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@Article{Domagala2012,
  author    = {Domagała, Sławomir and Fournier, Bertrand and Liebschner, Dorothee and Guillot, Benoît and Jelsch, Christian},
  journal   = {Acta Crystallogr Sect A},
  title     = {An improved experimental databank of transferable multipolar atom models – {ELMAM2}. {C}onstruction details and applications},
  year      = {2012},
  issn      = {0108-7673},
  month     = {Mar},
  number    = {3},
  pages     = {337–351},
  volume    = {68},
  crossref  = {ube},
  doi       = {10.1107/s0108767312008197},
  file      = {2012_Domagała_337.pdf:by-author/D/Domagała/2012_Domagała_337.pdf:PDF},
  groups    = {sg/Crystallography, am/Crystallography},
  owner     = {andrius},
  publisher = {International Union of Crystallography (IUCr)},
  timestamp = {2016.11.14},
  creationdate = {2016-11-14T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0108767312008197},
}

@Presentation{Rose2015,
  author    = {John Rose},
  title     = {{JVM} implementation challenges: why the future is hard but worth it},
  year      = {2015},
  file      = {2015_Rose.pdf:by-author/R/Rose/2015_Rose.pdf:PDF},
  owner     = {saulius},
  timestamp = {2019.05.01},
  creationdate = {2019-05-01T00:00:00},
  url       = {https://cr.openjdk.java.net/~jrose/pres/201502-JVMChallenges.pdf},
}

@Article{Sali1993,
  author    = {Andrej {\v{S}}ali and Tom L. Blundell},
  journal   = {Journal of Molecular Biology},
  title     = {Comparative protein modelling by satisfaction of spatial restraints},
  year      = {1993},
  pages     = {779--815},
  volume    = {234},
  doi       = {10.1006/jmbi.1993.1626},
  file      = {:by-author/Š/Šali/1993_Šali_779.pdf:PDF},
  keywords  = {Proteins; Structure Predicion},
  owner     = {andrius},
  timestamp = {2014.03.11},
  creationdate = {2014-03-11T00:00:00},
}

@Article{Saltenis2000,
  author     = {\v{S}altenis, Simonas and Jensen, Christian S. and Leutenegger, Scott T. and Lopez, Mario A.},
  journal    = {SIGMOD Rec.},
  title      = {Indexing the positions of continuously moving objects},
  year       = {2000},
  issn       = {0163-5808},
  pages      = {331--342},
  volume     = {29},
  abstract   = {The coming years will witness dramatic advances in wireless communications as well as positioning technologies. As a result, tracking the changing positions of objects capable of continuous movement is becoming increasingly feasible and necessary. The present paper proposes a novel, R-tree based indexing technique that supports the efficient querying of the current and projected future positions of such moving objects. The technique is capable of indexing objects moving in one-, two-, and three-dimensional space. Update algorithms enable the index to accommodate a dynamic data set, where objects may appear and disappear, and where changes occur in the anticipated positions of existing objects. A comprehensive performance study is reported.},
  address    = {New York, NY, USA},
  doi        = {10.1145/335191.335427},
  file       = {:by-author/S/Saltenis/2000_Saltenis_331.pdf:PDF},
  issue_date = {June 2000},
  owner      = {saulius},
  publisher  = {ACM},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url        = {http://doi.acm.org/10.1145/335191.335427},
}

@Article{Aakeroy2010,
  author    = {Aakeröy, Christer B. and Champness, Neil R. and Janiak, Christoph},
  journal   = {CrystEngComm},
  title     = {Recent advances in crystal engineering},
  year      = {2010},
  pages     = {22--43},
  volume    = {12},
  abstract  = {The articles published in the tenth anniversary issue of CrystEngComm are reviewed. The issue highlighted the state-of-the-art of crystal engineering and new trends and developing areas in crystal engineering. In particular{,} the following article emphasises developments in the areas of intermolecular interactions{,} notably hydrogen and halogen bonds; metal-organic frameworks or coordination polymers; polymorphism and solvates.},
  doi       = {10.1039/B919819A},
  file      = {2010_Aakeröy_22.pdf:by-author/A/Aakeröy/2010_Aakeröy_22.pdf:PDF},
  issue     = {1},
  keywords  = {Crystal Engineering; Metal-Organic Frameworks (MOF)},
  owner     = {saulius},
  publisher = {The Royal Society of Chemistry},
  timestamp = {2013.01.05},
  creationdate = {2013-01-05T00:00:00},
  url       = {http://dx.doi.org/10.1039/B919819A},
}

@Article{Aalten1996,
  author    = {van Aalten, Daan M. F. and Bywater, Robert P. and Findlay, John B. C. and Hendlich, Manfred and Hooft, Rob W. W. and Vriend, Gert},
  journal   = {Journal of Computer-Aided Molecular Design},
  title     = {{PRODRG}, a Program for Generating Molecular Topologies and Unique Molecular Descriptors from Coordinates of Small Molecules},
  year      = {1996},
  pages     = {255--262},
  volume    = {10},
  file      = {:by-author/v/vanAalten/1996_Aalten_255.pdf:PDF},
  keywords  = {Molecular Topology; Restrains},
  owner     = {andrius},
  timestamp = {2012.05.14},
  creationdate = {2012-05-14T00:00:00},
}

@Presentation{aashish2008,
  author       = {aashish},
  title        = {Measuring Program Similarity: Experiments with SPEC CPU benchmark suites},
  year         = {2008},
  organization = {Laboratory of Computer Architecture},
  school       = {University of Texas, Austin},
  file         = {:by-author/a/aashish/2008_aashish.ppt:PPT},
  keywords     = {Computer Science (CS)},
  owner        = {saulius},
  timestamp = {2015.03.03},
  creationdate = {2015-03-03T00:00:00},
}

@Article{Abadi1991,
  author           = {Martin Abadi and Luca Cardelli and Benjamin Pierce and Gordon Plotkin},
  journal          = {ACM Transactions on Programming Languages and Systems},
  title            = {Dynamic Typing in a Statically Typed Language},
  year             = {1991},
  pages            = {237--268},
  volume           = {23},
  creationdate     = {2008-07-28T00:00:00},
  doi              = {10.1145/103135.103138},
  file             = {1991_Abadi_TOPLAS_237--Dynamic_in_statically_language.pdf:by-author/A/Abadi/1991_Abadi_237.pdf:PDF},
  keywords         = {Computer Science (CS); Type Systems},
  modificationdate = {2023-04-23T10:11:20},
  owner            = {saulius},
  timestamp        = {2008.07.28},
}

@Article{Abadjieva1993,
  author    = {Abadjieva},
  journal   = {J. Mol. Biol.},
  title     = {Deletions within the {DNA} Recognition Subunit of {M.EcoR124I} that Identify a Region Involved in Protein-Protein Interactions between {HsdS} and {HsdM}},
  year      = {1993},
  pages     = {35},
  file      = {:by-author/A/Abadjieva/1993_Abadjieva_35.pdf:PDF},
  keywords  = {TypeI},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Abadjieva2003,
  author    = {Abadjieva, A. and Scarlett, G. and Janscák, P. and Dutta, C. F. and Firman, K.},
  journal   = {Folia microbiologica},
  title     = {Characterization of an EcoR124I restriction-modification enzyme produced from a deleted form of the DNA-binding subunit, which results in a novel DNA specificity.},
  year      = {2003},
  pages     = {319--28},
  volume    = {48},
  abstract  = {We purified and characterized both the methyltransferase and the endonuclease containing the HsdS delta 50 subunit (type I restriction endonucleases are composed of three subunits--HsdR required for restriction, HsdM required for methylation and HsdS responsible for DNA recognition) produced from the deletion mutation hsdS delta 50 of the type IC R-M system EcoR 124I; this mutant subunit lacks the C-terminal 163 residues of HsdS and produces a novel DNA specificity. Analysis of the purified HsDs delta 50 subunit indicated that during purification it is subject to partial proteolysis resulting in removal of approximately 1 kDa of the polypeptide at the C-terminus. This proteolysis prevented the purification of further deletion mutants, which were determined as having a novel DNA specificity in vivo. After biochemical characterization of the mutant DNA methyltransferase (MTase) and restriction endonuclease we found only one difference comparing with the wild-type enzyme--a significantly higher binding affinity of the MTase for the two substrates of hemimethylated and fully methylated DNA. This indicates that MTase delta 50 is less able to discriminate the methylation status of the DNA during its binding. However, the mutant MTase still preferred hemimethylated DNA as the substrate for methylation. We fused the hsdM and hsdS delta 50 genes and showed that the HsdM-HsdS delta 50 fusion protein is capable of dimerization confirming the model for assembly of this deletion mutant.},
  file      = {:by-author/A/Abadjieva/2003_Abadjieva_319.pdf:PDF},
  keywords  = {TypeI},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Abad-Zapatero2007,
  author    = {Abad-Zapatero, Cele},
  journal   = {Acta crystallographica. Section D, Biological crystallography},
  title     = {Notes of a protein crystallographer: quo vadis structural biology?},
  year      = {2007},
  pages     = {660--4},
  volume    = {63},
  doi       = {10.1107/S0907444907015053},
  file      = {:by-author/A/Abad-Zapatero/2007_Abad-Zapatero_660.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Abakumov2000,
  author    = {A.M. Abakumov and J. Hadermann and M.G. Rozova and B.Ph. Pavljuk and E.V. Antipov and O.I. Lebedev and G. van Tendeloo},
  journal   = {Journal of Solid State Chemistry},
  title     = {Synthesis and Crystal Structure of a New Complex Oxyfluoride La0.813Sr0.187Cu(O,F)3−δ},
  year      = {2000},
  issn      = {0022-4596},
  pages     = {189--196},
  volume    = {149},
  abstract  = {La8−xSrxCu8O20−δ (x=1.3, 1.5, and 1.9) compounds were fluorinated using XeF2 as a fluorinating agent. The formation of a new tetragonal complex oxyfluoride La0.813Sr0.187Cu(O, F)3−δ was observed. The structure of the new phase was refined using X-ray powder data (a=3.7921(3) Å, c=4.0515(4) Å, S. G. P4/mmm, R1=0.020, RP=0.045, RwP=0.057) and was confirmed by electron diffraction and high-resolution electron microscopy (HREM). The tetragonal distortion of the perovskite unit cell seems to be due to a Jahn–Teller deformation of the copper coordination environment with the formation of four short (1.896 Å) and two long (2.026 Å) Cu–(O, F) distances. Domains of the La0.813Sr0.187Cu(O, F)3−δ phase were observed by \{HREM\} inside a matrix of a slightly fluorinated initial phase.},
  doi       = {10.1006/jssc.1999.8521},
  file      = {:by-author/A/Abakumov/2000_Abakumov_189.pdf:pdf},
  keywords  = {Fluorination},
  owner     = {saulius},
  timestamp = {2015.10.09},
  creationdate = {2015-10-09T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/S0022459699985213},
}

@InProceedings{Abbi2008,
  author    = {Revlin Abbi and Elia El-Darzi and Christos Vasilakis and Peter Millard},
  booktitle = {Intelligent Systems, 2008. IS '08. 4th International IEEE Conference},
  title     = {Analysis of stopping criteria for the {EM} algorithm in the context of patient grouping according to length of stay},
  year      = {2008},
  month     = {sept.},
  pages     = {3-9 - 3-14},
  volume    = {1},
  abstract  = {The expectation maximisation (EM) algorithm is an iterative maximum likelihood procedure often used for estimating the parameters of a mixture model. Theoretically, increases in the likelihood function are guaranteed as the algorithm iteratively improves upon previously derived parameter estimates. The algorithm is considered to converge when all parameter estimates become stable and no further improvements can be made to the likelihood value. However, to reduce computational time, it is often common practice for the algorithm to be stopped before complete convergence using heuristic approaches. In this paper, we consider various stopping criteria and evaluate their effect on fitting Gaussian mixture models (GMMs) to patient length of stay (LOS) data. Although the GMM can be successfully fitted to positively skewed data such as LOS, the fitting procedure often requires many iterations of the EM algorithm. To our knowledge, no previous study has evaluated the effect of different stopping criteria on fitting GMMs to skewed distributions. Hence, the aim of this paper is to evaluate the effect of various stopping criteria in order to select and justify their use within a patient spell classification methodology. Results illustrate that criteria based on the difference in the likelihood value and on the GMM parameters may not always be a good indicator for stopping the algorithm. In fact we show that the values of the difference in the variance parameters should be used instead, as these parameters are the last to stabilise. In addition, we also specify threshold values for the other stopping criteria.},
  doi       = {10.1109/IS.2008.4670413},
  file      = {:by-author/A/Abbi/2008_Abbi_9.pdf:PDF},
  groups    = {am/Expectation maximisation},
  keywords  = {Expectation Maximisation; Gaussian Mixture Models},
  owner     = {andrius},
  timestamp = {2013.02.13},
  creationdate = {2013-02-13T00:00:00},
}

@Article{Abbott1976,
  author    = {Abbott, L. F.},
  journal   = {Physical Review B},
  title     = {Massless Particles with Continuous Spin Indices},
  year      = {1976},
  pages     = {2291--2294},
  volume    = {13},
  abstract  = {Massless representations of the Poincare group include states with continous spin indices. Free field operators corresponding to these states are constructed and are shown to obey noncausal commutation or anticommutation relations.},
  doi       = {10.1103/PhysRevD.13.2291},
  file      = {:by-author/A/Abbott/1976_Abbott_2291.pdf:PDF},
  issue     = {8},
  keywords  = {Physics; Spin},
  owner     = {saulius},
  publisher = {American Physical Society},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
  url       = {http://link.aps.org/doi/10.1103/PhysRevD.13.2291},
}

@TechReport{Abdelguerfi2002,
  author           = {Mahdi Abdelguerfi and Julie Givaudan and Kevin Shaw and Roy Ladner},
  institution      = {ACM},
  title            = {The 2-3{TR}-tree, a trajectory-oriented index structure for fully evolving valid-time spatio-temporal datasets},
  year             = {2002},
  abstract         = {Supporting large volumes of multi-dimensional data is an inherent characteristic of modern database applications, such as Geographical Information Systems (GIS), Computer Aided design (CAD), and Image and Multimedia Databases. Such databases need underlying systems with extended features like query languages, data models, and indexing methods, as compared to traditional databases, mainly because of the complexity of representing and retrieving data. The presented work deals with access methods for databases that accurately model the real world. More precisely, the focus is on index structures that can capture the time varying nature of moving objects, namely spatio-temporal structures. A new taxonomy to classify these structures has been defined according to dataset characteristics and query requirements. Then, a new spatio-temporal access method, the 2-3TR-tree, has been designed to process specific datasets and fulfill specific query requirements that no other existing spatio-temporal index could handle.},
  creationdate     = {2008-07-28T00:00:00},
  doi              = {10.1145/585147.585155},
  file             = {:by-author/A/Abdelguerfi/2002_Abdelguerfi.pdf:PDF},
  keywords         = {Indexing; R Tree; Spatio Temporal Databases; Taxonomy},
  modificationdate = {2024-08-28T11:58:31},
  owner            = {saulius},
  timestamp        = {2008.07.28},
}

@Proceedings{Abdessalem2006,
  title            = {Evaluation of Probabilistic Queries in Moving Objects Databases},
  year             = {2006},
  abstract         = {The representation of moving objects in spatial database systems has become an important research topic in recent years. As it is not realistic to track and store the location of objects at every time instant, one of the issues in this domain has to do with handling uncertainty in the location of moving objects. In this paper, we propose three statis- tical methods for computing probabilistic estimates about the location of a moving object at a certain time and show how to use them for evaluating probabilistic range queries. The focus is on applications dealing with the spatiotempo- ral behavior of non-network constrained moving objects, for monitoring or data-mining purposes, for instance.},
  author           = {Talel Abdessalem and Laurent Decreusefond and Jos{\'e} Moreira},
  creationdate     = {2008-07-28T00:00:00},
  doi              = {10.1145/1140104.1140109},
  file             = {:by-author/A/Abdessalem/2006_Abdessalem.pdf:PDF},
  keywords         = {Moving Objects; Spatio Temporal Databases; Spatio Temporal Uncertainty},
  modificationdate = {2023-04-23T10:12:34},
  owner            = {saulius},
  timestamp        = {2008.07.28},
}

@Article{Abel1826,
  author    = {Abel, N. H.},
  journal   = {Journal für die reine und angewandte Mathematik},
  title     = {Beweis der Unmöglichkeit, algebraische Gleichungen von höheren Graden als dem vierten allgemein aufzulösen},
  year      = {1826},
  pages     = {65--84},
  volume    = {1},
  file      = {1826_Abel_65.pdf:by-author/A/Abel/1826_Abel_65.pdf:PDF},
  groups    = {sg/Algebraic equations},
  keywords  = {Algebra; Algebraic Equations},
  owner     = {saulius},
  timestamp = {2016.04.13},
  creationdate = {2016-04-13T00:00:00},
  url       = {http://www.digizeitschriften.de/dms/img/?PID=PPN243919689_0001|log12},
}

@Article{Abrahams2000,
  author    = {Abrahams, Isaac and Ahmed, Aliya and Groombridge, Christopher J. and Hawkes, Geoffrey E. and Nunes, Teresa G.},
  journal   = {J. Chem. Soc.{,} Dalton Trans.},
  title     = {Cation distribution in cubic NaM(PO3)3 (M = Mg or Zn) using X-ray powder diffraction and solid state NMR},
  year      = {2000},
  pages     = {155--160},
  abstract  = {Solid state 23Na and 31P magic angle spinning nuclear magnetic resonance (MAS-NMR) spectroscopy and X-ray powder diffraction have been used in combination to study the structure of the model phosphate phases NaMg(PO3)3 and NaZn(PO3)3. The similar X-ray scattering of Na and Mg make determination of the cation distribution in NaMg(PO3)3 difficult using X-ray data alone. However{,} the structure of NaZn(PO3)3 was successfully refined and an initial model for the cation distribution in the magnesium analogue proposed. The 23Na and 31P solid state NMR data confirm the similarities between the two structures{,} while the 23Na also suggested three sodium sites in a 2[ratio]1[ratio]1 ratio{,} consistent with the proposed crystallographic model. This allowed for a successful refinement of the structure of NaMg(PO3)3{,} confirming that the structures are indeed isostructural. Both structures contain chains of (PO3)nn- with Na+ and Mg2+/Zn2+ ions in distorted octahedral sites located between the polyphosphate chains.},
  doi       = {10.1039/A906413C},
  file      = {:by-author/A/Abrahams/2000_Abrahams_155.pdf:pdf},
  issue     = {2},
  owner     = {saulius},
  publisher = {The Royal Society of Chemistry},
  timestamp = {2015.10.09},
  creationdate = {2015-10-09T00:00:00},
  url       = {http://dx.doi.org/10.1039/A906413C},
}

@Article{Abrahams1999,
  author    = {I. Abrahams and A.J. Bush and G.E. Hawkes and T. Nunes},
  journal   = {Journal of Solid State Chemistry},
  title     = {Structure and Oxide Ion Conductivity Mechanism in Bi2Al4O9 by Combined X-Ray and High-Resolution Neutron Powder Diffraction and 27Al Solid State \{NMR\}},
  year      = {1999},
  issn      = {0022-4596},
  pages     = {631--636},
  volume    = {147},
  abstract  = {The structure of Bi2Al4O9 has been refined using a combination of X-ray and high-resolution neutron powder diffraction. Iterative simulation of the 27Al \{MAS\} solid state \{NMR\} data confirms the presence of two Al sites, one octahedral and one tetrahedral, in an approximate 1:1 ratio. The structure of Bi2Al4O9 has been refined anisotropically in the orthorhombic space group Pbam, with a=7.7134(1), b=8.1139(2), c=5.6914(1) Å, and Z=2. The refinement terminated with Rwp=17.09% (X ray), 11.44% (neutron); Rex=4.52% (X ray), 3.22% (neutron). The structure consists of edge-sharing columns of AlO6 octahedra running parallel to the c-axis. These columns are linked by pairs of apex sharing AlO4 tetrahedra, with Bi atoms located between the columns. The Bi 6s2 lone pairs point toward vacant sites in the structure. A one-dimensional conductivity mechanism along the c-axis vector is proposed involving these sites.},
  doi       = {10.1006/jssc.1999.8427},
  file      = {:by-author/A/Abrahams/1999_Abrahams_631.pdf:pdf},
  owner     = {saulius},
  timestamp = {2015.10.09},
  creationdate = {2015-10-09T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/S002245969998427X},
}

@Article{Acharya2005,
  author    = {Acharya, K. Ravi and Lloyd, Matthew D.},
  journal   = {Trends in pharmacological sciences},
  title     = {The advantages and limitations of protein crystal structures.},
  year      = {2005},
  number    = {1},
  pages     = {10--14},
  volume    = {26},
  abstract  = {Crystal structure analysis using X-ray diffraction is, in many cases, the most advanced method available for obtaining high-resolution structural information about biological macromolecules. The ways in which X-ray diffraction data are collected and refined have a strong impact on the final quality of the structural models and the type and magnitude of their associated errors. It is becoming increasingly necessary for both structural and non-structural biologists to judge the reliability and accuracy of these models, which are being used in many aspects of research, including structure-based drug design, and to address detailed functional biological questions. In this article, we discuss how errors in these models arise and how they can be evaluated, and we argue for even more stringent validation checks and documentation of structures before deposition with the Protein Data Bank.},
  doi       = {10.1016/j.tips.2004.10.011},
  file      = {:by-author/A/Acharya/2005_Acharya_10.pdf:pdf},
  keywords  = {Structure Refinement; Validation; X-ray Crystallography},
  owner     = {saulius},
  pii       = {S0165-6147(04)00305-0},
  pubmed    = {15629199},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Article{Acharya2003,
  author    = {Parag Acharya},
  journal   = {Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology},
  title     = {Studies on the Non-covalent Interactions (Stereoelectronics, Stacking and Hydrogen Bonding) in the Self-assembly of DNA and RNA},
  year      = {2003},
  pages     = {1},
  volume    = {914},
  file      = {2003_Acharya_1.pdf:by-author/A/Acharya/2003_Acharya_1.pdf:PDF},
  keywords  = {Stacking},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Achilli2014,
  author     = {Achilli, Elisabetta and Minguzzi, Alessandro and Lugaresi, Ottavio and Locatelli, Cristina and Rondinini, Sandra and Spinolo, Giorgio and Ghigna, Paolo},
  journal    = {Journal of Spectroscopy},
  title      = {In situ dispersive {EXAFS} in electrocatalysis: the investigation of the local structure of {IrO} x in chronoamperometric conditions as a case study},
  year       = {2014},
  volume     = {2014},
  doi        = {10.1155/2014/480102},
  file       = {[PDF] from hindawi.com:by-author/A/Achilli/2014_Achilli.pdf:PDF;Snapshot:by-author/A/Achilli/2014_Achilli.html:URL},
  groups     = {sg/JAC2009, sg/NAR2012},
  owner      = {saulius},
  shorttitle = {In situ dispersive {EXAFS} in electrocatalysis},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url        = {http://www.hindawi.com/journals/jspec/2014/480102/abs/},
  urldate    = {2015-08-31},
}

@Article{Adam2002,
  author    = {Adam, David},
  journal   = {Nature},
  title     = {Citation analysis: The counting house},
  year      = {2002},
  issn      = {0028-0836},
  month     = feb,
  number    = {6873},
  pages     = {726--729},
  volume    = {415},
  abstract  = {Scientists' work is often evaluated using citation statistics compiled by a company called the ISI. But how useful and reliable are the data? David Adam gets the measure of citation analysis.},
  comment   = {10.1038/415726a},
  doi       = {10.1038/415726a},
  file      = {2002_Adam_726.pdf:by-author/A/Adam/2002_Adam_726.pdf:PDF},
  groups    = {sg/Bibliometrics},
  keywords  = {Criticism; Impact Factor (IF); Quality of Research},
  owner     = {saulius},
  timestamp = {2016.02.14},
  creationdate = {2016-02-14T00:00:00},
  url       = {http://dx.doi.org/10.1038/415726a},
}

@Article{Adams2008,
  author    = {Adams, Nico and Winter, Jerry and Murray-Rust, Peter and Rzepa, Henry S.},
  journal   = {Journal of chemical information and modeling},
  title     = {Chemical Markup, XML and the World-Wide Web. 8. Polymer Markup Language.},
  year      = {2008},
  pages     = {2118--28},
  volume    = {48},
  abstract  = {Polymers are among the most important classes of materials but are only inadequately supported by modern informatics. The paper discusses the reasons why polymer informatics is considerably more challenging than small molecule informatics and develops a vision for the computer-aided design of polymers, based on modern semantic web technologies. The paper then discusses the development of Polymer Markup Language (PML). PML is an extensible language, designed to support the (structural) representation of polymers and polymer-related information. PML closely interoperates with Chemical Markup Language (CML) and overcomes a number of the previously identified challenges.},
  doi       = {10.1021/ci8002123},
  file      = {:by-author/A/Adams/2008_Adams_2118.pdf:PDF},
  keywords  = {CML; Chemoinformatics; Crystallography; Data Formats; Data Management; X-ray Crystallography; XML},
  owner     = {saulius},
  timestamp = {2014.01.26},
  creationdate = {2014-01-26T00:00:00},
}

@InProceedings{Adams2009,
  author    = {Ryan Prescott Adams and Iain Murray and David J.C. MacKay},
  booktitle = {Proceedings of the 26 th International Conference on Machine Learning},
  title     = {Tractable Nonparametric Bayesian Inference in Poisson Processes with Gaussian Process Intensities},
  year      = {2009},
  abstract  = {The inhomogeneous Poisson process is a point process that has varying intensity across its domain (usually time or space). For nonparametric Bayesian modeling, the Gaussian process is a useful way to place a prior distribution on this intensity. The combina- tion of a Poisson process and GP is known as a Gaussian Cox process, or doubly-stochastic Poisson process. Likelihood-based inference in these models requires an intractable integral over an infinite-dimensional random function. In this paper we present the first approach to Gaussian Cox processes in which it is possible to perform inference without introducing approximations or finite- dimensional proxy distributions. We call our method the Sigmoidal Gaussian Cox Process, which uses a generative model for Poisson data to enable tractable inference via Markov chain Monte Carlo. We compare our methods to competing methods on synthetic data and apply it to several real-world data sets.},
  file      = {:by-author/A/Adams/2009_Adams.pdf:PDF},
  groups    = {sg/Bayesian},
  owner     = {saulius},
  timestamp = {2012.09.30},
  creationdate = {2012-09-30T00:00:00},
}

@Article{Adams2000,
  author    = {Stefan Adams},
  journal   = {Journal of Solid State Chemistry},
  title     = {\{CDW\} Superstructures in Hydrogen Molybdenum Bronzes HxMoO3},
  year      = {2000},
  issn      = {0022-4596},
  pages     = {75--87},
  volume    = {149},
  abstract  = {Hydrogen molybdenum bronzes HxMoO3 (0< x< 2) are consistently described as low-dimensional mixed conductors, whose properties under ambient conditions are controlled by charge density wave modulations. Proton conduction pathways in the bronzes are modeled by a bond valence approach. The redistribution of hydrogen during the intercalation process between two types of potential proton sites is simulated in a molecular mechanics study. Therefrom a structure model for the bronze phase \{II\} (0.85 < x < 1.04) is derived, which permits a Rietveld refinement of its previously unknown structure from powder X-ray data (space group I12/m1; a=14.5191(6) Å, b=3.7944(1) Å, c=7.7248(3) Å, β=93.743(2)° for x≈0.9). Both the doubling of the host cell along the c-axis in phase \{II\} and the 6×c superstructure found for phase I with x≈1/3 meet the expectations for quasi-one-dimensional Peierls distorted systems. Modifications in the structure, proton ordering, and properties of the bronzes are studied as a function of temperature. A time-resolved powder \{XRD\} investigation on the oxidation of phase \{II\} indicates the existence of a intermediate phase H0.6MoO3. The powder structure determination of this metastable phase (space group C2/m, a=14.543(2) Å, b=3.8520(4) Å, c=3.7691(4) Å, β= 90.73(1)°) indicates a redistribution of the protons during this oxidation step.},
  doi       = {10.1006/jssc.1999.8498},
  file      = {:by-author/A/Adams/2000_Adams_75.pdf:pdf},
  keywords  = {Molybdenum Bronze},
  owner     = {saulius},
  timestamp = {2015.10.09},
  creationdate = {2015-10-09T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/S0022459699984980},
}

@Article{Adams2011,
  author    = {Adams, Sam and de Castro, Pablo and Echenique, Pablo and Estrada, Jorge and Hanwell, Marcus and Murray-Rust, Peter and Sherwood, Paul and Thomas, Jens and Townsend, Joe},
  journal   = {Journal of Cheminformatics},
  title     = {The Quixote project: Collaborative and Open Quantum Chemistry data management in the Internet age},
  year      = {2011},
  issn      = {1758-2946},
  pages     = {38},
  volume    = {3},
  abstract  = {Computational Quantum Chemistry has developed into a powerful, efficient, reliable and increasingly routine tool for exploring the structure and properties of small to medium sized molecules. Many thousands of calculations are performed every day, some offering results which approach experimental accuracy. However, in contrast to other disciplines, such as crystallography, or bioinformatics, where standard formats and well-known, unified databases exist, this QC data is generally destined to remain locally held in files which are not designed to be machine-readable. Only a very small subset of these results will become accessible to the wider community through publication.In this paper we describe how the Quixote Project is developing the infrastructure required to convert output from a number of different molecular quantum chemistry packages to a common semantically rich, machine-readable format and to build respositories of QC results. Such an infrastructure offers benefits at many levels. The standardised representation of the results will facilitate software interoperability, for example making it easier for analysis tools to take data from different QC packages, and will also help with archival and deposition of results. The repository infrastructure, which is lightweight and built using Open software components, can be implemented at individual researcher, project, organisation or community level, offering the exciting possibility that in future many of these QC results can be made publically available, to be searched and interpreted just as crystallography and bioinformatics results are today.Although we believe that quantum chemists will appreciate the contribution the Quixote infrastructure can make to the organisation and and exchange of their results, we anticipate that greater rewards will come from enabling their results to be consumed by a wider community. As the respositories grow they will become a valuable source of chemical data for use by other disciplines in both research and education.The Quixote project is unconventional in that the infrastructure is being implemented in advance of a full definition of the data model which will eventually underpin it. We believe that a working system which offers real value to researchers based on tools and shared, searchable repositories will encourage early participation from a broader community, including both producers and consumers of data. In the early stages, searching and indexing can be performed on the chemical subject of the calculations, and well defined calculation meta-data. The process of defining more specific quantum chemical definitions, adding them to dictionaries and extracting them consistently from the results of the various software packages can then proceed in an incremental manner, adding additional value at each stage.Not only will these results help to change the data management model in the field of Quantum Chemistry, but the methodology can be applied to other pressing problems related to data in computational and experimental science.},
  doi       = {10.1186/1758-2946-3-38},
  file      = {2011_Adams_38.pdf:by-author/A/Adams/2011_Adams_38.pdf:PDF},
  keywords  = {Chemoinformatics; Data Management; Databases; Density Functional Theory (DFT); QM/MM; Quantum Mechanics (QM)},
  owner     = {saulius},
  pubmedid  = {21999363},
  timestamp = {2014.04.03},
  creationdate = {2014-04-03T00:00:00},
  url       = {http://www.jcheminf.com/content/3/1/38},
}

@Article{Addison1984,
  author    = {Addison, Anthony W. and Rao, T. Nageswara and Reedijk, Jan and van Rijn, Jacobus and Verschoor, Gerrit C.},
  journal   = {J. Chem. Soc., Dalton Trans.},
  title     = {Synthesis, structure, and spectroscopic properties of copper(II) compounds containing nitrogen–sulphur donor ligands; the crystal and molecular structure of aqua[1,7-bis(N-methylbenzimidazol-2′-yl)-2,6-dithiaheptane]copper(II) perchlorate},
  year      = {1984},
  issn      = {1364-5447},
  number    = {7},
  pages     = {1349--1356},
  doi       = {10.1039/dt9840001349},
  file      = {:by-author/A/Addison/1984_Addison_1349.pdf:PDF},
  keywords  = {Definition of Tau; Distortion Index; For COD Deposition; Metal Coordination},
  owner     = {saulius},
  publisher = {Royal Society of Chemistry (RSC)},
  timestamp = {2017.02.01},
  creationdate = {2017-02-01T00:00:00},
  url       = {http://dx.doi.org/10.1039/dt9840001349},
}

@TechReport{Adler2008,
  author      = {Robert Adler and John Ewing and Peter Taylor},
  institution = {Joint Committee on Quantitative Assessment of Research},
  title       = {Citation Statistics},
  year        = {2008},
  note        = {A report from the International Mathematical Union (IMU) in cooperation with the International Council of Industrial and Applied Mathematics (ICIAM) and the Institute of Mathematical Statistics (IMS)},
  abstract    = {This is a report about the use and misuse of citation data in the assessment of scientific research. The idea that research assessment must be done using "simple and objective" methods is increasingly prevalent today. The "simple and objective" methods are broadly interpreted as bibliometrics, that is, citation data and the statistics derived from them. There is a belief that citation statistics are inherently more accurate because they substitute simple numbers for complex judgments, and hence overcome the possible subjectivity of peer review. But this belief is unfounded ...},
  file        = {:by-author/A/Adler/2008_Adler.pdf:PDF},
  groups      = {sg/Bibliometrics},
  keywords    = {Impact Factors},
  owner       = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
  url         = {http://mathunion.org/fileadmin/IMU/Report/CitationStatistics.pdf},
}

@Presentation{Adrian2004a,
  author    = {Adrian},
  title     = {Patent Protection for Computer-Related Inventions},
  year      = {2004},
  file      = {:by-author/A/Adrian/2004_Adrian_slides.pdf:PDF},
  keywords  = {Patentai; Teise},
  owner     = {saulius},
  pages     = {slides},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Presentation{Adrian2004,
  author    = {Angela Adrian},
  title     = {Patent Protection for Computer-Related Inventions},
  year      = {2004},
  file      = {:by-author/A/Adrian/2004_Adrian_slides2.pdf:PDF},
  keywords  = {Patentai; Teise},
  owner     = {saulius},
  pages     = {slides2},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Conference{Aeschliman2010,
  author       = {Chad Aeschliman and Johnny Park and Avinash C. Kak},
  booktitle    = {European Conference on Computer Vision 2010},
  title        = {A Novel Parameter Estimation Algorithm for the Multivariate t-Distribution and Its Application to Computer Vision},
  year         = {2010},
  organization = {Purdue University},
  abstract     = {We present a novel algorithm for approximating the parameters of a multivariate t-distribution. At the expense of a slightly de- creased accuracy in the estimates, the proposed algorithm is significantly faster and easier to implement compared to the maximum likelihood estimates computed using the expectation-maximization algorithm. The formulation of the proposed algorithm also provides theoretical guidance for solving problems that are intractable with the maximum likelihood equations. In particular, we show how the proposed algorithm can be modified to give an incremental solution for fast online parameter estimation. Finally, we validate the effectiveness of the proposed algorithm by using the approximated t-distribution as a drop in replacement for the conventional Gaussian distribution in two computer vision applications: object recognition and tracking. In both cases the t-distribution gives better performance with no increase in computation.},
  file         = {:by-author/A/Aeschliman/2010_Aeschliman.pdf:PDF},
  groups       = {am/Student's t},
  owner        = {andrius},
  timestamp = {2016.03.04},
  creationdate = {2016-03-04T00:00:00},
  url          = {https://engineering.purdue.edu/RVL/Publications/Aeschliman2010ANovel.pdf},
}

@Article{Afonine2009,
  author           = {Afonine, Pavel V and Grosse-Kunstleve, Ralf W and Urzhumtsev, Alexandre and Adams, Paul D},
  journal          = {Journal of applied crystallography},
  title            = {Automatic multiple-zone rigid-body refinement with a large convergence radius.},
  year             = {2009},
  pages            = {607--615},
  volume           = {42},
  abstract         = {Rigid-body refinement is the constrained coordinate refinement of one or more groups of atoms that each move (rotate and translate) as a single body. The goal of this work was to establish an automatic procedure for rigid-body refinement which implements a practical compromise between runtime requirements and convergence radius. This has been achieved by analysis of a large number of trial refinements for 12 classes of random rigid-body displacements (that differ in magnitude of introduced errors), using both least-squares and maximum-likelihood target functions. The results of these tests led to a multiple-zone protocol. The final parameterization of this protocol was optimized empirically on the basis of a second large set of test refinements. This multiple-zone protocol is implemented as part of the phenix.refine program.},
  creationdate     = {2008-07-28T00:00:00},
  doi              = {10.1107/s0021889809023528},
  file             = {2009_Afonine_607.pdf:by-author/A/Afonine/2009_Afonine_607.pdf:PDF},
  keywords         = {Refinement; X-ray Crystallography},
  modificationdate = {2023-04-23T10:13:49},
  owner            = {saulius},
  timestamp        = {2008.07.28},
}

@Article{Afonine2004,
  author    = {Afonine, Pavel V. and Lunin, Vladimir Y. and Muzet, Nicolas and Urzhumtsev, Alexandre},
  journal   = {Acta Crystallographica Section D},
  title     = {On the possibility of the observation of valence electron density for individual bonds in proteins in conventional difference maps},
  year      = {2004},
  pages     = {260--274},
  volume    = {60},
  doi       = {10.1107/S0907444903026209},
  file      = {wd0012.pdf:by-author/A/Afonine/2004_Afonine_260.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444903026209},
}

@Manuscript{AfsharXXXX,
  author    = {Shahriar S. Afshar},
  title     = {Sharp Complementary Wave And Particle Behaviours In The Same welcher weg Experiment},
  year      = {XXXX},
  keywords  = {Quantum Mechanics (QM)},
  file      = {:by-author/A/Afshar/XXXX_Afshar_manuscript.pdf:PDF},
  owner     = {saulius},
  pages     = {manuscript},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Agard2004,
  author    = {Agard, Nicholas J. and Prescher, Jennifer A. and Bertozzi, Carolyn R.},
  journal   = {Journal of the American Chemical Society},
  title     = {A strain-promoted [3 + 2] azide-alkyne cycloaddition for covalent modification of biomolecules in living systems.},
  year      = {2004},
  pages     = {15046--7},
  volume    = {126},
  abstract  = {Selective chemical reactions that are orthogonal to the diverse functionality of biological systems have become important tools in the field of chemical biology. Two notable examples are the Staudinger ligation of azides and phosphines and the Cu(I)-catalyzed [3 + 2] cycloaddition of azides and alkynes ("click chemistry"). The Staudinger ligation has sufficient biocompatibility for performance in living animals but suffers from phosphine oxidation and synthetic challenges. Click chemistry obviates the requirement of phosphines, but the Cu(I) catalyst is toxic to cells, thereby precluding in vivo applications. Here we present a strain-promoted [3 + 2] cycloaddition between cyclooctynes and azides that proceeds under physiological conditions without the need for a catalyst. The utility of the reaction was demonstrated by selective modification of biomolecules in vitro and on living cells, with no apparent toxicity.},
  file      = {:by-author/A/Agard/2004_Agard_15046.pdf:PDF},
  keywords  = {Bioconjugation},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@Article{Agari2008,
  author    = {Agari, Yoshihiro and Yokoyama, Shigeyuki and Kuramitsu, Seiki and Shinkai, Akeo},
  journal   = {Proteins},
  title     = {X-ray crystal structure of a CRISPR-associated protein, Cse2, from Thermus thermophilus HB8.},
  year      = {2008},
  pages     = {1063--7},
  volume    = {73},
  file      = {:by-author/A/Agari/2008_Agari_1063.pdf:PDF},
  groups    = {sg/CRISPR-Cas},
  keywords  = {CRISPR},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Agarwal1980,
  author    = {Ramesh C. Agarwal},
  journal   = {Acta Crystallographica Section A},
  title     = {A new least-squares refinement technique based on the fast Fourier transform algorithm: {\em erratum}.},
  year      = {1980},
  pages     = {496},
  abstract  = {In Agarwal [Acta Cryst. (1978), A34, 791-809], equation (61) should read: c3 = 2Cm1 Cm2. All information is given in the Abstract.},
  doi       = {10.1107/S0567739480001052},
  file      = {:by-author/A/Agarwal/1980_Agarwal_496.pdf:PDF},
  keywords  = {Refinement; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
  url       = {http://scripts.iucr.org/cgi-bin/paper?S0567739480001052},
}

@Article{Agarwal1978,
  author    = {Agarwal, R. C.},
  journal   = {Acta Crystallographica Section A},
  title     = {A new least-squares refinement technique based on the fast Fourier transform algorithm},
  year      = {1978},
  pages     = {791--809},
  volume    = {34},
  abstract  = {A new atomic-parameters least-squares refinement method is presented which makes use of the fast Fourier transform algorithm at all stages of the computation. For large structures, the amount of computation is almost proportional to the size of the structure making it very attractive for large biological structures such as proteins. In addition the method has a radius of convergence of approximately 0.75 Å making it applicable at a very early stage of the structure-determination process. The method has been tested on hypothetical as well as real structures. The method has been used to refine the structure of insulin at 1.5 Å resolution, barium beauvuricin complex at 1.2 Å resolution, and myoglobin at 2 Å resolution. Details of the method and brief summaries of its applications are presented in the paper.},
  doi       = {10.1107/S0567739478001618},
  file      = {1978_Agarwal_791.pdf:by-author/A/Agarwal/1978_Agarwal_791.pdf:PDF},
  keywords  = {Algorithms; Structure Refinement; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2013.03.25},
  creationdate = {2013-03-25T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0567739478001618},
}

@Article{Aggarwal2013,
  author    = {Vaneet Aggarwal and Chao Tian and Vinay A. Vaishampayan and Yih{-}Farn Robin Chen},
  journal   = {CoRR},
  title     = {Distributed Data Storage Systems with Opportunistic Repair},
  year      = {2013},
  pages     = {1311.4096v1},
  volume    = {abs/1311.4096},
  abstract  = {The reliability of erasure-coded distributed storage systems, as measured by the mean time to data loss (MTTDL), depends on the repair bandwidth of the code. Repair-efficient codes provide reliability values several orders of magnitude better than conventional erasure codes. Current state of the art codes fix the number of helper nodes (nodes participating in repair) a priori. In practice, however, it is desirable to allow the number of helper nodes to be adaptively determined by the network traffic conditions. In this work, we propose an opportunistic repair framework to address this issue. It is shown that there exists a threshold on the storage overhead, below which such an opportunistic approach does not lose any efficiency from the optimal storage-repair-bandwidth tradeoff; i.e. it is possible to construct a code simultaneously optimal for different numbers of helper nodes. We further examine the benefits of such opportunistic codes, and derive the MTTDL improvement for two repair models: one with limited total repair bandwidth and the other with limited individual-node repair bandwidth. In both settings, we show orders of magnitude improvement in MTTDL. Finally, the proposed framework is examined in a network setting where a significant improvement in MTTDL is observed.},
  bibsource = {dblp computer science bibliography, http://dblp.org},
  biburl    = {http://dblp.uni-trier.de/rec/bib/journals/corr/AggarwalTVC13},
  file      = {2013_Aggarwal_1311.4096v1.pdf:by-author/A/Aggarwal/2013_Aggarwal_1311.4096v1.pdf:PDF},
  keywords  = {Distributed Storage; Reliability; Tahoe LAFS},
  owner     = {saulius},
  timestamp = {2014.10.21},
  creationdate = {2014-10-21T00:00:00},
  url       = {http://arxiv.org/abs/1311.4096},
}

@TechReport{Agrawal2004,
  author           = {Sanjay Agrawal and Vivek Narasayya and Beverly Yang},
  institution      = {Microsoft Research; Stanford University},
  title            = {Integrating Vertical and Horizontal Partitioning into Automated Physical Database Design},
  year             = {2004},
  abstract         = {In addition to indexes and materialized views, horizontal and vertical partitioning are important aspects of physical design in a relational database system that significantly impact performance. Horizontal partitioning also provides manageability; database administrators often require indexes and their underlying tables partitioned identically so as to make common operations such as backup/restore easier. While partitioning is important, incorporating partitioning makes the problem of automating physical design much harder since: (a) The choices of partitioning can strongly interact with choices of indexes and materialized views. (b) A large new space of physical design alternatives must be considered. (c) Manageability requirements impose a new constraint on the problem. In this paper, we present novel techniques for designing a scalable solution to this integrated physical design problem that takes both performance and manageability into account. We have implemented our techniques and evaluated it on Microsoft SQL Server. Our experiments highlight: (a) the importance of taking an integrated approach to automated physical design and (b) the scalability of our techniques.},
  creationdate     = {2008-07-28T00:00:00},
  doi              = {10.1145/1007568.1007609},
  file             = {:by-author/A/Agrawal/2004_Agrawal.pdf:PDF},
  modificationdate = {2023-04-23T10:14:01},
  owner            = {saulius},
  timestamp        = {2008.07.28},
}

@Article{Ahmad2008,
  author    = {Ahmad, Shandar and Keskin, Ozlem and Sarai, Akinori and Nussinov, Ruth},
  journal   = {Nucleic acids research},
  title     = {Protein-DNA interactions: structural, thermodynamic and clustering patterns of conserved residues in DNA-binding proteins.},
  year      = {2008},
  pages     = {5922--32},
  volume    = {36},
  abstract  = {Amino acid residues, which play important roles in protein function, are often conserved. Here, we analyze thermodynamic and structural data of protein-DNA interactions to explore a relationship between free energy, sequence conservation and structural cooperativity. We observe that the most stabilizing residues or putative hotspots are those which occur as clusters of conserved residues. The higher packing density of the clusters and available experimental thermodynamic data of mutations suggest cooperativity between conserved residues in the clusters. Conserved singlets contribute to the stability of protein-DNA complexes to a lesser extent. We also analyze structural features of conserved residues and their clusters and examine their role in identifying DNA-binding sites. We show that about half of the observed conserved residue clusters are in the interface with the DNA, which could be identified from their amino acid composition; whereas the remaining clusters are at the protein-protein or protein-ligand interface, or embedded in the structural scaffolds. In protein-protein interfaces, conserved residues are highly correlated with experimental residue hotspots, contributing dominantly and often cooperatively to the stability of protein-protein complexes. Overall, the conservation patterns of the stabilizing residues in DNA-binding proteins also highlight the significance of clustering as compared to single residue conservation.},
  file      = {:by-author/A/Ahmad/2008_Ahmad_5922.pdf:PDF},
  keywords  = {Readout},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Ahmad2006,
  author    = {Ahmad, Shandar and Kono, Hidetoshi and Araúzo-Bravo, Marcos J. and Sarai, Akinori},
  journal   = {Nucleic acids research},
  title     = {ReadOut: structure-based calculation of direct and indirect readout energies and specificities for protein-DNA recognition.},
  year      = {2006},
  pages     = {W124-7},
  volume    = {34},
  abstract  = {Protein-DNA interactions play a central role in regulatory processes at the genetic level. DNA-binding proteins recognize their targets by direct base-amino acid interactions and indirect conformational energy contribution from DNA deformations and elasticity. Knowledge-based approach based on the statistical analysis of protein-DNA complex structures has been successfully used to calculate interaction energies and specificities of direct and indirect readouts in protein-DNA recognition. Here, we have implemented the method as a webserver, which calculates direct and indirect readout energies and Z-scores, as a measure of specificity, using atomic coordinates of protein-DNA complexes. This server is freely available at http://gibk26.bse.kyutech.ac.jp/jouhou/readout/. The only input to this webserver is the Protein Data Bank (PDB) style coordinate data of atoms or the PDB code itself. The server returns total energy Z-scores, which estimate the degree of sequence specificity of the protein-DNA complex. This webserver is expected to be useful for estimating interaction energy and DNA conformation energy, and relative contributions to the specificity from direct and indirect readout. It may also be useful for checking the quality of protein-DNA complex structures, and for engineering proteins and target DNAs.},
  file      = {:by-author/A/Ahmad/2006_Ahmad_W124.pdf:PDF},
  keywords  = {Readout},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Ahn2008,
  author    = {Luis Ahn and Benjamin Maurer and Colin Mcmillen and David Abraham and Manuel Blum},
  journal   = {Science},
  title     = {reCAPTCHA: Human-Based Character Recognition via Web Security Measures},
  year      = {2008},
  pages     = {1465--1468},
  volume    = {321},
  abstract  = {CAPTCHAs (Completely Automated Public Turing test to tell Computers and Humans Apart) are widespread security measures on the World Wide Web that prevent automated programs from abusing online services. They do so by asking humans to perform a task that computers cannot yet perform, such as deciphering distorted characters. Our research explored whether such human effort can be channeled into a useful purpose: helping to digitize old printed material by asking users to decipher scanned words from books that computerized optical character recognition failed to recognize. We showed that this method can transcribe text with a word accuracy exceeding 99%, matching the guarantee of professional human transcribers. Our apparatus is deployed in more than 40,000 Web sites and has transcribed over 440 million words.},
  file      = {:by-author/A/Ahn/2008_Ahn_1465.pdf:PDF},
  owner     = {saulius},
  timestamp = {2011.12.13},
  creationdate = {2011-12-13T00:00:00},
}

@Article{Ahnert1997,
  author           = {Ahnert, P. and Patel, S. S.},
  journal          = {The Journal of biological chemistry},
  title            = {Asymmetric interactions of hexameric bacteriophage T7 DNA helicase with the 5'- and 3'-tails of the forked DNA substrate.},
  year             = {1997},
  pages            = {32267--73},
  volume           = {272},
  abstract         = {Bacteriophage T7 DNA helicase requires two noncomplementary single-stranded DNA (ssDNA) tails next to a double-stranded DNA (dsDNA) region to initiate DNA unwinding. The interactions of the helicase with the DNA were investigated using a series of forked DNAs. Our results show that the helicase interacts asymmetrically with the two tails of the forked DNA. When the helicase was preassembled on the forked DNA before the start of unwinding, a DNA with 15-nucleotide (nt) 3'-tail and 35-nt 5'-tail was unwound with optimal rates close to 60 base pairs/s at 18 degrees C. When the helicase was not preassembled on the DNA, a >65-nt long 5'-tail was required for maximal unwinding rates of 12 base pairs/s. We show that the helicase interacts specifically with the ssDNA region and maintains contact with both ssDNA strands during DNA unwinding, since conversion of the two ssDNA tails to dsDNA structures greatly inhibited unwinding, and the helicase was unable to unwind past a nick in the dsDNA region. These studies have provided new insights into the mechanism of DNA unwinding. We propose an exclusion model of DNA unwinding in which T7 helicase hexamer interacts mainly with the ssDNA strands during DNA unwinding, encircling the 5'-strand and excluding the 3'-strand from the hole.},
  creationdate     = {2008-07-28T00:00:00},
  doi              = {10.1074/jbc.272.51.32267},
  file             = {:by-author/A/Ahnert/1997_Ahnert_32267.pdf:PDF},
  keywords         = {T7; {gp41} Helicase},
  modificationdate = {2023-04-23T10:14:28},
  owner            = {em},
  timestamp        = {2008.07.28},
}

@Article{Akaike1974,
  author    = {Hirotugu Akaike},
  journal   = {IEEE Transactions on Automatic Control},
  title     = {A New Look at The Statistical Model Identification},
  year      = {1974},
  pages     = {716--723},
  volume    = {19},
  abstract  = {The history of the development of statistical hypothesis testing in time series analysis is reviewed briefly and it is pointed out that the hypothesis testing procedure is not adequately defined as the procedure for statistical model identification. The classical maximum likelihood estimation procedure is reviewed and a new estimate minimum information theoretical criterion (AIC) estimate (MAICE) which is designed for the purpose of statistical identification is introduced. When there are several competing models the MAICE is defined by the model and the maximum likelihood estimates of the parameters which give the minimum of AIC defined by AIC = (-2)log-(maximum likelihood) + 2(number of independently adjusted parameters within the model). MAICE provides a versatile procedure for statistical model identification which is free from the ambiguities inherent in the application of conventional hypothesis testing procedure. The practical utility of MAICE in time series analysis is demonstrated with some numerical examples.},
  doi       = {10.1109/TAC.1974.1100705},
  file      = {:by-author/A/Akaike/1974_Akaike_716.pdf:PDF},
  groups    = {am/Statistics, am/Model selection},
  owner     = {andrius},
  timestamp = {2012.11.25},
  creationdate = {2012-11-25T00:00:00},
}

@TechReport{Akers1993,
  author      = {Robert L. Akers},
  institution = {Computational Logic Inc.},
  title       = {Strong Static Type Checking for Functional Common Lisp},
  year        = {1993},
  abstract    = {This thesis presents a type system which supports the strong static type checking of programs developed in an applicative subset of the Common Lisp language. The Lisp subset is augmented with a guard construct for function definitions, which allows type restrictions to be placed on the arguments. Guards support the analysis and safe use of partial functions, like CAR, which are well-defined only for arguments of a certain type. A language of type descriptors characterizes the type domain. Descriptors are composed into function signatures which characterize the guard and which map various combinations of actual parameter types to possible result types. From a base of signatures for a small collection of primitive functions, the system infers signatures for newly submitted functions. The system includes a type inference algorithm which handles constructs beyond the constraints of ML-style systems. Most notable are the free use of CONS to construct objects of undeclared type and the use of IF forms whose two result components have unrelated types, resulting in ad hoc polymorphism. Accordingly, the type descriptor language accommodates disjunction, unrestricted CONS, recursive type forms, and ad hoc polymorphic function signatures. As with traditional type inference systems, unification is a central algorithm, but the richness of our type language complicates many component algorithms, including unification. Special treatment is given to recognizer functions, which are predicates determining whether an object is of a particular type. Type inference in this setting is undecidable, so the algorithm is heuristic and is not complete. The semantics of the system are in terms of a function which determines whether values satisfy descriptors with respect to a binding of type variables. The soundness of each signature emitted by the system is validated by a signature checker, whose properties are formally specified with respect to the formal semantics and proven to hold. The checker algorithm is substantially simpler than the inference algorithm, as it need not perform operations such as discovering closed recursive forms. Thus, its proof is both more straightforward to construct and easier to validate than a direct proof of the inference algorithm would be.},
  file        = {:by-author/A/Akers/1993_Akers_techreport.pdf:PDF},
  keywords    = {Computer Languages; Computer Science (CS); Lisp; Static Typing; Type Systems},
  owner       = {saulius},
  pages       = {techreport},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Akitt1977,
  author    = {Akitt, J. W.},
  journal   = {The Computer Journal},
  title     = {Function Minimisation Using the Nelder And Mead Simplex Method With Limited Arithmetic Precision: The Self Regenerative Simplex},
  year      = {1977},
  pages     = {84--85},
  volume    = {20},
  file      = {:by-author/A/Akitt/1977_Akitt_84.pdf:PDF},
  keywords  = {Computer Science (CS); Minimisation; Simplex Method},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Akiyama2010,
  author    = {Akiyama, Shuji},
  journal   = {Journal of Applied Crystallography},
  title     = {Quality control of protein standards for molecular mass determinations by small-angle X-ray scattering},
  year      = {2010},
  pages     = {237–243},
  volume    = {43},
  abstract  = {Small-angle X-ray scattering (SAXS) is a powerful technique with which to evaluate the size and shape of biological macromolecules in solution. Forward scattering intensity normalized relative to the particle concentration,I(0)/c,is useful as a good measure of molecular mass. A general method for deducing the molecular mass from SAXS data is to determine the ratio of I(0)/c of a target protein to that of a standard protein with known molecular mass. The accuracy of this interprotein calibration is affected considerably by the monodispersity of the prepared standard, as well as by the precision in estimating its concentration. In the present study, chromatographic fractionation followed by hydrodynamic characterization is proposed as an effective procedure by which to prepare aseries of monodispersed protein standards. The estimation of molecular mass within an average deviation of 8% is demonstrated using monodispersed bovine serum albumin as a standard. The present results demonstrate the importance of protein standard quality control in order to take full advantage of interprotein calibration},
  doi       = {10.1107/S002188981000138X},
  file      = {:by-author/A/Akiyama/2010_Akiyama_237.pdf:PDF},
  keywords  = {Molecular Weight (MW); SAXS},
  owner     = {em},
  timestamp = {2013.10.25},
  creationdate = {2013-10-25T00:00:00},
}

@Article{Akiyama1996,
  author    = {Akiyama, T. and Hogan, M. E.},
  journal   = {The Journal of biological chemistry},
  title     = {Microscopic DNA flexibility analysis. Probing the base composition and ion dependence of minor groove compression with an artificial dna bending agent.},
  year      = {1996},
  pages     = {29126--35},
  volume    = {271},
  abstract  = {We have used an artificial DNA bending agent to monitor the local flexibility of the DNA helix as a function of Mg2+ cation concentration, sequence, and temperature. A DNA bending agent was constructed from a pair of triple helix-forming oligonucleotides connected by a flexible polymeric linker, which, when the linker is short enough, causes a bend in a minor groove region separating the two sites of triple helix formation. The unique aspect of this system is that, since the bent region is not in direct contact with the linker or the triple helix-forming oligonucleotides, the free energy reflecting the bendability of the minor helix groove can be estimated from a comparison of binding affinity between the bent and unbent triple helices. A binding competition experiment and association and dissociation kinetic assays executed at 37 degrees C in the presence of 10 mM Mg2+ have revealed an extremely small difference in binding affinity between bent (50 degrees ) and straight triple helices, suggesting that DNA flexibility with respect to minor groove compression is extremely high and virtually independent of the sequence of the distorted duplex. This unexpectedly small difference in binding affinity was detected over the temperature range from 25 to 65 degrees C, and over a Mg2+ concentration range from 0.3 to 10 mM. Thus, these findings provide evidence that DNA bendability for minor groove compression is inherently high and independent of DNA sequence, temperature, or a 30-fold variation of Mg2+ ion concentration.},
  file      = {:by-author/A/Akiyama/1996_Akiyama_29126.pdf:PDF},
  keywords  = {Bending; Readout},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Alazard2007,
  author    = {Alazard, Robert and Mourey, Lionel and Ebel, Christine and Konarev, Peter V. and Petoukhov, Maxim V. and Svergun, Dmitri I. and Erard, Monique},
  journal   = {Nucleic acids research},
  title     = {Fine-tuning of intrinsic N-Oct-3 POU domain allostery by regulatory DNA targets.},
  year      = {2007},
  pages     = {4420--32},
  volume    = {35},
  abstract  = {The 'POU' (acronym of Pit-1, Oct-1, Unc-86) family of transcription factors share a common DNA-binding domain of approximately 160 residues, comprising so-called 'POUs' and 'POUh' sub-domains connected by a flexible linker. The importance of POU proteins as developmental regulators and tumor-promoting agents is due to linker flexibility, which allows them to adapt to a considerable variety of DNA targets. However, because of this flexibility, it has not been possible to determine the Oct-1/Pit-1 linker structure in crystallographic POU/DNA complexes. We have previously shown that the neuronal POU protein N-Oct-3 linker contains a structured region. Here, we have used a combination of hydrodynamic methods, DNA footprinting experiments, molecular modeling and small angle X-ray scattering to (i) structurally interpret the N-Oct-3-binding site within the HLA DRalpha gene promoter and deduce from this a novel POU domain allosteric conformation and (ii) analyze the molecular mechanisms involved in conformational transitions. We conclude that there might exist a continuum running from free to 'pre-bound' N-Oct-3 POU conformations and that regulatory DNA regions likely select pre-existing conformers, in addition to molding the appropriate DBD structure. Finally, we suggest that a specific pair of glycine residues in the linker might act as a major conformational switch.},
  file      = {:by-author/A/Alazard/2007_Alazard_4420.pdf:PDF},
  keywords  = {Experiment; SAXS; Shape},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Alberts2011,
  author    = {Bruce Alberts},
  journal   = {Science},
  title     = {Editor’s Note},
  year      = {2011},
  pages     = {1149},
  volume    = {332},
  abstract  = {The research article “A bacterium that can grow by using arsenic instead of phosphorus” by F. Wolfe-Simon et al. [p. 1163, (1)] was the subject of extensive discussion and criticism following its online publication. Science received a wide range of correspon- dence that raised specific concerns about the Research Article’s methods and interpretations. Eight Technical Comments that represent the main concerns, as well as a Technical Response by Wolfe-Simon et al., are published online with this issue at the addresses listed below (all were previously published in Science Express on 27 May). They have been peer-reviewed and revised according to Science’s standard procedure.},
  editor    = {Jennifer Sills},
  file      = {2011_Alberts_1149.pdf:by-author/A/Alberts/2011_Alberts_1149.pdf:PDF},
  keywords  = {Arsenic Instead of Phosphorus},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Alder1970,
  author           = {Alder, B. J. and Wainwright, T. B.},
  journal          = {Physical Review A},
  title            = {Decay of the Velocity Autocorrelation Function},
  year             = {1970},
  pages            = {18},
  volume           = {1},
  abstract         = {Molecular-dynamic studies of the behavior of the diffusion coefficient after a long time $s$ have shown that the velocity autocorrelation function decays as $s^{-1}$ for hard disks and as $s^{3/2}$ for hard spheres, at least at intermediate fluid densities. A hydrodynamic similarity solution of the decay in velocity of an initially moving volume element in an otherwise stationary compressible viscous fluid agrees with a decay of ($(\ethta s)^{-d/2}$) where $\etha{}$ is the viscosity and $d$ is the dimensionality of the system. The slow decay, which would lead to a divergent diffusion coefficient in two dimensions, is caused by a vortex flow pattern which has been quantitatively calculations.},
  creationdate     = {2008-07-28T00:00:00},
  doi              = {10.1103/physreva.1.18},
  file             = {1970_Alder_18.pdf:by-author/A/Alder/1970_Alder_18.pdf:PDF},
  groups           = {sg/Molecular dynamics},
  keywords         = {Hard Spheres; Molecular Dynamics (MD)},
  modificationdate = {2023-04-23T10:15:13},
  owner            = {saulius},
  timestamp        = {2008.07.28},
}

@Article{Alder1962,
  author           = {B. J. Alder and T. E. Wainwright},
  journal          = {Physical Review},
  title            = {Phase Transition in Elastic Disks},
  year             = {1962},
  pages            = {359--361},
  volume           = {127},
  creationdate     = {2008-07-28T00:00:00},
  doi              = {10.1103/physrev.127.359},
  file             = {1962_Alder_359.pdf:by-author/A/Alder/1962_Alder_359.pdf:PDF},
  groups           = {sg/Molecular dynamics},
  keywords         = {Hard Spheres; Molecular Dynamics (MD)},
  modificationdate = {2023-04-23T10:15:24},
  owner            = {saulius},
  timestamp        = {2008.07.28},
}

@Article{Alder1957,
  author           = {B. J. Alder and T. E. Wainwright},
  journal          = {Journal of Chemical Physics},
  title            = {Phase Transition for a Hard Sphere System},
  year             = {1957},
  pages            = {1208},
  volume           = {27},
  creationdate     = {2008-07-28T00:00:00},
  doi              = {10.1063/1.1743957},
  file             = {1957_Alder_1208.pdf:by-author/A/Alder/1957_Alder_1208.pdf:PDF},
  groups           = {sg/Molecular dynamics},
  keywords         = {Hard Spheres; Molecular Dynamics (MD); Physics},
  modificationdate = {2023-01-29T14:05:24},
  owner            = {saulius},
  timestamp        = {2008.07.28},
  url              = {http://jcp.aip.org/resource/1/jcpsa6/v27/i5/p1208_s1},
}

@Presentation{Aldrich2005,
  author    = {Jonathan Aldrich},
  title     = {Hoare Logic},
  year      = {2005},
  file      = {:by-author/A/Aldrich/2005_Aldrich_slides.pdf:PDF},
  groups    = {sg/Correctness proofs},
  keywords  = {Computer Science (CS); Correctness Proofs},
  owner     = {saulius},
  pages     = {slides},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Alexander2008,
  author    = {Nathan Alexander and Ahmad Al-Mestarihi and Marco Bortolus and Hassane Mchaourab and Jens Meiler},
  journal   = {Structure},
  title     = {De novo high-resolution protein structure determination from sparse spin-labeling {EPR} data},
  year      = {2008},
  month     = {feb},
  number    = {2},
  pages     = {181--195},
  volume    = {16},
  doi       = {10.1016/j.str.2007.11.015},
  file      = {:by-author/A/Alexander/2008_Alexander_181.pdf:PDF},
  keywords  = {ESR; Structure Solution Methods},
  owner     = {saulius},
  publisher = {Elsevier {BV}},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Alexieva2009,
  author    = {B. Alexieva and S. Stoitsova and V. Pavlova and Ts. Paunova and E. Nikolova},
  journal   = {Biotechnology \& Biotechnological Equipment},
  title     = {Whey protein concentrate as a protective agent against doxorubicin-induced cardiotoxicity in mice},
  year      = {2009},
  pages     = {493--497},
  volume    = {23},
  abstract  = {Whey proteins are considered as functional food ingredients which have high cysteine content and promote the biosynthesis of glutathione– the primary intracellular antioxidant. Doxorubicin (DOX) is one of the most active antitumor antibiotics in current use. The therapeutic value of DOX, however, is limited by its toxicity. Oxidative stress is one of the underlying mechanisms of DOX toxicity in noncancerous (nontargeted) tissues. We investigated the protective effect of whey protein concentrate against DOX toxicity and oxidative stress. The administration of DOX (20 mg/kg i.p.) to BALB/c mice caused significant decrease of tissue glutathione level in the heart and severe histopathological changes, examined by light and transmission electron microscopy. These biochemical and histological alterations were effectively attenuated on pretreatment with whey protein concentrate. We therefore concluded that the protective action of whey is due to the enhancement of tissue glutathione level which might have important cytoprotective effects on oxidative stress, induced by DOX treatment.},
  file      = {2009_Alexieva_493.pdf:by-author/A/Alexieva/2009_Alexieva_493.pdf:PDF},
  keywords  = {Cardiotoxicity; Doxorubicin; Glutathione; Small Molecule Drugs; Whey Proteins},
  owner     = {saulius},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
  url       = {http://www.diagnosisp.com/dp/journals/view_article.php?journal_id=1&archive=0&issue_id=22&article_id=702},
}

@Article{Alfakih199X,
  author    = {Abdo Y. Alfakih and Amir Khandani and Henry Wolkowicz},
  title     = {Solving Euclidean distance matrix completion problems via semidefinite programming},
  year      = {199X},
  pages     = {1},
  file      = {199X_Alfakih_1.pdf:by-author/A/Alfakih/199X_Alfakih_1.pdf:PDF},
  keywords  = {Distance Matrices; Mathematics},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Ali2006,
  author    = {Maruf M. U. Ali and S. Mark Roe and Cara K. Vaughan and Phillipe Meyer and Barry Panaretou and Peter W. Piper and Chrisostomos Prodromou and Laurence H. Pearl},
  journal   = {Nature},
  title     = {Crystal structure of an Hsp90– nucleotide–p23/Sba1 closed chaperone complex},
  year      = {2006},
  pages     = {1013--1017},
  volume    = {440},
  abstract  = {Recently, two new immobilized polysaccharides based CSPs, namely tris-(3,5-dimethylphenylcarbamate) derivatives of amylose and cellulose known as Chiralpak IA and Chiralpak IB were introduced, which may be used with a wide range of solvents including standard and prohibited ones. Several racemic piperidine-2,6-dione analogues [aminoglutethimide, p-nitro-glutethimide, p-nitro-5-aminoglutethimide, cyclohexylaminoglutethimide, phenglutarimide and thalidomide] have been resolved on Chiralpak IA and Chiralpak IB columns (25cmx0.46cm). The non-conventional mobile phases used were methyl-tert-butyl ether-THF (90:10, v/v) [I], 100% dichloromethane [II] and 100% acetonitrile [III] separately at a flow rate of 1.0mL/min using a UV detector at 254nm. The resolution factors for Chiralpak IA and Chiralpak IB columns were 1.00-5.33 and 0.33-0.67, respectively. Chiralpak IA column gave better results than Chiralpak IB column for the reported molecules using the developed HPLC conditions. Experimental conditions and the possible chiral recognition mechanisms have been discussed.},
  doi       = {10.1038/nature04716},
  file      = {:by-author/A/Ali/2006_Ali_1013.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Allan1998,
  author    = {Allan, B. W. and Beechem, J. M. and Lindstrom, W. M. and Reich, N. O.},
  journal   = {The Journal of biological chemistry},
  title     = {Direct real time observation of base flipping by the EcoRI DNA methyltransferase.},
  year      = {1998},
  pages     = {2368--73},
  volume    = {273},
  abstract  = {DNA methyltransferases are excellent prototypes for investigating DNA distortion and enzyme specificity because catalysis requires the extrahelical stabilization of the target base within the enzyme active site. The energetics and kinetics of base flipping by the EcoRI DNA methyltransferase were investigated by two methods. First, equilibrium dissociation constants (KDDNA) were determined for the binding of the methyltransferase to DNA containing abasic sites or base analogs incorporated at the target base. Consistent with a base flipping mechanism, tighter binding to oligonucleotides containing destabilized target base pairs was observed. Second, total intensity stopped flow fluorescence measurements of DNA containing 2-aminopurine allowed presteady-state real time observation of the base flipping transition. Following the rapid formation of an enzyme-DNA collision complex, a biphasic increase in total intensity was observed. The fast phase dominated the total intensity increase with a rate nearly identical to k(methylation) determined by rapid chemical quench-flow techniques (Reich, N. O., and Mashoon, N. (1993) J. Biol. Chem. 268, 9191-9193). The restacking of the extrahelical base also revealed biphasic kinetics with the recovered amplitudes from these off-rate experiments matching very closely to those observed during the base unstacking process. These results provide the first direct and continuous observation of base flipping and show that at least two distinct conformational transitions occurred at the flipped base subsequent to complex formation. Furthermore, our results suggest that the commitment to catalysis during the methylation of the target site is not determined at the level of the chemistry step but rather is mediated by prior intramolecular isomerization within the enzyme-DNA complex.},
  file      = {:by-author/A/Allan/1998_Allan_2368.pdf:PDF},
  keywords  = {MTases},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Allen2002,
  author    = {Allen, Frank H.},
  journal   = {Acta Crystallographica Section B},
  title     = {The Cambridge Structural Database: a quarter of a million crystal structures and rising},
  year      = {2002},
  pages     = {380--388},
  volume    = {58},
  abstract  = {The creation, maintenance, information content and availability of the Cambridge Structural Database are summarized. Statistics show that the CSD will contain at least half a million crystal structures by the year 2010.},
  doi       = {10.1107/S0108768102003890},
  file      = {2002_Allen_380.pdf:by-author/A/Allen/2002_Allen_380.pdf:PDF},
  keywords  = {CCDC; CSD; Data Access Policy; Data Management; Databases},
  owner     = {saulius},
  timestamp = {2014.06.30},
  creationdate = {2014-06-30T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0108768102003890},
}

@InBook{Allen2006,
  author           = {F. H. Allen and J. M. Barnard and A. P. F. Cook and S. R. Hall},
  chapter          = {4.8 Molecular Information File dictionary (MIF)},
  editor           = {Sydney Hall and Brian Mcmahon},
  pages            = {467--470},
  publisher        = {Springer},
  title            = {International Tables for Crystallography},
  year             = {2006},
  volume           = {G},
  creationdate     = {2013-11-14T00:00:00},
  doi              = {10.1107/97809553602060000748},
  file             = {2006_Allen_467.pdf:by-author/A/Allen/2006_Allen_467.pdf:PDF},
  groups           = {am/MIF},
  keywords         = {CIF; Crystallography; Data Formats; Data Management; MIF},
  modificationdate = {2023-08-07T10:23:05},
  owner            = {saulius},
  timestamp        = {2013.11.14},
}

@Article{Allen1995,
  author           = {Frank H. Allen and John M. Barnard and Anthony P. F. Cook and Sydney R. Hall},
  journal          = {Journal of Chemical Information and Computer Sciences},
  title            = {The {M}olecular {I}nformation {F}ile ({MIF}): Core Specifications of a New Standard Format for Chemical Data},
  year             = {1995},
  pages            = {412--427},
  volume           = {35},
  abstract         = {The initial core data definitions of a universal data exchange format for chemical information is proposed. The Molecular Information File (MIF) represents a coalescence of two major format developments: the Standard Molecular Data Format (SMD) and the Crystallographic Information File that conforms to the STAR (Self-Defining Text Archive and Retrieval) syntax. Essentially, the MIF is a re-expression of the major SMD concepts using STAR syntax. The core data items, defined here, cover chemical connectivity representations, stereochemistry, and associated data for complete 2D and 3D molecules and for 2D substructural queries.},
  creationdate     = {2012-10-21T00:00:00},
  doi              = {10.1021/ci00025a009},
  file             = {:by-author/A/Allen/1995_Allen_412.pdf:PDF},
  groups           = {am/MIF},
  keywords         = {CIF; Crystallography; Data Formats; Data Management; MIF; Molecular Information File},
  modificationdate = {2023-08-07T10:23:05},
  owner            = {saulius},
  timestamp        = {2012.10.21},
  url              = {http://pubs.acs.org/doi/abs/10.1021/ci00025a009},
}

@Article{Allen1994a,
  author    = {Allen, Frank H. and Garner, Stephanie E. Howard, Judith A. K. and Pitchford, Nigel A.},
  journal   = {Acta Crystallographica Section B},
  title     = {Symmetry-Modified Conformational Mapping and Classification of the Medium Rings from Crystallographic Data. {III}. endo-Unsaturated Seven-Membered Rings},
  year      = {1994},
  pages     = {395--404},
  volume    = {50},
  file      = {:by-author/A/Allen/1994_Allen_395.pdf:PDF},
  keywords  = {Cremer & Pople Parameters},
  owner     = {andrius},
  timestamp = {2012.08.15},
  creationdate = {2012-08-15T00:00:00},
}

@Article{Allen1996,
  author    = {Allen, Frank H. and Howard, Judith A. K. and Pitchford, Nigel A.},
  journal   = {Acta Crystallographica Section B},
  title     = {Symmetry-Modified Conformational Mapping and Classification of the Medium Rings from Crystallographic Data. {IV}. Cyclooctane and Related Eight-Membered Rings},
  year      = {1996},
  pages     = {882--891},
  volume    = {52},
  file      = {:by-author/A/Allen/1996_Allen_882.pdf:PDF},
  keywords  = {Cremer & Pople Parameters},
  owner     = {andrius},
  timestamp = {2012.08.15},
  creationdate = {2012-08-15T00:00:00},
}

@Article{Allen1993a,
  author    = {Allen, Frank H. and Howard, Judith A. K. and Pitchford, Nigel A.},
  journal   = {Acta Crystallographica Section B},
  title     = {Symmetry-Modified Conformational Mapping and Classification of the Medium Rings from Crystallographic Data. {I}. Cycloheptane},
  year      = {1993},
  pages     = {910--928},
  volume    = {49},
  file      = {:by-author/A/Allen/1993_Allen_910.pdf:PDF},
  keywords  = {Cremer & Pople Parameters},
  owner     = {andrius},
  timestamp = {2012.08.15},
  creationdate = {2012-08-15T00:00:00},
}

@Article{Allen1994,
  author    = {Allen, Frank H. and Howard, Judith A. K. and Pitchford, Nigel A. and Vinter, J. G.},
  journal   = {Acta Crystallographica Section B},
  title     = {Symmetry-Modified Conformational Mapping and Classification of the Medium Rings from Crystallographic Data. {II}. exo-Unsaturated and Heterocyclic Seven-Membered Rings},
  year      = {1994},
  pages     = {382--395},
  volume    = {50},
  file      = {:by-author/A/Allen/1994_Allen_382.pdf:PDF},
  keywords  = {Cremer & Pople Parameters},
  owner     = {andrius},
  timestamp = {2012.08.15},
  creationdate = {2012-08-15T00:00:00},
}

@Article{Allen2004,
  author           = {Allen, Frank H. and Johnson, Owen and Shields, Gregory P. and Smith, Barry R. and Towler, Matthew},
  journal          = {Journal of Applied Crystallography},
  title            = {{CIF} applications. {XV}. {\it {enCIFer}}: a program for viewing, editing and visualizing {CIF}s},
  year             = {2004},
  pages            = {335--338},
  volume           = {37},
  abstract         = {The enCIFer program permits the location, reporting and correction of syntax and format violations in single- or multi-block crystallographic information files (CIFs). The program also permits the editing of existing individual or looped data items and the addition of new data in these categories, and provides data-entry wizards for the addition of two types of standard information for small-molecule structural studies, namely publication data and chemical and physical property information. Facilities for the graphical visualization and manipulation of structure(s) in a CIF are also provided.},
  creationdate     = {2014-06-30T00:00:00},
  doi              = {10.1107/S0021889804003528},
  file             = {2004_Allen_335.pdf:by-author/A/Allen/2004_Allen_335.pdf:PDF},
  keywords         = {CIF; Data Presentation; EnCIFer; Software; X-ray Crystallography},
  modificationdate = {2023-08-07T10:23:05},
  owner            = {saulius},
  timestamp        = {2014.06.30},
  url              = {http://dx.doi.org/10.1107/S0021889804003528},
}

@Article{Allen1987,
  author    = {Frank H. Allen and Olga Kennard and David G. Watson and Lee Brammer and A. Guy Orpen and Robin Taylor},
  journal   = {J. Chem. Soc., Perkin Trans. 2},
  title     = {Tables of bond lengths determined by {X}-ray and neutron diffraction. {P}art 1. {B}ond lengths in organic compounds},
  year      = {1987},
  pages     = {S1-S19},
  abstract  = {The average lengths of bonds involving the elements H, B, C, N, O, F, Si, P, S, Cl, As, Se, Br, Te, and l in organic compounds are reported.},
  doi       = {10.1039/P298700000S1},
  file      = {:by-author/A/Allen/1987_Allen_S1.pdf:PDF},
  keywords  = {Restrains},
  owner     = {andrius},
  timestamp = {2013.04.22},
  creationdate = {2013-04-22T00:00:00},
  url       = {http://dx.doi.org/10.1039/P298700000S1},
}

@Article{Allen2005,
  author    = {Allen, Frank H. and Taylor, Robin},
  journal   = {Chemical communications (Cambridge, England)},
  title     = {Librarians, crystal structures and drug design.},
  year      = {2005},
  month     = {Sep},
  number    = {41},
  pages     = {5135--40},
  abstract  = {There are now 355,000 published crystal structures of organic and metal-organic compounds, all of which have been acquired, validated, chemically annotated and organised for searching in the Cambridge Structural Database (CSD). The CSD is used in rational drug design and is beginning to answer important questions relevant to the formulation of pharmaceutical active ingredients. The value and credibility of this research are ultimately dependent on the accuracy and completeness of the underlying crystal-structure data.},
  doi       = {10.1039/B511106B},
  file      = {:by-author/A/Allen/2005_Allen_5135.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://pubs.rsc.org/en/content/articlelanding/2005/cc/b511106b},
}

@Article{Allen1993,
  author           = {Allen, Jr., G. C. and Kornberg, A.},
  journal          = {The Journal of biological chemistry},
  title            = {Assembly of the primosome of DNA replication in Escherichia coli.},
  year             = {1993},
  pages            = {19204--9},
  volume           = {268},
  abstract         = {Assembly of the Escherichia coli primosome requires six proteins, PriA, PriB, PriC, DnaB, DnaC, and DnaT, acting at a primosome assembly site (pas) on an SSB-coated single-stranded (ss) DNA. Assembly is initiated by interactions of PriA and PriB with ssDNA and the pas. PriC, DnaB, DnaC, and DnaT then act on the PriA-PriB-DNA complex to yield the primosome. In the primosome, the dATPase (ATPase) of PriA becomes hyper-activated. In addition, the assembled primosome appears to block the pas, preventing it from activating additional PriA molecules. Either ATP alone or dATP in combination with GTP is sufficient for primosome assembly, while ATP or GTP provides for its maintenance during isolation. These nucleotide requirements can be reconciled with the need for ATP or dATP for DnaB-DnaC complex formation and hydrolysis of ATP or GTP by DnaB when it binds ssDNA. Such isolated primosomes contain a dATPase, the hallmark of PriA, and a GTPase indicative of DnaB. Further studies indicate that the isolated primosome contains the PriB replication activity in addition to PriA and DnaB.},
  creationdate     = {2008-07-28T00:00:00},
  doi              = {10.1016/s0021-9258(19)36500-7},
  file             = {:by-author/A/Allen/1993_Allen_19204.pdf:PDF},
  keywords         = {Ecoli; {gp41} Helicase},
  modificationdate = {2023-04-23T10:15:53},
  owner            = {em},
  timestamp        = {2008.07.28},
}

@Presentation{Allen2005a,
  author    = {Allen, Phil (?)},
  title     = {(History of Quantum Chemistry)},
  year      = {2005},
  file      = {2005_Allen_slides.pdf:by-author/A/Allen/2005_Allen_slides.pdf:PDF},
  keywords  = {Density Functional Theory (DFT); History},
  owner     = {saulius},
  timestamp = {2014.10.21},
  creationdate = {2014-10-21T00:00:00},
  url       = {http://felix.physics.sunysb.edu/~allen/Pdffiles/dft.pdf},
}

@Manuscript{Allison2004,
  author    = {John R. Allison and Emerson H. Tiller},
  title     = {The Business Method Patent Myth},
  year      = {2004},
  keywords  = {Patentai; Teise},
  file      = {:by-author/A/Allison/2004_Allison.doc:DOC},
  owner     = {saulius},
  timestamp = {2015.02.28},
  creationdate = {2015-02-28T00:00:00},
}

@InProceedings{deAlmeida2006,
  author    = {de Almeida, Victor Teixeira and G\"{u}ting, Ralf Hartmut},
  booktitle = {Proceedings of the 2006 ACM symposium on Applied computing},
  title     = {Using Dijkstra's Algorithm to Incrementally Find the K-Nearest Neighbors in Spatial Network Databases},
  year      = {2006},
  address   = {New York, NY, USA},
  pages     = {58--62},
  publisher = {ACM},
  series    = {SAC '06},
  abstract  = {One of the most important kinds of queries in Spatial Network Databases (SNDB) to support Location-Based Services (LBS) is the k-Nearest Neighbors (k-NN) query. Given a point in a network, e.g. a location of a car on a road network, and a set of points of interests, e.g. hotels, gas stations, etc., the k-NN query returns the k points of interest closest to the query point. The network distance is used in such a query instead of the Euclidean distance. Dijkstra's algorithm is a well known solution to this problem. In this paper, we propose a storage schema with a set of index structures to support an efficient execution of a slightly modified version of the Dijkstra's algorithm. We show in an experimental evaluation with generated data sets that our proposal is more efficient than the state-of-the-art solution to this problem.},
  doi       = {10.1145/1141277.1141291},
  file      = {:by-author/d/deAlmeida/2006_deAlmeida_58.pdf:PDF},
  isbn      = {1-59593-108-2},
  keywords  = {Index Structures; Location Based Services; Nearest Neighbors; Spatial Databases},
  location  = {Dijon, France},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://doi.acm.org/10.1145/1141277.1141291},
}

@Article{Alon2009,
  author    = {Uri Alon},
  journal   = {Molecular Cell},
  title     = {How To Give a Good Talk},
  year      = {2009},
  pages     = {165},
  volume    = {36},
  abstract  = {We depend on talks to communicate our work, and we spend much of our time as audience members in talks. However, few scientists are taught the well-established principles of giving good talks. Here, I describe how to prepare, present, and answer questions in a scientific talk. We will see how a talk prepared with a single premise and delivered with good eye contact is clear and enjoyable.},
  doi       = {10.1016/j.molcel.2009.10.007},
  file      = {:by-author/A/Alon/2009_Alon_165.pdf:PDF},
  owner     = {saulius},
  timestamp = {2013.03.22},
  creationdate = {2013-03-22T00:00:00},
}

@Article{Alonso2006,
  author    = {Alonso, Hernán and Bliznyuk, Andrey A. and Gready, Jill E.},
  journal   = {Medicinal research reviews},
  title     = {Combining docking and molecular dynamic simulations in drug design.},
  year      = {2006},
  pages     = {531--68},
  volume    = {26},
  abstract  = {A rational approach is needed to maximize the chances of finding new drugs, and to exploit the opportunities of potential new drug targets emerging from genomic and proteomic initiatives, and from the large libraries of small compounds now readily available through combinatorial chemistry. Despite a shaky early history, computer-aided drug design techniques can now be effective in reducing costs and speeding up drug discovery. This happy outcome results from development of more accurate and reliable algorithms, use of more thoughtfully planned strategies to apply them, and greatly increased computer power to allow studies with the necessary reliability to be performed. Our review focuses on applications and protocols, with the main emphasis on critical analysis of recent studies where docking calculations and molecular dynamics (MD) simulations were combined to dock small molecules into protein receptors. We highlight successes to demonstrate what is possible now, but also point out drawbacks and future directions. The review is structured to lead the reader from the simpler to more compute-intensive methods. Thus, while inexpensive and fast docking algorithms can be used to scan large compound libraries and reduce their size, more accurate but expensive MD simulations can be applied when a few selected ligand candidates remain. MD simulations can be used: during the preparation of the protein receptor before docking, to optimize its structure and account for protein flexibility; for the refinement of docked complexes, to include solvent effects and account for induced fit; to calculate binding free energies, to provide an accurate ranking of the potential ligands; and in the latest developments, during the docking process itself to find the binding site and correctly dock the ligand a priori.},
  file      = {:by-author/A/Alonso/2006_Alonso_531.pdf:PDF},
  keywords  = {Drug Design},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Aloy2003,
  author    = {Aloy, Patrick and Ceulemans, Hugo and Stark, Alexander and Russell, Robert B.},
  journal   = {Journal of molecular biology},
  title     = {The relationship between sequence and interaction divergence in proteins.},
  year      = {2003},
  number    = {5},
  pages     = {989--998},
  volume    = {332},
  abstract  = {There is currently a gap in knowledge between complexes of known three-dimensional structure and those known from other experimental methods such as affinity purifications or the two-hybrid system. This gap can sometimes be bridged by methods that extrapolate interaction information from one complex structure to homologues of the interacting proteins. To do this, it is important to know if and when proteins of the same type (e.g. family, superfamily or fold) interact in the same way. Here, we study interactions of known structure to address this question. We found all instances within the structural classification of proteins database of the same domain pairs interacting in different complexes, and then compared them with a simple measure (interaction RMSD). When plotted against sequence similarity we find that close homologues (30-40% or higher sequence identity) almost invariably interact the same way. Conversely, similarity only in fold (i.e. without additional evidence for a common ancestor) is only rarely associated with a similarity in interaction. The results suggest that there is a twilight zone of sequence similarity where it is not possible to say whether or not domains will interact similarly. We also discuss the rare instances of fold similarities interacting the same way, and those where obviously homologous proteins interact differently.},
  doi       = {10.1016/j.jmb.2003.07.006},
  file      = {:by-author/A/Aloy/2003_Aloy_989.pdf:pdf},
  keywords  = {Validation},
  owner     = {saulius},
  pii       = {S0022283603009999},
  pubmed    = {14499603},
  timestamp = {2016.12.12},
  creationdate = {2016-12-12T00:00:00},
}

@Article{Alterio2012,
  author    = {Alterio, Vincenzo and Di Fiore, Anna and D’Ambrosio, Katia and Supuran, Claudiu T. and De Simone, Giuseppina},
  journal   = {Chemical Reviews},
  title     = {Multiple Binding Modes of Inhibitors to Carbonic Anhydrases: How to Design Specific Drugs Targeting 15 Different Isoforms?},
  year      = {2012},
  pages     = {4421--4468},
  volume    = {112},
  doi       = {10.1021/cr200176r},
  file      = {:by-author/A/Alterio/2012_Alterio_4421.pdf:PDF},
  groups    = {sg/reviews},
  keywords  = {Carbonic Anhydrases; Inhibitors; Lidand; Review; {hCA}},
  owner     = {em},
  timestamp = {2013.02.21},
  creationdate = {2013-02-21T00:00:00},
}

@Article{Althorpe1999,
  author    = {Althorpe, N. J. and Chilley, P. M. and Thomas, A. T. and Brammar, W. J. and Wilkins, B. M.},
  journal   = {Molecular microbiology},
  title     = {Transient transcriptional activation of the Incl1 plasmid anti-restriction gene (ardA) and SOS inhibition gene (psiB) early in conjugating recipient bacteria.},
  year      = {1999},
  pages     = {133--42},
  volume    = {31},
  abstract  = {The ardA gene of the enterobacterial plasmid CollbP-9 acts to alleviate restriction of DNA by type I systems, while psiB inhibits induction of the bacterial SOS response. Both genes are transferred early in a round of bacterial conjugation as part of the plasmid leading region. We report here that ardA and psiB are transcribed transiently after their conjugative transport into the recipient cell. Transcript levels, monitored by competitive reverse transcription-polymerase chain reaction (RT-PCR) amplification of RNA templates, started to increase about 5 min after the initiation of conjugation in a cell population and probably before the first round of plasmid transfer was completed. Genetic evidence is given that the expression of ardA and psiB is activated when the genes enter the recipient cell on the transferring plasmid strand. It is proposed that these and other leading region genes function to promote the establishment of the immigrant plasmid in the new host and are expressed by transcription from promoters active only in single-stranded DNA.},
  file      = {:by-author/A/Althorpe/1999_Althorpe_133.pdf:PDF},
  keywords  = {Antirestriction},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Presentation{Altiparmak2007,
  author       = {Fatih Altiparmak and David Chiu and Hakan Ferhatosmanoglu},
  title        = {Incremental Quantization for Aging Data Streams},
  year         = {2007},
  organization = {Database Research Group, Dept. of Computer Science and Engineering},
  school       = {Ohio State University},
  file         = {:by-author/A/Altiparmak/2007_Altiparmak.ppt:PPT},
  keywords     = {Computer Science (CS); Continuous_data; Databases},
  owner        = {saulius},
  timestamp = {2015.03.03},
  creationdate = {2015-03-03T00:00:00},
}

@InBook{Altman2008,
  author           = {Altman, Micah},
  editor           = {Sobh, Tarek},
  pages            = {311--316},
  publisher        = {Springer Netherlands},
  title            = {A Fingerprint Method for Scientific Data Verification},
  year             = {2008},
  address          = {Dordrecht},
  isbn             = {978-1-4020-8741-7},
  abstract         = {This article discusses an algorithm (called "UNF") for verifying digital data matrices. This algorithm is now used in a number of software packages and digital library projects. We discuss the details of the algorithm, and offer an extension for normalization of time and duration data.},
  booktitle        = {Advances in Computer and Information Sciences and Engineering},
  comment          = {Cited by Rauber2016a.},
  creationdate     = {2016-11-21T00:00:00},
  doi              = {10.1007/978-1-4020-8741-7_57},
  file             = {2008_Altman_311.pdf:by-author/A/Altman/2008_Altman_311.pdf:PDF},
  keywords         = {Checksums; Computer Science (CS); Data Management; Fingerprints; Reproducible Research},
  modificationdate = {2023-01-03T09:22:34},
  owner            = {saulius},
  timestamp        = {2016.11.21},
  url              = {http://dx.doi.org/10.1007/978-1-4020-8741-7_57},
}

@Article{Altomare2015,
  author    = {Altomare, Angela and Corriero, Nicola and Cuocci, Corrado and Falcicchio, Aurelia and Moliterni, Anna and Rizzi, Rosanna},
  journal   = {J Appl Crystallogr},
  title     = {{QUALX2.0}: a qualitative phase analysis software using the freely available database {POW_COD}},
  year      = {2015},
  issn      = {1600-5767},
  month     = {Feb},
  number    = {2},
  pages     = {598–603},
  volume    = {48},
  doi       = {10.1107/s1600576715002319},
  file      = {:by-author/A/Altomare/2015_Altomare_598.pdf:PDF},
  keywords  = {Citing COD},
  owner     = {andrius},
  publisher = {International Union of Crystallography (IUCr)},
  timestamp = {2016.01.11},
  creationdate = {2016-01-11T00:00:00},
  url       = {http://dx.doi.org/10.1107/S1600576715002319},
}

@Article{Altschul1986,
  author           = {Altschul, S. F. and Erickson, B. W.},
  journal          = {Bulletin of mathematical biology},
  title            = {Optimal sequence alignment using affine gap costs.},
  year             = {1986},
  pages            = {603--16},
  volume           = {48},
  abstract         = {When comparing two biological sequences, it is often desirable for a gap to be assigned a cost not directly proportional to its length. If affine gap costs are employed, in other words if opening a gap costs v and each null in the gap costs u, the algorithm of Gotoh (1982,J. molec. Biol. 162, 705) finds the minimum cost of aligning two sequences in order M N steps. Gotoh's algorithm attempts to find only one from among possibly many optimal (minimum-cost) alignments, but does not always succeed. This paper provides an example for which this part of Gotoh's algorithm fails and describes an algorithm that finds all and only the optimal alignments. This modification of Gotoh's algorithm still requires order M N steps. A more precise form of path graph than previously used is needed to represent accurately all optimal alignments for affinegap costs.},
  creationdate     = {2013-07-01T00:00:00},
  doi              = {10.1007/BF02462326},
  file             = {:by-author/A/Altschul/1986_Altschul_603.pdf:PDF},
  keywords         = {Affine Gap Cost; Algorithm Failure; Algorithms; Alignment With Gaps; Bioinformatics; Bugs; Criticism; Gap Cost; Needleman-Wunsch Algorithm; Sequence Alignment},
  modificationdate = {2023-02-08T20:14:38},
  owner            = {saulius},
  timestamp        = {2013.07.01},
}

@Article{Alva2008,
  author    = {Alva, Vikram and Koretke, Kristin K. and Coles, Murray and Lupas, Andrei N.},
  journal   = {Current opinion in structural biology},
  title     = {Cradle-loop barrels and the concept of metafolds in protein classification by natural descent.},
  year      = {2008},
  pages     = {358--65},
  volume    = {18},
  abstract  = {Current classification systems for protein structure show many inconsistencies both within and between systems. The metafold concept was introduced to identify fold similarities by consensus and thus provide a more unified view of fold space. Using cradle-loop barrels as an example, we propose to use the metafold as the next hierarchical level above the fold, encompassing a group of topologically related folds for which a homologous relationship has been substantiated. We see this as an important step on the way to a classification of proteins by natural descent.},
  file      = {:by-author/A/Alva/2008_Alva_358.pdf:PDF},
  keywords  = {Evolution},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Alvarez2013,
  author    = {Santiago Alvarez},
  journal   = {Dalton Transactions},
  title     = {A cartography of the van der {W}aals territories},
  year      = {2013},
  pages     = {8617--8636},
  volume    = {42},
  abstract  = {The distribution of distances from atoms of a particular element E to a probe atom X (oxygen in most cases), both bonded and intermolecular non-bonded contacts, has been analyzed. In general, the distribution is characterized by a maximum at short EX distances corresponding to chemical bonds, followed by a range of unpopulated distances – the van der Waals gap – and a second maximum at longer distances – the van der Waals peak – superimposed on a random distribution function that roughly follows a d3 dependence. The analysis of more than five million interatomic “non-bonded” distances has led to the proposal of a consistent set of van der Waals radii for most naturally occurring elements, and its applicability to other element pairs has been tested for a set of more than three million data, all of them compared to over one million bond distances.},
  doi       = {10.1039/c3dt50599e},
  file      = {:by-author/A/Alvarez/2012_Alvarez_8617.pdf:PDF},
  keywords  = {Van Der Waals},
  owner     = {antanas},
  timestamp = {2014.06.19},
  creationdate = {2014-06-19T00:00:00},
  url       = {http://pubs.rsc.org/en/Content/ArticleLanding/2013/DT/c3dt50599e#!divAbstract},
}

@Manuscript{Alvis2011,
  author    = {Claire E. Alvis and Jeremiah J. Willcock and Kyle M. Carter and William E. Byrd and Daniel P. Friedman},
  title     = {cKanren: miniKanren with Constraints},
  year      = {2011},
  keywords  = {Computer Languages; Computer Science (CS); Oregon Workshop; Scheme},
  abstract  = {We present cKanren, a framework for constraint logic pro- gramming (CLP) in Scheme. cKanren subsumes miniKan- ren, a logic programming language embedded in Scheme. cKanren allows programmers to easily use, define, and com- bine different kinds of constraints. We provide two example constraint systems: one over finite domains and one over trees. The cKanren framework is designed to encourage an especially pure style of logic programming in which goals can be reordered arbitrarily without affecting a program’s semantics (with an important decidability-related caveat). We develop the complete implementation of the cKanren framework, written in R6RS Scheme extended with SRFI 39 parameters. We present the implementation of cKanren’s finite domain and disequality constraint solvers, and we provide introductions to miniKanren, cKanren, and numer- ous example programs, including the Send More Money cryptarithmetic puzzle and N-Queens.},
  file      = {:by-author/A/Alvis/2011_Alvis.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@TechReport{AMD2000,
  author      = {AMD},
  institution = {Advanced Micro Devices, Inc.},
  title       = {Linux Kernel Issue with Systems Using AGP Graphics},
  year        = {2000},
  file        = {:by-author/A/AMD/2000_AMD_appnote.pdf:PDF},
  keywords    = {Computer Science (CS); Linux; Operating Systems},
  owner       = {saulius},
  pages       = {appnote},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Ames1997,
  author    = {Ames, James B. and Ishima, Rieko and Tanaka, Toshiyuki and Gordon, Jeffrey I. and Stryer, Lubert and Ikura, Mitsuhiko},
  journal   = {Nature},
  title     = {Molecular mechanics of calcium–myristoyl switches},
  year      = {1997},
  issn      = {0028-0836},
  pages     = {198--202},
  volume    = {389},
  abstract  = {Many eukaryotic cellular and viral proteins have a covalently attached myristoyl group at the amino terminus. One such protein is recoverin, a calcium sensor in retinal rod cells, which controls the lifetime of photoexcited rhodopsin by inhibiting rhodopsin kinase. Recoverin has a relative molecular mass of 23,000 (Mr 23K), and contains an amino-terminal myristoyl group (or related acyl group) and four EF hands. The binding of two Ca2+ ions to recoverin leads to its translocation from the cytosol to the disc membrane,. In the Ca2+-free state, the myristoyl group is sequestered in a deep hydrophobic box, where it is clamped by multiple residues contributed by three of the EF hands. We have used nuclear magnetic resonance to show that Ca2+ induces the unclamping and extrusion of the myristoyl group, enabling it to interact with a lipid bilayer membrane. The transition is also accompanied by a 45-degree rotation of the amino-terminal domain relative to the carboxy-terminal domain, and many hydrophobic residues are exposed. The conservation of the myristoyl binding site and two swivels in recoverin homologues from yeast to humans indicates that calcium–myristoyl switches are ancient devices for controlling calcium-sensitive processes.},
  copyright = {© 1997 Nature Publishing Group},
  doi       = {10.1038/38310},
  file      = {Full Text PDF:by-author/A/Ames/1997_Ames_198.pdf:application/pdf;Snapshot:by-author/A/Ames/1997_Ames_198.html:text/html},
  groups    = {sg/biomolecular},
  language  = {en},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://www.nature.com/nature/journal/v389/n6647/abs/389198a0.html},
  urldate   = {2015-08-05},
}

@Article{Amin2015,
  author    = {Bengag Amin and Allem Rachida},
  journal   = {Biomolecular Research \& Therapeutics},
  title     = {Anti-inflammatory Activity Citrus Essence ({C}. sinensis and {C}. aurantium) Local to Chlef Region (algeria): {In} vivo study},
  year      = {2015},
  pages     = {126},
  volume    = {4},
  file      = {Bengag Amin and Allem Rachida - 2015 - Anti-inflammatory Activity Citrus Essence (C. Sine.pdf:by-author/A/Amin/2015_Amin_126.pdf:application/pdf},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://www.omicsgroup.org/journals/antiinflammatory-activity-citrus-essence-c-sinensis-and-c-aurantiumlocal-to-chlef-region-algeria-in-vivo-study-2167-7956-1000126.pdf},
  urldate   = {2015-09-07},
}

@Article{Amit1978,
  author    = {Amit, A. and Mester, L. and Klewe, B. and Furberg, S.},
  journal   = {Acta Chemica Scandinavica},
  title     = {The Crystal Structure of Serotonin Hydrogen Oxalate},
  year      = {1978},
  pages     = {267--270},
  volume    = {32a},
  doi       = {10.3891/acta.chem.scand.32a-0267},
  file      = {:by-author/A/Amit/1978_Amit_267.pdf:PDF},
  keywords  = {Crude Data for COD},
  owner     = {andrius},
  timestamp = {2013.05.17},
  creationdate = {2013-05-17T00:00:00},
}

@Article{Amorin2012,
  author    = {Amorín, Harvey and Chateigner, Daniel and Holc, Janez and Kosec, Marija and Alguero, Miguel and Ricote, Jesus},
  journal   = {Journal of the American Ceramic Society},
  title     = {Combined structural and quantitative texture analysis of morphotropic phase boundary {Pb} ({Mg}1/3Nb2/3) {O}3-{PbTiO}3 ceramics},
  year      = {2012},
  pages     = {2965--2971},
  volume    = {95},
  file      = {[PDF] from researchgate.net:by-author/A/Amorín/2012_Amorín_2965.pdf:application/pdf;Snapshot:by-author/A/Amorín/2012_Amorín_2965.html:text/html},
  groups    = {sg/JAC2009},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://onlinelibrary.wiley.com/doi/10.1111/j.1551-2916.2012.05261.x/pdf},
  urldate   = {2015-08-31},
}

@Article{An2002,
  author    = {An, Byeong-Kwan and Kwon, Soon-Ki and Jung, Sang-Don and Park, Soo Young},
  journal   = {Journal of the American Chemical Society},
  title     = {Enhanced emission and its switching in fluorescent organic nanoparticles},
  year      = {2002},
  issn      = {0002-7863},
  pages     = {14410--14415},
  volume    = {124},
  abstract  = {A new class of organic nanoparticles (CN-MBE nanoparticles) with a mean diameter of ca. 3040 nm, which exhibit a strongly enhanced fluorescence emission, were prepared by a simple reprecipitation method. CN-MBE (1-cyano-trans-1,2-bis-(4'-methylbiphenyl)ethylene) is very weakly fluorescent in solution, but the intensity is increased by almost 700 times in the nanoparticles. Enhanced emission in CN-MBE nanoparticles is attributed to the synergetic effect of intramolecular planarization and J-type aggregate formation (restricted excimer formation) in nanopaticles. On/off fluorescence switching for organic vapor was demonstrated with CN-MBE nanoparticles.},
  doi       = {10.1021/ja0269082},
  file      = {An et al. - 2002 - Enhanced Emission and Its Switching in Fluorescent.pdf:by-author/A/An/2002_An_14410.pdf:application/pdf;ACS Full Text Snapshot:by-author/A/An/2002_An_14410.html:text/html},
  groups    = {sg/chemical},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://dx.doi.org/10.1021/ja0269082},
  urldate   = {2015-08-21},
}

@Article{Anarbaev1995,
  author    = {Anarbaev, R. O. and Vladimirova, O. V. and Lavrik, O. I.},
  journal   = {European journal of biochemistry / FEBS},
  title     = {The interaction of synthetic templates with eukaryotic DNA primase.},
  year      = {1995},
  pages     = {60--7},
  volume    = {228},
  abstract  = {The template interaction of calf thymus and human placenta DNA primases has been investigated. Using oligothymidylates, we showed that a template consisting of ten monomeric units was the critical size for interaction with the enzyme. The hydrophobic effect is likely to be a major factor determining template recognition by the DNA primase. The correlation between the template affinity with the enzyme and the octanol-water hydrophobic scale confirms this suggestion. In addition, the electrostatic interaction between the phosphate group of the template and side chains on the enzyme probably increases template affinity. Using methylated poly(dA), we found that the first nucleotide base of the primer should be more hydrophobic than the corresponding nucleotide base of the template. A model for the mechanism of action of DNA primase is suggested on the basis of data presented in this study and previous findings. According to this model, (a) DNA primase binds ten nucleotides of the template; (b) the synthesis of primer up to the formation of a decamer occurs processively and competes with template binding of the enzyme; (c) the conditions under which the nucleotides are incorporated into the RNA product change during the extension of the primer, and these changes are responsible for switching from primase to polymerase activity. The template specificity of DNA primase is likely to play an important role in the initiation and regulation of DNA replication.},
  file      = {:by-author/A/Anarbaev/1995_Anarbaev_60.pdf:PDF},
  owner     = {em},
  timestamp = {2013.09.19},
  creationdate = {2013-09-19T00:00:00},
}

@Article{Anastas2003,
  author    = {Dina Anastas},
  journal   = {BioTeach Journal},
  title     = {The Hitchhiker's Guide to the RNA World},
  year      = {2003},
  pages     = {37--40},
  volume    = {1},
  abstract  = {The quest to reach a plausible hypothesis concerning the origin of life is ongoing. Today, we have conceptualized many workable hypotheses; however, a vigorous controversy has evolved over the past years concerning the nature of the origin of life. We’ll start first with theory of the “RNA world” that states that the first molecular systems to display the properties of self-replication and evolution were RNA molecules (Schwartz, 1993). Schwartz proposes that RNA molecules are in fact the first “living” things. What qualifies as “living” in this context is any system which is able to replicate itself and, in doing so, continually adapt by means of selection to a changing environment. Moreover, Bartel and Unrau, in their article “Constructing an RNA world” explain the popular theory of life’s origin that also states that the first biocatalysts were not made of protein but were made of RNA or a very similar polymer (1999). Many scientists have accepted this theory as the most satisfactory explanation for the origin of life. According to this theory, RNA first promoted the reaction required for life with the help of metals, pyridines, amino acids and other small-molecule cofactors. Later, these RNA molecules developed various abilities to synthesize coded polypeptides that served as more sophisticated cofactors. Eventually, RNA was replaced by DNA as the genetic polymer, and by proteins as the prominent biocatalysts. However, during the history of the scientific study of the origin of life, different models have attracted attention. These different models centre their basis on the origin of life using different theories: protein-centred, nucleic acid-centred, and other “precursor” hypothesis based models.},
  file      = {2003_Anastas_37.pdf:by-author/A/Anastas/2003_Anastas_37.pdf:PDF},
  keywords  = {Origin of Life; RNA World},
  owner     = {saulius},
  timestamp = {2013.09.27},
  creationdate = {2013-09-27T00:00:00},
  url       = {http://www.bioteach.ubc.ca/Journal/V01I01/3740RNAworld.pdf},
}

@Article{Andersen1980,
  author           = {Andersen, Hans C.},
  journal          = {The Journal of Chemical Physics},
  title            = {Molecular dynamics simulations at constant pressure and/or temperature},
  year             = {1980},
  number           = {4},
  pages            = {2384--2393},
  volume           = {72},
  abstract         = {In the molecular dynamics simulation method for fluids, the equations of motion for a collection of particles in a fixed volume are solved numerically. The energy, volume, and number of particles are constant for a particular simulation, and it is assumed that time averages of properties of the simulated fluid are equal to microcanonical ensemble averages of the same properties. In some situations, it is desirable to perform simulations of a fluid for particular values of temperature and/or pressure or under conditions in which the energy and volume of the fluid can fluctuate. This paper proposes and discusses three methods for performing molecular dynamics simulations under conditions of constant temperature and/or pressure, rather than constant energy and volume. For these three methods, it is shown that time averages of properties of the simulated fluid are equal to averages over the isoenthalpic–isobaric, canonical, and isothermal–isobaric ensembles. Each method is a way of describing the dynamics of a certain number of particles in a volume element of a fluid while taking into account the influence of surrounding particles in changing the energy and/or density of the simulated volume element. The influence of the surroundings is taken into account without introducing unwanted surface effects. Examples of situations where these methods may be useful are discussed.},
  comment          = {Discussed and cited in https://computecanada.github.io/molmodsim-md-theory-lesson-novice/07-thermostats/index.html and https://computecanada.github.io/molmodsim-md-theory-lesson-novice/reference.html.},
  creationdate     = {2016-02-24T00:00:00},
  doi              = {10.1063/1.439486},
  file             = {1980_Andersen_2384.pdf:by-author/A/Andersen/1980_Andersen_2384.pdf:PDF},
  groups           = {sg/Molecular dynamics},
  keywords         = {Molecular Dynamics (MD); Physics; Thermostat},
  modificationdate = {2023-01-29T13:09:09},
  owner            = {saulius},
  timestamp        = {2016.02.24},
  url              = {http://scitation.aip.org/content/aip/journal/jcp/72/4/10.1063/1.439486},
}

@TechReport{Anderson1987,
  author      = {Anderson, E. and Veith, G. D. and Weininger, D.},
  institution = {Environmental Research Laboratory-Duluth},
  title       = {{SMILES}: A line notation and computerized interpreter for chemical structures},
  year        = {1987},
  file        = {:by-author/A/Anderson/1987_Anderson.pdf:PDF},
  owner       = {andrius},
  timestamp = {2014.06.30},
  creationdate = {2014-06-30T00:00:00},
}

@Article{Anderson1986,
  author    = {Herbert Anderson},
  journal   = {Los Alamos Science},
  title     = {Metropolis, Monte Carlo and the MANIAC},
  year      = {1986},
  pages     = {96--107},
  volume    = {14},
  file      = {1986_Anderson_96.pdf:by-author/A/Anderson/1986_Anderson_96.pdf:PDF},
  groups    = {sg/Molecular dynamics},
  keywords  = {Molecular Dynamics (MD); Monte Carlo},
  owner     = {saulius},
  timestamp = {2011.10.21},
  creationdate = {2011-10-21T00:00:00},
}

@Article{Anderson2011,
  author    = {Kirsty M. Anderson and Michael R. Probert and Andrés E. Goeta and Jonathan W. Steed},
  journal   = {CrystEngComm},
  title     = {Size does matter -- the contribution of molecular volume, shape and flexibility to the formation of co-crystals and structures with Z' > 1},
  year      = {2011},
  pages     = {83--87},
  volume    = {13},
  doi       = {10.1039/c0ce00172d},
  file      = {:by-author/A/Anderson/2011_Anderson_83.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@Article{Anderson2006,
  author    = {Anderson, Megan J. and Hansen, Carl L. and Quake, Stephen R.},
  journal   = {Proceedings of the National Academy of Sciences of the United States of America},
  title     = {Phase knowledge enables rational screens for protein crystallization.},
  year      = {2006},
  pages     = {16746--51},
  volume    = {103},
  abstract  = {We show that knowledge of the phase behavior of a protein allows one to create a rational screen that increases the success rate of crystallizing challenging proteins. The strategy is based on using microfluidics to perform large numbers of protein solubility experiments across many different chemical conditions to identify reagents for crystallization experiments. Phase diagrams were generated for the identified reagents and used to design customized crystallization screens for every protein. This strategy was applied with a 75% success rate to the crystallization of 12 diverse proteins, most of which failed to crystallize when using traditional techniques. The overall diffraction success rate was 33%, about double what was achieved with conventional automation in large-scale protein structure consortia. The higher diffraction success rates are achieved by designing customized crystallization screens using the phase behavior information for each target. The identification of reagents based on an understanding of protein solubility and the use of phase diagrams in the design of individualized crystallization screens therefore promotes high crystallization rates and the production of diffraction-quality crystals.},
  file      = {:by-author/A/Anderson/2006_Anderson_16746.pdf:PDF},
  keywords  = {Crystallisation},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@Article{Anderson2003,
  author    = {Ross Anderson},
  journal   = {Upgrade},
  title     = {‘Trusted Computing’ and Competition Policy – Issues for Computing Professionals},
  year      = {2003},
  pages     = {35--41},
  volume    = {4},
  abstract  = {The most significant strategic development in information technology over the past year has been ‘Trusted Computing’ (TC). In this paper, the author gives an outline of TC, and sketch some of the possible effects on the computing business and the people who work in it.},
  file      = {Anderson_2003_35-trusted-computing.pdf:by-author/A/Anderson/2003_Anderson_35.pdf:PDF},
  keywords  = {Computer Science (CS)},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Andersson2000,
  author    = {Andersson, K. M. and Hovmöller, S.},
  journal   = {Acta crystallographica. Section D, Biological crystallography},
  title     = {The protein content in crystals and packing coefficients in different space groups.},
  year      = {2000},
  pages     = {789--90},
  volume    = {56},
  abstract  = {A precise way of estimating the packing coefficient, i.e. the ratio between the protein and unit-cell volume, or solvent content in protein crystals is given. At present, the solvent content is not given for most proteins in the Protein Data Bank and in many cases where it is given the values are dubious. The mean density of proteins in the crystalline form is around 1.22 g cm(-3), not 1.35 g cm(-3) as usually stated. This is equivalent to 19.5 A(3) per non-H atom. A statistical investigation of the average protein content and packing coefficient in different space groups is presented. The packing coefficients are generally higher in the most frequently occurring space groups than in the uncommon space groups. There is also a remarkable difference in frequency distribution for enantiomorphous pairs of space groups.},
  file      = {:by-author/A/Andersson/2000_Andersson_789.pdf:PDF},
  keywords  = {Density; Grow Krystal},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Andreini2012,
  author    = {Claudia Andreini and Gabriele Cavallaro and Serena Lorenzini},
  journal   = {Bioinformatics},
  title     = {{F}ind{G}eo: a tool for determining metal coordination geometry},
  year      = {2012},
  pages     = {1658--1660},
  volume    = {28},
  abstract  = {Summary: Metals are essential for the structure and function of many proteins and nucleic acids. The geometrical arrangement of the atoms that coordinate a metal in a biological macromolecule is an important determinant of the specificity and role of that metal. At present, however, this information can be retrieved only from the literature, which sometimes contains an improper or incorrect description of the geometry, and often lacks it altogether. Thus, we developed FindGeo to quickly and easily determine the coordination geometry of selected, or all, metals in a given structure. FindGeo works by superimposing the metal-coordinating atoms in the input structure to a library of templates with alternative ideal geometries, which are ranked by RMSD to identify the best geometry assignment. Availability: FindGeo is freely available as a web service and as a stand-alone program at http://metalweb.cerm.unifi.it/tools/findgeo/.},
  doi       = {10.1093/bioinformatics/bts246},
  file      = {:by-author/A/Andreini/2012_Andreini_1658.pdf:PDF},
  keywords  = {Metal Coordination},
  owner     = {antanas},
  timestamp = {2014.06.16},
  creationdate = {2014-06-16T00:00:00},
  url       = {http://bioinformatics.oxfordjournals.org/content/28/12/1658},
}

@Article{Andreini2013,
  author    = {Claudia Andreini and Gabriele Cavallaro and Serena Lorenzini and Antonio Rosato},
  journal   = {Nucleic Acids Research},
  title     = {{M}etal{PDB}: a database of metal sites in biological macromolecular structures},
  year      = {2013},
  pages     = {D312-D319},
  volume    = {41},
  abstract  = {We present here MetalPDB (freely accessible at http://metalweb.cerm.unifi.it), a novel resource aimed at conveying the information available on the three-dimensional (3D) structures of metal- binding biological macromolecules in a consistent and effective manner. This is achieved through the systematic and automated representation of metal- binding sites in proteins and nucleic acids by way of Minimal Functional Sites (MFSs). MFSs are 3D templates that describe the local environment around the metal(s) independently of the larger context of the macromolecular structure embedding the site(s), and are the central objects of MetalPDB design. MFSs are grouped into equistructural (broadly defined as sites found in corresponding positions in similar structures) and equivalent sites (equistructural sites that contain the same metals), allowing users to easily analyse similarities and vari- ations in metal–macromolecule interactions, and to link them to functional information. The web inter- face of MetalPDB allows access to a comprehensive overview of metal-containing biological structures, providing a basis to investigate the basic principles governing the properties of these systems. MetalPDB is updated monthly in an automated manner.},
  doi       = {10.1093/nar/gks1063},
  file      = {:by-author/A/Andreini/2013_Andreini_D312.pdf:PDF},
  owner     = {antanas},
  timestamp = {2013.12.09},
  creationdate = {2013-12-09T00:00:00},
  url       = {http://nar.oxfordjournals.org/content/41/D1/D312},
}

@Article{Andrejasic2008,
  author    = {Andrejašič, Miha and Pražnikar, Jure and Turk, Dušan},
  journal   = {Acta Crystallographica Section D, Biological Crystallography},
  title     = {{PURY}: a database of geometric restraints of hetero compounds for refinement in complexes with macromolecular structures.},
  year      = {2008},
  pages     = {1093--109},
  volume    = {64},
  abstract  = {The number and variety of macromolecular structures in complex with ;hetero' ligands is growing. The need for rapid delivery of correct geometric parameters for their refinement, which is often crucial for understanding the biological relevance of the structure, is growing correspondingly. The current standard for describing protein structures is the Engh-Huber parameter set. It is an expert data set resulting from selection and analysis of the crystal structures gathered in the Cambridge Structural Database (CSD). Clearly, such a manual approach cannot be applied to the vast and ever-growing number of chemical compounds. Therefore, a database, named PURY, of geometric parameters of chemical compounds has been developed, together with a server that accesses it. PURY is a compilation of the whole CSD. It contains lists of atom classes and bonds connecting them, as well as angle, chirality, planarity and conformation parameters. The current compilation is based on CSD 5.28 and contains 1978 atom classes and 32,702 bonding, 237,068 angle, 201,860 dihedral and 64,193 improper geometric restraints. Analysis has confirmed that the restraints from the PURY database are suitable for use in macromolecular crystal structure refinement and should be of value to the crystallographic community. The database can be accessed through the web server http://pury.ijs.si/, which creates topology and parameter files from deposited coordinates in suitable forms for the refinement programs MAIN, CNS and REFMAC. In the near future, the server will move to the CSD website http://pury.ccdc.cam.ac.uk/.},
  doi       = {10.1107/S0907444908027388},
  file      = {2008_Andrejašič_1093.pdf:by-author/A/Andrejasic/2008_Andrejasic_1093.pdf:PDF},
  keywords  = {Restrains},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Webpage{Andrew2006,
  author    = {Andrew},
  retrieved = {2008-07-28},
  title     = {Statistical Modeling, Causal Inference, and Social Science},
  url       = {http://www.stat.columbia.edu/~cook/movabletype/archives/bayesian_statistics/},
  month     = {July},
  year      = {2006},
  file      = {:by-author/A/Andrew/2006_Andrew.war:},
  groups    = {sg/Bayesian},
  keywords  = {Bayesian-statistics; Mathematics},
  owner     = {saulius},
  timestamp = {2015.03.02},
  creationdate = {2015-03-02T00:00:00},
}

@Article{Andrews2014,
  author    = {Andrews, Lawrence C. and Bernstein, Herbert J.},
  journal   = {Journal of Applied Crystallography},
  title     = {The geometry of Niggli reduction: {\it BGAOL} {--}embedding Niggli reduction and analysis of boundaries},
  year      = {2014},
  pages     = {346--359},
  volume    = {47},
  abstract  = {Niggli reduction can be viewed as a series of operations in a six-dimensional space derived from the metric tensor. An implicit embedding of the space of Niggli-reduced cells in a higher-dimensional space to facilitate calculation of distances between cells is described. This distance metric is used to create a program, BGAOL, for Bravais lattice determination. Results from BGAOL are compared with results from other metric based Bravais lattice determination algorithms. This embedding depends on understanding the boundary polytopes of the Niggli-reduced cone N in the six-dimensional space G6. This article describes an investigation of the boundary polytopes of the Niggli-reduced cone N in the six-dimensional space G6 by algebraic analysis and organized random probing of regions near one-, two-, three-, four-, five-, six-, seven- and eightfold boundary polytope intersections. The discussion of valid boundary polytopes is limited to those avoiding the mathematically interesting but crystallographically impossible cases of zero-length cell edges. Combinations of boundary polytopes without a valid intersection in the closure of the Niggli cone or with an intersection that would force a cell edge to zero or without neighboring probe points are eliminated. In all, 216 boundary polytopes are found. There are 15 five-dimensional boundary polytopes of the full G6 Niggli cone N.},
  doi       = {10.1107/S1600576713031002},
  file      = {2014_Andrews_346.pdf:by-author/A/Andrews/2014_Andrews_346.pdf:PDF},
  groups    = {sg/Cell reduction},
  keywords  = {Algorithms; Crystallographic Computing; Reduced Cell; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2014.03.27},
  creationdate = {2014-03-27T00:00:00},
  url       = {http://dx.doi.org/10.1107/S1600576713031002},
}

@Article{Andrews2013,
  author    = {Lawrence C. Andrews and Herbert J. Bernstein},
  journal   = {arXiv},
  title     = {The Geometry of Niggli Reduction I: The Boundary Polytopes of the Niggli Cone},
  year      = {2013},
  pages     = {1203.5146v4},
  abstract  = {Correct identification of the Bravais lattice of a crystal is an important step in structure solution. Niggli reduction is a commonly used technique. We investigate the boundary polytopes of the Niggli-reduced cone in the six-dimensional space G6 by algebraic analysis and organized random probing of regions near 1- through 8-fold boundary polytope intersections. We limit consideration of boundary polytopes to those avoiding the mathematically interesting but crystallographically impossible cases of 0 length cell edges. Combinations of boundary polytopes without a valid intersection in the closure of the Niggli cone or with an intersection that would force a cell edge to 0 or without neighboring probe points are eliminated. 216 boundary polytopes are found: 15 5-D boundary polytopes of the full G6 Niggli cone, 53 4-D boundary polytopes resulting from intersections of pairs of the 15 5-D boundary polytopes, 79 3-D boundary polytopes resulting from 2-fold, 3-fold and 4-fold intersections of the 15 5-D boundary polytopes, 55 2-D boundary polytopes resulting from 2-fold, 3-fold, 4-fold and higher intersections of the 15 5-D boundary polytopes, 14 1-D boundary polytopes resulting from 3-fold and higher intersections of the 15 5-D boundary polytopes. All primitive lattice types can be represented as combinations of the 15 5-D boundary polytopes. All non-primitive lattice types can be represented as combinations of the 15 5-D boundary polytopes and of the 7 special-position subspaces of the 5-D boundary polytopes. This study provides a new, simpler and arguably more intuitive basis set for the classification of lattice characters and helps to illuminate some of the complexities in Bravais lattice identification. The classification is intended to help in organizing database searches and in understanding which lattice symmetries are "close" to a given experimentally determined cell.},
  file      = {2013_Andrews_1203.5146v4.pdf:by-author/A/Andrews/2013_Andrews_1203.5146v4.pdf:PDF},
  groups    = {sg/Cell reduction},
  keywords  = {Algorithms; Reduced Cell},
  owner     = {saulius},
  timestamp = {2014.11.10},
  creationdate = {2014-11-10T00:00:00},
  url       = {http://arxiv.org/abs/1203.5146v4},
}

@Article{Andrews2013a,
  author    = {Lawrence C. Andrews and Herbert J. Bernstein},
  journal   = {arXiv},
  title     = {The Geometry of Niggli Reduction II: BGAOL -- Embedding Niggli Reduction},
  year      = {2013},
  pages     = {1305.6561v1},
  abstract  = {Niggli reduction can be viewed as a series of operations in a six-dimensional space derived from the metric tensor. An implicit embedding of the space of Niggli-reduced cells in a higher dimensional space to facilitate calculation of distances between cells is described. This distance metric is used to create a program, BGAOL, for Bravais lattice determination. Results from BGAOL are compared to the results from other metric-based Bravais lattice determination algorithms.},
  file      = {2013_Andrews_1305.6561v1.pdf:by-author/A/Andrews/2013_Andrews_1305.6561v1.pdf:PDF},
  groups    = {sg/Cell reduction},
  keywords  = {Algorithms; Reduced Cell},
  owner     = {saulius},
  timestamp = {2016.11.30},
  creationdate = {2016-11-30T00:00:00},
  url       = {https://arxiv.org/abs/1305.6561},
}

@Article{Andrews2011,
  author    = {Lawrence C. Andrews and Herbert J. Bernstein},
  title     = {A Monte Carlo Investigation of the Geometry of Niggli Reduction},
  year      = {2011},
  pages     = {preprint},
  abstract  = {Correct identification of the Bravais lattice of a crystal is an important early step in structure solution. Niggli reduction is a commonly used technique. We investigate the boundary manifolds of the Niggli-reduced cone in the six-dimensional space G6 by organized random probing of regions near 1-, 2-, 3-, 4-, 5-, 6-, 7- and 8-fold bound- ary manifold intersections. We limit our consideration of valid boundary manifolds to those avoiding the mathematically interesting but crystallographically impossible cases of zero length cell edges. Combinations of boundary manifolds without a valid intersection or with an intersection that would force a cell axis to zero or without neighboring probe points are eliminated. 215 boundary manifolds are found. There are 15 5-D boundary manifolds of the full G6 Niggli cone, 53 4-D boundary mani- folds resulting from intersections of pairs of the 15 5-D boundary manifolds, 72 3-D boundary manifolds resulting from the intersections of triples of the 15 5-D boundary manifolds, 47 2-D boundary manifolds resulting from the intersections of quadruples of the 15 5-D boundary manifolds, 20 1-D boundary manifolds resulting from the intersection of quintuples of the 15 5-D boundary manifolds, 6 1-D boundary man- ifolds resulting from the intersection of sextuples of the 15 5-D boundary manifolds and one each of 1-D boundary manifolds resulting from the intersection of 7 or 8 5-D boundary manifolds. The classification of the boundary manifolds into 5-, 4-, 3-, 2- and 1- dimensional boundary manifolds corresponds well to the Niggli classification and suggests other possible symmetries. All of the primitive lattice types can be represented as combinations of the 15 5- D boundary manifolds. All of the non-primitive lattice types can be represented as combinations of the 15 5-D boundary manifolds and of the 7 special-position subspaces of the 5-D boundary manifolds. This study provides a new, simpler, more intuitive basis set for the classification of lattice characters and helps to illuminate some of the complexities in Bravais lattice identification.},
  file      = {:by-author/A/Andrews/2011_Andrews_preprint.pdf:PDF},
  groups    = {sg/Cell reduction},
  keywords  = {Crystal Cell; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Andrews1988,
  author    = {Andrews, L. C. and Bernstein, H. J.},
  journal   = {Acta Crystallographica Section A},
  title     = {Lattices and reduced cells as points in 6-space and selection of {B}ravais lattice type by projections},
  year      = {1988},
  pages     = {1009--1018},
  volume    = {44},
  abstract  = {A characterization of crystallographic unit cells as vectors in a Euclidean six-dimensional space (E6 in the usual mathematical notation; here termed G6) is introduced, in which the non-triclinic Bravais lattice types form one-, two-, three- and four-dimensional linear subspaces. This formalism makes the determination of the 'best' Bravais lattice (or lattices) for a particular experimentally determined cell a process of determining Euclidean distances in G6 from the cell to its projections into the subspaces of the lattice types. The elements of vectors in the space are drawn from the Niggli matrix with the unsymmetrical elements doubled. A cell is first reduced and all its nearly Buerger-reduced cells are used in the distance determinations. Thus the smallest distance provides information about both the propriety of the lattice type selection and the instability of the cell reduction.},
  doi       = {10.1107/S0108767388006427},
  file      = {1988_Andrews_1009.pdf:by-author/A/Andrews/1988_Andrews_1009.pdf:PDF},
  groups    = {sg/Cell reduction},
  keywords  = {Algorithms; Crystallographic Computing; Reduced Cell; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2014.03.27},
  creationdate = {2014-03-27T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0108767388006427},
}

@Article{Andronico2011,
  author    = {Andronico, Alessio and Randall, Arlo and Benz, Ryan W. and Baldi, Pierre},
  journal   = {Journal of chemical information and modeling},
  title     = {Data-driven high-throughput prediction of the 3-{D} structure of small molecules: review and progress},
  year      = {2011},
  pages     = {760--76},
  volume    = {51},
  abstract  = {Accurate prediction of the 3-D structure of small molecules is essential in order to understand their physical, chemical, and biological properties, including how they interact with other molecules. Here, we survey the field of high-throughput methods for 3-D structure prediction and set up new target specifications for the next generation of methods. We then introduce COSMOS, a novel data-driven prediction method that utilizes libraries of fragment and torsion angle parameters. We illustrate COSMOS using parameters extracted from the Cambridge Structural Database (CSD) by analyzing their distribution and then evaluating the system's performance in terms of speed, coverage, and accuracy. Results show that COSMOS represents a significant improvement when compared to state-of-the-art prediction methods, particularly in terms of coverage of complex molecular structures, including metal-organics. COSMOS can predict structures for 96.4% of the molecules in the CSD (99.6% organic, 94.6% metal-organic), whereas the widely used commercial method CORINA predicts structures for 68.5% (98.5% organic, 51.6% metal-organic). On the common subset of molecules predicted by both methods, COSMOS makes predictions with an average speed per molecule of 0.15 s (0.10 s organic, 0.21 s metal-organic) and an average rmsd of 1.57 Å (1.26 Å organic, 1.90 Å metal-organic), and CORINA makes predictions with an average speed per molecule of 0.13s (0.18s organic, 0.08s metal-organic) and an average rmsd of 1.60 Å (1.13 Å organic, 2.11 Å metal-organic). COSMOS is available through the ChemDB chemoinformatics Web portal at http://cdb.ics.uci.edu/ .},
  doi       = {10.1021/ci100223t},
  file      = {:by-author/A/Andronico/2011_Andronico_760.pdf:PDF},
  keywords  = {Crystallography; Data Management; Databases; Restrains},
  owner     = {saulius},
  timestamp = {2012.09.24},
  creationdate = {2012-09-24T00:00:00},
  url       = {http://pubs.acs.org/doi/abs/10.1021/ci100223t},
}

@Article{Androulakis2008,
  author    = {Androulakis, Steve and Schmidberger, Jason and Bate, Mark A. and DeGori, Ross and Beitz, Anthony and Keong, Cyrus and Cameron, Bob and McGowan, Sheena and Porter, Corrine J. and Harrison, Andrew and Hunter, Jane and Martin, Jennifer L. and Kobe, Bostjan and Dobson, Renwick C. J. and Parker, Michael W. and Whisstock, James C. and Gray, Joan and Treloar, Andrew and Groenewegen, David and Dickson, Neil and Buckle, Ashley M.},
  journal   = {Acta Crystallographica Section D},
  title     = {Federated repositories of X-ray diffraction images},
  year      = {2008},
  pages     = {810--814},
  volume    = {64},
  abstract  = {There is a pressing need for the archiving and curation of raw X-ray diffraction data. This information is critical for validation, methods development and improvement of archived structures. However, the relatively large size of these data sets has presented challenges for storage in a single worldwide repository such as the Protein Data Bank archive. This problem can be avoided by using a federated approach, where each institution utilizes its institutional repository for storage, with a discovery service overlaid. Institutional repositories are relatively stable and adequately funded, ensuring persistence. Here, a simple repository solution is described, utilizing Fedora open-source database software and data-annotation and deposition tools that can be deployed at any site cheaply and easily. Data sets and associated metadata from federated repositories are given a unique and persistent handle, providing a simple mechanism for search and retrieval via web interfaces. In addition to ensuring that valuable data is not lost, the provision of raw data has several uses for the crystallographic community. Most importantly, structure determination can only be truly repeated or verified when the raw data are available. Moreover, the availability of raw data is extremely useful for the development of improved methods of image analysis and data processing.},
  doi       = {10.1107/S0907444908015540},
  file      = {2008_Androulakis_810.pdf:by-author/A/Androulakis/2008_Androulakis_810.pdf:PDF},
  keywords  = {Data Management; Databases; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2014.04.15},
  creationdate = {2014-04-15T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444908015540},
}

@Article{Anfinsen1973,
  author           = {Anfinsen, C B},
  journal          = {Science (New York, N.Y.)},
  title            = {Principles that govern the folding of protein chains.},
  year             = {1973},
  pages            = {223--30},
  volume           = {181},
  creationdate     = {2008-07-28T00:00:00},
  doi              = {10.1126/science.181.4096.223},
  file             = {1973_Anfinsen_223.pdf:by-author/A/Anfinsen/1973_Anfinsen_223.pdf:PDF},
  keywords         = {Folding; Protein Physics},
  modificationdate = {2023-04-23T10:16:59},
  owner            = {saulius},
  timestamp        = {2008.07.28},
}

@Article{Anfinsen1961,
  author    = {Anfinsen, C. B. and Haber, E. and Sela, M. and White, Jr, F. H.},
  journal   = {Proceedings of the National Academy of Sciences of the United States of America},
  title     = {The kinetics of formation of native ribonuclease during oxidation of the reduced polypeptide chain.},
  year      = {1961},
  pages     = {1309--14},
  volume    = {47},
  file      = {:by-author/A/Anfinsen/1961_Anfinsen_1309.pdf:PDF},
  keywords  = {Protein Denaturation},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Anisimov1991,
  author    = {Anisimov, Vladimir I. and Zaanen, Jan and Andersen, Ole K.},
  journal   = {Phys. Rev. B},
  title     = {Band theory and {M}ott insulators: {H}ubbard {U} instead of {S}toner {I}},
  year      = {1991},
  pages     = {943--954},
  volume    = {44},
  doi       = {10.1103/PhysRevB.44.943},
  file      = {:by-author/A/Anisimov/1991_Anisimov_943.pdf:PDF},
  issue     = {3},
  keywords  = {Density Functional Theory (DFT)},
  numpages  = {0},
  owner     = {andrius},
  publisher = {American Physical Society},
  timestamp = {2015.07.29},
  creationdate = {2015-07-29T00:00:00},
}

@Misc{ASCB2012,
  author    = {{Annual Meeting of The American Society for Cell Biology}},
  title     = {San Francisco Declaration on Research Assessment},
  year      = {2012},
  abstract  = {General Recommendation
1. Do not use journal-based metrics, such as Journal Impact Factors, as a surrogate measure of the quality of individual research articles, to assess an individual scientist’s contributions, or in hiring, promotion, or funding decisions.},
  file      = {:by-author/A/ASCB/2012_ASCB.pdf:PDF},
  groups    = {sg/Bibliometrics},
  keywords  = {Impact Factor (IF); Quality of Research; Research Assessment},
  owner     = {saulius},
  timestamp = {2017.02.11},
  creationdate = {2017-02-11T00:00:00},
  url       = {http://www.ascb.org/files/SFDeclarationFINAL.pdf},
}

@Article{anonymous2004,
  author    = {anonymous},
  title     = {The Entropy of the Classical Ideal Gas},
  year      = {2004},
  abstract  = {An analysis is presented of the probability distribution of particles and energy in a classical ideal gas of indistinguishable particles for the Matter and Interactions I (33.131) course.},
  file      = {:by-author/a/anonymous/2004_anonymous.pdf:PDF},
  keywords  = {Statistical Physics},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Manuscript{anonymous2003,
  author    = {anonymous},
  title     = {Real symmetric matrices},
  year      = {2003},
  file      = {:by-author/a/anonymous/2003_anonymous.pdf:PDF},
  owner     = {saulius},
  timestamp = {2011.12.13},
  creationdate = {2011-12-13T00:00:00},
}

@Misc{anonymous2000,
  author    = {anonymous},
  title     = {5.2 Matrix Norms},
  year      = {2000},
  file      = {:by-author/a/anonymous/2000_anonymous.pdf:PDF},
  owner     = {saulius},
  timestamp = {2011.12.13},
  creationdate = {2011-12-13T00:00:00},
  volume    = {2000},
}

@Manuscript{anonymous1999,
  author    = {anonymous},
  title     = {E. S. Fedorov, A. Schoenflies: In Memoriam},
  year      = {1999},
  keywords  = {A. Schoenflies; E. S. Fedorov; History; Spacegroups},
  url       = {http://www.iucr.org/__data/assets/pdf_file/0020/749/fedorov.pdf},
  file      = {1999_anonymous.pdf:by-author/a/anonymous/1999_anonymous.pdf:PDF},
  owner     = {saulius},
  timestamp = {2014.10.21},
  creationdate = {2014-10-21T00:00:00},
}

@Article{Anson1932,
  author    = {Anson, M. L. and Mirsky, A. E.},
  journal   = {The Journal of general physiology},
  title     = {THE EFFECT OF DENATURATION ON THE VISCOSITY OF PROTEIN SYSTEMS.},
  year      = {1932},
  pages     = {341--50},
  volume    = {15},
  abstract  = {The viscosity of a protein solution is increased by the denaturation of the protein. This is true both when there is the formation of protein aggregates which occlude water and when there is no aggregation. Under certain conditions, as a result of the aggregation following denaturation, a solution containing only one per cent of protein may be converted into a clear gel. The conditions for obtaining very viscous solutions containing little denatured protein are always close to the conditions for actual precipitation and under these conditions the viscosity is very sensitive to slight changes in the concentration of salts and hydrogen ions.},
  file      = {:by-author/A/Anson/1932_Anson_341.pdf:PDF},
  keywords  = {Protein Denaturation},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Anson1931,
  author    = {M. L. Anson and A. E. Mirsky},
  title     = {The Reversibility of Protein Coagulation},
  year      = {1931},
  file      = {:by-author/A/Anson/1931_Anson.pdf:PDF},
  keywords  = {Protein Denaturation},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Anson1931a,
  author    = {Anson, M. L. and Mirsky, A. E.},
  journal   = {The Journal of general physiology},
  title     = {Protein Coagulation and Its Reversal: Serum Albumin.},
  year      = {1931},
  pages     = {725--32},
  volume    = {14},
  abstract  = {1. It is possible to prepare crystalline, soluble, heat-coagulable serum albumin from coagulated serum albumin. 2. In the cases so far studied, the more soluble a denatured protein, the more easily its denaturation can be reversed.},
  file      = {:by-author/A/Anson/1931_Anson_725.pdf:PDF},
  keywords  = {Protein Denaturation},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Anson1931b,
  author    = {Anson, M. L. and Mirsky, A. E.},
  journal   = {The Journal of general physiology},
  title     = {Protein Coagulation and Its Reversal : Globin.},
  year      = {1931},
  pages     = {605--9},
  volume    = {14},
  abstract  = {1. The globin prepared from hemoglobin by the acid acetone method is denatured globin. 2. The denaturation and coagulation of globin by acid acetone are reversible. 3. Soluble globin can be obtained from the acid acetone globin even if the globin is first precipitated by trichloracetic acid or heated to 100 degrees C. 4. Hill and Holden's theory that they separated native globin from hemoglobin without any intermediate denaturation is not proven by their experiments.},
  file      = {:by-author/A/Anson/1931_Anson_605.pdf:PDF},
  keywords  = {Protein Denaturation},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Anson1929,
  author    = {Anson, M. L. and Mirsky, A. E.},
  journal   = {The Journal of general physiology},
  title     = {The Perparation of Completely Coagulated Hemoglobin.},
  year      = {1929},
  pages     = {121--32},
  volume    = {13},
  abstract  = {As a preliminary to the study of the reversal of the coagulation of hemoglobin several methods are described for the preparation of completely denatured and coagulated hemoglobin and the evidence is given that hemoglobin is a typical coagulable protein.},
  file      = {:by-author/A/Anson/1929_Anson_121.pdf:PDF},
  keywords  = {Protein Denaturation},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Anson1925,
  author    = {Anson, M. L. and Mirsky, A. E.},
  journal   = {The Journal of general physiology},
  title     = {On Some General Properties of Proteins.},
  year      = {1925},
  pages     = {169--79},
  volume    = {9},
  abstract  = {1. The processes of denaturation and coagulation of hemoglobin are like those of other proteins. 2. When hemoglobin is denatured it is probably depolymerized into hemochromogen. 3. When other proteins are denatured they, too, are probably depolymerized. Conversely, native proteins can be regarded as aggregates of denatured proteins. 4. The globins and histones are to be regarded as denatured proteins rather than as a distinct group of proteins. 5. The factors affecting the equilibrium between native and denatured proteins have been considered. 6. A non-polar group is uncovered when a protein is denatured. 7. It has been shown that judged by the two most sensitive tests for the specificity of proteins, it is only when proteins are in the native form that they are highly specific.},
  file      = {:by-author/A/Anson/1925_Anson_169.pdf:PDF},
  keywords  = {Protein Denaturation},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{BrianP.Anton2004,
  author    = {Brian P. Anton and Raleigh, Elisabeth A.},
  journal   = {Journal Of Bacteriology},
  title     = {Transposon-Mediated Linker Insertion Scanning Mutagenesis of the {E}scherichia coli {McrA} Endonuclease},
  year      = {2004},
  pages     = {5699–5707},
  volume    = {186},
  abstract  = {McrA is one of three functions that restrict modified foreign DNA in Escherichia coli K-12, affecting both methylated and hydroxymethylated substrates. We present here the first systematic analysis of the functional organization of McrA by using the GPS-LS insertion scanning system. We collected in-frame insertions of five amino acids at 46 independent locations and C-terminal truncations at 20 independent locations in the McrA protein. Each mutant was assayed for in vivo restriction of both methylated and hydroxymethylated bacterio- phage (M.HpaII-modified lambda and T4gt, respectively) and for induction of the E. coli SOS response in the pres- ence of M.HpaII methylation, indicative of DNA damage. Our findings suggest the presence of an N-terminal DNA-binding domain and a C-terminal catalytic nuclease domain connected by a linker region largely tolerant of amino acid insertions. DNA damage inflicted by a functional C-terminal domain is required for restriction of phage T4gt. Disruption of the N-terminal domain abolishes restriction of both substrates. Surprisingly, truncation mutations that spare the N-terminal domain do not mediate DNA damage, as measured by SOS induction, but nevertheless partially restrict M.HpaII-modified lambda in vivo. We suggest a common explanation for this “restriction without damage” and a similar observation seen in vivo with McrB, a component of another of the modified-DNA restriction functions. Briefly, we propose that unproductive site-specific binding of the pro- tein to a vulnerable position in the lambda genome disrupts the phage development program at an early stage. We also identified a single mutant, carrying an insertion in the N-terminal domain, which could fully restrict lambda but did not restrict T4gt at all. This mutant may have a selective impairment in substrate recognition, distinguish- ing methylated from hydroxymethylated substrates. The study shows that the technically easy insertion scan- ning method can provide a rich source of functional information when coupled with effective phenotype tests.},
  file      = {:by-author/A/Anton/2004_Anton_5699.pdf:PDF},
  keywords  = {McrA; Restriction Endonuclease (RE); TypeIV},
  owner     = {em},
  timestamp = {2013.02.21},
  creationdate = {2013-02-21T00:00:00},
}

@Article{Antos2006,
  author    = {Antos, John M. and Francis, Matthew B.},
  journal   = {Current opinion in chemical biology},
  title     = {Transition metal catalyzed methods for site-selective protein modification.},
  year      = {2006},
  pages     = {253--62},
  volume    = {10},
  abstract  = {The broad utility of protein bioconjugates has created a need for new and diverse strategies for site-selective protein modification. In particular, chemical reactions that target alternative amino acid side chains or unnatural functional groups are emerging as a valuable complement to more commonly used lysine- and cysteine-based strategies. Considering their widespread use in organic synthesis, reactions catalyzed by transition metals could provide a particularly powerful set of transformations for the continued expansion of the bioconjugation toolkit. Recent efforts to apply transition metal catalysis to protein modification have resulted in new methods for protein cross-linking, tryptophan modification, tyrosine modification, reductive amination of protein amines, and unnatural amino acid labeling. These strategies have substantially expanded the synthetic flexibility of protein modification, and thus the range of applications for which bioconjugates can be used in chemical biology and materials science.},
  file      = {:by-author/A/Antos/2006_Antos_253.pdf:PDF},
  keywords  = {Bioconjugation},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@Manuscript{AntoyXXXX,
  author    = {Sergio Antoy},
  title     = {Functional Pearl},
  year      = {XXXX},
  keywords  = {Alphametics; Computer Science (CS)},
  file      = {:by-author/A/Antoy/XXXX_Antoy.pdf:PDF},
  journal   = {J. Functional Programming},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Manuscript{Anvin2011,
  author    = {H. Peter Anvin},
  title     = {The mathematics of RAID-6},
  year      = {2011},
  month     = {Dec},
  url       = {http://kernel.org/pub/linux/kernel/people/hpa/raid6.pdf},
  file      = {:by-author/A/Anvin/2011_Anvin.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.11.27},
  creationdate = {2012-11-27T00:00:00},
}

@Article{Anzaldi2012,
  author    = {Anzaldi, Laura J. and Mu{\~{n}}oz-Fern{\'a}ndez, Daniel and Erill, Ivan},
  journal   = {BMC Bioinformatics},
  title     = {BioWord: A sequence manipulation suite for Microsoft Word},
  year      = {2012},
  issn      = {1471-2105},
  number    = {1},
  pages     = {1--7},
  volume    = {13},
  abstract  = {The ability to manipulate, edit and process DNA and protein sequences has rapidly become a necessary skill for practicing biologists across a wide swath of disciplines. In spite of this, most everyday sequence manipulation tools are distributed across several programs and web servers, sometimes requiring installation and typically involving frequent switching between applications. To address this problem, here we have developed BioWord, a macro-enabled self-installing template for Microsoft Word documents that integrates an extensive suite of DNA and protein sequence manipulation tools.},
  doi       = {10.1186/1471-2105-13-124},
  file      = {2012_Anzaldi_1.pdf:by-author/A/Anzaldi/2012_Anzaldi_1.pdf:PDF},
  keywords  = {Bioinformatics; Sequence Processing; Software Development},
  owner     = {saulius},
  timestamp = {2016.05.14},
  creationdate = {2016-05-14T00:00:00},
  url       = {http://dx.doi.org/10.1186/1471-2105-13-124},
}

@Article{Apostolakis2001,
  author    = {Apostolakis, Joannis and Hofmann, Detlef Walter Maria and Lengauer, Thomas},
  journal   = {Acta Crystallographica Section A},
  title     = {Derivation of a scoring function for crystal structure prediction},
  year      = {2001},
  pages     = {442--450},
  volume    = {57},
  doi       = {10.1107/S0108767301004810},
  file      = {bk0088.pdf:by-author/A/Apostolakis/2001_Apostolakis_442.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0108767301004810},
}

@InProceedings{Appel1987,
  author    = {Andrew W. Appel},
  title     = {Concise specifications of locally optimal code generators},
  year      = {1987},
  abstract  = {Dynamic programming allows locally optimal instruction selection for expression trees. More importantly, the algorithm allows concise and elegant specification of code generators. Aho, Ganapathi, and Tjiang have built the Twig code-generator-generator, which produces dynamic-programming code-generators from grammar-like specifications. Encoding a complex architecture as a grammar for a dynamic-programming codegenerator -generator shows the expressive power of the technique. Each instruction, addressing mode, register and class can be expressed individually in the grammar. The grammar can be factored much more readily than with the Graham-Glanville LR(1) algorithm, so it can be much more concise. Twig specifications for the VAX and MC68020 are described, and the corresponding code generators select very good (and under the right assumptions, optimal) instruction sequences. Limitations and possible improvements to the specification language are discussed. 1. Introduction One of the last...},
  comment   = {Concise specifications of locally optimal code generators Andrew W. Appel Department of Computer Science Princeton University Princeton, NJ 08544 ABSTRACT Dynamic programming allows locally optimal instruction selection for expression trees. More importantly, the algorithm allows concise and elegant specification of code generators. Aho, Ganapathi, and Tjiang have built the Twig code-generator-generator, which produces dynamic-programming code-generators from grammar-like specifications. Encoding a complex architecture as a grammar for a dynamic-programming code- generator-generator shows the expressive power of the technique. Each instruction, addressing mode, register and class can be expressed individually in the grammar. The grammar can be factored much more readily than with the Graham-Glanville LR(1) algo- rithm, so it can be much more concise. Twig specifications for the VAX and MC68020 are described, and the corresponding code generators select very good (and under the right assumptions, optimal) instruction sequences. Limitations and possible improvements to the specification language are discussed. 1. Introduction One of the last phases of a typical compiler is the translation of an intermediate representation of a compiled program into target-machine instructions. This instruction selection phase has been the subject of much research, with two primary goals: to find algorithms for selecting optimally efficient instruction sequences, and to find ways to automatically generate instruction selection programs from concise specifications of the target machine’s operations. This paper describes techniques for using Aho, Ganapathi, and Tjiang’s Twig[1], a code-generator genera- tor that uses tree matching and dynamic programming. The instruction sets of the DEC VAX and Motorola 68020 are used as a illustrative examples. The VAX architecture can be described with only 112 rules; the 68020 is somewhat more complicated. Some of the problems of using Twig are described, and solutions to these problems are proposed. 1.1. Optimal instruction selection An intermediate representation can be considered as a directed graph, in which edges point from uses of values to sources of values. Most of the work in optimal instruction selection has considered only trees -- graphs in which each source of a value has only one use. (The ‘‘trivial’’ sources, such as constants and the addresses of program variables, may have several uses; each use will be a leaf of the tree.) For more general graphs, optimal instruction selection becomes NP-complete[2, 3]. For trees, it is possible to find optimal solutions (with appropriate restrictions on the scope of the problem). For example, the problem of optimal register allocation[4, 5] can be solved using a simple bottom-up label- ling algorithm. Optimal instruction selection for machines with one class of general registers is solved using a bottom-up dynamic programming algorithm[6] (the algorithm uses dynamic programming in that},
  file      = {:by-author/A/Appel/1987_Appel.ps:PostScript;:by-author/A/Appel/1987_Appel.pdf:PDF},
  owner     = {saulius},
  timestamp = {2013.08.10},
  creationdate = {2013-08-10T00:00:00},
  url       = {http://www.cs.princeton.edu/~appel/papers/80.ps},
}

@Manuscript{Applequist1998,
  author    = {John Applequist},
  title     = {Tensors in a Nutshell},
  year      = {1998},
  file      = {:by-author/A/Applequist/1998_Applequist.pdf:PDF},
  owner     = {saulius},
  timestamp = {2013.03.22},
  creationdate = {2013-03-22T00:00:00},
}

@Webpage{Appleton1998,
  author    = {Brad Appleton and Stephen P. Berczuk and Ralph Cabrera and Robert Orenstein},
  retrieved = {2008-10-28},
  title     = {Streamed Lines: Branching Patterns for Parallel Software Developmen},
  url       = {http://www.bradapp.com/acme/branching/},
  year      = {1998},
  abstract  = {Most software version control systems provide mechanisms for branching into multiple lines of development and merging source code from one development line into another. However, the techniques, policies and guidelines for using these mechanisms are often misapplied or not fully understood. This is unfortunate, since the use or misuse of branching and merging can make or break a parallel software development project. Streamed Lines is a pattern language for organizing related lines of development into appropriately diverging and converging streams of source code changes.},
  file      = {:by-author/A/Appleton/1998_Appleton.war:WAR},
  keywords  = {Computer Science (CS); Software Development; Software Project Management; Version Control},
  owner     = {saulius},
  timestamp = {2015.03.02},
  creationdate = {2015-03-02T00:00:00},
}

@Article{Aqvist1986,
  author    = {Johan Åqvist},
  journal   = {Computers \& Chemistry},
  title     = {A Simple Way to Calculate the Axis of an α-helix},
  year      = {1986},
  pages     = {97--99},
  volume    = {10},
  abstract  = {A simple method to quickly and accurately calculate the axis of an a-helix. by least squares fitting to a cylindrical surface, is presented.The method is well suited for the analysis of molecular dynamics (MD) trajectories of proteins, and some test results on a recent MD simulation are given.},
  doi       = {10.1016/0097-8485(86)80002-X},
  file      = {:by-author/Å/Åqvist/1986_Åqvist_97.pdf:PDF},
  keywords  = {Helical Parameters; Protein Bioinformatics},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/009784858680002X},
}

@Article{Arad1987,
  author    = {Arad, T. and Piefke, J. and Gewitz, H. S. and Romberg, B. and Glotz, C. and Müssig, J. and Yonath, A. and Wittmann, H. G.},
  journal   = {Analytical biochemistry},
  title     = {The growth of ordered two-dimensional sheets of ribosomal particles from salt-alcohol mixtures.},
  year      = {1987},
  pages     = {113--7},
  volume    = {167},
  abstract  = {A procedure for the in vitro growth of well-ordered two-dimensional sheets from ribosomal particles using salts and salt-alcohol mixtures has been developed. Employing this procedure, ordered two-dimensional sheets of the wild type as well as of mutated 50 S ribosomal subunits from Bacillus stearothermophilus can readily be obtained. These sheets, stained with uranyl acetate or gold-thioglucose, are suitable for three-dimensional image reconstruction. They consist of relatively small unit cells with dimensions of 160 +/- 15 and 365 +/- 20 A. Diffraction patterns of electron micrographs of these sheets contain features to 25 A resolution.},
  file      = {:by-author/A/Arad/1987_Arad_113.pdf:PDF},
  keywords  = {Ribosome Structure},
  owner     = {saulius},
  timestamp = {2012.06.25},
  creationdate = {2012-06-25T00:00:00},
}

@Article{Aragones2013,
  author      = {J. L. Aragones and E. G. Noya and C. Valeriani and C. Vega},
  journal     = {J Chem Phys},
  title       = {Free energy calculations for molecular solids using GROMACS.},
  year        = {2013},
  pages       = {034104},
  volume      = {139},
  abstract    = {In this work, we describe a procedure to evaluate the free energy of molecular solids with the GROMACS molecular dynamics package. The free energy is calculated using the Einstein molecule method that can be regarded as a small modification of the Einstein crystal method. Here, the position and orientation of the molecules is fixed by using an Einstein field that binds with harmonic springs at least three non-collinear atoms (or points of the molecule) to their reference positions. The validity of the Einstein field is tested by performing free-energy calculations of methanol, water (ice), and patchy colloids molecular solids. The free energies calculated with GROMACS show a very good agreement with those obtained using Monte Carlo and with previously published results.},
  doi         = {10.1063/1.4812362},
  file        = {2013_Aragones_34104.pdf:by-author/A/Aragones/2013_Aragones_34104.pdf:PDF},
  groups      = {sg/Molecular dynamics},
  institution = {Departamento de Química Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain. aragones@mit.edu},
  language    = {eng},
  medline-pst = {ppublish},
  owner       = {saulius},
  pmid        = {23883007},
  timestamp = {2013.11.06},
  creationdate = {2013-11-06T00:00:00},
  url         = {http://dx.doi.org/10.1063/1.4812362},
}

@Article{Aragones2012,
  author      = {J. L. Aragones and C. Valeriani and C. Vega},
  journal     = {J Chem Phys},
  title       = {Note: Free energy calculations for atomic solids through the Einstein crystal/molecule methodology using GROMACS and LAMMPS.},
  year        = {2012},
  pages       = {146101},
  volume      = {137},
  abstract    = {In 1984 Frenkel and Ladd proposed the “Einstein crystal method,” a novel scheme to compute the free energy of a solid:1 the method is based on a thermodynamic integra- tion of the Helmholtz free energy in the canonical ensemble along a reversible path between the system of interest and an ideal Einstein crystal with the same structure as the real solid, whose Helmholtz free energy can be analytically computed. In the ideal Einstein crystal, particles are attached to their lattice positions via harmonic springs (of constant E). More recently, some of us have proposed the “Einstein molecule method,”[2,3] a variant of the Einstein crystal to compute the free energy of molecular solids. The main difference between both methods is the choice of the reference system. In the Einstein crystal the reference system is an ideal Einstein crystal with the constraint of the center-of-mass of the system kept fixed (to avoid a quasi-divergence of the integral of the free energy change from the reference system to the real solid). In the Einstein molecule the reference system is an ideal Einstein crystal with the constraint of the position of one particle kept fixed.},
  doi         = {10.1063/1.4758700},
  file        = {2012_Aragones_146101.pdf:by-author/A/Aragones/2012_Aragones_146101.pdf:PDF},
  language    = {eng},
  medline-pst = {ppublish},
  owner       = {saulius},
  pmid        = {23061870},
  timestamp = {2013.11.06},
  creationdate = {2013-11-06T00:00:00},
  url         = {http://dx.doi.org/10.1063/1.4758700},
}

@Article{Aras2014,
  author    = {Aras, Nadir and Yalçın, Şerife},
  journal   = {Journal of Analytical Atomic Spectrometry},
  title     = {Rapid identification of phosphorus containing proteins in electrophoresis gel spots by laser-induced breakdown spectroscopy, {LIBS}},
  year      = {2014},
  issn      = {1364-5544},
  pages     = {545--552},
  volume    = {29},
  abstract  = {A novel method for the rapid in-gel identification of phosphorus containing proteins, specifically casein and ovalbumin, prior to mass spectrometric analysis for the elucidation of phosphorylation sites was developed. After polyacrylamide gel-electrophoretic separation, staining and drying, protein bands were subjected to focused laser pulses at the center or the vicinity of the protein band. Phosphorus containing proteins were recognized from their prominent phosphorus lines in the luminous plasma formed by energetic laser pulses. The LIBS emission intensity of phosphorus lines at 253.5 nm and 255.3 nm has been optimized with respect to laser energy and detector timing parameters by using pure casein in the pellet form. The method was applied to casein, ovalbumin, two commercially available standard protein mixtures and proteins extracted from the canola plant. It was shown that LIBS was capable of identifying phosphorus containing proteins directly in the gel matrix in nanogram amounts. Mass spectrometric analysis of the ovalbumin spot after the in-gel digestion procedure has proved the accuracy of the technique. With the speed and spatial resolution that LIBS offers, this technique shows promise in the micro-local spotting of phosphorus containing proteins in the polyacrylamide gel matrix prior to MS analysis for the determination of the phosphorylation sites.},
  doi       = {10.1039/C3JA50225B},
  file      = {Aras and Yalçın - 2014 - Rapid identification of phosphorus containing prot.pdf:by-author/A/Aras/2014_Aras_545.pdf:application/pdf;Snapshot:by-author/A/Aras/2014_Aras_545.html:text/html},
  language  = {en},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://pubs.rsc.org/en/content/articlelanding/2014/ja/c3ja50225b},
  urldate   = {2015-09-30},
}

@InProceedings{Arbaugh1997,
  author    = {William A. Arbaugh and David J. Farber and Jonathan M. Smith},
  booktitle = {IEEE Security and Privacy Conference},
  title     = {A Secure and Reliable Bootstrap and Architecture},
  year      = {1997},
  publisher = {IEEE},
  file      = {:by-author/A/Arbaugh/1997_Arbaugh.pdf:PDF;:by-author/A/Arbaugh/1997_Arbaugh.ps:PostScript},
  owner     = {saulius},
  timestamp = {2015.02.25},
  creationdate = {2015-02-25T00:00:00},
}

@Article{Arber1966,
  author    = {Arber, Werner},
  journal   = {J. Mol. Biol.},
  title     = {Host Specificity of DNA produced by Escherichia coli: 9. Host-controlled Modification of Bacteriophage fd},
  year      = {1966},
  pages     = {483--496},
  volume    = {20},
  abstract  = {Host-controlled modification is shown to occur with four related msle-specific bacteriophage strains containing single-stranded DNA: fd, fl, Ml3 and F12. All four phages are restricted and modified in bacteria with B host speciilcity, the first three also in Pl-lysogenic cells. None of the phages is restricted in strains with K host specificity or carrying the episome RTF-2. The bacterial characters rsm, which control the B host specificity of h DNA, are also responsible for restriction and modification of phage fd. The apparent difference in K restriction, which is encountered by A, but not by fd, is thought to find its explanation in the small molecular size of fd DNA, on which K specificity sites might be lacking. Indeed, restriction and modification act on the DNA of fd: DNA from fd phages which infect restricting host cells is partially broken down to acid-soluble products. On the other hand, one-cycle growth of fd.B on non-restricting and non-modifying Kr-m- bacteria yields, among a majority of progeny of fd. Kr-m- phage, some phage particles with parental B host specificity, and they also have parental DNA as shown by density labelling of the infecting phage. The efficiency of such transfer of parental fd.B DNA was found to be 0.12 if measured after 18 minutes incubation of the infected cells. The implication of this transfer on the mechanism of phage DNA replication is discussed.},
  doi       = {10.1016/0022-2836(66)90004-0},
  file      = {1966_Arber_483.pdf:by-author/A/Arber/1966_Arber_483.pdf:PDF},
  keywords  = {EcorII; History; Restriction Endonucleases (REases)},
  owner     = {saulius},
  pmid      = {5338985},
  timestamp = {2016.12.04},
  creationdate = {2016-12-04T00:00:00},
}

@Article{Arber1962,
  author    = {Arber, Werner and Dussoix, Daisy},
  journal   = {Journal of Molecular Biology},
  title     = {Host specificity of DNA produced by Escherichia coli: I. Host controlled modification of bacteriophage λ},
  year      = {1962},
  issn      = {0022-2836},
  month     = {Jul},
  number    = {1},
  pages     = {18--36},
  volume    = {5},
  abstract  = {Lambda bacteriophage particles carry a “host specificity” determined by the bacterial strains on which they were produced. Upon infection of a different bacterial host (1) the phage DNA may be either accepted or rejected on the basis of this specificity, (2) if accepted, the phage multiplies and progeny phage are produced. Those progeny to which the parental phage DNA molecule is transferred, in either conserved or semi-conserved form, also receive the parental phage host specificity. All progeny containing only newly synthesized DNA receive only the specificity of the new bacterial host. It is concluded that host specificity is carried on the bacteriophage DNA.
Phage P1, present in a bacterial cell as either prophage or vegetative phage, imparts to λ DNA multiplying in the same cell a host specificity over and above that determined by the host itself. Such P1-induced specificity can be impressed equally well onto replicating and non-replicating λ DNA.},
  doi       = {10.1016/s0022-2836(62)80058-8},
  file      = {1962_Arber_18.pdf:by-author/A/Arber/1962_Arber_18.pdf:PDF},
  keywords  = {History; Restriction Endonucleases (REases)},
  owner     = {saulius},
  publisher = {Elsevier BV},
  timestamp = {2016.11.30},
  creationdate = {2016-11-30T00:00:00},
  url       = {http://dx.doi.org/10.1016/S0022-2836(62)80058-8},
}

@MastersThesis{Archambault2010,
  author    = {Erik Archambault and Christopher Pardy and John Hogeboom and Christopher Smith and Joshua Montgomery and Brian Tate},
  school    = {Worcester Polytechnic Institute},
  title     = {Fine-Grain Parallelism: An Investigative Study into the merits of Graphical Programming and a Fine-grain Execution Model},
  year      = {2010},
  month     = {March},
  file      = {2010_Archambault.pdf:by-author/A/Archambault/2010_Archambault.pdf:PDF},
  keywords  = {Graphical Programming; Parallel Computations; Programming Languages; SISAL; Single Assignment Languages},
  owner     = {saulius},
  timestamp = {2015.06.15},
  creationdate = {2015-06-15T00:00:00},
}

@InProceedings{Archambeau2003,
  author    = {Cédric Archambeau and John A. Lee and Michel Verleysen},
  booktitle = {ESANN'2003 proceedings - European Symposium on Artificial Neural Networks},
  title     = {On Convergence Problems of the {EM} Algorithm for Finite {G}aussian Mixtures},
  year      = {2003},
  month     = {April},
  pages     = {99--106},
  abstract  = {Efficient probability density function estimation is of primary interest in statistics. A popular approach for achieving this is the use of finite Gaussian mixture models. Based on the expectation-maximization algorithm, the maximum likelihood estimates of the model parameters can be iteratively computed in an elegant way. Unfortunately, in some cases the algorithm is not converging properly because of numerical difficulties. They are of two kinds: they can be associated to outliers or to repeated data samples. In this paper, we trace and discuss their origin while providing some theoretical evidence. As a matter of fact, both can be explained by the concept of isolation, which is leading to the width of the collapsing mixture component to become zero.},
  file      = {:by-author/A/Archambeau/2003_Archambeau_99.pdf:PDF},
  keywords  = {Expectation Maximisation; Gaussian Mixture Models},
  owner     = {andrius},
  timestamp = {2013.02.26},
  creationdate = {2013-02-26T00:00:00},
}

@Article{Arden1961,
  author     = {Arden, Bruce and Galler, Bernard A. and Graham, Robert M.},
  journal    = {Commun. ACM},
  title      = {Letter to the editor: criticisms of ALGOL 60},
  year       = {1961},
  issn       = {0001-0782},
  pages      = {309},
  volume     = {4},
  acmid      = {366625},
  address    = {New York, NY, USA},
  doi        = {10.1145/366622.366625},
  file       = {1961_Arden_309.pdf:by-author/A/Arden/1961_Arden_309.pdf:PDF},
  issue_date = {July 1961},
  keywords   = {Algol; Algol 60; Computer Science (CS); Criticism; Programming Languages},
  owner      = {saulius},
  publisher  = {ACM},
  timestamp = {2012.06.04},
  creationdate = {2012-06-04T00:00:00},
  url        = {http://doi.acm.org/10.1145/366622.366625},
}

@TechReport{Arens2003,
  author           = {Călin Arens and Jantien Stoter and Peter van Oosterom},
  institution      = {Section GIS-Technology, Department of Geodesy, Faculty of Civil Engineering and Geosciences, Delft University of Technology},
  title            = {Modelling 3d spatial objects in a geo-DBMS using a 3d primitive},
  year             = {2003},
  abstract         = {Geo-DBMSs make it possible to manage large spatial datasets in databases that can be accessed by multiple users at the same time. These spatial datasets usually contain 2D data, while more and more applications depend on 3D data. Some examples are 3D cadastres [1], telecommunications [2] and town planning [3]. These applications mainly come from the ever-growing tendency of using living space multifunctional by building in the vertical direction, e.g. apartments, buildings over spanning a road, tunnels and bridges [1]. The present Geo-DBMSs do not support 3D primitives, but 3D spatial objects can be modelled by using 2D primitives such as polygons. This is possible by using 3D coordinates, which are supported by the Geo-DBMSs. In this way, several 2D polygons bound a 3D object. These 2D polygons can be stored in one record (multi-polygon) or multiple records.},
  creationdate     = {2008-07-28T00:00:00},
  doi              = {10.1016/j.cageo.2004.05.013},
  file             = {:by-author/A/Arens/2003_Arens.pdf:PDF},
  modificationdate = {2023-04-23T10:17:09},
  owner            = {saulius},
  timestamp        = {2008.07.28},
}

@TechReport{Aretz2008,
  author      = {F.E.J. Kruseman Aretz},
  institution = {Centrum Wiskunde \& Informatica},
  title       = {A comparison between the ALGOL 60 implementations on the Electrologica X1 and the Electrologica X8},
  year        = {2008},
  month       = {September},
  note        = {REPORT SEN-E0801 SEPTEMBER 2008},
  abstract    = {We compare two ALGOL 60 implementations, both developed at the Mathematical Centre in Amsterdam, forerunner of the CWI. They were designed for Electrologica hardware, the EL X1 from 1958 and the EL X8 from 1965. The X1 did not support ALGOL 60 implementation at all. Its ALGOl 60 system was designed by Dijkstra and Zonneveld and completed in 1960. Although developed as an academic exercise it soon was heavily used and appreciated. The X8, successor of the X1 and (almost) upwards compatible to it, had a number of extensions chosen specifically to support ALGOL 60 implementation. The ALGOL 60 system, developed by Nederkoorn and Kruseman Aretz, was completed even before the first delivery of an X8. In this document we describe the two systems, demonstrating the progress in both hard- ware and software in a relatively short period.},
  file        = {2008_Aretz.pdf:by-author/A/Aretz/2008_Aretz.pdf:PDF},
  keywords    = {Algol; Compilers; Computer Science (CS); Computing History; Electrologica X1; Electrologica X8},
  owner       = {saulius},
  timestamp = {2016.10.29},
  creationdate = {2016-10-29T00:00:00},
  url         = {http://oai.cwi.nl/oai/asset/13677/13677D.pdf},
}

@TechReport{Aretz2003,
  author      = {F.E.J. Kruseman Aretz},
  institution = {Centrum voor Wiskunde en Informatica},
  title       = {The Dijkstra-Zonneveld ALGOL 60 compiler for the Electrologica X1. Historical note SEN, 2},
  year        = {2003},
  month       = {June},
  note        = {NOTE SEN-N0301 JUNE 30, 2003},
  abstract    = {In the summer of 1960 Edsger W. Dijkstra and Jaap A. Zonneveld put into operation the very first ALGOL 60 compiler in the world. Its code was never documented. This report contains the full assembly text of one of the latest versions of that compiler (from 1964). In order to make that text more accessible, an equivalent version in Pascal is added, together with eight chapters introducing the compiler and explaining its major features.},
  file        = {2003_Aretz.pdf:by-author/A/Aretz/2003_Aretz.pdf:PDF},
  issn        = {1386-3711},
  keywords    = {Algol; Compilers; Computer Science (CS); Computing History; Electrologica X1},
  owner       = {saulius},
  timestamp = {2016.10.29},
  creationdate = {2016-10-29T00:00:00},
  url         = {http://oai.cwi.nl/oai/asset/4155/04155D.pdf},
}

@Article{Armalyte2005,
  author    = {Armalyte, Elena and Bujnicki, Janusz M. and Giedriene, Jolanta and Gasiunas, Giedrius and Kosiński, Jan and Lubys, Arvydas},
  journal   = {The Journal of biological chemistry},
  title     = {Mva1269I: a monomeric type IIS restriction endonuclease from Micrococcus varians with two EcoRI- and FokI-like catalytic domains.},
  year      = {2005},
  pages     = {41584--94},
  volume    = {280},
  abstract  = {Type II restriction endonuclease Mva1269I recognizes an asymmetric DNA sequence 5'-GAATGCN / -3'/5'-NG / CATTC-3' and cuts top and bottom DNA strands at positions, indicated by the "/" symbol. Most restriction endonucleases require dimerization to cleave both strands of DNA. We found that Mva1269I is a monomer both in solution and upon binding of cognate DNA. Protein fold-recognition analysis revealed that Mva1269I comprises two "PD-(D/E)XK" domains. The N-terminal domain is related to the 5'-GAATTC-3'-specific restriction endonuclease EcoRI, whereas the C-terminal one resembles the nonspecific nuclease domain of restriction endonuclease FokI. Inactivation of the C-terminal catalytic site transformed Mva1269I into a very active bottom strand-nicking enzyme, whereas mutants in the N-terminal domain nicked the top strand, but only at elevated enzyme concentrations. We found that the cleavage of the bottom strand is a prerequisite for the cleavage of the top strand. We suggest that Mva1269I evolved the ability to recognize and to cleave its asymmetrical target by a fusion of an EcoRI-like domain, which incises the bottom strand within the target, and a FokI-like domain that completes the cleavage within the nonspecific region outside the target sequence. Our results have implications for the molecular evolution of restriction endonucleases, as well as for perspectives of engineering new restriction and nicking enzymes with asymmetric target sites.},
  doi       = {10.1074/jbc.M506775200},
  file      = {:by-author/A/Armalyte/2005_Armalyte_41584.pdf:PDF},
  keywords  = {BfiI; TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Arnott1974,
  author    = {Arnott, S. and Chandrasekaran, R. and Marttila, C. M.},
  journal   = {The Biochemical journal},
  title     = {Structures for polyinosinic acid and polyguanylic acid.},
  year      = {1974},
  pages     = {537--43},
  volume    = {141},
  abstract  = {X-ray-diffraction analysis of oriented, partially crystalline fibres of polyinosinic acid has resulted in a new molecular model. This model consists of four identical polynucleotide chains related to one another by a fourfold rotation axis. The coaxial helices are righthanded (screw symmetry 23(2)) and have an axial translation per residue h=0.341nm and a rotation per residue t=31.3 degrees . Incorporated in the model are standard bond lengths, bond angles and C-2-endo furanose rings. The nucleotide conformation angles, determined by linked-atom least-squares methods, are orthodox and the fit with the X-ray intensities is good. Each hypoxanthine base is linked to two others by hydrogen bonds involving O-6 and N-1. Further stability may arise from intrachain hydrogen bonds between each ribose hydroxyl group and the phosphate oxygen O-3. If guanine were to be substituted for hypoxanthine in an isogeometrical molecular structure, additional hydrogen bonds could be made between every N-2 and N-7.},
  file      = {:by-author/A/Arnott/1974_Arnott_537.pdf:PDF},
  keywords  = {DNA Structure},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Arora1997,
  author    = {Nidhi Arora and B. Jayaram},
  journal   = {Journal of Computational Chemistry},
  title     = {Strength of Hydrogen Bonds in α Helices},
  year      = {1997},
  pages     = {1245--1252},
  volume    = {18},
  file      = {:by-author/A/Arora/1997_Arora_1245.pdf:PDF},
  keywords  = {H Bonds; Protein Physics},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Arsuaga2005,
  author           = {Arsuaga, Javier and Vazquez, Mariel and McGuirk, Paul and Trigueros, Sonia and Sumners, De Witt and Roca, Joaquim},
  journal          = {Proceedings of the National Academy of Sciences of the United States of America},
  title            = {DNA knots reveal a chiral organization of DNA in phage capsids.},
  year             = {2005},
  pages            = {9165--9},
  volume           = {102},
  abstract         = {Icosahedral bacteriophages pack their double-stranded DNA genomes to near-crystalline density and achieve one of the highest levels of DNA condensation found in nature. Despite numerous studies, some essential properties of the packaging geometry of the DNA inside the phage capsid are still unknown. We present a different approach to the problems of randomness and chirality of the packed DNA. We recently showed that most DNA molecules extracted from bacteriophage P4 are highly knotted because of the cyclization of the linear DNA molecule confined in the phage capsid. Here, we show that these knots provide information about the global arrangement of the DNA inside the capsid. First, we analyze the distribution of the viral DNA knots by high-resolution gel electrophoresis. Next, we perform Monte Carlo computer simulations of random knotting for freely jointed polygons confined to spherical volumes. Comparison of the knot distributions obtained by both techniques produces a topological proof of nonrandom packaging of the viral DNA. Moreover, our simulations show that the scarcity of the achiral knot 4(1) and the predominance of the torus knot 5(1) over the twist knot 5(2) observed in the viral distribution of DNA knots cannot be obtained by confinement alone but must include writhe bias in the conformation sampling. These results indicate that the packaging geometry of the DNA inside the viral capsid is writhe-directed.},
  creationdate     = {2008-07-28T00:00:00},
  doi              = {10.1073/pnas.0409323102},
  file             = {Arsuaga_2005_9165-DNA-knots-in-phages.pdf:by-author/A/Arsuaga/2005_Arsuaga_9165.pdf:PDF},
  modificationdate = {2023-04-23T10:17:50},
  owner            = {saulius},
  timestamp        = {2008.07.28},
}

@Presentation{Artale2009,
  author    = {Alessandro Artale},
  title     = {Compilers -- Lecture VI. Semantic Analysis: Type Checking \& Symbol Table},
  year      = {2009},
  course    = {Compilers},
  lecture   = {Lecture VI.},
  school    = {Free University of Bolzano},
  file      = {:by-author/A/Artale/2009_Artale_slides.pdf:PDF},
  keywords  = {Compiler Symbol Tables; Computer Science (CS)},
  owner     = {saulius},
  pages     = {slides},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Arumugam2009,
  author    = {Arumugam, Sri Ranjini and Lee, Tae-Hee and Benkovic, Stephen J.},
  journal   = {The Journal of biological chemistry},
  title     = {Investigation of stoichiometry of T4 bacteriophage helicase loader protein (gp59).},
  year      = {2009},
  pages     = {29283--9},
  volume    = {284},
  abstract  = {The T4 bacteriophage helicase loader (gp59) is one of the main eight proteins that play an active role in the replisome. gp59 is a small protein (26 kDa) that exists as a monomer in solution and in the crystal. It binds preferentially to forked DNA and interacts directly with the T4 helicase (gp41), single-stranded DNA-binding protein (gp32), and polymerase (gp43). However, the stoichiometry and structure of the functional form are not very well understood. There is experimental evidence for a hexameric structure for the helicase (gp41) and the primase (gp61), inferring that the gp59 structure might also be hexameric. Various experimental approaches, including gel shift, fluorescence anisotropy, light scattering, and fluorescence correlation spectroscopy, have not provided a clearer understanding of the stoichiometry. In this study, we employed single-molecule photobleaching (smPB) experiments to elucidate the stoichiometry of gp59 on a forked DNA and to investigate its interaction with other proteins forming the primosome complex. smPB studies were performed with Alexa 555-labeled gp59 proteins and a forked DNA substrate. Co-localization experiments were performed using Cy5-labeled forked DNA and Alexa 555-labeled gp59 in the presence and absence of gp32 and gp41 proteins. A systematic study of smPB experiments and subsequent data analysis using a simple model indicated that gp59 on the forked DNA forms a hexamer. In addition, the presence of gp32 and gp41 proteins increases the stability of the gp59 complex, emphasizing their functional role in T4 DNA replication machinery.},
  file      = {:by-author/A/Arumugam/2009_Arumugam_29283.pdf:PDF},
  keywords  = {{gp41} Helicase},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Arun1987,
  author           = {Arun, K. S. and Huang, T. S. and Blostein, S. D.},
  journal          = {Pattern Analysis and Machine Intelligence, IEEE Transactions on},
  title            = {Least-squares fitting of two 3-{D} point sets},
  year             = {1987},
  issn             = {0162-8828},
  pages            = {698--700},
  volume           = {PAMI-9},
  abstract         = {Two point sets {pi} and {p'i}; i = 1, 2,..., N are related by p'i = Rpi + T + Ni, where R is a rotation matrix, T a translation vector, and Ni a noise vector. Given {pi} and {p'i}, we present an algorithm for finding the least-squares solution of R and T, which is based on the singular value decomposition (SVD) of a 3 × 3 matrix. This new algorithm is compared to two earlier algorithms with respect to computer time requirements.},
  comment          = {"It was shown in (Huang, Blostein, and Margerum) [3] that: If the least-squares solution to (1) is R and T, then ( p' ) and ( pi - Rp, - T ) have the same centroid". Contradicts Chen2004?},
  creationdate     = {2012-05-16T00:00:00},
  doi              = {10.1109/TPAMI.1987.4767965},
  file             = {1987_Arun_698.pdf:by-author/A/Arun/1987_Arun_698.pdf:PDF},
  groups           = {sg/Molecule superposion, sg/Superposition, sg/Bioinf. Algorithms},
  keywords         = {Algorithms; Structure Superposition},
  modificationdate = {2024-05-12T18:05:09},
  owner            = {saulius},
  timestamp        = {2012.05.16},
}

@Presentation{Arvind2011,
  author       = {Arvind},
  title        = {Modeling Processors},
  year         = {2011},
  organization = {MIT},
  file         = {:by-author/A/Arvind/2011_Arvind.pdf:PDF},
  keywords     = {CPU Design; Computer Science (CS); Electronics},
  month        = {February},
  owner        = {saulius},
  timestamp = {2015.03.11},
  creationdate = {2015-03-11T00:00:00},
  url          = {http://csg.csail.mit.edu/6.375},
}

@Article{Arwin2004,
  author    = {Arwin, Hans and Poksinski, Michal and Johansen, Knut},
  journal   = {Applied Optics},
  title     = {Total internal reflection ellipsometry: principles and applications},
  year      = {2004},
  pages     = {3028--3036},
  volume    = {43},
  doi       = {10.1364/AO.43.003028},
  file      = {:by-author/A/Arwin/2004_Arwin_3028.pdf:pdf},
  owner     = {saulius},
  timestamp = {2015.02.25},
  creationdate = {2015-02-25T00:00:00},
}

@Article{Arya1998,
  author    = {Arya, Sunil and Mount, David M. and Netanyahu, Nathan S. and Silverman, Ruth and Wu, Angela Y.},
  journal   = {J. ACM},
  title     = {An Optimal Algorithm for Approximate Nearest Neighbor Searching Fixed Dimensions},
  year      = {1998},
  issn      = {0004-5411},
  pages     = {891--923},
  volume    = {45},
  doi       = {10.1145/293347.293348},
  file      = {:by-author/A/Arya/1998_Arya_891.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://doi.acm.org/10.1145/293347.293348},
}

@Article{Ash1997,
  author    = {Ash, Sheila and Cline, Malcolm A. and Homer, R. Webster and Hurst, Tad and Smith, Gregory B.},
  journal   = {Journal of Chemical Information and Computer Sciences},
  title     = {{SYBYL} Line Notation ({SLN}): A Versatile Language for Chemical Structure Representation},
  year      = {1997},
  issn      = {0095-2338},
  month     = {Jan},
  number    = {1},
  pages     = {71–79},
  volume    = {37},
  abstract  = {SYBYL Line Notation (SLN) is an ASCII language used to represent chemical structures, including common organic molecules, macromolecules, polymers, and combinatorial libraries. SLN is also used to express substructural (2D) queries and includes a complete facility for Markush representation. This concise language is ideal for database storage of chemical entities as well as for network communication of structures and queries.},
  doi       = {10.1021/ci960109j},
  file      = {1997_Ash_71.pdf:by-author/A/Ash/1997_Ash_71.pdf:PDF},
  groups    = {sg/Crystallography, am/Crystallography},
  owner     = {andrius},
  publisher = {American Chemical Society (ACS)},
  timestamp = {2017.01.02},
  creationdate = {2017-01-02T00:00:00},
  url       = {http://dx.doi.org/10.1021/ci960109j},
}

@Article{Ashida2002,
  author           = {Ashida, Shingo and Nishimori, Isao and Tanimura, Masanobu and Onishi, Saburo and Shuin, Taro},
  journal          = {Journal of cancer research and clinical oncology},
  title            = {Effects of von Hippel-Lindau gene mutation and methylation status on expression of transmembrane carbonic anhydrases in renal cell carcinoma.},
  year             = {2002},
  pages            = {561--8},
  volume           = {128},
  creationdate     = {2008-07-28T00:00:00},
  doi              = {10.1007/s00432-002-0374-x},
  file             = {2002_Ashida_561.pdf:by-author/A/Ashida/2002_Ashida_561.pdf:PDF},
  groups           = {sg/cancer, sg/medicine},
  keywords         = {Carbonic Anhydrases},
  modificationdate = {2023-04-23T10:18:56},
  owner            = {saulius},
  timestamp        = {2008.07.28},
}

@Article{Ashino2010,
  author    = {Ashino, Toshihiro},
  journal   = {Data Science Journal},
  title     = {Materials Ontology: An Infrastructure for Exchanging Materials Information and Knowledge},
  year      = {2010},
  pages     = {54--61},
  volume    = {9},
  doi       = {10.2481/dsj.008-041},
  file      = {:by-author/A/Ashino/2010_Ashino_54.pdf:PDF},
  owner     = {andrius},
  timestamp = {2015.07.21},
  creationdate = {2015-07-21T00:00:00},
}

@Article{Assenberg2002,
  author           = {Assenberg, René and Weston, Anthony and Cardy, Don L N and Fox, Keith R},
  journal          = {Nucleic acids research},
  title            = {Sequence-dependent folding of DNA three-way junctions.},
  year             = {2002},
  pages            = {5142--50},
  volume           = {30},
  abstract         = {Three-way DNA junctions can adopt several different conformers, which differ in the coaxial stacking of the arms. These structural variants are often dominated by one conformer, which is determined by the DNA sequence. In this study we have compared several three-way DNA junctions in order to assess how the arrangement of bases around the branch point affects the conformer distribution. The results show that rearranging the different arms, while retaining their base sequences, can affect the conformer distribution. In some instances this generates a structure that appears to contain parallel coaxially stacked helices rather than the usual anti-parallel arrangement. Although the conformer equilibrium can be affected by the order of purines and pyrimidines around the branch point, this is not sufficient to predict the conformer distribution. We find that the folding of three-way junctions can be separated into two groups of dinucleotide steps. These two groups show distinctive stacking properties in B-DNA, suggesting there is a correlation between B-DNA stacking and coaxial stacking in DNA junctions.},
  creationdate     = {2008-07-28T00:00:00},
  doi              = {10.1093/nar/gkf637},
  file             = {2002_Assenberg_5142.pdf:by-author/A/Assenberg/2002_Assenberg_5142.pdf:PDF},
  keywords         = {Stacking},
  modificationdate = {2023-04-23T10:19:32},
  owner            = {saulius},
  timestamp        = {2008.07.28},
}

@Article{Aston2017,
  author    = {James C. Aston and Paul J. Saines},
  journal   = {Zeitschrift für anorganische und allgemeine Chemie},
  title     = {Transition-Metal Dependent Cation Disorder in the Chiral Cubic {AB} ({HCO}2 )3 Metal-Organic Frameworks (A = Li or Na, B = Mn or Co)},
  year      = {2017},
  month     = {jan},
  doi       = {10.1002/zaac.201600350},
  file      = {Aston2017.pdf:by-author/A/Aston/2017_Aston.pdf:PDF;:by-author/A/Aston/2017_Aston_a.pdf:PDF},
  groups    = {sg/MOF, sg/MOFs, am/MOFs},
  owner     = {saulius},
  publisher = {Wiley-Blackwell},
  timestamp = {2017.01.31},
  creationdate = {2017-01-31T00:00:00},
  url       = {https://doi.org/10.1002%2Fzaac.201600350},
}

@InProceedings{Astrachan2003,
  author    = {Owen Astrachan},
  booktitle = {Proceedings of the 34th SIGCSE technical symposium on Computer science education},
  title     = {Bubble Sort: An Archaeological Algorithmic Analysis},
  year      = {2003},
  address   = {New York, NY, USA},
  pages     = {1--5},
  publisher = {ACM},
  series    = {SIGCSE '03},
  abstract  = {Text books, including books for general audiences, invariably mention bubble sort in discussions of elementary sorting algorithms. We trace the history of bubble sort, its popularity, and its endurance in the face of pedagogical assertions that code and algorithmic examples used in early courses should be of high quality and adhere to established best practices. This paper is more an historical analysis than a philosophical treatise for the exclusion of bubble sort from books and courses. However, sentiments for exclusion are supported by Knuth [17], "In short, the bubble sort seems to have nothing to recommend it, except a catchy name and the fact that it leads to some interesting theoretical problems." Although bubble sort may not be a best practice sort, perhaps the weight of history is more than enough to compensate and provide for its longevity.},
  doi       = {10.1145/611892.611918},
  file      = {:by-author/A/Astrachan/2003_Astrachan_1.pdf:PDF},
  isbn      = {1-58113-648-X},
  keywords  = {Algorithm Analysis; Computer Science (CS); Sorting},
  location  = {Reno, Navada, USA},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
  url       = {http://doi.acm.org/10.1145/611892.611918},
}

@Article{Astumian2007,
  author    = {Astumian, R. Dean},
  journal   = {Proceedings of the National Academy of Sciences},
  title     = {Adiabatic operation of a molecular machine},
  year      = {2007},
  pages     = {19715--19718},
  volume    = {104},
  abstract  = {Operation of a molecular machine is often thought of as a “far from equilibrium” process in which energy released by some high free energy fuel molecule or by light is used to drive a nonequilibrium “power stroke” to do work on the environment. Here we discuss how a molecular machine can be operated arbitrarily close to chemical equilibrium and still perform significant work at an appreciable rate: micrometer per second velocities against piconewton loads. As a specific example, we focus on a motor based on a three-ring catenane similar to that discussed by Leigh [Leigh DA, Wong JKY, Dehez F, Zerbetto F (2003) Nature 424:174–179]. The machine moves through its working cycle under the influence of external modulation of the energies of the states, where the modulation is carried out slowly enough that the state probabilities obey a Boltzmann equilibrium distribution at every instant. The mechanism can be understood in terms of the geometric phase [Berry MV (1990) Phys Today 43(12):34–40] in which the system moves adiabatically around a closed loop in parameter space, completing, on average, nearly one-half mechanical cycle each time it does so. Because the system is very close to equilibrium at every instant, the efficiency can approach 100%.},
  doi       = {10.1073/pnas.0708040104},
  file      = {2007_Astumian_19715.pdf:by-author/A/Astumian/2007_Astumian_19715.pdf:PDF},
  keywords  = {Molecular Machines},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://www.pnas.org/content/104/50/19715.abstract},
}

@Article{Astumian1997,
  author           = {Astumian, R D},
  journal          = {Science (New York, N.Y.)},
  title            = {Thermodynamics and kinetics of a Brownian motor.},
  year             = {1997},
  pages            = {917--22},
  volume           = {276},
  creationdate     = {2008-07-28T00:00:00},
  doi              = {10.1126/science.276.5314.917},
  file             = {1997_Astumian_917.pdf:by-author/A/Astumian/1997_Astumian_917.pdf:PDF},
  keywords         = {Molecular Machines},
  modificationdate = {2023-04-23T10:20:02},
  owner            = {saulius},
  timestamp        = {2008.07.28},
}

@Article{Astumian1998,
  author           = {Astumian, R D and Derényi, I},
  journal          = {European biophysics journal : EBJ},
  title            = {Fluctuation driven transport and models of molecular motors and pumps.},
  year             = {1998},
  pages            = {474--89},
  volume           = {27},
  abstract         = {Non-equilibrium fluctuations can drive vectorial transport along an anisotropic structure in an isothermal medium by biasing the effect of thermal noise (kBT). Mechanisms based on this principle are often called Brownian ratchets and have been invoked as a possible explanation for the operation of biomolecular motors and pumps. We discuss the thermodynamics and kinetics for the operation of microscopic ratchet motors under conditions relevant to biology, showing how energy provided by external fluctuations or a non-equilibrium chemical reaction can cause unidirectional motion or uphill pumping of a substance. Our analysis suggests that molecular pumps such as Na,K-ATPase and molecular motors such as kinesin and myosin may share a common underlying mechanism.},
  creationdate     = {2008-07-28T00:00:00},
  doi              = {10.1007/s002490050158},
  file             = {Astumian_1998_474-molecular_motors_and_pumps.pdf:by-author/A/Astumian/1998_Astumian_474.pdf:PDF},
  modificationdate = {2023-04-23T10:20:13},
  owner            = {saulius},
  timestamp        = {2008.07.28},
}

@Article{Atanasiu2001a,
  author    = {Atanasiu, C. and Byron, O. and McMiken, H. and Sturrock, S. S. and Dryden, D. T.},
  journal   = {Nucleic acids research},
  title     = {Characterisation of the structure of ocr, the gene 0.3 protein of bacteriophage T7.},
  year      = {2001},
  pages     = {3059--68},
  volume    = {29},
  abstract  = {The product of gene 0.3 of bacteriophage T7, ocr, is a potent inhibitor of type I DNA restriction and modification enzymes. We have used biophysical methods to examine the mass, stability, shape and surface charge distribution of ocr. Ocr is a dimeric protein with hydrodynamic behaviour equivalent to a prolate ellipsoid of axial ratio 4.3 +/- 0.7:1 and mass of 27 kDa. The protein is resistant to denaturation but removal of the C-terminal region reduces stability substantially. Six amino acids, N4, D25, N43, D62, S68 and W94, are all located on the surface of the protein and N4 and S68 are also located at the interface between the two 116 amino acid monomers. Negatively charged amino acid side chains surround W94 but these side chains are not part of the highly acidic C-terminus after W94. Ocr is able to displace a short DNA duplex from the binding site of a type I enzyme with a dissociation constant of the order of 100 pM or better. These results suggest that ocr is of a suitable size and shape to effectively block the DNA binding site of a type I enzyme and has a large negatively charged patch on its surface. This charge distribution may be complementary to the charge distribution within the DNA binding site of type I DNA restriction and modification enzymes.},
  file      = {:by-author/A/Atanasiu/2001_Atanasiu_3059.pdf:PDF},
  keywords  = {Antirestriction},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Atanasiu2002,
  author    = {Atanasiu, C. and Su, T-J. and Sturrock, S. S. and Dryden, D. T. F.},
  journal   = {Nucleic acids research},
  title     = {Interaction of the ocr gene 0.3 protein of bacteriophage T7 with EcoKI restriction/modification enzyme.},
  year      = {2002},
  pages     = {3936--44},
  volume    = {30},
  abstract  = {The ocr protein, the product of gene 0.3 of bacteriophage T7, is a structural mimic of the phosphate backbone of B-form DNA. In total it mimics 22 phosphate groups over approximately 24 bp of DNA. This mimicry allows it to block DNA binding by type I DNA restriction enzymes and to inhibit these enzymes. We have determined that multiple ocr dimers can bind stoichiometrically to the archetypal type I enzyme, EcoKI. One dimer binds to the core methyltransferase and two to the complete bifunctional restriction and modification enzyme. Ocr can also bind to the component subunits of EcoKI. Binding affinity to the methyltransferase core is extremely strong with a large favourable enthalpy change and an unfavourable entropy change. This strong interaction prevents the dissociation of the methyltransferase which occurs upon dilution of the enzyme. This stabilisation arises because the interaction appears to involve virtually the entire surface area of ocr and leads to the enzyme completely wrapping around ocr.},
  file      = {:by-author/A/Atanasiu/2002_Atanasiu_3936.pdf:PDF},
  keywords  = {Antirestriction},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Athalye2006,
  author    = {Vikram S Athalye and Arvind Kumar},
  journal   = {Journal of Physics B: Atomic, Molecular and Optical Physics},
  title     = {Decoherence of superposition of molecular chiral states due to Rayleigh scattering},
  year      = {2006},
  pages     = {2633},
  volume    = {39},
  abstract  = {In this paper we investigate the effect of many Rayleigh scattering events on decoherence of superpositions of chiral states of a molecule, by taking these events as measurement-like interactions in the sense that the scattered photon state depends on the state of the molecule—both its centre-of-mass position and its chirality. This gives rise to two contributions to decoherence: one due to the position measurement and the other due to the chirality measurement. It is found that under identical conditions, the decoherence timescale for chiral molecules can be different from that for achiral molecules depending on the chiral sensitivity of scattering.},
  file      = {2006_Athalye_2633.pdf:by-author/A/Athalye/2006_Athalye_2633.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.05.16},
  creationdate = {2012-05-16T00:00:00},
  url       = {http://stacks.iop.org/0953-4075/39/i=12/a=002},
}

@Proceedings{Atkinson2011,
  title     = {Adapting Scheme-Like Macros to a C-Like Language},
  year      = {2011},
  abstract  = {ZL is a C++-compatible language in which high-level constructs, such as classes, are defined using macros over a C-like core. ZL’s parser and macro expander are similar to that of Scheme. Unlike Scheme, however, ZL must deal with C’s richer syntax. Specif- ically, support for context-sensitive parsing and multiple syntac- tic categories (expressions, statements, types, etc.) leads to novel strategies for parsing and macro expansion. In this paper we de- scribe ZL’s approach to parsing and macros.},
  author    = {Kevin Atkinson and Matthew Flatt},
  file      = {:by-author/A/Atkinson/2011_Atkinson.pdf:PDF},
  keywords  = {Computer Languages; Computer Science (CS); Oregon Workshop; Scheme},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
  url       = {http://www.schemeworkshop.org/2011/papers/Atkinson2011.pdf},
}

@Article{Attridge2001,
  author    = {Daniel J.M. Attridge},
  journal   = {Intellectual Property Quarterly},
  title     = {Challenging claims! patenting computer programs in Europe and the USA},
  year      = {2001},
  pages     = {22--49},
  volume    = {1},
  file      = {:by-author/A/Attridge/2001_Attridge_22.doc:DOC},
  keywords  = {Patentai; Teise},
  owner     = {saulius},
  timestamp = {2015.02.28},
  creationdate = {2015-02-28T00:00:00},
}

@InProceedings{Aung2003,
  author           = {Zeyar Aung and Wei Fu and Kian-Lee Tan},
  booktitle        = {Proceedings of the Eighth International Conference on Database Systems for Advanced Applications},
  title            = {An Efficient Index-based Protein Structure Database Searching Method},
  year             = {2003},
  abstract         = {In this paper, we present a novel indexing method called ProtDex to facilitate fast searching in 3-dimensional protein structure database. In ProtDex, we first build an index on the representative properties of all proteins in the database. When evaluating a query, with the help of the index, we filter out a small candidate list of proteins. Then, we can either directly report them, with their respective rankings, to the user, or do the expensive actual alignments on them upon user’s request. Preliminary experimental results show that our solution is up to 16 times faster than the popular DALI method for database searching task (without actual alignments), while its overall accuracy is only slightly inferior to that of DALI. The software is available upon request by sending emails to the authors.},
  creationdate     = {2008-07-28T00:00:00},
  doi              = {10.1109/dasfaa.2003.1192396},
  file             = {:by-author/A/Aung/2003_Aung.pdf:PDF},
  journal          = {Proceedings of the Eighth International Conference on Database Systems for Advanced Applications},
  modificationdate = {2023-04-23T10:20:31},
  owner            = {saulius},
  timestamp        = {2008.07.28},
}

@Article{Auslander1965,
  author    = {Louis Auslander},
  journal   = {Proceedings of the American Mathematical Society},
  title     = {An Account on the Theory of Crystallographic Groups},
  year      = {1965},
  pages     = {1230--1236},
  volume    = {16},
  file      = {:by-author/A/Auslander/1965_Auslander_1230.pdf:PDF},
  keywords  = {Spacegroups; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
  url       = {http://www.jstor.org/stable/2035904 .},
}

@Article{Austin2002,
  author    = {Peter C. Austin and Lawrence J. Brunner and Janet E. Hux},
  title     = {Bayeswatch: an overview of {Bayesian} statistics},
  year      = {2002},
  pages     = {277--286},
  volume    = {8},
  file      = {Peter C. Austin et al. - 2002 - Bayeswatch an overview of Bayesian statistics.pdf:by-author/A/Austin/2002_Austin_277.pdf:application/pdf},
  groups    = {sg/Clinical Trials},
  language  = {English},
  owner     = {saulius},
  timestamp = {2015.12.14},
  creationdate = {2015-12-14T00:00:00},
  url       = {http://www.biostat.jhsph.edu/~fdominic/teaching/bio656/references/BayesOverview.pdf},
  urldate   = {2015-12-12},
}

@Webpage{MathArchivesAuthors2008,
  author    = {MathArchives Authors},
  retrieved = {2008-10-28},
  title     = {Math Archives: Other Software Sites},
  url       = {http://archives.math.utk.edu/cgi-bin/all_software.html},
  year      = {2008},
  file      = {:by-author/A/Authors/2008_Authors.odt:},
  keywords  = {Computer Science (CS); Mathematical-programs; Programs},
  owner     = {saulius},
  timestamp = {2015.03.03},
  creationdate = {2015-03-03T00:00:00},
}

@MastersThesis{Au-Yeung2003,
  author    = {Susanna W. M. Au-Yeung},
  school    = {the University of London and the Imperial College of Science, Technology and Medicine},
  title     = {Finding Probability Distributions From Moments},
  year      = {2003},
  abstract  = {Using the moment sequence of a continuous probability function to regenerate the full distribution is a mathematical problem that has been investigated for many years. One method is to use a flexible distribution to approximate the densities by matching the moments of the two distributions. The results are of great interest, as they can be readily applied to response time analysis in concurrent systems, where obtaining moments is relatively easy but obtaining full distributions is hard. In this dissertation we look at the development of a tool that approximates densities when given the first four moments. The Generalized Lambda Distribution will be discussed in detail and we shall investigate the effectiveness of using it to approximate densities of well known probability distributions in addition to densities derived from response time analysis models.},
  file      = {2003_Au-Yeung_masterthesis.pdf:by-author/A/Au-Yeung/2003_Au-Yeung_masterthesis.pdf:PDF},
  owner     = {saulius},
  pages     = {mscthesis},
  timestamp = {2012.09.18},
  creationdate = {2012-09-18T00:00:00},
}

@Article{Avery1944,
  author    = {Avery, O.T. and MacLeod, C.M. and McCarty, M.},
  journal   = {J. Exp. Med.},
  title     = {Studies on the chemical nature of the substance inducing transformation of Pneumococcal types},
  year      = {1944},
  pages     = {137--159},
  volume    = {79},
  file      = {1944_Avery_137.pdf:by-author/A/Avery/1944_Avery_137.pdf:PDF},
  keywords  = {DNA; Transformation},
  owner     = {saulius},
  timestamp = {2012.11.21},
  creationdate = {2012-11-21T00:00:00},
  url       = {http://www.nature.com/nature/dna50/macLeodmccarty.pdf},
}

@Article{Aviram1974,
  author    = {Aviram, Arieh and Ratner, Mark A.},
  title     = {Molecular rectifiers},
  year      = {1974},
  pages     = {277--283},
  volume    = {29},
  abstract  = {The construction of a very simple electronic device, a rectifier, based on the use of a single organic molecule is discussed. The molecular rectifier consists of a donor pi system and an acceptor pi system, separated by a sigma-bonded (methylene) tunnelling bridge. The response of such a molecule to an applied field is calculated, and rectifier properties indeed appear.},
  file      = {Aviram and Ratner - 1974 - Molecular rectifiers.pdf:by-author/A/Aviram/1974_Aviram_277.pdf:application/pdf},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  urldate   = {2015-08-26},
}

@Article{Ayora2002,
  author           = {Ayora, Silvia and Weise, Frank and Mesa, Pablo and Stasiak, Andrzej and Alonso, Juan C.},
  journal          = {Nucleic acids research},
  title            = {Bacillus subtilis bacteriophage SPP1 hexameric DNA helicase, G40P, interacts with forked DNA.},
  year             = {2002},
  pages            = {2280--9},
  volume           = {30},
  abstract         = {SPP1-encoded replicative DNA helicase gene 40 product (G40P) is an essential product for phage replication. Hexameric G40P, in the presence of AMP-PNP, preferentially binds unstructured single-stranded (ss)DNA in a sequence-independent manner. The efficiency of ssDNA binding, nucleotide hydrolysis and the unwinding activity of G40P are affected in a different manner by different nucleotide cofactors. Nuclease protection studies suggest that G40P protects the 5' tail of a forked molecule, and the duplex region at the junction against exonuclease attack. G40P does not protect the 3' tail of a forked molecule from exonuclease attack. By using electron microscopy we confirm that the ssDNA transverses the centre of the hexameric ring. Our results show that hexameric G40P DNA helicase encircles the 5' tail, interacts with the duplex DNA at the ss-double-stranded DNA junction and excludes the 3' tail of the forked DNA.},
  creationdate     = {2008-07-28T00:00:00},
  doi              = {10.1093/nar/30.11.2280},
  file             = {:by-author/A/Ayora/2002_Ayora_2280.pdf:PDF},
  keywords         = {{gp41}; {gp41} Helicase},
  modificationdate = {2023-04-23T10:20:45},
  owner            = {em},
  timestamp        = {2008.07.28},
}

@TechReport{Azarani2003,
  author      = {Arezou Azarani},
  institution = {Corning},
  title       = {Automated High-Throughput Microdrop Crystallization Using Corning® CrystalEX™ 96 Well Protein Crystallization Microplates},
  year        = {2003},
  file        = {2003_Azarani.pdf:by-author/A/Azarani/2003_Azarani.pdf:PDF},
  keywords    = {Corning Plates; Crystallisation Plates; Protein Crystallisation},
  owner       = {saulius},
  timestamp = {2013.10.27},
  creationdate = {2013-10-27T00:00:00},
  url         = {http://www.level.com.tw/html/ezcatfiles/vipweb20/img/img/20297/96wellCrystalEXpaper.pdf},
}

@TechReport{AZUL2013,
  author      = {AZUL},
  institution = {AZUL Systems},
  title       = {Understanding Java Garbage Collection -- And What You Can Do About It},
  year        = {2013},
  file        = {2013_AZUL_v3.pdf:by-author/A/AZUL/2013_AZUL_v3.pdf:PDF},
  groups      = {sg/Garbage collectors, sg/Java},
  keywords    = {Computer Science (CS); Garbage Collection; Java},
  owner       = {saulius},
  timestamp = {2015.12.16},
  creationdate = {2015-12-16T00:00:00},
  url         = {http://www.azulsystems.com/sites/default/files/images/Understanding_Java_Garbage_Collection_v3.pdf},
}

@Article{Bohm2001,
  author    = {B\"{o}hm, Christian and Berchtold, Stefan and Keim, Daniel A.},
  journal   = {ACM Comput. Surv.},
  title     = {Searching in High-dimensional Spaces: Index Structures for Improving the Performance of Multimedia Databases},
  year      = {2001},
  issn      = {0360-0300},
  pages     = {322--373},
  volume    = {33},
  doi       = {10.1145/502807.502809},
  file      = {:by-author/B/Bohm/2001_Bohm_322.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://doi.acm.org/10.1145/502807.502809},
}

@InProceedings{Baars2002,
  author    = {Baars, Arthur I. and Swierstra, S. Doaitse},
  booktitle = {Proceedings of the seventh ACM SIGPLAN international conference on Functional programming},
  title     = {Typing Dynamic Typing},
  year      = {2002},
  address   = {New York, NY, USA},
  pages     = {157--166},
  publisher = {ACM},
  series    = {ICFP '02},
  doi       = {10.1145/581478.581494},
  file      = {:by-author/B/Baars/2002_Baars_157.pdf:PDF},
  isbn      = {1-58113-487-8},
  keywords  = {Computer Science (CS); Type Systems},
  location  = {Pittsburgh, PA, USA},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
  url       = {http://doi.acm.org/10.1145/581478.581494},
}

@Article{Babic2008,
  author      = {Andrea C Babic and Elizabeth J Little and Veena M Manohar and Jurate Bitinaite and Nancy C Horton},
  journal     = {J Mol Biol},
  title       = {DNA distortion and specificity in a sequence-specific endonuclease.},
  year        = {2008},
  month       = {Oct},
  number      = {1},
  pages       = {186--204},
  volume      = {383},
  abstract    = {Five new structures of the Q138F HincII enzyme bound to a total of three different DNA sequences and three different metal ions (Ca(2+), Mg(2+), and Mn(2+)) are presented. While previous structures were produced from soaking Ca(2+) into preformed Q138F HincII/DNA crystals, the new structures are derived from cocrystallization with Ca(2+), Mg(2+), or Mn(2+). The Mn(2)(+)-bound structure provides the first view of a product complex of Q138F HincII with cleaved DNA. Binding studies and a crystal structure show how Ca(2+) allows trapping of a Q138F HincII complex with noncognate DNA in a catalytically incompetent conformation. Many Q138F HincII/DNA structures show asymmetry, despite the binding of a symmetric substrate by a symmetric enzyme. The various complexes are fit into a model describing the different conformations of the DNA-bound enzyme and show how DNA conformational energetics determine DNA-cleavage rates by the Q138F HincII enzyme.},
  doi         = {10.1016/j.jmb.2008.08.032},
  file        = {2008_Babic_186.pdf:by-author/B/Babic/2008_Babic_186.pdf:PDF},
  institution = {Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, AZ 85721, USA.},
  keywords    = {Amino Acid Substitution; Base Sequence; Binding Sites; Catalytic Domain; Cations; Crystallization; Crystallography; DNA; Deoxyribonucleases; Dimerization; Divalent; Models; Molecular; Protein Conformation; Protein Structure; Quaternary; Recombinant Proteins; Substrate Specificity; Type II Site-Specific; X-Ray},
  owner       = {em},
  pii         = {S0022-2836(08)01025-5},
  pmid        = {18762194},
  timestamp = {2011.06.10},
  creationdate = {2011-06-10T00:00:00},
  url         = {http://dx.doi.org/10.1016/j.jmb.2008.08.032},
}

@Article{Babic2008a,
  author    = {Babic, Andrea C. and Little, Elizabeth J. and Manohar, Veena M. and Bitinaite, Jurate and Horton, Nancy C.},
  journal   = {Journal of molecular biology},
  title     = {DNA distortion and specificity in a sequence-specific endonuclease.},
  year      = {2008},
  pages     = {186--204},
  volume    = {383},
  abstract  = {Five new structures of the Q138F HincII enzyme bound to a total of three different DNA sequences and three different metal ions (Ca(2+), Mg(2+), and Mn(2+)) are presented. While previous structures were produced from soaking Ca(2+) into preformed Q138F HincII/DNA crystals, the new structures are derived from cocrystallization with Ca(2+), Mg(2+), or Mn(2+). The Mn(2)(+)-bound structure provides the first view of a product complex of Q138F HincII with cleaved DNA. Binding studies and a crystal structure show how Ca(2+) allows trapping of a Q138F HincII complex with noncognate DNA in a catalytically incompetent conformation. Many Q138F HincII/DNA structures show asymmetry, despite the binding of a symmetric substrate by a symmetric enzyme. The various complexes are fit into a model describing the different conformations of the DNA-bound enzyme and show how DNA conformational energetics determine DNA-cleavage rates by the Q138F HincII enzyme.},
  file      = {:by-author/B/Babic/2008_Babic_186.pdf:PDF},
  keywords  = {HincII; Indirect; Readout; TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Webpage{Backus1976,
  author    = {J.~W. Backus and F.~L. Bauer and J. Green and C. Katz and J. McCarthy and P. Naur and A.~J. Perlis and H. Rutishauser and K. Samelson and B. Vauquois and J.~H. Wegstein and A.~van Wijngaarden and M. Woodger},
  retrieved = {2015-03-06},
  title     = {Modified Report on the Algorithmic Language Algol 60},
  url       = {http://www.masswerk.at/algol60/modified_report.htm},
  year      = {1976},
  file      = {:by-author/B/Backus/1976_Backus.htm:URL},
  keywords  = {Algol; Algol 68; Computer Science (CS); Programming-languages},
  owner     = {saulius},
  timestamp = {2015.03.03},
  creationdate = {2015-03-03T00:00:00},
}

@Article{Backus1960,
  author     = {Backus, J. W. and Bauer, F. L. and Green, J. and Katz, C. and McCarthy, J. and Perlis, A. J. and Rutishauser, H. and Samelson, K. and Vauquois, B. and Wegstein, J. H. and van Wijngaarden, A. and Woodger, M.},
  journal    = {Commun. ACM},
  title      = {Report on the Algorithmic Language {ALGOL} 60},
  year       = {1960},
  issn       = {0001-0782},
  pages      = {299--314},
  volume     = {3},
  address    = {New York, NY, USA},
  doi        = {10.1145/367236.367262},
  editor     = {Naur, Peter},
  file       = {:by-author/B/Backus/1960_Backus_299.pdf:PDF},
  issue_date = {May 1960},
  keywords   = {Algol; Algol 60; Computer Science (CS); Programming Languages},
  owner      = {saulius},
  publisher  = {ACM},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
  url        = {http://doi.acm.org/10.1145/367236.367262},
}

@Presentation{Bader2006,
  author       = {Reinhold Bader and Georg Hager},
  title        = {OpenMP Programming: Correctness, Tuning, Examples},
  year         = {2006},
  organization = {LRZ; RRZE},
  file         = {:by-author/B/Bader/2006_Bader_slides.pdf:PDF},
  owner        = {saulius},
  pages        = {slides},
  timestamp = {2013.07.02},
  creationdate = {2013-07-02T00:00:00},
  url          = {http://www.lrz.de/services/software/parallel/openmp/Kurs/OpenMP_optex.pdf},
}

@Article{Badger2003,
  author    = {Badger, John},
  journal   = {Acta Crystallographica Section D},
  title     = {An evaluation of automated model-building procedures for protein crystallography},
  year      = {2003},
  pages     = {823--827},
  volume    = {59},
  doi       = {10.1107/S0907444903003792},
  file      = {dz0004.pdf:by-author/B/Badger/2003_Badger_823.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444903003792},
}

@Article{Badjakov2008,
  author    = {I. Badjakov and M. Nikolova and R. Gevrenova and V. Kondakova and E. Todorovska1 and A. Atanassov},
  journal   = {Biotechnology \& Biotechnological Equipment},
  title     = {Bioactive compounds in small fruits and their influence on human health},
  year      = {2008},
  pages     = {581--587},
  volume    = {22},
  abstract  = {The international tendency for growing and production of small fruits shows a permanent increasing. Bulgaria is a traditional important producer of small berries in Europe. A large variety of small fruit products are wide spread and typical for Bulgarian nutriment. Aside with the growing demand in production of small fruit, there is an obvious tendency in food quality, breeding and technology requirements improvement. Breeding purposes comprise improvement of many traits, but selection of disease resistant cultivars, with higher yield and improved consumers properties such as fruit color, shape, smell and transportation ability are among the most important tasks. Recent progress in molecular analyses and agriculture biotechnologies has enormous impact on selection, technology, testing, preservation and processing of agricultural products. Metabolomics assay as a new dimension in these studies and practice focuses the attention on the biochemical contents of cells and tissues, and has a rapidly growing significance in knowledge of small fruits value for human health. Berry fruits are very rich sources of bioactive compounds as phenolics and organic acid. Bioactive berry compounds, their characterization and utilization in functional foods and clinical assessment of antimicrobial properties for human health are among the major targets of contemporary research. Phenolic compounds in berries inhibit the growth of range of human pathogens. Especially raspberry, strawberry, cranberry, crowberries showed evidence of antimicrobial effects against bacterial pathogens as Salmonella and Staphylococcus. The evaluation of small fruit genetic resources for the presence of bioactive compounds and their properties as natural agents is of doubtless significance and will be with great benefit for breeders, food and pharmaceutical industry.},
  file      = {2008_Badjakov_581.pdf:by-author/B/Badjakov/2008_Badjakov_581.pdf:PDF},
  keywords  = {Bioactive Compounds; Human Health; Metabolomics; Small Fruits},
  owner     = {saulius},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
  url       = {http://www.diagnosisp.com/dp/journals/view_article.php?journal_id=1&archive=0&issue_id=17&article_id=468},
}

@Misc{Baggerly,
  author    = {Baggerly, Keith A.},
  title     = {Bioinformatics and reproducible research},
  file      = {Bioinformatics and Reproducible Research:by-author/B/Baggerly/XXXX_Baggerly.pdf:application/pdf},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://www.mdanderson.org/education-and-research/departments-programs-and-labs/departments-and-divisions/division-of-quantitative-sciences/pdf/keith-baggerly.pdf},
  urldate   = {2015-06-06},
}

@Presentation{Baggerly2014,
  author    = {Keith A. Baggerly},
  title     = {Reproducible Research in Bioinformatics},
  year      = {2014},
  file      = {Microarrays, Cell Lines, Drugs and Disease\: Predicting Response to Chemotherapy - Baggerly_panel_sept2014.pdf:by-author/B/Baggerly/2014_Baggerly.pdf:application/pdf},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://www.samsi.info/sites/default/files/Baggerly_panel_sept2014.pdf},
  urldate   = {2015-06-06},
}

@Article{Baggerly2009,
  author    = {Baggerly, Keith A. and Coombes, Kevin R.},
  journal   = {Ann. Appl. Stat.},
  title     = {Deriving chemosensitivity from cell lines: Forensic bioinformatics and reproducible research in high-throughput biology},
  year      = {2009},
  pages     = {1309--1334},
  volume    = {3},
  doi       = {10.1214/09-AOAS291},
  file      = {2009_Baggerly_1309.pdf:by-author/B/Baggerly/2009_Baggerly_1309.pdf:PDF},
  fjournal  = {The Annals of Applied Statistics},
  keywords  = {Bioinformatics; Forensic Bioinformatics; High-throughput; Tools},
  owner     = {saulius},
  publisher = {The Institute of Mathematical Statistics},
  timestamp = {2015.06.12},
  creationdate = {2015-06-12T00:00:00},
  url       = {http://dx.doi.org/10.1214/09-AOAS291},
}

@Article{Bagla2011,
  author    = {Bagla, Pallava},
  journal   = {Science (New York, N.Y.)},
  title     = {Traditional medicine. Piercing the veil of Ayurveda.},
  year      = {2011},
  pages     = {1491},
  volume    = {334},
  file      = {:by-author/B/Bagla/2011_Bagla_1491.pdf:PDF},
  keywords  = {Chemistry; Natural Compounds},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@Article{Bahn2002,
  author       = {Bahn, S. R. and Jacobsen, Karsten W.},
  journal      = {Computing in Science Engineering},
  title        = {An object-oriented scripting interface to a legacy electronic structure code},
  year         = {2002},
  issn         = {1521-9615},
  pages        = {56--66},
  volume       = {4},
  abstract     = {The authors have created an object-oriented scripting interface to a mature density functional theory code. The interface gives users a high-level, flexible handle on the code without rewriting the underlying number-crunching code. The authors also discuss the design issues and advantages of homogeneous interfaces},
  creationdate = {2015-11-23T00:00:00},
  doi          = {10.1109/5992.998641},
  file         = {2002_Bahn_56.pdf:by-author/B/Bahn/2002_Bahn_56.pdf:PDF},
  keywords     = {Chemistry; Computer Interfaces; Density Functional Theory (DFT); Density Functional Theory Code; Eigenvalues and Eigenfunctions; Equations; Jacobian Matrices; Legacy Code; Object Oriented Programming; Object-oriented Databases; Object-oriented Programming; Physics Computing; Quantum Mechanics (QM); Scripting Interface; User Interface; User Interfaces; Wave Functions},
  owner        = {saulius},
  timestamp    = {2015.11.23},
}

@Article{Baierlein2001,
  author    = {Baierlein},
  journal   = {American Journal of Physics},
  title     = {The elusive chemical potential},
  year      = {2001},
  pages     = {423},
  volume    = {69},
  abstract  = {This paper offers some qualitative understanding of the chemical potential, a topic that students invariably find difficult. Three “meanings” for the chemical potential are stated and then supported by analytical development. Two substantial applications—depression of the melting point and batteries—illustrate the chemical potential in action. The origin of the term “chemical potential” has its surprises, and a sketch of the history concludes the paper. © 2001 American Association of Physics Teachers.},
  doi       = {10.1119/1.1336839},
  file      = {:by-author/B/Baierlein/2001_Baierlein_423.pdf:PDF},
  keywords  = {Thermodynamics},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Manuscript{LeBail2008,
  author    = {Armel le Bail},
  title     = {Frontiers Between Crystal-structure Prediction and Determination by Powder Diffractometry},
  year      = {2008},
  keywords  = {Crystal Structure Prediction (CSP); Powder Diffraction; Prediction; Search-match; X-ray Crystallography},
  abstract  = {The fuzzy frontiers between structure determination by powder diffractometry and crystal structure prediction are discussed. The application of a search-match program combined with a database of more than 60,000 predicted powder diffraction patterns is demonstrated. Immediate structure solution (before indexing) is shown to be possible by this method if the discrepancies between the predicted crystal structure cell parameters and the actual ones are < 1%. Incomplete chemistry of the hypothetical models (missing interstitial cations, water molecules, etc) is not necessarily a barrier to a successful identification (in spite of inducing large intensity errors), provided the search-match is made with chemical restrictions on the elements present in both the virtual and experimental compounds.},
  file      = {:by-author/B/Bail/2008_Bail_p2d2.pdf:PDF},
  groups    = {sg/Crystal structure prediction},
  owner     = {saulius},
  pages     = {p2d2-manuscript},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@Article{Bailey2004,
  author    = {Chris Bailey and Stephen Pelc},
  title     = {UFO – Ubiquitous Forth Object},
  year      = {2004},
  abstract  = {The UFO will form a combination of CPU and operating system technology, namely a stack- machine CPU core, and a Forth operating system. However both of these components will have novel properties, in that a scaleable target instance can be generated, according to a trade-off between gate-count, speed, power, and computational performance. Simpler machines can emulate more complex ones, but at the cost of lower performance than a physical implementation of the more complex architecture.},
  file      = {:by-author/B/Bailey/2004_Bailey.pdf:PDF},
  keywords  = {Computer Science (CS); Stack Machines},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Electronic{Bailey2006,
  author    = {Nicholas P. Bailey and Thierry Cretegny and James P. Sethna, and Valerie R. Coffman and Andrew J. Dolgert and Christopher R Myers and Jakob Schiøtz and Jens Jørgen Mortensen},
  month     = {January},
  title     = {Digital Material: A flexible atomistic simulation code},
  url       = {http://arxiv.org/pdf/cond-mat/0601236},
  year      = {2006},
  eprint    = {cond-mat/0601236},
  file      = {2008_Bailey_1.pdf:by-author/B/Bailey/2006_Bailey.pdf:PDF},
  keywords  = {Simulations},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Bailey2007,
  author           = {Bailey, Scott and Eliason, William K. and Steitz, Thomas A.},
  journal          = {Science (New York, N.Y.)},
  title            = {Structure of hexameric DnaB helicase and its complex with a domain of DnaG primase.},
  year             = {2007},
  pages            = {459--63},
  volume           = {318},
  abstract         = {The complex between the DnaB helicase and the DnaG primase unwinds duplex DNA at the eubacterial replication fork and synthesizes the Okazaki RNA primers. The crystal structures of hexameric DnaB and its complex with the helicase binding domain (HBD) of DnaG reveal that within the hexamer the two domains of DnaB pack with strikingly different symmetries to form a distinct two-layered ring structure. Each of three bound HBDs stabilizes the DnaB hexamer in a conformation that may increase its processivity. Three positive, conserved electrostatic patches on the N-terminal domain of DnaB may also serve as a binding site for DNA and thereby guide the DNA to a DnaG active site.},
  creationdate     = {2008-07-28T00:00:00},
  doi              = {10.1126/science.1147353},
  file             = {:by-author/B/Bailey/2007_Bailey_459.pdf:PDF},
  keywords         = {Ecoli; {gp41} Helicase},
  modificationdate = {2023-04-23T10:20:55},
  owner            = {em},
  timestamp        = {2008.07.28},
}

@Article{Bailey2006a,
  author    = {Scott Bailey and Richard A. Wing and Thomas A. Steitz},
  journal   = {Cell},
  title     = {The Structure of T. aquaticus DNA Polymerase III Is Distinct from Eukaryotic Replicative DNA Polymerases},
  year      = {2006},
  issn      = {0092-8674},
  pages     = {893--904},
  volume    = {126},
  abstract  = {Summary The crystal structure of Thermus aquaticus DNA polymerase III α subunit reveals that the structure of the catalytic domain of the eubacterial replicative polymerase is unrelated to that of the eukaryotic replicative polymerase but rather belongs to the Polβ-like nucleotidyltransferase superfamily. A model of the polymerase complexed with both DNA and β-sliding clamp interacting with a reoriented binding domain and internal β binding site was constructed that is consistent with existing biochemical data. Within the crystal, two C-terminal domains are interacting through a surface that is larger than many dimer interfaces. Since replicative polymerases of eubacteria and eukaryotes/archaea are not homologous, the nature of the replicative polymerase in the last common ancestor is unknown. Although other possibilities have been proposed, the plausibility of a ribozyme DNA polymerase should be considered.},
  doi       = {10.1016/j.cell.2006.07.027},
  file      = {2006_Bailey_893.pdf:by-author/B/Bailey/2006_Bailey_893.pdf:PDF;mmc1.pdf Supplemental Data:by-author/B/Bailey/2006_Bailey_893_suppl/mmc1.pdf:PDF},
  keywords  = {PolIII},
  owner     = {saulius},
  timestamp = {2012.10.24},
  creationdate = {2012-10-24T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/S009286740601021X},
}

@Article{Bajpai2015,
  author       = {Bajpai, A. and Mukhopadhyay, A. and Krishna, M. S. and Govardhan, S. and Moorthy, J. N.},
  journal      = {{IUCrJ}},
  title        = {A fluorescent paramagnetic Mn metal–organic framework based on semi-rigid pyrene tetra­carboxylic acid: sensing of solvent polarity and explosive nitroaromatics},
  year         = {2015},
  issn         = {2052-2525},
  number       = {5},
  pages        = {552--562},
  volume       = {2},
  abstract     = {An Mn metal–organic framework (Mn-{MOF}), Mn-L, based on a pyrene-tetraacid linker (H4L), displays a respectable fluorescence quantum yield of 8.3\% in spite of the presence of the paramagnetic metal ions, due presumably to fixation of the metal ions in geometries that do not allow complete energy/charge-transfer quenching. Remarkably, the porous Mn-L {MOF} with ∼25\% solvent-accessible volume exhibits a heretofore unprecedented solvent-dependent fluorescence emission maximum, permitting its use as a probe of solvent polarity; the emission maxima in different solvents correlate excellently with Reichardt's solvent polarity parameter ({ETN}). Further, the applicability of Mn-L to the sensing of nitroaromatics via fluorescence quenching is demonstrated; the detection limit for {TNT} is shown to be 125 p.p.m. The results bring out the fact that {MOFs} based on paramagnetic metal ions can indeed find application when the quenching mechanisms are attenuated by certain geometries of the organic linkers of the {MOF}.},
  date         = {2015-09-01},
  doi          = {10.1107/S2052252515012506},
  file         = {Full Text PDF:by-author/B/Bajpai/2015_Bajpai_552.pdf:PDF;Snapshot:by-author/B/Bajpai/2015_Bajpai_552.html:URL},
  groups       = {sg/MOF, sg/MOFs, am/MOFs},
  journaltitle = {{IUCrJ}},
  keywords     = {Crystal Structure; Fluorescence; Metal-Organic Frameworks (MOF); Metal-organic Framework; Nitro­aromatics; Sensing; Solvatochromism},
  langid       = {english},
  owner        = {saulius},
  rights       = {http://creativecommons.org/licenses/by/2.0/uk},
  shortjournal = {{IUCrJ}},
  shorttitle   = {A fluorescent paramagnetic Mn metal–organic framework based on semi-rigid pyrene tetra­carboxylic acid},
  timestamp = {2017.01.29},
  creationdate = {2017-01-29T00:00:00},
  url          = {http://scripts.iucr.org/cgi-bin/paper?ed5005},
  urldate      = {2017-01-29},
}

@Article{Baker1996,
  author           = {Baker, E N and Blundell, T L and Vijayan, M and Dodson, E and Dodson, G and Gilliland, G I and Sussman, J L},
  journal          = {Nature},
  title            = {Crystallographic data deposition.},
  year             = {1996},
  pages            = {202},
  volume           = {379},
  creationdate     = {2008-07-28T00:00:00},
  doi              = {10.1038/379202a0},
  file             = {1996_Baker_202.pdf:by-author/B/Baker/1996_Baker_202.pdf:PDF;1996_Baker_202.djvu:by-author/B/Baker/1996_Baker_202.djvu:Djvu},
  keywords         = {Data Quality; X-ray Crystallography},
  modificationdate = {2023-04-23T10:21:11},
  owner            = {saulius},
  timestamp        = {2008.07.28},
}

@Article{Baker1996a,
  author    = {Baker, E. N. and Blundell, T. L. and Vijayan, M. and Dodson, E. and Dodson, G. and Gilliland, G. L. and Sussman, J. L.},
  journal   = {Biophysical Journal},
  title     = {Archival Journal Requirements for Data Deposition},
  year      = {1996},
  pages     = {2994},
  volume    = {70},
  file      = {:by-author/B/Baker/1996_Baker_2994.pdf:PDF},
  groups    = {sg/Bayesian},
  keywords  = {Bayesian Statistics; Mathematics},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Baker1991,
  author    = {Henry G. Baker},
  journal   = {ACM Sigplan Notices},
  title     = {Shallow Binding Makes Functional Arrays Fast},
  year      = {1991},
  pages     = {145--147},
  abstract  = {Access and update for random elements of arrays in imperative programming languages are O(1) operations. Implementing functional programming languages to achieve equivalent efficiency has proved difficult. We show how the straight-forward application of shallow binding to functional arrays automatically achieves O(1) update for single-threaded usage.},
  file      = {:by-author/B/Baker/1991_Baker_145.ps.gz:PostScript;:by-author/B/Baker/1991_Baker_145.pdf:PDF},
  owner     = {saulius},
  timestamp = {2015.02.27},
  creationdate = {2015-02-27T00:00:00},
}

@TechReport{Baker1991a,
  author      = {Henry G. Baker},
  institution = {Nimble Computer Corporation, 16231 Meadow Ridge Way, Encino, CA 91436},
  title       = {Shallow Binding Makes Functional Arrays Fast},
  year        = {1991},
  file        = {:by-author/B/Baker/1991_Baker. 1991), 145-147..war:WAR},
  keywords    = {Computer Science (CS); Functional; Languages},
  owner       = {saulius},
  timestamp = {2015.03.02},
  creationdate = {2015-03-02T00:00:00},
  url         = {http://home.pipeline.com/~hbaker1/ShallowArrays.html},
}

@Article{Baker2004,
  author           = {Baker, Nathan A},
  journal          = {Methods in enzymology},
  title            = {Poisson-Boltzmann methods for biomolecular electrostatics.},
  year             = {2004},
  pages            = {94--118},
  volume           = {383},
  creationdate     = {2008-07-28T00:00:00},
  doi              = {10.1016/s0076-6879(04)83005-2},
  file             = {2004_Baker_94.pdf:by-author/B/Baker/2004_Baker_94.pdf:PDF},
  keywords         = {Poisson-Boltzmann eq; Protein Physics; Solvatation},
  modificationdate = {2023-04-23T10:21:27},
  owner            = {saulius},
  timestamp        = {2008.07.28},
}

@Presentation{Balaji2010,
  author       = {Pavan Balaji},
  title        = {Introduction to Parallel Programming with MPI},
  year         = {2010},
  organization = {Argonne National Laboratory},
  email        = {balaji@mcs.anl.gov},
  file         = {:by-author/B/Balaji/2010_Balaji_slides.pdf:PDF},
  owner        = {saulius},
  pages        = {slides},
  timestamp = {2013.07.02},
  creationdate = {2013-07-02T00:00:00},
  url          = {http://www.mcs.anl.gov/~balaji/},
}

@Article{Balashov1956,
  author    = {Balashov, V.},
  journal   = {Acta Crystallographica},
  title     = {The choice of the unit cell in the triclinic system},
  year      = {1956},
  month     = {Mar},
  number    = {3},
  pages     = {319--320},
  volume    = {9},
  doi       = {10.1107/S0365110X56000905},
  file      = {1956_Balashov_319.pdf:by-author/B/Balashov/1956_Balashov_319.pdf:PDF},
  groups    = {sg/Cell sg/Reduction, sg/Cell reduction},
  keywords  = {Unit Cell},
  owner     = {saulius},
  timestamp = {2016.04.12},
  creationdate = {2016-04-12T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0365110X56000905},
}

@Article{Baldi2011,
  author    = {Baldi, Pierre},
  journal   = {Journal of chemical information and modeling},
  title     = {Data-driven high-throughput prediction of the 3-{D} structure of small molecules: review and progress. {A} response to the letter by the {C}ambridge {C}rystallographic {D}ata {C}entre},
  year      = {2011},
  pages     = {3029},
  volume    = {51},
  abstract  = {A response is presented to sentiments expressed in &quot;Data-Driven High-Throughput Prediction of the 3-D Structure of Small Molecules: Review and Progress. A Response from The Cambridge Crystallographic Data Centre&quot;, recently published in the Journal of Chemical Information and Modeling, (1) which may give readers a misleading impression regarding significant impediments to scientific research posed by the CCDC.},
  doi       = {10.1021/ci200460z},
  file      = {:by-author/B/Baldi/2011_Baldi_3029.pdf:PDF},
  groups    = {sg/JAC2009},
  keywords  = {COSMOS; CSD; Citing COD; Citing CrystalEye; Criticism; Crystallography; Data Management; Databases; Restrains},
  owner     = {saulius},
  timestamp = {2012.09.24},
  creationdate = {2012-09-24T00:00:00},
  url       = {http://pubs.acs.org/doi/abs/10.1021/ci200460z},
}

@Article{Baldwin2002,
  author    = {Robert L. Baldwin},
  journal   = {Biophysical Chemistry},
  title     = {John Schellman and his scientific work},
  year      = {2002},
  month     = {January},
  pages     = {9--13},
  abstract  = {In 1955 John Schellman wrote a paper estimating the stability of the α-helix in aqueous solution [1]. Four years earlier Pauling and Corey had proposed that the α-helix should be a major structural unit in proteins, but no one had yet seen an α-helix. Only in 1958, when Kendrew and co-workers determined the structure of the first protein (sperm whale myoglobin) at 0.6 nm resolution, could α-helices begin to be seen. So John's paper was on the cutting edge, to put it mildly. His was also the first modern paper on the energetics of protein folding: Kauzmann's landmark paper on the energetic importance of burying non-polar side chains in the interior of proteins appeared 4 years later in 1959.},
  doi       = {10.1016/S0301-4622(02)00194-1},
  file      = {2002_Baldwin_9.pdf:by-author/B/Baldwin/2002_Baldwin_9.pdf:PDF},
  keywords  = {Protein Folding; Thermodinamics; Urea Denaturation},
  owner     = {saulius},
  timestamp = {2015.03.13},
  creationdate = {2015-03-13T00:00:00},
  url       = {http://rbaldwin.stanford.edu/PDFs/john_schellman.pdf},
}

@Article{Baldwin2000,
  author           = {Baldwin, R. L. and Zimm, B. H.},
  journal          = {Proceedings of the National Academy of Sciences of the United States of America},
  title            = {Are denatured proteins ever random coils?},
  year             = {2000},
  pages            = {12391--2},
  volume           = {97},
  creationdate     = {2008-07-28T00:00:00},
  doi              = {10.1073/pnas.97.23.12391},
  file             = {:by-author/B/Baldwin/2000_Baldwin_12391.pdf:PDF},
  modificationdate = {2023-04-23T10:21:37},
  owner            = {saulius},
  timestamp        = {2008.07.28},
}

@Article{Balla1984,
  author    = {Prabhakara C. Balla and Andreas Antoniou},
  journal   = {IEEE Journal of Solid-State Circuits},
  title     = {Low power dissipation {MOS} ternary logic family},
  year      = {1984},
  pages     = {739--749},
  volume    = {sc-19},
  abstract  = {An MOS ternary-logic family is proposed, which is com- prised of a set of inverters, NOR gates, and NAN D gates. These gates are used to design basic ternary arithmetic and memory circuits. The circuits thus obtained are then used to synthesize complex ternary arithmetic circuits and shift registers. The ternary circuits developed are shown to have some significant advantages relative to other known ternary circuits like low power dissipation, and reduced propagation delay and component count. For a given dynamic range, the complexity of the new ternary circuits is shown to be comparable to that of corresponding binary circuits. Nevertheless, the associated reduction in the wordlength in the case of the ternary circuits tends to alleviate to a large extent the pin limitation problem associated with VLSI implementation. The paper concludes with an implementation of the cyclic convolution, an application in which a significant advantage can be gained through the use of ternary digital hardware.},
  file      = {:by-author/B/Balla/1984_Balla_739.pdf:},
  keywords  = {Computer Science (CS); Logic-circuits; Ternary},
  owner     = {saulius},
  timestamp = {2015.03.03},
  creationdate = {2015-03-03T00:00:00},
}

@Article{Ballell2005,
  author    = {Ballell, Lluis and Alink, Kirstin J. and Slijper, Monique and Versluis, Cees and Liskamp, Rob M. J. and Pieters, Roland J.},
  journal   = {Chembiochem: a European Journal of Chemical Biology},
  title     = {A New Chemical Probe for Proteomics of Carbohydrate-binding Proteins},
  year      = {2005},
  pages     = {291--5},
  volume    = {6},
  file      = {:by-author/B/Ballell/2005_Ballell_291.pdf:PDF},
  keywords  = {Bioconjugation},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@Article{Ballester2007,
  author           = {Ballester, Pedro J and Richards, W. Graham},
  journal          = {Proceedings of the Royal Society A: Mathematical, Physical and Engineering Science},
  title            = {Ultrafast shape recognition for similarity search in molecular databases},
  year             = {2007},
  pages            = {1307--1321},
  volume           = {463},
  abstract         = {Molecular databases are routinely screened for compounds that most closely resemble a molecule of known biological activity to provide novel drug leads. It is widely believed that three-dimensional molecular shape is the most discriminating pattern for biological activity as it is directly related to the steep repulsive part of the interaction potential between the drug-like molecule and its macromolecular target. However, efficient comparison of molecular shape is currently a challenge. Here, we show that a new approach based on moments of distance distributions is able to recognize molecular shape at least three orders of magnitude faster than current methodologies. Such an ultrafast method permits the identification of similarly shaped compounds within the largest molecular databases. In addition, the problematic requirement of aligning molecules for comparison is circumvented, as the proposed distributions are independent of molecular orientation. Our methodology could be also adapted to tackle similar hard problems in other fields, such as designing content-based Internet search engines for three-dimensional geometrical objects or performing fast similarity comparisons between proteins. From a broader perspective, we anticipate that ultrafast pattern recognition will soon become not only useful, but also essential to address the data explosion currently experienced in most scientific disciplines.},
  creationdate     = {2012-10-25T00:00:00},
  doi              = {10.1098/rspa.2007.1823},
  eprint           = {http://rspa.royalsocietypublishing.org/content/463/2081/1307.full.pdf+html},
  file             = {2007_Ballester_1307.pdf:by-author/B/Ballester/2007_Ballester_1307.pdf:PDF},
  keywords         = {Chemical Structure Search; Databases; Fingreprints; Three Dimensional Structures; Ultrafast Shape Recognition},
  modificationdate = {2023-12-24T19:17:40},
  owner            = {saulius},
  timestamp        = {2012.10.25},
  url              = {http://rspa.royalsocietypublishing.org/content/463/2081/1307.abstract},
}

@Misc{Ballester2006,
  author           = {Pedro J. Ballester and W. Graham Richards},
  howpublished     = {PDF poster/slides},
  month            = {September},
  note             = {NFCR Center for Computational Drug Discovery, University of Oxford, Oxford, UK},
  title            = {Ultrafast Shape Recognition for Similarity Search in Molecular Databases},
  year             = {2006},
  creationdate     = {2008-07-28T00:00:00},
  doi              = {10.1098/rspa.2007.1823},
  file             = {:by-author/B/Ballester/2006_Ballester.pdf:PDF},
  keywords         = {Chemical Structure Search; Databases; Fingreprints; Three Dimensional Structures; Ultrafast Shape Recognition},
  modificationdate = {2023-12-24T19:18:03},
  owner            = {saulius},
  timestamp        = {2008.07.28},
}

@Article{Balzer1967,
  author    = {Robert Balzer},
  journal   = {Information and Control},
  title     = {An 8-state minimal time solution to the firing squad synchronization problem},
  year      = {1967},
  issn      = {0019-9958},
  number    = {1},
  pages     = {22 - 42},
  volume    = {10},
  abstract  = {This paper presents a description of a general outline for a minimal time solution to the Firing Squad Synchronization Problem, and a solution of this form which is composed of machines with only eight states. The paper then discusses the verification of this minimal time solution by computer simulation, and gives the schema for the mathematical induction proof that the solution works for any length (the full proof is given in (Balzer, 1966)). The final part of the paper discusses some efforts to determine the minimal number of states needed for a minimal time solution. No four state minimal time solution exists. A reasonable set of conditions are presented for which no five state minimal time solution exists. Also, various eight state minimal time solutions exists.},
  doi       = {10.1016/S0019-9958(67)90032-0},
  file      = {1967_Balzer_22.pdf:by-author/B/Balzer/1967_Balzer_22.pdf:PDF},
  keywords  = {Celular Automata; Computer Science (CS)},
  owner     = {saulius},
  timestamp = {2016.07.17},
  creationdate = {2016-07-17T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/S0019995867900320},
}

@InProceedings{Bandi2004,
  author    = {Bandi, Nagender and Sun, Chengyu and Agrawal, Divyakant and El Abbadi, Amr},
  booktitle = {Proceedings of the Thirtieth international conference on Very large data bases - Volume 30},
  title     = {Hardware Acceleration in Commercial Databases: A Case Study of Spatial Operations},
  year      = {2004},
  pages     = {1021--1032},
  abstract  = {Traditional databases have focused on the is- sue of reducing I/O cost as it is the bottleneck in many operations. As databases become increasingly accepted in areas such as Geo- graphic Information Systems (GIS) and Bio- informatics, commercial DBMS need to sup- port data types for complex data such as spa- tial geometries and protein structures. These non-conventional data types and their asso- ciated operations present new challenges. In particular, the computational cost of some spatial operations can be orders of magnitude higher than the I/O cost. In order to im- prove the performance of spatial query pro- cessing, innovative solutions for reducing this computational cost are beginning to emerge. Recently, it has been proposed that hard- ware acceleration of an off-the-shelf graph- ics card can be used to reduce the compu- tational cost of spatial operations. However, this proposal is preliminary in that it es- tablishes the feasibility of the hardware as- sisted approach in a stand-alone setting but not in a real-world commercial database. In this paper we present an architecture to show how hardware acceleration of an off-the-shelf graphics card can be integrated into a popu- lar commercial database to speed up spatial queries. Extensive experimentation with real- world datasets shows that significant improve- ment in the performance of spatial operations can be achieved with this integration. The vi- ability of this approach underscores the signif- icance of a tighter integration of hardware ac- celeration into commercial databases for spa- tial applications.},
  file      = {:by-author/B/Bandi/2004_Bandi_1021.pdf:PDF},
  isbn      = {0-12-088469-0},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dl.acm.org/citation.cfm?id=1316689.1316777},
}

@Article{Bandyopadhyay2008,
  author    = {Bandyopadhyay, Anirban and Acharya, Somobrata},
  journal   = {Proceedings of the National Academy of Sciences of the United States of America},
  title     = {A 16-bit parallel processing in a molecular assembly.},
  year      = {2008},
  pages     = {3668--72},
  volume    = {105},
  abstract  = {A machine assembly consisting of 17 identical molecules of 2,3,5,6-tetramethyl-1-4-benzoquinone (DRQ) executes 16 instructions at a time. A single DRQ is positioned at the center of a circular ring formed by 16 other DRQs, controlling their operation in parallel through hydrogen-bond channels. Each molecule is a logic machine and generates four instructions by rotating its alkyl groups. A single instruction executed by a scanning tunneling microscope tip on the central molecule can change decisions of 16 machines simultaneously, in four billion (4(16)) ways. This parallel communication represents a significant conceptual advance relative to today's fastest processors, which execute only one instruction at a time.},
  doi       = {10.1073/pnas.0703105105},
  file      = {2008_Bandyopadhyay_3668.pdf:by-author/B/Bandyopadhyay/2008_Bandyopadhyay_3668.pdf:PDF},
  keywords  = {Molecular Machines},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Banerjee2005a,
  author    = {Arindam Banerjee and Inderjit S. Dhillon and Joydeep Ghosh and Suvrit Sra},
  journal   = {Journal of Machine Learning Research},
  title     = {Clustering on the Unit Hypersphere using von {M}ises-{F}isher Distributions},
  year      = {2005},
  pages     = {1–39},
  volume    = {6},
  abstract  = {Several large scale data mining applications, such as text categorization and gene expression analysis, involve high-dimensional data that is also inherently directional in nature. Often such data is L2 normalized so that it lies on the surface of a unit hypersphere. Popular models such as (mixtures of) multi-variate Gaussians are inadequate for characterizing such data. This paper proposes a generative mixture-model approach to clustering directional data based on the von Mises-Fisher (vMF) distribution, which arises naturally for data distributed on the unit hypersphere. In particular, we derive and analyze two variants of the Expectation Maximization (EM) framework for estimating the mean and concentration parameters of this mixture. Numerical estimation of the concentration parameters is non-trivial in high dimensions since it involves functional inversion of ratios of Bessel functions. We also formulate two clustering algorithms corresponding to the variants of EM that we derive. Our approach provides a theoretical basis for the use of cosine similarity that has been widely employed by the information retrieval community, and obtains the spherical kmeans algorithm (kmeans with cosine similarity) as a special case of both variants. Empirical results on clustering of high-dimensional text and gene-expression data based on a mixture of vMF distributions show that the ability to estimate the concentration parameter for each vMF component, which is not present in existing approaches, yields superior results, especially for difficult clustering tasks in high-dimensional spaces.},
  file      = {:by-author/B/Banerjee/2005_Banerjee_1.pdf:PDF},
  keywords  = {Clustering on Hyperspheres; Expectation Maximisation},
  owner     = {andrius},
  timestamp = {2013.02.27},
  creationdate = {2013-02-27T00:00:00},
}

@Electronic{Banerjee2003,
  author    = {Arindam Banerjee and Inderjit S. Dhillon and Joydeep Ghosh and Suvrit Sra},
  title     = {Expectation Maximization for Clustering on Hyperspheres},
  url       = {http://www.lans.ece.utexas.edu/~abanerjee/papers/05/banerjee05a.pdf},
  year      = {2003},
  abstract  = {High dimensional directional data is becoming increasingly important in contemporary ap- plications such as analysis of text and gene-expression data. A natural model for multi-variate directional data is provided by the von Mises-Fisher (vMF) distribution on the unit hyper- sphere that is analogous to multi-variate Gaussian distribution in R^d . In this paper, we propose modeling complex directional data as a mixture of vMF distributions. We derive and analyze two variants of the Expectation Maximization (EM) framework for estimating the parameters of this mixture. We also propose two clustering algorithms corresponding to these variants. An interesting aspect of our methodology is that the spherical kmeans algorithm (kmeans with cosine similarity) can be shown to be a special case of both our algorithms. Several results on gene expression and high-dimensional text datasets are presented to demonstrate the improved clusterings obtained by our algorithms.},
  file      = {:by-author/B/Banerjee/2003_Banerjee_1.pdf:PDF},
  keywords  = {Clustering on Hyperspheres; Expectation Maximisation},
  owner     = {andrius},
  pages     = {1--33},
  timestamp = {2012.08.16},
  creationdate = {2012-08-16T00:00:00},
}

@Article{Banerjee2004,
  author           = {Banerjee, Abir L and Swanson, Michael and Roy, Bidhan C and Jia, Xiao and Haldar, Manas K and Mallik, Sanku and Srivastava, D K},
  journal          = {Journal of the American Chemical Society},
  title            = {Protein surface-assisted enhancement in the binding affinity of an inhibitor for recombinant human carbonic anhydrase-II.},
  year             = {2004},
  pages            = {10875--83},
  volume           = {126},
  abstract         = {We elaborate on a novel strategy for enhancing the binding affinity of an active-site directed inhibitor by attaching a tether group, designed to interact with the surface-exposed histidine residue(s) of enzymes. In this approach, we have utilized the recombinant form of human carbonic anhydrase-II (hCA-II) as the enzyme source and benzenesulfonamide and its derivatives as inhibitors. The steady-state kinetic and the ligand binding data revealed that the attachment of iminodiacetate (IDA)-Cu(2+) to benzenesulfonamide (via a triethylene glycol spacer) enhanced its binding affinity for hCA-II by about 40-fold. No energetic contribution of either IDA or triethylene glycol spacer was found (at least in the ground state of the enzyme-inhibitor complex) when Cu(2+) was stripped off from the tether group-conjugated sulfonamide derivative. Arguments are presented that the overall strategy of enhancing the binding affinities of known inhibitors by attaching the IDA-Cu(2+) groups to interact with the surface-exposed histidine residues will find a general application in designing the isozyme-specific inhibitors as potential drugs.},
  creationdate     = {2008-07-28T00:00:00},
  doi              = {10.1021/ja047557p},
  file             = {2004_Banerjee_10875.pdf:by-author/B/Banerjee/2004_Banerjee_10875.pdf:PDF},
  groups           = {sg/inhibitors, sg/hCA2},
  keywords         = {Carbonic Anhydrases; Inhibitors},
  modificationdate = {2023-04-23T10:24:55},
  owner            = {saulius},
  timestamp        = {2008.07.28},
}

@MastersThesis{Banerjee2005,
  author    = {Kutty S. Banerjee},
  school    = {Department of computer science and the committee on graduate studies of Worcester Polytechnic Institute},
  title     = {Remote execution for mobile 3D graphics},
  year      = {2005},
  month     = {may},
  file      = {:by-author/B/Banerjee/2005_Banerjee_mscthesis.pdf:PDF},
  keywords  = {Computer Graphics; Computer Science (CS)},
  owner     = {saulius},
  pages     = {mscthesis},
  timestamp = {2012.09.27},
  creationdate = {2012-09-27T00:00:00},
  url       = {http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.102.579},
}

@Article{ProteinDataBank1973,
  author    = {Protein Data Bank},
  journal   = {Acta Crystallographica Section B},
  title     = {{Protein Data Bank}. Notes and News},
  year      = {1973},
  pages     = {1746},
  volume    = {29},
  abstract  = {The repository system for protein crystallographic data, annound in the scientific press in October 1971, is now operational. The data bank is administered jointly by the Cambridge Crystallographic Data Centre and the Brookhaven National Laboratory. The atomic coordinates for the following proteins are available for distribution on magnetic tape in machine readable form: 1. Cyanide methaemoglobin V from sea lamprey. 2. Cytochrome bs. 3. Basic pancreatic trypsin inhibitor. 4. Subtilisin BPN (Novo). 5. Tosyl c$\alpha$- chymotrypsin. 6. Bovine carboxypeptidase A$\alpha$. 7. L-Lactate dehydrogenase. 8. Myoglobin. 9. Rubredoxin.},
  doi       = {10.1107/S0567740873005467},
  file      = {:by-author/P/PDB/1973_PDB_1746.pdf:PDF},
  groups    = {am/PDB},
  keywords  = {Data Management; Databases; PDB; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2014.03.24},
  creationdate = {2014-03-24T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0567740873005467},
}

@Article{ProteinDataBank1971,
  author    = {Protein Data Bank},
  journal   = {Nature New Biology},
  title     = {Protein Data Bank},
  year      = {1971},
  pages     = {223},
  volume    = {233},
  doi       = {10.1038/newbio233223b0},
  file      = {:by-author/P/PDB/1971_PDB_223.pdf:PDF},
  groups    = {am/PDB},
  keywords  = {Data Management; Databases; PDB; Protein Crystallography; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2014.03.24},
  creationdate = {2014-03-24T00:00:00},
  url       = {http://www.nature.com/nature-newbio/journal/v233/n42/pdf/newbio233223b0.pdf},
}

@TechReport{Banker1990,
  author      = {Rajiv D. Banker and Srikant M. Datar and Chris F. Kemerer and Dani Zweig},
  institution = {International Center for Research on the Management of Technology},
  title       = {Software complexity and software maintenance costs},
  year        = {1990},
  file        = {:by-author/B/Banker/1990_Banker.pdf:PDF},
  keywords    = {Computer Science (CS); Software Design},
  owner       = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
  url         = {http://dspace.mit.edu/bitstream/handle/1721.1/49191/softwarecomplexi92sloa.pdf?sequence=1},
}

@Misc{Banks2011,
  author    = {Banks, David},
  title     = {Reproducible research: {A} range of response},
  year      = {2011},
  file      = {Banks - 2011 - Reproducible Research A Range of Response.pdf:by-author/B/Banks/2011_Banks.pdf:application/pdf},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://bioinformatics.mdanderson.org/Supplements/ReproRsch-All/Modified/ENAR/banksNotes.pdf},
  urldate   = {2015-06-06},
}

@MastersThesis{Bannerman2006,
  author    = {Marcus Bannerman},
  school    = {School of Chemical Engineering and Analytical Science School of The University of Manchester},
  title     = {Transport properties of asymmetric binary hard-sphere mixtures},
  year      = {2006},
  file      = {:by-author/B/Bannerman/2006_Bannerman_MEthesis.pdf:PDF},
  groups    = {sg/Molecular dynamics},
  keywords  = {Hard Spheres; Molecular Dynamics (MD)},
  owner     = {saulius},
  pages     = {MEthesis},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@Article{Baranauskiene2010,
  author      = {Lina Baranauskienė and Mika Hilvo and Jurgita Matulienė and Dmitrij Golovenko and Elena Manakova and Virginija Dudutienė and Vilma Michailovienė and Jolanta Torresan and Jelena Jachno and Seppo Parkkila and Alfonso Maresca and Claudiu T Supuran and Saulius Gražulis and Daumantas Matulis},
  journal     = {J Enzyme Inhib Med Chem},
  title       = {Inhibition and binding studies of carbonic anhydrase isozymes I, II and IX with benzimidazo[1,2-c][1,2,3]thiadiazole-7-sulphonamides.},
  year        = {2010},
  pages       = {863--870},
  volume      = {25},
  abstract    = {The binding and inhibition strength of a series of benzimidazo[1,2-c][1,2,3]thiadiazole-7-sulphonamides were determined for recombinant human carbonic anhydrase isoforms I, II, and IX. The inhibition strength was determined by a stop-flow method to measure carbon dioxide hydration. Inhibitor-enzyme binding was determined by two biophysical techniques--isothermal titration calorimetry and thermal shift assay. The co-crystal structure was determined by X-ray crystallography. Comparing the results obtained using three different inhibition and binding methods increased the accuracy of compound affinity ranking and the ability to determine compound inhibitory specificity towards a particular carbonic anhydrase isoform. In most cases, all three methods yielded the same results despite using very different approaches to measure the binding and inhibition reactions. Some of the compounds studied are submicromolar inhibitors of the isoform IX, a prominent cancer target.},
  doi         = {10.3109/14756360903571685},
  file        = {:/home/alexey/papers/by-author/B/Baranauskiene/2010_Baranauskiene_863.pdf:PDF},
  groups      = {sg/inhibitors},
  institution = {Laboratory of Biothermodynamics and Drug Design, Institute of Biotechnology, Graičiūno 8, Vilnius, Lithuania.},
  keywords    = {Algorithms; Antagonists /&/ Inhibitors/chemistry/genetics/metabolism; Antagonists /&/ Inhibitors/chemistry/metabolism; Antagonists /&/ Inhibitors/genetics/metabolism; Antigens; Antineoplastic Agents; Benzimidazoles; Calorimetry; Carbonic Anhydrase I; Carbonic Anhydrase II; Carbonic Anhydrase Inhibitors; Carbonic Anhydrases; Catalytic Domain; Chemistry/metabolism/pharmacology; Crystallography; Drug Effects; Genetics/metabolism; Humans; Kinetics; Ligands; Methods; Molecular Conformation; Neoplasm; Recombinant Proteins; Sulfonamides; Thiadiazoles; X-Ray},
  language    = {eng},
  medline-pst = {ppublish},
  owner       = {em},
  pmid        = {20166809},
  timestamp = {2013.02.18},
  creationdate = {2013-02-18T00:00:00},
  url         = {http://dx.doi.org/10.3109/14756360903571685},
}

@InProceedings{Barham2003,
  author    = {Barham, Paul and Dragovic, Boris and Fraser, Keir and Hand, Steven and Harris, Tim and Ho, Alex and Neugebauer, Rolf and Pratt, Ian and Warfield, Andrew},
  booktitle = {Proceedings of the nineteenth ACM symposium on Operating systems principles},
  title     = {Xen and the art of virtualization},
  year      = {2003},
  address   = {New York, NY, USA},
  pages     = {164--177},
  publisher = {ACM},
  series    = {SOSP '03},
  doi       = {10.1145/945445.945462},
  file      = {:by-author/B/Barham/2003_Barham_164.pdf:PDF},
  isbn      = {1-58113-757-5},
  keywords  = {Computer Science (CS); Virtualisation; Xen},
  location  = {Bolton Landing, NY, USA},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
  url       = {http://doi.acm.org/10.1145/945445.945462},
}

@Article{Barlow1988,
  author    = {Barlow, D. J. and Thornton, J. M.},
  journal   = {Journal of Molecular Biology},
  title     = {Helix geometry in proteins.},
  year      = {1988},
  pages     = {601--19},
  volume    = {201},
  abstract  = {In this report we describe a general survey of all helices found in 57 of the known protein crystal structures, together with a detailed analysis of 48 alpha-helices found in 16 of the structures that are determined to high resolution. The survey of all helices reveals a total of 291 alpha-helices, 71 3(10)-helices and no examples of pi-helices. The conformations of the observed helices are significantly different from the &quot;ideal&quot; linear structures. The mean phi, psi angles for the alpha- and 3(10)-helices found in proteins are, respectively, (-62 degrees, -41 degrees) and (-71 degrees, -18 degrees). A computer program, HBEND, is used to characterize and to quantify the different types of helix distortion. alpha-Helices are classified as regular or irregular, linear, curved or kinked. Of the 48 alpha-helices analysed, only 15% are considered to be linear; 17% are kinked, and 58% are curved. The curvature of helices is caused by differences in the peptide hydrogen bonding on opposite faces of the helix, reflecting carbonyl-solvent/side-chain interactions for the exposed residues, and packing constraints for residues involved in the hydrophobic core. Kinked helices arise either as a result of included proline residues, or because of conflicting requirements for the optimal packing of the helix side-chains. In alpha-helices where there are kinks caused by proline residues, we show that the angle of kink is relatively constant (approximately 26 degrees), and that there is minimal disruption of the helix hydrogen bonding. The proline residues responsible for the kinks are highly conserved, suggesting that these distortions may be structurally/functionally important.},
  file      = {:by-author/B/Barlow/1988_Barlow_601.pdf:PDF},
  keywords  = {Helical Parameters; Protein Bioinformatics},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Presentation{Barnard2003,
  author       = {John Barnard},
  title        = {Chemical Structure Representation and Search Systems},
  year         = {2003},
  organization = {Barnard Chemical Information Ltd},
  file         = {2003_Barnard_slides.ppt:by-author/B/Barnard/2003_Barnard_slides.ppt:PowerPoint},
  keywords     = {Crystallography; Data Formats; Data Management; Fingerprints; Molecular Information File; Morgan Fingerprints},
  owner        = {saulius},
  timestamp = {2014.01.26},
  creationdate = {2014-01-26T00:00:00},
}

@Article{Barnard1990,
  author    = {Barnard, John M.},
  journal   = {Journal of Chemical Information and Computer Sciences},
  title     = {Draft specification for revised version of the Standard Molecular Data (SMD) Format},
  year      = {1990},
  pages     = {81--96},
  volume    = {30},
  abstract  = {A paper describing the Standard Molecular Data Format, as developed by a group of European chemical and pharma- ceutical companies, was published in 1989.’ Copies of a technical description of the most recent version of it (version 4.3), dated February 4, 1987, have been distributed by the authors of that papera2 An open meeting held in Frankfurt, FRG, in May 1988 discussed this version of the Format and identified several areas in which it could usefully be extended or improved. Under the auspices of the Chemical Structure Association, a series of Technical Working Groups was established to examine the Format in detail and to make recommendations for a revised version. Some preliminary accounts of the conclusions of these groups have appeared el~ewhere.~” Questions of standardi- zation of chemical structure information, and the need for a suitable standard format for information exchange, are ad- dressed in several contributions to a recent symposium.6 This paper presents the conclusions of the Working Groups in the form of a draft specification for version 5.0 of SMD Format. Comments are invited on the draft and should be sent to the Technical Secretary at the address shown above. In the light of any comments received, further revisions may be made before a definitive specification for the Format is presented at an open meeting to be held in association with the 2nd International Meeting on Chemical Structures at the Leeuwenhorst Congress Center, Noordwijkerhout, The Netherlands, June 3-7, 1990.},
  doi       = {10.1021/ci00065a018},
  eprint    = {http://pubs.acs.org/doi/pdf/10.1021/ci00065a018},
  file      = {1990_Barnard_81.pdf:by-author/B/Barnard/1990_Barnard_81.pdf:PDF},
  keywords  = {Crystallography; Data Formats; Data Management; Molecular Information File},
  owner     = {saulius},
  timestamp = {2014.03.26},
  creationdate = {2014-03-26T00:00:00},
  url       = {http://pubs.acs.org/doi/abs/10.1021/ci00065a018},
}

@Manuscript{Barnes2014,
  author    = {Nicholas Barnes},
  title     = {The Memory Management Reference Articles: Memory management in various languages},
  year      = {2014},
  url       = {http://www.memorymanagement.org/articles/lang.html},
  abstract  = {This is a survey of memory management in various programming languages. We can't hope to cover all the programming languages in the world, so we've chosen some that are widely-used or that have particularly interesting memory management features.},
  file      = {:by-author/B/Barnes/2014_Barnes.odt:PDF},
  owner     = {saulius},
  timestamp = {2014.03.23},
  creationdate = {2014-03-23T00:00:00},
}

@Article{Barnes2010,
  author    = {Nick Barnes},
  journal   = {Nature},
  title     = {Publish your computer code: it is good enough},
  year      = {2010},
  pages     = {753},
  volume    = {467},
  doi       = {10.1038/467753a},
  file      = {:by-author/B/Barnes/2010_Barnes_753.pdf:PDF},
  keywords  = {Data Management},
  owner     = {saulius},
  timestamp = {2012.04.09},
  creationdate = {2012-04-09T00:00:00},
  url       = {http://www.nature.com/news/2010/101013/full/467753a.html},
}

@Article{Barnett2005,
  author    = {Barnett},
  title     = {Weakest-Precondition of Unstructured Programs},
  year      = {2005},
  abstract  = {Program verification systems typically transform a program into a logical expression which is then fed to a theorem prover. The logical expression represents the weakest precondition of the program relative to its specification;when (and if!) the theorem prover is able to prove the expression, then the program is considered correct. Computing such a logical expression for an imperative, structured program is straightforward, although there are issues having to do with loops and the efficiency both of the computation and of the complexity of the formula with respect to the theorem prover. This paper presents a novel approach for computing the weakest precondition of an unstructured program that is sound even in the presence of loops. The computation is efficient and the resulting logical expression provides more leeway for the theorem prover efficiently to attack the proof.},
  file      = {:by-author/B/Barnett/2005_Barnett.pdf:PDF},
  keywords  = {Computer Science (CS); Weakest Preconditions},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Barrett2004,
  author    = {Barrett, C. Paul and Hall, Benjamin A. and Noble, Martin E. M.},
  journal   = {Acta Crystallographica Section D},
  title     = {{\it Dynamite}: a simple way to gain insight into protein motions},
  year      = {2004},
  pages     = {2280--2287},
  volume    = {60},
  doi       = {10.1107/S0907444904019171},
  file      = {ba5065.pdf:by-author/B/Barrett/2004_Barrett_2280.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444904019171},
}

@Article{Barril2006,
  author    = {Barril, Xavier and Soliva, Robert},
  journal   = {Molecular BioSystems},
  title     = {Molecular Modelling},
  year      = {2006},
  pages     = {661},
  volume    = {2},
  doi       = {10.1039/B613461K},
  file      = {:by-author/B/Barril/2006_Barril_661.pdf:PDF},
  issue     = {12},
  keywords  = {Molecular Modelling},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
  url       = {http://dx.doi.org/10.1039/B613461K},
}

@Article{Barril2006a,
  author    = {Xavier Barril and Robert Soliva},
  journal   = {Molecular BioSystems},
  title     = {Molecular Modelling},
  year      = {2006},
  pages     = {660--681},
  volume    = {2},
  doi       = {10.1039/B613461K},
  file      = {:by-author/B/Barril/2006_Barril_660.1039b613461k.war:},
  keywords  = {Molecular-modeling},
  owner     = {saulius},
  timestamp = {2015.03.02},
  creationdate = {2015-03-02T00:00:00},
}

@Article{Barros2015,
  author     = {Barros, B. S. and de Oliveira, R. S. and Kulesza, J. and Melo, V. R. M. and Melo, D. M. A. and Alves Jr, S.},
  journal    = {Journal of Physics and Chemistry of Solids},
  title      = {Reddish-orange {Ca}3{ĄxAl}2O6: {xEu}3ž nanophosphors: fast synthesis and photophysical properties},
  year       = {2015},
  pages      = {90--94},
  volume     = {78},
  file       = {[PDF] from researchgate.net:by-author/B/Barros/2015_Barros_90.pdf:application/pdf},
  groups     = {sg/JAC2009},
  owner      = {saulius},
  shorttitle = {Reddish-orange {Ca}3{ĄxAl}2O6},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url        = {http://www.researchgate.net/profile/Braulio_Barros2/publication/269334801_Reddish-orange_Ca3-xAl2O6xEu3_nanophosphors_Fast_synthesis_and_photophysical_properties/links/54871a8d0cf2ef34478eb2ca.pdf},
  urldate    = {2015-08-31},
}

@Article{Barry1994,
  author           = {Barry, J. and Alberts, B.},
  journal          = {The Journal of biological chemistry},
  title            = {Purification and characterization of bacteriophage T4 gene 59 protein. A DNA helicase assembly protein involved in DNA replication.},
  year             = {1994},
  pages            = {33049--62},
  volume           = {269},
  abstract         = {The T4 bacteriophage gene 59 protein is required for normal T4 DNA replication. We have purified this protein to homogeneity in two steps and show that it binds both to single-stranded DNA and to the T4 gene 32 protein, a DNA single strand binding protein. In in vitro assays, covering DNA with 32 protein makes this DNA inaccessible to the 41 protein, the highly processive DNA helicase, that associates with the T4 DNA primase (gene 61 protein) to form an active primosome. However, the 59 protein brings about the rapid assembly of 41 protein onto single-stranded DNA, even if this DNA is covered with 32 protein. The 59 protein is therefore a DNA helicase assembly protein. The observed requirements for the 59 protein in the vivo T4 DNA replication are explained by there being two alternative pathways for loading the 41 protein onto a replication fork at early times of T4 DNA synthesis, with only a 59 protein-mediated pathway remaining operative for the recombination-mediated replication that dominates later in infection (Barry, J., and Alberts, B. M. (1994) J. Biol. Chem. 269, 33063-33068).},
  creationdate     = {2008-07-28T00:00:00},
  doi              = {10.1016/s0021-9258(20)30096-x},
  file             = {:by-author/B/Barry/1994_Barry_33049.pdf:PDF},
  keywords         = {{gp41} Helicase; {gp59}},
  modificationdate = {2023-04-23T10:25:12},
  owner            = {em},
  timestamp        = {2008.07.28},
}

@Article{Bart1999,
  author    = {Aldert Bart and Jacob Dankert and Arie van der Ende},
  journal   = {Molecular Microbiology},
  title     = {Operator sequences for the regulatory proteins of restriction modification systems},
  year      = {1999},
  pages     = {1275},
  volume    = {31},
  abstract  = {For some type II restriction modification (RM) systems, it has been shown that transcription of the methylase gene (M ) and the restriction endonuclease gene (R ) is regu- lated by the control gene (C ) product (Tao et al . 1991, J Bacteriol 173: 1367–1375). In these systems, C is located directly upstream of R , and in most systems M is located divergently from CR (Fig. 1). The control element is a short (Ϸ80 amino acids) protein containing a helix–turn– helix DNA-binding motif, distantly related to the well- known phage lambda cI regulator.},
  file      = {:by-author/B/Bart/1999_Bart_1275.pdf:PDF},
  keywords  = {Control Protein; Restriction Endonucleases (REases)},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Bartel2008,
  author    = {Joe Bartel and Martha Bartel},
  journal   = {The Computer Journal},
  title     = {Data Structures in Forth},
  year      = {2008},
  number    = {41},
  pages     = {9},
  file      = {:by-author/B/Bartel/2008_Bartel_9.pdf:PDF},
  keywords  = {Computer Science (CS); FORTH; Programming Languages},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Barthe1997,
  author    = {Gilles Barthe and Femke van Raamsdonk},
  title     = {Termination of algebraic type systems: the syntactic approach},
  year      = {1997},
  file      = {:by-author/B/Barthe/1997_Barthe.pdf:PDF},
  keywords  = {Computer Science (CS); Type Systems},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Bartlett1967,
  author    = {M. S. Bartlett},
  journal   = {Journal of the Royal Statistical Society. Series A (General)},
  title     = {Inference and Stochastic Processes},
  year      = {1967},
  pages     = {457--478},
  volume    = {130},
  abstract  = {The relation of statistical inference to the wider problem of all inductive inference is reviewed. For scientific inference in general the competing approaches are the hypothetical-deductive and the Bayesian, and the formalism of each is discussed in statistical contexts in terms of the two main concepts of probability -- chance and degree of belief. Inference problems arising with stochastic processes and time-seriesare considered against this background, and the author's own general attitude to statistical inference reiterated. Two appendices refer respectively to two specific technical problems (i) separating a discrete and a spectral density component, (ii) specification and inferencefor "nearest-neighbour" systems.},
  file      = {1967_Bartlett_457.pdf:by-author/B/Bartlett/1967_Bartlett_457.pdf:PDF},
  groups    = {sg/Bayesian},
  owner     = {saulius},
  timestamp = {2012.10.03},
  creationdate = {2012-10-03T00:00:00},
  url       = {http://www.jstor.org/stable/2982519},
}

@Article{Bartolucci2005,
  author    = {Bartolucci, Cecilia and Lamba, Doriano and Grazulis, Saulius and Manakova, Elena and Heumann, Hermann},
  journal   = {Journal of molecular biology},
  title     = {Crystal structure of wild-type chaperonin GroEL.},
  year      = {2005},
  pages     = {940--51},
  volume    = {354},
  abstract  = {The 2.9A resolution crystal structure of apo wild-type GroEL was determined for the first time and represents the reference structure, facilitating the study of structural and functional differences observed in GroEL variants. Until now the crystal structure of the mutant Arg13Gly, Ala126Val GroEL was used for this purpose. We show that, due to the mutations as well as to the presence of a crystallographic symmetry, the ring-ring interface was inaccurately described. Analysis of the present structure allowed the definition of structural elements at this interface, essential for understanding the inter-ring allosteric signal transmission. We also show unambiguously that there is no ATP-induced 102 degrees rotation of the apical domain helix I around its helical axis, as previously assumed in the crystal structure of the (GroEL-KMgATP)(14) complex, and analyze the apical domain movements. These results enabled us to compare our structure with other GroEL crystal structures already published, allowing us to suggest a new route through which the allosteric signal for negative cooperativity propagates within the molecule. The proposed mechanism, supported by known mutagenesis data, underlines the importance of the switching of salt bridges.},
  file      = {:by-author/B/Bartolucci/2005_Bartolucci_940.pdf:PDF},
  keywords  = {ATPase; Chaperonine; GroEL},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@InProceedings{Barton1991,
  author    = {Russell Barton and Ivey, John S., Jr.},
  booktitle = {Proceedings of the 1991 Winter Simulation Conference},
  title     = {Modifications of The Nelder-Mead Simplex Method for Stochastic Simulation Response Optimisation},
  year      = {1991},
  pages     = {945},
  file      = {:by-author/B/Barton/1991_Barton_945.pdf:PDF},
  keywords  = {Computer Science (CS); Minimisation; Simplex Method},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Barzilai1988,
  author    = {Jonathan Barzilai and Jonathan M. Borwein},
  journal   = {IMA Journal of Numerical Analysis},
  title     = {Two-Point Step Size Gradient Methods},
  year      = {1988},
  pages     = {141--148},
  file      = {:by-author/B/Barzilai/1988_Barzilai_141.pdf:PDF},
  owner     = {andrius},
  timestamp = {2012.11.29},
  creationdate = {2012-11-29T00:00:00},
}

@Article{Barzilay2011,
  author    = {Eli Barzilay and Ryan Culpepper and},
  title     = {Keeping it Clean with Syntax Parameters and Matthew Flatt},
  year      = {2011},
  abstract  = {Racket’s syntax parameters support the hygienic implementation of syntactic forms that would otherwise introduce implicit identifiers unhygienically.},
  file      = {:by-author/B/Barzilay/2011_Barzilay.pdf:PDF},
  keywords  = {Computer Languages; Computer Science (CS); Oregon Workshop; Scheme},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Bash1987,
  author    = {Bash, P. A. and Singh, U. C. and Langridge, R. and Kollman, P. A.},
  journal   = {Science (New York, N.Y.)},
  title     = {Free energy calculations by computer simulation.},
  year      = {1987},
  pages     = {564--8},
  volume    = {236},
  abstract  = {A fundamental problem in chemistry and biochemistry is understanding the role of solvation in determining molecular properties. Recent advances in statistical mechanical theory and molecular dynamics methodology can be used to solve this problem with the aid of supercomputers. By using these advances the free energies of solvation of all the chemical classes of amino acid side chains, four nucleic acid bases and other organic molecules can be calculated. The effect of a site-specific mutation on the stability of trypsin is predicted. The results are in good agreement with available experiments.},
  file      = {:by-author/B/Bash/1987_Bash_564.pdf:PDF},
  keywords  = {Molecular Dynamics (MD)},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Bates1999,
  author    = {Bates, S. and Roscoe, R. A. and Althorpe, N. J. and Brammar, W. J. and Wilkins, B. M.},
  journal   = {Microbiology (Reading, England)},
  title     = {Expression of leading region genes on IncI1 plasmid ColIb-P9: genetic evidence for single-stranded DNA transcription.},
  year      = {1999},
  pages     = {2655--62},
  volume    = {145 ( Pt 10)},
  abstract  = {The leading region of a plasmid is the first sector to enter the recipient cell in bacterial conjugation. This sector of IncI1 plasmid ColIb-P9 includes genes that are transcribed in a transient pulse early in the conjugatively infected cell to promote establishment of the immigrant plasmid. Evidence is presented that the burst of gene expression is regulated by a process which is independent of a repressor but dependent on the orientation of the genes on the unique plasmid strand transferred in conjugation. The nucleotide sequence of 11.7 kb of the leading region was determined and found to contain 10 ORFs; all are orientated such that the template strand for transcription corresponds to the transferred strand. The leading region contains three dispersed repeats of a sequence homologous to a novel promoter in ssDNA described by H. Masai &amp; K. Arai (1997, Cell 89, 897-907). It is proposed that the repeats are promoters that form in the transferring strand of ColIb to support transient transcription of genes transferred early in conjugation.},
  file      = {:by-author/B/Bates/1999_Bates_2655.pdf:PDF},
  keywords  = {Antirestriction},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Manuscript{Batista-Navarro2010,
  author    = {Riza Theresa Batista-Navarro and Sophia Ananiadou},
  title     = {Discovering Potential Drugs by Extracting Biological Activities of Natural Products},
  year      = {2010},
  keywords  = {Bioinformatics; Biological Activity; Chemoinformatics; Natural Language Processing; Natural Products},
  abstract  = {Natural products play an important role in drug discovery. Many of the drugs in the market today were discovered based on the study and synthesis of isolated natural products. The search for natural products is a non-trivial task: in a step known as dereplication, a natural product chemist has to determine what has already been reported to avoid re-isolating already known natural products. With the growth of scientific literature, however, this can become a daunting task.},
  file      = {2010_Batista-Navarro_manuscript.pdf:by-author/B/Batista-Navarro/2010_Batista-Navarro_manuscript.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Batsanov2001,
  author    = {S. S. Batsanov},
  journal   = {Inorganic Materials},
  title     = {Van der Waals Radii of Elements},
  year      = {2001},
  pages     = {871--885},
  volume    = {37},
  doi       = {10.1023/A:1011625728803},
  file      = {:by-author/B/Batsanov/2001_Batsanov_871.pdf:PDF},
  keywords  = {Van Der Waals Radii},
  owner     = {antanas},
  timestamp = {2014.06.26},
  creationdate = {2014-06-26T00:00:00},
}

@Manual{Baudin2010,
  title     = {{N}elder-{M}ead User’s Manual},
  author    = {Baudin},
  year      = {2010},
  abstract  = {In this document, we present the Nelder-Mead component provided in Scilab. The introduction gives a brief overview of the optimization features of the component and present an introductory example. Then we present some theory associated with the simplex, a geometric concept which is central in the Nelder-Mead algorithm. We present several method to compute an initial simplex. Then we present Spendley’s et al. fixed shape unconstrained optimization algorithm. Several numerical experiments are provided, which shows how this algorithm performs on well-scaled and badly scaled quadratics. In the final section, we present the Nelder-Mead variable shape unconstrained optimization algorithm. Several numerical experiments are presented, where some of these are counter examples, that is cases where the algorithms fails to converge on a stationnary point. In the appendix of this document, the interested reader will find a bibliography of simplex-based algorithms, along with an analysis of the various implementations which are available in several programming languages.},
  file      = {:by-author/B/Baudin/2010_Baudin.pdf:PDF},
  keywords  = {Computer Science (CS); Minimisation; Simplex Method},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Baudrit2006,
  author    = {C. Baudrit and D. Dubois},
  journal   = {Computational Statistics \& Data Analysis},
  title     = {Practical representations of incomplete probabilistic knowledge},
  year      = {2006},
  issn      = {0167-9473},
  pages     = {86 - 108},
  volume    = {51},
  abstract  = {The compact representation of incomplete probabilistic knowledge which can be encountered in risk evaluation problems, for instance in environmental studies is considered. Various kinds of knowledge are considered such as expert opinions about characteristics of distributions or poor statistical information. The approach is based on probability families encoded by possibility distributions and belief functions. In each case, a technique for representing the available imprecise probabilistic information faithfully is proposed, using different uncertainty frameworks, such as possibility theory, probability theory, and belief functions, etc. Moreover the use of probability–possibility transformations enables confidence intervals to be encompassed by cuts of possibility distributions, thus making the representation stronger. The respective appropriateness of pairs of cumulative distributions, continuous possibility distributions or discrete random sets for representing information about the mean value, the mode, the median and other fractiles of ill-known probability distributions is discussed in detail.},
  doi       = {10.1016/j.csda.2006.02.009},
  file      = {2006_Baudrit_86.pdf:by-author/B/Baudrit/2006_Baudrit_86.pdf:PDF},
  groups    = {sg/Possibility theory},
  keywords  = {Imprecise Probabilities},
  owner     = {saulius},
  timestamp = {2015.12.07},
  creationdate = {2015-12-07T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/S0167947306000454},
}

@Article{Bauknech1996,
  author    = {Henri Bauknecht and Andreas Zell and Harald Bayer and Paul Levi and Markus Wagener and Jens Sadowski and Johann Gasteiger},
  journal   = {Journal of Chemical Information and Computer Sciences},
  title     = {Locating Biologically Active Compounds in Medium-Sized Heterogeneous Datasets by Topological Autocorrelation Vectors: Dopamine and Benzodiazepine Agonists},
  year      = {1996},
  pages     = {1205--1213},
  volume    = {36},
  abstract  = {Electronic properties located on the atoms of a molecule such as partial atomic charges as well as electronegativity and polarizability values are encoded by an autocorrelation vector accounting for the constitution of a molecule. This encoding procedure is able to distinguish between compounds being dopamine agonists and those being benzodiazepine receptor agonists even after projection into a two-dimensional self-organizing network. The two types of compounds can still be distinguished if they are buried in a dataset of 8323 compounds of a chemical supplier catalog comprising a wide structural variety. The maps obtained by this sequence of events, calculation of empirical physicochemical effects, encoding in a topological autocorrelation vector, and projection by a self-organizing neural network, can thus be used for searching for structural similarity, and, in particular, for finding new lead structures with biological activity.},
  doi       = {10.1021/ci960346m},
  file      = {:by-author/B/Bauknecht/1996_Bauknecht_1205.pdf:PDF},
  keywords  = {Drug Design},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
  url       = {http://pubs.acs.org/doi/abs/10.1021/ci960346m},
}

@Article{Baumann2012,
  author    = {Baumann, Dominik and Sedlmaier, Stefan J. and Schnick, Wolfgang},
  journal   = {Angewandte Chemie International Edition},
  title     = {An Unprecedented AB2 Tetrahedra Network Structure Type in a High-Pressure Phase of Phosphorus Oxonitride (PON)},
  year      = {2012},
  issn      = {1521-3773},
  pages     = {4707--4709},
  volume    = {51},
  abstract  = {An unprecedented framework structure made up of tetrahedra has been discovered in a novel high-pressure polymorph of the phosphorus oxonitride PON by treating a single-source precursor at 12 GPa and 1250 °C. It is the first polymorph of PON that does not crystallize in a structure type known from SiO2.},
  doi       = {10.1002/anie.201200811},
  file      = {2012_Baumann_4707.pdf:by-author/B/Baumann/2012_Baumann_4707.pdf:PDF},
  keywords  = {Confirmation; High-pressure Chemistry; Nitrides; PCOD; Phosphorus; Solid-state Structures; Structure Elucidation; Structure Predicion},
  owner     = {saulius},
  publisher = {WILEY-VCH Verlag},
  timestamp = {2013.04.27},
  creationdate = {2013-04-27T00:00:00},
  url       = {http://dx.doi.org/10.1002/anie.201200811},
}

@Article{Baur1992,
  author    = {Baur, W. H. and Kassner, D.},
  journal   = {Acta Crystallographica Section B Structural Science},
  title     = {The perils of {Cc}: comparing the frequencies of falsely assigned space groups with their general population},
  year      = {1992},
  issn      = {0108-7681},
  month     = {Aug},
  number    = {4},
  pages     = {356–369},
  volume    = {48},
  doi       = {10.1107/s0108768191014726},
  file      = {1992_Baur_356.pdf:by-author/B/Baur/1992_Baur_356.pdf:PDF},
  owner     = {andrius},
  publisher = {International Union of Crystallography (IUCr)},
  timestamp = {2017.03.13},
  creationdate = {2017-03-13T00:00:00},
  url       = {http://dx.doi.org/10.1107/s0108768191014726},
}

@Article{Bayarri2004,
  author    = {M. J. Bayarri and J. O. Berger},
  journal   = {Statistical Science},
  title     = {The Interplay of Bayesian and Frequentist Analysis},
  year      = {2004},
  pages     = {58--80},
  volume    = {19},
  abstract  = {Statistics has struggled for nearly a century over the issue of whether the Bayesian or frequentist paradigm is superior. This debate is far from over and, indeed, should continue, since there are fundamental philosophical and pedagogical issues at stake. At the methodological level, however, the debate has become considerably muted, with the recognition that each approach has a great deal to contribute to statistical practice and each is actually essential for full development of the other approach. In this article, we embark upon a rather idiosyncratic walk through some of these issues.},
  doi       = {10.1214/088342304000000116},
  file      = {2004_Bayarri_58.pdf:by-author/B/Bayarri/2004_Bayarri_58.pdf:PDF},
  groups    = {sg/Bayesian},
  keywords  = {Admissibility; Bayesian Model Checking; Bayesian Statistics; Conditional Frequentist; Confidence Intervals; Consistency; Coverage; Design; Hierarchical Models; Nonparametric Bayes; Objective Bayesian Methods; P-values; Reference Priors; testing.},
  owner     = {saulius},
  timestamp = {2012.10.03},
  creationdate = {2012-10-03T00:00:00},
  url       = {http://projecteuclid.org/euclid.ss/1089808273},
}

@Article{Bayarri2000,
  author           = {M. J. Bayarri and James O. Berger},
  journal          = {Journal of the American Statistical Association},
  title            = {P Values for Composite Null Models},
  year             = {2000},
  pages            = {1127--1142},
  volume           = {95},
  abstract         = {The problem of investigating compatibility of an assumed model with the data is investigated in the situation when the assumed model has unknown parameters. The most frequently used measures of compatibility are p values, based on statistics T for which large values are deemed to indicate incompatibility of the data and the model. When the null model has unknown parameters, p values are not uniquely defined. The proposals for computing a p value in such a situation include the plug-in and similar p values on the frequentist side, and the predictive and posterior predictive p values on the Bayesian side. We propose two alternatives, the conditional predictive p value and the partial posterior predictive p value, and indicate their advantages from both Bayesian and frequentist perspectives.},
  creationdate     = {2012-10-03T00:00:00},
  file             = {2000_Bayarri_1127.pdf:by-author/B/Bayarri/2000_Bayarri_1127.pdf:PDF},
  groups           = {sg/Bayesian},
  keywords         = {Bayes Factors; Bayesian P-values; Bayesian Statistics; Conditioning; Model Checking; P-values; Predictive Distribution},
  modificationdate = {2022-11-13T17:30:14},
  owner            = {saulius},
  timestamp        = {2012.10.03},
  url              = {http://www.jstor.org/stable/2669749},
}

@Article{Bayarri2007,
  author           = {M. J. Bayarri and M. E. Castellanos},
  journal          = {Statistical Science},
  title            = {Bayesian Checking of the Second Levels of Hierarchical Models},
  year             = {2007},
  pages            = {322--343},
  volume           = {22},
  comment          = {Hierarchical models are increasingly used in many applications. Along with this increased use comes a desire to investigate whether the model is compatible with the observed data. Bayesian methods are well suited to eliminate the many (nuisance) parameters in these complicated models; in this paper we investigate Bayesian methods for model checking. Since we contemplate model checking as a preliminary, exploratory analysis, we con- centrate on objective Bayesian methods in which careful specification of an informative prior distribution is avoided. Numerous examples are given and different proposals are investigated and critically compared.},
  creationdate     = {2012-10-03T00:00:00},
  doi              = {10.1214/07-STS235},
  file             = {2007_Bayarri_322.pdf:by-author/B/Bayarri/2007_Bayarri_322.pdf:PDF},
  groups           = {sg/Bayesian},
  keywords         = {Bayesian Statistics; Conflict; Empirical-Bayes; Model Checking; Model Criticism; Objective Bayesian Methods; P-values; Partial Posterior Predictive; Posterior Predictive},
  modificationdate = {2022-11-13T17:30:36},
  owner            = {saulius},
  timestamp        = {2012.10.03},
  url              = {http://projecteuclid.org/euclid.ss/1199285031},
}

@Article{Beall2010,
  author           = {Jeffrey Beall},
  journal          = {Future Internet},
  title            = {Metadata for name disambiguation and collocation},
  year             = {2010},
  pages            = {fi2010001},
  abstract         = {Searching names of persons, families, and organizations is often difficult in online databases because different persons or organizations frequently share the same name and because a single person’s or organization’s name may appear in different forms in various online documents. Databases and search engines can use metadata as a tool to solve the problem of name ambiguity and name variation in online databases. This article describes the challenges names pose in information retrieval and some emerging name metadata databases that can help ameliorate the problems. Effective name disambiguation and collocation increase search precision and recall and can improve assessment of scholarly work.},
  creationdate     = {2014-03-23T00:00:00},
  doi              = {10.3390/fi2010001},
  file             = {:by-author/B/Beall/2010_Beall_fi2010001.pdf:PDF},
  keywords         = {Bibliography; Collocation; Databases; Information Retrieval; Metadata; Name Disambiguation; Names},
  modificationdate = {2024-10-13T08:50:09},
  owner            = {saulius},
  timestamp        = {2014.03.23},
}

@Article{Bearden1967,
  author    = {J. A. Bearden},
  journal   = {Reviews in Modern Physics},
  title     = {X-Ray Wavelengths},
  year      = {1967},
  pages     = {78--124},
  abstract  = {Inconsistencies in accepted values (in x units) of x-ray reference lines have recently been demonstrated, although all are supposedly based on "good" calcite crystals. Factors supporting the selection of the W $K\alpha_1$ line as {\it the X-ray Wavelength Standard} are critically discussed. A review is given of the experimental measurements which are used to establish the wavelength of this line on an absolute angstrom basis. Its value is $\lambda$ W $K\alpha_1$ = ($0.2090100\pm5$ ppm) Å. This may be used to define a new unit, denoted by Å$^*$, such that the W $K\alpha_1$ wavelength is exactely 0.2090100~Å$^*$; hence 1Å$^*$ = 1Å$\pm$5~ppm. The wavelengths of the Ag $K\alpha1$, Mo $K\alpha1$, Cu $K\alpha1$, and the Cr $K\alpha1$ have been established as secondary standards with probable error of approximately one part per million. Sixty-one additional z-ray lines have been used as reference values in a comprehensive review and reevaluation of more than 2700 emission and absorption wavelengths. The recommended wavelength values are listed in Å$^*$ units together with probable errors; corresponding energies are given in kwV. A second table lists the wavelengths in numerical order, and likewise includes their energies in keV.},
  doi       = {10.1103/RevModPhys.39.78},
  file      = {1967_Bearden_78.pdf:by-author/B/Bearden/1967_Bearden_78.pdf:PDF},
  keywords  = {Wavelength; X-ray Crystallography; X-rays},
  owner     = {saulius},
  timestamp = {2015.03.13},
  creationdate = {2015-03-13T00:00:00},
}

@Article{Beatty2005,
  author    = {Beatty, Kimberly E. and Xie, Fang and Wang, Qian and Tirrell, David A.},
  journal   = {Journal of the American Chemical Society},
  title     = {Selective dye-labeling of newly synthesized proteins in bacterial cells.},
  year      = {2005},
  pages     = {14150--1},
  volume    = {127},
  abstract  = {We describe fluorescence labeling of newly synthesized proteins in Escherichia coli cells by means of Cu(I)-catalyzed cycloaddition between alkynyl amino acid side chains and the fluorogenic dye 3-azido-7-hydroxycoumarin. The method involves co-translational labeling of proteins by the non-natural amino acids homopropargylglycine (Hpg) or ethynylphenylalanine (Eth) followed by treatment with the dye. As a demonstration, the model protein barstar was expressed and treated overnight with Cu(I) and 3-azido-7-hydroxycoumarin. Examination of treated cells by confocal microscopy revealed that strong fluorescence enhancement was observed only for alkynyl-barstar treated with Cu(I) and the reactive dye. The cellular fluorescence was punctate, and gel electrophoresis confirmed that labeled barstar was localized in inclusion bodies. Other proteins showed little fluorescence. Examination of treated cells by fluorimetry demonstrated that cultures supplemented with Eth or Hpg showed an 8- to 14-fold enhancement in fluorescence intensity after labeling. Addition of a protein synthesis inhibitor reduced the emission intensity to levels slightly above background, confirming selective labeling of newly synthesized proteins in the bacterial cell.},
  file      = {:by-author/B/Beatty/2005_Beatty_14150.pdf:PDF;2005_Beatty_14150-supp.pdf:by-author/B/Beatty/2005_Beatty_14150-supp.pdf:PDF},
  keywords  = {Bioconjugation; Protein Labeling},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Bebak1989,
  author    = {Bebak, H. and Buse, C. and Donner, W. T. and Hoever, P. and Jacob, H. and Klaus, H. and Pesch, J. and Roemelt, J. and Schilling, P. and B. Woost and C. Zirz},
  journal   = {Journal of Chemical Information and Computer Sciences},
  title     = {The standard molecular data format (SMD format) as an integration tool in computer chemistry},
  year      = {1989},
  pages     = {1--5},
  volume    = {29},
  abstract  = {The standard molecular data (SMD) format is described, providing a powerful tool for data exchange between chemically oriented programs. By its modular design it offers a broad application range and great flexibility with respect to future extensions; Le., definition of new information blocks is possible without affecting existing blocks. Furthermore, the SMD format includes the concept of superatom-representing subsets of a molecular structure or ensemblewhich offers a new strategy for economic and flexible storage of large molecules (proteins, polymers, etc.) and permits a new and consistent method for storage of reactions. This paper is not intended to be a technical report on the format, but the basic ideas and strategies guiding its design are presented.},
  doi       = {10.1021/ci00061a002},
  eprint    = {http://pubs.acs.org/doi/pdf/10.1021/ci00061a002},
  file      = {1989_Bebak_1.pdf:by-author/B/Bebak/1989_Bebak_1.pdf:PDF},
  keywords  = {Crystallography; Data Formats; Data Management; Molecular Information File},
  owner     = {saulius},
  timestamp = {2014.03.26},
  creationdate = {2014-03-26T00:00:00},
  url       = {http://pubs.acs.org/doi/abs/10.1021/ci00061a002},
}

@Webpage{Becher2009,
  author    = {Stephan Becher},
  retrieved = {2015-03-11},
  title     = {Introduction To StrongForth},
  url       = {http://www.arestlessmind.org/2009/02/03/intro.html},
  month     = {February},
  year      = {2009},
  abstract  = {The basic idea behind StrongForth is the wish to add strong static type checking to a Forth system. Previous Forth systems and standards (including ANS) were supposed to be typeless or untyped, which means they do not do any type checking at all. The interpreter and the compiler generally accept any word to be applied to the operands on the data and return stack. This behaviour grants total freedom to the programmer, but on the other side it is rather often a reason for type errors, which frequently cause system crashes and other more or less strange behaviour throughout the whole development phase.},
  file      = {2009_Becher.odt:by-author/B/Becher/2009_Becher.odt:OpenDocument text},
  keywords  = {Computer Science (CS); Forth; Programming Languages; Static Typing; Strong Typing},
  owner     = {saulius},
  timestamp = {2015.03.11},
  creationdate = {2015-03-11T00:00:00},
}

@Manuscript{Becher2000,
  author    = {Stephan Becher},
  title     = {strongForth 0.03 beta version},
  year      = {2000},
  keywords  = {Computer Science (CS); Forth; Programming Languages; Static Typing; Strong Typing},
  month     = {December},
  file      = {2000_Becher.txt:by-author/B/Becher/2000_Becher.txt:Text;2000_Becher.zip:by-author/B/Becher/2000_Becher.zip:ZIP},
  owner     = {saulius},
  timestamp = {2015.03.10},
  creationdate = {2015-03-10T00:00:00},
}

@Manual{Becher2000a,
  title     = {Introduction to strongForth},
  author    = {Stephan Becher},
  month     = {December},
  year      = {2000},
  file      = {2000_Becher.htm:by-author/B/Becher/2000_Becher.htm:URL;2000_Becher.zip:by-author/B/Becher/2000_Becher.zip:ZIP},
  keywords  = {Computer Science (CS); Forth; Programming Languages; Static Typing; Strong Typing},
  owner     = {saulius},
  timestamp = {2015.03.10},
  creationdate = {2015-03-10T00:00:00},
}

@Webpage{Beck2009,
  author    = {Kent Beck},
  retrieved = {2009-02-07},
  title     = {Simple Smalltalk Testing: With Pattern},
  url       = {http://www.xprogramming.com/testfram.htm},
  year      = {2009},
  file      = {:by-author/B/Beck/2009_Beck.war:},
  keywords  = {Computer Science (CS); Test Driven Development},
  owner     = {saulius},
  timestamp = {2015.03.02},
  creationdate = {2015-03-02T00:00:00},
}

@Book{Beck2002,
  author    = {Kent Beck},
  title     = {Test-Driven Development By Example},
  year      = {2002},
  file      = {:by-author/B/Beck/2002_Beck.pdf:PDF},
  keywords  = {Computer Science (CS); Test Driven Development},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@InProceedings{Beck1989,
  author    = {Kent Beck and Ward Cunningham},
  booktitle = {OOPSLA'89 Conference Proceedings},
  title     = {A Laboratory For Teaching: Object-Oriented Thinking},
  year      = {1989},
  month     = {October},
  abstract  = {It is difficult to introduce both novice and experienced procedural programmers to the anthropomorphic perspective necessary for object-oriented design. We introduce CRC cards, which characterize objects by class name, responsibilities, and collaborators, as a way of giving learners a direct experience of objects. We have found this approach successful in teaching novice programmers the concepts of objects, and in introducing experienced programmers to complicated existing designs.},
  file      = {:by-author/B/Beck/1989_Beck.war:},
  keywords  = {Computer Science (CS); OO-programming-design-analysis},
  owner     = {saulius},
  timestamp = {2015.03.02},
  creationdate = {2015-03-02T00:00:00},
  url       = {http://c2.com/doc/oopsla89/paper.html},
}

@Book{Beck2008,
  author    = {Mark Beck},
  publisher = {Whitman College},
  title     = {Physics 385L Quantum Mechanics Laboratory Manual},
  year      = {2008},
  file      = {:by-author/B/Beck/2008_Beck.pdf:PDF},
  keywords  = {Laboratory Manual; Quantum Mechanics (QM)},
  owner     = {saulius},
  timestamp = {2013.10.22},
  creationdate = {2013-10-22T00:00:00},
  url       = {http://www.pa.msu.edu/courses/2011fall/PHY431/Labs/QuantumOptics/1-Beck_QM_Manual.pdf},
}

@Article{Becke2014,
  author    = {Becke, Axel D.},
  journal   = {The Journal of Chemical Physics},
  title     = {Perspective: Fifty years of density-functional theory in chemical physics},
  year      = {2014},
  pages     = {18A301},
  volume    = {140},
  abstract  = {Since its formal inception in 1964–1965, Kohn-Sham density-functional theory (KS-DFT) has become the most popular electronic structure method in computational physics and chemistry. Its popularity stems from its beautifully simple conceptual framework and computational elegance. The rise of KS-DFT in chemical physics began in earnest in the mid 1980s, when crucial developments in its exchange-correlation term gave the theory predictive power competitive with well-developed wave-function methods. Today KS-DFT finds itself under increasing pressure to deliver higher and higher accuracy and to adapt to ever more challenging problems. If we are not mindful, however, these pressures may submerge the theory in the wave-function sea. KS-DFT might be lost. I am hopeful the Kohn-Sham philosophical, theoretical, and computational framework can be preserved. This Perspective outlines the history, basic concepts, and present status of KS-DFT in chemical physics, and offers suggestions for its future development.},
  doi       = {10.1063/1.4869598},
  file      = {2014_Becke_18A301.pdf:by-author/B/Becke/2014_Becke_18A301.pdf:PDF},
  keywords  = {Computational Chemistry; Density Functional Theory (DFT); Quantum Chemistry},
  owner     = {saulius},
  timestamp = {2014.07.21},
  creationdate = {2014-07-21T00:00:00},
  url       = {http://scitation.aip.org/content/aip/journal/jcp/140/18/10.1063/1.4869598},
}

@Article{Becker2006,
  author    = {Becker, Nils B. and Wolff, Lars and Everaers, Ralf},
  journal   = {Nucleic acids research},
  title     = {Indirect readout: detection of optimized subsequences and calculation of relative binding affinities using different DNA elastic potentials.},
  year      = {2006},
  pages     = {5638--49},
  volume    = {34},
  abstract  = {Essential biological processes require that proteins bind to a set of specific DNA sites with tuned relative affinities. We focus on the indirect readout mechanism and discuss its theoretical description in relation to the present understanding of DNA elasticity on the rigid base pair level. Combining existing parametrizations of elastic potentials for DNA, we derive elastic free energies directly related to competitive binding experiments, and propose a computationally inexpensive local marker for elastically optimized subsequences in protein-DNA co-crystals. We test our approach in an application to the bacteriophage 434 repressor. In agreement with known results we find that indirect readout dominates at the central, non-contacted bases of the binding site. Elastic optimization involves all deformation modes and is mainly due to the adapted equilibrium structure of the operator, while sequence-dependent elasticity plays a minor role. These qualitative observations are robust with respect to current parametrization uncertainties. Predictions for relative affinities mediated by indirect readout depend sensitively on the chosen parametrization. Their quantitative comparison with experimental data allows for a critical evaluation of DNA elastic potentials and of the correspondence between crystal and solution structures. The software written for the presented analysis is included as Supplementary Data.},
  file      = {:by-author/B/Becker/2006_Becker_5638.pdf:PDF},
  keywords  = {Readout},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Bedem2009,
  author    = {van den Bedem, Henry and Dhanik, Ankur and Latombe, Jean-Claude and Deacon, Ashley M.},
  journal   = {Acta Crystallographica Section D},
  title     = {Modeling discrete heterogeneity in X-ray diffraction data by fitting multi-conformers},
  year      = {2009},
  pages     = {1107--1117},
  volume    = {65},
  abstract  = {The native state of a protein is regarded to be an ensemble of conformers, which allows association with binding partners. While some of this structural heterogeneity is retained upon crystallization, reliably extracting heterogeneous features from diffraction data has remained a challenge. In this study, a new algorithm for the automatic modelling of discrete heterogeneity is presented. At high resolution, the authors' single multi-conformer model, with correlated structural features to represent heterogeneity, shows improved agreement with the diffraction data compared with a single-conformer model. The model appears to be representative of the set of structures present in the crystal. In contrast, below 2 Å resolution representing ambiguous electron density by correlated multi-conformers in a single model does not yield better agreement with the experimental data. Consistent with previous studies, this suggests that variability in multi-conformer models at lower resolution levels reflects uncertainty more than coordinated motion.},
  doi       = {10.1107/S0907444909030613},
  file      = {2009_Bedem_1107.pdf:by-author/B/Bedem/2009_Bedem_1107.pdf:PDF},
  keywords  = {Algorithms; Heterogeneity; Modeling; Multi-conformers; Protein Crystallography; Structure Refinement; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2013.03.25},
  creationdate = {2013-03-25T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444909030613},
}

@Article{Beebe1993,
  author    = {Nelson H. F. Beebe},
  journal   = {TUGboat},
  title     = {Bibliography Prettyprinting and Syntax Checking},
  year      = {1993},
  pages     = {395},
  file      = {:by-author/B/Beebe/1993_Beebe_395.pdf:PDF},
  keywords  = {Bibtex; Computer Science (CS)},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Beel2010,
  author    = {Jöran Beel and Bela Gipp and Erik Wilde},
  journal   = {Journal of Scholarly Publishing},
  title     = {{A}cademic {S}earch {E}ngine {O}ptimization ({ASEO}): Optimizing Scholarly Literature for {G}oogle {S}cholar \& Co.},
  year      = {2010},
  pages     = {176--190},
  volume    = {41},
  abstract  = {This article introduces and discusses the concept of academic search engine optimization (ASEO). Based on three recently conducted studies, guidelines are provided on how to optimize scholarly literature for academic search engines in general and for Google Scholar in particular. In addition, we briefly discuss the risk of researchers' illegitimately 'over-optimizing' their articles.},
  doi       = {10.3138/jsp.41.2.176},
  file      = {:by-author/B/Beel/2010_Beel_176.pdf:PDF},
  owner     = {andrius},
  timestamp = {2013.03.08},
  creationdate = {2013-03-08T00:00:00},
}

@Article{Been1988,
  author    = {Been, M D and Cech, T R},
  journal   = {Science (New York, N.Y.)},
  title     = {RNA as an RNA polymerase: net elongation of an RNA primer catalyzed by the Tetrahymena ribozyme.},
  year      = {1988},
  pages     = {1412--6},
  volume    = {239},
  file      = {1988_Been_1412.pdf:by-author/B/Been/1988_Been_1412.pdf:PDF},
  keywords  = {Ribozymes},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Beetham1976,
  author    = {Beetham,M. J. and Campbell,C. M.},
  journal   = {Proceedings of the Edinburgh Mathematical Society (Series 2)},
  title     = {A note on the Todd-Coxeter coset enumeration algorithm},
  year      = {1976},
  issn      = {1464-3839},
  pages     = {73--79},
  volume    = {20},
  abstract  = {In (8) Todd and Coxeter described an algorithm for enumerating the cosets of a finitely generated subgroup of finite index in a finitely presented group. Several authors ((1), (2), (5), (6), (7)) have discussed a modification of the algorithm to give also a presentation of the subgroup in terms of the given generators.},
  doi       = {10.1017/S0013091500015790},
  file      = {1976_Beetham_73.pdf:by-author/B/Beetham/1976_Beetham_73.pdf:PDF},
  issue     = {01},
  keywords  = {Algorithms},
  numpages  = {7},
  owner     = {saulius},
  timestamp = {2013.03.22},
  creationdate = {2013-03-22T00:00:00},
  url       = {http://journals.cambridge.org/article_S0013091500015790},
}

@Article{Behrend2008,
  author    = {Andreas Behrend and Christian Dorau and Rainer Manthey and Gereon Schüeller},
  title     = {Incremental View-Based Analysis of Stock Market Data Streams},
  year      = {2008},
  pages     = {269--275},
  abstract  = {In this paper we show the usefulness and feasibility of applying conventional SQL queries for analyzing a wide spectrum of data streams. As application area we have chosen the analysis of stock market data, mainly because this kind of application exhibits sufficiently many of those characteristics for which relational query technology can be considered a valuable instrument in a stream context. The resulting TInTo system is a tool for computing so-called technical indicators, numerical values calculated from a certain kind of stock market data, characterizing the development of stock prices over a given time period. Update propagation is used for the incremental recomputation of indicator views defined over a stream of continuously changing price data.},
  file      = {:by-author/B/Behrend/2008_Behrend_269.pdf:PDF},
  keywords  = {Computer Science (CS); Continuous; Databases},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Beichl2000,
  author    = {Beichl, I. and Sullivan, F.},
  journal   = {Computing in Science \& Engineering},
  title     = {The Metropolis Algorithm},
  year      = {2000},
  month     = {Feb},
  note      = {ISSN: 1521-9615 References Cited: 6 Cited by : 14 INSPEC Accession Number: 6463882 Date of Current Version: 06 August 2002},
  number    = {1},
  pages     = {65--69},
  volume    = {2},
  abstract  = {The Metropolis Algorithm has been the most successful and influential of all the members of the computational species that used to be called the "Monte Carlo method". Today, topics related to this algorithm constitute an entire field of computational science supported by a deep theory and having applications ranging from physical simulations to the foundations of computational complexity. Since the rejection method invention (J. von Neumann), it has been developed extensively and applied in a wide variety of settings. The Metropolis Algorithm can be formulated as an instance of the rejection method used for generating steps in a Markov chain},
  doi       = {10.1109/5992.814660},
  file      = {2000_Beichl_65.pdf:by-author/B/Beichl/2000_Beichl_65.pdf:PDF},
  groups    = {sg/Molecular dynamics},
  keywords  = {Molecular Dynamics (MD); Monte Carlo},
  owner     = {saulius},
  timestamp = {2011.10.21},
  creationdate = {2011-10-21T00:00:00},
  url       = {http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=814660&tag=1},
}

@Manual{Beitz2011,
  title     = {The {TEXshade} package: Typesetting nucleotide and peptide alignments},
  author    = {Eric Beitz},
  edition   = {v1.24},
  month     = {Dec},
  year      = {2011},
  abstract  = {Setting alignments of nucleotides and peptides for publication or presentation purposes is usually a time consuming two-step process. First, a scientific software is used for the calculation of the alignment. This is done in a few minutes. Then, in order to highlight special sequence relationships and to label positions and regions of interest a second software with high quality output capability is needed. Manipulating sequence alignments with standard word processing or graphics programs takes its time—often several hours—and simple layout changes such as re-breaking lines, say from 50 to 40 residues per line, elongate the working time considerably. TEXshade is an alignment shading software written in TEX/LATEX which can process multiple sequence alignments in the MSF, ALN and FASTA file format. It provides in addition to common shading algorithms special shading modes featuring functional aspects, e. g. charge or hydropathy, and a plenitude of commands for handling shading colors, text styles, labels, legends and even allows the user to define completely new shading modes. TEXshade combines highest flexibility and the habitual TEX output quality—with reasonable time expenditure.},
  file      = {:by-author/B/Beitz/2011_Beitz_manual.pdf:PDF},
  keywords  = {Latex},
  owner     = {andrius},
  timestamp = {2013.12.12},
  creationdate = {2013-12-12T00:00:00},
  url       = {http://www.uni-kiel.de/Pharmazie/chem/Prof_Beitz/pdf/texshade.pdf},
}

@Article{Bell1972,
  author    = {C. Gordon Bell and J. L Eggert and J. Grason and P. Williams},
  journal   = {IEEE Transactions on Computers},
  title     = {The Description and Use of Register Transfer Modules (RTM's)(R)},
  year      = {1972},
  issn      = {0018-9340},
  pages     = {495--500},
  volume    = {21},
  abstract  = {This note describes a set of register-transfer modules (RTM's) that are used as a basis for digital systems design. RTM's allow digital systems to be specified in a flow chart form with complete construction (wiring) information, thus obviating combinational and sequential switching circuit theory based design. The modules make extensive use of integrated circuitry. The note briefly describes the class of problems that RTM's can be used to solve, together with some of the module design decisions. The most important RTM's are described from the user's viewpoint, and two example designs are given.},
  acmid     = {1310467},
  address   = {Washington, DC, USA},
  doi       = {10.1109/T-C.1972.223548},
  file      = {:by-author/B/Bell/1972_Bell_495.pdf:PDF},
  keywords  = {Computer Architecture; Computer Science (CS); Hardware},
  numpages  = {6},
  owner     = {saulius},
  publisher = {IEEE Computer Society},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
  url       = {http://dx.doi.org/10.1109/T-C.1972.223548},
}

@Article{Bell2014,
  author    = {Bell, Ian H. and Wronski, Jorrit and Quoilin, Sylvain and Lemort, Vincent},
  journal   = {Industrial \&amp; engineering chemistry research},
  title     = {Pure and Pseudo-pure Fluid Thermophysical Property Evaluation and the Open-Source Thermophysical Property Library CoolProp.},
  year      = {2014},
  pages     = {2498--2508},
  volume    = {53},
  doi       = {10.1021/ie4033999},
  file      = {:by-author/B/Bell/2014_Bell_2498.pdf:PDF},
  owner     = {saulius},
  timestamp = {2014.03.23},
  creationdate = {2014-03-23T00:00:00},
}

@Article{Bell2006a,
  author    = {Jonathan Bell and Stuart Lewis},
  title     = {Using {OAI-PMH} and {METS} for exporting metadata and digital objects between repositories},
  year      = {2006},
  pages     = {techreport},
  file      = {:by-author/B/Bell/2006_Bell_techreport.pdf:PDF},
  keywords  = {Digital Repositries; Libraries; Metadata},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Bellamy2000,
  author           = {Bellamy, H D and Snell, E H and Lovelace, J and Pokross, M and Borgstahl, G E},
  journal          = {Acta crystallographica. Section D, Biological crystallography},
  title            = {The high-mosaicity illusion: revealing the true physical characteristics of macromolecular crystals.},
  year             = {2000},
  pages            = {986--95},
  volume           = {56},
  creationdate     = {2008-07-28T00:00:00},
  doi              = {10.1107/s0907444900007356},
  file             = {Bellamy_2000_986-highmosaicity.pdf:by-author/B/Bellamy/2000_Bellamy_986.pdf:PDF},
  modificationdate = {2023-04-23T10:26:21},
  owner            = {saulius},
  timestamp        = {2008.07.28},
}

@Article{Belogurov1995,
  author    = {Belogurov, A. A. and Delver, E. P.},
  journal   = {Nucleic acids research},
  title     = {A motif conserved among the type I restriction-modification enzymes and antirestriction proteins: a possible basis for mechanism of action of plasmid-encoded antirestriction functions.},
  year      = {1995},
  pages     = {785--7},
  volume    = {23},
  abstract  = {Antirestriction proteins Ard encoded by some self-transmissible plasmids specifically inhibit restriction by members of all three families of type I restriction-modification (R-M) systems in E.coli. Recently, we have identified the amino acid region, 'antirestriction' domain, that is conserved within different plasmid and phage T7-encoded antirestriction proteins and may be involved in interaction with the type I R-M systems. In this paper we demonstrate that this amino acid sequence shares considerable similarity with a well-known conserved sequence (the Argos repeat) found in the DNA sequence specificity (S) polypeptides of type I systems. We suggest that the presence of these similar motifs in restriction and antirestriction proteins may give a structural basis for their interaction and that the antirestriction action of Ard proteins may be a result of the competition between the 'antirestriction' domains of Ard proteins and the similar conserved domains of the S subunits that are believed to play a role in the subunit assembly of type I R-M systems.},
  file      = {:by-author/B/Belogurov/1995_Belogurov_785.pdf:PDF},
  keywords  = {Antirestriction},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Belogurov1993,
  author    = {Belogurov, A. A. and Delver, E. P. and Rodzevich, O. V.},
  journal   = {Journal of bacteriology},
  title     = {Plasmid pKM101 encodes two nonhomologous antirestriction proteins (ArdA and ArdB) whose expression is controlled by homologous regulatory sequences.},
  year      = {1993},
  pages     = {4843--50},
  volume    = {175},
  abstract  = {The IncN plasmid pKM101 (a derivative of R46) encodes the antirestriction protein ArdB (alleviation of restriction of DNA) in addition to another antirestriction protein, ArdA, described previously. The relevant gene, ardB, was located in the leading region of pKM101, about 7 kb from oriT. The nucleotide sequence of ardB was determined, and an appropriate polypeptide was identified in maxicells of Escherichia coli. Like ArdA, ArdB efficiently inhibits restriction by members of the three known families of type I systems of E. coli and only slightly affects the type II enzyme, EcoRI. However, in contrast to ArdA, ArdB is ineffective against the modification activity of the type I (EcoK) system. Comparison of deduced amino acid sequences of ArdA and ArdB revealed only one small region of similarity (nine residues), suggesting that this region may be somehow involved in the interaction with the type I restriction systems. We also found that the expression of both ardA and ardB genes is controlled jointly by two pKM101-encoded proteins, ArdK and ArdR, with molecular weights of about 15,000 and 20,000, respectively. The finding that the sequences immediately upstream of ardA and ardB share about 94% identity over 218 bp suggests that their expression may be controlled by ArdK and ArdR at the transcriptional level. Deletion studies and promoter probe analysis of these sequences revealed the regions responsible for the action of ArdK and ArdR as regulatory proteins. We propose that both types of antirestriction proteins may play a pivotal role in overcoming the host restriction barrier by self-transmissible broad-host-range plasmids. It seems likely that the ardKR-dependent regulatory system serves in this case as a genetic switch that controls the expression of plasmid-encoded antirestriction functions during mating.},
  file      = {:by-author/B/Belogurov/1993_Belogurov_4843.pdf:PDF},
  keywords  = {Antirestriction},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Belogurov1992,
  author    = {Belogurov, A. A. and Delver, E. P. and Rodzevich, O. V.},
  journal   = {Journal of bacteriology},
  title     = {IncN plasmid pKM101 and IncI1 plasmid ColIb-P9 encode homologous antirestriction proteins in their leading regions.},
  year      = {1992},
  pages     = {5079--85},
  volume    = {174},
  abstract  = {The IncN plasmid pKM101 (a derivative of R46), like the IncI1 plasmid ColIb-P9, carries a gene (ardA, for alleviation of restriction of DNA) encoding an antirestriction function. ardA was located about 4 kb from the origin of transfer, in the region transferred early during bacterial conjugation. The nucleotide sequence of ardA was determined, and an appropriate polypeptide with the predicted molecular weight of about 19,500 was identified in maxicells of Escherichia coli. Comparison of the deduced amino acid sequences of the antirestriction proteins of the unrelated plasmids pKM101 and ColIb (ArdA and Ard, respectively) revealed that these proteins have about 60% identity. Like ColIb Ard, pKM101 ArdA specifically inhibits both the restriction and modification activities of five type I systems of E. coli tested and does not influence type III (EcoP1) restriction or the 5-methylcytosine-specific restriction systems McrA and McrB. However, in contrast to ColIb Ard, pKM101 ArdA is effective against the type II enzyme EcoRI. The Ard proteins are believed to overcome the host restriction barrier during bacterial conjugation. We have also identified two other genes of pKM101, ardR and ardK, which seem to control ardA activity and ardA-mediated lethality, respectively. Our findings suggest that ardR may serve as a genetic switch that determines whether the ardA-encoded antirestriction function is induced during mating.},
  file      = {:by-author/B/Belogurov/1992_Belogurov_5079.pdf:PDF},
  keywords  = {Antirestriction},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Belsky2002,
  author    = {Belsky, Alec and Hellenbrandt, Mariette and Karen, Vicky Lynn and Luksch, Peter},
  journal   = {Acta Crystallographica Section B},
  title     = {New developments in the {Inorganic Crystal Structure Database (ICSD)}: accessibility in support of materials research and design},
  year      = {2002},
  pages     = {364--369},
  volume    = {58},
  abstract  = {The materials community in both science and industry use crystallographic data models on a daily basis to visualize, explain and predict the behavior of chemicals and materials. Access to reliable information on the structure of crystalline materials helps researchers concentrate experimental work in directions that optimize the discovery process. The Inorganic Crystal Structure Database (ICSD) is a comprehensive collection of more than 60000 crystal structure entries for inorganic materials and is produced cooperatively by Fachinformationszentrum Karlsruhe (FIZ), Germany, and the US National Institute of Standards and Technology (NIST). The ICSD is disseminated in computerized formats with scientific software tools to exploit the content of the database. Features of a new Windows-based graphical user interface for the ICSD are outlined, together with directions for future development in support of materials research and design.},
  doi       = {10.1107/S0108768102006948},
  file      = {:by-author/B/Belsky/2002_Belsky_364.pdf:PDF},
  keywords  = {Crystal Structure Data; ICSD; Inorganic Crystal Structure Database; Materials Design; Visualization Software; Windows-based Graphical User Interface},
  owner     = {andrius},
  timestamp = {2015.06.25},
  creationdate = {2015-06-25T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0108768102006948},
}

@Article{Belugina2011,
  author    = {Belugina, N. V. and Gainutdinov, R. V. and Tolstikhina, A. L. and Dolbinina, V. V. and Sorokina, N. I. and Alekseeva, O. A.},
  journal   = {Crystallography Reports},
  title     = {Nanorelief of the natural cleavage surface of triglycine sulphate crystals with substitutional and interstitial impurities},
  year      = {2011},
  issn      = {1562-689X},
  month     = {Nov},
  number    = {6},
  pages     = {1070--1076},
  volume    = {56},
  abstract  = {Ferroelectric triglycine sulphate crystals (T GS) with substitutional (LADTGS+ADP, DTGS) and interstitial (Cr) impurities have been studied by atomicforce microscopy, X-ray diffraction, and X-ray fluorescence. The nanorelief parameters of the mirror cleavage TGS(010) surface have been measured with a high accuracy. A correlation between the crystal defect density in the bulk and the cleavage surface nanorelief is revealed at the submicrometer level.},
  doi       = {10.1134/s1063774511030047},
  file      = {2011_Belugina_1070.pdf:by-author/B/Belugina/2011_Belugina_1070.pdf:PDF},
  keywords  = {Atomic Force Microscope; Crystal Surface; Erroelectric Crystals; Nice Crystal Photos; Triglycine Sulphate; X-ray Crystallography},
  owner     = {saulius},
  publisher = {Pleiades Publishing Ltd},
  timestamp = {2016.10.03},
  creationdate = {2016-10-03T00:00:00},
  url       = {http://dx.doi.org/10.1134/S1063774511030047},
}

@Article{Bemis1996,
  author    = {Bemis, Guy W. and Murcko, Mark A.},
  journal   = {Journal of Medicinal Chemistry},
  title     = {The Properties of Known Drugs. 1. Molecular Frameworks},
  year      = {1996},
  pages     = {2887--2893},
  volume    = {39},
  abstract  = {In order to better understand the common features present in drug molecules, we use shape description methods to analyze a database of commercially available drugs and prepare a list of common drug shapes. A useful way of organizing this structural data is to group the atoms of each drug molecule into ring, linker, framework, and side chain atoms. On the basis of the two-dimensional molecular structures (without regard to atom type, hybridization, and bond order), there are 1179 different frameworks among the 5120 compounds analyzed. However, the shapes of half of the drugs in the database are described by the 32 most frequently occurring frameworks. This suggests that the diversity of shapes in the set of known drugs is extremely low. In our second method of analysis, in which atom type, hybridization, and bond order are considered, more diversity is seen; there are 2506 different frameworks among the 5120 compounds in the database, and the most frequently occurring 42 frameworks account for only one-fourth of the drugs. We discuss the possible interpretations of these findings and the way they may be used to guide future drug discovery research.},
  comment   = {Cited by Hu2019.},
  doi       = {10.1021/jm9602928},
  eprint    = {http://pubs.acs.org/doi/pdf/10.1021/jm9602928},
  file      = {1996_Bemis_2887.pdf:by-author/B/Bemis/1996_Bemis_2887.pdf:PDF},
  owner     = {saulius},
  timestamp = {2013.04.01},
  creationdate = {2013-04-01T00:00:00},
  url       = {http://pubs.acs.org/doi/abs/10.1021/jm9602928},
}

@Article{Benenson2004,
  author           = {Benenson, Yaakov and Gil, Binyamin and Ben-Dor, Uri and Adar, Rivka and Shapiro, Ehud},
  journal          = {Nature},
  title            = {An autonomous molecular computer for logical control of gene expression.},
  year             = {2004},
  pages            = {423--9},
  volume           = {429},
  abstract         = {Early biomolecular computer research focused on laboratory-scale, human-operated computers for complex computational problems. Recently, simple molecular-scale autonomous programmable computers were demonstrated allowing both input and output information to be in molecular form. Such computers, using biological molecules as input data and biologically active molecules as outputs, could produce a system for 'logical' control of biological processes. Here we describe an autonomous biomolecular computer that, at least in vitro, logically analyses the levels of messenger RNA species, and in response produces a molecule capable of affecting levels of gene expression. The computer operates at a concentration of close to a trillion computers per microlitre and consists of three programmable modules: a computation module, that is, a stochastic molecular automaton; an input module, by which specific mRNA levels or point mutations regulate software molecule concentrations, and hence automaton transition probabilities; and an output module, capable of controlled release of a short single-stranded DNA molecule. This approach might be applied in vivo to biochemical sensing, genetic engineering and even medical diagnosis and treatment. As a proof of principle we programmed the computer to identify and analyse mRNA of disease-related genes associated with models of small-cell lung cancer and prostate cancer, and to produce a single-stranded DNA molecule modelled after an anticancer drug.},
  creationdate     = {2008-07-28T00:00:00},
  doi              = {10.1038/nature02551},
  file             = {Benenson_2004_423-computer_of_gene_expr.pdf:by-author/B/Benenson/2004_Benenson_423.pdf:PDF},
  modificationdate = {2023-04-23T10:26:47},
  owner            = {saulius},
  timestamp        = {2008.07.28},
}

@Article{Benkert2011,
  author    = {Pascal Benkert and Marco Biasini and Torsten Schwede},
  journal   = {Bioinformatics},
  title     = {Toward the estimation of the absolute quality of individual protein structure models},
  year      = {2011},
  pages     = {343--350},
  volume    = {27},
  abstract  = {Motivation: Quality assessment of protein structures is an important part of experimental structure validation and plays a crucial role in protein structure prediction, where the predicted models may contain substantial errors. Most current scoring functions are primarily designed to rank alternative models of the same sequence supporting model selection, whereas the prediction of the absolute quality of an individual protein model has received little attention in the field. However, reliable absolute quality estimates are crucial to assess the suitability of a model for specific biomedical applications. Results: In this work, we present a new absolute measure for the quality of protein models, which provides an estimate of the ‘degree of nativeness’ of the structural features observed in a model and describes the likelihood that a given model is of comparable quality to experimental structures. Model quality estimates based on the QMEAN scoring function were normalized with respect to the number of interactions. The resulting scoring function is independent of the size of the protein and may therefore be used to assess both monomers and entire oligomeric assemblies. Model quality scores for individual models are then expressed as ‘Z-scores’ in comparison to scores obtained for high-resolution crystal structures. We demonstrate the ability of the newly introduced QMEAN Z-score to detect experimentally solved protein structures containing significant errors, as well as to evaluate theoretical protein models. In a comprehensive QMEAN Z-score analysis of all experimental structures in the PDB, membrane proteins accumulate on one side of the score spectrum and thermostable proteins on the other. Proteins from the thermophilic organism Thermatoga maritima received significantly higher QMEAN Z-scores in a pairwise comparison with their homologous mesophilic counterparts, underlining the significance of the QMEAN Z-score as an estimate of protein stability. Availability: The Z-score calculation has been integrated in the QMEAN server available at: http://swissmodel.expasy.org/qmean.},
  doi       = {10.1093/bioinformatics/btq662},
  file      = {:by-author/B/Benkert/2011_Benkert_343.pdf:PDF},
  keywords  = {Proteins; Structure Prediction},
  owner     = {andrius},
  timestamp = {2013.12.04},
  creationdate = {2013-12-04T00:00:00},
}

@Article{Benkert2008,
  author    = {Benkert, Pascal and Tosatto, Silvio C. E. and Schomburg, Dietmar},
  journal   = {Proteins: Structure, Function, and Bioinformatics},
  title     = {{QMEAN}: A comprehensive scoring function for model quality assessment},
  year      = {2008},
  issn      = {1097-0134},
  pages     = {261--277},
  volume    = {71},
  abstract  = {In protein structure prediction, a considerable number of alternative models are usually produced from which subsequently the final model has to be selected. Thus, a scoring function for the identification of the best model within an ensemble of alternative models is a key component of most protein structure prediction pipelines. QMEAN, which stands for Qualitative Model Energy ANalysis, is a composite scoring function describing the major geometrical aspects of protein structures. Five different structural descriptors are used. The local geometry is analyzed by a new kind of torsion angle potential over three consecutive amino acids. A secondary structure-specific distance-dependent pairwise residue-level potential is used to assess long-range interactions. A solvation potential describes the burial status of the residues. Two simple terms describing the agreement of predicted and calculated secondary structure and solvent accessibility, respectively, are also included. A variety of different implementations are investigated and several approaches to combine and optimize them are discussed. QMEAN was tested on several standard decoy sets including a molecular dynamics simulation decoy set as well as on a comprehensive data set of totally 22,420 models from server predictions for the 95 targets of CASP7. In a comparison to five well-established model quality assessment programs, QMEAN shows a statistically significant improvement over nearly all quality measures describing the ability of the scoring function to identify the native structure and to discriminate good from bad models. The three-residue torsion angle potential turned out to be very effective in recognizing the native fold.},
  doi       = {10.1002/prot.21715},
  file      = {:by-author/B/Benkert/2008_Benkert_261.pdf:PDF},
  keywords  = {Proteins; Structure Prediction},
  owner     = {andrius},
  publisher = {Wiley Subscription Services, Inc., A Wiley Company},
  timestamp = {2013.12.04},
  creationdate = {2013-12-04T00:00:00},
  url       = {http://dx.doi.org/10.1002/prot.21715},
}

@Article{Benkovic2001,
  author           = {Benkovic, S. J. and Valentine, A. M. and Salinas, F.},
  journal          = {Annual review of biochemistry},
  title            = {Replisome-mediated {DNA} replication.},
  year             = {2001},
  pages            = {181--208},
  volume           = {70},
  abstract         = {The elaborate process of genomic replication requires a large collection of proteins properly assembled at a DNA replication fork. Several decades of research on the bacterium Escherichia coli and its bacteriophages T4 and T7 have defined the roles of many proteins central to DNA replication. These three different prokaryotic replication systems use the same fundamental components for synthesis at a moving DNA replication fork even though the number and nature of some individual proteins are different and many lack extensive sequence homology. The components of the replication complex can be grouped into functional categories as follows: DNA polymerase, helix destabilizing protein, polymerase accessory factors, and primosome (DNA helicase and DNA primase activities). The replication of DNA derives from a multistep enzymatic pathway that features the assembly of accessory factors and polymerases into a functional holoenzyme; the separation of the double-stranded template DNA by helicase activity and its coupling to the primase synthesis of RNA primers to initiate Okazaki fragment synthesis; and the continuous and discontinuous synthesis of the leading and lagging daughter strands by the polymerases. This review summarizes and compares and contrasts for these three systems the types, timing, and mechanism of reactions and of protein-protein interactions required to initiate, control, and coordinate the synthesis of the leading and lagging strands at a DNA replication fork and comments on their generality.},
  creationdate     = {2008-07-28T00:00:00},
  doi              = {10.1146/annurev.biochem.70.1.181},
  file             = {:by-author/B/Benkovic/2001_Benkovic_181.pdf:PDF},
  keywords         = {{gp41} Helicase},
  modificationdate = {2024-03-18T17:23:12},
  owner            = {em},
  timestamp        = {2008.07.28},
}

@Article{Ben‐Naim1977,
  author    = {Ben‐Naim, A.},
  journal   = {The Journal of Chemical Physics},
  title     = {Inversion of the Kirkwood–Buff theory of solutions: Application to the water–ethanol system},
  year      = {1977},
  pages     = {4884--4890},
  volume    = {67},
  abstract  = {A general procedure is outlined whereby experimental data such as partial molar volumes, isothermal compressibilities, and partial vapor pressures may be processed to obtain information on the extent of the affinity between two species in a mixture of two (or more) components. A particular example of the water–ethanol system is processed in this manner to obtain the quantities G αβ which are integrals over the pair correlation functions between two species α and β. This information is relevant to several topics of interest in the field of aqueous solutions, such as the solvation of solutes, hydrophobic interactions, and structural changes in the solvent brought by the addition of solutes to water. More generally it may be used to characterize the properties of various mixtures on a molecular level.},
  doi       = {10.1063/1.434669},
  file      = {1977_Ben‐Naim_4884.pdf:by-author/B/Ben‐Naim/1977_Ben‐Naim_4884.pdf:PDF},
  keywords  = {Kirkwood-Buff Theory; Protein Folding; Statistical Physics; Theory of Solutions},
  owner     = {saulius},
  timestamp = {2015.03.13},
  creationdate = {2015-03-13T00:00:00},
  url       = {http://scitation.aip.org/content/aip/journal/jcp/67/11/10.1063/1.434669},
}

@Article{Benner1991,
  author           = {Benner, S A and Ellington, A D},
  journal          = {Science (New York, N.Y.)},
  title            = {RNA world.},
  year             = {1991},
  pages            = {1232},
  volume           = {252},
  creationdate     = {2008-07-28T00:00:00},
  doi              = {10.1126/science.252.5010.1232-b},
  file             = {1991_Benner_1232.pdf:by-author/B/Benner/1991_Benner_1232.pdf:PDF},
  keywords         = {RNA World; Ribozymes},
  modificationdate = {2023-04-23T10:27:28},
  owner            = {saulius},
  timestamp        = {2008.07.28},
}

@Article{Ben-Shem2010,
  author           = {Ben-Shem, Adam and Jenner, Lasse and Yusupova, Gulnara and Yusupov, Marat},
  journal          = {Science (New York, N.Y.)},
  title            = {Crystal structure of the eukaryotic ribosome.},
  year             = {2010},
  pages            = {1203--9},
  volume           = {330},
  creationdate     = {2008-07-28T00:00:00},
  doi              = {10.1126/science.1194294},
  file             = {2010_Ben-Shem_1203.pdf:by-author/B/Ben-Shem/2010_Ben-Shem_1203.pdf:PDF},
  keywords         = {Protein Structures; Ribosome},
  modificationdate = {2023-04-23T10:27:46},
  owner            = {saulius},
  timestamp        = {2008.07.28},
}

@TechReport{Bentley1992,
  author      = {John L. Bentley and Lynn W. Jelinski and Brian W. Kernighan},
  institution = {AT\&T Bell Laboratories},
  title       = {CHEM -- A Program for typesetting Chemical Diagrams: User Manual},
  year        = {1992},
  month       = {Oct},
  note        = {chem for nroff manual},
  file        = {:by-author/B/Bentley/1992_Bentley_tr122.ps.gz:PDF},
  keywords    = {Groff; Manual; Nroff; Troff; Typesetting; Unix},
  owner       = {saulius},
  timestamp = {2012.11.20},
  creationdate = {2012-11-20T00:00:00},
  url         = {http://cm.bell-labs.com/cm/cs/cstr/122.ps.gz},
}

@TechReport{Bentley1991a,
  author      = {John L. Bentley and Brian W. Kernighan},
  institution = {AT\&T Bell Laboratories},
  title       = {Grap -- A Language for Typesetting Graphs: Tutorial and User Manual},
  year        = {1991},
  month       = {May},
  file        = {:by-author/B/Bentley/1991_Bentley.pdf:PDF;:by-author/B/Bentley/1991_Bentley.ps:PostScript;:by-author/B/Bentley/1991_Bentley_tr114.ps.gz:PDF},
  keywords    = {Computer Science (CS); Grap; Groff; Manual; Nroff; Troff; Typesetting; Unix},
  owner       = {saulius},
  timestamp = {2012.11.20},
  creationdate = {2012-11-20T00:00:00},
  url         = {http://cm.bell-labs.com/cm/cs/cstr/114.ps.gz},
}

@TechReport{Bentley1986,
  author      = {Jon L. Bentley and Brian W. Kernighan},
  institution = {AT\&T Bell Laboratories, and Murray Hill, New Jersey 07974},
  title       = {Tools for Printing Indexes},
  year        = {1986},
  month       = {October},
  file        = {:by-author/B/Bentley/1986_Bentley.ps:PostScript;:by-author/B/Bentley/1986_Bentley.pdf:PDF},
  keywords    = {Computer Science (CS); Groff; Roff; Troff; Typesetting; Unix},
  owner       = {saulius},
  timestamp = {2015.02.27},
  creationdate = {2015-02-27T00:00:00},
}

@InProceedings{Berchtold1996,
  author    = {Berchtold, Stefan and Keim, Daniel A. and Kriegel, Hans-Peter},
  booktitle = {Proceedings of the 22th International Conference on Very Large Data Bases},
  title     = {The X-tree: An Index Structure for High-Dimensional Data},
  year      = {1996},
  pages     = {28--39},
  abstract  = {In this paper,we proposea new method for index- ing large amountsof point and spatial datain high- dimensional space.An analysis shows that index structuressuch as the R*-tree are not adequatefor indexing high-dimensional data sets. The major problem of R-tree-basedindex structures is the overlap of the bounding boxes in the directory, which increases with growing dimension.To avoid this problem, we introduce a new organization of the directory which usesa split algorithm minimiz- ing overlap and additionally utilizes the conceptof supemodes. basic idea of overlap-minimizing The split and supernodes to keepthe directory ashi- is erarchicalaspossible,andat the sametime to avoid splits in the directory that would result in high over- lap. Our experiments show that for high-dimen- sional data,theX-tree outperformsthe well-known R*-tree and the TV-tree by up to two orders of magnitude.},
  file      = {:by-author/B/Berchtold/1996_Berchtold_28.pdf:PDF},
  isbn      = {1-55860-382-4},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dl.acm.org/citation.cfm?id=645922.673502},
}

@Article{Berendsen1984,
  author           = {Berendsen, H. J. C. and Postma, J. P. M. and van Gunsteren, W. F. and DiNola, A. and Haak, J. R.},
  journal          = {The Journal of Chemical Physics},
  title            = {Molecular dynamics with coupling to an external bath},
  year             = {1984},
  number           = {8},
  pages            = {3684--3690},
  volume           = {81},
  abstract         = {In molecular dynamics (MD) simulations the need often arises to maintain such parameters as temperature or pressure rather than energy and volume, or to impose gradients for studying transport properties in nonequilibrium MD. A method is described to realize coupling to an external bath with constant temperature or pressure with adjustable time constants for the coupling. The method is easily extendable to other variables and to gradients, and can be applied also to polyatomic molecules involving internal constraints. The influence of coupling time constants on dynamical variables is evaluated. A leap‐frog algorithm is presented for the general case involving constraints with coupling to both a constant temperature and a constant pressure bath.},
  comment          = {Discussed and cited in https://computecanada.github.io/molmodsim-md-theory-lesson-novice/07-thermostats/index.html and https://computecanada.github.io/molmodsim-md-theory-lesson-novice/reference.html.},
  creationdate     = {2016-02-23T00:00:00},
  doi              = {http://dx.doi.org/10.1063/1.448118},
  file             = {1984_Berendsen_3684.pdf:by-author/B/Berendsen/1984_Berendsen_3684.pdf:PDF},
  groups           = {sg/Molecular dynamics},
  keywords         = {Molecular Dynamics (MD); Thermostat},
  modificationdate = {2023-01-29T13:22:19},
  owner            = {saulius},
  timestamp        = {2016.02.23},
  url              = {http://scitation.aip.org/content/aip/journal/jcp/81/8/10.1063/1.448118},
}

@Manuscript{Berg1999,
  author    = {Van den Berg and Di Cerbo and Zimmermann},
  title     = {IBM/Computer Programs},
  year      = {1999},
  keywords  = {Patentai; Teise},
  file      = {:by-author/B/Berg/1999_Berg.doc:DOC},
  owner     = {saulius},
  timestamp = {2015.02.28},
  creationdate = {2015-02-28T00:00:00},
}

@Article{Berge2000,
  author           = {Berge, T and Ellis, D J and Dryden, D T and Edwardson, J M and Henderson, R M},
  journal          = {Biophysical journal},
  title            = {Translocation-independent dimerization of the EcoKI endonuclease visualized by atomic force microscopy.},
  year             = {2000},
  pages            = {479--84},
  volume           = {79},
  abstract         = {Bacterial type I restriction/modification systems are capable of performing multiple actions in response to the methylation pattern on their DNA recognition sequences. The enzymes making up these systems serve to protect the bacterial cells against viral infection by binding to their recognition sequences on the invading DNA and degrading it after extensive ATP-driven translocation. DNA cleavage has been thought to occur as the result of a collision between two translocating enzyme complexes. Using atomic force microscopy (AFM), we show here that EcoKI dimerizes rapidly when bound to a plasmid containing two recognition sites for the enzyme. Dimerization proceeds in the absence of ATP and is also seen with an EcoKI mutant (K477R) that is unable to translocate DNA. Only monomers are seen when the enzyme complex binds to a plasmid containing a single recognition site. Based on our results, we propose that the binding of EcoKI to specific DNA target sequences is accompanied by a conformational change that leads rapidly to dimerization. This event is followed by ATP-dependent translocation and cleavage of the DNA.},
  creationdate     = {2008-07-28T00:00:00},
  doi              = {10.1016/s0006-3495(00)76309-0},
  file             = {Berge_2000_479-EcoKI-translocation-AFM.pdf:by-author/B/Berge/2000_Berge_479.pdf:PDF},
  modificationdate = {2023-04-23T10:41:45},
  owner            = {saulius},
  timestamp        = {2008.07.28},
}

@Webpage{Berger2008,
  author    = {Daniel Berger},
  retrieved = {2008-10-28},
  title     = {Is QWERTY harming language design?},
  url       = {http://archive.oreilly.com/pub/post/is_qwerty_harming_language_des.html},
  month     = {May},
  year      = {2008},
  file      = {:by-author/B/Berger/2008_Berger.odt:},
  keywords  = {Computer Language Design; Computer Science (CS)},
  owner     = {saulius},
  timestamp = {2015.03.03},
  creationdate = {2015-03-03T00:00:00},
}

@Article{Berger1996,
  author           = {Berger, J M and Gamblin, S J and Harrison, S C and Wang, J C},
  journal          = {Nature},
  title            = {Structure and mechanism of DNA topoisomerase II.},
  year             = {1996},
  pages            = {225--32},
  volume           = {379},
  abstract         = {The crystal structure of a large fragment of yeast type II DNA topoisomerase reveals a heart-shaped dimeric protein with a large central hole. It provides a molecular model of the enzyme as an ATP-modulated clamp with two sets of jaws at opposite ends, connected by multiple joints. An enzyme with bound DNA can admit a second DNA duplex through one set of jaws, transport it through the cleaved first duplex, and expel it through the other set of jaws.},
  creationdate     = {2008-07-28T00:00:00},
  doi              = {10.1038/379225a0},
  file             = {1996_Berger_225.pdf:by-author/B/Berger/1996_Berger_225.pdf:PDF;:by-author/B/Berger/1996_Berger_225.djvu:Djvu},
  keywords         = {Protein Structures; Topoisomerase II},
  modificationdate = {2023-04-23T10:41:58},
  owner            = {saulius},
  timestamp        = {2008.07.28},
}

@Article{Berger1987,
  author           = {James O. Berger and Thomas Sellke},
  journal          = {Journal of the American Statistical Association},
  title            = {Testing a Point Null Hypothesis: The Irreconcilability of P Values and Evidence},
  year             = {1987},
  pages            = {112--122},
  volume           = {82},
  abstract         = {The problem of testing a point null hypothesis (or a "small interval" null hypothesis) is considered. Of interest is the relationship between the P value (or observed significance level) and conditional and Bayesian measures of evidence against the null hypothesis. Although one might presume that a small P value indicates the presence of strong evidence against the null, such is not necessarily the case. Expanding on earlier work [especially Edwards, Lindman, and Savage (1963) and Dickey (1977)], it is shown that actual evidence against a null (as measured, say, by posterior probability or comparative likelihood) can differ by an order of magnitude from the P value. For instance, data that yield a P value of .05, when testing a normal mean, result in a posterior probability of the null of at least .30 for any objective prior distribution. ("Objective" here means that equal prior weight is given the two hypotheses and that the prior is symmetric and nonincreasing away from the null; other definitions of "objective" will be seen to yield qualitatively similar results.) The overall conclusion is that P values can be highly misleading measures of the evidence provided by the data against the null hypothesis.},
  comment          = {"The overall conclusion is that P values can be highly misleading measures of the evidence provided by the data against the null hypothesis"},
  creationdate     = {2012-10-04T00:00:00},
  file             = {1987_Berger_112.pdf:by-author/B/Berger/1987_Berger_112.pdf:PDF},
  groups           = {sg/Bayesian},
  keywords         = {Bayesian Statistics; P-values},
  modificationdate = {2022-11-13T17:34:19},
  owner            = {saulius},
  timestamp        = {2012.10.04},
  url              = {http://www.jstor.org/stable/2289131?origin=JSTOR-pdf},
}

@Article{Berkhof2003,
  author    = {Johannes Berkhof and Iven van Mechelen and Andrew Gelman},
  journal   = {Statistica Sinica},
  title     = {A {B}ayesian Approach to The Selection And Testing of Mixture Models},
  year      = {2003},
  pages     = {423--442},
  volume    = {13},
  abstract  = {An important aspect of mixture modeling is the selection of the number of mixture components. In this paper, we discuss the Bayes factor as a selection tool. The discussion will focus on two aspects: computation of the Bayes factor and prior sensitivity. For the computation, we propose a variant of Chib’s estimator that accounts for the non-identifiability of the mixture components. To reduce the prior sensitivity of the Bayes factor, we propose to extend the model with a hyperprior. We further discuss the use of posterior predictive checks for examining the fit of the model. The ideas are illustrated by means of a psychiatric diagnosis example.},
  file      = {:by-author/B/Berkhof/2003_Berkhof_423.pdf:PDF},
  groups    = {sg/Bayesian},
  owner     = {andrius},
  timestamp = {2012.11.20},
  creationdate = {2012-11-20T00:00:00},
}

@Article{Berkholz2009,
  author    = {Berkholz, Donald S. and Shapovalov, Maxim V. and Dunbrack, Jr, Roland L. and Karplus, P. Andrew},
  journal   = {Structure (London, England : 1993)},
  title     = {Conformation dependence of backbone geometry in proteins.},
  year      = {2009},
  pages     = {1316--25},
  volume    = {17},
  abstract  = {Protein structure determination and predictive modeling have long been guided by the paradigm that the peptide backbone has a single, context-independent ideal geometry. Both quantum-mechanics calculations and empirical analyses have shown this is an incorrect simplification in that backbone covalent geometry actually varies systematically as a function of the phi and Psi backbone dihedral angles. Here, we use a nonredundant set of ultrahigh-resolution protein structures to define these conformation-dependent variations. The trends have a rational, structural basis that can be explained by avoidance of atomic clashes or optimization of favorable electrostatic interactions. To facilitate adoption of this paradigm, we have created a conformation-dependent library of covalent bond lengths and bond angles and shown that it has improved accuracy over existing methods without any additional variables to optimize. Protein structures derived from crystallographic refinement and predictive modeling both stand to benefit from incorporation of the paradigm.},
  doi       = {10.1016/j.str.2009.08.012},
  file      = {:by-author/B/Berkholz/2009_Berkholz_1316.pdf:PDF},
  keywords  = {X-ray Crystallography},
  owner     = {andrius},
  timestamp = {2012.05.30},
  creationdate = {2012-05-30T00:00:00},
}

@Article{Berl2000,
  author           = {Berl, V. and Huc, I. and Khoury, R. G. and Krische, M. J. and Lehn, J. M.},
  journal          = {Nature},
  title            = {Interconversion of single and double helices formed from synthetic molecular strands.},
  year             = {2000},
  pages            = {720--3},
  volume           = {407},
  abstract         = {Synthetic single-helical conformations are quite common, but the formation of double helices based on recognition between the two constituent strands is relatively rare. Known examples include duplex formation through base-pair-specific hydrogen bonding and stacking, as found in nucleic acids and their analogues, and polypeptides composed of amino acids with alternating L and D configurations. Some synthetic polymers and self-assembled fibres have double-helical winding induced by van der Waals interactions. A third mode of non-covalent interaction, coordination of organic ligands to metal ions, can give rise to double, triple and quadruple helices, although in this case the assembly is driven by the coordination geometry of the metal and the structure of the ligands, rather than by direct inter-strand complementarity. Here we describe a family of oligomeric molecules with bent conformations, which exhibit dynamic exchange between single and double molecular helices in solution, through spiral sliding of the synthetic oligomer strands. The bent conformations leading to the helical shape of the molecules result from intramolecular hydrogen bonding within 2'-pyridyl-2-pyridinecarboxamide units, with extensive intermolecular aromatic stacking stabilizing the double-stranded helices that form through dimerization.},
  creationdate     = {2008-07-28T00:00:00},
  doi              = {10.1038/35037545},
  file             = {:by-author/B/Berl/2000_Berl_720.pdf:PDF},
  modificationdate = {2023-04-23T10:42:17},
  owner            = {saulius},
  timestamp        = {2008.07.28},
}

@Article{Berman2003,
  author    = {Berman, Helen and Henrick, Kim and Nakamura, Haruki},
  journal   = {Nat Struct Mol Biol},
  title     = {Announcing the worldwide Protein Data Bank},
  year      = {2003},
  issn      = {1072-8368},
  pages     = {980--980},
  volume    = {10},
  abstract  = {In recognition of the growing international and interdisciplinary nature of structural biology, three organizations have formed a collaboration to oversee the newly formed worldwide Protein Data Bank (wwPDB; http://www.wwpdb.org/},
  comment   = {10.1038/nsb1203-980},
  doi       = {10.1038/nsb1203-980},
  file      = {2003_Berman_980.pdf:by-author/B/Berman/2003_Berman_980.pdf:PDF},
  groups    = {am/PDB},
  keywords  = {Crystallography; Data Access Policy; Data Management; Databases; PDB},
  owner     = {saulius},
  timestamp = {2013.01.30},
  creationdate = {2013-01-30T00:00:00},
  url       = {http://dx.doi.org/10.1038/nsb1203-980},
}

@Article{Berman2007,
  author    = {Berman, Helen and Henrick, Kim and Nakamura, Haruki and Markley, John L.},
  journal   = {Nucleic Acids Research},
  title     = {The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data},
  year      = {2007},
  pages     = {D301-D303},
  volume    = {35},
  abstract  = {The worldwide Protein Data Bank (wwPDB) is the international collaboration that manages the deposition, processing and distribution of the PDB archive. The online PDB archive is a repository for the coordinates and related information for more than 38 000 structures, including proteins, nucleic acids and large macromolecular complexes that have been determined using X-ray crystallography, NMR and electron microscopy techniques. The founding members of the wwPDB are RCSB PDB (USA), MSD-EBI (Europe) and PDBj (Japan) [H.M. Berman, K. Henrick and H. Nakamura (2003) Nature Struct. Biol., 10, 980]. The BMRB group (USA) joined the wwPDB in 2006. The mission of the wwPDB is to maintain a single archive of macromolecular structural data that are freely and publicly available to the global community. Additionally, the wwPDB provides a variety of services to a broad community of users. The wwPDB website at http://www.wwpdb.org/ provides information about services provided by the individual member organizations and about projects undertaken by the wwPDB.},
  doi       = {10.1093/nar/gkl971},
  eprint    = {http://nar.oxfordjournals.org/content/35/suppl_1/D301.full.pdf+html},
  file      = {:by-author/B/Berman/2007_Berman_D301.pdf:PDF},
  groups    = {am/PDB},
  keywords  = {Crystallographic Databases; PDB},
  owner     = {saulius},
  timestamp = {2014.09.08},
  creationdate = {2014-09-08T00:00:00},
  url       = {http://nar.oxfordjournals.org/content/35/suppl_1/D301.abstract},
}

@Article{Berman2012,
  author           = {Helen M. Berman and Gerard J. Kleywegt and Haruki Nakamura and John L. Markley},
  journal          = {Structure},
  title            = {The {P}rotein {D}ata {B}ank at 40: reflecting on the past to prepare for the future},
  year             = {2012},
  issn             = {0969-2126},
  pages            = {391--396},
  volume           = {20},
  abstract         = {A symposium celebrating the 40th anniversary of the Protein Data Bank archive (PDB), organized by the Worldwide Protein Data Bank, was held at Cold Spring Harbor Laboratory (CSHL) October 28–30, 2011. PDB40's distinguished speakers highlighted four decades of innovation in structural biology, from the early era of structural determination to future directions for the field.},
  creationdate     = {2014-07-07T00:00:00},
  doi              = {10.1016/j.str.2012.01.010},
  file             = {:by-author/B/Berman/2012_Berman_391.pdf:PDF},
  groups           = {am/PDB},
  modificationdate = {2024-08-15T18:46:35},
  owner            = {antanas},
  timestamp        = {2014.07.07},
  url              = {http://www.sciencedirect.com/science/article/pii/S0969212612000184},
}

@Article{Berman2008,
  author    = {Berman, Helen M.},
  journal   = {Acta Crystallographica Section A},
  title     = {The {Protein Data Bank}: a historical perspective},
  year      = {2008},
  month     = {Jan},
  number    = {1},
  pages     = {88--95},
  volume    = {64},
  abstract  = {The Protein Data Bank began as a grassroots effort in 1971. It has grown from a small archive containing a dozen structures to a major international resource for structural biology containing more than 40000 entries. The interplay of science, technology and attitudes about data sharing have all played a role in the growth of this resource.},
  doi       = {10.1107/S0108767307035623},
  file      = {2008_Berman_88.pdf:by-author/B/Berman/2008_Berman_88.pdf:PDF},
  groups    = {am/PDB},
  owner     = {andrius},
  timestamp = {2017.02.21},
  creationdate = {2017-02-21T00:00:00},
  url       = {https://doi.org/10.1107/S0108767307035623},
}

@Article{Berman2002,
  author    = {Berman, Helen M and Battistuz, Tammy and Bhat, T N and Bluhm, Wolfgang F and Bourne, Philip E and Burkhardt, Kyle and Feng, Zukang and Gilliland, Gary L and Iype, Lisa and Jain, Shri and Fagan, Phoebe and Marvin, Jessica and Padilla, David and Ravichandran, Veerasamy and Schneider, Bohdan and Thanki, Narmada and Weissig, Helge and Westbrook, John D and Zardecki, Christine},
  journal   = {Acta crystallographica. Section D, Biological crystallography},
  title     = {The Protein Data Bank.},
  year      = {2002},
  pages     = {899--907},
  volume    = {58},
  doi       = {10.1107/S0907444902003451},
  file      = {2002_Berman_899.pdf:by-author/B/Berman/2002_Berman_899.pdf:PDF},
  groups    = {am/PDB},
  keywords  = {Databases; History; PDB},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Berman2004,
  author    = {Helen M. Berman and Philip E. Bourne and John Westbrook},
  journal   = {Current Proteomics},
  title     = {The Protein Data Bank: A Case Study in Management of Community Data},
  year      = {2004},
  pages     = {49--57},
  abstract  = {As the sole repository for three-dimensional structure data of biological macromolecules, the Protein Data Bank (PDB) is an important resource for research in the academic, pharmaceutical, and biotechnology sectors. Over the years, the methods and speed of structure determination have changed as technology has improved. At the same time the methods for data collection, archiving, and distribution of the structural data in the PDB have also evolved. Concurrently, the community of data depositors and users has expanded. As of October 2003, the PDB archive contains approximately 23,000 released structures and the website receives over 160,000 hits per day. The lessons learned from the development of the PDB may be applicable to the ongoing development of new data and knowledge resources in proteomics},
  file      = {2004_Berman_49.pdf:by-author/B/Berman/2004_Berman_49.pdf:PDF},
  groups    = {am/PDB},
  keywords  = {Data Management; Databases; PDB; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2014.03.24},
  creationdate = {2014-03-24T00:00:00},
  url       = {http://www.sdsc.edu/pb/papers/currprot04.pdf},
}

@Article{Berman2006,
  author           = {Berman, Helen M and Burley, Stephen K and Chiu, Wah and Sali, Andrej and Adzhubei, Alexei and Bourne, Philip E and Bryant, Stephen H and Dunbrack, Jr, Roland L and Fidelis, Krzysztof and Frank, Joachim and Godzik, Adam and Henrick, Kim and Joachimiak, Andrzej and Heymann, Bernard and Jones, David and Markley, John L and Moult, John and Montelione, Gaetano T and Orengo, Christine and Rossmann, Michael G and Rost, Burkhard and Saibil, Helen and Schwede, Torsten and Standley, Daron M and Westbrook, John D},
  journal          = {Structure (London, England : 1993)},
  title            = {Outcome of a workshop on archiving structural models of biological macromolecules.},
  year             = {2006},
  pages            = {1211--7},
  volume           = {14},
  creationdate     = {2008-07-28T00:00:00},
  doi              = {10.1016/j.str.2006.06.005},
  file             = {2006_Berman_1211.pdf:by-author/B/Berman/2006_Berman_1211.pdf:PDF},
  keywords         = {Predicted Model Database},
  modificationdate = {2023-04-23T10:42:58},
  owner            = {saulius},
  timestamp        = {2008.07.28},
}

@Article{Berman2015,
  author       = {Berman, H. M. and Gabanyi, M. J. and Groom, C. R. and Johnson, J. E. and Murshudov, G. N. and Nicholls, R. A. and Reddy, V. and Schwede, T. and Zimmerman, M. D. and Westbrook, J. and Minor, W.},
  journal      = {{IUCrJ}},
  title        = {Data to knowledge: how to get meaning from your result},
  year         = {2015},
  issn         = {2052-2525},
  number       = {1},
  pages        = {45--58},
  volume       = {2},
  abstract     = {Structural and functional studies require the development of sophisticated `Big Data' technologies and software to increase the knowledge derived and ensure reproducibility of the data. This paper presents summaries of the Structural Biology Knowledge Base, the {VIPERdb} Virus Structure Database, evaluation of homology modeling by the Protein Model Portal, the {ProSMART} tool for conformation-independent structure comparison, the {LabDB} `super' laboratory information management system and the Cambridge Structural Database. These techniques and technologies represent important tools for the transformation of crystallographic data into knowledge and information, in an effort to address the problem of non-reproducibility of experimental results.},
  date         = {2015-01-01},
  doi          = {10.1107/S2052252514023306},
  file         = {Full Text PDF:by-author/B/Berman/2015_Berman_45.pdf:PDF;Snapshot:by-author/B/Berman/2015_Berman_45.html:URL},
  journaltitle = {{IUCrJ}},
  keywords     = {Big Data; Data Deposition; Databases; Knowledge Bases; Meaning From Data; PDB},
  langid       = {english},
  owner        = {saulius},
  rights       = {http://creativecommons.org/licenses/by/2.0/uk},
  shortjournal = {{IUCrJ}},
  shorttitle   = {Data to knowledge},
  timestamp = {2017.01.29},
  creationdate = {2017-01-29T00:00:00},
  url          = {http://scripts.iucr.org/cgi-bin/paper?dc5004},
  urldate      = {2017-01-29},
}

@Article{Berman1992,
  author    = {Helen M. Berman and Wilma K. Olson and David L. Beveridge and John Westbrook and Anke Gelbin and Tamas Demeny and S. H. Hsieh and A. R. Srinivasan and Bohdan Schneider},
  journal   = {Biophys. J.},
  title     = {The Nucleic Acid Database: A Comprehensive Relational Database of Three-Dimensional Structures of Nucleic Acids},
  year      = {1992},
  pages     = {751--759},
  volume    = {63},
  doi       = {10.1016/S0006-3495(92)81649-1},
  file      = {1992_Berman_751.pdf:by-author/B/Berman/1992_Berman_751.pdf:PDF},
  groups    = {am/NDB},
  keywords  = {NDB; Nucleic Acids Database; Scientific Databases; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2015.05.13},
  creationdate = {2015-05-13T00:00:00},
}

@Article{Berman2000,
  author    = {Berman, Helen M. and Westbrook, John and Feng, Zukang and Gilliland, Gary and Bhat, T. N. and Weissig, Helge and Shindyalov, Ilya N. and Bourne, Philip E.},
  journal   = {Nucleic Acids Research},
  title     = {The Protein Data Bank},
  year      = {2000},
  pages     = {235--242},
  volume    = {28},
  abstract  = {The Protein Data Bank (PDB; http://www.rcsb.org/pdb/ ) is the single worldwide archive of structural data of biological macromolecules. This paper describes the goals of the PDB, the systems in place for data deposition and access, how to obtain further information, and near-term plans for the future development of the resource.},
  doi       = {10.1093/nar/28.1.235},
  eprint    = {http://nar.oxfordjournals.org/content/28/1/235.full.pdf+html},
  file      = {2000_Berman_235.pdf:by-author/B/Berman/2000_Berman_235.pdf:PDF},
  groups    = {am/PDB},
  owner     = {saulius},
  timestamp = {2013.01.30},
  creationdate = {2013-01-30T00:00:00},
  url       = {http://nar.oxfordjournals.org/content/28/1/235.abstract},
}

@Article{Bernado2010,
  author    = {Bernado, Pau},
  journal   = {Eur Biophys J},
  title     = {Effect of interdomain dynamics on the structure determination of modular proteins by small-angle scattering},
  year      = {2010},
  pages     = {769–780},
  volume    = {39},
  abstract  = {Multidomain proteins in which consecutive globular regions are connected by linkers are prevalent in nature (Levitt in Proc Natl Acad Sci USA 106:11079–11084, 2009). Some members of this family have largely resisted structural characterization as a result of challenges associated with their inherent flexibility. Small-angle scattering (SAS) is often the method of choice for their structural study. An extensive set of simulated data for both flexible and rigid multidomain systems was analyzed and modeled using standard protocols. This study clearly shows that SAXS profiles obtained from highly flexible proteins can be wrongly interpreted as arising from a rigid structure. In this context, it would be important to identify features from the SAXS data or from the derived structural models that indicate interdomain motions to differentiate between these two scenarios. Features of SAXS data that identify flexible proteins are: (1) general attenuation of fine structure in the scattering profiles, which becomes more dramatic in Kratky representations, and (2) a reduced number of interdomain correlation peaks in p(r) functions that also present large Dmax values and a smooth decrease to 0. When modeling this dynamically averaged SAXS data, the structures obtained present characteristic trends: (1) ab initio models display a decrease in resolution, and (2) rigid-body models present highly extended conformations with a lack of interdomain contacts. The ensemble},
  file      = {:by-author/B/Bernadó/2010_Bernado_769.pdf:PDF},
  keywords  = {BUNCH; DAMMIN; EOM; SAXS},
  owner     = {em},
  timestamp = {2013.06.28},
  creationdate = {2013-06-28T00:00:00},
}

@Presentation{Bernado2010b,
  author    = {Pau Bernadó},
  title     = {Biomolecular Flexibility: New oportunites for Small-Angle Scattering},
  year      = {2010},
  file      = {:by-author/B/Bernadó/2010_Bernado_slides.ppt:PowerPoint},
  owner     = {saulius},
  timestamp = {2013.08.11},
  creationdate = {2013-08-11T00:00:00},
}

@Article{Bernado2010a,
  author    = {Bernado, Pau and Modig, Kristofer and Grela, Przemys1aw and Svergun, Dmitri I. and Tchorzewski, Marek and Pons, Miquel and Akke, Mikael},
  journal   = {Biophysical Journal},
  title     = {Structure and Dynamics of Ribosomal Protein L12: An Ensemble Model Based on SAXS and NMR Relaxation},
  year      = {2010},
  pages     = {2374--2382},
  volume    = {98},
  abstract  = {Ribosomal protein L12 is a two-domain protein that forms dimers mediated by its N-terminal domains. A 20-residue linker separates the N- and C-terminal domains. This linker results in a three-lobe topology with significant flexibility, known to be critical for efficient translation. Here we present an ensemble model of spatial distributions and correlation times for the domain reorientations of L12 that reconciles experimental data from small-angle x-ray scattering and nuclear magnetic resonance. We generated an ensemble of L12 conformations in which the structure of each domain is fixed but the domain orientations are variable. The ensemble reproduces the small-angle x-ray scattering data and the optimized correlation times of its reorientational eigenmodes fit the 15N relaxation data. The ensemble model reveals intrinsic conformational properties of L12 that help explain its function on the ribosome. The two C-terminal domains sample a large volume and extend further away from the ribosome anchor than expected for a random-chain linker, indicating that the flexible linker has residual order. Furthermore, the distances between each C-terminal domain and the anchor are anticorrelated, indicating that one of them is more retracted on average. We speculate that these properties promote the function of L12 to recruit translation factors and control their activity on the ribosome.},
  doi       = {10.1016/j.bpj.2010.02.012},
  file      = {:by-author/B/Bernadó/2010_Bernado_2374.pdf:PDF},
  keywords  = {EOM; SAXS},
  owner     = {em},
  timestamp = {2013.06.28},
  creationdate = {2013-06-28T00:00:00},
}

@Article{Bernado2007,
  author    = {Bernadó, Pau and Mylonas, Efstratios and Petoukhov, Maxim V. and Blackledge, Martin and Svergun, Dmitri I.},
  journal   = {Journal of the American Chemical Society},
  title     = {Structural characterization of flexible proteins using small-angle X-ray scattering.},
  year      = {2007},
  pages     = {5656--64},
  volume    = {129},
  abstract  = {Structural analysis of flexible macromolecular systems such as intrinsically disordered or multidomain proteins with flexible linkers is a difficult task as high-resolution techniques are barely applicable. A new approach, ensemble optimization method (EOM), is proposed to quantitatively characterize flexible proteins in solution using small-angle X-ray scattering (SAXS). The flexibility is taken into account by allowing for the coexistence of different conformations of the protein contributing to the experimental scattering pattern. These conformers are selected using a genetic algorithm from a pool containing a large number of randomly generated models covering the protein configurational space. Quantitative criteria are developed to analyze the EOM selected models and to determine the optimum number of conformers in the ensemble. Simultaneous fitting of multiple scattering patterns from deletion mutants, if available, provides yet more detailed local information about the structure. The efficiency of EOM is demonstrated in model and practical examples on completely or partially unfolded proteins and on multidomain proteins interconnected by linkers. In the latter case, EOM is able to distinguish between rigid and flexible proteins and to directly assess the interdomain contacts.},
  file      = {:by-author/B/Bernadó/2007_Bernado_5656.pdf:PDF},
  keywords  = {EOM; Flexible; SAXS},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@InProceedings{Bernardo2010,
  author    = {Jose M. Bernardo},
  booktitle = {Bayesian statistics},
  title     = {Integrated Objective Bayesian Estimation and Hypothesis Testing},
  year      = {2010},
  editor    = {J. M. Bernardo and M. J. Bayarri and J. O. Berger and A. P. Dawid and D. Heckerman and A. F. M. Smith and M. West},
  pages     = {1--68},
  publisher = {Oxford: Oxford University Press},
  volume    = {9},
  file      = {:by-author/B/Bernardo/2010_Bernardo.pdf:PDF},
  groups    = {sg/Bayesian},
  keywords  = {Bayesian Statistics},
  owner     = {saulius},
  timestamp = {2012.10.09},
  creationdate = {2012-10-09T00:00:00},
  url       = {http://isba.stat.duke.edu/events/valencia/publications.html},
}

@MastersThesis{Bernegger2013,
  author    = {Jan Bernegger},
  school    = {Distributed Computing Group, Computer Engineering and Networks Laboratory, ETH Z{\"u}rich},
  title     = {Collaborative OCR for Tabularized Data},
  year      = {2013},
  file      = {:by-author/B/Bernegger/2013_Bernegger.pdf:PDF},
  groups    = {sg/Text segmentation, sg/Document processing},
  keywords  = {Data Management; OCR},
  owner     = {saulius},
  timestamp = {2014.11.06},
  creationdate = {2014-11-06T00:00:00},
  url       = {ftp://ftp.tik.ee.ethz.ch/pub/students/2012-HS/SA-2012-26.pdf},
}

@Article{Bernhardt2012,
  author    = {Bernhardt, Harold},
  journal   = {Biology Direct},
  title     = {The RNA world hypothesis: the worst theory of the early evolution of life (except for all the others)},
  year      = {2012},
  issn      = {1745-6150},
  pages     = {23},
  volume    = {7},
  abstract  = {The problems associated with the RNA world hypothesis are well known. In the following I discuss some of these difficulties, some of the alternative hypotheses that have been proposed, and some of the problems with these alternative models. From a biosynthetic - as well as, arguably, evolutionary - perspective, DNA is a modified RNA, and so the chicken-and-egg dilemma of "which came first?" boils down to a choice between RNA and protein. This is not just a question of cause and effect, but also one of statistical likelihood, as the chance of two such different types of macromolecule arising simultaneously would appear unlikely. The RNA world hypothesis is an example of a 'top down' (or should it be 'present back'?) approach to early evolution: how can we simplify modern biological systems to give a plausible evolutionary pathway that preserves continuity of function? The discovery that RNA possesses catalytic ability provides a potential solution: a single macromolecule could have originally carried out both replication and catalysis. RNA - which constitutes the genome of RNA viruses, and catalyzes peptide synthesis on the ribosome - could have been both the chicken and the egg! However, the following objections have been raised to the RNA world hypothesis: (i) RNA is too complex a molecule to have arisen prebiotically; (ii) RNA is inherently unstable; (iii) catalysis is a relatively rare property of long RNA sequences only; and (iv) the catalytic repertoire of RNA is too limited. I will offer some possible responses to these objections in the light of work by our and other labs. Finally, I will critically discuss an alternative theory to the RNA world hypothesis known as 'proteins first', which holds that proteins either preceded RNA in evolution, or - at the very least - that proteins and RNA coevolved. I will argue that, while theoretically possible, such a hypothesis is probably unprovable, and that the RNA world hypothesis, although far from perfect or complete, is the best we currently have to help understand the backstory to contemporary biology.REVIEWERS:This article was reviewed by Eugene Koonin, Anthony Poole and Michael Yarus (nominated by Laura Landweber).},
  doi       = {10.1186/1745-6150-7-23},
  file      = {2012_Bernhardt_23.pdf:by-author/B/Bernhardt/2012_Bernhardt_23.pdf:PDF},
  keywords  = {Nucleic Acid Evolution; Nucleic Acid Structure; Prebiotic Evolution; RNA World},
  owner     = {saulius},
  pubmedid  = {22793875},
  timestamp = {2013.09.27},
  creationdate = {2013-09-27T00:00:00},
  url       = {http://www.biology-direct.com/content/7/1/23},
}

@Manuscript{Bernstein2002,
  author    = {Bernstein},
  title     = {A two-stage shift register for clocked Quantum-dot Cellular Automata},
  year      = {2002},
  keywords  = {Electronics},
  abstract  = {Quantum-Dot Cellular Automata (QCA) is a computational scheme utilizing the position of interacting single electrons within arrays of quantum dots (“cells”) to encode and process binary information. Clocked QCA architectures can provide power gain, logic level restoration and memory features. Using arrays of micron-sized metal dots, we experimentally demonstrate operation of a QCA latch-inverter and a two-stage shift register.},
  file      = {:by-author/B/Bernstein/2002_Bernstein_manuscript.pdf:PDF},
  groups    = {sg/Cellular automata},
  owner     = {saulius},
  pages     = {manuscript},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Bernstein2005,
  author    = {Bernstein, Daniel J.},
  title     = {Cache-timing Attacks on {AES}},
  year      = {2005},
  file      = {:by-author/B/Bernstein/2005_Bernstein.pdf:PDF},
  keywords  = {Computer Science (CS); Cryptography},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Bernstein1977,
  author    = {Frances C. Bernstein and Thomas F. Koetzle and Graheme J.B. Williams and Edgar F. Meyer Jr. and Michael D. Brice and John R. Rodgers and Olga Kennard and Takehiko Shimanouchi and Mitsuo Tasumi},
  journal   = {Journal of Molecular Biology},
  title     = {The protein data bank: A computer-based archival file for macromolecular structures},
  year      = {1977},
  issn      = {0022-2836},
  pages     = {535--542},
  volume    = {112},
  abstract  = {The Protein Data Bank is a computer-based archival file for macromolecular structures. The Bank stores in a uniform format atomic co-ordinates and partial bond connectivities, as derived from crystallographic studies. Text included in each data entry gives pertinent information for the structure at hand (e.g. species from which the molecule has been obtained, resolution of diffraction data, literature citations and specifications of secondary structure). In addition to atomic co-ordinates and connectivities, the Protein Data Bank stores structure factors and phases, although these latter data are not placed in any uniform format. Input of data to the Bank and general maintenance functions are carried out at Brookhaven National Laboratory. All data stored in the Bank are available on magnetic tape for public distribution, from Brookhaven (to laboratories in the Americans), Tokyo (Japan), and Cambridge (Europe and worldwide). A master file is maintained at Brookhaven and duplicate copies are stored in Cambridge and Tokyo. In the future, it is hoped to expand the scope of the Protein Data Bank to make available co-ordinates for standard structural types (e.g. α-helix, RNA double-stranded helix) and representative computer programs of utility in the study and interpretation of macromolecular structures.},
  doi       = {10.1016/S0022-2836(77)80200-3},
  file      = {1977_Bernstein_535.pdf:by-author/B/Bernstein/1977_Bernstein_535.pdf:PDF},
  groups    = {am/PDB},
  keywords  = {Data Management; Databases; PDB; Protein Crystallography; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2014.03.24},
  creationdate = {2014-03-24T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/S0022283677802003},
}

@Article{Bernstein2016,
  author           = {Bernstein, Herbert J. and Bollinger, John C. and Brown, I. David and Gražulis, Saulius and Hester, James R. and McMahon, Brian and Spadaccini, Nick and Westbrook, John D. and Westrip, Simon P.},
  journal          = {Journal of Applied Crystallography},
  title            = {Specification of the {Crystallographic Information File} format, version 2.0},
  year             = {2016},
  issn             = {1600-5767},
  month            = {Feb},
  number           = {1},
  pages            = {277--284},
  volume           = {49},
  abstract         = {Version 2.0 of the CIF format incorporates novel features implemented in STAR 2.0. Among these are an expanded character repertoire, new and more flexible forms for quoted data values, and new compound data types. The CIF 2.0 format is compared with both CIF 1.1 and STAR 2.0, and a formal syntax specification is provided.},
  creationdate     = {2016-01-08T00:00:00},
  doi              = {10.1107/s1600576715021871},
  file             = {:by-author/B/Bernstein/2016_Bernstein.pdf:PDF},
  groups           = {sg/CIF, am/CIF},
  keywords         = {CIF},
  modificationdate = {2023-08-07T10:23:04},
  owner            = {andrius},
  publisher        = {International Union of Crystallography (IUCr)},
  timestamp        = {2016.01.08},
  url              = {http://dx.doi.org/10.1107/S1600576715021871},
}

@Article{Berry2006a,
  author    = {Berry, Donald A.},
  journal   = {Nature Reviews Drug Discovery},
  title     = {Bayesian clinical trials},
  year      = {2006},
  issn      = {1474-1776},
  pages     = {27--36},
  volume    = {5},
  abstract  = {Bayesian statistical methods are being used increasingly in clinical research because the Bayesian approach is ideally suited to adapting to information that accrues during a trial, potentially allowing for smaller more informative trials and for patients to receive better treatment. Accumulating results can be assessed at any time, including continually, with the possibility of modifying the design of the trial, for example, by slowing (or stopping) or expanding accrual, imbalancing randomization to favour better-performing therapies, dropping or adding treatment arms, and changing the trial population to focus on patient subsets that are responding better to the experimental therapies. Bayesian analyses use available patient-outcome information, including biomarkers that accumulating data indicate might be related to clinical outcome. They also allow for the use of historical information and for synthesizing results of relevant trials. Here, I explain the rationale underlying Bayesian clinical trials, and discuss the potential of such trials to improve the effectiveness of drug development.},
  copyright = {© 2006 Nature Publishing Group},
  doi       = {10.1038/nrd1927},
  file      = {Berry - 2006 - Bayesian clinical trials.pdf:by-author/B/Berry/2006_Berry_27.pdf:PDF;Snapshot:by-author/B/Berry/2006_Berry_27.html:URL},
  groups    = {sg/Clinical Trials},
  language  = {en},
  owner     = {saulius},
  timestamp = {2015.12.14},
  creationdate = {2015-12-14T00:00:00},
  url       = {http://www.nature.com/nrd/journal/v5/n1/abs/nrd1927.html},
  urldate   = {2015-12-12},
}

@Article{Berry2004,
  author    = {Berry, Donald A.},
  journal   = {Statistical Science},
  title     = {Bayesian Statistics and the Efficiency and Ethics of Clinical Trials},
  year      = {2004},
  issn      = {0883-4237, 2168-8745},
  pages     = {175--187},
  volume    = {19},
  abstract  = {The Bayesian approach is being used increasingly in medical research. The flexibility of the Bayesian approach allows for building designs of clinical trials that have good properties of any desired sort. Examples include maximizing effective treatment of patients in the trial, maximizing information about the slope of a dose–response curve, minimizing costs, minimizing the number of patients treated, minimizing the length of the trial and combinations of these desiderata. They also include standard frequentist operating characteristics when these are important considerations. Posterior probabilities are updated via Bayes’ theorem on the basis of accumulating data. These are used to effect modifications of the trial’s course, including stopping accrual, extending accrual beyond that originally planned, dropping treatment arms, adding arms, etc. An important aspect of the approach I advocate is modeling the relationship between a trial’s primary endpoint and early indications of patient performance—auxiliary endpoints. This has several highly desirable consequences. One is that it improves the efficiency of adaptive trials because information is available sooner than otherwise.},
  doi       = {10.1214/088342304000000044},
  file      = {Berry - 2004 - Bayesian Statistics and the Efficiency and Ethics .pdf:by-author/B/Berry/2004_Berry_175.pdf:PDF;Snapshot:by-author/B/Berry/2004_Berry_175.html:URL},
  groups    = {sg/Clinical Trials},
  keywords  = {Adaptive Designs; Auxiliary Endpoints; Bayesian Updating; Clinical Ethics; Clinical Trials; Decision Analysis; Extraim Analyses; Predictive Probabilities},
  mrnumber  = {MR2086326},
  owner     = {saulius},
  timestamp = {2015.12.14},
  creationdate = {2015-12-14T00:00:00},
  url       = {http://projecteuclid.org/euclid.ss/1089808281},
  urldate   = {2015-12-12},
  zmnumber  = {1057.62096},
}

@Article{Berry2006,
  author    = {Berry, Ian M. and Dym, O. and Esnouf, R. M. and Harlos, K. and Meged, R. and Perrakis, A. and Sussman, J. L. and Walter, T. S. and Wilson, J. and Messerschmidt, Albrecht},
  journal   = {Acta crystallographica. Section D, Biological crystallography},
  title     = {SPINE high-throughput crystallization, crystal imaging and recognition techniques: current state, performance analysis, new technologies and future aspects.},
  year      = {2006},
  pages     = {1137--49},
  volume    = {62},
  abstract  = {This paper reviews the developments in high-throughput and nanolitre-scale protein crystallography technologies within the remit of workpackage 4 of the Structural Proteomics In Europe (SPINE) project since the project's inception in October 2002. By surveying the uptake, use and experience of new technologies by SPINE partners across Europe, a picture emerges of highly successful adoption of novel working methods revolutionizing this area of structural biology. Finally, a forward view is taken of how crystallization methodologies may develop in the future.},
  file      = {:by-author/B/Berry/2006_Berry_1137.pdf:PDF},
  keywords  = {Crystallisation},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@Article{Besnier2001,
  author    = {Besnier, C. E. and Kong, H.},
  journal   = {EMBO reports},
  title     = {Converting MlyI endonuclease into a nicking enzyme by changing its oligomerization state.},
  year      = {2001},
  pages     = {782--6},
  volume    = {2},
  abstract  = {N.BstNBI is a nicking endonuclease that recognizes the sequence GAGTC and nicks one DNA strand specifically. The Type IIs endonuclease, MlyI, also recognizes GAGTC, but cleaves both DNA strands. Sequence comparisons revealed significant similarities between N.BstNBI and MlyI. Previous studies showed that MlyI dimerizes in the presence of a cognate DNA, whereas N.BstNBI remains a monomer. This suggests that dimerization may be required for double-stranded cleavage. To test this hypothesis, we used a multiple alignment to design mutations to disrupt the dimerization function of MlyI. When Tyr491 and Lys494 were both changed to alanine, the mutated endonuclease, N.MlyI, no longer formed a dimer and cleaved only one DNA strand specifically. Thus, we have shown that changing the oligomerization state of an enzyme changes its enzymatic function. This experiment also established a protocol that could be applied to other Type IIs endonucleases in order to generate more novel nicking endonucleases.},
  file      = {:by-author/B/Besnier/2001_Besnier_782.pdf:PDF},
  keywords  = {BspD6I},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@Article{Bessen2000,
  author    = {Bessen},
  title     = {Sequential Innovation, Patents, and Imitation},
  year      = {2000},
  pages     = {WP00-01},
  abstract  = {How could such industries as software, semiconductors, and computers have been so innovative despite historically weak patent protection? We argue that if innovation is both sequential and complementary—as it certainly has been in those industries—competition can increase firms’ future profits thus offsetting short-term dissipation of rents. A simple model also shows that in such a dynamic industry, patent protection may reduce overall innovation and social welfare. The natural experiment that occurred when patent protection was extended to software in the 1980's provides a test of this model. Standard arguments would predict that R&D intensity and productivity should have increased among patenting firms. Consistent with our model, however, these increases did not occur. Other evidence supporting our model includes a distinctive pattern of cross-licensing in these industries and a positive relationship between rates of innovation and firm entry.},
  file      = {:by-author/B/Bessen/2000_Bessen_WP00.pdf:PDF},
  keywords  = {Economy; Patents; Sequential Innovation},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Best1979,
  author    = {D. J. Best and N. I. Fisher},
  journal   = {Journal of the Royal Statistical Society. Series C (Applied Statistics)},
  title     = {Efficient Simulation of the von {M}ises Distribution},
  year      = {1979},
  pages     = {152--157},
  volume    = {28},
  abstract  = {An algorithm is given to simulate samples from the von Mises distribution. A wrapped Cauchy density is used as an envelope to give an acceptance-rejection method which is both simple to program and fast for all values of the concentration parameter of the von Mises distribution.},
  file      = {:by-author/B/Best/1979_Best_152.pdf:PDF},
  owner     = {andrius},
  timestamp = {2012.12.07},
  creationdate = {2012-12-07T00:00:00},
}

@Article{Betz2013,
  author    = {Betz, Karin and Malyshev, Denis A. and Lavergne, Thomas and Welte, Wolfram and Diederichs, Kay and Romesberg, Floyd E. and Marx, Andreas},
  journal   = {Journal of the American Chemical Society},
  title     = {Structural Insights into DNA Replication without Hydrogen Bonds},
  year      = {2013},
  issn      = {1520-5126},
  month     = {Dec},
  number    = {49},
  pages     = {18637–18643},
  volume    = {135},
  doi       = {10.1021/ja409609j},
  file      = {:by-author/B/Betz/2013_Betz_18637.pdf:PDF},
  groups    = {am/Expanded genetic code},
  owner     = {andrius},
  publisher = {American Chemical Society (ACS)},
  timestamp = {2016.05.02},
  creationdate = {2016-05-02T00:00:00},
  url       = {http://dx.doi.org/10.1021/ja409609j},
}

@Manuscript{Bezhanishvili2006,
  author    = {Nick Bezhanishvili and Dick de Jongh},
  title     = {Intuitionistic Logic},
  year      = {2006},
  file      = {:by-author/B/Bezhanishvili/2006_Bezhanishvili.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.09.18},
  creationdate = {2012-09-18T00:00:00},
}

@Article{Bhattacharyya2000,
  author           = {Bhattacharyya, S. and Griep, M. A.},
  journal          = {Biochemistry},
  title            = {DnaB helicase affects the initiation specificity of Escherichia coli primase on single-stranded DNA templates.},
  year             = {2000},
  pages            = {745--752},
  volume           = {39},
  abstract         = {The effect of DnaB helicase on the initiation specificity of primase was studied biochemically using a series of single-stranded DNA templates in which each nucleotide of the trinucleotide d(CTG) initiation sequence was systematically varied. DnaB helicase accelerated the rate of primer syntheisis, prevented "overlong" primers from forming and decreased the initiation specificity of primase. In the presence of DnaB helicase, all trinucleotides could serve as the primer initiation site although there was a distinct preference for d(CAG). These data may explain the high chromosomal prevalence of octanucleotides containing CTG on the leading strand and its complement CAG on the lagging strand. The specificity of DnaB helicase places it on the lagging strand template where it stimulates the initiation of Okazaki fragment synthesis. In the absence of DnaB helicase, primase preferentially primed the d(CTG) template. In the presence of DnaB helicase, the initiation preference was not only altered but also the preferred initiating nucleotide was found to be GTP rather than ATP, for both the d(CTG) and the d(CAG) templates. This suggested that the specificity of primase for the d(CTG) initiation trinucleotide was predominantly unaffected in the absence of DnaB helicase on short ssDNA templates, whereas in conjunction with DnaB helicase, the specificity was altered and this alteration has significant implications in the replication of Escherichia coli chromosome in vivo.},
  creationdate     = {2008-07-28T00:00:00},
  file             = {:by-author/B/Bhattacharyya/2000_Bhattacharyya_745.pdf:PDF},
  keywords         = {Ecoli; {gp41} Helicase},
  modificationdate = {2023-04-23T10:43:41},
  owner            = {em},
  timestamp        = {2008.07.28},
}

@Article{Bhaya2011,
  author    = {Bhaya, Devaki and Davison, Michelle and Barrangou, Rodolphe},
  journal   = {Annual review of genetics},
  title     = {CRISPR-Cas systems in bacteria and archaea: versatile small RNAs for adaptive defense and regulation.},
  year      = {2011},
  pages     = {273--97},
  volume    = {45},
  abstract  = {Bacteria and archaea have evolved defense and regulatory mechanisms to cope with various environmental stressors, including virus attack. This arsenal has been expanded by the recent discovery of the versatile CRISPR-Cas system, which has two novel features. First, the host can specifically incorporate short sequences from invading genetic elements (virus or plasmid) into a region of its genome that is distinguished by clustered regularly interspaced short palindromic repeats (CRISPRs). Second, when these sequences are transcribed and precisely processed into small RNAs, they guide a multifunctional protein complex (Cas proteins) to recognize and cleave incoming foreign genetic material. This adaptive immunity system, which uses a library of small noncoding RNAs as a potent weapon against fast-evolving viruses, is also used as a regulatory system by the host. Exciting breakthroughs in understanding the mechanisms of the CRISPR-Cas system and its potential for biotechnological applications and understanding evolutionary dynamics are discussed.},
  file      = {:by-author/B/Bhaya/2011_Bhaya_273.pdf:PDF},
  groups    = {sg/CRISPR-Cas},
  keywords  = {CRISPR},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Bianco2005,
  author    = {Bianco, Piero R. and Hurley, Elizabeth M.},
  journal   = {Journal of molecular biology},
  title     = {The type I restriction endonuclease EcoR124I, couples ATP hydrolysis to bidirectional DNA translocation.},
  year      = {2005},
  pages     = {837--59},
  volume    = {352},
  abstract  = {Type I restriction endonuclease holoenzymes contain methylase (M), restriction (R) and specificity (S) subunits, present in an M2:R2:S1 stoichiometry. These enzymes bind to specific DNA sequences and translocate dsDNA in an ATP-dependent manner toward the holoenzyme anchored at the recognition sequence. Once translocation is impeded, DNA restriction, which functions to protect the host cell from invading DNA, takes place. Translocation and DNA cleavage are afforded by the two diametrically opposed R-subunits. To gain insight into the mechanism of translocation, a detailed characterization of the ATPase activity of EcoR124I was done. Results show that following recognition sequence binding, ATP hydrolysis-coupled, bidirectional DNA translocation by EcoR124I ensues, with the R-subunits transiently disengaging, on average, every 515 bp. Macroscopic processivity of 2031(+/-184)bp is maintained, as the R-subunits remain in close proximity to the DNA through association with the methyltransferase. Transient uncoupling of ATP hydrolysis from translocation results in 3.1(+/-0.4) ATP molecules being hydrolyzed per base-pair translocated per R-subunit. This is the first clear demonstration of the coupling of ATP hydrolysis to dsDNA translocation, albeit inefficient. Once translocation is impeded on supercoiled DNA, the DNA is cleaved. DNA cleavage inactivates the EcoR124I holoenzyme partially and reversibly, which explains the stoichiometric behaviour of type I restriction enzymes. Inactivated holoenzyme remains bound to the DNA at the recognition sequence and immediately releases the nascent ends. The release of nascent ends was demonstrated using a novel, fluorescence-based, real-time assay that takes advantage of the ability of the Escherichia coli RecBCD enzyme to unwind restricted dsDNA. The resulting unwinding of EcoR124I-restricted DNA by RecBCD reveals coordination between the restriction-modification and recombination systems that functions to destroy invading DNA efficiently. In addition, we demonstrate the displacement of EcoR124I following DNA cleavage by the translocating RecBCD enzyme, resulting in the restoration of catalytic function to EcoR124I.},
  file      = {:by-author/B/Bianco/2005_Bianco_837.pdf:PDF},
  keywords  = {TypeI},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Bianco1998,
  author           = {Piero R. Bianco and Robert B. Tracy and Stephen C. Kowalczykowski},
  journal          = {Frontiers in Bioscience},
  title            = {DNA strand exchange proteins: a biochemical and physical comparison},
  year             = {1998},
  pages            = {d570-603},
  volume           = {3},
  creationdate     = {2008-07-28T00:00:00},
  doi              = {10.2741/a304},
  file             = {:by-author/B/Bianco/1998_Bianco_d570.pdf:PDF},
  modificationdate = {2023-04-23T10:44:09},
  owner            = {saulius},
  timestamp        = {2008.07.28},
}

@Article{Bickel2012,
  author     = {Bickel, David R.},
  journal    = {Communications in Statistics - Theory and Methods},
  title      = {Coherent Frequentism: A Decision Theory Based on Confidence Sets},
  year       = {2012},
  issn       = {0361-0926},
  pages      = {1478--1496},
  volume     = {41},
  abstract   = {By representing fair betting odds according to one or more pairs of confidence set estimators, dual parameter distributions called confidence posteriors secure the coherence of actions without any prior distribution. This theory reduces to the maximization of expected utility when the pair of posteriors is induced by an exact or approximate confidence set estimator or when a reduction rule is applied to the pair. Unlike the p-value, the confidence posterior probability of an interval hypothesis is suitable as an estimator of the indicator of hypothesis truth since it converges to 1 if the hypothesis is true or to 0 otherwise.},
  doi        = {10.1080/03610926.2010.543302},
  file       = {Bickel - 2012 - Coherent Frequentism A Decision Theory Based on C.pdf:by-author/B/Bickel/2012_Bickel_1478.pdf:PDF;Snapshot:by-author/B/Bickel/2012_Bickel_1478.html:URL},
  groups     = {sg/Frequentist},
  owner      = {saulius},
  shorttitle = {Coherent {Frequentism}},
  timestamp = {2015.12.07},
  creationdate = {2015-12-07T00:00:00},
  url        = {http://dx.doi.org/10.1080/03610926.2010.543302},
  urldate    = {2015-12-07},
}

@Manuscript{Biddle2002,
  author    = {Peter Biddle and Paul England and Marcus Peinado and Bryan Willman},
  title     = {The Darknet and the Future of Content Distribution},
  year      = {2002},
  keywords  = {Computer Science (CS)},
  abstract  = {We investigate the darknet – a collection of networks and technologies used to share digital content. The darknet is not a separate physical network but an application and protocol layer riding on existing networks. Examples of darknets are peer-to-peer file sharing, CD and DVD copying, and key or password sharing on email and newsgroups. The last few years have seen vast increases in the darknet’s aggregate bandwidth, reliability, usability, size of shared library, and availability of search engines. In this paper we categorize and analyze existing and future darknets, from both the technical and legal perspectives. We speculate that there will be short-term impediments to the effectiveness of the darknet as a distribution mechanism, but ultimately the darknet-genie will not be put back into the bottle. In view of this hypothesis, we examine the relevance of content protection and content distribution architectures.},
  file      = {:by-author/B/Biddle/2002_Biddle.doc:DOC},
  owner     = {saulius},
  timestamp = {2015.02.28},
  creationdate = {2015-02-28T00:00:00},
}

@Article{Bienfait2013,
  author    = {Bienfait, Bruno and Ertl, Peter},
  journal   = {Journal of Cheminformatics},
  title     = {JSME: a free molecule editor in JavaScript},
  year      = {2013},
  issn      = {1758-2946},
  pages     = {24},
  volume    = {5},
  abstract  = {BACKGROUND:A molecule editor, i.e. a program facilitating graphical input and interactive editing of molecules, is an indispensable part of every cheminformatics or molecular processing system. Today, when a web browser has become the universal scientific user interface, a tool to edit molecules directly within the web browser is essential. One of the most popular tools for molecular structure input on the web is the JME applet. Since its release nearly 15years ago, however the web environment has changed and Java applets are facing increasing implementation hurdles due to their maintenance and support requirements, as well as security issues. This prompted us to update the JME editor and port it to a modern Internet programming language - JavaScript.SUMMARY:The actual molecule editing Java code of the JME editor was translated into JavaScript with help of the Google Web Toolkit compiler and a custom library that emulates a subset of the GUI features of the Java runtime environment. In this process, the editor was enhanced by additional functionalities including a substituent menu, copy/paste, drag and drop and undo/redo capabilities and an integrated help. In addition to desktop computers, the editor supports molecule editing on touch devices, including iPhone, iPad and Android phones and tablets. In analogy to JME the new editor is named JSME. This new molecule editor is compact, easy to use and easy to incorporate into web pages.CONCLUSIONS:A free molecule editor written in JavaScript was developed and is released under the terms of permissive BSD license. The editor is compatible with JME, has practically the same user interface as well as the web application programming interface. The JSME editor is available for download from the project web page http://peter-ertl.com/jsme/ webcite},
  doi       = {10.1186/1758-2946-5-24},
  file      = {2013_Bienfait_24.pdf:by-author/B/Bienfait/2013_Bienfait_24.pdf:PDF},
  keywords  = {Chemoinformatics; JavaScript; Molecule Editor},
  owner     = {saulius},
  pubmedid  = {23694746},
  timestamp = {2014.05.22},
  creationdate = {2014-05-22T00:00:00},
  url       = {http://www.jcheminf.com/content/5/1/24},
}

@Article{Biernacki2003,
  author     = {Biernacki, Christophe and Celeux, Gilles and Govaert, G{\'e}rard},
  journal    = {Comput. Stat. Data Anal.},
  title      = {Choosing starting values for the {EM} algorithm for getting the highest likelihood in multivariate {G}aussian mixture models},
  year       = {2003},
  issn       = {0167-9473},
  pages      = {561--575},
  volume     = {41},
  abstract   = {Simple methods to choose sensible starting values for the EM algorithm to get maximum likelihood parameter estimation in mixture models are compared. They are based on random initialization, using a classification EM algorithm (CEM), a Stochastic EM algorithm (SEM) or previous short runs of EM itself. Those initializations are included in a search/run/select strategy which can be compounded by repeating the three steps. They are compared in the context of multivariate Gaussian mixtures on the basis of numerical experiments on both simulated and real data sets in a target number of iterations. The main conclusions of those numerical experiments are the following. The simple random initialization which is probably the most employed way of initiating EM is often outperformed by strategies using CEM, SEM or shorts runs of EM before running EM. Also, it appears that compounding is generally profitable since using a single run of EM can often lead to suboptimal solutions. Otherwise, none of the experimental strategies can be regarded as the best one and it is difficult to characterize situations where a particular strategy can be expected to outperform the other ones. However, the strategy initiating EM with short runs of EM can be recommended. This strategy, which as far as we know was not used before the present study, has some advantages. It is simple, performs well in a lot of situations presupposing no particular form of the mixture to be fitted to the data and seems little sensitive to noisy data.},
  doi        = {10.1016/S0167-9473(02)00163-9},
  file       = {:by-author/B/Biernacki/2003_Biernacki_561.ps:PostScript},
  issue_date = {28 January 2003},
  keywords   = {Expectation Maximisation; Gaussian Mixture Models},
  owner      = {andrius},
  publisher  = {Elsevier Science Publishers B. V.},
  timestamp = {2013.03.26},
  creationdate = {2013-03-26T00:00:00},
}

@Article{Biesel1977,
  author           = {Biesel, H. R.},
  journal          = {Chromatographia},
  title            = {Recursive Calculation of the Standard Deviation with Increased Accuracy},
  year             = {1977},
  pages            = {173--175},
  volume           = {10},
  abstract         = {When calculating the standard deviation of a series of measured data the analyst often underestimates the influence of rounding errors that lead to wrong results. This paper presents a procedure which avoids this disadvantage, being especially suitable for use in minicomputers.},
  creationdate     = {2008-07-28T00:00:00},
  doi              = {10.1007/bf02262936},
  file             = {1977_Biesel_173.pdf:by-author/B/Biesel/1977_Biesel_173.pdf:PDF},
  keywords         = {Mathematics; On-line Calculations; Recursive Statistic; Standard Deviation},
  modificationdate = {2023-04-23T10:45:56},
  owner            = {saulius},
  timestamp        = {2008.07.28},
}

@Lecture{Biesiadka2004,
  author    = {J. Biesiadka and B. Loll and J. Kern and K.-D. Irrgang and P. Jordan and N. Krauss and P. Fromme and H. T. Witt and W. Saenger and A. Zouni},
  title     = {Crystal Structures of Cyanobacterial Photosystems I and II},
  year      = {2004},
  abstract  = {Oxygenic photosynthesis in plants, green algae and cyanobacteria is performed by photosystems I and II (PSI and PSII) embedded in the thylakoid membrane. They function in series, PSII oxidizing water to molecular (atmospheric) O2, H+ and electrons; the latter are transferred to PSI and from there via ferredoxin to NADP-reductase to provide NADPH+. The H+ released at PSII form a pH- gradient over the thylakoid membrane that drives ATP synthetase. ATP and NADH+ serve in dark reactions to reduce CO2 to carbohydrates. PSI and PSII from Synechococcus elongatus were solubilized from the thylakoid membrane using dodecylmaltoside as detergent and crystallized; they are fully active in the crystals. X-ray diffraction data were collected at synchrotrons DESY/Hamburg, ESRF/Grenoble, LURE/Paris and the structures determined at 2.5 Angstrom (PSI [1]) and 3.2 Angstrom (PSII [2]) resolution. In PSI, the amino acid sequences of the 12 polypeptides were fitted to the electron density, and 96 chlorophyll a, two phylloquinones, three Fe4S4 clusters, 22 carotenoids and four lipid molecules could be located. In PSII, 12 of the 17 subunits were identified in the electron density and the Mn-Cluster has been located (where water oxidation occurs) as well as 31 chlorophyll a, 4 Fe2+, plastoquinone QA, two pheophytins and one carotenoid. Of particular interest is the architecture of the electron transfer chains including the chlorophyll a "special pairs" P680 (PSII) and P700 (PSI). They are at the heart of the photosystems and drive photosynthesis, fueled by photons from sunlight that is collected by large antenna systems containing chlorophyll a and carotenoids. Acknowledgements to DFG-Sonderforschungsb- ereich 312 and 498 and Fonds der Chemischen Industrie. We are grateful for synchrotron beam time.},
  file      = {:by-author/B/Biesiadka/2004_Biesiadka_59.pdf:PDF},
  keywords  = {Obzor; Review},
  owner     = {em},
  pages     = {59},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Manuscript{Bihlmayer2007,
  author    = {Gustav Bihlmayer},
  title     = {Electronic structure of matter: Basics and DFT},
  year      = {2007},
  keywords  = {Density Functional Theory (DFT)},
  url       = {http://iffwww.iff.kfa-juelich.de/~gbihl/publ/iff_2007.pdf},
  file      = {2007_Bihlmayer_A3.pdf:by-author/B/Bihlmayer/2007_Bihlmayer_A3.pdf:PDF},
  owner     = {saulius},
  timestamp = {2014.04.15},
  creationdate = {2014-04-15T00:00:00},
}

@Manual{Bihorel2012,
  title     = {Package ‘neldermead’},
  author    = {Sebastien Bihorel},
  year      = {2012},
  file      = {:by-author/B/Bihorel/2012_Bihorel.pdf:PDF},
  keywords  = {Computer Science (CS); Minimisation; Simplex Method},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Bilan2012,
  author    = {Bilan, S. and Zotti, L. A. and Pauly, F. and Cuevas, J. C.},
  journal   = {Phys. Rev. B},
  title     = {Theoretical study of the charge transport through C${}_{60}$-based single-molecule junctions},
  year      = {2012},
  pages     = {205403},
  volume    = {85},
  doi       = {10.1103/PhysRevB.85.205403},
  file      = {2012_Bilan_205403.pdf:by-author/B/Bilan/2012_Bilan_205403.pdf:PDF},
  issue     = {20},
  keywords  = {Density Functional Theory (DFT); Single Molecule Switches},
  numpages  = {9},
  owner     = {saulius},
  publisher = {American Physical Society},
  timestamp = {2014.10.21},
  creationdate = {2014-10-21T00:00:00},
  url       = {http://link.aps.org/doi/10.1103/PhysRevB.85.205403},
}

@Article{Bindzus2014,
  author    = {Bindzus, Niels and Straasø, Tine and Wahlberg, Nanna and Becker, Jacob and Bjerg, Lasse and Lock, Nina and Dippel, Ann Christin and Iversen, Bo B.},
  journal   = {Acta crystallographica. Section A, Foundations and advances},
  title     = {Experimental determination of core electron deformation in diamond.},
  year      = {2014},
  pages     = {39--48},
  volume    = {70},
  abstract  = {Synchrotron powder X-ray diffraction data are used to determine the core electron deformation of diamond. Core shell contraction inherently linked to covalent bond formation is observed in close correspondence with theoretical predictions. Accordingly, a precise and physically sound reconstruction of the electron density in diamond necessitates the use of an extended multipolar model, which abandons the assumption of an inert core. The present investigation is facilitated by negligible model bias in the extraction of structure factors, which is accomplished by simultaneous multipolar and Rietveld refinement accurately determining an atomic displacement parameter (ADP) of 0.00181 (1) Å(2). The deconvolution of thermal motion is a critical step in experimental core electron polarization studies, and for diamond it is imperative to exploit the monatomic crystal structure by implementing Wilson plots in determination of the ADP. This empowers the electron-density analysis to precisely administer both the deconvolution of thermal motion and the employment of the extended multipolar model on an experimental basis.},
  doi       = {10.1107/S2053273313026600},
  file      = {:by-author/B/Bindzus/2014_Bindzus_39.pdf:PDF},
  owner     = {saulius},
  timestamp = {2014.03.23},
  creationdate = {2014-03-23T00:00:00},
}

@InProceedings{Bingham2001,
  author    = {Bingham, Ella and Mannila, Heikki},
  booktitle = {Proceedings of the seventh ACM SIGKDD international conference on Knowledge discovery and data mining},
  title     = {Random projection in dimensionality reduction: applications to image and text data},
  year      = {2001},
  pages     = {245--250},
  abstract  = {Random projections have recently emerged as a powerful method for dimensionality reduction. Theoretical results indicate that the method preserves distances quite nicely; however, empirical results are sparse. We present experimental results on using random projection as a dimensionality reduction tool in a number of cases, where the high dimensionality of the data would otherwise lead to burdensome computations. Our application areas are the processing of both noisy and noiseless images, and information retrieval in text documents. We show that projecting the data onto a random lower-dimensional subspace yields results comparable to conventional dimensionality reduction methods such as principal component analysis: the similarity of data vectors is preserved well under random projection. However, using random projections is computationally significantly less expensive than using, e.g., principal component analysis. We also show experimentally that using a sparse random matrix gives additional computational savings in random projection.},
  doi       = {10.1145/502512.502546},
  file      = {:by-author/B/Bingham/sigmod97.ps:PostScript;:by-author/B/Bingham/2001_Bingham_245.pdf:PDF},
  isbn      = {1-58113-391-X},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://doi.acm.org/10.1145/502512.502546},
}

@Manuscript{Binmore2006,
  author    = {Ken Binmore},
  title     = {Rational Decisions in Large Worlds},
  year      = {2006},
  keywords  = {Bayesian Statistics; Criticism},
  url       = {http://else.econ.ucl.ac.uk/papers/uploaded/266.pdf},
  abstract  = {This paper argues that we need to look beyond Bayesian decision theory for an answer to the general problem of making rational decisions under uncertainty. The view that Bayesian decision theory is only genuinely valid in a small world was asserted very firmly by Leonard Savage [18] when laying down the principles of the theory in his path-breaking Foundations of Statistics. He makes the distinction between small and large worlds in a folksy way by quoting the proverbs ”Look before you leap” and ”Cross that bridge when you come to it”. You are in a small world if it is feasible always to look before you leap. You are in a large world if there are some bridges that you cannot cross before you come to them.},
  file      = {2006_Binmore.pdf:by-author/B/Binmore/2006_Binmore.pdf:PDF},
  groups    = {sg/Bayesian},
  owner     = {saulius},
  timestamp = {2012.10.04},
  creationdate = {2012-10-04T00:00:00},
}

@Article{Biradha2002,
  author    = {Biradha, Kumar and Fujita, Makoto},
  journal   = {Angew. Chem. Int. Ed.},
  title     = {A Springlike 3D-Coordination Network That Shrinks or Swells in a Crystal-to-Crystal Manner upon Guest Removal or Readsorption},
  year      = {2002},
  issn      = {1521-3773},
  month     = {Sep},
  number    = {18},
  pages     = {3392--3395},
  volume    = {41},
  doi       = {10.1002/1521-3773(20020916)41:18<3392::aid-anie3392>3.0.co;2-v},
  file      = {2002_Biradha_3392.pdf:by-author/B/Biradha/2002_Biradha_3392.pdf:PDF},
  groups    = {sg/Crystal sponges, sg/Crystallisation, sg/MOF, sg/MOFs, am/MOFs},
  keywords  = {Chemical Crystalography; Crystallography; Porous Materials; X-ray Crystallography},
  owner     = {saulius},
  publisher = {Wiley-Blackwell},
  timestamp = {2016.05.14},
  creationdate = {2016-05-14T00:00:00},
  url       = {http://dx.doi.org/10.1002/1521-3773(20020916)41:18<3392::AID-ANIE3392>3.0.CO;2-V},
}

@Article{Birner2004,
  author           = {Birner, Peter and Preusser, Matthias and Gelpi, Ellen and Berger, Johannes and Gatterbauer, Brigitte and Ambros, Inge M and Ambros, Peter F and Acker, Till and Plate, Karl H and Harris, Adrian L and Hainfellner, Johannes A},
  journal          = {Clinical cancer research : an official journal of the American Association for Cancer Research},
  title            = {Expression of hypoxia-related tissue factors correlates with diminished survival of adjuvantly treated patients with chromosome 1p aberrant oligodendroglial neoplasms and therapeutic implications.},
  year             = {2004},
  pages            = {6567--71},
  volume           = {10},
  creationdate     = {2008-07-28T00:00:00},
  doi              = {10.1158/1078-0432.ccr-04-0617},
  file             = {2004_Birner_6567.pdf:by-author/B/Birner/2004_Birner_6567.pdf:PDF},
  groups           = {sg/cancer, sg/medicine},
  keywords         = {CA14; Carbonic Anhydrases},
  modificationdate = {2023-04-23T10:46:27},
  owner            = {saulius},
  timestamp        = {2008.07.28},
}

@Conference{Bish2013,
  author    = {D.L. Bish and D.F. Blake and D.T. Vaniman and S.J. Chipera and P. Sarrazin and R.V. Morris and D.W. Ming and A.H. Treiman and R.T. Downs and C. Achilles and S. Morrison and A. Yen and T. Bristow and J. Morookian and J. Farmer and J. Crisp and E. Rampe and E. Stolper and D. Des Marais and N. Spanovich and R. Anderson and {the MSL Science Team}},
  booktitle = {44th Lunar and Planetary Science Conference},
  title     = {First X-ray diffraction results from Mars science laboratory: mineralogy of Rocknest aeolian bedform at Gale crater.},
  year      = {2013},
  pages     = {1111},
  abstract  = {Numerous orbital and landed obser- vations of the martian surface suggest a reasonably uniform martian soil composition, likely as a result of global aeolian mixing [1, 2]. Chemical data for martian soils are abundant [e.g., 2, 3], and phase information has been provided by lander thermal emission and Mössbauer spectroscopic measurements [3, 4, 5, 6]. However, until now no X-ray diffraction (XRD) data were available for martian soil nor has XRD ever been used on another body apart from Earth. XRD is gener- ally considered the most definitive method for deter- mining the crystalline phases in solid samples, and it is the method of choice for determining mineralogy. CheMin’s first XRD analysis on Mars coincided with the 100th anniversary of the discovery of X-ray diffrac- tion by von Laue. Curiosity delivered scooped samples of loose, un- consolidated material (“soil”) acquired from an aeolian bedform at the Rocknest locality to instruments in the body of the rover (the laboratory). Imaging shows that the soil has a range of particle sizes, of 1-2 mm and smaller, presumably representing contributions from global, regional, and local sources.},
  file      = {:by-author/B/Bish/2013_Bish_1111.pdf:PDF},
  owner     = {saulius},
  timestamp = {2013.09.19},
  creationdate = {2013-09-19T00:00:00},
}

@Article{Bissantz2010,
  author    = {Bissantz, Caterina and Kuhn, Bernd and Stahl, Martin},
  journal   = {Journal of Medicinal Chemistry},
  title     = {A Medicinal Chemist’s Guide to Molecular Interactions},
  year      = {2010},
  pages     = {5061--5084},
  volume    = {53},
  abstract  = {Molecular recognition in biological systems relies on the existence of specific attractive interactions between two partner molecules. Structure-based drug design seeks to identify and optimize such interactions between ligands and their host molecules, typically proteins, given their three-dimensional structures. This optimization process requires knowledge about interaction geometries and approximate affinity contributions of attractive interactions that can be gleaned from crystal structure and associated affinity data. Here we compile and review the literature on molecular interactions as it pertains to medicinal chemistry through a combination of careful statistical analysis of the large body of publicly available X-ray structure data and experimental and theoretical studies of specific model systems. We attempt to extract key messages of practical value and complement references with our own searches of the CSDa,(1)},
  doi       = {10.1021/jm100112j},
  eprint    = {http://pubs.acs.org/doi/pdf/10.1021/jm100112j},
  file      = {2010_Bissantz_5061errata.pdf:by-author/B/Bissantz/2010_Bissantz_5061errata.pdf:PDF;2010_Bissantz_5061.pdf:by-author/B/Bissantz/2010_Bissantz_5061.pdf:PDF},
  keywords  = {Bioinformatics; Chemoinformatics; Drug Design},
  owner     = {saulius},
  timestamp = {2013.04.11},
  creationdate = {2013-04-11T00:00:00},
  url       = {http://pubs.acs.org/doi/abs/10.1021/jm100112j},
}

@Article{Bist2001,
  author    = {Bist, P. and Sistla, S. and Krishnamurthy, V. and Acharya, A. and Chandrakala, B. and Rao, D. N.},
  journal   = {Journal of molecular biology},
  title     = {S-adenosyl-L-methionine is required for DNA cleavage by type III restriction enzymes.},
  year      = {2001},
  pages     = {93--109},
  volume    = {310},
  abstract  = {The requirement of S-adenosyl-L-methionine (AdoMet) in the cleavage reaction carried out by type III restriction-modification enzymes has been investigated. We show that DNA restriction by EcoPI restriction enzyme does not take place in the absence of exogenously added AdoMet. Interestingly, the closely related EcoP15I enzyme has endogenously bound AdoMet and therefore does not require the addition of the cofactor for DNA cleavage. By employing a variety of AdoMet analogs, which differ structurally from AdoMet, this study demonstrates that the carboxyl group and any substitution at the epsilon carbon of methionine is absolutely essential for DNA cleavage. Such analogs could bring about the necessary conformational change(s) in the enzyme, which make the enzyme proficient in DNA cleavage. Our studies, which include native polyacrylamide gel electrophoresis, molecular size exclusion chromatography, UV, fluorescence and circular dichroism spectroscopy, clearly demonstrate that the holoenzyme and apoenzyme forms of EcoP15I restriction enzyme have different conformations. Furthermore, the Res and Mod subunits of the EcoP15I restriction enzyme can be separated by gel filtration chromatography in the presence of 2 M NaCl. Reconstitution experiments, which involve mixing of the isolated subunits, result in an apoenzyme form, which is restriction proficient in the presence of AdoMet. However, mixing the Res subunit with Mod subunit deficient in AdoMet binding does not result in a functional restriction enzyme. These observations are consistent with the fact that AdoMet is required for DNA cleavage. In vivo complementation of the defective mod allele with a wild-type mod allele showed that an active restriction enzyme could be formed. Furthermore, we show that while the purified c2-134 mutant restriction enzyme is unable to cleave DNA, the c2-440 mutant enzyme is able to cleave DNA albeit poorly. Taken together, these results suggest that AdoMet binding causes conformational changes in the restriction enzyme and is necessary to bring about DNA cleavage.},
  file      = {:by-author/B/Bist/2001_Bist_93.pdf:PDF},
  keywords  = {TypeIII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Biswas1999,
  author    = {Biswas, E. E. and Biswas, S. B.},
  journal   = {Biochemistry},
  title     = {Mechanism of DnaB helicase of Escherichia coli: structural domains involved in ATP hydrolysis, DNA binding, and oligomerization.},
  year      = {1999},
  pages     = {10919--28},
  volume    = {38},
  abstract  = {We describe the delineation of three distinct structural domains of the DnaB helicase of Escherichia coli: domain alpha, amino acid residues (aa) 1-156; domain beta, aa 157-302; and domain gamma, aa 303-471. Using mutants with deletion in these domains, we have examined their role(s) in hexamer formation, DNA-dependent ATPase, and DNA helicase activities. The mutant DnaBbetagamma protein, in which domain alpha was deleted, formed a hexamer; whereas the mutant DnaBalphabeta, in which domain gamma was deleted, could form only dimers. The dimerization of DnaBalphabeta was Mg(2+) dependent. These data suggest that the oligomerization of DnaB helicase involves at least two distinct protein-protein interaction sites; one of these sites is located primarily within domain beta (site 1), while the other interaction site is located within domain gamma (site 2). The mutant DnaBbeta, a polypeptide of 147 aa, where both domains alpha and gamma were deleted, displayed a completely functional ATPase activity. This domain, thus, constitutes the "central catalytic domain" for ATPase activity. The ATPase activity of DnaBalphabeta was kinetically comparable to that of DnaBbeta, indicating that domain alpha had little or no influence on the ATPase activity. In both cases, the ATPase activities were DNA independent. DnaBbetagamma had a DNA-dependent ATPase activity that was kinetically comparable to the ATPase activity of wild-type DnaB protein (wtDnaB), indicating a specific role for C-terminal domain gamma in enhancement of the ATPase activity of domain beta as well as in DNA binding. Mutant DnaBbetagamma, which lacked domain alpha, was devoid of any helicase activity pointing to a significant role for domain alpha. The major findings of this study are (i) domain beta contained a functional ATPase active site; (ii) domain gamma appeared to be the DNA binding domain and a positive regulator of the ATPase activity of domain beta; (iii) although domain alpha did not have any significant effect on the ATPase, DNA binding activities, or hexamer formation, it definitely plays a pivotal role in transducing the energy of ATP hydrolysis to DNA unwinding by the hexamer; and (iv) all three domains are required for helicase activity.},
  file      = {:by-author/B/Biswas/1999_Biswas_10919.pdf:PDF},
  keywords  = {{gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Bitinaite2002,
  author    = {Bitinaite, Jurate and Schildkraut, Ira},
  journal   = {Proceedings of the National Academy of Sciences of the United States of America},
  title     = {Self-generated DNA termini relax the specificity of SgrAI restriction endonuclease.},
  year      = {2002},
  pages     = {1164--9},
  volume    = {99},
  abstract  = {The primary target of SgrAI restriction endonuclease is a multiple sequence of the form 5'-CPu/CCGGPyG. Previous work had indicated that SgrAI must bind two recognition sites simultaneously for catalysis [Bilcock, D. T., Daniels, L. E., Bath, A. J. &amp; Halford, S. E. (1999) J. Biol. Chem. 274, 36379-36386]. In the present study, SgrAI is shown to cleave not only its canonical sequences, but also the sequences 5'-CPuCCGGPy(A,T,C) and 5'-CPuCCGGGG, both referred to as secondary sequences. On plasmid pSK7, SgrAI cleaves secondary sites 26-fold slower than the canonical site. However, the same plasmid, but without the canonical site, is cleaved 200-fold slower. We show that DNA termini generated by cleaving the canonical site for SgrAI assist in the cleavage of secondary sites. The SgrAI-termini in cis with respect to secondary site are markedly preferred over those in trans. The SgrAI-termini provided in a form of oligonucleotide duplex are also shown to stimulate canonical site cleavage. At a 40-fold molar excess of the SgrAI-termini over substrate, the SgrAI specificity is shown to improve by two orders of magnitude, because of concurrent 10-fold increase in the cleavage of canonical site and 50-fold decrease in the cleavage of secondary sites. The unconventional reaction pathway by which SgrAI utilizes the self-generated DNA termini to cleave its DNA targets has not been observed hitherto among type II restriction endonucleases. Based on our work and previous reports, a pathway of DNA binding and cleavage by the SgrAI restriction endonuclease is proposed.},
  file      = {:by-author/B/Bitinaite/2002_Bitinaite_1164.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Bittner1979,
  author    = {Bittner, M. and Burke, R. L. and Alberts, B. M.},
  journal   = {The Journal of biological chemistry},
  title     = {Purification of the T4 gene 32 protein free from detectable deoxyribonuclease activities.},
  year      = {1979},
  pages     = {9565--72},
  volume    = {254},
  abstract  = {Detailed procedures are presented which allow reproducible preparation of T4 gene 32 protein, a helix-destabilizing protein essential for DNA replication and genetic recombination in T4 bacteriophage-infected Escherichia coli cells. Although 32 protein can be purified to better than 99% homogeneity by any one of several procedures, these methods have been developed to remove trace amounts of contaminating deoxyribonucleases, which are present in high levels in the original infected cells. Two alternative preparations are presented, each involving three chromatographic steps. Both 32 proteins obtained are essentially "nuclease-free," when tested at physiological salt concentrations. However, we show here that the phenyl-Sepharose chromatography step, which is necessary to remove an exonuclease activity active only at low salt concentrations, also removes a second protein present in trace amounts. In some cases, retention of this second protein is desirable, since it is essential for obtaining RNA primed, de novo DNA chain starts in an in vitro DNA replication system, when this system is constructed by mixing highly purified preparations of each of the six replication proteins coded for by T4 genes 32, 43, 44, 62, 45, and 41.},
  file      = {:by-author/B/Bittner/1979_Bittner_9565.pdf:PDF},
  keywords  = {Solid-state Batteries (SSB); {gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Bjoerkman2012,
  author    = {T Björkman and A Gulans and A V Krasheninnikov and R M Nieminen},
  journal   = {Journal of Physics: Condensed Matter},
  title     = {Are we van der Waals ready?},
  year      = {2012},
  pages     = {424218},
  volume    = {24},
  abstract  = {We apply a range of density-functional-theory-based methods capable of describing van der Waals interactions with weakly bonded layered solids in order to investigate their accuracy for extended systems. The methods under investigation are the local-density approximation, semi-empirical force fields, non-local van der Waals density functionals and the random-phase approximation. We investigate the equilibrium geometries, elastic constants and binding energies of a large and diverse set of compounds and arrive at conclusions about the reliability of the different methods. The study also points to some directions of further development for the non-local van der Waals density functionals.},
  doi       = {10.1088/0953-8984/24/42/424218},
  file      = {:by-author/B/Bjorkman/2012_Bjorkman_424218.pdf:PDF},
  groups    = {sg/Crystal structure prediction},
  keywords  = {COD Deposition; Crystal Structure Prediction (CSP); Density Functional Theory (DFT)},
  owner     = {saulius},
  timestamp = {2013.04.12},
  creationdate = {2013-04-12T00:00:00},
  url       = {http://stacks.iop.org/0953-8984/24/i=42/a=424218},
}

@Article{Blochl1994,
  author    = {Bl\"ochl, Peter E. and Jepsen, O. and Andersen, O. K.},
  journal   = {Phys. Rev. B},
  title     = {Improved tetrahedron method for {Brillouin-zone} integrations},
  year      = {1994},
  pages     = {16223--16233},
  volume    = {49},
  doi       = {10.1103/PhysRevB.49.16223},
  file      = {:by-author/B/Blöchl/1994_Blöchl_16223.pdf:PDF},
  issue     = {23},
  keywords  = {Density Functional Theory (DFT)},
  numpages  = {0},
  owner     = {andrius},
  publisher = {American Physical Society},
  timestamp = {2015.05.07},
  creationdate = {2015-05-07T00:00:00},
  url       = {http://link.aps.org/doi/10.1103/PhysRevB.49.16223},
}

@Article{Black2007,
  author    = {Black, Andrew P. and Hutchinson, Norman C. and Jul, Eric and Levy, Henry M.},
  journal   = {Proceedings of the third ACM SIGPLAN conference on History of programming languages 2007},
  title     = {The Development of the Emerald Programming Language},
  year      = {2007},
  pages     = {11-1--11-51},
  abstract  = {Emerald is an object-based programming language and system designed and implemented in the Department of Computer Science at the University of Washington in the early and mid-1980s. The goal of Emerald was to simplify the construction of distributed applications. This goal was reflected at every level of the system: its object structure, the programming language design, the compiler implementation, and the run-time support. This paper describes the origins of the Emerald group, the forces that formed the language, the influences that Emerald has had on subsequent distributed systems and programming languages, and some of Emerald's more interesting technical innovations.},
  doi       = {10.1145/1238844.1238855},
  file      = {:by-author/B/Black/2007_Black_11.pdf:PDF},
  keywords  = {Abstract Types; Call-by-move; Computer Languages; Computer Science (CS); Distributed Programming; Eden; Emerald; Mobility; Object Mobility; Object-oriented Programming; Polymorphism; Remote Object Invocation; Remote Procedure Call; Type Conformity; Washington},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
  url       = {http://doi.acm.org/10.1145/1238844.1238855},
}

@Conference{Blake2013,
  author    = {D.F. Blake and D.L. Bish and R.V. Morris and R.T. Downs and A.H. Treiman and S.M. Morrison and S.J. Chipera and D.W. Ming and A.S. Yen and D.T. Vaniman and J. Grotzinger and J.A. Crisp and C.N. Achilles and E.B. Rampe and T.F. Bristow and P.C. Sarrazin, P. and J.D. Farmer and D.J.~Des Marais and E.M. Stolper and J.M. Morookian and M.A. Wilson and N. Spanovich and R.C. Anderson and {the~MSL~Science Team}},
  booktitle = {44th Lunar and Planetary Science Conference},
  title     = {Mineralogy and elemental composition of wind drift soil at Rocknest, Gale crater},
  year      = {2013},
  pages     = {1289},
  file      = {:by-author/B/Blake/2013_Blake_1289.pdf:PDF},
  owner     = {saulius},
  timestamp = {2013.09.19},
  creationdate = {2013-09-19T00:00:00},
}

@Article{Blanc2004,
  author    = {Blanc, E. and Roversi, P. and Vonrhein, C. and Flensburg, C. and Lea, S. M. and Bricogne, G.},
  journal   = {Acta Crystallographica Section D},
  title     = {Refinement of severely incomplete structures with maximum likelihood in {\it BUSTER{--}TNT}},
  year      = {2004},
  pages     = {2210--2221},
  volume    = {60},
  doi       = {10.1107/S0907444904016427},
  file      = {ba5067.pdf:by-author/B/Blanc/2004_Blanc_2210.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444904016427},
}

@Article{Blanchet2013,
  author    = {Blanchet, Clement E. and Svergun, Dmitri I.},
  journal   = {Annu. Rev. Phys. Chem.},
  title     = {Small-Angle X-Ray Scattering on Biological Macromolecules and Nanocomposites in Solution},
  year      = {2013},
  pages     = {37–54},
  volume    = {64},
  abstract  = {Small-angle X-ray scattering (SAXS) is a powerful method to study the structural properties of materials at the nanoscale. Recent progress in in- strumentation and analysis methods has led to rapidly growing applications of this technique for the characterization of biological macromolecules in solution. Ab initio and rigid-body modeling methods allow one to build three-dimensional, low-resolution models from SAXS data. With the new approaches, oligomeric states of proteins and macromolecular complexes can be assessed, chemical equilibria and kinetic reactions can be studied, and even flexible objects such as intrinsically unfolded proteins can be quanti- tatively characterized. This review describes the analysis methods of SAXS data from macromolecular solutions, ranging from the computation of over- all structural parameters to advanced three-dimensional modeling. The ef- ficiency of these methods is illustrated by recent applications to biological macromolecules and nanocomposite particles.},
  file      = {:by-author/B/Blanchet/2013_Blanchet_37.pdf:PDF},
  keywords  = {Ab Initio Methods; Flexible Macromolecules; Macromolecular Structure; Nanostructure; Review; Rigid-body Modeling; SAXS; Synchrotrons},
  owner     = {em},
  timestamp = {2013.10.01},
  creationdate = {2013-10-01T00:00:00},
}

@Article{Blanco2000,
  author    = {Blanco, Alvaro and Chomski, Emmanuel and Grabtchak, Serguei and Ibisate, Marta and John, Sajeev and Leonard, Stephen W. and Lopez, Cefe and Meseguer, Francisco and Miguez, Hernan and Mondia, Jessica P. and Ozin, Geoffrey A. and Toader, Ovidiu and van Driel, Henry M.},
  journal   = {Nature},
  title     = {Large-scale synthesis of a silicon photonic crystal with a complete three-dimensional bandgap near 1.5 micrometres},
  year      = {2000},
  issn      = {0028-0836},
  pages     = {437--440},
  volume    = {405},
  abstract  = {Photonic technology, using light instead of electrons as the information carrier, is increasingly replacing electronics in communication and information management systems. Microscopic light manipulation, for this purpose, is achievable through photonic bandgap materials, a special class of photonic crystals in which three-dimensional, periodic dielectric constant variations controllably prohibit electromagnetic propagation throughout a specified frequency band. This can result in the localization of photons, thus providing a mechanism for controlling and inhibiting spontaneous light emission that can be exploited for photonic device fabrication. In fact, carefully engineered line defects could act as waveguides connecting photonic devices in all-optical microchips, and infiltration of the photonic material with suitable liquid crystals might produce photonic bandgap structures (and hence light-flow patterns) fully tunable by an externally applied voltage. However, the realization of this technology requires a strategy for the efficient synthesis of high-quality, large-scale photonic crystals with photonic bandgaps at micrometre and sub-micrometre wavelengths, and with rationally designed line and point defects for optical circuitry. Here we describe single crystals of silicon inverse opal with a complete three-dimensional photonic bandgap centred on 1.46 m, produced by growing silicon inside the voids of an opal template of close-packed silica spheres that are connected by small 'necks' formed during sintering, followed by removal of the silica template. The synthesis method is simple and inexpensive, yielding photonic crystals of pure silicon that are easily integrated with existing silicon-based microelectronics.},
  copyright = {© 2000 Nature Publishing Group},
  doi       = {10.1038/35013024},
  file      = {Blanco et al. - 2000 - Large-scale synthesis of a silicon photonic crysta.pdf:by-author/B/Blanco/2000_Blanco_437.pdf:PDF;Snapshot:by-author/B/Blanco/2000_Blanco_437.html:URL},
  language  = {en},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://www.nature.com/nature/journal/v405/n6785/abs/405437a0.html},
  urldate   = {2015-08-21},
}

@Article{Blatov2007,
  author           = {Blatov, Vladislav A.},
  journal          = {Acta Crystallographica Section A Foundations of Crystallography},
  title            = {Topological relations between three-dimensional periodic nets. I. Uninodal nets},
  year             = {2007},
  issn             = {0108-7673},
  month            = {Jun},
  number           = {4},
  pages            = {329–343},
  volume           = {63},
  creationdate     = {2017-02-01T00:00:00},
  doi              = {10.1107/s0108767307022088},
  file             = {:by-author/B/Blatov/2007_Blatov_329.pdf:PDF},
  groups           = {sg/MOFs, am/MOFs, sg/MOF},
  keywords         = {Crystal Polymers; Enumeration; Metal-Organic Frameworks (MOF); Nets; Networks; Topology},
  modificationdate = {2022-11-30T18:53:44},
  owner            = {saulius},
  publisher        = {International Union of Crystallography (IUCr)},
  timestamp        = {2017.02.01},
  url              = {http://dx.doi.org/10.1107/S0108767307022088},
}

@Presentation{Blay2004,
  author       = {Sigal Blay},
  title        = {Calling {C} code from {R}. An introduction},
  year         = {2004},
  organization = {Dept. of Statistics and Actuarial Science, Simon Fraser University},
  file         = {2004_Blay_slides.pdf.ppt:by-author/B/Blay/2004_Blay_slides.pdf.ppt:PowerPoint},
  owner        = {andrius},
  timestamp = {2016.12.19},
  creationdate = {2016-12-19T00:00:00},
  url          = {http://www.sfu.ca/~sblay/R-C-interface.ppt},
}

@Article{Bleiholder2008,
  author    = {Bleiholder},
  title     = {Data Fusion},
  year      = {2008},
  file      = {:by-author/B/Bleiholder/2008_Bleiholder.pdf:PDF},
  keywords  = {Aggregation; Computer Science (CS); Databases},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Bleuit2001,
  author    = {Bleuit, J. S. and Xu, H. and Ma, Y. and Wang, T. and Liu, J. and Morrical, S. W.},
  journal   = {Proceedings of the National Academy of Sciences of the United States of America},
  title     = {Mediator proteins orchestrate enzyme-ssDNA assembly during T4 recombination-dependent DNA replication and repair.},
  year      = {2001},
  pages     = {8298--305},
  volume    = {98},
  abstract  = {Studies of recombination-dependent replication (RDR) in the T4 system have revealed the critical roles played by mediator proteins in the timely and productive loading of specific enzymes onto single-stranded DNA (ssDNA) during phage RDR processes. The T4 recombination mediator protein, uvsY, is necessary for the proper assembly of the T4 presynaptic filament (uvsX recombinase cooperatively bound to ssDNA), leading to the recombination-primed initiation of leading strand DNA synthesis. In the lagging strand synthesis component of RDR, replication mediator protein gp59 is required for the assembly of gp41, the DNA helicase component of the T4 primosome, onto lagging strand ssDNA. Together, uvsY and gp59 mediate the productive coupling of homologous recombination events to the initiation of T4 RDR. UvsY promotes presynaptic filament formation on 3' ssDNA-tailed chromosomes, the physiological primers for T4 RDR, and recent results suggest that uvsY also may serve as a coupling factor between presynapsis and the nucleolytic resection of double-stranded DNA ends. Other results indicate that uvsY stabilizes uvsX bound to the invading strand, effectively preventing primosome assembly there. Instead, gp59 directs primosome assembly to the displaced strand of the D loop/replication fork. This partitioning mechanism enforced by the T4 recombination/replication mediator proteins guards against antirecombination activity of the helicase component and ensures that recombination intermediates formed by uvsX/uvsY will efficiently be converted into semiconservative DNA replication forks. Although the major mode of T4 RDR is semiconservative, we present biochemical evidence that a conservative "bubble migration" mode of RDR could play a role in lesion bypass by the T4 replication machinery.},
  file      = {:by-author/B/Bleuit/2001_Bleuit_8298.pdf:PDF},
  keywords  = {Replisoma; {gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@PhdThesis{Blohmann2001,
  author    = {Blohmann},
  school    = {Fakultat der Physik der Ludwig-Maximilians-Universitat Munchen},
  title     = {Spin Representations of the q-Poincare Algebra},
  year      = {2001},
  file      = {:by-author/B/Blohmann/2001_Blohmann_phdthesis.pdf:PDF},
  keywords  = {Mathematics; Spin; Spinors},
  owner     = {saulius},
  pages     = {phdthesis},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Blomgren2000,
  author    = {Blomgren, G. E.},
  journal   = {Nature},
  title     = {Electrochemistry. Making a potential difference.},
  year      = {2000},
  pages     = {681--2},
  volume    = {407},
  file      = {:by-author/B/Blomgren/2000_Blomgren_681.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Bloom2009,
  author    = {Bloom, Linda B.},
  journal   = {DNA repair},
  title     = {Loading clamps for DNA replication and repair.},
  year      = {2009},
  pages     = {570--8},
  volume    = {8},
  abstract  = {Sliding clamps and clamp loaders were initially identified as DNA polymerase processivity factors. Sliding clamps are ring-shaped protein complexes that encircle and slide along duplex DNA, and clamp loaders are enzymes that load these clamps onto DNA. When bound to a sliding clamp, DNA polymerases remain tightly associated with the template being copied, but are able to translocate along DNA at rates limited by rates of nucleotide incorporation. Many different enzymes required for DNA replication and repair use sliding clamps. Clamps not only increase the processivity of these enzymes, but may also serve as an attachment point to coordinate the activities of enzymes required for a given process. Clamp loaders are members of the AAA+ family of ATPases and use energy from ATP binding and hydrolysis to catalyze the mechanical reaction of loading clamps onto DNA. Many structural and functional features of clamps and clamp loaders are conserved across all domains of life. Here, the mechanism of clamp loading is reviewed by comparing features of prokaryotic and eukaryotic clamps and clamp loaders.},
  file      = {:by-author/B/Bloom/2009_Bloom_570.pdf:PDF},
  keywords  = {{gp41} Helicase},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Webpage{Bloomberg2007,
  author    = {Bloomberg, D. S.},
  retrieved = {2016-02-05},
  title     = {Selected Papers on Image Processing and Image Analysis},
  url       = {https://tpgit.github.io/UnOfficialLeptDocs/leptonica/recent-pubs.html},
  language  = {English},
  year      = {2007},
  file      = {2007_Bloomberg.odt:by-author/B/Bloomberg/2007_Bloomberg.odt:OpenDocument text;2007_Bloomberg.pdf:by-author/B/Bloomberg/2007_Bloomberg.pdf:PDF},
  groups    = {sg/Text segmentation, sg/Document processing},
  keywords  = {Image Segmentation; OCR; Text Segmentation},
  owner     = {saulius},
  timestamp = {2016.02.05},
  creationdate = {2016-02-05T00:00:00},
}

@Conference{Bloomberg1996,
  author    = {D. S. Bloomberg},
  booktitle = {SPIE Conf. 2660, Doc. Rec. III},
  title     = {Textured reductions for document image analysis},
  year      = {1996},
  pages     = {160--174},
  file      = {1996_Bloomberg_160.pdf:by-author/B/Bloomberg/1996_Bloomberg_160.pdf:PDF},
  groups    = {sg/Text segmentation},
  keywords  = {Image Segmentation; OCR; Text Segmentation},
  owner     = {saulius},
  timestamp = {2015.05.27},
  creationdate = {2015-05-27T00:00:00},
  url       = {http://leptonica.com/papers/texred.pdf},
}

@Manuscript{Bloomenthal1997,
  author    = {Bloomenthal},
  title     = {Homogeneous Coordinates},
  year      = {1997},
  keywords  = {Computer Graphics; Computer Science (CS); Homogenous Coordinates},
  file      = {:by-author/B/Bloomenthal/1997_Bloomenthal.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Blount2008,
  author           = {Blount, Zachary D. and Borland, Christina Z. and Lenski, Richard E.},
  journal          = {Proceedings of the National Academy of Sciences of the United States of America},
  title            = {Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli.},
  year             = {2008},
  pages            = {7899--906},
  volume           = {105},
  abstract         = {The role of historical contingency in evolution has been much debated, but rarely tested. Twelve initially identical populations of Escherichia coli were founded in 1988 to investigate this issue. They have since evolved in a glucose-limited medium that also contains citrate, which E. coli cannot use as a carbon source under oxic conditions. No population evolved the capacity to exploit citrate for &gt;30,000 generations, although each population tested billions of mutations. A citrate-using (Cit+) variant finally evolved in one population by 31,500 generations, causing an increase in population size and diversity. The long-delayed and unique evolution of this function might indicate the involvement of some extremely rare mutation. Alternately, it may involve an ordinary mutation, but one whose physical occurrence or phenotypic expression is contingent on prior mutations in that population. We tested these hypotheses in experiments that &quot;replayed&quot; evolution from different points in that population's history. We observed no Cit+ mutants among 8.4 x 10(12) ancestral cells, nor among 9 x 10(12) cells from 60 clones sampled in the first 15,000 generations. However, we observed a significantly greater tendency for later clones to evolve Cit+, indicating that some potentiating mutation arose by 20,000 generations. This potentiating change increased the mutation rate to Cit+ but did not cause generalized hypermutability. Thus, the evolution of this phenotype was contingent on the particular history of that population. More generally, we suggest that historical contingency is especially important when it facilitates the evolution of key innovations that are not easily evolved by gradual, cumulative selection.},
  creationdate     = {2012-09-30T00:00:00},
  doi              = {10.1073/pnas.0803151105},
  file             = {:by-author/B/Blount/2008_Blount_7899.pdf:PDF},
  keywords         = {Evolution},
  modificationdate = {2023-08-05T22:32:16},
  owner            = {saulius},
  timestamp        = {2012.09.30},
}

@Article{Blum2007,
  author    = {Blum, Marc-Michael and Koglin, Alexander and Ruterjans, Heinz and Schoenborn, Benno and Langan, Paul and Chen, Julian C.-H.},
  journal   = {Acta Crystallographica Section F},
  title     = {Preliminary time-of-flight neutron diffraction study on diisopropyl fluorophosphatase (DFPase) from Loligo vulgaris},
  year      = {2007},
  pages     = {42–45},
  volume    = {63},
  abstract  = {The enzyme diisopropyl fluorophosphatase (DFPase) from Loligo vulgaris is capable of decontaminating a wide variety of toxic organophosphorus nerve agents. DFPase is structurally related to a number of enzymes, such as the medically important paraoxonase (PON). In order to investigate the reaction mechanism of this phosphotriesterase and to elucidate the protonation state of the active-site residues, large-sized crystals of DFPase have been prepared for neutron diffraction studies. Available H atoms have been exchanged through vapour diffusion against D2O-containing mother liquor in the capillary. A neutron data set has been collected to 2.2 A resolution on a relatively small 3 (0.43 mm ) crystal at the spallation source in Los Alamos. The sample size and asymmetric unit requirements for the feasibility of neutron diffraction studies are summarized.},
  doi       = {10.1107/S1744309106052924},
  file      = {:by-author/B/Blum/2006_Blum_42.pdf:PDF},
  keywords  = {Neutron Crystallography; Neutron Diffraction; Protein Crystallization},
  owner     = {em},
  timestamp = {2014.02.13},
  creationdate = {2014-02-13T00:00:00},
}

@Article{Blumenstiel2005,
  author    = {Blumenstiel, Justin P. and Hartl, Daniel L.},
  journal   = {Proceedings of the National Academy of Sciences of the United States of America},
  title     = {Evidence for maternally transmitted small interfering RNA in the repression of transposition in Drosophila virilis.},
  year      = {2005},
  pages     = {15965--70},
  volume    = {102},
  abstract  = {Hybrid dysgenesis in Drosophila is a syndrome of gonadal atrophy, sterility, and male recombination, and it occurs in the progeny of crosses between males that harbor certain transposable elements (TEs) and females that lack them. Known examples of hybrid dysgenesis in Drosophila melanogaster result from mobilization of individual families of TEs, such as the P element, the I element, or hobo. An example of hybrid dysgenesis in Drosophila virilis is unique in that multiple, unrelated families of TEs become mobilized, but a TE designated Penelope appears to play a major role. In all known examples of hybrid dysgenesis, the paternal germ line transmits the TEs in an active state, whereas the female germ line maintains repression of the TEs. The mechanism of maternal maintenance of repression is not known. Recent evidence suggests that the molecular machinery of RNA interference may function as an important host defense against TEs. This protection is mediated by the action of endogenous small interfering RNAs (siRNAs) composed of dsRNA molecules of 21-25 nt that can target complementary transcripts for destruction. In this paper, we demonstrate that endogenous siRNA derived from the Penelope element is maternally loaded in embryos through the female germ line in D. virilis. We also present evidence that the maternal inheritance of these endogenous siRNAs may contribute to maternal repression of Penelope.},
  file      = {:by-author/B/Blumenstiel/2005_Blumenstiel_15965.pdf:PDF},
  keywords  = {Mobile Genetic Elements},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@TechReport{Bochow2005,
  author      = {Anne Bochow and Alexandre Urzhumtsev},
  institution = {Physics Department, Faculty of Sciences and Technologies, University H. Poincaré Nancy 1, B.P. 239, 54506 Vandoeuvre-lès-Nancy, France},
  title       = {On the Fourier series truncation peaks at subatomic resolution},
  year        = {2005},
  abstract    = {Recently, several macromolecular structures have been resolved at a subatomic resolution as can be found in PDB (Berman et al., 2000; Berstein et al., 1977). At such a resolution, new structural details become visible at the corresponding Fourier maps. A small size of these details requires more careful analysis of the images of the electron density. In particular it is important to avoid confusion between signal and noise. The noise in Fourier maps can be attributed to several factors: errors in the experimental magnitudes, phase errors, Fourier series truncation. Some analysis of the first two sources of errors on macromolecular images at subatomic resolution has been reported previously (Afonine et al., 2004). This article addresses the role of errors in images caused by the resolution cut-off when this latter is unusually high for macromolecules, above 1 Å. The problem of Fourier series truncation is well known in macromolecular crystallography. At a very low resolution the ripples have a large scale and may systematically increase or decrease the values of the Fourier map in large regions. They complicate the definition of the correct molecular envelope. However, there are too few structural studies at such a resolution to bring much attention to this difficulty. At a conventional resolution of 2-3 Å, in general these errors do not pose particular difficulties due to a relatively weak effect. In most of cases, they are mentioned in relation to analysis of isolated ions or solvent molecules. It is known from many decades of studies on small molecules that at a subatomic resolution the noise caused by the series truncation is very significant. One of the main reasons for such increasing noise are very low values of the atomic displacement factor B which may reach 1-2 Å2 for such extremely well ordered structures. To decrease the noise in density deformation studies, this density is analysed at difference maps. The goal of the study presented here is to numerically compare the size of the density peaks due to density deformation with those caused by the series truncation. Not only the size of the noise peaks but also their shape is important to make a distinction between the noise and the signal. Both conventional and difference maps are studied.},
  file        = {:by-author/B/Bochow/2005_Bochow.sxw:;:by-author/B/Bochow/2005_Bochow.doc:DOC},
  keywords    = {X-ray Crystallography},
  owner       = {saulius},
  timestamp = {2015.02.28},
  creationdate = {2015-02-28T00:00:00},
  url         = {http://www.ccp4.ac.uk/newsletters/newsletter42/articles/Bochow_CCP4_2005_upd.doc},
}

@Article{Bochtler2007,
  author    = {Bochtler, Matthias and Chojnowski, Grzegorz},
  journal   = {Acta Crystallographica Section A},
  title     = {The highest reflection intensity in a resolution shell},
  year      = {2007},
  pages     = {146--155},
  volume    = {63},
  abstract  = {The Gumbel-Fisher-Tippett (GFT) extreme-value analysis is applied to evaluate the distribution, expectation value and standard deviation of the intensity J of the strongest reflection in a given resolution shell in the X-ray diffraction pattern of a crystal with many scattering atoms in the unit cell. For convenience, intensities are measured in units of the average reflection intensity in the resolution shell and, for simplicity, centric and acentric reflections are treated separately. For acentric reflections, the expectation value [mu] and standard deviation [sigma] of J are [mu] = ln n + [gamma] and [sigma] = [pi]/61/2, where n is the number of crystallographically independent reflections in the resolution shell and [gamma] ~ 0.577 is the Euler-Mascheroni constant. For centric reflections with expectation value 1 for the intensity, the corresponding expressions are [mu] = 2(ln n + [gamma]) - ln([pi] ln n) and [sigma] = 2[pi]/61/2 - [pi]/(61/2 ln n). Extensive numerical simulations show that these formulas are excellent approximations for random atom configurations at all resolutions, and good approximations for real protein crystal structures in the resolution range between 2.5 and 1.0 Å.},
  doi       = {10.1107/S0108767306052809},
  file      = {2007_Bochtler_146.pdf:by-author/B/Bochtler/2007_Bochtler_146.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.12.14},
  creationdate = {2012-12-14T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0108767306052809},
}

@Article{Bochtler2006,
  author       = {Matthias Bochtler and Roman H Szczepanowski and Gintautas Tamulaitis and Saulius Grazulis and Honorata Czapinska and Elena Manakova and Virginijus Siksnys},
  journal      = {EMBO J},
  title        = {Nucleotide flips determine the specificity of the Ecl18kI restriction endonuclease.},
  year         = {2006},
  month        = {May},
  number       = {10},
  pages        = {2219--2229},
  volume       = {25},
  abstract     = {Restricion endonuclease Ecl18kI is specific for the sequence /CCNGG and cleaves it before the outer C to generate 5 nt 5'-overhangs. It has been suggested that Ecl18kI is evolutionarily related to NgoMIV, a 6-bp cutter that cleaves the sequence G/CCGGC and leaves 4 nt 5'-overhangs. Here, we report the crystal structure of the Ecl18kI-DNA complex at 1.7 A resolution and compare it with the known structure of the NgoMIV-DNA complex. We find that Ecl18kI flips both central nucleotides within the CCNGG sequence and buries the extruded bases in pockets within the protein. Nucleotide flipping disrupts Watson-Crick base pairing, induces a kink in the DNA and shifts the DNA register by 1 bp, making the distances between scissile phosphates in the Ecl18kI and NgoMIV cocrystal structures nearly identical. Therefore, the two enzymes can use a conserved DNA recognition module, yet recognize different sequences, and form superimposable dimers, yet generate different cleavage patterns. Hence, Ecl18kI is the first example of a restriction endonuclease that flips nucleotides to achieve specificity for its recognition site.},
  creationdate = {2011-07-13T00:00:00},
  doi          = {10.1038/sj.emboj.7601096},
  file         = {2006_Bochtler_1.pdf:by-author/B/Bochtler/2006_Bochtler_1.pdf:PDF;2006_Bochtler_2219.pdf:by-author/B/Bochtler/2006_Bochtler_2219.pdf:PDF},
  institution  = {International Institute of Molecular and Cell Biology, Warsaw, Poland. MBochtler@iimcb.gov.pl},
  keywords     = {Amino Acid Sequence; Base Sequence; Binding Sites; Chemistry/genetics/metabolism; Chemistry/metabolism; Crystallography; DNA; Deoxyribonucleases; Dimerization; Macromolecular Substances; Models; Molecular; Molecular Sequence Data; Nucleic Acid Conformation; Nucleotides; Protein Structure; Substrate Specificity; Tertiary; Type II Site-Specific; X-Ray},
  language     = {eng},
  medline-pst  = {ppublish},
  owner        = {em},
  pii          = {7601096},
  pmid         = {16628220},
  timestamp    = {2011.07.13},
  url          = {http://dx.doi.org/10.1038/sj.emboj.7601096},
}

@Article{Bochtler2006a,
  author    = {Bochtler, Matthias and Szczepanowski, Roman H. and Tamulaitis, Gintautas and Grazulis, Saulius and Czapinska, Honorata and Manakova, Elena and Siksnys, Virginijus},
  journal   = {The EMBO journal},
  title     = {Nucleotide flips determine the specificity of the Ecl18kI restriction endonuclease.},
  year      = {2006},
  pages     = {2219--29},
  volume    = {25},
  abstract  = {Restricion endonuclease Ecl18kI is specific for the sequence /CCNGG and cleaves it before the outer C to generate 5 nt 5'-overhangs. It has been suggested that Ecl18kI is evolutionarily related to NgoMIV, a 6-bp cutter that cleaves the sequence G/CCGGC and leaves 4 nt 5'-overhangs. Here, we report the crystal structure of the Ecl18kI-DNA complex at 1.7 A resolution and compare it with the known structure of the NgoMIV-DNA complex. We find that Ecl18kI flips both central nucleotides within the CCNGG sequence and buries the extruded bases in pockets within the protein. Nucleotide flipping disrupts Watson-Crick base pairing, induces a kink in the DNA and shifts the DNA register by 1 bp, making the distances between scissile phosphates in the Ecl18kI and NgoMIV cocrystal structures nearly identical. Therefore, the two enzymes can use a conserved DNA recognition module, yet recognize different sequences, and form superimposable dimers, yet generate different cleavage patterns. Hence, Ecl18kI is the first example of a restriction endonuclease that flips nucleotides to achieve specificity for its recognition site.},
  file      = {:by-author/B/Bochtler/2006_Bochtler_2219.pdf:PDF},
  groups    = {sg/NgoMIV},
  keywords  = {Struct; TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Bochtler2006b,
  author    = {Matthias Bochtler and Roman H. Szczepanowski and Gintautas Tamulaitis and Saulius Grazulis and Honorata Czapinska and Elena Manakova and Virginijus Siksnys},
  journal   = {The EMBO Journal},
  title     = {Nucleotide flips determine the specificity of the {Ecl18kI} restriction endonuclease},
  year      = {2006},
  pages     = {1},
  file      = {:by-author/B/Bochtler/2006_Bochtler_1.pdf:PDF},
  keywords  = {Ecl18kI EcoRII; TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Boehm2004,
  author    = {Boehm},
  title     = {Garbage Collection in an Uncooperative Environment},
  year      = {2004},
  pages     = {manuscript},
  file      = {:by-author/B/Boehm/2004_Boehm_manuscript.pdf:PDF},
  groups    = {sg/Garbage collectors},
  keywords  = {Computer Science (CS); Garbage Collectors},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Boehm2001,
  author    = {Boehm},
  title     = {Bounding Space Usage of Conservative Garbage Collectors},
  year      = {2001},
  pages     = {techreport},
  file      = {:by-author/B/Boehm/2001_Boehm_techreport.pdf:PDF},
  groups    = {sg/Garbage collectors},
  keywords  = {Computer Science (CS); Garbage Collectors},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Boehm2000,
  author    = {Boehm},
  title     = {Fast Multiprocessor Memory Allocation and Garbage Collection},
  year      = {2000},
  pages     = {techreport},
  file      = {:by-author/B/Boehm/2000_Boehm_techreport.pdf:PDF},
  groups    = {sg/Garbage collectors},
  keywords  = {Computer Science (CS); Garbage Collectors},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Boehm2000a,
  author    = {Boehm},
  title     = {Reducing Garbage Collector Cache Misses},
  year      = {2000},
  pages     = {techrport},
  file      = {:by-author/B/Boehm/2000_Boehm_techrport.pdf:PDF},
  groups    = {sg/Garbage collectors},
  keywords  = {Computer Science (CS); Garbage Collectors},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Manual{Boehm1999,
  title     = {COCOMO II Model Definition Manual},
  author    = {Barry Boehm and Chris Abts and Brad Clark and Sunita Devnani-Chulani and Ellis Horowitz and Ray Madachy and Don Reifer and Rick Selby and Bert Steece},
  year      = {1999},
  file      = {1999_Boehm.pdf:by-author/B/Boehm/1999_Boehm.pdf:PDF},
  keywords  = {COCOMO; Computer Science (CS); Software Cost Estimation},
  owner     = {saulius},
  timestamp = {2015.11.22},
  creationdate = {2015-11-22T00:00:00},
  url       = {http://nas.uhcl.edu/boetticher/swen5230/modelman.pdf},
}

@Presentation{Boehm2012,
  author       = {Hans−J. Boehm},
  title        = {Memory Allocation Myths and Half−Truths},
  year         = {2012},
  organization = {Silicon Graphics},
  file         = {:by-author/B/Boehm/2012_Boehm.ps:PostScript;:by-author/B/Boehm/2012_Boehm.pdf:PDF},
  groups       = {sg/Garbage collectors},
  keywords     = {Computer Science (CS); Garbage Collection; Memory Allocation},
  owner        = {saulius},
  timestamp = {2015.02.27},
  creationdate = {2015-02-27T00:00:00},
  url          = {http://www.hpl.hp.com/personal/Hans_Boehm/gc/},
}

@Webpage{Boehm2004a,
  author    = {H. Boehm},
  retrieved = {2012-01-25},
  title     = {A garbage collector for C and C++},
  url       = {http://www.hboehm.info/gc/},
  year      = {2004},
  file      = {:by-author/B/Boehm/2004_Boehm.odt:},
  groups    = {sg/Garbage collectors},
  keywords  = {Computer Science (CS); Garbage Collectors},
  owner     = {saulius},
  timestamp = {2015.03.03},
  creationdate = {2015-03-03T00:00:00},
}

@TechReport{Boehm,
  author      = {Hans-J. Boehm},
  institution = {HP Labs},
  title       = {Conservative GC Algorithmic Overview},
  file        = {:by-author/B/Boehm/XXXX_Boehm.odt:},
  groups      = {sg/Garbage collectors},
  keywords    = {Computer Science (CS); Garbage Collectors},
  owner       = {saulius},
  retrieved   = {2012-01-25},
  timestamp = {2015.03.03},
  creationdate = {2015-03-03T00:00:00},
  url         = {http://www.hboehm.info/gc/gcdescr.html},
}

@TechReport{Boehm1996,
  author      = {Hans-J. Boehm},
  institution = {Xerox PARC},
  title       = {Simple Garbage-Collector-Safety},
  year        = {1996},
  abstract    = {A conservative garbage collector can typically be used with conventionally compiled programs written in C or Automatic garbage collection can significantly simplify C++. But two safety issues must be considered. First, the program development. It can also help to isolate program source code must not hide pointers from the garbage errors to one module by helping to ensure that no module can collector. This primarily requires stricter adherence to invalidate a data structure maintained by another. Though it existing restrictions in the language definition. Second, we is hard to quantify this benefit, most expert guesses seem to must ensure that the compiler will not perform place it in the range of 30-40% of program development time transformations that invalidate this requirement. for programs that manipulate complex linked data structures},
  file        = {:by-author/B/Boehm/1996_Boehm.pdf:PDF;:by-author/B/Boehm/1996_Boehm.ps.gz:PostScript},
  groups      = {sg/Garbage collectors},
  owner       = {saulius},
  timestamp = {2015.02.27},
  creationdate = {2015-02-27T00:00:00},
}

@TechReport{Boehm1993,
  author      = {Hans-Juergen Boehm},
  institution = {Xerox PARC},
  title       = {Space Efficient Conservative Garbage Collection},
  year        = {1993},
  file        = {:by-author/B/Boehm/1993_Boehm.ps.Z:PostScript;:by-author/B/Boehm/1993_Boehm.pdf:PDF},
  groups      = {sg/Garbage collectors},
  keywords    = {Computer Science (CS); Garbage Collectors},
  owner       = {saulius},
  timestamp = {2015.02.28},
  creationdate = {2015-02-28T00:00:00},
}

@TechReport{Boehm1991,
  author      = {Hans-J. Boehm and Alan J. Demers and Scott Shenker},
  institution = {Xerox PARC},
  title       = {Mostly Parallel Garbage Collection},
  year        = {1991},
  file        = {:by-author/B/Boehm/1991_Boehm.ps.Z:PostScript;:by-author/B/Boehm/1991_Boehm.pdf:PDF},
  groups      = {sg/Garbage collectors},
  keywords    = {Computer Science (CS); Garbage Collectors},
  owner       = {saulius},
  timestamp = {2015.02.28},
  creationdate = {2015-02-28T00:00:00},
}

@Article{Boekema2009,
  author    = {Boekema, Egbert J. and Folea, Mihaela and Kouřil, Roman},
  journal   = {Photosynthesis research},
  title     = {Single particle electron microscopy.},
  year      = {2009},
  pages     = {189--96},
  volume    = {102},
  abstract  = {Electron microscopy (EM) in combination with image analysis is a powerful technique to study protein structures at low, medium, and high resolution. Since electron micrographs of biological objects are very noisy, improvement of the signal-to-noise ratio by image processing is an integral part of EM, and this is performed by averaging large numbers of individual projections. Averaging procedures can be divided into crystallographic and non-crystallographic methods. The crystallographic averaging method, based on two-dimensional (2D) crystals of (membrane) proteins, yielded in solving atomic protein structures in the last century. More recently, single particle analysis could be extended to solve atomic structures as well. It is a suitable method for large proteins, viruses, and proteins that are difficult to crystallize. Because it is also a fast method to reveal the low-to-medium resolution structures, the impact of its application is growing rapidly. Technical aspects, results, and possibilities are presented.},
  file      = {:by-author/B/Boekema/2009_Boekema_189.pdf:PDF},
  keywords  = {CryoEM},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@Article{Bohannon2013,
  author    = {Bohannon, John},
  journal   = {Science},
  title     = {Who's Afraid of Peer Review?},
  year      = {2013},
  pages     = {60--65},
  volume    = {342},
  abstract  = {Dozens of open-access journals targeted in an elaborate Science sting accepted a spoof research article, raising questions about peer-review practices in much of the open-access world.},
  doi       = {10.1126/science.342.6154.60},
  eprint    = {http://www.sciencemag.org/content/342/6154/60.full.pdf},
  file      = {2013_Bohannon_60.pdf:by-author/B/Bohannon/2013_Bohannon_60.pdf:PDF},
  keywords  = {Data Quality; Peer-review; Scientific Publishing},
  owner     = {saulius},
  timestamp = {2013.10.30},
  creationdate = {2013-10-30T00:00:00},
  url       = {http://www.sciencemag.org/content/342/6154/60.short},
}

@Article{Boehm1983,
  author    = {Honsr Böhm},
  journal   = {American Mineralogist},
  title     = {Modulated structures at phasetransitions},
  year      = {1983},
  pages     = {11--17},
  volume    = {68},
  abstract  = {The characteristic features of modulated structureswhich appearas intermediate phases between a high-symmetry high temperature phase and a low temperature phase of lower symmetry are described. Two examples (NaNO2 and LiAlSiO+) are discussed. For NaNO2 previously published results are reviewed. For LiAlSiOa, the modulation of the structure is interpreted as being caused by the formation of domains which fluctuate in their width. This domain hypothesis is supported by model calculations. The course of structure determination is outlined.},
  file      = {:by-author/B/Bohm/1983_Bohm_11.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.10.15},
  creationdate = {2012-10-15T00:00:00},
}

@Article{Boisen1990,
  author    = {Boisen, Jr, M. B. and Gibbs, G. V. and Wondratschek, H.},
  journal   = {Acta Crystallographica Section A},
  title     = {Derivation of the normalizers of the space groups},
  year      = {1990},
  pages     = {545--552},
  volume    = {46},
  abstract  = {A method for the derivation of the affine normalizers of the space groups using matrix methods is presented. Published lists of normalizers have been verified, using matrix methods, both by hand and by computer. Generating matrices for the affine normalizers of triclinic and monoclinic space groups are listed.},
  doi       = {10.1107/S0108767390002434},
  file      = {1990_Boisen_545.pdf:by-author/B/Boisen/1990_Boisen_545.pdf:PDF},
  keywords  = {Spacegroups; Symmetry; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2014.05.08},
  creationdate = {2014-05-08T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0108767390002434},
}

@Article{Boissieu2013,
  author    = {de Boissieu, Marc},
  journal   = {Nat Mater},
  title     = {Quasicrystals: Model structures},
  year      = {2013},
  issn      = {1476-1122},
  pages     = {692--693},
  volume    = {12},
  abstract  = {Elucidating the relationship between the structure and magnetism of quasicrystals has long been a challenge. The discovery of an extended family of binary icosahedral quasicrystals with localized magnetic moments may be an important step in shedding light on this issue.},
  doi       = {10.1038/nmat3725},
  file      = {:by-author/d/deBoissieu/2013_Boissieu_692.pdf:pdf},
  owner     = {saulius},
  publisher = {Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},
  timestamp = {2015.10.09},
  creationdate = {2015-10-09T00:00:00},
  url       = {http://dx.doi.org/10.1038/nmat3725},
}

@Article{Boissieu2013a,
  author     = {de Boissieu, Marc},
  journal    = {Nature Materials},
  title      = {Quasicrystals: model structures},
  year       = {2013},
  issn       = {1476-1122},
  pages      = {692--693},
  volume     = {12},
  abstract   = {Elucidating the relationship between the structure and magnetism of quasicrystals has long been a challenge. The discovery of an extended family of binary icosahedral quasicrystals with localized magnetic moments may be an important step in shedding light on this issue.},
  copyright  = {© 2013 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},
  doi        = {10.1038/nmat3725},
  file       = {de Boissieu - 2013 - Quasicrystals Model structures.pdf:by-author/d/deBoissieu/2013_deBoissieu_692.pdf:PDF;Snapshot:by-author/d/deBoissieu/2013_deBoissieu_692.html:URL},
  language   = {en},
  owner      = {saulius},
  shorttitle = quasicrystals,
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url        = {http://www.nature.com/nmat/journal/v12/n8/full/nmat3725.html},
  urldate    = {2015-09-08},
}

@Article{Boissieu2012,
  author    = {Marc de Boissieu},
  title     = {Atomic structure of quasicrystals},
  year      = {2012},
  pages     = {965--976},
  volume    = {23},
  abstract  = {The 2011 Nobel Prize in chemistry has been awarded to Dan Shechtman for his discovery of quasi-crystals. The discovery has indeed been a breakthrough in crystallography and solid state physics and chemistry. After a brief introduction to the subject, we review some of the recent advances in the understanding of the atomic structure of icosahedral quasicrystals and in particular for the binary Cd–Yb type quasicrystal. Thanks to a combined analysis of periodic approximant, high quality synchrotron data, and the superspace approach, a detailed insight in the crystal chemistry of this binary quasicrystal as been achieved.},
  doi       = {10.1007/s11224-012-0004-4},
  file      = {Marc de Boissieu - 2012 - Atomic structure of quasicrystals.pdf:by-author/B/Boissieu/2012_Boissieu_965.pdf:application/pdf},
  language  = {English},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://download.springer.com/static/pdf/694/art%253A10.1007%252Fs11224-012-0004-4.pdf?originUrl=http%3A%2F%2Flink.springer.com%2Farticle%2F10.1007%2Fs11224-012-0004-4&token2=exp=1441722318~acl=%2Fstatic%2Fpdf%2F694%2Fart%25253A10.1007%25252Fs11224-012-0004-4.pdf%3ForiginUrl%3Dhttp%253A%252F%252Flink.springer.com%252Farticle%252F10.1007%252Fs11224-012-0004-4*~hmac=f3f8b8492f6a85948580335e0785a70f842f68f72e774957ed9df7b878e12953},
  urldate   = {2015-09-08},
}

@Article{Bolanz2013,
  author    = {Bolanz, Ralph Michael and Bläss, Ulrich and Ackermann, Sonia and Ciobotă, Valerian and Rösch, Petra and Tarcea, Nicolae and Popp, Jürgen and Majzlan, Juraj},
  journal   = {Clays and Clay Minerals},
  title     = {The effect of antimonate, arsenate, and phosphate on the transformation of ferrihydrite to goethite, hematite, feroxyhyte, and tripuhyite},
  year      = {2013},
  pages     = {11--25},
  volume    = {61},
  file      = {[PDF] from db-thueringen.de:by-author/B/Bolanz/2013_Bolanz_11.pdf:PDF;Snapshot:by-author/B/Bolanz/2013_Bolanz_11.html:URL},
  groups    = {sg/JAC2009, sg/NAR2012},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://ccm.geoscienceworld.org/content/61/1/11.short},
  urldate   = {2015-08-31},
}

@Article{Boldyreva2010,
  author    = {Boldyreva},
  journal   = {Journal of Applied Crystallography},
  title     = {Teaching general chemistry, solid-state chemistry and crystallography in one comprehensive undergraduate course: can the effect be synergistic?},
  year      = {2010},
  pages     = {1172},
  file      = {:by-author/B/Boldyreva/2010_Boldyreva_1172.pdf:PDF},
  keywords  = {Grow Krystal},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Manuscript{Bollinger2011,
  author           = {Bollinger, John},
  title            = {{CIF} - Changes to the specification},
  year             = {2011},
  keywords         = {CIF},
  month            = {Jul},
  url              = {http://www.iucr.org/__data/assets/pdf_file/0020/59420/cif2_syntax_changes-jcb20110728.pdf},
  creationdate     = {2015-07-29T00:00:00},
  file             = {:by-author/B/Bollinger/2011_Bollinger.pdf:PDF},
  modificationdate = {2023-08-07T10:23:05},
  owner            = {andrius},
  timestamp        = {2015.07.29},
}

@Article{Bollinger2016,
  author           = {Bollinger, John C.},
  journal          = {J Appl Crystallogr},
  title            = {A portable general-purpose application programming interface for {CIF 2.0}},
  year             = {2016},
  issn             = {1600-5767},
  month            = {Feb},
  number           = {1},
  volume           = {49},
  creationdate     = {2016-01-08T00:00:00},
  doi              = {10.1107/s1600576715021883},
  file             = {:by-author/B/Bollinger/2016_Bollinger.pdf:PDF},
  keywords         = {CIF},
  modificationdate = {2023-08-07T10:23:04},
  owner            = {andrius},
  publisher        = {International Union of Crystallography (IUCr)},
  timestamp        = {2016.01.08},
  url              = {http://dx.doi.org/10.1107/S1600576715021883},
}

@Manuscript{Bolton2009,
  author    = {Evan Bolton},
  title     = {PubChem Substructure Fingerprint},
  year      = {2009},
  keywords  = {Chemical Fingerprints; PubChem},
  url       = {http://astro.temple.edu/~tua87106/list_fingerprints.pdf},
  file      = {2009_Bolton.pdf:by-author/B/Bolton/2009_Bolton.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.07.07},
  creationdate = {2016-07-07T00:00:00},
}

@InBook{Bolton2008,
  author    = {Evan E. Bolton and Yanli Wang and Paul A. Thiessen and Stephen H. Bryant},
  chapter   = {Chapter 12 PubChem: Integrated Platform of Small Molecules and Biological Activities},
  editor    = {Ralph A. Wheeler and David C. Spellmeyer},
  pages     = {217--240},
  publisher = {Elsevier: Oxford, UK},
  title     = {Annual Reports in Computational Chemistry},
  year      = {2008},
  volume    = {4},
  abstract  = {PubChem is an open repository for experimental data identifying the biological activities of small molecules. PubChem contents include more than: 1,000 bioassays, 28 million bioassay test outcomes, 40 million substance contributed descriptions, and 19 million unique compound structures contributed from over 70 depositing organizations. PubChem provides a significant, publicly accessible platform for mining the biological information of small molecules.},
  doi       = {10.1016/S1574-1400(08)00012-1},
  file      = {2008_Bolton_217.pdf:by-author/B/Bolton/2008_Bolton_217.pdf:PDF;:by-author/B/Bolton/2008_Bolton_217manuscript.pdf:PDF},
  keywords  = {Computational Chemistry; Data Management; Databases},
  owner     = {saulius},
  timestamp = {2014.07.02},
  creationdate = {2014-07-02T00:00:00},
  url       = {ftp://ftp.ncbi.nlm.nih.gov/pubchem/publications/ARCC_PubChem_Integrated_Platform.pdf},
}

@Article{Boltzmann1877,
  author    = {Ludwig Boltzmann},
  journal   = {Sitzungsberichte der kaiserlichen Akademie der Wissenschaften},
  title     = {Über die Beziehung zwischen dem zweiten Hauptsatze des mechanischen Wärmetheorie und der Wahrscheinlichkeitsrechnung, respective den Sätzen über das Wärmegleichgewicht.},
  year      = {1877},
  pages     = {373--435},
  volume    = {LXXVI},
  file      = {:by-author/B/Boltzmann/1877_Boltzmann_373-translation.pdf:PDF},
  keywords  = {Entropy; Statistical Mechanics},
  owner     = {saulius},
  timestamp = {2012.04.08},
  creationdate = {2012-04-08T00:00:00},
}

@Presentation{Bolz2012,
  author     = {Carl Friedrich Bolz},
  title      = {PyPy: How to not write Virtual Machines for Dynamic Languages},
  year       = {2012},
  conference = {Dynamische Programmiersprachen},
  school     = {Institut für Informatik Heinrich-Heine-Universität Düsseldorf},
  file       = {:by-author/B/Bolz/2012_Bolz_presentation.pdf:PDF},
  owner      = {saulius},
  pages      = {presentation},
  timestamp = {2012.09.18},
  creationdate = {2012-09-18T00:00:00},
}

@Manuscript{Bolz2007,
  author    = {Carl Friedrich Bolz and Armin Rigo},
  title     = {How to {\em not} write Virtual Machines for Dynamic Languages},
  year      = {2007},
  abstract  = {Typical modern dynamic languages have a growing number of implementations. We explore the reasons for this situation, and the limitations it imposes on open source or academic communities that lack the resources to fine-tune and maintain them all. It is sometimes proposed that implementing dynamic languages on top of a standardized general-purpose object-oriented virtual machine (like Java or .NET) would help reduce this burden. We propose a complementary alternative to writing custom virtual machine (VMs) by hand, validated by the PyPy project: flexibly generating VMs from a high-level “specification”, inserting features and low-level details automatically – including good just-in-time compilers tuned to the dynamic language at hand. We believe this to be ultimately a better investment of efforts than the development of more and more advanced general-purpose object oriented VMs. In this paper we compare these two approaches in detail.},
  file      = {:by-author/B/Bolz/2007_Bolz.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.09.18},
  creationdate = {2012-09-18T00:00:00},
}

@Article{Bond2010,
  author    = {Bond, Andrew D.},
  journal   = {Journal of Applied Crystallography},
  title     = {Automated least-squares molecular overlay without {\it a priori} atomic correspondence or connectivity information},
  year      = {2010},
  pages     = {53--57},
  volume    = {43},
  doi       = {10.1107/S002188980904134X},
  file      = {2010_Bond_53.pdf:by-author/B/Bond/2010_Bond_53.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.02.15},
  creationdate = {2012-02-15T00:00:00},
  url       = {http://dx.doi.org/10.1107/S002188980904134X},
}

@Article{Bond2010a,
  author    = {Bond, Andrew D.},
  journal   = {CrystEngComm},
  title     = {Why do crystal structures waste molecular inversion symmetry?},
  year      = {2010},
  pages     = {2492--2500},
  volume    = {12},
  abstract  = {Single-component molecular crystal structures containing centrosymmetric molecules with non-centrosymmetric crystallographic site symmetry are retrieved from the Cambridge Structural Database. The distribution amongst space group types is comparable to that for molecular crystals in general{,} except that there is a significant decrease in the proportion of triclinic structures. The structures are analysed in terms of the symmetrical relationships between them and some specific chemical circumstances that lead to wasted molecular inversion symmetry are identified: (1) planar centrosymmetric molecules form locally centrosymmetric pairs through face-to-face ([small pi]-[small pi]) interactions and these pairs pack through edge-to-face interactions; (2) molecules form layers that are locally centrosymmetric but the symmetry within the layers is not compatible with the symmetry of the interlayer interactions. Although the non-centrosymmetric environments of isolated centrosymmetric molecules seem to be unusual{,} the symmetries of the identified structural fragments and the interactions between them are quite normal.},
  doi       = {10.1039/C001341B},
  file      = {2010_Bond_2492.pdf:by-author/B/Bond/2010_Bond_2492.pdf:PDF},
  issue     = {8},
  keywords  = {Crystal Engineering; High Z Structures},
  owner     = {saulius},
  publisher = {The Royal Society of Chemistry},
  timestamp = {2014.11.06},
  creationdate = {2014-11-06T00:00:00},
  url       = {http://dx.doi.org/10.1039/C001341B},
}

@Article{Bond2001,
  author    = {Bond, C. S. and Kvaratskhelia, M. and Richard, D. and White, M. F. and Hunter, W. N.},
  journal   = {Proceedings of the National Academy of Sciences of the United States of America},
  title     = {Structure of Hjc, a Holliday junction resolvase, from Sulfolobus solfataricus.},
  year      = {2001},
  pages     = {5509--14},
  volume    = {98},
  abstract  = {The 2.15-A structure of Hjc, a Holliday junction-resolving enzyme from the archaeon Sulfolobus solfataricus, reveals extensive structural homology with a superfamily of nucleases that includes type II restriction enzymes. Hjc is a dimer with a large DNA-binding surface consisting of numerous basic residues surrounding the metal-binding residues of the active sites. Residues critical for catalysis, identified on the basis of sequence comparisons and site-directed mutagenesis studies, are clustered to produce two active sites in the dimer, about 29 A apart, consistent with the requirement for the introduction of paired nicks in opposing strands of the four-way DNA junction substrate. Hjc displays similarity to the restriction endonucleases in the way its specific DNA-cutting pattern is determined but uses a different arrangement of nuclease subunits. Further structural similarity to a broad group of metal/phosphate-binding proteins, including conservation of active-site location, is observed. A high degree of conservation of surface electrostatic character is observed between Hjc and T4-phage endonuclease VII despite a complete lack of structural homology. A model of the Hjc-Holliday junction complex is proposed, based on the available functional and structural data.},
  file      = {:by-author/B/Bond/2001_Bond_5509.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Bondi1964,
  author    = {Bondi, A.},
  journal   = {The Journal of Physical Chemistry},
  title     = {van der Waals Volumes and Radii},
  year      = {1964},
  pages     = {441--451},
  volume    = {68},
  abstract  = {Intermolecular van der Waals radii of the nonmetallic elements have been assembled into a list of "recommended" values for volume calculations. These values have been arrived at by selecting the most reliable X-ray diffraction data those which could be reconciled with crystal density at 0 K. (to give reasonable packing density), gas kinetic collision cross section, critical density, and liquid state properties. A qualitative understanding of the nature of van der Waals radii is provided by correlation with the de Broglie wave length of the outermost valence electron. Tentative values for the van der Waals radii of metallic elements {--} in metal organic compounds {--} are proposed. The paper concludes with a list of increments for the volume of molecules impenetrable of thermal collision, the so-called van der Waals volume, and of the corresponding increments in area per molecule.},
  doi       = {10.1021/j100785a001},
  file      = {:by-author/B/Bondi/1964_Bondi_441.pdf:PDF},
  keywords  = {Bachelor's Thesis; Van Der Walls Radii},
  owner     = {antanas},
  timestamp = {2013.04.08},
  creationdate = {2013-04-08T00:00:00},
  url       = {http://pubs.acs.org/doi/abs/10.1021/j100785a001},
}

@Article{Boniecki2015,
  author    = {Boniecki, Michal J. and Lach, Grzegorz and Dawson, Wayne K. and Tomala, Konrad and Lukasz, Pawel and Soltysinski, Tomasz and Rother, Kristian M. and Bujnicki, Janusz M.},
  journal   = {Nucleic Acids Research},
  title     = {SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction},
  year      = {2015},
  pages     = {gkv1479},
  abstract  = {RNA molecules play fundamental roles in cellular processes. Their function and interactions with other biomolecules are dependent on the ability to form complex three-dimensional (3D) structures. However, experimental determination of RNA 3D structures is laborious and challenging, and therefore, the majority of known RNAs remain structurally uncharacterized. Here, we present SimRNA: a new method for computational RNA 3D structure prediction, which uses a coarse-grained representation, relies on the Monte Carlo method for sampling the conformational space, and employs a statistical potential to approximate the energy and identify conformations that correspond to biologically relevant structures. SimRNA can fold RNA molecules using only sequence information, and, on established test sequences, it recapitulates secondary structure with high accuracy, including correct prediction of pseudoknots. For modeling of complex 3D structures, it can use additional restraints, derived from experimental or computational analyses, including information about secondary structure and/or long-range contacts. SimRNA also can be used to analyze conformational landscapes and identify potential alternative structures.},
  doi       = {10.1093/nar/gkv1479},
  eprint    = {http://nar.oxfordjournals.org/content/early/2015/12/19/nar.gkv1479.full.pdf+html},
  file      = {2015_Boniecki_gkv1479.pdf:by-author/B/Boniecki/2015_Boniecki_gkv1479.pdf:PDF},
  groups    = {sg/applications},
  keywords  = {3D Structure; Coarse-grained Simulations; Monte Carlo Simulations; RNA; RNA Structure},
  owner     = {saulius},
  timestamp = {2016.03.04},
  creationdate = {2016-03-04T00:00:00},
  url       = {http://nar.oxfordjournals.org/content/early/2015/12/19/nar.gkv1479.abstract},
}

@Article{Bonnet2004,
  author    = {Bonnet, Pascal and Bryce, Richard A.},
  journal   = {Protein science : a publication of the Protein Society},
  title     = {Molecular dynamics and free energy analysis of neuraminidase-ligand interactions.},
  year      = {2004},
  pages     = {946--57},
  volume    = {13},
  abstract  = {We report molecular dynamics calculations of neuraminidase in complex with an inhibitor, 4-amino-2-deoxy-2,3-didehydro-N-acetylneuraminic acid (N-DANA), with subsequent free energy analysis of binding by using a combined molecular mechanics/continuum solvent model approach. A dynamical model of the complex containing an ionized Glu119 amino acid residue is found to be consistent with experimental data. Computational analysis indicates a major van der Waals component to the inhibitor-neuraminidase binding free energy. Based on the N-DANA/neuraminidase molecular dynamics trajectory, a perturbation methodology was used to predict the binding affinity of related neuraminidase inhibitors by using a force field/Poisson-Boltzmann potential. This approach, incorporating conformational search/local minimization schemes with distance-dependent dielectric or generalized Born solvent models, correctly identifies the most potent neuraminidase inhibitor. Mutation of the key ligand four-substituent to a hydrogen atom indicates no favorable binding free energy contribution of a hydroxyl group; conversely, cationic substituents form favorable electrostatic interactions with neuraminidase. Prospects for further development of the method as an analysis and rational design tool are discussed.},
  file      = {:by-author/B/Bonnet/2004_Bonnet_946.pdf:PDF},
  keywords  = {Protein Ligand Complexes},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Manuscript{Bonsangue1994,
  author    = {Bonsangue, Marcello M. and Kok, Joost N.},
  title     = {The Weakest Precondition Calculus: Recursion and Duality},
  year      = {1994},
  keywords  = {Computer Science (CS); Weakest Preconditions},
  comment   = {The original filename was "bonsangue94weakest.pdf", but it is no longer found on the Web as of 2014-11-21.},
  file      = {:by-author/B/Bonsangue/1994_Bonsangue.pdf:PDF},
  journal   = {Formal Aspects of Computing},
  note      = {This is a short version of [BK94]},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
  volume    = {6},
}

@Presentation{Borchardt-Ott2002,
  author    = {W. Borchardt-Ott},
  title     = {Crystallography. Crystal lattice and Indices and other topics},
  year      = {2002},
  lecture   = {Lecture 1},
  file      = {2002_Borchardt-Ott_slides.pdf:by-author/B/Borchardt-Ott/2002_Borchardt-Ott_slides.pdf:PDF},
  keywords  = {Crystallography; Lattices; Symmetry; Teaching},
  owner     = {saulius},
  timestamp = {2014.10.21},
  creationdate = {2014-10-21T00:00:00},
  url       = {http://www.uni-saarland.de/fileadmin/user_upload/Professoren/fr84_ProfMuecklich/lehre/crystallography/Lecture1-lattice-Indice.pdf},
}

@Article{Bordet1992,
  author    = {P. Bordet and J.J. Capponi and C. Chaillout and D. Chateigner and J. Chenavas and Th. Fournier and J.L. Hodeau and M. Marezio and M. Perroux and G. Thomas and A. Varela},
  journal   = {Physica C: Superconductivity},
  title     = {High Presure Synthesis and Structural Studies of R2CuO4 Compounds with R = Y, Tb, Dy, Ho, Er, Tm},
  year      = {1992},
  pages     = {178--188},
  volume    = {193},
  abstract  = {The title compounds have been prepared by high pressure/high temperature reaction. Thermogravimetric measurements indicate that they decompose a above ≈ 350°C in He flow. Electron microscopy and X-Ray powder and single crystal diffraction data are presented. They all reveal the presence of three types of superstructure, corresponding to different unit cells, which can be observed in different grains of the same sample. The results of an average structure refinement carried out with the unit cell, and symmetry of the T' phase are presented for the Tm2CuO4 compound. These results are compared with those obtained for Gd2CuO4.},
  doi       = {10.1016/0921-4534(92)90885-G},
  file      = {:by-author/B/Bordet/1992_Bordet_178.pdf:PDF},
  keywords  = {For COD Deposition; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/092145349290885G},
}

@Presentation{Bording2007,
  author    = {Phil Bording},
  title     = {Parallel Programming using MPI},
  year      = {2007},
  file      = {:by-author/B/Bording/2007_Bording.pdf:PDF},
  owner     = {saulius},
  timestamp = {2013.08.11},
  creationdate = {2013-08-11T00:00:00},
}

@Presentation{Bordoli2003,
  author       = {Lorenza Bordoli},
  title        = {Similarity Searches on Sequence Databases:BLAST, FASTA},
  year         = {2003},
  course       = {EMBnet Course},
  organization = {Swiss Institute of Bioinformatics},
  file         = {2003_Bordoli.pdf:by-author/B/Bordoli/2003_Bordoli.pdf:PDF},
  keywords     = {Algorithms; BLAST; Bioinformatics; FASTA; Sequence Alignment; Sequence Search},
  month        = {October},
  owner        = {saulius},
  timestamp = {2015.04.16},
  creationdate = {2015-04-16T00:00:00},
  url          = {http://www.ch.embnet.org/CoursEMBnet/Basel03/slides/BLAST_FASTA.pdf},
}

@Article{Borek2003,
  author    = {Borek, Dominika and Minor, Wladek and Otwinowski, Zbyszek},
  journal   = {Acta Crystallographica Section D},
  title     = {Measurement errors and their consequences in protein crystallography},
  year      = {2003},
  pages     = {2031--2038},
  volume    = {59},
  doi       = {10.1107/S0907444903020924},
  file      = {ba5035.pdf:by-author/B/Borek/2003_Borek_2031.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444903020924},
}

@Article{Boriack1995,
  author    = {P. Ann Boriack and David W. Christianson},
  journal   = {J. Med. Chem.},
  title     = {Secondary Interactions Significantly Removed from the Sulfonamide Binding Pocket of Carbonic Anhydrase II Influence Inhibitor Binding Constants},
  year      = {1995},
  pages     = {2286--2291},
  volume    = {38},
  file      = {:by-author/B/Boriack/1995_Boriack_2286.pdf:PDF},
  groups    = {sg/inhibitors, sg/hCA2},
  owner     = {saulius},
  timestamp = {2011.12.14},
  creationdate = {2011-12-14T00:00:00},
}

@Article{Boriack-Sjodin1998,
  author    = {Boriack-Sjodin, P A and Zeitlin, S and Chen, H H and Crenshaw, L and Gross, S and Dantanarayana, A and Delgado, P and May, J A and Dean, T and Christianson, D W},
  journal   = {Protein science : a publication of the Protein Society},
  title     = {Structural analysis of inhibitor binding to human carbonic anhydrase II.},
  year      = {1998},
  pages     = {2483--9},
  volume    = {7},
  abstract  = {X-ray crystal structures of carbonic anhydrase II (CAII) complexed with sulfonamide inhibitors illuminate the structural determinants of high affinity binding in the nanomolar regime. The primary binding interaction is the coordination of a primary sulfonamide group to the active site zinc ion. Secondary interactions fine-tune tight binding in regions of the active site cavity &gt;5 A away from zinc, and this work highlights three such features: (1) advantageous conformational restraints of a bicyclic thienothiazene-6-sulfonamide-1,1-dioxide inhibitor skeleton in comparison with a monocyclic 2,5-thiophenedisulfonamide skeleton; (2) optimal substituents attached to a secondary sulfonamide group targeted to interact with hydrophobic patches defined by Phe131, Leu198, and Pro202; and (3) optimal stereochemistry and configuration at the C-4 position of bicyclic thienothiazene-6-sulfonamides; the C-4 substituent can interact with His64, the catalytic proton shuttle. Structure-activity relationships rationalize affinity trends observed during the development of brinzolamide (Azopt), the newest carbonic anhydrase inhibitor approved for the treatment of glaucoma.},
  file      = {1998_Boriack-Sjodin_2483.pdf:by-author/B/Boriack-Sjodin/1998_Boriack-Sjodin_2483.pdf:PDF},
  groups    = {sg/inhibitors, sg/reviews, sg/hCA2},
  keywords  = {Binding; Carbonic Anhydrases},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Borisov2015,
  author    = {S. V. Borisov and S. A. Magarill and N. V. Pervukhina},
  journal   = {Russian Chemical Reviews},
  title     = {Crystallographic analysis of a series of inorganic compounds},
  year      = {2015},
  number    = {4},
  pages     = {393--421},
  volume    = {84},
  abstract  = {The method of crystallographic analysis relies on the mechanical-wave concept that treats the crystalline state as the result of ordering of atomic positions by families of parallel equidistant planes. Using this method, a large set of fluoride, oxide and sulfide structures was analyzed. The pseudo-translational ordering of various atomic groups (including the presence of cation and anion sublattices) in the structures of various classes of inorganic compounds was established. The crucial role of local ordering of heavy cations (coherent assembly) in the structures comprising large cluster fragments (Keggin polyanions, polyoxoniobates, etc .) is discussed. The role of symmetry and the regular distribution of heavy atoms in the formation of stable crystal structures, which is to be taken into account in the targeted design, is considered. The universality of configurations of atomic positions in the structures of various classes of inorganic compounds resulting from the ordering mechanism organized by mechanical (elastic) forces is demonstrated. The bibliography includes 158 references.},
  file      = {2015_Borisov_393.pdf:by-author/B/Borisov/2015_Borisov_393.pdf:PDF},
  keywords  = {For COD Deposition; Materials "genome"; Review; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2016.10.03},
  creationdate = {2016-10-03T00:00:00},
  url       = {http://stacks.iop.org/0036-021X/84/i=4/a=393},
}

@Article{Borisov2011,
  author    = {Borisov, S. V. and Magarill, S. A. and Pervukhina, N. V.},
  journal   = {Crystallography Reports},
  title     = {Analysis of atomic structures as the development of Belov’s “lattice” crystallography},
  year      = {2011},
  issn      = {1562-689X},
  month     = {Nov},
  number    = {6},
  pages     = {935--940},
  volume    = {56},
  doi       = {10.1134/s1063774511060046},
  file      = {2011_Borisov_935.pdf:by-author/B/Borisov/2011_Borisov_935.pdf:PDF},
  keywords  = {Materials "genome"; X-ray Crystallography},
  owner     = {saulius},
  publisher = {Pleiades Publishing Ltd},
  timestamp = {2016.10.03},
  creationdate = {2016-10-03T00:00:00},
  url       = {http://dx.doi.org/10.1134/S1063774511060046},
}

@Article{Bornhovd2004,
  author    = {Bornhövd},
  title     = {Adaptive Database Caching with DBCache},
  year      = {2004},
  file      = {:by-author/B/Bornhövd/2004_Bornhövd.pdf:PDF},
  keywords  = {Caching; Computer Science (CS); Databases},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Borysov2017,
  author    = {Borysov, Stanislav S. and Geilhufe, R. Matthias and Balatsky, Alexander V.},
  journal   = {PLOS ONE},
  title     = {Organic materials database: An open-access online database for data mining},
  year      = {2017},
  issn      = {1932-6203},
  month     = {Feb},
  number    = {2},
  pages     = {e0171501},
  volume    = {12},
  doi       = {10.1371/journal.pone.0171501},
  editor    = {Ostroverkhova, Oksana},
  file      = {2017_Borysov_0171501.pdf:by-author/B/Borysov/2017_Borysov_0171501.pdf:PDF},
  owner     = {andrius},
  publisher = {Public Library of Science (PLoS)},
  timestamp = {2017.04.25},
  creationdate = {2017-04-25T00:00:00},
  url       = {http://dx.doi.org/10.1371/journal.pone.0171501},
}

@Article{Boss2006,
  author    = {Boss, Christoph and Corminboeuf, Olivier and Grisostomi, Corinna and Meyer, Solange and Jones, Andrew F. and Prade, Lars and Binkert, Christoph and Fischli, Walter and Weller, Thomas and Bur, Daniel},
  journal   = {ChemMedChem},
  title     = {Achiral, Cheap, and Potent Inhibitors of Plasmepsins I, II, and IV},
  year      = {2006},
  issn      = {1860-7187},
  pages     = {1341--1345},
  volume    = {1},
  abstract  = {A novel class of molecules targeting aspartic proteinases from P. falciparum is described. Synthesis of these easily available, achiral, and highly potent molecules was supported by structural information and eventually allowed the identification of compounds highly active against three vacuolar aspartic proteinases. In a red blood cell assay, the growth of P. falciparum (strain K1) could be effectively prevented.},
  doi       = {10.1002/cmdc.200600223},
  file      = {2006_Boss_1341.pdf:by-author/B/Boss/2006_Boss_1341.pdf:PDF},
  keywords  = {Aspartic Proteases; Drug Design; Inhibitors; Malaria; Medicinal Chemistry},
  owner     = {saulius},
  publisher = {WILEY-VCH Verlag},
  timestamp = {2015.08.14},
  creationdate = {2015-08-14T00:00:00},
  url       = {http://dx.doi.org/10.1002/cmdc.200600223},
}

@Manuscript{Bottomley2004,
  author    = {Henry Bottomley},
  title     = {Maximum distance between the mode and the mean of a unimodal distribution},
  year      = {2004},
  month     = {Feb},
  abstract  = {The difference between the mean and the mode of a unimodal distribution is less than or equal to the square root of three times the standard deviation.},
  file      = {:by-author/B/Bottomley/2004_Bottomley.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.09.18},
  creationdate = {2012-09-18T00:00:00},
}

@Article{Boulesteix2010,
  author    = {Boulesteix, Anne-Laure},
  journal   = {Bioinformatics},
  title     = {Over-optimism in bioinformatics research},
  year      = {2010},
  pages     = {437--439},
  volume    = {26},
  doi       = {10.1093/bioinformatics/btp648},
  eprint    = {http://bioinformatics.oxfordjournals.org/content/26/3/437.full.pdf+html},
  file      = {2010_Boulesteix_437.pdf:by-author/B/Boulesteix/2010_Boulesteix_437.pdf:PDF},
  keywords  = {Bioinformatics; Criticism; Reproducible Research},
  owner     = {saulius},
  timestamp = {2015.06.12},
  creationdate = {2015-06-12T00:00:00},
  url       = {http://bioinformatics.oxfordjournals.org/content/26/3/437.short},
}

@Article{Boullay2012,
  author    = {Boullay, P. and Lutterotti, L. and Chateigner, D.},
  title     = {Quantitative analysis of electron diffraction ring patterns using the {MAUD} program},
  year      = {2012},
  file      = {[PDF] from ensicaen.fr:by-author/B/Boullay/XXXX_Boullay.pdf:application/pdf},
  groups    = {sg/JAC2009},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://www.ecole.ensicaen.fr/~chateign/danielc/abstracts/Boullay_abstract_EMC2012.pdf},
  urldate   = {2015-08-31},
}

@Article{Boullay2014,
  author    = {Boullay, P. and Lutterotti, L. and Chateigner, D. and Sicard, L.},
  journal   = {Acta Crystallographica Section A},
  title     = {Fast microstructure and phase analyses of nanopowders using combined analysis of transmission electron microscopy scattering patterns},
  year      = {2014},
  pages     = {448--456},
  volume    = {70},
  abstract  = {The full quantitative characterization of nanopowders using transmission electron microscopy scattering patterns is shown. This study demonstrates the feasibility of the application of so-called combined analysis, a global approach for phase identification, structure refinement, characterization of anisotropic crystallite sizes and shapes, texture analysis and texture variations with the probed scale, using electron diffraction patterns of TiO2 and Mn3O4 nanocrystal aggregates and platinum films. Electron diffraction pattern misalignments, positioning, and slight changes from pattern to pattern are directly integrated and refined within this approach. The use of a newly developed full-pattern search-match methodology for phase identification of nanopowders and the incorporation of the two-wave dynamical correction for diffraction patterns are also reported and proved to be efficient.},
  doi       = {10.1107/S2053273314009930},
  file      = {2014_Boullay_448.pdf:by-author/B/Boullay/2014_Boullay_448.pdf:PDF},
  keywords  = {Citing COD; FPSM; Material Identification; Powder Diffraction},
  owner     = {saulius},
  timestamp = {2014.11.06},
  creationdate = {2014-11-06T00:00:00},
  url       = {http://dx.doi.org/10.1107/S2053273314009930},
}

@Article{Boullay2014a,
  author    = {Boullay, P. and Lutterotti, L. and Chateigner, D. and Sicard, L.},
  journal   = {Acta Crystallographica Section A: Foundations and Advances},
  title     = {Fast microstructure and phase analyses of nanopowders using combined analysis of transmission electron microscopy scattering patterns},
  year      = {2014},
  pages     = {448--456},
  volume    = {70},
  file      = {[PDF] from researchgate.net:by-author/B/Boullay/2014_Boullay_448a.pdf:application/pdf},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://scripts.iucr.org/cgi-bin/paper?s2053273314009930},
  urldate   = {2015-08-31},
}

@Article{Bourgeois1971,
  author     = {Bourgeois, Fran\c{c}ois and Lassalle, Jean-Claude},
  journal    = {Commun. ACM},
  title      = {An extension of the Munkres algorithm for the assignment problem to rectangular matrices},
  year       = {1971},
  issn       = {0001-0782},
  pages      = {802--804},
  volume     = {14},
  acmid      = {362945},
  address    = {New York, NY, USA},
  doi        = {10.1145/362919.362945},
  file       = {:by-author/B/Bourgeois/1971_Bourgeois_802.pdf:PDF},
  issue_date = {Dec. 1971},
  keywords   = {Algorithms; Assignment Problem; Operations Research; Optimization Theory; Rectangular Matrices},
  numpages   = {3},
  owner      = {saulius},
  publisher  = {ACM},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
  url        = {http://doi.acm.org/10.1145/362919.362945},
}

@Manuscript{Bourhis2007,
  author    = {Luc J. Bourhis and Ralf W. Grosse-Kunstleve and Paul D. Adams},
  title     = {cctbx news},
  year      = {2007},
  keywords  = {CCTBX; X-ray Crystallography},
  url       = {http://cci.lbl.gov/publications/download/iucrcompcomm_nov2007.pdf},
  abstract  = {We describe recent developments of the Computational Crystallography Toolbox.},
  file      = {:by-author/B/Bourhis/2007_Bourhis.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Bourne1991,
  author    = {Bourne, Henry R. and Sanders, David A. and McCormic, Frank},
  title     = {The {GTPase} superfamily: conserved structure and molecular mechanism},
  year      = {1991},
  volume    = {349},
  file      = {Bourne et al. - 1991 - The GTPase superfamily conserved structure and mo.pdf:by-author/B/Bourne/1991_Bourne.pdf:application/pdf},
  groups    = {sg/biomolecular},
  language  = {English},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://www.pawelserver.com/rabs/files/0007.pdf},
  urldate   = {2015-08-05},
}

@Presentation{Bourne2010,
  author       = {Philip E. Bourne},
  title        = {Principles of DNA and RNA Structure},
  year         = {2010},
  course       = {Pharm 201/Bioinformatics I},
  lecture      = {Lecture 2},
  organization = {UCSD},
  school       = {Department of Pharmacology},
  file         = {:by-author/B/Bourne/2010_Bourne.ppt:PPT},
  keywords     = {Presentations},
  owner        = {saulius},
  timestamp = {2015.03.03},
  creationdate = {2015-03-03T00:00:00},
}

@Misc{Bourne1998,
  author    = {Philip E. Bourne and Ilya N. Shindyalov},
  title     = {A Database of Pairwise Aligned 3-D Structures for the Aceytlcholinesterases, Lipases and other Homologous Proteins},
  year      = {1998},
  abstract  = {The comparison of results from 3-D structure alignments obtained by a variety of different algorithms and those determined by domain experts reveals significant differences. Simply finding the best RMSD between the corresponding alpha carbon positions in two structures is not enough to match biologically meaningful features, and hence provide the most meaningful structure alignment. Yet an accurate comparative analysis of structure reveals a great deal about the biological function of related proteins. A recently described combinatorial extension algorithm has been further refined by the use of protein properties relevant to structural and functional features to provide good structure alignments. The resulting database of automated pairwise alignments is reported for acetylcholinesterase (9), lipases (15), haloalkane dehalogenase (11), and Cholesterol esterase (2) structures where more than 200 residues could be aligned with an RMSD less than 4.0Å. Results for the alignment of an acetylcholinesterase to a lipase is compared to the previously performed manual alignment. The database and associated tools for visualizing the structure alignments are available via the Web at the URL http://cl.sdsc.edu/align_db.html.},
  file      = {:by-author/B/Bourne/1998_Bourne.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Bourniquel2002,
  author    = {Bourniquel, Aude A. and Bickle, Thomas A.},
  journal   = {Biochimie},
  title     = {Complex restriction enzymes: NTP-driven molecular motors.},
  year      = {2002},
  pages     = {1047--59},
  volume    = {84},
  abstract  = {Survival is assuredly the prime directive for all living organisms either as individuals or as a species. One of the main challenges encountered by bacterial populations is the danger of bacteriophage attacks, since infection of a single bacterium may rapidly propagate, decimating the entire population. In order to protect themselves against this acute threat, bacteria have developed an array of defence mechanisms, which range from preventing the infection itself via interference with bacteriophage adsorption to the cell surface and prevention of phage DNA injection, to degradation of the injected phage DNA. This last defence mechanism is catalysed by the bacterial restriction-modification (R-M) systems, and in particular, by nucleoside 5'-triphosphate (NTP)-dependent restriction enzymes, e.g. type I and type III R-M systems or the modification-dependent endonucleases. Type I and type III restriction systems have dual properties. They may either act as methylases and protect the host's own DNA against restriction by methylating specific residues, or they catalyse ATP-dependent endonuclease activity so that invading foreign DNA lacking the host-specific methylation is degraded. These defence mechanism systems are further complemented by the presence of methylation-dependent, GTP-dependent endonucleases, that restricts specifically methylated DNA. Although all three types of endonucleases are structurally very different, they share a common functional mechanism. They recognise and bind to specific DNA sequences but do not cleave DNA within those target sites. They belong to the general class of DNA motor proteins, which use the free energy associated with nucleoside 5'-triphosphate hydrolysis to translocate DNA so that the subsequent DNA cleavage event occurs at a distance from the endonuclease recognition site. Moreover, DNA cleavage appears to be a random process triggered upon stalling of the DNA translocation process and requiring dimerisation of the bound endonucleases for a concerted break of both DNA strands. In this review, we present a detailed description and analysis of the functional mechanism of the three known NTP-dependent restriction systems: type I and type III restriction-modification enzymes, as well as the methylation-dependent McrBC endonuclease.},
  file      = {:by-author/B/Bourniquel/2002_Bourniquel_1047.pdf:PDF},
  keywords  = {TypeIII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Bouvier2007,
  author    = {Bouvier, Benjamin and Grubmüller, Helmut},
  journal   = {Biophysical journal},
  title     = {A molecular dynamics study of slow base flipping in DNA using conformational flooding.},
  year      = {2007},
  pages     = {770--86},
  volume    = {93},
  abstract  = {Individual DNA bases are known to be able to flip out of the helical stack, providing enzymes with access to the genetic information otherwise hidden inside the helix. Consequently, base flipping is a necessary first step to many more complex biological processes such as DNA transcription or replication. Much remains unknown about this elementary step, despite a wealth of experimental and theoretical studies. From the theoretical point of view, the involved timescale of milliseconds or longer requires the use of enhanced sampling techniques. In contrast to previous theoretical studies employing umbrella sampling along a predefined flipping coordinate, this study attempts to induce flipping without prior knowledge of the pathway, using information from a molecular dynamics simulation of a B-DNA fragment and the conformational flooding method. The relevance to base flipping of the principal components of the simulation is assayed, and a combination of modes optimally related to the flipping of the base through either helical groove is derived for each of the two bases of the central guanine-cytosine basepair. By applying an artificial flooding potential along these collective coordinates, the flipping mechanism is accelerated to within the scope of molecular dynamics simulations. The associated free energy surface is found to feature local minima corresponding to partially flipped states, particularly relevant to flipping in isolated DNA; further transitions from these minima to the fully flipped conformation are accelerated by additional flooding potentials. The associated free energy profiles feature similar barrier heights for both bases and pathways; the flipped state beyond is a broad and rugged attraction basin, only a few kcal/mol higher in energy than the closed conformation. This result diverges from previous works but echoes some aspects of recent experimental findings, justifying the need for novel approaches to this difficult problem: this contribution represents a first step in this direction. Important structural factors involved in flipping, both local (sugar-phosphate backbone dihedral angles) and global (helical axis bend), are also identified.},
  file      = {:by-author/B/Bouvier/2007_Bouvier_770.pdf:PDF},
  keywords  = {Molecular Dynamics (MD)},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Manuscript{Bove2004,
  author    = {Bove, V. Michael, Jr. and Wendy J. Plesniak and Tyeler Quentmeyer and James Barabas},
  title     = {Real-time Holographic Video Images With Commodity {PC} Hardware},
  year      = {2004},
  keywords  = {Computer Graphics; Computer Science (CS)},
  abstract  = {The MIT second-generation holographic video system is a real-time electro-holographic display. The system produces a single-color horizontal parallax only (HPO) holographic image. To reconstruct a three-dimensional image, the display uses a computed fringe pattern with an effective resolution of 256K samples wide by 144 lines high by 8 bits per sample. In this paper we first describe the implementation of a new computational subsystem for the display, replacing custom computing hardware with commodity PC graphics chips, and using OpenGL. We also report the implementation of stereogram computing techniques that employ the PC hardware acceleration to generate and update holographic images at rates of up to two frames per second. These innovations shrink the system’s physical footprint to fit on the table-top and mark the fastest rate at which full computation and update have been achieved on this system to date. Finally we present first results of implementing the Reconfigurable Image Projection (RIP) method of computing high- quality holograms on this new system.},
  file      = {:by-author/B/Bove/2004_Bove.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Bozic1996,
  author      = {D. Bozic and S. Grazulis and V. Siksnys and R. Huber},
  journal     = {J Mol Biol},
  title       = {Crystal structure of Citrobacter freundii restriction endonuclease Cfr10I at 2.15 A resolution.},
  year        = {1996},
  month       = {Jan},
  number      = {1},
  pages       = {176--186},
  volume      = {255},
  abstract    = {The X-ray crystal structure of Citrobacter freundii restriction endonuclease Cfr10I has been determined at a resolution of 2.15 A by multiple isomorphous replacement methods and refined to an R-factor of 19.64\%. The structure of Cfr10I represents the first structure of a restriction endonuclease recognizing a degenerated nucleotide sequence. Structural comparison of Cfr10I with previously solved structures of other restriction enzymes suggests that recognition of specific sequence occurs through contacts in the major and the minor grooves of DNA. The arrangement of the putative active site residues shows some striking differences from previously described restriction endonucleases and supports a two-metal-ion mechanism of catalysis.},
  doi         = {10.1006/jmbi.1996.0015},
  file        = {:by-author/B/Bozic/1996_Bozic_176.pdf:PDF},
  groups      = {sg/Cfr10I},
  institution = {Max-Planck-Institut für Biochemie, Planegg-Martinsried Germany.},
  keywords    = {Binding Sites; Citrobacter Freundii; Crystallography; DNA; Deoxyribonucleases; Models; Molecular; Protein Conformation; Protein Folding; Protein Structure; Secondary; Type II Site-Specific; X-Ray},
  owner       = {em},
  pii         = {S0022-2836(96)90015-7},
  pmid        = {8568865},
  timestamp = {2011.06.08},
  creationdate = {2011-06-08T00:00:00},
  url         = {http://dx.doi.org/10.1006/jmbi.1996.0015},
}

@Article{Bozic1996a,
  author    = {Bozic, D. and Grazulis, S. and Siksnys, V. and Huber, R.},
  journal   = {Journal of molecular biology},
  title     = {Crystal structure of Citrobacter freundii restriction endonuclease Cfr10I at 2.15 A resolution.},
  year      = {1996},
  pages     = {176--86},
  volume    = {255},
  abstract  = {The X-ray crystal structure of Citrobacter freundii restriction endonuclease Cfr10I has been determined at a resolution of 2.15 A by multiple isomorphous replacement methods and refined to an R-factor of 19.64%. The structure of Cfr10I represents the first structure of a restriction endonuclease recognizing a degenerated nucleotide sequence. Structural comparison of Cfr10I with previously solved structures of other restriction enzymes suggests that recognition of specific sequence occurs through contacts in the major and the minor grooves of DNA. The arrangement of the putative active site residues shows some striking differences from previously described restriction endonucleases and supports a two-metal-ion mechanism of catalysis.},
  file      = {:by-author/B/Bozic/1996_Bozic_176.pdf:PDF},
  groups    = {sg/Cfr10I},
  keywords  = {Struct; TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Brunger1992,
  author    = {Br{\"{u}}nger, Axel T.},
  journal   = {Nature},
  title     = {Free R value: a novel statistical quantity for assessing the accuracy of crystal structures},
  year      = {1992},
  pages     = {472--475},
  volume    = {355},
  abstract  = {The determination of macromolecular structure by crystallography involves fitting atomic models to the observed diffraction data. The traditional measure of the quality of this fit, and presumably the accuracy of the model, is the R value. Despite stereochemical restraints, it is possible to overfit or 'misfit' the diffraction data: an incorrect model can be refined to fairly good R values as several recent examples have shown. Here I propose a reliable and unbiased indicator of the accuracy of such models. By analogy with the cross-validation method of testing statistical models I define a statistical quantity (R(free) (T) that measures the agreement between observed and computed structure factor amplitudes for a 'test' set of reflections that is omitted in the modelling and refinement process. As examples show, there is a high correlation between R(free) (T) and the accuracy of the atomic model phases. This is useful because experimental phase information is usually inaccurate, incomplete or unavailable. I expect that R(free) (T) will provide a measure of the information content of recently proposed models of thermal motion and disorder, time-averaging and bulk solvent.},
  doi       = {10.1038/355472a0},
  file      = {1992_Brunger_472.pdf:by-author/B/Brünger/1992_Brünger_472.pdf:PDF;:by-author/B/Brunger/1992_Brunger_472.djvu:Djvu},
  keywords  = {Data Quality; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Brunger1987,
  author    = {Br{\"{u}}nger, Axel T. and Kuriyan, John and Karplus, Martin},
  journal   = {Science},
  title     = {Crystallographic {R} Factor Refinement by Molecular Dynamics},
  year      = {1987},
  pages     = {458--460},
  volume    = {235},
  file      = {:by-author/B/Brunger/1987_Brunger_458.pdf:PDF},
  keywords  = {Data Quality; Protein Structure; R Factor; Refinement; X-ray Crystallography},
  owner     = {andrius},
  timestamp = {2012.05.11},
  creationdate = {2012-05-11T00:00:00},
}

@Article{Bradley2005,
  author    = {Bradley, Philip and Misura, Kira M. S. and Baker, David},
  journal   = {Science (New York, N.Y.)},
  title     = {Toward high-resolution de novo structure prediction for small proteins.},
  year      = {2005},
  pages     = {1868--71},
  volume    = {309},
  abstract  = {The prediction of protein structure from amino acid sequence is a grand challenge of computational molecular biology. By using a combination of improved low- and high-resolution conformational sampling methods, improved atomically detailed potential functions that capture the jigsaw puzzle-like packing of protein cores, and high-performance computing, high-resolution structure prediction (&lt;1.5 angstroms) can be achieved for small protein domains (&lt;85 residues). The primary bottleneck to consistent high-resolution prediction appears to be conformational sampling.},
  file      = {:by-author/B/Bradley/2005_Bradley_1868.pdf:PDF},
  keywords  = {Structure Prediction},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Bragg1913,
  author    = {Bragg, W. H. and Bragg, W. L.},
  journal   = {Proceedings of the Royal Society of London A: Mathematical, Physical and Engineering Sciences},
  title     = {The Reflection of X-rays by Crystals},
  year      = {1913},
  issn      = {0950-1207},
  pages     = {428--438},
  volume    = {88},
  doi       = {10.1098/rspa.1913.0040},
  file      = {1913_Bragg_428.pdf:by-author/B/Bragg/1913_Bragg_428.pdf:PDF},
  keywords  = {Brag-Wulff Law; Bragg's Law; History; History of Science; X-ray Crystallography},
  owner     = {saulius},
  publisher = {The Royal Society},
  timestamp = {2015.03.02},
  creationdate = {2015-03-02T00:00:00},
}

@Article{Brameld1997,
  author    = {Ken Brameld and Siddharth Dasgupta and William A. Goddard III},
  journal   = {The Journal of Physical Chemistry B},
  title     = {Distance Dependent Hydrogen Bond Potentials for Nucleic Acid Base Pairs from ab Initio Quantum Mechanical Calculations (LMP2/cc-pVTZ)},
  year      = {1997},
  pages     = {4851--4859},
  volume    = {101},
  abstract  = {Hydrogen bonding between base pairs in nucleic acids is a key determinant of their structures. We have examined the distance dependence of the hydrogen bonding of AT-WC (Watson-Crick), GC-WC, and AT-H (Hoogsteen) base pairs using ab initio quantum mechanics, LMP2/cc-pVTZ(-f) energies at HF/cc-pVTZ(-f) optimized geometries. From these curves, we have extracted Morse potentials between the H atoms and the acceptor atoms that accurately reproduce the quantum mechanical energies for a range of geometries. Using these parameters, we have calculated the complexation energies of the remaining 26 possible pairwise combinations, and the agreement with previously reported ab initio calculations is excellent. We have also extracted off-diagonal Lennard-Jones 12-6 parameters to be used with the popular AMBER95 and CHARMM95 force fields that significantly improve their descriptions of the base-pairing energy and optimum geometry.},
  doi       = {10.1021/jp970199a},
  file      = {:by-author/B/Brameld/1997_Brameld_4851.pdf:PDF},
  keywords  = {H Bonds; Nucleic Acids},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
  url       = {http://pubs.acs.org/doi/abs/10.1021/jp970199a},
}

@Article{Branden1990,
  author    = {Carl-Ivar Brändén and T. Alwyn Jones},
  journal   = {Nature},
  title     = {Between objectivity and subjectivity},
  year      = {1990},
  pages     = {687--689},
  volume    = {343},
  abstract  = {Protein crystallography is an exacting trade, and the results may contain errors that are difficult to identify. It is the crystallographer's responsibility to make sure that incorrect protein structures do not reach the literature.},
  doi       = {10.1038/343687a0},
  file      = {1990_Branden_687.pdf:by-author/B/Brändén/1990_Brändén_687.pdf:PDF;:by-author/B/Branden/1990_Branden_687.djvu:Djvu},
  keywords  = {Data Quality; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://www.nature.com/nature/journal/v343/n6260/abs/343687a0.html},
}

@PhdThesis{Brandis1995,
  author    = {Marc Michael Brandis},
  school    = {ETH Zürich},
  title     = {Optimizing Compilers for Structured Programming Languages},
  year      = {1995},
  file      = {:by-author/B/Brandis/1995_Brandis.ps.gz:PostScript;:by-author/B/Brandis/1995_Brandis.pdf:PDF},
  number    = {Sciences},
  owner     = {saulius},
  timestamp = {2013.08.10},
  creationdate = {2013-08-10T00:00:00},
}

@Article{Bray1983,
  author    = {Gary Bray},
  journal   = {ACM SIGAda Ada Letters},
  title     = {Implementation implications of {A}da generics},
  year      = {1983},
  number    = {2},
  pages     = {62--71},
  volume    = {III},
  doi       = {10.1145/989971.989974},
  file      = {:by-author/B/Bray/1983_Bray_62.pdf:PDF},
  keywords  = {Ada; Computer Science (CS); Generic Types; Programming Languages},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Breternitz2015,
  author    = {Breternitz, Joachim and Gregory, Duncan},
  journal   = {Crystals},
  title     = {The Search for Hydrogen Stores on a Large Scale; A Straightforward and Automated Open Database Analysis as a First Sweep for Candidate Materials},
  year      = {2015},
  pages     = {617--633},
  volume    = {5},
  doi       = {10.3390/cryst5040617},
  file      = {:by-author/B/Breternitz/2015_Breternitz_617.pdf:PDF},
  keywords  = {Citing COD},
  owner     = {andrius},
  timestamp = {2015.12.07},
  creationdate = {2015-12-07T00:00:00},
}

@Article{Breton1996,
  author    = {Breton, R. and Housset, D. and Mazza, C. and Fontecilla-Camps, J. C.},
  journal   = {Structure (London, England : 1993)},
  title     = {The structure of a complex of human 17beta-hydroxysteroid dehydrogenase with estradiol and NADP+ identifies two principal targets for the design of inhibitors.},
  year      = {1996},
  number    = {8},
  pages     = {905--915},
  volume    = {4},
  abstract  = {BACKGROUND:The steroid hormone 17beta-estradiol is important in the genesis and development of human breast cancer. Its intracellular concentration is regulated by 17beta-hydroxysteroid dehydrogenase, which catalyzes the reversible reduction of estrone to 17beta-estradiol. This enzyme is thus an important target for inhibitor design. The precise localization and orientation of the substrate and cofactor in the active site is of paramount importance for the design of such inhibitors, and for an understanding of the catalytic mechanism. RESULTS:The structure of recombinant human 17beta-hydroxysteroid dehydrogenase of type 1 (17beta-HSD1) in complex with estradiol at room temperature has been determined at 1.7 A resolution, and a ternary 17betaHSD1-estradiol-NADP+ complex at -150 degrees C has been solved and refined at 2.20 A resolution. The structures show that estradiol interacts with the enzyme through three hydrogen bonds (involving side chains of Ser142, Tyr155 and His221), and hydrophobic interactions between the core of the steroid and nine other residues. The NADP+ molecule binds in an extended conformation, with the nicotinamide ring close to the estradiol molecule. CONCLUSIONS:From the structure of the complex of the enzyme with the substrate and cofactor of the oxidation reaction, the orientation of the substrates for the reduction reaction can be deduced with confidence. A triangular hydrogen-bond network between Tyr155, Ser142 and O17 from estradiol probably facilitates the deprotonation of the reactive tyrosine, while the conserved Lys159 appears not to be directly involved in catalysis. Both the steroid-binding site and the NADPH-binding site can be proposed as targets for the design of inhibitors.},
  doi       = {10.1016/S0969-2126(96)00098-6},
  file      = {:by-author/B/Breton/1996_Breton_905.pdf:PDF},
  keywords  = {17β-hydroxysteroid Dehydrogenase; Complex; Estradiol; NADP+; Structure Refinement; Validation; X-ray Crystallography; X-ray Structure},
  owner     = {saulius},
  pubmed    = {8805577},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Article{Breton2001,
  author    = {Breton, S},
  journal   = {JOP : Journal of the pancreas},
  title     = {The cellular physiology of carbonic anhydrases.},
  year      = {2001},
  pages     = {159--64},
  volume    = {2},
  abstract  = {Carbonic anhydrases are zinc metalloenzymes that catalyze the reversible hydration of CO(2) to form HCO(3)(-) and protons according to the following reaction: CO(2) + H(2)O &lt;=&gt; H(2)CO(3) &lt;=&gt; HCO(3)(-) + H(+). The first reaction is catalyzed by carbonic anhydrase and the second reaction occurs instantaneously. The carbonic anhydrase (CA) gene family includes ten enzymatically active members, which are major players in many physiological processes, including renal and male reproductive tract acidification, bone resorption, respiration, gluconeogenesis, signal transduction, and formation of gastric acid. The newly identified CA IX (previously called MN) and CA XII are related to cell proliferation and oncogenesis. Carbonic anhydrase isozymes have different kinetic properties and they are present in various tissues and in various cell compartments. CA I, II, III and VII are cytoplasmic, CA V is mitochondrial, and CA VI is present in salivary secretions. CA IV, IX, XII and XIV are membrane proteins: CA IV is a glycosyl-phosphatidylinositol-anchored protein, and CA IX, XII and XIV are transmembrane proteins. The present work will focus on the roles of CA II and CA IV in transepithelial proton secretion and bicarbonate reabsorption processes. The localization of these isoforms in selected epithelia that are involved in net acid/base transport, such as kidney proximal tubules and collecting ducts, and tubules from the male reproductive tract will be reviewed.},
  file      = {2001_Breton_159.pdf:by-author/B/Breton/2001_Breton_159.pdf:PDF},
  groups    = {sg/physiology},
  keywords  = {Carbonic Anhydrases},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Webpage{Bretthorst1998,
  author    = {G. Larry Bretthorst},
  retrieved = {2008-07-28},
  title     = {Edwin T. Jaynes -- Bibliography},
  url       = {http://bayes.wustl.edu/etj/node1.html},
  year      = {1998},
  file      = {:by-author/B/Bretthorst/1998_Bretthorst._Jaynes_-_Bibliography.war:},
  groups    = {sg/Bayesian},
  keywords  = {Bayesian-statistics; Mathematics},
  owner     = {saulius},
  timestamp = {2015.03.02},
  creationdate = {2015-03-02T00:00:00},
}

@Article{Bricogne2003,
  author    = {Bricogne, G. and Vonrhein, C. and Flensburg, C. and Schiltz, M. and Paciorek, W.},
  journal   = {Acta Crystallographica Section D},
  title     = {Generation, representation and flow of phase information in structure determination: recent developments in and around {\it SHARP} 2.0},
  year      = {2003},
  pages     = {2023--2030},
  volume    = {59},
  doi       = {10.1107/S0907444903017694},
  file      = {ba5047.pdf:by-author/B/Bricogne/2003_Bricogne_2023.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444903017694},
}

@Article{Briggs2000,
  author    = {Mark S. Briggs and D. Dougal Burns and Michael E. Cooper and Susan J. Gregory},
  journal   = {Chemical Communications},
  title     = {A pH sensitive fluorescent cyanine dye for biological applications},
  year      = {2000},
  number    = {23},
  pages     = {2323--2324},
  abstract  = {A pentamethine cyanine dye has been synthesised that is fluorescent when protonated{,} becoming non-fluorescent upon proton abstraction. The probe has a p of 7.5{,} with observable changes in the fluorescent emission properties across a pH range of 6.0-8.0{,} therefore providing a useful probe for studying pH in biological media.},
  doi       = {10.1039/b007108k},
  file      = {2000_Briggs_2323.pdf:by-author/B/Briggs/2000_Briggs_2323.pdf:PDF},
  keywords  = {{pH} Sensitive DNA Base Analogues},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@InProceedings{Brinkhoff1996,
  author    = {Brinkhoff, T. and Kriegel, H.-P. and Seeger, B.},
  booktitle = {Data Engineering, 1996. Proceedings of the Twelfth International Conference on},
  title     = {Parallel Processing of Spatial Joins Using R-trees},
  year      = {1996},
  pages     = {258--265},
  abstract  = {We show that spatial joins are very suitable to be processed on a parallel hardware platform. The parallel system is equipped with a so called shared virtual memory which is well suited for the design and implementation of parallel spatial join algorithms. We start with an algorithm that consists of three phases: task creation, task assignment and parallel task execution. In order to reduce CPU and I/O cost, the three phases are processed in a fashion that preserves spatial locality. Dynamic load balancing is achieved by splitting tasks into smaller ones and reassigning some of the smaller tasks to idle processors. In an experimental performance comparison, we identify the advantages and disadvantages of several variants of our algorithm. The most efficient one shows an almost optimal speed up under the assumption that the number of disks is sufficiently large},
  doi       = {10.1109/ICDE.1996.492114},
  file      = {:by-author/B/Brinkhoff/1996_Brinkhoff_258.pdf:PDF},
  keywords  = {Almost Optimal Speed up; Dynamic Load Balancing; Experimental Performance Comparison; Parallel Algorithms; Parallel Hardware Platform; Parallel Processing; Parallel Programming; Parallel Spatial Join Algorithms; Parallel System; Parallel Task Execution; R Trees; Relational Algebra; Resource Allocation; Shared Virtual Memory; Spatial Data Structures; Spatial Joins; Spatial Locality; Task Assignment; Task Creation; Tree Data Structures; Virtual Storage; Visual Databases},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Brinkley1988,
  author    = {Brinkley, J. F. and Altman, R. B. and Duncan, B. S. and Buchanan, B. G. and Jardetzky, O.},
  journal   = {Journal of chemical information and computer sciences},
  title     = {Heuristic refinement method for the derivation of protein solution structures: validation on cytochrome b562.},
  year      = {1988},
  pages     = {194--210},
  volume    = {28},
  abstract  = {A method is described for determining the family of protein structures compatible with solution data obtained primarily from nuclear magnetic resonance (NMR) spectroscopy. Starting with all possible conformations, the method systematically excludes conformations until the remaining structures are only those compatible with the data. The apparent computational intractability of this approach is reduced by assembling the protein in pieces, by considering the protein at several levels of abstraction, by utilizing constraint satisfaction methods to consider only a few atoms at a time, and by utilizing artificial intelligence methods of heuristic control to decide which actions will exclude the most conformations. Example results are presented for simulated NMR data from the known crystal structure of cytochrome b562 (103 residues). For 10 sample backbones an average root-mean-square deviation from the crystal of 4.1 A was found for all alpha-carbon atoms and 2.8 A for helix alpha-carbons alone. The 10 backbones define the family of all structures compatible with the data and provide nearly correct starting structures for adjustment by any of the current structure determination methods.},
  doi       = {10.1021/ci00060a005},
  file      = {:by-author/B/Brinkley/1988_Brinkley_194.pdf:PDF},
  keywords  = {Description of NMR Structures},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
  url       = {http://pubs.acs.org/doi/abs/10.1021/ci00060a005},
}

@Article{Britten1969,
  author    = {Britten, R. J. and Davidson, E. H.},
  journal   = {Science},
  title     = {Gene Regulation for Higher Cells: A Theory},
  year      = {1969},
  issn      = {1095-9203},
  month     = {Jul},
  number    = {3891},
  pages     = {349–357},
  volume    = {165},
  doi       = {10.1126/science.165.3891.349},
  file      = {1969_Britten_349.pdf:by-author/B/Britten/1969_Britten_349.pdf:PDF},
  groups    = {am/RNA activation},
  owner     = {andrius},
  publisher = {American Association for the Advancement of Science (AAAS)},
  timestamp = {2016.10.04},
  creationdate = {2016-10-04T00:00:00},
  url       = {http://dx.doi.org/10.1126/science.165.3891.349},
}

@Article{Brodersen2003,
  author    = {Brodersen, D. E. and Clemons, Jr, W. M. and Carter, A. P. and Wimberly, B. T. and Ramakrishnan, V.},
  journal   = {Acta Crystallographica Section D},
  title     = {Phasing the 30S ribosomal subunit structure},
  year      = {2003},
  pages     = {2044--2050},
  volume    = {59},
  doi       = {10.1107/S0907444903017669},
  file      = {ba5037.pdf:by-author/B/Brodersen/2003_Brodersen_2044.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444903017669},
}

@Manuscript{Broline2005,
  author    = {Duane Broline},
  title     = {Generators and Relations, Isomorphisms and Cosets},
  year      = {2005},
  keywords  = {Abstract Algebra; Coset Enumeration; GAP; Group Representation},
  url       = {http://www.ux1.eiu.edu/~cfdmb/gap/3530_03fa/lab3.pdf},
  abstract  = {One of the ways that groups in GAP are specified is through generators and relations. There are man y subtle diffculties and much deep mathematics in this area, ho w ev er, the basic idea is not all that hard. An alphab et is a set of sym b ols. A w ord is a string of sym b ols from the alphab et. F or example, if the alphab et w ere f a; b g , words in the alphab et would b e aaabbaa , aba , and ababaab . In addition to the w ords con taining one or more sym b ols, there is the sp ecial word, , represen ting the \word with no symbols. Let W be the set of all w ords in some alphab et. The op eration of juxtap osition (placing next to eac h other), denes an asso ciativ e asso ciativ e op eration on W . The w ord is the iden tit y of this op eration. With the addition of \rewriting rules" the set can giv e rise to a group. A t w o-w a y rewriting rule is an expression of the form w 1 $ w 2 , where w 1 and w 2 are w ords in some alphab et. Suc h a rule allo ws us to c hange the w ords in an alphab et. F or example, the rule w 1 $ w 2 means that if ev er w 1 is a part of a larger w ord, then that p ortion of the w ord consisting of w 1 made b e replaced b y w 2 and, con v ersely , an o ccurrence of w 2 ma y b e replaced b y w 1 .},
  file      = {2005_Broline.pdf:by-author/B/Broline/2005_Broline.pdf:PDF},
  owner     = {saulius},
  timestamp = {2013.10.20},
  creationdate = {2013-10-20T00:00:00},
}

@Article{Brooijmans2010,
  author    = {Brooijmans, Natasja and Humblet, Christine},
  journal   = {Chemical Biology \& Drug Design},
  title     = {Chemical Space Sampling in Virtual Screening by Different Crystal Structures},
  year      = {2010},
  issn      = {1747-0285},
  pages     = {472--479},
  volume    = {76},
  abstract  = {Retrospective virtual screening experiments were carried out to investigate the effects of combining hit lists from different crystal structures of the same target using consensus scoring. An in-house High Throughput Screening (HTS) dataset from PI3K-γ was used and docked against five diverse PI3K-γ crystal structures. The results show that consensus scoring prioritizes compounds that score moderately against individual crystal structures and is thus complementary to individual crystal structure screening leading to an increase in the diversity of hits. Enrichment factors (EFs) of the consensus score for two or three structures are often as high as or higher than the EF of the individual structures used in the consensus score. Combining four or five structures in the consensus score generally yields lower enrichments. Compounds in the top 500 of the consensus score that are also found in the top 500 of an individual X-ray structure used in the consensus score calculations yield the largest number of hits with the lowest number of false positives.},
  doi       = {10.1111/j.1747-0285.2010.01041.x},
  file      = {2010_Brooijmans_472.pdf:by-author/B/Brooijmans/2010_Brooijmans_472.pdf:PDF},
  keywords  = {Binding Sites; Computer Aided Design; Crystallography: X Ray; Docking; Drug Design; Models: Molecular; Protein Conformation; Protein Kinases},
  owner     = {saulius},
  publisher = {Blackwell Publishing Ltd},
  timestamp = {2013.04.01},
  creationdate = {2013-04-01T00:00:00},
  url       = {http://dx.doi.org/10.1111/j.1747-0285.2010.01041.x},
}

@Article{Brooks1983,
  author    = {Brooks, Bernard R. and Bruccoleri, Robert E. and Olafson, Barry D. and States, David J. and Swaminathan, S. and Karplus, Martin},
  journal   = {Journal of Computational Chemistry},
  title     = {{CHARMM}: A program for macromolecular energy, minimization, and dynamics calculations},
  year      = {1983},
  issn      = {1096-987X},
  number    = {2},
  pages     = {187–217},
  volume    = {4},
  doi       = {10.1002/jcc.540040211},
  file      = {1983_Brooks_187.pdf:by-author/B/Brooks/1983_Brooks_187.pdf:PDF},
  groups    = {sg/Crystallography, am/Crystallography},
  owner     = {andrius},
  publisher = {Wiley-Blackwell},
  timestamp = {2016.11.22},
  creationdate = {2016-11-22T00:00:00},
  url       = {http://dx.doi.org/10.1002/jcc.540040211},
}

@Manuscript{BrooksXXXX,
  author    = {Brooks, Christopher H.},
  title     = {An Introduction to Amoeba},
  year      = {XXXX},
  keywords  = {Computer Science (CS); Minimisation; Simplex Method},
  file      = {:by-author/B/Brooks/XXXX_Brooks.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@InBook{Brooks1995,
  author    = {Brooks, Jr., Frederick Phillips},
  publisher = {Addison Wesley Longman, Inc.},
  title     = {The Mythical Man-Month},
  year      = {1995},
  file      = {1995_Brooks.pdf:by-author/B/Brooks/1995_Brooks.pdf:PDF},
  groups    = {sg/Software project management},
  owner     = {saulius},
  timestamp = {2015.11.22},
  creationdate = {2015-11-22T00:00:00},
  url       = {http://phoenix.goucher.edu/~kelliher/f2010/cs245/theMythicalManMonth.pdf},
}

@Manuscript{Brooks1986,
  author       = {Brooks, Jr., Frederick P.},
  title        = {No Silver Bullet — Essence and Accident in Software Engineering},
  year         = {1986},
  keywords     = {Computer Science (CS); Software Engineering; Software Project Management},
  organization = {University of North Carolina at Chapel Hill},
  url          = {http://faculty.salisbury.edu/~xswang/Research/Papers/SERelated/no-silver-bullet.pdf},
  abstract     = {There is no single development, in either technology or management technique, which by itself promises even one order-of-magnitude improvement within a decade in productivity, in reliability, in simplicity.},
  file         = {1986_Brooks.pdf:by-author/B/Brooks/1986_Brooks.pdf:PDF},
  groups       = {sg/Software project management},
  owner        = {saulius},
  timestamp = {2015.12.09},
  creationdate = {2015-12-09T00:00:00},
}

@Article{Brophy1997,
  author    = {James M. Brophy and Lawrence Joseph},
  journal   = {The Lancet},
  title     = {Bayesian interim statistical analysis of randomised trials},
  year      = {1997},
  pages     = {1166--1168},
  volume    = {349},
  file      = {James M. Brophy and Lawrence Joseph - 1997 - Bayesian interim statistical analysis of randomise.pdf:by-author/B/Brophy/1997_Brophy_1166.pdf:application/pdf},
  groups    = {sg/Clinical Trials},
  language  = {English},
  owner     = {saulius},
  timestamp = {2015.12.14},
  creationdate = {2015-12-14T00:00:00},
  url       = {http://www.medicine.mcgill.ca/epidemiology/Joseph/publications/Methodological/lancet1997.pdf},
  urldate   = {2015-12-12},
}

@Article{Bross-Walch2005,
  author    = {Bross-Walch, Nadja and Kühn, Till and Moskau, Detlef and Zerbe, Oliver},
  journal   = {Chemistry \&amp; biodiversity},
  title     = {Strategies and tools for structure determination of natural products using modern methods of NMR spectroscopy.},
  year      = {2005},
  pages     = {147--77},
  volume    = {2},
  file      = {:by-author/B/Bross-Walch/2005_Bross-Walch_147.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Browman2008,
  author    = {Browman},
  title     = {The use and misuse of bibliometric indices in evaluating scholarly performance},
  year      = {2008},
  file      = {:by-author/B/Browman/2008_Browman.pdf:PDF},
  groups    = {sg/Bibliometrics},
  keywords  = {Impact Factors},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Presentation{Brown2010,
  author    = {Brown},
  title     = {Shape Determination: Application to Proteins},
  year      = {2010},
  file      = {:by-author/B/Brown/2010_Brown_slides2.pdf:PDF},
  keywords  = {SAXS},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Presentation{Brown2010a,
  author    = {Brown},
  title     = {Rigid Body Refinement: Applications to Proteins},
  year      = {2010},
  file      = {:by-author/B/Brown/2010_Brown_slides.pdf:PDF},
  keywords  = {SAXS},
  owner     = {em},
  pages     = {slides},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Manuscript{Brown2007,
  author    = {Curtis Brown},
  title     = {Alternative Formulations of Propositional Logic},
  year      = {2007},
  file      = {:by-author/B/Brown/2007_Brown.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.09.18},
  creationdate = {2012-09-18T00:00:00},
}

@Article{Brown2007a,
  author    = {Brown, Eric N. and Ramaswamy, S.},
  journal   = {Acta crystallographica. Section D, Biological crystallography},
  title     = {Quality of protein crystal structures.},
  year      = {2007},
  pages     = {941--50},
  volume    = {63},
  abstract  = {The genomics era has seen the propagation of numerous databases containing easily accessible data that are routinely used by investigators to interpret results and generate new ideas. Most investigators consider data extracted from scientific databases to be error-free. However, data generated by all experimental techniques contain errors and some, including the coordinates in the Protein Data Bank (PDB), also integrate the subjective interpretations of experimentalists. This paper explores the determinants of protein structure quality metrics used routinely by protein crystallographers. These metrics are available for most structures in the database, including the R factor, R(free), real-space correlation coefficient, Ramachandran violations etc. All structures in the PDB were analyzed for their overall quality based on nine different quality metrics. Multivariate statistical analysis revealed that while technological improvements have increased the number of structures determined, the overall quality of structures has remained constant. The quality of structures deposited by structural genomics initiatives are generally better than the quality of structures from individual investigator laboratories. The most striking result is the association between structure quality and the journal in which the structure was first published. The worst offenders are the apparently high-impact general science journals. The rush to publish high-impact work in the competitive atmosphere may have led to the proliferation of poor-quality structures.},
  doi       = {10.1107/S0907444907033847},
  file      = {:by-author/B/Brown/2007_Brown_941.pdf:PDF},
  groups    = {sg/Bibliometrics},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Brown2009,
  author    = {Brown, Ian David},
  journal   = {Chem. Rev.},
  title     = {Recent Developments in the Methods and Applications of the Bond Valence Model},
  year      = {2009},
  issn      = {1520-6890},
  month     = {Dec},
  number    = {12},
  pages     = {6858–6919},
  volume    = {109},
  doi       = {10.1021/cr900053k},
  file      = {2009_Brown_6858.pdf:by-author/B/Brown/2009_Brown_6858.pdf:PDF},
  groups    = {sg/Crystallography, am/Crystallography},
  owner     = {andrius},
  publisher = {American Chemical Society (ACS)},
  timestamp = {2016.11.14},
  creationdate = {2016-11-14T00:00:00},
  url       = {http://dx.doi.org/10.1021/cr900053k},
}

@Article{Brown1996b,
  author           = {I. D. Brown},
  journal          = {J. Res. Natl. Inst. Stand. Technol.},
  title            = {CIF (Crystallographic Information File): A Standard for Crystallographic Data Interchange},
  year             = {1996},
  pages            = {341--346},
  volume           = {101},
  creationdate     = {2015-05-13T00:00:00},
  file             = {1996_Brown_341.pdf:by-author/B/Brown/1996_Brown_341.pdf:PDF},
  keywords         = {CIF},
  modificationdate = {2023-08-07T10:23:05},
  owner            = {saulius},
  timestamp        = {2015.05.13},
  url              = {http://nvlpubs.nist.gov/nistpubs/jres/101/3/j3brow.pdf},
}

@Article{Brown1983,
  author    = {Brown, I. D.},
  journal   = {Acta Crystallographica Section A},
  title     = {The standard crystallographic file structure},
  year      = {1983},
  pages     = {216--224},
  volume    = {39},
  abstract  = {This paper describes a file structure that has been developed by a joint working party of the Data and Computing Commissions of the International Union of Crystallography. It is intended as a standard that can be used by those wishing to transfer any type of crystallographic data from one laboratory or program system to another.},
  doi       = {10.1107/S0108767383000495},
  file      = {1983_Brown_216.pdf:by-author/B/Brown/1983_Brown_216.pdf:PDF},
  keywords  = {Crystallography; Crystallography File Formats; Data Management; File Formats; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2013.09.18},
  creationdate = {2013-09-18T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0108767383000495},
}

@Article{Brown2002,
  author           = {I. David Brown and Brian McMahon},
  journal          = {Acta Crystallographica Section B},
  title            = {{CIF}: the computer language of crystallography},
  year             = {2002},
  pages            = {317--324},
  volume           = {58},
  abstract         = {The Crystallographic Information File (CIF) was adopted in 1990 by the International Union of Crystallography as a file structure for the archiving and distribution of crystallographic information. The CIF standard is now well established and is in regular use for reporting crystal structure determinations to Acta Crystallographica and other journals. The structure of CIF is ̄exible and extensible and is compatible with other evolving standards. It is well suited to relational and object-oriented models, and is being adopted by the crystallographic databases. This paper reviews the development of CIF and describes its salient features. Future extension of the standard to include implementation of methods will allow CIF to exploit the potential of advanced information-handling software.},
  creationdate     = {2013-02-06T00:00:00},
  doi              = {10.1107/S0108768102003464},
  file             = {:by-author/B/Brown/2002_Brown_317.pdf:PDF},
  keywords         = {CIF},
  modificationdate = {2023-08-07T10:23:05},
  owner            = {andrius},
  timestamp        = {2013.02.06},
}

@Article{Brown2016,
  author    = {Brown, Jr., Gordon E.},
  journal   = {Elements},
  title     = {The Pyramids of Giza and Archimedes’ Palimpsest: What Would Indiana Jones Think of Modern Approaches to Archaeology?},
  year      = {2016},
  issn      = {1811-5217},
  month     = {Feb},
  number    = {1},
  pages     = {3–4},
  volume    = {12},
  doi       = {10.2113/gselements.12.1.3},
  file      = {2016_Brown_3.pdf:by-author/B/Brown/2016_Brown_3.pdf:PDF},
  keywords  = {Archeology; Palimpsest; X-ray; X-ray Flourescense},
  owner     = {saulius},
  publisher = {GeoScienceWorld},
  timestamp = {2016.03.23},
  creationdate = {2016-03-23T00:00:00},
  url       = {http://dx.doi.org/10.2113/gselements.12.1.3},
}

@Article{Brown2011,
  author    = {Brown, Nathan},
  journal   = {Wiley Interdisciplinary Reviews: Computational Molecular Science},
  title     = {Algorithms for chemoinformatics},
  year      = {2011},
  issn      = {1759-0884},
  pages     = {716--726},
  volume    = {1},
  abstract  = {The field of chemoinformatics makes use of a great number of different computational algorithms from mathematics and computer science as well as algorithms that are defined explicitly for challenges specific to chemoinformatics. This article provides an overview of algorithms and algorithmic complexity together with a review of common algorithmic design paradigms. These approaches are then given context with a set of relevant examples from chemoinformatics with definitions of the algorithms and, where relevant, graphical explanations. © 2011 John Wiley & Sons, Ltd. WIREs Comput Mol Sci 2011 1 716-726 DOI: 10.1002/wcms.42},
  doi       = {10.1002/wcms.42},
  file      = {2011_Brown_716.pdf:by-author/B/Brown/2011_Brown_716.pdf:PDF},
  owner     = {saulius},
  publisher = {John Wiley \& Sons, Inc.},
  timestamp = {2014.10.18},
  creationdate = {2014-10-18T00:00:00},
  url       = {http://dx.doi.org/10.1002/wcms.42},
}

@Article{Brown1996,
  author    = {Nigel P. Brown and Christine A. Orengo and William R. Taylor},
  journal   = {Computers \& Chemistry},
  title     = {A protein structure comparison methodology},
  year      = {1996},
  issn      = {0097-8485},
  pages     = {359--380},
  volume    = {20},
  doi       = {10.1016/0097-8485(95)00062-3},
  file      = {1996_Brown_359.pdf:by-author/B/Brown/1996_Brown_359.pdf:PDF},
  groups    = {sg/Molecule superposion, sg/Superposition, sg/Bioinf. Algorithms},
  keywords  = {Algorithms; Structure Superposition; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2012.05.16},
  creationdate = {2012-05-16T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/0097848595000623},
}

@Article{Brown1991,
  author    = {A. S. Brown and M. A. Spackman},
  journal   = {Acta Crystallographica Section A Foundations of Crystallography},
  title     = {A model study of the $\upkappa$-refinement procedure for fitting valence electron densities},
  year      = {1991},
  month     = {jan},
  number    = {1},
  pages     = {21--29},
  volume    = {47},
  doi       = {10.1107/S0108767390009163},
  file      = {:by-author/B/Brown/1991_Brown_21.pdf:PDF},
  keywords  = {Refinement; X-ray Crystallography},
  owner     = {saulius},
  publisher = {International Union of Crystallography ({IUCr})},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Brown1992,
  author    = {Tom Brown and Olga Kennard},
  journal   = {Current Opinion in Structural Biology},
  title     = {Structural basis of DNA mutagenesis},
  year      = {1992},
  pages     = {354--360},
  volume    = {2},
  abstract  = {The scope of this review covers those NMR and X-ray crystallographic structural analyses that have been carried out in recent months on a number of mutagenic lesions, mismatched base pairs and a mutational hotspot in synthetic DNA duplexes. The structure of DNA duplexes containing the mutagenic bases O(6)-methyl deoxyguanosine, O(6)-ethyl deoxyguanosine, 8-hydroxydeoxyguanosine and 1,N(6)-ethenodeoxyadeno- sine are discussed. Recent studies on DNA duplexes containing G-A mismatched base pairs are also reviewed. Finally, an important study of a dodecamer containing a sequence corresponding to a hotspot for frameshift mutagenesis is described. This structure contains a novel type of groove backbone interaction and novel base mispairing which suggest a molecular model for frameshift substitution mutagenesis.},
  file      = {1992_Brown_354.pdf:by-author/B/Brown/1992_Brown_354.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Browne2006,
  author    = {Browne, Wesley R and Feringa, Ben L},
  journal   = {Nature nanotechnology},
  title     = {Making molecular machines work.},
  year      = {2006},
  pages     = {25--35},
  volume    = {1},
  abstract  = {In this review we chart recent advances in what is at once an old and very new field of endeavour--the achievement of control of motion at the molecular level including solid-state and surface-mounted rotors, and its natural progression to the development of synthetic molecular machines. Besides a discussion of design principles used to control linear and rotary motion in such molecular systems, this review will address the advances towards the construction of synthetic machines that can perform useful functions. Approaches taken by several research groups to construct wholly synthetic molecular machines and devices are compared. This will be illustrated with molecular rotors, elevators, valves, transporters, muscles and other motor functions used to develop smart materials. The demonstration of molecular machinery is highlighted through recent examples of systems capable of effecting macroscopic movement through concerted molecular motion. Several approaches to illustrate how molecular motor systems have been used to accomplish work are discussed. We will conclude with prospects for future developments in this exciting field of nanotechnology.},
  file      = {2006_Browne_25.pdf:by-author/B/Browne/2006_Browne_25.pdf:PDF},
  keywords  = {Molecular Machines},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Browne2006a,
  author    = {Wesley R. Browne and Ben L. Feringa},
  journal   = {Nature Nanotechnology},
  title     = {Making molecular machines work},
  year      = {2006},
  pages     = {25--35},
  volume    = {1},
  abstract  = {In this review we chart recent advances in what is at once an old and very new field of endeavour — the achievement of control of motion at the molecular level including solid-state and surface-mounted rotors, and its natural progression to the development of synthetic molecular machines. Besides a discussion of design principles used to control linear and rotary motion in such molecular systems, this review will address the advances towards the construction of synthetic machines that can perform useful functions. Approaches taken by several research groups to construct wholly synthetic molecular machines and devices are compared. This will be illustrated with molecular rotors, elevators, valves, transporters, muscles and other motor functions used to develop smart materials. The demonstration of molecular machinery is highlighted through recent examples of systems capable of effecting macroscopic movement through concerted molecular motion. Several approaches to illustrate how molecular motor systems have been used to accomplish work are discussed. We will conclude with prospects for future developments in this exciting field of nanotechnology.},
  doi       = {10.1038/nnano.2006.45},
  file      = {:by-author/B/Browne/2006_Browne_25.war:},
  keywords  = {Molecular-machines},
  owner     = {saulius},
  timestamp = {2015.03.02},
  creationdate = {2015-03-02T00:00:00},
}

@TechReport{Brozycki2008,
  author      = {John Brozycki},
  institution = {SANS Institute},
  title       = {Detecting and Preventing Anonymous Proxy Usage},
  year        = {2008},
  abstract    = {Many organizations filter the Internet sites that their users may view. They do this for legitimate reasons that include preventing hostile work environments for their users, protecting network assets and data from malicious code or theft, and complying with regulations and company policies. Anonymous proxy services allow users to bypass most filtering systems. This paper explores methods organizations may use to detect and prevent anonymous proxy usage.},
  file        = {:by-author/B/Brozycki/2008_Brozycki.pdf:PDF},
  owner       = {saulius},
  timestamp = {2013.03.22},
  creationdate = {2013-03-22T00:00:00},
}

@Article{Brumley2003,
  author    = {David Brumley and Dan Boneh},
  title     = {Remote Timing Attacks are Practical},
  year      = {2003},
  abstract  = {Timing attacks are usually used to attack weak computing devices such as smartcards. We show that timing attacks apply to general software systems. Specifically, we devise a timing attack against OpenSSL. Our experiments show that we can extract private keys from an OpenSSL-based web server running on a machine in the local network. Our results demonstrate that timing attacks against network servers are practical and therefore security systems should defend against them.},
  file      = {:by-author/B/Brumley/2003_Brumley.pdf:PDF},
  keywords  = {Computer Science (CS); Cryptography},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Brunger1998,
  author    = {Brunger, A T and Adams, P D and Clore, G M and DeLano, W L and Gros, P and Grosse-Kunstleve, R W and Jiang, J S and Kuszewski, J and Nilges, M and Pannu, N S and Read, R J and Rice, L M and Simonson, T and Warren, G L},
  journal   = {Acta Crystallogr D Biol Crystallogr},
  title     = {Crystallography \& NMR system: A new software suite for macromolecular structure determination},
  year      = {1998},
  month     = {Sep},
  pages     = {905--21},
  volume    = {54(Pt 5)},
  abstract  = {A new software suite, called Crystallography & NMR System (CNS), has been developed for macromolecular structure determination by X-ray crystallography or solution nuclear magnetic resonance (NMR) spectroscopy. In contrast to existing structure-determination programs, the architecture of CNS is highly flexible, allowing for extension to other structure-determination methods, such as electron microscopy and solid-state NMR spectroscopy. CNS has a hierarchical structure: a high-level hypertext markup language (HTML) user interface, task-oriented user input files, module files, a symbolic structure-determination language (CNS language), and low-level source code. Each layer is accessible to the user. The novice user may just use the HTML interface, while the more advanced user may use any of the other layers. The source code will be distributed, thus source-code modification is possible. The CNS language is sufficiently powerful and flexible that many new algorithms can be easily implemented in the CNS language without changes to the source code. The CNS language allows the user to perform operations on data structures, such as structure factors, electron-density maps, and atomic properties. The power of the CNS language has been demonstrated by the implementation of a comprehensive set of crystallographic procedures for phasing, density modification and refinement. User-friendly task-oriented input files are available for nearly all aspects of macromolecular structure determination by X-ray crystallography and solution NMR},
  address   = {The Howard Hughes Medical Institute, Yale University, New Haven, CT 06511, USA, and Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA. brunger@laplace.csb.yale.edu},
  doi       = {10.1107/S0907444998003254},
  file      = {1998_Brunger_905.pdf:by-author/B/Brunger/1998_Brunger_905.pdf:PDF},
  keywords  = {Refinement; X-ray Crystallography; macromolecular crystallography. CNS},
  owner     = {em},
  timestamp = {2016.06.16},
  creationdate = {2016-06-16T00:00:00},
  url       = {http://www.ncbi.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&dopt=abstract&list_uids=9757107},
}

@Article{Bruenger1998,
  author    = {Brünger, Axel T and Adams, Paul D and Rice, Luke M},
  journal   = {Current Opinion in Structural Biology},
  title     = {Recent developments for the efficient crystallographic refinement of macromolecular structures},
  year      = {1998},
  issn      = {0959-440X},
  month     = {Oct},
  number    = {5},
  pages     = {606--611},
  volume    = {8},
  abstract  = {Macromolecular crystallographic refinement has recently been made more efficient by the use of cross-validated maximum likelihood targets and torsion-angle molecular dynamics simulated annealing. In combination with automated model building methods, the amount of manual intervention required to complete and refine a structure is greatly reduced.},
  doi       = {10.1016/S0959-440X(98)80152-8},
  file      = {:by-author/B/Brünger/1998_Brünger_606.pdf:pdf},
  keywords  = {Structure Refinement; Validation; X-ray Crystallography},
  owner     = {saulius},
  pii       = {S0959-440X(98)80152-8},
  publisher = {Elsevier BV},
  pubmed    = {9818265},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
  url       = {http://dx.doi.org/10.1016/S0959-440X(98)80152-8},
}

@Article{Brunger2009,
  author    = {Brunger, Axel T and DeLaBarre, Byron and Davies, Jason M and Weis, William I},
  journal   = {Acta crystallographica. Section D, Biological crystallography},
  title     = {X-ray structure determination at low resolution.},
  year      = {2009},
  pages     = {128--33},
  volume    = {65},
  file      = {2009_Brunger_128.pdf:by-author/B/Brunger/2009_Brunger_128.pdf:PDF},
  keywords  = {Structure Determination; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Brunger1989,
  author    = {Brünger, A. T. and Karplus, M. and Petsko, G. A.},
  journal   = {Acta Crystallogr Sect A},
  title     = {Crystallographic refinement by simulated annealing: application to crambin},
  year      = {1989},
  issn      = {0108-7673},
  month     = {Jan},
  number    = {1},
  pages     = {50–61},
  volume    = {45},
  doi       = {10.1107/s0108767388009195},
  file      = {1989_Brünger_50.pdf:by-author/B/Brünger/1989_Brünger_50.pdf:PDF},
  groups    = {sg/Crystallography, am/Crystallography},
  owner     = {andrius},
  publisher = {International Union of Crystallography (IUCr)},
  timestamp = {2016.11.22},
  creationdate = {2016-11-22T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0108767388009195},
}

@Article{Bruno2014,
  author    = {Bruno, IanJ. and Groom, ColinR.},
  journal   = {Journal of Computer-Aided Molecular Design},
  title     = {A crystallographic perspective on sharing data and knowledge},
  year      = {2014},
  issn      = {0920-654X},
  pages     = {1--8},
  abstract  = {The crystallographic community is in many ways an exemplar of the benefits and practices of sharing data. Since the inception of the technique, virtually every published crystal structure has been made available to others. This has been achieved through the establishment of several specialist data centres, including the Cambridge Crystallographic Data Centre, which produces the Cambridge Structural Database. Containing curated structures of small organic molecules, some containing a metal, the database has been produced for almost 50 years. This has required the development of complex informatics tools and an environment allowing expert human curation. As importantly, a financial model has evolved which has, to date, ensured the sustainability of the resource. However, the opportunities afforded by technological changes and changing attitudes to sharing data make it an opportune moment to review current practices.},
  doi       = {10.1007/s10822-014-9780-9},
  file      = {2014_Bruno_1.pdf:by-author/B/Bruno/2014_Bruno_1.pdf:PDF},
  keywords  = {CCDC; CSD; Crystallography; Data; Knowledge; Sharing; Sustainability},
  language  = {English},
  owner     = {saulius},
  publisher = {Springer International Publishing},
  timestamp = {2014.09.02},
  creationdate = {2014-09-02T00:00:00},
  url       = {http://dx.doi.org/10.1007/s10822-014-9780-9},
}

@Article{Bruno2004,
  author    = {Bruno, Ian J. and Cole, Jason C. and Kessler, Magnus and Luo, Jie and Sam Motherwell, W. D. and Purkis, Lucy H. and Smith, Barry R. and Taylor, Robin},
  journal   = {J. Chem. Inf. Comput. Sci.},
  title     = {Retrieval of Crystallographically-Derived Molecular Geometry Information},
  year      = {2004},
  pages     = {2133--2144},
  volume    = {44},
  doi       = {10.1021/ci049780b},
  file      = {:by-author/B/Bruno/2004_Bruno_2133.pdf:PDF},
  owner     = {andrius},
  timestamp = {2012.06.01},
  creationdate = {2012-06-01T00:00:00},
}

@PhdThesis{Bruns1997,
  author    = {Glenn R. Bruns},
  school    = {University of Edinburgh},
  title     = {Process Abstraction in the Verication of Temporal Properties},
  year      = {1997},
  file      = {:by-author/B/Bruns/1997_Bruns.pdf:PDF;:by-author/B/Bruns/1997_Bruns.ps:PostScript},
  owner     = {saulius},
  timestamp = {2015.02.25},
  creationdate = {2015-02-25T00:00:00},
}

@Article{Brunzelle2003,
  author    = {Brunzelle, Joseph S. and Shafaee, Padram and Yang, Xiaojing and Weigand, Steve and Ren, Zhong and Anderson, Wayne F.},
  journal   = {Acta Crystallographica Section D},
  title     = {Automated crystallographic system for high-throughput protein structure determination},
  year      = {2003},
  pages     = {1138--1144},
  volume    = {59},
  doi       = {10.1107/S0907444903008199},
  file      = {gr2333.pdf:by-author/B/Brunzelle/2003_Brunzelle_1138.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444903008199},
}

@Article{Bryant1995,
  author    = {Bryant, F. O. and Cutler, H. G. and Burla, M. C. and Newton, M. G.},
  journal   = {Acta Crystallographica Section C},
  title     = {Duclauxin Ethyl Acetate Solvate, 2C${\sb 29}$H${\sb 22}$O${\sb 11}$.C${\sb 4}$H${\sb 8}$O${\sb 2}$},
  year      = {1995},
  pages     = {437--440},
  volume    = {51},
  doi       = {10.1107/S010827019400394X},
  file      = {:by-author/B/Bryant/1995_Bryant_437.pdf:PDF},
  owner     = {saulius},
  timestamp = {2013.03.22},
  creationdate = {2013-03-22T00:00:00},
  url       = {http://dx.doi.org/10.1107/S010827019400394X},
}

@Article{Brymora2012,
  author    = {Brymora, Katarzyna and Calvayrac, Florent},
  journal   = {arXiv preprint arXiv:1205.1842},
  title     = {Ligand effects on the electronic structure and magnetism of magnetite surfaces},
  year      = {2012},
  file      = {[PDF] from arxiv.org:by-author/B/Brymora/2012_Brymora.pdf:PDF;Snapshot:by-author/B/Brymora/2012_Brymora.html:URL},
  groups    = {sg/NAR2012},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://arxiv.org/abs/1205.1842},
  urldate   = {2015-08-31},
}

@Article{Buchsbaum2007,
  author    = {Buchsbaum, Christian and Schmidt, Martin U.},
  journal   = {Acta Crystallographica Section B},
  title     = {Rietveld refinement of a wrong crystal structure},
  year      = {2007},
  pages     = {926--932},
  volume    = {63},
  doi       = {10.1107/S0108768107050823},
  file      = {av5092.pdf:by-author/B/Buchsbaum/2007_Buchsbaum_926.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0108768107050823},
}

@Article{Bucksch1971,
  author    = {Bucksch, R.},
  journal   = {Journal of Applied Crystallography},
  title     = {The conversion of reduced cells to conventional cells by algebraic means},
  year      = {1971},
  pages     = {156--159},
  volume    = {4},
  doi       = {10.1107/S0021889871006526},
  file      = {:by-author/B/Bucksch/1971_Bucksch_156.pdf:PDF},
  keywords  = {Algorithms; Niggli Cell; Reduced Cell; Unit Cell; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2014.11.06},
  creationdate = {2014-11-06T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0021889871006526},
}

@Presentation{Buechler2007,
  author       = {Steven Buechler},
  title        = {Statistical Models in R: Some Examples},
  year         = {2007},
  organization = {Department of Mathematics, 276B Hurley Hall; 1-6233},
  file         = {2007_Buechler.pdf:by-author/B/Buechler/2007_Buechler.pdf:PDF},
  groups       = {sg/Statistics with R},
  keywords     = {R; Statistics},
  owner        = {saulius},
  timestamp = {2016.01.07},
  creationdate = {2016-01-07T00:00:00},
  url          = {http://www3.nd.edu/~steve/Rcourse/Lecture8v1.pdf},
}

@Article{Buerger1957,
  author    = {Buerger, M. J.},
  journal   = {Zeitschrift für Kristallographie - Crystalline Materials},
  title     = {Reduced Cells},
  year      = {1957},
  pages     = {42--60},
  volume    = {109},
  abstract  = {Several authors have erroneously stated that the endpoint of the DELAUNAY reduction is the reduced cell, although DELAUNAY himself was well aware of the literature on reduced cells and avoided using the term in connection with his reduction. The nature of the reduced cell and the cell resulting from the DELAUNAY reduction are discussed. There are several reasons for preferring the reduced cell. The popularity which the cell resulting from the DELAUNAY reduction has achieved appears to be due to the fact that no one has made a point of developing methods for finding the reduced cell. In this paper the following three methods of finding the reduced cell from an arbitrary primitive cell are presented: (1) a simple graphical method, (2) an analytical method suitable for digital computers, and (3) an algorithm which is not only simpler, but which converges to its result more rapidly than the DELAUNAY reduction. NIGGLI has already prepared the ground for identifying the crystal system and lattice type from the scalar representation of the reduced cell. Some of his results are presented in more convenient tabular form},
  doi       = {10.1524/zkri.1957.109.16.42},
  file      = {1957_Buerger_42.pdf:by-author/B/Buerger/1957_Buerger_42.pdf:PDF},
  groups    = {sg/Cell sg/Reduction, sg/Cell reduction},
  keywords  = {Reduced Cell},
  owner     = {saulius},
  timestamp = {2014.11.19},
  creationdate = {2014-11-19T00:00:00},
}

@Article{Bujalowski2000,
  author    = {Bujalowski, W. and Jezewska, M. J.},
  journal   = {Biochemistry},
  title     = {Kinetic mechanism of nucleotide cofactor binding to Escherichia coli replicative helicase DnaB protein. stopped-flow kinetic studies using fluorescent, ribose-, and base-modified nucleotide analogues.},
  year      = {2000},
  pages     = {2106--22},
  volume    = {39},
  abstract  = {The kinetic mechanism of binding nucleotide cofactors to the Escherichia coli primary replicative helicase DnaB protein has been studied, using the fluorescence stopped-flow technique. The experiments have been performed with fluorescent ATP and ADP analogues bearing the modification on the ribose, MANT-AMP-PNP and MANT-ADP, and on the base, epsilonAMP-PNP and epsilonADP. Association of the DnaB helicase with nucleotide cofactors is characterized by four relaxation times that indicate that the binding occurs by a minimum of four-steps. The simplest mechanism which can describe the data is a four-step sequential process where the bimolecular binding step is followed by three isomerization steps. This mechanism is described by the following equation: [equation in text]. The binding mechanism is independent of the location of the nucleotide cofactor modification and is an intrinsic property of the DnaB helicase-nucleotide system. Quantitative amplitude analyses, using the matrix projection operator technique, allowed us to determine specific fluorescence changes accompanying the formation of all intermediates relative to the fluorescence of the free nucleotide. It shows that the major conformational change of the DnaB helicase-nucleotide complex occurs in the formation of the (H-N)(1). Moreover, the value of the bimolecular rate constant, k(1), is 3-4 orders of magnitude lower than the value expected for the diffusion-controlled reaction. These results indicate that the determined first step includes formation of the collision and an additional transition of the enzyme-nucleotide complex. The obtained results provide evidence of profoundly different conformational states of the ribose and base regions of the nucleotide-binding site in different intermediates. The sequential nature of the mechanism of the nucleotide binding to the DnaB helicase indicates the lack of the existence of a kinetically significant conformational equilibrium of the helicase protomer and the DnaB hexamer prior to the binding. The significance of these results for the functioning of the DnaB helicase is discussed.},
  file      = {:by-author/B/Bujalowski/2000_Bujalowski_2106.pdf:PDF},
  keywords  = {Ecoli; {gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Bujalowski1994,
  author    = {Bujalowski, W. and Klonowska, M. M. and Jezewska, M. J.},
  journal   = {The Journal of biological chemistry},
  title     = {Oligomeric structure of Escherichia coli primary replicative helicase DnaB protein.},
  year      = {1994},
  pages     = {31350--8},
  volume    = {269},
  abstract  = {The oligomeric structure of the Escherichia coli primary replicative helicase DnaB protein in relation to the functions of the enzyme and the energetics of its stability has been characterized. Sedimentation equilibrium, sedimentation velocity, and ligand binding studies show that, in solutions containing magnesium ions, the DnaB helicase exists as a stable hexamer over a wide protein concentration range (approximately 10(-7) to 10(-5) M (hexamer)). The sedimentation coefficient of the hexamer (s0(20,w) = 10.3 +/- 0.3 S) provides an apparent frictional ratio of 1.09 +/- 0.03, which suggests that the hexamer has a nonspherical shape and, when modeled as a prolate ellipsoid of revolution, has an axial ratio of a/b = 2.6 +/- 0.6. Magnesium ions play a crucial structural role in stabilizing the hexameric structure of the DnaB helicase. In the absence of Mg2+, the DnaB protein forms a trimer that, at low protein concentrations, dissociates into monomers. Analysis of the sedimentation data indicates that the dimerization of the trimers into the active DnaB hexamer is accompanied by an uptake of approximately 4 magnesium cations. The sedimentation coefficient of the DnaB monomer (s0(20,w) = 2.8 +/- 0.3 S) provides an apparent frictional ratio of 1.22 +/- 0.05, which indicates that the monomer has an elongated structure with an axial ratio of a/b = 5.2 +/- 0.8 when modeled as a prolate ellipsoid of revolution. Analysis of the ratio of the sedimentation coefficients (the sedimentation ratio) of the DnaB hexamer and monomer, which depends solely on the shape of the protomer and the mode of aggregation, strongly suggests that elongated DnaB promoters aggregate with cyclic symmetry in which the protomer-protomer contacts are limited to only two neighboring subunits.},
  file      = {:by-author/B/Bujalowski/1994_Bujalowski_31350.pdf:PDF},
  keywords  = {Ecoli; {gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Bujdak2006,
  author    = {Bujdák, Juraj and Remko, Milan and Rode, Bernd M},
  journal   = {Journal of colloid and interface science},
  title     = {Selective adsorption and reactivity of dipeptide stereoisomers in clay mineral suspension.},
  year      = {2006},
  pages     = {304--8},
  volume    = {294},
  abstract  = {Preferential adsorption of dipeptide diastereomers (dialanine, Val-Ala) on clay mineral surfaces was observed. Significantly higher adsorption of dipeptides composed from only one type of enantiomer of amino acid units in comparison to those containing both L- and D-type of amino acid units in their molecules, was experimentally proven. This selectivity was explained in terms of different hydrophobic properties of diastereomers, which are probably controlled by intramolecular interactions between nonpolar and polar parts of dipeptide molecules affected by their stereochemistry. A significantly higher reactivity of stereoisomers composed from the same type of amino acid enantiomers to form amide bonds was proven as well. Theoretical study could distinguish different properties of the diastereomers. The results of the calculations indicate possible effects of molecular stability in the stereoselectivity during the adsorption and reactions of Ala(2) diastereomers.},
  doi       = {10.1016/j.jcis.2005.07.046},
  file      = {2006_Bujdák_304.pdf:by-author/B/Bujdák/2006_Bujdák_304.pdf:PDF;tables.csv:by-author/B/Bujdák/2006_Bujdák_304/tables.csv:CSV},
  keywords  = {Chemical Prebiotic; Evolution},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Bujdak2003,
  author    = {J. Bujdák and B.M. Rode},
  journal   = {Catalysis Letters},
  title     = {Peptide bond formation on the surface of activated alumina: peptide chain elongation},
  year      = {2003},
  pages     = {149--154},
  volume    = {91},
  abstract  = {Reactions of the dipeptides Gly2 , Ala2 Þ themselves and in combination with amino acids (AA) (glycine, alanine, valine, leucine, proline) and glycine oligopeptides Gly3, Gly4 , Gly5 on activated alumina surface were investigated. Reactions of glycine oligopeptides led to the formation of longer-chain oligomers up to Gly11. Combinations of Gly2 with other amino acids led to various reactions proceeding by different reaction mechanisms. In the reactions of Gly2 with AA, cyclic anhydride cyc(Gly2) formation was followed by AA addition and molecular rearrangement leading to the formation of Gly-Gly-AA tripeptides. In the reaction of Ala2 with glycine, this type of reaction apparently does not proceed readily, although very high yields of cyc(Ala2) are formed. The reactivities of the individual components are not always reflected in reactions of their mixtures.},
  doi       = {10.1023/B:CATL.0000007148.33571.f7},
  file      = {2003_Bujdák_149.pdf:by-author/B/Bujdák/2003_Bujdák_149.pdf:PDF},
  keywords  = {Chemical Prebiotic; Evolution},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Bujdak2001,
  author    = {Bujdák, J and Rode, B M},
  journal   = {Amino acids},
  title     = {Activated alumina as an energy source for peptide bond formation: consequences for mineral-mediated prebiotic processes.},
  year      = {2001},
  pages     = {281--91},
  volume    = {21},
  abstract  = {The catalytic properties of various forms of alumina were tested for alanine dimerization reaction. The catalytic efficiency of alumina depends on the structure, as well as on acid/base properties of the catalyst. The highest yields of Ala2 were achieved on activated alumina with surface of neutral pH (about 3% conversion after 2 weeks). Thermal analysis of Ala + alumina reaction systems shows that the thermal behavior of amino acid changes substantially in contact with the activated surface of the alumina catalyst. The reaction of Ala is detected as being strongly endothermic by differential thermal analysis of pure amino acid (above 250 degrees C). The alanine endothermic reaction is shifted substantially to lower values (below 200 degrees C) and hardly detectable if activated alumina is present. The reaction mechanism of amino acid activation on alumina surface and its significance for mineral-catalyzed prebiotic peptide bond formation are discussed.},
  doi       = {10.1007/s007260170014},
  file      = {2001_Bujdák_281.pdf:by-author/B/Bujdák/2001_Bujdák_281.pdf:PDF},
  keywords  = {Chemical Prebiotic; Evolution},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Bujdak1999,
  author    = {Juraj Bujdák and Bernd M. Rode},
  journal   = {Journal of Molecular Catalysis A: Chemical},
  title     = {The effect of clay structure on peptide bond formation catalysis},
  year      = {1999},
  pages     = {129--136},
  volume    = {144},
  abstract  = {The catalytic efficiency in peptide bond formation of various clays was tested by reactions of glycine (gly), diglycine (gly2), glycine+alanine (ala), gly2+ala. The main effects of clay structure and composition resulted as following: (1) Clay composition influences the activation of reactant molecules at clay particle edges. (2) Acidity (basicity) of the clay surface can change on the state of the reactant. (3) The clay structure is related to suspension stability and thus accessibility of clay catalytic sites. Mg-rich trioctahedral clays hectorite (smectite) and talc are the most efficient catalysts. Oligomerization of gly and gly2 proceeds on all clays, whereas oligopeptides including ala units are formed with much lower yields and only on the most efficient catalysts. Besides dipeptides and other linear peptides, also cyclic anhydride (diketopiperazine) is formed with relatively high yields from diglycine. Cyclic anhydrides can directly act in the formation of the linear oligopeptides by ring opening molecular rearrangement and addition of another amino acid (oligopeptide).},
  doi       = {10.1016/S1381-1169(98)00342-2},
  file      = {1999_Bujdák_129.pdf:by-author/B/Bujdák/1999_Bujdák_129.pdf:PDF},
  keywords  = {Chemical Prebiotic; Evolution},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Bujdak1999a,
  author    = {Bujdák, J and Rode, B M},
  journal   = {Origins of life and evolution of the biosphere : the journal of the International Society for the Study of the Origin of Life},
  title     = {Silica, alumina and clay catalyzed peptide bond formation: enhanced efficiency of alumina catalyst.},
  year      = {1999},
  pages     = {451--61},
  volume    = {29},
  abstract  = {Catalytic efficiencies of clay (hectorite), silica and alumina were tested in peptide bond formation reactions of glycine (Gly), alanine (Ala), proline (Pro), valine (Val) and leucine (Leu). The reactions were performed as drying/wetting (hectorite) and temperature fluctuation (silica and alumina) experiments at 85 degrees C. The reactivity of amino acids decreased in order Gly &gt; Ala &gt; Pro approximately Val approximately Leu. The highest catalytic efficiency was observed for alumina, the only catalyst producing oligopeptides in all investigated reaction systems. The peptide bond formation on alumina is probably catalyzed by the same sites and via similar reaction mechanisms as some alumina-catalyzed dehydration reactions used in industrial chemistry.},
  doi       = {10.1023/A:1006524703513},
  file      = {1999_Bujdák_451.pdf:by-author/B/Bujdák/1999_Bujdák_451.pdf:PDF},
  keywords  = {Chemical Prebiotic},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Bujdak1997,
  author    = {Jurai Bujdák and Bernd M. Rode},
  journal   = {React. Kinet. Catal. Lett.},
  title     = {Glycine oligomerization on silica and alumina},
  year      = {1997},
  pages     = {281--286},
  volume    = {62},
  abstract  = {Oligomerization of glycine (gly) and diglycine (gly2) on silica and alumina was observed in experiments simulating wetting-drying cycles at 80°C. Glycine produces less than 1% total yield of gly2 and diketopiperazine (DKP) after one week. In experiments starting from gly2, more than 10% DKP is formed. Formation of higher oligomers (gly3–gly6) proceeded as well, with 3.8% and 5.1% total yields on silica and alumina surfaces respectively.},
  doi       = {10.1007/BF02475464},
  file      = {1997_Bujdák_281.pdf:by-author/B/Bujdák/1997_Bujdák_281.pdf:PDF},
  keywords  = {Chemical Prebiotic; Evolution},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Bujdak1996,
  author    = {Bujdák, J and Rode, B M},
  journal   = {Journal of molecular evolution},
  title     = {The effect of smectite composition on the catalysis of peptide bond formation.},
  year      = {1996},
  pages     = {326--33},
  volume    = {43},
  abstract  = {Clay-catalyzed glycine and diglycine oligomerizations were performed as drying/wetting cycles at 80 degrees C. Two trioctahedral smectites (hectorite and saponite), three pure montmorillonites, a ferruginous smectite, an Fe(II)-rich smectite, and three smectites containing goethite admixture were used as catalysts. Highest peptide bond formation was found with trioctahedral smectites. About 7% of glycine was converted to diglycine and diketopiperazine on hectorite after 7 days. In the case of dioctahedral smectites, highest yields were achieved using clays with a negative-layer charge localized in the octahedral sheets (up to 2% of converted glycine after 7 days). The presence of Fe(II) in clay is reflected in a higher efficiency in catalyzing amino acid dimerization (about 3.5% of converted glycine after 7 days). The possible significance of the results for prebiotic chemistry is discussed.},
  doi       = {10.1007/BF02339007},
  file      = {1996_Bujdák_326.pdf:by-author/B/Bujdák/1996_Bujdák_326.pdf:PDF},
  keywords  = {Chemical Prebiotic; Evolution},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Bujnicki2003,
  author    = {Bujnicki},
  title     = {Molecular Phylogenetics Of Restriction Endonucleases},
  year      = {2003},
  file      = {:by-author/B/Bujnicki/2003_Bujnicki.pdf:PDF},
  keywords  = {Obzor},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Bujnicki2001,
  author    = {Bujnicki, J. M.},
  journal   = {Acta biochimica Polonica},
  title     = {Understanding the evolution of restriction-modification systems: clues from sequence and structure comparisons.},
  year      = {2001},
  pages     = {935--67},
  volume    = {48},
  abstract  = {Restriction-modification (RM) systems comprise two opposing enzymatic activities: a restriction endonuclease, that targets specific DNA sequences and performs endonucleolytic cleavage, and a modification methyltransferase that renders these sequences resistant to cleavage. Studies on molecular genetics and biochemistry of RM systems have been carried out over the past four decades, laying foundations for modern molecular biology and providing important models for mechanisms of highly specific protein-DNA interactions. Although the number of known, relevant sequences 3D structures of RM proteins is growing steadily, we do not fully understand their functional diversities from an evolutionary perspective and we are not yet able to engineer new sequence specificities based on rational approaches. Recent findings on the evolution of RM systems and on their structures and mechanisms of action have led to a picture in which conserved modules with defined function are shared between different RM proteins and other enzymes involved in nucleic acid biochemistry. On the other hand, it has been realized that some of the modules have been replaced in the evolution by unrelated domains exerting similar function. The aim of this review is to give a survey on the recent progress in the field of structural phylogeny of RM enzymes with special emphasis on studies of sequence-structure-function relationships and emerging potential applications in biotechnology.},
  file      = {:by-author/B/Bujnicki/2001_Bujnicki_935.pdf:PDF},
  keywords  = {Evolution; TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Manuscript{Bukhari2010,
  author    = {Syed Saqib Bukhari and Faisal Shafait and Thomas M. Breuel},
  title     = {Improved Document Image Segmentation Algorithm using Multiresolution Morphology},
  year      = {2010},
  keywords  = {Image Segmentation; OCR; Text Segmentation},
  url       = {http://www.dfki.de/web/forschung/publikationen/renameFileForDownload?filename=Bukhari-text-image-segmentation-DRR11.pdf&file_id=uploads_830},
  abstract  = {Page segmentation into text and non-text components is an essential preprocessing step before OCR operation. If this is not done properly, an OCR classification engine produces garbage text due to the presence of non- text components. This paper describes improvements to the text/image segmentation algorithm described by Bloomberg, 1 which is also available in his open-source Leptonica library. 2 The modifications result in significant improvements over Bloomberg’s algorithm on UW-III, UNLV, ICDAR 2009 page segmentation competition test images and circuit diagram datasets.},
  comment   = {Cites, discusses and claims to improve the Bloomberg's text image segmentation algorithm},
  file      = {2010_Bukhari.pdf:by-author/B/Bukhari/2010_Bukhari.pdf:PDF},
  groups    = {sg/Text segmentation},
  owner     = {saulius},
  timestamp = {2016.02.05},
  creationdate = {2016-02-05T00:00:00},
}

@Manuscript{Bull2013,
  author    = {Larry Bull and Julian Holley and Ben De Lacy Costello and Andrew Adamatzky},
  title     = {Toward {T}uring’s {A}-type Unorganised Machines in an Unconventional Substrate: a Dynamic Representation in Compartmentalised Excitable Chemical Media},
  year      = {2013},
  url       = {http://arxiv.org/abs/1212.1344},
  abstract  = {Turing presented a general representation scheme by which to achieve artificial intelligence - unorganised machines. Significantly, these were a form of discrete dynamical system and yet such representations remain relatively unexplored. Further, at the same time as also suggesting that natural evolution may provide inspiration for search mechanisms to design machines, he noted that mechanisms inspired by the social aspects of learning may prove useful. This paper presents initial results from consideration of using Turing's dynamical representation within an unconventional substrate - networks of Belousov-Zhabotinsky vesicles - designed by an imitation-based, i.e., cultural, approach. Turing's representation scheme is also extended to include a fuller set of Boolean functions at the nodes of the recurrent networks.},
  file      = {:by-author/B/Bull/2013_Bull_1.pdf:PDF},
  owner     = {andrius},
  timestamp = {2012.12.17},
  creationdate = {2012-12-17T00:00:00},
}

@Presentation{Bullard2001,
  author    = {Bullard},
  title     = {A Brief Introduction to Bayesian Statistics},
  year      = {2001},
  file      = {:by-author/B/Bullard/2001_Bullard_handouts.pdf:PDF},
  groups    = {sg/Bayesian},
  keywords  = {Bayesian Statistics; Mathematics},
  owner     = {saulius},
  pages     = {handouts},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@InProceedings{Buneman2008,
  author    = {Buneman, Peter and Cheney, James and Tan, Wang-Chiew and Vansummeren, Stijn},
  booktitle = {Proceedings of the twenty-seventh ACM SIGMOD-SIGACT-SIGART symposium on Principles of database systems},
  title     = {Curated databases},
  year      = {2008},
  address   = {New York, NY, USA},
  pages     = {1--12},
  publisher = {ACM},
  series    = {PODS '08},
  abstract  = {Curated databases are databases that are populated and updated with a great deal of human effort. Most reference works that one traditionally found on the reference shelves of libraries – dictionaries, encyclopedias, gazetteers etc. – are now curated databases. Since it is now easy to publish databases on the web, there has been an explosion in the number of new curated databases used in scientific research. The value of curated databases lies in the organization and the quality of the data they contain. Like the paper reference works they have replaced, they usually represent the efforts of a dedicated group of people to produce a definitive description of some subject area. Curated databases present a number of challenges for database research. The topics of annotation, provenance, and citation are central, because curated databases are heavily cross-referenced with, and include data from, other databases, and much of the work of a curator is annotating existing data. Evolution of structure is important because these databases often evolve from semistructured representations, and because they have to accommodate new scientific dis- coveries. Much of the work in these areas is in its infancy, but it is beginning to provide suggest new research for both theory and practice. We discuss some of this research and emphasize the need to find appropriate models of the processes associated with curated databases.},
  acmid     = {1376918},
  doi       = {10.1145/1376916.1376918},
  file      = {2008_Buneman_1.pdf:by-author/B/Buneman/2008_Buneman_1.pdf:PDF},
  isbn      = {978-1-60558-152-1},
  keywords  = {Annotation; Archiving; Curation; Databases; Provenance},
  location  = {Vancouver, Canada},
  numpages  = {12},
  owner     = {saulius},
  timestamp = {2012.10.25},
  creationdate = {2012-10-25T00:00:00},
  url       = {http://doi.acm.org/10.1145/1376916.1376918},
}

@Article{Buneman2016,
  author     = {Buneman, Peter and Davidson, Susan and Frew, James},
  journal    = {Commun. ACM},
  title      = {Why Data Citation is a Computational Problem},
  year       = {2016},
  issn       = {0001-0782},
  month      = aug,
  number     = {9},
  pages      = {50--57},
  volume     = {59},
  abstract   = {Using database views to define citable units is the key to specifying and generating citations to data.},
  acmid      = {2893181},
  address    = {New York, NY, USA},
  doi        = {10.1145/2893181},
  file       = {2016_Buneman_50.pdf:by-author/B/Buneman/2016_Buneman_50.pdf:PDF},
  groups     = {sg/Methods and tools},
  issue_date = {September 2016},
  keywords   = {Data Citation; Reproducible Research},
  numpages   = {8},
  owner      = {saulius},
  publisher  = {ACM},
  timestamp = {2016.11.17},
  creationdate = {2016-11-17T00:00:00},
  url        = {http://doi.acm.org/10.1145/2893181},
}

@Article{Buneman2002a,
  author           = {Peter Buneman and Sanjeev Khanna and Keishi Tajima and Wang-Chiew Tan},
  journal          = {ACM Transactions on Database Systems},
  title            = {Archiving scientific data},
  year             = {2004},
  issn             = {1557-4644},
  month            = mar,
  number           = {1},
  pages            = {2},
  volume           = {29},
  abstract         = {Archiving is important for scientific data, where it is necessary to record all past versions of a database in order to verify findings based upon a specific version. Much scientific data is held in a hierachical format and has a key structure that provides a canonical identification for each element of the hierarchy. In this article, we exploit these properties to develop an archiving technique that is both efficient in its use of space and preserves the continuity of elements through versions of the database, something that is not provided by traditional minimum-edit-distance diff approaches. The approach also uses timestamps. All versions of the data are merged into one hierarchy where an element appearing in multiple versions is stored only once along with a timestamp. By identifying the semantic continuity of elements and merging them into one data structure, our technique is capable of providing meaningful change descriptions, the archive allows us to easily answer certain temporal queries such as retrieval of any specific version from the archive and finding the history of an element. This is in contrast with approaches that store a sequence of deltas where such operations may require undoing a large number of changes or significant reasoning with the deltas.},
  creationdate     = {2012-10-25T00:00:00},
  doi              = {10.1145/974750.974752},
  file             = {:by-author/B/Buneman/2004_Buneman_2.pdf:PDF},
  keywords         = {Archiving; Data Management; Data Reuse; Databases; Scientific Data},
  modificationdate = {2024-05-17T16:06:05},
  owner            = {saulius},
  publisher        = {Association for Computing Machinery (ACM)},
  timestamp        = {2012.10.25},
}

@InProceedings{Buneman2002,
  author           = {Peter Buneman and Sanjeev Khanna and Keishi Tajima and Wang-Chiew Tan},
  booktitle        = {Proceedings of ACM SIGMOD International Conference on Management of Data},
  title            = {Archiving scientific data},
  year             = {2002},
  address          = {Madison, Wisconsin},
  month            = jun,
  pages            = {1--12},
  publisher        = {ACM},
  series           = {SIGMOD/PODS02},
  collection       = {SIGMOD/PODS02},
  creationdate     = {2012-10-25T00:00:00},
  doi              = {10.1145/564691.564693},
  file             = {2002_Buneman_1.pdf:by-author/B/Buneman/2002_Buneman_1.pdf:PDF},
  keywords         = {Archiving; Data Management; Data Reuse; Databases; Scientific Data},
  modificationdate = {2024-05-17T16:03:44},
  owner            = {saulius},
  status           = {ref},
  timestamp        = {2012.10.25},
  url              = {http://homepages.inf.ed.ac.uk/opb/papers/sigmod2002.pdf},
}

@Article{Bunn1994,
  author    = {Ann M. Cappalonga Bunn and Richard S. Alexander and David W. Christianson},
  journal   = {J. Am. Chem. Soc.},
  title     = {Mapping Protein-Peptide Affinity: Binding of Peptidylsulfonamide Inhibitors to Human Carbonic Anhydrase II},
  year      = {1994},
  pages     = {5063--5068},
  volume    = {116},
  file      = {1994_Cappalonga_5063.pdf:by-author/B/Bunn/1994_Bunn_5063.pdf:PDF},
  groups    = {sg/modelling, sg/hCA2},
  keywords  = {Inhibitors},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Bunouf2010,
  author    = {Bunouf},
  title     = {On Bayesian Analysis in Multistage Designs},
  year      = {2010},
  abstract  = {A new Bayesian approach to multistage hypothesis testing is considered. The corrected Jeffreys prior is derived using Jeffreys’ criterion on likelihood associated with the design information. Based on the principle of design impartiality, the Bayes factor as posterior-based evidential measure can be generalized to multistage testing, so that the decision boundaries reflect equal evidence for hypotheses over stages. Effect of prior correction on design parameters and on Bayesian inference upon test termination is studied. The use of the prior as the default objective choice in multistage hypothesis testing is discussed. In an extension to point estimation in multistage binomial designs, we consider another class of priors which generalizes the corrected Jeffreys prior. The transposition of the beta parameters of Haldane’s and the uniform priors for fixed binomial experiments yields bias-corrected versions of these priors in multistage designs.},
  file      = {:by-author/B/Bunouf/2010_Bunouf.pdf:PDF},
  groups    = {sg/Bayesian},
  keywords  = {Bayes Factor; Bayesian Statistics; Beta-J Distribution; Frequentist Characteristics; Jeffreys' Criterion; Likelihood Principle; Mathematics; Objective Prior},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Manuscript{Burbank1960,
  author    = {R.D. Burbank},
  title     = {Molecular Structure in Crystal Aggregates of Linear Polyethylene},
  year      = {1960},
  keywords  = {Polyethylene; Structures},
  month     = {November},
  abstract  = {Crystal aggregates of linear polyethylene have been studied in the electron microscope. Twinning has been observed to occur across (530) planes, and possibly across (120) planes. Crystal morphologies have been observed which exhibit (530) and (5.110) faces. Electron interference ejjlects have been observed which give rise to contrast lines and figures which frequently are parallel to crystallographic directions. These observations, and those of others, have been interprcterl in terms of recently proposed ideas on molecular chain folding. It is suggested that chain folds may lie in a variety of fold planes or fold surfaces which are normal, or nearly normal, to the crystal lamellae. I t is shown that a continuity of fold structure is necessary and possible across a wide variety of bounclaries delineating regions of different fold structure. It is shown that these structural concepts are compatible with recently proposed idcas on the growth of lamellar polymer crystals and can suggest new details of the growth process.},
  file      = {:by-author/B/Burbank/1960_Burbank_1627.pdf:PDF},
  journal   = {The Bell System Technical Report},
  owner     = {saulius},
  pages     = {1627--1663},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@Article{Burgi2003,
  author    = {Hans-Beat Bürgi and Silvia C. Capelli},
  journal   = {Helvetica Chimica Acta},
  title     = {Getting More out of Crystal-Structure Analyses},
  year      = {2003},
  pages     = {1625--1640},
  volume    = {86},
  file      = {:by-author/B/Bürgi/2003_Bürgi_1625.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Burke1985,
  author    = {Burke, R. L. and Munn, M. and Barry, J. and Alberts, B. M.},
  journal   = {The Journal of biological chemistry},
  title     = {Purification and properties of the bacteriophage T4 gene 61 RNA priming protein.},
  year      = {1985},
  pages     = {1711--22},
  volume    = {260},
  abstract  = {The bacteriophage T4 gene 61 protein is required, together with the gene 41 protein and single-stranded DNA, for the synthesis of the pentaribonucleotides that are used as primers for the start of each new Okazaki DNA fragment during T4 DNA replication. Using this priming activity as an assay, we have purified the 61 protein to essential homogeneity in milligram amounts. The priming activity was identified with the product of T4 gene 61 by using two-dimensional polyacrylamide gel electrophoresis to compare all of the T4-induced proteins in wild-type and mutant infections; the purified protein co-migrates with the only detectable protein missing in a 61- mutant infection. The purified 61 protein is shown to bind to the T4 helix-destabilizing protein (gene 32 protein) and to both single-stranded and double-stranded DNA. We have failed to detect any ribonucleotide polymerizing activity in either the 61 protein or the 41 protein alone; both the 61 and 41 proteins must be present to observe any synthesis of oligoribonucleotides.},
  file      = {:by-author/B/Burke/1985_Burke_1711.pdf:PDF},
  keywords  = {Primase; {gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Burkhardt2006,
  author    = {Burkhardt, Kyle and Schneider, Bohdan and Ory, Jeramia},
  journal   = {PLoS computational biology},
  title     = {A biocurator perspective: annotation at the Research Collaboratory for Structural Bioinformatics Protein Data Bank.},
  year      = {2006},
  pages     = {e99},
  volume    = {2},
  file      = {:by-author/B/Burkhardt/2006_Burkhardt_e99.pdf:PDF},
  keywords  = {Databases; PDB; PDB Curator Tasks},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@Article{Burkhardt1967,
  author    = {Burkhardt, W.H.},
  journal   = {Computing},
  title     = {Generating test programs from syntax},
  year      = {1967},
  issn      = {0010-485X},
  pages     = {53--73},
  volume    = {2},
  abstract  = {Summary The many faces of programming and systems development demand an immense amount of mechanical routine work. The present paper tries to explain some areas where automation of many tasks may be of great help. One special area, where progress seems to lag behind unduly, can be found in debugging, testing, and diagnosing systems. Here we attempted the generation of programs automatically from a definition of a problem and the characteristics of programs for its solution by a software system, which has been specially designed for this purpose. It has been indicated how the ideas underlying this project may be applied successfully to other areas. Zusammenfassung Bei der Programmierung und Systementwicklung wird zu einem erheblichen Umfang mechanische Routinearbeit erfordert. Der vorliegende Beitrag grenzt verschiedene Gebiete ab, wo mehrere Aufgabenlösungen automatisiert werden können. Ein Spezialgebiet, in welchem die Techniken auf niedrigem Stand zurückgeblieben scheinen, findet sich im Analysieren und Ausprüfen von Systemprogrammen. Hier haben wir versucht, Programme durch ein System automatisch zu erzeugen, ausgehend von einer Definition des Problems und den Charakteristiken seiner Lösung. Dieses System war zu diesem Zweck entwickelt worden. Ferner wird angedeutet, wie die Ideen, auf denen dieser Beitrag beruht, auf andere Gebiete erfolgreich angewendet werden können.},
  doi       = {10.1007/BF02235512},
  file      = {1967_Burkhardt_53.pdf:by-author/B/Burkhardt/1967_Burkhardt_53.pdf:PDF},
  keywords  = {Computer Science (CS); Programming Languages; Software Testing; Syntax},
  language  = {English},
  owner     = {saulius},
  publisher = {Springer-Verlag},
  timestamp = {2015.11.22},
  creationdate = {2015-11-22T00:00:00},
  url       = {http://dx.doi.org/10.1007/BF02235512},
}

@Article{Burla1989,
  author    = {Burla, M. C. and Camalli, M. and Cascarano, G. and Giacovazzo, C. and Polidori, G. and Spagna, R. and Viterbo, D.},
  journal   = {J. Appl. Cryst.},
  title     = {{\it SIR}88 {--} a direct-methods program for the automatic solution of crystal structures},
  year      = {1989},
  pages     = {389--393},
  volume    = {22},
  doi       = {10.1107/S0021889889004103},
  file      = {1989_Burla_389.pdf:by-author/B/Burla/1989_Burla_389.pdf:PDF},
  keywords  = {Software; Structure Solution; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0021889889004103},
}

@Article{Burla2003,
  author    = {Burla, Maria Cristina and Carrozzini, Benedetta and Cascarano, Giovanni Luca and Giacovazzo, Carmelo and Polidori, Giampiero},
  journal   = {Acta Crystallographica Section D},
  title     = {SAD or MAD phasing: location of the anomalous scatterers},
  year      = {2003},
  pages     = {662--669},
  volume    = {59},
  doi       = {10.1107/S0907444903002129},
  file      = {wd0004.pdf:by-author/B/Burla/2003_Burla_662.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444903002129},
}

@Article{Burla2000,
  author    = {Burla, Maria Cristina and Carrozzini, Benedetta and Cascarano, Giovanni Luca and Giacovazzo, Carmelo and Polidori, Giampiero},
  journal   = {Journal of Applied Crystallography},
  title     = {Solving crystal structures in {\it P}1: an automated procedure for finding an allowed origin in the correct space group},
  year      = {2000},
  pages     = {307--311},
  volume    = {33},
  abstract  = {Crystal structure solution in {\it P}1 may be particularly suitable for complex crystal structures crystallizing in other space groups. However, additional efforts and human intervention are often necessary to locate correctly the structural model so obtained with respect to an allowed origin of the actual space group. An automatic procedure is described which is able to perform such a task, allowing the routine passage to the correct space group and the subsequent structure refinement. Some tests are presented proving the effectiveness of the procedure.},
  doi       = {10.1107/S0021889800000157},
  file      = {2000_Burla_307.pdf:by-author/B/Burla/2000_Burla_307.pdf:PDF},
  keywords  = {Algorithms; Spacegroups; Symmetry; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2015.06.15},
  creationdate = {2015-06-15T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0021889800000157},
}

@Manuscript{Burtsev1999,
  author    = {Alexey A. Burtsev},
  title     = {Interrupt mechanism for threaded code interpreter},
  year      = {1999},
  keywords  = {Computer Science (CS); Threaded Code},
  url       = {http://www.complang.tuwien.ac.at/anton/euroforth/ef99/burtsev99.pdf},
  abstract  = {Various methods to support interrupt mechanism in programming systems, based on threaded code techniques, are analysed. Threaded code interpreters, which support interrupt handling at the level of machine code, have serious demerits. Another method of interruption for interpreter of threaded code are suggested. It makes possible to interrupt program only at the level of threaded code. It means, that body of interrupt handler will be executed not at the same moment, when the interruption is raised, but just after that moment, when the interpreter completes execution of its current command (primitive procedure, which body are defined in machine code). Realization of interrupt mechanism according to this suggested method for DSSP (Forth-like system, developed in Moscow University) are described. Advantages of new interrupt technique for threaded code interpreter, especially concerning parallel programming and exception handling, are explained.},
  file      = {:by-author/B/Burtsev/1999_Burtsev.pdf:PDF},
  groups    = {sg/Threaded code},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Burzlaff1982,
  author    = {H. Burzlaff and A. Hountas},
  journal   = {J. Appl. Cryst.},
  title     = {Computer program for the derivation of symmetry operations from the space-group symbols},
  year      = {1982},
  pages     = {464--467},
  volume    = {15},
  file      = {1982_Burzlaff_464.pdf:by-author/B/Burzlaff/1982_Burzlaff_464.pdf:PDF},
  keywords  = {Spacegroup Symbols; Spacegroups; Symmetry},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Burzlaff1980,
  author    = {H. Burzlaff and H. Zimmermann},
  journal   = {Zeitschrift für Kristallographie},
  title     = {On the choice of origins in the description of space groups},
  year      = {1980},
  pages     = {151--179},
  volume    = {153},
  abstract  = {The set of origins available in the description of space groups is investigated with respect to equivalence. Privileged origins may be derived employing two different criteria: (i) A unique origin can be found for each short international space-group symbol by the application of simple rules (origin related to the symbol). (ii) The first standard settings of the International Tables (1952) are chosen such that the set of equivalent origins is a subset of the origins of their affine or Euclidean normalizers respectively. A list of the affine normalizers for space groups with higher than monoclinic symmetry is presented.},
  doi       = {10.1524/zkri.1980.153.3-4.151},
  file      = {1980_Burzlaff_151.pdf:by-author/B/Burzlaff/1980_Burzlaff_151.pdf:PDF},
  groups    = {sg/Cell reduction},
  keywords  = {Spacegroups; Symmetry; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2014.05.13},
  creationdate = {2014-05-13T00:00:00},
  url       = {http://www.degruyter.com/view/j/zkri.1980.153.issue-3-4/zkri.1980.153.3-4.151/zkri.1980.153.3-4.151.xml},
}

@Article{Buseck1992,
  author    = {Buseck, Peter R. and Tsipursky, Semeon J. and Hettich, Robert},
  journal   = {Science},
  title     = {Fullerenes from the geological environment},
  year      = {1992},
  issn      = {0036-8075, 1095-9203},
  pages     = {215--217},
  volume    = {257},
  abstract  = {By means of high-resoluton transmission electron microscopy, both C60 and C70 fullerenes have been found in a, carbon-rich Precambrian rock from Russia The fullerenes were confirmed by Fourier transform mass spectrometry with both laser desorption and thermal desorption/electron-capture methods to verify that the fullerenes were indeed present in the geological sample and were not generated by the laser ionization event. The mass spectra were measured under conditions sufficient to resolve the 13C/12C isotopic ratios for C60 and C70 and indicate that these ratios correspond to the normal range of isotopic values.},
  doi       = {10.1126/science.257.5067.215},
  file      = {Full Text PDF:by-author/B/Buseck/1992_Buseck_215.pdf:PDF;Snapshot:by-author/B/Buseck/1992_Buseck_215.html:URL},
  language  = {en},
  owner     = {saulius},
  pmid      = {17794751},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://www.sciencemag.org/content/257/5067/215},
  urldate   = {2015-07-06},
}

@Article{Busing1964,
  author    = {Busing, W. R. and Levy, H. A.},
  journal   = {Acta Crystallographica},
  title     = {The effect of thermal motion on the estimation of bond lengths from diffraction measurements},
  year      = {1964},
  issn      = {0365-110X},
  month     = {Feb},
  number    = {2},
  pages     = {142–146},
  volume    = {17},
  doi       = {10.1107/s0365110x64000408},
  file      = {1964_Busing_142.pdf:by-author/B/Busing/1964_Busing_142.pdf:PDF},
  groups    = {sg/Crystallography, am/Crystallography},
  owner     = {andrius},
  publisher = {International Union of Crystallography (IUCr)},
  timestamp = {2016.12.21},
  creationdate = {2016-12-21T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0365110X64000408},
}

@Manuscript{Butkus2008,
  author    = {Justas Butkus and Audrius Kazlauskas and Laura Radžiūtė and Mantas Viržintas},
  title     = {Erdvinių duomenų bazių indeksavimas},
  year      = {2008},
  keywords  = {Computer Science (CS); Databases; Spatial Databases Indexing},
  file      = {:by-author/B/Butkus/2008_Butkus.doc:DOC},
  owner     = {saulius},
  timestamp = {2015.02.28},
  creationdate = {2015-02-28T00:00:00},
}

@Manuscript{Butkus2009,
  author    = {Justas Butkus and Emilis Kukė},
  title     = {Deklaratyvus, komponentinis programavimas MVC šablone},
  year      = {2009},
  keywords  = {Computer Science (CS); MVC},
  file      = {:by-author/B/Butkus/2009_Butkus_manuscript.odt:OpenDocument text},
  journal   = {Mokslas – Lietuvos ateitis},
  number    = {1},
  owner     = {saulius},
  timestamp = {2015.10.09},
  creationdate = {2015-10-09T00:00:00},
  volume    = {1},
}

@Article{Butler2013,
  author    = {Declan Butler},
  journal   = {Nature},
  title     = {Investigating journals: The dark side of publishing},
  year      = {2013},
  pages     = {433--435},
  volume    = {495},
  abstract  = {The explosion in open-access publishing has fuelled the rise of questionable operators.},
  doi       = {10.1038/495433a},
  file      = {2013_Butler_433.pdf:by-author/B/Butler/2013_Butler_433.pdf:PDF},
  keywords  = {Communication Policy; Open Access; Publishing; Research Management; Scientific Publication},
  owner     = {saulius},
  timestamp = {2013.04.03},
  creationdate = {2013-04-03T00:00:00},
  url       = {http://www.nature.com/news/investigating-journals-the-dark-side-of-publishing-1.12666},
}

@Webpage{Butterworth2012,
  author    = {Neil Butterworth},
  retrieved = {2016.11.25},
  title     = {All About EOF},
  url       = {https://latedev.wordpress.com/2012/12/04/all-about-eof/},
  month     = {Dec},
  year      = {2012},
  file      = {:by-author/B/Butterworth/2012_Butterworth.pdf:PDF},
  owner     = {andrius},
  timestamp = {2016.11.25},
  creationdate = {2016-11-25T00:00:00},
}

@Article{Buttingsrud2007,
  author    = {Buttingsrud, Bård and King, Ross Donald and Alsberg, Bjørn Kåre},
  journal   = {Journal of Chemometrics},
  title     = {An alignment-free methodology for modelling field-based 3D-structure activity relationships using inductive logic programming},
  year      = {2007},
  pages     = {509},
  volume    = {21},
  abstract  = {Traditional 3D-quantitative structure–activity relationship (QSAR)/structure–activity relationship (SAR) methodologies are sensitive to the quality of an alignment step which is required to make molecular structures comparable. Even though many methods have been proposed to solve this problem, they often result in a loss of model interpretability. The requirement of alignment is a restriction imposed by traditional regression methods due to their failure to represent relations between data objects directly. Inductive logic programming (ILP) is a class of machine-learning methods able to describe relational data directly. We propose a new methodology which is aimed at using the richness in molecular interaction fields (MIFs) without being restricted by any alignment procedure. A set of MIFs is computed and further compressed by finding their minima corresponding to the sites of strongest interaction between a molecule and the applied test probe. ILP uses these minima to build easily interpretable rules about activity expressed as pharmacophore rules in the powerful language of first-order logic. We use a set of previously published inhibitors of factor Xa of the benzamidine family to discuss the problems, requirements and advantages of the new methodology. Copyright © 2007 John Wiley & Sons, Ltd.},
  doi       = {10.1002/cem.1056},
  file      = {:by-author/B/Buttingsrud/2007_Buttingsrud_509.pdf:PDF},
  keywords  = {Alignment-free; Drug Design; Inductive Logic Programming (ILP); MIF-ILP; Molecular Field Extrema; Molecular Interaction Field (MIF); Quantitative Structure-activity Relationship (QSAR); Quantitative Structure-property Relationship (QSPR); Structure-activity Relationship (SAR)},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
  url       = {http://dx.doi.org/10.1002/cem.1056},
}

@Article{Buttner1992,
  author    = {R. H. Buttner and E. N. Maslen},
  journal   = {Acta Cryst. B},
  title     = {Structural Parameters and Electron Difference Density in BaTiO_3},
  year      = {1992},
  pages     = {764--769},
  volume    = {48},
  file      = {:by-author/B/Buttner/1992_Buttner_764.pdf:PDF},
  keywords  = {For COD Deposition; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@Presentation{Bylaska2010,
  author    = {Eric J. Bylaska},
  title     = {Introduction to Plane-Wave Basis Sets and Pseudopotential Theory},
  year      = {2010},
  school    = {Pacific Northwest National Laboratory},
  file      = {:by-author/B/Bylaska/2010_Bylaska.pdf:PDF},
  keywords  = {Density Functional Theory (DFT)},
  owner     = {saulius},
  timestamp = {2014.11.06},
  creationdate = {2014-11-06T00:00:00},
  url       = {http://www.nwchem-sw.org/images/Pw-lecture.pdf},
}

@Article{Byrd2005,
  author    = {Byrd, Alicia K. and Raney, Kevin D.},
  journal   = {Biochemistry},
  title     = {Increasing the length of the single-stranded overhang enhances unwinding of duplex DNA by bacteriophage T4 Dda helicase.},
  year      = {2005},
  pages     = {12990--7},
  volume    = {44},
  abstract  = {Dda has been shown previously to be active as a monomer for DNA unwinding [Nanduri et al. (2002) Proc. Natl. Acad. Sci. U.S.A. 99, 14722] and streptavidin displacement [Byrd and Raney (2004) Nat. Struct. Mol. Biol. 11, 531]. However, its activity for streptavidin displacement increased as a function of the length of single-stranded DNA. We investigated whether Dda exhibited enhanced DNA unwinding of partially duplex DNA substrates as a function of increasing the length of the single-stranded overhangs. DNA substrates were prepared containing 16 base pairs and single-stranded overhangs of 4, 6, 8, 12, 16, 20, and 24 nucleotides. Under single turnover conditions in the presence of excess enzyme, the quantity of DNA unwound increased significantly as the length of the single strand overhang increased. Increased processivity was observed when the DNA substrate contained longer single-stranded overhangs. Equilibrium binding studies indicated that Dda bound to the substrates containing the longer overhangs significantly better than the shorter overhangs. To determine whether the increased processivity for unwinding was due to multiple molecules of Dda or due to the increased binding affinity to the longer overhangs, DNA unwinding was conducted under pre-steady-state conditions, which favor binding of monomeric Dda. Under pre-steady-state conditions, the quantity of product decreased somewhat as the single-stranded length increased, from 12 to 24 nucleotides. Thus, when monomeric Dda is required to translocate longer distances prior to unwinding, processivity is lowered. Taken together, these results indicate that enhanced binding to the longer single-stranded overhangs was not responsible for enhanced processivity under conditions of excess enzyme. Rather, multiple molecules of Dda bound to the same substrate exhibit greater processivity for DNA unwinding.},
  file      = {:by-author/B/Byrd/2005_Byrd_12990.pdf:PDF},
  keywords  = {{gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Manuscript{Cabral2006,
  author    = {Bruno Cabral and Paulo Marques},
  title     = {Making Exception Handling Work},
  year      = {2006},
  keywords  = {Computer Science (CS); Exception Handling},
  url       = {https://www.usenix.org/legacy/event/hotdep06/tech/prelim_papers/cabral/cabral.pdf},
  abstract  = {Most modern programming languages rely on exceptions for dealing with errors. Although exception handling was a significant improvement over other mechanisms like checking return codes, it’s far from perfect. In fact, it can be argued that this mechanism is seriously flawed. In this paper we argue that exception handling should be automatically done at the runtime/operating system level. The motivation is similar to the one that lead to garbage collection: memory management was a tedious and error prone process, thus virtual machines included support for taking care of it. We believe that many exceptions can be automatically dealt with, and recovered, as long as appropriate mechanisms exist in the runtime environment. We believe that this approach may dramatically influence the way programming languages are designed and significantly contribute to having more robust code, being actually developed with much less programming effort.},
  comment   = {https://www.usenix.org/conference/hotdep-06/making-exception-handling-work},
  file      = {:by-author/C/Cabral/2006_Cabral.pdf:PDF},
  groups    = {sg/Garbage collectors},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Calderone2004,
  author    = {Calderone, Vito},
  journal   = {Acta Crystallographica Section D},
  title     = {Practical aspects of the integration of different software in protein structure solution},
  year      = {2004},
  pages     = {2150--2155},
  volume    = {60},
  doi       = {10.1107/S0907444904019055},
  file      = {ba5059.pdf:by-author/C/Calderone/2004_Calderone_2150.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444904019055},
}

@Article{Caldes2001,
  author    = {Caldes, M. T. and Deniard, P. and Zou, X. D. and Marchand, R. and Diot, N. and Brec, R.},
  journal   = {Micron (Oxford, England : 1993)},
  title     = {Solving modulated structures by X-ray and electron crystallography.},
  year      = {2001},
  pages     = {497--507},
  volume    = {32},
  abstract  = {X-ray diffraction can be used for accurately determining not only classical, ordinary structures, but also modulated ones. For structures with weak modulations, the modulation induced satellite reflections are often hard to be observed by X-ray diffraction, but they appear clearly in electron diffraction. In these cases, X-ray diffraction will give only average structures whereas electron diffraction will yield information about the modulations. Sr(1.4)Ta(0.6)O(2.9) is a complex modulated compound with weak modulation and small modulated domains. Here we demonstrate the power of combining X-ray and electron crystallography for studying modulated structures on powders. The modulations of Sr(1.4)Ta(0.6)O(2.9) were determined from electron diffraction (SAED) and high resolution electron microscopy (HREM) images. With specially developed image processing techniques, the weak modulations were enhanced, facilitating the interpretation of HREM images in terms of atomic structure.},
  file      = {:by-author/C/Caldes/2001_Caldes_497.pdf:PDF},
  owner     = {saulius},
  timestamp = {2013.03.22},
  creationdate = {2013-03-22T00:00:00},
}

@Presentation{Caliste2010,
  author     = {Damien Caliste},
  title      = {Sharing electronic data within {ETSF}},
  year       = {2010},
  conference = {Cecam tutorial "Basic techniques and tools for development and maintenance of atomic-scale software"},
  file       = {:by-author/C/Caliste/2010_Caliste_slides.pdf:PDF},
  groups     = {am/ETSF},
  owner      = {andrius},
  timestamp = {2016.01.25},
  creationdate = {2016-01-25T00:00:00},
  url        = {http://www.cecam.org/upload/talk/presentation_5264.pdf},
}

@Article{Caliste2008,
  author    = {D. Caliste and Y. Pouillon and M.J. Verstraete and V. Olevano and X. Gonze},
  journal   = {Computer Physics Communications},
  title     = {Sharing electronic structure and crystallographic data with {ETSF\_IO}},
  year      = {2008},
  issn      = {0010-4655},
  pages     = {748--758},
  volume    = {179},
  abstract  = {We present a library of routines whose main goal is to read and write exchangeable files (NetCDF file format) storing electronic structure and crystallographic information. It is based on the specification agreed inside the European Theoretical Spectroscopy Facility (ETSF). Accordingly, this library is nicknamed ETSF_IO. The purpose of this article is to give both an overview of the ETSF_IO library and a closer look at its usage. ETSF_IO is designed to be robust and easy to use, close to Fortran read and write routines. To facilitate its adoption, a complete documentation of the input and output arguments of the routines is available in the package, as well as six tutorials explaining in detail various possible uses of the library routines. Program summary Program title: ETSF_IO Catalogue identifier: AEBG_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEBG_v1_0.html Program obtainable from: \{CPC\} Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Gnu Lesser General Public License No. of lines in distributed program, including test data, etc.: 63 156 No. of bytes in distributed program, including test data, etc.: 363 390 Distribution format: tar.gz Programming language: Fortran 95 Computer: All systems with a Fortran95 compiler Operating system: All systems with a Fortran95 compiler Classification: 7.3, 8 External routines: NetCDF, http://www.unidata.ucar.edu/software/netcdf Nature of problem: Store and exchange electronic structure data and crystallographic data independently of the computational platform, language and generating software Solution method: Implement a library based both on NetCDF file format and an open specification (http://etsf.eu/index.php?page=standardization)},
  doi       = {10.1016/j.cpc.2008.05.007},
  file      = {2008_Caliste_748.pdf:by-author/C/Caliste/2008_Caliste_748.pdf:PDF},
  groups    = {am/ETSF},
  keywords  = {Crystallographic Computing; Data Management; NetCDF},
  owner     = {saulius},
  timestamp = {2013.08.20},
  creationdate = {2013-08-20T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/S0010465508001963},
}

@Article{Calisto2005,
  author    = {Calisto, Bárbara M. and Pich, Oscar Q. and Piñol, Jaume and Fita, Ignacio and Querol, Enrique and Carpena, Xavier},
  journal   = {Journal of molecular biology},
  title     = {Crystal structure of a putative type I restriction-modification S subunit from Mycoplasma genitalium.},
  year      = {2005},
  pages     = {749--62},
  volume    = {351},
  abstract  = {The crystal structure of the eubacteria Mycoplasma genitalium ORF MG438 polypeptide, determined by multiple anomalous dispersion and refined at 2.3 A resolution, reveals the organization of S subunits from the Type I restriction and modification system. The structure consists of two globular domains, with about 150 residues each, separated by a pair of 40 residue long antiparallel alpha-helices. The globular domains correspond to the variable target recognition domains (TRDs), as previously defined for S subunits on sequence analysis, while the two helices correspond to the central (CR1) and C-terminal (CR2) conserved regions, respectively. The structure of the MG438 subunit presents an overall cyclic topology with an intramolecular 2-fold axis that superimposes the N and the C-half parts, each half containing a globular domain and a conserved helix. TRDs are found to be structurally related with the small domain of the Type II N6-adenine DNA MTase TaqI. These relationships together with the structural peculiarities of MG438, in particular the presence of the intramolecular quasi-symmetry, allow the proposal of a model for S subunits recognition of their DNA targets in agreement with previous experimental results. In the crystal, two subunits of MG438 related by a crystallographic 2-fold axis present a large contact area mainly involving the symmetric interactions of a cluster of exposed hydrophobic residues. Comparison with the recently reported structure of an S subunit from the archaea Methanococcus jannaschii highlights the structural features preserved despite a sequence identity below 20%, but also reveals important differences in the globular domains and in their disposition with respect to the conserved regions.},
  file      = {:by-author/C/Calisto/2005_Calisto_749.pdf:PDF},
  keywords  = {TypeI},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Calladine1982,
  author    = {Calladine, C. R.},
  journal   = {Journal of molecular biology},
  title     = {Mechanics of sequence-dependent stacking of bases in B-DNA.},
  year      = {1982},
  pages     = {343--52},
  volume    = {161},
  file      = {:by-author/C/Calladine/1982_Calladine_343.pdf:PDF},
  keywords  = {Calladine Rules; Readout},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Callaway2012,
  author    = {Callaway, Ewen},
  journal   = {Nature},
  title     = {Studies slow the human DNA clock.},
  year      = {2012},
  pages     = {343--4},
  volume    = {489},
  abstract  = {The story of human ancestors used to be writ only in bones and tools, but since the 1960s DNA has given its own version of events. Some results were revelatory, such as when DNA studies showed that all modern humans descended from ancestors who lived in Africa more than 100,000 years ago. Others were baffling, suggesting that key events in human evolution happened at times that flatly contradicted the archaeology. Now archaeologists and geneticists are beginning to tell the same story, thanks to improved estimates of DNA’s mutation rate — the molecular clock that underpins genetic dating1–4. “It’s incredibly vindicating to finally have some reconciliation between genetics and archaeology,” says Jeff Rose, an archaeologist at the University of Birmingham, UK. Archaeologists and geneticists may now be able to tackle nuanced questions about human history with greater confidence in one another’s data. “They do have to agree,” says Aylwyn Scally, an evolutionary genomicist at the Wellcome Trust Sanger Institute in Hinxton, UK. “There was a real story.”},
  file      = {:by-author/C/Callaway/2012_Callaway_343.pdf:PDF},
  keywords  = {Anthropology; DNA Clock; Human Evolution},
  owner     = {saulius},
  timestamp = {2013.01.08},
  creationdate = {2013-01-08T00:00:00},
}

@InCollection{Callender2011,
  author    = {Craig Callender},
  booktitle = {The Continuum Companion to the Philosophy of Science},
  publisher = {Continuum},
  title     = {Philosophy of Science and Metaphysics},
  year      = {2011},
  pages     = {33--54},
  file      = {:by-author/C/Callender/2011_Callender_33.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.09.30},
  creationdate = {2012-09-30T00:00:00},
}

@Article{Calogero2008,
  author    = {F. Calogero and F. Leyvraz},
  journal   = {New Journal of Physics},
  title     = {Spontaneous reversal of irreversible processes in a many-body Hamiltonian evolution},
  year      = {2008},
  pages     = {023042},
  volume    = {10},
  abstract  = {Recently a technique has been introduced to Ω-modify a Hamiltonian so that the Ω-modifiedHamiltonian thereby produced is isochronous: all its solutions are periodic in all degrees of freedom with the same period \tilde{T} =2\pi /\Omega . In this paper—after briefly reviewing this approach—we focus in particular on the Ω-modified version of the most general realistic many-body problem whose behavior, over time intervals much shorter than the isochrony period \tilde{T} , differs only marginally from the thermodynamically irreversible evolution of the corresponding, unmodified and realistic many-body system. We discuss the (apparently paradoxical) periodic recurrence of the irreversible processes occurring in this Ω-modified model, implying a periodic reversal of its irreversible behavior. We then discuss the equilibrium statistical mechanics of this Ω-modified model, including the compatibility of standard thermodynamic notions such as entropy with the peculiar phenomenology featured by its time evolution. The theoretical discussion is complemented by numerically simulated examples of the molecular dynamics yielded by the (standard and classical) Hamiltonian describing (many) particles interacting pairwise via potentials of Lennard–Jones type and via harmonic potentials in two-dimensional space, and by its Ω-modified version. In the latter case, the simulation displays (approximate) returns to configurations away from thermodynamic equilibrium after relaxation to equilibrium had occurred.},
  doi       = {10.1088/1367-2630/10/2/023042},
  file      = {:by-author/C/Calogero/2008_Calogero_023042.pdf:PDF},
  keywords  = {Spontaneous; Statistical Physics},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
  url       = {http://stacks.iop.org/1367-2630/10/i=2/a=023042},
}

@Webpage{Cameron1998,
  author      = {Robert D. Cameron},
  retrieved   = {2008-07-28},
  title       = {REX: XML Shallow Parsing with Regular Expressions},
  url         = {http://www.cs.sfu.ca/~cameron/REX.html},
  institution = {School of Computing Science, Simon Fraser University},
  month       = {November},
  year        = {1998},
  abstract    = {The syntax of XML is simple enough that it is possible to parse an XML document into a list of its markup and text items using a single regular expression. Such a shallow parse of an XML document can be very useful for the construction of a variety of lightweight XML processing tools. However, complex regular expressions can be difficult to construct and even more difficult to read. Using a form of literate programming for regular expressions, this paper documents a set of XML shallow parsing expressions that can be used a basis for simple, correct, efficient, robust and language-independent XML shallow parsing. Complete shallow parser implementations of less than 50 lines each in Perl, JavaScript and Lex/Flex are also given.},
  file        = {:by-author/C/Cameron/1998_Cameron.war:},
  keywords    = {Computer Science (CS); XML},
  owner       = {saulius},
  timestamp = {2015.03.02},
  creationdate = {2015-03-02T00:00:00},
}

@TechReport{Campbell2010,
  author      = {Greg Campbell},
  institution = {U.S. Department of Health and Human Services Food and Drug Administration Center for Devices and Radiological Health Division of Biostatistics Office of Surveillance and Biometrics},
  title       = {Guidance Documents (Medical Devices and Radiation-Emitting Products) - Guidance for the Use of {Bayesian} Statistics in Medical Device Clinical Trials},
  year        = {2010},
  type        = {WebContent},
  abstract    = {OSB/DB},
  file        = {2010_Campbell.pdf:by-author/H/Health/2010_Campbell.pdf:PDF;2010_Campbell.html:by-author/H/Health/2010_Campbell.html:URL},
  groups      = {sg/Clinical Trials},
  language    = {en},
  owner       = {saulius},
  timestamp = {2015.12.14},
  creationdate = {2015-12-14T00:00:00},
  url         = {http://www.fda.gov/MedicalDevices/DeviceRegulationandGuidance/GuidanceDocuments/ucm071072.htm},
  urldate     = {2015-12-12},
}

@Manuscript{Cann1991,
  author    = {David Cann},
  title     = {Retire Fortran? A Debate Rekindled},
  year      = {1991},
  keywords  = {Computer Science (CS); Fortran; Programming Languages; Sisal},
  url       = {http://www.fortranstatement.com/SisalVsFORTRAN_LLNL.pdf},
  abstract  = {In the May 1984 issue of Physics Today, Jim McGraw debated David Kuck and Michael Wolfe on the question of retiring Fortran. They adressed such questions as: Is Fortran the best tool for decomposing problems for parallel execution? Is Fortran the programming language we should carry into the 21st century? Are there alternatives? While McGraw argued forcefully in favor of retiring Fortran, concerns about performace crippled his position. He could not rebut the claim that only Fortran could provide the performance required for scientific computing. In this report, we use the current performance of CRAY Sisal, a functional language for large-scale scientific computing, to counter that claim. Of McGraw had had our data in 1984, he coul dhave countered what some say is the only defence in favor of keeping Fortran. The results show that we can move beyond the constraints of imperative programming. We can raise the level of abstraction and {\it retain performance}.},
  file      = {:by-author/C/Cann/1991_Cann_preprint.pdf:PDF},
  owner     = {saulius},
  pages     = {preprint},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Presentation{Cantrell1999,
  author    = {Cantrell},
  title     = {Boolean Algebra (1)},
  year      = {1999},
  file      = {:by-author/C/Cantrell/1999_Cantrell_slides.pdf:PDF},
  keywords  = {Boolean Algebra; Computer Architecture; Computer Science (CS)},
  owner     = {saulius},
  pages     = {slides},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@InProceedings{Cao2007,
  author    = {Yingjun Cao and Lingchu Yu and Alade Tokuta and Paul P. Wang},
  booktitle = {Innovative Algorithms and Techniques in Automation, Industrial Electronics and Telecommunications},
  title     = {A Random Approach to Study the Stability of Fuzzy Logic Networks},
  year      = {2007},
  editor    = {T. Sobh et al.},
  pages     = {17--21},
  publisher = {Springer},
  abstract  = {In this paper, we propose a general network model, fuzzy logic network (FLN), and study its stability and conver- gence properties. The convergence property was first deduced theoretically. Then a random approach was adopted to simulate the convergence speed and steady-state properties for a variety of fuzzy logical functions. The simulation results show that MV logi- cal function causes the system to be on the edge of chaos when the number of nodes increases. Thus this logical function is more use- ful to infer real complex networks, such as gene regulatory net- works.},
  file      = {:by-author/C/Cao/2007_Cao_17.pdf:PDF},
  owner     = {saulius},
  timestamp = {2013.08.11},
  creationdate = {2013-08-11T00:00:00},
}

@Article{Capkauskaite2010,
  author      = {Edita Čapkauskaitė and Lina Baranauskienė and Dmitrij Golovenko and Elena Manakova and Saulius Gražulis and Sigitas Tumkevičius and Daumantas Matulis},
  journal     = {Bioorg Med Chem},
  title       = {Indapamide-like benzenesulfonamides as inhibitors of carbonic anhydrases I, II, VII, and XIII.},
  year        = {2010},
  pages       = {7357--7364},
  volume      = {18},
  abstract    = {A series of novel 2-chloro-5-[(1-benzimidazolyl- and 2-benzimidazolylsulfanyl)acetyl]benzene-sulfonamides were designed and synthesized. Their binding to recombinant human carbonic anhydrase (hCA) isozymes I, II, VII, and XIII was determined by isothermal titration calorimetry and thermal shift assay. The designed S-alkylated benzimidazole derivatives exhibited stronger binding than the indapamide-like N-alkylated benzimidazoles, with the K(d) reaching about 50-100 nM with drug-targeted hCAs VII and XIII. The cocrystal structures of selected compounds with hCA II were determined by X-ray crystallography, and structural features of the binding event were revealed.},
  doi         = {10.1016/j.bmc.2010.09.016},
  file        = {:by-author/C/Capkauskaitė/2010_Capkauskaite_7357.pdf:PDF},
  groups      = {sg/inhibitors},
  institution = {Laboratory of Biothermodynamics and Drug Design, Institute of Biotechnology, Graičiūno 8, Vilnius LT-02241, Lithuania.},
  keywords    = {Antagonists /&/ Inhibitors/genetics/metabolism; Binding Sites; Carbonic Anhydrase I; Carbonic Anhydrase II; Carbonic Anhydrase Inhibitors; Carbonic Anhydrases; Chemical Synthesis/chemistry/pharmacology; Chemistry; Chemistry/genetics/metabolism; Crystallography; Humans; Indapamide; Kinetics; Protein Binding; Protein Structure; Recombinant Proteins; Sulfonamides; Tertiary; X-Ray},
  language    = {eng},
  medline-pst = {ppublish},
  owner       = {em},
  pii         = {S0968-0896(10)00831-X},
  pmid        = {20926301},
  timestamp = {2013.02.18},
  creationdate = {2013-02-18T00:00:00},
  url         = {http://dx.doi.org/10.1016/j.bmc.2010.09.016},
}

@Article{Capkauskaite2012,
  author    = {Čapkauskaitė, Edita and Zubrienė, Asta and Baranauskienė, Lina and Tamulaitienė, Giedrė and Manakova, Elena and Kairys, Visvaldas and Gražulis, Saulius and Tumkevičius, Sigitas and Matulis, Daumantas},
  journal   = {European journal of medicinal chemistry},
  title     = {Design of [(2-pyrimidinylthio)acetyl]benzenesulfonamides as inhibitors of human carbonic anhydrases.},
  year      = {2012},
  pages     = {259--70},
  volume    = {51},
  abstract  = {A series of [(2-pyrimidinylthio)acetyl]benzenesulfonamides were designed and synthesized. Their binding affinities as inhibitors of several recombinant human carbonic anhydrase (CA) isozymes were determined by isothermal titration calorimetry (ITC) and thermal shift assay (TSA). A group of compounds containing a chlorine atom in the benzenesulfonamide ring were found to exhibit higher selectivity but lower binding affinity toward tested CAs. The crystal structures of selected compounds in complex with CA II were determined to atomic resolution. Docking studies were performed to compare the binding modes of experimentally determined crystallographic structures with computational prediction of the pyrimidine derivative binding to CA II. Several compounds bound to select CAs with single-digit nanomolar affinities and could be used as leads for inhibitor development toward a select CA isozyme.},
  doi       = {10.1016/j.ejmech.2012.02.050},
  file      = {:by-author/C/Capkauskaitė/2012_Capkauskaite_259.pdf:PDF},
  groups    = {sg/inhibitors},
  keywords  = {Crystal Structure; Inhibitors; Pyrimidines; {hCA}},
  owner     = {saulius},
  timestamp = {2012.05.02},
  creationdate = {2012-05-02T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/S0223523412001419},
}

@Article{Capkauskaite2013,
  author      = {Edita Čapkauskaitė and Asta Zubrienė and Alexey Smirnov and Jolanta Torresan and Miglė Kišonaitė and Justina Kazokaitė and Joana Gylytė and Vilma Michailovienė and Vaida Jogaitė and Elena Manakova and Saulius Gražulis and Sigitas Tumkevičius and Daumantas Matulis},
  journal     = {Bioorg Med Chem},
  title       = {Benzenesulfonamides with pyrimidine moiety as inhibitors of human carbonic anhydrases I, II, VI, VII, XII, and XIII.},
  year        = {2013},
  month       = {Nov},
  note        = {BVTL BNSTL pdb/4KNJ, pdb/4KNN, pdb/4KP5, pdb/4KNI, pdb/4KNM, pdb/4KP8},
  number      = {22},
  pages       = {6937--6947},
  volume      = {21},
  abstract    = {Two groups of benzenesulfonamide derivatives, bearing pyrimidine moieties, were designed and synthesized as inhibitors of carbonic anhydrases (CA). Their binding affinities to six recombinant human CA isoforms I, II, VI, VII, XII, and XIII were determined by the thermal shift assay (TSA). The binding of several inhibitors was measured by isothermal titration calorimetry (ITC). Direct demonstration of compound inhibition was achieved by determining the inhibition constant by stopped-flow CO2 hydration assay. The most potent compounds demonstrated selectivity towards isoform I and affinities of 0.5nM. The crystal structures of selected compounds in complex with CA II, XII, and XIII were determined to atomic resolution. Compounds described here were compared with previously published pyrimidinebenzenesulfonamides.(1) Systematic structure-activity analysis of 40 compound interactions with six isoforms yields clues for the design of compounds with greater affinities and selectivities towards target CA isoforms.},
  comment     = {Acknowledgments This research was funded by a Grant (No. LIG-09/2012) from the Research Council of Lithuania. Diffraction data were collected at the EMBL/DESY, Hamburg, P14 beamline at PETRA III storage ring and X11 at DORIS storage ring. Access to the measurement facilities was funded by the FP7-REGPOT-2009-1 program (project 245721 MoBiLi). M.K. and A.S. acknowledge support by project ‘Promotion of Student Scientific Activities’ (VP1-3.1-ŠMM-01-V-02-003) from the Research Council of Lithuania. This project is funded by the Republic of Lithuania and European Social Fund under the 2007–2013 Human Resources Development Operational Programme’s priority 3. Authors thank Zita Liutkevičiūtė and Vytautas Smirnovas for the help with mass spectrometry analysis of synthetic compounds and proteins and local contacts at the EMBL beamlines Dr. G. Bourenkov and Dr. M. Cianci for the help with beamline operation.},
  doi         = {10.1016/j.bmc.2013.09.029},
  file        = {2013_Capkauskaite_6937.pdf:by-author/C/Capkauskaitė/2013_Capkauskaite_6937.pdf:PDF},
  groups      = {sg/inhibitors},
  institution = {Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Graičiūno 8, Vilnius LT-02241, Lithuania.},
  keywords    = {Crystal Structures; Inhibitors; Pirimidines; {hCA}},
  language    = {eng},
  medline-pst = {ppublish},
  owner       = {em},
  pii         = {S0968-0896(13)00809-2},
  pmid        = {24103428},
  timestamp = {2013.10.30},
  creationdate = {2013-10-30T00:00:00},
  url         = {http://dx.doi.org/10.1016/j.bmc.2013.09.029},
}

@TechReport{Caravita2011,
  author      = {Ruggero Caravita},
  institution = {CERN openlab},
  title       = {Implementation and test of MLFit application using OpenMP and MPI parallel technlogies},
  year        = {2011},
  month       = {aug},
  file        = {:by-author/C/Caravita/2011_Caravita_slides.pdf:PDF},
  owner       = {saulius},
  pages       = {slides},
  timestamp = {2013.07.02},
  creationdate = {2013-07-02T00:00:00},
}

@TechReport{Cardelli1995,
  author      = {Luca Cardelli},
  institution = {Digital Equipment Corporation, Systems Research Center, 130 Lytton Ave, Palo Alto, CA 94301, USA},
  title       = {A Language with Distributed Scope},
  year        = {1995},
  month       = {May},
  abstract    = {Obliq is a lexically-scoped, untyped, interpreted lan- guage that supports distributed object-oriented computation. Obliq objects have state and are local to a site. Obliq computations can roam over the network, while maintaining network connections. Distributed lexical scoping is the key mechanism for managing distributed computations.},
  file        = {:by-author/C/Cardelli/1995_Cardelli.ps:PostScript;:by-author/C/Cardelli/1995_Cardelli.pdf:PDF},
  keywords    = {Computer Science (CS); Obliq; Programming Languages},
  owner       = {saulius},
  timestamp = {2015.02.27},
  creationdate = {2015-02-27T00:00:00},
}

@Article{Cardone2009,
  author    = {Fabio Cardone and Roberto Mignani and Andrea Petrucci},
  journal   = {Physics Letters A},
  title     = {Piezonuclear decay of thorium},
  year      = {2009},
  pages     = {1956--1958},
  volume    = {373},
  doi       = {10.1016/j.physleta.2009.03.067},
  file      = {:by-author/C/Cardone/2009_Cardone_1956.pdf:PDF},
  keywords  = {Physics; Radioactive Decay},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@InProceedings{Cardoze1998,
  author    = {David E. Cardoze and Leonard J. Schulman},
  booktitle = {Foundations of Computer Science, 1998. Proceedings. 39th Annual Symposium on},
  title     = {Pattern Matching for Spatial Point Sets},
  year      = {1998},
  pages     = {156--165},
  doi       = {10.1109/SFCS.1998.743439},
  file      = {:by-author/C/Cardoze/1998_Cardoze_156.pdf:PDF},
  owner     = {andrius},
  timestamp = {2013.05.28},
  creationdate = {2013-05-28T00:00:00},
}

@Presentation{Carlin2012,
  author    = {Bradley P. Carlin},
  title     = {Bayesian Adaptive Methods for Clinical Trials},
  year      = {2012},
  file      = {2012_Carlin.pdf:by-author/C/Carlin/2012_Carlin.pdf:PDF},
  groups    = {sg/Clinical Trials},
  owner     = {saulius},
  timestamp = {2015.12.14},
  creationdate = {2015-12-14T00:00:00},
  url       = {http://www.biostat.umn.edu/~brad/7440/slidePfizer-UofM2012.pdf},
  urldate   = {2015-12-12},
}

@Article{Carlson1931,
  author    = {Carlson, A. J.},
  journal   = {Science (New York, N.Y.)},
  title     = {Science And The Supernatural.},
  year      = {1931},
  pages     = {217--25},
  volume    = {73},
  file      = {:by-author/C/Carlson/1931_Carlson_217.pdf:PDF},
  keywords  = {Epistemology; Philosophy},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@Article{Carlson2006,
  author    = {J. A. Carlson and M. D. Olmstead and M. Beck},
  journal   = {Am. J. Phys.},
  title     = {Quantum mysteries tested: An experiment implementing Hardy’s test of local realism},
  year      = {2006},
  pages     = {180--186},
  volume    = {74},
  abstract  = {We have performed a test of local realism using entangled photons produced by spontaneous parametric downconversion. This experimental test is based on an idea originally proposed by Hardy for a test of local realism without inequalities, although our experiment actually measures an inequality as any experiment must. We find a more-than-70 standard deviation violation of the predictions of local realism. The experimental effort required for this test is essentially the same as that required for a test of a Bell inequality. However, this test is based on concepts that are easier to understand and more compelling than those behind the original Bell inequality},
  doi       = {10.1119/1.2167764},
  file      = {2006_Carlson_180.pdf:by-author/C/Carlson/2006_Carlson_180.pdf:PDF},
  keywords  = {Bell's Inequalities; Quantum Correlations; Quantum Mechanics (QM)},
  owner     = {saulius},
  timestamp = {2013.10.22},
  creationdate = {2013-10-22T00:00:00},
  url       = {http://people.whitman.edu/~beckmk/QM/Hardy/Carlson_ajp.pdf},
}

@Article{Carolan2015,
  author    = {Carolan, Jacques and Harrold, Christopher and Sparrow, Chris and Martín-López, Enrique and Russell, Nicholas J. and Silverstone, Joshua W. and Shadbolt, Peter J. and Matsuda, Nobuyuki and Oguma, Manabu and Itoh, Mikitaka and Marshall, Graham D. and Thompson, Mark G. and Matthews, Jonathan C. F. and Hashimoto, Toshikazu and O’Brien, Jeremy L. and Laing, Anthony},
  journal   = {Science},
  title     = {Universal linear optics},
  year      = {2015},
  issn      = {0036-8075, 1095-9203},
  pages     = {711--716},
  volume    = {349},
  abstract  = {Linear optics underpins fundamental tests of quantum mechanics and quantum technologies. We demonstrate a single reprogrammable optical circuit that is sufficient to implement all possible linear optical protocols up to the size of that circuit. Our six-mode universal system consists of a cascade of 15 Mach-Zehnder interferometers with 30 thermo-optic phase shifters integrated into a single photonic chip that is electrically and optically interfaced for arbitrary setting of all phase shifters, input of up to six photons, and their measurement with a 12-single-photon detector system. We programmed this system to implement heralded quantum logic and entangling gates, boson sampling with verification tests, and six-dimensional complex Hadamards. We implemented 100 Haar random unitaries with an average fidelity of 0.999 ± 0.001. Our system can be rapidly reprogrammed to implement these and any other linear optical protocol, pointing the way to applications across fundamental science and quantum technologies. Complex quantum optical circuitry Encoding and manipulating information in the states of single photons provides a potential platform for quantum computing and communication. Carolan et al. developed a reconfigurable integrated waveguide device fabricated in a glass chip (see the Perspective by Rohde and Dowling). The device allowed for universal linear optics transformations on six wave-guides using 15 integrated Mach-Zehnder interferometers, each of which was individually programmable. Functional performance in a number of applications in optics and quantum optics demonstrates the versatility of the device's reprogrammable architecture. Science, this issue p. 711; see also p. 696},
  doi       = {10.1126/science.aab3642},
  file      = {Carolan et al. - 2015 - Universal linear optics.pdf:by-author/C/Carolan/2015_Carolan_711.pdf:PDF;Snapshot:by-author/C/Carolan/2015_Carolan_711.html:URL},
  language  = {en},
  owner     = {saulius},
  pmid      = {26160375},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://www.sciencemag.org/content/349/6249/711},
  urldate   = {2015-09-10},
}

@InBook{Carpinelli2000,
  author    = {Carpinelli},
  chapter   = {6},
  pages     = {214--266},
  title     = {CPU Design},
  year      = {2000},
  file      = {:by-author/C/Carpinelli/2000_Carpinelli_214.pdf:PDF},
  keywords  = {CPU Design; Computer Science (CS)},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Carrascoza2014,
  author    = {Carrascoza, Francisco and Zaric, Snezana and Silaghi-Dumitrescu, Radu},
  journal   = {Journal of molecular graphics \&amp; modelling},
  title     = {Computational study of protein secondary structure elements: Ramachandran plots revisited.},
  year      = {2014},
  pages     = {125--133},
  volume    = {50},
  abstract  = {Potential energy surface (PES) were built for nineteen amino acids using density functional theory (PW91 and DFT M062X/6-311**). Examining the energy as a function of the φ/ψ dihedral angles in the allowed regions of the Ramachandran plot, amino acid groups that share common patterns on their PES plots and global minima were identified. These patterns show partial correlation with their structural and pharmacophoric features. Differences between these computational results and the experimentally noted permitted conformations of each amino acid are rationalized on the basis of attractive intra- and inter-molecular non-covalent interactions. The present data are focused on the intrinsic properties of an amino acid - an element which to our knowledge is typically ignored, as larger models are always used for the sake of similarity to real biological polypeptides.},
  doi       = {10.1016/j.jmgm.2014.04.001},
  file      = {:by-author/C/Carrascoza/2014_Carrascoza_125.pdf:pdf},
  keywords  = {Structure Refinement; Validation; X-ray Crystallography},
  owner     = {saulius},
  pii       = {S1093-3263(14)00046-1},
  pubmed    = {24793053},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@TechReport{Carreira-Perpinan2000,
  author      = {Carreira-Perpinan},
  institution = {Dept. of Computer Science, University of Sheffield, UK},
  title       = {Mode-finding for mixtures of Gaussian distributions},
  year        = {2000},
  month       = {August},
  note        = {Technical Report CS–99–03},
  number      = {CS–99–03},
  abstract    = {I consider the problem of finding all the modes of a mixture of multivariate Gaussian distributions, which has applications in clustering and regression. I derive exact formulas for the gradient and Hessian and give a partial proof that the number of modes cannot be more than the number of components, and are contained in the convex hull of the component centroids. Then, I develop two exhaustive mode search algorithms: one based on combined quadratic maximisation and gradient ascent and the other one based on a fixed-point iterative scheme. Appropriate values for the search control parameters are derived by taking into account theoretical results regarding the bounds for the gradient and Hessian of the mixture. The significance of the modes is quantified locally (for each mode) by error bars, or confidence intervals (estimated using the values of the Hessian at each mode); and globally by the sparseness of the mixture, measured by its differential entropy (estimated through bounds). I conclude with some reflections about bump-finding.},
  file        = {2000_Carreira-Perpinan_tr.pdf:by-author/C/Carreira-Perpinan/2000_Carreira-Perpinan_tr.pdf:PDF},
  owner       = {saulius},
  pages       = {tr-CS-99-03},
  timestamp = {2012.09.18},
  creationdate = {2012-09-18T00:00:00},
}

@Article{Carson2007,
  author    = {Carson, Mike and Johnson, David H. and McDonald, Heather and Brouillette, Christie and Delucas, Lawrence J.},
  journal   = {Acta crystallographica. Section D, Biological crystallography},
  title     = {His-tag impact on structure.},
  year      = {2007},
  pages     = {295--301},
  volume    = {63},
  abstract  = {Crystallographers are increasingly determining structures of protein constructs that include His tags. Many have taken for granted that these tags have little effect on the native structure. This paper surveys and compares crystal structures with and without His tags. It is observed that actual refined tag residues fitted into density occur in less that 10% of the tagged sequences. However, higher resolution crystals are observed when this occurs. It is shown that these purification tags generally have no significant effect on the structure of the native protein. Resolution and R factors are not affected, but the overall B factors are slightly higher. Additional annotation in the PDB format to make tag definition explicit is suggested.},
  doi       = {10.1107/S0907444906052024},
  file      = {:by-author/C/Carson/2007_Carson_295.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Carte2008,
  author    = {Carte, Jason and Wang, Ruiying and Li, Hong and Terns, Rebecca M and Terns, Michael P.},
  journal   = {GENES \& DEVELOPMENT},
  title     = {Cas6 is an endoribonuclease that generates guide RNAs for invader defense in prokaryotes},
  year      = {2008},
  pages     = {489–3496},
  volume    = {22},
  abstract  = {An RNA-based gene silencing pathway that protects bacteria and archaea from viruses and other genome invaders is hypothesized to arise from guide RNAs encoded by CRISPR loci and proteins encoded by the cas genes. CRISPR loci contain multiple short invader-derived sequences separated by short repeats. The presence of virus-specific sequences within CRISPR loci of prokaryotic genomes confers resistance against corresponding viruses. The CRISPR loci are transcribed as long RNAs that must be processed to smaller guide RNAs. Here we identified Pyrococcus furiosus Cas6 as a novel endoribonuclease that cleaves CRISPR RNAs within the repeat sequences to release individual invader targeting RNAs. Cas6 interacts with a specific sequence motif in the 5؅ region of the CRISPR repeat element and cleaves at a defined site within the 3؅ region of the repeat. The 1.8 angstrom crystal structure of the enzyme reveals two ferredoxin-like folds that are also found in other RNA-binding proteins. The predicted active site of the enzyme is similar to that of tRNA splicing endonucleases, and concordantly, Cas6 activity is metal-independent. cas6 is one of the most widely distributed CRISPR-associated genes. Our findings indicate that Cas6 functions in the generation of CRISPR-derived guide RNAs in numerous bacteria and archaea.},
  doi       = {10.1101/gad.1742908},
  file      = {2008_Carte_3489.pdf:by-author/C/Carte/2008_Carte_3489.pdf:PDF},
  groups    = {sg/CRISPR-Cas},
  keywords  = {CRISPR; CasE; Cascade},
  owner     = {em},
  timestamp = {2013.01.07},
  creationdate = {2013-01-07T00:00:00},
}

@Article{Carter1988,
  author    = {Carter, Charles W. and Baldwin, Eric T. and Frick, Lloyd},
  journal   = {Journal of Crystal Growth},
  title     = {Statistical design of experiments for protein crystal growth and the use of a precrystallization assay},
  year      = {1988},
  issn      = {0022-0248},
  month     = {Jul},
  number    = {1-3},
  pages     = {60--73},
  volume    = {90},
  abstract  = {Statistical design of crystallization experiments greatly reduces the amount of protein necessary to find conditions for crystal growth and leads naturally to a useful data base for improving crystallization conditions in cases where the initial trials do not produce adequate results. Although it is counterintuitive to vary simultaneously all the factors to be screened, this apparent loss of control over experimental parameters actually costs very little in terms of the statistical strength of inferences to be drawn from the resulting data. We have used incomplete factorial designs to crystallize all of the proteins we are now studying (tryptophanyl-tRNA synthetase, cytidine deaminase, and a manganese catalase). In each case we used a rudimentary microscopic examination to determine the experimental outcomes. From these data we have generated for each protein a “factor profile” showing the relative importance of the factors studied. In at least one case, the specific information in this profile lead to a substantial improvement in the crystals we were able to grow. Considerable potential power lies in the ability to feed information obtained from all experiments in an initial trial back into the design of subsequent improvements in crystal growth conditions. Exploitation of this feedback is limited by the accuracy of the experimental assay procedure. Microscopic examination has many limitations, including subjectivity and low precision. More importantly, it can be seriously misleading if kinetic factors force suitable nuclei to shower as a microcrystalline array which is mistakenly taken to be a precipitate. The dilution curve assay based on dynamic light scattering was developed (Kam et al., J. Mol. Biol. 123 (1978) 539-555) from the concept that hydrodynamic measurements at different protein concentrations could reflect thermodynamic interactions in aggregates without forcing the system to produce macroscopic manifestations. Hence, it should discriminate between cases involving a kinetic barrier to large crystal growth and those where thermodynamic interactions between molecules are poor. Preliminary measurements of the dilution curves of phosphoglucomutase in ammonium sulfate solutions with and without PEG-400 suggest that the dilution curve can identify microcrystalline samples.},
  doi       = {10.1016/0022-0248(88)90299-0},
  file      = {1988_Carter_60.pdf:by-author/C/Carter/1988_Carter_60.pdf:PDF},
  keywords  = {Crystallisation; Incomplete Factorial Designs; X-ray Crystallography},
  owner     = {saulius},
  publisher = {Elsevier BV},
  timestamp = {2016.04.19},
  creationdate = {2016-04-19T00:00:00},
  url       = {http://dx.doi.org/10.1016/0022-0248(88)90299-0},
}

@Article{Cartwright2004,
  author    = {Robert Cartwright and Mike Fagan},
  journal   = {SIGPLAN Not.},
  title     = {Soft Typing},
  year      = {2004},
  pages     = {412--428},
  volume    = {39},
  acmid     = {989435},
  address   = {New York, NY, USA},
  doi       = {10.1145/989393.989435},
  file      = {2004_Cartwright_SIGPLAN_Notices_412--Soft_typing.pdf:by-author/C/Cartwright/2004_Cartwright_412.pdf:PDF},
  keywords  = {Computer Science (CS); Type Systems},
  owner     = {saulius},
  publisher = {ACM},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Carugo2005,
  author    = {Oliviero Carugo and Kristina Djinović Carugo},
  journal   = {Trends in Biochemical Sciences},
  title     = {When X-rays modify the protein structure: radiation damage at work},
  year      = {2005},
  issn      = {0968-0004},
  pages     = {213--219},
  volume    = {30},
  abstract  = {The majority of 3D structures of macromolecules are currently determined by macromolecular crystallography, which employs the diffraction of X-rays on single crystals. However, during diffraction experiments, the X-rays can damage the protein crystals by ionization processes, especially when powerful X-ray sources at synchrotron facilities are used. This process of radiation damage generates photo-electrons that can get trapped in protein moieties. The 3D structure derived from such experiments can differ remarkably from the structure of the native molecule. Recently, the crystal structures of different oxidation states of horseradish peroxidase and nickel-containing superoxide dismutase were determined using crystallographic redox titration performed during the exposure of the crystals to the incident X-ray beam. Previous crystallographic analyses have not shown the distinct structures of the active sites associated with the redox state of the structural features of these enzymes. These new studies show that, for protein moieties that are susceptible to radiation damage and prone to reduction by photo-electrons, care is required in both the design of the diffraction experiment and the analysis and interpretation.},
  doi       = {10.1016/j.tibs.2005.02.009},
  file      = {2005_Carugo_213.pdf:by-author/C/Carugo/2005_Carugo_213.pdf:PDF},
  keywords  = {Protein Crystallography; Radiation Damage; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2014.03.24},
  creationdate = {2014-03-24T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/S0968000405000575},
}

@Article{Carugo2001,
  author    = {Carugo, Oliviero and Pongor, Sándor},
  journal   = {Protein Science},
  title     = {A normalized root-mean-spuare distance for comparing protein three-dimensional structures},
  year      = {2001},
  issn      = {1469-896X},
  pages     = {1470--1473},
  volume    = {10},
  abstract  = {The degree of similarity of two protein three-dimensional structures is usually measured with the root-mean-square distance between equivalent atom pairs. Such a similarity measure depends on the dimension of the proteins, that is, on the number of equivalent atom pairs. The present communication presents a simple procedure to make the root-mean-square distances between pairs of three-dimensional structures independent of their dimensions. This normalization may be useful in evolutionary and fold classification studies as well as in simple comparisons between different structural models.},
  doi       = {10.1110/ps.690101},
  file      = {2001_Carugo_1470.pdf:by-author/C/Carugo/2001_Carugo_1470.pdf:PDF},
  keywords  = {Root Mean Square Distance; Structure Classification; Structure Comparison; Three-dimensional Similarity},
  owner     = {saulius},
  publisher = {Cold Spring Harbor Laboratory Press},
  timestamp = {2012.05.15},
  creationdate = {2012-05-15T00:00:00},
  url       = {http://dx.doi.org/10.1110/ps.690101},
}

@Article{Carvajal-Moreno2015,
  author    = {Carvajal-Moreno, Carvajal-Moreno},
  title     = {Mycotoxins that affect the human cardiovascular system},
  year      = {2015},
  pages     = {124},
  volume    = {4},
  copyright = {Creative Commons Attribution License},
  doi       = {10.4172/2167-7956.1000124},
  file      = {Carvajal-Moreno - 2015 - Mycotoxins that Affect the Human Cardiovascular Sy.pdf:by-author/C/Carvajal-Moreno/2015_Carvajal-Moreno_124.pdf:application/pdf},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://www.omicsgroup.org/journals/mycotoxins-that-affect-the-human-cardiovascular-system-2167-7956-1000124.pdf},
  urldate   = {2015-09-07},
}

@Article{Casas2015,
  author    = {Casas, Lluís and Estop, Eugènia},
  journal   = {Journal of Chemical Education},
  title     = {Virtual and Printed 3D Models for Teaching Crystal Symmetry and Point Groups},
  year      = {2015},
  abstract  = {Both, virtual and printed 3D crystal models can help students and teachers deal with chemical education topics such as symmetry and point groups. In the present paper, two freely downloadable tools (interactive PDF files and a mobile app) are presented as examples of the application of 3D design to study point-symmetry. The use of 3D printing to produce tangible crystal models is also explored. A series of dissection puzzles that will be especially useful for teaching crystallographic concepts such as asymmetric unit and general/special positions is presented. Educators are encouraged to use the presented tools in their classes, and we expect our work to inspire other college educators to design and share similar tools.},
  doi       = {10.1021/acs.jchemed.5b00147},
  eprint    = {http://dx.doi.org/10.1021/acs.jchemed.5b00147},
  file      = {2015_Casas_prepprint.pdf:by-author/C/Casas/2015_Casas_prepprint.pdf:PDF},
  keywords  = {3D Printing; Crystallographic Edication},
  owner     = {saulius},
  timestamp = {2015.06.12},
  creationdate = {2015-06-12T00:00:00},
  url       = {http://dx.doi.org/10.1021/acs.jchemed.5b00147},
}

@Article{Casas2009,
  author    = {L. Casas and C. Mantell and M. Rodríguez and A. Torres and F.A. Macías and E. Martínez de la Ossa},
  journal   = {Chemical Engineering Journal},
  title     = {Extraction of natural compounds with biological activity from sunflower leaves using supercritical carbon dioxide},
  year      = {2009},
  issn      = {1385-8947},
  pages     = {301--306},
  volume    = {152},
  abstract  = {The application of supercritical carbon dioxide in the extraction of bioactive compounds from Helianthus annuus L. (sunflower) has been investigated. The influence of different variables, including pre-treatment of the sample, temperature and pressure, was investigated. The samples were either dried or congealed and the extraction conditions were as follows: temperatures of 35, 40, 45 and 50&#xa0;°C, and pressures of 100, 200, 300, 400 and 500&#xa0;bar. The best extraction yields were achieved on using a dried sample at a temperature of 50&#xa0;°C and a pressure of 500&#xa0;bar. The bioactivities of the extracts obtained under the different sets of conditions were compared. The best activity profiles were obtained for the dried samples extracted with supercritical carbon dioxide at 500&#xa0;bar and congealed samples extracted at 50&#xa0;°C and 500&#xa0;bar.},
  doi       = {10.1016/j.cej.2007.06.027},
  file      = {2009_Casas_301.pdf:by-author/C/Casas/2009_Casas_301.pdf:PDF},
  keywords  = {Bioinformatics; Biological Activity; Chemoinformatics; Natural Language Processing; Natural Products; Sunflower},
  owner     = {saulius},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/S1385894707004330},
}

@Article{Casas1992,
  author    = {Jose R. Casas-Finet and Kenneth R. Fischer and Richard L. Karpel},
  journal   = {PNAS},
  title     = {Structural basis for the nucleic acid binding cooperativity of bacteriophage T4 gene 32 protein: The (Lys/Arg)3(Ser/Thr)2 (LAST) motif},
  year      = {1992},
  pages     = {1050--1054},
  volume    = {89},
  abstract  = {To identify the functional residues of the N-terminal B region of bacteriophage T4 gene 32 protein involved in its cooperative binding to single-stranded nucleic acids, a process dependent on homotypic protein-protein in- teraction, we have studied the interaction of the protein with synthetic peptides containing different portions of this domain. Gel-permeation chromatography showed that a 6-acryloyl-2- dimethylaminonaphthalene (acrylodan)-labeled fluorescent peptide corresponding to the first 17 residues of gene 32 protein formed a complex with whole protein. The fluorescence was blue-shifted 14 nm upon interaction with intact protein, and somewhat less so (7-11 mm) with cleavage products of the protein lacking B domains. The intrinsic tryptophan fluores- cence of whole and truncated protein was quenched by this peptide and by the nonderivatized peptide. The peptide bound tightly to truncated protein at both 0.015 and 0.44 M Na+, with a stoichiometry of 1:1. Similar tryptophan quenching or acry- lodan blue shifts were obtained with peptides corresponding to residues 1-9 and 3-8, but not residues 14, 5-9, or 5-17, indicating that the essential amino acids are contained within positions 3-8, Lys-Arg-Lys-Ser-Thr-Ala. Several other DNA binding proteins contain a LAST motif with documented involvement of these residues in nucleic acid interaction. The amino acid and coding sequence of residues 110-114, a region proposed to be involved in nucleic acid binding, is virtually identical to that of residues 3-7. Based on these observations, we have formulated a model for the cooperative interactions of gene 32 protein with single-stranded nucleic acids.},
  file      = {:by-author/C/Casas-Finet/1992_Casas-Finet_1050.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Cascarano1991,
  author    = {Cascarano, G. and Giacovazzo, C.},
  journal   = {J. Appl. Cryst.},
  title     = {Automatic searching of an asymmetric unit from the space-group symbol},
  year      = {1991},
  pages     = {1071--1072},
  volume    = {24},
  abstract  = {A program for the automatic definition of an asymmetric unit is described. Starting from the space-group symbol, an asymmetric unit is automatically calculated by means of a simple algorithm in the case of space groups up to the orthorhombic system. For higher symmetry a tabulation is used.},
  file      = {1991_Cascarano_1071.pdf:by-author/C/Cascarano/1991_Cascarano_1071.pdf:PDF},
  keywords  = {Spacegroup Symbols; Spacegroups; Symmetry},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Castagna2005,
  author    = {Castagna},
  journal   = {PPDP},
  title     = {A Gentle Introduction to Semantic Subtyping},
  year      = {2005},
  pages     = {198--208},
  file      = {:by-author/C/Castagna/2005_Castagna_PPDP.pdf:PDF},
  keywords  = {Computer Science (CS); Type Systems},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Presentation{Castro2006,
  author    = {Alberto Castro},
  title     = {A Primer in Density Functional Theory},
  year      = {2006},
  file      = {:by-author/C/Castro/2006_Castro_slides.pdf:PDF},
  keywords  = {Density Functional Theory (DFT); Presentations},
  owner     = {saulius},
  pages     = {slides},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Cavasotto2007,
  author    = {Claudion N. Cavasotto and Andrew J. W. Orry},
  journal   = {Current Topics in Medical Chemistry},
  title     = {Ligand design and Structure-based Virtual Screening in Drug Discovery},
  year      = {2007},
  pages     = {1006--1014},
  volume    = {7},
  file      = {:by-author/C/Cavasotto/2007_Cavasotto_1006.pdf:PDF},
  keywords  = {Docking},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@Article{Cavasotto2007a,
  author    = {Cavasotto, Claudio N. and Andrew J. W. Orry},
  journal   = {Current Topics in Medicinal Chemistry},
  title     = {Ligand Docking and Structure-based Virtual Screning in Drug Discovery},
  year      = {2007},
  pages     = {1006--1014},
  volume    = {7},
  file      = {2007_Cavasotto_1006.pdf:by-author/C/Cavasotto/2007_Cavasotto_1006.pdf:PDF},
  keywords  = {Docking},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Webpage{Rietveld,
  author    = {CCP14},
  retrieved = {2008-07-28},
  title     = {Hugo Rietveld \& Alan Hewat Fortran source code for Profile Refinement},
  url       = {http://www.ccp14.ac.uk/ccp/web-mirrors/hewat-rietveld/index.html},
  year      = {1978},
  file      = {:by-author/C/CCP14/1978_CCP14.war:},
  keywords  = {Rietveld Refinement},
  owner     = {saulius},
  timestamp = {2015.03.02},
  creationdate = {2015-03-02T00:00:00},
}

@Webpage{CCP141969,
  author    = {CCP14},
  retrieved = {2008-07-28},
  title     = {Classic Hugo Rietveld Source Code online: Original Hugo M. Rietveld Report - RCN-104 - Reactor Centrum Nederland},
  url       = {http://www.ccp14.ac.uk/ccp/web-mirrors/hugorietveld/riet-report/index.html},
  year      = {1969},
  file      = {:by-author/C/CCP14/1969_CCP14._Rietveld_Report_-_Reactor_Centrium_Nederland_-_April_1969.war:},
  keywords  = {Rietveld Refinement},
  owner     = {saulius},
  timestamp = {2015.03.02},
  creationdate = {2015-03-02T00:00:00},
}

@Article{CCP4CollaborativeComputationalProject1994,
  author    = {CCP4 (Collaborative Computational Project, Number 4)},
  journal   = {Acta Cryst D},
  title     = {The CCP4 suite: programs for protein crystallography},
  year      = {1994},
  pages     = {760--763},
  volume    = {50},
  abstract  = {The CCP4 (Collaborative Computational Project, number 4) program suite is a collection of programs and associated data and subroutine libraries which can be used for macromolecular structure determination by X-ray crystallography. The suite is designed to be flexible, allowing users a number of methods of achieving their aims and so there may be more than one program to cover each function. The programs are written mainly in standard Fortran77. They are from a wide variety of sources but are connected by standard data file formats. The package has been ported to all the major platforms under both Unix and VMS. The suite is distributed by anonymous ftp from Daresbury Laboratory and is widely used throughout the world.},
  file      = {:by-author/C/CCP4/1994_CCP4_760.pdf:PDF},
  keywords  = {CCP4; Protein Crystallography},
  owner     = {em},
  timestamp = {2011.10.17},
  creationdate = {2011-10-17T00:00:00},
}

@Webpage{CECAM2015,
  author    = {CECAM},
  retrieved = {2016-01-20},
  title     = {The Electronic Structure Library},
  url       = {http://esl.cecam.org/mediawiki/index.php/Main_Page},
  site      = {http://esl.cecam.org/},
  siteurl   = {http://esl.cecam.org/},
  year      = {2015},
  file      = {2015_CECAM.odt:by-author/C/CECAM/2015_CECAM.odt:OpenDocument text;2015_CECAM.pdf:by-author/C/CECAM/2015_CECAM.pdf:PDF},
  keywords  = {CECAM; Data Formats; Electronic Structure; Library},
  owner     = {saulius},
  timestamp = {2016.01.20},
  creationdate = {2016-01-20T00:00:00},
}

@Article{Cederbaum2013,
  author    = {Cederbaum, Lorenz S.},
  journal   = {The Journal of Chemical Physics},
  title     = {The exact molecular wavefunction as a product of an electronic and a nuclear wavefunction},
  year      = {2013},
  pages     = {224110},
  volume    = {138},
  abstract  = {The Born-Oppenheimer approximation is a basic approximation in molecular science. In this approximation, the total molecular wavefunction is written as a product of an electronic and a nuclear wavefunction.Hunter [Int. J. Quantum Chem.9, 237 (Year: 1975)]10.1002/qua.560090205 has argued that the exact total wavefunction can also be factorized as such a product. In the present work, a variational principle is introduced which shows explicitly that the total wavefunction can be exactly written as such a product. To this end, a different electronic Hamiltonian has to be defined. The Schrödinger equation for the electronic wavefunction follows from the variational ansatz and is presented. As in the Born-Oppenheimer approximation, the nuclear motion is shown to proceed in a potential which is the electronic energy. In contrast to the Born-Oppenheimer approximation, the separation of the center of mass can be carried out exactly. The electronic Hamiltonian and the equation of motion of the nuclei resulting after the exact separation of the center of mass motion are explicitly given. A simple exactly solvable model is used to illustrate some aspects of the theory.},
  doi       = {10.1063/1.4807115},
  file      = {2013_Cederbaum_224110.pdf:by-author/C/Cederbaum/2013_Cederbaum_224110.pdf:PDF},
  keywords  = {Computational Chemistry; Density Functional Theory (DFT); Quantum Chemistry},
  owner     = {saulius},
  timestamp = {2014.07.21},
  creationdate = {2014-07-21T00:00:00},
  url       = {http://scitation.aip.org/content/aip/journal/jcp/138/22/10.1063/1.4807115},
}

@Article{Cedergren1987,
  author    = {Robert Cedergren and Henri Grosjean},
  journal   = {Biosystems},
  title     = {On the primacy of primordial RNA},
  year      = {1987},
  issn      = {0303-2647},
  pages     = {175--180},
  volume    = {20},
  abstract  = {The ability of \{RNA\} to catalyze biochemical reactions is used to develop a self-consistent picture of how a primordial \{RNA\} could have given rise to the necessary factors and processes of early life forms. Essential to this proposal is the impact of \{RNA\} structural domains, “selected” by thermodynamic criteria, on the structure of early proteins (exons) and the assembly of functional complexes. Based on this analysis, the chronological appearance of informational molecules follows the order: primordial RNA, proteins whose structures are determined by primordial \{RNA\} sequences and finally DNA.},
  doi       = {10.1016/0303-2647(87)90043-8},
  file      = {1987_Cedergren_175.pdf:by-author/C/Cedergren/1987_Cedergren_175.pdf:PDF},
  keywords  = {RNA; RNA World},
  owner     = {saulius},
  timestamp = {2013.09.27},
  creationdate = {2013-09-27T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/0303264787900438},
}

@Article{Celeux2000,
  author    = {Gilles Celeux and Merrilee Hurn and Christian P. Robert},
  journal   = {Journal of the American Statistical Association},
  title     = {Computational and Inferential Difficulties with Mixture Posterior Distributions},
  year      = {2000},
  pages     = {957--970},
  volume    = {95},
  abstract  = {This article deals with both exploration and interpretation problems related to posterior distributions for mixture models. The specification of mixture posterior distributions means that the presence of k! modes is known immediately. Standard Markov chain Monte Carlo (MCMC) techniques usually have difficulties with well-separated modes such as occur here; the MCMC sampler stays within a neighborhood of a local mode and fails to visit other equally important modes. We show that exploration of these modes can be imposed using tempered transitions. However, if the prior distribution does not distinguish between the different components, then the posterior mixture distribution is symmetric and standard estimators such as posterior means cannot be used. We propose alternatives for Bayesian inference for permutation invariant posteriors, including a clustering device and alternative appropriate loss functions.},
  doi       = {10.1080/01621459.2000.10474285},
  file      = {:by-author/C/Celeux/2000_Celeux_957.pdf:PDF},
  groups    = {sg/Bayesian},
  owner     = {andrius},
  timestamp = {2012.11.21},
  creationdate = {2012-11-21T00:00:00},
}

@Manual{CellMatricCorporation2005,
  title     = {User Manual And Tutorials For The Cell Matrix Mod 88},
  author    = {CellMatricCorporation},
  year      = {2005},
  file      = {:by-author/C/CellMatricCorporation/2005_CellMatricCorporation_usermanual.pdf:PDF},
  groups    = {sg/Cell Matrix},
  keywords  = {Cell Matrix; Computer Science (CS)},
  owner     = {saulius},
  pages     = {usermanual},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
  url       = {http://www.cellmatrix.com/},
}

@Article{Cesnaviciene2003,
  author    = {Egle Cesnaviciene and Goda Mitkaite and Kornelijus Stankevicius and Arvydas Janulaitis and Arvydas Lubys},
  journal   = {Nucleic Acids Research},
  title     = {Esp1396I restriction--modification system: structural organization and mode of regulation},
  year      = {2003},
  pages     = {743--749},
  volume    = {31},
  abstract  = {Esp1396I restriction--modification (RM) system recognizes an interrupted palindromic DNA sequ- ence 5¢-CCA(N)5TGG-3¢. The Esp1396I RM system was found to reside on pEsp1396, a 5.6 kb plasmid naturally occurring in Enterobacter sp. strain RFL1396. The nucleotide sequence of the entire 5622 bp pEsp1396 plasmid was determined on both strands. Identi®ed genes for DNA methyltrans- ferase (esp1396IM) and restriction endonuclease (esp1396IR) are transcribed convergently. The restriction endonuclease gene is preceded by the small ORF (esp1396IC) that possesses a strong helix-turn-helix motif and resembles regulatory proteins found in PvuII, BamHI and few other RM systems. Gene regulation studies revealed that C.Esp1396I acts as both a repressor of methylase expression and an activator of regulatory protein and restriction endonuclease expression. Our data indicate that C protein from Esp1396I RM system activates the expression of the Enase gene, which is co-transcribed from the promoter of regulatory gene, by the mechanism of coupled translation.},
  doi       = {10.1093/nar/gkg135},
  file      = {2003_Cesnaviciene_743.pdf:by-author/C/Cesnaviciene/2003_Cesnaviciene_743.pdf:PDF},
  owner     = {em},
  timestamp = {2013.08.11},
  creationdate = {2013-08-11T00:00:00},
}

@Article{Cha1986,
  author    = {Cha, T. A. and Alberts, B. M.},
  journal   = {The Journal of biological chemistry},
  title     = {Studies of the DNA helicase-RNA primase unit from bacteriophage T4. A trinucleotide sequence on the DNA template starts RNA primer synthesis.},
  year      = {1986},
  pages     = {7001--10},
  volume    = {261},
  abstract  = {The purified DNA replication proteins encoded by genes 41 and 61 of bacteriophage T4 catalyze efficient RNA primer synthesis on a single-stranded DNA template. In the presence of additional T4 replication proteins, we demonstrate that the template sequences 5'-GTT-3' and 5'-GCT-3' serve as necessary and sufficient signals for RNA primer-dependent initiation of new DNA chains. These chains start with primers that have the sequences pppApCpNpNpN and pppGpCpNpNpN, where N can be any one of the four ribonucleotides. Each primer is initiated from the T (A-start primers) or C (G-start primers) in the center of the recognized template sequence. A subset of the DNA chain starts is observed when one of the four ribonucleoside triphosphates used as the substrates for primer synthesis is omitted; the starts observed reveal that both pentaribonucleotide and tetraribonucleotide primers can be used for efficient initiation of new DNA chains, whereas primers that are only 3 nucleotides long are inactive. It was known previously that, when 61 protein is present in catalytic amounts, the 41 and 61 proteins are both required for observing RNA primer synthesis. However, by raising the concentration of the 61 protein to a much higher level, a substantial amount of RNA-primed DNA synthesis is obtained in the absence of 41 protein. The DNA chains made are initiated by primers that seem to be identical to those made when both 41 and 61 proteins are present; however, only those template sites containing the 5'-GCT-3' sequence are utilized. The 61 protein is, therefore, the RNA primase, whereas the 41 protein should be viewed as a DNA helicase that is required (presumably via a 41/61 complex) for efficient primase recognition of both the 5'-GCT-3' and 5'-GTT-3' DNA template sequences.},
  file      = {:by-author/C/Cha/1986_Cha_7001.pdf:PDF},
  keywords  = {Replisoma; {gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Chaitin1975,
  author    = {Gregory J. Chaitin},
  journal   = {Scientific American},
  title     = {Randomness and Mathematical Proof},
  year      = {1975},
  pages     = {47--52},
  volume    = {232},
  abstract  = {Although randomness can be precisely defined and can even be measured, a given number cannot be proved to be random. This enigma establishes a limit to what is possible in mathematics.},
  file      = {:by-author/C/Chaitin/1975_Chaitin_47.war:},
  keywords  = {Mathematics},
  owner     = {saulius},
  timestamp = {2015.03.02},
  creationdate = {2015-03-02T00:00:00},
  url       = {http://www.cs.umaine.edu/~chaitin/sciamer.html},
}

@Article{Chaka1996,
  author    = {Chaka, A. M. and Zaniewski, R. and Youngs, W. and Tessier, C. and Klopman, G.},
  journal   = {Acta Crystallographica Section B},
  title     = {Predicting the Crystal Structure of Organic Molecular Materials},
  year      = {1996},
  pages     = {165--183},
  volume    = {52},
  abstract  = {This paper describes a novel method for predicting the crystal structure of organic molecular materials which employs a series of successive approximations to focus on structures of high probability, without resorting to a brute force search and energy minimization of all possible structures. The problem of multiple local minima is overcome by assuming that the crystal structure is closely packed, thereby eliminating 217 of the 230 possible space groups. Configurations within the 13 remaining space groups are searched by rotating the reference molecule about Cartesian axes in rotational increments of 15°. Initial energy minimization is performed using (6-12) Lennard-Jones pair potentials to produce a set of closely packed structures. The structures are then refined with the introduction of a Coulombic potential calculated using molecular multipole moments. This method has successfully located local minima which correspond to the observed crystal structures of several saturated and unsaturated hydro-C atoms with no a priori information provided. For large polycyclic aromatic hydrocarbons, additional refinements of the energy calculations are required to distinguish the experimental structure from a small number of closely packed structures. Our methodology for a priori crystal structure prediction represents the most efficient algorithm presented to date, in a field where the first successes have only been described within the past year and have been few and far between. Since our algorithm is capable of locating a large number of reasonable structures with similar energy in a short period of time, and is more likely to locate a minimum corresponding to the experimental structure, our program provides a superior framework to determine the level of theory required to calculate the intermolecular potential. For all but highly asymmetric hydrocarbons, however, distinguishing the observed structure from a large number of highly probable structures requires more rigorously calculated intermolecular interactions than pair potentials, plus an ad hoc electrostatic potential, and is thus beyond the scope of this paper. All calculations were performed on the Ohio Supercomputer Center's Cray Y-MP.},
  doi       = {10.1107/S0108768195006987},
  file      = {:by-author/C/Chaka/1996_Chaka_165.pdf:PDF},
  groups    = {sg/Crystal structure prediction},
  keywords  = {Crystal Structure Prediction (CSP)},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0108768195006987},
}

@Article{Chakraborty2008,
  author    = {Chakraborty},
  title     = {A Short Introduction to Hoare Logic},
  year      = {2008},
  pages     = {slides},
  file      = {:by-author/C/Chakraborty/2008_Chakraborty_slides.pdf:PDF},
  groups    = {sg/Correctness proofs},
  keywords  = {Computer Science (CS); Correctness Proofs},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Presentation{Chalabine2007,
  author    = {Chalabine},
  title     = {Compiler Construction},
  year      = {2007},
  file      = {:by-author/C/Chalabine/2007_Chalabine_slides.pdf:PDF},
  keywords  = {Compiler Symbol Tables; Computer Science (CS)},
  owner     = {saulius},
  pages     = {slides},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Chalin2006,
  author    = {Chalin},
  title     = {Towards Support for Non-null Types and Non-null-by-default in Java},
  year      = {2006},
  file      = {:by-author/C/Chalin/2006_Chalin.pdf:PDF},
  keywords  = {Computer Science (CS); Non Null},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Chalin2005,
  author    = {Chalin},
  title     = {Non-null References by Default in the Java Modeling Language},
  year      = {2005},
  pages     = {techreport},
  file      = {:by-author/C/Chalin/2005_Chalin_techreport.pdf:PDF},
  keywords  = {Computer Science (CS); Non Null},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Chalker2009,
  author    = {Chalker, Justin M. and Bernardes, Gonçalo J. L. and Lin, Yuya A. and Davis, Benjamin G.},
  journal   = {Chem. Asian J.},
  title     = {Chemical Modification of Proteins at Cysteine: Opportunities in Chemistry and Biology},
  year      = {2009},
  pages     = {630 – 640},
  volume    = {4},
  doi       = {10.1002/asia.200800427},
  file      = {2009_Chalker_630.pdf:by-author/C/Chalker/2009_Chalker_630.pdf:PDF},
  keywords  = {Chemical Miodification; Cysteine},
  owner     = {em},
  timestamp = {2013.01.07},
  creationdate = {2013-01-07T00:00:00},
}

@Article{Chamizo1997,
  author    = {Fernando Chamizo and Antonio Córdoba},
  journal   = {Journal of number theory},
  title     = {One-Dimensional Crystals and Quadratic Residues},
  year      = {1997},
  pages     = {101--104},
  volume    = {65},
  file      = {1997_Chamizo_101.pdf:by-author/C/Chamizo/1997_Chamizo_101.pdf:PDF},
  owner     = {saulius},
  timestamp = {2015.05.05},
  creationdate = {2015-05-05T00:00:00},
  url       = {http://www.uam.es/personal_pdi/ciencias/acordoba/documentos/articulos/One-dimensionalcrystals.pdf},
}

@Manuscript{Chan,
  author    = {Agnes Chan and Yair Frankel and Yiannis Tsiounis},
  title     = {Easy come -- easy go divisible cash},
  year      = {1998},
  abstract  = {Recently, there has been an interest in creating practical anonymous electronic cash with the ability to conduct payments of exact amounts, as is typically the practice in physical payment systems. The most general solution for such payments is to allow electronic coins to be divisible (e.g., each coin can be spent incrementally but total purchases are limited to the monetary value of the coin). In Crypto'95, T. Okamoto presented the first efficient divisible, anonymous (but linkable) off-line e-cash scheme requiring only O(log N) computations for each of the withdrawal, payment and deposit procedures, where N = (total coin value)/ (smallest divisible unit) is the divisibility precision. However, the zero-knowledge protocol used for the creation of a blinded unlinkable coin by Okamoto is quite ineffcient and is used only at set-up to make the system efficient. Incorporating "unlinkable" blinding only in the set-up, however, limits the level of anonymity offered by allowing the linking of all coins withdrawn|rather than a more desirable anonymity which allows only linking of subcoins of a withdrawn coin. In this paper we make a further step towards practicality of complete (i.e., divisible) anonymous e-cash by presenting a solution where all procedures (set-up, withdrawal, payment and deposit) are bounded by tens of exponentiations; in particular we improve on Okamoto's result by 3 orders of magnitude, while the size of the coin remains about 300 Bytes, based on a 512 bit modulus. Moreover, the protocols are compatible with tracing methods used for "fair" or "revokable" anonymous cash},
  file      = {:by-author/C/Chan/1998_Chan_manuscript.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.10.15},
  creationdate = {2012-10-15T00:00:00},
}

@InProceedings{Chan2009,
  author    = {Edward P.F. Chan and Jie Zhang},
  booktitle = {Proceedings of the 11th International Symposium on Advances in Spatial and Temporal Databases},
  title     = {Efficient Evaluation of Static and Dynamic Optimal Route Queries on a Massive Graph},
  year      = {2009},
  pages     = {386--391},
  doi       = {10.1007/978-3-642-02982-0_26},
  file      = {:by-author/C/Chan/2009_Chan_386.pdf:PDF},
  isbn      = {978-3-642-02981-3},
  keywords  = {Distance Materialization; Optimal Route Queries; Route Query Evaluation; Static and Dynamic Graphs},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1007/978-3-642-02982-0_26},
}

@Article{Chan2007,
  author    = {Chan, Siu-hong and Bao, Yongming and Ciszak, Ewa and Laget, Sophie and Xu, Shuang-yong},
  journal   = {Nucleic acids research},
  title     = {Catalytic domain of restriction endonuclease BmrI as a cleavage module for engineering endonucleases with novel substrate specificities.},
  year      = {2007},
  pages     = {6238--48},
  volume    = {35},
  abstract  = {Creating endonucleases with novel sequence specificities provides more possibilities to manipulate DNA. We have created a chimeric endonuclease (CH-endonuclease) consisting of the DNA cleavage domain of BmrI restriction endonuclease and C.BclI, a controller protein of the BclI restriction-modification system. The purified chimeric endonuclease, BmrI198-C.BclI, cleaves DNA at specific sites in the vicinity of the recognition sequence of C.BclI. Double-strand (ds) breaks were observed at two sites: 8 bp upstream and 18 bp within the C-box sequence. Using DNA substrates with deletions of C-box sequence, we show that the chimeric endonuclease requires the 5' half of the C box only for specific cleavage. A schematic model is proposed for the mode of protein-DNA binding and DNA cleavage. The present study demonstrates that the BmrI cleavage domain can be used to create combinatorial endonucleases that cleave DNA at specific sequences dictated by the DNA-binding partner. The resulting endonucleases will be useful in vitro and in vivo to create ds breaks at specific sites and generate deletions.},
  file      = {:by-author/C/Chan/2007_Chan_6238.pdf:PDF},
  owner     = {em},
  timestamp = {2013.09.19},
  creationdate = {2013-09-19T00:00:00},
}

@Article{Chandonia2006,
  author    = {Chandonia, John-Marc and Brenner, Steven E.},
  journal   = {Science (New York, N.Y.)},
  title     = {The impact of structural genomics: expectations and outcomes.},
  year      = {2006},
  pages     = {347--51},
  volume    = {311},
  abstract  = {Structural genomics (SG) projects aim to expand our structural knowledge of biological macromolecules while lowering the average costs of structure determination. We quantitatively analyzed the novelty, cost, and impact of structures solved by SG centers, and we contrast these results with traditional structural biology. The first structure identified in a protein family enables inference of the fold and of ancient relationships to other proteins; in the year ending 31 January 2005, about half of such structures were solved at a SG center rather than in a traditional laboratory. Furthermore, the cost of solving a structure at the most efficient SG center in the United States has dropped to one-quarter of the estimated cost of solving a structure by traditional methods. However, the efficiency of the top structural biology laboratories-even though they work on very challenging structures-is comparable to that of SG centers; moreover, traditional structural biology papers are cited significantly more often, suggesting greater current impact.},
  file      = {:by-author/C/Chandonia/2006_Chandonia_347.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Chandrasekar2013,
  author    = {Chandrasekar, Jagadeeswaran and Silverman, Scott K.},
  journal   = {Proceedings of the National Academy of Sciences},
  title     = {Catalytic DNA with phosphatase activity},
  year      = {2013},
  abstract  = {Catalytic DNA sequences (deoxyribozymes, DNA enzymes, or DNAzymes) have been identified by in vitro selection for various catalytic activities. Expanding the limits of DNA catalysis is an important fundamental objective and may facilitate practical utility of catalysts that can be obtained from entirely unbiased (random) sequence populations. In this study, we show that DNA can catalyze Zn2+-dependent phosphomonoester hydrolysis of tyrosine and serine side chains (i.e., exhibit phosphatase activity). The best deoxyribozyme decreases the half-life for phosphoserine hydrolysis from as high as >1010 y to <1 h. The phosphatase activity also occurs with nonpeptidic substrates but with reduced efficiency, indicating a preference for phosphopeptides. The newly identified deoxyribozymes can function with multiple turnover using free peptide substrates, have activity in the presence of human cell lysate or BSA, and catalyze dephosphorylation of a larger protein substrate, suggesting broader application of DNA catalysts as artificial phosphatases.},
  doi       = {10.1073/pnas.1221946110},
  eprint    = {http://www.pnas.org/content/early/2013/03/15/1221946110.full.pdf+html},
  file      = {2013_Chandrasekar_1221946110.pdf:by-author/C/Chandrasekar/2013_Chandrasekar_1221946110.pdf:PDF},
  keywords  = {DNA; DNA Catalytic Activity; DNA Enzymes; DNAzymes; Deoxyribozymes; Ribozymes},
  owner     = {saulius},
  timestamp = {2013.05.06},
  creationdate = {2013-05-06T00:00:00},
  url       = {http://www.pnas.org/content/early/2013/03/15/1221946110.abstract},
}

@Article{Chang2005,
  author    = {Chang, Chung-I and Ihara, Kentaro and Chelliah, Yogarany and Mengin-Lecreulx, Dominique and Wakatsuki, Soichi and Deisenhofer, Johann},
  journal   = {Proceedings of the National Academy of Sciences of the United States of America},
  title     = {Structure of the ectodomain of Drosophila peptidoglycan-recognition protein LCa suggests a molecular mechanism for pattern recognition.},
  year      = {2005},
  pages     = {10279--84},
  volume    = {102},
  abstract  = {The peptidoglycan-recognition protein LCa (PGRP-LCa) is a transmembrane receptor required for activation of the Drosophila immune deficiency pathway by monomeric Gram-negative peptidoglycan. We have determined the crystal structure of the ectodomain of PGRP-LCa at 2.5-A resolution and found two unique helical insertions in the LCa ectodomain that disrupt an otherwise L-shaped peptidoglycan-docking groove present in all other known PGRP structures. The deficient binding of PGRP-LCa to monomeric peptidoglycan was confirmed by biochemical pull-down assays. Recognition of monomeric peptidoglycan involves both PGRP-LCa and -LCx. We showed that association of the LCa and LCx ectodomains in vitro depends on monomeric peptidoglycan. The presence of a defective peptidoglycan-docking groove, while preserving a unique role in mediating monomeric peptidoglycan induction of immune response, suggests that PGRP-LCa recognizes the exposed structural features of a monomeric muropeptide when the latter is bound to and presented by the ectodomain of PGRP-LCx. Such features include N-acetyl glucosamine and the anhydro bond in the glycan of the muropeptide, which have been demonstrated to be critical for immune stimulatory activity.},
  file      = {Chang_2005_10279-struct_Drosofila_LCa.pdf:by-author/C/Chang/2005_Chang_10279.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Chang2013,
  author    = {E.-E. Chang and Tse-Lun Chen and Shu-Yuan Pan and Yi-Hung Chen and Pen-Chi Chiang},
  journal   = {Journal of Hazardous Materials},
  title     = {Kinetic modeling on {CO2} capture using basic oxygen furnace slag coupled with cold-rolling wastewater in a rotating packed bed},
  year      = {2013},
  issn      = {0304-3894},
  pages     = {937 - 946},
  volume    = {260},
  abstract  = {In this study, direct and indirect carbonation of basic oxygen furnace slag (BOFS) coupled with cold-rolling wastewater (CRW) was carried out via a rotating packed bed (RPB). The solid products were qualitatively characterized by scanning electron microscopy (SEM) and X-ray diffraction (XRD) and quantitatively analyzed with thermogravimetric analysis (TGA). The leachate was analyzed with inductively coupled plasma-optical emission spectroscopy (ICP-OES). The results indicate that the maximum achievable carbonation conversion (MACC) of BOFS was 90.7%, corresponding to a capture capacity of 0.277 g CO2 /g of BOFS, by direct carbonation with CRW under a rotation speed of 750 rpm at 30 ◦ C for 20 min. In addition, CO2 mass balance among the gas, liquid, and solid phases within an RPB was well-developed, with an error less than 10%, to confirm the actual CO2 capture capacity of BOFS with precision and accuracy. Furthermore, a reaction kinetic model based on mass balance was established to determine the reaction rate constant for various liquid agents (CRW and pure water). It was concluded that co-utilization of alkaline wastes including BOFS and CRW via the RPB is a novel approach for both enhancing CO2 capture capacity and reducing the environmental impacts of alkaline wastes.},
  doi       = {10.1016/j.jhazmat.2013.06.052},
  file      = {:by-author/C/Cheng/2013_Cheng_937.pdf:PDF},
  groups    = {sg/NAR2012},
  keywords  = {Citing COD},
  owner     = {andrius},
  timestamp = {2013.10.31},
  creationdate = {2013-10-31T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/S0304389413004524},
}

@Article{Chapman2007,
  author    = {Adriane Chapman and H. V. Jagadish},
  journal   = {IEEE Data Eng. Bull.},
  title     = {Issues in Building Practical Provenance Systems},
  year      = {2007},
  pages     = {38--43},
  volume    = {30},
  abstract  = {The importance of maintaining provenance has been widely recognized, particularly with respect to highly-manipulated data. However, there are few deployed databases that provide provenance informa- tion with their data. We have constructed a database of protein interactions (MiMI), which is heavily used by biomedical scientists, by manipulating and integrating data from several popular biological sources. The provenance stored provides key information for assisting researchers in understanding and trusting the data. In this paper, we describe several desiderata for a practical provenance system, based on our experience from this system. We discuss the challenges that these requirements present, and outline solutions to several of these challenges that we have implemented. Our list of a dozen or so desiderata includes: efficiently capturing provenance from external applications; managing provenance size; and presenting provenance in a usable way. For example, data is often manipulated via provenance- unaware processes, but the associated provenance must still be tracked and stored. Additionally, prove- nance information can grow to outrageous proportions if it is either very rich or fine-grained, or both. Finally, when users view provenance data, they can usually understand a SELECT manipulation, but “why did the bcgCoalesce [1] manipulation output that?”},
  bibsource = {DBLP, http://dblp.uni-trier.de},
  ee        = {http://sites.computer.org/debull/A07dec/chapman.pdf},
  file      = {2007_Chapman_38.pdf:by-author/C/Chapman/2007_Chapman_38.pdf:PDF},
  keywords  = {Bioinformatics; Data Management; Databases; Provenance},
  owner     = {saulius},
  timestamp = {2012.10.25},
  creationdate = {2012-10-25T00:00:00},
}

@Presentation{Chapman2009,
  author    = {Barbara Chapman and Lei Huang},
  title     = {How OpenMP is Compiled},
  year      = {2009},
  school    = {University of Houston},
  file      = {:by-author/C/Chapman/2009_Chapman_slides.pdf:PDF},
  owner     = {saulius},
  pages     = {slides},
  timestamp = {2013.07.02},
  creationdate = {2013-07-02T00:00:00},
}

@Article{Chapman2011,
  author    = {Chapman, Henry N. and Fromme, Petra and Barty, Anton and White, Thomas A. and Kirian, Richard A. and Aquila, Andrew and Hunter, Mark S. and Schulz, Joachim and DePonte, Daniel P. and Weierstall, Uwe and Doak, R. Bruce and Maia, Filipe R. N. C. and Martin, Andrew V. and Schlichting, Ilme and Lomb, Lukas and Coppola, Nicola and Shoeman, Robert L. and Epp, Sascha W. and Hartmann, Robert and Rolles, Daniel and Rudenko, Artem and Foucar, Lutz and Kimmel, Nils and Weidenspointner, Georg and Holl, Peter and Liang, Mengning and Barthelmess, Miriam and Caleman, Carl and Boutet, Sébastien and Bogan, Michael J. and Krzywinski, Jacek and Bostedt, Christoph and Bajt, Saša and Gumprecht, Lars and Rudek, Benedikt and Erk, Benjamin and Schmidt, Carlo and Hömke, André and Reich, Christian and Pietschner, Daniel and Strüder, Lothar and Hauser, Günter and Gorke, Hubert and Ullrich, Joachim and Herrmann, Sven and Schaller, Gerhard and Schopper, Florian and Soltau, Heike and Kühnel, Kai-Uwe and Messerschmidt, Marc and Bozek, John D. and Hau-Riege, Stefan P. and Frank, Matthias and Hampton, Christina Y. and Sierra, Raymond G. and Starodub, Dmitri and Williams, Garth J. and Hajdu, Janos and Timneanu, Nicusor and Seibert, M. Marvin and Andreasson, Jakob and Rocker, Andrea and Jönsson, Olof and Svenda, Martin and Stern, Stephan and Nass, Karol and Andritschke, Robert and Schröter, Claus-Dieter and Krasniqi, Faton and Bott, Mario and Schmidt, Kevin E. and Wang, Xiaoyu and Grotjohann, Ingo and Holton, James M. and Barends, Thomas R. M. and Neutze, Richard and Marchesini, Stefano and Fromme, Raimund and Schorb, Sebastian and Rupp, Daniela and Adolph, Marcus and Gorkhover, Tais and Andersson, Inger and Hirsemann, Helmut and Potdevin, Guillaume and Graafsma, Heinz and Nilsson, Björn and Spence, John C. H.},
  journal   = {Nature},
  title     = {Femtosecond X-ray protein nanocrystallography.},
  year      = {2011},
  pages     = {73--7},
  volume    = {470},
  abstract  = {X-ray crystallography provides the vast majority of macromolecular structures, but the success of the method relies on growing crystals of sufficient size. In conventional measurements, the necessary increase in X-ray dose to record data from crystals that are too small leads to extensive damage before a diffraction signal can be recorded. It is particularly challenging to obtain large, well-diffracting crystals of membrane proteins, for which fewer than 300 unique structures have been determined despite their importance in all living cells. Here we present a method for structure determination where single-crystal X-ray diffraction 'snapshots' are collected from a fully hydrated stream of nanocrystals using femtosecond pulses from a hard-X-ray free-electron laser, the Linac Coherent Light Source. We prove this concept with nanocrystals of photosystem I, one of the largest membrane protein complexes. More than 3,000,000 diffraction patterns were collected in this study, and a three-dimensional data set was assembled from individual photosystem I nanocrystals (∼200 nm to 2 μm in size). We mitigate the problem of radiation damage in crystallography by using pulses briefer than the timescale of most damage processes. This offers a new approach to structure determination of macromolecules that do not yield crystals of sufficient size for studies using conventional radiation sources or are particularly sensitive to radiation damage.},
  file      = {:by-author/C/Chapman/2011_Chapman_73.pdf:PDF},
  keywords  = {X Ray Lasers; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Chapyzhenka1999,
  author    = {Chapyzhenka},
  title     = {sTTAck: Stack Transport Triggered Architecture},
  year      = {1999},
  file      = {:by-author/C/Chapyzhenka/1999_Chapyzhenka.pdf:PDF},
  keywords  = {Computer Architecture; Computer Science (CS); Hardware},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Charles2006,
  author    = {Charles, Mathieu and Veesler, Stéphane and Bonneté, Françoise},
  journal   = {Acta crystallographica. Section D, Biological crystallography},
  title     = {MPCD: a new interactive on-line crystallization data bank for screening strategies.},
  year      = {2006},
  pages     = {1311--8},
  volume    = {62},
  abstract  = {The Marseille Protein Crystallization Database (MPCD) is a new crystallization database, freely accessible via http://www.crmcn.univ-mrs.fr/mpcd/, populated with information found in the BMCD and CYCLOP. This new online database includes details about macromolecules (such as name, pI, molecular weight, number of subunits), crystallization conditions, methods and additives used in an easy-to-compare table form. It allows users to choose their own crystallization parameters, to create tables for further analysis and also to enter new proteins and crystallization conditions in order to supplement this database. As an essential tool in structural biology, this crystallization database will be highly relevant to crystal growers, when connected to the Protein Data Bank, for the crystallogenesis of a variety of structurally distinct molecules and assemblies, and to macromolecular and biomaterial researchers designing structures.},
  doi       = {10.1107/S0907444906027594},
  file      = {:by-author/C/Charles/2006_Charles_1311.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Charlton2006,
  author    = {Charlton},
  title     = {Program Verification with Interacting Analysis Plugins},
  year      = {2006},
  file      = {:by-author/C/Charlton/2006_Charlton.pdf:PDF},
  groups    = {sg/Correctness proofs},
  keywords  = {Computer Science (CS); Correctness Proofs},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Chateigner2010a,
  author     = {Chateigner, Daniel},
  title      = {Combined analysis: structure-texture-microstructure-phase-stresses-reflectivity determination by x-ray and neutron scattering},
  year       = {2010},
  file       = {[PDF] from archives-ouvertes.fr:by-author/C/Chateigner/2010_Chateigner.pdf:application/pdf},
  groups     = {sg/JAC2009},
  owner      = {saulius},
  shorttitle = {Combined analysis},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url        = {https://cel.archives-ouvertes.fr/cel-00109040/document},
  urldate    = {2015-08-31},
}

@InProceedings{Chateigner2011,
  author    = {Chateigner, Daniel and Blanchart, Philippe and Deniel, Sarah and Lutterotti, Luca and Wenk, Hans Rudolf},
  booktitle = {Advances in science and technology},
  title     = {Characterization of microstructure and crystallographic texture of silicate and phyllosilicate ceramics},
  year      = {2011},
  pages     = {13--22},
  publisher = {Trans Tech Publ},
  volume    = {68},
  file      = {[PDF] from researchgate.net:by-author/C/Chateigner/2011_Chateigner_13.pdf:PDF;Snapshot:by-author/C/Chateigner/2011_Chateigner_13.html:URL},
  groups    = {sg/JAC2009},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://www.scientific.net/AST.68.13},
  urldate   = {2015-08-31},
}

@Article{Chateigner2014,
  author    = {Chateigner, Daniel and Grazulis, Saulius and Butkus, Justas and Merkys, Andrius and Daškevič, Adriana and Pérez, Olivier and Pepponi, Giancarlo and Lutterotti, Luca and Olozábal, Miguel Quirós and Le Bail, Armel and {others}},
  title     = {News in open structure and property databases},
  year      = {2014},
  file      = {[PDF] from ensicaen.fr:by-author/C/Chateigner/2014_Chateigner.pdf:PDF},
  groups    = {sg/JAC2009, sg/NAR2012},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://www.ecole.ensicaen.fr/~chateign/danielc/abstracts/Chateigner_abstract_AFC2013.pdf},
  urldate   = {2015-08-31},
}

@Article{Chateigner2015,
  author    = {Chateigner, Daniel and Grazulis, Saulius and Pérez, Olivier and Pepponi, Giancarlo and Lutterotti, Luca},
  title     = {{COD}, {PCOD}, {TCOD}, {MPOD}… open structure and property databases},
  year      = {2015},
  file      = {[PDF] from ensicaen.fr:by-author/C/Chateigner/2015_Chateigner.pdf:PDF},
  groups    = {sg/JAC2009, sg/NAR2012, sg/COD, am/COD, am/TCOD, am/MPOD},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://www.ecole.ensicaen.fr/~chateign/danielc/abstracts/Chateigner_abstract_JNCO2013.pdf},
  urldate   = {2015-08-31},
}

@Article{Chateigner2000,
  author    = {D. Chateigner and C. Hedegaard and H.-R. Wenk},
  journal   = {Journal of Structural Geology},
  title     = {Mollusc shell microstructures and crystallographic textures},
  year      = {2000},
  pages     = {1723},
  volume    = {22},
  file      = {2000_Chateigner_1723.pdf:by-author/C/Chateigner/2000_Chateigner_1723.pdf:PDF},
  keywords  = {Textures; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Chateigner2010,
  author     = {Chateigner, Daniel and Ouhenia, S. and Krauss, C. and Hedegaard, C. and Gil, O. and Morales, M. and Lutterotti, L. and Rousseau, M. and Lopez, E.},
  journal    = {Materials Science and Engineering: A},
  title      = {Voyaging around nacre with the {X}-ray shuttle: from bio-mineralisation to prosthetics via mollusc phylogeny},
  year       = {2010},
  pages      = {37--51},
  volume     = {528},
  file       = {[PDF] from ensicaen.fr:by-author/C/Chateigner/2010_Chateigner_37.pdf:PDF;Snapshot:by-author/C/Chateigner/2010_Chateigner_37.html:URL},
  groups     = {sg/JAC2009},
  owner      = {saulius},
  shorttitle = {Voyaging around nacre with the {X}-ray shuttle},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url        = {http://www.sciencedirect.com/science/article/pii/S0921509310007707},
  urldate    = {2015-08-31},
}

@InProceedings{Chatterjee2004,
  author    = {Chatterjee, Ramkrishna and Arun, Gopalan and Agarwal, Sanjay and Speckhard, Ben and Vasudevan, Ramesh},
  booktitle = {Proceedings of the 26th International Conference on Software Engineering},
  title     = {Using Applications of Data Versioning in Database Application Development},
  year      = {2004},
  address   = {Washington, DC, USA},
  pages     = {315--325},
  publisher = {IEEE Computer Society},
  series    = {ICSE '04},
  abstract  = {Database applications such as enterprise resource planning systems and customer relationship management systems are widely used software systems. Development and testing of database applications is difficult because the program execution depends on the persistent state stored in the database. In this paper we show that how versioning of the persistent data stored in the database can solve some critical problems in the development and testing of database applications can be solved by versioning the data stored in the database. Our solution framework is based on long transaction management, a well-researched branch of database systems. We also present empirical experimental results that show the proposed framework's effectiveness in practice.},
  acmid     = {999436},
  file      = {2004_Chatterjee_315.pdf:by-author/C/Chatterjee/2004_Chatterjee_315.pdf:PDF},
  isbn      = {0-7695-2163-0},
  keywords  = {Computer Science (CS); Data Versioning; Reproducible Research},
  numpages  = {11},
  owner     = {saulius},
  timestamp = {2016.11.21},
  creationdate = {2016-11-21T00:00:00},
  url       = {http://dl.acm.org/citation.cfm?id=998675.999436},
}

@Article{Chayen2002,
  author    = {Chayen, Naomi E. and Saridakis, Emmanuel},
  journal   = {Acta Crystallographica Section D},
  title     = {Protein crystallization for genomics: towards high-throughput optimization techniques},
  year      = {2002},
  pages     = {921--927},
  volume    = {58},
  doi       = {10.1107/S0907444902005322},
  file      = {gr2234.pdf:by-author/C/Chayen/2002_Chayen_921.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444902005322},
}

@Article{Chazalette2004,
  author    = {Chazalette, Celine and Masereel, Bernard and Rolin, Stéphanie and Thiry, Anne and Scozzafava, Andrea and Innocenti, Alessio and Supuran, Claudiu T},
  journal   = {Bioorganic \&amp; medicinal chemistry letters},
  title     = {Carbonic anhydrase inhibitors. Design of anticonvulsant sulfonamides incorporating indane moieties.},
  year      = {2004},
  pages     = {5781--6},
  volume    = {14},
  file      = {2004_Chazalette_5781.pdf:by-author/C/Chazalette/2004_Chazalette_5781.pdf:PDF},
  groups    = {sg/inhibitors},
  keywords  = {Carbonic Anhydrases},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Presentation{Chee2000,
  author    = {Daniel Chee and N. Lindsley-Griffin},
  title     = {Crystal Interfacial Angles (and other properties) (?)},
  year      = {2000},
  file      = {2000_Chee_slides.ppt:by-author/C/Chee/2000_Chee_slides.ppt:PowerPoint},
  keywords  = {Crystal Properties; Mineral Properties; Mineralogy},
  owner     = {saulius},
  timestamp = {2016.10.16},
  creationdate = {2016-10-16T00:00:00},
  url       = {http://www.geol.umd.edu/~kaufman/NLG_pp/minsecond.ppt},
}

@Manuscript{TheRoyalSocietyofChemistry1998,
  author    = {The Royal Society of Chemistry},
  title     = {Final refined positional parameters for norbornene (C7H10) at 105 K},
  year      = {1998},
  keywords  = {Rietveld Refinement},
  file      = {:by-author/C/Chemistry/1998_Chemistry.doc:DOC},
  owner     = {saulius},
  timestamp = {2015.02.28},
  creationdate = {2015-02-28T00:00:00},
}

@Article{Chen2010a,
  author    = {Chen},
  title     = {Abstraction of Object Graphs in Program Verification},
  year      = {2010},
  file      = {:by-author/C/Chen/2010_Chen.pdf:PDF},
  groups    = {sg/Correctness proofs},
  keywords  = {Computer Science (CS); Correctness Proofs},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Chen2000,
  author    = {Chen, B. and Zhou, G. and Kim, M. and Chishti, Y. and Hussey, R. E. and Ely, B. and Skehel, J. J. and Reinherz, E. L. and Harrison, S. C. and Wiley, D. C.},
  journal   = {The Journal of biological chemistry},
  title     = {Expression, purification, and characterization of gp160e, the soluble, trimeric ectodomain of the simian immunodeficiency virus envelope glycoprotein, gp160.},
  year      = {2000},
  pages     = {34946--53},
  volume    = {275},
  abstract  = {The envelope glycoprotein, gp160, of simian immunodeficiency virus (SIV) shares approximately 25% sequence identity with gp160 from the human immunodeficiency virus, type I, indicating a close structural similarity. As a result of binding to cell surface CD4 and co-receptor (e.g. CCR5 and CXCR4), both SIV and human immunodeficiency virus gp160 mediate viral entry by membrane fusion. We report here the characterization of gp160e, the soluble ectodomain of SIV gp160. The ectodomain has been expressed in both insect cells and Chinese hamster ovary (CHO)-Lec3.2.8.1 cells, deficient in enzymes necessary for synthesizing complex oligosaccharides. Both the primary and a secondary proteolytic cleavage sites between the gp120 and gp41 subunits of gp160 were mutated to prevent cleavage and shedding of gp120. The purified, soluble glycoprotein is shown to be trimeric by chemical cross-linking, gel filtration chromatography, and analytical ultracentrifugation. It forms soluble, tight complexes with soluble CD4 and a number of Fab fragments from neutralizing monoclonal antibodies. Soluble complexes were also produced of enzymatically deglycosylated gp160e and of gp160e variants with deletions in the variable segments.},
  file      = {:by-author/C/Chen/2000_Chen_34946.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Chen2004,
  author           = {Chen, Chuanbo and Li, Qishen},
  journal          = {Acta Crystallographica Section A},
  title            = {{RETRACTED}: A strict solution for the optimal superimposition of protein structures},
  year             = {2004},
  pages            = {201--203},
  volume           = {60},
  abstract         = {Existing methods for the optimal superimposition of one vector set on another in the comparison of parts or the whole of related protein molecules are based on the precondition that the centroids of the two sets are coincident. As a result, the translation components of the transformation are artificially removed from the superimposition process. This is obviously not strict in the mathematical sense. The theorem presented in this paper is a strict solution for the optimal superimposition of two vector sets, which is in fact the problem of the weighted optimal rigid superimposition of two vector sets. Examples show its advantages compared with the method of simply coinciding the centroids of the two vector sets for the translation transformation.},
  comment          = {"Thus we can say that the precondition that the centroids of the two vector sets coincide is not strictly fulfilled, and the superimposition obtained based on it is in fact not optimal."},
  creationdate     = {2012-05-16T00:00:00},
  doi              = {10.1107/S0108767304003654},
  file             = {2004_Chen_201.pdf:by-author/C/Chen/2004_Chen_201.pdf:PDF},
  groups           = {sg/Molecule superposion, sg/Superposition, sg/Bioinf. Algorithms},
  keywords         = {Algorithms; Retracted; Structure Superposition},
  modificationdate = {2024-05-12T21:55:43},
  owner            = {saulius},
  timestamp        = {2012.05.16},
  url              = {http://dx.doi.org/10.1107/S0108767304003654},
}

@Article{Chen1998,
  author    = {Chen, Jiangang and McAllister, Michael A. and Lee, Jeehiun K. and Houk, K. N.},
  journal   = {The Journal of Organic Chemistry},
  title     = {Short, Strong Hydrogen Bonds in the Gas Phase and in Solution: Theoretical Exploration of pKa Matching and Environmental Effects on the Strengths of Hydrogen Bonds and Their Potential Roles in Enzymatic Catalysis},
  year      = {1998},
  pages     = {4611--4619},
  volume    = {63},
  abstract  = {Short, strong hydrogen bonds are common in charged systems in the gas phase, but the importance of such bonding in enzymatic catalysis has been the subject of considerable controversy. Confusion has arisen about the relationship among bond strength, the “low-barrier” or “no-barrier” nature of the hydrogen bonding, the role of pKa matching, the covalent or electrostatic nature of the bonding, and the role of solvation on the strengths of these types of hydrogen bonds. We have attempted to strip away the “Alice in Wonderland” quality of the definitions in this field by defining, through high-level calculations, when short-strong hydrogen bonds do and do not occur. The strengths and geometries of several types of hydrogen bonds involving anions have been investigated by ab initio quantum mechanical calculations. For a series of enols hydrogen-bonded to enolates, the strengths of the short, strong gas-phase hydrogen bonds are linearly related to the differences between the proton affinities (PA) of the two anions which share the proton. The bond strength is also related to the O···O distance between them. There is no discontinuity at ΔPA = 0, and hydrogen-bonding becomes even stronger in a computational experiment when the PA of the H-bond acceptor exceeds that of the donor. “Low-barrier” hydrogen bonds with single-well minima after inclusion of zero-point energies occur when ΔPA is near 0, but no special stability accrues when the double-well minimum becomes single-well. The maleic/fumaric and mesaconic/citraconic systems studied by Drueckhammer have been investigated computationally. The influence of solvation on hydrogen-bond strength was studied using solvent cavity models. Small increases in dielectric constant from the gas-phase value (ε = 1) rapidly reduce the strengths of charged hydrogen bonds. Short, strong hydrogen bonds occur only with charged systems, and only then in nonpolar (ε < 10) environments. Alternative mechanisms are often available to account for enzymatic catalysis; the example of orotidine monophosphate decarboxylase is discussed.},
  doi       = {10.1021/jo972262y},
  file      = {:by-author/C/Chen/1998_Chen_4611.pdf:PDF},
  keywords  = {H Bonds; Protein Physics},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
  url       = {http://pubs.acs.org/doi/abs/10.1021/jo972262y},
}

@Article{Chen2005,
  author    = {Chen, J and Röcken, C and Hoffmann, J and Krüger, S and Lendeckel, U and Rocco, A and Pastorekova, S and Malfertheiner, P and Ebert, M P A},
  journal   = {Gut},
  title     = {Expression of carbonic anhydrase 9 at the invasion front of gastric cancers.},
  year      = {2005},
  pages     = {920--7},
  volume    = {54},
  file      = {2005_Chen_920.pdf:by-author/C/Chen/2005_Chen_920.pdf:PDF},
  groups    = {sg/cancer, sg/medicine, sg/physiology, sg/hCA9},
  keywords  = {Carbonic Anhydrases},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Chen2005a,
  author    = {Ji Chen and Scott K. Spear and Jonathan G. Huddleston and Robin D. Rogers},
  journal   = {Green Chemistry},
  title     = {Polyethylene glycol and solutions of polyethylene glycol as green reaction media},
  year      = {2005},
  pages     = {64--82},
  volume    = {7},
  file      = {2005_Chen_64.pdf:by-author/C/Chen/2005_Chen_64.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Chen2014,
  author    = {Chen, Joe P. J. and Spence, John C. H. and Millane, Rick P.},
  journal   = {Acta Crystallographica Section A},
  title     = {Direct phasing in femtosecond nanocrystallography. I. Diffraction characteristics},
  year      = {2014},
  pages     = {143--153},
  volume    = {70},
  abstract  = {X-ray free-electron lasers solve a number of difficulties in protein crystallography by providing intense but ultra-short pulses of X-rays, allowing collection of useful diffraction data from nanocrystals. Whereas the diffraction from large crystals corresponds only to samples of the Fourier amplitude of the molecular transform at the Bragg peaks, diffraction from very small crystals allows measurement of the diffraction amplitudes between the Bragg samples. Although highly attenuated, these additional samples offer the possibility of iterative phase retrieval without the use of ancillary experimental data [Spence et al. (2011). Opt. Express, 19, 2866-2873]. This first of a series of two papers examines in detail the characteristics of diffraction patterns from collections of nanocrystals, estimation of the molecular transform and the noise characteristics of the measurements. The second paper [Chen et al. (2014). Acta Cryst. A70, 154-161] examines iterative phase-retrieval methods for reconstructing molecular structures in the presence of the variable noise levels in such data.},
  doi       = {10.1107/S2053273313032038},
  file      = {:by-author/C/Chen/2014_Chen_143.pdf:PDF},
  owner     = {saulius},
  timestamp = {2014.03.23},
  creationdate = {2014-03-23T00:00:00},
  url       = {http://dx.doi.org/10.1107/S2053273313032038},
}

@Article{Chen2008,
  author    = {Jing-Chao Chen},
  journal   = {Software-Practice And Experience},
  title     = {Symmetry Partition Sort},
  year      = {2008},
  pages     = {761--773},
  abstract  = {In this paper, we propose a useful replacement for quicksort-style utility functions. The replacement is called Symmetry Partition Sort, the principle of which is similar to that of Proportion Extend Sort. The main characteristic of the new algorithm is that it always places partially sorted inputs (used as a basis for proportional extensions) at each end of an array when entering the partitioning routine. This is advantageous in speeding up the processing for partitioning. The library function we developed based on the new algorithm is more attractive than the Psort library function introduced in 2004 because of its simple implementation mechanism, clearer source code, and faster operation with a performance guarantee of O(n log n). Increased robustness and adaptivity also make it highly competitive as a library function.},
  file      = {:by-author/C/Chen/2008_Chen_761.pdf:PDF},
  keywords  = {Algorithms; Computer Science (CS); Sorting},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@InProceedings{Li1998,
  author    = {Chen, Li and Choubey, Rupesh and Rundensteiner, Elke A.},
  booktitle = {Proceedings of the 6th ACM international symposium on Advances in geographic information systems},
  title     = {Bulk Insertions into R-Trees Using the Small-Tree-Large-Tree Approach},
  year      = {1998},
  address   = {New York, NY, USA},
  pages     = {161--162},
  publisher = {ACM},
  series    = {GIS '98},
  abstract  = {Previous work on bulk loading data focussed at building multidimensional index structures from scratch while the problem of bulk insertions into existing index structures has been largely overlooked. In this paper, we now propose the STLT (Srnall-Tree-Large-Tree) technique, which as opposed to the current technique of inserting data one by one, bulk inserts entire new datasets into an active R-tree. STLT considers the new dataset as an R-tree itself (small tree), identifies and prepares a suitable location in the original R-tree (large tree) for insertion and lastly performs the insert of the small tree into the large tree. Our experiments confirm that for skewed datasets STLT consistently outperforms existing techniques (by up to 65%) for data insertion, while generating an index structure with comparable query retrieval performance.},
  doi       = {10.1145/288692.288722},
  file      = {:by-author/C/Chen/1998_Chen_161.pdf:PDF},
  isbn      = {1-58113-115-1},
  location  = {Washington, D.C., United States},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://doi.acm.org/10.1145/288692.288722},
}

@Article{Chen1991,
  author    = {Chen, L. Q. and Rose, J. P. and Breslow, E. and Yang, D. and Chang, W. R. and Furey, Jr, W. F. and Sax, M. and Wang, B. C.},
  journal   = {Proceedings of the National Academy of Sciences of the United States of America},
  title     = {Crystal structure of a bovine neurophysin II dipeptide complex at 2.8 A determined from the single-wavelength anomalous scattering signal of an incorporated iodine atom.},
  year      = {1991},
  pages     = {4240--4},
  volume    = {88},
  abstract  = {The crystal structure of a dipeptide complex of bovine neurophysin II has been solved at 2.8 A resolution solely by using single-wavelength anomalous scattering data from a single iodinated derivative. The asymmetric unit is an elongated tetramer of dimensions 110 x 40 x 30 A, composed of two dimers related by pseudo twofold symmetry. Each monomer consists of two homologous layers, each with four antiparallel beta-strands. The two regions are connected by a helix followed by a long loop. Monomer-monomer contacts involve antiparallel beta-sheet interactions, which form a dimer with two layers of eight beta-strands. One peptide per monomer occupies the principal hormone-binding pocket formed by part of the amino-terminal region and parts of the connecting helix and loop, with binding to protein consistent with conclusions drawn from solution studies. Dimer-dimer contacts involve the Tyr49 region adjacent to this site. A fifth dipeptide, of unknown biological significance, helps to stabilize one of the monomer-monomer interfaces and the tetramer-tetramer network in the crystal.},
  file      = {:by-author/C/Chen/1991_Chen_4240.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Chen2001,
  author    = {Chen, S. and Gunasekera, A. and Zhang, X. and Kunkel, T. A. and Ebright, R. H. and Berman, H. M.},
  journal   = {Journal of molecular biology},
  title     = {Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: alteration of DNA binding specificity through alteration of DNA kinking.},
  year      = {2001},
  pages     = {75--82},
  volume    = {314},
  abstract  = {The catabolite activator protein (CAP) sharply bends DNA in the CAP-DNA complex, introducing a DNA kink, with a roll angle of approximately 40 degrees and a twist angle of approximately 20 degrees, between positions 6 and 7 of the DNA half-site, 5'-A(1)A(2)A(3)T(4)G(5)T(6)G(7)A(8)T(9)C(10)T(11)-3' (&quot;primary kink&quot;). CAP recognizes the base-pair immediately 5' to the primary-kink site, T:A(6), through an &quot;indirect-readout&quot; mechanism involving sequence effects on the energetics of primary-kink formation. CAP recognizes the base-pair immediately 3' to the primary-kink site, G:C(7), through a &quot;direct-readout&quot; mechanism involving formation of a hydrogen bond between Glu181 of CAP and G:C(7). Here, we report that substitution of the carboxylate side-chain of Glu181 of CAP by the one-methylene-group-shorter carboxylate side-chain of Asp changes DNA binding specificity at position 6 of the DNA half site, changing specificity for T:A(6) to specificity for C:G(6), and we report a crystallographic analysis defining the structural basis of the change in specificity. The Glu181--&gt;Asp substitution eliminates the primary kink and thus eliminates indirect-readout-based specificity for T:A(6). The Glu181--&gt;Asp substitution does not eliminate hydrogen-bond formation with G:C(7), and thus does not eliminate direct-readout-based specificity for G:C(7).},
  file      = {:by-author/C/Chen/2001_Chen_75.pdf:PDF},
  keywords  = {DNA Protein; Indirect; Readout},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@InProceedings{Chen2009,
  author    = {Shuo Chen and Ziqing Mao and Yi-Min Wang and Ming Zhang},
  booktitle = {IEEE S\&P’09 proceedings},
  title     = {Pretty-Bad-Proxy: An Overlooked Adversary in Browsers’ HTTPS Deployments},
  year      = {2009},
  abstract  = {HTTPS is designed to provide secure web communications over insecure networks. The protocol itself has been rigorously designed and evaluated by assuming the network as an adversary. This paper is motivated by our curiosity about whether such an adversary has been carefully examined when HTTPS is integrated into the browser/web systems. We focus on a specific adversary named “Pretty-Bad- Proxy” (PBP). PBP is a malicious proxy targeting browsers’ rendering modules above the HTTP/HTTPS layer. It attempts to break the end-to-end security guarantees of HTTPS without breaking any cryptographic scheme. We discovered a set of vulnerabilities exploitable by a PBP: in many realistic network environments where attackers can sniff the browser traffic, they can steal sensitive data from an HTTPS server, fake an HTTPS page and impersonate an authenticated user to access an HTTPS server. These vulnerabilities reflect the neglects in the design of modern browsers – they affect all major browsers and a large number of websites. We believe that the PBP adversary has not been rigorously examined in the browser/web industry. The vendors of the affected browsers have all confirmed the vulnerabilities reported in this paper. Most of them have patched or planned on patching their browsers. We believe the attack scenarios described in this paper may only be a subset of the vulnerabilities under PBP. Thus further (and more rigorous) evaluations of the HTTPS deployments in browsers appear to be necessary.},
  file      = {:by-author/C/Chen/2009_Chen.pdf:PDF},
  keywords  = {Browser Security; Computer Science (CS); Computer Security; HTTPS Deployment},
  owner     = {saulius},
  timestamp = {2013.01.18},
  creationdate = {2013-01-18T00:00:00},
  url       = {http://research.microsoft.com/apps/pubs/default.aspx?id=79323},
}

@InProceedings{Chen2004a,
  author    = {Sibao Chen and Haixian Wang and Bin Luo},
  booktitle = {Third International Conference on Image and Graphics (ICIG’04)},
  title     = {Greedy {EM} Algorithm for Robust T-Mixture Modeling},
  year      = {2004},
  pages     = {548--551},
  publisher = {Institute of Electrical \& Electronics Engineers (IEEE)},
  comment   = {This paper concerns a greedy EM algorithm for t-mixture modeling, which is more robust than Gaussian mixture modeling when a typical points exist or the set of data has heavy tail. Local Kullback divergence is used to determine how to insert new component. The greedy algorithm obviates the complicated initialization. The results are comparable to that of split-and-merge EM algorithm while the proposed algorithm is faster. Also the by product of a sequence of mixture models is useful for model selection. Experiments of synthetic data clustering and unsupervised color image segmentation are given.},
  doi       = {10.1109/icig.2004.76},
  file      = {:by-author/C/Chen/2004_Chen_548.pdf:PDF},
  groups    = {am/Student's t, am/Expectation maximisation},
  isbn      = {http://id.crossref.org/isbn/0-7695-2244-0},
  owner     = {andrius},
  timestamp = {2016.03.21},
  creationdate = {2016-03-21T00:00:00},
  url       = {http://dx.doi.org/10.1109/ICIG.2004.76},
}

@InProceedings{Chen2004b,
  author    = {Si-Bao Chen and Bin Luo},
  booktitle = {Proceedings of 2004 International Conference on Machine Learning and Cybernetics (IEEE Cat. No.04EX826)},
  title     = {Robust t-mixture modelling with {SMEM} algorithm},
  year      = {2004},
  pages     = {3689--3694},
  publisher = {Institute of Electrical \& Electronics Engineers (IEEE)},
  volume    = {6},
  abstract  = {Multivariate t-mixture modelling is more robust than Gaussian mixture modelling to a set of data containing a group or groups of observations with longer than Gaussian tails or a typical observations. To alleviate the problem of local convergence of the traditional EM algorithm, a split-and-merge operation is introduced into the EM algorithm for multivariate t-mixtures. The split-and-merge equations are first presented theoretically and then a new merge method is acquired. Accordingly, a modified EM algorithm is constructed. Experiments of data clustering and unsupervised color image segmentation are given.},
  doi       = {10.1109/icmlc.2004.1380451},
  file      = {:by-author/C/Chen/2004_Chen_3689.pdf:PDF},
  groups    = {am/Student's t, am/Expectation maximisation},
  isbn      = {0-7803-8403-2},
  owner     = {andrius},
  timestamp = {2016.03.21},
  creationdate = {2016-03-21T00:00:00},
  url       = {http://dx.doi.org/10.1109/ICMLC.2004.1380451},
}

@Article{Chen1999,
  author    = {Tzung-Shi Chen and Chih-Yung Chang and Jang-Ping Sheu and Gwo-John Yu},
  journal   = {Proc. Natl. Sci. Counc. ROC(A)},
  title     = {A Fault-Tolerant Model for Replication in Distributed-File Systems},
  year      = {1999},
  pages     = {402},
  file      = {:by-author/C/Chen/1999_Chen_402.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.09.18},
  creationdate = {2012-09-18T00:00:00},
}

@Article{Chen2010,
  author    = {Chen, Vincent B. and Arendall, III, W. Bryan and Headd, Jeffrey J. and Keedy, Daniel A. and Immormino, Robert M. and Kapral, Gary J. and Murray, Laura W. and Richardson, Jane S. and Richardson, David C.},
  journal   = {Acta Crystallographica Section D},
  title     = {{\it MolProbity}: all-atom structure validation for macromolecular crystallography},
  year      = {2010},
  pages     = {12--21},
  volume    = {66},
  abstract  = {MolProbity is a structure-validation web service that provides broad-spectrum solidly based evaluation of model quality at both the global and local levels for both proteins and nucleic acids. It relies heavily on the power and sensitivity provided by optimized hydrogen placement and all-atom contact analysis, complemented by updated versions of covalent-geometry and torsion-angle criteria. Some of the local corrections can be performed automatically in MolProbity and all of the diagnostics are presented in chart and graphical forms that help guide manual rebuilding. X-ray crystallography provides a wealth of biologically important molecular data in the form of atomic three-dimensional structures of proteins, nucleic acids and increasingly large complexes in multiple forms and states. Advances in automation, in everything from crystallization to data collection to phasing to model building to refinement, have made solving a structure using crystallography easier than ever. However, despite these improvements, local errors that can affect biological interpretation are widespread at low resolution and even high-resolution structures nearly all contain at least a few local errors such as Ramachandran outliers, flipped branched protein side chains and incorrect sugar puckers. It is critical both for the crystallographer and for the end user that there are easy and reliable methods to diagnose and correct these sorts of errors in structures. MolProbity is the authors' contribution to helping solve this problem and this article reviews its general capabilities, reports on recent enhancements and usage, and presents evidence that the resulting improvements are now beneficially affecting the global database.},
  doi       = {10.1107/S0907444909042073},
  file      = {:by-author/C/Chen/2010_Chen_12.pdf:PDF},
  keywords  = {Grow Krystal},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444909042073},
}

@Article{Chen2003,
  author    = {Chen, Yong and Jung, Gun-Young and Ohlberg, Douglas A. A. and Li, Xuema and Stewart, Duncan R. and Jeppesen, Jan O. and Nielsen, Kent A. and Stoddart, J. Fraser and Williams, R. Stanley},
  journal   = {Nanotechnology},
  title     = {Nanoscale molecular-switch crossbar circuits},
  year      = {2003},
  issn      = {0957-4484},
  pages     = {462},
  volume    = {14},
  abstract  = {Molecular electronics offer an alternative pathway to construct nanoscale circuits in which the critical dimension is naturally associated with molecular sizes. We describe the fabrication and testing of nanoscale molecular-electronic circuits that comprise a molecular monolayer of [2]rotaxanes sandwiched between metal nanowires to form an 8 × 8 crossbar within a 1 µm2 area. The resistance at each cross point of the crossbar can be switched reversibly. By using each cross point as an active memory cell, crossbar circuits were operated as rewritable, nonvolatile memory with a density of 6.4 Gbits cm−2. By setting the resistances at specific cross points, two 4 × 4 subarrays of the crossbar were configured to be a nanoscale demultiplexer and multiplexer that were used to read memory bits in a third subarray.},
  doi       = {10.1088/0957-4484/14/4/311},
  file      = {Chen et al. - 2003 - Nanoscale molecular-switch crossbar circuits.pdf:by-author/C/Chen/2003_Chen_462.pdf:PDF;Snapshot:by-author/C/Chen/2003_Chen_462.html:URL},
  groups    = {sg/chemical, sg/electronics},
  language  = {en},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://iopscience.iop.org/0957-4484/14/4/311},
  urldate   = {2015-08-05},
}

@Article{Chen2003a,
  author    = {Chen, Yong and Ohlberg, Douglas A. A. and Li, Xuema and Stewart, Duncan R. and Williams, R. Stanley and Jeppesen, Jan O. and Nielsen, Kent A. and Stoddart, J. Fraser and Olynick, Deirdre L. and Anderson, Erik},
  journal   = {Applied Physics Letters},
  title     = {Nanoscale molecular-switch devices fabricated by imprint lithography},
  year      = {2003},
  issn      = {0003-6951, 1077-3118},
  pages     = {1610--1612},
  volume    = {82},
  abstract  = {Nanoscale molecular-electronic devices comprising a single molecular monolayer of bistable [2]rotaxanes sandwiched between two 40-nm metal electrodes were fabricated using imprint lithography. Bistable current–voltage characteristics with high on–off ratios and reversible switching properties were observed. Such devices may function as basic elements for future ultradense electronic circuitry.},
  doi       = {10.1063/1.1559439},
  file      = {Full Text PDF:by-author/C/Chen/2003_Chen_1610.pdf:PDF;Snapshot:by-author/C/Chen/2003_Chen_1610.html:URL},
  groups    = {sg/chemical},
  keywords  = {Electrical Properties; Electrodes; Monolayers; Nanofabrication; Nanolithography},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://scitation.aip.org/content/aip/journal/apl/82/10/10.1063/1.1559439},
  urldate   = {2015-08-05},
}

@Article{Chen2000a,
  author           = {Yu Wai Chen and Eleanor J. Dodson and Gerard J. Kleywegt},
  journal          = {Structure},
  title            = {Does {NMR} mean “not for molecular replacement”? Using {NMR}-based search models to solve protein crystal structures},
  year             = {2000},
  issn             = {0969-2126},
  number           = {11},
  pages            = {R213--R220},
  volume           = {8},
  abstract         = {Molecular replacement (MR) is a very effective method to solve the phase problem in X-ray crystallography [1]. If a search model with reasonable structural homology is available, MR can often accelerate structure solution by avoiding the need for tedious preparation of heavy-atom or selenomethionine derivatives. However, the success of MR depends critically on the similarity between the search model and the target structure. There is a widely accepted rule-of-thumb which states that if the overall root mean square deviation (rmsd) between equivalent Cα atoms exceeds ∼1.5 Å, it is difficult or impossible to obtain a clear solution. For the structure determination of small macromolecules up to ∼30 kDa, nuclear magnetic resonance (NMR) spectroscopy is a powerful alternative to X-ray crystallography and contributes a substantial fraction of the depositions in the Protein Data Bank (PDB). However, employing NMR structures as search models to solve a crystal structure by MR is not always successful, even if the NMR structure is that of the same protein. Two problems are commonly encountered: the true MR solution is poorly discriminated from (or buried among) false solutions, and there is poor behavior or failure during refinement even when a correct MR solution is found and fairly high-resolution crystallographic data is available. But thanks to advances in methodology and ever-increasing computing power, we are now in a better position to tackle such difficult problems.},
  creationdate     = {2016-12-11T00:00:00},
  doi              = {10.1016/S0969-2126(00)00524-4},
  file             = {:by-author/C/Chen/2000_Chen_R213.pdf:PDF},
  keywords         = {Structure Refinement; Validation; X-ray Crystallography},
  modificationdate = {2024-08-15T18:47:26},
  owner            = {saulius},
  timestamp        = {2016.12.11},
  url              = {http://www.sciencedirect.com/science/article/pii/S0969212600005244},
}

@TechReport{Chen2013,
  author      = {Yih-Farn Chen and Scott Daniels and Marios Hadjieleftheriou and Pingkai Liu and Chao Tian and Vinay Vaishampayan},
  institution = {AT\&T Labs-Research, Shannon Laboratory},
  title       = {Distributed Storage Evaluation on a Three-Wide Inter-Data Center Deployment},
  year        = {2013},
  abstract    = {The demand for cloud storage is exploding as an ever increasing number of enterprises and consumers are storing and processing their data in the cloud. Hence, distributed object storage solutions (e.g., Tahoe-LAFS, Riak, Swift, HDFS) are becoming very critical components of any cloud infrastructure. These systems are able to offer good reliability by distributing redundant information across a large number of commodity servers, easily achieving up to 10 nines of reliability. One drawback of these systems is that they are usually designed for deployment within a single data center, where node-to-node latencies are small. Geo-replication (i.e., distributing redundant information across data centers) for most open-source storage systems is, to the best of our knowledge, accomplished by asynchronously mirroring a given deployment. Given that geo- replication is critical for ensuring very high degrees of reliability (e.g., for achieving 16 nines), in this work we evaluate how these storage systems perform when they are directly deployed in a WAN setting. To this end, three popular distributed object stores, namely Quantcast-QFS, Swift and Tahoe-LAFS, are considered and tested on a three-wide data center environment and our findings are reported.},
  file        = {2013_Chen.pdf:by-author/C/Chen/2013_Chen.pdf:PDF},
  keywords    = {Computer Science (CS); Distributed Storage; Reliability; Tahoe-LAFS},
  owner       = {saulius},
  timestamp = {2016.11.23},
  creationdate = {2016-11-23T00:00:00},
  url         = {http://web2-clone.research.att.com/export/sites/att_labs/techdocs/TD_101264.pdf},
}

@Article{Cheng2007,
  author    = {Cheng, Jackie Y. W. and Ko, John S. N. and Chen, Ronald Y. L. and Ng, Emil M. L.},
  journal   = {Schizophrenia research},
  title     = {Meta-regression analysis using latitude as moderator of paternal age related schizophrenia risk: high ambient temperature induced de novo mutations or is it related to the cold?},
  year      = {2008},
  pages     = {71--6},
  volume    = {99},
  abstract  = {While the season of birth, latitude and first admission effects suggest higher risk of schizophrenia with cold climate, the high ambient temperature induced de novo mutation hypothesis suggests the opposite. We conducted a systematic review and meta-analysis (4 case-control studies and 5 cohort studies). We used annual mean daily temperature and latitude of study sites as direct and indirect measures of ambient temperature respectively. Using case-control studies conducted in the Northern hemisphere for meta-regression, high latitude and low ambient temperature were found to increase paternal age related schizophrenia risk significantly. More research is needed to support the de novo mutation hypothesis.},
  file      = {:by-author/C/Cheng/2008_Cheng_71.pdf:PDF},
  keywords  = {Drug Design},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Cheng2001,
  author    = {Cheng, X. and Roberts, R. J.},
  journal   = {Nucleic Acids Research},
  title     = {AdoMet-dependent methylation, DNA methyltransferases and base flipping.},
  year      = {2001},
  pages     = {3784--95},
  volume    = {29},
  abstract  = {Twenty AdoMet-dependent methyltransferases (MTases) have been characterized structurally by X-ray crystallography and NMR. These include seven DNA MTases, five RNA MTases, four protein MTases and four small molecule MTases acting on the carbon, oxygen or nitrogen atoms of their substrates. The MTases share a common core structure of a mixed seven-stranded beta-sheet (6 downward arrow 7 upward arrow 5 downward arrow 4 downward arrow 1 downward arrow 2 downward arrow 3 downward arrow) referred to as an 'AdoMet-dependent MTase fold', with the exception of a protein arginine MTase which contains a compact consensus fold lacking the antiparallel hairpin strands (6 downward arrow 7 upward arrow). The consensus fold is useful to identify hypothetical MTases during structural proteomics efforts on unannotated proteins. The same core structure works for very different classes of MTase including those that act on substrates differing in size from small molecules (catechol or glycine) to macromolecules (DNA, RNA and protein). DNA MTases use a 'base flipping' mechanism to deliver a specific base within a DNA molecule into a typically concave catalytic pocket. Base flipping involves rotation of backbone bonds in double-stranded DNA to expose an out-of-stack nucleotide, which can then be a substrate for an enzyme-catalyzed chemical reaction. The phenomenon is fully established for DNA MTases and for DNA base excision repair enzymes, and is likely to prove general for enzymes that require access to unpaired, mismatched or damaged nucleotides within base-paired regions in DNA and RNA. Several newly discovered MTase families in eukaryotes (DNA 5mC MTases and protein arginine and lysine MTases) offer new challenges in the MTase field.},
  doi       = {10.1093/nar/29.18.3784},
  file      = {:by-author/C/Cheng/2001_Cheng_3784.pdf:PDF},
  keywords  = {HhaI},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
  url       = {http://nar.oxfordjournals.org/content/29/18/3784.abstract},
}

@Article{Chepelev2008,
  author    = {N. Chepelev and L. Chepelev and M.D. Alamgir and A. Golshani},
  journal   = {Biotechnology \& Biotechnological Equipment},
  title     = {Large-scale protein-protein interaction detection approaches: past, present and future},
  year      = {2008},
  pages     = {513--529},
  volume    = {22},
  abstract  = {Protein-protein interaction elucidation is of immense importance to biology, medicine, and related fields. It is now realized that various diseases such as different types of cancers, Alzheimer’s disease, etc, require an integrated view of protein interaction networks. To aid in deciphering these networks, a number of methods have been developed including yeast two-hybrid analysis, tandem affinity purification tagging, as well as protein microarray technologies. In this article, we discuss some of the most important trends and technologies of the past, reflect on their present, and explore some exciting future directions in the field of large-scale protein-protein interaction detection. We argue that the future of the protein interaction elucidation field lies in the development of novel and/or improved high-throughput techniques that generate reproducible and most importantly, quantitative data.},
  file      = {2008_Chepelev_513.pdf:by-author/C/Chepelev/2008_Chepelev_513.pdf:PDF},
  keywords  = {Protein Chip; Protein Interaction Map; Proteome; TAP Tag; Y2H Analysis},
  owner     = {saulius},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
  url       = {http://www.diagnosisp.com/dp/journals/view_article.php?journal_id=1&archive=0&issue_id=17&article_id=456},
}

@Article{Chernyshev1999,
  author    = {V. V. Chernyshev and A. V. Yatsenko and V. A. Tafeenko and E. J. Sonneveld and H. Schenk and V. A. Makarov},
  journal   = {Powder Diffraction},
  title     = {Crystal and molecular structure of 1-amino-4-methoxycarbonyl-3-methyl-8-oxopyrazolo[1,5-a]pyrimidine monohydrate from laboratory powder data},
  year      = {1999},
  pages     = {289--292},
  volume    = {14},
  doi       = {10.1017/S0885715600010708},
  file      = {:by-author/C/Chernyshev/1999_Chernyshev_289.war:},
  keywords  = {Rietveld Refinement},
  owner     = {saulius},
  timestamp = {2015.03.02},
  creationdate = {2015-03-02T00:00:00},
}

@Manuscript{Cheshire1996,
  author    = {Stuart Cheshire and Mary Baker},
  title     = {Internet Mobility 4x4},
  year      = {1996},
  keywords  = {Computer Science (CS)},
  url       = {http://www.stuartcheshire.org/papers/InternetMobility4x4/},
  abstract  = {Mobile IP protocols allow mobile hosts to send and receive packets addressed with their home network IP address, regardless of the IP address of their current point of attachment in the Internet. While some recent work in Mobile IP focuses on a couple of specific routing optimizations for sending packets to and from mobile hosts [Joh96] [Mon96], we show that a variety of different optimizations are appropriate in different circumstances. The best choice, which may vary on a connection-by-connection or even on a packet-by-packet basis, depends on three factors: the characteristics the protocol should optimize, the permissiveness of the networks over which the packets travel, and the level of mobile-awareness of the hosts with which the mobile host corresponds. Of the sixteen possible routing choices that we identify, we describe the seven that are most useful and discuss their benefits and limitations. These optimizations range from the most costly, which provides completely transparent mobility in all networks, to the most economical, which does not attempt to conceal location information. In particular, hosts should retain the option to communicate conventionally without using Mobile IP whenever appropriate. Further, we show that all optimizations can be described using a 4x4 grid of packet characteristics. This makes it easier for a mobile host, through a series of tests, to determine which of the currently available optimizations is the best to use for any given correspondent host.},
  file      = {:by-author/C/Cheshire/1996_Cheshire.war:},
  owner     = {saulius},
  timestamp = {2015.03.02},
  creationdate = {2015-03-02T00:00:00},
}

@Article{Cheung2009,
  author    = {Kwok Cheung and Hunter, J. and Drennan, J.},
  journal   = {Intelligent Systems, IEEE},
  title     = {{MatSeek}: An Ontology-Based Federated Search Interface for Materials Scientists},
  year      = {2009},
  issn      = {1541-1672},
  pages     = {47--56},
  volume    = {24},
  abstract  = {By providing an integrated Web interface to the critical materials science databases and analytical tools, MatSeek represents a significant advance toward a full-fledged materials-informatics workbench.},
  doi       = {10.1109/MIS.2009.13},
  file      = {:by-author/C/Cheung/2009_Cheung_47.pdf:PDF},
  owner     = {andrius},
  timestamp = {2015.07.21},
  creationdate = {2015-07-21T00:00:00},
}

@Presentation{Cheung2010,
  author       = {Peter Cheung},
  title        = {Clocking Strategies in {VLSI} Systems},
  year         = {2010},
  organization = {Department of Electrical \& Electronic Engineering Imperial College London},
  file         = {:by-author/C/Cheung/2010_Cheung_slides.pdf:PDF},
  owner        = {andrius},
  timestamp = {2013.03.08},
  creationdate = {2013-03-08T00:00:00},
}

@Article{Chevalier2002,
  author    = {Chevalier, Brett S and Kortemme, Tanja and Chadsey, Meggen S and Baker, David and Monnat, Raymond J and Stoddard, Barry L},
  journal   = {Molecular cell},
  title     = {Design, activity, and structure of a highly specific artificial endonuclease.},
  year      = {2002},
  pages     = {895--905},
  volume    = {10},
  abstract  = {We have generated an artificial highly specific endonuclease by fusing domains of homing endonucleases I-DmoI and I-CreI and creating a new 1400 A(2) protein interface between these domains. Protein engineering was accomplished by combining computational redesign and an in vivo protein-folding screen. The resulting enzyme, E-DreI (Engineered I-DmoI/I-CreI), binds a long chimeric DNA target site with nanomolar affinity, cleaving it precisely at a rate equivalent to its natural parents. The structure of an E-DreI/DNA complex demonstrates the accuracy of the protein interface redesign algorithm and reveals how catalytic function is maintained during the creation of the new endonuclease. These results indicate that it may be possible to generate novel highly specific DNA binding proteins from homing endonucleases.},
  file      = {Chevalier_2002_895-high_spec_artificial_nuc.pdf:by-author/C/Chevalier/2002_Chevalier_895.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Chib1995,
  author    = {Siddhartha Chib and Edward Greenberg},
  journal   = {The Americal Statistitian},
  title     = {Understanding the {M}etropolis--{H}astings algorithm},
  year      = {1995},
  pages     = {327--335},
  volume    = {49},
  file      = {:by-author/C/Chib/1995_Chib_327.pdf:PDF},
  keywords  = {Metropolis Hastings; Monte Carlo},
  owner     = {saulius},
  timestamp = {2012.10.04},
  creationdate = {2012-10-04T00:00:00},
}

@Article{Chiche1990,
  author    = {Chiche, L and Gregoret, L M and Cohen, F E and Kollman, P A},
  journal   = {Proceedings of the National Academy of Sciences},
  title     = {Protein model structure evaluation using the solvation free energy of folding.},
  year      = {1990},
  pages     = {3240--3243},
  volume    = {87},
  abstract  = {A systematic study of solvation free energy of folding for proteins with known crystallographic structures is presented. There is a linear relationship between the solvation free energy of folding and the protein size. This relationship, which can be rationalized by a simple model of chain folding, allows prediction of the solvation free energy of folding for proteins for which no high resolution structures are available. All misfolded structures analyzed show solvation free energies higher than predicted; however, some of the misfolded structures have values close enough to the predicted values so that one must be very careful when using such a criterion to check the correctness of a protein model.},
  doi       = {10.1073/pnas.87.8.3240},
  eprint    = {http://www.pnas.org/content/87/8/3240.full.pdf},
  file      = {1990_Chiche_3240.pdf:by-author/C/Chiche/1990_Chiche_3240.pdf:PDF},
  keywords  = {Bioinformatics; Free Energy; Hydrophobicity; Protein Folding},
  owner     = {saulius},
  timestamp = {2015.06.22},
  creationdate = {2015-06-22T00:00:00},
  url       = {http://www.pnas.org/content/87/8/3240.abstract},
}

@Article{Valinluck2004,
  author    = {V. Chin and V. Valinluck and S. Magaki and J. Ryu},
  journal   = {Nucleic Acids Research},
  title     = {{KpnBI} is the prototype of a new family ({IE}) of bacterial type {I} restriction-modification system},
  year      = {2004},
  pages     = {e138},
  volume    = {32},
  doi       = {10.1093/nar/gnh134},
  file      = {:by-author/V/Valinluck/2004_Valinluck_e138.pdf:PDF},
  keywords  = {TypeIII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Chisnall2015,
  author     = {Chisnall, David and Rothwell, Colin and Watson, Robert N.M. and Woodruff, Jonathan and Vadera, Munraj and Moore, Simon W. and Roe, Michael and Davis, Brooks and Neumann, Peter G.},
  journal    = {SIGPLAN Not.},
  title      = {Beyond the PDP-11: Architectural Support for a Memory-Safe C Abstract Machine},
  year       = {2015},
  issn       = {0362-1340},
  month      = mar,
  number     = {4},
  pages      = {117--130},
  volume     = {50},
  abstract   = {We propose a new memory-safe interpretation of the C abstract machine that provides stronger protection to benefit security and debugging. Despite ambiguities in the specification intended to provide implementation flexibility, contemporary implementations of C have converged on a memory model similar to the PDP-11, the original target for C. This model lacks support for memory safety despite well-documented impacts on security and reliability. Attempts to change this model are often hampered by assumptions embedded in a large body of existing C code, dating back to the memory model exposed by the original C compiler for the PDP-11. Our experience with attempting to implement a memory-safe variant of C on the CHERI experimental microprocessor led us to identify a number of problematic idioms. We describe these as well as their interaction with existing memory safety schemes and the assumptions that they make beyond the requirements of the C specification. Finally, we refine the CHERI ISA and abstract model for C, by combining elements of the CHERI capability model and fat pointers, and present a softcore CPU that implements a C abstract machine that can run legacy C code with strong memory protection guarantees.},
  acmid      = {2694367},
  address    = {New York, NY, USA},
  doi        = {10.1145/2775054.2694367},
  file       = {2015_Chisnall_117.pdf:by-author/C/Chisnall/2015_Chisnall_117.pdf:PDF},
  issue_date = {April 2015},
  keywords   = {Bounds Checking; C Language; Capabilities; Code Generation; Compiler Construction; Compilers; LLVM; Memory Protection; Memory Safety; Processor Design; Security},
  numpages   = {14},
  owner      = {saulius},
  publisher  = {ACM},
  timestamp = {2016.10.05},
  creationdate = {2016-10-05T00:00:00},
  url        = {http://doi.acm.org/10.1145/2775054.2694367},
}

@Article{Chisolm2012,
  author    = {Chisolm, Eric},
  journal   = {arXiv:1205.5935 [math-ph]},
  title     = {Geometric Algebra},
  year      = {2012},
  month     = may,
  note      = {arXiv: 1205.5935},
  pages     = {1205.5935},
  abstract  = {This is an introduction to geometric algebra, an alternative to traditional vector algebra that expands on it in two ways: 1. In addition to scalars and vectors, it defines new objects representing subspaces of any dimension. 2. It defines a product that's strongly motivated by geometry and can be taken between any two objects. For example, the product of two vectors taken in a certain way represents their common plane. This system was invented by William Clifford and is more commonly known as Clifford algebra. It's actually older than the vector algebra that we use today (due to Gibbs) and includes it as a subset. Over the years, various parts of Clifford algebra have been reinvented independently by many people who found they needed it, often not realizing that all those parts belonged in one system. This suggests that Clifford had the right idea, and that geometric algebra, not the reduced version we use today, deserves to be the standard "vector algebra." My goal in these notes is to describe geometric algebra from that standpoint and illustrate its usefulness. The notes are work in progress; I'll keep adding new topics as I learn them myself.},
  annote    = {Comment: 92 pages and 1 figure},
  file      = {2012_Chisolm_1205.5935.pdf:by-author/C/Chisolm/2012_Chisolm_1205.5935.pdf:PDF},
  keywords  = {Algebra; Geometric Algebra; Mathematical Physics; Mathematics},
  owner     = {saulius},
  timestamp = {2016.03.30},
  creationdate = {2016-03-30T00:00:00},
  url       = {http://arxiv.org/abs/1205.5935},
  urldate   = {2016-03-30},
}

@InProceedings{Chiticariu2005,
  author    = {Chiticariu, Laura and Tan, Wang-Chiew and Vijayvargiya, Gaurav},
  booktitle = {Proceedings of the 2005 ACM SIGMOD international conference on Management of data},
  title     = {DBNotes: a post-it system for relational databases based on provenance},
  year      = {2005},
  address   = {New York, NY, USA},
  pages     = {942--944},
  publisher = {ACM},
  series    = {SIGMOD '05},
  abstract  = {We demonstrate DBNotes, a Post-It note system for relational databases where every piece of data may be associated with zero or more notes (or annotations). These annotations are transparently propagated along as data is being transformed. The method by which annotations are propagated is based on provenance (aka lineage): the annotations associated with a piece of data d in the result of a transformation consist of the annotations associated with each piece of data in the source where d is copied from. One immediate application of this system is to use annotations to systematically trace the provenance and flow of data. If every piece of source data is attached with an annotation that describes its address (i.e., origins), then the annotations of a piece of data in the result of a transformation describe its provenance. Hence, one can easily determine the provenance of data through a sequence of transformation steps simply by examining the annotations. Annotations can also be used to store additional information about data. Since a database schema is often proprietary, the ability to insert new information about data without having to change the underlying schema is a useful feature. For example, an error report could be attached to an erroneous piece of data, and this error report will be propagated to other databases along transformations, thus notifying other users of the error. Overall, the annotations on the result of a transformation can also provide an estimate on the quality of the resulting database.},
  acmid     = {1066296},
  doi       = {10.1145/1066157.1066296},
  file      = {2005_Chiticariu_942.pdf:by-author/C/Chiticariu/2005_Chiticariu_942.pdf:PDF},
  isbn      = {1-59593-060-4},
  keywords  = {Annotation; Data Management; Databases},
  location  = {Baltimore, Maryland},
  numpages  = {3},
  owner     = {saulius},
  timestamp = {2012.10.25},
  creationdate = {2012-10-25T00:00:00},
  url       = {http://doi.acm.org/10.1145/1066157.1066296},
}

@Article{Chitre2007,
  author    = {Mandar A. Chitre and John R. Potter and S. H. Ong},
  journal   = {IEEE Transactions on Communications},
  title     = {Viterbi Decoding of Convolutional Codes in Symmetric α-Stable Noise},
  year      = {2007},
  pages     = {2230--2233},
  volume    = {55},
  abstract  = {Algorithms developed with a Gaussian noise assump- tion perform poorly in impulsive noise, such as that described by the symmetric α-stable (SαS) distribution. We investigate the performance of antipodal signaling and Viterbi decoding of con- volutional codes in SαS noise. We demonstrate that the p-norm branch metric is robust in SαS noise},
  file      = {:by-author/C/Chitre/2007_Chitre_2230.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.09.18},
  creationdate = {2012-09-18T00:00:00},
}

@Article{Chittaboina2005,
  author    = {Srinivas Chittaboina and Fang Xie and Qian Wang},
  journal   = {Tetrahedron Letters},
  title     = {One-pot synthesis of triazole-linked glycoconjugates},
  year      = {2005},
  issn      = {0040-4039},
  pages     = {2331--2336},
  volume    = {46},
  abstract  = {Highly efficient one-pot synthesis of 1,2,3-triazole-linked glycoconjugates was presented involving a Cu(I) catalyzed 1,3-dipolar cycloaddition as the key step. It offers a convenient route to prepare neoglycoconjugates derived from unprotected saccharides or peracetylated saccharides.},
  doi       = {10.1016/j.tetlet.2005.01.175},
  file      = {:by-author/C/Chittaboina/2005_Chittaboina_2331.pdf:PDF},
  keywords  = {Bioconjugation},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/S0040403905002674},
}

@Article{Chiu2004,
  author    = {Chiu, Joyce and March, Paul E. and Lee, Ryan and Tillett, Daniel},
  journal   = {Nucleic acids research},
  title     = {Site-directed, Ligase-Independent Mutagenesis (SLIM): a single-tube methodology approaching 100% efficiency in 4 h.},
  year      = {2004},
  pages     = {e174},
  volume    = {32},
  abstract  = {Site-directed, Ligase-Independent Mutagenesis (SLIM) is a novel PCR-mediated mutagenesis approach that can accommodate all three sequence modification types (insertion, deletion and substitution). The method utilizes an inverse PCR amplification of the template by two tailed long primers and two short primers in a single reaction with all steps carried out in one tube. The tailed primers are designed to contain the desired mutation on complementary overhangs at the terminus of PCR products. Upon post-amplification denaturation and re-annealing, heteroduplex formation between the mixed PCR products creates the desired clonable mutated plasmid. The technique is highly robust and suitable for applications in high-throughput gene engineering and library constructions. In this study, SLIM was employed to create sequence insertions, deletion and substitution within bacteriophage T7 gene 5. The overall efficiency for obtaining the desired product was &gt;95%.},
  file      = {:by-author/C/Chiu/2004_Chiu_e174.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Chmiel2005a,
  author    = {Agnieszka A Chmiel and Janusz M. Bujnicki and Krzysztof J. Skowronek},
  journal   = {BMC Structural Biology},
  title     = {A homology model of restriction endonuclease {SfiI} in complex with {DNA}},
  year      = {2005},
  pages     = {5:2},
  file      = {:by-author/C/Chmiel/2005_Chmiel_5\:2.pdf:PDF},
  keywords  = {Evolution; TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Chmiel2005,
  author    = {Chmiel, Agnieszka A. and Radlinska, Monika and Pawlak, Sebastian D. and Krowarsch, Daniel and Bujnicki, Janusz M. and Skowronek, Krzysztof J.},
  journal   = {Protein engineering, design \&amp; selection : PEDS},
  title     = {A theoretical model of restriction endonuclease NlaIV in complex with DNA, predicted by fold recognition and validated by site-directed mutagenesis and circular dichroism spectroscopy.},
  year      = {2005},
  pages     = {181--9},
  volume    = {18},
  abstract  = {Restriction enzymes (REases) are commercial reagents commonly used in DNA manipulations and mapping. They are regarded as very attractive models for studying protein-DNA interactions and valuable targets for protein engineering. Their amino acid sequences usually show no similarities to other proteins, with rare exceptions of other REases that recognize identical or very similar sequences. Hence, they are extremely hard targets for structure prediction and modeling. NlaIV is a Type II REase, which recognizes the interrupted palindromic sequence GGNNCC (where N indicates any base) and cleaves it in the middle, leaving blunt ends. NlaIV shows no sequence similarity to other proteins and virtually nothing is known about its sequence-structure-function relationships. Using protein fold recognition, we identified a remote relationship between NlaIV and EcoRV, an extensively studied REase, which recognizes the GATATC sequence and whose crystal structure has been determined. Using the 'FRankenstein's monster' approach we constructed a comparative model of NlaIV based on the EcoRV template and used it to predict the catalytic and DNA-binding residues. The model was validated by site-directed mutagenesis and analysis of the activity of the mutants in vivo and in vitro as well as structural characterization of the wild-type enzyme and two mutants by circular dichroism spectroscopy. The structural model of the NlaIV-DNA complex suggests regions of the protein sequence that may interact with the 'non-specific' bases of the target and thus it provides insight into the evolution of sequence specificity in restriction enzymes and may help engineer REases with novel specificities. Before this analysis was carried out, neither the three-dimensional fold of NlaIV, its evolutionary relationships or its catalytic or DNA-binding residues were known. Hence our analysis may be regarded as a paradigm for studies aiming at reducing 'white spaces' on the evolutionary landscape of sequence-function relationships by combining bioinformatics with simple experimental assays.},
  file      = {:by-author/C/Chmiel/2005_Chmiel_181.pdf:PDF},
  keywords  = {TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Cho2014,
  author    = {Cho, A.},
  journal   = {Science},
  title     = {Breakthrough lost in coin toss?},
  year      = {2014},
  issn      = {1095-9203},
  month     = {Oct},
  number    = {6205},
  pages     = {22--23},
  volume    = {346},
  doi       = {10.1126/science.346.6205.22},
  file      = {2014_Cho_22.pdf:by-author/C/Cho/2014_Cho_22.pdf:PDF},
  groups    = {sg/Measurements},
  keywords  = {Measurement; Wavepacket Reduction},
  owner     = {saulius},
  publisher = {American Association for the Advancement of Science (AAAS)},
  timestamp = {2016.04.04},
  creationdate = {2016-04-04T00:00:00},
  url       = {http://dx.doi.org/10.1126/science.346.6205.22},
}

@Article{Cho2007,
  author    = {Cho, Eunsook and Gwak, Hyesun and Chun, Inkoo},
  journal   = {International journal of pharmaceutics},
  title     = {Formulation and evaluation of ondansetron nasal delivery systems.},
  year      = {2008},
  pages     = {101--7},
  volume    = {349},
  abstract  = {This study aimed to formulate and evaluate nasal delivery systems containing ondansetron hydrochloride. In the in vitro study, the permeation rate with the addition of 10% polyethylene glycol 300 (PEG 300) to aqueous solution containing 0.01% benzalkonium chloride (BC) and 10% sulfobutylether beta-cyclodextrin sodium salt (SBCD) was somewhat more rapid up to 1.5h compared to the addition of 10% PG. The permeation flux increased as the drug concentration increased regardless of the vehicles used. The addition of nicotinamide or chitosan to aqueous drug solution (40 mg/ml) with 10% PEG 300 and 0.01% BC rather decreased permeation rate and delayed lag time. Even though cyclodextrins including SBCD or dimethyl-ss-cyclodextrin failed to show permeation enhancing effects of ondansetron hydrochloride, the addition of 10% SBCD to aqueous solution containing 10% PEG 300 and 0.01% BC could be a good candidate for ondansetron nasal delivery systems because of its safety profile, stable storage in refrigerator and solubilizing effect. With the above formulation, the nasal delivery system increased AUC0-2h and Cmax by 2.1 and 1.7 times compared to those of oral delivery, respectively while there was no difference found in AUC0-2h with intravenous administration. Therefore, the nasal delivery system of ondansetron hydrochloride formulated in this study was feasible for nasal administration.},
  file      = {:by-author/C/Cho/2008_Cho_101.pdf:PDF},
  keywords  = {Molecular Dynamics (MD)},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Choi2006,
  author           = {Vicky Choi},
  journal          = {Journal of Chemical Information and Modeling},
  title            = {On updating torsion angles of molecular conformations},
  year             = {2006},
  pages            = {438--444},
  volume           = {46},
  creationdate     = {2011-12-14T00:00:00},
  doi              = {10.1021/ci050253h},
  file             = {:by-author/C/Choi/2006_Choi_438.pdf:PDF},
  keywords         = {Dihedral Angles; Molecular Modelling; Torsion Angles},
  modificationdate = {2024-04-08T13:18:24},
  owner            = {saulius},
  timestamp        = {2011.12.14},
}

@Article{Chothia1986,
  author    = {Chothia, C. and Lesk, A. M.},
  journal   = {The EMBO journal},
  title     = {The relation between the divergence of sequence and structure in proteins},
  year      = {1986},
  number    = {4},
  pages     = {823--826},
  volume    = {5},
  abstract  = {Homologous proteins have regions which retain the same general fold and regions where the folds differ. For pairs of distantly related proteins (residue identity approximately 20%), the regions with the same fold may comprise less than half of each molecule. The regions with the same general fold differ in structure by amounts that increase as the amino acid sequences diverge. The root mean square deviation in the positions of the main chain atoms, delta, is related to the fraction of mutated residues, H, by the expression: delta(A) = 0.40 e1.87H.},
  file      = {:by-author/C/Chothia/1986_Chothia_823.pdf:pdf},
  keywords  = {Validation},
  owner     = {saulius},
  pmc       = {PMC1166865},
  pubmed    = {3709526},
  timestamp = {2016.12.12},
  creationdate = {2016-12-12T00:00:00},
  url       = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1166865/},
}

@Article{Christensen1995a,
  author    = {Christensen},
  title     = {Methods for Handling Exceptions in Object-oriented Programming Languages},
  year      = {1995},
  pages     = {mscthesis2},
  file      = {:by-author/C/Christensen/1995_Christensen_mscthesis2.pdf:PDF},
  keywords  = {Computer Science (CS); Exception Handling},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Christensen1967,
  author    = {C.J. Christensen and A. Nielsen and A. Bahnsen and W.K. Brown and B.M. Rustad},
  journal   = {Physics Letters B},
  title     = {The half-life of the free neutron},
  year      = {1967},
  issn      = {0370-2693},
  number    = {1},
  pages     = {11--13},
  volume    = {26},
  abstract  = {A measurement of the half-life of the free neutron yields T12 = 10.80 ± 0.16 min.},
  doi       = {10.1016/0370-2693(67)90532-1},
  file      = {1967_Christensen_11.pdf:by-author/C/Christensen/1967_Christensen_11.pdf:PDF},
  keywords  = {Half-life; Neutron; Nuclear Physics; Nucleon; Physics},
  owner     = {saulius},
  timestamp = {2016.01.18},
  creationdate = {2016-01-18T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/0370269367905321},
}

@Article{Christensen2004,
  author    = {Christensen, Janne Ørskov and Schultz, Kirsten and Mollgaard, Birgitte and Kristensen, Henning Gjelstrup and Mullertz, Anette},
  journal   = {European journal of pharmaceutical sciences : official journal of the European Federation for Pharmaceutical Sciences},
  title     = {Solubilisation of poorly water-soluble drugs during in vitro lipolysis of medium- and long-chain triacylglycerols.},
  year      = {2004},
  pages     = {287--96},
  volume    = {23},
  abstract  = {The partitioning of poorly soluble drugs into an aqueous micellar phase was exploited using an in vitro lipid digestion model, simulating the events taking place during digestion of acylglycerols in the duodenum. The aqueous micellar phase was isolated after ultracentrifugation of samples obtained at different degrees of triacylglycerol hydrolysis. Flupentixol, 1'-[4-[1-(4-fluorophenyl)-1-H-indol-3-yl]-1-butyl]spiro[iso-benzofuran-1(3H), 4' piperidine] (LU 28-179) and probucol were studied. The effect of the alkyl chain length of the triacylglycerol was studied using a medium-chain triacylglycerol (MCT) and a long-chain triacylglycerol (LCT), respectively. In general, an oil solution was used as the lipid source in the model. Samples were analysed in regard to micellar size, lipid composition and drug concentration. During lipolysis, the content of lipolytic products in the aqueous micellar phase increased. The micellar size (R(H) approximately 3 nm) only increased when long-chain lipolytic products were incorporated in the mixed micelles (R(H) approximately 7.8 nm). Flupentixol was quickly transferred to the mixed micelles due to high solubility in this phase (100% released). A tendency towards higher solubilisation of LU 28-179, when it was administered in the LCT (approximately 24% released) compared to when it was administered in the MCT (approximately 15% released) at 70% hydrolysis, and a lagphase was observed. There was no difference in the solubilisation of probucol using MCT or LCT ( approximately 20% released), respectively. Differences in the physicochemical properties of the drugs resulted in differences in their distribution between the phases arising during lipolysis.},
  file      = {:by-author/C/Christensen/2004_Christensen_287.pdf:PDF},
  keywords  = {TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@MastersThesis{Christensen1995,
  author    = {Morten Mikael Christensen},
  school    = {Department of Mathematics and Computer Science, Odense University},
  title     = {Methods for Handling Exceptions in Object-oriented Programming Languages},
  year      = {1995},
  file      = {:by-author/C/Christensen/1995_Christensen_mscthesis.pdf:PDF},
  keywords  = {Computer Science (CS); Exception Handling},
  owner     = {saulius},
  pages     = {mscthesis},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Christopher1996,
  author    = {Christopher, J. A. and Swanson, R. and Baldwin, T. O.},
  journal   = {Computers \&amp; chemistry},
  title     = {Algorithms for finding the axis of a helix: fast rotational and parametric least-squares methods.},
  year      = {1996},
  pages     = {339--45},
  volume    = {20},
  abstract  = {Several methods for finding the axis of a helix are presented and compared. The most accurate determines the helix axis as the axis of rotation necessary to map point i to point i + 1 of the helix. The fastest method calculates the helix axis as the best-fit line through the coordinates by a three-dimensional parametric linear least-squares algorithm, taking advantage of the sequential nature of the data.},
  file      = {:by-author/C/Christopher/1996_Christopher_339.pdf:PDF},
  keywords  = {Helical Parameters; Protein Bioinformatics},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Chu2010,
  author    = {Chu, Y. and Yue, X. and Younger, S. T. and Janowski, B. A. and Corey, D. R.},
  journal   = {Nucleic Acids Research},
  title     = {Involvement of argonaute proteins in gene silencing and activation by RNAs complementary to a non-coding transcript at the progesterone receptor promoter},
  year      = {2010},
  issn      = {1362-4962},
  month     = {Jul},
  number    = {21},
  pages     = {7736–7748},
  volume    = {38},
  doi       = {10.1093/nar/gkq648},
  file      = {2010_Chu_7736.pdf:by-author/C/Chu/2010_Chu_7736.pdf:PDF},
  groups    = {am/RNA activation},
  owner     = {andrius},
  publisher = {Oxford University Press (OUP)},
  timestamp = {2016.09.14},
  creationdate = {2016-09-14T00:00:00},
  url       = {http://dx.doi.org/10.1093/nar/gkq648},
}

@Article{Chung2007,
  author    = {Chun-Wa Chung},
  journal   = {Acta Crystallographica Section D},
  title     = {The Use of Biophysical Methods Increases Success in Obtaining Liganded Crystal Structures},
  year      = {2007},
  pages     = {62--71},
  volume    = {63},
  abstract  = {In attempts to determine the crystal structure of small molecule-protein complexes, a common frustration is the absence of ligand binding once the protein structure has been solved. While the first structure, even with no ligand bound (apo), can be a cause for celebration, the solution of dozens of apo structures can give an unwanted sense of déjà vu. Much time and material is wasted on unsuccessful experiments, which can have a serious impact on productivity and morale. There are many reasons for the lack of observed binding in crystals and this paper highlights some of these. Biophysical methods may be used to confirm and optimize solution conditions to increase the success rate of crystallizing protein-ligand complexes. As there are an overwhelming number of biophysical methods available, some of the factors that need to be considered when choosing the most appropriate technique for a given system are discussed. Finally, a few illustrative examples where biophysical methods have proven helpful in real systems are given.},
  doi       = {10.1107/S0907444906051869},
  file      = {:by-author/C/Chung/2007_Chung_62.pdf:PDF},
  owner     = {saulius},
  timestamp = {2011.12.16},
  creationdate = {2011-12-16T00:00:00},
}

@Article{Chung2007a,
  author    = {St. Clare Chung and Miklos Schulz},
  title     = {Bayesian Designs for Clinical Trials in Early Drug Development},
  year      = {2007},
  number    = {6},
  volume    = {3},
  file      = {Microsoft Word - Bayesian - 0706_bayesian.pdf:by-author/C/Chung/2007_Chung.pdf:application/pdf},
  groups    = {sg/Clinical Trials},
  language  = {English},
  owner     = {saulius},
  timestamp = {2015.12.14},
  creationdate = {2015-12-14T00:00:00},
  url       = {http://www.scian.com/media/488/0706_bayesian.pdf},
  urldate   = {2015-12-12},
}

@Article{Chung1999,
  author    = {Chung, S. Y. and Subbiah, S.},
  journal   = {Proteins},
  title     = {Validation of NMR side-chain conformations by packing calculations.},
  year      = {1999},
  pages     = {184--94},
  volume    = {35},
  abstract  = {The precision and accuracy of protein structures determined by nuclear magnetic resonance (NMR) spectroscopy depend on the completeness of input experimental data set. Typically, rather than a single structure, an ensemble of up to 20 equally representative conformers is generated and routinely deposited in the Protein Database. There are substantially more experimentally derived restraints available to define the main-chain coordinates than those of the side chains. Consequently, the side-chain conformations among the conformers are more variable and less well defined than those of the backbone. Even when a side chain is determined with high precision and is found to adopt very similar orientations among all the conformers in the ensemble, it is possible that its orientation might still be incorrect. Thus, it would be helpful if there were a method to assess independently the side-chain orientations determined by NMR. Recently, homology modeling by side-chain packing algorithms has been shown to be successful in predicting the side-chain conformations of the buried residues for a protein when the main-chain coordinates and sequence information are given. Since the main-chain coordinates determined by NMR are consistently more reliable than those of the side-chains, we have applied the side-chain packing algorithms to predict side-chain conformations that are compatible with the NMR-derived backbone. Using four test cases where the NMR solution structures and the X-ray crystal structure of the same protein are available, we demonstrate that the side-chain packing method can provide independent validation for the side-chain conformations of NMR structures. Comparison of the side-chain conformations derived by side-chain packing prediction and by NMR spectroscopy demonstrates that when there is agreement between the NMR model and the predicted model, on average 78% of the time the X-ray structure also concurs. While the side-chain packing method can confirm the reliable residue conformations in NMR models, more importantly, it can also identify the questionable residue conformations with an accuracy of 60%. This validation method can serve to increase the confidence level for potential users of structural models determined by NMR.},
  file      = {:by-author/C/Chung/1999_Chung_184.pdf:PDF},
  keywords  = {Protein Bioinformatics; Quality Estimation},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Chung2014,
  author    = {Chung, Yongchul G. and Camp, Jeffrey and Haranczyk, Maciej and Sikora, Benjamin J. and Bury, Wojciech and Krungleviciute, Vaiva and Yildirim, Taner and Farha, Omar K. and Sholl, David S. and Snurr, Randall Q.},
  journal   = {Chemistry of Materials},
  title     = {Computation-Ready, Experimental Metal–Organic Frameworks: A Tool To Enable High-Throughput Screening of Nanoporous Crystals},
  year      = {2014},
  issn      = {1520-5002},
  month     = {Nov},
  number    = {21},
  pages     = {6185--6192},
  volume    = {26},
  abstract  = {Experimentally refined crystal structures for metal–organic frameworks (MOFs) often include solvent molecules and partially occupied or disordered atoms. This creates a major impediment to applying high-throughput computational screening to MOFs. To address this problem, we have constructed a database of MOF structures that are derived from experimental data but are immediately suitable for molecular simulations. The computation-ready, experimental (CoRE) MOF database contains over 4700 porous structures with publically available atomic coordinates. Important physical and chemical properties including the surface area and pore dimensions are reported for these structures. To demonstrate the utility of the database, we performed grand canonical Monte Carlo simulations of methane adsorption on all structures in the CoRE MOF database. We investigated the structural properties of the CoRE MOFs that govern methane storage capacity and found that these relationships agree well with those derived recently from a large database of hypothetical MOFs.},
  doi       = {10.1021/cm502594j},
  file      = {2014_Chung_6185.pdf:by-author/C/Chung/2014_Chung_6185.pdf:PDF},
  groups    = {sg/MOF, sg/MOFs, am/MOFs},
  keywords  = {Metal-Organic Frameworks (MOF)},
  owner     = {saulius},
  publisher = {American Chemical Society (ACS)},
  timestamp = {2016.12.27},
  creationdate = {2016-12-27T00:00:00},
  url       = {http://dx.doi.org/10.1021/cm502594j},
}

@InProceedings{Ciaccia1997,
  author    = {Ciaccia, Paolo and Patella, Marco and Zezula, Pavel},
  booktitle = {Proceedings of the 23rd International Conference on Very Large Data Bases},
  title     = {M-tree: An Efficient Access Method for Similarity Search in Metric Spaces},
  year      = {1997},
  address   = {San Francisco, CA, USA},
  pages     = {426--435},
  publisher = {Morgan Kaufmann Publishers Inc.},
  series    = {VLDB '97},
  abstract  = {A new access method, called M-tree, is proposed to organize and search large data sets from a generic "metric space", i.e. where object proximity is only defined by a distance function satisfying the positivity, symmetry, and triangle inequality postulates. We detail algorithms for insertion of objects and split management, which keep the M-tree always balanced - several heuristic split alternatives are considered and experimentally evaluated. Algorithms for similarity (range and k-nearest neighbors) queries are also described. Results from extensive experimentation with a prototype system are reported, considering as the performance criteria the number of page I/O's and the number of distance computations. The results demonstrate that the M-tree indeed extends the domain of applicability beyond the traditional vector spaces, performs reasonably well in high-dimensional data spaces, and scales well in case of growing files.},
  file      = {:by-author/C/Ciaccia/1997_Ciaccia_426.pdf:PDF},
  isbn      = {1-55860-470-7},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dl.acm.org/citation.cfm?id=645923.671005},
}

@PhdThesis{Cid-Dresdner1964,
  author    = {Hilda Cid-Dresdner},
  school    = {Massachusetts Institute of Technology},
  title     = {Crystal Structures of the Turquois-group Minerals},
  year      = {1964},
  file      = {:by-author/C/Cid-Dresdner/1964_Cid-Dresdner_phdthesis.pdf:PDF},
  keywords  = {History; X-ray Crystallography},
  owner     = {saulius},
  pages     = {phdthesis},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Cieplak2001,
  author    = {T. Cieplak and J.L. Wisniewski},
  journal   = {Molecules},
  title     = {A New Effective Algorithm for the Unambiguous Identification of the Stereochemical Characteristics of Compounds During Their Registration in Databases},
  year      = {2001},
  pages     = {915--926},
  volume    = {6},
  abstract  = {A new effective algorithm for handling of geometry at chiral centers for the processing of stereochemical structures during their unambiguous registration in databases was designed, programmed and implemented. The chemical and mathematical reasoning behind the algorithm are discussed in detail. Its advantages- in comparison to the methods used so far - are illustrated for the manual as well as for the computer- assisted assignment of stereodescriptors based on the CIP ranking procedure.},
  doi       = {10.3390/61100915},
  file      = {:by-author/C/Cieplak/2001_Cieplak_915.pdf:PDF},
  keywords  = {CIP; Chirality; Determinant Algorithm; Stereochemistry; Stereodescriptors},
  owner     = {saulius},
  timestamp = {2014.01.26},
  creationdate = {2014-01-26T00:00:00},
  url       = {http://www.mdpi.com/1420-3049/6/11/915},
}

@InProceedings{Cieslewicz2006,
  author    = {John Cieslewicz and Jonathan Berry and Bruce Hendrickson and Kenneth A. Ross},
  booktitle = {Proceedings of the Second International Workshop on Data Management on New Hardware},
  title     = {Realizing Parallelism in Database Operations: Insights from a Massively Multithreaded Architecture},
  year      = {2006},
  abstract  = {A new trend in processor design is increased on-chip support for multithreading in the form of both chip multiprocessors and simultaneous multithreading. Recent research in data- base systems has begun to explore increased thread-level parallelism made possible by these new multicore and mul- tithreaded processors. The question of how best to use this new technology remains open, particularly as the number of cores per chip and threads per core increase. In this paper we use an existing massively multithreaded architecture, the Cray MTA-2, to explore the implications that a larger de- gree of on-chip multithreading may have for parallelism in database operations. We find that parallelism in database operations is easy to achieve on the MTA-2 and that, with little effort, parallelism can be made to scale linearly with the number of available processor cores.},
  doi       = {10.1145/1140402.1140408},
  file      = {:by-author/C/Cieslewicz/2006_Cieslewicz.pdf:PDF},
  isbn      = {1-59593-466-9},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://doi.acm.org/10.1145/1140402.1140408},
}

@Article{Ciriminna2013,
  author    = {Ciriminna, Rosaria and Pagliaro, Mario},
  journal   = {Chemistry Central journal},
  title     = {On the use of the h-index in evaluating chemical research.},
  year      = {2013},
  pages     = {132},
  volume    = {7},
  doi       = {10.1186/1752-153X-7-132},
  file      = {:by-author/C/Ciriminna/2013_Ciriminna_132.pdf:PDF},
  owner     = {saulius},
  timestamp = {2014.03.23},
  creationdate = {2014-03-23T00:00:00},
  url       = {http://journal.chemistrycentral.com/content/7/1/132},
}

@Article{Cizek1966,
  author    = {Čížek, Jiří},
  journal   = {The Journal of Chemical Physics},
  title     = {On the Correlation Problem in Atomic and Molecular Systems. Calculation of Wavefunction Components in Ursell‐Type Expansion Using Quantum‐Field Theoretical Methods},
  year      = {1966},
  pages     = {4256--4266},
  volume    = {45},
  abstract  = {A method is suggested for the calculation of the matrix elements of the logarithm of an operator which gives the exact wavefunction when operating on the wavefunction in the one‐electron approximation. The method is based on the use of the creation and annihilation operators, hole—particle formalism, Wick's theorem, and the technique of Feynman‐like diagrams. The connection of this method with the configuration‐interaction method as well as with the perturbation theory in the quantum‐field theoretical form is discussed. The method is applied to the simple models of nitrogen and benzene molecules. The results are compared with those obtained with the configuration‐interaction method considering all possible configurations within the chosen basis of one‐electron functions.},
  doi       = {10.1063/1.1727484},
  file      = {1966_Čížek_4256.pdf:by-author/Č/Čížek/1966_Čížek_4256.pdf:PDF},
  keywords  = {Computational Chemistry; Density Functional Theory (DFT); Quantum Chemistry},
  owner     = {saulius},
  timestamp = {2014.07.21},
  creationdate = {2014-07-21T00:00:00},
  url       = {http://scitation.aip.org/content/aip/journal/jcp/45/11/10.1063/1.1727484},
}

@Article{Clark1989,
  author    = {Clark, Matthew and Cramer, Richard D. and Van Opdenbosch, Nicole},
  journal   = {Journal of Computational Chemistry},
  title     = {Validation of the general purpose {T}ripos 5.2 force field},
  year      = {1989},
  issn      = {1096-987X},
  month     = {Dec},
  number    = {8},
  pages     = {982–1012},
  volume    = {10},
  doi       = {10.1002/jcc.540100804},
  file      = {1989_Clark_982.pdf:by-author/C/Clark/1989_Clark_982.pdf:PDF},
  groups    = {sg/Crystallography, am/Crystallography},
  owner     = {andrius},
  publisher = {Wiley-Blackwell},
  timestamp = {2017.01.03},
  creationdate = {2017-01-03T00:00:00},
  url       = {http://dx.doi.org/10.1002/jcc.540100804},
}

@Article{Clark2002,
  author    = {Clark, Peter A.},
  journal   = {Medical science monitor : international medical journal of experimental and clinical research},
  title     = {AIDS research in developing countries: do the ends justify the means?},
  year      = {2002},
  pages     = {ED5-16},
  volume    = {8},
  abstract  = {Concrete ethical standards for human research are clearly stipulated in both international and national codes of ethics, and are meant to protect human subjects, especially the most vulnerable. A recent clinical study conducted from 1994 to 1997 by Dr. Thomas C, Quinn, M.D. has fueled the debate raging in the scientific community regarding the ethics of clinical AIDS research in developing countries. Quinn's conducted a community-based, randomized, controlled study of 15,127 rural Ugandans to determine whether intermittent antibiotic treatment to reduce the prevalence of other sexually transmitted diseases would also reduce the rate of HIV transmission. Subsequently, the study identified 415 couples in which one partner was HIV positive and one was initially HIV negative and followed them prospectively for up to 30 months. Researchers were not permitted to inform the seronegative partner of the HIV status of the other partner. As a result, 90 of the initially HIV negative partners (21.7%) seroconverted during a follow-up period of 30 months. To allow for research studies in developing countries that are not permitted in the United States appears to make the Third World equivalent to a 'research sweat shop'. Developing nations offer easy access to patients, reduced costs, and less stringent regulations. This appears to create a double standard for medical research that is both ethically and humanly unacceptable, especially when other viable option exist. To allow relativism to seep into the international and national ethical standards will open the door to an idea that condones the possible abuse of those least able to protect themselves. Researchers have an ethical responsibility to uphold the integrity of these ethical standards. Failure to do so today may have a devastating impact on humanity in the future.},
  file      = {:by-author/C/Clark/2002_Clark_ED5.pdf:PDF},
  keywords  = {MSM},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Manuscript{Clarke2000,
  author      = {Kevin A. Clarke},
  title       = {The Effect of Priors on Approximate Bayes Factors from MCMC Output},
  year        = {2000},
  institution = {University of Michigan, Department of Political Science},
  keywords    = {Bayesian Statistics},
  abstract    = {The MCMC approach to calculating approximate Bayes factors is considered. The calculation, consisting of a log-likelihood, a prior, and a posterior, presents an excellent opportunity to observe directly the effects of priors on Bayes factors. Three empirical examples demonstrate that Bayes factors are sensitive to a combination of the prior variance and the difference in the number of parameters between the rival models.},
  file        = {:by-author/C/Clarke/2000_Clarke.pdf:PDF},
  groups      = {sg/Bayesian},
  owner       = {saulius},
  timestamp = {2012.09.30},
  creationdate = {2012-09-30T00:00:00},
}

@Article{Clark2011,
  author           = {Clark, Alex M.},
  journal          = {Journal of Chemical Information and Modeling},
  title            = {Accurate specification of molecular structures: the case for zero-order bonds and explicit hydrogen counting},
  year             = {2011},
  issn             = {1549-960X},
  month            = {Dec},
  number           = {12},
  pages            = {3149--3157},
  volume           = {51},
  creationdate     = {2021-06-29T16:22:06+0300},
  doi              = {10.1021/ci200488k},
  file             = {:by-author/C/Clark/2011_Clark_3149.pdf:PDF;:by-author/C/Clark/2011_Clark_3149_suppl/ci200488k_si_001.pdf:PDF},
  modificationdate = {2022-12-03T18:22:33},
  owner            = {andrius},
  publisher        = {American Chemical Society (ACS)},
  timestamp        = {2021.06.29},
  url              = {https://pubs.acs.org/doi/pdf/10.1021/ci200488k},
}

@Article{Clarke2012,
  author    = {Laura Clarke and Xiangqun Zheng-Bradley and Richard Smith and Eugene Kulesha and Chunlin Xiao and Iliana Toneva and Brendan Vaughan and Don Preuss and Rasko Leinonen and Martin Shumway and Stephen Sherry and Paul Flicek and The 1000 Genomes Project Consortium},
  journal   = {Nature Methods},
  title     = {The 1000 Genomes Project: data management and community access},
  year      = {2012},
  pages     = {459--462},
  volume    = {9},
  doi       = {10.1038/nmeth.1974},
  file      = {2012_Clarke_459.pdf:by-author/C/Clarke/2012_Clarke_459.pdf:PDF;Supplementary information:by-author/C/Clarke/2012_Clarke_459suppl.pdf:PDF},
  keywords  = {Databases; Genomes},
  owner     = {saulius},
  timestamp = {2012.06.13},
  creationdate = {2012-06-13T00:00:00},
}

@Article{Clegg1981,
  author    = {Clegg, W.},
  journal   = {Acta Crystallographica Section A},
  title     = {Cell reduction and lattice symmetry determination},
  year      = {1981},
  pages     = {913--915},
  volume    = {37},
  abstract  = {Simple inspection of the reduced form of a unit cell can fail to detect the correct lattice symmetry, because of the effects of measurement errors, computer rounding errors and uncertainties in interpretation of almost equal numbers. A procedure which is insensitive to these effects consists of the generation of a list of lattice vectors sorted on length, together with angles between pairs of them. The list includes the edges, face diagonals and body diagonals of the reduced cell, and the sums and differences of any of these which are similar in length. The correct unit cell is easily recognized in the vector list.},
  doi       = {10.1107/S0567739481001952},
  file      = {1981_Clegg_913.pdf:by-author/C/Clegg/1981_Clegg_913.pdf:PDF},
  keywords  = {Crystallographic Computing; Reduced Cell; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2014.03.27},
  creationdate = {2014-03-27T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0567739481001952},
}

@Article{Clemons2001,
  author    = {Clemons, Jr, W. M. and Brodersen, D. E. and McCutcheon, J. P. and May, J. L. and Carter, A. P. and Morgan-Warren, R. J. and Wimberly, B. T. and Ramakrishnan, V.},
  journal   = {Journal of molecular biology},
  title     = {Crystal structure of the 30 S ribosomal subunit from Thermus thermophilus: purification, crystallization and structure determination.},
  year      = {2001},
  pages     = {827--43},
  volume    = {310},
  abstract  = {We describe the crystallization and structure determination of the 30 S ribosomal subunit from Thermus thermophilus. Previous reports of crystals that diffracted to 10 A resolution were used as a starting point to improve the quality of the diffraction. Eventually, ideas such as the addition of substrates or factors to eliminate conformational heterogeneity proved less important than attention to detail in yielding crystals that diffracted beyond 3 A resolution. Despite improvements in technology and methodology in the last decade, the structure determination of the 30 S subunit presented some very challenging technical problems because of the size of the asymmetric unit, crystal variability and sensitivity to radiation damage. Some steps that were useful for determination of the atomic structure were: the use of anomalous scattering from the LIII edges of osmium and lutetium to obtain the necessary phasing signal; the use of tunable, third-generation synchrotron sources to obtain data of reasonable quality at high resolution; collection of derivative data precisely about a mirror plane to preserve small anomalous differences between Bijvoet mates despite extensive radiation damage and multi-crystal scaling; the pre-screening of crystals to ensure quality, isomorphism and the efficient use of scarce third-generation synchrotron time; pre-incubation of crystals in cobalt hexaammine to ensure isomorphism with other derivatives; and finally, the placement of proteins whose structures had been previously solved in isolation, in conjunction with biochemical data on protein-RNA interactions, to map out the architecture of the 30 S subunit prior to the construction of a detailed atomic-resolution model.},
  file      = {:by-author/C/Clemons/2001_Clemons_827.pdf:PDF},
  keywords  = {Ribosome Structure},
  owner     = {saulius},
  timestamp = {2012.06.25},
  creationdate = {2012-06-25T00:00:00},
}

@Article{Clerch1996,
  author    = {Berta Clerch and Eusebi Rivera and Montserrat Llagostera},
  journal   = {Journal of Bacteriology},
  title     = {Identification of a pKM101 Region Which Confers a Slow Growth Rate and Interferes with Susceptibility to Quinolone in Escherichia coli AB1157},
  year      = {1996},
  pages     = {5568--5572},
  volume    = {178},
  file      = {1996_Clerch_5568.pdf:by-author/C/Clerch/1996_Clerch_5568.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Click2009,
  author      = {Timothy H Click and George A Kaminski},
  journal     = {J Phys Chem B},
  title       = {Reproducing basic pKa values for turkey ovomucoid third domain using a polarizable force field.},
  year        = {2009},
  pages       = {7844--7850},
  volume      = {113},
  abstract    = {We have extended our previous studies of calculating acidity constants for the acidic residues found in the turkey ovomucoid third domain protein (OMTKY3) by determining the relative pKa values for the basic residues (Lys13, Arg21, Lys29, Lys34, His52, and Lys55). A polarizable force field (PFF) was employed. The values of the pKa were found by direct comparison of energies of solvated protonated and deprotonated forms of the protein. Poisson-Boltzmann (PBF) and surface generalized Born (SGB) continuum solvation models represent the hydration, and a nonpolarizable fixed-charge OPLS-AA force field was used for comparison. Our results indicate that (i) the pKa values of the basic residues can be found in close agreement with the experimental values when a PFF is used in conjunction with the PBF solvation model, (ii) it is sufficient to take into the account only the residues which are in close proximity (hydrogen bonded) to the residue in question, and (iii) the PBF solvation model is superior to the SGB solvation model for these pKa calculations. The average error with the PBF/PFF model is only 0.7 pH unit, compared with 2.2 and 6.1 units for the PBF/OPLS and SGB/OPLS, respectively. The maximum deviation of the PBF/PFF results from the experimental values is 1.7 pH units compared with 6.0 pH units for the PBF/OPLS. Moreover, the best results were obtained while using an advanced nonpolar energy calculation scheme. The overall conclusion is that this methodology and force field are suitable for the accurate assessment of pKa shifts for both acidic and basic protein residues.},
  doi         = {10.1021/jp809412e},
  file        = {2009_Click_7844.pdf:by-author/C/Click/2009_Click_7844.pdf:PDF},
  institution = {Department of Chemistry, Central Michigan University, Mt. Pleasant, Michigan 48859, USA.},
  keywords    = {Animals; Arginine; Chemistry; Histidine; Hydrogen-Ion Concentration; Lysine; Models; Molecular; Ovomucin; PKa; Protein Physics; Protein Structure; Tertiary; Turkeys},
  language    = {eng},
  medline-pst = {ppublish},
  owner       = {saulius},
  pmid        = {19432439},
  timestamp = {2011.10.13},
  creationdate = {2011-10-13T00:00:00},
  url         = {http://dx.doi.org/10.1021/jp809412e},
}

@Article{Clowney1996,
  author    = {Clowney, Lester and Jain, Shri C. and Srinivasan, A. R. and Westbrook, John and Olson, Wilma K. and Berman, Helen M.},
  journal   = {Journal of the American Chemical Society},
  title     = {Geometric Parameters in Nucleic Acids: Nitrogenous Bases},
  year      = {1996},
  pages     = {509--518},
  volume    = {118},
  file      = {:by-author/C/Clowney/1996_Clowney_509.pdf:PDF},
  keywords  = {X-ray Crystallography},
  owner     = {andrius},
  timestamp = {2012.05.18},
  creationdate = {2012-05-18T00:00:00},
}

@Article{Cocozaki2012,
  author    = {Cocozaki, Alexis I. and Ramia, Nancy F. and Shao, Yaming and Hale, Caryn R. and Terns, Rebecca M. and Terns, and Michael P. and Li, Hong},
  journal   = {Structure},
  title     = {Structure of the Cmr2 Subunit of the CRISPR-Cas RNA Silencing Complex},
  year      = {2012},
  pages     = {545–553},
  volume    = {20},
  doi       = {10.1016/j.str.2012.01.018},
  file      = {:by-author/C/Cocozaki/2012_Cocosaki_545.pdf:PDF},
  groups    = {sg/CRISPR-Cas},
  keywords  = {CRISPR; Cas Complex; Cmr Complex; Cmr2; Crystal Structure},
  owner     = {em},
  timestamp = {2013.10.01},
  creationdate = {2013-10-01T00:00:00},
}

@Article{Cohen2008,
  author    = {E. G. D. Cohen},
  journal   = {arXiv},
  title     = {Entropy, probability and dynamics},
  year      = {2008},
  pages     = {0807.1268v2},
  file      = {:by-author/C/Cohen/2008_Cohen_0807.1268v2.pdf:PDF},
  keywords  = {Entropy; Statistical Mechanics},
  owner     = {saulius},
  timestamp = {2012.04.08},
  creationdate = {2012-04-08T00:00:00},
}

@Manuscript{Cohen2001,
  author    = {Julie E. Cohen and Mark A. Lemley},
  title     = {Patent scope and innovation in the software industry},
  year      = {2001},
  keywords  = {Patentai; Teise},
  file      = {:by-author/C/Cohen/2001_Cohen.doc:DOC},
  owner     = {saulius},
  timestamp = {2015.02.28},
  creationdate = {2015-02-28T00:00:00},
}

@Manuscript{Cohen1999,
  author    = {Larry Cohen},
  title     = {The patenting of software},
  year      = {1999},
  keywords  = {Patentai; Teise},
  file      = {:by-author/C/Cohen/1999_Cohen.doc:DOC},
  owner     = {saulius},
  timestamp = {2015.02.28},
  creationdate = {2015-02-28T00:00:00},
}

@Article{Cohen2004,
  author    = {Cohen, Serge X. and Morris, Richard J. and Fernandez, Francisco J. and Ben Jelloul, Marouane and Kakaris, Mattheos and Parthasarathy, Venkataraman and Lamzin, Victor S. and Kleywegt, Gerard J. and Perrakis, Anastassis},
  journal   = {Acta Crystallographica Section D},
  title     = {Towards complete validated models in the next generation of {\it ARP}/{\it wARP}},
  year      = {2004},
  pages     = {2222--2229},
  volume    = {60},
  doi       = {10.1107/S0907444904027556},
  file      = {ba5068.pdf:by-author/C/Cohen/2004_Cohen_2222.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444904027556},
}

@Article{Cohen-Karni2011,
  author    = {Cohen-Karni, Devora and Xu, Derrick and Apone, Lynne and Fomenkov, Alexey and Sun, Zhiyi and Davis, Paul J. and Morey Kinney, Shannon R. and Yamada-Mabuchi, Megumu and Xu, Shuang-yong and Devis, Theodore and Pradhan, Sriharsa and Roberts, Richard J. and Zheng, Yu},
  journal   = {PNAS},
  title     = {The MspJI family of modification-dependent restriction endonucleases for epigenetic studies},
  year      = {2011},
  pages     = {11040–11045},
  volume    = {108},
  abstract  = {MspJI is a novel modification-dependent restriction endonuclease that cleaves at a fixed distance away from the modification site. Here, we present the biochemical characterization of several MspJI homologs, including FspEI, LpnPI, AspBHI, RlaI, and SgrTI. All of the enzymes specifically recognize cytosine C5 modification (methylation or hydroxymethylation) in DNA and cleave at a constant distance (N12 ∕N16 ) away from the modified cytosine. Each displays its own sequence context preference, favoring different nucleotides flanking the modified cytosine. By cleaving on both sides of fully modified CpG sites, they allow the extraction of 32-base long fragments around the modified sites from the genomic DNA. These enzymes provide powerful tools for direct interrogation of the epigenome. For example, we show that RlaI, an enzyme that prefers m CWG but not m CpG sites, generates digestion patterns that differ between plant and mammalian genomic DNA, highlighting the difference between their epigenomic patterns. In addition, we demonstrate that deep sequencing of the digested DNA fragments generated from these enzymes provides a feasible method to map the modified sites in the genome. Altogether, the MspJI family of enzymes represent appealing tools of choice for method development in DNA epigenetic studies.},
  doi       = {10.1073/pnas.1018448108},
  file      = {:by-author/C/Cohen-Karni/2011_Cohen-Karni_11040.pdf:PDF},
  keywords  = {AspBHI; FspEI; LpnPI; Methyl-directed; Modification-dependent; MspJI; MspJI Family; REase; Restriction Endonuclease (RE); RlaI; SgrTI; TypeIV},
  owner     = {em},
  timestamp = {2013.10.29},
  creationdate = {2013-10-29T00:00:00},
}

@Article{CoimbatoreNarayanan2014,
  author    = {Coimbatore Narayanan, Buvaneswari and John Westbrook and Saheli Ghosh and Anton I. Petrov and Blake Sweeney and Craig L. Zirbel and Neocles B. Leontis and Helen M. Berman},
  journal   = {Nucleic Acids Res.},
  title     = {The Nucleic Acid Database: new features and capabilities},
  year      = {2014},
  pages     = {D114-D122},
  volume    = {42},
  doi       = {10.1093/nar/gkt980},
  file      = {2014_Narayanan_D114.pdf:by-author/N/Narayanan/2014_Narayanan_D114.pdf:PDF},
  groups    = {am/NDB},
  keywords  = {NDB; Nucleic Acids Database; Scientific Databases; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2015.05.13},
  creationdate = {2015-05-13T00:00:00},
}

@Article{Colandene1998,
  author    = {Colandene, J. D. and Topal, M. D.},
  journal   = {Proceedings of the National Academy of Sciences of the United States of America},
  title     = {The domain organization of NaeI endonuclease: separation of binding and catalysis.},
  year      = {1998},
  pages     = {3531--6},
  volume    = {95},
  abstract  = {NaeI is a remarkable type II restriction endonuclease. It must bind two recognition sequences to cleave DNA, forms a covalent protein-DNA intermediate, and is only 1 aa change away from topoisomerase and recombinase activity. The latter activities apparently derive from reactivation of a cryptic DNA ligase active site. Here, we demonstrate that NaeI has two protease-resistant domains, involving approximately the N-terminal and C-terminal halves of the protein, linked by a protease-accessible region of 30 aa. The domains were purified by cloning. The C-terminal domain was shown by gel mobility-shift assay to have approximately 8-fold lower DNA-binding ability than intact NaeI. Analytical ultracentrifugation showed this domain to be a monomer in solution. The N-terminal domain, which contains the catalytic region defined by random mutagenesis, did not bind DNA and was a mixture of different-sized complexes in solution implying that it mediates self-association. DNA greatly inhibited proteolysis of the linker region. The results identify the DNA-binding domain, imply that DNA cleavage and recognition are independent and separable, and lead us to speculate about a cleft-like structure for NaeI.},
  file      = {:by-author/C/Colandene/1998_Colandene_3531.pdf:PDF},
  keywords  = {TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Cole2016,
  author    = {Cole, Jason C. and Groom, Colin R. and Korb, Oliver and McCabe, Patrick and Shields, Gregory P.},
  journal   = {Journal of Chemical Information and Modeling},
  title     = {Knowledge-Based Optimization of Molecular Geometries Using Crystal Structures},
  year      = {2016},
  issn      = {1549-960X},
  month     = {Apr},
  number    = {4},
  pages     = {652–661},
  volume    = {56},
  doi       = {10.1021/acs.jcim.5b00712},
  file      = {2016_Cole_652.pdf:by-author/C/Cole/2016_Cole_652.pdf:PDF},
  groups    = {sg/Crystallography, am/Crystallography},
  owner     = {andrius},
  publisher = {American Chemical Society (ACS)},
  timestamp = {2016.12.29},
  creationdate = {2016-12-29T00:00:00},
  url       = {http://dx.doi.org/10.1021/acs.jcim.5b00712},
}

@Article{Coles2005,
  author    = {Coles, Simon J and Day, Nick E and Murray-Rust, Peter and Rzepa, Henry S and Zhang, Yong},
  journal   = {Organic \&amp; biomolecular chemistry},
  title     = {Enhancement of the chemical semantic web through the use of InChI identifiers.},
  year      = {2005},
  pages     = {1832--4},
  volume    = {3},
  doi       = {10.1039/B502828K},
  file      = {2005_Coles_1832.pdf:by-author/C/Coles/2005_Coles_1832.pdf:PDF},
  keywords  = {Chemoinformatics},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@TechReport{Collberg1997,
  author      = {Christian S. Collberg},
  institution = {Department of Computer Science, The University of Auckland, Private Bag 92019, Auckland, New Zealand},
  title       = {Reverse Interpretation + Mutation Analysis = Automatic Retargeting},
  year        = {1997},
  abstract    = {There are three popular methods for constructing highly retargetable compilers: (1) the compiler emits abstract ma- chine code which is interpreted at run-time, (2) the compiler emits C code which is subsequently compiled to machine code by the native C compiler, or (3) the compiler's code- generator is generated by a back-end generator from a formal machine description produced by the compiler writer. These methods incur high costs at run-time, compile- time, or compiler-construction time, respectively. In this paper we will describe a novel method which promises to signi cantly reduce the e ort required to retar- get a compiler to a new architecture, while at the same time producing fast and e ective compilers. The basic idea is to use the native C compiler at compiler construction time to discover architectural features of the new architecture. From this information a formal machine description is produced. Given this machine description, a native code-generator can be generated by a back-end generator such as BEG or burg.},
  file        = {:by-author/C/Collberg/1997_Collberg.ps.gz:PostScript;:by-author/C/Collberg/1997_Collberg.pdf:PDF},
  owner       = {saulius},
  timestamp = {2015.02.27},
  creationdate = {2015-02-27T00:00:00},
}

@Book{Collins-Sussman2011,
  author    = {Ben Collins-Sussman and Brian W. Fitzpatrick and C. Michael Pilato},
  title     = {Version Control with Subversion},
  year      = {2011},
  file      = {2011_Collins-Sussman.pdf:by-author/C/Collins-Sussman/2011_Collins-Sussman.pdf:PDF},
  keywords  = {Computer Science (CS); Software Development; Subversion; Version Control},
  owner     = {saulius},
  timestamp = {2016.11.06},
  creationdate = {2016-11-06T00:00:00},
  url       = {http://svnbook.red-bean.com/},
}

@Article{Collman2006,
  author    = {James P. Collman and Neal K. Devaraj and Todd P. A. Eberspacher and Christopher E. D. Chidsey},
  journal   = {Langmuir},
  title     = {Mixed Azide-Terminated Monolayers: A Platform for Modifying Electrode Surfaces},
  year      = {2006},
  pages     = {2457--2464},
  abstract  = {We have prepared and characterized mixed self-assembled-monolayers (SAM) on gold electrodes from azido alkane thiols and various ω-functionalized alkane thiols. In the presence of copper(I) catalysts these azide-modified surfaces are shown to react rapidly and quantitatively with terminal acetylenes forming 1,2,3-triazoles, via “click” chemistry. The initial azide substituents can be identified and monitored using both grazing-angle infrared (IR) and X-ray photoelectron spectrosopies. Acetylenes possessing redox-active ferrocene substituents react with the azide-terminated mixed SAMs and electrochemical measurements of the ferrocene-modified SAM electrodes have been used to quantify the redox centers attached to these platforms. Time-resolved electrochemical measurements have enabled us to follow the formation of these ferrocene centers and thus to measure the rate of the surface “click” reaction. Under optimal conditions this well-behaved second-order reaction takes place with a rate constant of 1×10 3 M -1 sec -1 . Typical reaction times of several minutes were realized using micromolar concentrations of acetylene. These techniques have been used to construct well-characterized, covalently-modified monolayers that can be employed as functional electrode surfaces.},
  doi       = {10.1021/la052947},
  file      = {:by-author/C/Collman/2006_Collman_2457.war:WAR},
  keywords  = {Azide; Click Chemistry; Click-chemistry; Kinetics; Self-Assembled Monolayers; Surface Reaction},
  owner     = {saulius},
  timestamp = {2015.03.02},
  creationdate = {2015-03-02T00:00:00},
}

@Article{Colmenarejo2003,
  author    = {Colmenarejo, Gonzalo},
  journal   = {Medicinal research reviews},
  title     = {In silico prediction of drug-binding strengths to human serum albumin.},
  year      = {2003},
  pages     = {275--301},
  volume    = {23},
  abstract  = {Drug binding to Human Serum Albumin (HSA) is an area of intense research. The pharmacokinetics and pharmacodynamics of drugs are strongly affected by their binding to this protein. In this article, the field is reviewed, as well as our models to predict drug-binding affinities to HSA from drug structure. The physiological role of HSA is described, as well as its influence in drug action. The crystal structures of this protein are discussed, emphasizing the two drug-binding sites and the fatty acids binding sites observed therein. The advantages of using high-performance affinity chromatography to rapidly screen drugs for HSA binding are explained. The different QSAR models for HSA binding of restricted families of drugs (both from other groups and our group) are enumerated. Finally, a detailed description of our general models to predict drug-binding strengths to HSA from structure is given. It is expected for these models to be useful in drug design and pharmaceutical research.},
  file      = {:by-author/C/Colmenarejo/2003_Colmenarejo_275.pdf:PDF},
  keywords  = {Drug Design},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Colon2014,
  author    = {Colon, Yamil J. and Snurr, Randall Q.},
  journal   = {Chem. Soc. Rev.},
  title     = {High-throughput computational screening of metal-organic frameworks},
  year      = {2014},
  pages     = {5735--5749},
  volume    = {43},
  abstract  = {There is an almost unlimited number of metal-organic frameworks (MOFs). This creates exciting opportunities but also poses a problem: how do we quickly find the best MOFs for a given application? Molecular simulations have advanced sufficiently that many MOF properties - especially structural and gas adsorption properties - can be predicted computationally{,} and molecular modeling techniques are now used increasingly to guide the synthesis of new MOFs. With increasing computational power and improved simulation algorithms{,} it has become possible to conduct high-throughput computational screening to identify promising MOF structures and uncover structure-property relations. We review these efforts and discuss future directions in this new field.},
  doi       = {10.1039/C4CS00070F},
  file      = {2014_Colon_5735.pdf:by-author/C/Colon/2014_Colon_5735.pdf:PDF},
  groups    = {sg/MOF, sg/MOFs, am/MOFs},
  issue     = {16},
  keywords  = {Metal-Organic Frameworks (MOF)},
  owner     = {saulius},
  publisher = {The Royal Society of Chemistry},
  timestamp = {2017.02.10},
  creationdate = {2017-02-10T00:00:00},
  url       = {http://dx.doi.org/10.1039/C4CS00070F},
}

@Article{Colonnese2011,
  author    = {Stefania Colonnese and Stefano Rinauro and Gaetano Scarano},
  journal   = {IEEE Signal Processing Letters},
  title     = {Fast Maximum Likelihood Scale Parameter Estimation From Histogram Measurements},
  year      = {2011},
  pages     = {474--477},
  volume    = {18},
  abstract  = {In this letter, we address the problem of estimating a parameter acting as a scale factor on the observations probability density function (pdf), i.e. a scale parameter. Histogram based Max- imum Likelihood (ML) estimation of a scale parameter requires the evaluation of a discrete scale correlation. We show how ML estima- tion can be implemented by means of a computationally efficient Discrete Fourier Transform based procedure, when geometric his- togram sampling is adopted. As a case study, we analyze a gain esti- mator for general QAM constellations. Simulation results and theo- retical performance analysis show that the presented ML estimator outperforms selected state of the art estimators, approaching the Cramér–Rao Lower Bound (CRLB) for a wide range of SNR.},
  file      = {:by-author/C/Colonnese/2011_Colonnese_474.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.09.18},
  creationdate = {2012-09-18T00:00:00},
}

@Article{Colquhoun2014,
  author    = {Colquhoun, D.},
  journal   = {Royal Society Open Science},
  title     = {An investigation of the false discovery rate and the misinterpretation of p-values},
  year      = {2014},
  issn      = {2054-5703},
  month     = {Nov},
  number    = {3},
  pages     = {140216},
  volume    = {1},
  abstract  = {If you use p=0.05 to suggest that you have made a discovery, you will be wrong at least 30% of the time. If, as is often the case, experiments are underpowered, you will be wrong most of the time. This conclusion is demonstrated from several points of view. First, tree diagrams which show the close analogy with the screening test problem. Similar conclusions are drawn by repeated simulations of t-tests. These mimic what is done in real life, which makes the results more persuasive. The simulation method is used also to evaluate the extent to which effect sizes are over-estimated, especially in underpowered experiments. A script is supplied to allow the reader to do simulations themselves, with numbers appropriate for their own work. It is concluded that if you wish to keep your false discovery rate below 5%, you need to use a three-sigma rule, or to insist on p≤0.001. And never use the word ‘significant’.},
  doi       = {10.1098/rsos.140216},
  file      = {2014_Colquhoun_140216.pdf:by-author/C/Colquhoun/2014_Colquhoun_140216.pdf:PDF},
  groups    = {sg/Bayesian, sg/Clinical Trials, sg/Non-reproducibility, sg/R Uses},
  keywords  = {Bayesian Statistics; Criticism; P-values; Statistics},
  owner     = {saulius},
  publisher = {The Royal Society},
  timestamp = {2016.10.24},
  creationdate = {2016-10-24T00:00:00},
  url       = {http://dx.doi.org/10.1098/rsos.140216},
}

@Article{Colquhoun2007,
  author    = {David Colquhoun},
  journal   = {Physiology News},
  title     = {How to get good science},
  year      = {2007},
  pages     = {12--14},
  volume    = {69},
  file      = {Colquhoun.qxp - colquhoun-goodscience-jp-version-2007.pdf:by-author/C/Colquhoun/2007_Colquhoun_12.pdf:application/pdf},
  groups    = {sg/Bibliometrics},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://dcscience.net/colquhoun-goodscience-jp-version-2007.pdf},
  urldate   = {2015-07-06},
}

@Manuscript{Colquhoun2007a,
  author    = {David Colquhoun},
  title     = {How to get good science},
  year      = {2007},
  url       = {http://www.dcscience.net/goodscience.pdf},
  file      = {goodscience.pdf:by-author/C/Colquhoun/2007_Colquhoun.pdf:application/pdf},
  groups    = {sg/Bibliometrics},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  urldate   = {2015-07-06},
}

@Periodical{IUCrComputingCommission2008,
  title     = {Commission on Crystallographic Computing Newsletter},
  year      = {2008},
  editor    = {Lachlan Cranswick},
  month     = {October},
  number    = {9},
  author    = {IUCr Computing Commission},
  file      = {:by-author/I/IUCr-Computing-Commission/2008_IUCr-Computing-Commission.pdf:PDF},
  keywords  = {IUCr Computing Commission; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@InCollection{Connolly2007,
  author    = {Bernard A. Connolly and Hsiao-Hui Liu and Damian Parry and Lisa E. Engler and Michael R. Kurpiewski and Linda Jen-Jacobson},
  booktitle = {DNA–Protein Interactions: Principles and Protocols},
  publisher = {Humana Press Inc., Totowa, NJ},
  title     = {Assay of Restriction Endonucleases Using Oligonucleotides},
  year      = {2007},
  editor    = {T. Moss},
  pages     = {465--86},
  series    = {Methods in Molecular Biology},
  volume    = {148},
  abstract  = {This review covers the isolation and structure determination of triterpenoids including squalene derivatives, lanostanes, cycloartanes, dammaranes, euphanes, tirucallanes, tetranortriterpenoids, quassinoids, lupanes, oleananes, friedelanes, uranes, hopanes, isomalabaricanes and saponins. The literature from January to December 2004 is reviewed and 243 references are cited.},
  file      = {:by-author/C/Connolly/2007_Connolly_465.pdf:PDF},
  journal   = {Methods in Molecular Biology},
  keywords  = {TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@InBook{Connolly1997,
  author    = {Bernard~A. Connolly and Hsiao-Hui Liu and Damian Parry and Lisa~E. Engler and Michael~R. Kurpiewski and Linda Jen-Jacobson},
  chapter   = {Assay of Restriction Endonucleases Using Oligonucleotides},
  editor    = {T. Moss},
  pages     = {465--490},
  publisher = {Humana Press},
  title     = {DNA–Protein Interactions: Principles and Protocols},
  year      = {1997},
  series    = {Methods in Molecular Biology},
  volume    = {148},
  booktitle = {Methods in Molecular Biology},
  file      = {:by-author/C/Connolly/1997_Connolly_465.pdf:PDF},
  owner     = {em},
  timestamp = {2013.09.19},
  creationdate = {2013-09-19T00:00:00},
}

@Article{Connolly1985,
  author    = {Michael L. Connolly},
  journal   = {Journal of Molecular Graphics},
  title     = {Depth-buffer algorithms for molecular modelling},
  year      = {1985},
  issn      = {0263-7855},
  pages     = {19 - 24},
  volume    = {3},
  abstract  = {Methods for drawing sophisticated pictures of molecules on colour-raster graphics terminals are presented. These methods utilize depth buffers, which store, for each pixel, not only a colour and a shade, but also a z coordinate or depth. Depth buffers make it convenient to combine several different molecular representations into a single picture. The algorithms can produce cutaway views of protein interiors, cross-sections of proteinprotein interfaces, and translucent solvent-accessible surfaces through which the chemical structure may be seen.},
  doi       = {10.1016/0263-7855(85)80009-6},
  file      = {1985_Connolly_19.pdf:by-author/C/Connolly/1985_Connolly_19.pdf:PDF},
  keywords  = {Algorithms; Computer Graphics; Molecular Graphics; Raster Graphics; Z-buffer},
  owner     = {saulius},
  timestamp = {2014.01.26},
  creationdate = {2014-01-26T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/0263785585800096},
}

@Manuscript{Conrad2005,
  author    = {Brian Conrad},
  title     = {Stokes' Theorem on Riemannian manifolds (or Div, Grad, Curl, and all that)},
  year      = {2005},
  keywords  = {Differential Geometry; Field Theory; Mathematics; Riemannian Manifolds},
  url       = {http://math.stanford.edu/~conrad/diffgeomPage/handouts/stokesthm.pdf},
  file      = {2005_Conrad.pdf:by-author/C/Conrad/2005_Conrad.pdf:PDF},
  groups    = {sg/Field theory, sg/Riemann geometry},
  owner     = {saulius},
  timestamp = {2016.06.02},
  creationdate = {2016-06-02T00:00:00},
}

@Manual{Conroy1999,
  title     = {Sirius reference manual},
  author    = {Alan Conroy and Conroy},
  year      = {1999},
  file      = {:by-author/C/Conroy/1999_Conroy.txt:Text},
  keywords  = {Bytecode Interpreters; Computer Science (CS); Sirius; Virtual Machines},
  owner     = {saulius},
  timestamp = {2015.03.10},
  creationdate = {2015-03-10T00:00:00},
  url       = {http://siriuspl.sourceforge.net/},
}

@Manual{Conroy1999a,
  title     = {Sirius virtual machine internals manual},
  author    = {Alan Conroy and Conroy},
  year      = {1999},
  file      = {:by-author/C/Conroy/1999_Conroy_a.txt:Text},
  keywords  = {Bytecode Interpreters; Computer Science (CS); Sirius; Virtual Machines},
  owner     = {saulius},
  timestamp = {2015.03.10},
  creationdate = {2015-03-10T00:00:00},
  url       = {http://siriuspl.sourceforge.net/internals.txt},
}

@InProceedings{Consel1990,
  author    = {Charles Consel},
  booktitle = {LFP '90 Proceedings of the 1990 ACM conference on LISP and functional programming},
  title     = {Binding time analysis for high order untyped functional languages},
  year      = {1990},
  pages     = {264--272},
  abstract  = {When some inputs of a program are known at compile-time, certain expressions can be processed statically; this is the basis of the notion of partial evaluation. Identifying these early computations can be determined independently of the actual values of the input by a static analysis called binding time analysis. Then, to process a program, one simply follows the binding time information: evaluate compile-time expressions and defer the others to run-time. Using abstract interpretation, we present a binding time analysis for an untyped functional language which provides an effective treatment of both higher order functions and data structures. To our knowledge it is the first such analysis. It has been implemented and is used in a partial evaluator for a side-effect free dialect of Scheme. The analysis is general enough, however, to be valid for non-strict typed functional languages such as Haskell. Our approach and the system we have developed solve and go beyond the open problem of partially evaluating higher order functions described in [3] since we also provide a method to handle data structures. Our analysis improves on previous work [5, 15, 4] in that: (1) it treats both higher order functions and data structures, (2) it does not impose syntactic restrictions on the program being processed, and (3) it does not require a preliminary phase to collect the set of possible functions that may occur at each site of application.},
  file      = {1990_Consel_264.pdf:by-author/C/Consel/1990_Consel_264.pdf:PDF},
  keywords  = {Computer Science (CS); Type Systems},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{TheUniProtConsortium2015,
  author    = {The UniProt Consortium},
  journal   = {Nucleic Acids Research},
  title     = {UniProt: a hub for protein information},
  year      = {2015},
  number    = {D1},
  pages     = {D204-D212},
  volume    = {43},
  abstract  = {UniProt is an important collection of protein sequences and their annotations, which has doubled in size to 80 million sequences during the past year. This growth in sequences has prompted an extension of UniProt accession number space from 6 to 10 characters. An increasing fraction of new sequences are identical to a sequence that already exists in the database with the majority of sequences coming from genome sequencing projects. We have created a new proteome identifier that uniquely identifies a particular assembly of a species and strain or subspecies to help users track the provenance of sequences. We present a new website that has been designed using a user-experience design process. We have introduced an annotation score for all entries in UniProt to represent the relative amount of knowledge known about each protein. These scores will be helpful in identifying which proteins are the best characterized and most informative for comparative analysis. All UniProt data is provided freely and is available on the web at http://www.uniprot.org/.},
  doi       = {10.1093/nar/gku989},
  eprint    = {http://nar.oxfordjournals.org/content/43/D1/D204.full.pdf+html},
  file      = {:by-author/U/UniProt/2015_TheUniProtConsortium_D204.pdf:PDF},
  keywords  = {Databases; Genomes; Protein Sequences; SwissProt; UNiProt},
  owner     = {saulius},
  timestamp = {2016.05.29},
  creationdate = {2016-05-29T00:00:00},
  url       = {http://nar.oxfordjournals.org/content/43/D1/D204.abstract},
}

@Article{Constantinopoulos2006,
  author    = {Constantinopoulos, C. and Titsias, M. K. and Likas, A.},
  journal   = {IEEE Trans. Pattern Anal. Machine Intell.},
  title     = {Bayesian feature and model selection for {Gaussian} mixture models},
  year      = {2006},
  issn      = {0162-8828},
  month     = {Jun},
  number    = {6},
  pages     = {1013--1018},
  volume    = {28},
  abstract  = {We present a Bayesian method for mixture model training that simultaneously treats the feature selection and the model selection problem. The method is based on the integration of a mixture model formulation that takes into account the saliency of the features and a Bayesian approach to mixture learning that can be used to estimate the number of mixture components. The proposed learning algorithm follows the variational framework and can simultaneously optimize over the number of components, the saliency of the features, and the parameters of the mixture model. Experimental results using high-dimensional artificial and real data illustrate the effectiveness of the method.},
  doi       = {10.1109/tpami.2006.111},
  file      = {:by-author/C/Constantinopoulos/2006_Constantinopoulos_1013.pdf:PDF},
  groups    = {am/Gaussian},
  owner     = {andrius},
  publisher = {Institute of Electrical \& Electronics Engineers (IEEE)},
  timestamp = {2016.03.21},
  creationdate = {2016-03-21T00:00:00},
  url       = {http://www.aueb.gr/users/mtitsias/papers/TPAMI06.pdf},
}

@Article{LoConte2002,
  author    = {Loredana Lo Conte and Steven E. Brenner and Tim J. P. Hubbard and Cyrus Chothia and Alexey G. Murzin},
  journal   = {Nucleic Acids Research},
  title     = {SCOP database in 2002: refinements accommodate structural genomics},
  year      = {2002},
  pages     = {264--267},
  volume    = {30},
  abstract  = {The SCOP (Structural Classification of Proteins) database is a comprehensive ordering of all proteins of known structure, according to their evolutionary and structural relationships. Protein domains in SCOP are grouped into species and hierarchically classified into families, superfamilies, folds and classes. Recently, we introduced a new set of features with the aim of standardizing access to the database, and providing a solid basis to manage the increasing number of experimental structures expected from structural genomics projects. These features include: a new set of identifiers, which uniquely identify each entry in the hierarchy; a compact repre- sentation of protein domain classification; a new set of parseable files, which fully describe all domains in SCOP and the hierarchy itself. These new features are reflected in the ASTRAL compendium. The SCOP search engine has also been updated, and a set of links to external resources added at the level of domain entries. SCOP can be accessed at http:// scop.mrc-lmb.cam.ac.uk/scop.},
  file      = {LoConte_2002_264-SCOP_2002.pdf:by-author/L/LoConte/2002_LoConte_264.pdf:PDF},
  keywords  = {Bioinformatics; Classification; Protein Folds; SCOP},
  owner     = {saulius},
  timestamp = {2012.11.20},
  creationdate = {2012-11-20T00:00:00},
}

@InProceedings{Cook1971,
  author    = {Stephen A. Cook},
  booktitle = {Proceedings of the third annual ACM symposium on Theory of computing},
  title     = {The Complexity of Theorem-Proving Procedures},
  year      = {1971},
  address   = {New York, NY, USA},
  pages     = {151--158},
  publisher = {ACM},
  series    = {STOC '71},
  acmid     = {805047},
  doi       = {10.1145/800157.805047},
  file      = {:by-author/C/Cook/1971_Cook_151.pdf:PDF},
  location  = {Shaker Heights, Ohio, USA},
  numpages  = {8},
  owner     = {andrius},
  timestamp = {2013.05.06},
  creationdate = {2013-05-06T00:00:00},
  url       = {http://doi.acm.org/10.1145/800157.805047},
}

@Article{Cooper2007,
  author    = {Cooper, David R. and Boczek, Tomasz and Grelewska, Katarzyna and Pinkowska, Malgorzata and Sikorska, Malgorzata and Zawadzki, Michal and Derewenda, Zygmunt},
  journal   = {Acta crystallographica. Section D, Biological crystallography},
  title     = {Protein crystallization by surface entropy reduction: optimization of the SER strategy.},
  year      = {2007},
  pages     = {636--45},
  volume    = {63},
  abstract  = {A strategy of rationally engineering protein surfaces with the aim of obtaining mutants that are distinctly more susceptible to crystallization than the wild-type protein has previously been suggested. The strategy relies on replacing small clusters of two to three surface residues characterized by high conformational entropy with alanines. This surface entropy reduction (or SER) method has proven to be an effective salvage pathway for proteins that are difficult to crystallize. Here, a systematic comparison of the efficacy of using Ala, His, Ser, Thr and Tyr to replace high-entropy residues is reported. A total of 40 mutants were generated and screened using two different procedures. The results reaffirm that alanine is a particularly good choice for a replacement residue and identify tyrosines and threonines as additional candidates that have considerable potential to mediate crystal contacts. The propensity of these mutants to form crystals in alternative screens in which the normal crystallization reservoir solutions were replaced with 1.5 M NaCl was also examined. The results were impressive: more than half of the mutants yielded a larger number of crystals with salt as the reservoir solution. This method greatly increased the variety of conditions that yielded crystals. Taken together, these results suggest a powerful crystallization strategy that combines surface engineering with efficient screening using standard and alternate reservoir solutions.},
  doi       = {10.1107/S0907444907010931},
  file      = {:by-author/C/Cooper/2007_Cooper_636.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Cooper2007a,
  author      = {David R Cooper and Tomasz Boczek and Katarzyna Grelewska and Malgorzata Pinkowska and Malgorzata Sikorska and Michal Zawadzki and Zygmunt Derewenda},
  journal     = {Acta Crystallogr D Biol Crystallogr},
  title       = {Protein crystallization by surface entropy reduction: optimization of the SER strategy.},
  year        = {2007},
  month       = {May},
  number      = {Pt 5},
  pages       = {636--645},
  volume      = {63},
  abstract    = {A strategy of rationally engineering protein surfaces with the aim of obtaining mutants that are distinctly more susceptible to crystallization than the wild-type protein has previously been suggested. The strategy relies on replacing small clusters of two to three surface residues characterized by high conformational entropy with alanines. This surface entropy reduction (or SER) method has proven to be an effective salvage pathway for proteins that are difficult to crystallize. Here, a systematic comparison of the efficacy of using Ala, His, Ser, Thr and Tyr to replace high-entropy residues is reported. A total of 40 mutants were generated and screened using two different procedures. The results reaffirm that alanine is a particularly good choice for a replacement residue and identify tyrosines and threonines as additional candidates that have considerable potential to mediate crystal contacts. The propensity of these mutants to form crystals in alternative screens in which the normal crystallization reservoir solutions were replaced with 1.5 M NaCl was also examined. The results were impressive: more than half of the mutants yielded a larger number of crystals with salt as the reservoir solution. This method greatly increased the variety of conditions that yielded crystals. Taken together, these results suggest a powerful crystallization strategy that combines surface engineering with efficient screening using standard and alternate reservoir solutions.},
  doi         = {10.1107/S0907444907010931},
  file        = {:by-author/C/Cooper/2007_Cooper_636.pdf:PDF},
  institution = {Department of Molecular Physiology and Biological Physics and Integrated Center for Structure-Function Innovation, University of Virginia, Charlottesville, Virginia 22908-0736, USA.},
  keywords    = {Chemistry; Crystallization; Mutagenesis; Proteins; Surface Properties},
  language    = {eng},
  medline-pst = {ppublish},
  owner       = {em},
  pii         = {S0907444907010931},
  pmid        = {17452789},
  timestamp = {2016.06.09},
  creationdate = {2016-06-09T00:00:00},
  url         = {http://dx.doi.org/10.1107/S0907444907010931},
}

@Article{Copeland1999,
  author    = {Copeland},
  title     = {Super {T}uring-Machines},
  year      = {1999},
  pages     = {preprint},
  file      = {:by-author/C/Copeland/1999_Copeland_preprint.pdf:PDF},
  keywords  = {Computer Science (CS); Super Turing Computations},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Copley2007,
  author    = {Shelley D. Copley and Eric Smith and Harold J. Morowitz},
  journal   = {Bioorganic Chemistry},
  title     = {The origin of the {RNA} world: Co-evolution of genes and metabolism},
  year      = {2007},
  issn      = {0045-2068},
  pages     = {430--443},
  volume    = {35},
  abstract  = {Discoveries demonstrating that \{RNA\} can serve genetic, catalytic, structural, and regulatory roles have provided strong support for the existence of an \{RNA\} World that preceded the origin of life as we know it. Despite the appeal of this idea, it has been difficult to explain how macromolecular \{RNAs\} emerged from small molecules available on the early Earth. We propose here a mechanism by which mutual catalysis in a pre-biotic network initiated a progression of stages characterized by ever larger and more effective catalysts supporting a proto-metabolic network, and the emergence of \{RNA\} as the dominant macromolecule due to its ability to both catalyze chemical reactions and to be copied in a template-directed manner. This model suggests that many features of modern life, including the biosynthetic pathways leading to simple metabolites, the structures of organic and metal ion cofactors, homochirality, and template-directed replication of nucleic acids, arose long before the \{RNA\} World and were retained as pre-biotic systems became more sophisticated.},
  doi       = {10.1016/j.bioorg.2007.08.001},
  file      = {2007_Copley_430.pdf:by-author/C/Copley/2007_Copley_430.pdf:PDF},
  keywords  = {Origins of Life; RNA World},
  owner     = {saulius},
  timestamp = {2013.09.27},
  creationdate = {2013-09-27T00:00:00},
  url       = {http://tuvalu.santafe.edu/~desmith/PDF_pubs/Copley_BOG.pdf},
}

@TechReport{Corden2010,
  author      = {Martyn J. Corden and David Kreitzer},
  institution = {Software Solutions Group, Intel Corporation},
  title       = {Consistency of Floating-Point Results using the Intel® Compiler or Why doesn’t my application always give the same answer?},
  year        = {2010},
  file        = {:by-author/C/Corden/2010_Corden.pdf:PDF},
  keywords    = {Computer Science (CS); Floating Point Arithmetics},
  owner       = {saulius},
  timestamp = {2012.09.26},
  creationdate = {2012-09-26T00:00:00},
}

@Article{Cordero2008,
  author    = {Beatriz Cordero and Verónica Gómez and Ana E. Platero-Prats and Marc Revés and Jorge Echeverría and Eduard Cremades and Flavia Barragán and Santiago Alvarez},
  journal   = {Dalton Transactions},
  title     = {Covalent radii revisited},
  year      = {2008},
  pages     = {2832--2838},
  abstract  = {A new set of covalent atomic radii has been deduced from crystallographic data for most of the elements with atomic numbers up to 96. The proposed radii show a well behaved periodic dependence that allows us to interpolate a few radii for elements for which structural data is lacking, notably the noble gases. The proposed set of radii therefore fills most of the gaps and solves some inconsistencies in currently used covalent radii. The transition metal and lanthanide contractions as well as the differences in covalent atomic radii between low spin and high spin configurations in transition metals are illustrated by the proposed radii set.},
  doi       = {10.1039/b801115j},
  file      = {:by-author/C/Cordero/2008_Cordero_2832.pdf:PDF},
  owner     = {andrius},
  timestamp = {2013.04.17},
  creationdate = {2013-04-17T00:00:00},
  url       = {http://pubs.rsc.org/en/Content/ArticleLanding/2008/DT/b801115j#!divAbstract},
}

@Article{Corn2006,
  author    = {Corn, Jacob E. and Berger, James M.},
  journal   = {Nucleic acids research},
  title     = {Regulation of bacterial priming and daughter strand synthesis through helicase-primase interactions.},
  year      = {2006},
  pages     = {4082--8},
  volume    = {34},
  abstract  = {The replisome is a multi-component molecular machine responsible for rapidly and accurately copying the genome of an organism. A central member of the bacterial replisome is DnaB, the replicative helicase, which separates the parental duplex to provide templates for newly synthesized daughter strands. A unique RNA polymerase, the DnaG primase, associates with DnaB to repeatedly initiate thousands of Okazaki fragments per replication cycle on the lagging strand. A number of studies have shown that the stability and frequency of the interaction between DnaG and DnaB determines Okazaki fragment length. More recent work indicates that each DnaB hexamer associates with multiple DnaG molecules and that these primases can coordinate with one another to regulate their activities at a replication fork. Together, disparate lines of evidence are beginning to suggest that Okazaki fragment initiation may be controlled in part by crosstalk between multiple primases bound to the helicase.},
  file      = {:by-author/C/Corn/2006_Corn_4082.pdf:PDF},
  keywords  = {{gp41} Helicase},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Corn2005,
  author    = {Corn, Jacob E. and Pease, Paul J. and Hura, Greg L. and Berger, James M.},
  journal   = {Molecular cell},
  title     = {Crosstalk between primase subunits can act to regulate primer synthesis in trans.},
  year      = {2005},
  pages     = {391--401},
  volume    = {20},
  abstract  = {The coordination of primase function within the replisome is an essential but poorly understood feature of lagging strand synthesis. By using crystallography and small-angle X-ray scattering (SAXS), we show that functional elements of bacterial primase transition between two dominant conformations: an extended form that uncouples a regulatory domain from its associated RNA polymerase core and a compact state that sequesters the regulatory region from the site of primer synthesis. FRET studies and priming assays reveal that the regulatory domain of one primase subunit productively associates with nucleic acid that is bound to the polymerase domain of a second protomer in trans. This intersubunit interaction allows primase to select initiation sites on template DNA and implicates the regulatory domain as a "molecular brake" that restricts primer length. Our data suggest that the replisome may cooperatively use multiple primases and this conformational switch to control initiation frequency, processivity, and ultimately, Okazaki fragment synthesis.},
  file      = {:by-author/C/Corn/2005_Corn_391.pdf:PDF},
  keywords  = {{gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Cortecchia2016,
  author    = {Daniele Cortecchia and Cesare Soci and Massimo Cametti and Annamaria Petrozza and Javier Mart{\'{\i}}-Rujas},
  journal   = {{ChemPlusChem}},
  title     = {Crystal Engineering of a Two-Dimensional Lead-Free Perovskite with Functional Organic Cations by Second-Sphere Coordination},
  year      = {2016},
  month     = {nov},
  doi       = {10.1002/cplu.201600477},
  file      = {:by-author/C/Cortecchia/2016_Cortecchia_a.pdf:PDF;Cortecchia2016.pdf:by-author/C/Cortecchia/2016_Cortecchia.pdf:PDF},
  groups    = {sg/MOF, sg/MOFs, am/MOFs},
  owner     = {saulius},
  publisher = {Wiley-Blackwell},
  timestamp = {2017.01.31},
  creationdate = {2017-01-31T00:00:00},
  url       = {https://doi.org/10.1002%2Fcplu.201600477},
}

@Manuscript{Costa2008,
  author    = {Costa},
  title     = {Characterization of Complex Networks: A Survey of Measurements},
  year      = {2008},
  keywords  = {Algorithms},
  abstract  = {Each complex network (or class of networks) presents specific topologi- cal features which characterize its connectivity and highly influence the dy- namics of processes executed on the network. The analysis, discrimination, and synthesis of complex networks therefore rely on the use of measurements capable of expressing the most relevant topological features. This article presents a survey of such measurements. It includes general considerations about complex network characterization, a brief review of the principal mod- els, and the presentation of the main existing measurements. Important re- lated issues covered in this work comprise the representation of the evolution of complex networks in terms of trajectories in several measurement spaces, the analysis of the correlations between some of the most traditional mea- surements, perturbation analysis, as well as the use of multivariate statistics for feature selection and network classification. Depending on the network and the analysis task one has in mind, a specific set of features may be cho- sen. It is hoped that the present survey will help the proper application and interpretation of measurements.},
  file      = {:by-author/C/Costa/2008_Costa_1.pdf:PDF},
  owner     = {andrius},
  pages     = {1},
  timestamp = {2012.05.07},
  creationdate = {2012-05-07T00:00:00},
}

@Article{Costa2008a,
  author    = {Costa, Alessandro and van Duinen, Gijs and Medagli, Barbara and Chong, James and Sakakibara, Nozomi and Kelman, Zvi and Nair, Satish K. and Patwardhan, Ardan and Onesti, Silvia},
  journal   = {The EMBO journal},
  title     = {Cryo-electron microscopy reveals a novel DNA-binding site on the MCM helicase.},
  year      = {2008},
  pages     = {2250--8},
  volume    = {27},
  abstract  = {The eukaryotic MCM2-7 complex is recruited at origins of replication during the G1 phase and acts as the main helicase at the replication fork during the S phase of the cell cycle. To characterize the interplay between the MCM helicase and DNA prior to the melting of the double helix, we determined the structure of an archaeal MCM orthologue bound to a 5.6-kb double-stranded DNA segment, using cryo-electron microscopy. DNA wraps around the N-terminal face of a single hexameric ring. This interaction requires a conformational change within the outer belt of the MCM N-terminal domain, exposing a previously unrecognized helix-turn-helix DNA-binding motif. Our findings provide novel insights into the role of the MCM complex during the initiation step of DNA replication.},
  file      = {:by-author/C/Costa/2008_Costa_2250.pdf:PDF},
  keywords  = {CryoEM},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@Manuscript{Cottenier2010,
  author    = {Cottenier},
  title     = {Computational materials science for the next generations: addressing the Inverse Problem by a computed property database},
  year      = {2010},
  keywords  = {Manuscripts},
  file      = {:by-author/C/Cottenier/2010_Cottenier_manuscript.pdf:PDF},
  owner     = {saulius},
  pages     = {manuscript},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Presentation{Cottenier2015,
  author       = {Stefaan Cottenier},
  title        = {Bringing {DFT} codes back to the test bench: what did we learn?},
  year         = {2015},
  conference   = {CECAM},
  organization = {EPFL},
  file         = {2015_Cottenier_handouts.pdf:by-author/C/Cottenier/2015_Cottenier_handouts.pdf:PDF},
  keywords     = {Accuracy; Density Functional Theory (DFT); Precision; TCOD; Theoretical Calculations; Validation},
  owner        = {saulius},
  timestamp = {2015.06.15},
  creationdate = {2015-06-15T00:00:00},
}

@Presentation{Coudert2010,
  author    = {François-Xavier Coudert},
  title     = {DFT with plane waves, pseudopotentials},
  year      = {2010},
  file      = {:by-author/C/Coudert/2010_Coudert.pdf:PDF},
  keywords  = {Density Functional Theory (DFT)},
  owner     = {saulius},
  timestamp = {2014.11.06},
  creationdate = {2014-11-06T00:00:00},
  url       = {http://www.phenix.cnrs.fr/IMG/pdf/dft-pw.pdf},
}

@Article{Coudert2016,
  author    = {Coudert, François-Xavier and Fuchs, Alain H.},
  journal   = {Coordination Chemistry Reviews},
  title     = {Computational characterization and prediction of metal–organic framework properties},
  year      = {2016},
  issn      = {0010-8545},
  month     = {Jan},
  pages     = {211–236},
  volume    = {307},
  abstract  = {In this introductory review, we give an overview of the computational chemistry methods commonly used in the field of metal–organic frameworks (MOFs), to describe or predict the structures themselves and characterize their various properties, either at the quantum chemical level or through classical molecular simulation. We discuss the methods for the prediction of crystal structures, geometrical properties and large-scale screening of hypothetical MOFs, as well as their thermal and mechanical properties. A separate section deals with the simulation of adsorption of fluids and fluid mixtures in MOFs.},
  doi       = {10.1016/j.ccr.2015.08.001},
  file      = {2016_Coudert_211.pdf:by-author/C/Coudert/2016_Coudert_211.pdf:PDF},
  groups    = {sg/MOFs, am/MOFs},
  owner     = {andrius},
  publisher = {Elsevier BV},
  timestamp = {2017.01.12},
  creationdate = {2017-01-12T00:00:00},
  url       = {http://dx.doi.org/10.1016/j.ccr.2015.08.001},
}

@Article{Coulibaly2007,
  author    = {Coulibaly, Fasséli and Chiu, Elaine and Ikeda, Keiko and Gutmann, Sascha and Haebel, Peter W. and Schulze-Briese, Clemens and Mori, Hajime and Metcalf, Peter},
  journal   = {Nature},
  title     = {The molecular organization of cypovirus polyhedra.},
  year      = {2007},
  pages     = {97--101},
  volume    = {446},
  abstract  = {Cypoviruses and baculoviruses are notoriously difficult to eradicate because the virus particles are embedded in micrometre-sized protein crystals called polyhedra. The remarkable stability of polyhedra means that, like bacterial spores, these insect viruses remain infectious for years in soil. The environmental persistence of polyhedra is the cause of significant losses in silkworm cocoon harvests but has also been exploited against pests in biological alternatives to chemical insecticides. Although polyhedra have been extensively characterized since the early 1900s, their atomic organization remains elusive. Here we describe the 2 A crystal structure of both recombinant and infectious silkworm cypovirus polyhedra determined using crystals 5-12 micrometres in diameter purified from insect cells. These are the smallest crystals yet used for de novo X-ray protein structure determination. We found that polyhedra are made of trimers of the viral polyhedrin protein and contain nucleotides. Although the shape of these building blocks is reminiscent of some capsid trimers, polyhedrin has a new fold and has evolved to assemble in vivo into three-dimensional cubic crystals rather than icosahedral shells. The polyhedrin trimers are extensively cross-linked in polyhedra by non-covalent interactions and pack with an exquisite molecular complementarity similar to that of antigen-antibody complexes. The resulting ultrastable and sealed crystals shield the virus particles from environmental damage. The structure suggests that polyhedra can serve as the basis for the development of robust and versatile nanoparticles for biotechnological applications such as microarrays and biopesticides.},
  file      = {:by-author/C/Coulibaly/2007_Coulibaly_97.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Manuscript{Courtney1995,
  author       = {Antony Courtney},
  title        = {Phantom: A Language Overview},
  year         = {1995},
  keywords     = {Computer Science (CS); Phantom; Programming Languages},
  month        = {May},
  organization = {Department of Computer Science, Trinity College Dublin},
  school       = {Trinity College Dublin},
  abstract     = {Phantom is a new interpreted language designed to address many of the prob- lems which arise when developing large-scale, interactive, distributed applications such as distributed conferencing systems, multi-player games or collaborative work tools. To meet the requirements of this application domain, Phantom combines the distributed lexical scoping semantics of Obliq with a substantial language core. The language is based on a safe, extended subset of Modula-3, and supports a num- ber of modern programming features, including: static structural-equivalence typ- ing, objects, interfaces, lightweight threads, exceptions, garbage collection, higher- order functions, lambda expressions, a keyword binding mechanism, dynamically sized lists, slice indexing notation, and type-safe implicit declarations. This paper presents an overview of each of the key features of the language core,},
  file         = {:by-author/C/Courtney/1995_Courtney.ps:PostScript;:by-author/C/Courtney/1995_Courtney.pdf:PDF},
  groups       = {sg/Garbage collectors},
  owner        = {saulius},
  timestamp = {2015.02.27},
  creationdate = {2015-02-27T00:00:00},
}

@Manual{Courtney1995a,
  title        = {Phantom Reference Manual},
  author       = {Antony Courtney},
  month        = {May},
  organization = {Department of Computer Science, Trinity College Dublin},
  year         = {1995},
  file         = {:by-author/C/Courtney/1995_Courtney_a.ps:PostScript;:by-author/C/Courtney/1995_Courtney_a.pdf:PDF},
  keywords     = {Computer Science (CS); Phantom; Programming Languages},
  owner        = {saulius},
  school       = {Trinity College Dublin},
  timestamp = {2015.02.27},
  creationdate = {2015-02-27T00:00:00},
}

@Article{Cousineau2010,
  author    = {Denis Cousineau and Sylvain Chartier},
  journal   = {International Journal of Psychological Research},
  title     = {Outliers detection and treatment: a review},
  year      = {2010},
  number    = {1},
  pages     = {58--67},
  volume    = {3},
  file      = {:by-author/C/Cousineau/2010_Cousineau_58.pdf:PDF},
  groups    = {am/Outliers},
  owner     = {andrius},
  timestamp = {2016.06.30},
  creationdate = {2016-06-30T00:00:00},
  url       = {http://revistas.usb.edu.co/index.php/IJPR/article/view/844},
}

@Article{Coutsias2005,
  author    = {Coutsias, Evangelos A. and Seok, Chaok and Dill, Ken A.},
  journal   = {Journal of Computational Chemistry},
  title     = {Rotational superposition and least squares: The {SVD} and quaternions approaches yield identical results. {R}eply to the preceding comment by {G}. {K}neller},
  year      = {2005},
  issn      = {1096-987X},
  pages     = {1663--1665},
  volume    = {26},
  abstract  = {A widely used way to compare the structures of biomolecules or solid bodies is to translate and rotate one structure with respect to the other to minimize the root-mean-square deviation (RMSD). We present a simple derivation, based on quaternions, for the optimal solid body transformation (rotation-translation) that minimizes the RMSD between two sets of vectors. We prove that the quaternion method is equivalent to the well-known formula due to Kabsch. We analyze the various cases that may arise, and give a complete enumeration of the special cases in terms of the arrangement of the eigenvalues of a traceless, 4 × 4 symmetric matrix. A key result here is an expression for the gradient of the RMSD as a function of model parameters. This can be useful, for example, in finding the minimum energy path of a reaction using the elastic band methods or in optimizing model parameters to best fit a target structure.},
  doi       = {10.1002/jcc.20316},
  file      = {:by-author/C/Coutsias/2005_Coutsias_1663.pdf:PDF},
  keywords  = {Least Squares; Rotational Superposition},
  owner     = {saulius},
  publisher = {Wiley Subscription Services, Inc., A Wiley Company},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1002/jcc.20316},
}

@Article{Coutsias2004,
  author           = {Coutsias, Evangelos A. and Seok, Chaok and Dill, Ken A.},
  journal          = {Journal of Computational Chemistry},
  title            = {Using quaternions to calculate {RMSD}},
  year             = {2004},
  pages            = {1849--1857},
  volume           = {25},
  abstract         = {A widely used way to compare the structures of biomolecules or solid bodies is to translate and rotate one structure with respect to the other to minimize the root-mean-square deviation (RMSD). We present a simple derivation, based on quaternions, for the optimal solid body transformation (rotation-translation) that minimizes the RMSD between two sets of vectors. We prove that the quaternion method is equivalent to the well-known formula due to Kabsch. We analyze the various cases that may arise, and give a complete enumeration of the special cases in terms of the arrangement of the eigenvalues of a traceless, 4 x 4 symmetric matrix. A key result here is an expression for the gradient of the RMSD as a function of model parameters. This can be useful, for example, in finding the minimum energy path of a reaction using the elastic band methods or in optimizing model parameters to best fit a target structure.},
  comment          = {Demonstrates that at the optimal superposition the barycenters of the pint sets coincide. Contradicts Chen2004?},
  creationdate     = {2008-07-28T00:00:00},
  doi              = {10.1002/jcc.20110},
  file             = {:by-author/C/Coutsias/2004_Coutsias_1849.pdf:PDF},
  groups           = {sg/Molecule superposion, sg/Superposition, sg/Bioinf. Algorithms},
  keywords         = {Algorithms; Quaternions; Structure Superposition; X-ray Crystallography},
  modificationdate = {2024-05-12T20:42:09},
  owner            = {saulius},
  timestamp        = {2008.07.28},
  url              = {http://dx.doi.org/10.1002/jcc.20110},
}

@Article{Cowan-Jacob2007,
  author    = {Cowan-Jacob, Sandra W. and Fendrich, Gabriele and Floersheimer, Andreas and Furet, Pascal and Liebetanz, Janis and Rummel, Gabriele and Rheinberger, Paul and Centeleghe, Mario and Fabbro, Doriano and Manley, Paul W.},
  journal   = {Acta crystallographica. Section D, Biological crystallography},
  title     = {Structural biology contributions to the discovery of drugs to treat chronic myelogenous leukaemia.},
  year      = {2007},
  pages     = {80--93},
  volume    = {63},
  abstract  = {Chronic myelogenous leukaemia (CML) results from the Bcr-Abl oncoprotein, which has a constitutively activated Abl tyrosine kinase domain. Although most chronic phase CML patients treated with imatinib as first-line therapy maintain excellent durable responses, patients who have progressed to advanced-stage CML frequently fail to respond or lose their response to therapy owing to the emergence of drug-resistant mutants of the protein. More than 40 such point mutations have been observed in imatinib-resistant patients. The crystal structures of wild-type and mutant Abl kinase in complex with imatinib and other small-molecule Abl inhibitors were determined, with the aim of understanding the molecular basis of resistance and to aid in the design and optimization of inhibitors active against the resistance mutants. These results are presented in a way which illustrates the approaches used to generate multiple structures, the type of information that can be gained and the way that this information is used to support drug discovery.},
  doi       = {10.1107/S0907444906047287},
  file      = {:by-author/C/Cowan-Jacob/2007_Cowan-Jacob_80.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Presentation{Cowles2007,
  author    = {Kate Cowles},
  title     = {Using MPI (MPICH) in C programs on our cluster},
  year      = {2007},
  file      = {:by-author/C/Cowles/2007_Cowles.pdf:PDF},
  owner     = {saulius},
  timestamp = {2013.08.11},
  creationdate = {2013-08-11T00:00:00},
}

@Presentation{Cowtan2005,
  author    = {Cowtan},
  title     = {Crystallographic Symmetry in Real and Reciprocal Space},
  year      = {2005},
  file      = {:by-author/C/Cowtan/2005_Cowtan_slides.pdf:PDF},
  keywords  = {Presentations},
  owner     = {saulius},
  pages     = {slides},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Cozzetto2007,
  author    = {Cozzetto, Domenico and Kryshtafovych, Andriy and Ceriani, Michele and Tramontano, Anna},
  journal   = {Proteins: Structure, Function, and Bioinformatics},
  title     = {Assessment of predictions in the model quality assessment category},
  year      = {2007},
  pages     = {175--183},
  volume    = {69},
  abstract  = {The article presents our evaluation of the predictions submitted to the model quality assessment (QA) category in CASP7. In this newly introduced category, predictors were asked to provide quality estimates for protein structure models. The QA category uses the automatically produced models that are traditionally distributed to CASP participants as input for predictions. Predictors were asked to provide an index of the quality of these individual models (QM1) as well as an index for the expected correctness of each of their residues (QM2). We computed the correlation between the observed and predicted quality of the models and of the individual residues achieved by the participating groups and evaluated the statistical significance of the differences. We also compared the results with those obtained by a “naïve predictor” that assigns a quality score related to how close the model is to the structure of the most similar protein of known structure. The aims of a method for assessing the overall quality of a model can be twofold: selecting the best (or one of the best) model(s) among a set of plausible choices, or assigning a nonrelative quality value to an individual model. The applications of the two strategies are different, albeit equally important. Our assessment of the QA category demonstrates that methods for addressing the first task effectively do exist, while there is room for improvement as far as the second aspect is concerned. Notwithstanding the limited number of groups submitting predictions for residue-level accuracy, our data demonstrate that a respectable accuracy in this task can be achieved by methods relying on the comparison of different models for the same target. Proteins 2007. © 2007 Wiley-Liss, Inc.},
  doi       = {10.1002/prot.21669},
  file      = {:by-author/C/Cozzetto/2007_Cozzetto_175.pdf:PDF},
  keywords  = {Protein Bioinformatics; Quality Estimation},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
  url       = {http://dx.doi.org/10.1002/prot.21669},
}

@Presentation{Cozzini2005,
  author    = {Stefano Cozzini},
  title     = {MPI tutorial},
  year      = {2005},
  course    = {Democritos/ICTP course in “Tools for computational physics"},
  file      = {:by-author/C/Cozzini/2005_Cozzini_slides.pdf:PDF},
  owner     = {saulius},
  pages     = {slides},
  timestamp = {2013.07.02},
  creationdate = {2013-07-02T00:00:00},
  url       = {http://www.democritos.it/events/computational_physics/lecture_stefano4.pdf},
}

@Manuscript{Cremer2011,
  author    = {Jacques Cr\'{e}mer},
  title     = {A very minimal introduction to TikZ*},
  year      = {2011},
  keywords  = {Latex},
  school    = {Toulouse School of Economics},
  url       = {http://bit.ly/gNfVn9},
  abstract  = {The aim of this document is to provide the minimum useful introduction to the Tik Z package (written by Till Tantau), which enables you to do nice figures in LATEX. I hope it will encourage for further exploration, but I also believe that at least 70% of the figures found in the economic literature can be drawn with the commands I present here. There are certainly mistakes left in this document. Be careful and if you find a mistake, drop me an e-mail! The latest version of this document can be found at http://bit.ly/gNfVn9.},
  file      = {:by-author/C/Cremer/2011_Cremer_manuscript.pdf:PDF},
  owner     = {andrius},
  timestamp = {2013.08.15},
  creationdate = {2013-08-15T00:00:00},
}

@Article{Craik2010,
  author    = {Craik, David J. and Mylne, Joshua S. and Daly, Norelle L.},
  journal   = {Cell. Mol. Life Sci.},
  title     = {Cyclotides: macrocyclic peptides with applications in drug design and agriculture},
  year      = {2010},
  pages     = {9--16},
  volume    = {67},
  abstract  = {Cyclotides are disulfide-rich peptides from plants that are exceptionally stable as a result of their unique cyclic cystine knot structural motif. Their natural role is thought to be as plant defence agents, most notably against insect pests, but they also have potential applications in drug design and agriculture. This article identifies gaps in current knowledge on cyclotides and suggests future directions for research into this fascinating family of ultra-stable mini-proteins.},
  doi       = {10.1007/s00018-009-0159-3},
  file      = {:by-author/C/Craik/2010_Craik_9.pdf:PDF},
  keywords  = {Circular Proteins; Cyclic Cystine Knot; Cyclisation; Kalata B1; Review; Small Peptides},
  owner     = {em},
  timestamp = {2013.10.01},
  creationdate = {2013-10-01T00:00:00},
}

@Webpage{Cramer2008,
  author    = {John G. Cramer},
  retrieved = {2008-12-27},
  title     = {A Farewell to Copenhagen?},
  url       = {http://www.analogsf.com/0410/altview2.shtml},
  year      = {2008},
  file      = {:by-author/C/Cramer/2008_Cramer.war:},
  keywords  = {Quantum-mechanics},
  owner     = {saulius},
  timestamp = {2015.03.02},
  creationdate = {2015-03-02T00:00:00},
}

@Article{Crampton2006,
  author    = {Crampton, Donald J. and Ohi, Melanie and Qimron, Udi and Walz, Thomas and Richardson, Charles C.},
  journal   = {Journal of molecular biology},
  title     = {Oligomeric states of bacteriophage T7 gene 4 primase/helicase.},
  year      = {2006},
  pages     = {667--77},
  volume    = {360},
  abstract  = {Electron microscopic and crystallographic data have shown that the gene 4 primase/helicase encoded by bacteriophage T7 can form both hexamers and heptamers. After cross-linking with glutaraldehyde to stabilize the oligomeric protein, hexamers and heptamers can be distinguished either by negative stain electron microscopy or electrophoretic analysis using polyacrylamide gels. We find that hexamers predominate in the presence of either dTTP or beta,gamma-methylene dTTP whereas the ratio between hexamers and heptamers is nearly the converse in the presence of dTDP. When formed, heptamers are unable to efficiently bind either single-stranded DNA or double-stranded DNA. We postulate that a switch between heptamer to hexamer may provide a ring-opening mechanism for the single-stranded DNA binding pathway. Accordingly, we observe that in the presence of both nucleoside di- and triphosphates the gene 4 protein exists as a hexamer when bound to single-stranded DNA and as a mixture of heptamer and hexamer when not bound to single-stranded DNA. Furthermore, altering regions of the gene 4 protein postulated to be conformational switches for dTTP-dependent helicase activity leads to modulation of the heptamer to hexamer ratio.},
  file      = {:by-author/C/Crampton/2006_Crampton_667.pdf:PDF},
  keywords  = {{gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Manuscript{Cranswick2000,
  author    = {Lachlan M. D. Cranswick},
  title     = {Freely available software tools for chemical crystallography},
  year      = {2000},
  keywords  = {Software; X-ray Crystallography},
  url       = {http://www.ccp14.ac.uk/poster-talks/bca2000/ccp14_all.zip},
  file      = {:by-author/C/Cranswick/2000_Cranswick.doc:Word},
  owner     = {saulius},
  timestamp = {2015.03.10},
  creationdate = {2015-03-10T00:00:00},
}

@Manuscript{Cranswick2000a,
  author    = {Lachlan M. D. Cranswick},
  title     = {Turning raw data into results: freely available crystallographic software via the internet. Overview},
  year      = {2000},
  keywords  = {Software; X-ray Crystallography},
  url       = {http://www.ccp14.ac.uk/poster-talks/chalk-river-feb2000/chalk-river.zip},
  file      = {:by-author/C/Cranswick/2000_Cranswick_a.doc:Word},
  owner     = {saulius},
  timestamp = {2015.03.10},
  creationdate = {2015-03-10T00:00:00},
}

@Manuscript{Cranswick1999,
  author    = {Lachlan M. D. Cranswick},
  title     = {Collaborative Computational Project number 14 for Single Crystal and Powder Diffraction: An Introduction},
  year      = {1999},
  url       = {http://www.ccp14.ac.uk/poster-talks/chalk-river-feb2000/chalk-river.zip},
  file      = {:by-author/C/Cranswick/1999_Cranswick.doc:Word},
  owner     = {saulius},
  timestamp = {2015.03.10},
  creationdate = {2015-03-10T00:00:00},
}

@InProceedings{Craver2001,
  author    = {Scott A. Craver and Min Wu and Bede Liu},
  booktitle = {Proceedings of the 10th USENIX Security Symposium},
  title     = {Reading Between the Lines: Lessons from the SDMI Challenge},
  year      = {2001},
  file      = {:by-author/C/Craver/2001_Craver.pdf:PDF},
  keywords  = {Computer Science (CS); Security; Unix; Usenix},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Crawford1983,
  author    = {Crawford, J. F.},
  journal   = {Nuclear Instruments and Methods},
  title     = {A non-iterative method for fitting circular arcs to measured points},
  year      = {1983},
  pages     = {223--225},
  volume    = {211},
  file      = {1983_Crawford_223.pdf:by-author/C/Crawford/1983_Crawford_223.pdf:PDF},
  groups    = {sg/Arc fitting, sg/Bioinf. Algorithms},
  keywords  = {Arc Fitting; Mathematics},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Cremer1984,
  author    = {Dieter Cremer},
  journal   = {Acta Crystallographica Section B},
  title     = {On the Correct Usage of the {C}remer-{P}ople Puckering Parameters as Quantitative Descriptorsof Ring Shapes - a Reply to Recent Criticism by {P}etit, {D}illen and {G}eise},
  year      = {1984},
  pages     = {498--500},
  volume    = {40},
  file      = {:by-author/C/Cremer/1984_Cremer_498.pdf:PDF},
  keywords  = {Cremer & Pople Parameters},
  owner     = {andrius},
  timestamp = {2012.08.02},
  creationdate = {2012-08-02T00:00:00},
}

@Article{Cremer1980,
  author    = {Dieter Cremer},
  journal   = {Israel Journal of Chemistry},
  title     = {A General Definition of Ring Substituent Positions},
  year      = {1980},
  pages     = {12--19},
  volume    = {20},
  file      = {:by-author/C/Cremer/1980_Cremer_12.pdf:PDF},
  keywords  = {Cremer & Pople Parameters},
  owner     = {andrius},
  timestamp = {2012.08.02},
  creationdate = {2012-08-02T00:00:00},
}

@Article{Cremer1975a,
  author    = {Cremer, D. and Pople, J. A.},
  journal   = {Journal of the American Chemical Society},
  title     = {A General Definition of Ring Puckering Coordinates},
  year      = {1975},
  pages     = {1354--1358},
  volume    = {6},
  file      = {:by-author/C/Cremer/1975_Cremer_1354.pdf:PDF},
  keywords  = {Cremer & Pople Parameters},
  owner     = {andrius},
  timestamp = {2012.07.13},
  creationdate = {2012-07-13T00:00:00},
}

@Article{Cremer1975b,
  author    = {Cremer, D. and Pople, J. A.},
  journal   = {Journal of the American Chemical Society},
  title     = {Molecular Orbital Theory of the Electronic Structure of Organic Compounds. {XXIII}. Pseudorotation in Saturated Five-Membered Ring Compounds},
  year      = {1975},
  pages     = {1358--1367},
  volume    = {6},
  file      = {:by-author/C/Cremer/1975_Cremer_1358.pdf:PDF},
  keywords  = {Cremer & Pople Parameters},
  owner     = {andrius},
  timestamp = {2012.07.13},
  creationdate = {2012-07-13T00:00:00},
}

@Article{Crick1970,
  author    = {Crick, F. H.},
  journal   = {Science (New York, N.Y.)},
  title     = {DNA: test of structure?},
  year      = {1970},
  pages     = {1694},
  volume    = {167},
  file      = {:by-author/C/Crick/1970_Crick_1694.pdf:PDF},
  keywords  = {DNA Structure},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Crick1952,
  author    = {Crick, F. H. C.},
  journal   = {Nature},
  title     = {Is alpha-keratin a coiled coil?},
  year      = {1952},
  pages     = {882--3},
  volume    = {170},
  file      = {:by-author/C/Crick/1952_Crick_882.pdf:PDF},
  keywords  = {Alpha Helices; Protein Structure},
  owner     = {saulius},
  timestamp = {2012.11.21},
  creationdate = {2012-11-21T00:00:00},
  url       = {http://www.nature.com/nature/focus/crick/pdf/crick170.pdf},
}

@Article{Crippen2004,
  author    = {Crippen, Gordon M.},
  journal   = {Biopolymers},
  title     = {Statistical mechanics of protein folding by cluster distance geometry.},
  year      = {2004},
  pages     = {278--89},
  volume    = {75},
  abstract  = {This is our second type of model for protein folding where the configurational parameters and the effective potential energy function are chosen in such a way that all conformations are described and the canonical partition function can be evaluated analytically. Structure is described in terms of distances between pairs of sequentially contiguous blocks of eight residues, and all possible conformations are grouped into 71 subsets in terms of bounds on these distances. The energy is taken to be a sum of pairwise interactions between such blocks. The 210 energy parameters were adjusted so that the native folds of 32 small proteins are favored in free energy over the denatured state. We then found 146 proteins having negligible sequence similarity to any of the training proteins, yet the free energy of the respective correct native states were favored over the denatured state.},
  file      = {:by-author/C/Crippen/2004_Crippen_278.pdf:PDF},
  keywords  = {Distance Geometry; Protein Bioinformatics},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Crooks1997,
  author    = {Gavin E. Crooks and David Chandler},
  journal   = {Physical Review E},
  title     = {Gaussian statistics of the hard-sphere fluid},
  year      = {1997},
  pages     = {4217--4221},
  volume    = {56},
  file      = {1997_Crooks_4217.pdf:by-author/C/Crooks/1997_Crooks_4217.pdf:PDF},
  groups    = {sg/Molecular dynamics},
  keywords  = {Hard Spheres; Molecular Dynamics (MD)},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Crosson2002,
  author    = {Crosson, Sean and Moffat, Keith},
  journal   = {The Plant Cell},
  title     = {Photoexcited structure of a plant photoreceptor domain reveals a light-driven molecular switch},
  year      = {2002},
  issn      = {1040-4651, 1532-298X},
  pages     = {1067--1075},
  volume    = {14},
  abstract  = {The phototropins are flavoprotein kinases that control phototropic bending, light-induced chloroplast movement, and stomatal opening in plants. Two flavin mononucleotide binding light, oxygen, or voltage (LOV) domains are the sites for initial photochemistry in these blue light photoreceptors. We have determined the steady state, photoexcited crystal structure of a flavin-bound LOV domain. The structure reveals a unique photochemical switch in the flavin binding pocket in which the absorption of light drives the formation of a reversible covalent bond between a highly conserved Cys residue and the flavin cofactor. This provides a molecular picture of a cysteinyl-flavin covalent adduct, the presumed signaling species that leads to phototropin kinase activation and subsequent signal transduction. We identify closely related LOV domains in two eubacterial proteins that suggests the light-induced conformational change evident in this structure is an ancient biomolecular response to light, arising before the appearance of plants.},
  doi       = {10.1105/tpc.010475},
  file      = {Full Text PDF:by-author/C/Crosson/2002_Crosson_1067.pdf:PDF;Snapshot:by-author/C/Crosson/2002_Crosson_1067.html:URL},
  groups    = {sg/biomolecular, sg/MOFs, am/MOFs},
  language  = {en},
  owner     = {saulius},
  pmid      = {12034897},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://www.plantcell.org/content/14/5/1067},
  urldate   = {2015-08-05},
}

@Article{Crothers1998,
  author    = {Crothers, D. M.},
  journal   = {Proceedings of the National Academy of Sciences of the United States of America},
  title     = {DNA curvature and deformation in protein-DNA complexes: a step in the right direction.},
  year      = {1998},
  pages     = {15163--5},
  volume    = {95},
  file      = {:by-author/C/Crothers/1998_Crothers_15163.pdf:PDF},
  keywords  = {DNA Protein; Readout},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Cruickshank1956,
  author    = {Cruickshank, D. W. J.},
  journal   = {Acta Crystallographica},
  title     = {Errors in Bond Lengths Due to Rotational Oscillations of Molecules},
  year      = {1956},
  pages     = {757--758},
  volume    = {9},
  doi       = {10.1107/S0365110X56002059},
  file      = {:by-author/C/Cruickshank/1956_Cruickshank_757.pdf:PDF},
  owner     = {andrius},
  timestamp = {2013.05.09},
  creationdate = {2013-05-09T00:00:00},
}

@Article{Cruz-Cabeza2012,
  author    = {Cruz-Cabeza, Aurora J. and Liebeschuetz, John W. and Allen, Frank H.},
  journal   = {CrystEngComm},
  title     = {Systematic conformational bias in small-molecule crystal structures is rare and explicable},
  year      = {2012},
  issn      = {1466-8033},
  number    = {20},
  pages     = {6797},
  volume    = {14},
  abstract  = {Analysis of the Cambridge Structural Database, together with DFT and crystal structure prediction calculations, show that the observation of higher-energy planar conformers of biphenyl (BP) and cyclobutane (CB) is possible because of improved intermolecular interactions in their crystal structures. Such intermolecular/intramolecular energy compensation almost always occurs when crystallographic and molecular symmetry elements coincide. For BP and CB, almost exclusively, a crystallographic inversion centre coincides with a centre of symmetry in a Ci-symmetric molecule. We conclude that the observation of higher energy conformers (with the compensation of conformational energies up to ≈8–10 kJ.mol.−1 above the global minimum) together with this symmetry coincidence is rare. The work shows that concerns, expressed by some drug discovery chemists and other scientists, that conformations observed in crystal structures are systematically biased due to ‘crystal packing effects’ is overstated: only 16% of BP and CB fragments are exactly planar in small-molecule crystal structures, while the remaining conformations are close to their gas-phase energy minima. Thus, crystal structure conformations are good guides to conformational preferences in other phases and in other applications, e.g. in conformer generation or in the study of protein–ligand binding.},
  doi       = {10.1039/c2ce25585e},
  file      = {2012_Cruz-Cabeza_6797.pdf:by-author/C/Cruz-Cabeza/2012_Cruz-Cabeza_6797.pdf:PDF},
  groups    = {sg/Crystallography, am/Crystallography},
  owner     = {andrius},
  publisher = {Royal Society of Chemistry (RSC)},
  timestamp = {2016.11.18},
  creationdate = {2016-11-18T00:00:00},
  url       = {http://dx.doi.org/10.1039/c2ce25585e},
}

@Presentation{Cuevas2014,
  author       = {Juan Carlos Cuevas},
  title        = {Introduction to Density Functional Theory},
  year         = {2014},
  organization = {Institut f{\"u}r Theoretische Festk{\"o}rperphysik},
  school       = {Universit{\"a}t Karlsruhe (Germany)},
  file         = {2014_Cuevas_DFTslides.pdf:by-author/C/Cuevas/2014_Cuevas_DFTslides.pdf:PDF},
  keywords     = {Density Functional Theory (DFT)},
  owner        = {saulius},
  timestamp = {2014.10.21},
  creationdate = {2014-10-21T00:00:00},
  url          = {https://www.uam.es/personal_pdi/ciencias/jcuevas/Talks/JC-Cuevas-DFT.pdf},
}

@PhdThesis{Cuevas1999,
  author    = {Juan Carlos Cuevas},
  school    = {Universidad Autonoma de Madrid},
  title     = {Electronic Transport in Normal and Superconducting Nanocontacts},
  year      = {1999},
  file      = {1999_Cuevas_thesis.pdf:by-author/C/Cuevas/1999_Cuevas_thesis.pdf:PDF},
  owner     = {saulius},
  timestamp = {2014.10.21},
  creationdate = {2014-10-21T00:00:00},
  url       = {https://www.uam.es/personal_pdi/ciencias/jcuevas/Publications/thesis.pdf},
}

@Article{Cuevas2003,
  author    = {J C Cuevas and J Heurich and F Pauly and W Wenzel and Gerd Schön},
  journal   = {Nanotechnology},
  title     = {Theoretical description of the electrical conduction in atomic and molecular junctions},
  year      = {2003},
  pages     = {R29},
  volume    = {14},
  abstract  = {We present a theoretical analysis of the electronic transport through atomic and molecular junctions. The main goal of this work is to show how the electronic structure of single atoms and molecules controls the macroscopic electrical properties of the circuits in which they are used as building blocks. In particular, we review our work on three basic problems that have received special experimental attention in recent years: (i) the conductance of a single-atom contact, (ii) the conductance of a hydrogen molecule and (iii) the current through single organic molecules.},
  file      = {2003_Cuevas_R29.pdf:by-author/C/Cuevas/2003_Cuevas_R29.pdf:PDF},
  owner     = {saulius},
  timestamp = {2014.10.21},
  creationdate = {2014-10-21T00:00:00},
  url       = {http://stacks.iop.org/0957-4484/14/i=8/a=201},
}

@Article{Curran2009,
  author    = {Curran, Patrick J. and Hussong, Andrea M.},
  journal   = {Psychological methods},
  title     = {Integrative data analysis: the simultaneous analysis of multiple data sets.},
  year      = {2009},
  pages     = {81--100},
  volume    = {14},
  abstract  = {There are both quantitative and methodological techniques that foster the development and maintenance of a cumulative knowledge base within the psychological sciences. Most noteworthy of these techniques is meta-analysis, which allows for the synthesis of summary statistics drawn from multiple studies when the original data are not available. However, when the original data can be obtained from multiple studies, many advantages stem from the statistical analysis of the pooled data. The authors define integrative data analysis (IDA) as the analysis of multiple data sets that have been pooled into one. Although variants of IDA have been incorporated into other scientific disciplines, the use of these techniques is much less evident in psychology. In this article the authors present an overview of IDA as it may be applied within the psychological sciences, discuss the relative advantages and disadvantages of IDA, describe analytic strategies for analyzing pooled individual data, and offer recommendations for the use of IDA in practice.},
  file      = {:by-author/C/Curran/2009_Curran_81.pdf:PDF},
  keywords  = {Data Management},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@Article{Curtarolo2005,
  author    = {Stefano Curtarolo and Dane Morgan and Gerbrand Ceder},
  journal   = {Computer Coupling of Phase Diagrams and Thermochemistry},
  title     = {Accuracy of ab initio methods in predicting the crystal structures of metals: A review of 80 binary alloys},
  year      = {2005},
  pages     = {163--211},
  volume    = {29},
  file      = {2005_Curtarolo_163.pdf:by-author/C/Curtarolo/2005_Curtarolo_163.pdf:PDF},
  keywords  = {Density Functional Theory (DFT)},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Curtarolo2012,
  author    = {Stefano Curtarolo and Wahyu Setyawan and Shidong Wang and Junkai Xue and Kesong Yang and Richard H. Taylor and Lance J. Nelson and Gus L.W. Hart and Stefano Sanvito and Marco Buongiorno-Nardelli and Natalio Mingo and Ohad Levy},
  journal   = {Computational Materials Science},
  title     = {{AFLOWLIB.ORG}: A distributed materials properties repository from high-throughput ab initio calculations},
  year      = {2012},
  issn      = {0927-0256},
  pages     = {227--235},
  volume    = {58},
  abstract  = {Empirical databases of crystal structures and thermodynamic properties are fundamental tools for materials research. Recent rapid proliferation of computational data on materials properties presents the possibility to complement and extend the databases where the experimental data is lacking or difficult to obtain. Enhanced repositories that integrate both computational and empirical approaches open novel opportunities for structure discovery and optimization, including uncovering of unsuspected compounds, metastable structures and correlations between various characteristics. The practical realization of these opportunities depends on a systematic compilation and classification of the generated data in addition to an accessible interface for the materials science community. In this paper we present an extensive repository, aflowlib.org, comprising phase-diagrams, electronic structure and magnetic properties, generated by the high-throughput framework AFLOW. This continuously updated compilation currently contains over 150,000 thermodynamic entries for alloys, covering the entire composition range of more than 650 binary systems, 13,000 electronic structure analyses of inorganic compounds, and 50,000 entries for novel potential magnetic and spintronics systems. The repository is available for the scientific community on the website of the materials research consortium, aflowlib.org.},
  doi       = {10.1016/j.commatsci.2012.02.002},
  file      = {:by-author/C/Curtarolo/2012_Curtarolo_227.pdf:PDF},
  keywords  = {Density Functional Theory (DFT)},
  owner     = {andrius},
  timestamp = {2015.07.29},
  creationdate = {2015-07-29T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/S0927025612000687},
}

@Article{Cymerman2005,
  author    = {Iwona A. Cymerman and Gregor Meiss and Janusz M. Bujnicki},
  journal   = {Bioinformatics},
  title     = {{DNase II} is a member of the phospholipase {D} superfamily},
  year      = {2005},
  pages     = {preprint},
  file      = {:by-author/C/Cymerman/2005_Cymerman_preprint.pdf:PDF},
  keywords  = {Evolution},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Cyranoski2012,
  author    = {Cyranoski, David},
  journal   = {Nature},
  title     = {Retraction record rocks community.},
  year      = {2012},
  pages     = {346--7},
  volume    = {489},
  abstract  = {One of the biggest purges of the scientific literature in history is finally getting under way. After more than a decade of suspicion about the work of anaesthesiolo- gist Yoshitaka Fujii, formerly of Toho Univer- sity in Tokyo, investigations by journals and universities have concluded that he fabri- cated data on an epic scale. At least half of the roughly 200 papers he authored on responses to drugs after surgery are in line for retraction in the coming months.},
  file      = {:by-author/C/Cyranoski/2012_Cyranoski_346.pdf:PDF},
  keywords  = {Data Management; Scientific Fraud},
  owner     = {saulius},
  timestamp = {2013.01.08},
  creationdate = {2013-01-08T00:00:00},
}

@Article{Czyzowicz1985,
  author     = {Czyzowicz, Jurek and Iglewski, Michal},
  journal    = {SIGPLAN Not.},
  title      = {Implementing Generic Types in Modula-2},
  year       = {1985},
  issn       = {0362-1340},
  pages      = {26--32},
  volume     = {20},
  abstract   = {In SIGPLAN Notices, vol. 20, #6., June 1985 R. S. Wiener and R. F. Sincovec presented "Two Approaches to Implementing Generic Data Structures in Modula-2". Our paper presents a third solution which attempts to avoid or at least diminish the effects of some shortcomings existing in Wiener and Sincovec's approaches.},
  acmid      = {382623},
  address    = {New York, NY, USA},
  doi        = {10.1145/382086.382623},
  file       = {1985_Czyzowicz_26.pdf:by-author/C/Czyzowicz/1985_Czyzowicz_26.pdf:PDF},
  groups     = {sg/Generic types, sg/Modula-2},
  issue_date = {Dec. 1985},
  numpages   = {7},
  owner      = {saulius},
  publisher  = {ACM},
  timestamp = {2015.12.16},
  creationdate = {2015-12-16T00:00:00},
  url        = {http://doi.acm.org/10.1145/382086.382623},
}

@Article{Arcy2007,
  author    = {D'Arcy, Allan and Villard, Frederic and Marsh, May},
  journal   = {Acta crystallographica. Section D, Biological crystallography},
  title     = {An automated microseed matrix-screening method for protein crystallization.},
  year      = {2007},
  pages     = {550--4},
  volume    = {63},
  abstract  = {A microseed-matrix procedure has been established with the aim of influencing the nucleation event in standard crystallization screens. The method is based on the original description of matrix seeding described by Ireton &amp; Stoddard (2004, Acta Cryst. D60, 601-605). Seed stocks are produced using a simple "seed-bead" method. The protein, reservoir solutions and seed stocks are pipetted simultaneously using a three-bore dispensing tip in drops of 0.6 microl total volume. The number and type of hits produced with the proteins tested in this study has been increased and it is believed that this method could be generally applicable to proteins where little or no nucleation is normally observed.},
  doi       = {10.1107/S0907444907007652},
  file      = {:by-author/D/DArcy/2007_DArcy_550.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Ursi2005,
  author    = {D'Ursi, Pasqualina and Salvi, Erika and Fossa, Paola and Milanesi, Luciano and Rovida, Ermanna},
  journal   = {BMC Bioinformatics},
  title     = {Modelling the interaction of steroid receptors with endocrine disrupting chemicals},
  year      = {2005},
  pages     = {S10},
  volume    = {6},
  abstract  = {Background The organic polychlorinated compounds like dichlorodiphenyltrichloroethane with its metabolites and polychlorinated biphenyls are a class of highly persistent environmental contaminants. They have been recognized to have detrimental health effects both on wildlife and humans acting as endocrine disrupters due to their ability of mimicking the action of the steroid hormones, and thus interfering with hormone response. There are several experimental evidences that they bind and activate human steroid receptors. However, despite the growing concern about the toxicological activity of endocrine disrupters, molecular data of the interaction of these compounds with biological targets are still lacking. Results We have used a flexible docking approach to characterize the molecular interaction of seven endocrine disrupting chemicals with estrogen, progesterone and androgen receptors in the ligand-binding domain. All ligands docked in the buried hydrophobic cavity corresponding to the hormone steroid pocket. The interaction was characterized by multiple hydrophobic contacts involving a different number of residues facing the binding pocket, depending on ligands orientation. The EDC ligands did not display a unique binding mode, probably due to their lipophilicity and flexibility, which conferred them a great adaptability into the hydrophobic and large binding pocket of steroid receptors. Conclusion Our results are in agreement with toxicological data on binding and allow to describe a pattern of interactions for a group of ECD to steroid receptors suggesting the requirement of a hydrophobic cavity to accommodate these chlorine carrying compounds. Although the affinity is lower than for hormones, their action can be brought about by a possible synergistic effect.},
  doi       = {10.1186/1471-2105-6-S4-S10},
  file      = {:by-author/D/DUrsi/2005_DUrsi_S10.pdf:PDF},
  owner     = {saulius},
  publisher = {Springer (Biomed Central Ltd.)},
  timestamp = {2013.08.10},
  creationdate = {2013-08-10T00:00:00},
  url       = {http://dx.doi.org/10.1186/1471-2105-6-S4-S10},
}

@Article{Dafforn2007,
  author    = {Dafforn, Timothy R.},
  journal   = {Acta crystallographica. Section D, Biological crystallography},
  title     = {So how do you know you have a macromolecular complex?},
  year      = {2007},
  pages     = {17--25},
  volume    = {63},
  abstract  = {Protein in crystal form is at an extremely high concentration and yet retains the complex secondary structure that defines an active protein. The protein crystal itself is made up of a repeating lattice of protein-protein and protein-solvent interactions. The problem that confronts any crystallographer is to identify those interactions that represent physiological interactions and those that do not. This review explores the tools that are available to provide such information using the original crystal liquor as a sample. The review is aimed at postgraduate and postdoctoral researchers who may well be coming up against this problem for the first time. Techniques are discussed that will provide information on the stoichiometry of complexes as well as low-resolution information on complex structure. Together, these data will help to identify the physiological complex.},
  doi       = {10.1107/S0907444906047044},
  file      = {:by-author/D/Dafforn/2007_Dafforn_17.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Dalby1992,
  author    = {Dalby, Arthur and Nourse, James G. and Hounshell, W. Douglas and Gushurst, Ann K. I. and Grier, David L. and Leland, Burton A. and Laufer, John},
  journal   = {Journal of Chemical Information and Computer Sciences},
  title     = {Description of several chemical structure file formats used by computer programs developed at Molecular Design Limited},
  year      = {1992},
  pages     = {244--255},
  volume    = {32},
  doi       = {10.1021/ci00007a012},
  eprint    = {http://pubs.acs.org/doi/pdf/10.1021/ci00007a012},
  file      = {:by-author/D/Dalby/1992_Dalby_244.pdf:PDF},
  keywords  = {SDF; Structures Data File},
  owner     = {antanas},
  timestamp = {2014.07.02},
  creationdate = {2014-07-02T00:00:00},
  url       = {http://pubs.acs.org/doi/abs/10.1021/ci00007a012},
}

@Article{Dalhus2009,
  author    = {Dalhus, Bjørn and Arvai, Andrew S and Rosnes, Ida and Olsen, Øyvind E and Backe, Paul H and Alseth, Ingrun and Gao, Honghai and Cao, Weiguo and Tainer, John A and Bjørås, Magnar},
  journal   = {Nature structural \&amp; molecular biology},
  title     = {Structures of endonuclease V with DNA reveal initiation of deaminated adenine repair.},
  year      = {2009},
  pages     = {138--43},
  volume    = {16},
  file      = {2009_Dalhus_138.pdf:by-author/D/Dalhus/2009_Dalhus_138.pdf:PDF},
  keywords  = {HhaI},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{DallAntonia2003,
  author    = {Dall'Antonia, Fabio and Baker, Patrick J. and Schneider, Thomas R.},
  journal   = {Acta Crystallographica Section D},
  title     = {Optimization of selenium substructures as obtained from {\it SHELXD}},
  year      = {2003},
  pages     = {1987--1994},
  volume    = {59},
  doi       = {10.1107/S0907444903017670},
  file      = {ba5039.pdf:by-author/D/DallAntonia/2003_DallAntonia_1987.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444903017670},
}

@InProceedings{Dalle2012,
  author           = {Dalle, Olivier},
  booktitle        = {Proceedings of the Winter Simulation Conference},
  title            = {On Reproducibility and Traceability of Simulations},
  year             = {2012},
  pages            = {244},
  publisher        = {Winter Simulation Conference},
  series           = {WSC '12},
  abstract         = {Reproducibility of experiments is the pillar of a rigorous scientific approach. However, simulation-based experiments often fail to meet this fundamental requirement. In this paper, we first revisit the definition of reproducibility in the context of simulation. Then, we give a comprehensive review of issues that make this highly desirable feature so difficult to obtain. Given that experimental (in-silico) science is only one of the many applications of simulation, our analysis also explores the needs and benefits of providing the simulation reproducibility property for other kinds of applications. Coming back to scientific applications, we give a few examples of solutions proposed for solving the above issues. Finally, going one step beyond reproducibility, we also discuss in our conclusion the notion of traceability and its potential use in order to improve the simulation methodology.},
  acmid            = {2430088},
  articleno        = {244},
  creationdate     = {2016-11-07T00:00:00},
  file             = {2012_Dalle_224.pdf:by-author/D/Dalle/2012_Dalle_224.pdf:PDF},
  keywords         = {Computer Science (CS); Reproducibility; Reproducible Research; Simulation},
  location         = {Berlin, Germany},
  modificationdate = {2023-01-02T19:39:20},
  numpages         = {12},
  owner            = {saulius},
  timestamp        = {2016.11.07},
  url              = {http://dl.acm.org/citation.cfm?id=2429759.2430088},
}

@Presentation{Damasceno2010,
  author    = {Tiago Sommer Damasceno},
  title     = {Parallel Programming Using OpenMP},
  year      = {2010},
  file      = {:by-author/D/Damasceno/2010_Damasceno_slides.pdf:PDF},
  owner     = {saulius},
  pages     = {slides},
  timestamp = {2013.07.02},
  creationdate = {2013-07-02T00:00:00},
}

@Article{Damm2006,
  author           = {Damm, Kelly L. and Carlson, Heather A.},
  journal          = {Biophysical journal},
  title            = {Gaussian-weighted {RMSD} superposition of proteins: a structural comparison for flexible proteins and predicted protein structures.},
  year             = {2006},
  pages            = {4558--73},
  volume           = {90},
  abstract         = {Many proteins contain flexible structures such as loops and hinged domains. A simple root mean square deviation (RMSD) alignment of two different conformations of the same protein can be skewed by the difference between the mobile regions. To overcome this problem, we have developed a novel method to overlay two protein conformations by their atomic coordinates using a Gaussian-weighted RMSD (wRMSD) fit. The algorithm is based on the Kabsch least-squares method and determines an optimal transformation between two molecules by calculating the minimal weighted deviation between the two coordinate sets. Unlike other techniques that choose subsets of residues to overlay, all atoms are included in the wRMSD overlay. Atoms that barely move between the two conformations will have a greater weighting than those that have a large displacement. Our superposition tool has produced successful alignments when applied to proteins for which two conformations are known. The transformation calculation is heavily weighted by the coordinates of the static region of the two conformations, highlighting the range of flexibility in the overlaid structures. Lastly, we show how wRMSD fits can be used to evaluate predicted protein structures. Comparing a predicted fold to its experimentally determined target structure is another case of comparing two protein conformations of the same sequence, and the degree of alignment directly reflects the quality of the prediction.},
  creationdate     = {2012-05-15T00:00:00},
  doi              = {10.1529/biophysj.105.066654},
  file             = {:by-author/D/Damm/2006_Damm_4558.pdf:PDF;manuscript:by-author/D/Damm/2006_Damm_4558_manuscript.pdf:PDF},
  groups           = {sg/Molecule superposion, sg/Superposition, sg/Bioinf. Algorithms},
  keywords         = {Structure Superposition},
  modificationdate = {2024-05-12T14:49:28},
  owner            = {saulius},
  timestamp        = {2012.05.15},
}

@Article{Daniels2008,
  author    = {Karen E. Daniels and Oliver Brausch and Werner Pesch and Eberhard Bodenschatz},
  journal   = {J. Fluid Mech.},
  title     = {Competition and bistability of ordered undulations and undulation chaos in inclined layer convection},
  year      = {2008},
  pages     = {261},
  abstract  = {Experimental and theoretical investigations of undulation patterns in high-pressure, inclined layer gas convection at a Prandtl number near unity are reported. Particular focus is given to the competition between the spatiotemporal chaotic state of undulation chaos and stationary patterns of ordered undulations. In experiments a competition and bistability between the two states is observed, with ordered undulations most prevalent at higher Rayleigh number. The spectral pattern entropy, spatial correlation lengths, and defect statistics are used to characterize the competing states. The experiments are complemented by a theoretical analysis of the Oberbeck-Boussinesq equations. The stability region of the ordered undulation as a function of their wavevectors and the Rayleigh number is obtained with Galerkin techniques. In addition, direct numerical simulations are used to investigate the spatiotemporal dynamics. In the simulations both ordered undulations and undulation chaos were observed dependent on initial conditions. Experiment and theory are found to agree well.},
  file      = {:by-author/D/Daniels/2008_Daniels_261.pdf:PDF},
  owner     = {saulius},
  timestamp = {2013.07.25},
  creationdate = {2013-07-25T00:00:00},
  url       = {http://arxiv.org/abs/nlin/0702006v1},
}

@Article{Daniels2003,
  author    = {Daniels, Lucy E. and Wood, Katie M. and Scott, David J. and Halford, Stephen E.},
  journal   = {Journal of molecular biology},
  title     = {Subunit assembly for DNA cleavage by restriction endonuclease SgrAI.},
  year      = {2003},
  pages     = {579--91},
  volume    = {327},
  abstract  = {The SgrAI endonuclease usually cleaves DNA with two recognition sites more rapidly than DNA with one site, often converting the former directly to the products cut at both sites. In this respect, SgrAI acts like the tetrameric restriction enzymes that bind two copies of their target sites before cleaving both sites concertedly. However, by analytical ultracentrifugation, SgrAI is a dimer in solution though it aggregates to high molecular mass species when bound to its specific DNA sequence. Its reaction kinetics indicate that it uses different mechanisms to cleave DNA with one and with two SgrAI sites. It cleaves the one-site DNA in the style of a dimeric restriction enzyme acting at an individual site, mediating neither interactions in trans, as seen with the tetrameric enzymes, nor subunit associations, as seen with the monomeric enzymes. In contrast, its optimal reaction on DNA with two sites involves an association of protein subunits: two dimers bound to sites in cis may associate to form a tetramer that has enhanced activity, which then cleaves both sites concurrently. The mode of action of SgrAI differs from all restriction enzymes characterised previously, so this study extends the range of mechanisms known for restriction endonucleases.},
  file      = {:by-author/D/Daniels/2003_Daniels_579.pdf:PDF},
  keywords  = {SgrAI; TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Das2006,
  author    = {Das, Payel and Moll, Mark and Stamati, Hernán and Kavraki, Lydia E. and Clementi, Cecilia},
  journal   = {Proceedings of the National Academy of Sciences of the United States of America},
  title     = {Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear dimensionality reduction.},
  year      = {2006},
  pages     = {9885--90},
  volume    = {103},
  abstract  = {The definition of reaction coordinates for the characterization of a protein-folding reaction has long been a controversial issue, even for the "simple" case in which one single free-energy barrier separates the folded and unfolded ensemble. We propose a general approach to this problem to obtain a few collective coordinates by using nonlinear dimensionality reduction. We validate the usefulness of this method by characterizing the folding landscape associated with a coarse-grained protein model of src homology 3 as sampled by molecular dynamics simulations. The folding free-energy landscape projected on the few relevant coordinates emerging from the dimensionality reduction can correctly identify the transition-state ensemble of the reaction. The first embedding dimension efficiently captures the evolution of the folding process along the main folding route. These results clearly show that the proposed method can efficiently find a low-dimensional representation of a complex process such as protein folding.},
  file      = {:by-author/D/Das/2006_Das_9885.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Das2002,
  author    = {Das, Undurti},
  journal   = {Medical science monitor : international medical journal of experimental and clinical research},
  title     = {A radical approach to cancer.},
  year      = {2002},
  pages     = {RA79-92},
  volume    = {8},
  abstract  = {Reactive oxygen species are known to be potentially dangerous, but are also needed for signal-transduction pathways. Tumor cells have relatively low amounts of superoxide dismutase (SOD), which quenches superoxide anion (O2(-*)), and as a result of a higher level of aerobic metabolism, higher concentrations of O2(-*) , compared to normal cells. But this may not be true of all tumor cells. Some tumor cells have relatively higher amounts of vitamin E, a potent anti-oxidant, and a higher level of anaerobic metabolism, resulting in a balance that is tilted more towards higher anti-oxidant capacity. In both instances of higher aerobic and anaerobic metabolism methods designed to augment free radical generation in tumor cells can cause their death. It is suggested that free radicals and lipid peroxides suppress the expression of Bcl-2, activate caspases and shorten telomere, and thus inducing apoptosis of tumor cells. Ionizing radiation, anthracyclines, bleomycin and cytokines produce free radicals and thus are useful as anti-cancer agents. But they also produce many side-effects. 2-methoxyoestradiol and polyunsaturated fatty acids (PUFAs) inhibit SODs and cause an increase of O2(-*) in tumor cells leading to their death. In addition, PUFAs (especially gamma-linolenic acid), 2-methoxyoestradiol and thalidomide may possess anti-angiogenic activity. This suggests that free radicals can suppress angiogenesis. Limited clinical studies done with gamma-linolenic acid showed that it can regress human brain gliomas without any significant side-effects. Thus, PUFAs, thalidomide and 2-methoxyoestradiol or their derivatives may offer a new radical approach to the treatment of cancer.},
  file      = {:by-author/D/Das/2002_Das_RA79.pdf:PDF},
  keywords  = {MSM},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@InBook{Dattorro2006,
  author    = {Dattorro, Jon},
  chapter   = {Chapter 4. Euclidean Distance Matrix},
  pages     = {219--314},
  publisher = {Meboo Publishing USA},
  title     = {Convex Optimization \& Euclidean Distance Geometry},
  year      = {2006},
  file      = {2006_Dattorro_219.pdf:by-author/D/Dattorro/2006_Dattorro_219.pdf:PDF},
  keywords  = {Distance Matrices; Mathematics},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Daujotyte2000,
  author    = {Daujotyte, D. and Klimasauskas, S.},
  journal   = {Nucleic acids symposium series},
  title     = {Affinity photo-crosslinking study of the DNA base flipping pathway by HhaI methyltransferase.},
  year      = {2000},
  number    = {44},
  pages     = {271--2},
  abstract  = {HhaI DNA methyltransferase flips the inner cytosine in the recognition sequence 5'-GCGC-3' out of the DNA helix and into the catalytic site for methylation. To identify intermediate states on the base-flipping pathway, affinity photo-crosslinking experiments were performed with synthetic dodecamer duplexes containing modified bases 2-thiothymine (2sT) or 4-thiothymine (4sT) at the target base position. Here we show that the DNA strand containing 2sT, but not 4sT, covalently cross-links to the HhaI methyltransferase upon irradiation at 340-360 nm.},
  file      = {:by-author/D/Daujotyte/2000_Daujotyte_271.pdf:PDF},
  keywords  = {HhaI},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Daujotyte2004,
  author    = {Daujotyte, Dalia and Serva, Saulius and Vilkaitis, Giedrius and Merkiene, Egle and Venclovas, Ceslovas and Klimasauskas, Saulius},
  journal   = {Structure (London, England : 1993)},
  title     = {HhaI DNA methyltransferase uses the protruding Gln237 for active flipping of its target cytosine.},
  year      = {2004},
  pages     = {1047--55},
  volume    = {12},
  abstract  = {Access to a nucleotide by its rotation out of the DNA helix (base flipping) is used by numerous DNA modification and repair enzymes. Despite extensive studies of the paradigm HhaI methyltransferase, initial events leading to base flipping remained elusive. Here we demonstrate that the replacement of the target C:G pair with the 2-aminopurine:T pair in the DNA or shortening of the side chain of Gln237 in the protein severely perturb base flipping, but retain specific DNA binding. Kinetic analyses and molecular modeling suggest that a steric interaction between the protruding side chain of Gln237 and the target cytosine in B-DNA reduces the energy barrier for flipping by 3 kcal/mol. Subsequent stabilization of an open state by further 4 kcal/mol is achieved through specific hydrogen bonding of the side chain to the orphan guanine. Gln237 thus plays a key role in actively opening the target C:G pair by a "push-and-bind" mechanism.},
  file      = {:by-author/D/Daujotyte/2004_Daujotyte_1047.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Dauter2003,
  author    = {Dauter, Zbigniew},
  journal   = {Acta Crystallographica Section D},
  title     = {Twinned crystals and anomalous phasing},
  year      = {2003},
  pages     = {2004--2016},
  volume    = {59},
  doi       = {10.1107/S0907444903021085},
  file      = {ba5041.pdf:by-author/D/Dauter/2003_Dauter_2004.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444903021085},
}

@Article{Dauter2001,
  author    = {Dauter, Zbigniew and Adamiak, Dorota A.},
  journal   = {Acta Crystallographica Section D},
  title     = {Anomalous signal of phosphorus used for phasing DNA oligomer: importance of data redundancy},
  year      = {2001},
  pages     = {990--995},
  volume    = {57},
  doi       = {10.1107/S0907444901006382},
  file      = {gr2143.pdf:by-author/D/Dauter/2001_Dauter_990.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444901006382},
}

@Article{Dauter2002,
  author    = {Dauter, Zbigniew and Dauter, Miroslawa and Dodson, Eleanor},
  journal   = {Acta Crystallographica Section D},
  title     = {Jolly SAD},
  year      = {2002},
  pages     = {494--506},
  volume    = {58},
  doi       = {10.1107/S090744490200118X},
  file      = {gr2203.pdf:by-author/D/Dauter/2002_Dauter_494.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S090744490200118X},
}

@Article{Dauter2000,
  author    = {Dauter, Z. and Dauter, M. and Rajashankar, K. R.},
  journal   = {Acta crystallographica. Section D, Biological crystallography},
  title     = {Novel approach to phasing proteins: derivatization by short cryo-soaking with halides.},
  year      = {2000},
  pages     = {232--7},
  volume    = {56},
  abstract  = {A quick (less than 1 min) soak of protein crystals in a cryo-solution containing bromide or iodide anions leads to incorporation of these anomalous scatterers into the ordered solvent region around the protein molecules. These halide anions provide a convenient way of phasing through their anomalous scattering signal: bromides using multiwavelength anomalous dispersion (MAD) and bromides and/or iodides using single-wavelength anomalous dispersion (SAD) or single isomorphous replacement with anomalous scattering (SIRAS) methods. This approach has been tested successfully on four different proteins and has been used to solve the structure of a new protein of molecular weight 30 kDa.},
  file      = {:by-author/D/Dauter/2000_Dauter_232.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Davenport2001,
  author    = {R. John Davenport},
  journal   = {Science},
  title     = {Ribozymes. Making Copies in the RNA World},
  year      = {2001},
  pages     = {1278},
  volume    = {292},
  doi       = {10.1126/science.292.5520.1278a},
  file      = {:by-author/D/Davenport/2001_Davenport_1278.war:},
  keywords  = {Ribozymes},
  owner     = {saulius},
  timestamp = {2015.03.02},
  creationdate = {2015-03-02T00:00:00},
}

@Article{David2008,
  author    = {David, W I F and Shankland, K},
  journal   = {Acta crystallographica. Section A, Foundations of crystallography},
  title     = {Structure determination from powder diffraction data.},
  year      = {2008},
  pages     = {52--64},
  volume    = {64},
  file      = {2008_David_52.pdf:by-author/D/David/2008_David_52.pdf:PDF},
  keywords  = {Powder Diffraction; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Davies2002,
  author    = {Douglas R. Davies and Heidrun Interthal and James J. Champoux and Wim G.J. Hol},
  journal   = {Structure},
  title     = {The Crystal Structure of Human Tyrosyl-DNA Phosphodiesterase, Tdp1},
  year      = {2002},
  pages     = {237–248},
  volume    = {10},
  file      = {Davies_2002_237-TyrP_structure.pdf:by-author/D/Davies/2002_Davies_237–248.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Davies2004,
  author    = {Davies, Douglas R and Interthal, Heidrun and Champoux, James J and Hol, Wim G J},
  journal   = {Journal of medicinal chemistry},
  title     = {Explorations of peptide and oligonucleotide binding sites of tyrosyl-DNA phosphodiesterase using vanadate complexes.},
  year      = {2004},
  pages     = {829--37},
  volume    = {47},
  abstract  = {Tyrosyl-DNA phosphodiesterase (Tdp1) catalyzes the hydrolysis of a phosphodiester bond between a tyrosine residue and a DNA 3' phosphate and functions as a DNA repair enzyme that cleaves stalled topoisomerase I-DNA complexes. We previously determined a procedure to crystallize a quaternary complex containing Tdp1, vanadate, a DNA oligonucleotide, and a tyrosine-containing peptide that mimics the transition state for hydrolysis of the Tdp1 substrate. Here, the ability of vanadate to accept a variety of different ligands is exploited to produce several different quaternary complexes with a variety of oligonucleotides, and peptides or a tyrosine analogue, in efforts to explore the binding properties of the Tdp1 DNA and peptide binding clefts. Eight crystal structures of Tdp1 with vanadate, oligonucleotides, and peptides or peptide analogues were determined. These structures demonstrated that Tdp1 is able to bind substituents with limited sequence variation in the polypeptide moiety and also bind oligonucleotides with sequence variation at the 3' end. Additionally, the tyrosine analogue octopamine can replace topoisomerase I derived peptides as the apical ligand to vanadate. The versatility of this system suggests that the formation of quaternary complexes around vanadate could be adapted to become a useful method for structure-based inhibitor design and has the potential to be generally applicable to other enzymes that perform chemistry on phosphate esters.},
  file      = {Davies_2004_829-Tdp1-VO4.pdf:by-author/D/Davies/2004_Davies_829.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Davies2003,
  author    = {Davies, Douglas R and Interthal, Heidrun and Champoux, James J and Hol, Wim G J},
  journal   = {Chemistry \&amp; biology},
  title     = {Crystal structure of a transition state mimic for Tdp1 assembled from vanadate, DNA, and a topoisomerase I-derived peptide.},
  year      = {2003},
  pages     = {139--47},
  volume    = {10},
  file      = {Davies_2003_139-Tdp1-VO4.pdf:by-author/D/Davies/2003_Davies_139.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Davies1999,
  author    = {Davies, G. P. and Kemp, P. and Molineux, I. J. and Murray, N. E.},
  journal   = {Journal of molecular biology},
  title     = {The DNA translocation and ATPase activities of restriction-deficient mutants of Eco KI.},
  year      = {1999},
  pages     = {787--96},
  volume    = {292},
  abstract  = {Eco KI, a type I restriction enzyme, specifies DNA methyltransferase, ATPase, endonuclease and DNA translocation activities. One subunit (HsdR) of the oligomeric enzyme contributes to those activities essential for restriction. These activities involve ATP-dependent DNA translocation and DNA cleavage. Mutations that change amino acids within recognisable motifs in HsdR impair restriction. We have used an in vivo assay to monitor the effect of these mutations on DNA translocation. The assay follows the Eco KI-dependent entry of phage T7 DNA from the phage particle into the host cell. Earlier experiments have shown that mutations within the seven motifs characteristic of the DEAD-box family of proteins that comprise known or putative helicases severely impair the ATPase activity of purified enzymes. We find that the mutations abolish DNA translocation in vivo. This provides evidence that these motifs are relevant to the coupling of ATP hydrolysis to DNA translocation. Mutations that identify an endonuclease motif similar to that found at the active site of type II restriction enzymes and other nucleases have been shown to abolish DNA nicking activity. When conservative changes are made at these residues, the enzymes lack nuclease activity but retain the ability to hydrolyse ATP and to translocate DNA at wild-type levels. It has been speculated that nicking may be necessary to resolve the topological problems associated with DNA translocation by type I restriction and modification systems. Our experiments show that loss of the nicking activity associated with the endonuclease motif of Eco KI has no effect on ATPase activity in vitro or DNA translocation of the T7 genome in vivo.},
  file      = {:by-author/D/Davies/1999_Davies_787.pdf:PDF},
  keywords  = {TypeI},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Davies1999a,
  author    = {Davies, G. P. and Martin, I. and Sturrock, S. S. and Cronshaw, A. and Murray, N. E. and Dryden, D. T.},
  journal   = {Journal of molecular biology},
  title     = {On the structure and operation of type I DNA restriction enzymes.},
  year      = {1999},
  pages     = {565--79},
  volume    = {290},
  abstract  = {Type I DNA restriction enzymes are large, molecular machines possessing DNA methyltransferase, ATPase, DNA translocase and endonuclease activities. The ATPase, DNA translocase and endonuclease activities are specified by the restriction (R) subunit of the enzyme. We demonstrate that the R subunit of the Eco KI type I restriction enzyme comprises several different functional domains. An N-terminal domain contains an amino acid motif identical with that forming the catalytic site in simple restriction endonucleases, and changes within this motif lead to a loss of nuclease activity and abolish the restriction reaction. The central part of the R subunit contains amino acid sequences characteristic of DNA helicases. We demonstrate, using limited proteolysis of this subunit, that the helicase motifs are contained in two domains. Secondary structure prediction of these domains suggests a structure that is the same as the catalytic domains of DNA helicases of known structure. The C-terminal region of the R subunit can be removed by elastase treatment leaving a large fragment, stable in the presence of ATP, which can no longer bind to the other subunits of Eco KI suggesting that this domain is required for protein assembly. Considering these results and previous models of the methyltransferase part of these enzymes, a structural and operational model of a type I DNA restriction enzyme is presented.},
  file      = {:by-author/D/Davies/1999_Davies_565.pdf:PDF},
  keywords  = {TypeI},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Manuscript{Davies1998,
  author    = {Simon Davies},
  title     = {Computer program claims: the final frontier for software inventions},
  year      = {1998},
  keywords  = {Patentai; Teise},
  file      = {:by-author/D/Davies/1998_Davies.doc:DOC},
  owner     = {saulius},
  timestamp = {2015.02.28},
  creationdate = {2015-02-28T00:00:00},
}

@Article{Davis2005,
  author    = {Ian W. Davis and W. Bryan Arendall III and David C. Richardson and Jane S. Richardson},
  journal   = {Structure},
  title     = {The Backrub Motion: How Protein Backbone Shrugs When a Sidechain Dances},
  year      = {2005},
  pages     = {265},
  file      = {:by-author/D/Davis/2005_Davis_265.pdf:PDF},
  keywords  = {Grow Krystal},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Davis2012,
  author      = {Joel G Davis and Kamil P Gierszal and Ping Wang and Dor Ben-Amotz},
  journal     = {Nature},
  title       = {Water structural transformation at molecular hydrophobic interfaces.},
  year        = {2012},
  month       = {Nov},
  number      = {7425},
  pages       = {582--585},
  volume      = {491},
  abstract    = {Hydrophobic hydration is considered to have a key role in biological processes ranging from membrane formation to protein folding and ligand binding. Historically, hydrophobic hydration shells were thought to resemble solid clathrate hydrates, with solutes surrounded by polyhedral cages composed of tetrahedrally hydrogen-bonded water molecules. But more recent experimental and theoretical studies have challenged this view and emphasized the importance of the length scales involved. Here we report combined polarized, isotopic and temperature-dependent Raman scattering measurements with multivariate curve resolution (Raman-MCR) that explore hydrophobic hydration by mapping the vibrational spectroscopic features arising from the hydrophobic hydration shells of linear alcohols ranging from methanol to heptanol. Our data, covering the entire 0-100 °C temperature range, show clear evidence that at low temperatures the hydration shells have a hydrophobically enhanced water structure with greater tetrahedral order and fewer weak hydrogen bonds than the surrounding bulk water. This structure disappears with increasing temperature and is then, for hydrophobic chains longer than ~1 nm, replaced by a more disordered structure with weaker hydrogen bonds than bulk water. These observations support our current understanding of hydrophobic hydration, including the thermally induced water structural transformation that is suggestive of the hydrophobic crossover predicted to occur at lengths of ~1 nm (refs 5, 9, 10, 14).},
  doi         = {10.1038/nature11570},
  file        = {:by-author/D/Davis/2012_Davis_582.pdf:PDF},
  institution = {Purdue University, Department of Chemistry, West Lafayette, Indiana 47907, USA.},
  keywords    = {1-Butanol; Chemistry; Hydrogen Bonding; Hydrophobic and Hydrophilic Interactions; Molecular Structure; Raman; Spectrum Analysis; Temperature; Vibration; Water},
  language    = {eng},
  medline-pst = {ppublish},
  owner       = {alexey},
  pii         = {nature11570},
  pmid        = {23172216},
  timestamp = {2016.03.01},
  creationdate = {2016-03-01T00:00:00},
  url         = {http://dx.doi.org/10.1038/nature11570},
}

@Article{Davis2013,
  author       = {Joel G Davis and Blake M Rankin and Kamil P Gierszal and Dor Ben-Amotz},
  journal      = {Nat Chem},
  title        = {On the cooperative formation of non-hydrogen-bonded water at molecular hydrophobic interfaces.},
  year         = {2013},
  month        = {Sep},
  number       = {9},
  pages        = {796--802},
  volume       = {5},
  abstract     = {The unique structural, dynamical and chemical properties of air/water and oil/water interfaces are thought to play a key role in various biological, geological and environmental processes. For example, non-hydrogen-bonded ('dangling') OH groups--which create surface defects in water's hydrogen bonding network and are experimentally detected at both macroscopic (air/water or oil/water) and microscopic (dissolved hydrophobic molecule) interfaces--are thought to catalyse some chemical reactions. However, how the size, curvature or charge of the exposed hydrophobic surface influences water's propensity to form dangling OH defects has not yet been established quantitatively. Here we use Raman multivariate curve resolution to probe spectroscopically the hydrophobic hydration shell and, using a statistical multisite analysis, we show that such interfacial dangling OH structures are entropically stabilized and their formation is cooperative (the probability that a non-hydrogen-bonded OH group will form depends nonlinearly on the hydrophobic surface area). We thus expose an important difference between the chemical properties of molecular and macroscopic oil/water interfaces.},
  creationdate = {2016-03-01T00:00:00},
  doi          = {10.1038/nchem.1716},
  file         = {:by-author/D/Davis/2013_Davis_1.pdf:PDF},
  institution  = {Purdue University, Department of Chemistry, West Lafayette, Indiana 47907, USA.},
  keywords     = {Air; Chemistry; Hydrogen Bonding; Hydrophobic and Hydrophilic Interactions; Hydroxides; Oils; Temperature; Thermodynamics; Water},
  language     = {eng},
  medline-pst  = {ppublish},
  owner        = {alexey},
  pii          = {nchem.1716},
  pmid         = {23965683},
  timestamp    = {2016.03.01},
  url          = {http://dx.doi.org/10.1038/nchem.1716},
}

@Article{Davis2015,
  author      = {Joel G Davis and Samual R Zukowski and Blake M Rankin and Dor Ben-Amotz},
  journal     = {J Phys Chem B},
  title       = {Influence of a Neighboring Charged Group on Hydrophobic Hydration Shell Structure.},
  year        = {2015},
  month       = {Jul},
  number      = {29},
  pages       = {9417--9422},
  volume      = {119},
  abstract    = {Raman multivariate curve resolution (Raman-MCR), as well as quantum and classical calculations, are used to probe water structural changes in the hydration shells of carboxylic acids and tetraalkyl ammonium ions with various aliphatic chain lengths. The results reveal that water molecules in the hydration shell around the hydrophobic chains undergo a temperature and chain length dependent structural transformation resembling that previously observed in aqueous solutions of n-alcohols. Deprotonation of the carboxylic acid headgroup (at pH ∼ 7) is found to suppress the onset of the hydration-shell structural transformation around the nearest aliphatic methylene group. Tetraalkyl ammonium cations are found to more strongly suppress the water structural transformation, perhaps reflecting the greater intramolecular charge delocalization and suppression of dangling OH defects in water's tetrahedral H-bond network. The observed coupling between ionic and hydrophobic groups, as well as the associated charge asymmetry, may influence the hydrophobicity of proteins and other materials.},
  doi         = {10.1021/jp510641a},
  file        = {:by-author/D/Davis/2014_Davis_0000.pdf:PDF},
  institution = {Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States.},
  language    = {eng},
  medline-pst = {ppublish},
  owner       = {alexey},
  pmid        = {25415181},
  timestamp = {2016.03.01},
  creationdate = {2016-03-01T00:00:00},
  url         = {http://dx.doi.org/10.1021/jp510641a},
}

@TechReport{Davoli1994,
  author      = {Michael Kenneth Davoli},
  institution = {Departament of Computer Science and Engineering, Auburn University},
  title       = {Scalable, Full-matrix Least-squares Refinement of Small Molecular Structures on a Distributed Memory Multiprocessing System},
  year        = {1994},
  file        = {:by-author/D/Davoli/1994_Davoli_techreport.pdf:PDF},
  keywords    = {Refinement; X-ray Crystallography},
  owner       = {saulius},
  pages       = {techreport},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Manuscript{Dawid1966,
  author    = {A. P. Dawid and M. Stone and J. V. Zidek},
  title     = {Critique of E. T. Jaynes's "Paradoxes of Probability Theory"},
  year      = {1966},
  keywords  = {Bayesian-statistics; Mathematics},
  file      = {:by-author/D/Dawid/1966_Dawid.PS.bz2:PS BZ2},
  groups    = {sg/Bayesian},
  owner     = {saulius},
  timestamp = {2015.03.03},
  creationdate = {2015-03-03T00:00:00},
}

@TechReport{Dawkins2009,
  author      = {Bill Dawkins and Ramamurthy Krithivas and Arnold Jones},
  institution = {SNIA},
  title       = {Common RAID Disk Data Format Specification},
  year        = {2009},
  month       = {Mar},
  note        = {This document has been released and approved by the SNIA. The SNIA believes that the ideas, methodologies and technologies described in this document accurately represent the SNIA goals and are appropriate for widespread distribution. Suggestion for revision should be directed to http://www.snia.org/feedback/.},
  abstract    = {In today’s IT environments, there are several reasons why system administrators would wish to change the internal RAID solutions they are using. For example, many servers are shipped with a RAID solution implemented on the motherboard (ROMB). ROMB solutions allow RAID formats to be applied to the disks internal to the server. As the server’s data set grows, the administrator often finds s/he needs to move to a larger direct attached storage (DAS) solution with external JBODs. The system administrator would like to move the internal disks and their data to the DAS system’s external JBODs. One method of migration is to backup a RAID group, transfer the disks to the new storage system, reconfigure the disks as a new RAID group behind the new RAID controller, and restore the data from the backup device. This time consuming procedure also carries some risk of data loss. A better method would be to move the disks with data-in-place from one RAID implementation to another. Unfortunately, the different methods for storing configuration information prohibit data-in-place migration between systems from different storage vendors. The SNIA Common RAID Disk Data Format Technical Working Group was chartered define a standard data structure describing how data is formatted across the disks in a RAID group. This specification defines the Common RAID Disk Data Format (DDF) structure. The DDF structure allows a basic level of interoperability between different suppliers of RAID technology. The Common RAID DDF structure benefits storage users by enabling data-in-place migration among systems from different vendors. Part of the specification defines how data is distributed for many basic RAID levels. This is necessary to precisely document how data is formatted for RAID levels indicated by the DDF structure. The DDF TWG recognizes that the formats described do not represent all methods for implementing the defined RAID levels. The SNIA does not imply that specification formats represent a preferred RAID implementation. Reviewers of this specification are encouraged to suggest alternate RAID level formats for inclusion into future revisions of the specification.},
  comment     = {Version 2.0 Revision 19},
  file        = {:by-author/D/Dawkins/2009_Dawkins_trv2.0r19.pdf:PDF},
  owner       = {saulius},
  pages       = {trv2.0r19},
  timestamp = {2012.11.27},
  creationdate = {2012-11-27T00:00:00},
  url         = {http://www.snia.org/sites/default/files/SNIA_DDF_Technical_Position_v2.0.pdf},
}

@InBook{Dawson2003,
  author    = {Michael R.W. Dawson},
  chapter   = {11},
  title     = {Perceptrons And Logic Gates},
  year      = {2003},
  booktitle = {Trains Of Thought},
  file      = {:by-author/D/Dawson/2003_Dawson.pdf:PDF},
  keywords  = {Boolean Algebra; Computer Architecture; Computer Science (CS)},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Day2012,
  author           = {Day, Nick and Downing, Jim and Adams, Sam and England, N. W. and Murray-Rust, Peter},
  journal          = {Journal of Applied Crystallography},
  title            = {{CrystalEye}: automated aggregation, semantification and dissemination of the world’s open crystallographic data},
  year             = {2012},
  pages            = {316--323},
  volume           = {45},
  abstract         = {CrystalEye automatically aggregates crystallographic data from web resources (the supplementary data to articles on publishers’ web sites) into a structured XML-based repository, and then adds value to that open data by providing methods to easily browse, search and to keep up-to-date with the latest published information.},
  creationdate     = {2015-02-11T00:00:00},
  doi              = {10.1107/S0021889812006462},
  file             = {:./by-author/D/Day/2012_Day_316.pdf:PDF},
  modificationdate = {2023-07-17T19:56:45},
  owner            = {antanas},
  timestamp        = {2015.02.11},
}

@PhdThesis{Day2008,
  author           = {Nicholas Elliot Day},
  school           = {University of Cambridge},
  title            = {Automated Analysis and Validation of Open Chemical Data},
  year             = {2008},
  month            = {nov},
  abstract         = {Methods to automatically extract Open Data from the chemical literature, validate it, and use it to validate theory are examined. Chemical identifiers which assist the automatic location of chemical struc- tures using commercial Web search engines are investigated. The IUPAC International Chemical Idenfitifer (InChI) gives almost 100% recall and pre- cision, though is shown to be too long for present search engines. A com- bination of InChI and InChIKey, a shorter, fixed-length hash of the InChI string, is concluded to be the best current method of identifying structures. The proportion of published, Open Crystallographic Information Files (CIFs) that are valid with respect to the specification is shown to be im- proving, and is around 99% in 2007. The error rate in the conversion of valid CIFs to Chemical Markup Language (CML) is less than 0.2%. The machine generation of connection tables from CIFs requires many heuristics, and in some cases it is impossible to deduce the exact connection table. CrystalEye, a fully-automated system for the reformulation of the frag- mented crystallographic Web into a structured XML-based repository is de- scribed. Published, Open CIFs can be located and aggregated programmat- ically with almost 100% recall. It is shown that, by converting CIF data to CML, software can be created to use the latest Web standards and tech- nologies to enhance the ability of Web users to browse, find, keep updated, download and reuse the latest published crystallography. A workflow for the high-throughput calculation of solid-state geometry using a semi-empirical method is described. A wide-range of organic and inorganic systems provided by CrystalEye are used to test both the data and the method. Several errors in the method are discovered, many of which can be attributed to the parameterization process. An Open NMR experiment to perform high-throughput prediction of 13 C chemical shifts using a GIAO protocol is described. The data and analysis were provided on publicly-available webpages to enable crowdsourcing, which assisted in discovering an error rate of 6.1% in the starting data. The protocol was refined during the work and shown to have an average unsigned error of 2.24ppm for 13 C nuclei of small, rigid molecules; comparable to the errors observed elsewhere for general structures using HOSE and Neural Network methods.},
  creationdate     = {2013-09-19T00:00:00},
  file             = {2008_Day_phdthesis.pdf:by-author/D/Day/2008_Day_phdthesis.pdf:PDF},
  keywords         = {CIF; Crystallography; Data Management; NMR; X-ray Crystallography},
  modificationdate = {2023-08-07T10:23:05},
  owner            = {saulius},
  timestamp        = {2013.09.19},
  url              = {https://www.repository.cam.ac.uk/bitstream/handle/1810/238467/ned24-thesis-corrected-1_A1b.pdf?sequence=1},
}

@Article{Day2011,
  author           = {Nick E. Day and Peter Murray-Rust and Simon M. Tyrrell},
  journal          = {J. Appl. Cryst.},
  title            = {CIFXML: A Schema and Toolkit for Managing CIFs in XML},
  year             = {2011},
  pages            = {628--634},
  volume           = {44},
  abstract         = {CIFXML applies the XML strategies and technologies to create a general interface for processing CIF documents that conform to the CIF syntax and DDL1. Both a DTD and an XML schema for CIFs are presented. CIFs can be read, edited, validated syntactically, sorted, normalized, filtered, stored as an XML document object model, transformed and output. CIFXOM provides an easy way of converting CIFs to XML and vice versa using Java.},
  creationdate     = {2013-09-19T00:00:00},
  doi              = {10.1107/S0021889811011058},
  file             = {2011_Day_628.pdf:by-author/D/Day/2011_Day_628.pdf:PDF},
  keywords         = {CIF; CML; Chemoinformatics; Crystallography; Data Formats; Data Management; X-ray Crystallography; XML},
  modificationdate = {2023-08-07T10:23:05},
  owner            = {saulius},
  timestamp        = {2013.09.19},
  url              = {http://journals.iucr.org/j/issues/2011/03/00/he5526},
}

@Article{Backer1991,
  author    = {De Backer, O. and Colson, C.},
  journal   = {Journal of bacteriology},
  title     = {Two-step cloning and expression in Escherichia coli of the DNA restriction-modification system StyLTI of Salmonella typhimurium.},
  year      = {1991},
  pages     = {1321--7},
  volume    = {173},
  abstract  = {The StyLTI restriction-modification system is common to most strains of the genus Salmonella, including Salmonella typhimurium. We report here the two-step cloning of the genes controlling the StyLTI system. The StyLTI methylase gene (mod) was cloned first. Then, the companion endonuclease gene (res) was introduced on a compatible vector. A strain of S. typhimurium sensitive to the coliphage lambda was constructed and used to select self-modifying recombinant phages from a Res- Mod+ S. typhimurium genomic library in the lambda EMBL4 cloning vector. The methylase gene of one of these phages was then subcloned in pBR328 and transferred into Escherichia coli. In the second step, the closely linked endonuclease and methylase genes were cloned together on a single DNA fragment inserted in pACYC184 and introduced into the Mod+ E. coli strain obtained in the first step. Attempts to transform Mod- E. coli or S. typhimurium strains with this Res+ Mod+ plasmid were unsuccessful, whereas transformation of Mod+ strains occurred at a normal frequency. This can be understood if the introduction of the StyLTI genes into naive hosts is lethal because of degradation of host DNA by restriction activity; in contrast to most restriction-modification systems, StyLTI could not be transferred into naive hosts without killing them. In addition, it was found that strains containing only the res gene are viable and lack restriction activity in the absence of the companion mod gene. This suggests that expression of the StyLTI endonuclease activity requires at least one polypeptide involved in the methylation activity, as is the case for types I and III restriction-modification systems but not for type II systems.},
  file      = {:by-author/D/DeBacker/1991_Backer_1321.pdf:PDF},
  keywords  = {TypeI},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{DeLasPenas2014,
  author    = {De Las Pe{\~{n}}as, Ma. Louise Antonette N. and Loyola, Mark L. and Basilio, Antonio M. and Santoso, Eko Budi},
  journal   = {Acta Crystallographica Section A},
  title     = {Symmetry groups of single-wall nanotubes},
  year      = {2014},
  pages     = {12--23},
  volume    = {70},
  abstract  = {This work investigates the symmetry properties of single-wall carbon nanotubes and their structural analogs, which are nanotubes consisting of different kinds of atoms. The symmetry group of a nanotube is studied by looking at symmetries and color fixing symmetries associated with a coloring of the tiling by hexagons in the Euclidean plane which, when rolled, gives rise to a geometric model of the nanotube. The approach is also applied to nanotubes with non-hexagonal symmetry arising from other isogonal tilings of the plane.},
  doi       = {10.1107/S2053273313023887},
  file      = {:by-author/D/DeLasPenas/2014_DeLasPenas_12.pdf:PDF},
  owner     = {saulius},
  timestamp = {2014.03.23},
  creationdate = {2014-03-23T00:00:00},
  url       = {http://dx.doi.org/10.1107/S2053273313023887},
}

@Article{DeSimone2005,
  author    = {De Simone, Giuseppina and Di Fiore, Anna and Valeria Menchise and Carlo Pedone and Jochen Antel and Angela Casini and Andrea Scozzafava and Michael Wurlb and Claudiu T. Supuran},
  journal   = {Bioorganic \& Medicinal Chemistry Letters},
  title     = {Carbonic anhydrase inhibitors. Zonisamide is an effective inhibitor of the cytosolic isozyme II and mitochondrial isozyme V: solution and X-ray crystallographic studies},
  year      = {2005},
  pages     = {2315--2320},
  volume    = {15},
  file      = {2005_DeSimone_2315.pdf:by-author/D/DeSimone/2005_DeSimone_2315.pdf:PDF},
  groups    = {sg/inhibitors, sg/hCA2, sg/hCA5},
  keywords  = {Carbonic Anhydrases},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Debattista2005,
  author    = {K. Debattista and V. Sundstedt and F. Pereira and A. Chalmers},
  title     = {Selective Parallel Rendering for High-Fidelity Graphics},
  year      = {2005},
  file      = {:by-author/D/Debattista/2005_Debattista.pdf:PDF},
  keywords  = {Computer Graphics; Computer Science (CS)},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Debreczeni2003,
  author    = {Debreczeni, Judit {\'{E}}. and Bunk{\'{o}}czi, G{\'{a}}bor and Ma, Qingjun and Blaser, Heiko and Sheldrick, George M.},
  journal   = {Acta Crystallographica Section D},
  title     = {In-house measurement of the sulfur anomalous signal and its use for phasing},
  year      = {2003},
  pages     = {688--696},
  volume    = {59},
  doi       = {10.1107/S0907444903002646},
  file      = {wd0005.pdf:by-author/D/Debreczeni/2003_Debreczeni_688.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444903002646},
}

@Article{Debye1913,
  author    = {Debye, P.},
  journal   = {Annalen der Physik},
  title     = {Interferenz von Röntgenstrahlen und Wärmebewegung},
  year      = {1913},
  issn      = {1521-3889},
  pages     = {49--92},
  volume    = {348},
  doi       = {10.1002/andp.19133480105},
  file      = {1913_Debye_49.pdf:by-author/D/Debye/1913_Debye_49.pdf:PDF},
  keywords  = {Atomic Displacement Parameters; Crystallography; Debye-Waller Factor; X-ray Crystallography},
  owner     = {saulius},
  publisher = {WILEY-VCH Verlag},
  timestamp = {2013.05.03},
  creationdate = {2013-05-03T00:00:00},
  url       = {http://dx.doi.org/10.1002/andp.19133480105},
}

@TechReport{Decai2005,
  author      = {Jiao Decai and David Sinclair},
  institution = {School of Computing, Dublin City University, Glasnevin, Dublin 9, Ireland},
  title       = {A Weakest Precondition Calculus for Applied π-Calculus},
  year        = {2005},
  month       = {November},
  file        = {:by-author/D/Decai/2005_Decai.pdf:PDF},
  keywords    = {Computer Science (CS); Weakest Preconditions},
  owner       = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Degtyarenko2000,
  author    = {Degtyarenko, K.},
  journal   = {Bioinformatics (Oxford, England)},
  title     = {Bioinorganic motifs: towards functional classification of metalloproteins.},
  year      = {2000},
  pages     = {851--64},
  volume    = {16},
  abstract  = {The habitat of bioinorganic motifs (BIMs) is at the interface of biological inorganic chemistry and bioinformatics. BIM is defined as a common structural feature shared by functionally related, but not necessarily homologous, proteins, and consisting of the metal atom(s) and first coordination shell ligands. BIMs appear to be suitable for classification of metal centres at any level, from groups of unrelated proteins with similar function to different functional states of the same protein, and for description of possible evolutionary relationships of metalloproteins. However, they have not attracted wide attention from the bioinformatics community. Although their presence is appreciated, they are difficult to predict-therefore the current 'high-throughput' initiatives are likely to miss or ignore them altogether. The protein sequence databases do not distinguish between proteins containing different prosthetic groups (unless they have different sequences) or between apo- and holoprotein. On the other hand, the protein structure databases include data on 'hetero compounds' of various origin but these data are often inconsistent. A number of specialized databases dealing with BIMs and attempts to classify them are reviewed. SUPPLEMENTARY INFORMATION: The additional bibliography and list of Internet resources on bioinorganic chemistry are available at http://www.ebi.ac.uk/ approximately kirill/biometal/},
  file      = {:by-author/D/Degtyarenko/2000_Degtyarenko_851.pdf:PDF},
  keywords  = {Bioinformatics},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@Article{Deibert1999,
  author    = {Deibert, M. and Grazulis, S. and Janulaitis, A. and Siksnys, V. and Huber, R.},
  journal   = {The EMBO journal},
  title     = {Crystal structure of MunI restriction endonuclease in complex with cognate DNA at 1.7 A resolution.},
  year      = {1999},
  pages     = {5805--16},
  volume    = {18},
  abstract  = {The MunI restriction enzyme recognizes the palindromic hexanucleotide sequence C/AATTG (the '/' indicates the cleavage site). The crystal structure of its active site mutant D83A bound to cognate DNA has been determined at 1.7 A resolution. Base-specific contacts between MunI and DNA occur exclusively in the major groove. While DNA-binding sites of most other restriction enzymes are comprised of discontinuous sequence segments, MunI combines all residues involved in the base-specific contacts within one short stretch (residues R115-R121) located at the N-terminal region of the 3(10)4 helix. The outer CG base pair of the recognition sequence is recognized solely by R115 through hydrogen bonds made by backbone and side chain atoms to both bases. The mechanism of recognition of the central AATT nucleotides by MunI is similar to that of EcoRI, which recognizes the G/AATTC sequence. The local conformation of AATT deviates from the typical B-DNA form and is remarkably similar to EcoRI-DNA. It appears to be essential for specific hydrogen bonding and recognition by MunI and EcoRI.},
  file      = {:by-author/D/Deibert/1999_Deibert_5805.pdf:PDF},
  keywords  = {Struct; TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Deibert2000,
  author       = {M. Deibert and S. Grazulis and G. Sasnauskas and V. Siksnys and R. Huber},
  journal      = {Nat. Struct. Biol.},
  title        = {Structure of the tetrameric restriction endonuclease NgoMIV in complex with cleaved DNA.},
  year         = {2000},
  month        = {Sep},
  number       = {9},
  pages        = {792--799},
  volume       = {7},
  abstract     = {The crystal structure of the NgoMIV restriction endonuclease in complex with cleaved DNA has been determined at 1.6 A resolution. The crystallographic asymmetric unit contains a protein tetramer and two DNA molecules cleaved at their recognition sites. This is the first structure of a tetrameric restriction enzyme-DNA complex. In the tetramer, two primary dimers are arranged back to back with two oligonucleotides bound in clefts on opposite sides of the tetramer. The DNA molecules retain a B-type conformation and have an enclosed angle between their helical axes of 60 degrees. Sequence-specific interactions occur in both the major and minor grooves. Two Mg2+ ions are located close to the cleaved phosphate at the active site of NgoMIV. Biochemical experiments show that interactions between the recognition sites within the tetramer greatly increase DNA cleavage efficiency.},
  creationdate = {2011-06-10T00:00:00},
  doi          = {10.1038/79032},
  file         = {2000_Deibert_792.pdf:by-author/D/Deibert/2000_Deibert_792.pdf:PDF},
  groups       = {sg/NgoMIV},
  institution  = {Max-Planck-Institut für Biochemie, D-82152 Planegg-Martinsried, Germany. markus.deibert@cii.de},
  keywords     = {Amino Acid Sequence; Base Sequence; Binding Sites; Chemistry/genetics/metabolism; Chemistry/metabolism; Crystallography; DNA; DNA-Binding Proteins; Deoxyribonucleases; Dimerization; Endonucleases; Enzymology; Genetics; Magnesium; Metabolism; Models; Molecular; Molecular Sequence Data; Neisseria Gonorrhoeae; Nucleic Acid; Nucleic Acid Conformation; Plasmids; Protein Structure; Quaternary; Regulatory Sequences; Secondary; Sequence Alignment; Structure-activity Relationship (SAR); Substrate Specificity; Type II Site-Specific; X-Ray},
  language     = {eng},
  medline-pst  = {ppublish},
  owner        = {em},
  pmid         = {10966652},
  timestamp    = {2011.06.10},
  url          = {http://dx.doi.org/10.1038/79032},
}

@Article{Deibert2000a,
  author    = {Deibert, M. and Grazulis, S. and Sasnauskas, G. and Siksnys, V. and Huber, R.},
  journal   = {Nature structural biology},
  title     = {Structure of the tetrameric restriction endonuclease NgoMIV in complex with cleaved DNA.},
  year      = {2000},
  pages     = {792--9},
  volume    = {7},
  abstract  = {The crystal structure of the NgoMIV restriction endonuclease in complex with cleaved DNA has been determined at 1.6 A resolution. The crystallographic asymmetric unit contains a protein tetramer and two DNA molecules cleaved at their recognition sites. This is the first structure of a tetrameric restriction enzyme-DNA complex. In the tetramer, two primary dimers are arranged back to back with two oligonucleotides bound in clefts on opposite sides of the tetramer. The DNA molecules retain a B-type conformation and have an enclosed angle between their helical axes of 60 degrees. Sequence-specific interactions occur in both the major and minor grooves. Two Mg2+ ions are located close to the cleaved phosphate at the active site of NgoMIV. Biochemical experiments show that interactions between the recognition sites within the tetramer greatly increase DNA cleavage efficiency.},
  file      = {:by-author/D/Deibert/2000_Deibert_792.pdf:PDF},
  groups    = {sg/NgoMIV},
  keywords  = {TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Deiters2003,
  author    = {Deiters, Alexander and Cropp, T. Ashton and Mukherji, Mridul and Chin, Jason W. and Anderson, J. Christopher and Schultz, Peter G.},
  journal   = {Journal of the American Chemical Society},
  title     = {Adding amino acids with novel reactivity to the genetic code of Saccharomyces cerevisiae.},
  year      = {2003},
  pages     = {11782--3},
  volume    = {125},
  abstract  = {Using a novel genetic selection, we have identified a series of mutants of the E. coli tyrosyl-tRNA synthetase that selectively charge an amber suppressor tRNA with p-(propargyloxy)phenylalanine and p-azidophenylalanine in yeast. These evolved tRNA-synthetase pairs can be used to site-specifically label proteins with functional groups orthogonal to normal biological chemistries. As an example, we have shown that proteins containing these amino acids can be efficiently bioconjugated with small organic molecules by a [3 + 2] cycloaddition reaction that is mild enough for the manipulation of biological samples.},
  file      = {:by-author/D/Deiters/2003_Deiters_11782.pdf:PDF},
  keywords  = {Bioconjugation},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@Article{Deiters2003a,
  author    = {Deiters, Alexander and Cropp, T. Ashton and Mukherji, Mridul and Chin, Jason W. and Anderson, J. Christopher and Schultz, Peter G.},
  journal   = {Journal of the American Chemical Society},
  title     = {Adding amino acids with novel reactivity to the genetic code of Saccharomyces cerevisiae.},
  year      = {2003},
  pages     = {supporting-info},
  volume    = {125},
  file      = {:by-author/D/Deiters/2003_Deiters_supporting.pdf:PDF},
  keywords  = {Bioconjugation},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@Article{Dekker2004,
  author    = {Carien Dekker and Lesley Haire and Guy Dodson},
  journal   = {Journal of Applied Crystallography},
  title     = {Vapour-diffusion protein crystallization in newly designed pore strips},
  year      = {2004},
  pages     = {862--866},
  volume    = {37},
  doi       = {10.1107/S0021889804018928},
  file      = {2004_Dekker_862.pdf:by-author/D/Dekker/2004_Dekker_862.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Delagoutte2001,
  author    = {Delagoutte, E. and von Hippel, P. H.},
  journal   = {Biochemistry},
  title     = {Molecular mechanisms of the functional coupling of the helicase (gp41) and polymerase (gp43) of bacteriophage T4 within the DNA replication fork.},
  year      = {2001},
  pages     = {4459--77},
  volume    = {40},
  abstract  = {Processive strand-displacement DNA synthesis with the T4 replication system requires functional "coupling" between the DNA polymerase (gp43) and the helicase (gp41). To define the physical basis of this functional coupling, we have used analytical ultracentrifugation to show that gp43 is a monomeric species at physiological protein concentrations and that gp41 and gp43 do not physically interact in the absence of DNA, suggesting that the functional coupling between gp41 and gp43 depends significantly on interactions modulated by the replication fork DNA. Results from strand-displacement DNA synthesis show that a minimal gp41-gp43 replication complex can perform strand-displacement synthesis at approximately 90 nts/s in a solution containing poly(ethylene glycol) to drive helicase loading. In contrast, neither the Klenow fragment of Escherichia coli DNA polymerase I nor the T7 DNA polymerase, both of which are nonprocessive polymerases, can carry out strand-displacement DNA synthesis with gp41, suggesting that the functional helicase-polymerase coupling may require the homologous system. However, we show that a heterologous helicase-polymerase pair can work if the polymerase is processive. Strand-displacement DNA synthesis using the gp41 helicase with the T4 DNA polymerase holoenzyme or the phage T7 DNA polymerase-thioredoxin complex, both of which are processive, proceeds at the rate of approximately 250 nts/s. However, replication fork assembly is less efficient with the heterologous helicase-polymerase pair. Therefore, a processive (homologous or heterologous) "trailing" DNA polymerase is sufficient to improve gp41 processivity and unwinding activity in the elongation stage of the helicase reaction, and specific T4 helicase-polymerase coupling becomes significant only in the assembly (or initiation) stage.},
  file      = {:by-author/D/Delagoutte/2001_Delagoutte_4459.pdf:PDF},
  keywords  = {Replisoma; {gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Delagoutte2003,
  author    = {Delagoutte, Emmanuelle and Von Hippel, Peter H.},
  journal   = {The Journal of biological chemistry},
  title     = {Function and assembly of the bacteriophage T4 DNA replication complex: interactions of the T4 polymerase with various model DNA constructs.},
  year      = {2003},
  pages     = {25435--47},
  volume    = {278},
  abstract  = {Complexes formed between DNA polymerase and genomic DNA at the replication fork are key elements of the replication machinery. We used sedimentation velocity, fluorescence anisotropy, and surface plasmon resonance to measure the binding interactions between bacteriophage T4 DNA polymerase (gp43) and various model DNA constructs. These results provide quantitative insight into how this replication polymerase performs template-directed 5' --&gt; 3' DNA synthesis and how this function is coordinated with the activities of the other proteins of the replication complex. We find that short (single- and double-stranded) DNA molecules bind a single gp43 polymerase in a nonspecific (overlap) binding mode with moderate affinity (Kd approximately 150 nm) and a binding site size of approximately 10 nucleotides for single-stranded DNA and approximately 13 bp for double-stranded DNA. In contrast, gp43 binds in a site-specific (nonoverlap) mode and significantly more tightly (Kd approximately 5 nm) to DNA constructs carrying a primer-template junction, with the polymerase covering approximately 5 nucleotides downstream and approximately 6-7 bp upstream of the 3'-primer terminus. The rate of this specific binding interaction is close to diffusion-controlled. The affinity of gp43 for the primer-template junction is modulated specifically by dNTP substrates, with the next "correct" dNTP strengthening the interaction and an incorrect dNTP weakening the observed binding. These results are discussed in terms of the individual steps of the polymerase-catalyzed single nucleotide addition cycle and the replication complex assembly process. We suggest that changes in the kinetics and thermodynamics of these steps by auxiliary replication proteins constitute a basic mechanism for protein coupling within the replication complex.},
  file      = {:by-author/D/Delagoutte/2003_Delagoutte_25435.pdf:PDF},
  keywords  = {{gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Delaunay1933,
  author    = {Delaunay, B.},
  journal   = {Zeitschrift für Kristallographie - Crystalline Materials},
  title     = {Neue Darstellung der geometrischen Kristallographie},
  year      = {1933},
  pages     = {109--149},
  volume    = {84},
  doi       = {10.1524/zkri.1933.84.1.109},
  file      = {1933_Delaunay_109.pdf:by-author/D/Delaunay/1933_Delaunay_109.pdf:PDF},
  groups    = {sg/Cell sg/Reduction, sg/Cell reduction},
  keywords  = {Reduced Cell},
  owner     = {saulius},
  timestamp = {2014.11.18},
  creationdate = {2014-11-18T00:00:00},
}

@Article{Delic2008,
  author    = {Delic, Kemal A. and Walker, Martin Anthony},
  journal   = {Ubiquity},
  title     = {Emergence of the Academic Computing Clouds},
  year      = {2008},
  issn      = {1530-2180},
  pages     = {1:1-1:1},
  volume    = {2008},
  abstract  = {Computational grids are very large-scale aggregates of communication and computation resources enabling new types of applications and bringing several benefits of economy-of-scale. The first computational grids were established in academic environments during the previous decade, and today are making inroads into the realm of corporate and enterprise computing. Very recently, we observe the emergence of cloud computing as a new potential super structure for corporate, enterprise and academic computing. While cloud computing shares the same original vision of grid computing articulated in the 1990s by Foster, Kesselman and others, there are significant differences. In this paper, we first briefly outline the architecture, technologies and standards of computational grids. We then point at some of notable examples of academic use of grids and sketch the future of research in grids. In the third section, we draw some architectural lines of cloud computing, hint at the design and technology choices and indicate some future challenges. In conclusion, we claim that academic computing clouds might appear soon, supporting the emergence of Science 2.0 activities, some of which we list shortly.},
  address   = {New York, NY, USA},
  articleno = {1},
  doi       = {10.1145/1414663.1414664},
  file      = {:by-author/D/Delic/2008_Delic_1\:1.pdf:PDF},
  owner     = {saulius},
  publisher = {ACM},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://doi.acm.org/10.1145/1414663.1414664},
}

@Article{Deller2015,
  author    = {Deller, Marc C. and Rupp, Bernhard},
  journal   = {Journal of Computer-Aided Molecular Design},
  title     = {Models of protein–ligand crystal structures: trust, but verify},
  year      = {2015},
  issn      = {1573-4951},
  month     = {Feb},
  number    = {9},
  pages     = {817–836},
  volume    = {29},
  abstract  = {X-ray crystallography provides the most accurate models of protein–ligand structures. These models serve as the foundation of many computational methods including structure prediction, molecular modelling, and structure-based drug design. The success of these computational methods ultimately depends on the quality of the underlying protein–ligand models. X-ray crystallography offers the unparalleled advantage of a clear mathematical formalism relating the experimental data to the protein–ligand model. In the case of X-ray crystallography, the primary experimental evidence is the electron density of the molecules forming the crystal. The first step in the generation of an accurate and precise crystallographic model is the interpretation of the electron density of the crystal, typically carried out by construction of an atomic model. The atomic model must then be validated for fit to the experimental electron density and also for agreement with prior expectations of stereochemistry. Stringent validation of protein–ligand models has become possible as a result of the mandatory deposition of primary diffraction data, and many computational tools are now available to aid in the validation process. Validation of protein–ligand complexes has revealed some instances of overenthusiastic interpretation of ligand density. Fundamental concepts and metrics of protein–ligand quality validation are discussed and we highlight software tools to assist in this process. It is essential that end users select high quality protein–ligand models for their computational and biological studies, and we provide an overview of how this can be achieved.},
  doi       = {10.1007/s10822-015-9833-8},
  file      = {2015_Deller_817.pdf:by-author/D/Deller/2015_Deller_817.pdf:PDF},
  groups    = {sg/Crystallography, am/Crystallography, am/Data quality},
  owner     = {andrius},
  publisher = {Springer Nature},
  timestamp = {2016.12.27},
  creationdate = {2016-12-27T00:00:00},
  url       = {http://dx.doi.org/10.1007/s10822-015-9833-8},
}

@Article{Delver1991,
  author    = {Delver, E. P. and Kotova, V. U. and Zavilgelsky, G. B. and Belogurov, A. A.},
  journal   = {Journal of bacteriology},
  title     = {Nucleotide sequence of the gene (ard) encoding the antirestriction protein of plasmid colIb-P9.},
  year      = {1991},
  pages     = {5887--92},
  volume    = {173},
  abstract  = {The IncI1 plasmid ColIb-P9 was found to encode an antirestriction function. The relevant gene, ard (alleviation of restriction of DNA), maps about 5 kb from the origin of transfer, in the region transferred early during bacterial conjugation. Ard inhibits both restriction and modification by each of the four type I systems of Escherichia coli tested, but it had no effect on restriction by either EcoRI, a type II system, or EcoP1, a type III system. The nucleotide sequence of the ColIb ard gene was determined; the predicted molecular weight of the Ard polypeptide is 19,193. The proposed polypeptide chain contains an excess of 25 negatively charged amino acids, suggesting that its overall character is very acidic. Deletion analysis of the gene revealed that the Ard protein contained a distinct functional domain located in the COOH-terminal half of the polypeptide. We suggest that the biological role of the ColIb Ard protein is associated with overcoming host-controlled restriction during bacterial conjugation.},
  file      = {:by-author/D/Delver/1991_Delver_5887.pdf:PDF},
  keywords  = {Antirestriction},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Demir2010,
  author    = {Demir, Emek and Cary, Michael P. and Paley, Suzanne and Fukuda, Ken and Lemer, Christian and Vastrik, Imre and Wu, Guanming and D'Eustachio, Peter and Schaefer, Carl and Luciano, Joanne and Schacherer, Frank and Martinez-Flores, Irma and Hu, Zhenjun and Jimenez-Jacinto, Veronica and Joshi-Tope, Geeta and Kandasamy, Kumaran and Lopez-Fuentes, Alejandra C. and Mi, Huaiyu and Pichler, Elgar and Rodchenkov, Igor and Splendiani, Andrea and Tkachev, Sasha and Zucker, Jeremy and Gopinath, Gopal and Rajasimha, Harsha and Ramakrishnan, Ranjani and Shah, Imran and Syed, Mustafa and Anwar, Nadia and Babur, Ozgün and Blinov, Michael and Brauner, Erik and Corwin, Dan and Donaldson, Sylva and Gibbons, Frank and Goldberg, Robert and Hornbeck, Peter and Luna, Augustin and Murray-Rust, Peter and Neumann, Eric and Reubenacker, Oliver and Samwald, Matthias and van Iersel, Martijn and Wimalaratne, Sarala and Allen, Keith and Braun, Burk and Whirl-Carrillo, Michelle and Cheung, Kei-Hoi and Dahlquist, Kam and Finney, Andrew and Gillespie, Marc and Glass, Elizabeth and Gong, Li and Haw, Robin and Honig, Michael and Hubaut, Olivier and Kane, David and Krupa, Shiva and Kutmon, Martina and Leonard, Julie and Marks, Debbie and Merberg, David and Petri, Victoria and Pico, Alex and Ravenscroft, Dean and Ren, Liya and Shah, Nigam and Sunshine, Margot and Tang, Rebecca and Whaley, Ryan and Letovksy, Stan and Buetow, Kenneth H. and Rzhetsky, Andrey and Schachter, Vincent and Sobral, Bruno S. and Dogrusoz, Ugur and McWeeney, Shannon and Aladjem, Mirit and Birney, Ewan and Collado-Vides, Julio and Goto, Susumu and Hucka, Michael and Le Novère, Nicolas and Maltsev, Natalia and Pandey, Akhilesh and Thomas, Paul and Wingender, Edgar and Karp, Peter D. and Sander, Chris and Bader, Gary D.},
  journal   = {Nature biotechnology},
  title     = {The BioPAX community standard for pathway data sharing.},
  year      = {2010},
  pages     = {935--42},
  volume    = {28},
  abstract  = {Biological Pathway Exchange (BioPAX) is a standard language to represent biological pathways at the molecular and cellular level and to facilitate the exchange of pathway data. The rapid growth of the volume of pathway data has spurred the development of databases and computational tools to aid interpretation; however, use of these data is hampered by the current fragmentation of pathway information across many databases with incompatible formats. BioPAX, which was created through a community process, solves this problem by making pathway data substantially easier to collect, index, interpret and share. BioPAX can represent metabolic and signaling pathways, molecular and genetic interactions and gene regulation networks. Using BioPAX, millions of interactions, organized into thousands of pathways, from many organisms are available from a growing number of databases. This large amount of pathway data in a computable form will support visualization, analysis and biological discovery.},
  doi       = {10.1038/nbt.1666},
  file      = {:by-author/D/Demir/2010_Demir_935.pdf:PDF},
  keywords  = {Data Management},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@Article{Dempster1977,
  author    = {A. P. Dempster and N. M. Laird and D. B. Rubin},
  journal   = {Journal of the Royal Statistical Society},
  title     = {Maximum Likelihood from Incomplete Data via the {EM} Algorithm},
  year      = {1977},
  pages     = {1--38},
  volume    = {39},
  abstract  = {A broadly applicable algorithm for computing maximum likelihood estimates from incomplete data is presented at various levels of generality. Theory showing the monotone behaviour of the likelihood and convergence of the algorithm is derived. Many examples are sketched, including missing value situations, applications to grouped, censored or truncated data, finite mixture models, variance component estimation, hyperparameter estimation, iteratively reweighted least squares and factor analysis.},
  file      = {:by-author/D/Dempster/1977_Dempster_1.pdf:PDF},
  keywords  = {Expectation Maximisation},
  owner     = {andrius},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
  url       = {http://links.jstor.org/sici?sici=0035-9246%281977%2939%3A1%3C1%3AMLFIDV%3E2.0.CO%3B2-Z},
}

@Article{Deng2012,
  author    = {Deng, Hexiang and Grunder, Sergio and Cordova, Kyle E. and Valente, Cory and Furukawa, Hiroyasu and Hmadeh, Mohamad and Gándara, Felipe and Whalley, Adam C. and Liu, Zheng and Asahina, Shunsuke and Kazumori, Hiroyoshi and O'Keeffe, Michael and Terasaki, Osamu and Stoddart, J. Fraser and Yaghi, Omar M.},
  journal   = {Science (New York, N.Y.)},
  title     = {Large-pore apertures in a series of metal-organic frameworks.},
  year      = {2012},
  pages     = {1018--23},
  volume    = {336},
  abstract  = {We report a strategy to expand the pore aperture of metal-organic frameworks (MOFs) into a previously unattained size regime (&gt;32 angstroms). Specifically, the systematic expansion of a well-known MOF structure, MOF-74, from its original link of one phenylene ring (I) to two, three, four, five, six, seven, nine, and eleven (II to XI, respectively), afforded an isoreticular series of MOF-74 structures (termed IRMOF-74-I to XI) with pore apertures ranging from 14 to 98 angstroms. All members of this series have noninterpenetrating structures and exhibit robust architectures, as evidenced by their permanent porosity and high thermal stability (up to 300°C). The pore apertures of an oligoethylene glycol-functionalized IRMOF-74-VII and IRMOF-74-IX are large enough for natural proteins to enter the pores.},
  doi       = {10.1126/science.1220131},
  file      = {:by-author/D/Deng/2012_Deng_1018.pdf:PDF},
  groups    = {sg/MOF, sg/MOFs, am/MOFs},
  keywords  = {Metal-Organic Frameworks (MOF); Proteins},
  owner     = {saulius},
  timestamp = {2013.01.05},
  creationdate = {2013-01-05T00:00:00},
}

@Article{Dennett2010,
  author    = {Daniel C. Dennett},
  journal   = {Evolutionary Psychology},
  title     = {Preachers Who Are Not Believers},
  year      = {2010},
  pages     = {122},
  volume    = {8},
  abstract  = {There are systemic features of contemporary Christianity that create an almost invisible class of non-believing clergy, ensnared in their ministries by a web of obligations, constraints, comforts, and community. Exemplars from five Protestant denominations, Southern Baptist, United Church of Christ, Presbyterian, Methodist and Church of Christ, were found and confidentially interviewed at length about their lives, religious education and indoctrination, aspirations, problems and ways of coping. The in-depth, qualitative interviews formed the basis for profiles of all five, together with general observations about their predicaments and how they got into them. The authors anticipate that the discussion generated on the Web (at On Faith, the Newsweek/Washington Post website on religion, http://newsweek.washingtonpost.com/onfaith//2010/03/disbelief_in_the_pulpit/all.html) and on other websites will facilitate a larger study that will enable the insights of this pilot study to be clarified, modified, and expanded.},
  file      = {:by-author/D/Dennett/2010_Dennett_122.pdf:PDF},
  keywords  = {Clergy; Disbelief; Interviews; Protestantism; Qualitative; Religijotyra; Religion},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@Webpage{Denton2005,
  author      = {William Denton},
  retrieved   = {2008-07-28},
  title       = {Gödel's Incompleteness Theorem},
  url         = {https://www.miskatonic.org/godel.html},
  institution = {Miskatonic University Press},
  month       = {December},
  year        = {2005},
  file        = {:by-author/D/Denton/2005_Denton.war:},
  keywords    = {Goedel's Theorem},
  owner       = {saulius},
  timestamp = {2015.03.02},
  creationdate = {2015-03-02T00:00:00},
}

@Article{DePristo2004,
  author    = {DePristo, Mark A and de Bakker, Paul I W and Blundell, Tom L},
  journal   = {Structure (London, England : 1993)},
  title     = {Heterogeneity and inaccuracy in protein structures solved by X-ray crystallography.},
  year      = {2004},
  pages     = {831--8},
  volume    = {12},
  file      = {DePristo_2004_831-Inaccuracy-in-Xray.pdf:by-author/D/DePristo/2004_DePristo_831.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Der2008,
  author    = {A. Dér},
  journal   = {Biotechnology \& Biotechnological Equipment},
  title     = {Salts, interfacial water and protein conformation},
  year      = {2008},
  pages     = {629--633},
  volume    = {22},
  abstract  = {A phenomenological theory of salt-induced Hofmeister phenomena is presented, based on a relation between protein solubility in salt solutions and protein-water interfacial tension. As a generalization of previous treatments, it implies that both kosmotropic salting-out and chaotropic salting-in are manifested via salt-induced changes of the hydrophobic/hydrophilic properties of protein-water interfaces. The theory is applied to describe the salt-dependent free energy profiles of proteins as a function of their water-exposed surface area. On this basis, three classes of protein conformation have been distinguished. The new formalism accounts for the diverse manifestations of salt effects on protein conformation, dynamics and stability, and resolves the puzzle of chaotropes stabilizing certain proteins (and other anomalies). It is also shown that the relation between interfacial tension and protein structural stability is straightforwardly linked to protein conformational fluctuations, providing a keystone for the microscopic interpretation of Hofmeister effects. Implications of the results concerning the use of Hofmeister effects in the experimental study of protein function are discussed.},
  file      = {2008_Dér_629.pdf:by-author/D/Der/2008_Dér_629.pdf:PDF},
  keywords  = {Conformational Fluctuations; Hofmeister Effects; Interfacial Energy; Noncovalent Interactions; Protein Physics; Water},
  owner     = {saulius},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
  url       = {http://www.diagnosisp.com/dp/journals/view_article.php?journal_id=1&archive=0&issue_id=17&article_id=475},
}

@Article{DesSoye2015,
  author    = {Des Soye, Benjamin J and Patel, Jaymin R and Isaacs, Farren J and Jewett, Michael C},
  journal   = {Current Opinion in Chemical Biology},
  title     = {Repurposing the translation apparatus for synthetic biology},
  year      = {2015},
  issn      = {1367-5931},
  month     = {Oct},
  pages     = {83--90},
  volume    = {28},
  doi       = {10.1016/j.cbpa.2015.06.008},
  file      = {:by-author/D/DesSoye/2015_DesSoye_83.pdf:PDF},
  groups    = {am/Expanded genetic code},
  owner     = {andrius},
  publisher = {Elsevier BV},
  timestamp = {2016.05.31},
  creationdate = {2016-05-31T00:00:00},
  url       = {http://dx.doi.org/10.1016/j.cbpa.2015.06.008},
}

@Presentation{deVries2006,
  author    = {deVries},
  title     = {{D}ijkstra’s Weakest Precondition},
  year      = {2006},
  file      = {:by-author/d/deVries/2006_deVries_slides.pdf:PDF},
  groups    = {sg/Correctness proofs},
  keywords  = {Computer Science (CS); Correctness Proofs},
  owner     = {saulius},
  pages     = {slides},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Dewar1986,
  author    = {Michael J. S. Dewar and Merz, Kenneth M., Jr.},
  journal   = {Journal of the American Chemical Society},
  title     = {Thermal Rearrangements of C10H8 Species; Benzvalene Analogues and the Automerization of Naphthalene},
  year      = {1986},
  pages     = {5146--5153},
  volume    = {108},
  doi       = {10.1021/ja00277a019},
  file      = {:by-author/D/Dewar/1986_Dewar_5146.pdf:PDF},
  keywords  = {Azulene},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
  url       = {http://pubs.acs.org/doi/abs/10.1021/ja00277a019},
}

@Article{DeWitt1990,
  author    = {DeWitt, David J. and Gray, Jim},
  journal   = {SIGMOD Rec.},
  title     = {Parallel database systems: the future of database processing or a passing fad?},
  year      = {1990},
  issn      = {0163-5808},
  pages     = {104--112},
  volume    = {19},
  abstract  = {The concept of parallel database machines consisting of exotic hardware has been replaced by a fairly conventional shared-nothing hardware base along with a highly parallel dataflow software architecture. Such a design provides speedup and scaleup in processing relational database queries. This paper reviews the techniques used by such systems, and surveys current commercial and research systems.},
  doi       = {10.1145/122058.122071},
  file      = {:by-author/D/DeWitt/1990_DeWitt_104.pdf:PDF},
  owner     = {saulius},
  publisher = {ACM},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://doi.acm.org/10.1145/122058.122071},
}

@Article{DeWitte1997,
  author    = {DeWitte, Robert S. and Ishchenko, Alexey V. and Shakhnovich, Eugene I.},
  journal   = {Journal of the American Chemical Society},
  title     = {SMoG:  de Novo Design Method Based on Simple, Fast, and Accurate Free Energy Estimates. 2. Case Studies in Molecular Design},
  year      = {1997},
  pages     = {4608--4617},
  volume    = {119},
  abstract  = {In this paper, we summarize three ligand design studies performed using the program SMoG, which was developed in our lab. The aim of this presentation is to communicate through examples the potential of this method:  the richness of the molecules that can be developed and the ease with which they are found. In particular, we present suggestions for ligands to Src SH3 domain (specificity pocket and LP site) and CD4.},
  doi       = {10.1021/ja963689+},
  file      = {:by-author/D/DeWitte/1997_DeWitte_4608.pdf:PDF},
  keywords  = {Ligand Design},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
  url       = {http://pubs.acs.org/doi/abs/10.1021/ja963689%2B},
}

@Article{Dey2013,
  author    = {Dey, Chandan and Kundu, Tanay and Biswal, Bishnu P. and Mallick, Arijit and Banerjee, Rahul},
  journal   = {Acta Crystallogr Sect B Struct Sci},
  title     = {Crystalline metal-organic frameworks (MOFs): synthesis, structure and function},
  year      = {2013},
  issn      = {2052-5206},
  month     = {Dec},
  number    = {1},
  pages     = {3--10},
  volume    = {70},
  abstract  = {Metal-organic frameworks (MOFs) are a class of hybrid network supramolecular solid materials comprised of organized organic linkers and metal cations. They can display enormously high surface areas with tunable pore size and functionality, and can be used as hosts for a range of guest molecules. Since their discovery, MOFs have experienced widespread exploration for their applications in gas storage, drug delivery and sensing. This article covers general and modern synthetic strategies to prepare MOFs, and discusses their structural diversity and properties with respect to application perspectives.},
  doi       = {10.1107/s2052520613029557},
  file      = {2013_Dey_3.pdf:by-author/D/Dey/2013_Dey_3.pdf:PDF},
  groups    = {sg/MOF, sg/MOFs, am/MOFs},
  keywords  = {Metal-Organic Frameworks (MOF)},
  owner     = {saulius},
  publisher = {International Union of Crystallography (IUCr)},
  timestamp = {2016.05.17},
  creationdate = {2016-05-17T00:00:00},
  url       = {http://dx.doi.org/10.1107/S2052520613029557},
}

@Booklet{DFG1998,
  title     = {Vorschläge zur Sicherung guter wissenschaftlicher Praxis: Empfehlungen der Kommission „Selbstkontrolle in der Wissenschaft“},
  author    = {DFG},
  year      = {1998},
  file      = {:by-author/D/DFG/1998_DFG.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.09.18},
  creationdate = {2012-09-18T00:00:00},
}

@Article{DiCosmo2003,
  author    = {Di Cosmo, Roberto},
  journal   = {Upgrade},
  title     = {Legal Tools to Protect Software: Choosing the Right One},
  year      = {2003},
  pages     = {21--23},
  volume    = {4},
  file      = {DiCosmo_2003_21-open-ideas.pdf:by-author/D/DiCosmo/2003_DiCosmo_21.pdf:PDF},
  keywords  = {Computer Science (CS)},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{DiCostanzo2003,
  author    = {Di Costanzo, Luigi and Forneris, Federico and Geremia, Silvano and Randaccio, Lucio},
  journal   = {Acta crystallographica. Section D, Biological crystallography},
  title     = {Phasing protein structures using the group-subgroup relation.},
  year      = {2003},
  pages     = {1435--9},
  volume    = {59},
  file      = {2003_Costanzo_1435.pdf:by-author/D/DiCostanzo/2003_DiCostanzo_1435.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{DiFiore2005,
  author    = {Di Fiore, Anna and De Simone, Giuseppina and Valeria Menchise and Carlo Pedone and Angela Casini and Andrea Scozzafavab and Claudiu T. Supuran},
  journal   = {Bioorganic \& Medicinal Chemistry Letters},
  title     = {Carbonic anhydrase inhibitors: X-ray crystal structure of a benzenesulfonamide strong CA II and CA IX inhibitor bearing a pentafluorophenylaminothioureido tail in complex with isozyme II},
  year      = {2005},
  pages     = {1937--1942},
  volume    = {15},
  abstract  = {N-1-(4-Sulfamoylphenyl)-N-4-pentafluorophenyl-thiosemicarbazide was prepared by the reaction of 4-isothiocyanato- benzenesulfonamide with pentafluorophenyl hydrazine, and proved to be an effective inhibitor of several isozymes of the zinc enzyme carbonic anhydrase (CA, EC 4.2.1.1), such as CA I, II, and IX. Against the physiologically relevant isozymes hCA II and hCA IX, the compound showed inhibition constants in the range of 15–19 nM, whereas it was less effective as a hCA I inhibitor (KI of 78 nM). The high-resolution X-ray crystal structure of its adduct with hCA II showed the inhibitor to bind within the hydro- phobic half of the enzyme active site, making extensive and strong van der Waals contacts with amino acid residues Gln92, Val121, Phe131, Leu198, Thr200, Pro202, in addition to the coordination of the sulfonamide nitrogen to the Zn(II) ion of the active site, and participation of the SO2NH2 group to a network of hydrogen bonds involving residues Thr199 and Glu106. These results are helpful for the design of better CA II or CA IX inhibitors based on the thioureido-benzenesulfonamide motif, with potential applications as anti-glaucoma or anti-cancer drugs.},
  doi       = {10.1016/j.bmcl.2005.01.086},
  file      = {2005_DiFiore_1937.pdf:by-author/D/DiFiore/2005_DiFiore_1937.pdf:PDF},
  groups    = {sg/inhibitors, sg/hCA2, sg/hCA9},
  keywords  = {Carbonic Anhydrases},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{DiFiore2008,
  author    = {Di Fiore, Anna and Carlo Pedone and Jochen Antel and Harald Waldeck and Andreas Witte and Michael Wurl and Andrea Scozzafava and Claudiu T. Supuran and De Simone, Giuseppina},
  journal   = {Bioorganic \& Medicinal Chemistry Letters},
  title     = {Carbonic anhydrase inhibitors: The X-ray crystal structure of ethoxzolamide complexed to human isoform II reveals the importance of thr200 and gln92 for obtaining tight-binding inhibitors},
  year      = {2008},
  pages     = {2669--2674},
  volume    = {18},
  doi       = {10.1016/j.bmcl.2008.03.023},
  file      = {2008_DiFiore_2669.pdf:by-author/D/DiFiore/2008_DiFiore_2669.pdf:PDF},
  groups    = {sg/inhibitors, sg/hCA2},
  keywords  = {Carbonic Anhydrases; Inhibitors},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Diaconis2004,
  author    = {Persi Diaconis},
  journal   = {SIAM News},
  title     = {A Frequentist Does This, A Bayesian That},
  year      = {2004},
  number    = {2},
  volume    = {37},
  file      = {:by-author/D/Diaconis/2004_Diaconis.war:},
  groups    = {sg/Bayesian},
  keywords  = {Bayesian-statistics; Mathematics},
  owner     = {saulius},
  timestamp = {2015.03.02},
  creationdate = {2015-03-02T00:00:00},
  url       = {http://www.siam.org/siamnews/03-04/Bayesian.htm},
}

@TechReport{Diaconu2014,
  author      = {Cristinel Diaconu and Sabine Kraml and Christian Surace and Daniel Chateigner and Thérèse Libourel Rouge},
  institution = {LIRMM},
  title       = {{PREDON} Scientific Data Preservation 2014},
  year        = {2014},
  file        = {:by-author/D/Diaconu/2014_Diaconu.pdf:PDF},
  keywords    = {COD; Data Preservation; Database},
  owner       = {antanas},
  timestamp = {2015.10.01},
  creationdate = {2015-10-01T00:00:00},
  url         = {http://hal.in2p3.fr/in2p3-00959072},
}

@Article{Diamond1984,
  author    = {Diamond},
  title     = {Methods and Applications in Crystallographic Computing},
  year      = {1984},
  file      = {:by-author/D/Diamond/1984_Diamond.pdf:PDF},
  keywords  = {Crystallographic Computing; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Diamond1992,
  author           = {Diamond, R.},
  journal          = {Protein science : a publication of the Protein Society},
  title            = {On the multiple simultaneous superposition of molecular structures by rigid body transformations},
  year             = {1992},
  issn             = {1469-896X},
  month            = oct,
  number           = {10},
  pages            = {1279--1287},
  volume           = {1},
  abstract         = {A method of optimally superimposing n coordinate sets on each other by rigid body transformations, which minimizes the sum of all n (n - 1)/2 pairwise residuals, is presented. In the solution phase the work load is approximately linear on n, is independent of the size of the structures, is independent of their initial orientations, and terminates in one cycle if n = 2 of if the coordinate sets are exactly superposable, and otherwise takes a number of cycles dependent only on genuine shape differences. Enantiomorphism, if present, is detected, in which case the option exists to reverse or not to reverse the chirality of relevant coordinate sets. The method also offers a rational approach to the problem of multiple minima and has successfully identified four distinct minima in such a case. Source code, which is arranged to enable the study of the disposition of domains in multidomain structures, is available from the author.},
  creationdate     = {2008-07-28T00:00:00},
  doi              = {10.1002/pro.5560011006},
  file             = {:by-author/D/Diamond/1992_Diamond_1279.pdf:PDF},
  groups           = {sg/Molecule superposion, sg/Superposition, sg/Bioinf. Algorithms},
  keywords         = {Algorithms; Structure Superposition; X-ray Crystallography},
  modificationdate = {2024-05-12T17:23:11},
  owner            = {saulius},
  publisher        = {Wiley},
  timestamp        = {2008.07.28},
}

@Article{Diamond1988,
  author           = {Diamond, R.},
  journal          = {Acta Crystallographica Section A},
  title            = {A note on the rotational superposition problem},
  year             = {1988},
  pages            = {211--216},
  volume           = {44},
  comment          = {"It is well known that the optimal rotational superposition is achieved if the data sets are referred to their respective centroids as origins". Contradicts Chen2004?},
  creationdate     = {2012-05-15T00:00:00},
  doi              = {10.1107/S0108767387010535},
  file             = {1988_Diamond_211.pdf:by-author/D/Diamond/1988_Diamond_211.pdf:PDF},
  groups           = {sg/Molecule superposion, sg/Superposition, sg/Bioinf. Algorithms},
  keywords         = {Algorithms; Structure Superposition; X-ray Crystallography},
  modificationdate = {2024-05-12T14:53:46},
  owner            = {saulius},
  timestamp        = {2012.05.15},
  url              = {http://dx.doi.org/10.1107/S0108767387010535},
}

@Article{Diamond1976,
  author    = {R. Diamond},
  journal   = {Acta Crystallographica Section A},
  title     = {On the comparison of conformations using linear and quadratic transformations},
  year      = {1976},
  pages     = {1--10},
  volume    = {32},
  abstract  = {A means is developed whereby coordinate sets for related molecules may be compared in such a way as to express rigorously the relationship between them in terms of position, orientation, homogeneous strain and curvature. It is thought that such curvatures may be of value in characterizing hinge regions of allosteric enzymes. The method is illustrated with examples taken from haemoglobin and myoglobin},
  doi       = {10.1107/S0567739476000016},
  file      = {:by-author/D/Diamond/1976_Diamond_1.pdf:PDF},
  groups    = {sg/Molecule superposion, sg/Superposition, sg/Bioinf. Algorithms},
  keywords  = {Algorithms; Structure Superposition; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Diamond1966,
  author    = {Robert Diamond},
  journal   = {Acta Cryst.},
  title     = {A Mathematical Model-Building Procedure for Proteins},
  year      = {1966},
  pages     = {253--266},
  volume    = {21},
  abstract  = {The procedure is intended primarily as an intermediate step between the interpretation of an electron density map of medium resolution and the refinement of the structure. The procedure builds a represen- tation of a polypeptide using images of amino acids as determined in small structures, rendered suitably flexible by rotations about single bonds (and other lines if required) and uses the method of least squares to fold the resulting chain and side chains to approach the guide points (derived from the electron den- sity map or otherwise) as closely as possible. Thus an idealized structure can be derived from a selec- tion of rough coordinates and a knowledge of the sequence. The procedure is also capable (with limita- tions) of bridging uncertain regions. Some novel mathematical techniques of general interest are described and employed. These include reversion and a sliding filter as means of combating non-linearity. The sliding filter is a means of sup- pressing large shifts by excluding from the least-squares process those eigenvectors of the normal matrix which have small eigenvalues. This is done in a manner depending on the residual. A means of achieving accurate rotations in three dimensions without setting up a matrix is also given},
  doi       = {10.1107/S0365110X6600269X},
  file      = {:by-author/D/Diamond/1966_Diamond_253.pdf:PDF},
  keywords  = {Algorithms; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2011.12.21},
  creationdate = {2011-12-21T00:00:00},
}

@Article{Diaz-Chao2014,
  author    = {Díaz-Chao, P. and Giovannelli, F. and Lebedev, O. and Chateigner, D. and Lutterotti, L. and Delorme, F. and Guilmeau, E.},
  journal   = {Journal of the European Ceramic Society},
  title     = {Textured {Al}-doped {ZnO} ceramics with isotropic grains},
  year      = {2014},
  pages     = {4247--4256},
  volume    = {34},
  file      = {[PDF] from researchgate.net:by-author/D/Díaz-Chao/2014_Díaz-Chao_4247.pdf:PDF;Snapshot:by-author/D/Díaz-Chao/2014_Díaz-Chao_4247.html:URL},
  groups    = {sg/JAC2009},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/S095522191400377X},
  urldate   = {2015-08-31},
}

@Article{Dickerson1998,
  author       = {Dickerson, R. E.},
  journal      = {Nucleic acids research},
  title        = {{DNA} bending: the prevalence of kinkiness and the virtues of normality.},
  year         = {1998},
  pages        = {1906--1926},
  volume       = {26},
  abstract     = {DNA bending in 86 complexes with sequence-specific proteins has been examined using normal vector plots, matrices of normal vector angles between all base pairs in the helix, and one-digit roll/slide/twist tables. FREEHELIX, a new program especially designed to analyze severely bent and kinked duplexes, generates the foregoing quantities plus local roll, tilt, twist, slide, shift and rise parameters that are completely free of any assumptions about an overall helix axis. In nearly every case, bending results from positive roll at pyrimidine-purine base pair steps: C-A (= T-G), T-A, or less frequently C-G, in a direction that compresses the major groove. Normal vector plots reveal three well-defined types of bending among the 86 examples: (i) localized kinks produced by positive roll at one or two discrete base pairs steps, (ii) three-dimensional writhe resulting from positive roll at a series of adjacent base pairs steps, or (iii) continuous curvature produced by alternations of positive and negative roll every 5 bp, with side-to-side zig-zag roll at intermediate position. In no case is tilt a significant component of the bending process. In sequences with two localized kinks, such as CAP and IHF, the dihedral angle formed by the three helix segments is a linear function of the number of base pair steps between kinks: dihedral angle = 36 degrees x kink separation. Twenty-eight of the 86 examples can be described as major bends, and significant elements in the recognition of a given base sequence by protein. But even the minor bends play a role in fine-tuning protein/DNA interactions. Sequence-dependent helix deformability is an important component of protein/DNA recognition, alongside the more generally recognized patterns of hydrogen bonding. The combination of FREEHELIX, normal vector plots, full vector angle matrices, and one-digit roll/slide/twist tables affords a rapid and convenient method for assessing bending in DNA.},
  creationdate = {2012-11-09T00:00:00},
  doi          = {10.1093/nar/26.8.1906},
  file         = {:by-author/D/Dickerson/1998_Dickerson_1906.pdf:PDF},
  keywords     = {Bacterial Proteins; Base Composition; Base Sequence; Bending; Binding Sites; Chemistry; Computer Simulation; DNA; DNA Restriction Enzymes; DNA-Binding Proteins; FREEHELIX; Homeodomain Proteins; Humans; Integration Host Factors; Metabolism; Models; Molecular; Nucleic Acid Conformation; Protein Structure; RNA Cap-Binding Proteins; RNA-Binding Proteins; Readout; Repressor Proteins; Secondary; Software; TATA Box; TATA-Box Binding Protein; Transcription Factors; Viral Proteins; Viral Regulatory and Accessory Proteins; YR},
  owner        = {em},
  timestamp    = {2012.11.09},
}

@Article{Dickerson1983a,
  author    = {Dickerson, R. E.},
  journal   = {Journal of molecular biology},
  title     = {Base sequence and helix structure variation in B and A DNA.},
  year      = {1983},
  pages     = {419--41},
  volume    = {166},
  abstract  = {The observed propeller twist in base-pairs of crystalline double-helical DNA oligomers improves the stacking overlap along each individual helix strand. But, as proposed by Calladine, it also leads to clash or steric hindrance between purines at adjacent base-pairs on opposite strands of the helix. This clash can be relieved by: (1) decreasing the local helix twist angle between base-pairs; (2) opening up the roll angle between base-pairs on the side on which the clash occurs; (3) separating purines by sliding base-pairs along their long axes so that the purines are partially pulled out of the stack (leading to equal but opposite alterations in main-chain torsion angle delta at the two ends of the base-pair); and (4) flattening the propeller twist of the offending base-pairs. Simple sum functions, sigma 1 through sigma 4, are defined, by which the expected local variation in helix twist, base roll angle, torsion angle delta and propeller twist may be calculated from base sequence. All four functions are quite successful in predicting the behavior of B DNA. Only the helix twist and base roll functions are applicable to A DNA, and the helix twist function begins to fail for an A helical RNA/DNA hybrid. Within these limits, the sequence-derived sum functions match the observed helix parameter variation quite closely, with correlation coefficients greater than 0.900 in nearly all cases. Implications of this sequence-derived helix parameter variation for repressor-operator interactions are considered.},
  file      = {:by-author/D/Dickerson/1983_Dickerson_419.pdf:PDF},
  keywords  = {Calladine Rules; Readout},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Dickerson1982,
  author    = {Dickerson, R E and Drew, H R and Conner, B N and Wing, R M and Fratini, A V and Kopka, M L},
  journal   = {Science (New York, N.Y.)},
  title     = {The anatomy of A-, B-, and Z-DNA.},
  year      = {1982},
  pages     = {475--85},
  volume    = {216},
  file      = {1982_Dickerson_475.pdf:by-author/D/Dickerson/1982_Dickerson_475.pdf:PDF},
  keywords  = {Readout; Stacking},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Dickerson1983,
  author    = {Dickerson, R E and Kopka, M L and Pjura, P},
  journal   = {Proceedings of the National Academy of Sciences of the United States of America},
  title     = {A random-walk model for helix bending in B-DNA.},
  year      = {1983},
  pages     = {7099--103},
  volume    = {80},
  abstract  = {The double-helical B-DNA dodecamer of sequence d(C-G-C-G-A-A-T-T-C-G-C-G) has been refined independently from x-ray crystal structure analyses in five different variants: d(C-G-C-G-A-A-T-T-C-G-C-G) at 16 K, at room temperature, and with bound cis-diamminedichloroplatinum(II), and d(C-G-C-G-A-A-T-T-brC-G-C-G) in 60% 2-methyl-2,4-pentanediol at 20 degrees C and 7 degrees C. These helices display overall axial bends of 22 degrees, 18 degrees, 17 degrees, 14 degrees, and 3 degrees, respectively, providing an opportunity to investigate the nature of the bending process in B-DNA. Bending from one base pair to the next is best described as a stochastic or random-walk process, having forward, retrograde, and sidewise individual steps, but with an overall sense of bending. Individual steps almost always involve rolling of adjacent base pairs over one another along their long axes, not a tilting or wedge displacement that lifts neighboring base pairs apart at one end. A slight preference is observed for bending the double helix in a direction that compresses the major groove rather than the minor, and this is intuitively reasonable in view of the narrowness of the minor groove and its occupation by the spine of hydration that stabilizes the B form of DNA. This model predicts that, when DNA is wound around the nucleosome core, it should not be smoothly curved but should exhibit discrete bends every five base pairs as proposed by Zhurkin et al. [Zhurkin, V.B., Lysov, Y. P. &amp; Ivanov, V. I. (1979) Nucleic Acids Res. 6, 1081-1096)]. Sharper bends may occur at alternate positions, where the major groove faces the nucleosome core.},
  file      = {1983_Dickerson_7099.pdf:by-author/D/Dickerson/1983_Dickerson_7099.pdf:PDF},
  keywords  = {Readout; Stacking},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Webpage{Diederichs2014,
  author    = {Kay Diederichs},
  retrieved = {2016-12-21},
  title     = {XDS Wiki},
  url       = {http://strucbio.biologie.uni-konstanz.de/xdswiki},
  language  = {English},
  month     = {November},
  site      = {http://strucbio.biologie.uni-konstanz.de/},
  siteurl   = {http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Main_Page},
  year      = {2014},
  file      = {2014_Diederichs_XDSwiki.odt:by-author/D/Diederichs/2014_Diederichs_XDSwiki.odt:OpenDocument text;2014_Diederichs_XDSwiki.pdf:by-author/D/Diederichs/2014_Diederichs_XDSwiki.pdf:PDF},
  keywords  = {Data Reduction; Reflection Integration; Software; X-ray Crystallography; XDS},
  owner     = {saulius},
  timestamp = {2016.12.21},
  creationdate = {2016-12-21T00:00:00},
}

@Presentation{Diederichs2013,
  author    = {Kay Diederichs},
  title     = {XDS},
  year      = {2013},
  school    = {Protein Crystallography / Molecular Bioinformatics, University of Konstanz, Germany},
  file      = {2013_Diederichs_slides.pdf:by-author/D/Diederichs/2013_Diederichs_slides.pdf:PDF},
  keywords  = {Data Reduction; Reflection Integration; Software; X-ray Crystallography; XDS},
  owner     = {saulius},
  timestamp = {2016.12.21},
  creationdate = {2016-12-21T00:00:00},
  url       = {http://www.xtal.iqfr.csic.es/MCS2013/KD-MCS2013-XDS.pdf},
}

@Presentation{Diederichs2009,
  author    = {Kay Diederichs},
  title     = {Using XDS - a practical perspective},
  year      = {2009},
  file      = {2009_Diederichs_slides.pdf:by-author/D/Diederichs/2009_Diederichs_slides.pdf:PDF},
  keywords  = {Data Reduction; Reflection Integration; Software; X-ray Crystallography; XDS},
  owner     = {saulius},
  timestamp = {2016.12.21},
  creationdate = {2016-12-21T00:00:00},
  url       = {http://www.ccp4.ac.uk/schools/Japan-2010/tutorials/xds/Diederichs26th.pdf},
}

@Article{Diederichs1994,
  author    = {Diederichs, K.},
  journal   = {Journal of Applied Crystallography},
  title     = {{\it SUPERIMPOSE} {--} a program for the unambiguous structural superposition of spatially related molecules, including macromolecules},
  year      = {1994},
  pages     = {436--437},
  volume    = {27},
  doi       = {10.1107/S0021889894000920},
  file      = {1994_Diederichs_436.pdf:by-author/D/Diederichs/1994_Diederichs_436.pdf:PDF},
  groups    = {sg/Molecule superposion, sg/Superposition, sg/Bioinf. Algorithms},
  keywords  = {Structure Comparison; Structure Superposition},
  owner     = {saulius},
  timestamp = {2012.05.15},
  creationdate = {2012-05-15T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0021889894000920},
}

@Article{Diederichs2003,
  author    = {Diederichs, Kay and McSweeney, Sean and Ravelli, Raimond B. G.},
  journal   = {Acta Crystallographica Section D},
  title     = {Zero-dose extrapolation as part of macromolecular synchrotron data reduction},
  year      = {2003},
  pages     = {903--909},
  volume    = {59},
  doi       = {10.1107/S0907444903006516},
  file      = {wd0009.pdf:by-author/D/Diederichs/2003_Diederichs_903.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444903006516},
}

@Article{Dieterich2006,
  author    = {Dieterich, Daniela C. and Link, A. James and Graumann, Johannes and Tirrell, David A. and Schuman, Erin M.},
  journal   = {Proceedings of the National Academy of Sciences of the United States of America},
  title     = {Selective identification of newly synthesized proteins in mammalian cells using bioorthogonal noncanonical amino acid tagging (BONCAT).},
  year      = {2006},
  pages     = {9482--7},
  volume    = {103},
  abstract  = {In both normal and pathological states, cells respond rapidly to environmental cues by synthesizing new proteins. The selective identification of a newly synthesized proteome has been hindered by the basic fact that all proteins, new and old, share the same pool of amino acids and thus are chemically indistinguishable. We describe here a technology, based on the cotranslational introduction of azide groups into proteins and the chemoselective tagging of azide-labeled proteins with an alkyne affinity tag, to separate and identify, specifically, the newly synthesized proteins in mammalian cells. Incorporation of the azide-bearing amino acid azidohomoalanine is unbiased, not toxic, and does not increase protein degradation. As a first demonstration of the method, we report the selective purification and identification of 195 metabolically labeled proteins with multidimensional liquid chromatography in-line with tandem MS. Furthermore, in combination with leucine-based mass tagging, candidates were immediately validated as newly synthesized proteins. The identified proteins, synthesized in a 2-h window, possess a broad range of biochemical properties and span most functional gene ontology categories. This technology makes it possible to address the temporal and spatial characteristics of newly synthesized proteomes in any cell type.},
  file      = {:by-author/D/Dieterich/2006_Dieterich_9482.pdf:PDF},
  keywords  = {Bioconjugation},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@Article{Dietmann2001,
  author    = {Sabine Dietmann and Liisa Holm},
  journal   = {Nature Structural Biology},
  title     = {Identification of homology in protein structure classification},
  year      = {2001},
  pages     = {953--957},
  volume    = {11},
  file      = {Dietman_2001_953-structure_homology_identif.pdf:by-author/D/Dietmann/2001_Dietmann_953.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Dietzel2008,
  author    = {Pascal D. C. Dietzel and Richard Blom and Helmer Fjellv{\aa}g},
  journal   = {European Journal of Inorganic Chemistry},
  title     = {Base-Induced Formation of Two Magnesium Metal-Organic Framework Compounds with a Bifunctional Tetratopic Ligand},
  year      = {2008},
  month     = {aug},
  number    = {23},
  pages     = {3624--3632},
  volume    = {2008},
  comment   = {Describes synthesis cited in: "Large-Pore Apertures in a Series of Metal-Organic Frameworks", Hexiang Deng et al. Science 336, 1018 (2012); DOI: 10.1126/science.1220131.},
  doi       = {10.1002/ejic.200701284},
  file      = {Dietzel2008.pdf:by-author/D/Dietzel/2008_Dietzel_3624.pdf:PDF},
  groups    = {sg/MOF, sg/MOFs, am/MOFs},
  keywords  = {Synthesis},
  owner     = {saulius},
  publisher = {Wiley-Blackwell},
  timestamp = {2017.01.31},
  creationdate = {2017-01-31T00:00:00},
}

@Manuscript{Dijkstra2000,
  author    = {Edsger W. Dijkstra},
  title     = {Programming: from craft to scientific discipline},
  year      = {2000},
  keywords  = {Computer Science (CS); Structured-programming},
  file      = {:by-author/D/Dijkstra/2000_Dijkstra.PDF:},
  note      = {EWD566},
  owner     = {saulius},
  timestamp = {2015.03.03},
  creationdate = {2015-03-03T00:00:00},
}

@Manuscript{Dijkstra1976,
  author    = {Edsger W. Dijkstra},
  title     = {The characterization of semantics},
  year      = {1976},
  keywords  = {Computer Science (CS); Structured-programming},
  file      = {:by-author/D/Dijkstra/1976_Dijkstra.PDF:},
  note      = {EWD401},
  owner     = {saulius},
  timestamp = {2015.03.03},
  creationdate = {2015-03-03T00:00:00},
}

@Webpage{Dijkstra1976a,
  author    = {Edsger W. Dijkstra},
  retrieved = {2010-03-05},
  title     = {Programming: from craft to scientific discipline},
  url       = {http://www.cs.utexas.edu/users/EWD/transcriptions/EWD05xx/EWD566.html},
  year      = {1976},
  file      = {:by-author/D/Dijkstra/1976_Dijkstra.odt:},
  keywords  = {Computer Science (CS); Structured-programming},
  note      = {EWD566},
  owner     = {saulius},
  timestamp = {2015.03.03},
  creationdate = {2015-03-03T00:00:00},
}

@Manuscript{Dijkstra1975,
  author    = {Edsger W. Dijkstra},
  title     = {Guarded commands, non-determinacy and formal derivation of programs},
  year      = {1975},
  keywords  = {Computer Science (CS); Structured-programming},
  file      = {:by-author/D/Dijkstra/1975_Dijkstra.PDF:PDF},
  note      = {EWD472},
  owner     = {saulius},
  timestamp = {2015.03.03},
  creationdate = {2015-03-03T00:00:00},
}

@Webpage{Dijkstra1972,
  author    = {Edsger W. Dijkstra},
  retrieved = {2010-09-07},
  title     = {The Humble Programmer},
  url       = {http://www.cs.utexas.edu/~EWD/transcriptions/EWD03xx/EWD340.html},
  year      = {1972},
  file      = {:by-author/D/Dijkstra/1972_Dijkstra.odt:},
  keywords  = {Computer Science (CS); Software-design},
  note      = {EWD340},
  owner     = {saulius},
  timestamp = {2015.03.03},
  creationdate = {2015-03-03T00:00:00},
}

@Article{Dijkstra1968,
  author     = {Dijkstra, Edsger W.},
  journal    = {Commun. ACM},
  title      = {The structure of the \“THE\”-multiprogramming system},
  year       = {1968},
  issn       = {0001-0782},
  pages      = {341--346},
  volume     = {11},
  acmid      = {363143},
  address    = {New York, NY, USA},
  doi        = {10.1145/363095.363143},
  file       = {1968_Dijkstra_341.pdf:by-author/D/Dijkstra/1968_Dijkstra_341.pdf:PDF},
  issue_date = {May 1968},
  keywords   = {Computer Science (CS); Cooperating Sequential Processes; Input Output Buffering; Multiprocessing; Multiprogramming; Multiprogramming System; Operating System; Processor Sharing; Program Verification; Real-time Debugging; Synchronizing Primitives; System Hierarchy; System Levels; System Structure},
  numpages   = {6},
  owner      = {saulius},
  publisher  = {ACM},
  timestamp = {2012.05.17},
  creationdate = {2012-05-17T00:00:00},
  url        = {http://doi.acm.org/10.1145/363095.363143},
}

@Article{Dijkstra1968a,
  author     = {Dijkstra, Edsger W.},
  journal    = {Commun. ACM},
  title      = {Go to Statement Considered Harmful},
  year       = {1968},
  issn       = {0001-0782},
  pages      = {147--148},
  volume     = {11},
  address    = {New York, NY, USA},
  doi        = {10.1145/362929.362947},
  file       = {:by-author/D/Dijkstra/1968_Dijkstra_147.pdf:PDF;:by-author/D/Dijkstra/1968_Dijkstra_147-orig.pdf:PDF},
  issue_date = {March 1968},
  keywords   = {Computer Science (CS); Programming Culture},
  owner      = {saulius},
  publisher  = {ACM},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
  url        = {http://doi.acm.org/10.1145/362929.362947},
}

@Manuscript{Dijkstra1968b,
  author    = {Dijkstra, Edsger W.},
  title     = {The structure of the {THE}-multiprogramming system ({EDW}196)},
  year      = {1968},
  keywords  = {Computer Science (CS); Cooperating Sequential Processes; Input Output Buffering; Multiprocessing; Multiprogramming; Multiprogramming System; Operating System; Processor Sharing; Program Verification; Real-time Debugging; Synchronizing Primitives; System Hierarchy; System Levels; System Structure},
  url       = {http://www.cs.utexas.edu/~EWD/ewd01xx/EWD196.PDF},
  file      = {1968_Dijkstra.pdf:by-author/D/Dijkstra/1968_Dijkstra.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.10.29},
  creationdate = {2016-10-29T00:00:00},
}

@Article{Dijkstra1961,
  author    = {Edsger W. Dijkstra},
  journal   = {Commun. ACM},
  title     = {Letter to the editor: defense of {ALGOL} 60},
  year      = {1961},
  pages     = {502--503},
  volume    = {4},
  bibdate   = {2003-11-20},
  bibsource = {DBLP, http://dblp.uni-trier.de/db/journals/cacm/cacm4.htmlDijkstra61},
  file      = {1961_Dijkstra_502.pdf:by-author/D/Dijkstra/1961_Dijkstra_502.pdf:PDF},
  keywords  = {Algol; Algol 60; Call by Name; Computer Science (CS); Jensen's Device; Programming Languages},
  owner     = {saulius},
  timestamp = {2012.06.04},
  creationdate = {2012-06-04T00:00:00},
  url       = {http://doi.acm.org/10.1145/366813.366844},
}

@PhdThesis{Dijkstra1959,
  author    = {Dijkstra, E. W.},
  school    = {Communication with an automatic computer},
  title     = {Communication with an Automatic Computer},
  year      = {1959},
  file      = {1959_Dijkstra_phdthesis.pdf:by-author/D/Dijkstra/1959_Dijkstra_phdthesis.pdf:PDF},
  keywords  = {Computer Science (CS); Computing History; Electrologica X1},
  owner     = {saulius},
  timestamp = {2016.10.29},
  creationdate = {2016-10-29T00:00:00},
  url       = {http://www.cs.utexas.edu/users/EWD/PhDthesis/PhDthesis.PDF},
}

@TechReport{Dijkstra1978,
  author      = {Dijkstra, Edsger W. and Leslie Lamport and A. J. Martin and C. S. Scholten and E. F. M. Steffens},
  institution = {Burroughs, Plataanstraat 5, NL-4565 Neunen, The Netherlands},
  title       = {On-the-flye garbage collection: an excercise in cooperation},
  year        = {1978},
  note        = {EWD496A},
  file        = {:by-author/D/Dijkstra/1978_Dijkstra_EWD496A.pdf:PDF},
  groups      = {sg/Garbage collectors},
  keywords    = {Computer Science (CS); Garbage Collectors},
  owner       = {saulius},
  pages       = {EWD496A},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{DiMatteo2001,
  author    = {Dimatteo, Ilaria and Genovese, Christopher R. and Kass, Robert E.},
  journal   = {Biometrika},
  title     = {Bayesian curve-fitting with free-knot splines},
  year      = {2001},
  pages     = {1055--1071},
  volume    = {88},
  abstract  = {We describe a Bayesian method, for fitting curves to data drawn from an exponential family, that uses splines for which the number and locations of knots are free parameters. The method uses reversible-jump Markov chain Monte Carlo to change the knot configurations and a locality heuristic to speed up mixing. For nonnormal models, we approximate the integrated likelihood ratios needed to compute acceptance probabilities by using the Bayesian information criterion, BIC, under priors that make this approximation accurate. Our technique is based on a marginalised chain on the knot number and locations, but we provide methods for inference about the regression coefficients, and functions of them, in both normal and nonnormal models. Simulation results suggest that the method performs well, and we illustrate the method in two neuroscience applications.},
  doi       = {10.1093/biomet/88.4.1055},
  eprint    = {http://biomet.oxfordjournals.org/content/88/4/1055.full.pdf+html},
  file      = {:by-author/D/DiMatteo/2001_DiMatteo_1055.pdf:PDF},
  owner     = {andrius},
  timestamp = {2015.12.14},
  creationdate = {2015-12-14T00:00:00},
  url       = {http://biomet.oxfordjournals.org/content/88/4/1055.abstract},
}

@Article{Ding2003,
  author    = {Ding, Haitao and Qiu, Shihong and Li, Songlin and Symersky, Jindrich and Green, Todd J and Luo, Ming},
  journal   = {Acta crystallographica. Section D, Biological crystallography},
  title     = {Expression, purification, crystallization of fragments from the C-terminal region of DFF45/ICAD.},
  year      = {2003},
  pages     = {1323--6},
  volume    = {59},
  file      = {Ding_2003_1323-DFF45_Cterm_cryst.pdf:by-author/D/Ding/2003_Ding_1323.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Diot2000,
  author    = {N. Diot and P. Bénard-Rocherullé and R. Marchand},
  journal   = {Powder Diffraction},
  title     = {X-ray powder diffraction data and Rietveld refinement for Ln 6 WO 12 (Ln = Y, Ho)},
  year      = {2000},
  pages     = {220--226},
  volume    = {15},
  file      = {:by-author/D/Diot/2000_Diot_220.war:},
  keywords  = {Rietveld Refinement},
  owner     = {saulius},
  timestamp = {2015.03.02},
  creationdate = {2015-03-02T00:00:00},
  url       = {http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=PODIE2000015000004000220000001&idtype=cvips&gifs=yes},
}

@Article{Dirichlet1850,
  author    = {Dirichlet, Lejeune G.},
  journal   = {Journal für die reine und angewandte Mathematik},
  title     = {Über die Reduction der positiven quadratischen Formen mit drei unbestimmten ganzen Zahlen},
  year      = {1850},
  pages     = {221--239},
  volume    = {40},
  file      = {1850_Dirichlet_221.pdf:by-author/D/Dirichlet/1850_Dirichlet_221.pdf:PDF},
  groups    = {sg/Cell reduction, sg/Quadratic forms},
  keywords  = {Cell Reduction; Quadratic Forms; Reduction},
  owner     = {saulius},
  timestamp = {2016.04.13},
  creationdate = {2016-04-13T00:00:00},
  url       = {http://www.digizeitschriften.de/dms/img/?PID=GDZPPN002146894},
}

@Article{Dittrich2013,
  author    = {Dittrich, B. and Hübschle, C. B. and Pröpper, K. and Dietrich, F. and Stolper, T. and Holstein, J. J.},
  journal   = {Acta Crystallogr Sect B Struct Sci},
  title     = {The generalized invariom database ({GID})},
  year      = {2013},
  issn      = {2052-5192},
  month     = {Mar},
  number    = {2},
  pages     = {91–104},
  volume    = {69},
  doi       = {10.1107/s2052519213002285},
  file      = {2013_Dittrich_91.pdf:by-author/D/Dittrich/2013_Dittrich_91.pdf:PDF},
  groups    = {sg/Crystallography, am/Crystallography},
  owner     = {andrius},
  publisher = {International Union of Crystallography (IUCr)},
  timestamp = {2016.11.14},
  creationdate = {2016-11-14T00:00:00},
  url       = {http://dx.doi.org/10.1107/S2052519213002285},
}

@Article{Dixit2006,
  author    = {Surjit B. Dixit and David L. Beveridge},
  journal   = {Bioinformatics},
  title     = {Structual Bioinformatics of DNA: A Web Based Tool for the Analysis of Molecular Dynamics Results and Structure Prediction},
  year      = {2006},
  pages     = {1007--1009},
  volume    = {22},
  abstract  = {Summary: We report here the release of a web-based tool (MDDNA) to study and model the fine structural details of DNA on the basis of data extracted from a set of molecular dynamics (MD) trajectories of DNA sequences involving all the unique tetranucleotides. The dynamic web interface can be employed to analyze the first neighbor sequence context effects on the 10 unique dinucleotide steps of DNA. Functionality is included to build all atom models of any user-defined sequence based on the MD results. The backend of this interface is a relational database storing the conformational details of DNA obtained in 39 different MD simulation trajectories comprising all the 136 unique tetranucleotide steps. Examples of the use of this data to predict DNA structures are included.Availability:http://humphry.chem.wesleyan.edu:8080/MDDNAContact:sdixit@wesleyan.eduSupplementary information: Supplementary data including color figures are available at Bioinformatics online.},
  doi       = {10.1093/bioinformatics/btl059},
  file      = {:by-author/D/Dixit/2006_Dixit_1007.pdf:PDF},
  keywords  = {DNA Structure},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
  url       = {http://bioinformatics.oxfordjournals.org/content/22/8/1007.abstract},
}

@Article{Dixon2009,
  author    = {Dixon, Nicholas E.},
  journal   = {Nature},
  title     = {DNA replication: prime-time looping.},
  year      = {2009},
  pages     = {854--5},
  volume    = {462},
  file      = {:by-author/D/Dixon/2009_Dixon_854.pdf:PDF},
  keywords  = {{gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Dlakic1995,
  author    = {Dlakic, M. and Harrington, R. E.},
  journal   = {The Journal of biological chemistry},
  title     = {Bending and torsional flexibility of G/C-rich sequences as determined by cyclization assays.},
  year      = {1995},
  pages     = {29945--52},
  volume    = {270},
  abstract  = {The structural polymorphism of DNA is a vital aspect of its biological function. However, it has become increasingly apparent in recent years that DNA polymorphism is a complicated, multidimensional phenomenon that includes not only static sequence-directed structures but dynamic effects as well, including influences of counterions and sequence context. In order to address some of these additional factors that govern DNA conformation, we have used T4 ligase-mediated cyclization to investigate bending in a series of DNA sequences containing the GGGCCC.GGGCCC motif in different sequence contexts including various helical phasings with (A)5-tracts. We present evidence for curvature in GGGCCC.GGGCCC and (A)5-tract motifs in the presence of physiological levels of Mg2+ and show that these motifs curve through similar but oppositely directed bending angles under these ionic strength conditions. Although these two sequence motifs appear to bend similarly, our results suggest significant differences in stiffness and stability of curvature between them. We also show that under the same experimental conditions, the CTAG-CTAG sequence element possesses unusual torsional flexibility and that this appears to be associated with the central TA.TA dinucleotide. The results underscore the need to include sequence context and specific ion effects as well as a dynamic basis in more complete predictive models for functionally related DNA polymorphism.},
  file      = {:by-author/D/Dlakic/1995_Dlakic_29945.pdf:PDF},
  keywords  = {Bending; Readout},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Dobrzanska2006,
  author    = {Dobrzańska, Liliana and Lloyd, Gareth O. and Esterhuysen, Catharine and Barbour, Leonard J.},
  journal   = {Angewandte Chemie International Edition},
  title     = {Guest-induced conformational switching in a single crystal},
  year      = {2006},
  issn      = {1521-3773},
  pages     = {5856--5859},
  volume    = {45},
  copyright = {Copyright © 2006 WILEY-VCH Verlag GmbH \& Co. KGaA, Weinheim},
  doi       = {10.1002/anie.200602057},
  file      = {Dobrzańska et al. - 2006 - Guest-Induced Conformational Switching in a Single.pdf:by-author/D/Dobrzańska/2006_Dobrzańska_5856.pdf:PDF;Snapshot:by-author/D/Dobrzańska/2006_Dobrzańska_5856.html:URL},
  groups    = {sg/chemical},
  keywords  = {Cooperative Phenomena; Crystal Engineering; Host-guest Systems; Phase Transitions; Solvatochromism},
  language  = {en},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://onlinelibrary.wiley.com/doi/10.1002/anie.200602057/abstract},
  urldate   = {2015-08-21},
}

@Article{Dodson2003,
  author    = {Dodson, Eleanor},
  journal   = {Acta Crystallographica Section D},
  title     = {Is it jolly SAD?},
  year      = {2003},
  pages     = {1958--1965},
  volume    = {59},
  doi       = {10.1107/S0907444903020936},
  file      = {ba5053.pdf:by-author/D/Dodson/2003_Dodson_1958.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444903020936},
}

@Article{Dodson1998,
  author    = {Dodson, Eleanor},
  journal   = {Acta Crystallographica Section D},
  title     = {The Role of Validation in Macromolecular Crystallography},
  year      = {1998},
  pages     = {1109--1118},
  volume    = {54},
  abstract  = {The importance of validation techniques in X-ray structure determination and their relation to refinement procedures are discussed, with particular reference to atomic resolution structures. The requirements of deposition and publication, and the role of validation tools in this are analysed. The need for a rigorously defined file format is emphasized.},
  file      = {:by-author/D/Dodson/1998_Dodson_1109.pdf:PDF},
  owner     = {andrius},
  timestamp = {2012.06.10},
  creationdate = {2012-06-10T00:00:00},
}

@Article{Dodson2001,
  author    = {Dodson, Eleanor J.},
  journal   = {Acta Crystallographica Section D},
  title     = {Using electron-microscopy images as a model for molecular replacement},
  year      = {2001},
  pages     = {1405--1409},
  volume    = {57},
  doi       = {10.1107/S0907444901013415},
  file      = {ba5018.pdf:by-author/D/Dodson/2001_Dodson_1405.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444901013415},
}

@Article{Dodson2000,
  author    = {Dodson, M. S.},
  journal   = {Bioconjugate chemistry},
  title     = {Dimethyl suberimidate cross-linking of oligo(dT) to DNA-binding proteins.},
  year      = {2000},
  pages     = {876--9},
  volume    = {11},
  abstract  = {Dimethyl suberimidate is a bifunctional reagent that is used for cross-linking the protein components of oligomeric macromolecules. In this report, dimethyl suberimidate is shown to specifically cross-link oligo(dT) of varying lengths to the DNA-binding subunits of a multimeric helicase-primase encoded by herpes simplex virus type 1. This result indicates that dimethyl suberimidate and other imidoester cross-linking reagents may be useful for characterizing the interaction of oligo(dT) with proteins that bind single-stranded DNA.},
  file      = {:by-author/D/Dodson/2000_Dodson_876.pdf:PDF},
  keywords  = {{gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Webpage{Dominus1999,
  author    = {M-J. Dominus},
  retrieved = {2009-01-09},
  title     = {Strong Typing},
  url       = {http://perl.plover.com/yak/typing/notes.html},
  year      = {1999},
  file      = {:by-author/D/Dominus/1999_Dominus.war:},
  keywords  = {Computer Science (CS); Type-systems},
  owner     = {saulius},
  timestamp = {2015.03.02},
  creationdate = {2015-03-02T00:00:00},
}

@Article{Dong1995,
  author    = {Dong, F. and Gogol, E. P. and von Hippel, P. H.},
  journal   = {The Journal of biological chemistry},
  title     = {The phage T4-coded DNA replication helicase (gp41) forms a hexamer upon activation by nucleoside triphosphate.},
  year      = {1995},
  pages     = {7462--73},
  volume    = {270},
  abstract  = {Sedimentation and high performance liquid chromatography studies show that the functional DNA replication helicase of bacteriophage T4 (gp41) exists primarily as a dimer at physiological protein concentrations, assembling from gp41 monomers with an association constant of approximately 10(6) M-1. Cryoelectron microscopy, analytical ultracentrifugation, and protein-protein cross-linking studies demonstrate that the binding of ATP or GTP drives the assembly of these dimers into monodisperse hexameric complexes, which redissociate following depletion of the purine nucleotide triphosphatase (PuTP) substrates by the DNA-stimulated PuTPase activity of the helicase. The hexameric state of gp41 can be stabilized for detailed study by the addition of the nonhydrolyzable PuTP analogs ATP gamma S and GTP gamma S and is not significantly affected by the presence of ADP, GDP, or single-stranded or forked DNA template constructs, although some structural details of the hexameric complex may be altered by DNA binding. Our results also indicate that the active gp41 helicase exists as a hexagonal trimer of asymmetric dimers, and that the hexamer is probably characterized by D3 symmetry. The assembly pathway of the gp41 helicase has been analyzed, and its structure and properties compared with those of other helicases involved in a variety of cellular processes. Functional implications of such structural organization are also considered.},
  file      = {:by-author/D/Dong/1995_Dong_7462.pdf:PDF;:by-author/D/Dong/1995_Dong_7462.war:WAR archive},
  keywords  = {Oligomer; {gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Dong1996,
  author    = {Dong, F. and von Hippel, P. H.},
  journal   = {The Journal of biological chemistry},
  title     = {The ATP-activated hexameric helicase of bacteriophage T4 (gp41) forms a stable primosome with a single subunit of T4-coded primase (gp61).},
  year      = {1996},
  pages     = {19625--31},
  volume    = {271},
  abstract  = {We have examined the formation of the primosome subassembly of the bacteriophage T4-coded DNA replication (elongation) complex from its helicase, primase, and DNA components. Previously, we had shown that the T4 helicase (gp41) exists in solution in a stable monomer left and right arrow dimer equilibrium at physiological protein (and salt) concentrations and forms a hexamer upon activation by ATP (or GTP) binding (Dong, F., Gogol, E. P., and von Hippel, P. H.(1995) J. Biol. Chem. 270, 7462-7473). Here we report that the T4 primase (gp61) is a monomer in solution under the same conditions, and that the ATP-activated helicase binds to a single gp61 primase molecule on appropriate DNA templates to reconstitute a stable primosome. We show that: (i) the gp41 helicase alone does not form a stable complex with DNA templates, although this helicase by itself can carry out moderately processive ATP-driven translocation along single-stranded DNA (Young, M. C., Schultz, D. E., Ring, D., and von Hippel, P. H.(1994) J. Mol. Biol. 235, 1447-1458); (ii) the primase alone does form a stable complex with DNA; (iii) the helicase can bind to the primase-DNA complex in the presence of ATP or GTP to form a stable ternary complex; (iv) this complex consists of six helicase subunits and one primase subunit; and (v) the reconstituted primosome is stable for at least 10 to 20 min after NTP cleavage and dissociation of the hydrolysis products. These results strongly suggest that the functional T4 DNA replication primosome consists of an integrated 6:1 helicase-primase complex bound to DNA, and that the ATP-activated helicase hexamer remains intact throughout the processive DNA replication process.},
  file      = {:by-author/D/Dong/1996_Dong_19625.pdf:PDF},
  keywords  = {Gel; {gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Dong2002,
  author    = {Qunfeng Dong and Zhijun Wu},
  journal   = {Journal of Global Optimization},
  title     = {A linear-time algorithm for solving the molecular distance geometry problem with exact inter-atomic distances},
  year      = {2002},
  pages     = {365--375},
  volume    = {22},
  abstract  = {We describe a linear-time algorithm for solving the molecular distance geometry problem with exact distances between all pairs of atoms. This problem needs to be solved in every iteration of general distance geometry algorithms for protein modeling such as the EMBED algorithm by Crippen and Havel (Distance Geometry and Molecular Conformation, Wiley, 1988). However, previous approaches to the problem rely on decomposing an distance matrix or minimizing an error function and require $O(n^2)$ to $O(n^3)$ floating point operations. The linear-time algorithm will provide a much more efficient approach to the problem, especially in large-scale applications. It exploits the problem structure and hence is able to identify infeasible data more easily as well.},
  file      = {:by-author/D/Dong/2002_Dong_365.pdf:PDF},
  keywords  = {Distance Geometry; Distance Matrix; Strucure Reconstruction},
  owner     = {saulius},
  timestamp = {2011.12.14},
  creationdate = {2011-12-14T00:00:00},
}

@Article{Dong2006,
  author    = {Dong, Wei},
  title     = {Migrating Linux VServers},
  year      = {2006},
  abstract  = {The interaction between processes has always been an obstacle to the migration of single running processes. On the other extreme, the migration of a whole running system, both in a physical machine of a virtual machine, is not that hard. In this project, we want to find out a point lying in between where we can do the migration with both correctness and low cost. The Linux VServer is used in the project to create isolated contexts which limit the interaction of processes in the boundary of such context, and the migration is carried out at the level of whole isolated context. The results of the project prove this a feasible solution.},
  file      = {:by-author/D/Dong/2006_Dong.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Dong2005,
  author    = {Zeyuan Dong and Xin Huang and Shizhong Mao and Junqiu Liu and Guimin Luo and Jiacong Shen},
  journal   = {Chemistry Letters},
  title     = {A Synthetic Bifunctional Enzyme Model with Superoxide Dismutase and Glutathione Peroxidase Activities},
  year      = {2005},
  pages     = {X},
  file      = {:by-author/D/Dong/2005_Dong_X.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Donhauser2001,
  author    = {Donhauser, Z. J. and Mantooth, B. A. and Kelly, K. F. and Bumm, L. A. and Monnell, J. D. and Stapleton, J. J. and Price, D. W. and Rawlett, A. M. and Allara, D. L. and Tour, J. M. and Weiss, P. S.},
  journal   = {Science},
  title     = {Conductance switching in single molecules through conformational changes},
  year      = {2001},
  issn      = {0036-8075, 1095-9203},
  pages     = {2303--2307},
  volume    = {292},
  abstract  = {We tracked over time the conductance switching of single and bundled phenylene ethynylene oligomers isolated in matrices of alkanethiolate monolayers. The persistence times for isolated and bundled molecules in either the ON or OFF switch state range from seconds to tens of hours. When the surrounding matrix is well ordered, the rate at which the inserted molecules switch is low. Conversely, when the surrounding matrix is poorly ordered, the inserted molecules switch more often. We conclude that the switching is a result of conformational changes in the molecules or bundles, rather than electrostatic effects of charge transfer.},
  doi       = {10.1126/science.1060294},
  file      = {Full Text PDF:by-author/D/Donhauser/2001_Donhauser_2303.pdf:PDF;Snapshot:by-author/D/Donhauser/2001_Donhauser_2303.html:URL},
  groups    = {sg/chemical},
  language  = {en},
  owner     = {saulius},
  pmid      = {11423655},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://www.sciencemag.org/content/292/5525/2303},
  urldate   = {2015-08-05},
}

@Article{Donmez2006,
  author    = {Donmez, Ilker and Patel, Smita S.},
  journal   = {Nucleic acids research},
  title     = {Mechanisms of a ring shaped helicase.},
  year      = {2006},
  pages     = {4216--24},
  volume    = {34},
  abstract  = {Bacteriophage T7 helicase (T7 gene 4 helicase-primase) is a prototypical member of the ring-shaped family of helicases, whose structure and biochemical mechanisms have been studied in detail. T7 helicase assembles into a homohexameric ring that binds single-stranded DNA in its central channel. Using RecA-type nucleotide binding and sensing motifs, T7 helicase binds and hydrolyzes several NTPs, among which dTTP supports optimal protein assembly, DNA binding and unwinding activities. During translocation along single stranded DNA, the subunits of the ring go through dTTP hydrolysis cycles one at a time, and this probably occurs also during DNA unwinding. Interestingly, the unwinding speed of T7 helicase is an order of magnitude slower than its translocation rate along single stranded DNA. The slow unwinding rate is greatly stimulated when DNA synthesis by T7 DNA polymerase is coupled to DNA unwinding. Using the T7 helicase as an example, we highlight critical findings and discuss possible mechanisms of helicase action.},
  file      = {:by-author/D/Donmez/2006_Donmez_4216.pdf:PDF},
  keywords  = {{gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Donnay1943,
  author    = {Donnay, Joseph Désiré Hubert},
  journal   = {American Mineralogist},
  title     = {Rules for the conventional orientation of crystals},
  year      = {1943},
  month     = {May},
  number    = {5},
  pages     = {313--328},
  volume    = {28},
  abstract  = {The following rules are recommended for the conventional orientation of a crystal. They are intended to apply to all systematic descriptions, either morphological or structural.},
  file      = {1943_Donnay_313.pdf:by-author/D/Donnay/1943_Donnay_313.pdf:PDF},
  groups    = {sg/Cell reduction},
  keywords  = {Reduction; Unit Cell},
  owner     = {saulius},
  timestamp = {2016.04.12},
  creationdate = {2016-04-12T00:00:00},
  url       = {http://www.minsocam.org/ammin/AM28/AM28_313.pdf},
}

@Article{Donnay1943a,
  author    = {Donnay, Joseph Désiré Hubert},
  journal   = {American Mineralogist},
  title     = {Rules for the conventional orientation of crystals: a correction},
  year      = {1943},
  month     = {July-August},
  number    = {7-8},
  pages     = {470},
  volume    = {28},
  abstract  = {Errata: Page 319, first line, read „to discard the αβ rule . . . etc.“ The space group of lorandite in the Peacock setting (Am. Minerol., 28, 326, 1943) was represented by P2/x, with glide-component 1/2(a+2c), and the criterion for the zone [(h0l)] was expressed as "(h+2l) even." As Dr. M. J. Buerger kindly pointed out to me, this method of symbolizing the space group is unnecessarily complicated. It is equivalent to the simpler notation P2/a (with criterion "h even"), for a glide-component 1/2a has the same efiect as a glide-component 1/2(a+2c).},
  file      = {1943_Donnay_470.pdf:by-author/D/Donnay/1943_Donnay_470.pdf:PDF},
  groups    = {sg/Cell reduction},
  keywords  = {Reduction; Unit Cell},
  owner     = {saulius},
  timestamp = {2016.04.12},
  creationdate = {2016-04-12T00:00:00},
  url       = {http://www.minsocam.org/ammin/AM28/AM28_470.pdf},
}

@Article{Donnay1943b,
  author    = {Donnay, Joseph Désiré Hubert},
  journal   = {American Mineralogist},
  title     = {Resetting a triclinic unit-cell in the conventional orientation},
  year      = {1943},
  month     = {September-October},
  number    = {9-10},
  pages     = {507},
  volume    = {28},
  abstract  = {The rules for the conventional orientation of a triclinic crystal (Donnay and Mélon, 1933; Donnay, Tunell, and Barth, 1934; Donnay,1943) are the following. The axes must be: (1) chosen along the shortest three translations; (2) named so as to satisfy the condition c<a<b; (3) oriented so that the axial cross is right-handed, with α and β both obtuse},
  file      = {1943_Donnay_507.pdf:by-author/D/Donnay/1943_Donnay_507.pdf:PDF},
  groups    = {sg/Cell sg/Reduction, sg/Cell reduction},
  keywords  = {Reduction; Unit Cell},
  owner     = {saulius},
  timestamp = {2016.04.12},
  creationdate = {2016-04-12T00:00:00},
  url       = {http://www.minsocam.org/ammin/AM28/AM28_507.pdf},
}

@Article{Donner1996,
  author    = {Donner, Wolfgang T.},
  journal   = {Journal of Chemical Information and Computer Sciences},
  title     = {Economic Aspects of Chemical Information†},
  year      = {1996},
  pages     = {937--941},
  volume    = {36},
  abstract  = {Important chemical information is contained in a unique way in the Beilstein handbook as well as in the database with its own search engine (CrossFire). This electronic form is one important component of a chemical information management system needed in industrial R&D. The necessary investment for such a system also needs an economic justification. Effective use of any such system containing chemical information from different sources will be enhanced considerably by the use of CAS Registry Numbers.},
  doi       = {10.1021/ci950248l},
  file      = {:by-author/D/Donner/1996_Donner_937.pdf:PDF},
  keywords  = {Chemical Databases},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
  url       = {http://pubs.acs.org/doi/abs/10.1021/ci950248l},
}

@Article{Donnini2011,
  author    = {Serena Donnini and Florian Tegeler and Gerrit Groenhof and Helmut Grubmüller},
  journal   = {Journal of Chemical Theory and Computation},
  title     = {Constant pH Molecular Dynamics in Explicit Solvent with λ-Dynamics},
  year      = {2011},
  note      = {PMID: 21687785},
  number    = {6},
  pages     = {1962--1978},
  volume    = {7},
  abstract  = {pH is an important parameter in condensed-phase systems, because it determines the protonation state of titratable groups and thus influences the structure, dynamics, and function of molecules in solution. In most force field simulation protocols, however, the protonation state of a system (rather than its pH) is kept fixed and cannot adapt to changes of the local environment. Here, we present a method, implemented within the MD package GROMACS, for constant pH molecular dynamics simulations in explicit solvent that is based on the λ-dynamics approach. In the latter, the dynamics of the titration coordinate λ, which interpolates between the protonated and deprotonated states, is driven by generalized forces between the protonated and deprotonated states. The hydration free energy, as a function of pH, is included to facilitate constant pH simulations. The protonation states of titratable groups are allowed to change dynamically during a simulation, thus reproducing average protonation probabilities at a certain pH. The accuracy of the method is tested against titration curves of single amino acids and a dipeptide in explicit solvent.},
  doi       = {10.1021/ct200061r},
  eprint    = {http://dx.doi.org/10.1021/ct200061r},
  file      = {2011_Donnini_1962.pdf:by-author/D/Donnini/2011_Donnini_1962.pdf:PDF},
  groups    = {sg/Molecular dynamics},
  keywords  = {Molecular Dynamics (MD); Simulations; Thermostat},
  owner     = {saulius},
  timestamp = {2016.02.23},
  creationdate = {2016-02-23T00:00:00},
  url       = {http://dx.doi.org/10.1021/ct200061r},
}

@Article{Donohue1969,
  author    = {Donohue, J.},
  journal   = {Science (New York, N.Y.)},
  title     = {Fourier analysis and the structure of DNA.},
  year      = {1969},
  pages     = {1091--6},
  volume    = {165},
  file      = {:by-author/D/Donohue/1969_Donohue_1091.pdf:PDF},
  keywords  = {DNA Structure},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Donohue1956,
  author    = {Donohue, J.},
  journal   = {Proceedings of the National Academy of Sciences of the United States of America},
  title     = {HYDROGEN-BONDED HELICAL CONFIGURATIONS OF POLYNUCLEOTIDES.},
  year      = {1956},
  pages     = {60--5},
  volume    = {42},
  file      = {:by-author/D/Donohue/1956_Donohue_60.pdf:PDF},
  keywords  = {DNA Structure},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Donohue1949,
  author    = {Donohue, J. and Schomaker, V.},
  journal   = {Acta Crystallographica},
  title     = {The use of punched cards in molecular structure determinations. {III}. Structure-factor calculations of {X}-ray crystallography},
  year      = {1949},
  issn      = {0365-110X},
  month     = {Dec},
  number    = {6},
  pages     = {344--347},
  volume    = {2},
  abstract  = {A method is described whereby the rapid calculation of the structure factors of X-ray crystallography is accomplished on punched cards and International Business Machines. The method is sufficiently flexible to allow its application to any space group. The principles set forth may also be applied to other formerly laborious calculations, such as the application of the method of least squares to crystal-structure determinations.},
  doi       = {10.1107/s0365110x49000904},
  file      = {1949_Donohue_344.pdf:by-author/D/Donohue/1949_Donohue_344.pdf:PDF},
  keywords  = {Computations; History; X-ray Crystallography},
  owner     = {saulius},
  publisher = {International Union of Crystallography (IUCr)},
  timestamp = {2017.01.07},
  creationdate = {2017-01-07T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0365110X49000904},
}

@Manuscript{Dooijes2006,
  author      = {Dooijes, E. H.},
  title       = {Trends in computer technology},
  year        = {2006},
  institution = {Computer Museum, Department of Computer Science, University of Amsterdam},
  keywords    = {Computer Science (CS); Computing History},
  month       = {May},
  file        = {:by-author/D/Dooijes/2006_Dooijes.pdf:PDF},
  owner       = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Manuscript{Dooijes2000,
  author      = {Dooijes, E. H.},
  title       = {Old computers, now and in the future},
  year        = {2000},
  institution = {Department of Computer Science, University of Amsterdam, Kruislaan 403, 1098SJ Amsterdam, The Netherlands},
  keywords    = {Computer Science (CS); Computing History},
  month       = {December},
  abstract    = {In this paper we discuss some of the problems we have experienced while putting together and maintaining a fairly extensive collection of 'antique' computer equipment.},
  file        = {:by-author/D/Dooijes/2000_Dooijes.pdf:PDF},
  owner       = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Webpage{Dopertchouk2000,
  author    = {Oleg Dopertchouk},
  retrieved = {2011-07-21},
  title     = {Simple Bounding-Sphere Collision Detection},
  url       = {http://www.gamedev.net/page/resources/_/technical/math-and-physics/simple-bounding-sphere-collision-detection-r1234},
  month     = {November},
  year      = {2000},
  abstract  = {Collision detection is an important part of most 3D games. Shooting enemies, avoiding (or failing to avoid) obstacles, even simply staying on the ground usually requires some form of collision-detection. It's a vast subject and there are many excellent articles written about it. However, most of them concern the more sophisticated algorithms, such as BSP and the simple bounding-sphere check receives no more than a passing mention. It is a quite simple procedure but it still could be very useful and there are a couple of subtle points involved. So I thought perhaps I should write something about it.},
  file      = {:by-author/D/Dopertchouk/2000_Dopertchouk.odt:},
  groups    = {sg/Molecular dynamics},
  keywords  = {Hard-spheres; Molecular-dynamics},
  owner     = {saulius},
  timestamp = {2015.03.03},
  creationdate = {2015-03-03T00:00:00},
}

@Lecture{Doran2015,
  author    = {Chris Doran},
  title     = {GA2015 – Lecture 4 - Geometric Algebra},
  year      = {2015},
  file      = {Microsoft PowerPoint - GA2015_Lecture4.pptx - GA2015_Lecture4.pdf:by-author/D/Doran/2015_Doran.pdf:PDF;Snapshot:by-author/D/Doran/2015_Doran.html:URL},
  keywords  = {Computer Algorithms; Geometric Algebra; Haskel; Mathematics},
  owner     = {saulius},
  timestamp = {2016.04.05},
  creationdate = {2016-04-05T00:00:00},
  url       = {http://geometry.mrao.cam.ac.uk/2015/10/ga2015-lecture-4/},
  urldate   = {2016-03-30},
}

@Lecture{Doran2015a,
  author    = {Chris Doran},
  title     = {GA2015 – Lecture 3 - Geometric Algebra},
  year      = {2015},
  file      = {Microsoft PowerPoint - GA2015_Lecture3.pptx - GA2015_Lecture3.pdf:by-author/D/Doran/2015_Doran_a.pdf:PDF;Snapshot:by-author/D/Doran/2015_Doran_a.html:URL},
  keywords  = {Computer Algorithms; Geometric Algebra; Haskel; Mathematics},
  owner     = {saulius},
  timestamp = {2016.04.05},
  creationdate = {2016-04-05T00:00:00},
  url       = {http://geometry.mrao.cam.ac.uk/2015/10/ga2015-lecture-3/},
  urldate   = {2016-03-30},
}

@Lecture{Doran2015b,
  author    = {Chris Doran},
  title     = {GA2015 – Lecture 2 - Geometric Algebra},
  year      = {2015},
  file      = {Microsoft PowerPoint - GA2015_Lecture2.pptx - GA2015_Lecture2.pdf:by-author/D/Doran/2015_Doran_b.pdf:PDF;Snapshot:by-author/D/Doran/2015_Doran_b.html:URL},
  keywords  = {Computer Algorithms; Geometric Algebra; Haskel; Mathematics},
  owner     = {saulius},
  timestamp = {2016.04.05},
  creationdate = {2016-04-05T00:00:00},
  url       = {http://geometry.mrao.cam.ac.uk/2015/10/ga2015-lecture-2/},
  urldate   = {2016-03-30},
}

@Lecture{Doran2015c,
  author    = {Chris Doran},
  title     = {GA2015 – Lecture 1 - Geometric Algebra},
  year      = {2015},
  file      = {Microsoft PowerPoint - GA2015_Lecture1.pptx - GA2015_Lecture1.pdf:by-author/D/Doran/2015_Doran_c.pdf:PDF;Snapshot:by-author/D/Doran/2015_Doran_c.html:URL},
  keywords  = {Computer Algorithms; Geometric Algebra; Haskel; Mathematics},
  owner     = {saulius},
  timestamp = {2016.04.05},
  creationdate = {2016-04-05T00:00:00},
  url       = {http://geometry.mrao.cam.ac.uk/2015/10/ga2015-lecture-1/},
  urldate   = {2016-03-30},
}

@Lecture{Doran2015d,
  author    = {Chris Doran},
  title     = {GA2015 – Lecture 5 - Geometric Algebra},
  year      = {2015},
  file      = {Microsoft PowerPoint - GA2015_Lecture5.pptx - GA2015_Lecture5.pdf:by-author/D/Doran/2015_Doran_d.pdf:PDF;Snapshot:by-author/D/Doran/2015_Doran_d.html:URL},
  keywords  = {Computer Algorithms; Geometric Algebra; Haskel; Mathematics},
  owner     = {saulius},
  timestamp = {2016.04.05},
  creationdate = {2016-04-05T00:00:00},
  url       = {http://geometry.mrao.cam.ac.uk/2015/10/ga2015-lecture-5/},
  urldate   = {2016-03-30},
}

@Lecture{Doran2015e,
  author    = {Chris Doran},
  title     = {GA2015 – Lecture 6 - Geometric Algebra},
  year      = {2015},
  file      = {GA2015_Lecture6.pdf:by-author/D/Doran/2015_Doran_e.pdf:PDF;Snapshot:by-author/D/Doran/2015_Doran_e.html:URL},
  keywords  = {Computer Algorithms; Geometric Algebra; Haskel; Mathematics},
  owner     = {saulius},
  timestamp = {2016.04.05},
  creationdate = {2016-04-05T00:00:00},
  url       = {http://geometry.mrao.cam.ac.uk/2015/11/ga2015-lecture-6/},
  urldate   = {2016-03-30},
}

@Lecture{Doran2015f,
  author    = {Chris Doran},
  title     = {GA2015 – Lecture 7 - Geometric Algebra},
  year      = {2015},
  file      = {GA2015_Lecture7.pdf:by-author/D/Doran/2015_Doran_f.pdf:PDF;Snapshot:by-author/D/Doran/2015_Doran_f.html:URL},
  keywords  = {Computer Algorithms; Geometric Algebra; Haskel; Mathematics},
  owner     = {saulius},
  timestamp = {2016.04.05},
  creationdate = {2016-04-05T00:00:00},
  url       = {http://geometry.mrao.cam.ac.uk/2015/11/ga2015-lecture-7/},
  urldate   = {2016-03-30},
}

@Lecture{Doran2015g,
  author    = {Chris Doran},
  title     = {GA2015 – Lecture 8 - Geometric Algebra},
  year      = {2015},
  file      = {Microsoft PowerPoint - GA2015_Lecture8.pptx - GA2015_Lecture8.pdf:by-author/D/Doran/2015_Doran_g.pdf:PDF;Snapshot:by-author/D/Doran/2015_Doran_g.html:URL},
  keywords  = {Computer Algorithms; Geometric Algebra; Haskel; Mathematics},
  owner     = {saulius},
  timestamp = {2016.04.05},
  creationdate = {2016-04-05T00:00:00},
  url       = {http://geometry.mrao.cam.ac.uk/2015/11/ga2015-lecture-8/},
  urldate   = {2016-03-30},
}

@InBook{Doran2003,
  author    = {Chris Doran and Anthony Lasenby},
  chapter   = {Introduction},
  pages     = {1--19},
  publisher = {Cambridge University Press},
  title     = {Geometric algebra for physicists},
  year      = {2003},
  file      = {2003_Doran.pdf:by-author/D/Doran/2003_Doran.pdf:PDF},
  keywords  = {Algebra; Geometric Algebra; Mathematics},
  owner     = {saulius},
  timestamp = {2016.03.30},
  creationdate = {2016-03-30T00:00:00},
  url       = {http://catdir.loc.gov/catdir/samples/cam033/2002035182.pdf},
}

@TechReport{Dorward1997,
  author      = {Sean Dorward and Rob Pike and David Leo Presotto and Dennis M. Ritchie and Howard Trickey and Phil Winterbottom},
  institution = {Computing Science Research Center, Lucent Technologies, Bell Labs, Murray Hill, New Jersey, USA},
  title       = {The Inferno Operating System},
  year        = {1997},
  abstract    = {Inferno is an operating system for creating and supporting distributed services. It was originally developed by the Computing Science Research Center of Bell Labs, the R&D arm of Lucent Technologies, and further developed by other groups in Lucent. Inferno was designed specifically as a commercial product, both for licensing in the marketplace and for use within new Lucent offerings. It encapsulates many years of Bell Labs research in operating systems, languages, on-the-fly compilers, graphics, security, networking and portability.},
  file        = {:by-author/D/Dorward/1997_Dorward.war:},
  keywords    = {Computer Science (CS)},
  owner       = {saulius},
  timestamp = {2015.03.02},
  creationdate = {2015-03-02T00:00:00},
  url         = {http://www.vitanuova.com/inferno/papers/bltj.html},
}

@Article{Doudna2002,
  author    = {Doudna, Jennifer A and Rath, Virginia L},
  journal   = {Cell},
  title     = {Structure and function of the eukaryotic ribosome: the next frontier.},
  year      = {2002},
  pages     = {153--6},
  volume    = {109},
  abstract  = {As the catalytic and regulatory centers of protein synthesis in cells, ribosomes are central to many aspects of cell and structural biology. Recent work highlights the unique properties and complexity of eukaryotic ribosomes and their component rRNAs and proteins.},
  file      = {2002_Doudna_153.pdf:by-author/D/Doudna/2002_Doudna_153.pdf:PDF},
  keywords  = {Protein Structures; Ribosome},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Douglas2003,
  author    = {Douglas, Keith},
  title     = {Super-{T}uring Computation: A Case Study Analysis},
  year      = {2003},
  file      = {:by-author/D/Douglas/2003_Douglas.pdf:PDF},
  keywords  = {Computer Science (CS); Super Turing Computations},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Dowell2001,
  author    = {Dowell, Robin and Jokerst, Rodney and Day, Allen and Eddy, Sean and Stein, Lincoln},
  journal   = {BMC Bioinformatics},
  title     = {The Distributed Annotation System},
  year      = {2001},
  issn      = {1471-2105},
  pages     = {7},
  volume    = {2},
  abstract  = {BACKGROUND:Currently, most genome annotation is curated by centralized groups with limited resources. Efforts to share annotations transparently among multiple groups have not yet been satisfactory.RESULTS:Here we introduce a concept called the Distributed Annotation System (DAS). DAS allows sequence annotations to be decentralized among multiple third-party annotators and integrated on an as-needed basis by client-side software. The communication between client and servers in DAS is defined by the DAS XML specification. Annotations are displayed in layers, one per server. Any client or server adhering to the DAS XML specification can participate in the system; we describe a simple prototype client and server example.CONCLUSIONS:The DAS specification is being used experimentally by Ensembl, WormBase, and the Berkeley Drosophila Genome Project. Continued success will depend on the readiness of the research community to adopt DAS and provide annotations. All components are freely available from the project website http://www.biodas.org/ webcite.},
  doi       = {10.1186/1471-2105-2-7},
  file      = {2001_Dowell_2-7.pdf:by-author/D/Dowell/2001_Dowell_2-7.pdf:PDF},
  keywords  = {Bioinformatics; Databases},
  owner     = {saulius},
  pubmedid  = {11667947},
  timestamp = {2012.10.25},
  creationdate = {2012-10-25T00:00:00},
  url       = {http://www.biomedcentral.com/1471-2105/2/7},
}

@Article{Downing2008,
  author    = {Downing, Jim and Murray-Rust, Peter and Tonge, Alan P. and Morgan, Peter and Rzepa, Henry S. and Cotterill, Fiona and Day, Nick and Harvey, Matt J.},
  journal   = {Journal of Chemical Information and Modeling},
  title     = {SPECTRa: The Deposition and Validation of Primary Chemistry Research Data in Digital Repositories},
  year      = {2008},
  pages     = {1571--1581},
  volume    = {48},
  abstract  = {The SPECTRa (Submission, Preservation and Exposure of Chemistry Teaching and Research Data) project has investigated the practices of chemists in archiving and disseminating primary chemical data from academic research laboratories. To redress the loss of the large amount of data never archived or disseminated, we have developed software for data publication into departmental and institutional Open Access digital repositories (DSpace). Data adhering to standard formats in selected disciplines (crystallography, NMR, computational chemistry) is transformed to XML (CML, Chemical Markup Language) which provides added validation. Context-specific chemical metadata and persistent Handle identifiers are added to enable long-term data reuse. It was found essential to provide an embargo mechanism, and policies for operating this and other processes are presented.},
  doi       = {10.1021/ci7004737},
  eprint    = {http://pubs.acs.org/doi/pdf/10.1021/ci7004737},
  file      = {2008_Downing_1571.pdf:by-author/D/Downing/2008_Downing_1571.pdf:PDF},
  keywords  = {CML; Chemoinformatics; Computational Chemistry},
  owner     = {saulius},
  timestamp = {2014.07.17},
  creationdate = {2014-07-17T00:00:00},
  url       = {http://pubs.acs.org/doi/abs/10.1021/ci7004737},
}

@Article{Downs1989,
  author    = {Geoffrey M. Downs and Valerie J. Gillet and John D. Holliday and Michael F. Lynch},
  journal   = {J. Chem. Inf. Comput. Sci.},
  title     = {Review of Ring Perception Algorithms for Chemical Graphs},
  year      = {1989},
  pages     = {172--187},
  volume    = {29},
  abstract  = {Current ring perception algorithms for use on chemical graphs concentrate on processing specific structures. In this review, the various published ring perception algorithms are classified according to the initial ring set obtained, and each algorithm or method of perception is described in detail. The final ring sets obtained are discussed in terms of their suitability for use in representing the ring systems in structurally explicit parts of generic chemical structures.},
  doi       = {10.1021/ci00063a007},
  file      = {1989_Downs_172.pdf:by-author/D/Downs/1989_Downs_172.pdf:PDF},
  keywords  = {Ring Perception},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Presentation{Downs2013,
  author       = {Robert T. Downs},
  title        = {Curiosity: Results from the Mars Science Laboratory},
  year         = {2013},
  organization = {NASA/JPL-Caltech/MSSS},
  file         = {2013_Downs_slides.pdf:by-author/D/Downs/2013_Downs_slides.pdf:PDF},
  keywords     = {Crystallography; Curiosity Rover; Mars Exploration; Mineralogy; Powder Diffraction; X-ray Crystallography},
  owner        = {saulius},
  timestamp = {2013.09.10},
  creationdate = {2013-09-10T00:00:00},
  url          = {http://www.geo.arizona.edu/~downs/xtal/Dallas_Downs_Aug2013.pdf},
}

@Article{Downs1993,
  author    = {R. T. Downs and K. L. Bartelmehs and G. V. Gibbs and Boisen, Jr., M. B.},
  journal   = {American Mineralogist},
  title     = {Interactive software for calculating and displaying X-ray or neutron powder diffractometer patterns of crystalline materials},
  year      = {1993},
  pages     = {1104--1107},
  volume    = {78},
  file      = {1993_Downs_1104.pdf:by-author/D/Downs/1993_Downs_1104.pdf:PDF},
  keywords  = {Algorithms; Mineralogy; Powder Diffraction; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Downs2003,
  author           = {Robert T. Downs and Michelle Hall-Wallace},
  journal          = {American Mineralogist},
  title            = {The American Mineralogist crystal structure database},
  year             = {2003},
  pages            = {247--250},
  volume           = {88},
  creationdate     = {2008-07-28T00:00:00},
  eprint           = {https://pubs.geoscienceworld.org/msa/ammin/article-abstract/88/1/247/43886/The-American-Mineralogist-crystal-structure},
  file             = {:by-author/D/Downs/2003_Downs_247.pdf:PDF},
  keywords         = {AMCSD; Databases; Mineralogy},
  modificationdate = {2024-01-11T08:30:12},
  owner            = {saulius},
  timestamp        = {2008.07.28},
  url              = {http://geo.arizona.edu/xtal/group/pdf/am88_247.pdf},
}

@Article{Dreele1990,
  author    = {Robert B. Von Dreele},
  journal   = {Los Alamos Science},
  title     = {Crystal Symmetry Groups},
  year      = {1990},
  pages     = {152--157},
  volume    = {19},
  file      = {:by-author/D/Dreele/1990_Dreele_152.pdf:PDF},
  owner     = {antanas},
  timestamp = {2013.05.26},
  creationdate = {2013-05-26T00:00:00},
  url       = {http://worldebookfair.com/eBooks/WPLBN0002113450-Los-Alamos-Science-No--19--1990-by-Robert-B--Von-Dreele.aspx},
}

@Article{Dreele1990a,
  author    = {Robert B. Von Dreele},
  journal   = {Los Alamos Science},
  title     = {{X}-Ray and Neutron Crystallography : A Powerful Combination},
  year      = {1990},
  pages     = {132--151},
  volume    = {19},
  file      = {:by-author/D/Dreele/1990_Dreele_132.pdf:PDF},
  owner     = {antanas},
  timestamp = {2013.05.26},
  creationdate = {2013-05-26T00:00:00},
  url       = {http://worldebookfair.com/eBooks/WPLBN0002113450-Los-Alamos-Science-No--19--1990-by-Robert-B--Von-Dreele.aspx},
}

@Article{Dreier1996,
  author    = {Dreier, J. and Bickle, T. A.},
  journal   = {Journal of molecular biology},
  title     = {ATPase activity of the type IC restriction-modification system EcoR124II.},
  year      = {1996},
  pages     = {960--9},
  volume    = {257},
  abstract  = {We have investigated the ATPase activity of the type IC restriction-modification (R-M) system EcoR124II. As with all type I R-M systems EcoR 124II requires ATP hydrolysis to cut DNA. We determined the KM for ATP to be 10(-5) to 10(-4) M. By measuring ATP hydrolysis under different conditions and by simultaneously monitoring DNA restriction, methylation and ATP hydrolysis we propose that the order of events during restriction is: (1) binding of EcoR124II to a non-methylated recognition sequence, (2) start of DNA-dependent ATP hydrolysis which continues even after restriction is complete, (3) restriction of DNA, (4) methylation of the product. Non-cleavable DNA substrates, such as recognition site containing oligonucleotides, also support ATP hydrolysis. Methylation can also occur prior to ATP hydrolysis and prevent DNA degradation.},
  file      = {:by-author/D/Dreier/1996_Dreier_960.pdf:PDF},
  keywords  = {TypeI},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Dreier1996a,
  author    = {Dreier, J. and MacWilliams, M. P. and Bickle, T. A.},
  journal   = {Journal of molecular biology},
  title     = {DNA cleavage by the type IC restriction-modification enzyme EcoR124II.},
  year      = {1996},
  pages     = {722--33},
  volume    = {264},
  abstract  = {Type I restriction-modification systems bind to non-palindromic, bipartite recognition sequences. Although these enzymes methylate specific adenine residues within their recognition sequences, they cut DNA at sites up to several thousand base-pairs away. We have investigated the mechanism of how EcoR124II, a type IC restriction-modification system, selects the cleavage site. Restriction studies with different DNA constructs revealed that circular DNA requires only one non-methylated recognition sequence to be cut, whereas linear DNA needs at least two such sites. Cleavage of linear DNA is independent of site orientation. Further investigations of the linear substrates revealed a mechanism whereby the double-strand break is introduced between two recognition sequences. We propose a model for the selection of restriction sites by type I enzymes where two EcoR124II complexes bind to two recognition sequences. Lack of methylation at a site stimulates the enzyme to translocate DNA on both sides of the recognition sequence. Thus the two complexes approach each other and, at the point where they meet, they interact to introduce a double-strand break in the DNA.},
  file      = {:by-author/D/Dreier/1996_Dreier_722.pdf:PDF},
  keywords  = {TypeI},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Drmac2009,
  author    = {Zlatko Drmač},
  journal   = {SIAM Journal on Matrix Analysis and Applications},
  title     = {A global convergence proof for cyclic jacobi methods with block rotations},
  year      = {2009},
  pages     = {1329--1350},
  volume    = {31},
  abstract  = {This paper introduces a globally convergent block (column- and row-) cyclic Jacobi method for diagonalization of Hermitian matrices and for computation of the singular value decomposition of general matrices. It is shown that a block rotation (a generalization of the Jacobi $2\times2$ rotation) can be computed and implemented in a particular way to guarantee global convergence. The proof includes the convergence of the eigenspaces in the general case of multiple eigenvalues. This solves a long standing open problem of convergence of block cyclic Jacobi methods.},
  file      = {2009_Drmač_1329.pdf:by-author/D/Drmač/2009_Drmač_1329.pdf:PDF},
  owner     = {saulius},
  timestamp = {2011.12.13},
  creationdate = {2011-12-13T00:00:00},
}

@Article{Dryden2001,
  author    = {Dryden, D. T. and Murray, N. E. and Rao, D. N.},
  journal   = {Nucleic acids research},
  title     = {Nucleoside triphosphate-dependent restriction enzymes.},
  year      = {2001},
  pages     = {3728--41},
  volume    = {29},
  abstract  = {The known nucleoside triphosphate-dependent restriction enzymes are hetero-oligomeric proteins that behave as molecular machines in response to their target sequences. They translocate DNA in a process dependent on the hydrolysis of a nucleoside triphosphate. For the ATP-dependent type I and type III restriction and modification systems, the collision of translocating complexes triggers hydrolysis of phosphodiester bonds in unmodified DNA to generate double-strand breaks. Type I endonucleases break the DNA at unspecified sequences remote from the target sequence, type III endonucleases at a fixed position close to the target sequence. Type I and type III restriction and modification (R-M) systems are notable for effective post-translational control of their endonuclease activity. For some type I enzymes, this control is mediated by proteolytic degradation of that subunit of the complex which is essential for DNA translocation and breakage. This control, lacking in the well-studied type II R-M systems, provides extraordinarily effective protection of resident DNA should it acquire unmodified target sequences. The only well-documented GTP-dependent restriction enzyme, McrBC, requires methylated target sequences for the initiation of phosphodiester bond cleavage.},
  file      = {:by-author/D/Dryden/2001_Dryden_3728.pdf:PDF},
  keywords  = {Obzor},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Dryden2011,
  author    = {Dryden, David T. F. and Edwardson, J. M. and Henderson, Robert M.},
  journal   = {Nucleic acids research},
  title     = {DNA translocation by type III restriction enzymes: a comparison of current models of their operation derived from ensemble and single-molecule measurements.},
  year      = {2011},
  pages     = {4525--31},
  volume    = {39},
  abstract  = {Much insight into the interactions of DNA and enzymes has been obtained using a number of single-molecule techniques. However, recent results generated using two of these techniques-atomic force microscopy (AFM) and magnetic tweezers (MT)-have produced apparently contradictory results when applied to the action of the ATP-dependent type III restriction endonucleases on DNA. The AFM images show extensive looping of the DNA brought about by the existence of multiple DNA binding sites on each enzyme and enzyme dimerisation. The MT experiments show no evidence for looping being a requirement for DNA cleavage, but instead support a diffusive sliding of the enzyme on the DNA until an enzyme-enzyme collision occurs, leading to cleavage. Not only do these two methods appear to disagree, but also the models derived from them have difficulty explaining some ensemble biochemical results on DNA cleavage. In this 'Survey and Summary', we describe several different models put forward for the action of type III restriction enzymes and their inadequacies. We also attempt to reconcile the different models and indicate areas for further experimentation to elucidate the mechanism of these enzymes.},
  file      = {:by-author/D/Dryden/2011_Dryden_4525.pdf:PDF},
  keywords  = {TypeIII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Dryden2001a,
  author    = {D. T. F. Dryden and Noreen E. Murray and D. N. Rao},
  journal   = {Nucleic Acids Research},
  title     = {Nucleoside triphosphate-dependent restriction enzymes},
  year      = {2001},
  pages     = {3728a},
  file      = {:by-author/D/Dryden/2001_Dryden_3728a.pdf:PDF},
  keywords  = {Obzor},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Dube2006,
  author    = {Dube, Danielle H. and Prescher, Jennifer A. and Quang, Chi N. and Bertozzi, Carolyn R.},
  journal   = {Proceedings of the National Academy of Sciences of the United States of America},
  title     = {Probing mucin-type O-linked glycosylation in living animals.},
  year      = {2006},
  pages     = {4819--24},
  volume    = {103},
  abstract  = {Changes in O-linked protein glycosylation are known to correlate with disease states but are difficult to monitor in a physiological setting because of a lack of experimental tools. Here, we report a technique for rapid profiling of O-linked glycoproteins in living animals by metabolic labeling with N-azidoacetylgalactosamine (GalNAz) followed by Staudinger ligation with phosphine probes. After injection of mice with a peracetylated form of GalNAz, azide-labeled glycoproteins were observed in a variety of tissues, including liver, kidney, and heart, in serum, and on isolated splenocytes. B cell glycoproteins were robustly labeled with GalNAz but T cell glycoproteins were not, suggesting fundamental differences in glycosylation machinery or metabolism. Furthermore, GalNAz-labeled B cells could be selectively targeted with a phosphine probe by Staudinger ligation within the living animal. Metabolic labeling with GalNAz followed by Staudinger ligation provides a means for proteomic analysis of this posttranslational modification and for identifying O-linked glycoprotein fingerprints associated with disease.},
  file      = {:by-author/D/Dube/2006_Dube_4819.pdf:PDF},
  keywords  = {Bioconjugation},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@Article{Dubois2007,
  author    = {Dubois},
  title     = {Possibility Theory as a Basis for Qualitative Decision Theory},
  year      = {2007},
  abstract  = {A counterpart to von Neumann and Morgenstern' expected utility theory is proposed in the framework of possibility theory. The existence of a utility function, representing a preference ordering among possibility distributions (on the consequences of decision-maker's actions) that satisfies a series of axioms pertaining to decision-maker's behavior, is established. The obtained utility is a generalization of Wald's criterion, which is recovered in case of total ignorance; when ignorance is only partial, the utility takes into account the fact that some situations are more plausible than others. Mathematically, the qualitative utility is nothing but the necessity measure of a fuzzy event in the sense of possibility theory (a so-called Sugeno integral). The possibilistic representation of uncertainty, which only requires a linearly ordered scale, is qualitative in nature. Only max, min and order-reversing operations are used on the scale. The axioms express a risk-averse behavior of the decision maker and correspond to a pessimistic view of what may happen. The proposed qualitative utility function is currently used in flexible constraint satisfaction problems under incomplete information. It can also be used in association with possibilistic logic, which is tailored to reasoning under incomplete states of knowledge.},
  file      = {:by-author/D/Dubois/2007_Dubois.pdf:PDF},
  groups    = {sg/Bayesian, sg/Possibility theory},
  keywords  = {Mathematics; Non Bayesian Updating},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Dubois2006,
  author    = {Dubois},
  title     = {Possibility Theory and Statistical Reasoning},
  year      = {2006},
  file      = {:by-author/D/Dubois/2006_Dubois.pdf:PDF},
  groups    = {sg/Bayesian, sg/Possibility theory},
  keywords  = {Mathematics; Non Bayesian Updating},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Dubois2006a,
  author     = {Dubois, Didier},
  journal    = {Comput. Stat. Data Anal.},
  title      = {Possibility Theory and Statistical Reasoning},
  year       = {2006},
  issn       = {0167-9473},
  pages      = {47--69},
  volume     = {51},
  abstract   = {Numerical possibility distributions can encode special convex families of probability measures. The connection between possibility theory and probability theory is potentially fruitful in the scope of statistical reasoning when uncertainty due to variability of observations should be distinguished from uncertainty due to incomplete information. This paper proposes an overview of numerical possibility theory. Its aim is to show that some notions in statistics are naturally interpreted in the language of this theory. First, probabilistic inequalites (like Chebychev's) offer a natural setting for devising possibility distributions from poor probabilistic information. Moreover, likelihood functions obey the laws of possibility theory when no prior probability is available. Possibility distributions also generalize the notion of confidence or prediction intervals, shedding some light on the role of the mode of asymmetric probability densities in the derivation of maximally informative interval substitutes of probabilistic information. Finally, the simulation of fuzzy sets comes down to selecting a probabilistic representation of a possibility distribution, which coincides with the Shapley value of the corresponding consonant capacity. This selection process is in agreement with Laplace indifference principle and is closely connected with the mean interval of a fuzzy interval. It sheds light on the ''defuzzification'' process in fuzzy set theory and provides a natural definition of a subjective possibility distribution that sticks to the Bayesian framework of exchangeable bets. Potential applications to risk assessment are pointed out.},
  acmid      = {1648302},
  address    = {Amsterdam, The Netherlands, The Netherlands},
  doi        = {10.1016/j.csda.2006.04.015},
  file       = {2006_Dubois_47.pdf:by-author/D/Dubois/2006_Dubois_47.pdf:PDF},
  groups     = {sg/Bayesian, sg/Possibility theory},
  issue_date = {November, 2006},
  keywords   = {Confidence Intervals; Imprecise Probability; Possibility Theory; Uncertainty Propagation},
  numpages   = {23},
  owner      = {saulius},
  publisher  = {Elsevier Science Publishers B. V.},
  timestamp = {2015.12.07},
  creationdate = {2015-12-07T00:00:00},
  url        = {http://dx.doi.org/10.1016/j.csda.2006.04.015},
}

@Article{Dubois2003,
  author    = {D. Dubois and H. Prade},
  title     = {Possibility Theory and its Applications: A Retrospective and Prospective View},
  year      = {2003},
  pages     = {3},
  abstract  = {Possibility theory is an uncertainty theory devoted to the handling of incomplete infohation. It is similar to a large extent to probability theory because it is based on set-functions. It differs from probability theory because it uses a pair of dual set functions (possibility and necessity measures) instead of only one. Besides, it is not additive and makes sense on ordinal structures. Possibility theory has been coined by Zadeh in 1978, and was mainly proposed as a framework for translating.natura1 language information into fuzzy constraints on an underlying feature space. However, it was already introduced as a full-fledged approach to uncertainty in the late forties by the Economist G.L.S. Shackle, who called "degree of potential surprize" of ari event the degree of necessity of the opposite event. Independently, in the late sixties, possibility measures were also suggested by the philosopher L.J. Cohen ("Baconian probabilities"), and comparative counterparts of possibility measures were first defined by the philosopher David Lewis. After a overview of these pioneering contributions, the talk will present the two main directions along which possibility theory has developed: qualitative and quantitative. Both approaches share the same basic "maxitivity" axiom. But they differ when it comes to conditioning and independence notions. Qualitative possibility measures can be valued on any totally ordered set (especially a finite one). They lead to inconsistency-tolerant extensions of propositional logic such as possibilistic logic, and provide a natural semantic setting for non-monotonic reasoning, whose computational complexity remains close to the one of propositional logic. Decision-theoretic justifications of qualitative possibility have been recently devised, in the style of Savage theory. Qualitative counterparts of expected utility take the form of Sugeno integrals specialized to possibility and necessity of fuzzy events. Quantitative possibility theory has several branches: a degree of possibility can be viewed as an upper probability bound, a possibility distribution can be viewed as a likelihood function, and it can also encode probability distributions with extreme values. Extracting a confidence interval from a probability distribution, or devising a probabilistic inequality can be viewed as moving from a probabilistic to a possibilistic representation. Possibilistic mean values can be defined using Choquet integrals, and come close to defuzzification methods. .The connection between possibility measures and imprecise probabilistic reasoning is especially promising, based on recent deep works by De Cooman and Walley. Besides, possibility theory has offered a natural semantic framework for devising a typology of fuzzy rules, distinguishing rules whose purpose is to propagate uncertainty through reasoning steps, from rules whose main purpose is similarity-based interpolation. More recently, a distinction has been made between positive and negative information, corresponding respectively to observed data, examples on the one hand, and constraints ruling out impossible situations on the other hand. This bipolar view has shed new light on the debate between conjunctive and implicative representation of rules. Implicative representations focus on exceptions to rules and have a negative flavor, while conjunctive representations point out the examples of the rules and highlight their positive side. Adding to the framework the notion of guaranteed possibility measure (replacing the maximum by the minimum in the definition of a possiblity measure) makes it possible to capture the bipolarity of information, including when fuzzy sets are involved. It provides a sound interpretation of interval-valued fuzzy sets. Lastly, possibility theory also offers a framework for preference modeling (using fuzzy constraints). Both prioritized and soft constraints can be captured by possibility distributions. Possibility offers a natural setting for fuzzy optimization whose aim is to balance the levels of satisfaction of multiple fuzzy constraints (instead of minimizing an overall cost). Bipolarity can be captured as well in preference modeling (defining what is more or less rejected and what is more or less desired independently). Possibility theory has potential for capturing some of the semantics of legal reasoning as well (distinguishing what is more or less forbidden from what is implicitly permitted, and what is explicitly permitted ). Existing applications of possibility theory can be found in scheduling and other problem-solving tasks, database querying, diagnosis, belief revision, case-based reasoning, risk analysis, statistics with h z z y data and imprecise probabilities.},
  file      = {:by-author/D/Dubois/2003_Dubois_3.pdf:PDF},
  groups    = {sg/Bayesian, sg/Possibility theory},
  keywords  = {Mathematics; Non Bayesian Updating},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Presentation{Dubois2003a,
  author       = {D. Dubois and H. Prade},
  title        = {Possibility Theory and its applications: a retrospective and prospective view},
  year         = {2003},
  organization = {IRIT-CNRS, Université Paul Sabatier, 31062 TOULOUSE FRANCE},
  file         = {:by-author/D/Dubois/2003_Dubois.ppt:PPT},
  groups       = {sg/Possibility theory},
  keywords     = {Possibility-theory; Presentations},
  owner        = {saulius},
  timestamp = {2015.03.03},
  creationdate = {2015-03-03T00:00:00},
}

@Article{Dubois2001,
  author    = {Dubois, J. and St -Pierre, C.},
  journal   = {Diagnostic microbiology and infectious disease},
  title     = {In vitro activity of ABT-773 versus macrolides and quinolones against resistant respiratory tract pathogens.},
  year      = {2001},
  pages     = {35--40},
  volume    = {40},
  abstract  = {ABT-773, a novel ketolide, was compared to erythromycin, azithromycin, clarithromycin, ciprofloxacin, ofloxacin, levofloxacin, moxifloxacin, gatifloxacin, and gemifloxacin against antibiotic-resistant strains recently isolated from patients with respiratory tract infections. MICs were determined by agar dilution using standard NCCLS methodology. ABT-773 (MIC(90) 0.06 mg/L) was more active than the macrolides (MIC(90) &gt; or = 2 mg/L) and fluoroquinolones (MIC(90) &gt; or = 0.5 mg/L) against penicillin-resistant Streptococcus pneumoniae. The fluoroquinolones were the most active agents tested against beta-lactamase-positive Haemophilus influenzae (MIC(90) &lt; or = 0.01-0.06 mg/L), against which ABT-773 (MIC(90) 4 mg/L) was comparable to azithromycin and two- and four-fold more active than erythromycin and clarithromycin, respectively. Against beta-lactamase positive Moraxella catarrhalis, the activity of ABT-773 (MIC(90) 0.06 mg/L) was comparable to gemifloxacin, trovafloxacin, levofloxacin, and ciprofloxacin (MIC(90) 0.03-0.06 mg/L) and 4- to eightfold greater than that of clarithromycin, gatifloxacin, and erythromycin. These data suggest ABT-773 could be a valuable compound for the treatment of respiratory tract infections, including those resistant to usual oral therapy.},
  file      = {:by-author/D/Dubois/2001_Dubois_35.pdf:PDF},
  groups    = {sg/Bayesian},
  keywords  = {Mathematics; Non Bayesian Updating},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Duda2005,
  author    = {Duda, David M and Tu, Chingkuang and Fisher, S Zoë and An, Haiqain and Yoshioka, Craig and Govindasamy, Lakshmanan and Laipis, Philip J and Agbandje-McKenna, Mavis and Silverman, David N and McKenna, Robert},
  journal   = {Biochemistry},
  title     = {Human carbonic anhydrase III: structural and kinetic study of catalysis and proton transfer.},
  year      = {2005},
  pages     = {10046--53},
  volume    = {44},
  abstract  = {The residue phenylalanine 198 (Phe 198) is a prominent cause of the lower activity of human carbonic anhydrase III (HCA III) compared with HCA II and other isozymes which have leucine at this site. We report the crystal structures of HCA III and the site-directed mutant F198L HCA III, both at 2.1 A resolution, and the enhancement of catalytic activity by exogenous proton donors containing imidazole rings. Both enzymes had a hexahistidine extension at the carboxy-terminal end, used to aid in purification, that was ordered in the crystal structures bound in the active site cavity of an adjacent symmetry-related enzyme. This observation allowed us to comment on a number of possible binding sites for imidazole and derivatives as exogenous proton donors/acceptors in catalysis by HCA III. Kinetic and structural evidence indicates that the phenyl side chain of Phe 198 in HCA III, about 5 A from the zinc, is a steric constriction in the active site, may cause altered interactions at the zinc-bound solvent, and is a binding site for the activation of catalysis by histidylhistidine. This suggests that sites of activation of the proton-transfer pathway in carbonic anhydrase are closer to the zinc than considered in previous studies.},
  file      = {2005_Duda_10046.pdf:by-author/D/Duda/2005_Duda_10046.pdf:PDF},
  groups    = {sg/hCA2},
  keywords  = {CA3; Carbonic Anhydrases},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@InProceedings{Duda1999,
  author    = {Kenneth J. Duda and David R. Cheriton},
  title     = {Borrowed-Virtual-Time (BVT) scheduling: supporting latency-sensitive threads in a general-purpose scheduler},
  year      = {1999},
  abstract  = {Systems need to run a larger and more diverse set of applica- tions, from real-time to interactive to batch, on uniprocessor and multiprocessor platforms. However, most schedulers ei- ther do not address latency requirements or are specialized to complex real-time paradigms, limiting their applicability to general-purpose systems. In this paper, we present Borrowed-Virtual-Time (BVT) Scheduling, showing that it provides low-latency for real- time and interactive applications yet weighted sharing of the CPU across applications according to system policy, even with thread failure at the real-time level, all with a low-overhead implementation on multiprocessors as well as uniprocessors. It makes minimal demands on application developers, and can be used with a reservation or admission control module for hard real-time applications.},
  file      = {:by-author/D/Duda/1999_Duda.pdf:PDF},
  journal   = {SOSP},
  keywords  = {Computer Science (CS); Linux; Operating Systems; Scheduling},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Dudas2005,
  author    = {Dudas, Kathleen C. and Kreuzer, Kenneth N.},
  journal   = {The Journal of biological chemistry},
  title     = {Bacteriophage T4 helicase loader protein gp59 functions as gatekeeper in origin-dependent replication in vivo.},
  year      = {2005},
  pages     = {21561--9},
  volume    = {280},
  abstract  = {Bacteriophage T4 initiates origin-dependent replication via an R-loop mechanism in vivo. During in vitro reactions, the phage-encoded gp59 stimulates loading of the replicative helicase, gp41, onto branched intermediates, including origin R-loops. However, although gp59 is essential for recombination-dependent replication from D-loops, it does not appear to be required for origin-dependent replication in vivo. In this study, we have analyzed the origin-replicative intermediates formed during infections that are deficient in gp59 and other phage replication proteins. During infections lacking gp59, the initial replication forks from two different T4 origins actively replicated both leading- and lagging-strands. However, the retrograde replication forks from both origins were abnormal in the gp59-deficient infections. The lagging-strand from the initial fork was elongated as a new leading-strand in the retrograde direction without lagging-strand synthesis, whereas in the wild-type, leading- and lagging-strand synthesis appeared to be coupled. These results imply that gp59 inhibits the polymerase holoenzyme in vivo until the helicase-primase (gp41-gp61) complex is loaded, and we thereby refer to gp59 as a gatekeeper. We also found that all origin-replicative intermediates were absent in infections deficient in the helicase gp41 or the single-strand-binding protein gp32, regardless of whether gp59 was present or absent. These results argue that replication from the origin in vivo is dependent on both the helicase and single-strand-binding protein and demonstrate that the strong replication defect of gene 41 and 32 single mutants is not caused by gp59 inhibition of the polymerase.},
  file      = {:by-author/D/Dudas/2005_Dudas_21561.pdf:PDF},
  keywords  = {{gp41} Helicase; {gp59}},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@PhdThesis{Dudik2007,
  author    = {Miroslav Dudík},
  school    = {Princeton University},
  title     = {Maximum entropy density estimation and modeling geographic distributions of species},
  year      = {2007},
  abstract  = {Maximum entropy (maxent) approach, formally equivalent to maximum likelihood, is a widely used density-estimation method. When input datasets are small, maxent is likely to overfit. Overfitting can be eliminated by various smoothing techniques, such as regularization and constraint relaxation, but theory explaining their prop- erties is often missing or needs to be derived for each case separately. In this dis- sertation, we propose a unified treatment for a large and general class of smoothing techniques. We provide fully general guarantees on their statistical performance and propose optimization algorithms with complete convergence proofs. As special cases, we can easily derive performance guarantees for many known regularization types including L1 and L2-squared regularization. Furthermore, our general approach enables us to derive entirely new regularization functions with superior statistical guarantees. The new regularization functions use information about the structure of the feature space, incorporate information about sample selection bias, and combine information across several related density-estimation tasks. We propose algorithms solving a large and general subclass of generalized maxent problems, including all discussed in the dissertation, and prove their convergence. Our convergence proofs generalize techniques based on information geometry and Bregman divergences as well as those based more directly on compactness. As an application of maxent, we discuss an important problem in ecology and con- servation: the problem of modeling geographic distributions of species. Here, small sample sizes hinder accurate modeling of rare and endangered species. Generalized maxent offers several advantages over previous techniques. In particular, general- ized maxent addresses the problem in a statistically sound manner and allows prin- cipled extensions to situations when data collection is biased or when we have access to data on many related species. The utility of our unified approach is demonstrated in comprehensive experiments on large real-world datasets. We find that general- ized maxent is among the best-performing species-distribution modeling techniques. Our experiments also show that the contributions of this dissertation, i.e., regulari- zation strategies, bias-removal approaches, and multiple-estimation techniques, all significantly improve the predictive performance of maxent.},
  file      = {:by-author/D/Dudik/2007_Dudik_phdthesis.pdf:PDF},
  keywords  = {MaxEnt; Maximum Entropy},
  owner     = {saulius},
  timestamp = {2012.10.16},
  creationdate = {2012-10-16T00:00:00},
}

@Article{Dudutiene2007,
  author    = {Dudutiene, Virginija and Baranauskiene, Lina and Matulis, Daumantas},
  journal   = {Bioorganic \&amp; medicinal chemistry letters},
  title     = {Benzimidazo[1,2-c][1,2,3]thiadiazole-7-sulfonamides as inhibitors of carbonic anhydrase.},
  year      = {2007},
  pages     = {3335--8},
  volume    = {17},
  file      = {2007_Dudutiene_3335.pdf:by-author/D/Dudutiene/2007_Dudutiene_3335.pdf:PDF},
  groups    = {sg/inhibitors},
  keywords  = {Carbonic Anhydrases; Inhibitors},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Dudutiene2014,
  author      = {Virginija Dudutienė and Jurgita Matulienė and Alexey Smirnov and David D Timm and Asta Zubrienė and Lina Baranauskienė and Vaida Morkūnaitė and Joana Smirnovienė and Vilma Michailovienė and Vaida Juozapaitienė and Aurelija Mickevičiūtė and Justina Kazokaitė and Sandra Bakšytė and Aistė Kasiliauskaitė and Jelena Jachno and Jurgita Revuckienė and Miglė Kišonaitė and Vilma Pilipuitytė and Eglė Ivanauskaitė and Goda Milinavičiūtė and Vytautas Smirnovas and Vilma Petrikaitė and Visvaldas Kairys and Vytautas Petrauskas and Povilas Norvaišas and Darius Lingė and Paulius Gibieža and Edita Capkauskaitė and Audrius Zakšauskas and Egidijus Kazlauskas and Elena Manakova and Saulius Gražulis and John E Ladbury and Daumantas Matulis},
  journal     = {J Med Chem},
  title       = {Discovery and characterization of novel selective inhibitors of carbonic anhydrase IX.},
  year        = {2014},
  month       = {Oct},
  note        = {BVTL BNRSTL pdb/4PYX, pdb/4PYY, pdb/4Q0L, pdb/4PZH, pdb/4Q06, pdb/4Q08, pdb/4Q09, pdb/4Q07},
  pages       = {9435--9446},
  volume      = {57},
  abstract    = {Human carbonic anhydrase IX (CA IX) is highly expressed in tumor tissues and its selective inhibition provides potential target for treatment against numerous cancers. Development of potent, highly selective inhibitors against this target remains an unmet need in anti-cancer therapeutics. A series of fluorinated benzenesulfonamides with substituents on the benzene ring were designed and synthesized. Several of these exhibited a highly potent and selective inhibition profile against CA IX. Three fluorine atoms significantly increased the affinity by withdrawing electrons and lowering the pKa of the benzene sulfonamide group. The bulky ortho substituents such as cyclooctyl or even cyclododecyl groups fit to the hydrophobic pocket in the active site of CA IX but not CA II, as shown by the compound cocrystal structure with the chimeric CA IX. The strongest inhibitor of recombinant human CA IX catalytic domain produced in human cells achieved the affinity of 50 pM. However, the high affinity diminished the selectivity. The most selective compound for CA IX exhibited 10 nM affinity. The compound which showed the best balance between affinity and selectivity properties bound with 1 nM affinity. The inhibitors described in this work provide the basis for novel anticancer therapeutics targeting CA IX.},
  comment     = {ACKNOWLEDGMENTS !!! This research was funded by a grant from the Research Council of Lithuania (LIG-09/2012). The authors are grateful for grant FP7-REGPOT-2009-1 “MoBiLi”, agreement no. 245721, and COST projects TD0905 and CM0804.},
  doi         = {10.1021/jm501003k},
  file        = {:by-author/D/Dudutiene/2014_Dudutiene_9435.pdf:PDF},
  groups      = {sg/inhibitors, sg/hCA9},
  language    = {eng},
  medline-pst = {aheadofprint},
  owner       = {alexey},
  pmid        = {25358084},
  timestamp = {2014.11.10},
  creationdate = {2014-11-10T00:00:00},
  url         = {http://dx.doi.org/10.1021/jm501003k},
}

@Article{Dudutiene2013,
  author      = {Virginija Dudutienė and Asta Zubrienė and Alexey Smirnov and Joana Gylytė and David Timm and Elena Manakova and Saulius Gražulis and Daumantas Matulis},
  journal     = {Bioorg Med Chem},
  title       = {4-Substituted-2,3,5,6-tetrafluorobenzenesulfonamides as inhibitors of carbonic anhydrases I, II, VII, XII, and XIII.},
  year        = {2013},
  month       = {Jan},
  note        = {BVTL BNRSTL pdb/4HT2, pdb/4HU1, pdb/4HT0},
  abstract    = {A series of 4-substituted-2,3,5,6-tetrafluorobenezenesulfonamides were synthesized and their binding potencies as inhibitors of recombinant human carbonic anhydrase isozymes I, II, VII, XII, and XIII were determined by the thermal shift assay, isothermal titration calorimetry, and stop-flow CO(2) hydration assay. All fluorinated benzenesulfonamides exhibited nanomolar binding potency toward tested CAs and fluorinated benzenesulfonamides posessed higher binding potency than non-fluorinated compounds. The crystal structures of 4-[(4,6-dimethylpyrimidin-2-yl)thio]-2,3,5,6-tetrafluorobenzenesulfonamide in complex with CA II and CA XII, and 2,3,5,6-tetrafluoro-4-[(2-hydroxyethyl)sulfonyl]benzenesulfonamide in complex with CA XIII were determined. The observed dissociation constants for several fluorinated compounds reached subnanomolar range for CA I isozyme. The affinity and the selectivity of the compounds towards tested isozymes are presented.},
  comment     = {Acknowledgements This research was funded by a grant (No. MIP-067/2011) from the Research Council of Lithuania. The authors also acknowledge FP7-REGPOT-2009-1 grant ‘MoBiLi’, agreement No. 245721, the COST projects TD0905 and CM0804, and Professor Claudiu Supuran and his group for teaching the measurement of CA inhibition by the stop-flow hydration assay. The authors thank Zita Liutkeviciute for help with the mass spectrometry analysis of the synthetic com- pounds. Crystallographic measurements were performed at the EMBL DESY beamlines in Hamburg. The authors thank local con- tacts, Dr. Gleb Bourenkov and Dr. Michele Cianci, for the help with beamline operation. SG and EM travels to Hamburg were sup- ported in part by the European Community’s Research Infrastruc- ture Action under the Sixth Framework Programme ‘Structuring the European Research Area Specific Programme’ (contract Num- ber RII3-CT-2004-506008) and by the MoBiLi project. AS acknowl- edges support by the project ‘Promotion of Student Scientific Activities’ (VP1-3.1-ŠMM-01-V-02-003) from the Research Council of Lithuania.},
  doi         = {10.1016/j.bmc.2013.01.008},
  file        = {:by-author/D/Dudutiene/2013_Dudutiene_2093.pdf:PDF},
  groups      = {sg/inhibitors},
  institution = {Department of Biothermodynamics and Drug Design,Vilnius University Institute of Biotechnology, Graičiūno 8, Vilnius LT-02241, Lithuania.},
  keywords    = {Crystal Structure; VD-10 Inhibitors; {hCA}},
  language    = {eng},
  medline-pst = {aheadofprint},
  owner       = {em},
  pii         = {S0968-0896(13)00037-0},
  pmid        = {23394791},
  timestamp = {2013.02.18},
  creationdate = {2013-02-18T00:00:00},
  url         = {http://dx.doi.org/10.1016/j.bmc.2013.01.008},
}

@Article{Dudutiene2015,
  author      = {Virginija Dudutienė and Asta Zubrienė and Alexey Smirnov and David D Timm and Joana Smirnovienė and Justina Kazokaitė and Vilma Michailovienė and Audrius Zakšauskas and Elena Manakova and Saulius Gražulis and Daumantas Matulis},
  journal     = {ChemMedChem},
  title       = {Functionalization of Fluorinated Benzenesulfonamides and Their Inhibitory Properties toward Carbonic Anhydrases.},
  year        = {2015},
  pages       = {662--687},
  volume      = {10},
  abstract    = {Substituted tri- and tetrafluorobenzenesulfonamides were designed, synthesized, and evaluated as high-affinity and isoform-selective carbonic anhydrase (CA) inhibitors. Their binding affinities for recombinant human CA I, II, VA, VI, VII, XII, and XIII catalytic domains were determined by fluorescent thermal shift assay, isothermal titration calorimetry, and a stopped-flow CO2 hydration assay. Variation of the substituents at the 2-, 3-, and 4-positions yielded compounds with a broad range of binding affinities and isoform selectivities. Several 2,4-substituted-3,5,6-trifluorobenzenesulfonamides were effective CA XIII inhibitors with high selectivity over off-target CA I and CA II. 3,4-Disubstituted-2,5,6-trifluorobenzenesulfonamides bound CAs with higher affinity than 2,4-disubstituted-3,5,6-trifluorobenzenesulfonamides. Many such fluorinated benzenesulfonamides were found to be nanomolar inhibitors of CA II, CA VII, tumor-associated CA IX and CA XII, and CA XIII. X-ray crystal structures of inhibitors bound in the active sites of several CA isoforms provide structure-activity relationship information for inhibitor binding affinities and selectivity.},
  doi         = {10.1002/cmdc.201402490},
  file        = {:by-author/D/Dudutiene/2015_Dudutiene_0000.pdf:PDF},
  groups      = {sg/inhibitors},
  institution = {Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Graičiūno 8, Vilnius 02241 (Lithuania).},
  language    = {eng},
  medline-pst = {ppublish},
  owner       = {alexey},
  pmid        = {25758852},
  timestamp = {2015.04.08},
  creationdate = {2015-04-08T00:00:00},
  url         = {http://dx.doi.org/10.1002/cmdc.201402490},
}

@Article{Dumas2015,
  author    = {Dumas, Anaelle and Lercher, Lukas and Spicer, Christopher D. and Davis, Benjamin G.},
  journal   = {Chem. Sci.},
  title     = {Designing logical codon reassignment - Expanding the chemistry in biology},
  year      = {2015},
  pages     = {50--69},
  volume    = {6},
  abstract  = {Over the last decade{,} the ability to genetically encode unnatural amino acids (UAAs) has evolved rapidly. The programmed incorporation of UAAs into recombinant proteins relies on the reassignment or suppression of canonical codons with an amino-acyl tRNA synthetase/tRNA (aaRS/tRNA) pair{,} selective for the UAA of choice. In order to achieve selective incorporation{,} the aaRS should be selective for the designed tRNA and UAA over the endogenous amino acids and tRNAs. Enhanced selectivity has been achieved by transferring an aaRS/tRNA pair from another kingdom to the organism of interest{,} and subsequent aaRS evolution to acquire enhanced selectivity for the desired UAA. Today{,} over 150 non-canonical amino acids have been incorporated using such methods. This enables the introduction of a large variety of structures into proteins{,} in organisms ranging from prokaryote{,} yeast and mammalian cells lines to whole animals{,} enabling the study of protein function at a level that could not previously be achieved. While most research to date has focused on the suppression of {'}non-sense{'} codons{,} recent developments are beginning to open up the possibility of quadruplet codon decoding and the more selective reassignment of sense codons{,} offering a potentially powerful tool for incorporating multiple amino acids. Here{,} we aim to provide a focused review of methods for UAA incorporation with an emphasis in particular on the different tRNA synthetase/tRNA pairs exploited or developed{,} focusing upon the different UAA structures that have been incorporated and the logic behind the design and future creation of such systems. Our hope is that this will help rationalize the design of systems for incorporation of unexplored unnatural amino acids{,} as well as novel applications for those already known.},
  doi       = {10.1039/C4SC01534G},
  file      = {:by-author/D/Dumas/2015_Dumas_50.pdf:PDF},
  groups    = {am/Expanded genetic code},
  issue     = {1},
  owner     = {andrius},
  publisher = {The Royal Society of Chemistry},
  timestamp = {2016.05.04},
  creationdate = {2016-05-04T00:00:00},
  url       = {http://dx.doi.org/10.1039/C4SC01534G},
}

@Article{DuninHorkawicz2006,
  author    = {Stanislaw Dunin-Horkawicz and Marcin Feder and Janusz M Bujnicki},
  journal   = {BMC genomics},
  title     = {Phylogenomic analysis of the GIY-YIG nuclease superfamily.},
  year      = {2006},
  pages     = {98},
  volume    = {7},
  file      = {2006_Dunin-Horkawicz_98.pdf:by-author/D/Dunin-Horkawicz/2006_Dunin-Horkawicz_98.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@Article{Dunitz1999,
  author    = {Jack D. Dunitz},
  journal   = {Chemical Communications},
  title     = {A curiously short carbon–carbon double bond?},
  year      = {1999},
  pages     = {2547},
  file      = {:by-author/D/Dunitz/1999_Dunitz_2547.pdf:PDF},
  keywords  = {Crystallography},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Dunitz1995,
  author    = {Dunitz, J. D.},
  journal   = {Acta Crystallographica Section B Structural Science},
  title     = {Phase changes and chemical reactions in molecular crystals},
  year      = {1995},
  issn      = {01087681},
  pages     = {619--631},
  volume    = {51},
  doi       = {10.1107/S0108768194012036},
  file      = {Dunitz - 1995 - Phase changes and chemical reactions in molecular .pdf:by-author/D/Dunitz/1995_Dunitz_619.pdf:application/pdf},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://scripts.iucr.org/cgi-bin/paper?S0108768194012036},
  urldate   = {2015-08-21},
}

@Article{Dunitz1988,
  author    = {Jack D. Dunitz and Verner Schomaker and Kenneth N. Trueblood},
  journal   = {J . Phys. Chem.},
  title     = {Interpretation of Atomic Displacement Parameters from Diffraction Studies of Crystals},
  year      = {1988},
  pages     = {856--867},
  volume    = {92},
  abstract  = {Anisotropic Gaussian displacement parameters (ADP's), routinely obtained from crystal structure analyses, define the second moments of atomic probability distribution functions and hence provide information about averaged displacements of atoms from their mean positions in crystals. From the ADP's alone it is not possible to derive rigorous conclusions about crystal or molecular vibrations, but simple models involving correlated motions of groups of atoms are often capable of reproducing the observed ADP's and their temperature dependence. The possibilities and limitations of such models are discussed. Judiciously exercised and interpreted, the analysis of ADP's can yield quantities such as mean-square libration amplitudes that are not easily obtainable by other physical methods.},
  file      = {:by-author/D/Dunitz/1988_Dunitz_856.pdf:PDF},
  keywords  = {Atomic Displacement Parameters},
  owner     = {andrius},
  timestamp = {2013.04.12},
  creationdate = {2013-04-12T00:00:00},
}

@Article{Dunker1998,
  author    = {A. K. Dunker and E. Garner and S. Guilliot and P. Romero and K. Albrecht and Hart and Z. Obradovic and C. Kissinger and J. E. Villafranca},
  journal   = {Pac. Symp. Biocomput.},
  title     = {Protein disorder and the evolution of molecular recognition: theory, predictions and observations},
  year      = {1998},
  pages     = {473--484},
  abstract  = {Observations going back more than 20' years show that regions in proteins with disordered backbones can play roles in their binding to other molecules; typically, the disordered regions become ordered upon complex formation. Thought-experiments with Schulz Diagrams, which are defined herein, suggest that disorder-to-order transitions are required for natural selection to operate separately on affinity and specificity. Separation of affinity and specificity may be essential for fine-tuning the molecular interaction networks that comprise the living state. For low affinity, high specificity interactions, our analysis suggests that natural selection would parse the amino acids conferring flexibility in the unbound state from those conferring specificity in the bound state. For high affinity, low specificity or for high affinity, multiple specificity interactions, our analysis suggests that the disorder-to-order transitions enable alternative packing interactions between side chains to accommodate the different binding targets. Disorder-to-order transitions upon binding also have significant kinetic implications as well, by having complex effects on both on- and off-rates. Current data are insufficient to decide on these proposals, but sequence and structure analysis on two examples support further investigations of the role of disorder-to-order transitions upon binding.},
  file      = {1998_Dunker_473.pdf:by-author/D/Dunker/1998_Dunker_473.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.09.30},
  creationdate = {2012-09-30T00:00:00},
  url       = {http://www.ncbi.nlm.nih.gov/pubmed/9697205},
}

@Article{Dunlop2003,
  author    = {Dunlop, Kirsty V. and Hazes, Bart},
  journal   = {Acta Crystallographica Section D},
  title     = {When less is more: a more efficient vapour-diffusion protocol},
  year      = {2003},
  pages     = {1797--1800},
  volume    = {59},
  doi       = {10.1107/S0907444903017414},
  file      = {en5016.pdf:by-author/D/Dunlop/2003_Dunlop_1797.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444903017414},
}

@Presentation{Dunn2010,
  author    = {Corey Dunn},
  title     = {An Introduction to the Riemann Curvature Tensor and Differential Geometry},
  year      = {2010},
  file      = {2010_Dunn.pdf:by-author/D/Dunn/2010_Dunn.pdf:PDF},
  keywords  = {Differential Geometry; Riemann},
  owner     = {saulius},
  timestamp = {2016.02.27},
  creationdate = {2016-02-27T00:00:00},
  url       = {http://www.math.csusb.edu/faculty/dunn/lecture1.pdf},
}

@Article{Dunten2008,
  author      = {Pete W Dunten and Elizabeth J Little and Mark T Gregory and Veena M Manohar and Michael Dalton and David Hough and Jurate Bitinaite and Nancy C Horton},
  journal     = {Nucleic Acids Res.},
  title       = {The structure of SgrAI bound to DNA; recognition of an 8 base pair target.},
  year        = {2008},
  month       = {Sep},
  number      = {16},
  pages       = {5405--5416},
  volume      = {36},
  abstract    = {The three-dimensional X-ray crystal structure of the 'rare cutting' type II restriction endonuclease SgrAI bound to cognate DNA is presented. SgrAI forms a dimer bound to one duplex of DNA. Two Ca(2+) bind in the enzyme active site, with one ion at the interface between the protein and DNA, and the second bound distal from the DNA. These sites are differentially occupied by Mn(2+), with strong binding at the protein-DNA interface, but only partial occupancy of the distal site. The DNA remains uncleaved in the structures from crystals grown in the presence of either divalent cation. The structure of the dimer of SgrAI is similar to those of Cfr10I, Bse634I and NgoMIV, however no tetrameric structure of SgrAI is observed. DNA contacts to the central CCGG base pairs of the SgrAI canonical target sequence (CR|CCGGYG, | marks the site of cleavage) are found to be very similar to those in the NgoMIV/DNA structure (target sequence G|CCGGC). Specificity at the degenerate YR base pairs of the SgrAI sequence may occur via indirect readout using DNA distortion. Recognition of the outer GC base pairs occurs through a single contact to the G from an arginine side chain located in a region unique to SgrAI.},
  doi         = {10.1093/nar/gkn510},
  file        = {2008_Dunten_1.pdf:by-author/D/Dunten/2008_Dunten_1.pdf:PDF},
  institution = {Stanford Synchrotron Radiation Laboratory, Stanford University, Menlo Park, CA 94025, USA.},
  keywords    = {Allosteric Regulation; Base Pairing; Binding Sites; Calcium; Crystallography; DNA; Deoxyribonucleases; Manganese; Models; Molecular; Protein Binding; Type II Site-Specific; X-Ray},
  owner       = {em},
  pii         = {gkn510},
  pmid        = {18701646},
  timestamp = {2011.06.08},
  creationdate = {2011-06-08T00:00:00},
  url         = {http://dx.doi.org/10.1093/nar/gkn510},
}

@Article{Dunten2008a,
  author    = {Pete W. Dunten and Elizabeth J. Little and Mark T. Gregory and Veena M. Manohar and Michael Dalton and David Hough and Jurate Bitinaite and Nancy C. Horton},
  journal   = {Nucleic Acids Research},
  title     = {The structure of {SgrAI} bound to {DNA}; recognition of an 8 base pair target},
  year      = {2008},
  pages     = {1--12},
  file      = {:by-author/D/Dunten/2008_Dunten_1.pdf:PDF},
  keywords  = {Struct; TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Dunten2009,
  author       = {Pete W Dunten and Elizabeth J Little and Nancy C Horton},
  journal      = {Acta Crystallogr D Biol Crystallogr},
  title        = {The restriction enzyme SgrAI: structure solution via combination of poor MIRAS and MR phases.},
  year         = {2009},
  month        = {Apr},
  number       = {Pt 4},
  pages        = {393--398},
  volume       = {65},
  abstract     = {Uninterpretable electron-density maps were obtained using either MIRAS phases or MR phases in attempts to determine the structure of the type II restriction endonuclease SgrAI bound to DNA. While neither solution strategy was particularly promising (map correlation coefficients of 0.29 and 0.22 with the final model, respectively, for the MIRAS and MR phases and Phaser Z scores of 4.0 and 4.3 for the rotation and translation searches), phase combination followed by density modification gave a readily interpretable map. MR with a distantly related model located a dimer in the asymmetric unit and provided the correct transformation to use in averaging electron density between SgrAI subunits. MIRAS data sets with low substitution and MR solutions from only distantly related models should not be ignored, as poor-quality starting phases can be significantly improved. The bootstrapping strategy employed to improve the initial MIRAS phases is described.},
  creationdate = {2011-06-08T00:00:00},
  doi          = {10.1107/S0907444909003266},
  file         = {2009_Dunten_393.pdf:by-author/D/Dunten/2009_Dunten_393.pdf:PDF},
  institution  = {Stanford Synchrotron Radiation Laboratory, Stanford University, Menlo Park, CA 94025, USA. pete@slac.stanford.edu},
  keywords     = {Algorithms; Cations; Chemical; Crystallization; Crystallography; Deoxyribonucleases; Divalent; Models; Molecular; Oligodeoxyribonucleotides; Protein Binding; Protein Conformation; Streptomyces Griseus; Type II Site-Specific; X-Ray},
  owner        = {em},
  pii          = {S0907444909003266},
  pmid         = {19307723},
  timestamp    = {2011.06.08},
  url          = {http://dx.doi.org/10.1107/S0907444909003266},
}

@Article{Dunten2009a,
  author    = {Dunten, Pete W. and Little, Elizabeth J. and Horton, Nancy C.},
  journal   = {Acta crystallographica. Section D, Biological crystallography},
  title     = {The restriction enzyme SgrAI: structure solution via combination of poor MIRAS and MR phases.},
  year      = {2009},
  pages     = {393--8},
  volume    = {65},
  abstract  = {Uninterpretable electron-density maps were obtained using either MIRAS phases or MR phases in attempts to determine the structure of the type II restriction endonuclease SgrAI bound to DNA. While neither solution strategy was particularly promising (map correlation coefficients of 0.29 and 0.22 with the final model, respectively, for the MIRAS and MR phases and Phaser Z scores of 4.0 and 4.3 for the rotation and translation searches), phase combination followed by density modification gave a readily interpretable map. MR with a distantly related model located a dimer in the asymmetric unit and provided the correct transformation to use in averaging electron density between SgrAI subunits. MIRAS data sets with low substitution and MR solutions from only distantly related models should not be ignored, as poor-quality starting phases can be significantly improved. The bootstrapping strategy employed to improve the initial MIRAS phases is described.},
  file      = {:by-author/D/Dunten/2009_Dunten_393.pdf:PDF},
  keywords  = {SgrAI; TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Dunwell2000,
  author    = {Dunwell, J M and Khuri, S and Gane, P J},
  journal   = {Microbiology and molecular biology reviews : MMBR},
  title     = {Microbial relatives of the seed storage proteins of higher plants: conservation of structure and diversification of function during evolution of the cupin superfamily.},
  year      = {2000},
  pages     = {153--79},
  volume    = {64},
  abstract  = {This review summarizes the recent discovery of the cupin superfamily (from the Latin term "cupa," a small barrel) of functionally diverse proteins that initially were limited to several higher plant proteins such as seed storage proteins, germin (an oxalate oxidase), germin-like proteins, and auxin-binding protein. Knowledge of the three-dimensional structure of two vicilins, seed proteins with a characteristic beta-barrel core, led to the identification of a small number of conserved residues and thence to the discovery of several microbial proteins which share these key amino acids. In particular, there is a highly conserved pattern of two histidine-containing motifs with a varied intermotif spacing. This cupin signature is found as a central component of many microbial proteins including certain types of phosphomannose isomerase, polyketide synthase, epimerase, and dioxygenase. In addition, the signature has been identified within the N-terminal effector domain in a subgroup of bacterial AraC transcription factors. As well as these single-domain cupins, this survey has identified other classes of two-domain bicupins including bacterial gentisate 1, 2-dioxygenases and 1-hydroxy-2-naphthoate dioxygenases, fungal oxalate decarboxylases, and legume sucrose-binding proteins. Cupin evolution is discussed from the perspective of the structure-function relationships, using data from the genomes of several prokaryotes, especially Bacillus subtilis. Many of these functions involve aspects of sugar metabolism and cell wall synthesis and are concerned with responses to abiotic stress such as heat, desiccation, or starvation. Particular emphasis is also given to the oxalate-degrading enzymes from microbes, their biological significance, and their value in a range of medical and other applications.},
  file      = {Dunwell_2000_153_cupin_superfam.pdf:by-author/D/Dunwell/2000_Dunwell_153.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Duran-Frigola2013,
  author    = {Miquel Duran-Frigola and Roberto Mosca and Patrick Aloy},
  journal   = {Chemistry \& Biology},
  title     = {Structural Systems Pharmacology: The Role of 3{D} Structures in Next-Generation Drug Development},
  year      = {2013},
  pages     = {674--684},
  volume    = {20},
  abstract  = {Structural systems pharmacology offers a novel way of approaching drug discovery by considering the global physiological environment of protein targets, and the effects derived of tinkering with them, without losing the key molecular details. In this article, we review some recent advances in the structural annotation of cell networks and discuss their potential impact on some of the hottest areas of drug development. In particular, we analyze recent structure-based strategies to target networks, protein interaction interfaces and allosteric sites, and how they will help in the development of more potent and specific treatments. Finally, we propose that mapping genetic variations onto protein networks, beyond the pharmacological targets, can rationalize interindividual variability in drug response, giving valuable hints to advance toward personalized medicine.},
  doi       = {10.1016/j.chembiol.2013.03.004},
  file      = {:by-author/D/Duran-Frigola/2013_Duran-Frigola_674.pdf:PDF},
  owner     = {antanas},
  timestamp = {2013.12.12},
  creationdate = {2013-12-12T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/S1074552113000872},
}

@Manuscript{Durbeck2000,
  author    = {Lisa J. K. Durbeck and Nicholas J. Macias},
  title     = {The Cell Matrix: An Architecture for Nanocomputing},
  year      = {2000},
  keywords  = {Cell-matrix; Computer Science (CS)},
  url       = {http://www.cellmatrix.com/entryway/products/pub/nano/nano.html},
  abstract  = {Much effort has been put into the development of atomic-scale switches, and more recently toward the construction of computers from atomic-scale components. A larger goal is the development of an atomic-scale universal assembler, which could construct any electronic circuit, not just a specific CPU. We propose the insertion of a level of indirection into the process of constructing these specific or general builders. Rather than building physically heterogeneous systems that implement various digital circuits, we propose that the builder construct physically homogeneous, undifferentiated hardware that is later, after manufacture, differentiated into various digital circuits. This achieves the immediate goal of achieving specific CPU and memory architectures using atomic-scale switches. At the same time, it achieves the larger goal of being able to construct any digital circuit, using the same fixed manufacturing process. Moreover, this opens the way to implementing fundamentally new types of circuits, including dynamic, massively parallel, self-modifying ones. Additionally, the specific architecture in question is not particularly complex, making it easier to construct than most specific architectures. We have developed a computing architecture that fits this more attainable manufacturing goal. We have also been developing the extra step introduced into the process, that is, taking undifferentiated hardware and differentiating it efficiently and cheaply into desirable circuitry. The architecture presented here is physically simpler than a CPU or memory or field-programmable gate array. All system function is represented within the atomic unit of the system, called a cell. This unit is repeated over and over to form a multidimensional matrix of cells. In addition to being general purpose, the architecture is highly scalable, so much so that it appears to provide access to the differentiation and use of trillion trillion switch hardware. This is not possible with an FPGA architecture, because its gate array is configured serially, and serial configuration of trillion trillion switch hardware would take years. This paper describes the cell in detail and describes how networks of cells in a matrix are used to create small circuits. It also describes a sample application of the architecture that makes beneficial use of high switch counts.},
  file      = {:by-author/D/Durbeck/2000_Durbeck.war:},
  groups    = {sg/Cell Matrix},
  owner     = {saulius},
  retrieved = {2009-01-31},
  timestamp = {2015.03.02},
  creationdate = {2015-03-02T00:00:00},
}

@Article{Dussoix1965,
  author    = {Dussoix, Daisy and Arber, Werner},
  journal   = {Journal of Molecular Biology},
  title     = {Host specificity of DNA produced by Escherichia coli: IV. Host Specificity of Infectious DNA from Bacteriophage Lambda},
  year      = {1965},
  issn      = {0022-2836},
  month     = {Feb},
  number    = {2},
  pages     = {238--246},
  volume    = {11},
  abstract  = {DNA extracted with phenol from bacteriophage λ gives rise to phage production after uptake by helper-infected, competent recipient cells (Kaiser, 1962). Under our experimental conditions, the number of infective centres obtained by infection of Escherichia coli K12 is about 10−3 per phage equivalent of DNA from λ·K or from λ·K(Pl). But on K12(P1) recipient cells only λ·K(Pl) DNA infects with an efficiency of 10−3, while λ·K DNA gives about 100 times less infective centres. The same factor of restriction for λ·K is found in controls done by infection of the competent cells with intact phage particles instead of the phage DNA. Similarly, restrictions displayed by K12 against phage grown on E. coli B or E. coli C and those displayed by B against phage grown on K12 or C are found to hold true for DNA preparations. E. coli C accepts all tested λ DNA with about the same efficiency. We conclude that the phenol extraction does not affect the host specificity of the phage DNA. One-cycle growth of A initiated by infection of K12 with λ·K(Pl) DNA confirms this result: the parental Pi-directed host specificity is transferred into the phage progeny, and it is found only in such phage particles that also inherit one strand of the infecting DNA molecule. The stability of the association of DNA with its host specificity is further revealed by its resistance to various physical, chemical and enzymic treatments of the λ DNA.
It is significant with respect to the understanding of the mechanism of competence of bacteria for infection with A DNA that only non-restricted phage acts as a good helper.},
  doi       = {10.1016/s0022-2836(65)80054-7},
  file      = {1965_Dussoix_238.pdf:by-author/D/Dussoix/1965_Dussoix_238.pdf:PDF},
  groups    = {sg/general},
  keywords  = {History; Restriction Endonucleases (REases)},
  owner     = {saulius},
  publisher = {Elsevier BV},
  timestamp = {2016.11.30},
  creationdate = {2016-11-30T00:00:00},
  url       = {http://dx.doi.org/10.1016/S0022-2836(65)80054-7},
}

@Article{Dussoix1962,
  author    = {Dussoix, Daisy and Arber, Werner},
  journal   = {Journal of Molecular Biology},
  title     = {Host specificity of DNA produced by Escherichia coli: II. Control over acceptance of DNA from infecting phage λ},
  year      = {1962},
  issn      = {0022-2836},
  month     = {Jul},
  number    = {1},
  pages     = {37--49},
  volume    = {5},
  doi       = {10.1016/s0022-2836(62)80059-x},
  file      = {1962_Dussoix_37.pdf:by-author/D/Dussoix/1962_Dussoix_37.pdf:PDF},
  keywords  = {History; Restriction Endonucleases (REases)},
  owner     = {saulius},
  publisher = {Elsevier BV},
  timestamp = {2016.11.30},
  creationdate = {2016-11-30T00:00:00},
  url       = {http://dx.doi.org/10.1016/S0022-2836(62)80059-X},
}

@Article{Dusterhoft1991,
  author    = {Düsterhöft, A. and Erdmann, D. and Kröger, M.},
  journal   = {Nucleic acids research},
  title     = {Stepwise cloning and molecular characterisation of the {HgiDI} restriction-modification system from Herpetosiphon giganteus {Hpa2}},
  year      = {1991},
  pages     = {1049--1056},
  volume    = {19},
  abstract  = {The restriction-modification system HgiDI from Herpetosiphon giganteus strain Hpa2 has been cloned in E. coli in a two-step procedure. Selection of the methyltransferase (M.HgiDI) gene in vitro was performed using the heterologous restriction endonuclease AhaII, an isoschizomer of Acyl and HgiDI (GRCGYC). Cloning of the complete HgiDI endonuclease (R.HgiDI) gene could only be achieved in recipient cells harbouring a recombinant plasmid, which was expressing the corresponding methyltransferase and could thereby prevent the host from self-destruction of its genetic material. The HgiDI restriction-modification system was sequenced and functionally correlated with two open reading frames of 309 (M) and 359 (R) codons. In homology studies M.HgiDI showed significant similarities to 20 other m5C-methyltransferases and turned out to be the most compact enzyme of this group described so far. Initial attempts for overexpression of M.HgiDI and partial purification of R.HgiDI have been successful.},
  file      = {:by-author/D/Düsterhöft/1991_Dusterhoft_1049.pdf:PDF},
  keywords  = {TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Manuscript{Dusto2008,
  author    = {Dusto},
  title     = {Index Librorum Prohibitorum: The History, Philosophy, and Impact of the Index of Prohibited Books},
  year      = {2008},
  keywords  = {Religijotyra},
  file      = {:by-author/D/Dusto/2008_Dusto.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@PhdThesis{Dybvig1987,
  author    = {R. Kent Dybvig},
  school    = {University of North Carolina at Chapel Hill},
  title     = {Three Implementation Models for {S}cheme},
  year      = {1987},
  abstract  = {This dissertation presents three implementation models for the Scheme Programming Language. The first is a heap-based model used in some form in most Scheme implementations to date; the second is a new stack-based model that is considerably more efficient than the heap-based model at executing most programs; and the third is a new string-based model intended for use in a multiple-processor implementation of Scheme. The heap-based model allocates several important data structures in a heap, including actual parameter lists, binding environments, and call frames. The stack-based model allocates these same structures on a stack whenever possible. This results in less heap allocation, fewer memory references, shorter instruction sequences, less garbage collection, and more efficient use of memory. The string-based model allocates versions of these structures right in the program text, which is represented as a string of symbols. In the string-based model, Scheme programs are translated into an FFP language designed specifically to support Scheme. Programs in this language are directly executed by the FFP machine, a multiple-processor string-reduction computer. The stack-based model is of immediate practical benefit; it is the model used by the author’s Chez Scheme system, a high-performance implementation of Scheme. The string-based model will be useful for providing Scheme as a high-level alternative to FFP on the FFP machine once the machine is realized.},
  file      = {:by-author/D/Dybvig/1987_Dybvig_phdthesis.pdf:PDF},
  groups    = {sg/Garbage collectors},
  owner     = {andrius},
  timestamp = {2013.02.08},
  creationdate = {2013-02-08T00:00:00},
}

@Article{Easun2017,
  author    = {Easun, Timothy L. and Moreau, Florian and Yan, Yong and Yang, Sihai and Schröder, Martin},
  journal   = {Chem. Soc. Rev.},
  title     = {Structural and dynamic studies of substrate binding in porous metal–organic frameworks},
  year      = {2017},
  issn      = {1460-4744},
  number    = {1},
  pages     = {239--274},
  volume    = {46},
  abstract  = {Porous metal–organic frameworks (MOFs) are the subject of considerable research interest because of their high porosity and capability of specific binding to small molecules, thus underpinning a wide range of materials functions such as gas adsorption, separation, drug delivery, catalysis, and sensing. MOFs, constructed by the designed assembly of metal ions and functional organic linkers, are an emerging class of porous materials with extended porous structures containing periodic binding sites. MOFs thus provide a new platform for the study of the chemistry and reactivity of small molecules in confined pores using advanced diffraction and spectroscopic techniques. In this review, we focus on recent progress in experimental investigations on the crystallographic, dynamic and kinetic aspects of substrate binding within porous MOFs. In particular, we focus on studies on host–guest interactions involving open metal sites or pendant functional groups in the pore as the primary binding sites for guest molecules.},
  doi       = {10.1039/c6cs00603e},
  file      = {2017_Easun_239.pdf:by-author/E/Easun/2017_Easun_239.pdf:PDF},
  groups    = {sg/MOFs, am/MOFs, sg/MOF},
  keywords  = {Metal-Organic Frameworks (MOF); Review},
  owner     = {saulius},
  publisher = {Royal Society of Chemistry (RSC)},
  timestamp = {2017.01.16},
  creationdate = {2017-01-16T00:00:00},
  url       = {http://dx.doi.org/10.1039/c6cs00603e},
}

@Article{Ebihara2006,
  author    = {Ebihara, Akio and Yao, Min and Masui, Ryoji and Tanaka, Isao and Yokoyama, Shigeyuki and Kuramitsu, Seiki},
  journal   = {Protein science : a publication of the Protein Society},
  title     = {Crystal structure of hypothetical protein TTHB192 from Thermus thermophilus HB8 reveals a new protein family with an RNA recognition motif-like domain.},
  year      = {2006},
  pages     = {1494--9},
  volume    = {15},
  abstract  = {We have determined the crystal structure of hypothetical protein TTHB192 from Thermus thermophilus HB8 at 1.9 A resolution. This protein is a member of the Escherichia coli ygcH sequence family, which contains approximately 15 sequence homologs of bacterial origin. These homologs have a high isoelectric point. The crystal structure reveals that TTHB192 consists of two independently folded domains, and that each domain exhibits a ferredoxin-like fold with a four-stranded antiparallel beta-sheet packed on one side by alpha-helices. These two tandem domains face each other to generate a beta-sheet platform. TTHB192 displays overall structural similarity to Sex-lethal protein and poly(A)-binding protein fragments. These proteins have RNA binding activity which is supported by a beta-sheet platform formed by two tandem repeats of an RNA recognition motif domain with signature sequence motifs on the beta-sheet surface. Although TTHB192 does not have the same signature sequence motif as the RNA recognition motif domain, the presence of an evolutionarily conserved basic patch on the beta-sheet platform could be functionally relevant for nucleic acid-binding. This report shows that TTHB192 and its sequence homologs adopt an RNA recognition motif-like domain and provides the first testable functional hypothesis for this protein family.},
  file      = {:by-author/E/Ebihara/2006_Ebihara_1494.pdf:PDF},
  groups    = {sg/CRISPR-Cas},
  keywords  = {CRISPR},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Echalier2004,
  author    = {Echalier, A. and Glazer, R. L. and F{\"{u}}l{\"{o}}p, V. and Geday, M. A.},
  journal   = {Acta Crystallographica Section D},
  title     = {Assessing crystallization droplets using birefringence},
  year      = {2004},
  pages     = {696--702},
  volume    = {60},
  doi       = {10.1107/S0907444904003154},
  file      = {en5030.pdf:by-author/E/Echalier/2004_Echalier_696.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444904003154},
}

@Manual{Eddy2010,
  title        = {{HMMER} User’s Guide},
  author       = {Sean R. Eddy},
  edition      = {3.0},
  month        = {Mar},
  organization = {Janelia Farm Research Campus},
  year         = {2010},
  file         = {:by-author/E/Eddy/2010_Eddy_manual.pdf:PDF},
  keywords     = {Proteins; Structure Predicion},
  owner        = {andrius},
  timestamp = {2014.01.09},
  creationdate = {2014-01-09T00:00:00},
}

@Article{Eddy2004,
  author    = {Sean R. Eddy},
  title     = {What is {Bayesian} statistics?},
  year      = {2004},
  pages     = {1177--1178},
  volume    = {22},
  file      = {Sean R Eddy - 2004 - What is Bayesian statistics.pdf:by-author/E/Eddy/2004_Eddy_1177.pdf:application/pdf},
  groups    = {sg/Clinical Trials},
  language  = {English},
  owner     = {saulius},
  timestamp = {2015.12.14},
  creationdate = {2015-12-14T00:00:00},
  url       = {ftp://selab.janelia.org/pub/publications/Eddy-ATG3/Eddy-ATG3-reprint.pdf},
  urldate   = {2015-12-12},
}

@Manuscript{Edelsbrunner2012,
  author           = {Herbert Edelsbrunner},
  title            = {Introduction to {B}io-{G}eometry},
  year             = {2012},
  keywords         = {Algorithms; Bioinformatics; Convex Hull; Molecular Geometry; Structure Superposition; Topology},
  month            = {Jan},
  url              = {http://users.cs.duke.edu/~edels/Papers/2012-T-01-BioGeometry.pdf},
  author_sort      = {Edelsbrunner, Herbert},
  calibreid        = {805},
  comment          = {Another URLs where this document or its versions were found: https://vdocuments.mx/2012-t-01-biogeometry.html [accessed 2024-05-12T11:40+03:00]. Proves that the centroids must coincide upon optimal superposition – contradicts Chen2004?},
  creationdate     = {2016-11-04T00:00:00},
  file             = {2012_Edelsbrunner.pdf:by-author/E/Edelsbrunner/2012_Edelsbrunner.pdf:PDF},
  formats          = {pdf},
  groups           = {sg/Molecule superposion, sg/Superposition, sg/Bioinf. Algorithms},
  languages        = {eng},
  library_name     = {calibre},
  modificationdate = {2024-05-12T20:59:43},
  note             = {Downloaded from: http://users.cs.duke.edu/\~edels/Papers/2012-T-01-BioGeometry.pdf},
  owner            = {saulius},
  size             = {3337805 octets},
  tags             = {Bioinformatics, Mathematics, Algebra, Algorithms},
  timestamp        = {2016.11.04},
  title_sort       = {Introduction to Bio-Geometry},
  uuid             = {2feda523-7a1f-4c20-b878-c41619b5bf76},
  volume           = {1},
}

@Article{editorial2010,
  author    = {editorial},
  title     = {Scientific writing 101},
  year      = {2010},
  pages     = {139},
  file      = {:by-author/e/editorial/2010_editorial_139.pdf:PDF},
  keywords  = {Scientific Publications; Writing Guides},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{editorial2009a,
  author    = {editorial},
  title     = {Data’s shameful neglect},
  year      = {2009},
  pages     = {145},
  file      = {:by-author/e/editorial/2009_editorial_145.pdf:PDF},
  keywords  = {Data Management; Data Publication; Preservation; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Editorial2008,
  author    = {Editorial},
  journal   = {Nature Chemical Biology},
  title     = {Metals in chemical biology},
  year      = {2008},
  pages     = {143},
  volume    = {4},
  doi       = {10.1038/nchembio0308-143},
  file      = {:./by-author/e/editorial/2008_editorial_143.pdf:PDF},
  owner     = {antanas},
  timestamp = {2013.12.09},
  creationdate = {2013-12-09T00:00:00},
  url       = {http://www.nature.com/nchembio/journal/v4/n3/full/nchembio0308-143.html},
}

@Article{Editorial1996,
  author    = {Editorial},
  journal   = {Nature},
  title     = {Reinforcing access to research data},
  year      = {1996},
  pages     = {191},
  volume    = {379},
  abstract  = {The existence of public domain databases adds an obligation to some authors to deposit data. The situation with research materials is less clear-cut. It is time, nevertheless, for a change in {\em Nature's} policies.},
  doi       = {10.1038/379191a0},
  file      = {:by-author/e/editorial/1996_editorial_191.pdf:PDF;:by-author/N/NatureEditorial/1996_NatureEditorial_191.djvu:Djvu},
  keywords  = {Data Access Policy; Data Management; Data Quality; Databases; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://www.nature.com/nature/journal/v379/n6562/pdf/379191a0.pdf},
}

@Article{Editorial1996a,
  author    = {Editorial},
  journal   = {Nature},
  title     = {How not to protect databases},
  year      = {1996},
  pages     = {293},
  file      = {:by-author/e/editorial/1996_editorial_293.pdf:PDF},
  keywords  = {Copyrights; Patents; Trademarks},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Edwards1963,
  author    = {Ward Edwards and Harold Lindman and Leonard J. Savag},
  journal   = {Psychological Review},
  title     = {Bayesian Statistical Inference for Psychological Research},
  year      = {1963},
  pages     = {193--242},
  volume    = {70},
  abstract  = {Bayesian statistics, a currently controversial viewpoint concerning statistical inference, is based on a definition of probability as a particular measure of the opinions of ideally consistent people. Statistical inference is modification of these opinions in the light of evidence, and Bayes' theorem specifies how such modifications should be made. The tools of Bayesian statistics include the theory of specific distributions and the principle of stable estimation, which specifies when actual prior opinions may be satisfactorily approximated by a uniform distribution. A common feature of many classical significance tests is that a sharp null hypothesis is compared with a diffuse alternative hypothesis. Often evidence which, for a Bayesian statistician, strikingly supports the null hypothesis leads to rejection of that hypothesis by standard classical procedures. The likelihood principle emphasized in Bayesian statistics implies, among other things, that the rules governing when data collection stops are irrelevant to data interpretation. It is entirely appropriate to collect data until a point has been proven or disproven, or until the data collector runs out of time, money, or patience.},
  file      = {:by-author/E/Edwards/1963_Edwards_193.pdf:PDF},
  groups    = {sg/Bayesian},
  keywords  = {Bayesian Statistics},
  owner     = {saulius},
  timestamp = {2012.09.30},
  creationdate = {2012-09-30T00:00:00},
}

@Manuscript{Eeckhout2005,
  author    = {Lieven Eeckhout and John Sampson and Brad Calder},
  title     = {Exploiting Program Microarchitecture Independent Characteristics and Phase Behavior for Reduced Benchmark Suite Simulation},
  year      = {2005},
  keywords  = {Computer Architecture; Computer Science (CS); Performance Comparison},
  abstract  = {Modern architecture research relies heavily on detailed pipeline simulation. Simulating the full execution of an industry standard benchmark can take weeks to complete. Simulating the full execution of the whole benchmark suite for one architecture configuration can take months. To address this issue researchers have examined using targetted sampling based on phase behavior to significantly reduce the simulation time of each program in the benchmark suite. However, even with this sampling approach, simulating the full benchmark suite across a large range of architecture designs can take days to weeks to complete.},
  file      = {:by-author/E/Eeckhout/2005_Eeckhout.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Efremova2006,
  author    = {Efremova, S. V.},
  title     = {Water treatment with a shungite sorbent and biosorbents on its base},
  year      = {2006},
  issn      = {1070-4272},
  pages     = {397--402},
  volume    = {79},
  doi       = {10.1134/S1070427206030128},
  file      = {Water treatment with a shungite sorbent and biosorbents on its base - art%3A10.1134%2FS1070427206030128.pdf:by-author/E/Efremova/2006_Efremova_397.pdf:application/pdf},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://download.springer.com/static/pdf/718/art%253A10.1134%252FS1070427206030128.pdf?originUrl=http%3A%2F%2Flink.springer.com%2Farticle%2F10.1134%2FS1070427206030128&token2=exp=1436175912~acl=%2Fstatic%2Fpdf%2F718%2Fart%25253A10.1134%25252FS1070427206030128.pdf%3ForiginUrl%3Dhttp%253A%252F%252Flink.springer.com%252Farticle%252F10.1134%252FS1070427206030128*~hmac=0e7d2c215d50a49e545a796c384d3d295e8a3d8504f3b35224337896e70d373b},
  urldate   = {2015-07-06},
}

@Article{Efron1973,
  author    = {Bradley Efron and Carl Morris},
  journal   = {Journal of the American Statistical Association},
  title     = {Stein's estimation rule and its competitors -- an empirical Bayes approach},
  year      = {1973},
  pages     = {117--130},
  volume    = {68},
  abstract  = {Stein's estimator for k normal means is known to dominate the MLE if k ≥ 3. In this article we ask if Stein's estimator is any good in its own right. Our answer is yes: the positive part version of Stein's estimator is one member of a class of "good" rules that have Bayesian properties and also dominate the MLE. Other members of this class are also useful in various situations. Our approach is by means of empirical Bayes ideas. In the later sections we discuss rules for more complicated estimation problems, and conclude with results from empirical linear Bayes rules in non-normal cases.},
  file      = {:by-author/E/Efron/1973_Efron_117.pdf:PDF},
  groups    = {sg/Bayesian},
  keywords  = {Bayesian Statistics; Inadmissible MLE Estimators; Maximum Likelihood; Statistical Estimation; Stein's Rule},
  owner     = {saulius},
  timestamp = {2012.10.10},
  creationdate = {2012-10-10T00:00:00},
  url       = {http://links.jstor.org/sici?sici=0162-1459%28197303%2968%3A341%3C117%3ASERAIC%3E2.0.CO%3B2-T},
}

@Article{Egami1988,
  author    = {T. Egami and S. J. Poon},
  journal   = {Materials Science and Engineering},
  title     = {Atomic Structure of Quasicrystals},
  year      = {1988},
  pages     = {323--329},
  volume    = {99},
  abstract  = {Progress in the determination of the atomic struc- ture of quasicrystalline solids via pair distribution func- tion analysis obtained by X-ray and neutron diffraction is reviewed. Common features of the local structure in these solids are described, followed by the discussion on the mechanism of stabilization of quasi-crystals by long-range internal stress fields.},
  doi       = {10.1016/0025-5416(88)90350-3},
  file      = {:by-author/E/Egami/1988_Egami_323.pdf:pdf},
  owner     = {saulius},
  timestamp = {2015.10.09},
  creationdate = {2015-10-09T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/0025541688903503},
}

@Article{Egelman1995,
  author    = {Egelman, E. H. and Yu, X. and Wild, R. and Hingorani, M. M. and Patel, S. S.},
  journal   = {Proceedings of the National Academy of Sciences of the United States of America},
  title     = {Bacteriophage T7 helicase/primase proteins form rings around single-stranded DNA that suggest a general structure for hexameric helicases.},
  year      = {1995},
  pages     = {3869--73},
  volume    = {92},
  abstract  = {Most helicases studied to date have been characterized as oligomeric, but the relation between their structure and function has not been understood. The bacteriophage T7 gene 4 helicase/primase proteins act in T7 DNA replication. We have used electron microscopy, three-dimensional reconstruction, and protein crosslinking to demonstrate that both proteins form hexameric rings around single-stranded DNA. Each subunit has two lobes, so the hexamer appears to be two-tiered, with a small ring stacked on a large ring. The single-stranded DNA passes through the central hole of the hexamer, and the data exclude substantial wrapping of the DNA about or within the protein ring. Further, the hexamer binds DNA with a defined polarity as the smaller ring of the hexamer points toward the 5' end of the DNA. The similarity in three-dimensional structure of the T7 gene 4 proteins to that of the Escherichia coli RuvB helicase suggests that polar rings assembled around DNA may be a general feature of numerous hexameric helicases involved in DNA replication, transcription, recombination, and repair.},
  file      = {:by-author/E/Egelman/1995_Egelman_3869.pdf:PDF},
  keywords  = {T7; {gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Manuscript{Eger2013,
  author    = {Thomas Eger and Marc Scheufen and Daniel Meierrieks},
  title     = {The Determinants of Open Access Publishing: Survey Evidence from Germany},
  year      = {2013},
  keywords  = {Open Access Publishing},
  url       = {http://ssrn.com/abstract=2232675},
  abstract  = {We discuss the results of a survey conducted in fall 2012 and covering 2,151 researchers in Germany. We show that there are significant differences between the scientific disciplines with respect to researcher’s awareness of and experience with both open access (OA) journals and self-archiving. Our results reveal that the relevance of OA within a discipline may explain why researchers from particular disciplines do (not) publish OA. Besides, several aspects like copyright law, age, profession or the inherent reward system of a discipline play a role. As a consequence, the paper emphasizes that a “one-size-fits-all” approach as promoted by most recent policy approaches is little promising for providing an effective framework for shaping the future of scholarly publishing.},
  file      = {:by-author/E/Eger/2013_Eger.pdf:PDF},
  owner     = {saulius},
  timestamp = {2013.10.18},
  creationdate = {2013-10-18T00:00:00},
}

@TechReport{Egner2004,
  author      = {Sebastian Egner and Richard A. Kelsey and Michael Sperber},
  institution = {Indiana University},
  title       = {Cleaning up the Tower: Numbers in {S}cheme},
  year        = {2004},
  abstract    = {The R 5 RS specification of numerical operations leads to unportable and intransparent behavior of programs. Specifically, the notion of “exact/inexact numbers ” and the misleading distinction between “real ” and “rational ” numbers are two primary sources of confusion. Consequently, the way R 5 RS organizes numbers is significantly less useful than it could be. Based on this diagnosis, we propose to abandon the concept of exact/inexact numbers from Scheme altogether. In this paper, we examine designs in which exact and inexact rounding operations are explicitly separated, while there is no distinction between exact and inexact numbers. Through examining alternatives and practical ramifications, we arrive at an alternative proposal for the design of the numerical operations in Scheme.},
  file        = {:by-author/E/Egner/2004_Egner.pdf:PDF},
  owner       = {andrius},
  timestamp = {2013.02.14},
  creationdate = {2013-02-14T00:00:00},
}

@Article{Eigen1971,
  author    = {Eigen, Manfred},
  journal   = {Naturwissenschaften},
  title     = {Selforganization of matter and the evolution of biological macromolecules},
  year      = {1971},
  issn      = {1432-1904},
  number    = {10},
  pages     = {465--523},
  volume    = {58},
  doi       = {10.1007/BF00623322},
  file      = {1971_Eigen_465.pdf:by-author/E/Eigen/1971_Eigen_465.pdf:PDF},
  keywords  = {Evolution; Mathematical Models},
  owner     = {saulius},
  timestamp = {2016.06.24},
  creationdate = {2016-06-24T00:00:00},
  url       = {http://dx.doi.org/10.1007/BF00623322},
}

@InCollection{Einstein1997,
  author    = {Albert Einstein},
  booktitle = {The Collected Papers of Albert Einstein},
  publisher = {Princeton University Press},
  title     = {The Foundation of the General Theory of Relativity},
  year      = {1997},
  editor    = {A.~J. Kox and Martin~J. Klein and Robert Schulmann},
  pages     = {146--200},
  file      = {:by-author/E/Einstein/1997_Einstein_147translation.pdf:PDF},
  keywords  = {Reliatyvumo Teorija},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@InCollection{Einstein1916,
  author    = {Albert Einstein},
  booktitle = {The Collected Papers of Albert Einstein},
  publisher = {Princeton University Press},
  title     = {Die Grundlagen der allgemeinen Relativitätstheorie [The Foundation of the General Theory of Relativity]},
  year      = {1916},
  pages     = {284--339},
  file      = {:by-author/E/Einstein/1916_Einstein_769.pdf:PDF},
  journal   = {Annalen der Physik},
  keywords  = {Reliatyvumo Teorija},
  language  = {German, English},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Einstein1935,
  author    = {A. Einstein and B. Podolsky and N. Rosen},
  journal   = {Physical Review},
  title     = {Can Quantum-Mechanical Description of Physical Reality Be Considered Complete?},
  year      = {1935},
  pages     = {777--780},
  volume    = {47},
  file      = {1935_Einstein_777.pdf:by-author/E/Einstein/1935_Einstein_777.pdf:PDF},
  keywords  = {Quantum Mechanics (QM)},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Eisenberg2006,
  author    = {Eisenberg, E. and Baram, A.},
  journal   = {Physical review. E, Statistical, nonlinear, and soft matter physics},
  title     = {Analysis of the ordering transition of hard disks through the Mayer cluster expansion.},
  year      = {2006},
  pages     = {025104},
  volume    = {73},
  abstract  = {The available virial coefficients for the two-dimensional hard-disks model are transformed into a matrix representation of the thermodynamic potentials, which allows for an accurate description of the whole fluid phase, up to the phase transition. We find that the fluid phase terminates at the transition point, implying a second-order phase transition in accordance with the Kosterlitz-Thouless-Halperin-Nelson-Young scenario of a transition into a hexatic phase. The density and pressure at the transition are calculated from the available first ten virial coefficients, and are found to be in excellent agreement with recent Monte-Carlo calculations. Finally, we calculate the equation of state in the critical region.},
  file      = {:by-author/E/Eisenberg/2006_Eisenberg_025104.pdf:PDF;:by-author/E/Eisenberg/2006_Eisenberg_025104-manuscript.pdf:PDF},
  keywords  = {Hard Spheres; Molecular Dynamics (MD)},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Eisenschmidt2005,
  author       = {Kristin Eisenschmidt and Thomas Lanio and András Simoncsits and Albert Jeltsch and Vera Pingoud and Wolfgang Wende and Alfred Pingoud},
  journal      = {Nucleic Acids Res},
  title        = {Developing a programmed restriction endonuclease for highly specific DNA cleavage.},
  year         = {2005},
  number       = {22},
  pages        = {7039--7047},
  volume       = {33},
  abstract     = {Specific cleavage of large DNA molecules at few sites, necessary for the analysis of genomic DNA or for targeting individual genes in complex genomes, requires endonucleases of extremely high specificity. Restriction endonucleases (REase) that recognize DNA sequences of 4-8 bp are not sufficiently specific for this purpose. In principle, the specificity of REases can be extended by fusion to sequence recognition modules, e.g. specific DNA-binding domains or triple-helix forming oligonucleotides (TFO). We have chosen to extend the specificity of REases using TFOs, given the combinatorial flexibility this fusion offers in addressing a short, yet precisely recognized restriction site next to a defined triple-helix forming site (TFS). We demonstrate here that the single chain variant of PvuII (scPvuII) covalently coupled via the bifunctional cross-linker N-(gamma-maleimidobutryloxy) succinimide ester to a TFO (5'-NH2-[CH2](6 or 12)-MPMPMPMPMPPPPPPT-3', with M being 5-methyl-2'-deoxycytidine and P being 5-[1-propynyl]-2'-deoxyuridine), cleaves DNA specifically at the recognition site of PvuII (CAGCTG) if located in a distance of approximately one helical turn to a TFS (underlined) complementary to the TFO ('addressed' site: 5'-TTTTTTTCTCTCTCTCN(approximately 10)CAGCTG-3'), leaving 'unaddressed' PvuII sites intact. The preference for cleavage of an 'addressed' compared to an 'unaddressed' site is >1000-fold, if the cleavage reaction is initiated by addition of Mg2+ ions after preincubation of scPvuII-TFO and substrate in the absence of Mg2+ ions to allow triple-helix formation before DNA cleavage. Single base pair substitutions in the TFS prevent addressed DNA cleavage by scPvuII-TFO.},
  creationdate = {2016-06-16T00:00:00},
  doi          = {10.1093/nar/gki1009},
  file         = {:by-author/E/Eisenschmidt/2005_Eisenschmidt_7039.pdf:PDF},
  institution  = {Institut für Biochemie, Justus-Liebig-Universität, Heinrich-Buff-Ring 58, D-35392 Giessen, Germany.},
  keywords     = {Chemistry; Chemistry/metabolism; Cross-Linking Reagents; DNA; Deoxyribonucleases; Design; Oligonucleotides; Restriction Endonuclease (RE); Specificity; Substrate Specificity; Succinimides; Type II Site-Specific},
  language     = {eng},
  medline-pst  = {epublish},
  owner        = {em},
  pii          = {33/22/7039},
  pmid         = {16356926},
  timestamp    = {2016.06.16},
  url          = {http://dx.doi.org/10.1093/nar/gki1009},
}

@Article{Eisenstein1851,
  author    = {G. Eisenstein},
  journal   = {Journal für die reine und angewandte Mathematik},
  title     = {Tabelle der reducirten positiven ternären quadratischen Formen, nebst den Resultaten neuer Forschungen über diese Formen, in besonderer Rücksicht auf ihre tabellarische Berechnung},
  year      = {1851},
  pages     = {141--190},
  volume    = {41},
  file      = {1851_Eisenstein_141.pdf:by-author/E/Eisenstein/1851_Eisenstein_141.pdf:PDF},
  groups    = {sg/Cell reduction, sg/Quadratic forms},
  keywords  = {Cell Reduction; Quadratic Forms; Reduction},
  owner     = {saulius},
  timestamp = {2016.04.12},
  creationdate = {2016-04-12T00:00:00},
  url       = {http://gdz.sub.uni-goettingen.de/dms/load/img/?PID=GDZPPN002147181&physid=PHYS_0146},
}

@Article{Eisenstein1991,
  author    = {Eisenstein, M. and Sharon, R. and Berkovitch-Yellin, Z. and Gewitz, H. S. and Weinstein, S. and Pebay-Peyroula, E. and Roth, M. and Yonath, A.},
  journal   = {Biochimie},
  title     = {The interplay between X-ray crystallography, neutron diffraction, image reconstruction, organo-metallic chemistry and biochemistry in structural studies of ribosomes.},
  year      = {1991},
  pages     = {879--86},
  volume    = {73},
  abstract  = {Crystals of ribosomes, their complexes with components of protein biosynthesis, their natural, mutated and modified subunits, have been subjected to X-ray and neutron crystallographic analyses. Electron microscopy and 3-dimensional image reconstruction, supported by biochemistry, genetic, functional and organo-metallic studies were employed for facilitating phasing of the crystallographic data. For example, a monofunctional multi heavy-atom cluster (undecagold) was designed for covalent and quantitative binding to ribosomes. The modified particles were crystallized isomorphously with the native ones. Their difference-Patterson maps contain indications for the usefulness of these derivatives for subsequent phasing. Models of the ribosome and its large subunit were reconstructed from tilt series of 2-dimensional sheets. The comparison of the various reconstructed images enabled an initial assessment of the reliability of these models and led to tentative assignments of several functional features. These include the presumed sites for binding mRNA and for codon-anticodon interactions, the path taken by the nascent protein chain and the mode for tRNA binding to ribosomes. These assignments assisted in the design of biologically meaningful crystal systems. The reconstructed models are being used to identify structural features in initial density maps derived from X-ray and neutron diffraction data.},
  file      = {:by-author/E/Eisenstein/1991_Eisenstein_879.pdf:PDF},
  keywords  = {Ribosome Structure},
  owner     = {saulius},
  timestamp = {2012.06.25},
  creationdate = {2012-06-25T00:00:00},
}

@TechReport{Ekdahl2007,
  author      = {Patrik Ekdahl and Ben Smeets},
  institution = {1) Department of Information Technology, Lund University, PO Box 118, S-221 00 Lund, Sweden. Email: Patrik.Ekdahl@it.lth.se; 2) Ericsson Mobile Communications AB, Scheelevagen 7, S-221 83 Lund, Sweden. Email: Ben.Smeets@ecs.ericsson.se},
  title       = {Incremental Authentication of Tree-Structured Document},
  year        = {2007},
  abstract    = {A new message authentication code (MAC) is described that exploits the tree structure present in many modern document formats, e.g. SGML and XML. The new code supports incremental updating of the cryptographic checksum in the process of making incremental changes to the document. Theoretical bounds on the probability of a successful substitution attack are derived. Through experimental results we demonstrate that for randomly chosen messages the success proba- bility of such an attack will be smaller and is easily identi ed.},
  file        = {:by-author/E/Ekdahl/2007_Ekdahl.pdf:PDF},
  keywords    = {Computer Science (CS); Cryptography; Incremental Cryptography},
  owner       = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Ekland1995,
  author    = {Ekland, E H and Szostak, J W and Bartel, D P},
  journal   = {Science (New York, N.Y.)},
  title     = {Structurally complex and highly active RNA ligases derived from random RNA sequences.},
  year      = {1995},
  pages     = {364--70},
  volume    = {269},
  file      = {1995_Ekland_364.pdf:by-author/E/Ekland/1995_Ekland_364.pdf:PDF},
  keywords  = {Ribozymes},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Ellington1997,
  author    = {Ellington, Andrew D. and Robertson, Michael P. and Bull, Jim},
  journal   = {Science},
  title     = {Ribozymes in Wonderland},
  year      = {1997},
  issn      = {0036-8075, 1095-9203},
  pages     = {546--547},
  doi       = {10.1126/science.276.5312.546},
  file      = {:by-author/E/Ellington/1997_Ellington_546._276_(5312)_546_--_Science.war:},
  keywords  = {Ribozymes},
  language  = {en},
  owner     = {saulius},
  pmid      = {9148415},
  timestamp = {2015.03.02},
  creationdate = {2015-03-02T00:00:00},
  url       = {http://www.sciencemag.org/content/276/5312/546},
  urldate   = {2015-03-07},
}

@TechReport{Ellis1993,
  author      = {John R. Ellis and David L. Detlefs},
  institution = {Xerox Corporation, Palo Alto Research Center, 3333 Coyote Hill Road, Palo Alto, California 94304},
  title       = {Safe, Efficient Garbage Collection for C++},
  year        = {1993},
  file        = {:by-author/E/Ellis/1993_Ellis_techreport.pdf:PDF},
  groups      = {sg/Garbage collectors},
  keywords    = {C++; Computer Science (CS); Garbage Collectors; Memory Management; Programming Languages},
  owner       = {saulius},
  pages       = {techreport},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Manuscript{Ellison2000,
  author    = {Carl Ellison and Bruce Schneier},
  title     = {Ten Risks of PKI: What You're not Being Told about Public Key Infrastructure},
  year      = {2000},
  keywords  = {Computer Science (CS)},
  url       = {https://www.schneier.com/paper-pki.pdf},
  file      = {:by-author/E/Ellison/2000_Ellison.txt:},
  owner     = {saulius},
  timestamp = {2015.03.10},
  creationdate = {2015-03-10T00:00:00},
}

@Lecture{Elofsson2012,
  author       = {Arne Elofsson},
  title        = {Classical papers in bioinformatics},
  year         = {2012},
  organization = {Scilifelab, Stockholm},
  file         = {2012_Elofsson_lectures.odt:by-author/E/Elofsson/2012_Elofsson_lectures.odt:OpenDocument text},
  owner        = {saulius},
  timestamp = {2013.04.01},
  creationdate = {2013-04-01T00:00:00},
  url          = {http://bioinfo.se/classical/},
}

@Article{Elsevier1997,
  author    = {Elsevier},
  journal   = {Polyhedron},
  title     = {Deposition of crystallographic data : Information and instructions to authors of papers containing or comprising crystal structure determination},
  year      = {1997},
  issn      = {0277-5387},
  pages     = {III},
  volume    = {16},
  doi       = {10.1016/S0277-5387(97)90141-8},
  file      = {1997_Elsevier_III.pdf:by-author/E/Elsevier/1997_Elsevier_III.pdf:PDF},
  keywords  = {Crystallography; Data Access Policy; Data Management},
  owner     = {saulius},
  timestamp = {2013.01.09},
  creationdate = {2013-01-09T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/S0277538797901418},
}

@Article{Elsevier1996,
  author    = {Elsevier},
  journal   = {Polyhedron},
  title     = {Deposition of Crystallographic Data},
  year      = {1996},
  issn      = {0277-5387},
  pages     = {II},
  volume    = {15},
  doi       = {10.1016/S0277-5387(96)80013-1},
  file      = {1996_Elsevier_II.pdf:by-author/E/Elsevier/1996_Elsevier_II.pdf:PDF},
  keywords  = {Crystallography; Data Access Policy; Data Management},
  owner     = {saulius},
  timestamp = {2013.01.09},
  creationdate = {2013-01-09T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/S0277538796800131},
}

@Manuscript{Elts2004,
  author    = {Ekaterina Elts},
  title     = {Comparative analysis of PVM and MPI for the development of physical applications on parallel clusters},
  year      = {2004},
  file      = {:by-author/E/Elts/2004_Elts.pdf:PDF},
  owner     = {saulius},
  timestamp = {2013.07.02},
  creationdate = {2013-07-02T00:00:00},
}

@Article{Emberly2003,
  author    = {Emberly, Eldon G. and Kirczenow, George},
  journal   = {Physical Review Letters},
  title     = {The smallest molecular switch},
  year      = {2003},
  number    = {18},
  volume    = {91},
  doi       = {10.1103/PhysRevLett.91.188301},
  file      = {Emberly - 2003 - The Smallest Molecular Switch.pdf:by-author/E/Emberly/2003_Emberly.pdf:PDF;Phys. Rev. Lett. 91, 188301 (2003) - The Smallest Molecular Switch:by-author/E/Emberly/2003_Emberly.html:URL},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
}

@Article{Embleton2001,
  author    = {Embleton, M. L. and Siksnys, V. and Halford, S. E.},
  journal   = {Journal of molecular biology},
  title     = {DNA cleavage reactions by type II restriction enzymes that require two copies of their recognition sites.},
  year      = {2001},
  pages     = {503--14},
  volume    = {311},
  abstract  = {Several type II restriction endonucleases interact with two copies of their target sequence before they cleave DNA. Three such enzymes, NgoMIV, Cfr10I and NaeI, were tested on plasmids with one or two copies of their recognition sites, and on catenanes containing two interlinked rings of DNA with one site in each ring. The enzymes showed distinct patterns of behaviour. NgoMIV and NaeI cleaved the plasmid with two sites faster than that with one site and the catenanes at an intermediate rate, while Cfr10I gave similar steady-state rates on all three substrates. Both Cfr10I and NgoMIV converted the majority of the substrates with two sites directly to the products cut at both sites, while NaeI cleaved just one site at a time. All three enzymes thus synapse two DNA sites through three-dimensional space before cleaving DNA. With Cfr10I and NgoMIV, both sites are cleaved in one turnover, in a manner consistent with their tetrameric structures, while the cleavage of a single site by NaeI indicates that the second site acts not as a substrate but as an activator, as reported previously. The complexes spanning two sites have longer lifetimes on catenanes with one site in each ring than on circular DNA with two sites, which indicates that the catenanes have more freedom for site juxtaposition than plasmids with sites in cis.},
  file      = {:by-author/E/Embleton/2001_Embleton_503.pdf:PDF},
  groups    = {sg/Cfr10I, sg/NgoMIV},
  keywords  = {Tetra; TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Embleton2001a,
  author      = {M. L. Embleton and V. Siksnys and S. E. Halford},
  journal     = {J Mol Biol},
  title       = {DNA cleavage reactions by type II restriction enzymes that require two copies of their recognition sites.},
  year        = {2001},
  month       = {Aug},
  number      = {3},
  pages       = {503--514},
  volume      = {311},
  abstract    = {Several type II restriction endonucleases interact with two copies of their target sequence before they cleave DNA. Three such enzymes, NgoMIV, Cfr10I and NaeI, were tested on plasmids with one or two copies of their recognition sites, and on catenanes containing two interlinked rings of DNA with one site in each ring. The enzymes showed distinct patterns of behaviour. NgoMIV and NaeI cleaved the plasmid with two sites faster than that with one site and the catenanes at an intermediate rate, while Cfr10I gave similar steady-state rates on all three substrates. Both Cfr10I and NgoMIV converted the majority of the substrates with two sites directly to the products cut at both sites, while NaeI cleaved just one site at a time. All three enzymes thus synapse two DNA sites through three-dimensional space before cleaving DNA. With Cfr10I and NgoMIV, both sites are cleaved in one turnover, in a manner consistent with their tetrameric structures, while the cleavage of a single site by NaeI indicates that the second site acts not as a substrate but as an activator, as reported previously. The complexes spanning two sites have longer lifetimes on catenanes with one site in each ring than on circular DNA with two sites, which indicates that the catenanes have more freedom for site juxtaposition than plasmids with sites in cis.},
  doi         = {10.1006/jmbi.2001.4892},
  file        = {2001_Embleton_503.pdf:by-author/E/Embleton/2001_Embleton_503.pdf:PDF},
  groups      = {sg/Cfr10I, sg/NgoMIV},
  institution = {Department of Biochemistry, University of Bristol, Bristol, BS8 1TD, UK.},
  keywords    = {Bacterial Proteins; Base Sequence; Binding Sites; DNA; DNA-Binding Proteins; Deoxyribonucleases; Endonucleases; Gene Dosage; Kinetics; Nucleic Acid; Plasmids; Repetitive Sequences; Substrate Specificity; Type II Site-Specific},
  owner       = {em},
  pii         = {S0022-2836(01)94892-2},
  pmid        = {11493004},
  timestamp = {2011.06.10},
  creationdate = {2011-06-10T00:00:00},
  url         = {http://dx.doi.org/10.1006/jmbi.2001.4892},
}

@Article{Emsley2004b,
  author    = {Emsley, Paul and Cowtan, Kevin},
  journal   = {Acta Crystallogr D Biol Crystallogr},
  title     = {Coot: model-building tools for molecular graphics},
  year      = {2004},
  pages     = {2126--32},
  volume    = {60},
  abstract  = {CCP4mg is a project that aims to provide a general-purpose tool for structural biologists, providing tools for X-ray structure solution, structure comparison and analysis, and publication-quality graphics. The map-fitting tools are available as a stand-alone package, distributed as 'Coot'.},
  address   = {York Structural Biology Laboratory, University of York, Heslington, York YO10 5YW, England. emsley@ysbl.york.ac.uk},
  doi       = {10.1107/S0907444904019158},
  file      = {:by-author/E/Emsley/2004_Emsley_2126.pdf:PDF},
  isbn      = {0907-4449},
  keywords  = {CCP4; COOT; Coot; Protein Crystallography},
  owner     = {em},
  timestamp = {2011.10.17},
  creationdate = {2011-10-17T00:00:00},
  url       = {http://view.ncbi.nlm.nih.gov/pubmed/15572765},
}

@Article{Emsley2010,
  author    = {Emsley, P. and Lohkamp, B. and Scott, W. G. and Cowtan, K.},
  journal   = {Acta Crystallographica Section D},
  title     = {Features and development of {\it Coot}},
  year      = {2010},
  pages     = {486--501},
  volume    = {66},
  abstract  = {{\it Coot} is a molecular-graphics application for model building and validation of biological macromolecules. The program displays electron-density maps and atomic models and allows model manipulations such as idealization, real-space refinement, manual rotation/translation, rigid-body fitting, ligand search, solvation, mutations, rotamers and Ramachandran idealization. Furthermore, tools are provided for model validation as well as interfaces to external programs for refinement, validation and graphics. The software is designed to be easy to learn for novice users, which is achieved by ensuring that tools for common tasks are `discoverable' through familiar user-interface elements (menus and toolbars) or by intuitive behaviour (mouse controls). Recent developments have focused on providing tools for expert users, with~customisable key bindings, extensions and an extensive scripting interface. The software is under rapid development, but has already achieved very widespread use within the crystallographic community. The current state of the software is presented, with a description of the facilities available and of some of the underlying methods employed.},
  doi       = {10.1107/S0907444910007493},
  file      = {2010_Emsley_486.pdf:by-author/E/Emsley/2010_Emsley_486.pdf:PDF},
  keywords  = {Coot; Model Building},
  owner     = {saulius},
  timestamp = {2015.05.08},
  creationdate = {2015-05-08T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444910007493},
}

@InProceedings{Encheva2007,
  author    = {S. Encheva and S. Tumin},
  booktitle = {Innovative Algorithms and Techniques in Automation, Industrial Electronics and Telecommunications},
  title     = {Safe Logon with Free Lightweight Technologies},
  year      = {2007},
  editor    = {T. Sobh et al.},
  pages     = {5--9},
  publisher = {Springer},
  abstract  = {In this paper we address some security problems and issues about implementing Web applications and Web services. In order to do this, we first identify trust relationships among users and systems. In particular, we look into the problems of a secure communication between two parties over insecure channels using a signed digital envelope. We propose a simple and secure way of sign-on into Web applications without using enterprise user- identification and password pair. We try to adhere to simplicity principle in our modeling of the system. By using simple model and free lightweight technologies, we show that it is possible to implement secure Web applications and services.},
  file      = {:by-author/E/Encheva/2007_Encheva_5.pdf:PDF},
  owner     = {saulius},
  timestamp = {2013.08.11},
  creationdate = {2013-08-11T00:00:00},
}

@Article{Enemark2006,
  author    = {Enemark, Eric J. and Joshua-Tor, Leemor},
  journal   = {Nature},
  title     = {Mechanism of DNA translocation in a replicative hexameric helicase.},
  year      = {2006},
  pages     = {270--5},
  volume    = {442},
  abstract  = {The E1 protein of papillomavirus is a hexameric ring helicase belonging to the AAA + family. The mechanism that couples the ATP cycle to DNA translocation has been unclear. Here we present the crystal structure of the E1 hexamer with single-stranded DNA discretely bound within the hexamer channel and nucleotides at the subunit interfaces. This structure demonstrates that only one strand of DNA passes through the hexamer channel and that the DNA-binding hairpins of each subunit form a spiral 'staircase' that sequentially tracks the oligonucleotide backbone. Consecutively grouped ATP, ADP and apo configurations correlate with the height of the hairpin, suggesting a straightforward DNA translocation mechanism. Each subunit sequentially progresses through ATP, ADP and apo states while the associated DNA-binding hairpin travels from the top staircase position to the bottom, escorting one nucleotide of single-stranded DNA through the channel. These events permute sequentially around the ring from one subunit to the next.},
  file      = {:by-author/E/Enemark/2006_Enemark_270.pdf:PDF},
  keywords  = {Struktur; {gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Engh2002,
  author    = {Richard A. Engh and Dirk Bossemeyer},
  journal   = {Pharmacology \& Therapeutics},
  title     = {Structural aspects of protein kinase control—role of conformational flexibility},
  year      = {2002},
  issn      = {0163-7258},
  pages     = {99--111},
  volume    = {93},
  abstract  = {Protein kinases catalyze the phosphotransfer reaction fundamental to most signaling and regulatory processes in the eukaryotic cell. Absolute control of individual protein kinase activity is, therefore, of utmost importance to signaling fidelity in the cell. Mechanisms for activity modulation, including complete and reversible inactivation, have been shown by crystal structures of many active and inactive protein kinases. The structures of inactivated kinases, compared with those of active and catalytically competent kinases such as the protein kinase A catalytic subunit, highlight recurring structural alterations among a set of elements of the catalytic kinase core. These ‘activity modulation sites’ apparently comprise the principal evolved mechanisms for control of enzyme activity in the catalytic domain. In combination, they enable diverse physiological regulatory mechanisms operative for most protein kinases. Identification and characterization of these sites should impact strategies for discovery and design of target-specific therapeutic drugs as the range of structural variations for specific kinases becomes known. The principle site, the ATP-binding pocket, is the target of many physiological regulators and also most experimental or therapeutic inhibitors, which typically block it in a competitive or allosteric fashion. Co-crystallization studies with protein kinase A and other kinases have revealed binding features of several classes of protein kinase inhibitors. Ligand-induced structural changes are common and tend to optimize buried surface areas. The ability to optimize binding energies arising from the hydrophobic effect creates a logarithmic dependence of binding energy on buried surface areas. Exceptions to this rule arise for specific inhibitor classes, and possibly also as artifacts of structure determination.},
  doi       = {10.1016/S0163-7258(02)00180-8},
  file      = {2002_Engh_99.pdf:by-author/E/Engh/2002_Engh_99.pdf:PDF},
  keywords  = {Protein Kinase A},
  owner     = {saulius},
  timestamp = {2013.04.01},
  creationdate = {2013-04-01T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/S0163725802001808},
}

@InBook{Engh2006,
  author    = {Engh, Richard A. and Huber, Robert},
  chapter   = {18.3},
  editor    = {Michael G. Rossmann and Eddy Arnold},
  pages     = {382--392},
  publisher = {Kluwer Academic Publishers},
  title     = {Structure quality and target parameters},
  year      = {2006},
  note      = {by International Union of Crystallography},
  volume    = {F},
  file      = {:by-author/E/Engh/2006_Engh_382.pdf:PDF;references:by-author/E/Engh/2006_Engh_382references.pdf:PDF},
  keywords  = {Restrains},
  owner     = {saulius},
  timestamp = {2012.05.09},
  creationdate = {2012-05-09T00:00:00},
}

@Article{Engh1991,
  author    = {Engh, Richard A. and Huber, Robert},
  journal   = {Acta Crystallographica Section A},
  title     = {Accurate bond and angle parameters for {X}-ray protein structure refinement},
  year      = {1991},
  pages     = {392--400},
  volume    = {47},
  file      = {:by-author/E/Engh/1991_Engh_392.pdf:PDF},
  keywords  = {Restrains},
  owner     = {andrius},
  timestamp = {2012.05.04},
  creationdate = {2012-05-04T00:00:00},
}

@Article{Englander2003,
  author    = {Englander, Joan J and Del Mar, Charyl and Li, Will and Englander, S Walter and Kim, Jack S and Stranz, David D and Hamuro, Yoshitomo and Woods, Jr, Virgil L},
  journal   = {Proceedings of the National Academy of Sciences of the United States of America},
  title     = {Protein structure change studied by hydrogen-deuterium exchange, functional labeling, and mass spectrometry.},
  year      = {2003},
  pages     = {7057--62},
  volume    = {100},
  abstract  = {An automated high-throughput, high-resolution deuterium exchange HPLC-MS method (DXMS) was used to extend previous hydrogen exchange studies on the position and energetic role of regulatory structure changes in hemoglobin. The results match earlier highly accurate but much more limited tritium exchange results, extend the analysis to the entire sequence of both hemoglobin subunits, and identify some energetically important changes. Allosterically sensitive amide hydrogens located at near amino acid resolution help to confirm the reality of local unfolding reactions and their use to evaluate resolved structure changes in terms of allosteric free energy.},
  file      = {Englander_2003_7057-hydrogen_exchange.pdf:by-author/E/Englander/2003_Englander_7057.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@InProceedings{Engler1996a,
  author    = {Dawson R. Engler},
  booktitle = {IN PLDI ’96: PROCEEDINGS OF THE ACM SIGPLAN 1996 CONFERENCE ON PROGRAMMING LANGUAGE DESIGN AND IMPLEMENTATION},
  title     = {VCODE: A retargetable, extensible, very fast dynamic code generation system},
  year      = {1996},
  pages     = {160--170},
  file      = {1996_Engler_160.pdf:by-author/E/Engler/1996_Engler_160.pdf:PDF},
  groups    = {sg/Compiler construction},
  keywords  = {Code Generation; Compiler Construction},
  owner     = {saulius},
  timestamp = {2015.08.07},
  creationdate = {2015-08-07T00:00:00},
  url       = {http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.225.1780},
}

@InProceedings{Engler1996,
  author    = {Dawson R. Engler and Wilson C. Hsieh and M. Frans Kaashoek},
  booktitle = {In Symposium on Principles of Programming Languages},
  title     = {`C: A Language for High-Level, Efficient, and Machine-independent Dynamic Code Generation},
  year      = {1996},
  pages     = {131--144},
  file      = {1996_Engler_131.pdf:by-author/E/Engler/1996_Engler_131.pdf:PDF},
  groups    = {sg/Compiler construction},
  keywords  = {Code Generation; Compiler Construction},
  owner     = {saulius},
  timestamp = {2015.08.07},
  creationdate = {2015-08-07T00:00:00},
  url       = {http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.18.5716},
}

@Article{Ennifar2002,
  author    = {Ennifar, E. and Carpentier, P. and Ferrer, J.-L. and Walter, P. and Dumas, P.},
  journal   = {Acta Crystallographica Section D},
  title     = {X-ray-induced debromination of nucleic acids at the Br{\it K} absorption edge and implications for MAD phasing},
  year      = {2002},
  pages     = {1262--1268},
  volume    = {58},
  doi       = {10.1107/S0907444902009526},
  file      = {gr2254.pdf:by-author/E/Ennifar/2002_Ennifar_1262.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444902009526},
}

@Article{Epinat2003,
  author    = {Epinat, Jean-Charles and Arnould, Sylvain and Chames, Patrick and Rochaix, Pascal and Desfontaines, Dominique and Puzin, Clémence and Patin, Amélie and Zanghellini, Alexandre and Pâques, Frédéric and Lacroix, Emmanuel},
  journal   = {Nucleic acids research},
  title     = {A novel engineered meganuclease induces homologous recombination in yeast and mammalian cells.},
  year      = {2003},
  pages     = {2952--62},
  volume    = {31},
  abstract  = {Homologous gene targeting is the ultimate tool for reverse genetics, but its use is often limited by low efficiency. In a number of recent studies, site- specific DNA double-strand breaks (DSBs) have been used to induce efficient gene targeting. Engineering highly specific, dedicated DNA endonucleases is the key to a wider usage of this technology. In this study, we present two novel, chimeric meganucleases, derived from homing endonucleases. The first one is able to induce recombination in yeast and mammalian cells, whereas the second cleaves a novel (chosen) DNA target site. These results are a first step toward the generation of custom endonucleases for the purpose of targeted genome engineering.},
  file      = {Epinat_2003_2952-engineered-meganuclease.pdf:by-author/E/Epinat/2003_Epinat_2952.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Eppstein2004,
  author     = {Eppstein, David},
  journal    = {SIGACT News},
  title      = {On the {NP}-completeness of Cryptarithms},
  year       = {1987},
  issn       = {0163-5700},
  pages      = {38--40},
  volume     = {18},
  address    = {New York, NY, USA},
  doi        = {10.1145/24658.24662},
  file       = {:by-author/E/Eppstein/1987_Eppstein_38.pdf:PDF},
  issue_date = {April 1987},
  keywords   = {Alphametics; Computer Science (CS)},
  owner      = {saulius},
  publisher  = {ACM},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
  url        = {http://doi.acm.org/10.1145/24658.24662},
}

@InProceedings{Erdogmus2005,
  author    = {Erdogmus},
  booktitle = {IEEE Transactions on Software Engineering},
  title     = {On the Effectiveness of Test-first Approach to Programming},
  year      = {2005},
  pages     = {1},
  file      = {:by-author/E/Erdogmus/2005_Erdogmus_1.pdf:PDF},
  keywords  = {Computer Science (CS); Test Driven Development},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Ericsson2010,
  author    = {G. Ericsson and S. Pomp and H. Sjöstrand and E. Traneus},
  journal   = {Physics Letters A},
  title     = {Piezonuclear reactions – do they really exist?},
  year      = {2010},
  pages     = {750--753},
  volume    = {374},
  abstract  = {In a number of recent articles in this journal F. Cardone and collaborators have claimed the observation of several striking nuclear phenomena which they attribute to “piezonuclear reactions”. One such claim [F. Cardone, R. Mignani, A. Petrucci, Phys. Lett. A 373 (2009) 1956] is that subjecting a solution of 228Th to cavitation leads to a “transformation” of thorium nuclei that is 104 times faster than the normal nuclear decay for this isotope. In a “Comment” [G. Ericsson, S. Pomp, H. Sjöstrand, E. Traneus, Phys. Lett. A 373 (2009) 3795] to the thorium work, we have criticized the evidence provided for this claim. In a “Reply” [F. Cardone, R. Mignani, A. Petrucci, Phys. Lett. A 373 (2009) 3797] Cardone et al. answer only some minor points but avoid addressing the real issue. The information provided in their Reply displays a worrying lack of control of their experimental situation and the data they put forward as evidence for their claims. We point out several shortcomings and errors in the described experimental preparations, set-up and reporting, as well as in the data analysis. We conclude that the evidence presented by Cardone et al. is insufficient to justify their claims of accelerated thorium decay (by “piezonuclear reactions” or otherwise).},
  doi       = {10.1016/j.physleta.2009.11.067},
  file      = {:by-author/E/Ericsson/2010_Ericsson_750.pdf:PDF},
  keywords  = {Physics; Radioactive Decay},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/S037596010901500X},
}

@Manuscript{Erlebach2005,
  author    = {Pavel Erlebach and Tomáš Vojnar},
  title     = {Automated Formal Verification of Programs with Dynamic Data Structures Using State-of-the-Art Tools},
  year      = {2005},
  keywords  = {Computer Science (CS); Correctness Proofs; Program Verification; Programming Languages},
  abstract  = {This paper investigates capabilities of two advanced state-of-the-art tools— namely Pale and TVLA—for automated formal verification of programs manipulating unbounded dynamic data structures. We consider verification of operations dealing with binary search trees over which we want to verify the basic correctness of pointer manipu- lations (no null pointer dereferences, etc.) as well as the sortedness requirement of binary search trees. Unlike in other works, we want to verify the full sortedness requirement, i.e. that all nodes in the left subtree of a node n are smaller than n, and all nodes in the right subtree of n are bigger than n (and not just the relation between a node and its direct subnodes). For the needs of verifying this property in the TVLA tool, we provide a new kind of instrumentation predicate that allows one to handle such a property.},
  file      = {:by-author/E/Erlebach/2005_Erlebach.pdf:PDF},
  groups    = {sg/Correctness proofs},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Erlich2017,
  author    = {Erlich, Yaniv and Zielinski, Dina},
  journal   = {Science},
  title     = {{DNA} {F}ountain enables a robust and efficient storage architecture},
  year      = {2017},
  issn      = {1095-9203},
  month     = {Mar},
  number    = {6328},
  pages     = {950–954},
  volume    = {355},
  doi       = {10.1126/science.aaj2038},
  file      = {2017_Erlich_950.pdf:by-author/E/Erlich/2017_Erlich_950.pdf:PDF},
  owner     = {andrius},
  publisher = {American Association for the Advancement of Science (AAAS)},
  timestamp = {2017.03.09},
  creationdate = {2017-03-09T00:00:00},
  url       = {http://dx.doi.org/10.1126/science.aaj2038},
}

@TechReport{Erlingsson1996,
  author      = {Ulfar Erlingsson and Alexander V. Konstantinou},
  institution = {Computer Science Department, Rensselaer Polytechnic Institute, Troy, NY 12180},
  title       = {Implementing the C+ Standard Template Library in Ada 95},
  year        = {1996},
  month       = {January},
  abstract    = {The Standard Template Library (STL), a recent addition to the ANSI C+ standard, provides a set of well structured generic C+ components that work together in a seamless way" SL94]. The popularity of STL stems from its combination of an orthogonal design, solid theoretical foundation, and strong emphasis on e ciency. This paper presents a design scheme for implementing the C+ STL library components in Ada, using features introduced in the 1995 Ada standard Ada95a]. Discussion is based on a prototype Ada 95 implementation, segments of which illustrate the paper. This work was prepared under the supervision of Dr. David Musser at Rensselaer Polytechnic Institute.},
  file        = {:by-author/E/Erlingsson/1996_Erlingsson.ps:PostScript;:by-author/E/Erlingsson/1996_Erlingsson.pdf:PDF},
  keywords    = {Ada; C++; Computer Science (CS); Programming Languages; Templates},
  owner       = {saulius},
  timestamp = {2015.02.27},
  creationdate = {2015-02-27T00:00:00},
}

@Webpage{Ertl2011,
  author    = {Anton Ertl},
  retrieved = {2008-07-28},
  title     = {Threaded Code},
  url       = {http://www.complang.tuwien.ac.at/forth/threaded-code.html},
  month     = {May},
  year      = {2011},
  abstract  = {Threaded code is a technique for implementing virtual machine interpreters. There are various ways to implement interpreters: Some of the more popular are: Direct string interpretation. Compilation into a tree (typically, an abstract syntax tree) and interpret that tree. Compilation into a virtual machine, and interpret the virtual machine code. If you are interested in performance, the virtual machine approach is the way to go (because fetching and decoding is simpler, and therefore faster). If you are not interested in performance (yet), you still may want to consider the virtual machine approach, because it often is as simple as the others. Threaded code, in its original meaning [bell73], is one of the techniques for implementing virtual machine interpreters. Nowadays, at least the Forth community uses the term threading for almost any technique used for implementing Forth's virtual machine.},
  file      = {:by-author/E/Ertl/2011_Ertl.html:},
  groups    = {sg/Threaded code},
  keywords  = {Computer Science (CS); Threaded-code},
  owner     = {saulius},
  timestamp = {2015.03.03},
  creationdate = {2015-03-03T00:00:00},
}

@InBook{Ertl2002,
  author           = {Anton M. Ertl and Gregg, David},
  editor           = {Horspool, R. Nigel},
  pages            = {5--8},
  publisher        = {Springer Berlin Heidelberg},
  title            = {Building an Interpreter with Vmgen},
  year             = {2002},
  address          = {Berlin, Heidelberg},
  isbn             = {978-3-540-45937-8},
  abstract         = {Vmgen automates many of the tasks of writing the virtual machine part of an interpreter, resulting in less coding, debugging and maintenance effort. This paper gives some quantitative data about the source code and generated code for a vmgen-based interpreter, and gives some examples demonstrating the simplicity of using vmgen. Vmgen is available at http://www.complang.tuwien.ac.at/anton/vmgen/.},
  booktitle        = {Compiler Construction: 11th International Conference, CC 2002 Held as Part of the Joint European Conferences on Theory and Practice of Software, ETAPS 2002 Grenoble, France, April 8--12, 2002 Proceedings},
  creationdate     = {2016-10-06T00:00:00},
  doi              = {10.1007/3-540-45937-5_2},
  file             = {:by-author/E/Ertl/2002_Ertl_5.pdf:PDF},
  groups           = {sg/Stack machines, sg/Threaded code},
  keywords         = {Compiler Construction; Computer Science (CS); Stack Machines},
  modificationdate = {2024-11-08T22:12:10},
  owner            = {saulius},
  timestamp        = {2016.10.06},
  url              = {http://dx.doi.org/10.1007/3-540-45937-5_2},
}

@TechReport{Ertl2001,
  author      = {M. Anton Ertl},
  institution = {TU Wien},
  title       = {Threaded Code Variations and Optimizations},
  year        = {2001},
  abstract    = {Forth has been traditionally implementad as indirect threaded code, where the code for non-primitives is the code-field address of the word. To ge tmaximum benefit from combining sequences of primitives into superinstructions, the code produced for a non-primitive shole be a primitive followed by a parameter (e.g. lit addr for variables). This paper takes alook at the steps from a traditional threaded-code implementation to superinstructions, and at the size and speed effects of the various steps. The use of superinstructions gives speedups of up to a factor of 2 on large benchmarks on processors with branch target buffers, but requires more space for the primitives and the optimisation tables, and als a little more space for the threaded code.},
  file        = {:by-author/E/Ertl/2001_Ertl.pdf:PDF},
  groups      = {sg/Threaded code},
  keywords    = {Compiler Optimisation; Computer Science (CS); Stack Machines; Threaded Code},
  owner       = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@TechReport{Ertl1999,
  author      = {M. Anton Ertl},
  institution = {Institut fur Computersprachen, Technische Universitat Wien, Argentinierstra e 8, A-1040 Wien},
  title       = {Is Forth Code Compact? A Case Study},
  year        = {1999},
  abstract    = {Forth advocates often claim that Forth code is smaller, faster, and requires less development time than equivalent programs in other languages. This paper investigates this claim by comparing a num- ber of parser generators written in various lan- guages with respect to source code size. The small- est parser generator (14 lines) in this comparison is written in Forth, and the other Forth program is smaller than the others in its class by a factor of 8 or more however, the Forth programs do not have all the features of their counterparts. I took a closer look at Gray (in Forth) and Coco/R (in Modula-2) and found that several Forth features missing from Modula-2 give Gray more than a factor of three advantage over Coco/R (even if the other size differences were solely due to differences in functionality): run-time code generation access to the parser and a simple, exible syntax and Forth's dictionary.},
  file        = {:by-author/E/Ertl/1999_Ertl.pdf:PDF},
  groups      = {sg/Threaded code},
  keywords    = {Compiler Optimisation; Computer Science (CS); Forth; Programmimng Languages; Threaded Code},
  owner       = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@TechReport{Ertl1998a,
  author    = {M. Anton Ertl},
  title     = {State-smartness -- Why it is Evil and How to Exorcise it},
  year      = {1998},
  file      = {:by-author/E/Ertl/1998_Ertl.ps.gz:PostScript;:by-author/E/Ertl/1998_Ertl.pdf:PDF},
  owner     = {saulius},
  timestamp = {2015.02.27},
  creationdate = {2015-02-27T00:00:00},
}

@PhdThesis{Ertl1996,
  author           = {Martin Anton Ertl},
  school           = {Technischen Universitat Wien, Technisch-Naturwissenschaftliche Fakultat},
  title            = {Implementation of Stack-Based Languages on Register Machines},
  year             = {1996},
  creationdate     = {2015-02-27T00:00:00},
  file             = {:by-author/E/Ertl/1996_Ertl.ps.gz:PostScript;:by-author/E/Ertl/1996_Ertl.pdf:PDF},
  keywords         = {Compilers; Computer Architecture; Computer Science (CS); FORTH; Register Machines; Stack Machines},
  modificationdate = {2023-01-03T09:12:21},
  owner            = {saulius},
  timestamp        = {2015.02.27},
}

@TechReport{Ertl1995a,
  author      = {M. Anton Ertl},
  institution = {Institut fur Computersprachen, Technische Universitat Wien, Argentinierstra e 8, A-1040 Wien},
  title       = {Stack Caching for Interpreters},
  year        = {1995},
  abstract    = {An interpreter can spend a significant part of its execution time on accessing arguments of virtual machine instructions. This paper explores two methods to reduce this overhead for virtual stack machines by caching top-of-stack values in (real machine) registers. The dynamic method is based on having, for every possible state of the cache, one specialized version of the whole interpreter; the execution of an instruction usually changes the state of the cache and the next instruction is executed in the version corresponding to the new state. In the static method a state machine that keeps track of the cache state is added to the compiler. Common instructions exist in specialized versions for several states, but it is not necessary to have a version of every instruction for every cache state. Stack manipulation instructions are optimized away.},
  file        = {:by-author/E/Ertl/1995_Ertl.ps.gz:PostScript;:by-author/E/Ertl/1995_Ertl.pdf:PDF},
  owner       = {saulius},
  timestamp = {2015.02.27},
  creationdate = {2015-02-27T00:00:00},
}

@Article{Ertl1992,
  author    = {M. Anton Ertl},
  journal   = {EuroForth},
  title     = {A New Approach to Forth Native and Code Generation},
  year      = {1992},
  pages     = {73--78},
  abstract  = {RAFTS is a framework for applying state of the art compiler technology to the compilation of Forth. The heart of RAFTS is a simple method for transforming Forth programs into data ow graphs and static single assignment form. Standard code generation and optimization techniques can be applied to programs in these forms. Speci cally, RAFTS uses interprocedural register allocation to eliminate nearly all stack accesses. It also removes nearly all stack pointer updates. Inli-ning and tail call optimization reduce the call over- head. RAFTS compiles all of Forth, including difcult cases like unknown stack heights, PICK, ROLL and EXECUTE. And last, but not least, RAFTS is designed for interactive Forth},
  file      = {:by-author/E/Ertl/1992_Ertl_73.ps.gz:PostScript;:by-author/E/Ertl/1992_Ertl_73.pdf:PDF},
  owner     = {saulius},
  timestamp = {2015.02.27},
  creationdate = {2015-02-27T00:00:00},
}

@TechReport{Ertl1992a,
  author      = {M. Anton Ertl},
  institution = {Institut fur Computersprachen, Technische Universitat Wien},
  title       = {A Portable Forth Engine},
  year        = {1992},
  file        = {:by-author/E/Ertl/1992_Ertl.pdf:PDF;:by-author/E/Ertl/1992_Ertl.ps:PostScript},
  owner       = {saulius},
  timestamp = {2015.02.25},
  creationdate = {2015-02-25T00:00:00},
}

@Manuscript{Ertl1995,
  author    = {M. Anton Ertl and Martin Maierhofer},
  title     = {Translating Forth to Efficient C},
  year      = {1995},
  abstract  = {An automatic translator can translate Forth into C code which the current generation of optimizing C compilers compiles to e cient machine code. I.e., the resulting code keeps stack items in registers and rarely updates the stack pointer. This paper presents a simple translation method that produces e cient C code, describes an implementation of the method and presents results achieved with this implementation: The translated code is 4.5-7.5 times faster than Gforth (the fastest measured interpretive system), 1.33 times faster than BigForth 386 (a native code compiler), and smaller than Gforth's threaded code.},
  file      = {:by-author/E/Ertl/1995_Ertl_a.ps.gz:PostScript;:by-author/E/Ertl/1995_Ertl_a.pdf:PDF},
  groups    = {sg/Threaded code},
  owner     = {saulius},
  timestamp = {2015.02.27},
  creationdate = {2015-02-27T00:00:00},
}

@TechReport{Ertl1998,
  author      = {M. Anton Ertl and Christian Pirker},
  institution = {Institut fur Computersprachen, Technische Universitat Wien, Argentinierstra e 8, A-1040 Wien},
  title       = {Compilation of Stack-Based Languages (Abschlußbericht)},
  year        = {1998},
  abstract    = {RAFTS is a framework for applying state of the art compiler technology to the compilation of stackbased languages like Forth and Postscript. The special needs of stack-based languages are an e cient stack representation, fast procedure calls, and fast compilation. RAFTS addresses the stack representation problem by allocating stack items to registers such that most stack accesses in the source program are register accesses in the machine language program, and by eliminating most stack pointer up- dates. To achieve fast calls, RAFTS performs these optimizations interprocedurally and also performs procedure inlining and tail call optimization. Fast compilation is achieved by selecting fast algorithms and implementing them e ciently. Until now we have implemented the basic block part of RAFTS and a part of the work necessary for inlining and interprocedural optimizations.},
  file        = {:by-author/E/Ertl/1998_Ertl_a.ps.gz:PostScript;:by-author/E/Ertl/1998_Ertl_a.pdf:PDF},
  owner       = {saulius},
  timestamp = {2015.02.27},
  creationdate = {2015-02-27T00:00:00},
  url         = {http://www.complang.tuwien.ac.at/papers/ertl%26pirker98.ps.gz},
}

@TechReport{Ertl1997,
  author      = {M. Anton Ertl and Christian Pirker},
  institution = {Institut fur Computersprachen, Technische Universitat Wien, Argentinierstra e 8, A-1040 Wien},
  title       = {The Structure of a Forth Native Code Compiler},
  year        = {1997},
  abstract    = {Writing a sophisticated Forth native code compiler program to be read, and generate code then, poses some tasks that are not discussed in compiler but may have to execute a part of the program text books. Some of these tasks arise from speci c before everything is read. Together with the language features, others from the requirement for requirement to compile as late as possible, this very fast compilation to maintain interactivity. In has led to implementing code generation on this paper we describe some of the more interesting EXECUTE (Section 3.2). data structures and algorithms used in the RAFTS Strati cation of de nitions (i.e., de ne before prototype.},
  file        = {:by-author/E/Ertl/1997_Ertl.ps.gz:PostScript;:by-author/E/Ertl/1997_Ertl.pdf:PDF},
  owner       = {saulius},
  timestamp = {2015.02.27},
  creationdate = {2015-02-27T00:00:00},
}

@TechReport{Ertl1996a,
  author      = {M. Anton Ertl and Christian Pirker},
  institution = {Institut fur Computersprachen, Technische Universitat Wien, Argentinierstra e 8, A-1040 Wien, Austria},
  title       = {RAFTS for Basic Blocks: A progress report on Forth Native Code Compilation},
  year        = {1996},
  abstract    = {RAFTS is a framework for applying state of the art compiler technology to the compila- tion of stack-based languages, in particular Forth. This paper describes our experiences and ndings in implementing the basic block (straight-line code) part of RAFTS; it also presents empirical results: the basic block part is the simplest part of RAFTS, but without the other parts it is hardly better than existing techniques, because in Forth basic blocks are very short (there are few basic blocks with more than two useful instructions).},
  file        = {:by-author/E/Ertl/1996_Ertl_a.ps.gz:PostScript;:by-author/E/Ertl/1996_Ertl_a.pdf:PDF},
  owner       = {saulius},
  timestamp = {2015.02.27},
  creationdate = {2015-02-27T00:00:00},
}

@Article{Eschenmoser1999,
  author    = {Eschenmoser, A},
  journal   = {Science (New York, N.Y.)},
  title     = {Chemical etiology of nucleic acid structure.},
  year      = {1999},
  pages     = {2118--24},
  volume    = {284},
  file      = {1999_Eschenmoser_2118.pdf:by-author/E/Eschenmoser/1999_Eschenmoser_2118.pdf:PDF},
  keywords  = {Stacking},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Esnouf1999,
  author    = {Esnouf, R M},
  journal   = {Acta Crystallogr D Biol Crystallogr},
  title     = {Further additions to MolScript version 1.4, including reading and contouring of electron-density maps},
  year      = {1999},
  month     = {Apr},
  number    = {Pt 4},
  pages     = {938--40},
  volume    = {55},
  abstract  = {MolScript is one of the most popular programs for the generation of publication-quality figures and the recent re-working of the program should ensure its continued popularity. However, some functionality of particular interest to crystallographers is not part of the standard program. A modified MolScript version 1.4 has been described previously, with more flexible colouring schemes among its new features. This report describes further enhancements to MolScript version 1.4, including facilities for drawing rods for helices and ribbons for oligonucleotides and allowing several formats of electron-density maps to be read and contoured using either lines or smoothed triangulated surfaces.},
  address   = {The Rega Institute for Medical Research, Katholieke Universiteit Leuven, Minder-broedersstraat 10, B-3000 Leuven, Belgium. esnouf@rega.kuleuven.ac.be},
  doi       = {10.1107/S0907444998017363},
  file      = {1999_Esnouf_938.pdf:by-author/E/Esnouf/1999_Esnouf_938.pdf:PDF},
  isbn      = {0907-4449},
  keywords  = {Molecular Graphics; Molscript},
  owner     = {em},
  timestamp = {2016.06.16},
  creationdate = {2016-06-16T00:00:00},
  url       = {http://view.ncbi.nlm.nih.gov/pubmed/10089341},
}

@Presentation{Estrade2010,
  author    = {Estrade, B.},
  title     = {Hybrid Programming with MPI and OpenMP},
  year      = {2010},
  file      = {:by-author/E/Estrade/2010_Estrade_slides.pdf:PDF},
  owner     = {saulius},
  pages     = {slides},
  timestamp = {2013.07.02},
  creationdate = {2013-07-02T00:00:00},
}

@Article{Etzkorn2004,
  author    = {Etzkorn, Christopher and Horton, Nancy C.},
  journal   = {Biochemistry},
  title     = {Ca2+ binding in the active site of HincII: implications for the catalytic mechanism.},
  year      = {2004},
  pages     = {13256--70},
  volume    = {43},
  abstract  = {The 2.8 A crystal structure of the type II restriction endonuclease HincII bound to Ca(2+) and cognate DNA containing GTCGAC is presented. The DNA is uncleaved, and one calcium ion is bound per active site, in a position previously described as site I in the related blunt cutting type II restriction endonuclease EcoRV [Horton, N. C., Newberry, K. J., and Perona, J. J. (1998) Proc. Natl. Acad. Sci. U.S.A. 95 (23), 13489-13494], as well as that found in other related enzymes. Unlike the site I metal in EcoRV, but similar to that of PvuII, NgoMIV, BamHI, BglII, and BglI, the observed calcium cation is directly ligated to the pro-S(p) oxygen of the scissile phosphate. A calcium ion-ligated water molecule is well positioned to act as the nucleophile in the phosphodiester bond cleavage reaction, and is within hydrogen bonding distance of the conserved active site lysine (Lys 129), as well as the pro-R(p) oxygen of the phosphate group 3' of the scissile phosphate, suggesting possible roles for these groups in the catalytic mechanism. Kinetic data consistent with an important role for the 3'-phosphate group in DNA cleavage by HincII are presented. The previously observed sodium ion [Horton, N. C., Dorner, L. F., and Perona, J. J. (2002) Nat. Struct. Biol. 9, 42-47] persists in the active sites of the Ca(2+)-bound structure; however, kinetic data show little effect on the single-turnover rate of DNA cleavage in the absence of Na(+) ions.},
  file      = {:by-author/E/Etzkorn/2004_Etzkorn_13256.pdf:PDF},
  groups    = {sg/NgoMIV},
  keywords  = {Catalysis; HincII; TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Etzkorn2004a,
  author      = {Christopher Etzkorn and Nancy C Horton},
  journal     = {J Mol Biol},
  title       = {Mechanistic insights from the structures of HincII bound to cognate DNA cleaved from addition of Mg2+ and Mn2+.},
  year        = {2004},
  month       = {Oct},
  number      = {4},
  pages       = {833--849},
  volume      = {343},
  abstract    = {The three-dimensional X-ray crystal structures of HincII bound to cognate DNA containing GTCGAC and Mn(2+) or Mg(2+), at 2.50A and 2.95A resolution, respectively, are presented. In both structures, the DNA is found cleaved, and the positions of the active-site groups, cleaved phosphate group, and 3' oxygen atom of the leaving group are in very similar positions. Two highly occupied Mn(2+) positions are found in each active site of the four crystallographically independent subunit copies in the HincII/DNA/Mn(2+) structure. The manganese ion closest to the previously identified single Ca(2+) position of HincII is shifted 1.7A and has lost direct ligation to the active-site aspartate residue, Asp127. A Mn(2+)-ligated water molecule in a position analogous to that seen in the HincII/DNA/Ca(2+) structure, and proposed to be the attacking nucleophile, is beyond hydrogen bonding distance from the active-site lysine residue, Lys129, but remains within hydrogen bonding distance from the proRp oxygen atom of the phosphate group 3' to the scissile phosphate group. In addition, the position of the cleaved phosphate group is on the opposite side of the axis connecting the two metal ions relative to that found in the BamHI/product DNA/Mn(2+) structure. Mechanistic implications are discussed, and a model for the two-metal-ion mechanism of DNA cleavage by HincII is proposed.},
  doi         = {10.1016/j.jmb.2004.08.082},
  file        = {2004_Etzkorn_13256.pdf:by-author/E/Etzkorn/2004_Etzkorn_13256.pdf:PDF},
  institution = {Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, AZ 85721, USA.},
  keywords    = {Aspartic Acid; Bacteria; Crystallography; DNA; Deoxyribonucleases; Glutamic Acid; Magnesium; Manganese; Phosphates; Protein Structure; Tertiary; Type II Site-Specific; X-Ray},
  owner       = {em},
  pii         = {S0022-2836(04)01082-4},
  pmid        = {15476804},
  timestamp = {2011.06.10},
  creationdate = {2011-06-10T00:00:00},
  url         = {http://dx.doi.org/10.1016/j.jmb.2004.08.082},
}

@Article{Etzkorn2004b,
  author      = {Christopher Etzkorn and Nancy C Horton},
  journal     = {Biochemistry},
  title       = {Ca2+ binding in the active site of HincII: implications for the catalytic mechanism.},
  year        = {2004},
  month       = {Oct},
  number      = {42},
  pages       = {13256--13270},
  volume      = {43},
  abstract    = {The 2.8 A crystal structure of the type II restriction endonuclease HincII bound to Ca(2+) and cognate DNA containing GTCGAC is presented. The DNA is uncleaved, and one calcium ion is bound per active site, in a position previously described as site I in the related blunt cutting type II restriction endonuclease EcoRV [Horton, N. C., Newberry, K. J., and Perona, J. J. (1998) Proc. Natl. Acad. Sci. U.S.A. 95 (23), 13489-13494], as well as that found in other related enzymes. Unlike the site I metal in EcoRV, but similar to that of PvuII, NgoMIV, BamHI, BglII, and BglI, the observed calcium cation is directly ligated to the pro-S(p) oxygen of the scissile phosphate. A calcium ion-ligated water molecule is well positioned to act as the nucleophile in the phosphodiester bond cleavage reaction, and is within hydrogen bonding distance of the conserved active site lysine (Lys 129), as well as the pro-R(p) oxygen of the phosphate group 3' of the scissile phosphate, suggesting possible roles for these groups in the catalytic mechanism. Kinetic data consistent with an important role for the 3'-phosphate group in DNA cleavage by HincII are presented. The previously observed sodium ion [Horton, N. C., Dorner, L. F., and Perona, J. J. (2002) Nat. Struct. Biol. 9, 42-47] persists in the active sites of the Ca(2+)-bound structure; however, kinetic data show little effect on the single-turnover rate of DNA cleavage in the absence of Na(+) ions.},
  doi         = {10.1021/bi0490082},
  file        = {2004_Etzkorn_13256.pdf:by-author/E/Etzkorn/2004_Etzkorn_13256.pdf:PDF},
  groups      = {sg/NgoMIV},
  institution = {Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, Arizona 85721, USA.},
  keywords    = {Bacterial; Binding Sites; Calcium-Binding Proteins; Catalysis; Catalytic Domain; Crystallography; DNA; DNA-Binding Proteins; Deoxyribonucleases; Haemophilus Influenzae; Hydrolysis; Models; Molecular; Protein; Protein Conformation; Protein Subunits; Structural Homology; Substrate Specificity; Type II Site-Specific; X-Ray},
  owner       = {em},
  pmid        = {15491133},
  timestamp = {2011.06.10},
  creationdate = {2011-06-10T00:00:00},
  url         = {http://dx.doi.org/10.1021/bi0490082},
}

@Article{Evans1983,
  author    = {Denis J. Evans and G.P. Morriss},
  journal   = {Chemical Physics},
  title     = {Isothermal-isobaric molecular dynamics},
  year      = {1983},
  issn      = {0301-0104},
  number    = {1},
  pages     = {63 - 66},
  volume    = {77},
  abstract  = {We combine the Doll's tensor hamiltonian for flow deformation with Gauss' principle of least constraint to develop classical equations of motion for which the temperature and hydrostatic pressure are constants of the motion. These equations of motion define a molecular dynamics algorithm for which N, T, p are the independent thermodynamic state variables.},
  doi       = {10.1016/0301-0104(83)85065-4},
  file      = {1983_Evans_63.pdf:by-author/E/Evans/1983_Evans_63.pdf:PDF},
  groups    = {sg/Molecular dynamics},
  keywords  = {Molecular Dynamics (MD); Thermostats},
  owner     = {saulius},
  timestamp = {2016.02.24},
  creationdate = {2016-02-24T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/0301010483850654},
}

@Article{Evans1984,
  author    = {Evans, Denis J. and Morriss, Gary P.},
  journal   = {The Journal of Chemical Physics},
  title     = {Comment on ‘‘Extensions of the molecular dynamics simulation method. II. Isothermal systems’’},
  year      = {1984},
  number    = {8},
  pages     = {3749--3750},
  volume    = {81},
  abstract  = {Haile and Gupta have given derivations of isothermal equations of motion for a system of N particles. The first derivation, based on generalized potentials, gives equations of motion which are derivable from a Hamiltonian and hence have four rather than three constants of the motion. These equations of motion have no obvious relevance to equilibrium statistical mechanics. Derivations which lead to isothermal equations of motion which have direct utility to statistical mechanics have been given by Evans, Hoover, and Nosé.},
  doi       = {10.1063/1.448095},
  file      = {1984_Evans_3749.pdf:by-author/E/Evans/1984_Evans_3749.pdf:PDF},
  groups    = {sg/Molecular dynamics},
  keywords  = {Molecular Dynamics (MD); Polemics; Thermostats},
  owner     = {saulius},
  timestamp = {2016.02.24},
  creationdate = {2016-02-24T00:00:00},
  url       = {http://scitation.aip.org/content/aip/journal/jcp/81/8/10.1063/1.448095},
}

@Article{Evans2003,
  author    = {Evans, Gwyndaf and Bricogne, G{\'{e}}rard},
  journal   = {Acta Crystallographica Section D},
  title     = {Triiodide derivatization in protein crystallography},
  year      = {2003},
  pages     = {1923--1929},
  volume    = {59},
  doi       = {10.1107/S0907444903012897},
  file      = {ba5032.pdf:by-author/E/Evans/2003_Evans_1923.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444903012897},
}

@PhdThesis{Evans2000,
  author    = {Matt Evans},
  school    = {University of Nebraska-Lincoln},
  title     = {FTFS: The Design of A Fault Tolerant Distributed File-System},
  year      = {2000},
  file      = {2000_Evans_phdthesis.pdf:by-author/E/Evans/2000_Evans_phdthesis.pdf:PDF},
  owner     = {saulius},
  pages     = {PhD-thesis},
  timestamp = {2012.09.18},
  creationdate = {2012-09-18T00:00:00},
}

@Article{Evans2005,
  author    = {Evans, Michael J. and Saghatelian, Alan and Sorensen, Erik J. and Cravatt, Benjamin F.},
  journal   = {Nature biotechnology},
  title     = {Target discovery in small-molecule cell-based screens by in situ proteome reactivity profiling.},
  year      = {2005},
  pages     = {1303--7},
  volume    = {23},
  abstract  = {Chemical genomics aims to discover small molecules that affect biological processes through the perturbation of protein function. However, determining the protein targets of bioactive compounds remains a formidable challenge. We address this problem here through the creation of a natural product-inspired small-molecule library bearing protein-reactive elements. Cell-based screening identified a compound, MJE3, that inhibits breast cancer cell proliferation. In situ proteome reactivity profiling revealed that MJE3, but not other library members, covalently labeled the glycolytic enzyme phosphoglycerate mutase 1 (PGAM1), resulting in enzyme inhibition. Interestingly, MJE3 labeling and inhibition of PGAM1 were observed exclusively in intact cells. These results support the hypothesis that cancer cells depend on glycolysis for viability and promote PGAM1 as a potential therapeutic target. More generally, the incorporation of protein-reactive compounds into chemical genomics screens offers a means to discover targets of bioactive small molecules in living systems, thereby enabling downstream mechanistic investigations.},
  file      = {:by-author/E/Evans/2005_Evans_1303.pdf:PDF},
  keywords  = {Bioconjugation},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@Article{Evans2012a,
  author    = {Phil Evans},
  journal   = {Science},
  title     = {Resolving Some Old Problems in Protein Crystallography},
  year      = {2012},
  pages     = {986--987},
  volume    = {336},
  abstract  = {Scientific conclusions should be supported by the observed data. However, in x-ray crystallography, the raw diffraction data are rather remotely connected to the final coordinates of the molecule because the experimental data undergo a Fourier transform during the analysis. Thus, any individual feature of the structural model—where a particular atom is located—depends on all of the measured diffraction intensities. Also, the phase information essential for this reconstruction is lost in the experiment (the “phase problem”). Although the coordinate model is repeatedly tested against the data in the course of structure solution, it is common practice to choose what data to use early in the process. Two papers in this issue suggest in different ways that crystallographers have often been excluding useful data from structure determination. On page1030, Karplus and Diederichs (1) show that the “resolution” of data sets is frequently underestimated, so that the final model is not as good as it could be. On page 1033, Liu et al. (2) show that averaging data from multiple crystals can give helpful information for solving the phase problem by using intrinsic sulfur atoms in the protein, circumventing the need to introduce heavier atoms.},
  doi       = {10.1126/science.1222162},
  file      = {2012_Evans_986.pdf:by-author/E/Evans/2012_Evans_986.pdf:PDF},
  keywords  = {Data Quality; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2014.03.24},
  creationdate = {2014-03-24T00:00:00},
  url       = {http://www.xtal.iqfr.csic.es/Cristalografia/archivos_08/Resolving-Some-Old-Problems-in-Protein-Crystallography.pdf},
}

@Article{Evans2006,
  author    = {Evans, Philip},
  journal   = {Acta Crystallogr D Biol Crystallogr},
  title     = {Scaling and assessment of data quality},
  year      = {2006},
  month     = {Jan},
  number    = {Pt 1},
  pages     = {72--82},
  volume    = {62},
  abstract  = {The various physical factors affecting measured diffraction intensities are discussed, as are the scaling models which may be used to put the data on a consistent scale. After scaling, the intensities can be analysed to set the real resolution of the data set, to detect bad regions (e.g. bad images), to analyse radiation damage and to assess the overall quality of the data set. The significance of any anomalous signal may be assessed by probability and correlation analysis. The algorithms used by the CCP4 scaling program SCALA are described. A requirement for the scaling and merging of intensities is knowledge of the Laue group and point-group symmetries: the possible symmetry of the diffraction pattern may be determined from scores such as correlation coefficients between observations which might be symmetry-related. These scoring functions are implemented in a new program POINTLESS},
  address   = {MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, England. pre@mrc-lmb.cam.ac.uk},
  file      = {2006_Evans_72.pdf:by-author/E/Evans/2006_Evans_72.pdf:PDF},
  owner     = {em},
  timestamp = {2016.06.16},
  creationdate = {2016-06-16T00:00:00},
  url       = {http://www.ncbi.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&dopt=abstract&list_uids=16369096},
}

@Article{Evans2003a,
  author    = {Evans, Philip},
  journal   = {Acta Crystallographica Section D},
  title     = {Phasing the AP2 core complex with Xe, Hg and Se},
  year      = {2003},
  pages     = {2039--2043},
  volume    = {59},
  doi       = {10.1107/S0907444903017840},
  file      = {ba5045.pdf:by-author/E/Evans/2003_Evans_2039.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444903017840},
}

@Article{Evans2012,
  author    = {P.W. Evans and Huw Price and K.~B. Wharton},
  journal   = {The British Journal for the Philosophy of Science},
  title     = {New Slant on the EPR-Bell Experiment},
  year      = {2012},
  pages     = {1–28},
  abstract  = {The best case for thinking that quantum mechanics is nonlocal rests on Bell’s Theorem, and later results of the same kind. However, the correlations characteristic of Einstein– Podolsky–Rosen (EPR)–Bell (EPRB) experiments also arise in familiar cases elsewhere in quantum mechanics (QM), where the two measurements involved are timelike rather than spacelike separated; and in which the correlations are usually assumed to have a local causal explanation, requiring no action-at-a-distance (AAD). It is interesting to ask how this is possible, in the light of Bell’s Theorem. We investigate this question, and present two options. Either (i) the new cases are nonlocal too, in which case AAD is more widespread in QM than has previously been appreciated (and does not depend on en- tanglement, as usually construed); or (ii) the means of avoiding AAD in the new cases extends in a natural way to EPRB, removing AAD in these cases too. There is a third option, viz., that the new cases are strongly disanalogous to EPRB. But this option requires an argument, so far missing, that the physical world breaks the symmetries which otherwise support the analogy. In the absence of such an argument, the orthodox combination of views—action-at-a-distance in EPRB, but local causality in its timelike analogue—is less well established than it is usually assumed to be},
  doi       = {10.1093/bjps/axr052},
  file      = {:by-author/E/Evans/2012_Evans.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.09.18},
  creationdate = {2012-09-18T00:00:00},
  url       = {http://bjps.oxfordjournals.org/content/early/2012/04/26/bjps.axr052.abstract},
}

@Article{Evans2007,
  author    = {Evans, Philip R.},
  journal   = {Acta Crystallographica Section D},
  title     = {An introduction to stereochemical restraints},
  year      = {2007},
  pages     = {58--61},
  volume    = {63},
  abstract  = {At the resolution available from most macromolecular crystals, the X-ray data alone are insufficient to lead to a chemically reasonable structure, so stereochemical restraints are essential. These usually restrain bond lengths, bond angles, planes and chiral volumes. The definition of these restraints and where the values come from are described. A dictionary entry contains information about the atom types, their connectivity and all the appropriate restraints. Torsion angles are not usually restrained, but they do have optimum values. In the special case of flexible five- and six-membered rings, including pentose and hexose sugars, the ring pucker is defined by combinations of torsion angles and the pucker affects the position of substituents.},
  doi       = {10.1107/S090744490604604X},
  file      = {2007_Evans_58.pdf:by-author/E/Evans/2007_Evans_58.pdf:PDF},
  keywords  = {Restrains},
  owner     = {saulius},
  timestamp = {2012.05.23},
  creationdate = {2012-05-23T00:00:00},
  url       = {http://dx.doi.org/10.1107/S090744490604604X},
}

@Article{Evgenev2000,
  author    = {Michael B. Evgen’ev and Zelentsova, Helena and Poluectova, Helena and George T. Lyozin and Veleikodvorskaja, Vera and Pyatkov, K. I. and Lev A. Zhivotovsky and Margaret G. Kidwell},
  journal   = {PNAS},
  title     = {Mobile elements and chromosomal evolution in the virilis group of Drosophila},
  year      = {2000},
  pages     = {11337--11342},
  volume    = {97},
  abstract  = {Species of the virilis group of Drosophila differ by multiple inversions and chromosome fusions that probably accompanied, or led to, speciation. Drosophila virilis has the primitive karyotype for the group, and natural populations are exceptional in having no chromosomal polymorphisms. We report that the genomic locations of Penelope and Ulysses transposons are nonrandomly distributed in 12 strains of D. virilis. Furthermore, Penelope and Ulysses insertion sites in D. virilis show a statistically significant association with the breakpoints of inversions found in other species of the virilis group. Sixteen newly induced chromosomal rearrangements were isolated from the progeny of D. virilis hybrid dysgenic crosses, including 12 inversions, 2 translocations, and 2 deletions. Penelope and Ulysses were associated with the breakpoints of over half of these new rearrangements. Many rearrangement breakpoints also coincide with the chromosomal locations of Penelope and Ulysses insertions in the parental strains and with breakpoints of inversions previously established for other species of the group. Analysis of homologous sequences from D. virilis and Drosophila lummei indicated that Penelope insertion sites were closely, but not identically, located at the nucleotide sequence level. Overall, these results indicate that Penelope and Ulysses insert in a limited number of genomic locations and are consistent with the possibility that these elements play an important role in the evolution of the virilis species group.},
  doi       = {10.1073/pnas.210386297},
  file      = {:by-author/E/Evgenev/2000_Evgenev_11337.pdf:PDF},
  owner     = {saulius},
  timestamp = {2013.08.10},
  creationdate = {2013-08-10T00:00:00},
}

@Article{Evgenev1997,
  author    = {Michael B. Evgen’ev and Helena Zelentsova and Natalia Shostak and Marina Kozitsina and Victor Barskyi and Dirk-henner L. Ankenau and Victor G. Corces},
  journal   = {Proc. Natl. Acad. Sci. USA},
  title     = {Penelope and a new family of transposable elements and its possible and role in hybrid dysgenesis in Drosophila and virilis},
  year      = {1997},
  pages     = {196--201},
  volume    = {94},
  file      = {:by-author/E/Evgenev/1997_Evgenev_196.pdf:PDF},
  owner     = {saulius},
  timestamp = {2013.08.10},
  creationdate = {2013-08-10T00:00:00},
}

@Article{Eynden2011,
  author    = {Eynden},
  title     = {Managing and Sharing Data},
  year      = {2011},
  file      = {:by-author/E/Eynden/2011_Eynden.pdf:PDF},
  keywords  = {Data Management},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@Article{Eysenbach2006,
  author    = {Eysenbach, Gunther},
  journal   = {PLoS Biol},
  title     = {Citation Advantage of Open Access Articles},
  year      = {2006},
  issn      = {1545-7885},
  month     = {May},
  number    = {5},
  pages     = {e157},
  volume    = {4},
  abstract  = {Open access (OA) to the research literature has the potential to accelerate recognition and dissemination of research findings, but its actual effects are controversial. This was a longitudinal bibliometric analysis of a cohort of OA and non-OA articles published between June 8, 2004, and December 20, 2004, in the same journal (PNAS: Proceedings of the National Academy of Sciences). Article characteristics were extracted, and citation data were compared between the two groups at three different points in time: at “quasi-baseline” (December 2004, 0–6 mo after publication), in April 2005 (4–10 mo after publication), and in October 2005 (10–16 mo after publication). Potentially confounding variables, including number of authors, authors' lifetime publication count and impact, submission track, country of corresponding author, funding organization, and discipline, were adjusted for in logistic and linear multiple regression models. A total of 1,492 original research articles were analyzed: 212 (14.2% of all articles) were OA articles paid by the author, and 1,280 (85.8%) were non-OA articles. In April 2005 (mean 206 d after publication), 627 (49.0%) of the non-OA articles versus 78 (36.8%) of the OA articles were not cited (relative risk = 1.3 [95% Confidence Interval: 1.1–1.6]; p = 0.001). 6 mo later (mean 288 d after publication), non-OA articles were still more likely to be uncited (non-OA: 172 [13.6%], OA: 11 [5.2%]; relative risk = 2.6 [1.4–4.7]; p < 0.001). The average number of citations of OA articles was higher compared to non-OA articles (April 2005: 1.5 [SD = 2.5] versus 1.2 [SD = 2.0]; Z = 3.123; p = 0.002; October 2005: 6.4 [SD = 10.4] versus 4.5 [SD = 4.9]; Z = 4.058; p < 0.001). In a logistic regression model, controlling for potential confounders, OA articles compared to non-OA articles remained twice as likely to be cited (odds ratio = 2.1 [1.5–2.9]) in the first 4–10 mo after publication (April 2005), with the odds ratio increasing to 2.9 (1.5–5.5) 10–16 mo after publication (October 2005). Articles published as an immediate OA article on the journal site have higher impact than self-archived or otherwise openly accessible OA articles. We found strong evidence that, even in a journal that is widely available in research libraries, OA articles are more immediately recognized and cited by peers than non-OA articles published in the same journal. OA is likely to benefit science by accelerating dissemination and uptake of research findings.},
  doi       = {10.1371/journal.pbio.0040157},
  editor    = {Tenopir, CarolEditor},
  file      = {2006_Eysenbach_e157.pdf:by-author/E/Eysenbach/2006_Eysenbach_e157.pdf:PDF},
  groups    = {sg/Bibliometrics},
  keywords  = {Article Impatc; Citation Counts; Open Access},
  owner     = {saulius},
  publisher = {Public Library of Science (PLoS)},
  timestamp = {2016.10.16},
  creationdate = {2016-10-16T00:00:00},
  url       = {http://dx.doi.org/10.1371/journal.pbio.0040157},
}

@Article{Faber2002,
  author    = {Faber, John and Fawcett, Tim},
  journal   = {Acta Crystallographica Section B},
  title     = {The Powder Diffraction File: present and future},
  year      = {2002},
  month     = {Jun},
  number    = {3 Part 1},
  pages     = {325--332},
  volume    = {58},
  abstract  = {The International Centre for Diffraction Data (ICDD) produces the Powder Diffraction File (PDF). This paper discusses some of the seminal events in the history of producing this primary reference for powder diffraction. Recent key events that center on collaborative initiatives have led to an enormous jump in entry population for the PDF. Collective efforts to editorialize the PDF are ongoing and provide enormous added value to the file. Recently, the ICDD has created a new series of the PDF, designated PDF-4. These relational database structures are being used to house the PDF of the future. The design and benefits of the PDF-4 are described.},
  doi       = {10.1107/S0108768102003312},
  file      = {2002_Faber_325.pdf:by-author/F/Faber/2002_Faber_325.pdf:PDF},
  keywords  = {Digitized Powder Patterns; ICDD; Materials Design; PDF; Powder Diffraction File},
  owner     = {saulius},
  timestamp = {2016.10.16},
  creationdate = {2016-10-16T00:00:00},
  url       = {https://doi.org/10.1107/S0108768102003312},
}

@Article{Fagg2004,
  author       = {Graham E. Fagg and Jack J. Dongarra},
  journal      = {International Journal of High Performance Computing Applications},
  title        = {Building and using an Fault Tolerant MPI implementation},
  year         = {2004},
  pages        = {353},
  abstract     = {In this paper we discuss the design and use of a fault-tol- erant MPI (FT-MPI) that handles process failures in a way beyond that of the original MPI static process model. FT- MPI allows the semantics and associated modes of failures to be explicitly controlled by an application via a modified functionality within the standard MPI 1.2 API. Given is an overview of the FT-MPI semantics, architecture design, example usage and sample applications. A short discus- sion is given on the consequences of designing a fault-tol- erant MPI both in terms of how such an implementation handles failures at multiple levels internally as well as how existing applications can use new features while still remaining within the MPI standard.},
  doi          = {10.1177/1094342004046052},
  file         = {2004_Fagg_353manuscript.pdf:by-author/F/Fagg/2004_Fagg_353.pdf:PDF;2004_Fagg_353.pdf:by-author/F/Fagg/2004_Fagg_353.pdf:PDF},
  organization = {High Performance Computing Center Stuttgart, Allmandring 30, D-70550 Stuttgart, Germany; Department of Computer Science, Suite 413, 1122 Volunteer Blvd., University of Tennessee, Knoxville, TN-37996-3450, USA.},
  owner        = {saulius},
  timestamp = {2013.07.02},
  creationdate = {2013-07-02T00:00:00},
  url          = {http://www.netlib.org/utk/people/JackDongarra/PAPERS/154_2004_building-and-using-a-fault-tolerant-mpi-implementation.pdf},
}

@Article{Faginas-Lago2014,
  author    = {Faginas-Lago, Noelia and Albertí, Margarita and Costantini, Alessandro and Laganà, Antonio and Lombardi, Andrea and Pacifici, Leonardo},
  journal   = {Journal of molecular modeling},
  title     = {An innovative synergistic grid approach to the computational study of protein aggregation mechanisms},
  year      = {2014},
  pages     = {1--9},
  volume    = {20},
  file      = {[PDF] from researchgate.net:by-author/F/Faginas-Lago/2014_Faginas-Lago_1.pdf:PDF;Snapshot:by-author/F/Faginas-Lago/2014_Faginas-Lago_1.html:URL},
  groups    = {sg/JAC2009},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://link.springer.com/article/10.1007/s00894-014-2226-4},
  urldate   = {2015-08-31},
}

@TechReport{Fahndrich2003,
  author      = {Manuel Fähndrich and K. Rustan M. Leino},
  institution = {Microsoft Research, One Microsoft Way, Redmond, WA 98052, USA},
  title       = {Declaring and Checking Non-null Types in an Object-Oriented Language},
  year        = {2003},
  abstract    = {Distinguishing non-null references from possibly-null refer- ences at the type level can detect null-related errors in object- oriented programs at compile-time. This paper gives a pro- posal for retrofitting a language such as C# or Java with non-null types. It addresses the central complications that arise in constructors, where declared non-null fields may not yet have been initialized, but the partially constructed ob- ject is already accessible. The paper reports experience with an implementation for annotating and checking null-related properties in C# programs.},
  file        = {:by-author/F/Fahndrich/2003_Fahndrich.pdf:PDF},
  keywords    = {Computer Science (CS); Non Null},
  owner       = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Falini1996,
  author    = {Falini, Giuseppe and Albeck, Shira and Weiner, Steve and Addadi, Lia},
  journal   = {Science},
  title     = {Control of Aragonite or Calcite Polymorphism by Mollusk Shell Macromolecules},
  year      = {1996},
  pages     = {67--69},
  volume    = {271},
  abstract  = {Many mineralizing organisms selectively form either calcite or aragonite, two polymorphs of calcium carbonate with very similar crystalline structures. Understanding how these organisms achieve this control has represented a major challenge in the field of biomineralization. Macromolecules extracted from the aragonitic shell layers of some mollusks induced aragonite formation in vitro when preadsorbed on a substrate of β-chitin and silk fibroin. Macromolecules from calcitic shell layers induced mainly calcite formation under the same conditions. The results suggest that these macromolecules are responsible for the precipitation of either aragonite or calcite in vivo.},
  doi       = {10.1126/science.271.5245.67},
  eprint    = {http://www.sciencemag.org/content/271/5245/67.full.pdf},
  file      = {1996_Falini_67.pdf:by-author/F/Falini/1996_Falini_67.pdf:PDF},
  keywords  = {Textures; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://www.sciencemag.org/content/271/5245/67.abstract},
}

@Article{Fang2012,
  author    = {Fang, F. C. and Steen, R. G. and Casadevall, A.},
  journal   = {Proceedings of the National Academy of Sciences},
  title     = {Misconduct accounts for the majority of retracted scientific publications},
  year      = {2012},
  issn      = {1091-6490},
  month     = {Oct},
  number    = {42},
  pages     = {17028–17033},
  volume    = {109},
  date      = {2017-06-16},
  doi       = {10.1073/pnas.1212247109},
  file      = {2012_Fang_1212247109.pdf:by-author/F/Fang/2012_Fang_1212247109.pdf:PDF},
  owner     = {andrius},
  publisher = {Proceedings of the National Academy of Sciences},
  timestamp = {2017.06.16},
  creationdate = {2017-06-16T00:00:00},
  url       = {http://dx.doi.org/10.1073/pnas.1212247109},
}

@Article{Far2012,
  author    = {Far, Leila Babaie and Souri, Bubak and Heidari, Masoumeh and Roshan, K.},
  journal   = {Iran J Environ Health Sci Engineer},
  title     = {Evaluation of iron and manganese-coated pumice application for the removal of as (v) from aqueous solutions},
  year      = {2012},
  pages     = {2746--9},
  volume    = {9},
  file      = {[PDF] from biomedcentral.com:by-author/F/Far/2012_Far_2746.pdf:application/pdf},
  groups    = {sg/JAC2009},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://www.biomedcentral.com/content/pdf/1735-2746-9-21.pdf},
  urldate   = {2015-08-31},
}

@Article{Faria1990,
  author    = {J. Lima-de-Faria and E. Hellner and F. Liebau and E. Makovicky and E. Parthé},
  journal   = {Acta Crystallographica Section A},
  title     = {Nomenclature of {I}norganic {S}tructure {T}ypes. {R}eport of the {I}nternational {U}nion of {C}rystallography {C}ommission on {C}rystallographic {N}omenclature {S}ubcommittee on the {N}omenclature of {I}norganic {S}tructure {T}ypes},
  year      = {1990},
  pages     = {1--11},
  volume    = {46},
  doi       = {10.1107/S0108767389008834},
  file      = {:by-author/L/Lima-de-Faria/1990_Lima-de-Faria_1.pdf:PDF},
  owner     = {antanas},
  timestamp = {2014.06.17},
  creationdate = {2014-06-17T00:00:00},
  url       = {http://scripts.iucr.org/cgi-bin/paper?S0108767389008834},
}

@Article{Farrell2006,
  author    = {Farrell, Patrick J. and Rogers-Stewart, Katrina},
  journal   = {Journal of Statistical Computation and Simulation},
  title     = {Comprehensive study of tests for normality and symmetry: extending the {S}piegelhalter test},
  year      = {2006},
  pages     = {803–816},
  volume    = {76},
  doi       = {10.1080/10629360500109023},
  file      = {:by-author/F/Farrell/2006_Farrell_803.pdf:PDF},
  keywords  = {Statistical Tests},
  owner     = {andrius},
  timestamp = {2012.09.13},
  creationdate = {2012-09-13T00:00:00},
}

@Article{Faust2008,
  author    = {Faust, Annette and Panjikar, Santosh and Mueller, Uwe and Parthasarathy, Venkataraman and Schmidt, Andrea and Lamzin, Victor S. and Weiss, Manfred S.},
  journal   = {Journal of Applied Crystallography},
  title     = {A tutorial for learning and teaching macromol{\-}ecular crystallography},
  year      = {2008},
  pages     = {1161--1172},
  volume    = {41},
  abstract  = {Five experiments have been designed to be used for teaching macromolecular crystallography. The three proteins used in this tutorial are all commercially available; they can be easily and reproducibly crystallized and mounted for diffraction data collection. For each of the five experiments the raw images and the processed data of a sample diffraction data set as well as the refined coordinates and phases are provided for teaching the steps of data processing and structure determination.},
  doi       = {10.1107/S0021889808032494},
  file      = {2008_Faust_1161.pdf:by-author/F/Faust/2008_Faust_1161.pdf:PDF},
  keywords  = {Automated Structure Determination; Data Processing; Diffraction Data Collection; Macromolecular Crystallography; Protein Crystallization},
  owner     = {saulius},
  timestamp = {2015.04.03},
  creationdate = {2015-04-03T00:00:00},
  url       = {http://scripts.iucr.org/cgi-bin/paper?S0021889808032494},
}

@Article{Faust2010,
  author    = {Faust, Annette and Puehringer, Sandra and Darowski, Nora and Panjikar, Santosh and Diederichs, Kay and Mueller, Uwe and Weiss, Manfred S.},
  journal   = {Journal of Applied Crystallography},
  title     = {Update on the tutorial for learning and teaching macromolecular crystallography},
  year      = {2010},
  pages     = {1230--1237},
  volume    = {43},
  abstract  = {Two new experiments (single isomorphous replacement including anomalous-scattering effects and radiation damage-induced phasing) have been designed to complement the five experiments (sulfur single-wavelength anomalous diffraction, multiple-wavelength anomalous diffraction, molecular replacement, ion binding and ligand binding) of the first edition of the previously described tutorial for learning and teaching macromolecular crystallography [Faust, Panjikar, Mueller, Parthasarathy, Schmidt, Lamzin & Weiss (2008). {\it J. Appl. Cryst.} {\bf 41}, 1161{--}1172]. Furthermore, the tutorial has been re-organized and in part re-written to reflect the comments and suggestions of users. The most significant overhaul was applied to the data-processing part of the tutorial. Nevertheless, the convenient features that all of the utilized proteins used are commercially available and that they can be easily and reproducibly crystallized and mounted for diffraction data collection have been retained. Also, for all of the seven experiments the raw diffraction images and the processed data are provided for illustrating and teaching the steps of data processing and structure determination.},
  doi       = {10.1107/S0021889810028189},
  file      = {2010_Faust_1230.pdf:by-author/F/Faust/2010_Faust_1230.pdf:PDF},
  keywords  = {Crystallographic Education; Data Processing; Ion Binding; Ligand Binding; MIR; Molecular Replacement; RIP; SIRAS; Structure Determination; Sulfur SIR},
  owner     = {saulius},
  timestamp = {2015.04.03},
  creationdate = {2015-04-03T00:00:00},
  url       = {http://scripts.iucr.org/cgi-bin/paper?S0021889810028189},
}

@Article{Favell1969,
  author    = {Favell, J.},
  journal   = {Journal of the experimental analysis of behavior},
  title     = {A two-relay flip-flop.},
  year      = {1969},
  pages     = {190},
  volume    = {12},
  file      = {:by-author/F/Favell/1969_Favell_190.pdf:PDF},
  keywords  = {Electronics},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Feagan2007,
  author    = {Feagan, Lance and Rohrer, Justin and Garrett, Alexander and Amthauer, Heather and Komp, Ed and Johnson, David and Hock, Adam and Clark, Terry and Lushington, Gerald and Minden, Gary and Frost, Victor},
  journal   = {Source Code for Biology and Medicine},
  title     = {Bioinformatics process management: information flow via a computational journal},
  year      = {2007},
  issn      = {1751-0473},
  pages     = {9},
  volume    = {2},
  abstract  = {This paper presents the Bioinformatics Computational Journal (BCJ), a framework for conducting and managing computational experiments in bioinformatics and computational biology. These experiments often involve series of computations, data searches, filters, and annotations which can benefit from a structured environment. Systems to manage computational experiments exist, ranging from libraries with standard data models to elaborate schemes to chain together input and output between applications. Yet, although such frameworks are available, their use is not widespread-ad hoc scripts are often required to bind applications together. The BCJ explores another solution to this problem through a computer based environment suitable for on-site use, which builds on the traditional laboratory notebook paradigm. It provides an intuitive, extensible paradigm designed for expressive composition of applications. Extensive features facilitate sharing data, computational methods, and entire experiments. By focusing on the bioinformatics and computational biology domain, the scope of the computational framework was narrowed, permitting us to implement a capable set of features for this domain. This report discusses the features determined critical by our system and other projects, along with design issues. We illustrate the use of our implementation of the BCJ on two domain-specific examples.},
  doi       = {10.1186/1751-0473-2-9},
  file      = {2007_Feagan_1.pdf:by-author/F/Feagan/2007_Feagan_1.pdf:PDF},
  keywords  = {Databases; Managing Bioinformatics Compuations; PDB},
  owner     = {saulius},
  pubmedid  = {18053179},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://www.scfbm.org/content/2/1/9},
}

@Book{FEBS2012,
  author    = {FEBS},
  editor    = {FEBS},
  publisher = {FEBS},
  title     = {The FEBS Journal: poster presentations. Abstracts},
  year      = {2012},
  number    = {Suppl. 1},
  volume    = {279},
  file      = {:by-author/F/FEBS/2012_FEBS_abstracts.pdf:PDF},
  owner     = {em},
  pages     = {52--576},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Feder2005,
  author    = {Marcin Feder and Janusz M. Bujnicki},
  journal   = {BMC Genomics},
  title     = {Identification of a new family of putative {PD-(D/E)XK} nucleases with unusual phylogenomic distribution and a new type of the active site},
  year      = {2005},
  pages     = {6:21},
  doi       = {10.1186/1471-2164-6-21},
  file      = {:by-author/F/Feder/2005_Feder_6\:21.pdf:PDF},
  keywords  = {Evolution},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Fedorov2003,
  author     = {Fedorov, Roman and Schlichting, Ilme and Hartmann, Elisabeth and Domratcheva, Tatjana and Fuhrmann, Markus and Hegemann, Peter},
  journal    = {Biophysical Journal},
  title      = {Crystal structures and molecular mechanism of a light-induced signaling switch: the phot-{LOV}1 domain from chlamydomonas reinhardtii},
  year       = {2003},
  issn       = {0006-3495},
  pages      = {2474--2482},
  volume     = {84},
  abstract   = {Phot proteins (phototropins and homologs) are blue-light photoreceptors that control mechanical processes like phototropism, chloroplast relocation, or guard-cell opening in plants. Phot receptors consist of two flavin mononucleotide (FMN)-binding light, oxygen, or voltage (LOV) domains and a C-terminal serine/threonine kinase domain. We determined crystal structures of the LOV1 domain of Phot1 from the green alga Chlamydomonas reinhardtii in the dark and illuminated state to 1.9 Å and 2.8 Å resolution, respectively. The structure resembles that of LOV2 from Adiantum (Crosson, S. and K. Moffat. 2001. Proc. Natl. Acad. Sci. USA. 98:2995–3000). In the resting dark state of LOV1, the reactive Cys-57 is present in two conformations. Blue-light absorption causes formation of a proposed active signaling state that is characterized by a covalent bond between the flavin C4a and the thiol of Cys-57. There are differences around the FMN chromophore but no large overall conformational changes. Quantum chemical calculations based on the crystal structures revealed the electronic distribution in the active site during the photocycle. The results suggest trajectories for electrons, protons, and the active site cysteine and offer an interpretation of the reaction mechanism.},
  doi        = {10.1016/S0006-3495(03)75052-8},
  file       = {ScienceDirect Full Text PDF:by-author/F/Fedorov/2003_Fedorov_2474.pdf:PDF;ScienceDirect Snapshot:by-author/F/Fedorov/2003_Fedorov_2474.html:URL},
  groups     = {sg/biomolecular, sg/MOFs, am/MOFs},
  owner      = {saulius},
  shorttitle = {Crystal structures and molecular mechanism of a light-induced signaling switch},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url        = {http://www.sciencedirect.com/science/article/pii/S0006349503750528},
  urldate    = {2015-08-05},
}

@Manuscript{Feess2012,
  author    = {Eberhard Feess and Marc Scheufen},
  title     = {Academic copyright in the publishing game: A contest perspective},
  year      = {2012},
  keywords  = {Open Access Publishing},
  url       = {http://ssrn.com/abstract=1793867},
  file      = {:by-author/F/Feess/2012_Feess.pdf:PDF},
  owner     = {saulius},
  timestamp = {2013.10.18},
  creationdate = {2013-10-18T00:00:00},
}

@Article{Feferman2002,
  author    = {Feferman},
  title     = {Penrose’s Godelian argument},
  year      = {2002},
  file      = {:by-author/F/Feferman/2002_Feferman.pdf:PDF},
  keywords  = {Goedel's Theorem},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Book{Feigin1987,
  author    = {Feigin and Svergun},
  editor    = {George W. Taylor},
  publisher = {Plenum Press},
  title     = {Structure Analysis of Small-Angle X-Ray and Neutron Scattering},
  year      = {1987},
  file      = {:by-author/F/Feigin/1987_Feigin.pdf:PDF},
  keywords  = {Review; SAXS; Theory},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Manuscript{Feinberg2008,
  author    = {Feinberg},
  title     = {A Simple and Affordable TTL Processor for the Classroom},
  year      = {2008},
  keywords  = {CPU Design; Computer Architecture; Computer Science (CS); Hardware},
  file      = {:by-author/F/Feinberg/2008_Feinberg.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@TechReport{Feinberg2007,
  author      = {Feinberg, David},
  institution = {Carnegie Mellon University, Computer Science Department, School of Computer Science},
  title       = {A Simple and Affordable TTL Processor for the Classroom},
  year        = {2007},
  doi         = {10.1080/08993400601165412},
  file        = {:by-author/F/Feinberg/2007_Feinberg.pdf:PDF},
  keywords    = {CPU Design; Computer Science (CS); Electronics; Teaching},
  owner       = {saulius},
  timestamp = {2015.03.11},
  creationdate = {2015-03-11T00:00:00},
  url         = {http://repository.cmu.edu/compsci/596},
}

@Article{Felder2003,
  author    = {Richard M. Felder and Rebecca Brent},
  journal   = {Chemical Engineering Education},
  title     = {Learning by doing},
  year      = {2003},
  pages     = {282--283},
  file      = {2003_Felder_282.pdf:by-author/F/Felder/2003_Felder_282.pdf:PDF},
  keywords  = {Teaching},
  owner     = {saulius},
  timestamp = {2014.03.24},
  creationdate = {2014-03-24T00:00:00},
  url       = {http://www4.ncsu.edu/unity/lockers/users/f/felder/public/Columns/Active.pdf},
}

@Manuscript{Fellas1999,
  author    = {John Fellas},
  title     = {The patentability of software-related inventions in the United States},
  year      = {1999},
  keywords  = {Patentai; Teise},
  file      = {:by-author/F/Fellas/1999_Fellas.doc:DOC},
  owner     = {saulius},
  timestamp = {2015.02.28},
  creationdate = {2015-02-28T00:00:00},
}

@Article{Felsenstein1988,
  author    = {Joseph Felsenstein},
  journal   = {Ann. Rev. Genet.},
  title     = {Phylogenies from molecular sequences: inference and reliability},
  year      = {1988},
  pages     = {521--565},
  volume    = {22},
  file      = {1988_Felsenstein_521.pdf:by-author/F/Felsenstein/1988_Felsenstein_521.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.07.18},
  creationdate = {2012-07-18T00:00:00},
}

@Article{Fenn2006,
  author    = {Fenn},
  journal   = {The PracTEX Journal},
  title     = {Managing Citations and Your Bibliography with {BibTEX}},
  year      = {2006},
  abstract  = {This article gives a brief introduction to managing citations and to preparing a list of references with BibTEX.},
  file      = {:by-author/F/Fenn/2006_Fenn.pdf:PDF},
  keywords  = {Bibtex; Computer Science (CS)},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Fennick2008,
  author    = {Fennick, Jacob R. and Keith, J. Brandon and Leonard, Robert H. and Truong, Thanh N. and Lewis, James P.},
  journal   = {Journal of Applied Crystallography},
  title     = {A cyberenvironment for crystallography and materials science and an integrated user interface to the Crystallography Open Database and Predicted Crystallography Open Database},
  year      = {2008},
  pages     = {471--475},
  volume    = {41},
  abstract  = {With the advent and subsequent evolution of the Internet the ways in which computational crystallographic research is conducted have dramatically changed. Consequently, secure, robust and efficient means of accessing remote data and computational resources have become a necessity. At present scientists in computational crystallography access remote data and resources via separate technologies, namely SSH and Web services. Computational Science and Engineering Online (CSE-Online) combines these two methods into a single seamless environment while simultaneously addressing issues such as stability with regard to Internet interruption. Presently CSE-Online contains several applications which are useful to crystallographers; however, continued development of new tools is necessary. Toward this end a Java application capable of running in CSE-Online, namely the Crystallography Open Database User Interface (CODUI), has been developed, which allows users to search for crystal structures stored in the Crystallography Open Database and Predicted Crystallography Open Database, to export structural data for visualization, or to input structural data in other CSE-Online applications.},
  doi       = {10.1107/S0021889808000381},
  file      = {:by-author/F/Fennick/2008_Fennick_471.pdf:PDF},
  keywords  = {COD; Citing COD},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0021889808000381},
}

@Article{Feringa2001,
  author     = {Feringa, Ben L.},
  journal    = {Accounts of Chemical Research},
  title      = {In control of motion:  from molecular switches to molecular motors},
  year       = {2001},
  issn       = {0001-4842},
  pages      = {504--513},
  volume     = {34},
  abstract   = {The design of molecular systems in which controlled linear and rotary motion can be achieved under the influence of an external signal is a major endeavor toward future nanoscale machinery. In this Account we describe the development of molecular switches and the discoveries that culminated in the first light-driven molecular motor. Various chiral optical molecular switches and their use as trigger elements to control organization and functions will be discussed. The construction of the first and second generation molecular motors is presented.},
  doi        = {10.1021/ar0001721},
  file       = {Feringa - 2001 - In Control of Motion From Molecular Switches to .pdf:by-author/F/Feringa/2001_Feringa_504.pdf:application/pdf;ACS Full Text Snapshot:by-author/F/Feringa/2001_Feringa_504.html:text/html},
  groups     = {sg/chemical},
  owner      = {saulius},
  shorttitle = {In control of motion},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url        = {http://dx.doi.org/10.1021/ar0001721},
  urldate    = {2015-08-05},
}

@Article{Feringa2000,
  author    = {Feringa, Ben L. and van Delden, Richard A. and Koumura, Nagatoshi and Geertsema, Edzard M.},
  journal   = {Chemical Reviews},
  title     = {Chiroptical molecular switches},
  year      = {2000},
  issn      = {0009-2665},
  pages     = {1789--1816},
  volume    = {100},
  doi       = {10.1021/cr9900228},
  file      = {Feringa et al. - 2000 - Chiroptical Molecular Switches.pdf:by-author/F/Feringa/2000_Feringa_1789.pdf:application/pdf;ACS Full Text Snapshot:by-author/F/Feringa/2000_Feringa_1789.html:text/html},
  groups    = {sg/chemical},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://dx.doi.org/10.1021/cr9900228},
  urldate   = {2015-08-05},
}

@Article{Fermi1934,
  author    = {Fermi, E.},
  journal   = {Z. Physik},
  title     = {Versuch einer Theorie der β-Strahlen},
  year      = {1934},
  issn      = {1434-601X},
  month     = {Mar},
  number    = {3-4},
  pages     = {161--177},
  volume    = {88},
  doi       = {10.1007/bf01351864},
  file      = {1934_Fermi_161.pdf:by-author/F/Fermi/1934_Fermi_161.pdf:PDF},
  owner     = {saulius},
  publisher = {Springer Science + Business Media},
  timestamp = {2016.03.19},
  creationdate = {2016-03-19T00:00:00},
  url       = {http://dx.doi.org/10.1007/BF01351864},
}

@Article{Fernandez-Remolar2015,
  author    = {Fernández-Remolar, David C. and Santamaría, Joan and Amils, Ricardo and Parro, Victor and Gómez-Ortíz, D. and Izawa, Matthew RM and Banerjee, Neil R. and Pérez Rodríguez, Raúl and Rodríguez, Nuria and López-Martínez, Nieves},
  journal   = {Journal of Geophysical Research: Biogeosciences},
  title     = {Formation of iron-rich shelled structures by microbial communities},
  year      = {2015},
  pages     = {147--168},
  volume    = {120},
  file      = {[PDF] from researchgate.net:by-author/F/Fernández-Remolar/2015_Fernández-Remolar_147.pdf:application/pdf;Snapshot:by-author/F/Fernández-Remolar/2015_Fernández-Remolar_147.html:text/html},
  groups    = {sg/JAC2009},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://onlinelibrary.wiley.com/doi/10.1002/2014JG002745/full},
  urldate   = {2015-08-31},
}

@Article{Ferreiro2005,
  author    = {Ferreiro, Diego U. and Dellarole, Mariano and Nadra, Alejandro D. and de Prat-Gay, Gonzalo},
  journal   = {The Journal of biological chemistry},
  title     = {Free energy contributions to direct readout of a DNA sequence.},
  year      = {2005},
  pages     = {32480--4},
  volume    = {280},
  abstract  = {The energetic contributions of individual DNA-contacting side chains to specific DNA recognition in the human papillomavirus 16 E2C-DNA complex is small (less than 1.0 kcal mol(-1)), independent of the physical and chemical nature of the interaction, and is strictly additive. The sum of the individual contributions differs 1.0 kcal mol(-1) from the binding energy of the wild-type protein. This difference corresponds to the contribution from the deformability of the DNA, known as &quot;indirect readout.&quot; Thus, we can dissect the energetic contribution to DNA binding into 90% direct and 10% indirect readout components. The lack of high energy interactions indicates the absence of &quot;hot spots,&quot; such as those found in protein-protein interfaces. These results are compatible with a highly dynamic and &quot;wet&quot; protein-DNA interface, yet highly specific and tight, where individual interactions are constantly being formed and broken.},
  file      = {:by-author/F/Ferreiro/2005_Ferreiro_32480.pdf:PDF},
  keywords  = {Readout},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Ferreti1981,
  author    = {Luca Ferretti and Vittorio Sgaramella},
  journal   = {Nucleic Acids Research},
  title     = {Spedfic and reversible inhibition of the blunt end joining activity of the {T4} {DNA} ligase},
  year      = {1981},
  pages     = {3695},
  file      = {:by-author/F/Ferreti/1981_Ferreti_3695.pdf:PDF},
  keywords  = {TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Presentation{Ferris2009,
  author    = {Jim Ferris},
  title     = {An RNA World Scenario for the Origins of Life: Montmorillonite Clay-Catalyzed Formation of RNA Oligomers},
  year      = {2009},
  file      = {2009_Ferris_slides.pdf:by-author/F/Ferris/2009_Ferris_slides.pdf:PDF},
  keywords  = {Origins of Life; RNA World},
  owner     = {saulius},
  timestamp = {2013.09.27},
  creationdate = {2013-09-27T00:00:00},
  url       = {http://hudsonvalleyrnaclub.org/course/rna_lecture2_ferris090909.pdf},
}

@Article{Ferro1977,
  author    = {Dino R. Ferro and Jan Hermans},
  journal   = {Acta Crystallographica Section A},
  title     = {A different best rigid-body molecular fit routine},
  year      = {1977},
  pages     = {345--347},
  volume    = {33},
  abstract  = {A different algorithm which gives a least-squares fit between two sets of atoms is described [cf. Nyburg (1974). Acta Cryst. B30, 251-253]. With this algorithm the coordinates of the moving set of atoms are changed only once.},
  doi       = {10.1107/S0567739477000862},
  file      = {:by-author/F/Ferro/1977_Ferro_345.pdf:PDF},
  groups    = {sg/Molecule superposion, sg/Superposition, sg/Bioinf. Algorithms},
  keywords  = {Algorithms; Structure Superposition; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://scripts.iucr.org/cgi-bin/paper?S0567739477000862},
}

@Article{Fersht2009,
  author    = {Fersht, Alan},
  journal   = {Proceedings of the National Academy of Sciences of the United States of America},
  title     = {The most influential journals: Impact Factor and Eigenfactor.},
  year      = {2009},
  pages     = {6883--4},
  volume    = {106},
  file      = {:by-author/F/Fersht/2009_Fersht_6883.pdf:PDF},
  groups    = {sg/Bibliometrics},
  keywords  = {Impact Factors},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Festersen,
  author    = {Festersen, S. and Elsen, A. and Runge, B. and Koops, C. T. and Seeck, O. H. and Deutsch, M. and Ocko, B. and Magnussen, O. M. and Murphy, B. M.},
  title     = {Potential-induced adlayer formation and crystal nucleation at the mercury-electrolyte interface},
  file      = {[PDF] from desy.de:by-author/F/Festersen/XXXX_Festersen.pdf:application/pdf},
  groups    = {sg/NAR2012},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://photon-science.desy.de/annual_report/files/2012/20122137.pdf},
  urldate   = {2015-08-31},
}

@Article{Fichtner1986,
  author    = {Konrad Fichtner},
  journal   = {Computers \& Mathematics with Applications},
  title     = {Non-space-group symmetry in crystallography},
  year      = {1986},
  issn      = {0898-1221},
  pages     = {751 - 762},
  volume    = {12},
  abstract  = {After presenting the basic ideas of the characterization of symmetries of a “classical crystal” with its three-dimensional periodicity, approaches are discussed to describing relevant features of certain crystal structures by additional symmetries. Application and usefulness of some conceptions of non-space-group symmetries are illustrated by examples. Polytype structures or \{OD\} structures in the sense of Dornberger-Schiff are discussed in more detail.},
  doi       = {http://dx.doi.org/10.1016/0898-1221(86)90421-9},
  file      = {1986_Fichtner_751.pdf:by-author/F/Fichtner/1986_Fichtner_751.pdf:PDF},
  keywords  = {Crystallography; Spacegroups; Symmetry},
  owner     = {saulius},
  timestamp = {2015.10.10},
  creationdate = {2015-10-10T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/0898122186904219},
}

@PhdThesis{Fielding2000,
  author           = {Roy Thomas Fielding},
  school           = {University of California, Irvine},
  title            = {Architectural styles and the design of network-based software architectures},
  year             = {2000},
  creationdate     = {2016-10-28T00:00:00},
  file             = {2000_Fielding.pdf:by-author/F/Fielding/2000_Fielding.pdf:PDF},
  groups           = {sg/Web sg/applications},
  keywords         = {Computer Science (CS); REST; Web Applications},
  modificationdate = {2023-07-17T15:43:25},
  owner            = {saulius},
  timestamp        = {2016.10.28},
  url              = {https://www.ics.uci.edu/~fielding/pubs/dissertation/top.htm},
}

@Article{Figueiredo2002,
  author    = {Figueiredo, M.A.T. and Jain, A.K.},
  journal   = {IEEE Trans. Pattern Anal. Mach. Intell.},
  title     = {Unsupervised learning of finite mixture models},
  year      = {2002},
  issn      = {0162-8828},
  month     = {Mar},
  number    = {3},
  pages     = {381–396},
  volume    = {24},
  doi       = {10.1109/34.990138},
  file      = {:by-author/F/Figueiredo/2002_Figueiredo_381.pdf:PDF},
  groups    = {am/Gaussian, am/Expectation maximisation},
  owner     = {andrius},
  publisher = {Institute of Electrical \& Electronics Engineers (IEEE)},
  timestamp = {2016.06.29},
  creationdate = {2016-06-29T00:00:00},
  url       = {http://dx.doi.org/10.1109/34.990138},
}

@Article{Figueras1996,
  author    = {John Figueras},
  journal   = {J. Chem. Inf. Comput. Sci.},
  title     = {Ring Perception Using Breadth-First Search},
  year      = {1996},
  note      = {From: http://search.cpan.org/~itub/Chemistry-Ring-0.20/lib/Chemistry/Ring/Find.pm 2009.06.29 1) Leach, A. R.; Dolata, D. P.; Prout, P. Automated Conformational Analysis and Structure Generation: Algorithms for Molecular Perception J. Chem. Inf. Comput. Sci. 1990, 30, 316-324 2) Figueras, J. Ring perception using breadth-first search. J. Chem. Inf. Comput. Sci. 1996, 36, 986-991. Ref. 2 is only used for find_ring, not for find_rings, because it has been shown that the overall SSSR method in ref 2 has bugs. Ref 1 inspired find_rings, which depends on find_ring.},
  pages     = {986--991},
  volume    = {36},
  abstract  = {Combining breadth-first search with new ideas for uncovering embedded rings in complex systems1 yields a very fast routine for ring perception. With large structures, the new routine is orders of magnitude faster than depth-first ring detection, a result expected on the basis of recent work that establishes polynomial order for BFS.},
  file      = {1996_Figueras_986.pdf:by-author/F/Figueras/1996_Figueras_986.pdf:PDF},
  keywords  = {Ring Perception},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Fillingame2000,
  author    = {Fillingame, R. H.},
  journal   = {Nature structural biology},
  title     = {Getting to the bottom of the F1-ATPase.},
  year      = {2000},
  pages     = {1002--4},
  volume    = {7},
  file      = {:by-author/F/Fillingame/2000_Fillingame_1002.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Manuscript{Findlay2002,
  author    = {Andrew Findlay},
  title     = {Security with LDAP},
  year      = {2002},
  keywords  = {Account Management; Computer Management; Computer Science (CS); Computer Security; LDAP},
  month     = {February},
  url       = {https://www.skills-1st.co.uk/papers/security-with-ldap-jan-2002/security-with-ldap.singlesided.pdf},
  abstract  = {It is possible to use LDAP as a Network Information Service as well as for the more traditional white-pages service. This requires support from operating systems and has new security implications. This paper examines how open-source implementations are rising to the challenge. This paper was first presented at the UKUUG Winter Conference in February 2002.},
  file      = {2002_Findlay.pdf:by-author/F/Findlay/2002_Findlay.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.05.06},
  creationdate = {2016-05-06T00:00:00},
}

@Article{Finet1998,
  author    = {Finet, S and Bonneté, F and Frouin, J and Provost, K and Tardieu, A},
  journal   = {European biophysics journal : EBJ},
  title     = {Lysozyme crystal growth, as observed by small angle X-ray scattering, proceeds without crystallization intermediates.},
  year      = {1998},
  pages     = {263--71},
  volume    = {27},
  abstract  = {A combination of small angle X-ray scattering and gel techniques was used to follow the kinetics of protein crystal growth as a function of time. Hen egg white lysozyme, at different protein concentrations, was used as a model system. A new sample holder was designed, in which supersaturation is induced in the presence of salt by decreasing the temperature. It had been shown previously that a decrease in temperature and/or an increase in crystallizing agent induces an increase in the attractive interactions present in the lysozyme solutions, the lysozyme remaining monomeric. In the present paper we show that similar behaviour is observed in NaCl when agarose gels are used. During crystal growth, special attention was paid to determine whether oligomers were formed as the protein in solution was incorporated in the newly formed crystals. From these first series of experiments, we did not find any indication of oligomer formation between monomer in solution and crystal. The results obtained are in agreement with the hypothesis that lysozyme crystals in NaCl grow by addition of monomeric particles.},
  file      = {Finet_1998_263.pdf:by-author/F/Finet/1998_Finet_263.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Finger2007,
  author    = {Finger, Larry W. and Kroeker, Martin and Toby, Brian H.},
  journal   = {Journal of Applied Crystallography},
  title     = {{\it DRAWxtl}, an open-source computer program to produce crystal structure drawings},
  year      = {2007},
  pages     = {188--192},
  volume    = {40},
  abstract  = {The computer program DRAWxtl produces crystal structure drawings in the form of an interactive screen representation, as well as VRML files for use on web pages and in classroom teaching, and creates input files for the popular Persistence of Vision Raytracer (POV-Ray) rendering program for publication-quality graphics, including generation of stereo pairs. DRAWxtl output produces the standard kinds of graphical representations: spheres, ellipsoids, bonds and polyhedra of any complexity. In addition, it can draw arrows to represent magnetic moments, show capped cones to indicate the location of lone-pair electrons and display Fourier contours in three dimensions. A unique feature of this program is the ability to plot incommensurately modulated and composite structures. This open-source program can be used with operating systems as diverse as Windows (9X, NT, 2000 and XP), Mac OS X, Linux and most other varieties of Unix.},
  doi       = {10.1107/S0021889806051557},
  file      = {2007_Finger_188.pdf:by-author/F/Finger/2007_Finger_188.pdf:PDF},
  keywords  = {Graphics; Software; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0021889806051557},
}

@Article{Fioravanti2007,
  author    = {Fioravanti, Emanuela and Vellieux, Frédéric M D and Amara, Patricia and Madern, Dominique and Weik, Martin},
  journal   = {Journal of synchrotron radiation},
  title     = {Specific radiation damage to acidic residues and its relation to their chemical and structural environment.},
  year      = {2007},
  pages     = {84--91},
  volume    = {14},
  abstract  = {Intense synchrotron radiation produces specific structural and chemical damage to crystalline proteins even at 100 K. Carboxyl groups of acidic residues (Glu, Asp) losing their definition is one of the major effects observed. Here, the susceptibilities to X-ray damage of acidic residues in tetrameric malate dehydrogenase from Haloarcula marismortui are investigated. The marked excess of acidic residues in this halophilic enzyme makes it an ideal target to determine how specific damage to acidic residues is related to their structural and chemical environment. Four conclusions are drawn. (i) Acidic residues interacting with the side-chains of lysine and arginine residues are less affected by radiation damage than those interacting with serine, threonine and tyrosine side-chains. This suggests that residues with higher pK(a) values are more vulnerable to damage than those with a lower pK(a). However, such a correlation was not found when calculated pK(a) values were inspected. (ii) Acidic side-chains located in the enzymatic active site are the most radiation-sensitive ones. (iii) Acidic residues in the internal cavity formed by the four monomers and those involved in crystal contacts appear to be particularly susceptible. (iv) No correlation was found between radiation susceptibility and solvent accessibility.},
  file      = {2007_Fioravanti_84.pdf:by-author/F/Fioravanti/2007_Fioravanti_84.pdf:PDF},
  keywords  = {Protein Physics; Radiation Damage},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Fiore2008,
  author    = {Anna di Fiore and Carlo Pedone and Jochen Antel and Harald Waldeck and Andreas Witte and Michael Wurl and Andrea Scozzafava and Claudiu T. Supuran and Giuseppina De Simone},
  journal   = {Bioorganic \& Medicinal Chemistry Letters},
  title     = {Carbonic anhydrase inhibitors: The X-ray crystal structure of ethoxzolamide complexed to human isoform II reveals the importance of thr200 and gln92 for obtaining tight-binding inhibitors},
  year      = {2008},
  pages     = {2669--2674},
  volume    = {18},
  abstract  = {Ethoxzolamide, an almost forgotten inhibitor of the metalloenzyme carbonic anhydrase (CA, EC 4.2.1.1), is the only classical inhibitor whose structure in adduct with any isoform was not reported yet. We report here the inhibition data of this molecule with the 12 catalytically active mammalian isozymes (CA I–CA XIV) and the X-ray crystal structure with the cytosolic, ubiquitous isoform CA II. These data are presumably useful for the design of novel CA inhibitors, targeting various CA isozymes, considering that ethoxzolamide was already the lead molecule to obtain the second generation inhibitors, dorzolamide and brinzolamide, clinically used antiglaucoma agents with topical action, as well as various other investigational agents.},
  doi       = {10.1016/j.bmcl.2008.03.023},
  file      = {:by-author/F/Fiore/2008_Fiore_2669.pdf:PDF},
  groups    = {sg/inhibitors, sg/hCA2},
  keywords  = {Carbonic Anhydrases; Ethoxzolamide; Inhibitors; Protein Crystallography},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/S0960894X08002989},
}

@Article{Fiorio2010,
  author    = {Fiorio, Carlo V. and Hajivassiliou, Vassilis A. and Phillips, Peter C. B.},
  journal   = {Econometrics Journal},
  title     = {Bimodal t-ratios: the impact of thick tails on inference},
  year      = {2010},
  issn      = {1368-423X},
  pages     = {271--289},
  volume    = {13},
  abstract  = {Summary  This paper studies the distribution of the classical t-ratio with data generated from distributions with no finite moments and shows how classical testing is affected by bimodality. A key condition in generating bimodality is independence of the observations in the underlying data-generating process (DGP). The paper highlights the strikingly different implications of lack of correlation versus statistical independence in DGPs with infinite moments and shows how standard inference can be invalidated in such cases, thereby pointing to the need for adapting estimation and inference procedures to the special problems induced by thick-tailed (TT) distributions. The paper presents theoretical results for the Cauchy case and develops a new distribution termed the ‘double-Pareto’, which allows the thickness of the tails and the existence of moments to be determined parametrically. It also investigates the relative importance of tail thickness in case of finite moments by using TT distributions truncated on a compact support, showing that bimodality can persist even in such cases. Simulation results highlight the dangers of relying on naive testing in the face of TT distributions. Novel density estimation kernel methods are employed, given that our theoretical results yield cases that exhibit density discontinuities.},
  doi       = {10.1111/j.1368-423X.2010.00315.x},
  file      = {:by-author/F/Fiorio/2010_Fiorio_271.pdf:PDF},
  keywords  = {Bimodality; Cauchy; Double Pareto; T Ratio; Thick Tails},
  owner     = {saulius},
  publisher = {Blackwell Publishing Ltd},
  timestamp = {2012.09.18},
  creationdate = {2012-09-18T00:00:00},
  url       = {http://dx.doi.org/10.1111/j.1368-423X.2010.00315.x},
}

@Article{Firman2000,
  author    = {Firman and Dutta and Weiserova and Janscak},
  journal   = {Molecular Biology Today},
  title     = {The Role of Subunit Assembly in the Functional Control of Type {I} Restriction-Modification Enzymes},
  year      = {2000},
  pages     = {35--41},
  file      = {:by-author/F/Firman/2000_Firman_35.pdf:PDF},
  keywords  = {TypeI},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Firman2000a,
  author    = {Firman, K. and Szczelkun, M. D.},
  journal   = {The EMBO journal},
  title     = {Measuring motion on DNA by the type I restriction endonuclease EcoR124I using triplex displacement.},
  year      = {2000},
  pages     = {2094--102},
  volume    = {19},
  abstract  = {The type I restriction enzyme EcoR124I cleaves DNA following extensive linear translocation dependent upon ATP hydrolysis. Using protein-directed displacement of a DNA triplex, we have determined the kinetics of one-dimensional motion without the necessity of measuring DNA or ATP hydrolysis. The triplex was pre-formed specifically on linear DNA, 4370 bp from an EcoR124I site, and then incubated with endonuclease. Upon ATP addition, a distinct lag phase was observed before the triplex-forming oligonucleotide was displaced with exponential kinetics. As the distance between type I and triplex sites was shortened, the lag time decreased whilst the displacement reaction remained exponential. This is indicative of processive DNA translocation followed by collision with the triplex and oligonucleotide displacement. A linear relationship between lag duration and inter-site distance gives a translocation velocity of 400+/-32 bp/s at 20 degrees C. Furthermore, the data can only be explained by bi-directional translocation. An endonuclease with only one of the two HsdR subunits responsible for motion could still catalyse translocation. The reaction is less processive, but can 'reset' in either direction whenever the DNA is released.},
  file      = {:by-author/F/Firman/2000_Firman_2094.pdf:PDF},
  keywords  = {TypeI},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{First2013,
  author    = {Eric L. First and Christodoulos A. Floudas},
  journal   = {Microporous and Mesoporous Materials},
  title     = {MOFomics: Computational pore characterization of metal–organic frameworks},
  year      = {2013},
  issn      = {1387-1811},
  pages     = {32--39},
  volume    = {165},
  abstract  = {Microporous materials, such as zeolites and metal–organic frameworks (MOFs), are commonly considered for shape-selective separations and catalysis. With the large number of known and hypothetical structures available, computational techniques are needed to identify the most promising structures for applications of interest. We have developed an automated computational framework based on optimization, geometry, and graph algorithms to fully characterize the three-dimensional pore structures of MOFs. Our methods automatically identify the portals, channels, and cages of a MOF and describe their geometry and connectivity. Furthermore, we calculate quantities of interest including pore size distribution, accessible volume, accessible surface area, pore limiting diameter, and largest cavity diameter. Our computational framework has been applied to over 800 experimental MOFs, including zeolitic imidazolate frameworks (ZIFs), and over 1600 hypothetical MOFs. MOFomics, an online database of pore characterizations and the first web tool for MOFs that allows user submissions, is made freely available to the scientific communit (http://helios.princeton.edu/mofomics/).},
  doi       = {10.1016/j.micromeso.2012.07.049},
  file      = {2013_First_32.pdf:by-author/F/First/2013_First_32.pdf:PDF},
  groups    = {sg/MOF, sg/NAR2012, sg/MOFs, am/MOFs},
  keywords  = {Citing COD; Metal-Organic Frameworks (MOF)},
  owner     = {saulius},
  timestamp = {2012.12.13},
  creationdate = {2012-12-13T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/S1387181112004817},
}

@Article{Fiscella1998,
  author    = {Fiscella, R G},
  journal   = {American journal of health-system pharmacy : AJHP : official journal of the American Society of Health-System Pharmacists},
  title     = {Costs of glaucoma medications.},
  year      = {1998},
  pages     = {272--5},
  volume    = {55},
  file      = {1998_Fiscella_272.pdf:by-author/F/Fiscella/1998_Fiscella_272.pdf:PDF},
  groups    = {sg/medicine},
  keywords  = {Carbonic Anhydrases},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Fischer2010,
  author    = {Fischer, H. and de Oliveira Neto, M. and Napolitano, H.B. and Polikarpov, I. and Craievich, A.F.},
  journal   = {Journal of Applied Crystallography},
  title     = {Determination of the molecular weight of proteins in solution from a single small-angle X-ray scattering measurement on a relative scale},
  year      = {2010},
  pages     = {101--109},
  volume    = {43},
  abstract  = {This paper describes a new and simple method to determine the molecular weight of proteins in dilute solution, with an error smaller than ~10%, by using the experimental data of a single small-angle X-ray scattering (SAXS) curve measured on a relative scale. This procedure does not require the measurement of SAXS intensity on an absolute scale and does not involve a comparison with another SAXS curve determined from a known standard protein. The proposed procedure can be applied to monodisperse systems of proteins in dilute solution, either in monomeric or multimeric state, and it has been successfully tested on SAXS data experimentally determined for proteins with known molecular weights. It is shown here that the molecular weights determined by this procedure deviate from the known values by less than 10% in each case and the average error for the test set of 21 proteins was 5.3%. Importantly, this method allows for an unambiguous determination of the multimeric state of proteins with known molecular weights.},
  doi       = {10.1107/S0021889809043076},
  file      = {:by-author/F/Fischer/2010_Fischer_101.pdf:PDF;:by-author/F/Fisher/2010_Fisher_101.pdf:PDF},
  keywords  = {Molecular Weight (MW); SAXS},
  owner     = {em},
  timestamp = {2013.06.28},
  creationdate = {2013-06-28T00:00:00},
}

@Article{Fischer2004,
  author    = {Fischer, Hannes and Polikarpov, Igor and Craievich, Aldo F.},
  journal   = {Protein science : a publication of the Protein Society},
  title     = {Average protein density is a molecular-weight-dependent function.},
  year      = {2004},
  pages     = {2825--8},
  volume    = {13},
  abstract  = {The mass density of proteins is a relevant basic biophysical quantity. It is also a useful input parameter, for example, for three-dimensional structure determination by protein crystallography and studies of protein oligomers in solution by analytic ultracentrifugation. We have performed a critical analysis of published, theoretical, and experimental investigations about this issue and concluded that the average density of proteins is not a constant as often assumed. For proteins with a molecular weight below 20 kDa, the average density exhibits a positive deviation that increases for decreasing molecular weight. A simple molecular-weight-depending function is proposed that provides a more accurate estimate of the average protein density.},
  file      = {:by-author/F/Fischer/2004_Fischer_2825.pdf:PDF},
  keywords  = {Density; Grow Krystal},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Fischer1988,
  author    = {Reinhard X. Fischer and Ekkehart Tillmanns},
  journal   = {Acta Crystallographica Section C},
  title     = {The equivalent isotropic displacement factor},
  year      = {1988},
  pages     = {775--776},
  volume    = {44},
  doi       = {10.1107/S0108270187012745},
  file      = {:by-author/F/Fischer/1988_Fischer_775.pdf:PDF},
  keywords  = {Atomic Displacement Parameters},
  owner     = {andrius},
  timestamp = {2013.04.14},
  creationdate = {2013-04-14T00:00:00},
}

@Presentation{Fisher2007,
  author    = {Robert D. Fisher and Heidi Scubert},
  title     = {Phasing in Macromolecular Crystallography},
  year      = {2007},
  file      = {:by-author/F/Fisher/2007_Fisher.ppt:PPT},
  keywords  = {Presentations},
  owner     = {saulius},
  timestamp = {2015.03.03},
  creationdate = {2015-03-03T00:00:00},
}

@Article{Fisher2012,
  author    = {Fisher, S. Zoë and Aggarwal, Mayank and Kovalevsky, Andrey Y. and Silverman, David N. and McKenna, Robert},
  journal   = {J Am Chem Soc.},
  title     = {Neutron diffraction of acetazolamide-bound human carbonic anhydrase II reveals atomic details of drug binding},
  year      = {2012},
  pages     = {14726--14729},
  volume    = {134},
  abstract  = {Carbonic anhydrases (CAs) catalyze the hydration of CO2 forming HCO3− and a proton, an important reaction for many physiological processes including respiration, fluid secretion, and pH regulation. As such, CA isoforms are prominent clinical targets for treating various diseases. The clinically used acetazolamide (AZM) is a sulfonamide that binds with high affinity to human CA isoform II (HCA II). There are several X-ray structures available of AZM bound to various CA isoforms, but these complexes do not show the charged state of AZM, or hydrogen (H) atom positions of the protein and solvent. Neutron diffraction is a useful technique for directly observing H atoms and the mapping of H-bonding networks that can greatly contribute to rational drug design. To this end the neutron structure of H/D exchanged HCA II crystals in complex with AZM was determined. The structure reveals the molecular details of AZM binding and the charged state of the bound drug. This represents the first determined neutron structure of a clinically used drug bound to its target.},
  doi       = {10.1021/ja3068098},
  file      = {:by-author/F/Fisher/2012_Fisher_14726.pdf:PDF},
  groups    = {sg/hCA2},
  keywords  = {AZM; Neutron Diffraction; Protein Crystallization; {hCA}2},
  owner     = {em},
  timestamp = {2014.02.13},
  creationdate = {2014-02-13T00:00:00},
}

@Article{Fisher2005,
  author    = {Fisher, Zoë and Hernandez Prada, Jose A and Tu, Chingkuang and Duda, David and Yoshioka, Craig and An, Haiqian and Govindasamy, Lakshmanan and Silverman, David N and McKenna, Robert},
  journal   = {Biochemistry},
  title     = {Structural and kinetic characterization of active-site histidine as a proton shuttle in catalysis by human carbonic anhydrase II.},
  year      = {2005},
  pages     = {1097--105},
  volume    = {44},
  abstract  = {In the catalysis of the hydration of carbon dioxide and dehydration of bicarbonate by human carbonic anhydrase II (HCA II), a histidine residue (His64) shuttles protons between the zinc-bound solvent molecule and the bulk solution. To evaluate the effect of the position of the shuttle histidine and pH on proton shuttling, we have examined the catalysis and crystal structures of wild-type HCA II and two double mutants: H64A/N62H and H64A/N67H HCA II. His62 and His67 both have their side chains extending into the active-site cavity with distances from the zinc approximately equivalent to that of His64. Crystal structures were determined at pH 5.1-10.0, and the catalysis of the exchange of (18)O between CO(2) and water was assessed by mass spectrometry. Efficient proton shuttle exceeding a rate of 10(5) s(-)(1) was observed for histidine at positions 64 and 67; in contrast, relatively inefficient proton transfer at a rate near 10(3) s(-)(1) was observed for His62. The observation, in the crystal structures, of a completed hydrogen-bonded water chain between the histidine shuttle residue and the zinc-bound solvent does not appear to be required for efficient proton transfer. The data suggest that the number of intervening water molecules between the donor and acceptor supporting efficient proton transfer in HCA II is important, and furthermore suggest that a water bridge consisting of two intervening water molecules is consistent with efficient proton transfer.},
  file      = {2005_Fisher_1097.pdf:by-author/F/Fisher/2005_Fisher_1097.pdf:PDF},
  groups    = {sg/hCA2},
  keywords  = {Carbonic Anhydrases},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Fitelson2008,
  author    = {Branden Fitelson and Neil Thomason},
  journal   = {The Australasian Journal of Logic},
  title     = {Bayesians sometimes cannot ignore even very implausible theories (even ones that have not yet been thought of )},
  year      = {2008},
  pages     = {25--36},
  volume    = {6},
  abstract  = {In applying Bayes’s theorem to the history of science, Bayesians sometimes assume – often without argument – that they can safely ignore very implausible theories. This assumption is false, both in that it can seriously distort the history of science as well as the mathematics and the applicability of Bayes’s theorem. There are intuitively very plausible counter-examples. In fact, one can ignore very implausible or unknown theories only if at least one of two conditions is satisfied: (i) one is certain that there are no unknown theories which explain the phenomenon in question, or (ii) the likelihood of at least one of the known theories used in the calculation of the posterior is reasonably large. Often in the history of science, a very surprising phenomenon is observed, and neither of these criteria is satisfied.},
  file      = {:by-author/F/Fitelson/2008_Fitelson_25.pdf:PDF},
  groups    = {sg/Bayesian},
  keywords  = {Bayesian Statistics; Criticism},
  owner     = {saulius},
  timestamp = {2012.10.03},
  creationdate = {2012-10-03T00:00:00},
  url       = {http://philosophy.unimelb.edu.au/ajl/2008/2008_2.pdf},
}

@Manuscript{Fitelson2007,
  author    = {Branden Fitelson and Neil Thomason},
  title     = {Bayesians sometimes cannot ignore even very implausible theories (even ones that have not yet been thought of)},
  year      = {2007},
  keywords  = {Bayesian Statistics; Criticism},
  url       = {http://fitelson.org/hiti.pdf},
  abstract  = {In applying Bayes’s theorem to the history of science, Bayesians sometimes assume – often without argument – that they can safely ignore very implausible theories. This assumption is false, both in that it can seriously distort the history of science as well as the mathematics and the applicability of Bayes’s theorem. There are intuitively very plausible counter-examples. In fact, one can ignore very implausible or unknown theories only if at least one of two conditions is satisfied: (i) one is certain that there are no unknown theories which explain the phenomenon in question, or (ii) the likelihood of at least one of the known theories used in the calculation of the posterior is reasonably large. Often in the history of science, a very surprising phenomenon is observed, and neither of these criteria is satisfied.},
  file      = {:by-author/F/Fitelson/2007_Fitelson.pdf:PDF},
  groups    = {sg/Bayesian},
  owner     = {saulius},
  timestamp = {2012.09.30},
  creationdate = {2012-09-30T00:00:00},
}

@Article{Fitz2007,
  author    = {Daniel Fitz and Hannes Reiner and Bernd Michael Rode},
  journal   = {Pure and Applied Chemistry},
  title     = {Chemical evolution toward the origin of life},
  year      = {2007},
  pages     = {2101--2117},
  volume    = {79},
  abstract  = {Numerous hypotheses about how life on earth could have started can be found in the literature. In this article, we give an overview about the most widespread ones and try to point out which of them might have occurred on the primordial earth with highest probability from a chemical point of view. The idea that a very early stage of life was the "RNA world" encounters crucial problems concerning the formation of its building blocks and their stability in a prebiotic environment. Instead, it seems much more likely that a "peptide world" originated first and that RNA and DNA took up their part at a much later stage. It is shown that amino acids and peptides can be easily formed in a realistic primordial scenario and that these biomolecules can start chemical evolution without the help of RNA. The origin of biohomochirality seems strongly related to the most probable formation of the first peptides via the salt-induced peptide formation (SIPF) reaction.},
  doi       = {10.1351/pac200779122101},
  file      = {2007_Fitz_2101.pdf:by-author/F/Fitz/2007_Fitz_2101.pdf:PDF},
  keywords  = {Amino Acids; Chemical Evolution; Chemical Prebiotic; Evolution; Origin of Life; Peptides; Prebiotic Chemistry},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@InBook{Fitzgerald2006,
  author           = {P. M. D. Fitzgerald and J. D. Westbrook and P. E. Bourne and B. McMahon and K. D. Watenpaugh and H. M. Berman},
  chapter          = {3.6. Classification and use of macromolecular data},
  editor           = {S. R. Hall and B. McMahon},
  pages            = {144--198},
  publisher        = {International Union of Crystallography},
  title            = {International Tables for Crystallography},
  year             = {2006},
  volume           = {G},
  creationdate     = {2008-07-28T00:00:00},
  doi              = {10.1107/97809553602060000107},
  file             = {2006_Fitzgerald_144.pdf:by-author/F/Fitzgerald/2006_Fitzgerald_144.pdf:PDF},
  keywords         = {CIF; Databases; PDB; {mmCIF}},
  modificationdate = {2023-08-07T10:23:05},
  owner            = {saulius},
  timestamp        = {2008.07.28},
}

@InBook{Fitzgerald2006a,
  author           = {P. M. D. Fitzgerald and J. D. Westbrook and P. E. Bourne and B. McMahon and K. D. Watenpaugh and H. M. Berman},
  chapter          = {4.5. Macromolecular dictionary (mmCIF)},
  editor           = {S. R. Hall and B. McMahon},
  pages            = {295--443},
  publisher        = {International Union of Crystallography},
  title            = {International Tables for Crystallography},
  year             = {2006},
  volume           = {G},
  creationdate     = {2008-07-28T00:00:00},
  doi              = {10.1107/97809553602060000745},
  file             = {2006_Fitzgerald_295.pdf:by-author/F/Fitzgerald/2006_Fitzgerald_295.pdf:PDF},
  groups           = {sg/CIF, am/CIF},
  keywords         = {CIF; {mmCIF}},
  modificationdate = {2023-08-07T10:23:05},
  owner            = {saulius},
  timestamp        = {2008.07.28},
}

@Article{Flack2013,
  author    = {Flack, Howard D.},
  journal   = {Acta crystallographica. Section C, Crystal structure communications},
  title     = {Absolute-structure reports.},
  year      = {2013},
  pages     = {803--7},
  volume    = {69},
  abstract  = {All the 139 noncentrosymmetric crystal structures published in Acta Crystallographica Section C between January 2011 and November 2012 inclusive have been used as the basis of a detailed study of the reporting of absolute structure. These structure determinations cover a wide range of space groups, chemical composition and resonant-scattering contribution. Defining A and D as the average and difference of the intensities of Friedel opposites, their level of fit has been examined using 2AD and selected-D plots. It was found, regardless of the expected resonant-scattering contribution to Friedel opposites, that the Friedel-difference intensities are often dominated by random uncertainty and systematic error. An analysis of data collection strategy is provided. It is found that crystal-structure determinations resulting in a Flack parameter close to 0.5 may not necessarily be from crystals twinned by inversion. Friedifstat is shown to be a robust estimator of the resonant-scattering contribution to Friedel opposites, very little affected by the particular space group of a structure nor by the occupation of special positions. There is considerable confusion in the text of papers presenting achiral noncentrosymmetric crystal structures. Recommendations are provided for the optimal way of treating noncentrosymmetric crystal structures for which the experimenter has no interest in determining the absolute structure.},
  doi       = {10.1107/S0108270113014789},
  file      = {:by-author/F/Flack/2013_Flack_803.pdf:PDF},
  owner     = {saulius},
  timestamp = {2014.03.23},
  creationdate = {2014-03-23T00:00:00},
}

@Article{Flack2008,
  author    = {Flack, H D and Bernardinelli, G},
  journal   = {Acta crystallographica. Section A, Foundations of crystallography},
  title     = {Applications and properties of the Bijvoet intensity ratio.},
  year      = {2008},
  pages     = {484--93},
  volume    = {64},
  file      = {2008_Flack_484.pdf:by-author/F/Flack/2008_Flack_484.pdf:PDF},
  keywords  = {Flack Parameter; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Flack2008a,
  author    = {Flack, H. D. and Bernardinelli, G.},
  journal   = {Chirality},
  title     = {The use of X-ray crystallography to determine absolute configuration.},
  year      = {2008},
  pages     = {681--90},
  volume    = {20},
  abstract  = {Essential background on the determination of absolute configuration by way of single-crystal X-ray diffraction (XRD) is presented. The use and limitations of an internal chiral reference are described. The physical model underlying the Flack parameter is explained. Absolute structure and absolute configuration are defined and their similarities and differences are highlighted. The necessary conditions on the Flack parameter for satisfactory absolute-structure determination are detailed. The symmetry and purity conditions for absolute-configuration determination are discussed. The physical basis of resonant scattering is briefly presented and the insights obtained from a complete derivation of a Bijvoet intensity ratio by way of the mean-square Friedel difference are exposed. The requirements on least-squares refinement are emphasized. The topics of right-handed axes, XRD intensity measurement, software, crystal-structure evaluation, errors in crystal structures, and compatibility of data in their relation to absolute-configuration determination are described. Characterization of the compounds and crystals by the physicochemical measurement of optical rotation, CD spectra, and enantioselective chromatography are presented. Some simple and some complex examples of absolute-configuration determination using combined XRD and CD measurements, using XRD and enantioselective chromatography, and in multiply-twinned crystals clarify the technique. The review concludes with comments on absolute-configuration determination from light-atom structures.},
  file      = {:by-author/F/Flack/2008_Flack_681.pdf:PDF},
  keywords  = {Absolute Configuration; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Flack2000,
  author           = {H. D. Flack and G. Bernardinelli},
  journal          = {Journal of Applied Crystallography},
  title            = {Reporting and evaluating absolute-structure and absolute-configuration determinations},
  year             = {2000},
  pages            = {1143--1148},
  volume           = {33},
  abstract         = {Detailed practical and numerical information is provided for undertaking and evaluating absolute-structure and absolute-configuration determinations. The interpretation of numerical values of x, the Flack [Acta Cryst. (1983), A39, 876-881] parameter, and its standard uncertainty u are explained in terms of the inversion-distinguishing power. Moreover, the conditions to obtain reliable values of x(u) are detailed. Further explanatory material is provided on the use of right-handed axes, valid intensity data, the application to macromolecular structures, the dangers of polar-dispersion errors, Euclidean normalizers of space groups, the detection and reporting of molecular symmetry, enantiopurity and optical activity in solution. New CIF data names are introduced.},
  creationdate     = {2008-07-28T00:00:00},
  doi              = {10.1107/S0021889800007184},
  file             = {2000_Flack_1143.pdf:by-author/F/Flack/2000_Flack_1143.pdf:PDF},
  keywords         = {CIF; Crystallography; Flack Parameter; X-ray Crystallography},
  modificationdate = {2023-08-07T10:23:05},
  owner            = {saulius},
  timestamp        = {2008.07.28},
  url              = {http://journals.iucr.org/j/issues/2000/04/00/ks0021/index.html},
}

@Article{Flack1999,
  author    = {Flack, H. D. and Bernardinelli, G.},
  journal   = {Acta crystallographica. Section A, Foundations of crystallography},
  title     = {Absolute structure and absolute configuration.},
  year      = {1999},
  pages     = {908--915},
  volume    = {55},
  file      = {1999_Flack_908.pdf:by-author/F/Flack/1999_Flack_908.pdf:PDF},
  keywords  = {Flack Parameter; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Flack1980,
  author    = {Flack, H. D. and Vincent, M. G. and Vincent, J. A.},
  journal   = {Acta Crystallographica Section A},
  title     = {Testing for serial correlation in intensity data},
  year      = {1980},
  pages     = {495--496},
  volume    = {36},
  abstract  = {An example of the use of the Durbin-Watson d statistic to test for positive and negative serial correlation is presented. It is found that the diffractometer data tested do not suffer from serial correlation.},
  doi       = {10.1107/S0567739480001040},
  file      = {:by-author/F/Flack/1980_Flack_495.pdf:PDF},
  keywords  = {Refinement; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0567739480001040},
}

@Article{Flajolet1990,
  author    = {Flajolet, P.},
  journal   = {Computing},
  title     = {On Adaptive Sampling},
  year      = {1990},
  pages     = {391--400},
  volume    = {43},
  abstract  = {We analyze the storage/accuracy trade-off of an adaptive sampling algorithm due to Wegman that makes it possible to evaluate probabilistically the number of distinct elements in a large file stored on disk.},
  doi       = {10.1007/BF02241657},
  file      = {:by-author/F/Flajolet/1990_Flajolet_391.pdf:PDF},
  groups    = {am/Approximate counting},
  keywords  = {Adaptive Sampling; Algorithms},
  owner     = {andrius},
  timestamp = {2012.05.07},
  creationdate = {2012-05-07T00:00:00},
  url       = {http://algo.inria.fr/flajolet/Publications/Flajolet90.pdf},
}

@Article{Flajolet1985a,
  author    = {Philippe Flajolet},
  journal   = {BIT},
  title     = {Approximate Counting: A Detailed Analysis},
  year      = {1985},
  pages     = {113--134},
  file      = {:by-author/F/Flajolet/1985_Flajolet_113.pdf:PDF},
  groups    = {am/Approximate counting},
  owner     = {andrius},
  timestamp = {2012.11.26},
  creationdate = {2012-11-26T00:00:00},
}

@Article{Flajolet1985,
  author    = {Flajolet, Philippe and Martin, G. Nigel},
  journal   = {Journal of Computer And System Sciences},
  title     = {Probabilistic Counting Algorithms for Data Base Applications},
  year      = {1985},
  pages     = {182--209},
  abstract  = {This paper introduces a class of probabilistic counting algorithms with which one can estimate the number of distinct elements in a large collection of data (typically a large file stored on disk) in a single pass using only a small additional storage (typically less than a hundred binary words) and only a few operations per element scanned. The algorithms are based on statistical observations made on bits of hashed values of records. They are by construction totally insensitive to the replicative structure of elements in the file; they can be used in the context of distributed systems without any degradation of performances and prove especially useful in the context of data bases query optimisation.},
  file      = {:by-author/F/Flajolet/1985_Flajolet_182.pdf:PDF},
  groups    = {am/Approximate counting},
  keywords  = {Adaptive Sampling; Algorithms},
  owner     = {andrius},
  timestamp = {2012.05.07},
  creationdate = {2012-05-07T00:00:00},
}

@Manuscript{Flatt2007,
  author    = {Matthew Flatt},
  title     = {Inside PLT MzScheme},
  year      = {2007},
  keywords  = {Computer Science (CS); Garbage Collectors},
  file      = {:by-author/F/Flatt/2007_Flatt.pdf:PDF},
  groups    = {sg/Garbage collectors},
  number    = {December},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Fletcher2003,
  author    = {Fletcher, Graham and Mason, Sean and Terrett, Jon and Soloviev, Mikhail},
  journal   = {Journal of nanobiotechnology},
  title     = {Self-assembly of proteins and their nucleic acids.},
  year      = {2003},
  pages     = {1},
  volume    = {1},
  abstract  = {We have developed an artificial protein scaffold, herewith called a protein vector, which allows linking of an in-vitro synthesised protein to the nucleic acid which encodes it through the process of self-assembly. This protein vector enables the direct physical linkage between a functional protein and its genetic code. The principle is demonstrated using a streptavidin-based protein vector (SAPV) as both a nucleic acid binding pocket and a protein display system. We have shown that functional proteins or protein domains can be produced in vitro and physically linked to their DNA in a single enzymatic reaction. Such self-assembled protein-DNA complexes can be used for protein cloning, the cloning of protein affinity reagents or for the production of proteins which self-assemble on a variety of solid supports. Self-assembly can be utilised for making libraries of protein-DNA complexes or for labelling the protein part of such a complex to a high specific activity by labelling the nucleic acid associated with the protein. In summary, self-assembly offers an opportunity to quickly generate cheap protein affinity reagents, which can also be efficiently labelled, for use in traditional affinity assays or for protein arrays instead of conventional antibodies.},
  file      = {Fletcher_2003_1.pdf:by-author/F/Fletcher/2003_Fletcher_1.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Floresta2013a,
  author    = {Floresta, D.L. and Ardisson, J.D. and Fagundes, M. and Fabris, J.D. and Macedo, W.A.A.},
  journal   = {Hyperfine Interactions},
  title     = {Oxidation states of iron as an indicator of the techniques used to burn clays and handcraft archaeological {T}upiguarani ceramics by ancient human groups in {M}inas {G}erais, {B}razil},
  year      = {2013},
  issn      = {0304-3843},
  pages     = {1--9},
  abstract  = {Ceramics of the Tupiguarani Tradition typically have in common the burning characteristics, their forms and decoration motifs. Dating such ceramic pieces with the radiocarbon method indicate that these artifacts were probably handcrafted between 1,500 and 500 years before the present. Fragments ceramic utensils were collected in the archaeological site of Beltrão, in the municipality of Corinto, state of Minas Gerais, Brazil. A fragment of about 50 mm in diameter and 15 mm thick, with a color gradation across the ceramic wall ranging from red, on one side, grayish, in the middle, and orange, on the opposite side, was selected for a more detailed examination. The fragment was transversely cut and a series of subsamples were separated from different points along the piece wall, in layer segments of ∼3 mm. All subsamples were analyzed with Mössbauer spectroscopy at room temperature and 80 K. Results reveal that hematite is the magnetically ordered phase. A Fe2+ component (relative spectral area, 50 %) appears for the grayish subsample. According to these first results, the red subsample seems to be the side that had direct contact with fire used to burn the precursor clay in air. The grayish middle layer is probably due to the clay mixed with some ashes. Mössbauer data reveal that the orange layer, corresponding to the opposite side of the ceramic relatively to the direct fire, does contain about the same Fe2+ :Fe3+ ratio but much lower proportion of α-Fe2 O3 than the red layer.},
  doi       = {10.1007/s10751-012-0743-z},
  file      = {:by-author/F/Floresta/2013_Floresta_1.pdf:PDF},
  keywords  = {Citing COD},
  owner     = {andrius},
  publisher = {Springer Netherlands},
  timestamp = {2013.02.19},
  creationdate = {2013-02-19T00:00:00},
}

@Article{Floresta2015,
  author    = {Floresta, D.L. and Fagundes, M. and Fabris, J.D. and Ardisson, J.D.},
  journal   = {Hyperfine Interactions},
  title     = {Iron-containing pigment from an archaeological rupestrian painting of the Planalto Tradition in Minas Gerais, Brazil},
  year      = {2015},
  issn      = {0304-3843},
  pages     = {29--40},
  volume    = {232},
  doi       = {10.1007/s10751-015-1182-4},
  file      = {[PDF] from researchgate.net:by-author/F/Floresta/2015_Floresta_29.pdf:PDF},
  groups    = {sg/JAC2009, sg/NAR2012},
  keywords  = {Archaeometry; CEMS; Iron Oxides; Mössbauer Spectrometry; Rock Art},
  language  = {English},
  owner     = {saulius},
  publisher = {Springer International Publishing},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://www.researchgate.net/profile/Jose_Fabris/publication/276430636_Iron-containing_pigment_from_an_archaeological_rupestrian_painting_of_the_Planalto_Tradition_in_Minas_Gerais_Brazil/links/555cf6e508ae6f4dcc8bd230.pdf},
  urldate   = {2015-08-31},
}

@Article{Floresta2014,
  author    = {Floresta, D. L. and Ardisson, J. D. and Fagundes, M. and Fabris, J. D. and Macedo, W. A. A.},
  journal   = {Hyperfine Interactions},
  title     = {Oxidation states of iron as an indicator of the techniques used to burn clays and handcraft archaeological tupiguarani ceramics by ancient human groups in minas gerais, brazil},
  year      = {2014},
  pages     = {121--129},
  volume    = {224},
  file      = {[PDF] from beijing.com.cn:by-author/F/Floresta/2014_Floresta_121.pdf:PDF;Snapshot:by-author/F/Floresta/2014_Floresta_121.html:URL},
  groups    = {sg/JAC2009, sg/NAR2012},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://link.springer.com/article/10.1007/s10751-012-0743-z},
  urldate   = {2015-08-31},
}

@Article{Floresta2013,
  author    = {Floresta, D. L. and Fagundes, M. and Fabris, J. D. and Ardisson, J. D.},
  title     = {Nuclear gamma resonance absorption (moessbauer) spectroscopy as an archaeometric technique to assess chemical states of iron in a tupiguarani ceramic artifact from corinto, minas gerais, brazil},
  year      = {2013},
  file      = {[PDF] from iaea.org:by-author/F/Floresta/2013_Floresta.pdf:PDF},
  groups    = {sg/JAC2009, sg/NAR2012},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://www.iaea.org/inis/collection/NCLCollectionStore/_Public/45/110/45110539.pdf},
  urldate   = {2015-08-31},
}

@Article{Flower1996,
  author    = {Flower, D R},
  journal   = {The Biochemical journal},
  title     = {The lipocalin protein family: structure and function.},
  year      = {1996},
  pages     = {1--14},
  volume    = {318 ( Pt 1)},
  abstract  = {The lipocalin protein family is a large group of small extracellular proteins. The family demonstrates great diversity at the sequence level; however, most lipocalins share three characteristic conserved sequence motifs, the kernel lipocalins, while a group of more divergent family members, the outlier lipocalins, share only one. Belying this sequence dissimilarity, lipocalin crystal structures are highly conserved and comprise a single eight-stranded continuously hydrogen-bonded antiparallel beta-barrel, which encloses an internal ligand-binding site. Together with two other families of ligand-binding proteins, the fatty-acid-binding proteins (FABPs) and the avidins, the lipocalins form part of an overall structural superfamily: the calycins. Members of the lipocalin family are characterized by several common molecular-recognition properties: the ability to bind a range of small hydrophobic molecules, binding to specific cell-surface receptors and the formation of complexes with soluble macromolecules. The varied biological functions of the lipocalins are mediated by one or more of these properties. In the past, the lipocalins have been classified as transport proteins; however, it is now clear that the lipocalins exhibit great functional diversity, with roles in retinol transport, invertebrate cryptic coloration, olfaction and pheromone transport, and prostaglandin synthesis. The lipocalins have also been implicated in the regulation of cell homoeostasis and the modulation of the immune response, and, as carrier proteins, to act in the general clearance of endogenous and exogenous compounds.},
  file      = {Flower_1996_1-Lipocalin_family.pdf:by-author/F/Flower/1996_Flower_1.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Presentation{Fluri2002,
  author    = {Beat Fluri},
  title     = {System Software},
  year      = {2002},
  file      = {:by-author/F/Fluri/2002_Fluri_slides.pdf:PDF},
  keywords  = {Computer Science (CS); Operating Systems},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Lecture{Fluri2002a,
  author    = {Beat Fluri and Jürg Gutknecht},
  title     = {System-Software},
  year      = {2002},
  file      = {:by-author/F/Fluri/2002_Fluri.pdf:PDF},
  keywords  = {Computer Science (CS); Operating Systems},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Foadi2011,
  author    = {Foadi, James and Evans, Gwyndaf},
  journal   = {Acta crystallographica. Section A, Foundations of crystallography},
  title     = {On the allowed values for the triclinic unit-cell angles.},
  year      = {2011},
  pages     = {93--5},
  volume    = {67},
  file      = {2011_Foadi_93.pdf:by-author/F/Foadi/2011_Foadi_93.pdf:PDF},
  keywords  = {Spacegroups; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Manuscript{Fober2009,
  author           = {Thomas Fober and Eyke Hüllermeier},
  title            = {Fuzzy modeling of labeled point cloud superposition for the comparison of protein binding sites},
  year             = {2009},
  keywords         = {Structure Superposition},
  creationdate     = {2012-05-15T00:00:00},
  file             = {:by-author/F/Fober/2009_Fober.pdf:PDF},
  groups           = {sg/Molecule superposion, sg/Superposition, sg/Bioinf. Algorithms},
  modificationdate = {2024-05-12T14:25:08},
  owner            = {saulius},
  timestamp        = {2012.05.15},
}

@Article{Fogolari2005,
  author    = {Fogolari, Federico and Tosatto, Silvio C E},
  journal   = {Protein science : a publication of the Protein Society},
  title     = {Application of MM/PBSA colony free energy to loop decoy discrimination: toward correlation between energy and root mean square deviation.},
  year      = {2005},
  pages     = {889--901},
  volume    = {14},
  abstract  = {Accurate free energy estimation is needed in many predictive tasks. The molecular mechanics/Poisson-Boltzmann solvent accessible surface area (MM/PBSA) approach has proven to be accurate. However, the correlation between the estimated free energy and the distance (e.g., root mean square deviation [RMSD]) from the most stable conformation is hindered by the strong free energy dependence on minor conformational variations. In this paper, a protocol for MM/PBSA free energy estimation is designed and tested on several loop decoy sets. We show that further integration of MM/PBSA free energy estimator with the colony energy approach makes the correlation between the free energy and RMSD from the native structure apparent, for the test sets on which it could be applied. Our results suggest that (1) the MM/PBSA free energy estimator is able to detect native-like structures for most decoy sets, and (2) application of the colony energy approach greatly hampers the MM/energy strong dependence on minor conformational changes.},
  file      = {2005_Fogolari_889.pdf:by-author/F/Fogolari/2005_Fogolari_889.pdf:PDF},
  keywords  = {Poisson-Boltzmann eq; Protein Physics; Solvatation},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Fokine2003,
  author    = {Fokine, Andrei and Lunina, Natalia and Lunin, Vladimir and Urzhumtsev, Alexandre},
  journal   = {Acta Crystallographica Section D},
  title     = {Connectivity-based {\it ab initio} phasing at different solvent levels},
  year      = {2003},
  pages     = {850--858},
  volume    = {59},
  doi       = {10.1107/S0907444903004359},
  file      = {fw0023.pdf:by-author/F/Fokine/2003_Fokine_850.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444903004359},
}

@Article{Fomel,
  author    = {Fomel, Sergey and Claerbout, Jon F.},
  title     = {Reproducible research},
  file      = {Fomel and Claerbout - Reproducible Research.pdf:by-author/F/Fomel/XXXX_Fomel.pdf:application/pdf},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://www.computer.org/csdl/mags/cs/2009/01/mcs2009010005.pdf},
  urldate   = {2015-06-06},
}

@Article{Fonfara2012,
  author    = {Fonfara, Ines and Curth, Ute and Pingoud, Alfred and Wende, Wolfgang},
  journal   = {Nucleic acids research},
  title     = {Creating highly specific nucleases by fusion of active restriction endonucleases and catalytically inactive homing endonucleases.},
  year      = {2012},
  pages     = {847--60},
  volume    = {40},
  abstract  = {Zinc-finger nucleases and TALE nucleases are produced by combining a specific DNA-binding module and a non-specific DNA-cleavage module, resulting in nucleases able to cleave DNA at a unique sequence. Here a new approach for creating highly specific nucleases was pursued by fusing a catalytically inactive variant of the homing endonuclease I-SceI, as DNA binding-module, to the type IIP restriction enzyme PvuII, as cleavage module. The fusion enzymes were designed to recognize a composite site comprising the recognition site of PvuII flanked by the recognition site of I-SceI. In order to reduce activity on PvuII sites lacking the flanking I-SceI sites, the enzymes were optimized so that the binding of I-SceI to its sites positions PvuII for cleavage of the composite site. This was achieved by optimization of the linker and by introducing amino acid substitutions in PvuII which decrease its activity or disturb its dimer interface. The most specific variant showed a more than 1000-fold preference for the addressed composite site over an unaddressed PvuII site. These results indicate that using a specific restriction enzyme, such as PvuII, as cleavage module, offers an alternative to the otherwise often used catalytic domain of FokI, which by itself does not contribute to the specificity of the engineered nuclease.},
  file      = {:by-author/F/Fonfara/2012_Fonfara_847.pdf:PDF},
  keywords  = {Design; Restriction Endonuclease (RE); Specificity},
  owner     = {em},
  timestamp = {2013.09.19},
  creationdate = {2013-09-19T00:00:00},
}

@Article{Font-Bardia2012,
  author    = {Font-Bardia},
  journal   = {Handbook of instrumental techniques from CCiTUB},
  title     = {X-ray single crystal and powder diffraction: possibilities and applications},
  year      = {2012},
  pages     = {MT9},
  file      = {:by-author/F/Font-Bardia/2012_Font-Bardia_MT9.pdf:PDF},
  owner     = {saulius},
  timestamp = {2015.02.17},
  creationdate = {2015-02-17T00:00:00},
  url       = {http://diposit.ub.edu/dspace/bitstream/2445/32164/1/MT09%20-%20Single%20Crystal%20and%20Powder%20X-ray%20Diffraction_ed2.pdf},
}

@Webpage{Forcada2002,
  author      = {Mikel L. Forcada},
  retrieved   = {2015-03-07},
  title       = {What functions can a neuron compute?},
  url         = {http://www.dlsi.ua.es/~mlf/nnafmc/pbook/node11.html},
  institution = {Universitat d'Alacant, Dept. Llenguatges i Sistemes Informàtics, E-03071 Alacant (Spain)},
  year        = {2002},
  file        = {:by-author/F/Forcada/2002_Forcada.war:},
  keywords    = {Computer Science (CS)},
  owner       = {saulius},
  timestamp = {2015.03.02},
  creationdate = {2015-03-02T00:00:00},
}

@Webpage{Forcada2002a,
  author      = {Mikel L. Forcada},
  retrieved   = {2008-07-28},
  title       = {Neural Networks: Automata and Formal Models of Computation},
  url         = {http://www.dlsi.ua.es/~mlf/nnafmc/pbook/pbook.html},
  institution = {Universitat d'Alacant, Dept. Llenguatges i Sistemes Informàtics, E-03071 Alacant (Spain)},
  month       = {January},
  year        = {2002},
  file        = {:by-author/F/Forcada/2002_Forcada_a.war:},
  keywords    = {Computer Science (CS)},
  owner       = {saulius},
  timestamp = {2015.03.02},
  creationdate = {2015-03-02T00:00:00},
}

@TechReport{DataManagementTaskForce2009,
  author      = {Data Management Task Force},
  institution = {European Strategy Forum on Research Infrastructures},
  title       = {e-IRG Report on Data Management},
  year        = {2009},
  month       = {December},
  file        = {:by-author/d/data-anagement-task-force/2009_data-anagement-task-force.pdf:PDF},
  keywords    = {Data Management; Preservation},
  owner       = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@InProceedings{Fornari2004,
  author    = {Fornari, Miguel Rodrigues and Iochpe, Cirano},
  booktitle = {Proceedings of the 12th annual ACM international workshop on Geographic information systems},
  title     = {A spatial hash join algorithm suited for small buffer size},
  year      = {2004},
  address   = {New York, NY, USA},
  pages     = {118--126},
  publisher = {ACM},
  series    = {GIS '04},
  abstract  = {In this paper, a new algorithm for spatial join operations is introduced. The so-called NRQB (No Replication with Quadtrees and Buckets Spatial Merge Join) enhances the original PBSM by partitioning the space according to the spatial distribution of the objects. In addition, a hash file is created for each input data set and used to enhance both the storage of and the access to the minimum bounding rectan- gles (MBR) of the respective set elements. The paper also presents a performance evaluation of the proposed algorithm relying on the results obtained by the execution of a series of test cases concerning different spatial join scenarios. In each test case, the response time of NRQB is compared with that of some well-known algorithms. The test cases were con- ducted with both synthetic and real data sets. The results showed that the new algorithm is best suited for smaller buffer sizes, which are typical of mobile devices and database systems for desktop computers.},
  doi       = {10.1145/1032222.1032241},
  file      = {:by-author/F/Fornari/2004_Fornari_118.pdf:PDF},
  isbn      = {1-58113-979-9},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://doi.acm.org/10.1145/1032222.1032241},
}

@Article{Fortnow2009,
  author     = {Fortnow, Lance},
  journal    = {Commun. ACM},
  title      = {The status of the P versus NP problem},
  year       = {2009},
  issn       = {0001-0782},
  pages      = {78--86},
  volume     = {52},
  abstract   = {It's one of the fundamental mathematical problems of our time, and its importance grows with the rise of powerful computers.},
  acmid      = {1562186},
  address    = {New York, NY, USA},
  doi        = {10.1145/1562164.1562186},
  file       = {2009_Fortnow_78.pdf:by-author/F/Fortnow/2009_Fortnow_78.pdf:PDF},
  issue_date = {September 2009},
  numpages   = {9},
  owner      = {saulius},
  publisher  = {ACM},
  timestamp = {2012.05.30},
  creationdate = {2012-05-30T00:00:00},
  url        = {http://doi.acm.org/10.1145/1562164.1562186},
}

@Manuscript{Foster2007,
  author    = {Jeffrey S. Foster},
  title     = {Publication list},
  year      = {2007},
  keywords  = {Computer Science (CS)},
  url       = {http://www.cs.umd.edu/~jfoster/publications.shtml},
  file      = {:by-author/F/Foster/2007_Foster.war:},
  owner     = {saulius},
  timestamp = {2015.03.02},
  creationdate = {2015-03-02T00:00:00},
}

@Article{Fouineau2013,
  author    = {Fouineau, J. and Brymora, K. and Ourry, L. and Mammeri, F. and Yaacoub, N. and Calvayrac, F. and Ammar-Merah, S. and Greneche, J.-M.},
  journal   = {The Journal of Physical Chemistry C},
  title     = {Synthesis, {Mössbauer} characterization, and {Ab} initio modeling of iron oxide nanoparticles of medical interest functionalized by dopamine},
  year      = {2013},
  pages     = {14295--14302},
  volume    = {117},
  file      = {[PDF] from researchgate.net:by-author/F/Fouineau/2013_Fouineau_14295.pdf:application/pdf;Snapshot:by-author/F/Fouineau/2013_Fouineau_14295.html:text/html},
  groups    = {sg/NAR2012},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://pubs.acs.org/doi/abs/10.1021/jp4027942},
  urldate   = {2015-08-31},
}

@Article{Fouts2005,
  author    = {Fouts, Derrick E. and Mongodin, Emmanuel F. and Mandrell, Robert E. and Miller, William G. and Rasko, David A. and Ravel, Jacques and Brinkac, Lauren M. and DeBoy, Robert T. and Parker, Craig T. and Daugherty, Sean C. and Dodson, Robert J. and Durkin, A. Scott and Madupu, Ramana and Sullivan, Steven A. and Shetty, Jyoti U. and Ayodeji, Mobolanle A. and Shvartsbeyn, Alla and Schatz, Michael C. and Badger, Jonathan H. and Fraser, Claire M. and Nelson, Karen E.},
  journal   = {PLoS biology},
  title     = {Major structural differences and novel potential virulence mechanisms from the genomes of multiple campylobacter species.},
  year      = {2005},
  pages     = {e15},
  volume    = {3},
  abstract  = {Sequencing and comparative genome analysis of four strains of Campylobacter including C. lari RM2100, C. upsaliensis RM3195, and C. coli RM2228 has revealed major structural differences that are associated with the insertion of phage- and plasmid-like genomic islands, as well as major variations in the lipooligosaccharide complex. Poly G tracts are longer, are greater in number, and show greater variability in C. upsaliensis than in the other species. Many genes involved in host colonization, including racR/S, cadF, cdt, ciaB, and flagellin genes, are conserved across the species, but variations that appear to be species specific are evident for a lipooligosaccharide locus, a capsular (extracellular) polysaccharide locus, and a novel Campylobacter putative licABCD virulence locus. The strains also vary in their metabolic profiles, as well as their resistance profiles to a range of antibiotics. It is evident that the newly identified hypothetical and conserved hypothetical proteins, as well as uncharacterized two-component regulatory systems and membrane proteins, may hold additional significant information on the major differences in virulence among the species, as well as the specificity of the strains for particular hosts.},
  file      = {:by-author/F/Fouts/2005_Fouts_e15.pdf:PDF},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Book{Fowler2002,
  author    = {Martin Fowler and David Rice and Matthew Foemmel and Edward Hieatt and Robert Mee and Randy Stafford},
  publisher = {Addison Wesley},
  title     = {Patterns of Enterprise Application Architecture},
  year      = {2002},
  month     = {November},
  file      = {:by-author/F/Fowler/2002_Fowler.chm:CHM},
  keywords  = {Computer Science (CS); Software Design Patterns; Software Development},
  owner     = {saulius},
  timestamp = {2015.03.11},
  creationdate = {2015-03-11T00:00:00},
}

@Article{Fox2015,
  author      = {Jerome M Fox and Kyungtae Kang and Woody Sherman and Annie Héroux and G. Madhavi Sastry and Mostafa Baghbanzadeh and Matthew R Lockett and George M Whitesides},
  journal     = {J Am Chem Soc},
  title       = {Interactions between Hofmeister anions and the binding pocket of a protein.},
  year        = {2015},
  month       = {Mar},
  number      = {11},
  pages       = {3859--3866},
  volume      = {137},
  abstract    = {This paper uses the binding pocket of human carbonic anhydrase II (HCAII, EC 4.2.1.1) as a tool to examine the properties of Hofmeister anions that determine (i) where, and how strongly, they associate with concavities on the surfaces of proteins and (ii) how, upon binding, they alter the structure of water within those concavities. Results from X-ray crystallography and isothermal titration calorimetry show that most anions associate with the binding pocket of HCAII by forming inner-sphere ion pairs with the Zn(2+) cofactor. In these ion pairs, the free energy of anion-Zn(2+) association is inversely proportional to the free energetic cost of anion dehydration; this relationship is consistent with the mechanism of ion pair formation suggested by the "law of matching water affinities". Iodide and bromide anions also associate with a hydrophobic declivity in the wall of the binding pocket. Molecular dynamics simulations suggest that anions, upon associating with Zn(2+), trigger rearrangements of water that extend up to 8 Å away from their surfaces. These findings expand the range of interactions previously thought to occur between ions and proteins by suggesting that (i) weakly hydrated anions can bind complementarily shaped hydrophobic declivities, and that (ii) ion-induced rearrangements of water within protein concavities can (in contrast with similar rearrangements in bulk water) extend well beyond the first hydration shells of the ions that trigger them. This study paints a picture of Hofmeister anions as a set of structurally varied ligands that differ in size, shape, and affinity for water and, thus, in their ability to bind to—and to alter the charge and hydration structure of—polar, nonpolar, and topographically complex concavities on the surfaces of proteins.},
  doi         = {10.1021/jacs.5b00187},
  file        = {2015_Fox_3859.pdf:by-author/F/Fox/2015_Fox_3859.pdf:PDF},
  institution = {§The Kavli Institute for Bionano Science and Technology, Harvard University, 29 Oxford Street, Cambridge, Massachusetts 02138, United States.},
  keywords    = {Anions; Binding Sites; Carbonic Anhydrase II; Chemistry/metabolism; Coenzymes; Humans; Models; Molecular; Protein Binding; Protein Conformation; Protein Stability; Thermodynamics; Zinc},
  language    = {eng},
  medline-pst = {ppublish},
  owner       = {alexey},
  pmid        = {25738615},
  timestamp = {2016.08.29},
  creationdate = {2016-08-29T00:00:00},
  url         = {http://dx.doi.org/10.1021/jacs.5b00187},
}

@Article{Francisco2002,
  author    = {Françisco, M. Raymo},
  journal   = {Advanced Materials},
  title     = {Digital processing and communication with molecular switches},
  year      = {2002},
  pages     = {401--414},
  volume    = {14},
  file      = {Françisco - 2002 - Digital Processing and Communication with Molecula.pdf:by-author/F/Françisco/2002_Françisco_401.pdf:application/pdf},
  groups    = {sg/chemical, sg/electronics},
  language  = {English},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://m4ul4n4.synthasite.com/resources/Digital%20Processing%20and%20Communication.pdf},
  urldate   = {2015-08-26},
}

@Article{Frank1997,
  author    = {Frank, D. E. and Saecker, R. M. and Bond, J. P. and Capp, M. W. and Tsodikov, O. V. and Melcher, S. E. and Levandoski, M. M. and Record, Jr, M. T.},
  journal   = {Journal of Molecular Biology},
  title     = {Thermodynamics of the interactions of lac repressor with variants of the symmetric lac operator: effects of converting a consensus site to a non-specific site.},
  year      = {1997},
  pages     = {1186--206},
  volume    = {267},
  abstract  = {What are the thermodynamic consequences of the stepwise conversion of a highly specific (consensus) protein-DNA interface to one that is nonspecific? How do the magnitudes of key favorable contributions to complex stability (burial of hydrophobic surfaces and reduction of DNA phosphate charge density) change as the DNA sequence of the specific site is detuned? To address these questions we investigated the binding of lac repressor (LacI) to a series of 40 bp fragments carrying symmetric (consensus) and variant operator sequences over a range of temperatures and salt concentrations. Variant DNA sites contained symmetrical single and double base-pair substitutions at positions 4 and/or 5 [sequence: see text] in each 10 bp half site of the symmetric lac operator (Osym). Non-specific interactions were examined using a 40 bp non-operator DNA fragment. Disruption of the consensus interface by a single symmetrical substitution reduces the observed equilibrium association constant (K(obs)) for Osym by three to four orders of magnitude; double symmetrical substitutions approach the six orders in magnitude difference between specific and non-specific binding to a 40 bp fragment. At these adjacent positions in the consensus site, the free energy effects of multiple substitutions are non-additive: the first reduces /deltaG(obs)o/ by 3 to 5 kcal mol(-1), approximately halfway to the non-specific level, whereas the second is less deleterious, reducing /deltaG(obs)o/ by less than 3 kcal mol(-1). Variant-specific dependences of K(obs) on temperature and salt concentration characterize these LacI-operator interactions. In general, binding constants and standard free energies of binding both exhibit characteristic extrema near 290 K. As a consequence, both the enthalpic and entropic contributions to stability of Osym and variant complexes change from positive (i.e. entropy driven) at lower temperatures to negative (i.e. enthalpy driven) at higher temperatures, indicating that the heat capacity change upon binding, deltaC(obs)o, is large and negative. In general, /deltaC(obs)o/ decreases as the specificity and stability of the variant complex decreases. Stabilities of complexes of LacI with Osym and all variant operators are strongly [salt]-dependent. Binding constants for the variant complexes exhibit a power-dependence on [salt] that is larger in magnitude (i.e. more negative) than for Osym, but no obvious trend relates changes in contributions from the polyelectrolyte effect and the observed reductions in stability (delta deltaG(obs)o). These variant-specific thermodynamic signatures provide novel insights into the consequences of converting a consensus interface to a less specific one; such insights are not obtained from comparisons at the level of delta deltaG(obs)o. We propose that this variant-specific behavior arises from a strong effect of operator sequence on the extent of induced conformational changes in the protein (and possibly also in the DNA site) which accompany binding.},
  file      = {:by-author/F/Frank/1997_Frank_1186.pdf:PDF},
  keywords  = {Jen Jacobson},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Frank1945,
  author    = {Frank, Henry S. and Evans, Marjorie W.},
  journal   = {The Journal of Chemical Physics},
  title     = {Free Volume and Entropy in Condensed Systems III. Entropy in Binary Liquid Mixtures; Partial Molal Entropy in Dilute Solutions; Structure and Thermodynamics in Aqueous Electrolytes},
  year      = {1945},
  pages     = {507--532},
  volume    = {13},
  abstract  = {The ideas of the first and second papers in this series, which make it possible to interpret entropy data in terms of a physical picture, are applied to binary solutions, and equations are derived relating energy and volume changes when a solution is formed to the entropy change for the process. These equations are tested against data obtained by various authors on mixtures of normal liquids, and on solutions of non‐polar gases in normal solvents. Good general agreement is found, and it is concluded that in such solutions the physical picture of molecules moving in a ``normal'' manner in each others' force fields is adequate. As would be expected, permanent gases, when dissolved in normal liquids, loosen the forces on neighboring solvent molecules producing a solvent reaction which increases the partial molal entropy of the solute.Entropies of vaporization from aqueous solutions diverge strikingly from the normal behavior established for non‐aqueous solutions. The nature of the deviations found for non‐polar solutes in water, together with the large effect of temperature upon them, leads to the idea that the water forms frozen patches or microscopic icebergs around such solute molecules, the extent of the iceberg increasing with the size of the solute molecule. Such icebergs are apparently formed also about the non‐polar parts of the molecules of polar substances such as alcohols and amines dissolved in water, in agreement with Butler's observation that the increasing insolubility of large non‐polar molecules is an entropy effect. The entropies of hydration of ions are discussed from the same point of view, and the conclusion is reached that ions, to an extent which depends on their sizes and charges, may cause a breaking down of water structure as well as a freezing or saturation of the water nearest them. Various phenomena recorded in the literature are interpreted in these terms. The influence of temperature on certain salting‐out coefficients is interpreted in terms of entropy changes. It appears that the salting‐out phenomenon is at least partly a structural effect. It is suggested that structural influences modify the distribution of ions in an electrolytesolution, and reasons are given for postulating the existence of a super‐lattice structure in solutions of LaCl3 and of EuCl3. An example is given of a possible additional influence of structural factors upon reacting tendencies in aqueous solutions.},
  doi       = {10.1063/1.1723985},
  file      = {1945_Frank_507.pdf:by-author/F/Frank/1945_Frank_507.pdf:PDF},
  keywords  = {Entropy; Hydrophobic Effect; Simple Solute Systems},
  owner     = {saulius},
  timestamp = {2015.03.13},
  creationdate = {2015-03-13T00:00:00},
  url       = {http://scitation.aip.org/content/aip/journal/jcp/13/11/10.1063/1.1723985},
}

@Presentation{Franke2010,
  author    = {Franke},
  title     = {Ab-Initio Modelling. {DAMMIN} and {DAMMIF}},
  year      = {2010},
  file      = {:by-author/F/Franke/2010_Franke_slides.pdf:PDF},
  keywords  = {SAXS},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Franke2009,
  author    = {Franke, Daniel and Svergun, Dmitri I.},
  journal   = {Journal of Applied Crystallography},
  title     = {{\it DAMMIF}, a program for rapid {\it ab-initio} shape determination in small-angle scattering},
  year      = {2009},
  pages     = {342--346},
  volume    = {42},
  doi       = {10.1107/S0021889809000338},
  file      = {2009_Franke_342.pdf:by-author/F/Franke/2009_Franke_342.pdf:PDF},
  keywords  = {DAMMIF; SAXS},
  owner     = {em},
  timestamp = {2013.01.02},
  creationdate = {2013-01-02T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0021889809000338},
}

@Article{Franklin1953,
  author    = {Franklin, R. E. and Gosling, R. G.},
  journal   = {Nature},
  title     = {Evidence for 2-chain helix in crystalline structure of sodium deoxyribonucleate.},
  year      = {1953},
  pages     = {156--7},
  volume    = {172},
  file      = {:by-author/F/Franklin/1953_Franklin_156.pdf:PDF},
  keywords  = {DNA Structure},
  owner     = {saulius},
  timestamp = {2012.11.21},
  creationdate = {2012-11-21T00:00:00},
  url       = {http://www.nature.com/nature/dna50/franklingosling2.pdf},
}

@Article{Franklin1953a,
  author    = {Franklin, R. E. and Gosling, R. G.},
  journal   = {Nature},
  title     = {Molecular configuration in sodium thymonucleate.},
  year      = {1953},
  pages     = {740--1},
  volume    = {171},
  file      = {:by-author/F/Franklin/1953_Franklin_740.pdf:PDF},
  keywords  = {DNA Structure},
  owner     = {saulius},
  timestamp = {2012.11.21},
  creationdate = {2012-11-21T00:00:00},
  url       = {http://www.nature.com/nature/dna50/franklingosling.pdf},
}

@Article{Franz1997,
  author    = {Michael Franz},
  journal   = {Software -- Concepts and Tools},
  title     = {The Programming Language Lagoona -- A Fresh Look at Object Orientation},
  year      = {1997},
  pages     = {14--26},
  abstract  = {Lagoona is a strongly typed object-oriented programming language based on Oberon. Lacking the "class" construct found in traditional object-oriented languages, Lagoona separates many of the ocncerns usually subsumed by classes, such as encapsulation, structure and behavior, turning them into independent language constructs. Its rich data model can express the difference between specialisation and combination, two relations that are otherwise often both mapped into subtyping. In contrast to most strongly typed object-oriented languages, Lagoona's messages are not subordinate to classes, but are stand-alone entities that can be combined with arbitrary objects. A delegation mechanism is provided by which objects can forward received messages even if the don not "understand" their contents. Lagoona's particular message-send semantics makes the construction of extensible systems simple and elegant.},
  file      = {:by-author/F/Franz/1997_Franz_14.pdf:PDF},
  keywords  = {Computer Science (CS); Lagoona; Programming Languages},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@PhdThesis{Franz1994,
  author    = {Michael Franz},
  school    = {Swiss Federal Institute of Technology Zurich},
  title     = {Code Generation On the Fly: A Key to Portable Software},
  year      = {1994},
  note      = {Also available at http://oberon2005.oberoncore.ru/paper/eth10497.pdf (as of 2015-03-05)},
  file      = {:by-author/F/Franz/1994_Franz_doctorthesis.pdf:PDF},
  keywords  = {Computer Science (CS); Dissertations},
  owner     = {saulius},
  pages     = {doctorthesis},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
  url       = {http://e-collection.library.ethz.ch/eserv/eth:39291/eth-39291-01.pdf},
}

@Manuscript{Franz2003,
  author    = {Michael Franz and Peter H. Fröhlich and Andreas Gal},
  title     = {Supporting Software Composition at the Programming-Language Level},
  year      = {2003},
  keywords  = {Component-oriented Software Development; Computer Science (CS); Distributed Extensibility; Lagoona; Language Paradigms Beyond Object-oriented Programming; Programming Languages},
  url       = {http://dx.doi.org/10.1016/j.scico.2004.11.004},
  abstract  = {We are in the midst of a paradigm shift toward component-oriented software development, and significant progress has been made in understanding and harnessing this new paradigm. Somewhat strangely then, the new paradigm does not currently extend all the way down to how the components themselves are constructed. While we have composition architectures and languages that describe how systems are put together out of such atomic program parts, the parts themselves are still constructed based on a previous paradigm, object-oriented programming. We argue that this represents a mismatch that is holding back compositional software design: many of the assumptions that underly object-oriented systems simply do not apply in the open and dynamic contexts of component software environments. What, then, would a programming language look like that supported component-oriented pro- gramming at the smallest granularity? Our project to develop such a language, Lagoona, tries to provide an answer to this question. This paper motivates the new key concepts behind Lagoona and briefly describes their realization (using Lagoona itself as the imple- mentation language) in the context of Microsoft’s .NET environment.},
  file      = {:by-author/F/Franz/2003_Franz.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Presentation{Franzen2007,
  author    = {Franzen, Stefan},
  title     = {Density Functional Theory Calculations},
  year      = {2007},
  file      = {2007_Franzen_slides.pdf:by-author/F/Franzen/2007_Franzen_slides.pdf:PDF},
  keywords  = {Density Functional Theory (DFT); Molpro},
  owner     = {saulius},
  timestamp = {2014.10.21},
  creationdate = {2014-10-21T00:00:00},
  url       = {http://www4.ncsu.edu/~franzen/public_html/CH795Z/lecture/DFT_Method.pdf},
}

@Article{Fraser1991,
  author           = {Christopher W. Fraser and David R. Hanson},
  journal          = {Software -- practice and experience},
  title            = {A Code Generation Interface for ANSI C},
  year             = {1991},
  pages            = {963--988},
  volume           = {21},
  abstract         = {lcc is a retargetable, production compiler for ANSI C; it has been ported to the VAX, Motorola 68020, SPARC, and MIPS R3000, and some versions have been in use for over a year and a half. It is smaller and faster than generally available alternatives, and its local code is comparable. This paper describes the interface between the target-independent front end and the target-dependent back ends. The interface consists of shared data structures, a few functions, and a dag language. While this approach couples the front and back ends tightly, it results in efficient, compact compilers. The interface is illustrated by detailing a code generator that emits naive VAX code.},
  creationdate     = {2012-10-21T00:00:00},
  doi              = {10.1002/spe.4380210906},
  file             = {:by-author/F/Fraser/1991_Fraser_963.pdf:PDF},
  keywords         = {C Compilers; C Language; Code Generation; Compiler Design; Computer Science (CS); Lcc},
  modificationdate = {2022-11-04T09:15:10},
  owner            = {saulius},
  timestamp        = {2012.10.21},
}

@Article{Fraser1992,
  author    = {Christopher W. Fraser and David R. Hanson and Todd A. Proebsting},
  journal   = {ACM Letters on Programming Languages and Systems},
  title     = {Engineering a Simple, Efficient Code Generator Generator},
  year      = {1992},
  pages     = {213--226},
  volume    = {1},
  abstract  = {Many code generator generators use tree pattern matching and dynamic programming. This note describes a simple program that generates matchers that are fast, compact, and easy to understand. It is simpler than common alternatives: 200–700 lines of Icon or 950 lines of C versus 3000 lines of C for Twig and 5000 for burg. Its matchers run up to 25 times faster than Twig’s. They are necessarily slower than burg’s BURS (bottom-up rewrite system) matchers but they are more flexible and still practical.},
  file      = {:by-author/F/Fraser/1992_Fraser_213.pdf:PDF},
  keywords  = {Code Generation; Compiler Design; Computer Science (CS)},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Fraser2011,
  author    = {Fraser, James S. and van den Bedem, Henry and Samelson, Avi J. and Lang, P. Therese and Holton, James M. and Echols, Nathaniel and Alber, Tom},
  journal   = {Proceedings of the National Academy of Sciences},
  title     = {Accessing protein conformational ensembles using room-temperature X-ray crystallography},
  year      = {2011},
  pages     = {16247--16252},
  volume    = {108},
  abstract  = {Modern protein crystal structures are based nearly exclusively on X-ray data collected at cryogenic temperatures (generally 100 K). The cooling process is thought to introduce little bias in the functional interpretation of structural results, because cryogenic temperatures minimally perturb the overall protein backbone fold. In contrast, here we show that flash cooling biases previously hidden structural ensembles in protein crystals. By analyzing available data for 30 different proteins using new computational tools for electron-density sampling, model refinement, and molecular packing analysis, we found that crystal cryocooling remodels the conformational distributions of more than 35% of side chains and eliminates packing defects necessary for functional motions. In the signaling switch protein, H-Ras, an allosteric network consistent with fluctuations detected in solution by NMR was uncovered in the room-temperature, but not the cryogenic, electron-density maps. These results expose a bias in structural databases toward smaller, overpacked, and unrealistically unique models. Monitoring room-temperature conformational ensembles by X-ray crystallography can reveal motions crucial for catalysis, ligand binding, and allosteric regulation.},
  doi       = {10.1073/pnas.1111325108},
  eprint    = {http://www.pnas.org/content/108/39/16247.full.pdf+html},
  file      = {2011_Fraser_16247.pdf:by-author/F/Fraser/2011_Fraser_16247.pdf:PDF},
  keywords  = {Cryo Cooling; Energy Landscape; Protein Conformational Dynamics; Protein Crystallography; Proteins; Temperature Dependence; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2013.03.25},
  creationdate = {2013-03-25T00:00:00},
  url       = {http://www.pnas.org/content/108/39/16247.abstract},
}

@Presentation{Fratesi2005,
  author    = {Guido Fratesi},
  title     = {XCRYSDEN – a short tutorial},
  year      = {2005},
  course    = {Cagliari},
  comment   = {Referenced from the Quantum-Espresso tutorial list on http://www.fisica.uniud.it/~giannozz/QE-Tutorial/},
  file      = {2005_Fratesi_slides.pdf:by-author/F/Fratesi/2005_Fratesi_slides.pdf:PDF},
  keywords  = {Chemoinformatics; Computation Chemistry; Density Functional Theory (DFT); Molecular Vizialisation; Quantum Chemistry; Quantum-espresso},
  owner     = {saulius},
  timestamp = {2014.07.21},
  creationdate = {2014-07-21T00:00:00},
  url       = {http://www.fisica.uniud.it/~giannozz/QE-Tutorial/tutorial_xcrysden.pdf},
}

@Article{Fratini1982,
  author    = {Fratini, A. V. and Kopka, M. L. and Drew, H. R. and Dickerson, R. E.},
  journal   = {The Journal of biological chemistry},
  title     = {Reversible bending and helix geometry in a B-DNA dodecamer: CGCGAATTBrCGCG.},
  year      = {1982},
  pages     = {14686--707},
  volume    = {257},
  abstract  = {A double-helical B-DNA dodecamer has been analyzed by single crystal x-ray diffraction methods and refined independently in four variants: sequence CGCGAATTCGCG at 20 degrees C and at 16 K, and CGCGAATTBrCGCG in 60\% methylpentanediol at 20 and at 7 degrees C. The first three forms show a 14-19 degrees bend in overall helix axis, but the fourth is straight and unbent. Detailed comparisons of the various forms have led to a better understanding of helix geometry and bending. Structural principles can be understood best if organized under four headings: 1) intrinsic geometry of the sugar rings, 2) stacking and relative motion of base pairs, 3) geometry of the connecting phosphate backbone, and 4) mechanics of bending in B-DNA. The observed bending is neither completely localized nor smooth and continuous, but an intermediate compromise that can be termed "annealed kinking."},
  file      = {1982_Fratini_14686.pdf:by-author/F/Fratini/1982_Fratini_14686.pdf:PDF;3bdn.pdb:by-author/F/Fratini/1982_Fratini_14686/3bdn.pdb:PDB;4bna.pdb:by-author/F/Fratini/1982_Fratini_14686/4bna.pdb:PDB;4bna-sym.pdb:by-author/F/Fratini/1982_Fratini_14686/4bna-sym.pdb:PDB;4bna-sphere.pdb:by-author/F/Fratini/1982_Fratini_14686/4bna-sphere.pdb:PDB},
  keywords  = {DNA Structure; RY; Readout; Stacking},
  owner     = {em},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Manuscript{Freedman2000,
  author    = {C. D. Freedman},
  title     = {Software And Computer-Related Business-Method Inventions: Must Europe Adopt American Patent Culture?},
  year      = {2000},
  keywords  = {Patentai; Teise},
  file      = {:by-author/F/Freedman/2000_Freedman.RTF:DOC},
  owner     = {saulius},
  timestamp = {2015.02.28},
  creationdate = {2015-02-28T00:00:00},
}

@Article{Freedman1999,
  author    = {David Freedman},
  journal   = {The Annals of Statistics},
  title     = {On the {B}ernstein–von {M}ises theorem with infinite-dimensional parameters},
  year      = {1999},
  pages     = {1119--1140},
  volume    = {27},
  abstract  = {If there are many independent, identically distributed observations governed by a smooth, finite-dimensional statistical model, the Bayes estimate and the maximum likelihood estimate will be close. Furthermore, the posterior distribution of the parameter vector around the posterior mean will be close to the distribution of the maximum likelihood estimate around truth. Thus, Bayesian confidence sets have good frequentist coverage properties, and conversely. However, even for the simplest infinite-dimensional models, such results do not hold. The object here is to give some examples.},
  doi       = {10.1214/aos/1017938917},
  file      = {1999_Freedman_1119.pdf:by-author/F/Freedman/1999_Freedman_1119.pdf:PDF},
  groups    = {sg/Bayesian},
  keywords  = {Bayesian Statistics; Criticism},
  owner     = {saulius},
  timestamp = {2012.10.04},
  creationdate = {2012-10-04T00:00:00},
  url       = {http://projecteuclid.org/DPubS?service=UI&version=1.0&verb=Display&handle=euclid.aos/1017938917},
}

@Article{Freer1980,
  author    = {Freer, A. A. and Gilmore, C. J.},
  journal   = {Acta Crystallographica Section A},
  title     = {The use of higher invariants in {\it MULTAN}},
  year      = {1980},
  pages     = {470},
  volume    = {36},
  abstract  = {A method of using quartets and quintets in the direct-methods program MULTAN is described with several successful applications.},
  doi       = {10.1107/S0567739480000988},
  file      = {:by-author/F/Freer/1980_Freer_470.pdf:PDF},
  keywords  = {Direct Methods; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0567739480000988},
}

@Article{Freire2008,
  author       = {Ernesto Freire},
  journal      = {Drug Discov Today},
  title        = {Do enthalpy and entropy distinguish first in class from best in class?},
  year         = {2008},
  month        = {Oct},
  number       = {19-20},
  pages        = {869--874},
  volume       = {13},
  abstract     = {A drug molecule should bind to its target with high affinity and selectivity. Because the binding affinity is a combined function of the binding enthalpy and the binding entropy, extremely high affinity requires that both terms contribute favorably to binding. The binding enthalpy, however, is notoriously more difficult to optimize than the binding entropy, a fact that has resulted in thermodynamically unbalanced molecules that do not achieve optimal potency. In fact, with current technologies, the enthalpic optimization of drug candidates may take years and only appear in second-generation products. Within that context, it is not surprising that structure/activity relationships (SARs) that explicitly incorporate the interplay between enthalpy and entropy and accelerate the optimization process are being developed and gaining popularity.},
  creationdate = {2016-06-06T00:00:00},
  doi          = {10.1016/j.drudis.2008.07.005},
  file         = {2008_Freire_869.pdf:by-author/F/Freire/2008_Freire_869.pdf:PDF},
  institution  = {Department of Biology, Johns Hopkins University, Baltimore, MD 21218, United States. ef@jhu.edu},
  keywords     = {Animals; Chemistry; Drug; Drug Design; Entropy; Humans; Hydrogen Bonding; Ligands; Pharmaceutical Preparations; Receptors; Thermodynamics},
  language     = {eng},
  medline-pst  = {ppublish},
  owner        = {alexey},
  pii          = {S1359-6446(08)00266-3},
  pmid         = {18703160},
  timestamp    = {2016.06.06},
  url          = {http://dx.doi.org/10.1016/j.drudis.2008.07.005},
}

@Article{Frick2001,
  author    = {Frick, D. N. and Richardson, C. C.},
  journal   = {Annual review of biochemistry},
  title     = {DNA primases.},
  year      = {2001},
  pages     = {39--80},
  volume    = {70},
  abstract  = {DNA primases are enzymes whose continual activity is required at the DNA replication fork. They catalyze the synthesis of short RNA molecules used as primers for DNA polymerases. Primers are synthesized from ribonucleoside triphosphates and are four to fifteen nucleotides long. Most DNA primases can be divided into two classes. The first class contains bacterial and bacteriophage enzymes found associated with replicative DNA helicases. These prokaryotic primases contain three distinct domains: an amino terminal domain with a zinc ribbon motif involved in binding template DNA, a middle RNA polymerase domain, and a carboxyl-terminal region that either is itself a DNA helicase or interacts with a DNA helicase. The second major primase class comprises heterodimeric eukaryotic primases that form a complex with DNA polymerase alpha and its accessory B subunit. The small eukaryotic primase subunit contains the active site for RNA synthesis, and its activity correlates with DNA replication during the cell cycle.},
  file      = {:by-author/F/Frick/2001_Frick_39.pdf:PDF},
  keywords  = {Ecoli; {gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Frick1999,
  author    = {Frick, D. N. and Richardson, C. C.},
  journal   = {The Journal of biological chemistry},
  title     = {Interaction of bacteriophage T7 gene 4 primase with its template recognition site.},
  year      = {1999},
  pages     = {35889--98},
  volume    = {274},
  abstract  = {The primase fragment of the bacteriophage T7 63-kDa gene 4 helicase/primase protein contains the 271 N-terminal amino acid residues and lacks helicase activity. The primase fragment catalyzes the synthesis of oligoribonucleotides at rates similar to those catalyzed by the full-length protein in the presence of a 5-nucleotide DNA template containing a primase recognition site (5'-GGGTC-3', 5'-TGGTC-3', 5'-GTGTC-3', or 5'-TTGTC-3'). Although it is not copied into the oligoribonucleotides, the cytosine at the 3'-position is essential for synthesis and template binding. Two nucleotides flanking the 3'-end of the recognition site are required for tight DNA binding and rapid oligoribonucleotide synthesis. Nucleotides added to the 5'-end have no effect on the rate of oligoribonucleotide synthesis or the affinity of the primase for DNA. The binding of either ATP or CTP significantly increases the affinity of the primase for its DNA template. DNA lacking a primase recognition site does not inhibit oligoribonucleotide synthesis, suggesting that the primase binds DNA in a sequence-specific manner. The affinity of the primase for templates is weak, ranging from 10 to 150 microM. The tight DNA binding (&lt;1 microM) observed with the 63-kDa gene 4 protein occurs via interactions between DNA templates and the helicase domain.},
  file      = {:by-author/F/Frick/1999_Frick_35889.pdf:PDF},
  keywords  = {T7; {gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Fricke2003,
  author    = {Fricke, William M and Brill, Steven J},
  journal   = {Genes \&amp; development},
  title     = {Slx1-Slx4 is a second structure-specific endonuclease functionally redundant with Sgs1-Top3.},
  year      = {2003},
  pages     = {1768--78},
  volume    = {17},
  file      = {2003_Fricke_1768.pdf:by-author/F/Fricke/2003_Fricke_1768.pdf:PDF},
  keywords  = {Nucleases},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@PhdThesis{Friedel2013,
  author    = {Caroline Friedel},
  school    = {Fakult{\"{a}}t f{\"{u}}r Mathematik, Informatik und Statistik der Ludwig--Maximilians--Universit{\"{a}}t M{\"{u}}nchen},
  title     = {Bioinformatics methods for the biological interpretation of high-throughput experiments},
  year      = {2013},
  type      = {Habilitation thesis Habilitationsschrift},
  file      = {:by-author/F/Friedel/2013_Friedel.pdf:PDF},
  keywords  = {Bioinformatics},
  owner     = {saulius},
  timestamp = {2014.03.24},
  creationdate = {2014-03-24T00:00:00},
  url       = {http://www.bio.ifi.lmu.de/webfm_send/3624},
}

@Article{Friedel1999,
  author    = {P. Friedel and D. Jehnichen and J. Bergmann and T. Taut and A. Haase},
  journal   = {Advances in X-Ray Analysis},
  title     = {Application of Rietveld Refinement Combined with Force Field Energy Minimization to Structure Investigation of Cyclo-tris(2,6=pyridylformamidine)},
  year      = {1999},
  pages     = {593--600},
  volume    = {41},
  abstract  = {The structure refinement of X-ray powder data using the Rietveld method often results in false minima, i.e. not necessarily the energetically favored result. By introducing force fields as a new type of constraint into the recently developed BGMN program, a fully featured X-ray Rietveld system was created. With the model of bonding and nonbonding interactions, it was finally possible to refine the crystal structure of an aromatic trimer. By means of simple powder diffraction measurements, a set of structural data was ob- tained which was fitted mathematically to a structural model containing the geometry optimization by ab initio calculations, the indexing of diffraction pattern, the search of reasonable space group and the structure refinement under force field constraints. As an example, it was found that cycle-tris(2,6-pyridyl formamidine) crystallizes in a monoclinic unit cell with a = 28.17 A, b = 14.68 A, c = 4.43 A, 8 = 90.04 deg. The symmetry was determined as P2, /c, unique axis b, cell choice 3, Z = 4. The expected threefold symmetry of the cyclic compound was slightly disturbed. The best approximation was obtained when water molecules were packed additionally into the unit cell.},
  file      = {:by-author/F/Friedel/1999_Friedel_593.pdf:PDF},
  keywords  = {Powder Diffraction; Rietveld Refinement},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Manuscript{Fries2001,
  author    = {Christian P. Fries},
  title     = {A recursive formula for the Kurtosis of an approximation to the distribution of share prices},
  year      = {2001},
  keywords  = {Kurtosis; Mathematics; Recursive Statistic},
  file      = {2001_Fries_1.pdf:by-author/F/Fries/2001_Fries_1.pdf:PDF},
  owner     = {saulius},
  pages     = {1},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Friesner2004,
  author    = {Friesner, Richard A. and Banks, Jay L. and Murphy, Robert B. and Halgren, Thomas A. and Klicic, Jasna J. and Mainz, Daniel T. and Repasky, Matthew P. and Knoll, Eric H. and Shelley, Mee and Perry, Jason K. and Shaw, David E. and Francis, Perry and Shenkin, Peter S.},
  journal   = {Journal of Medicinal Chemistry},
  title     = {Glide:  A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking Accuracy},
  year      = {2004},
  pages     = {1739--1749},
  volume    = {47},
  abstract  = {Unlike other methods for docking ligands to the rigid 3D structure of a known protein receptor, Glide approximates a complete systematic search of the conformational, orientational, and positional space of the docked ligand. In this search, an initial rough positioning and scoring phase that dramatically narrows the search space is followed by torsionally flexible energy optimization on an OPLS-AA nonbonded potential grid for a few hundred surviving candidate poses. The very best candidates are further refined via a Monte Carlo sampling of pose conformation; in some cases, this is crucial to obtaining an accurate docked pose. Selection of the best docked pose uses a model energy function that combines empirical and force-field-based terms. Docking accuracy is assessed by redocking ligands from 282 cocrystallized PDB complexes starting from conformationally optimized ligand geometries that bear no memory of the correctly docked pose. Errors in geometry for the top-ranked pose are less than 1 Å in nearly half of the cases and are greater than 2 Å in only about one-third of them. Comparisons to published data on rms deviations show that Glide is nearly twice as accurate as GOLD and more than twice as accurate as FlexX for ligands having up to 20 rotatable bonds. Glide is also found to be more accurate than the recently described Surflex method.},
  doi       = {10.1021/jm0306430},
  eprint    = {http://pubs.acs.org/doi/pdf/10.1021/jm0306430},
  file      = {2004_Friesner_1739.pdf:by-author/F/Friesner/2004_Friesner_1739.pdf:PDF},
  owner     = {saulius},
  timestamp = {2013.04.01},
  creationdate = {2013-04-01T00:00:00},
  url       = {http://pubs.acs.org/doi/abs/10.1021/jm0306430},
}

@Article{Frigge1989,
  author              = {Frigge, Michael and Hoaglin, David C. and Iglewicz, Boris},
  journal             = {The American Statistician},
  title               = {Some Implementations of the Boxplot},
  year                = {1989},
  issn                = {00031305},
  pages               = {50--54},
  volume              = {43},
  abstract            = {An increasing number of statistical software packages offer exploratory data displays and summaries. For one of these, the graphical technique known as the boxplot, a selective survey of popular software packages revealed several definitions. These alternative constructions arise from different choices in computing quartiles and the fences that determine whether an observation is "outside" and thus plotted individually. We examine these alternatives and their consequences, discuss related background for boxplots (such as the probability that a sample contains one or more outside observations and the average proportion of outside observations in a sample), and offer recommendations that lead to a single standard form of the boxplot.},
  file                = {:by-author/F/Frigge/1989_Frigge_50.pdf:PDF},
  jstor_articletype   = {research-article},
  jstor_formatteddate = {Feb., 1989},
  language            = {English},
  owner               = {saulius},
  publisher           = {American Statistical Association},
  timestamp = {2012.09.18},
  creationdate = {2012-09-18T00:00:00},
  url                 = {http://www.jstor.org/stable/2685173},
}

@Manuscript{Frohlich2001,
  author    = {Peter H. Fröhlich and Michael Franz},
  title     = {On Certain Basic Properties of Component-Oriented Programming Languages},
  year      = {2001},
  keywords  = {Computer Science (CS); Lagoona; Programming Languages},
  abstract  = {The essence of component-oriented programming is a new understanding of extensibility in which the development and integration of extensions is a distributed activity, not a cen- tralized one as in previous software development paradigms. Component-oriented programming languages must therefore be designed to have certain basic properties that support rather than impede the distributed extensibility of software systems. We discuss a number of existing language mech- anisms in this regard and provide examples from Lagoona, an experimental component-oriented programming language we are developing.},
  file      = {:by-author/F/Fröhlich/2001_Fröhlich.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Frost2005,
  author    = {Frost, Laura S. and Leplae, Raphael and Summers, Anne O. and Toussaint, Ariane},
  journal   = {Nature reviews. Microbiology},
  title     = {Mobile genetic elements: the agents of open source evolution.},
  year      = {2005},
  pages     = {722--32},
  volume    = {3},
  abstract  = {Horizontal genomics is a new field in prokaryotic biology that is focused on the analysis of DNA sequences in prokaryotic chromosomes that seem to have originated from other prokaryotes or eukaryotes. However, it is equally important to understand the agents that effect DNA movement: plasmids, bacteriophages and transposons. Although these agents occur in all prokaryotes, comprehensive genomics of the prokaryotic mobile gene pool or 'mobilome' lags behind other genomics initiatives owing to challenges that are distinct from cellular chromosomal analysis. Recent work shows promise of improved mobile genetic element (MGE) genomics and consequent opportunities to take advantage - and avoid the dangers - of these 'natural genetic engineers'. This review describes MGEs, their properties that are important in horizontal gene transfer, and current opportunities to advance MGE genomics.},
  file      = {:by-author/F/Frost/2005_Frost_722.pdf:PDF},
  keywords  = {Obzor},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Fruk2005,
  author    = {Ljiljana Fruk and Melissa O'Neal and Kyle P. Chiang and Gerbrand Koster and Otger Campas},
  journal   = {Molecular BioSystems},
  title     = {Hot off the Press},
  year      = {2005},
  pages     = {351--353},
  volume    = {1},
  doi       = {10.1039/b514923c},
  file      = {:by-author/F/Fruk/2005_Fruk_351.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Fu1997,
  author    = {Fu, Zheng-Qing And Fan, Hai-Fu},
  journal   = {Journal of Applied Crystallography},
  title     = {A computer program to derive (3+1)-dimensional symmetry operations from two-line symbols},
  year      = {1997},
  pages     = {73--78},
  volume    = {30},
  doi       = {10.1107/S0021889896006711},
  file      = {1997_Zheng-Qing_73.pdf:by-author/Z/Zheng-Qing/1997_Zheng-Qing_73.pdf:PDF},
  keywords  = {Spacegroups; Superspacegroups; Symmetry},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0021889896006711},
}

@Article{Fu2004,
  author    = {Fu, Zheng-Qing and Rose, John P. and Wang, Bi-Cheng},
  journal   = {Acta Crystallographica Section D},
  title     = {Monitoring the anomalous scattering signal and noise levels in X-ray diffraction of crystals},
  year      = {2004},
  pages     = {499--506},
  volume    = {60},
  doi       = {10.1107/S0907444904000617},
  file      = {dz0019.pdf:by-author/F/Fu/2004_Fu_499.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444904000617},
}

@PhdThesis{Fuentes-Prior2001,
  author    = {Pablo Fuentes-Prior},
  school    = {Fakultät für Chemie der Technischen Universität München},
  title     = {Structural Investigations of Coagulation Factors},
  year      = {2001},
  file      = {:by-author/F/Fuentes-Prior/2001_Fuentes-Prior_phdthesis.pdf:PDF},
  keywords  = {Disertacijos},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@Article{Fujii2007,
  author    = {Fujii, Satoshi and Kono, Hidetoshi and Takenaka, Shigeori and Go, Nobuhiro and Sarai, Akinori},
  journal   = {Nucleic acids research},
  title     = {Sequence-dependent DNA deformability studied using molecular dynamics simulations.},
  year      = {2007},
  pages     = {6063--74},
  volume    = {35},
  abstract  = {Proteins recognize specific DNA sequences not only through direct contact between amino acids and bases, but also indirectly based on the sequence-dependent conformation and deformability of the DNA (indirect readout). We used molecular dynamics simulations to analyze the sequence-dependent DNA conformations of all 136 possible tetrameric sequences sandwiched between CGCG sequences. The deformability of dimeric steps obtained by the simulations is consistent with that by the crystal structures. The simulation results further showed that the conformation and deformability of the tetramers can highly depend on the flanking base pairs. The conformations of xATx tetramers show the most rigidity and are not affected by the flanking base pairs and the xYRx show by contrast the greatest flexibility and change their conformations depending on the base pairs at both ends, suggesting tetramers with the same central dimer can show different deformabilities. These results suggest that analysis of dimeric steps alone may overlook some conformational features of DNA and provide insight into the mechanism of indirect readout during protein-DNA recognition. Moreover, the sequence dependence of DNA conformation and deformability may be used to estimate the contribution of indirect readout to the specificity of protein-DNA recognition as well as nucleosome positioning and large-scale behavior of nucleic acids.},
  file      = {:by-author/F/Fujii/2007_Fujii_6063.pdf:PDF},
  groups    = {sg/applications},
  keywords  = {Readout},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Fujii2007a,
  author       = {Satoshi Fujii and Hidetoshi Kono and Shigeori Takenaka and Nobuhiro Go and Akinori Sarai},
  journal      = {Nucleic Acids Res},
  title        = {Sequence-dependent DNA deformability studied using molecular dynamics simulations.},
  year         = {2007},
  number       = {18},
  pages        = {6063--6074},
  volume       = {35},
  abstract     = {Proteins recognize specific DNA sequences not only through direct contact between amino acids and bases, but also indirectly based on the sequence-dependent conformation and deformability of the DNA (indirect readout). We used molecular dynamics simulations to analyze the sequence-dependent DNA conformations of all 136 possible tetrameric sequences sandwiched between CGCG sequences. The deformability of dimeric steps obtained by the simulations is consistent with that by the crystal structures. The simulation results further showed that the conformation and deformability of the tetramers can highly depend on the flanking base pairs. The conformations of xATx tetramers show the most rigidity and are not affected by the flanking base pairs and the xYRx show by contrast the greatest flexibility and change their conformations depending on the base pairs at both ends, suggesting tetramers with the same central dimer can show different deformabilities. These results suggest that analysis of dimeric steps alone may overlook some conformational features of DNA and provide insight into the mechanism of indirect readout during protein-DNA recognition. Moreover, the sequence dependence of DNA conformation and deformability may be used to estimate the contribution of indirect readout to the specificity of protein-DNA recognition as well as nucleosome positioning and large-scale behavior of nucleic acids.},
  creationdate = {2011-11-25T00:00:00},
  doi          = {10.1093/nar/gkm627},
  file         = {2007_Fujii_6063.pdf:by-author/F/Fujii/2007_Fujii_6063.pdf:PDF},
  groups       = {sg/applications},
  institution  = {Department of Bioscience and Bioinformatics, Kyushu Institute of Technology (KIT) 680-4 Kawazu, Iizuka, Fukuoka 820-8502, Japan.},
  keywords     = {Base Sequence; Chemistry; Computer Simulation; Crystallography; DNA; DNA-Binding Proteins; Dimerization; Models; Molecular; Nucleic Acid Conformation; Nucleosomes; X-Ray},
  language     = {eng},
  medline-pst  = {ppublish},
  owner        = {em},
  pii          = {gkm627},
  pmid         = {17766249},
  timestamp    = {2011.11.25},
  url          = {http://dx.doi.org/10.1093/nar/gkm627},
}

@Article{Fujikawa-Adachi1999,
  author    = {Fujikawa-Adachi, K and Nishimori, I and Taguchi, T and Onishi, S},
  journal   = {Genomics},
  title     = {Human carbonic anhydrase XIV (CA14): cDNA cloning, mRNA expression, and mapping to chromosome 1.},
  year      = {1999},
  pages     = {74--81},
  volume    = {61},
  abstract  = {A full-length cDNA clone of a human carbonic anhydrase XIV (HGMW-approved gene symbol CA14) was obtained and sequenced. The cDNA sequence was 1757 bp long and was predicted to encode a 337-amino-acid polypeptide with a molecular mass of 37.6 kDa. The deduced amino acid sequence of CA XIV showed an overall similarity of 29-46% to other active CA isozymes. The highest percentage similarity was with a transmembrane CA isoform, CA XII. As observed for CA XII, CA XIV has hydrophobic segments at both termini of the deduced protein for a putative signal sequence and a transmembrane domain. CA XIV showed low activity and was sensitive to acetazolamide, but not to sulfonamide. Northern blot analysis demonstrated an approximately 1.7-kb transcript in the adult human heart, brain, liver, and skeletal muscle. RNA dot-blot analysis for CA XIV mRNA expression showed a strong signal in all parts of the human brain and a weaker signal in the colon, small intestine, urinary bladder, and kidney. RT-PCR analysis showed an intense signal in the liver and spinal cord and a faint signal in the kidney. No CA XIV mRNA was seen in the salivary gland and pancreas. In contrast, CA XII mRNA was expressed in the kidney, salivary gland, and pancreas, but not in the liver or spinal cord. The CA XIV gene was localized to human chromosome 1q21. These findings indicate genetically distinct but closely related isoforms of human transmembrane CAs, CA XII and CA XIV, which have different patterns of tissue-specific expression.},
  file      = {1999_Fujikawa-Adachi_74.pdf:by-author/F/Fujikawa-Adachi/1999_Fujikawa-Adachi_74.pdf:PDF},
  groups    = {sg/hCA14},
  keywords  = {CA14; Carbonic Anhydrases},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Fujita2012,
  author    = {Fujita, Daishi and Suzuki, Kosuke and Sato, Sota and Yagi-Utsumi, Maho and Yamaguchi, Yoshiki and Mizuno, Nobuhiro and Kumasaka, Takashi and Takata, Masaki and Noda, Masanori and Uchiyama, Susumu and Kato, Koichi and Fujita, Makoto},
  journal   = {Nature Communications},
  title     = {Protein encapsulation within synthetic molecular hosts},
  year      = {2012},
  month     = oct,
  pages     = {1093},
  volume    = {3},
  abstract  = {Protein encapsulation has long attracted many chemists and biologists because of its potential to control the structure and functions of proteins, but has been a daunting challenge because of their incommensurably larger size compared with common synthetic hosts. Here we report the encapsulation of a small protein, ubiquitin, within giant coordination cages. The protein was attached to one bidentate ligand and, upon addition of Pd(II) ions (M) and additional ligands (L), M12L24 coordination nanocages self-assembled around the protein. Because of the well-defined host framework, the protein-encapsulated structure could be analysed by NMR spectroscopy, ultracentrifugation and X-ray crystallography.},
  doi       = {10.1038/ncomms2093},
  file      = {2012_Fujita_1093.pdf:by-author/F/Fujita/2012_Fujita_1093.pdf:PDF},
  groups    = {sg/MOF, sg/MOFs, am/MOFs},
  keywords  = {Metal-Organic Frameworks (MOF); Molecular Sponges},
  owner     = {saulius},
  publisher = {Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},
  timestamp = {2016.12.20},
  creationdate = {2016-12-20T00:00:00},
  url       = {http://dx.doi.org/10.1038/ncomms2093},
}

@Article{Fulton2000,
  author    = {William Fulton},
  journal   = {Bulletin (new Series) of the American Mathematical Society},
  title     = {Eigenvalues, Invariant Factors, Highest Weights, and Schubert Calculus},
  year      = {2000},
  pages     = {209--249},
  volume    = {27},
  file      = {:by-author/F/Fulton/2000_Fulton_209.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@Article{Funari2000,
  author    = {Funari, S. S. and Rapp, G. and Perbandt, M. and Dierks, K. and Vallazza, M. and Betzel, C. and Erdmann, V. A. and Svergun, D. I.},
  journal   = {The Journal of biological chemistry},
  title     = {Structure of free Thermus flavus 5 S rRNA at 1.3 nm resolution from synchrotron X-ray solution scattering.},
  year      = {2000},
  pages     = {31283--8},
  volume    = {275},
  abstract  = {The shape of free Thermus flavus 5 S rRNA in solution at 1.3 nm resolution is restored from synchrotron x-ray scattering data using an ab initio simulated annealing algorithm. The free 5 S rRNA is a bent elongated molecule displaying a compact central region and two projecting arms, similar to those of the tRNA. The atomic models of the 5 S rRNA domains A-D-E and B-C in the form of elongated helices can be well accommodated within the shape, yielding a tentative model of the structure of the free 5 S rRNA in solution. Its comparison with the recent protein-RNA map in the ribosome (Svergun, D. I., and Nierhaus, K. H. (2000) J. Biol. Chem. 275, 14432-14439) indicates that the 5 S rRNA becomes essentially more compact upon complex formation with specific ribosomal proteins. A conceivable conformational change involves rotation of the B-C domain toward the A-D-E domain. The model of free 5 S rRNA displays no interactions between domains E and C, but such interactions are possible in the bound molecule.},
  file      = {:by-author/F/Funari/2000_Funari_31283.pdf:PDF},
  keywords  = {Domain; SAXS; TRNA},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Furuta2012,
  author    = {Furuta, Yoshikazu and Kobayashi, Ichizo},
  journal   = {Nucleic Acids Research},
  title     = {Movement of {DNA} sequence recognition domains between non-orthologous proteins},
  year      = {2012},
  pages     = {9218–9232},
  volume    = {40},
  abstract  = {Comparisons of proteins show that they evolve through the movement of domains. However, in many cases, the underlying mechanisms remain unclear. Here, we observed the movements of DNA recognition domains between non-orthologous proteins within a prokaryote genome. Restriction–modification (RM) systems, consisting of a sequence-specific DNA methyltransferase and a restriction enzyme, contribute to maintenance/evolution of genomes/epigenomes. RM systems limit horizontal gene transfer but are themselves mobile. We compared Type III RM systems in Helicobacter pylori genomes and found that target recognition domain (TRD) sequences are mobile, moving between different orthologous groups that occupy unique chromosomal locations. Sequence comparisons suggested that a likely underlying mechanism is movement through homologous recombination of similar DNA sequences that encode amino acid sequence motifs that are conserved among Type III DNA methyltransferases. Consistent with this movement, incongruence was observed between the phylogenetic trees of TRD regions and other regions in proteins. Horizontal acquisition of diverse TRD sequences was suggested by detection of homologs in other Helicobacter species and distantly related bacterial species. One of these RM systems in H. pylori was inactivated by insertion of another RM system that likely transferred from an oral bacterium. TRD movement represents a novel route for diversification of DNA-interacting proteins.},
  doi       = {10.1093/nar/gks681},
  file      = {:by-author/F/Furuta/2012_Furuta_9218.pdf:PDF},
  keywords  = {Restriction Endonucleases (REases); Review},
  owner     = {em},
  timestamp = {2013.01.17},
  creationdate = {2013-01-17T00:00:00},
}

@Article{Fuxreiter2002,
  author    = {Fuxreiter, Monika and Simon, István},
  journal   = {Protein science : a publication of the Protein Society},
  title     = {Protein stability indicates divergent evolution of PD-(D/E)XK type II restriction endonucleases.},
  year      = {2002},
  pages     = {1978--83},
  volume    = {11},
  abstract  = {Type II restriction endonucleases recognize 4-8 base-pair-long DNA sequences and catalyze their cleavage with remarkable specificity. Crystal structures of the PD-(DE)XK superfamily revealed a common alpha/beta core motif and similar active site. In contrast, these enzymes show little sequence similarity and use different strategies to interact with their substrate DNA. The intriguing question is whether this enzyme family could have evolved from a common origin. In our present work, protein structure stability elements were analyzed and compared in three parts of PD-(DE)XK type II restriction endonucleases: (1) core motif, (2) active-site residues, and (3) residues playing role in DNA recognition. High correlation was found between the active-site residues and those stabilization factors that contribute to preventing structural decay. DNA recognition sites were also observed to participate in stabilization centers. It indicates that recognition motifs and active sites in PD-(DE)XK type II restriction endonucleases should have been evolutionary more conserved than other parts of the structure. Based on this observation it is proposed that PD-(DE)XK type II restriction endonucleases have developed from a common ancestor with divergent evolution.},
  file      = {:by-author/F/Fuxreiter/2002_Fuxreiter_1978.pdf:PDF},
  keywords  = {Evolution; TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Fuxreiter2011,
  author    = {Fuxreiter, Monika and Simon, Istvan and Bondos, Sarah},
  journal   = {Trends in biochemical sciences},
  title     = {Dynamic protein-DNA recognition: beyond what can be seen.},
  year      = {2011},
  pages     = {415--23},
  volume    = {36},
  abstract  = {Traditionally, specific DNA recognition is thought to rely on static contacts with the bases or phosphates. Recent results, however, indicate that residues far outside the binding context can crucially influence selectivity or binding affinity via transient, dynamic interactions with the DNA binding interface. These regions usually do not adopt a well-defined structure, even when bound to DNA, and thus form a fuzzy complex. Here, we propose the existence of a dynamic DNA readout mechanism, wherein distant segments modulate conformational preferences, flexibility or spacing of the DNA binding motifs or serve as competitive partners. Despite their low sequence similarity, these intrinsically disordered regions are often conserved at the structural level, and exploited for regulation of the transcription machinery via protein-protein interactions, post-translational modifications or alternative splicing.},
  file      = {:by-author/F/Fuxreiter/2011_Fuxreiter_415.pdf:PDF},
  keywords  = {Readout},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Fuzo2011,
  author    = {Fuzo, Carlos A. and Degr{\`e}ve, L{\'e}o},
  journal   = {Journal of Molecular Modeling},
  title     = {Effect of the thermostat in the molecular dynamics simulation on the folding of the model protein chignolin},
  year      = {2011},
  issn      = {0948-5023},
  number    = {6},
  pages     = {2785--2794},
  volume    = {18},
  abstract  = {Molecular dynamics simulations of the model protein chignolin with explicit solvent were carried out, in order to analyze the influence of the Berendsen thermostat on the evolution and folding of the peptide. The dependence of the peptide behavior on temperature was tested with the commonly employed thermostat scheme consisting of one thermostat for the protein and another for the solvent. The thermostat coupling time of the protein was increased to infinity, when the protein is not in direct contact with the thermal bath, a situation known as minimally invasive thermostat. In agreement with other works, it was observed that only in the last situation the instantaneous temperature of the model protein obeys a canonical distribution. As for the folding studies, it was shown that, in the applications of the commonly utilized thermostat schemes, the systems are trapped in local minima regions from which it has difficulty escaping. With the minimally invasive thermostat the time that the protein needs to fold was reduced by two to three times. These results show that the obstacles to the evolution of the extended peptide to the folded structure can be overcome when the temperature of the peptide is not directly controlled.},
  doi       = {10.1007/s00894-011-1282-2},
  file      = {2011_Fuzo_2785.pdf:by-author/F/Fuzo/2011_Fuzo_2785.pdf:PDF},
  groups    = {sg/Molecular dynamics},
  keywords  = {Molecular Dynamics (MD); Simulation; Thermostat},
  owner     = {saulius},
  timestamp = {2016.02.23},
  creationdate = {2016-02-23T00:00:00},
  url       = {http://dx.doi.org/10.1007/s00894-011-1282-2},
}

@Webpage{fvdl2006,
  author    = {fvdl},
  retrieved = {2008-07-28},
  title     = {Thread: Initial DSCM experiences},
  url       = {http://www.opensolaris.org/jive/thread.jspa?threadID=5823&tstart=0},
  month     = {February},
  year      = {2006},
  file      = {:by-author/f/fvdl/2006_fvdl.war:},
  keywords  = {Computer Science (CS)},
  owner     = {saulius},
  timestamp = {2015.03.02},
  creationdate = {2015-03-02T00:00:00},
}

@Webpage{Gadbois2012,
  author    = {David Gadbois and Charles Fiterman and David Chase and Marc Shapiro and Kelvin Nilsen and Paul Haahr and Nick Barnes and Pekka P. Pirinen},
  retrieved = {2012-01-25},
  title     = {GC FAQ -- algorithms},
  url       = {http://www.iecc.com/gclist/GC-algorithms.html},
  year      = {2012},
  file      = {:by-author/G/Gadbois/2012_Gadbois.html:},
  groups    = {sg/Garbage collectors},
  keywords  = {Computer Science (CS); Garbage Collectors},
  owner     = {saulius},
  timestamp = {2015.03.03},
  creationdate = {2015-03-03T00:00:00},
}

@Article{Galan2016,
  author    = {Galan, Elena and Perrin, Mickael Lucien and Lutz, Martin and Zant, Herre S. J. van der and Grozema, Ferdinand and Eelkema, Rienk},
  journal   = {Organic \& Biomolecular Chemistry},
  title     = {Synthesis of 1,2-biphenylethane based single-molecule diodes},
  year      = {2016},
  issn      = {1477-0539},
  month     = jan,
  abstract  = {We describe the synthesis of novel biphenylethane-based wires for molecular electronics. Exceptional single-molecule diode behavior was predicted for unsymmetrically substituted biphenylethane derivatives, synthesized here using the so far unexplored unsymmetrically substituted 1,2-bis(4-bromophenyl)ethanes as key intermediates, which were obtained from the corresponding tolane precursor by selective hydrogenation.},
  doi       = {10.1039/C6OB00008H},
  file      = {2016_Galan.pdf:by-author/G/2016_Galan.pdf:PDF},
  groups    = {sg/chemical, sg/electronics},
  keywords  = {Molecular Circuits; Molecular Diode; Molecular Switches; Nanotechnology},
  language  = {en},
  owner     = {saulius},
  timestamp = {2016.01.20},
  creationdate = {2016-01-20T00:00:00},
  url       = {http://pubs.rsc.org/en/content/articlelanding/2016/ob/c6ob00008h},
  urldate   = {2016-01-20},
}

@Article{Galbraith2011,
  author    = {Galbraith},
  title     = {Algorithms for the Closest and Shortest Vector Problems},
  year      = {2011},
  pages     = {chapter18},
  file      = {:by-author/G/Galbraith/2011_Galbraith_chapter18.pdf:PDF},
  keywords  = {Closest Vector Problem; Simulations},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Galburt2002,
  author    = {Galburt, Eric A. and Stoddard, Barry L.},
  journal   = {Biochemistry},
  title     = {Catalytic mechanisms of restriction and homing endonucleases.},
  year      = {2002},
  pages     = {13851--60},
  volume    = {41},
  abstract  = {The catalytic mechanisms of type II restriction endonucleases and homing endonucleases are discussed and compared. Brief reviews of the chemistry of phosphoryl transfers and canonical one-metal and two-metal endonucleolytic mechanisms are provided along with possible future directions in the study of endonuclease active sites. The discussion of type II restriction endonucleases is comprised of a description of the general architecture of the canonical active site structural motif followed by more in-depth examples of one- and two-metal mechanisms. The homing endonuclease section is comprised of four sections describing what is known regarding the cleavage mechanisms of the four group I intron homing endonuclease families: LAGLIDADG, His-Cys box, H-N-H, and GIY-YIG.},
  file      = {:by-author/G/Galburt/2002_Galburt_13851.pdf:PDF},
  keywords  = {Obzor},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Galburt2000,
  author    = {Galburt, E. A. and Stoddard, B. L.},
  journal   = {Nature structural biology},
  title     = {Restriction endonucleases: one of these things is not like the others.},
  year      = {2000},
  pages     = {89--91},
  volume    = {7},
  abstract  = {The crystal structure of the restriction endonuclease BglII in complex with its DNA target site has been determined. The DNA binding mode and chemistry of catalysis are observed to differ from BamHI which cleaves a similar target site. These observations indicate that more divergence has occurred within this family of proteins than originally thought.},
  file      = {:by-author/G/Galburt/2000_Galburt_89.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Galiulin2003,
  author    = {R. V. Galiulin},
  journal   = {Crystallography Reports},
  title     = {To the 150th Anniversary of the Birth of Evgraf Stepanovich Fedorov (1853–1919). Irregularities in the Fate of the Theory of Regularity},
  year      = {2003},
  pages     = {899--913},
  volume    = {48},
  file      = {2003_Galiulin_899.pdf:by-author/G/Galiulin/2003_Galiulin_899.pdf:PDF},
  keywords  = {Fedorov; History; Spacegroups; Symmetry},
  owner     = {saulius},
  timestamp = {2014.10.21},
  creationdate = {2014-10-21T00:00:00},
  url       = {http://www.galiulin.narod.ru/crys03_6.pdf.pdf},
}

@Article{Gallagher1998,
  author    = {Gallagher, K. and Sharp, K.},
  journal   = {Biophysical journal},
  title     = {Electrostatic contributions to heat capacity changes of DNA-ligand binding.},
  year      = {1998},
  pages     = {769--76},
  volume    = {75},
  abstract  = {Significant heat capacity changes (DeltaCp) often accompany protein unfolding, protein binding, and specific DNA-ligand binding reactions. Such changes are widely used to analyze contributions arising from hydrophobic and polar hydration. Current models relate the magnitude of DeltaCp to the solvent accessible surface area (ASA) of the molecule. However, for many binding systems-particularly those involving non-peptide ligands-these models predict a DeltaCp that is significantly different from the experimentally measured value. Electrostatic interactions provide a potential source of heat capacity changes and do not scale with ASA. Using finite-difference Poisson-Boltzmann methods (FDPB), we have determined the contribution of electrostatics to the DeltaCp associated with binding for DNA binding reactions involving the ligands DAPI, netropsin, lexitropsin, and the lambda repressor binding domain.},
  file      = {:by-author/G/Gallagher/1998_Gallagher_769.pdf:PDF},
  keywords  = {Heat Capacity; Protein Physics},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Galvez2010,
  author    = {Enrique J. Galvez},
  journal   = {Am. J. Phys.},
  title     = {Qubit quantum mechanics with correlated-photon experiments},
  year      = {2010},
  pages     = {510--519},
  volume    = {78},
  doi       = {10.1119/1.3337692},
  file      = {2010_Galvez_510.pdf:by-author/G/Galvez/2010_Galvez_510.pdf:PDF},
  keywords  = {Quantum Computers; Quantum Computing; Quantum Mechanics (QM); Teaching},
  owner     = {saulius},
  timestamp = {2013.10.22},
  creationdate = {2013-10-22T00:00:00},
  url       = {http://www.colgate.edu/portaldata/imagegallerywww/98c178dc-7e5b-4a04-b0a1-a73abf7f13d5/ImageGallery/qubit-quantum-mechanics.pdf},
}

@Manuscript{Galvez2007,
  author    = {Enrique J. Galvez and Mark Beck},
  title     = {Quantum Optics Experiments with Single Photons for Undergraduate Laboratories},
  year      = {2007},
  keywords  = {Quantum Mechanics (QM); Teaching},
  url       = {https://spie.org/etop/2007/etop07expX.pdf},
  file      = {2007_Galvez.pdf:by-author/G/Galvez/2007_Galvez.pdf:PDF},
  owner     = {saulius},
  timestamp = {2014.07.21},
  creationdate = {2014-07-21T00:00:00},
}

@Article{Gandara2014,
  author    = {Felipe Gándara and Thomas D. Bennett},
  journal   = {{IUCrJ}},
  title     = {Crystallography of metal--organic frameworks},
  year      = {2014},
  month     = {oct},
  number    = {6},
  pages     = {563--570},
  volume    = {1},
  abstract  = {Metal–organic frameworks (MOFs) are one of the most intensely studied material types in recent times. Their networks, resulting from the formation of strong bonds between inorganic and organic building units, offer unparalled chemical diversity and pore environments of growing complexity. Therefore, advances in single-crystal X-ray diffraction equipment and techniques are required to characterize materials with increasingly larger surface areas, and more complex linkers. In addition, whilst structure solution from powder diffraction data is possible, the area is much less populated and we detail the current efforts going on here. We also review the growing number of reports on diffraction under non-ambient conditions, including the response of MOF structures to very high pressures. Such experiments are important due to the expected presence of stresses in proposed applications of MOFs – evidence suggesting rich and complex behaviour. Given the entwined and inseparable nature of their structure, properties and applications, it is essential that the field of structural elucidation is able to continue growing and advancing, so as not to provide a rate-limiting step on characterization of their properties and incorporation into devices and applications. This review has been prepared with this in mind.},
  doi       = {10.1107/S2052252514020351},
  file      = {2014_Gándara_563.pdf:by-author/G/Gándara/2014_Gándara_563.pdf:PDF},
  groups    = {sg/MOF, sg/MOFs, am/MOFs},
  keywords  = {Crystal Growth; Metal-Organic Frameworks (MOF); Non-ambient Crystallography},
  owner     = {saulius},
  publisher = {International Union of Crystallography ({IUCr})},
  timestamp = {2017.01.29},
  creationdate = {2017-01-29T00:00:00},
  url       = {http://dx.doi.org/10.1107/S2052252514020351},
}

@Article{Gang2009,
  author    = {Wu Gang and Cai Li and Li Qin},
  journal   = {Journal of Semiconductors},
  title     = {Ternary Logic Circuit Design Based on Single Electron Transistors},
  year      = {2009},
  pages     = {025011},
  file      = {:by-author/G/Gang/2009_Gang_025011.pdf:PDF},
  keywords  = {Computer Science (CS); Logic Circuits; Ternary},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Gangisetty2005,
  author    = {Gangisetty, Omkaram and Jones, Charles E. and Bhagwat, Medha and Nossal, Nancy G.},
  journal   = {The Journal of biological chemistry},
  title     = {Maturation of bacteriophage T4 lagging strand fragments depends on interaction of T4 RNase H with T4 32 protein rather than the T4 gene 45 clamp.},
  year      = {2005},
  pages     = {12876--87},
  volume    = {280},
  abstract  = {In the bacteriophage T4 DNA replication system, T4 RNase H removes the RNA primers and some adjacent DNA before the lagging strand fragments are ligated. This 5'-nuclease has strong structural and functional similarity to the FEN1 nuclease family. We have shown previously that T4 32 protein binds DNA behind the nuclease and increases its processivity. Here we show that T4 RNase H with a C-terminal deletion (residues 278-305) retains its exonuclease activity but is no longer affected by 32 protein. T4 gene 45 replication clamp stimulates T4 RNase H on nicked or gapped substrates, where it can be loaded behind the nuclease, but does not increase its processivity. An N-terminal deletion (residues 2-10) of a conserved clamp interaction motif eliminates stimulation by the clamp. In the crystal structure of T4 RNase H, the binding sites for the clamp at the N terminus and for 32 protein at the C terminus are located close together, away from the catalytic site of the enzyme. By using mutant T4 RNase H with deletions in the binding site for either the clamp or 32 protein, we show that it is the interaction of T4 RNase H with 32 protein, rather than the clamp, that most affects the maturation of lagging strand fragments in the T4 replication system in vitro and T4 phage production in vivo.},
  file      = {:by-author/G/Gangisetty/2005_Gangisetty_12876.pdf:PDF},
  keywords  = {{gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Webpage{Ganssle2005,
  author    = {Jack Ganssle},
  retrieved = {2010-09-07},
  title     = {Subtract software costs by adding CPUs},
  url       = {http://www.embedded.com/design/other/4006449/Subtract-software-costs-by-adding-CPUs},
  year      = {2005},
  abstract  = {The best way to get a project done on time is to break it into smaller, more manageable chunks. That theory works better than some programmers suspect, extending even into multiprocessing systems. Jack Ganssle shows how breaking one big program into smaller programs that each run on their own processor can work wonders on performance, schedules, and sanity.},
  file      = {:by-author/G/Ganssle/2005_Ganssle.odt:},
  keywords  = {Computer Science (CS); Software-design},
  owner     = {saulius},
  timestamp = {2015.03.03},
  creationdate = {2015-03-03T00:00:00},
}

@Article{Gantz2016,
  author    = {Gantz, Valentino M. and Bier, Ethan},
  journal   = {BioEssays},
  title     = {The dawn of active genetics},
  year      = {2016},
  issn      = {1521-1878},
  pages     = {50--63},
  volume    = {38},
  abstract  = {On December 18, 2014, a yellow female fly quietly emerged from her pupal case. What made her unique was that she had only one parent carrying a mutant allele of this classic recessive locus. Then, one generation later, after mating with a wild-type male, all her offspring displayed the same recessive yellow phenotype. Further analysis of other such yellow females revealed that the construct causing the mutation was converting the opposing chromosome with 95% efficiency. These simple results, seen also in mosquitoes and yeast, open the door to a new era of genetics wherein the laws of traditional Mendelian inheritance can be bypassed for a broad variety of purposes. Here, we consider the implications of this fundamentally new form of “active genetics,” its applications for gene drives, reversal and amplification strategies, its potential for contributing to cell and gene therapy strategies, and ethical/biosafety considerations associated with such active genetic elements. Also watch the Video Abstract.},
  doi       = {10.1002/bies.201500102},
  file      = {2016_Gantz_50.pdf:by-author/G/Gantz/2016_Gantz_50.pdf:PDF},
  groups    = {sg/CRISPR-Cas},
  keywords  = {Active Genetics; Copy Cat Element; Drosophila; ERACR; Gene Drive; MCR; Mutagenic Chain Reaction},
  owner     = {saulius},
  timestamp = {2016.01.05},
  creationdate = {2016-01-05T00:00:00},
  url       = {http://dx.doi.org/10.1002/bies.201500102},
}

@Article{Gao2010,
  author    = {Fuchang Gao and Lixing Han},
  journal   = {Computational Optimization and Applications},
  title     = {Implementing the Nelder-Mead simplex algorithm with adaptive parameters},
  year      = {2010},
  issn      = {0926-6003},
  pages     = {259--277},
  volume    = {51},
  doi       = {10.1007/s10589-010-9329-3},
  file      = {:by-author/G/Gao/2010_Gao_259.pdf:PDF},
  issue     = {1},
  keywords  = {Computer Science (CS); Minimisation; Simplex Method},
  owner     = {saulius},
  publisher = {Springer US},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
  url       = {http://dx.doi.org/10.1007/s10589-010-9329-3},
}

@Article{Gao2005,
  author    = {Gao, Haixiao and Ayub, Maximiliano Juri and Levin, Mariano J and Frank, Joachim},
  journal   = {Proceedings of the National Academy of Sciences of the United States of America},
  title     = {The structure of the 80S ribosome from Trypanosoma cruzi reveals unique rRNA components.},
  year      = {2005},
  pages     = {10206--11},
  volume    = {102},
  abstract  = {We present analysis, by cryo-electron microscopy and single-particle reconstruction, of the structure of the 80S ribosome from Trypanosoma cruzi, the kinetoplastid protozoan pathogen that causes Chagas disease. The density map of the T. cruzi 80S ribosome shows the phylogenetically conserved eukaryotic rRNA core structure, together with distinctive structural features in both the small and large subunits. Remarkably, a previously undescribed helical structure appears in the small subunit in the vicinity of the mRNA exit channel. We propose that this rRNA structure likely participates in the recruitment of ribosome onto the 5' end of mRNA, in facilitating and modulating the initiation of translation that is unique to the trypanosomes.},
  file      = {Gao_2005_10206-struct_80S_ribosome_T.cruzi.pdf:by-author/G/Gao/2005_Gao_10206.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Gao2013,
  author    = {Gao, H. and Otero-de-la-Roza, A. and Aouadi, S. M. and Johnson, E. R. and Martini, A.},
  journal   = {Modelling and Simulation in Materials Science and Engineering},
  title     = {An empirical model for silver tantalate},
  year      = {2013},
  pages     = {055002},
  volume    = {21},
  file      = {[PDF] from researchgate.net:by-author/G/Gao/2013_Gao_055002.pdf:application/pdf;Snapshot:by-author/G/Gao/2013_Gao_055002.html:text/html},
  groups    = {sg/JAC2009},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://iopscience.iop.org/0965-0393/21/5/055002},
  urldate   = {2015-08-31},
}

@Article{Garbett2012,
  author      = {Garbett, Nichola C. and Chaires, Jonathan B.},
  journal     = {Expert Opin Drug Discov},
  title       = {Thermodynamic studies for drug design and screening.},
  year        = {2012},
  month       = {Apr},
  number      = {4},
  pages       = {299--314},
  volume      = {7},
  abstract    = {A key part of drug design and development is the optimization of molecular interactions between an engineered drug candidate and its binding target. Thermodynamic characterization provides information about the balance of energetic forces driving binding interactions and is essential for understanding and optimizing molecular interactions.This review discusses the information that can be obtained from thermodynamic measurements and how this can be applied to the drug development process. Current approaches for the measurement and optimization of thermodynamic parameters are presented, specifically higher throughput and calorimetric methods. Relevant literature for this review was identified in part by bibliographic searches for the period 2004 - 2011 using the Science Citation Index and PUBMED and the keywords listed below.The most effective drug design and development platform comes from an integrated process utilizing all available information from structural, thermodynamic and biological studies. Continuing evolution in our understanding of the energetic basis of molecular interactions and advances in thermodynamic methods for widespread application are essential to realize the goal of thermodynamically driven drug design. Comprehensive thermodynamic evaluation is vital early in the drug development process to speed drug development toward an optimal energetic interaction profile while retaining good pharmacological properties. Practical thermodynamic approaches, such as enthalpic optimization, thermodynamic optimization plots and the enthalpic efficiency index, have now matured to provide proven utility in the design process. Improved throughput in calorimetric methods remains essential for even greater integration of thermodynamics into drug design.},
  doi         = {10.1517/17460441.2012.666235},
  file        = {2012_Garbett_299.pdf:by-author/G/Garbett/2012_Garbett_299.pdf:PDF},
  institution = {Biophysics Core Facility, University of Louisville, James Graham Brown Cancer Center, Clinical and Translational Research Building, 505 South Hancock Street, Louisville, KY 40202, USA. nichola.garbett@louisville.edu},
  keywords    = {Binding Sites; Calorimetry; Crystallography; Differential Scanning; Drug Design; Fluorescence; Humans; Ligands; Magnetic Resonance Spectroscopy; Models; Molecular; Thermodynamics; X-Ray},
  language    = {eng},
  medline-pst = {ppublish},
  owner       = {saulius},
  pmid        = {22458502},
  timestamp = {2016.03.05},
  creationdate = {2016-03-05T00:00:00},
  url         = {http://dx.doi.org/10.1517/17460441.2012.666235},
}

@Article{Garcia1999,
  author    = {García, L. R. and Molineux, I. J.},
  journal   = {Proceedings of the National Academy of Sciences of the United States of America},
  title     = {Translocation and specific cleavage of bacteriophage T7 DNA in vivo by EcoKI.},
  year      = {1999},
  pages     = {12430--5},
  volume    = {96},
  abstract  = {Infection of Escherichia coli containing the type I restriction enzyme EcoKI by bacteriophage T7 0.3 mutants leads to restriction during the late stages of genome entry and during DNA replication. Patterns of cleavage in vivo suggest that some cutting occurs near the midpoint of two recognition sites, consistent with the idea that EcoKI translocates DNA bidirectionally through itself and cuts when two enzyme molecules collide. Rapid ejection of a 0.3(+) T7 genome from a bacteriophage lambda particle results in degradation of the infecting DNA by EcoKI, showing that the normal T7 DNA translocation process delays restriction. A unique recognition site inserted at the genomic left end allows EcoKI to function as a molecular motor and to translocate the remaining 39 kilobases of T7 DNA into the cell.},
  file      = {:by-author/G/García/1999_Garcia_12430.pdf:PDF},
  keywords  = {TypeI},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Garcia-Garibay2005,
  author    = {Garcia-Garibay, Miguel A},
  journal   = {Proceedings of the National Academy of Sciences of the United States of America},
  title     = {Crystalline molecular machines: encoding supramolecular dynamics into molecular structure.},
  year      = {2005},
  pages     = {10771--6},
  volume    = {102},
  abstract  = {Crystalline molecular machines represent an exciting new branch of crystal engineering and materials science with important implications to nanotechnology. Crystalline molecular machines are crystals built with molecules that are structurally programmed to respond collectively to mechanic, electric, magnetic, or photonic stimuli to fulfill specific functions. One of the main challenges in their construction derives from the picometric precision required for their mechanic operation within the close-packed, self-assembled environment of crystalline solids. In this article, we outline some of the general guidelines for their design and apply them for the construction of molecular crystals with units intended to emulate macroscopic gyroscopes and compasses. Recent advances in the preparation, crystallization, and dynamic characterization of these interesting systems offer a foothold to the possibilities and help highlight some avenues for future experimentation.},
  file      = {2005_Garcia-Garibay_10771.pdf:by-author/G/Garcia-Garibay/2005_Garcia-Garibay_10771.pdf:PDF},
  keywords  = {Molecular Machines},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Garcia-Pacios2008,
  author    = {M. Garcia-Pacios and J.Á. Fernández-Higuero and I. de la Arada and J.L.R. Arrondo},
  journal   = {Biotechnology \& Biotechnological Equipment},
  title     = {Protein stability studied by infrared spectroscopy},
  year      = {2008},
  pages     = {625--628},
  volume    = {22},
  abstract  = {Infrared structural analysis usually implies a mathematical approach to extract the information contained in the protein amide bands. Thermal profiles have been used to help in the understanding of protein stability. A new approach, generalized 2D-IR correlational spectroscopy, has been recently introduced. This approach performs a correlation analysis of the dynamic fluctuations caused by an external perturbation, to enhance spectral resolution. By using a combination of these three approaches we have studied the thermal unfolding of several soluble and membrane proteins showing that the various secondary structure elements unfold at different temperatures showing a different stability, which is more dependent on the protein topology rather than on secondary structure.},
  file      = {2008_Garcia-Pacios_625.pdf:by-author/G/Garcia-Pacios/2008_Garcia-Pacios_625.pdf:PDF},
  keywords  = {Amide Bond; FTIR; Infrared Spectroscopy; Protein Physics; Protein Stability},
  owner     = {saulius},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
  url       = {http://www.diagnosisp.com/dp/journals/view_article.php?journal_id=1&archive=0&issue_id=17&article_id=474},
}

@Article{Garfield1990,
  author    = {Eugene Garfield},
  journal   = {Essays of an Information Scientist: Journalology},
  title     = {Journal Citation Studies. 52. The Multifaceted Structure Of Crystallography Research. Part 1. Core Journals, High Impact Papers, and Current Research Fronts},
  year      = {1990},
  pages     = {327--336},
  volume    = {13},
  file      = {:by-author/G/Garfield/1990_Garfield_327.pdf:PDF},
  groups    = {sg/Bibliometrics},
  keywords  = {Impact Factors},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Garman2003,
  author    = {Garman, Elspeth and Murray, James W.},
  journal   = {Acta Crystallographica Section D},
  title     = {Heavy-atom derivatization},
  year      = {2003},
  pages     = {1903--1913},
  volume    = {59},
  doi       = {10.1107/S0907444903012794},
  file      = {ba5042.pdf:by-author/G/Garman/2003_Garman_1903.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444903012794},
}

@InBook{Garman2007,
  author           = {Elspeth Garman and Robin L. Owen},
  pages            = {1--18},
  publisher        = {Humana Press},
  title            = {Cryocrystallography of macromolecules. Practice and optimization},
  year             = {2007},
  isbn             = {1597452661},
  abstract         = {Techniques for flash-cooling protein crystals to around 100K (–173°C) for data collection have developed enormously in the last decade, to the extent that cryocrystallography is now standard practice. The main advantage of these methods is the vastly reduced rate of radiation damage to protein crystals in the X-ray beam at cryogenic temperatures over room temperature, extending their lifetimes so that complete datasets can be collected from a single crystal. The practical application of the techniques has become somewhat anecdotal and rather fixed within individual laboratories. This chapter gives step-by-step guidelines for flash-cooling crystals and some of the rationale for the recommended procedures. Optimization of the entire cryoprotocol can give substantial improvements to both the resolution and quality of the data, often resulting in more straightforward structure solution and subsequent model refinement. Attention to seemingly insignificant details can have a real impact on the usefulness of the final dataset, and are thus worth addressing.},
  creationdate     = {2012-10-21T00:00:00},
  doi              = {10.1385/1-59745-266-1:1},
  file             = {:by-author/G/Garman/2007_Garman_1.pdf:PDF},
  keywords         = {Cryocrystallography; Cryogen; Cryoprotectant; Cryoprotection; Cryostat; Ice; Mosaicity; Protocols; Radiation Damage},
  modificationdate = {2024-08-15T17:44:42},
  owner            = {saulius},
  timestamp        = {2012.10.21},
}

@Article{Garnier1978,
  author    = {Garnier, J. and Osguthorpe, D.J. and Robson, B.},
  journal   = {Journal of Molecular Biology},
  title     = {Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins},
  year      = {1978},
  issn      = {0022-2836},
  month     = {Mar},
  number    = {1},
  pages     = {97–120},
  volume    = {120},
  abstract  = {(1) Co-operation between a laboratory interested in developing the theory for protein secondary structure prediction methods and a laboratory interested in applying and comparing such methods has led to the development of a simple predictive algorithm. (2) Four-state predictions, in which each residue is unambiguously assigned one conformational state of α-helix, extended chain, reverse turn or coil, predict 49% of residue states correctly (in a sample of 26 proteins) when the overall helix and extended-chain content is not taken into account. (3) When the relative abundances of helix, extended chain, reverse turn and coil observed by X-ray crystallography are taken into account, a single constant for each protein and type of conformation can be used to bias the prediction. When predictions are optimized in this way, 63% of all residue states are unambiguously and correctly assigned. (4) By analysing the nature of the bias required, proteins can be classified into helix-rich types, pleated-sheet-rich types, and so on. It is shown that, if the type of protein can be determined even approximately by circular dichroism, 57% of residue states can be correctly predicted without taking into account the X-ray structure. Further, comparable predictions can be obtained if, instead of circular dichroism, preliminary predictions are made to assess the protein type. (5) It is emphasized that the numbers quoted here depend on the method used to assess accuracy, and the algorithm is shown to be at least as good as, and usually superior to, the reported prediction methods assessed in the same way. (6) Ways of further enhancing predictions by the use of additional information from hydrophobic triplets and homologous sequences are also explored. Hydro-phobic triplet information does not significantly improve predictive power and it is concluded that this information is used by proteins in the next stage of folding. On the other hand, the use of homologous sequences appears to be very promising. (7) The implication of these results in protein folding is discussed.},
  doi       = {10.1016/0022-2836(78)90297-8},
  file      = {1978_Garnier_97.pdf:by-author/G/Garnier/1978_Garnier_97.pdf:PDF},
  owner     = {andrius},
  publisher = {Elsevier BV},
  timestamp = {2017.03.28},
  creationdate = {2017-03-28T00:00:00},
  url       = {http://dx.doi.org/10.1016/0022-2836(78)90297-8},
}

@Manuscript{Gartner1999,
  author    = {Gärtner},
  title     = {Fast and Robust Smallest Enclosing Balls},
  year      = {1999},
  keywords  = {Algorithms; Computer Science (CS); Smallest Enclosing Balls},
  file      = {:by-author/G/Gärtner/1999_Gärtner.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Garvie2000,
  author    = {Garvie, C. W. and Phillips, S. E.},
  journal   = {Structure (London, England : 1993)},
  title     = {Direct and indirect readout in mutant Met repressor-operator complexes.},
  year      = {2000},
  pages     = {905--14},
  volume    = {8},
  file      = {:by-author/G/Garvie/2000_Garvie_905.pdf:PDF},
  keywords  = {DNA Protein; Readout},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Garvie2001,
  author    = {Garvie, C. W. and Wolberger, C.},
  journal   = {Molecular cell},
  title     = {Recognition of specific DNA sequences.},
  year      = {2001},
  pages     = {937--46},
  volume    = {8},
  abstract  = {Proteins that recognize specific DNA sequences play a central role in the regulation of transcription. The tremendous increase in structural information on protein-DNA complexes has uncovered a remarkable structural diversity in DNA binding folds, while at the same time revealing common themes in binding to target sites in the genome.},
  file      = {:by-author/G/Garvie/2001_Garvie_937.pdf:PDF},
  keywords  = {DNA Protein; Readout},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Gasiunas2012,
  author    = {Gasiunas, Giedrius and Barrangou, Rodolphe and Horvath, Philippe and Siksnys, Virginijus},
  journal   = {Proceedings of the National Academy of Sciences},
  title     = {{Cas9–crRNA} ribonucleoprotein complex mediates specific {DNA} cleavage for adaptive immunity in bacteria},
  year      = {2012},
  pages     = {E2579},
  volume    = {109},
  abstract  = {Clustered, regularly interspaced, short palindromic repeats (CRISPR)/CRISPR-associated (Cas) systems provide adaptive immunity against viruses and plasmids in bacteria and archaea. The silencing of invading nucleic acids is executed by ribonucleoprotein complexes preloaded with small, interfering CRISPR RNAs (crRNAs) that act as guides for targeting and degradation of foreign nucleic acid. Here, we demonstrate that the Cas9–crRNA complex of the Streptococcus thermophilus CRISPR3/Cas system introduces in vitro a double-strand break at a specific site in DNA containing a sequence complementary to crRNA. DNA cleavage is executed by Cas9, which uses two distinct active sites, RuvC and HNH, to generate site-specific nicks on opposite DNA strands. Results demonstrate that the Cas9–crRNA complex functions as an RNA-guided endonuclease with RNA-directed target sequence recognition and protein-mediated DNA cleavage. These findings pave the way for engineering of universal programmable RNA-guided DNA endonucleases.},
  doi       = {10.1073/pnas.1208507109},
  file      = {2012_Gasiunas_E2579.pdf:by-author/G/Gasiunas/2012_Gasiunas_E2579.pdf:PDF},
  groups    = {sg/CRISPR-Cas},
  keywords  = {CRISPR; Cas9},
  owner     = {em},
  timestamp = {2013.01.03},
  creationdate = {2013-01-03T00:00:00},
}

@Article{Gaspari2016,
  author      = {Roberto Gaspari and Chris Rechlin and Andreas Heine and Giovanni Bottegoni and Walter Rocchia and Daniel Schwarz and Jörg Bomke and Hans-Dieter Gerber and Gerhard Klebe and Andrea Cavalli},
  journal     = {J Med Chem},
  title       = {Kinetic and Structural Insights into the Mechanism of Binding of Sulfonamides to Human Carbonic Anhydrase by Computational and Experimental Studies.},
  year        = {2016},
  month       = {May},
  number      = {9},
  pages       = {4245--4256},
  volume      = {59},
  abstract    = {The binding of sulfonamides to human carbonic anhydrase II (hCAII) is a complex and long-debated example of protein-ligand recognition and interaction. In this study, we investigate the para-substituted n-alkyl and hydroxyethylene-benzenesulfonamides, providing a complete reconstruction of their binding pathway to hCAII by means of large-scale molecular dynamics simulations, density functional calculations, surface plasmon resonance (SPR) measurements, and X-ray crystallography experiments. Our analysis shows that the protein-ligand association rate (kon) dramatically increases with the ligand's hydrophobicity, pointing to the existence of a prebinding stage largely stabilized by a favorable packing of the ligand's apolar moieties with the hCAII "hydrophobic wall". The characterization of the binding pathway allows an unprecedented understanding of the structure-kinetic relationship in hCAII/benzenesulfonamide complexes, depicting a paradigmatic scenario for the multistep binding process in protein-ligand systems.},
  doi         = {10.1021/acs.jmedchem.5b01643},
  file        = {2016_Gaspari_4245.pdf:by-author/G/Gaspari/2016_Gaspari_4245.pdf:PDF},
  institution = {Department of Pharmacy and Biotechnology, University of Bologna , 40126 Bologna, Italy.},
  language    = {eng},
  medline-pst = {ppublish},
  owner       = {alexey},
  pmid        = {26700575},
  timestamp = {2016.09.05},
  creationdate = {2016-09-05T00:00:00},
  url         = {http://dx.doi.org/10.1021/acs.jmedchem.5b01643},
}

@Manuscript{Gassanenko1999,
  author    = {Gassanenko, M. L.},
  title     = {Threaded Code Execution and Return Address Manipulations from the Lambda Calculus Viewpoint},
  year      = {1999},
  keywords  = {Computer Science (CS); Threaded Code},
  abstract  = {This paper presents a lambda-calculus-based formal model of Forth's mechanism of code execution. This model is able to cope with control transfers implemented via the interpretation stack changes, a Forth technique that rarely can be found in other programming languages. The formal model may be used in compiler construction, program verification, and in computer science lecture courses.},
  file      = {:by-author/G/Gassanenko/1999_Gassanenko.pdf:PDF},
  groups    = {sg/Threaded code},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Gauchet2006,
  author    = {Gauchet, Cécile and Labadie, Guillermo R. and Poulter, C. Dale},
  journal   = {Journal of the American Chemical Society},
  title     = {Regio- and chemoselective covalent immobilization of proteins through unnatural amino acids.},
  year      = {2006},
  pages     = {9274--5},
  volume    = {128},
  abstract  = {A general approach was developed for the regio- and chemoselective covalent immobilization of soluble proteins on glass surfaces through an unnatural amino acid created by post-translationally modifying the cysteine residue in a CaaX recognition motif with functional groups suitable for &quot;click&quot; chemistry or a Staudinger ligation. Farnesyl diphosphate analogues bearing omega-azide or omega-alkyne moieties were attached to the cysteine residue in Cys-Val-Ile-Ala motifs at the C-termini of engineered versions of green fluorescent protein (GFP) and glutathione S-transferase (GST) by protein farnesyltransferase. The derivatized proteins were attached to glass slides bearing linkers containing azide (&quot;click&quot; chemistry) or phosphine (Staudinger ligation) groups. &quot;Click&quot;-immobilized proteins were detected by fluorescently labeled antibodies and remained attached to the slide through two cycles of stripping under stringent conditions at 80 degrees C. GFP immobilized by a Staudinger ligation was detected by directly imagining the GFP fluorophore over a period of 6 days. These methods for covalent immobilization of proteins should be generally applicable. CaaX recognition motifs can easily be appended to the C-terminus of a cloned protein by a simple modification of the corresponding gene, and virtually any soluble protein or peptide bearing a CaaX motif is a substrate for protein farnesyltransferase.},
  file      = {:by-author/G/Gauchet/2006_Gauchet_9274.pdf:PDF},
  keywords  = {Bioconjugation},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@InCollection{Gayvoronsky2015,
  author    = {Gayvoronsky, V. Ya and Popov, A. S. and Brodyn, M. S. and Uklein, A. V. and Multian, V. V. and Shul’zhenko, O. O.},
  booktitle = {Nanocomposites, nanophotonics, nanobiotechnology, and applications},
  publisher = {Springer},
  title     = {The effect of sintering temperature on linear and nonlinear optical properties of {YAG} nanoceramics},
  year      = {2015},
  pages     = {147--164},
  file      = {[PDF] from researchgate.net:by-author/G/Gayvoronsky/2015_Gayvoronsky_147.pdf:application/pdf;Snapshot:by-author/G/Gayvoronsky/2015_Gayvoronsky_147.html:text/html},
  groups    = {sg/NAR2012},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://link.springer.com/chapter/10.1007/978-3-319-06611-0_13},
  urldate   = {2015-08-31},
}

@Article{Geierstanger1994,
  author    = {Geierstanger, B. H. and Mrksich, M. and Dervan, P. B. and Wemmer, D. E.},
  journal   = {Science (New York, N.Y.)},
  title     = {Design of a G.C-specific DNA minor groove-binding peptide.},
  year      = {1994},
  pages     = {646--50},
  volume    = {266},
  abstract  = {A four-ring tripeptide containing alternating imidazole and pyrrole carboxamides specifically binds six-base pair 5'-(A,T)GCGC(A,T)-3' sites in the minor groove of DNA. The designed peptide has a specificity completely reversed from that of the tripyrrole distamycin, which binds A,T sequences. Structural studies with nuclear magnetic resonance revealed that two peptides bound side-by-side and in an antiparallel orientation in the minor groove. Each of the four imidazoles in the 2:1 ligand-DNA complex recognized a specific guanine amino group in the GCGC core through a hydrogen bond. Targeting a designated four-base pair G.C tract by this synthetic ligand supports the generality of the 2:1 peptide-DNA motif for sequence-specific minor groove recognition of DNA.},
  file      = {:by-author/G/Geierstanger/1994_Geierstanger_646.pdf:PDF},
  keywords  = {Direct; Readout; Struct},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Gelbin1996,
  author    = {Gelbin, Anke and Schneider, Bohdan and Clowney, Lester and Hsieh, Shu-Hsin and Olson, Wilma K. and Berman, Helen M.},
  journal   = {Journal of the American Chemical Society},
  title     = {Geometric Parameters in Nucleic Acids: Sugar and Phosphate Constituents},
  year      = {1996},
  pages     = {519--529},
  volume    = {118},
  file      = {:by-author/G/Gelbin/1996_Gelbin_519.pdf:PDF},
  keywords  = {X-ray Crystallography},
  owner     = {andrius},
  timestamp = {2012.05.11},
  creationdate = {2012-05-11T00:00:00},
}

@Article{Gelman2009,
  author    = {Gelman},
  journal   = {Statistical Science},
  title     = {Bayes, Jeffreys, Prior Distributions and the Philosophy of Statistics},
  year      = {2009},
  pages     = {176--178},
  volume    = {24},
  doi       = {10.1214/09-STS284D},
  file      = {:by-author/G/Gelman/2009_Gelman_176.pdf:PDF},
  groups    = {sg/Bayesian},
  keywords  = {Bayesian Statistics; Mathematics},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Gelman2013,
  author    = {Gelman, Andrew and Shalizi, Cosma Rohilla},
  journal   = {British Journal of Mathematical and Statistical Psychology},
  title     = {Philosophy and the practice of {B}ayesian statistics},
  year      = {2013},
  issn      = {2044-8317},
  pages     = {8--38},
  volume    = {66},
  abstract  = {A substantial school in the philosophy of science identifies Bayesian inference with inductive inference and even rationality as such, and seems to be strengthened by the rise and practical success of Bayesian statistics. We argue that the most successful forms of Bayesian statistics do not actually support that particular philosophy but rather accord much better with sophisticated forms of hypothetico-deductivism. We examine the actual role played by prior distributions in Bayesian models, and the crucial aspects of model checking and model revision, which fall outside the scope of Bayesian confirmation theory. We draw on the literature on the consistency of Bayesian updating and also on our experience of applied work in social science. Clarity about these matters should benefit not just philosophy of science, but also statistical practice. At best, the inductivist view has encouraged researchers to fit and compare models without checking them; at worst, theorists have actively discouraged practitioners from performing model checking because it does not fit into their framework.},
  doi       = {10.1111/j.2044-8317.2011.02037.x},
  file      = {:by-author/G/Gelman/2013_Gelman_8.pdf:PDF},
  groups    = {sg/Bayesian},
  keywords  = {Bayesian Statistics; Criticism},
  owner     = {saulius},
  publisher = {Blackwell Publishing Ltd},
  timestamp = {2012.09.30},
  creationdate = {2012-09-30T00:00:00},
  url       = {http://dx.doi.org/10.1111/j.2044-8317.2011.02037.x},
}

@Manuscript{Gelman2011,
  author       = {Andrew Gelman and Cosma Rohilla Shalizi},
  title        = {Philosophy and the practice of {B}ayesian statistics},
  year         = {2011},
  keywords     = {Bayesian Statistics; Criticism},
  organization = {Department of Statistics and Department of Political Science, Columbia University;Statistics Department, Carnegie Mellon University},
  abstract     = {A substantial school in the philosophy of science identifies Bayesian inference with inductive inference and even rationality as such, and seems to be strengthened by the rise and practical success of Bayesian statistics. We argue that the most successful forms of Bayesian statistics do not actually support that particular philosophy but rather accord much better with sophisticated forms of hypothetico-deductivism. We examine the actual role played by prior distributions in Bayesian models, and the crucial aspects of model checking and model revision, which fall outside the scope of Bayesian confirmation theory. We draw on the literature on the consistency of Bayesian updating and also on our experience of applied work in social science. Clarity about these matters should benefit not just philosophy of science, but also statistical practice. At best, the inductivist view has encouraged researchers to fit and compare models without checking them; at worst, theorists have actively discouraged practitioners from performing model checking because it does not fit into their frame- work.},
  file         = {2011_Gelman.pdf:by-author/G/Gelman/2011_Gelman.pdf:PDF},
  groups       = {sg/Bayesian},
  owner        = {saulius},
  timestamp = {2012.09.22},
  creationdate = {2012-09-22T00:00:00},
}

@Article{Gemmen2006,
  author    = {Gemmen, Gregory J. and Millin, Rachel and Smith, Douglas E.},
  journal   = {Nucleic acids research},
  title     = {DNA looping by two-site restriction endonucleases: heterogeneous probability distributions for loop size and unbinding force.},
  year      = {2006},
  pages     = {2864--77},
  volume    = {34},
  abstract  = {Proteins interacting at multiple sites on DNA via looping play an important role in many fundamental biochemical processes. Restriction endonucleases that must bind at two recognition sites for efficient activity are a useful model system for studying such interactions. Here we used single DNA manipulation to study sixteen known or suspected two-site endonucleases. In eleven cases (BpmI, BsgI, BspMI, Cfr10I, Eco57I, EcoRII, FokI, HpaII, NarI, Sau3AI and SgrAI) we found that substitution of Ca2+ for Mg2+ blocked cleavage and enabled us to observe stable DNA looping. Forced disruption of these loops allowed us to measure the frequency of looping and probability distributions for loop size and unbinding force for each enzyme. In four cases we observed bimodal unbinding force distributions, indicating conformational heterogeneity and/or complex binding energy landscapes. Measured unlooping events ranged in size from 7 to 7500 bp and the most probable size ranged from less than 75 bp to nearly 500 bp, depending on the enzyme. In most cases the size distributions were in much closer agreement with theoretical models that postulate sharp DNA kinking than with classical models of DNA elasticity. Our findings indicate that DNA looping is highly variable depending on the specific protein and does not depend solely on the mechanical properties of DNA.},
  file      = {:by-author/G/Gemmen/2006_Gemmen_2864.pdf:PDF},
  groups    = {sg/Cfr10I},
  keywords  = {Tetra; TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Genest1986,
  author    = {Genest, Christian and Zidek, James V.},
  journal   = {Statistical Science},
  title     = {Combining Probability Distributions: A Critique and an Annotated Bibliography},
  year      = {1986},
  pages     = {114--135},
  volume    = {1},
  abstract  = {This paper addresses the problem of aggregating a number of expert opinions which have been expressed in some numerical form in order to reflect individual uncertainty vis-a-vis a quantity of interest. The primary focus is consensus belief formation and expert use, although some relevant aspects of group decision making are also reviewed. A taxonomy of solutions is presented which serves as the framework for a survey of recent theoretical developments in the area. A number of current research directions are mentioned and an extensive, current annotated bibliography is included.},
  doi       = {10.1214/ss/1177013825},
  file      = {:by-author/G/Genest/1986_Genest_114.pdf:PDF},
  groups    = {sg/Bayesian},
  keywords  = {Bayesian Inference; Expert Opinions; Group Decisions},
  owner     = {andrius},
  publisher = {The Institute of Mathematical Statistics},
  timestamp = {2014.05.21},
  creationdate = {2014-05-21T00:00:00},
  url       = {http://dx.doi.org/10.1214/ss/1177013825},
}

@Article{Genick2007,
  author    = {Genick, Ulrich K.},
  journal   = {Acta Crystallographica Section D},
  title     = {Structure-factor extrapolation using the scalar approximation: theory, applications and limitations},
  year      = {2007},
  pages     = {1029--1041},
  volume    = {63},
  doi       = {10.1107/S0907444907038164},
  file      = {ea5067.pdf:by-author/G/Genick/2007_Genick_1029.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444907038164},
}

@Article{Genis2009,
  author      = {Caroli Genis and Katherine H Sippel and Nicolette Case and Wengang Cao and Balendu Sankara Avvaru and Lawrence J Tartaglia and Lakshmanan Govindasamy and Chingkuang Tu and Mavis Agbandje-McKenna and David N Silverman and Charles J Rosser and Robert McKenna},
  journal     = {Biochemistry},
  title       = {Design of a carbonic anhydrase IX active-site mimic to screen inhibitors for possible anticancer properties.},
  year        = {2009},
  pages       = {1322--1331},
  volume      = {48},
  abstract    = {Recently, a convincing body of evidence has accumulated suggesting that the overexpression of carbonic anhydrase isozyme IX (CA IX) in some cancers contributes to the acidification of the extracellular matrix, which in turn promotes the growth and metastasis of the tumor. These observations have made CA IX an attractive drug target for the selective treatment of certain cancers. Currently, there is no available X-ray crystal structure of CA IX, and this lack of availability has hampered the rational design of selective CA IX inhibitors. In light of these observations and on the basis of structural alignment homology, using the crystal structure of carbonic anhydrase II (CA II) and the sequence of CA IX, a double mutant of CA II with Ala65 replaced by Ser and Asn67 replaced by Gln has been constructed to resemble the active site of CA IX. This CA IX mimic has been characterized kinetically using (18)O-exchange and structurally using X-ray crystallography, alone and in complex with five CA sulfonamide-based inhibitors (acetazolamide, benzolamide, chlorzolamide, ethoxzolamide, and methazolamide), and compared to CA II. This structural information has been evaluated by both inhibition studies and in vitro cytotoxicity assays and shows a correlated structure-activity relationship. Kinetic and structural studies of CA II and CA IX mimic reveal chlorzolamide to be a more potent inhibitor of CA IX, inducing an active-site conformational change upon binding. Additionally, chlorzolamide appears to be cytotoxic to prostate cancer cells. This preliminary study demonstrates that the CA IX mimic may provide a useful model to design more isozyme-specific CA IX inhibitors, which may lead to development of new therapeutic treatments of some cancers.},
  doi         = {10.1021/bi802035f},
  file        = {2009_Genis_1322.pdf:by-author/G/Genis/2009_Genis_1322.pdf:PDF},
  groups      = {sg/chimerae, sg/hCA9},
  institution = {Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, Florida 32610, USA.},
  keywords    = {Amino Acid Sequence; Analysis/chemistry/pharmacology; Antigens; Antineoplastic Agents; Antitumor; Blotting; Carbonic Anhydrase Inhibitors; Carbonic Anhydrases; Catalytic Domain; Cell Death; Cell Line; Cell Proliferation; Chemistry/metabolism; Crystallography; Drug Design; Drug Effects; Drug Screening Assays; Humans; Kinetics; Metabolism; Molecular Mimicry; Molecular Sequence Data; Neoplasm; Protein; Proto-Oncogene Proteins C-bcl-2; Sequence Alignment; Structural Homology; Tumor; Western; X-Ray},
  language    = {eng},
  medline-pst = {ppublish},
  owner       = {alexey},
  pii         = {10.1021/bi802035f},
  pmid        = {19170619},
  timestamp = {2012.12.27},
  creationdate = {2012-12-27T00:00:00},
  url         = {http://dx.doi.org/10.1021/bi802035f},
}

@Article{Gentleman2005,
  author    = {Gentleman, Robert},
  journal   = {Statistical applications in genetics and molecular biology},
  title     = {Reproducible research: a bioinformatics case study.},
  year      = {2005},
  pages     = {Article2},
  volume    = {4},
  abstract  = {While scientific research and the methodologies involved have gone through substantial technological evolution the technology involved in the publication of the results of these endeavors has remained relatively stagnant. Publication is largely done in the same manner today as it was fifty years ago. Many journals have adopted electronic formats, however, their orientation and style is little different from a printed document. The documents tend to be static and take little advantage of computational resources that might be available. Recent work, Gentleman and Temple Lang (2003), suggests a methodology and basic infrastructure that can be used to publish documents in a substantially different way. Their approach is suitable for the publication of papers whose message relies on computation. Stated quite simply, Gentleman and Temple Lang (2003) propose a paradigm where documents are mixtures of code and text. Such documents may be self-contained or they may be a component of a compendium which provides the infrastructure needed to provide access to data and supporting software. These documents, or compendiums, can be processed in a number of different ways. One transformation will be to replace the code with its output -- thereby providing the familiar, but limited, static document. &lt;p /&gt; In this paper we apply these concepts to a seminal paper in bioinformatics, namely The Molecular Classification of Cancer, Golub et al (1999). The authors of that paper have generously provided data and other information that have allowed us to largely reproduce their results. Rather than reproduce this paper exactly we demonstrate that such a reproduction is possible and instead concentrate on demonstrating the usefulness of the compendium concept itself.},
  doi       = {10.2202/1544-6115.1034},
  file      = {2005_Gentleman_Article2.pdf:by-author/G/Gentleman/2005_Gentleman_Article2.pdf:PDF},
  keywords  = {Data Management; Reproducible Research},
  owner     = {saulius},
  timestamp = {2015.06.12},
  creationdate = {2015-06-12T00:00:00},
}

@Article{Gentleman2007,
  author    = {Robert Gentleman and Duncan Temple Lang},
  journal   = {Journal of Computational and Graphical Statistics},
  title     = {Statistical analyses and reproducible research},
  year      = {2007},
  pages     = {1--23},
  volume    = {16},
  doi       = {10.1198/106186007X178663},
  file      = {Statistical Analyses and Reproducible Research - 106186007X178663:by-author/G/Gentleman/2007_Gentleman_1.pdf:application/pdf},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://www.tandfonline.com/doi/pdf/10.1198/106186007X178663},
  urldate   = {2015-06-06},
}

@Article{vanGenuchten1991,
  author    = {Michiel van Genuchten},
  journal   = {IEEE Transactions on Software Engineering},
  title     = {Why is Software Late? An Empirical Study of Reasons For Delav in Software Development},
  year      = {1991},
  pages     = {582--590},
  volume    = {17},
  abstract  = {This paper describes a study of the reasons for delay in software development that was carried out in 1988 and 1989 in a Software Engineering Department. The aim of the study was to gain an insight into the reasons for differences between plans and reality in development activities in order to be able to take actions for improvement. A classification was used to determine the reasons. One hundred and sixty activities, comprising over 15 000 hours of work, have been analyzed. Actions have been taken in the Department as a result of the study. These actions should enable future projects to follow the plan more closely. The actions for improvement include the introduction of maintenance weeks. Similar studies in other software development departments have shown that the reasons varied widely from one department to another. It is recommended that every department should gain an insight into its reasons for delay in software development so as to be able to take appropriate actions for improvement.},
  file      = {:by-author/G/Genuchten/1991_vanGenuchten_582.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.09.18},
  creationdate = {2012-09-18T00:00:00},
}

@Manuscript{Genz1998,
  author    = {Alan Genz and Robert E. Kass},
  title     = {BAYESPACK: A Collection of Numerical Integration Software for Bayesian Analysis},
  year      = {1998},
  keywords  = {Algorithms; Bayesian Statistics; Computer Programs},
  file      = {:by-author/G/Genz/1998_Genz.pdf:PDF;:by-author/G/Genz/1998_Genz.ps:PostScript},
  groups    = {sg/Bayesian},
  owner     = {saulius},
  timestamp = {2013.08.10},
  creationdate = {2013-08-10T00:00:00},
}

@Article{Georgieva2007,
  author    = {Georgieva, Dilyana G. and Kuil, Maxim E. and Oosterkamp, Tjerk H. and Zandbergen, Henny W. and Abrahams, Jan Pieter},
  journal   = {Acta crystallographica. Section D, Biological crystallography},
  title     = {Heterogeneous nucleation of three-dimensional protein nanocrystals.},
  year      = {2007},
  pages     = {564--70},
  volume    = {63},
  abstract  = {Nucleation is the rate-limiting step in protein crystallization. Introducing heterogeneous substrates may in some cases lower the energy barrier for nucleation and thereby facilitate crystal growth. To date, the mechanism of heterogeneous protein nucleation remains poorly understood. In this study, the nucleating properties of fragments of human hair in crystallization experiments have been investigated. The four proteins that were tested, lysozyme, glucose isomerase, a polysaccharide-specific Fab fragment and potato serine protease inhibitor, nucleated preferentially on the hair surface. Macrocrystals and showers of tiny crystals of a few hundred nanometres thickness were obtained also under conditions that did not produce crystals in the absence of the nucleating agent. Cryo-electron diffraction showed that the nanocrystals diffracted to at least 4 A resolution. The mechanism of heterogeneous nucleation was studied using confocal fluorescent microscopy which demonstrated that the protein is concentrated on the nucleating surface. A substantial accumulation of protein was observed on the sharp edges of the hair's cuticles, explaining the strong nucleating activity of the surface.},
  doi       = {10.1107/S0907444907007810},
  file      = {:by-author/G/Georgieva/2007_Georgieva_564.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Germaneau2013,
  author    = {Éric Germaneau and Gang Su and Qing-Rong Zheng},
  journal   = {Journal of Physics: Condensed Matter},
  title     = {New boron nitride structures {B4N4}: a first-principles random searching application},
  year      = {2013},
  pages     = {125504},
  volume    = {25},
  abstract  = {The present investigation searched for new boron nitride (BN) polymorphs by means of first-principles simulations. The ab initio random structure searching strategy was implemented. The electronic and mechanical properties and equation of states of three new metastable B 4 N 4 crystal forms with equilibrium energies close to the most stable BN form, c-BN, are presented. Results show either dynamically stable semiconductors or insulators, one of which is even slightly harder than c-BN. The equation of states is also presented and a phase transition is predicted.},
  doi       = {10.1088/0953-8984/25/12/125504},
  file      = {:by-author/G/Germaneau/2013_Germaneau_125504.pdf:PDF},
  keywords  = {Citing COD},
  owner     = {andrius},
  timestamp = {2013.03.05},
  creationdate = {2013-03-05T00:00:00},
  url       = {http://stacks.iop.org/0953-8984/25/i=12/a=125504},
}

@Article{Germaneau2013a,
  author     = {Germaneau, Éric and Su, Gang and Zheng, Qing-Rong},
  journal    = {Journal of Physics: Condensed Matter},
  title      = {New boron nitride structures {B}4N4: a first-principles random searching application},
  year       = {2013},
  pages      = {125504},
  volume     = {25},
  file       = {[PDF] from researchgate.net:by-author/G/Germaneau/2013_Germaneau_125504b.pdf:application/pdf;[PDF] from researchgate.net:by-author/G/Germaneau/2013_Germaneau_125504a.pdf:application/pdf;Snapshot:by-author/G/Germaneau/2013_Germaneau_125504a.html:text/html;Snapshot:by-author/G/Germaneau/2013_Germaneau_125504.html:text/html},
  groups     = {sg/JAC2009, sg/NAR2012},
  owner      = {saulius},
  shorttitle = {New boron nitride structures {B}4N4},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url        = {http://iopscience.iop.org/0953-8984/25/12/125504},
  urldate    = {2015-08-31},
}

@Article{Gerogiannis2009,
  author    = {Gerogiannis, Demetrios and Nikou, Christophoros and Likas, Aristidis},
  journal   = {Image and Vision Computing},
  title     = {The mixtures of {Student’s t-distributions} as a robust framework for rigid registration},
  year      = {2009},
  issn      = {0262-8856},
  month     = {Aug},
  number    = {9},
  pages     = {1285--1294},
  volume    = {27},
  abstract  = {The problem of registering images or point sets is addressed. At first, a pixel similarity-based algorithm for the rigid registration between single and multimodal images is presented. The images may present dissimilarities due to noise, missing data or outlying measures. The method relies on the partitioning of a reference image by a Student’s t-mixture model (SMM). This partition is then projected onto the image to be registered. The main idea is that a t-component in the reference image corresponds to a t-component in the image to be registered. If the images are correctly registered the distances between the corresponding components is minimized. Moreover, the extension of the method to the registration of point clouds is also proposed. The use of SMM components is justified by the property that they have heavier tails than standard Gaussians, thus providing robustness to outliers. Experimental results indicate that, even in the case of low SNR or important amount of dissimilarities due to temporal changes, the proposed algorithm compares favorably to the mutual information method for image registration and to the Iterative Closest Points (ICP) algorithm for the alignment of point sets.},
  doi       = {10.1016/j.imavis.2008.11.013},
  file      = {:by-author/G/Gerogiannis/2008_Gerogiannis_1285.pdf:PDF},
  groups    = {am/Student's t, am/Expectation maximisation},
  keywords  = {Expectation Maximisation},
  owner     = {andrius},
  publisher = {Elsevier BV},
  timestamp = {2016.03.14},
  creationdate = {2016-03-14T00:00:00},
  url       = {http://www.cs.uoi.gr/~arly/papers/imavis09.pdf},
}

@Article{Geschwindner2015,
  author      = {Stefan Geschwindner and Johan Ulander and Patrik Johansson},
  journal     = {J Med Chem},
  title       = {Ligand Binding Thermodynamics in Drug Discovery: Still a Hot Tip?},
  year        = {2015},
  month       = {Aug},
  number      = {16},
  pages       = {6321--6335},
  volume      = {58},
  abstract    = {The use of ligand binding thermodynamics has been proposed as a potential success factor to accelerate drug discovery. However, despite the intuitive appeal of optimizing binding enthalpy, a number of factors complicate routine use of thermodynamic data. On a macroscopic level, a range of experimental parameters including temperature and buffer choice significantly influence the observed thermodynamic signatures. On a microscopic level, solute effects, structural flexibility, and cooperativity lead to nonlinear changes in enthalpy. This multifactorial character hides essential enthalpy contributions of intermolecular contacts, making them experimentally nonobservable. In this perspective, we present three case studies, reflect on some key factors affecting thermodynamic signatures, and investigate their relation to the hydrophobic effect, enthalpy-entropy compensation, lipophilic ligand efficiency, and promiscuity. The studies highlight that enthalpy and entropy cannot be used as direct end points but can together with calculations increase our understanding of ligand binding and identify interesting outliers that do not behave as expected.},
  doi         = {10.1021/jm501511f},
  file        = {2015_Geschwindner_0000.pdf:by-author/G/Geschwindner/2015_Geschwindner_0000.pdf:PDF},
  institution = {D Mölndal , S-43183 Mölndal, Sweden.},
  keywords    = {Algorithms; Animals; Drug Discovery; Entropy; Humans; Ligands; Methods/trends; Thermodynamics},
  language    = {eng},
  medline-pst = {ppublish},
  owner       = {alexey},
  pmid        = {25915439},
  timestamp = {2016.06.06},
  creationdate = {2016-06-06T00:00:00},
  url         = {http://dx.doi.org/10.1021/jm501511f},
}

@Article{Getling2003,
  author    = {Getling, A. V. and Brausch, O.},
  journal   = {Physical review. E, Statistical, nonlinear, and soft matter physics},
  title     = {Cellular flow patterns and their evolutionary scenarios in three-dimensional Rayleigh-Bénard convection.},
  year      = {2003},
  pages     = {046313},
  volume    = {67},
  abstract  = {The evolution of three-dimensional, cellular convective flows in a plane horizontal layer of a Boussinesq fluid heated from below is studied numerically. Slow motion in the form of a spatially periodic pattern of hexagonal cells is introduced initially. In a further development, the flow can undergo a sequence of transitions between various cell types. The features of the flow evolution agree with the idea of the flow seeking an optimal scale. In particular, two-vortex polygonal cells may form at some evolution stages, with an annular planform of the upflow region and downflows localized in both central and peripheral regions of the cells. If short-wave hexagons are stable, they exhibit a specific, stellate fine structure.},
  file      = {:by-author/G/Getling/2003_Getling_046313.pdf:PDF},
  keywords  = {Benards Cells},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@Manuscript{Geyer2003,
  author    = {Charles J. Geyer},
  title     = {Maximum Likelihood in R},
  year      = {2003},
  file      = {:by-author/G/Geyer/2003_Geyer.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.09.18},
  creationdate = {2012-09-18T00:00:00},
}

@Presentation{Ghahramani2006,
  author     = {Zoubin Ghahramani},
  title      = {Non-parametric Bayesian Methods},
  year       = {2006},
  conference = {Uncertainty in Artificial Intelligence},
  school     = {Gatsby Computational Neuroscience Unit, University College London, UK Center for Automated Learning and Discovery Carnegie Mellon University, USA},
  email      = {zoubin@gatsby.ucl.ac.uk},
  file       = {:by-author/G/Ghahramani/2006_Ghahramani_slides.pdf:PDF},
  groups     = {sg/Bayesian},
  keywords   = {Bayesian Statistics},
  owner      = {saulius},
  pages      = {slides},
  timestamp = {2012.09.30},
  creationdate = {2012-09-30T00:00:00},
  url        = {http://www.gatsby.ucl.ac.uk},
}

@Article{Ghahramani2000,
  author    = {Ghahramani, Z.},
  journal   = {Nature},
  title     = {Computational neuroscience. Building blocks of movement.},
  year      = {2000},
  pages     = {682--3},
  volume    = {407},
  file      = {:by-author/G/Ghahramani/2000_Ghahramani_682.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Ghiringhelli2015,
  author    = {Ghiringhelli, Luca M. and Vybiral, Jan and Levchenko, Sergey V. and Draxl, Claudia and Scheffler, Matthias},
  journal   = {Phys. Rev. Lett.},
  title     = {Big Data of Materials Science: Critical Role of the Descriptor},
  year      = {2015},
  pages     = {105503},
  volume    = {114},
  abstract  = {Statistical learning of materials properties or functions so far starts with a largely silent, nonchallenged step: the choice of the set of descriptive parameters (termed descriptor). However, when the scientific connection between the descriptor and the actuating mechanisms is unclear, the causality of the learned descriptor-property relation is uncertain. Thus, a trustful prediction of new promising materials, identification of anomalies, and scientific advancement are doubtful. We analyze this issue and define requirements for a suitable descriptor. For a classic example, the energy difference of zinc blende or wurtzite and rocksalt semiconductors, we demonstrate how a meaningful descriptor can be found systematically.},
  doi       = {10.1103/PhysRevLett.114.105503},
  file      = {2015_Ghiringhelli_105503.pdf:by-author/G/Ghiringhelli/2015_Ghiringhelli_105503.pdf:PDF},
  issue     = {10},
  keywords  = {Data Management; Databases; Material Properties; NoMaD},
  numpages  = {5},
  owner     = {saulius},
  publisher = {American Physical Society},
  timestamp = {2015.04.02},
  creationdate = {2015-04-02T00:00:00},
  url       = {http://link.aps.org/doi/10.1103/PhysRevLett.114.105503},
}

@Article{Ghosh2003,
  author    = {Ghosh, Anirban and Bansal, Manju},
  journal   = {Acta Crystallographica Section D},
  title     = {A glossary of DNA structures from A to Z},
  year      = {2003},
  pages     = {620--626},
  volume    = {59},
  doi       = {10.1107/S0907444903003251},
  file      = {hv0005.pdf:by-author/G/Ghosh/2003_Ghosh_620.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444903003251},
}

@Article{Giacovazzo2004,
  author    = {Giacovazzo, Carmelo and Siliqi, Dritan},
  journal   = {Acta Crystallographica Section D},
  title     = {Phasing {\it via} SAD/MAD data: the method of the joint probability distribution functions},
  year      = {2004},
  pages     = {73--82},
  volume    = {60},
  doi       = {10.1107/S0907444903022406},
  file      = {dz0017.pdf:by-author/G/Giacovazzo/2004_Giacovazzo_73.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444903022406},
}

@Article{Giannozzi2009,
  author    = {Paolo Giannozzi and Stefano Baroni and Nicola Bonini and Matteo Calandra and Roberto Car and Carlo Cavazzoni and Davide Ceresoli and Guido L Chiarotti and Matteo Cococcioni and Ismaila Dabo and Andrea Dal Corso and Stefano de Gironcoli and Stefano Fabris and Guido Fratesi and Ralph Gebauer and Uwe Gerstmann and Christos Gougoussis and Anton Kokalj and Michele Lazzeri and Layla Martin-Samos and Nicola Marzari and Francesco Mauri and Riccardo Mazzarello and Stefano Paolini and Alfredo Pasquarello and Lorenzo Paulatto and Carlo Sbraccia and Sandro Scandolo and Gabriele Sclauzero and Ari P Seitsonen and Alexander Smogunov and Paolo Umari and Renata M. Wentzcovitch},
  journal   = {Journal of Physics: Condensed Matter},
  title     = {QUANTUM ESPRESSO: a modular and open-source software project for quantum simulations of materials},
  year      = {2009},
  pages     = {395502},
  volume    = {21},
  abstract  = {QUANTUM ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling, based on density-functional theory, plane waves, and pseudopotentials (norm-conserving, ultrasoft, and projector-augmented wave). The acronym ESPRESSO stands for opEn Source Package for Research in Electronic Structure, Simulation, and Optimization . It is freely available to researchers around the world under the terms of the GNU General Public License. QUANTUM ESPRESSO builds upon newly-restructured electronic-structure codes that have been developed and tested by some of the original authors of novel electronic-structure algorithms and applied in the last twenty years by some of the leading materials modeling groups worldwide. Innovation and efficiency are still its main focus, with special attention paid to massively parallel architectures, and a great effort being devoted to user friendliness. QUANTUM ESPRESSO is evolving towards a distribution of independent and interoperable codes in the spirit of an open-source project, where researchers active in the field of electronic-structure calculations are encouraged to participate in the project by contributing their own codes or by implementing their own ideas into existing codes.},
  doi       = {10.1088/0953-8984/21/39/395502},
  file      = {2009_Giannozzi_395502.pdf:by-author/G/Giannozzi/2009_Giannozzi_395502.pdf:PDF},
  keywords  = {Ab Initio; Materials; Quantum Espresso; Quantum Mechanics (QM); Simulations},
  owner     = {saulius},
  timestamp = {2015.01.12},
  creationdate = {2015-01-12T00:00:00},
  url       = {http://stacks.iop.org/0953-8984/21/i=39/a=395502},
}

@Article{Gibbons2000,
  author    = {Gibbons, C. and Montgomery, M. G. and Leslie, A. G. and Walker, J. E.},
  journal   = {Nature structural biology},
  title     = {The structure of the central stalk in bovine F(1)-ATPase at 2.4 A resolution.},
  year      = {2000},
  pages     = {1055--61},
  volume    = {7},
  abstract  = {The central stalk in ATP synthase, made of gamma, delta and epsilon subunits in the mitochondrial enzyme, is the key rotary element in the enzyme's catalytic mechanism. The gamma subunit penetrates the catalytic (alpha beta)(3) domain and protrudes beneath it, interacting with a ring of c subunits in the membrane that drives rotation of the stalk during ATP synthesis. In other crystals of F(1)-ATPase, the protrusion was disordered, but with crystals of F(1)-ATPase inhibited with dicyclohexylcarbodiimide, the complete structure was revealed. The delta and epsilon subunits interact with a Rossmann fold in the gamma subunit, forming a foot. In ATP synthase, this foot interacts with the c-ring and couples the transmembrane proton motive force to catalysis in the (alpha beta)(3) domain.},
  file      = {:by-author/G/Gibbons/2000_Gibbons_1055.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Giffin2007,
  author    = {Adom Giffin and Ariel Caticha},
  journal   = {AIP Conference Proceedings},
  title     = {Updating Probabilities with Data and Moments},
  year      = {2007},
  pages     = {74--84},
  volume    = {954},
  abstract  = {We use the method of Maximum (relative) Entropy to process information in the form of observed data and moment constraints. The generic "canonical" form of the posterior distribution for the problem of simultaneous updating with data and moments is obtained. We discuss the general problem of non-commuting constraints, when they should be processed sequentially and when simultaneously. As an illustration, the multinomial example of die tosses is solved in detail for two superficially similar but actually very different problems.},
  doi       = {10.1063/1.2821302},
  editor    = {Kevin H. Knuth and Ariel Caticha and Julian L. Center and Adom Giffin and Carlos C. Rodriguez},
  file      = {2007_Giffin_74.pdf:by-author/G/Giffin/2007_Giffin_74.pdf:PDF},
  groups    = {sg/Bayesian},
  keywords  = {Bayes Methods; Bayesian Statistics; Data Analysis; MaxEnt; Maximum Entropy; Maximum Entropy Methods; Probability},
  owner     = {saulius},
  publisher = {AIP},
  timestamp = {2012.10.07},
  creationdate = {2012-10-07T00:00:00},
  url       = {http://link.aip.org/link/?APC/954/74/1},
}

@Article{Gil2012,
  author    = {Joseph (Yossi) Gil and Keren Lenz},
  journal   = {Journal of Object Technology},
  title     = {Keyword- and Default- Parameters in JAVA},
  year      = {2012},
  pages     = {1},
  volume    = {11},
  abstract  = {Overloading is a highly controversial programming language mech- anism by which different methods of the same class are allowed to bear the same name. Despite the criticism, JAVA programmers make extensive use of this mechanism—not just because it is available, but also because the language does not provide an alternative for defining multiple constructors, and because it is useful for expressing similarity of services provided by a class. In a previous paper we argued that more than 60% of the overloading cases are “justifiable” and that in 35% of the cases overloading is used for emulating a default arguments mechanism. Based on these results, this paper argues that most “justifiable” uses of overloading are better done with a combination of keyword parameters and default parameters parameter definition mechanisms, and describes our extension of the JAVA compiler which adds these two features to the language.},
  doi       = {10.5381/jot.2012.11.1.a1},
  file      = {:by-author/G/Gil/2012_Gil_1.pdf:PDF},
  owner     = {saulius},
  timestamp = {2015.02.17},
  creationdate = {2015-02-17T00:00:00},
  url       = {http://www.jot.fm/issues/issue_2012_04/article1.pdf},
}

@Article{Gilbert2006,
  author    = {Gilbert, Scott M and Whitson, Jared M and Mansukhani, Mahesh and Buttyan, Ralph and Benson, Mitchell C and Olsson, Carl A and Sawczuk, Ihor S and McKiernan, James M},
  journal   = {Urology},
  title     = {Detection of carbonic anhydrase-9 gene expression in peripheral blood cells predicts risk of disease recurrence in patients with renal cortical tumors.},
  year      = {2006},
  pages     = {942--5},
  volume    = {67},
  file      = {2006_Gilbert_942.pdf:by-author/G/Gilbert/2006_Gilbert_942.pdf:PDF},
  groups    = {sg/cancer, sg/medicine, sg/hCA9},
  keywords  = {CA9; Carbonic Anhydrases},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@InBook{Gilbert1999,
  author    = {Walter Gilbert and Sandro J. de Souza},
  chapter   = {Introns and the RNA World},
  editor    = {Raymond F. Gesteland},
  pages     = {221--231},
  publisher = {Cold Spring Harbor Laboratory Press},
  title     = {The RNA World},
  year      = {1999},
  edition   = {2nd},
  abstract  = {The RNA World is a hypothesis about the origin of life based on the view that the most critical event is the emergence of a self-replicating molecule, a molecule that can both copy itself and mutate and, hence, evolve to more efficient copying (Gilbert 1986). Evolution works on variation and selection, and selection is always measured in terms of more efficient multiplication, the ability to make more of the entity in question. The concept of an RNA World is a way of answering the basic problem of what was the molecular biology involved at the beginning of life. Our understanding of the molecular basis of biology today is in terms of a genetic material, commonly DNA, translated through an apparatus involving RNA and the mechanism of protein synthesis to specify the positions of 20 amino acids in protein enzymes. That picture of life, in which the genetic material is of one chemical kind, DNA, made up of four bases, a second chemical, RNA, is used for structural and transfer purposes, and the enzymatic activities in the cell are a third chemical kind made up of 20 ingredient amino acids, creates a complex paradox in trying to formulate how life could have begun. This paradox was resolved by two realizations. One was that RNA is likely to be more primary than DNA, but the picture of an RNA–protein world, in which RNA is the genetic material specifying the positions of amino acids in proteins, still left one with a complex problem of beginnings. The second realization, however, was that there was no intrinsic reason that enzymatic activity must be limited to proteins. The discovery of the first two RNA enzymes showed that RNA molecules could carry out the phosphodiester bond transfers needed for RNA synthesis (Kruger et al. 1982; Guerrier-Takada et al. 1983).},
  comment   = {ISBN: 9780879695613},
  file      = {1999_Gilbert_221.pdf:by-author/G/Gilbert/1999_Gilbert_221.pdf:PDF},
  keywords  = {RNA World},
  owner     = {saulius},
  timestamp = {2013.09.27},
  creationdate = {2013-09-27T00:00:00},
  url       = {http://rna.cshl.edu/content/free/chapters/09_rna_world_2nd.pdf},
}

@Article{Gildea2011,
  author           = {Richard J. Gildea and Luc J. Bourhis and Oleg V. Dolomanov and Ralf W. Grosse-Kunstleve and Horst Puschmann and Paul D. Adams and Judith A. K. Howard},
  journal          = {Journal of Applied Crystallography},
  title            = {{iotbx.cif}: a comprehensive {CIF} toolbox},
  year             = {2011},
  pages            = {1259--1263},
  volume           = {44},
  abstract         = {iotbx.cif is a new software module for the development of applications that make use of the CIF format. Comprehensive tools are provided for input, output and validation of CIFs, as well as for interconversion with high-level cctbx [Grosse-Kunstleve, Sauter, Moriarty & Adams (2002). J. Appl. Cryst. 35, 126–136] crystallographic objects. The interface to the library is written in Python, whilst parsing is carried out using a compiled parser, combining the performance of a compiled language (C++) with the benefits of using an interpreted language.},
  creationdate     = {2013-02-06T00:00:00},
  doi              = {10.1107/S0021889811041161},
  file             = {:by-author/G/Gildea/2011_Gildea_1259.pdf:PDF},
  keywords         = {CIF},
  modificationdate = {2023-08-07T10:23:05},
  owner            = {andrius},
  timestamp        = {2013.02.06},
}

@Article{Gilden1989,
  author    = {Gilden, D L and Proffitt, D R},
  journal   = {Journal of experimental psychology. Human perception and performance},
  title     = {Understanding collision dynamics.},
  year      = {1989},
  pages     = {372--83},
  volume    = {15},
  abstract  = {In two experiments we investigated people's ability to judge the relative mass of two objects involved in a collision. It was found that judgments of relative mass were made on the basis of two heuristics. Roughly stated, these heuristics were (a) an object that ricochets backward upon impact is less massive than the object that it hit, and (b) faster moving objects are less massive. A heuristic model of judgment is proposed that postulates that different sources of information in any event may have different levels of salience for observers and that heuristic access is controlled by the rank ordering of salience. It was found that observers ranked dissimilarity in mass on the basis of the relative salience of angle and velocity information and not proportionally to the distal mass ratio. This heuristic model was contrasted with the notion that people can veridically extract dynamic properties of motion events when the kinematic data are sufficient for their specification.},
  file      = {1989_Gilden_372.pdf:by-author/G/Gilden/1989_Gilden_372.pdf:PDF},
  groups    = {sg/Molecular dynamics},
  keywords  = {Hard Spheres; Molecular Dynamics (MD)},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Gilliland2001,
  author    = {Gary L. Gilliland},
  journal   = {Journal of Research of the National Institute of Standards and Technology},
  title     = {Macromolecular Crystallography and Structural Biology Databases at NIST},
  year      = {2001},
  pages     = {1155--1173},
  volume    = {106},
  abstract  = {In the late 1970s, macromolecular crystal- lography at NIST began with collabora- tion between NIST and NIH to establish a single-crystal neutron diffractometer. This instrument was constructed and em- ployed to solve a number of crystal struc- tures: bovine ribonuclease A, bovine-ri- bonuclease-uridine vanadate complex, and porcine insulin. In the mid 1980s a Biomolecular Structure Group was cre- ated establishing NIST capabilities in biomolecular singe-crystal x-ray diffrac- tion. The group worked on a variety of structural problems until joining the NIST/UMBI Center for Advanced Research in Biotechnology (CARB) in 1987. Crys- tallographic studies at CARB were then fo- cused on protein engineering efforts that included among others chymosin, subtilisin BPN' , interleukin 1␤, and glutathione S- transferase. Recently, the structural biology efforts have centered on enzymes in the chorismate metabolic pathways involved in amino acid biosynthesis and in structural genomics that involves determining the structures of “hypothetical” proteins to aid in assigning function. In addition to crystallographic studies, structural biology database activities began with the formal establishment of the Biological Macro- molecule Crystallization Database in 1989. Later, in 1997, NIST in partnership with Rutgers and UCSD formed the Research Collaboratory for Structural Bioinformat- ics that successfully acquired the Protein Data Bank. The NIST efforts in these ac- tivities have focused on data uniformity, es- tablishing and maintaining the physical archive, and working with the NMR com- munity.},
  file      = {:by-author/G/Gilliland/2001_Gilliland_1155.pdf:PDF},
  keywords  = {Databases; Macromolecular Crystallography; Neutron Crystallography; Protein Crystallography; Proteins; Structural Biology Databases; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2012.05.02},
  creationdate = {2012-05-02T00:00:00},
  url       = {http://www.nist.gov/jres},
}

@Article{Gilson2007,
  author    = {Michael K. Gilson and Huan-Xiang Zhou},
  journal   = {Annu. Rev. Biophys. Biomol. Struct.},
  title     = {Calculation of Protein-Ligand Binding Affinities},
  year      = {2007},
  pages     = {21--42},
  volume    = {36},
  abstract  = {Accurate methods of computing the affinity of a small molecule with a protein are needed to speed the discovery of new medications and biological probes. This paper reviews physics-based models of binding, beginning with a summary of the changes in potential energy, solvation energy, and configurational entropy that influence affinity, and a theoretical overview to frame the discussion of specific computational approaches. Important advances are reported in modeling protein-ligand energetics, such as the incorporation of electronic polarization and the use of quantum mechanical methods. Recent calculations suggest that changes in configurational entropy strongly oppose binding and must be included if accurate affinities are to be obtained. The linear interaction energy (LIE) and molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) methods are analyzed, as are free energy pathway methods, which show promise and may be ready for more extensive testing. Ultimately, major improvements in modeling accuracy will likely require advances on multiple fronts, as well as continued validation against experiment.},
  doi       = {10.1146/annurev.biophys.36.040306.132550},
  file      = {2007_Gilson_21.pdf:by-author/G/Gilson/2007_Gilson_21.pdf:PDF},
  keywords  = {Molecular Modelling},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Girard2003,
  author    = {Girard, {\'{E}}ric and Stelter, Meike and Vicat, Jean and Kahn, Richard},
  journal   = {Acta Crystallographica Section D},
  title     = {A new class of lanthanide complexes to obtain high-phasing-power heavy-atom derivatives for macromolecular crystallography},
  year      = {2003},
  pages     = {1914--1922},
  volume    = {59},
  doi       = {10.1107/S0907444903020511},
  file      = {ba5052.pdf:by-author/G/Girard/2003_Girard_1914.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444903020511},
}

@Article{Gkoutos2001,
  author    = {Gkoutos, Georgios V. and Murray-Rust, Peter and Rzepa, Henry S. and Wright, Michael},
  journal   = {Journal of Chemical Information and Computer Sciences},
  title     = {Chemical Markup, XML, and the World-Wide Web. 3. Toward a Signed Semantic Chemical Web of Trust},
  year      = {2001},
  pages     = {1124--1130},
  volume    = {41},
  abstract  = {We describe how a collection of documents expressed in XML-conforming languages such as CML and XHTML can be authenticated and validated against digital signatures which make use of established X.509 certificate technology. These can be associated either with specific nodes in the XML document or with the entire document. We illustrate this with two examples. An entire journal article expressed in XML has its individual components digitally signed by separate authors, and the collection is placed in an envelope and again signed. The second example involves using a software robot agent to acquire a collection of documents from a specified URL, to perform various operations and transformations on the content, including expressing molecules in CML, and to automatically sign the various components and deposit the result in a repository. We argue that these operations can used as components for building what we term an authenticated and semantic chemical web of trust.},
  doi       = {10.1021/ci000406v},
  eprint    = {http://pubs.acs.org/doi/pdf/10.1021/ci000406v},
  file      = {2001_Gkoutos_1124.pdf:by-author/G/Gkoutos/2001_Gkoutos_1124.pdf:PDF},
  keywords  = {CML; Chemoinformatics; Crystallography; Data Formats; Data Management; X-ray Crystallography; XML},
  owner     = {saulius},
  timestamp = {2014.06.24},
  creationdate = {2014-06-24T00:00:00},
  url       = {http://pubs.acs.org/doi/abs/10.1021/ci000406v},
}

@Article{Gledhill2007,
  author    = {Gledhill, Jonathan R and Montgomery, Martin G and Leslie, Andrew G W and Walker, John E},
  journal   = {Proceedings of the National Academy of Sciences of the United States of America},
  title     = {Mechanism of inhibition of bovine F1-ATPase by resveratrol and related polyphenols.},
  year      = {2007},
  pages     = {13632--7},
  volume    = {104},
  abstract  = {The structures of F(1)-ATPase from bovine heart mitochondria inhibited with the dietary phytopolyphenol, resveratrol, and with the related polyphenols quercetin and piceatannol have been determined at 2.3-, 2.4- and 2.7-A resolution, respectively. The inhibitors bind to a common site in the inside surface of an annulus made from loops in the three alpha- and three beta-subunits beneath the "crown" of beta-strands in their N-terminal domains. This region of F(1)-ATPase forms a bearing to allow the rotation of the tip of the gamma-subunit inside the annulus during catalysis. The binding site is a hydrophobic pocket between the C-terminal tip of the gamma-subunit and the beta(TP) subunit, and the inhibitors are bound via H-bonds mostly to their hydroxyl moieties mediated by bound water molecules and by hydrophobic interactions. There are no equivalent sites between the gamma-subunit and either the beta(DP) or the beta(E) subunit. The inhibitors probably prevent both the synthetic and hydrolytic activities of the enzyme by blocking both senses of rotation of the gamma-subunit. The beneficial effects of dietary resveratrol may derive in part by preventing mitochondrial ATP synthesis in tumor cells, thereby inducing apoptosis.},
  file      = {2007_Gledhill_13632.pdf:by-author/G/Gledhill/2007_Gledhill_13632.pdf:PDF},
  keywords  = {ATPase Resveratrol; Inhibitors; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Gogo2005,
  author    = {A. Gogo and W. D. Snyder and M. Beck},
  journal   = {Physical Review A},
  title     = {Comparing quantum and classical correlations in a quantum eraser},
  year      = {2005},
  pages     = {052103},
  volume    = {71},
  abstract  = {We have demonstrated the operation of a quantum eraser based on a polarization interferometer. Which-path information is erased not by modifying the interferometer apparatus, but instead by modifying the information obtained from measurements performed on a second beam, whose polarization is correlated with that of the interferometer beam. We compare the results obtained when the two beams are in an entangled state s quantum correlations d and in a mixed state s classical correlations d . We find that classical correlations can mimic most, but not all, of the quantum-mechanical behavior.},
  doi       = {10.1103/PhysRevA.71.052103},
  file      = {:by-author/G/Gogo/2005_Gogo_052103.pdf:PDF},
  keywords  = {Bell's Inequalities; Quantum Correlations; Quantum Mechanics (QM)},
  owner     = {saulius},
  paperid   = {052103},
  timestamp = {2013.10.22},
  creationdate = {2013-10-22T00:00:00},
  url       = {http://people.whitman.edu/~beckmk/QM/qe/qe.pdf},
}

@Presentation{Goins2000,
  author       = {Goins},
  title        = {Tape Technology 2000 The Exciting Future of Magnetic Tape},
  year         = {2000},
  organization = {THIC Inc.},
  file         = {:by-author/G/Goins/2000_Goins_slides.pdf:PDF},
  keywords     = {Computer Science (CS); Databases; Organisation},
  owner        = {saulius},
  pages        = {slides},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Goldberg2000,
  author    = {Billi Goldberg and Raphael B. Stricker},
  journal   = {J. theor. Biol.},
  title     = {Bridging the Gap: Human Diploid Cell Strains and the Origin of AIDS},
  year      = {2000},
  pages     = {497--503},
  volume    = {204},
  abstract  = {Recent descriptions of the first human and chimpanzee cases of human immunodeficiency virus type 1 (HIV-1)-related retroviral infections dating from 1959 have stirred interest in the origin of AIDS. Although the theory of a chimpanzee origin of HIV-1 with cross-species transfer to man has now gained popularity, a more likely scenario is that chimps and humans were infected by an HIV-1 precursor virus derived from a contaminated poliovaccine. The reason for the rapidity and ease of cross-species transfer of this precursor virus has not been elucidated. We hypothesize that the poliovaccine was passaged in a human diploid cell strain. This simple manipulation allowed the retrovirus to adapt to human tissues and may have spawned the AIDS pandemic.},
  doi       = {10.1006/jtbi.2000.2033},
  file      = {Goldberg_2000_497.pdf:by-author/G/Goldberg/2000_Goldberg_497.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Goldberg1991,
  author     = {Goldberg, David},
  journal    = {ACM Comput. Surv.},
  title      = {What every computer scientist should know about floating-point arithmetic},
  year       = {1991},
  issn       = {0360-0300},
  pages      = {5--48},
  volume     = {23},
  abstract   = {Floating-point arithmetic is considered an esotoric subject by many people. This is rather surprising, because floating-point is ubiquitous in computer systems: Almost every language has a floating-point datatype; computers from PCs to supercomputers have floating-point accelerators; most compilers will be called upon to compile floating-point algorithms from time to time; and virtually every operating system must respond to floating-point exceptions such as overflow This paper presents a tutorial on the aspects of floating-point that have a direct impact on designers of computer systems. It begins with background on floating-point representation and rounding error, continues with a discussion of the IEEE floating-point standard, and concludes with examples of how computer system builders can better support floating point.},
  acmid      = {103163},
  address    = {New York, NY, USA},
  doi        = {10.1145/103162.103163},
  file       = {1991_Goldberg.pdf:by-author/G/Goldberg/1991_Goldberg.pdf:PDF;1991_Goldberg.ps:by-author/G/Goldberg/1991_Goldberg.ps:PostScript;1991_Goldberg_5.pdf:by-author/G/Goldberg/1991_Goldberg_5.pdf:PDF},
  issue_date = {March 1991},
  keywords   = {Computer Science (CS); Denormalized Number; Exception; Floating Point; Floating Point Arithmetics; Floating Point Standard; Gradual Underflow; Guard Digit; NaN; Overflow; Relative Error; Rounding Error; Rounding Mode; Ulp; Underflow},
  numpages   = {44},
  owner      = {saulius},
  publisher  = {ACM},
  timestamp = {2012.09.27},
  creationdate = {2012-09-27T00:00:00},
  url        = {http://doi.acm.org/10.1145/103162.103163},
}

@Article{Golden1998,
  author    = {Golden, B L and Gooding, A R and Podell, E R and Cech, T R},
  journal   = {Science (New York, N.Y.)},
  title     = {A preorganized active site in the crystal structure of the Tetrahymena ribozyme.},
  year      = {1998},
  pages     = {259--64},
  volume    = {282},
  file      = {1998_Golden_259.pdf:by-author/G/Golden/1998_Golden_259.pdf:PDF},
  keywords  = {Ribozymes},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Goldfarb2014,
  author    = {Goldfarb, T. and Sberro, H. and Weinstock, E. and Cohen, O. and Doron, S. and Charpak-Amikam, Y. and Afik, S. and Ofir, G. and Sorek, R.},
  journal   = {The EMBO Journal},
  title     = {BREX is a novel phage resistance system widespread in microbial genomes},
  year      = {2014},
  issn      = {1460-2075},
  pages     = {169--183},
  volume    = {34},
  abstract  = {The perpetual arms race between bacteria and phage has resulted in the evolution of efficient resistance systems that protect bacteria from phage infection. Such systems, which include the CRISPR‐Cas and restriction‐modification systems, have proven to be invaluable in the biotechnology and dairy industries. Here, we report on a six‐gene cassette in Bacillus cereus which, when integrated into the Bacillus subtilis genome, confers resistance to a broad range of phages, including both virulent and temperate ones. This cassette includes a putative Lon‐like protease, an alkaline phosphatase domain protein, a putative RNA‐binding protein, a DNA methylase, an ATPase‐domain protein, and a protein of unknown function. We denote this novel defense system BREX (Bacteriophage Exclusion) and show that it allows phage adsorption but blocks phage DNA replication. Furthermore, our results suggest that methylation on non‐palindromic TAGGAG motifs in the bacterial genome guides self/non‐self discrimination and is essential for the defensive function of the BREX system. However, unlike restriction‐modification systems, phage DNA does not appear to be cleaved or degraded by BREX, suggesting a novel mechanism of defense. Pan genomic analysis revealed that BREX and BREX‐like systems, including the distantly related Pgl system described in Streptomyces coelicolor, are widely distributed in ~10% of all sequenced microbial genomes and can be divided into six coherent subtypes in which the gene composition and order is conserved. Finally, we detected a phage family that evades the BREX defense, implying that anti‐BREX mechanisms may have evolved in some phages as part of their arms race with bacteria.},
  doi       = {10.15252/embj.201489455},
  file      = {:by-author/G/Goldfarb/2014_Goldfarb_169.pdf:PDF},
  groups    = {sg/CRISPR-Cas},
  owner     = {saulius},
  publisher = {EMBO},
  timestamp = {2015.02.25},
  creationdate = {2015-02-25T00:00:00},
  url       = {http://dx.doi.org/10.15252/embj.201489455},
}

@Article{Goldman1993,
  author    = {Goldman, A. I. and Kelton, R. F.},
  journal   = {Rev. Mod. Phys.},
  title     = {Quasicrystals and crystalline approximants},
  year      = {1993},
  pages     = {213--230},
  volume    = {65},
  doi       = {10.1103/RevModPhys.65.213},
  file      = {1993_Goldman_213.pdf:by-author/G/Goldman/1993_Goldman_213.pdf:PDF},
  issue     = {1},
  keywords  = {Periodic Approximants; Qusicrystals},
  numpages  = {0},
  owner     = {saulius},
  publisher = {American Physical Society},
  timestamp = {2014.08.05},
  creationdate = {2014-08-05T00:00:00},
  url       = {http://link.aps.org/doi/10.1103/RevModPhys.65.213},
}

@Article{Goldschmidt2007a,
  author      = {Lukasz Goldschmidt and David R. Cooper and Zygmunt S. Derewenda and David Eisenberg},
  journal     = {Protein Sci},
  title       = {Toward rational protein crystallization: A Web server for the design of crystallizable protein variants.},
  year        = {2007},
  month       = {Aug},
  number      = {8},
  pages       = {1569--1576},
  volume      = {16},
  abstract    = {Growing well-diffracting crystals constitutes a serious bottleneck in structural biology. A recently proposed crystallization methodology for "stubborn crystallizers" is to engineer surface sequence variants designed to form intermolecular contacts that could support a crystal lattice. This approach relies on the concept of surface entropy reduction (SER), i.e., the replacement of clusters of flexible, solvent-exposed residues with residues with lower conformational entropy. This strategy minimizes the loss of conformational entropy upon crystallization and renders crystallization thermodynamically favorable. The method has been successfully used to crystallize more than 15 novel proteins, all stubborn crystallizers. But the choice of suitable sites for mutagenesis is not trivial. Herein, we announce a Web server, the surface entropy reduction prediction server (SERp server), designed to identify mutations that may facilitate crystallization. Suggested mutations are predicted based on an algorithm incorporating a conformational entropy profile, a secondary structure prediction, and sequence conservation. Minor considerations include the nature of flanking residues and gaps between mutation candidates. While designed to be used with default values, the server has many user-controlled parameters allowing for considerable flexibility. Within, we discuss (1) the methodology of the server, (2) how to interpret the results, and (3) factors that must be considered when selecting mutations. We also attempt to benchmark the server by comparing the server's predictions with successful SER structures. In most cases, the structure yielding mutations were easily identified by the SERp server. The server can be accessed at http://www.doe-mbi.ucla.edu/Services/SER.},
  doi         = {10.1110/ps.072914007},
  file        = {:by-author/G/Goldschmidt/2007_Goldschmidt_1569.pdf:PDF},
  institution = {Howard Hughes Medical Institute, University of California, Los Angeles-DOE Institute of Genomics and Proteomics, Los Angeles, California 90095-1570, USA.},
  keywords    = {Amino Acid Sequence; Animals; Chemistry/genetics; Conserved Sequence; Crystallization; Crystallography; Entropy; Humans; Internet; Molecular Sequence Data; Mutation; Protein Structure; Proteins; Secondary; Software; Surface Properties; User-Computer Interface; X-Ray},
  language    = {eng},
  medline-pst = {ppublish},
  owner       = {em},
  pii         = {16/8/1569},
  pmid        = {17656576},
  timestamp = {2016.06.09},
  creationdate = {2016-06-09T00:00:00},
  url         = {http://dx.doi.org/10.1110/ps.072914007},
}

@Manuscript{Goldsmith2004,
  author    = {John Goldsmith},
  title     = {Review of The Legacy of Zellig Harris: Language and information into the 21st century. Volume 1: Philosophy of science, syntax and semantics. Edited by Bruce Nevin},
  year      = {2004},
  keywords  = {Lingvistika},
  file      = {:by-author/G/Goldsmith/2004_Goldsmith.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Golovenko2009,
  author       = {Dmitrij Golovenko and Elena Manakova and Giedre Tamulaitiene and Saulius Grazulis and Virginijus Siksnys},
  journal      = {Nucleic Acids Res},
  title        = {Structural mechanisms for the 5'-CCWGG sequence recognition by the N- and C-terminal domains of EcoRII.},
  year         = {2009},
  month        = {Oct},
  number       = {19},
  pages        = {6613--6624},
  volume       = {37},
  abstract     = {EcoRII restriction endonuclease is specific for the 5'-CCWGG sequence (W stands for A or T); however, it shows no activity on a single recognition site. To activate cleavage it requires binding of an additional target site as an allosteric effector. EcoRII dimer consists of three structural units: a central catalytic core, made from two copies of the C-terminal domain (EcoRII-C), and two N-terminal effector DNA binding domains (EcoRII-N). Here, we report DNA-bound EcoRII-N and EcoRII-C structures, which show that EcoRII combines two radically different structural mechanisms to interact with the effector and substrate DNA. The catalytic EcoRII-C dimer flips out the central T:A base pair and makes symmetric interactions with the CC:GG half-sites. The EcoRII-N effector domain monomer binds to the target site asymmetrically in a single defined orientation which is determined by specific hydrogen bonding and van der Waals interactions with the central T:A pair in the major groove. The EcoRII-N mode of the target site recognition is shared by the large class of higher plant transcription factors of the B3 superfamily.},
  creationdate = {2011-07-11T00:00:00},
  doi          = {10.1093/nar/gkp699},
  file         = {2009_Golovenko_6613.pdf:by-author/G/Golovenko/2009_Golovenko_6613.pdf:PDF},
  institution  = {Institute of Biotechnology, Graiciuno 8, LT-02241 Vilnius, Lithuania.},
  keywords     = {Base Pairing; Base Sequence; Chemistry; DNA; DNA Methylation; Deoxyribonucleases; Models; Molecular; Protein Structure; Tertiary; Type II Site-Specific},
  language     = {eng},
  medline-pst  = {ppublish},
  owner        = {em},
  pii          = {gkp699},
  pmid         = {19729506},
  timestamp    = {2011.07.11},
  url          = {http://dx.doi.org/10.1093/nar/gkp699},
}

@Article{Golovenko2009a,
  author    = {Dmitrij Golovenko and Elena Manakova and Giedre Tamulaitiene and Saulius Grazulis and Virginijus Siksnys},
  journal   = {Nucleic acids research},
  title     = {Structural mechanisms for the {5'-CCWGG} sequence recognition by the {N-} and {C-terminal} domains of {EcoRII}},
  year      = {2009},
  pages     = {suppl},
  file      = {:by-author/G/Golovenko/2009_Golovenko_suppl.pdf:PDF},
  keywords  = {Struct; TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Golovenko2009b,
  author    = {Golovenko, Dmitrij and Manakova, Elena and Tamulaitiene, Giedre and Grazulis, Saulius and Siksnys, Virginijus},
  journal   = {Nucleic acids research},
  title     = {Structural mechanisms for the 5'-CCWGG sequence recognition by the N- and C-terminal domains of EcoRII.},
  year      = {2009},
  pages     = {6613--24},
  volume    = {37},
  abstract  = {EcoRII restriction endonuclease is specific for the 5'-CCWGG sequence (W stands for A or T); however, it shows no activity on a single recognition site. To activate cleavage it requires binding of an additional target site as an allosteric effector. EcoRII dimer consists of three structural units: a central catalytic core, made from two copies of the C-terminal domain (EcoRII-C), and two N-terminal effector DNA binding domains (EcoRII-N). Here, we report DNA-bound EcoRII-N and EcoRII-C structures, which show that EcoRII combines two radically different structural mechanisms to interact with the effector and substrate DNA. The catalytic EcoRII-C dimer flips out the central T:A base pair and makes symmetric interactions with the CC:GG half-sites. The EcoRII-N effector domain monomer binds to the target site asymmetrically in a single defined orientation which is determined by specific hydrogen bonding and van der Waals interactions with the central T:A pair in the major groove. The EcoRII-N mode of the target site recognition is shared by the large class of higher plant transcription factors of the B3 superfamily.},
  file      = {:by-author/G/Golovenko/2009_Golovenko_6613.pdf:PDF},
  keywords  = {Struct; TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Golovenko2014a,
  author    = {Golovenko, Dmitrij and Manakova, Elena and Zakrys, Linas and Zaremba, Mindaugas and Sasnauskas, Giedrius and Grazulis, Saulius and Siksnys, Virginijus},
  journal   = {Nucleic Acids Res.},
  title     = {Structural insight into the specificity of the B3 DNA-binding domains provided by the co-crystal structure of the C-terminal fragment of BfiI restriction enzyme},
  year      = {2014},
  pages     = {1--10},
  volume    = {42},
  abstract  = {The B3 DNA-binding domains (DBDs) of plant transcription factors (TF) and DBDs of EcoRII and BfiI restriction endonucleases (EcoRII-N and BfiI-C) share a common structural fold, classified as the DNA-binding pseudobarrel. The B3 DBDs in the plant TFs recognize a diverse set of target se- quences. The only available co-crystal structure of the B3-like DBD is that of EcoRII-N (recognition sequence 50 -CCTGG-30 ). In order to understand the structural and molecular mechanisms of specificity of B3 DBDs, we have solved the crystal structure of BfiI-C (recognition sequence 50 -ACTGGG-30 ) complexed with 12-bp cognate oligoduplex. Structural comparison of BfiI-C–DNA and EcoRII-N–DNA complexes reveals a conserved DNA-binding mode and a conserved pattern of interactions with the phosphodiester backbone. The determinants of the target specificity are located in the loops that emanate from the conserved structural core. The BfiI-C–DNA structure presented here expands a range of templates for modeling of the DNA-bound complexes of the B3 family of plant TFs.},
  doi       = {10.1093/nar/gkt1368},
  file      = {:by-author/G/Golovenko/2014_Golovenko_gkt1368.pdf:PDF},
  keywords  = {B3 Domain; BfiI; Crystal Structure; DBD; EcoRII; Protein Crystallography; Restriction Endonuclease (RE); Type IIS},
  owner     = {em},
  timestamp = {2014.01.14},
  creationdate = {2014-01-14T00:00:00},
}

@Article{Golovenko2014,
  author       = {Dmitrij Golovenko and Elena Manakova and Linas Zakrys and Mindaugas Zaremba and Giedrius Sasnauskas and Saulius Gražulis and Virginijus Siksnys},
  journal      = {Nucleic Acids Res},
  title        = {Structural insight into the specificity of the B3 DNA-binding domains provided by the co-crystal structure of the C-terminal fragment of BfiI restriction enzyme.},
  year         = {2014},
  month        = {Apr},
  number       = {6},
  pages        = {4113--4122},
  volume       = {42},
  abstract     = {The B3 DNA-binding domains (DBDs) of plant transcription factors (TF) and DBDs of EcoRII and BfiI restriction endonucleases (EcoRII-N and BfiI-C) share a common structural fold, classified as the DNA-binding pseudobarrel. The B3 DBDs in the plant TFs recognize a diverse set of target sequences. The only available co-crystal structure of the B3-like DBD is that of EcoRII-N (recognition sequence 5'-CCTGG-3'). In order to understand the structural and molecular mechanisms of specificity of B3 DBDs, we have solved the crystal structure of BfiI-C (recognition sequence 5'-ACTGGG-3') complexed with 12-bp cognate oligoduplex. Structural comparison of BfiI-C-DNA and EcoRII-N-DNA complexes reveals a conserved DNA-binding mode and a conserved pattern of interactions with the phosphodiester backbone. The determinants of the target specificity are located in the loops that emanate from the conserved structural core. The BfiI-C-DNA structure presented here expands a range of templates for modeling of the DNA-bound complexes of the B3 family of plant TFs.},
  creationdate = {2016-06-09T00:00:00},
  doi          = {10.1093/nar/gkt1368},
  file         = {2014_Golovenko_gkt1368.pdf:by-author/G/Golovenko/2014_Golovenko_gkt1368.pdf:PDF},
  institution  = {Department of Protein-DNA Interactions, Institute of Biotechnology, Vilnius University, Graičiūno 8, LT-02241, Vilnius, Lithuania.},
  keywords     = {Chemistry; Chemistry/genetics; Crystallography; DNA; DNA-Binding Proteins; Deoxyribonucleases; Models; Molecular; Mutation; Protein Binding; Protein Structure; Tertiary; Type II Site-Specific; X-Ray},
  language     = {eng},
  medline-pst  = {ppublish},
  owner        = {em},
  pii          = {gkt1368},
  pmid         = {24423868},
  timestamp    = {2016.06.09},
  url          = {http://dx.doi.org/10.1093/nar/gkt1368},
}

@Article{Gomberg1900,
  author    = {Gomberg, M.},
  journal   = {Journal of the American Chemical Society},
  title     = {An instance of trivalent carbon: triphenylmethyl},
  year      = {1900},
  pages     = {757--771},
  volume    = {22},
  doi       = {10.1021/ja02049a006},
  eprint    = {http://dx.doi.org/10.1021/ja02049a006},
  file      = {1900_Gomberg_757.pdf:by-author/G/Gomberg/1900_Gomberg_757.pdf:PDF},
  keywords  = {History; Stabile Radical},
  owner     = {saulius},
  timestamp = {2014.11.19},
  creationdate = {2014-11-19T00:00:00},
  url       = {http://dx.doi.org/10.1021/ja02049a006},
}

@Manuscript{Gonggrijp2006,
  author    = {Rop Gonggrijp and Willem-Jan Hengeveld and Andreas Bogk and Dirk Engling and Hannes Mehnert and Frank Rieger and Pascal Scheffers and Barry Wels},
  title     = {Nedap/Groenendaal ES3B voting computer: a security analysis},
  year      = {2006},
  keywords  = {Computer Science (CS); Voting Machine Security},
  abstract  = {90% of the of the votes in The Netherlands are cast on the Nedap/ Groenendaal ES3B voting computer. With very minor modifications, the same computer is also being used in parts of Germany and France. Use of this machine in Ireland is currently on hold after significant doubts were raised concerning its suitability for elections. This paper details how we installed new software in Nedap ES3B voting computers. It details how anyone, when given brief access to the devices at any time before the election, can gain complete and virtually undetectable control over the election results. It also shows how radio emanations from an unmodified ES3B can be received at several meters distance and be used to tell who votes what.},
  file      = {:by-author/G/Gonggrijp/2006_Gonggrijp.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Gonzalez2003,
  author    = {Gonz{\'{a}}lez, Ana},
  journal   = {Acta Crystallographica Section D},
  title     = {Faster data-collection strategies for structure determination using anomalous dispersion},
  year      = {2003},
  pages     = {315--322},
  volume    = {59},
  doi       = {10.1107/S0907444902022138},
  file      = {he0309.pdf:by-author/G/Gonzalez/2003_Gonzalez_315.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444902022138},
}

@Article{Gonzalez2003a,
  author    = {Gonz{\'{a}}lez, Ana},
  journal   = {Acta Crystallographica Section D},
  title     = {Optimizing data collection for structure determination},
  year      = {2003},
  pages     = {1935--1942},
  volume    = {59},
  doi       = {10.1107/S0907444903017700},
  file      = {ba5033.pdf:by-author/G/Gonzalez/2003_Gonzalez_1935.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444903017700},
}

@Article{Gonze2008,
  author    = {Xavier Gonze and C.-O. Almbladh and A. Cucca and D. Caliste and C. Freysoldt and M. A. L. Marques and V. Olevano and Yann Pouillon and M. J. Verstraete},
  journal   = {CoRR},
  title     = {Specification of an extensible and portable file format for electronic structure and crystallographic data},
  year      = {2008},
  volume    = {abs/0805.0192},
  abstract  = {In order to allow different software applications, in constant evolution, to interact and exchange data, flexible file formats are needed. A file format specification for different types of content has been elaborated to allow communication of data for the software developed within the European Network of Excellence "NANOQUANTA", focusing on first-principles calculations of materials and nanosystems. It might be used by other software as well, and is described here in detail. The format relies on the NetCDF binary input/output library, already used in many different scientific communities, that provides flexibility as well as portability accross languages and platforms. Thanks to NetCDF, the content can be accessed by keywords, ensuring the file format is extensible and backward compatible.},
  bibsource = {DBLP, http://dblp.uni-trier.de},
  ee        = {http://arxiv.org/abs/0805.0192},
  file      = {2008_Gonze_0805.0192v1.pdf:by-author/G/Gonze/2008_Gonze_0805.0192v1.pdf:PDF},
  keywords  = {Data Management; File Formats; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2013.08.20},
  creationdate = {2013-08-20T00:00:00},
}

@TechReport{Gonze2008a,
  author      = {X. Gonze and C.-O. Almbladh and A. Cucca and D. Caliste and M. Marques and C. Freysoldt and V. Olevano and Y. Pouillon and F. Sottile and M. Verstraete},
  institution = {European Theoretical Spectroscopy Facility},
  title       = {Specification of file formats for {ETSF} Specification version 3.3. Second revision for this version ({SpecFF ETSF3.3})},
  year        = {2008},
  file        = {:by-author/G/Gonze/2008_Gonze.pdf:PDF},
  groups      = {am/ETSF},
  owner       = {andrius},
  timestamp = {2016.01.20},
  creationdate = {2016-01-20T00:00:00},
  url         = {http://www.etsf.eu/system/files/SpecFFETSF_v3.3.pdf},
}

@Article{Goodman1991,
  author    = {Irwin R Goodman and Hung T Nguyen and Gerald S Rogers},
  journal   = {Journal of Mathematical Analysis and Applications},
  title     = {On the scoring approach to admissibility of uncertainty measures in expert systems},
  year      = {1991},
  issn      = {0022-247X},
  pages     = {550 - 594},
  volume    = {159},
  abstract  = {This paper arose from our need to rigorize, clarify, and address fully the results of Lindley's paper (Scoring rules and the inevitability of probability, Internat. Statist. Rev. 50, (1982), 1–26). Herein, we develop a calculus of admissibility in a game theoretic setting. In the case of an additive aggregation function, it is shown that decomposable measures, such as those used in fuzzy logics, are admissible. Also, the problem of the admissibility of the Dempster-Shafer belief functions is investigated via the concept of random sets. It is shown that the class of admissible measures in a scoring framework depends on the assumptions concerning the aggregation function in use. In particular, for nonadditive aggregation functions, an admissible measure may not be transformable to a finitely additive probability measure.},
  doi       = {10.1016/0022-247X(91)90214-K},
  file      = {1991_Goodman_550.pdf:by-author/G/Goodman/1991_Goodman_550.pdf:PDF},
  groups    = {sg/Probability theory, sg/Bayesian},
  keywords  = {Bayesian Statistics; Expert Systems; Knowledge Representation; Possibility Theory; Uncertainty Representation},
  owner     = {saulius},
  timestamp = {2015.12.07},
  creationdate = {2015-12-07T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/0022247X9190214K},
}

@Article{Goodsell1994,
  author    = {Goodsell, D. S. and Dickerson, R. E.},
  journal   = {Nucleic acids research},
  title     = {Bending and curvature calculations in B-DNA.},
  year      = {1994},
  pages     = {5497--503},
  volume    = {22},
  abstract  = {A simple program, BEND, has been written to calculate the magnitude of local bending and macroscopic curvature at each point along an arbitrary B-DNA sequence, using any desired bending model that specifies values of twist, roll and tilt as a function of sequence. The program has been used to evaluate six different DNA bending models in three categories. Two are bent non-A-tract models: (a) A new model based on the nucleosome positioning data of Satchwell et al 1986 (J. Mol. Biol. 191, 659-675), (b) The model of Calladine et al 1988 (J. Mol. Biol. 201, 127-137). Three are bent A-tract models: (c) The wedge model of Bolshoy et al 1991 (Proc. Natl. Acad. Sci. USA 88, 2312-2316), (d) The model of Cacchione et al 1989 (Biochem. 28, 8706-8713), (e) A reversed version of model (b). The last is a junction model: (f) The model of Koo &amp; Crothers 1988 (Proc. Natl. Acad. Sci. USA 85, 1763-1767). Although they have widely different assumptions and values for twist, roll and tilt, all six models correctly predict experimental A-tract curvature as measured by gel retardation and cyclization kinetics, but only the new nucleosome positioning model is successful in predicting curvature in regions containing phased GGGCCC sequences. This model--showing local bending at mixed sequence DNA, strong bends at the sequence GGC, and straight, rigid A-tracts--is the only model consistent with both solution data from gel retardation and cyclization kinetics and structural data from x-ray crystallography.},
  file      = {:by-author/G/Goodsell/1994_Goodsell_5497.pdf:PDF},
  keywords  = {Readout},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Gopinath2013,
  author    = {Gopinath, Krishnamoorthy and Venclovas, {\v{C}}eslovas and Ioerger, Thomas R. and Sacchettini, James C. and McKinney, John D. and Mizrahi, Valerie and Warner, Digby F.},
  journal   = {Open Biology},
  title     = {A vitamin {B12} transporter in {M}ycobacterium tuberculosis},
  year      = {2013},
  number    = {2},
  pages     = {120175--120175},
  volume    = {3},
  abstract  = {Vitamin B12-dependent enzymes function in core biochemical pathways in Mycobacterium tuberculosis, an obligate pathogen whose metabolism in vivo is poorly understood. Although M. tuberculosis can access vitamin B12 in vitro, it is uncertain whether the organism is able to scavenge B12 during host infection. This question is crucial to predictions of metabolic function, but its resolution is complicated by the absence in the M. tuberculosis genome of a direct homologue of BtuFCD, the only bacterial B12 transport system described to date. We applied genome-wide transposon mutagenesis to identify M. tuberculosis mutants defective in their ability to use exogenous B12. A small proportion of these mapped to Rv1314c, identifying the putative PduO-type ATP : co(I)rrinoid adenosyltransferase as essential for B12 assimilation. Most notably, however, insertions in Rv1819c dominated the mutant pool, revealing an unexpected function in B12 acquisition for an ATP-binding cassette (ABC)-type protein previously investigated as the mycobacterial BacA homologue. Moreover, targeted deletion of Rv1819c eliminated the ability of M. tuberculosis to transport B12 and related corrinoids in vitro. Our results establish an alternative to the canonical BtuCD-type system for B12 uptake in M. tuberculosis, and elucidate a role in B12 metabolism for an ABC protein implicated in chronic mycobacterial infection.},
  doi       = {10.1098/rsob.120175},
  file      = {:by-author/G/Gopinath/2013_Gopinath_120175.pdf:PDF;:by-author/G/Gopinath/2013_Gopinath_120175_suppl.pdf:PDF},
  owner     = {andrius},
  timestamp = {2014.04.04},
  creationdate = {2014-04-04T00:00:00},
  url       = {http://rsob.royalsocietypublishing.org/content/3/2/120175.abstract},
}

@Article{Gore2012,
  author    = {Swanand Gore and Sameer Velankar and Gerard J. Kleywegt},
  journal   = {Acta Crystallographica Section D},
  title     = {Implementing an {X}-ray validation pipeline for the {P}rotein {D}ata {B}ank},
  year      = {2012},
  pages     = {478--483},
  volume    = {68},
  abstract  = {There is an increasing realisation that the quality of the biomacromolecular structures deposited in the Protein Data Bank (PDB) archive needs to be assessed critically using established and powerful validation methods. The Worldwide Protein Data Bank (wwPDB) organization has convened several Validation Task Forces (VTFs) to advise on the methods and standards that should be used to validate all of the entries already in the PDB as well as all structures that will be deposited in the future. The recommendations of the X-ray VTF are currently being implemented in a software pipeline. Here, ongoing work on this pipeline is briefly described as well as ways in which validation-related information could be presented to users of structural data.},
  doi       = {10.1107/S0907444911050359},
  file      = {:by-author/G/Gore/2012_Gore_478.pdf:PDF},
  keywords  = {Crystallography; Validation},
  owner     = {andrius},
  timestamp = {2014.08.15},
  creationdate = {2014-08-15T00:00:00},
}

@Article{Gormley2000,
  author    = {Gormley, N. A. and Bath, A. J. and Halford, S. E.},
  journal   = {The Journal of biological chemistry},
  title     = {Reactions of BglI and other type II restriction endonucleases with discontinuous recognition sites.},
  year      = {2000},
  pages     = {6928--36},
  volume    = {275},
  abstract  = {Type II restriction enzymes generally recognize continuous sequences of 4-8 consecutive base pairs on DNA, but some recognize discontinuous sites where the specified sequence is interrupted by a defined length of nonspecific DNA. To date, a mechanism has been established for only one type II endonuclease with a discontinuous site, SfiI at GGCCNNNNNGGCC (where N is any base). In contrast to orthodox enzymes such as EcoRV, dimeric proteins that act at a single site, SfiI is a tetramer that interacts with two sites before cleaving DNA. BglI has a similar recognition sequence (GCCNNNNNGGC) to SfiI but a crystal structure like EcoRV. BglI and several other endonucleases with discontinuous sites were examined to see if they need two sites for their DNA cleavage reactions. The enzymes included some with sites containing lengthy segments of nonspecific DNA, such as XcmI (CCANNNNNNNNNTGG). In all cases, they acted at individual sites. Elongated recognition sites do not necessitate unusual reaction mechanisms. Other experiments on BglI showed that it bound to and cleaved DNA in the same manner as EcoRV, thus further delineating a distinct group of restriction enzymes with similar structures and a common reaction mechanism.},
  file      = {:by-author/G/Gormley/2000_Gormley_6928.pdf:PDF},
  keywords  = {TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@InProceedings{Gosink2008,
  author      = {Gosink, L. J. and Wu, K. and Bethel, E. W. and Owens, J. D. and Joy, K. I.},
  booktitle   = {BNL-729E},
  title       = {Bin-Hash Indexing: A Parallel Method for Fast Query Processing},
  year        = {2008},
  abstract    = {This paper presents a new parallel indexing data structure for answering queries. The index, called Bin-Hash, offers extremely high levels of concurrency, and is therefore well- suited for the emerging commodity of parallel processors, such as multi-cores, cell processors, and general purpose graphics processing units (GPU). The Bin-Hash approach first bins the base data, and then partitions and separately stores the values in each bin as a perfect spatial hash table. To answer a query, we first determine whether or not a record satisfies the query conditions based on the bin boundaries. For the bins with records that can not be resolved, we examine the spatial hash tables. The procedures for examining the bin numbers and the spatial hash tables offer the maximum possible level of concurrency; all records are able to be evaluated by our procedure independently in parallel. Additionally, our Bin-Hash procedures access much smaller amounts of data than similar parallel methods, such as the projection index. This smaller data footprint is critical for certain parallel processors, like GPUs, where memory resources are limited. To demonstrate the effectiveness of Bin-Hash, we implement it on a GPU using the data-parallel programming language CUDA. The concurrency offered by the Bin-Hash index allows us to fully utilize the GPU’s massive parallelism in our work; over 12,000 records can be simultaneously evaluated at any one time. We show that our new query processing method is an order of magnitude faster than current state-of-the-art CPU-based indexing technologies. Additionally, we compare our performance to existing GPU-based projection index strategies.},
  file        = {2008_Gosink.pdf:by-author/G/Gosink/2008_Gosink.pdf:PDF},
  institution = {Lawrence Berkeley National Laboratory},
  owner       = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url         = {http://www.escholarship.org/uc/item/0nr5t4hg},
}

@TechReport{Gough2000,
  author      = {K. John Gough},
  institution = {Queensland University of Technology},
  title       = {Stacking them up: a Comparison of Virtual Machines},
  year        = {2000},
  file        = {:by-author/G/Gough/2000_Gough.pdf:PDF;:by-author/G/Gough/2000_Gough.ps:PostScript},
  owner       = {saulius},
  timestamp = {2015.02.25},
  creationdate = {2015-02-25T00:00:00},
}

@Article{Gould2005,
  author    = {Gould, Stephen McQ and Tawfik, Dan S},
  journal   = {Biochemistry},
  title     = {Directed evolution of the promiscuous esterase activity of carbonic anhydrase II.},
  year      = {2005},
  pages     = {5444--52},
  volume    = {44},
  abstract  = {A promiscuous activity of an existing enzyme can confer an evolutionary advantage by providing an immediate response to a new selection pressure and a starting point for the divergence of a new enzyme. This work seeks to examine how this process might take place. Human carbonic anhydrase II (hCAII) is an enzyme that evolved to catalyze the reversible hydration of CO(2) and performs this task at a remarkable rate (k(cat) approximately 10(6) s(-)(1)). hCAII also exhibits promiscuous activity toward highly activated esters such as 4-nitrophenyl acetate. We describe a much weaker esterase activity of hCAII toward the bulkier and much less activated ester substrate 2-naphthyl acetate (2NA). Directed evolution of hCAII produced a variant with 40-fold higher rates toward 2NA, owing to two mutations: one within the active site (Ala65Val) and one at its mouth (Thr200Ala). Structure-activity studies suggest that these mutations led to adaptation of the active site for bulkier substrates and for the catalysis of nonactivated esters. The mutations did not, however, significantly alter the native activity of hCAII. Our results support the notion that the evolution of a new function can be driven by mutations that increase a promiscuous function (which serves as the starting point for the evolutionary process) but do not harm the native function.},
  file      = {2005_Gould_5444.pdf:by-author/G/Gould/2005_Gould_5444.pdf:PDF},
  groups    = {sg/hCA2},
  keywords  = {Carbonic Anhydrases},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Goulon2007,
  author    = {Goulon, A. and Picot, T. and Duprat, A. and Dreyfus, G.},
  journal   = {SAR and QSAR in Environmental Research},
  title     = {Predicting activities without computing descriptors: graph machines for {QSAR}},
  year      = {2007},
  pages     = {141--153},
  volume    = {18},
  abstract  = {We describe graph machines, an alternative approach to traditional machine-learning-based QSAR, which circumvents the problem of designing, computing and selecting molecular descriptors. In that approach, which is similar in spirit to recursive networks, molecules are considered as structured data, represented as graphs. For each example of the data set, a mathematical function (graph machine) is built, whose structure reflects the structure of the molecule under consideration; it is the combination of identical parameterised functions, called “node functions” (e.g. a feedforward neural network). The parameters of the node functions, shared both within and across the graph machines, are adjusted during training with the “shared weights” technique. Model selection is then performed by traditional cross-validation. Therefore, the designer's main task consists in finding the optimal complexity for the node function. The efficiency of this new approach has been demonstrated in many QSAR or QSPR tasks, as well as in modelling the activities of complex chemicals (e.g. the toxicity of a family of phenols or the anti-HIV activities of HEPT derivatives). It generally outperforms traditional techniques without requiring the selection and computation of descriptors. §Presented at the 12th International Workshop on Quantitative Structure-Activity Relationships in Environmental Toxicology (QSAR2006), 8–12 May 2006, Lyon, France.},
  doi       = {10.1080/10629360601054313},
  file      = {:by-author/G/Goulon/2007_Goulon_141.pdf:PDF},
  owner     = {andrius},
  timestamp = {2015.03.09},
  creationdate = {2015-03-09T00:00:00},
  url       = {http://dx.doi.org/10.1080/10629360601054313},
}

@Manuscript{Gove2013,
  author    = {Darryl Gove and Nawal Copty and Michael Wong},
  title     = {Leveraging OpenMP infrastructure for language level parallelisation},
  year      = {2013},
  file      = {:by-author/G/Gove/2013_Gove.pdf:PDF},
  owner     = {saulius},
  timestamp = {2013.07.02},
  creationdate = {2013-07-02T00:00:00},
}

@Article{Govers1980,
  author    = {Govers, H. A. J. and de Kruif, C. G.},
  journal   = {Acta Crystallographica Section A},
  title     = {Intermolecular energy and structure of tetrathiafulvalene (TTF) stacks from atom{--}atom potentials},
  year      = {1980},
  pages     = {428--432},
  volume    = {36},
  abstract  = {The lattice energy of isolated, regular tetrathiafulvalene stacks was minimized for a longitudinal slip of the molecules relative to each other at constant intermolecular separation and transverse slip. The van der Waals and repulsive interactions were calculated from atom-atom potentials. A simple expression is presented for the electrostatic interaction in neutral and charged stacks. This electrostatic contribution was calculated from CNDO/2 atomic point charges. The latter contribution proved to be negligible for stacks built up from neutral molecules. For these stacks the minimum of the lattice energy is achieved at a slip of 0.1-0.2 Å below the observed values. Eclipsed stacks, with zero slip, appeared to be only 3.35 kJ mol-1 less stable than slipped ones. In stacks built up from positively charged molecules the van der Waals and repulsive contributions are dominated completely by the electrostatic interaction. These stacks tend to a structure with infinite slip.},
  doi       = {10.1107/S0567739480000927},
  file      = {:by-author/G/Govers/1980_Govers_428.pdf:PDF},
  keywords  = {Molecular Modelling},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0567739480000927},
}

@Article{Gowers2004,
  author    = {Gowers, Darren M. and Bellamy, Stuart R. W. and Halford, Stephen E.},
  journal   = {Nucleic acids research},
  title     = {One recognition sequence, seven restriction enzymes, five reaction mechanisms.},
  year      = {2004},
  pages     = {3469--79},
  volume    = {32},
  abstract  = {The diversity of reaction mechanisms employed by Type II restriction enzymes was investigated by analysing the reactions of seven endonucleases at the same DNA sequence. NarI, KasI, Mly113I, SfoI, EgeI, EheI and BbeI cleave DNA at several different positions in the sequence 5'-GGCGCC-3'. Their reactions on plasmids with one or two copies of this sequence revealed five distinct mechanisms. These differ in terms of the number of sites the enzyme binds, and the number of phosphodiester bonds cleaved per turnover. NarI binds two sites, but cleaves only one bond per DNA-binding event. KasI also cuts only one bond per turnover but acts at individual sites, preferring intact to nicked sites. Mly113I cuts both strands of its recognition sites, but shows full activity only when bound to two sites, which are then cleaved concertedly. SfoI, EgeI and EheI cut both strands at individual sites, in the manner historically considered as normal for Type II enzymes. Finally, BbeI displays an absolute requirement for two sites in close physical proximity, which are cleaved concertedly. The range of reaction mechanisms for restriction enzymes is thus larger than commonly imagined, as is the number of enzymes needing two recognition sites.},
  file      = {:by-author/G/Gowers/2004_Gowers_3469.pdf:PDF},
  keywords  = {Evolution; TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Graaf2004,
  author    = {Jeroen van de Graaf and Osvaldo Carvalho},
  title     = {Reflecting on {X.509} and {LDAP}, or {H}ow separating identity and attributes could simplify a {PKI}},
  year      = {2004},
  abstract  = {X.509 certificates can be used to store attributes about its owner, and so can on-line directory systems such as LDAP. In this paper we explore the option of putting little or no data in the certificate itself, and all data in LDAP databases. We show how this approach completely changes the role of the Registration Authority, resulting in a more flexible PKI. In particular it leads to a way to implement Single Sign On, allowing hosting organizations to fully specify and modify access control lists, and for mechanisms in which the user can have some control over which information he shows to which organization.},
  file      = {:by-author/G/Graaf/2004_Graaf.pdf:PDF},
  keywords  = {Computer Science (CS); Cryptography},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@TechReport{Graefe1992,
  author      = {Goetz Graefe},
  institution = {University of Colorado at Boulder, Computer Science Department},
  title       = {Query Evaluation Techniques for Large Databases},
  year        = {1992},
  month       = {June},
  file        = {:by-author/G/Graefe/1992_Graefe.htm:},
  keywords    = {Computer Science (CS); Databases; Spatial Databases Indexing},
  owner       = {saulius},
  timestamp = {2015.03.03},
  creationdate = {2015-03-03T00:00:00},
  url         = {http://www.cse.iitb.ac.in/~maloo/ddp/queryeval-large-db.pdf},
}

@Article{Grandori1998,
  author    = {Grandori, R and Khalifah, P and Boice, J A and Fairman, R and Giovanielli, K and Carey, J},
  journal   = {The Journal of biological chemistry},
  title     = {Biochemical characterization of WrbA, founding member of a new family of multimeric flavodoxin-like proteins.},
  year      = {1998},
  pages     = {20960--6},
  volume    = {273},
  abstract  = {The protein WrbA had been identified as an Escherichia coli stationary-phase protein that copurified and coimmunoprecipitated with the tryptophan repressor. Sequences homologous to WrbA have been reported in several species of yeast and plants. We previously showed that this new family of proteins displays low but structurally significant sequence similarity with flavodoxins and that its members are predicted to share the alpha/beta core of the flavodoxin fold but with a short conserved insertion unique to the new family, which could account for reports that some family members may be dimeric in solution. The general sequence similarity to flavodoxins suggests that the members of the new family might bind FMN, but their wide evolutionary distribution indicates that, unlike the flavodoxins, these proteins may be ubiquitous. In this paper, we report the purification and biochemical characterization of WrbA, demonstrating that the protein binds FMN specifically and is a multimer in solution. The FMN binding constant is weaker than for many flavodoxins, being approximately 2 microM at 25 degreesC in 0. 1 mM sodium phosphate, pH 7.2. The protein participates in a dimer-tetramer equilibrium over a wide range of solution conditions, with a midpoint at approximately 1.4 microM. One FMN binds per monomer and has no apparent effect on the multimerization equilibrium. WrbA has no effect on the affinity or mode of DNA binding by the tryptophan repressor; thus, its physiological role remains unclear. Although many proteins with flavodoxin-like domains are known to be multimers, WrbA is apparently the first characterized case in which multimerization is associated directly with the flavodoxin-like domain itself.},
  file      = {Grandori_1998_20960.pdf:by-author/G/Grandori/1998_Grandori_20960.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Graney2013,
  author    = {Graney, Christopher M.},
  journal   = {Phys. Today},
  title     = {Revisiting Riccioli’s free-fall calculations},
  year      = {2013},
  issn      = {0031-9228},
  pages     = {8},
  volume    = {66},
  doi       = {10.1063/pt.3.1898},
  file      = {:by-author/G/Graney/2013_Graney_8.pdf:PDF},
  owner     = {saulius},
  publisher = {AIP Publishing},
  timestamp = {2015.02.25},
  creationdate = {2015-02-25T00:00:00},
  url       = {http://dx.doi.org/10.1063/PT.3.1898},
}

@TechReport{Graney2012,
  author      = {Christopher M. Graney},
  institution = {Jefferson Community \& Technical College},
  title       = {Doubting, Testing, and Confirming Galileo. A translation of Giovanni and Battista Riccioli’s and experiments regarding the motion of a falling body, as reported in his 1651 Almagestum Novum},
  year        = {2012},
  number      = {College},
  comment     = {The Italian astronomer Giovanni Battista Riccioli is commonly credited with performing the first precise experiments to determine the acceleration of a freely falling body. Riccioli has been discussed by historians of science, sometimes positively but often not, but translations of his work into modern languages are not readily available. Presented here is a translation of his experiments regarding the nature of the motion of a falling body. Riccioli provides a thorough description of his experiments, and his data are quite good. He appears to have a model approach to science: He attacks the question of free fall with the expectation of disproving Galileo’s ideas, yet he is convinced by his data that Galileo is indeed correct, and he promptly informs a former protégée of Galileo’s of the results.},
  file        = {:by-author/G/Graney/2012_Graney_.pdf:PDF},
  owner       = {saulius},
  timestamp = {2015.02.25},
  creationdate = {2015-02-25T00:00:00},
}

@Article{Graney2012a,
  author    = {Graney, Christopher M.},
  journal   = {Phys. Today},
  title     = {Anatomy of a fall: Giovanni Battista Riccioli and the story of g},
  year      = {2012},
  issn      = {0031-9228},
  pages     = {36},
  volume    = {65},
  doi       = {10.1063/pt.3.1716},
  file      = {:by-author/G/Graney/2012_Graney_36.pdf:PDF},
  owner     = {saulius},
  publisher = {AIP Publishing},
  timestamp = {2015.02.25},
  creationdate = {2015-02-25T00:00:00},
  url       = {http://dx.doi.org/10.1063/PT.3.1716},
}

@Article{Granlund2015,
  author    = {Granlund, L. and Billinge, S. J. L. and Duxbury, P. M.},
  journal   = {Acta Crystallographica Section A: Foundations and Advances},
  title     = {Algorithm for systematic peak extraction from atomic pair distribution functions},
  year      = {2015},
  pages     = {0--0},
  volume    = {71},
  file      = {[PDF] from columbia.edu:by-author/G/Granlund/2015_Granlund.pdf:application/pdf},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://scripts.iucr.org/cgi-bin/paper?S2053273315005276},
  urldate   = {2015-08-31},
}

@Article{Grant1996,
  author    = {Grant, J. A. and Gallardo, M. A. and Pickup, B. T.},
  journal   = {Journal of Computational Chemistry},
  title     = {A fast method of molecular shape comparison: A simple application of a {G}aussian description of molecular shape},
  year      = {1996},
  issn      = {1096-987X},
  pages     = {1653--1666},
  volume    = {17},
  abstract  = {A Gaussian description of molecular shape is used to compare the shapes of two molecules by analytically optimizing their volume intersection. The method is applied to predict the relative orientation of ligand series binding to the proteins, thrombin, HIV protease, and thermolysin. The method is also used to quantify the degree of chirality of asymmetric molecules and to investigate the chirality of biphenyl and the amino acids. The shape comparison method uses the newly described shape multipoles that can also be used to describe the inherent shape of molecules. Some results of calculated shape quadrupoles are given for the ligands used in this work. © 1996 by John Wiley & Sons, Inc.},
  doi       = {10.1002/(SICI)1096-987X(19961115)17:14<1653::AID-JCC7>3.0.CO;2-K},
  file      = {:by-author/G/Grant/1996_Grant_1654.pdf:PDF},
  owner     = {andrius},
  publisher = {John Wiley \& Sons, Inc.},
  timestamp = {2014.11.11},
  creationdate = {2014-11-11T00:00:00},
  url       = {http://dx.doi.org/10.1002/(SICI)1096-987X(19961115)17:14<1653::AID-JCC7>3.0.CO;2-K},
}

@Article{Gratias2008,
  author    = {D. Gratias and M. Quiquandon},
  journal   = {Philosophical Magazine},
  title     = {Structures of quasicrystals: Where are the atoms?},
  year      = {2008},
  pages     = {1887--1903},
  volume    = {88},
  abstract  = {This paper is an attempt to present a chronological review of the structural concepts that have been developed to characterize quasicrystals, starting from the experimental discovery of D. Shechtman and the concomitant theoretical definition of quasicrystal as proposed by D. Levine and P. Steinhardt, up to the present research in the field. The largest part of the paper is a discussion of the specific points that make the atomic structure determination of quasicrystals an original and difficult scientific challenge. We finally discuss the soundness of our knowledge of the actual atomic structure in quasicrystals: we do have quite a solid idea of where the atoms are but we are not sure about the distribution of the chemical species.},
  doi       = {10.1080/14786430801971474},
  eprint    = {http://dx.doi.org/10.1080/14786430801971474},
  file      = {2008_Gratias_1887.pdf:by-author/G/Gratias/2008_Gratias_1887.pdf:PDF},
  owner     = {saulius},
  timestamp = {2015.10.18},
  creationdate = {2015-10-18T00:00:00},
  url       = {http://dx.doi.org/10.1080/14786430801971474},
}

@Article{Graves-Woodward1997,
  author    = {Graves-Woodward, K. L. and Gottlieb, J. and Challberg, M. D. and Weller, S. K.},
  journal   = {The Journal of biological chemistry},
  title     = {Biochemical analyses of mutations in the HSV-1 helicase-primase that alter ATP hydrolysis, DNA unwinding, and coupling between hydrolysis and unwinding.},
  year      = {1997},
  pages     = {4623--30},
  volume    = {272},
  abstract  = {Herpes simplex virus type 1 encodes a heterotrimeric helicase-primase composed of the products of the UL5, UL52, and UL8 genes. UL5 possesses six motifs conserved among superfamily 1 of helicase proteins. Substitutions of conserved residues in each motif abolishes DNA replication in vivo (Zhu, L., and Weller, S. K. (1992) J. Virol. 66, 469-479). Purified UL5.52 harboring a Gly to Ala change in motif V retains primase and helicase activities in vitro but exhibits a higher KM for single-stranded DNA and lower DNA-dependent ATPase activity (Graves-Woodward, K. L., and Weller, S. K. (1996) J. Biol. Chem. 272, 13629-13635). We have purified and characterized six other subcomplexes with residue changes in the UL5 helicase motifs. Each variant subcomplex displays at least wild type or greater levels of primase and DNA binding activities, but all are defective in helicase activity. Mutations in motifs I and II exhibit profound decreases in DNA-dependent ATPase activity. Mutations in motifs III-VI decrease DNA-dependent ATPase activity 3-6-fold. Since mutations in motifs III, IV, V, and VI do not eliminate ATP hydrolysis or DNA binding, we propose that they may be involved in the coupling of these two activities to the process of DNA unwinding. This analysis represents the first comprehensive structure-function analysis of the conserved motifs in helicase superfamily 1.},
  file      = {:by-author/G/Graves-Woodward/1997_Graves-Woodward_4623.pdf:PDF},
  keywords  = {{gp41} Helicase},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Gray2005,
  author     = {Gray, Jim and Liu, David T. and Nieto-Santisteban, Maria and Szalay, Alex and DeWitt, David J. and Heber, Gerd},
  journal    = {SIGMOD Rec.},
  title      = {Scientific Data Management in the Coming Decade},
  year       = {2005},
  issn       = {0163-5808},
  pages      = {34--41},
  volume     = {34},
  abstract   = {Scientific instruments and computer simulations are creating vast data stores that require new scientific methods to analyze and organize the data. Data volumes are approximately doubling each year. Since these new instruments have extraordinary precision, the data quality is also rapidly improving. Analyzing this data to find the subtle effects missed by previous studies requires algorithms that can simultaneously deal with huge datasets and that can find very subtle effects --- finding both needles in the haystack and finding very small haystacks that were undetected in previous measurements.},
  address    = {New York, NY, USA},
  doi        = {10.1145/1107499.1107503},
  file       = {:by-author/G/Gray/2005_Gray_34.pdf:PDF},
  issue_date = {December 2005},
  numpages   = {8},
  owner      = {saulius},
  publisher  = {ACM},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url        = {http://doi.acm.org/10.1145/1107499.1107503},
}

@PhdThesis{Grazulis2000,
  author    = {Saulius Grazulis},
  school    = {Fakultät für Chemie der Technischen Universität München},
  title     = {Structure and function of the restriction endonucleases Bse634I and MunI},
  year      = {2000},
  file      = {2000_Grazulis_phdthesis.pdf:by-author/G/Grazulis/2000_Grazulis_phdthesis.pdf:PDF},
  groups    = {sg/Bse634I structures, sg/Bse634I},
  owner     = {saulius},
  timestamp = {2012.09.18},
  creationdate = {2012-09-18T00:00:00},
}

@Presentation{Grazulis2013,
  author       = {Saulius Gražulis},
  title        = {{F/LOSS} for Open Science: {C}rystallography {O}pen {D}atabase},
  year         = {2013},
  organization = {Vilnius University Institute of Biotechnology},
  file         = {:by-author/G/Gražulis/2013_Gražulis_slides.pdf:PDF},
  owner        = {andrius},
  timestamp = {2013.05.06},
  creationdate = {2013-05-06T00:00:00},
}

@Article{Grazulis2009,
  author    = {Gražulis, Saulius and Chateigner, Daniel and Downs, Robert T. and Yokochi, A. F. T. and Quirós, Miguel and Lutterotti, Luca and Manakova, Elena and Butkus, Justas and Moeck, Peter and Le Bail, Armel},
  journal   = {Journal of Applied Crystallography},
  title     = {{C}rystallography {O}pen {D}atabase {--} an open-access collection of crystal structures},
  year      = {2009},
  pages     = {726--729},
  volume    = {42},
  abstract  = {The Crystallography Open Database (COD), which is a project that aims to gather all available inorganic, metal-organic and small organic molecule structural data in one database, is described. The database adopts an open-access model. The COD currently contains ~80 000 entries in crystallographic information file format, with nearly full coverage of the International Union of Crystallography publications, and is growing in size and quality.},
  doi       = {10.1107/S0021889809016690},
  file      = {2009_Gražulis_726.pdf:by-author/G/Gražulis/2009_Gražulis_726.pdf:PDF},
  groups    = {sg/COD, am/COD},
  keywords  = {COD; Crystallography; Data Access Policy; Data Management; Databases},
  owner     = {saulius},
  timestamp = {2011.01.05},
  creationdate = {2011-01-05T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0021889809016690},
}

@Article{Grazulis2012,
  author           = {Gražulis, Saulius and Daškevič, Adriana and Merkys, Andrius and Chateigner, Daniel and Lutterotti, Luca and Quirós, Miguel and Serebryanaya, Nadezhda R. and Moeck, Peter and Downs, Robert T. and Le Bail, Armel},
  journal          = {Nucleic Acids Research},
  title            = {{C}rystallography {O}pen {D}atabase ({COD}): an open-access collection of crystal structures and platform for world-wide collaboration},
  year             = {2012},
  pages            = {D420-D427},
  volume           = {40},
  abstract         = {Using an open-access distribution model, the Crystallography Open Database (COD, http://www.crystallography.net) collects all known ‘small molecule / small to medium sized unit cell’ crystal structures and makes them available freely on the Internet. As of today, the COD has aggregated ∼150 000 structures, offering basic search capabilities and the possibility to download the whole database, or parts thereof using a variety of standard open communication protocols. A newly developed website provides capabilities for all registered users to deposit published and so far unpublished structures as personal communications or pre-publication depositions. Such a setup enables extension of the COD database by many users simultaneously. This increases the possibilities for growth of the COD database, and is the first step towards establishing a world wide Internet-based collaborative platform dedicated to the collection and curation of structural knowledge.},
  creationdate     = {2011-12-29T00:00:00},
  doi              = {10.1093/nar/gkr900},
  file             = {:by-author/G/Gražulis/2012_Gražulis_D420.pdf:PDF},
  groups           = {sg/COD, am/COD, am/My papers},
  keywords         = {CIF; COD; Crystallographic Databases; Crystallography; Data Management; Scientific Databases},
  modificationdate = {2024-04-27T11:28:09},
  owner            = {saulius},
  timestamp        = {2011.12.29},
  url              = {http://nar.oxfordjournals.org/content/40/D1/D420.abstract},
}

@Article{Grazulis2002,
  author       = {Saulius Grazulis and Markus Deibert and Renata Rimseliene and Remigijus Skirgaila and Giedrius Sasnauskas and Arunas Lagunavicius and Vladimir Repin and Claus Urbanke and Robert Huber and Virginijus Siksnys},
  journal      = {Nucleic Acids Res},
  title        = {Crystal structure of the Bse634I restriction endonuclease: comparison of two enzymes recognizing the same DNA sequence.},
  year         = {2002},
  month        = {Feb},
  number       = {4},
  pages        = {876--885},
  volume       = {30},
  abstract     = {Crystal structures of Type II restriction endonucleases demonstrate a conserved common core and active site residues but diverse structural elements involved in DNA sequence discrimination. Comparative structural analysis of restriction enzymes recognizing the same nucleotide sequence might therefore contribute to our understanding of the structural diversity of specificity determinants within restriction enzymes. We have solved the crystal structure of the Bacillus stearothermophilus restriction endonuclease Bse634I by the multiple isomorphous replacement technique to 2.17 A resolution. Bse634I is an isoschisomer of the Cfr10I restriction enzyme whose crystal structure has been reported previously. Comparative structural analysis of the first pair of isoschisomeric enzymes revealed conserved structural determinants of sequence recognition and catalysis. However, conformations of the N-terminal subdomains differed between Bse634I/Cfr10I, suggesting a rigid body movement that might couple DNA recognition and catalysis. Structural similarities extend to the quaternary structure level: crystal contacts suggest that Bse634I similarly to Cfr10I is arranged as a tetramer. Kinetic analysis reveals that Bse634I is able to interact simultaneously with two recognition sites supporting the tetrameric architecture of the protein. Thus, restriction enzymes Bse634I, Cfr10I and NgoMIV, recognizing overlapping nucleotide sequences, exhibit a conserved tetrameric architecture that is of functional importance.},
  creationdate = {2011-06-08T00:00:00},
  file         = {2002_Grazulis_876.pdf:by-author/G/Grazulis/2002_Grazulis_876.pdf:PDF},
  groups       = {sg/Cfr10I, sg/NgoMIV, sg/Bse634I structures, sg/Bse634I},
  institution  = {Max-Planck Institut für Biochemie, Abt. Strukturforschung, Am Klopferspitz 18a, D-82152 Martinsried (bei München), Germany. grazulis@ibt.lt},
  keywords     = {Base Sequence; Binding Sites; Catalytic Domain; Citrobacter Freundii; Conserved Sequence; Crystallography; DNA; Deoxyribonucleases; Geobacillus Stearothermophilus; Kinetics; Metals; Models; Molecular; Plasmids; Protein Structure; Quaternary; Substrate Specificity; Superhelical; Tertiary; Type II Site-Specific; X-Ray},
  owner        = {em},
  pmid         = {11842098},
  timestamp    = {2011.06.08},
}

@Article{Grazulis2005,
  author    = {Grazulis, Saulius and Manakova, Elena and Roessle, Manfred and Bochtler, Matthias and Tamulaitiene, Giedre and Huber, Robert and Siksnys, Virginijus},
  journal   = {Proceedings of the National Academy of Sciences of the United States of America},
  title     = {Structure of the metal-independent restriction enzyme BfiI reveals fusion of a specific DNA-binding domain with a nonspecific nuclease.},
  year      = {2005},
  pages     = {15797--802},
  volume    = {102},
  abstract  = {Among all restriction endonucleases known to date, BfiI is unique in cleaving DNA in the absence of metal ions. BfiI represents a different evolutionary lineage of restriction enzymes, as shown by its crystal structure at 1.9-A resolution. The protein consists of two structural domains. The N-terminal catalytic domain is similar to Nuc, an EDTA-resistant nuclease from the phospholipase D superfamily. The C-terminal DNA-binding domain of BfiI exhibits a beta-barrel-like structure very similar to the effector DNA-binding domain of the Mg(2+)-dependent restriction enzyme EcoRII and to the B3-like DNA-binding domain of plant transcription factors. BfiI presumably evolved through domain fusion of a DNA-recognition element to a nonspecific nuclease akin to Nuc and elaborated a mechanism to limit DNA cleavage to a single double-strand break near the specific recognition sequence. The crystal structure suggests that the interdomain linker may act as an autoinhibitor controlling BfiI catalytic activity in the absence of a specific DNA sequence. A psi-blast search identified a BfiI homologue in a Mesorhizobium sp. BNC1 bacteria strain, a plant symbiont isolated from an EDTA-rich environment.},
  doi       = {10.1073/pnas.0507949102},
  file      = {:by-author/G/Grazulis/2005_Grazulis_15797.pdf:PDF},
  keywords  = {Struct; TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Grazulis2015,
  author    = {Gražulis, Saulius and Merkys, Andrius and Vaitkus, Antanas and Okulič-Kazarinas, Mykolas},
  journal   = {Journal of Applied Crystallography},
  title     = {Computing stoichiometric molecular composition from crystal structures},
  year      = {2015},
  number    = {1},
  pages     = {85--91},
  volume    = {48},
  doi       = {10.1107/S1600576714025904},
  file      = {Grazulis et al. - 2015 - Computing stoichiometric molecular composition fro.pdf:by-author/G/Grazulis/2015_Grazulis.pdf:application/pdf;Snapshot:by-author/G/Grazulis/2015_Grazulis.html:text/html;kk5188sup1.zip:by-author/G/Grazulis/2015_Grazulis.zip:application/octet-stream},
  groups    = {sg/COD, am/COD, am/My papers},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://scripts.iucr.org/cgi-bin/paper?S1600576714025904},
  urldate   = {2015-08-31},
}

@Article{Grazulis2015a,
  author    = {Gražulis, Saulius and Merkys, Andrius and Vaitkus, Antanas and Okulič-Kazarinas, Mykolas},
  journal   = {Journal of Applied Crystallography},
  title     = {Computing stoichiometric molecular composition from crystal structures},
  year      = {2015},
  pages     = {85--91},
  volume    = {48},
  abstract  = {Crystallographic investigations deliver high-accuracy information about positions of atoms in crystal unit cells. For chemists, however, the structure of a molecule is most often of interest. The structure must thus be reconstructed from crystallographic files using symmetry information and chemical properties of atoms. Most existing algorithms faithfully reconstruct separate molecules but not the overall stoichiometry of the complex present in a crystal. Here, an algorithm that can reconstruct stoichiometrically correct multimolecular ensembles is described. This algorithm uses only the crystal symmetry information for determining molecule numbers and their stoichiometric ratios. The algorithm can be used by chemists and crystallographers as a standalone implementation for investigating above-molecular ensembles or as a function implemented in graphical crystal analysis software. The greatest envisaged benefit of the algorithm, however, is for the users of large crystallographic and chemical databases, since it will permit database maintainers to generate stoichiometrically correct chemical representations of crystal structures automatically and to match them against chemical databases, enabling multidisciplinary searches across multiple databases.},
  doi       = {10.1107/S1600576714025904},
  file      = {:by-author/G/Gražulis/2015_Gražulis_85.pdf:PDF},
  groups    = {sg/COD, am/COD, am/My papers},
  owner     = {andrius},
  timestamp = {2015.01.29},
  creationdate = {2015-01-29T00:00:00},
  url       = {http://dx.doi.org/10.1107/S1600576714025904},
}

@Article{Grazulis2015b,
  author    = {Gražulis, Saulius and Sarjeant, Amy Alexis and Moeck, Peter and Stone-Sundberg, Jennifer and Snyder, Trevor J. and Kaminsky, Werner and Oliver, Allen G. and Stern, Charlotte L. and Dawe, Louise N. and Rychkov, Denis A. and Losev, Evgeniy A. and Boldyreva, Elena V. and Tanski, Joseph M. and Bernstein, Joel and Rabeh, Wael M. and Kantardjieff, Katherine A.},
  journal   = {Journal of Applied Crystallography},
  title     = {Crystallographic education in the 21st century},
  year      = {2015},
  month     = {Dec},
  number    = {6},
  pages     = {1964--1975},
  volume    = {48},
  abstract  = {There are many methods that can be used to incorporate concepts of crystallography into the learning experiences of students, whether they are in elementary school, at university or part of the public at large. It is not always critical that those who teach crystallography have immediate access to diffraction equipment to be able to introduce the concepts of symmetry, packing or molecular structure in an age- and audience-appropriate manner. Crystallography can be used as a tool for teaching general chemistry concepts as well as general research techniques without ever having a student determine a crystal structure. Thus, methods for younger students to perform crystal growth experiments of simple inorganic salts, organic compounds and even metals are presented. For settings where crystallographic instrumentation is accessible (proximally or remotely), students can be involved in all steps of the process, from crystal growth, to data collection, through structure solution and refinement, to final publication. Several approaches based on the presentations in the MS92 Microsymposium at the IUCr 23rd Congress and General Assembly are reported. The topics cover methods for introducing crystallography to undergraduate students as part of a core chemistry curriculum; a successful short-course workshop intended to bootstrap researchers who rely on crystallography for their work; and efforts to bring crystallography to secondary school children and non-science majors. In addition to these workshops, demonstrations and long-format courses, open-format crystallographic databases and three-dimensional printed models as tools that can be used to excite target audiences and inspire them to pursue a deeper understanding of crystallography are described.},
  doi       = {10.1107/S1600576715016830},
  file      = {2015_Gražulis_1964.pdf:by-author/G/Grazulis/2015_Gražulis_1964.pdf:PDF},
  groups    = {sg/COD, am/COD},
  keywords  = {Crystallography; Databases; Education; Teaching},
  owner     = {saulius},
  timestamp = {2016.02.04},
  creationdate = {2016-02-04T00:00:00},
  url       = {http://dx.doi.org/10.1107/S1600576715016830},
}

@Article{Green2007,
  author    = {Green, Jonathan E. and Wook Choi, Jang and Boukai, Akram and Bunimovich, Yuri and Johnston-Halperin, Ezekiel and DeIonno, Erica and Luo, Yi and Sheriff, Bonnie A. and Xu, Ke and Shik Shin, Young and Tseng, Hsian-Rong and Stoddart, J. Fraser and Heath, James R.},
  journal   = {Nature},
  title     = {A 160-kilobit molecular electronic memory patterned at 1011 bits per square centimetre},
  year      = {2007},
  issn      = {0028-0836},
  pages     = {414--417},
  volume    = {445},
  abstract  = {The primary metric for gauging progress in the various semiconductor integrated circuit technologies is the spacing, or pitch, between the most closely spaced wires within a dynamic random access memory (DRAM) circuit. Modern DRAM circuits have 140 nm pitch wires and a memory cell size of 0.0408 m2. Improving integrated circuit technology will require that these dimensions decrease over time. However, at present a large fraction of the patterning and materials requirements that we expect to need for the construction of new integrated circuit technologies in 2013 have 'no known solution'. Promising ingredients for advances in integrated circuit technology are nanowires, molecular electronics and defect-tolerant architectures, as demonstrated by reports of single devices and small circuits. Methods of extending these approaches to large-scale, high-density circuitry are largely undeveloped. Here we describe a 160,000-bit molecular electronic memory circuit, fabricated at a density of 1011 bits cm-2 (pitch 33 nm; memory cell size 0.0011 m2), that is, roughly analogous to the dimensions of a DRAM circuit projected to be available by 2020. A monolayer of bistable, [2]rotaxane molecules served as the data storage elements. Although the circuit has large numbers of defects, those defects could be readily identified through electronic testing and isolated using software coding. The working bits were then configured to form a fully functional random access memory circuit for storing and retrieving information.},
  copyright = {© 2007 Nature Publishing Group},
  doi       = {10.1038/nature05462},
  file      = {Green et al. - 2007 - A 160-kilobit molecular electronic memory patterne.pdf:by-author/G/Green/2007_Green_414.pdf:application/pdf;Snapshot:by-author/G/Green/2007_Green_414.html:text/html},
  groups    = {sg/chemical, sg/electronics},
  language  = {en},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://www.nature.com/nature/journal/v445/n7126/full/nature05462.html},
  urldate   = {2015-10-09},
}

@Article{Green1992,
  author    = {Green, R and Szostak, J W},
  journal   = {Science (New York, N.Y.)},
  title     = {Selection of a ribozyme that functions as a superior template in a self-copying reaction.},
  year      = {1992},
  pages     = {1910--5},
  volume    = {258},
  file      = {1992_Green_1910.pdf:by-author/G/Green/1992_Green_1910.pdf:PDF},
  keywords  = {Ribozymes},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Greene2007,
  author    = {Greene, Charles H. and Pershing, Andrew J.},
  journal   = {Science (New York, N.Y.)},
  title     = {Oceans. Climate drives sea change.},
  year      = {2007},
  pages     = {1084--5},
  volume    = {315},
  file      = {:by-author/G/Greene/2007_Greene_1084.pdf:PDF},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Manuscript{Greenwade1993,
  author    = {George D. Greenwade},
  title     = {Documents related to the LaTeX3 project},
  year      = {1993},
  keywords  = {Computer Language Design; Computer Science (CS); Latex3},
  month     = {June},
  file      = {:by-author/G/Greenwade/1993_Greenwade.htm:},
  owner     = {saulius},
  timestamp = {2015.03.03},
  creationdate = {2015-03-03T00:00:00},
}

@Manual{Gregor2009,
  title     = {Boost.MPI},
  author    = {Douglas Gregor and Matthias Troyer},
  year      = {2009},
  file      = {:by-author/G/Gregor/2009_Gregor.pdf:PDF},
  owner     = {saulius},
  timestamp = {2013.07.02},
  creationdate = {2013-07-02T00:00:00},
}

@Article{Gressmann2005,
  author    = {Gressmann, Helga and Linz, Bodo and Ghai, Rohit and Pleissner, Klaus-Peter and Schlapbach, Ralph and Yamaoka, Yoshio and Kraft, Christian and Suerbaum, Sebastian and Meyer, Thomas F. and Achtman, Mark},
  journal   = {PLoS genetics},
  title     = {Gain and loss of multiple genes during the evolution of Helicobacter pylori.},
  year      = {2005},
  pages     = {e43},
  volume    = {1},
  abstract  = {Sequence diversity and gene content distinguish most isolates of Helicobacter pylori. Even greater sequence differences differentiate distinct populations of H. pylori from different continents, but it was not clear whether these populations also differ in gene content. To address this question, we tested 56 globally representative strains of H. pylori and four strains of Helicobacter acinonychis with whole genome microarrays. Of the weighted average of 1,531 genes present in the two sequenced genomes, 25% are absent in at least one strain of H. pylori and 21% were absent or variable in H. acinonychis. We extrapolate that the core genome present in all isolates of H. pylori contains 1,111 genes. Variable genes tend to be small and possess unusual GC content; many of them have probably been imported by horizontal gene transfer. Phylogenetic trees based on the microarray data differ from those based on sequences of seven genes from the core genome. These discrepancies are due to homoplasies resulting from independent gene loss by deletion or recombination in multiple strains, which distort phylogenetic patterns. The patterns of these discrepancies versus population structure allow a reconstruction of the timing of the acquisition of variable genes within this species. Variable genes that are located within the cag pathogenicity island were apparently first acquired en bloc after speciation. In contrast, most other variable genes are of unknown function or encode restriction/modification enzymes, transposases, or outer membrane proteins. These seem to have been acquired prior to speciation of H. pylori and were subsequently lost by convergent evolution within individual strains. Thus, the use of microarrays can reveal patterns of gene gain or loss when examined within a phylogenetic context that is based on sequences of core genes.},
  file      = {:by-author/G/Gressmann/2005_Gressmann_e43.pdf:PDF},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Gridi-Bennadji2009,
  author    = {F. Gridi-Bennadji and D. Chateigner and G. Di Vita and P. Blanchart},
  journal   = {Journal of the European Ceramic Society},
  title     = {Mechanical properties of textured ceramics from muscovite–kaolinite alternate layers},
  year      = {2009},
  pages     = {preprint},
  volume    = {29},
  abstract  = {An organized network of mullite anisotropic crystals embedded in a silico-aluminate matrix material is obtained at interfaces of sintered alternate layers of muscovite and kaolinite minerals. The nucleation and growth of mullite anisotropic crystals occur preferentially along the muscovite basal planes through topotactic reaction with the high temperature form of muscovite. Simultaneously to structural transformations, dehydroxylation of muscovite induces an exfoliation process, which is temperature and time dependent. The kinetics of this process was controlled using an appropriate thermal cycle and uniaxial load. During sintering, the control of mullite size mainly depends in temperature and the addition of a small quantity of low-temperature liquid phase also favors the growth of mullite. But liquid induces the weakening of the organization degree of the mullite network. Quantitative texture analysis (QTA) and SEM were used to characterize microstructural characteristics. Flexural strength, Young modulus and fracture toughness are closely related to size and organization degree of the mullite network. In general, mullite length favors the increase of strength and fracture toughness. But a high organization degree of the mullite network favors the occurrence of interconnected crystals and increases mechanical properties.},
  doi       = {10.1016/j.jeurceramsoc.2009.01.004},
  file      = {:by-author/G/Gridi-Bennadji/2009_Gridi-Bennadji_preprint.pdf:PDF},
  keywords  = {COD; Mullite; Muscovite-kaolinite Alternate Layers; Textured Ceramics},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/S0955221909000089},
}

@Article{Griep1997,
  author    = {Griep, M. A. and Adkins, B. J. and Hromas, D. and Johnson, S. and Miller, J.},
  journal   = {Biochemistry},
  title     = {The tyrosine photophysics of a primase-derived peptide are sensitive to the peptide's zinc-bound state: proof that the bacterial primase hypothetical zinc finger sequence binds zinc.},
  year      = {1997},
  pages     = {544--53},
  volume    = {36},
  abstract  = {A 35-amino acid peptide corresponding to the putative "zinc finger" sequence of primase was prepared to study its zinc binding properties. When zinc was added to the peptide, it was found that the fluorescence quantum yield of the single tyrosine increased by 46% and the average lifetime by 34%. The binding stoichiometry was one zinc per peptide. Below pH 6.0 and above pH 8.5, the zinc-peptide binding affinity was less than 1 microM and could be accurately determined. Interpolation from those binding constants suggested that the affinity at pH 7.5 was between 10 and 100 nM. The absorption spectrum of the cobalt(II)-peptide complex was consistent with tetrahedral metal coordination by three sulfur and one imidazole nitrogen ligands. The peptide affinity for cobalt was less than for zinc, indicating metal specificity. Analysis of the fluorescence intensity pH profile, circular dichroism spectra, the effect of extrinsic quenchers indicated that at neutral pH (1) the free peptide up into a structure to place the tyrosine in an environment protected from solvent, (2) the peptide bound zinc via its three cysteines and one of its histidines resulting in little change to the polypeptide secondary structure or to the tyrosine solvent accessibility, and (3) when the peptide bound zinc, it bound directly to or caused the immobilization of the groups that had been intramolecularly collisionally quenching the tyrosine which resulted in the observed increases in tyrosine quantum yield and lifetime.},
  file      = {:by-author/G/Griep/1997_Griep_544.pdf:PDF},
  keywords  = {Ecoli; {gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Webpage{Griffiths2004,
  author    = {Tom Griffiths},
  retrieved = {2008-07-28},
  title     = {A reading list on Bayesian methods},
  url       = {http://www.cog.brown.edu/~gruffydd/bayes.html},
  year      = {2004},
  file      = {:by-author/G/Griffiths/2004_Griffiths.war:},
  groups    = {sg/Bayesian},
  keywords  = {Bayesian Statistics; Mathematics},
  owner     = {saulius},
  timestamp = {2015.03.02},
  creationdate = {2015-03-02T00:00:00},
}

@Presentation{Griffiths2010,
  author    = {Tom Griffiths and Charles Kemp and Josh Tenenbaum},
  title     = {Bayesian models of inductive learning},
  year      = {2010},
  file      = {:by-author/G/Griffiths/2010_Griffiths_slides.ppt:PowerPoint},
  groups    = {sg/Bayesian},
  keywords  = {Bayesian Statistics},
  owner     = {saulius},
  timestamp = {2012.10.03},
  creationdate = {2012-10-03T00:00:00},
}

@Article{Grigaite2002,
  author    = {Grigaite, R. and Maneliene, Z. and Janulaitis, A.},
  journal   = {Nucleic acids research},
  title     = {AarI, a restriction endonuclease from Arthrobacter aurescens SS2-322, which recognizes the novel non-palindromic sequence 5'-CACCTGC(N)4/8-3'.},
  year      = {2002},
  pages     = {e123},
  volume    = {30},
  abstract  = {A new type II restriction endonuclease AarI has been isolated from Arthrobacter aurescens SS2-322. AarI recognizes the non-palindromic heptanucleotide sequence 5'-CACCTGC(N)4/8-3' and makes a staggered cut at the fourth and eighth bases downstream of the target duplex producing a four base 5'-protruding end. AarI activity is stimulated by oligodeoxyribonucleotide duplexes containing an enzyme-specific recognition sequence.},
  file      = {:by-author/G/Grigaite/2002_Grigaite_e123.pdf:PDF},
  keywords  = {BfiI; TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Grimmer1975,
  author    = {Grimmer, H.},
  journal   = {Acta Crystallographica Section A},
  title     = {The relation between reduced and conventional unit cells for centred monoclinic lattices},
  year      = {1975},
  pages     = {15--18},
  volume    = {31},
  doi       = {10.1107/S0567739475000034},
  file      = {:by-author/G/Grimmer/1975_Grimmer_15.pdf:PDF},
  keywords  = {Algorithms; Niggli Cell; Reduced Cell; Unit Cell; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2014.11.06},
  creationdate = {2014-11-06T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0567739475000034},
}

@Article{Grimmer1975a,
  author    = {Grimmer, H.},
  journal   = {Acta Crystallographica Section A},
  title     = {Corrections to the relation between reduced and conventional unit cells for centred monoclinic lattices},
  year      = {1975},
  pages     = {858--859},
  volume    = {31},
  doi       = {10.1107/S0567739475001891},
  file      = {:by-author/G/Grimmer/1975_Grimmer_858.pdf:PDF},
  keywords  = {Algorithms; Niggli Cell; Reduced Cell; Unit Cell; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2014.11.06},
  creationdate = {2014-11-06T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0567739475001891},
}

@PhdThesis{Grinberg2002,
  author    = {Victor A. Grinberg},
  school    = {Northeastern University},
  title     = {Advanced strategies for coset enumeration},
  year      = {2002},
  file      = {2002_Grinberg_thesis.pdf:by-author/G/Grinberg/2002_Grinberg_thesis.pdf:PDF},
  keywords  = {Algorithms},
  owner     = {saulius},
  timestamp = {2013.07.18},
  creationdate = {2013-07-18T00:00:00},
  url       = {http://www.ccs.neu.edu/home/victor/},
}

@Article{Groll2000,
  author    = {Groll, M. and Bajorek, M. and Köhler, A. and Moroder, L. and Rubin, D. M. and Huber, R. and Glickman, M. H. and Finley, D.},
  journal   = {Nature structural biology},
  title     = {A gated channel into the proteasome core particle.},
  year      = {2000},
  pages     = {1062--7},
  volume    = {7},
  abstract  = {The core particle (CP) of the yeast proteasome is composed of four heptameric rings of subunits arranged in a hollow, barrel-like structure. We report that the CP is autoinhibited by the N-terminal tails of the outer (alpha) ring subunits. Crystallographic analysis showed that deletion of the tail of the alpha 3-subunit opens a channel into the proteolytically active interior chamber of the CP, thus derepressing peptide hydrolysis. In the latent state of the particle, the tails prevent substrate entry by imposing topological closure on the CP. Inhibition by the alpha-subunit tails is relieved upon binding of the regulatory particle to the CP to form the proteasome holoenzyme.},
  file      = {:by-author/G/Groll/2000_Groll_1062.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Gromilov2011,
  author    = {Gromilov, S. A. and Bykova, E. A. and Borisov, S. V.},
  journal   = {Crystallography Reports},
  title     = {Algorithms, software, and examples of pseudotranslational sublattice analysis for crystal structures},
  year      = {2011},
  issn      = {1562-689X},
  month     = {Nov},
  number    = {6},
  pages     = {947--952},
  volume    = {56},
  abstract  = {Software for analyzing pseudotranslational sublattices (PTSs) in crystal structures is described. This software makes it possible to enumerate triads of reflections, sort them out with respect to different char acteristics, calculate linear and angular subcell parameters, and express the sublattice vectors in terms of the initial lattice vectors. The solution to the most widespread problems is illustrated by the example of the well known [Ru(NH3)6]Cl3 and [CuL](NO3)(ReO4) crystal structures (L is 4,6,6trimethyl1,9diamino3,7diazanon3en) and the structure of mineral iltisite, which is still unknown. In all cases we observed a tendency of crystal structures to have a higher symmetry, which was noted by Academician Belov in his time.},
  doi       = {10.1134/s1063774511060101},
  file      = {2011_Gromilov_947.pdf:by-author/G/Gromilov/2011_Gromilov_947.pdf:PDF},
  keywords  = {For COD Deposition; X-ray Crystallography},
  owner     = {saulius},
  publisher = {Pleiades Publishing Ltd},
  timestamp = {2016.10.03},
  creationdate = {2016-10-03T00:00:00},
  url       = {http://dx.doi.org/10.1134/S1063774511060101},
}

@Article{Groom2011,
  author    = {Groom, Colin R.},
  journal   = {Journal of chemical information and modeling},
  title     = {Data-driven high-throughput prediction of the 3-{D} structure of small molecules: review and progress. {A} response from the {C}ambridge {C}rystallographic {D}ata {C}entre},
  year      = {2011},
  pages     = {2787},
  volume    = {51},
  doi       = {10.1021/ci2002523},
  file      = {:by-author/G/Groom/2011_Groom_2787.pdf:PDF},
  keywords  = {COSMOS; CSD; Crystallography; Data Access Policy; Data Management; Databases},
  owner     = {saulius},
  timestamp = {2012.09.24},
  creationdate = {2012-09-24T00:00:00},
  url       = {http://pubs.acs.org/doi/abs/10.1021/ci2002523},
}

@Article{Groom2014,
  author    = {Groom, Colin R. and Allen, Frank H.},
  journal   = {Angewandte Chemie International Edition},
  title     = {The {C}ambridge {S}tructural {D}atabase in Retrospect and Prospect},
  year      = {2014},
  issn      = {1521-3773},
  pages     = {662--671},
  volume    = {53},
  abstract  = {The Cambridge Crystallographic Data Centre (CCDC) was established in 1965 to record numerical, chemical and bibliographic data relating to published organic and metal–organic crystal structures. The Cambridge Structural Database (CSD) now stores data for nearly 700 000 structures and is a comprehensive and fully retrospective historical archive of small-molecule crystallography. Nearly 40 000 new structures are added each year. As X-ray crystallography celebrates its centenary as a subject, and the CCDC approaches its own 50th year, this article traces the origins of the CCDC as a publicly funded organization and its onward development into a self-financing charitable institution. Principally, however, we describe the growth of the CSD and its extensive associated software system, and summarize its impact and value as a basis for research in structural chemistry, materials science and the life sciences, including drug discovery and drug development. Finally, the article considers the CCDC’s funding model in relation to open access and open data paradigms.},
  doi       = {10.1002/anie.201306438},
  file      = {2014_Groom_662.pdf:by-author/G/Groom/2014_Groom_662.pdf:PDF},
  groups    = {sg/CSD},
  keywords  = {CCDC Origins and Development; Crystal Structure Database; Drug Discovery; Drug Formulation; Structure Correlation},
  owner     = {saulius},
  publisher = {WILEY-VCH Verlag},
  timestamp = {2014.03.23},
  creationdate = {2014-03-23T00:00:00},
  url       = {http://dx.doi.org/10.1002/anie.201306438},
}

@Article{Groom2016,
  author           = {Groom, Colin R. and Bruno, Ian J. and Lightfoot, Matthew P. and Ward, Suzanna C.},
  journal          = {Acta Crystallographica Section B},
  title            = {The Cambridge Structural Database},
  year             = {2016},
  month            = {Apr},
  number           = {2},
  pages            = {171--179},
  volume           = {72},
  abstract         = {The Cambridge Structural Database (CSD) contains a complete record of all published organic and metal{--}organic small-molecule crystal structures. The database has been in operation for over 50years and continues to be the primary means of sharing structural chemistry data and knowledge across disciplines. As well as structures that are made public to support scientific articles, it includes many structures published directly as CSD Communications. All structures are processed both computationally and by expert structural chemistry editors prior to entering the database. A key component of this processing is the reliable association of the chemical identity of the structure studied with the experimental data. This important step helps ensure that data is widely discoverable and readily reusable. Content is further enriched through selective inclusion of additional experimental data. Entries are available to anyone through free CSD community web services. Linking services developed and maintained by the CCDC, combined with the use of standard identifiers, facilitate discovery from other resources. Data can also be accessed through CCDC and third party software applications and through an application programming interface.},
  creationdate     = {2016-10-16T00:00:00},
  doi              = {10.1107/S2052520616003954},
  file             = {2016_Groom_171.pdf:by-author/G/Groom/2016_Groom_171.pdf:PDF},
  keywords         = {CIF; CIF Archive; CSD; Crystal Structure Database; Open Data},
  modificationdate = {2023-08-07T10:23:04},
  owner            = {saulius},
  timestamp        = {2016.10.16},
  url              = {https://doi.org/10.1107/S2052520616003954},
}

@Presentation{Gropp1999,
  author    = {William Gropp},
  title     = {Tutorial on MPI: The Message-Passing Interface},
  year      = {1999},
  file      = {:by-author/G/Gropp/1999_Gropp_slides.pdf:PDF},
  owner     = {saulius},
  pages     = {slides},
  timestamp = {2013.07.02},
  creationdate = {2013-07-02T00:00:00},
  url       = {http://www.mcs.anl.gov/mpi/tutorial/gropp/talk.html},
}

@InBook{Grosjean2007,
  author    = {Henri Grosjean and Tairo Oshima},
  chapter   = {How Nucleic Acids Cope with High Temperature},
  editor    = {C. Gerday and N. Glansdorff},
  pages     = {39--56},
  publisher = {ASM Press},
  title     = {Physiology and Biochemistry of Extremophiles},
  year      = {2007},
  abstract  = {Thermophilic organisms are a subgroup of extremophiles which are defined as having an opti- mum growth temperature above 45°C for moderate thermophiles, above 65°C for extreme thermophiles, and above 80°C for hyperthermophiles, some of which, such as Pyrococcus, Pyrobaculum, and Methanopyrus, are able to grow optimally at tem- peratures as high as 100 to 105°C (even higher in vegetative state or under high pressure). The hyperthermophilic genera are mostly Archaea, except for Thermotoga and Aquifex genus that belong to Bacte- ria. They thrive in very hot terrestrial habitats such as geysers, hot springs, and hot sediments of volcanic eruptions or near deep-sea hydrothermal vents and undersea volcanoes. The moderate thermophiles can be found almost everywhere, while most extreme thermophiles are found essentially in moderately hot environments (for details, see other chapters in this volume).},
  file      = {:by-author/G/Grosjean/2007_Grosjean_39.pdf:PDF},
  keywords  = {Nucleic Acid Structure; Thermophiles},
  owner     = {saulius},
  timestamp = {2013.09.27},
  creationdate = {2013-09-27T00:00:00},
}

@Article{Grosse-Kunstleve2002,
  author    = {R. W. Grosse-Kunstleve and P. D. Adams},
  journal   = {Journal of Applied Crystallography},
  title     = {On the Handling of Atomic Anisotropic Displacement Parameters},
  year      = {2002},
  pages     = {477--480},
  volume    = {35},
  doi       = {10.1107/S0021889802008580},
  file      = {2002_Grosse-Kunstleve_477.pdf:by-author/G/Grosse-Kunstleve/2002_Grosse-Kunstleve_477.pdf:PDF},
  keywords  = {Anisotropic B Factors; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Grosse-Kunstleve1999,
  author    = {Grosse-Kunstleve, R. W.},
  journal   = {Acta crystallographica. Section A, Foundations of crystallography},
  title     = {Algorithms for deriving crystallographic space-group information.},
  year      = {1999},
  pages     = {383--395},
  volume    = {55},
  doi       = {10.1107/S0108767398010186},
  file      = {1999_Grosse-Kunstleve_383.pdf:by-author/G/Grosse-Kunstleve/1999_Grosse-Kunstleve_383.pdf:PDF},
  keywords  = {Spacegroup Symbols; Spacegroups; Symmetry},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://scripts.iucr.org/cgi-bin/paper?S0108767398010186},
}

@Article{Grosse-Kunstleve2003,
  author    = {Grosse-Kunstleve, R. W. and Adams, P. D.},
  journal   = {Acta Crystallographica Section D},
  title     = {On symmetries of substructures},
  year      = {2003},
  pages     = {1974--1977},
  volume    = {59},
  doi       = {10.1107/S0907444903021206},
  file      = {ba5051.pdf:by-author/G/Grosse-Kunstleve/2003_Grosse-Kunstleve_1974.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444903021206},
}

@Article{Grosse-Kunstleve2003a,
  author    = {Grosse-Kunstleve, R. W. and Adams, P. D.},
  journal   = {Acta Crystallographica Section D},
  title     = {Substructure search procedures for macromolecular structures},
  year      = {2003},
  pages     = {1966--1973},
  volume    = {59},
  doi       = {10.1107/S0907444903018043},
  file      = {ba5048.pdf:by-author/G/Grosse-Kunstleve/2003_Grosse-Kunstleve_1966.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444903018043},
}

@Article{Grosse-Kunstleve2002a,
  author    = {Grosse-Kunstleve, R W and Adams, P D},
  journal   = {Acta crystallographica. Section A, Foundations of crystallography},
  title     = {Algorithms for deriving crystallographic space-group information. II. Treatment of special positions.},
  year      = {2002},
  pages     = {60--5},
  volume    = {58},
  file      = {2002_Grosse-Kunstleve_60.pdf:by-author/G/Grosse-Kunstleve/2002_Grosse-Kunstleve_60.pdf:PDF;:by-author/G/Grosse-Kunstleve/2002_Grosse-Kunstleve_60manuscript.pdf:PDF},
  keywords  = {Special Positions},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Grosse-Kunstleve1997,
  author    = {R. W. Grosse-Kunstleve and L. B. McCusker and Ch. Baerlocher},
  journal   = {J. Appl. Cryst.},
  title     = {Powder Diffraction Data and Crystal Chemical Information Combined in an Automated Structure Determination Procedure for Zeolites},
  year      = {1997},
  pages     = {985--995},
  volume    = {30},
  abstract  = {Abstract The FOCUS method, in which both crystal chemical information and powder diffraction data are included in the structure determination process, is presented. FOCUS combines automatic Fourier recycling with a specialized topology search specific to zeolites, which can be described as having three-dimensional fourconnected framework structures. The capabilities of FOCUS have been tested with seven examples of medium to high complexity. The method was then applied to three novel zeolite structures and a promising model could be obtained in each case. Experience shows that the approach of using chemical and geometric knowledge can compensate for some of the information that is lost as a result of the overlap problem. At the same time, there is an intrinsic disadvantage: any method based on assumptions of certain structural properties is also limited to materials which conform to these assumptions. Examples which show the consequences of relaxing the structural assumptions are also given.},
  file      = {1997_Grosse-Kunstleve_985.pdf:by-author/G/Grosse-Kunstleve/1997_Grosse-Kunstleve_985.pdf:PDF},
  keywords  = {Powder Diffraction; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@Article{Grosse-Kunstleve2004,
  author    = {Grosse-Kunstleve, R. W. and Sauter, N. K. and Adams, P. D.},
  journal   = {Acta Crystallographica. Section A, Foundations of Crystallography},
  title     = {Numerically Stable Algorithms for the Computation of Reduced Unit Cells},
  year      = {2004},
  pages     = {1--6},
  volume    = {60},
  abstract  = {The computation of reduced unit cells is an important building block for a number of crystallographic applications, but unfortunately it is very easy to demonstrate that the conventional implementation of cell reduction algorithms is not numerically stable. A numerically stable implementation of the Niggli-reduction algorithm of Krivý &amp; Gruber [Acta Cryst. (1976), A32, 297-298] is presented. The stability is achieved by consistently using a tolerance in all floating-point comparisons. The tolerance must be greater than the accumulated rounding errors. A second stable algorithm is also presented, the minimum reduction, that does not require using a tolerance. It produces a cell with minimum lengths and all angles acute or obtuse. The algorithm is a simplified and modified version of the Buerger-reduction algorithm of Gruber [Acta Cryst. (1973), A29, 433-440]. Both algorithms have been enhanced to generate a change-of-basis matrix along with the parameters of the reduced cell.},
  doi       = {10.1107/S010876730302186X},
  file      = {:by-author/G/Grosse-Kunstleve/2004_Grosse-Kunstleve_1.pdf:PDF},
  groups    = {sg/Cell sg/Reduction, sg/Cell reduction},
  keywords  = {Crystal Cell; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
  url       = {http://dx.doi.org/10.1107/S010876730302186X},
}

@TechReport{Grosse-Kunstleve2011,
  author      = {Grosse-Kunstleve, Ralf W. and Peter H. Zwart and Pavel V. Afonine and Thomas R. Ioerger and Paul D. Adams},
  institution = {University of California},
  title       = {CCTBX news},
  year        = {2011},
  abstract    = {We describe recent developments of the Computational Crystallography Toolbox.},
  file        = {:by-author/G/Grosse-Kunstleve/2011_Grosse-Kunstleve_92.pdf:PDF},
  owner       = {saulius},
  pages       = {92},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@Manuscript{Grothoff2007,
  author    = {Christian Grothoff and Krista Grothoff and Tzvetan Horozov and Jussi T. Lindgren},
  title     = {An Encoding for Censorship-Resistant Sharing},
  year      = {2007},
  abstract  = {This paper describes ECRS, a content encoding scheme for censorship-resistant peer-to-peer networking. The proposed encoding mech- anism supports both efficient dissemination of encrypted data as well as encrypted queries over this data. Intermediaries can verify that an encrypted response matches an encrypted query without being able to decrypt either. Furthermore, ECRS allows users to share files encrypted under descriptive keys which are the basis for querying the network for content. With the proposed scheme, effective load balancing and swarm distribution are possible. The encoding mechanism handles data in small chunks, which can also be efficiently encoded on demand from the plain- text. The proposed encoding is conceptually simple and easy to imple- ment.},
  file      = {:by-author/G/Grothoff/2007_Grothoff.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.09.18},
  creationdate = {2012-09-18T00:00:00},
}

@Manual{TheGAPGroup2015,
  title     = {{GAP} --- {A} tutorial},
  author    = {The GAP Group},
  year      = {2015},
  file      = {GAP --- A Tutorial - manual.pdf:by-author/G/Group/2015_Group.pdf:application/pdf},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://www.gap-system.org/Manuals/doc/tut/manual.pdf},
  urldate   = {2015-10-02},
}

@Article{Groves2007,
  author    = {Groves, Matthew R. and Müller, Ingrid B. and Kreplin, Xandra and Müller-Dieckmann, Jochen},
  journal   = {Acta crystallographica. Section D, Biological crystallography},
  title     = {A method for the general identification of protein crystals in crystallization experiments using a noncovalent fluorescent dye.},
  year      = {2007},
  pages     = {526--35},
  volume    = {63},
  abstract  = {A technique is described whereby the addition of low concentrations (millimolar to micromolar) of the fluorescent dye 1,8-ANS to the protein solution prior to crystallization results in crystallization experiments in which protein crystals are strongly contrasted above background artifacts when exposed to low-intensity UV radiation. As 1,8-ANS does not covalently modify the protein sample, no further handling or purification steps are necessary. The system has been tested on a wide variety of protein samples and it has been shown that the addition of 1,8-ANS has no discernible effect on the crystallization frequencies or crystallization conditions of these proteins. As 1,8-ANS interacts with a wide variety of proteins, this is proposed to be a general solution for the automated classification of protein crystallization images and the detection of protein crystals. The results also demonstrate the expected discrimination between salt and protein crystals, as well as allowing the straightforward identification of small crystals that grow in precipitate or under a protein skin.},
  doi       = {10.1107/S0907444906056137},
  file      = {:by-author/G/Groves/2007_Groves_526.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Gruber1989,
  author    = {Gruber, B.},
  journal   = {Acta Crystallographica Section A},
  title     = {Reduced cells based on extremal principles},
  year      = {1989},
  pages     = {123--131},
  volume    = {45},
  doi       = {10.1107/S0108767388010621},
  file      = {:by-author/G/Gruber/1989_Gruber_123.pdf:PDF},
  keywords  = {Algorithms; Niggli Cell; Reduced Cell; Unit Cell; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2014.11.06},
  creationdate = {2014-11-06T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0108767388010621},
}

@Article{Gruber1973,
  author    = {Gruber, B.},
  journal   = {Acta Crystallographica Section A},
  title     = {The relationship between reduced cells in a general Bravais lattice},
  year      = {1973},
  pages     = {433--440},
  volume    = {29},
  abstract  = {It is shown that in a three-dimensional Bravais lattice at most 5 different cells based on the shortest three non-coplanar translations (Buerger cells) may exist. Their mutual relationship is found and two procedures are proposed to find all these cells if one of them is known. That cell which corresponds to the reduced quadratic form is indicated. For any of the 14 types of Bravais lattice the number of different Buerger cells is ascertained.},
  doi       = {10.1107/S0567739473001063},
  file      = {1973_Gruber_433.pdf:by-author/G/Gruber/1973_Gruber_433.pdf:PDF},
  groups    = {sg/Cell sg/Reduction, sg/Cell reduction},
  keywords  = {Buerger Cell; Niggli Cell; Reduced Cell; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2014.03.27},
  creationdate = {2014-03-27T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0567739473001063},
}

@Article{Gruber2007,
  author    = {Gruber, Jan and Zawaira, Alexander and Saunders, Rhodri and Barrett, C. Paul and Noble, Martin E. M.},
  journal   = {Acta crystallographica. Section D, Biological crystallography},
  title     = {Computational analyses of the surface properties of protein-protein interfaces.},
  year      = {2007},
  pages     = {50--7},
  volume    = {63},
  abstract  = {Several potential applications of structural biology depend on discovering how one macromolecule might recognize a partner. Experiment remains the best way to answer this question, but computational tools can contribute where this fails. In such cases, structures may be studied to identify patches of exposed residues that have properties common to interaction surfaces and the locations of these patches can serve as the basis for further modelling or for further experimentation. To date, interaction surfaces have been proposed on the basis of unusual physical properties, unusual propensities for particular amino-acid types or an unusually high level of sequence conservation. Using the CXXSurface toolkit, developed as a part of the CCP4MG program, a suite of tools to analyse the properties of surfaces and their interfaces in complexes has been prepared and applied. These tools have enabled the rapid analysis of known complexes to evaluate the distribution of (i) hydrophobicity, (ii) electrostatic complementarity and (iii) sequence conservation in authentic complexes, so as to assess the extent to which these properties may be useful indicators of probable biological function.},
  doi       = {10.1107/S0907444906046762},
  file      = {:by-author/G/Gruber/2007_Gruber_50.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Gruen2002,
  author    = {Gruen, Mathias and Chang, Kathy and Serbanescu, Irina and Liu, David R.},
  journal   = {Nucleic acids research},
  title     = {An in vivo selection system for homing endonuclease activity.},
  year      = {2002},
  pages     = {e29},
  volume    = {30},
  abstract  = {Homing endonucleases are enzymes that catalyze the highly sequence-specific cleavage of DNA. We have developed an in vivo selection in Escherichia coli that links cell survival with homing endonuclease-mediated DNA cleavage activity and sequence specificity. Using this selection, wild-type and mutant variants of three homing endonucleases were characterized without requiring protein purification and in vitro analysis. This selection system may facilitate the study of sequence-specific DNA cleaving enzymes, and selections based on this work may enable the evolution of homing endonucleases with novel activities or specificities.},
  file      = {:by-author/G/Gruen/2002_Gruen_e29.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Webpage{Grundy2000,
  author    = {Jim Grundy},
  retrieved = {2011-12-19},
  title     = {Exercise 13: Hoare Logic},
  url       = {http://cs.anu.edu.au/student/comp8033/ex13.html},
  month     = {March},
  year      = {2000},
  file      = {:by-author/G/Grundy/2000_Grundy.odt:},
  keywords  = {Comp8033; Computer Science (CS); Correctness-proofs; Student},
  owner     = {saulius},
  timestamp = {2015.03.03},
  creationdate = {2015-03-03T00:00:00},
}

@Presentation{Gruene2011,
  author    = {Tim Grüne},
  title     = {Data Integration with XDS},
  year      = {2011},
  file      = {2011_Grüne_slides.pdf:by-author/G/Grüne/2011_Grüne_slides.pdf:PDF},
  keywords  = {Data Reduction; Reflection Integration; Software; X-ray Crystallography; XDS},
  month     = {June},
  owner     = {saulius},
  timestamp = {2016.12.21},
  creationdate = {2016-12-21T00:00:00},
  url       = {http://shelx.uni-ac.gwdg.de/~tg/teaching/anl-ccp4/pdfs/ccp4-2011_tgruene_xds.pdf},
}

@PhdThesis{Gruner2002,
  author    = {Sibylle Annette Wunneda Gruner},
  school    = {Fakultät für Chemie der Technischen Universität München},
  title     = {Carbohydrate-Based Mimetics in Drug Design: Sugar Amino Acids as Structural Templates and Key Residues of Bioactive Peptidomimetics},
  year      = {2002},
  file      = {:by-author/G/Gruner/2002_Gruner_dissertation.pdf:PDF},
  owner     = {saulius},
  pages     = {dissertation},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Presentation{Grunwald1994,
  author       = {Dirk Grunwald and Ben Zorn},
  title        = {Correctness in Dynamic Storage Allocation},
  year         = {1994},
  conference   = {USENIX'94 Invited Talk},
  organization = {University of Colorado at Boulder},
  file         = {:by-author/G/Grunwald/1994_Grunwald.ps.bz2:PS BZ2;:by-author/G/Grunwald/1994_Grunwald.pdf:PDF},
  keywords     = {Computer Science (CS); Memory Allocators; Memory Management},
  month        = {June},
  owner        = {saulius},
  timestamp = {2015.03.03},
  creationdate = {2015-03-03T00:00:00},
}

@Presentation{Grunwald2007,
  author    = {Peter Grünwald},
  title     = {The Catch-Up Phenomenon},
  year      = {2007},
  file      = {:by-author/G/Grünwald/2007_Grunwald_slides.pdf:PDF},
  groups    = {sg/Bayesian},
  keywords  = {Bayesian Statistics},
  owner     = {saulius},
  pages     = {slides},
  timestamp = {2012.09.30},
  creationdate = {2012-09-30T00:00:00},
  url       = {http://www.grunwald.nl},
}

@Article{Grunwald2008,
  author    = {Peter Grünwald and Steven de Rooij and Tim van Erven},
  journal   = {Information Theory Workshop, 2008. ITW '08. IEEE},
  title     = {The Catch-Up Phenomenon},
  year      = {2008},
  pages     = {259--260},
  abstract  = {We consider inference based on a countable set of models (sets of probability distributions), focusing on two tasks: model selection and model averaging. In model selection tasks, the goal is to select the model that best explains the given data. In model averaging, the goal is to find the weighted combination of models that leads to the best prediction of future data from the same source.},
  file      = {:by-author/G/Grünwald/2008_Grunwald_259.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.09.30},
  creationdate = {2012-09-30T00:00:00},
  url       = {http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=4578662},
}

@Article{Grzesiuk2002,
  author    = {Grzesiuk, Wiesław and Kondracka, Agnieszka and Słoń, Milena and Wojda, Marzena and Nauman, Janusz},
  journal   = {Medical science monitor : international medical journal of experimental and clinical research},
  title     = {Salt iodination as a effective method of iodine supplementation.},
  year      = {2002},
  pages     = {CR288-91},
  volume    = {8},
  file      = {:by-author/G/Grzesiuk/2002_Grzesiuk_CR288.pdf:PDF},
  keywords  = {MSM},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Gu2011,
  author    = {Gu, Zhi-Yuan and Chen, Ying-Jun and Jiang, Jun-Qing and Yan, Xiu-Ping},
  journal   = {Chemical communications (Cambridge, England)},
  title     = {Metal-organic frameworks for efficient enrichment of peptides with simultaneous exclusion of proteins from complex biological samples.},
  year      = {2011},
  pages     = {4787--9},
  volume    = {47},
  abstract  = {Metal-organic frameworks MIL-53, MIL-100 and MIL-101 demonstrate efficient enrichment of peptides with simultaneous exclusion of proteins from complex biological samples.},
  doi       = {10.1039/C1CC10579E},
  file      = {:by-author/G/Gu/2011_Gu_4787.pdf:PDF},
  keywords  = {Bioconjugation; Metal-Organic Frameworks (MOF); Peptides},
  owner     = {saulius},
  timestamp = {2013.01.05},
  creationdate = {2013-01-05T00:00:00},
}

@Article{Guan2017,
  author    = {Cao Guan and Ximeng Liu and Weina Ren and Xin Li and Chuanwei Cheng and John Wang},
  journal   = {Advanced Energy Materials},
  title     = {Rational Design of Metal-Organic Framework Derived Hollow {NiCo}2 O4 Arrays for Flexible Supercapacitor and Electrocatalysis},
  year      = {2017},
  month     = {jan},
  pages     = {1602391},
  doi       = {10.1002/aenm.201602391},
  file      = {:by-author/G/Guan/2017_Guan_1602391.pdf:PDF},
  groups    = {sg/MOF, sg/MOFs, am/MOFs},
  owner     = {saulius},
  publisher = {Wiley-Blackwell},
  timestamp = {2017.01.31},
  creationdate = {2017-01-31T00:00:00},
  url       = {https://doi.org/10.1002%2Faenm.201602391},
}

@Article{Guan2017a,
  author    = {Jinju Guan and Yu Hu and Yu Wang and Hongfeng Li and Zhiling Xu and Tao Zhang and Peng Wu and Suoying Zhang and Gengwu Xiao and Wenlan Ji and Linjie Li and Meixuan Zhang and Yun Fan and Lin Li and Bing Zheng and Weina Zhang and Wei Huang and Fengwei Huo},
  journal   = {Advanced Materials},
  title     = {Controlled Encapsulation of Functional Organic Molecules within Metal-Organic Frameworks: In Situ Crystalline Structure Transformation},
  year      = {2017},
  month     = {jan},
  pages     = {1606290},
  comment   = {Can in-situ encapsulation be used for our analytic purposes, even for proteins? (S.G.)},
  doi       = {10.1002/adma.201606290},
  file      = {:by-author/G/Guan/2017_Guan_1606290.pdf:PDF},
  groups    = {sg/MOF, sg/MOFs, am/MOFs},
  keywords  = {In Situ Crystalline Structure Transformation; Synthesis},
  owner     = {saulius},
  publisher = {Wiley-Blackwell},
  timestamp = {2017.01.31},
  creationdate = {2017-01-31T00:00:00},
  url       = {https://doi.org/10.1002%2Fadma.201606290},
}

@Article{Gubler1992,
  author    = {Gubler, M. and Braguglia, D. and Meyer, J. and Piekarowicz, A. and Bickle, T. A.},
  journal   = {The EMBO journal},
  title     = {Recombination of constant and variable modules alters DNA sequence recognition by type IC restriction-modification enzymes.},
  year      = {1992},
  pages     = {233--40},
  volume    = {11},
  abstract  = {EcoR124 and EcoDXXI are allelic type I restriction-modification (R-M) systems whose specificity genes consist of common structural elements: two variable regions are separated by a constant, homologous region containing a number of repetitive sequence elements. In vitro recombination of variable and constant elements has led to fully active, hybrid R-M systems exhibiting new and predictable target site specificities. Methylation of synthetic DNA sequences with purified, hybrid modification methylases was used to confirm the proposed recognition sequences. The results clearly demonstrate the correlation between protein domains and target site specificity. Our data suggest that a bacterial population may switch the recognition sequences of its type I R-M system by single recombination events and thus is able to maintain a prokaryotic analogue of the immune system of variable specificity.},
  file      = {:by-author/G/Gubler/1992_Gubler_233.pdf:PDF},
  keywords  = {TypeI},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Lecture{Gudmundsson2016,
  author    = {Sigmundur Gudmundsson},
  title     = {An Introduction to Riemannian Geometry},
  year      = {2016},
  course    = {Lecture Notes in Mathematics},
  school    = {Lund University},
  file      = {2016_Gudmundsson.pdf:by-author/G/Gudmundsson/2016_Gudmundsson.pdf:PDF},
  keywords  = {Differential Geometry; Riemann},
  owner     = {saulius},
  timestamp = {2016.02.27},
  creationdate = {2016-02-27T00:00:00},
  url       = {http://www.matematik.lu.se/matematiklu/personal/sigma/Riemann.pdf},
}

@Manuscript{Gueheneuc2002,
  author    = {Yann-Gaël Guéhéneuc},
  title     = {Virtual Machines},
  year      = {2002},
  keywords  = {Computer Science (CS); Virtual Machines},
  file      = {:by-author/G/Gueheneuc/2002_Gueheneuc.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Guggenheim1999,
  author    = {Stephen Guggenheim and Wudi Zhan},
  journal   = {American Mineralogist},
  title     = {Crystal Structures of Two Partially Dehydrated Chlorites: The “Modified” Chlorite Structure},
  year      = {1999},
  pages     = {1415--1421},
  volume    = {84},
  abstract  = {Chromian clinochlore-IIb-4 (triclinic) and Ilb-2 (monoclinic) polytypes from the Day Book Body, North Carolina, were heated to 650 degrees C for 5 hours and air quenched. Single-crystal X-ray refinements of the (metastable) product phases resulted in R = wR = 0.056 and R = wR = 0.061 for the triclinic and monoclinic forms, respectively. The heat-treated triclinic from has C1 symmetry and cell parameters a = 5.368(1), b = 9.297(2), c = 14.215(6) Aa, alpha = 89.86(3), beta = 97.15(3), gamma = 89.98(2) degrees , and V = 703.95(36) Aa 3 , and the monoclinic form has a = 5.372(1), b = 9.291(2), c = 14.270(7) Aa, beta = 97.34(3) degrees , and V = 706.4(4) Aa 3 in C2/m symmetry. The product structures are topotactic with the parent phases, with the 2:1 layer of the product nearly identical to that of the parent. Dehydroxylation of the interlayer of the parent produces two quasi-planar sets of atoms between adjacent 2:1 layers. Although, based on the refinement of the average structure, the cations and anions are apparently disordered in these planes, cations (Mg, Al, Cr) must have three oxygen atom nearest neighbors and oxygen atoms must be coordinated to three cations. Apparent disorder is related to lateral displacements of the interlayer planes within the (001) plane. Interlayer-site to interlayer-site distances are near 1.8 Aa. Second nearest-neighbor distances for most of the interlayer sites are short, near 2.3 Aa. A model is proposed where, at high temperatures, the interlayer planes become more extended and planar, but the planes "crumple" upon cooling to more closely approach higher-order nearest-neighbor atoms. These changes upon cooling might be a significant driving force for additional cation and anion ordering in the interlayer, since the interlayer sites have very different second nearest-neighbor environments. Thus, with appropriate cooling rates, cation ordering possibly may be obtained. However, the development of an ordered pattern of cations and anions may also be dependent on kinetics; decomposition is favored over time because of the instability of threefold-coordinated interlayer ions.},
  file      = {:by-author/G/Guggenheim/1999_Guggenheim_1415.pdf:PDF},
  keywords  = {For COD Deposition; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
  url       = {http://ammin.geoscienceworld.org/content/84/9/1415.abstract},
}

@Article{Guha2006,
  author    = {Guha, Rajarshi and Howard, Michael T. and Hutchison, Geoffrey R. and Murray-Rust, Peter and Rzepa, Henry and Steinbeck, Christoph and Wegner, Jörg and Willighagen, Egon L.},
  journal   = {Journal of Chemical Information and Modeling},
  title     = {The Blue Obelisk -- Interoperability in Chemical Informatics},
  year      = {2006},
  pages     = {991--998},
  volume    = {46},
  abstract  = {The Blue Obelisk Movement (http://www.blueobelisk.org/) is the name used by a diverse Internet group promoting reusable chemistry via open source software development, consistent and complimentary chemoinformatics research, open data, and open standards. We outline recent examples of cooperation in the Blue Obelisk group:  a shared dictionary of algorithms and implementations in chemoinformatics algorithms drawing from our various software projects; a shared repository of chemoinformatics data including elemental properties, atomic radii, isotopes, atom typing rules, and so forth; and Web services for the platform-independent use of chemoinformatics programs.},
  doi       = {10.1021/ci050400b},
  eprint    = {http://pubs.acs.org/doi/pdf/10.1021/ci050400b},
  file      = {2006_Guha_991.pdf:by-author/G/Guha/2006_Guha_991.pdf:PDF},
  keywords  = {Data Access Policy; Data Management; Databases},
  owner     = {saulius},
  timestamp = {2014.05.14},
  creationdate = {2014-05-14T00:00:00},
  url       = {http://pubs.acs.org/doi/abs/10.1021/ci050400b},
}

@Article{Guinepain2005,
  author    = {Guinepain, Sylvain and Gruenwald, Le},
  journal   = {SIGMOD Rec.},
  title     = {Research issues in automatic database clustering},
  year      = {2005},
  issn      = {0163-5808},
  pages     = {33--38},
  volume    = {34},
  abstract  = {While a lot of work has been published on clustering of data on storage medium, little has been done about automating this process. This is an important area because with data proltferation, human attention has become a precious and expensive resource. Our goal is to develop an automatic and dynamic database clustering technique that will dynamically re-cluster a database with little intervention of a database administrator (DBA) and maintain an acceptable quevy response time at all times. In this paper we describe the issues that need to be solved when developing such a technique.},
  doi       = {10.1145/1058150.1058157},
  file      = {:by-author/G/Guinepain/2005_Guinepain_33.pdf:PDF},
  owner     = {saulius},
  publisher = {ACM},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://doi.acm.org/10.1145/1058150.1058157},
}

@Presentation{Gunzburger2012,
  author    = {Max Gunzburger},
  title     = {Parallel algorithm for spherical Delaunay triangulations and spherical centroidal Voronoi tessellations},
  year      = {2012},
  file      = {2012_Gunzburger_slides.pdf:by-author/G/Gunzburger/2012_Gunzburger_slides.pdf:PDF},
  keywords  = {Algorithms; Triangulation; Voronoi Triangulation},
  owner     = {saulius},
  timestamp = {2014.10.21},
  creationdate = {2014-10-21T00:00:00},
  url       = {http://www-old.newton.ac.uk/programmes/AMM/seminars/2012102415109.pdf},
}

@Article{Guo2014,
  author    = {Guo, Dan and Barry, Liam and Lin, Sharon Szu Hua and Huang, Vera and Li, Long-Cheng},
  journal   = {RNA Biology},
  title     = {{RNAa} in action: From the exception to the norm},
  year      = {2014},
  issn      = {1555-8584},
  month     = {Oct},
  number    = {10},
  pages     = {1221–1225},
  volume    = {11},
  doi       = {10.4161/15476286.2014.972853},
  file      = {:by-author/G/Guo/2014_Guo_1221.pdf:PDF},
  groups    = {am/RNA activation},
  owner     = {andrius},
  publisher = {Informa UK Limited},
  timestamp = {2016.08.22},
  creationdate = {2016-08-22T00:00:00},
  url       = {http://dx.doi.org/10.4161/15476286.2014.972853},
}

@Article{Guo2015,
  author    = {Guo, Peng and Shin, Jiho and Greenaway, Alex G. and Min, Jung Gi and Su, Jie and Choi, Hyun June and Liu, Leifeng and Cox, Paul A. and Hong, Suk Bong and Wright, Paul A. and Zou, Xiaodong},
  journal   = {Nature},
  title     = {A zeolite family with expanding structural complexity and embedded isoreticular structures},
  year      = {2015},
  issn      = {0028-0836},
  pages     = {74--78},
  volume    = {524},
  abstract  = {The prediction and synthesis of new crystal structures enable the targeted preparation of materials with desired properties. Among porous solids, this has been achieved for metal-organic frameworks, but not for the more widely applicable zeolites, where new materials are usually discovered using exploratory synthesis. Although millions of hypothetical zeolite structures have been proposed, not enough is known about their synthesis mechanism to allow any given structure to be prepared. Here we present an approach that combines structure solution with structure prediction, and inspires the targeted synthesis of new super-complex zeolites. We used electron diffraction to identify a family of related structures and to discover the structural /`coding/' within them. This allowed us to determine the complex, and previously unknown, structure of zeolite ZSM-25 (ref. 8), which has the largest unit-cell volume of all known zeolites (91,554 cubic angstroms) and demonstrates selective CO2 adsorption. By extending our method, we were able to predict other members of a family of increasingly complex, but structurally related, zeolites and to synthesize two more-complex zeolites in the family, PST-20 and PST-25, with much larger cell volumes (166,988 and 275,178 cubic angstroms, respectively) and similar selective adsorption properties. Members of this family have the same symmetry, but an expanding unit cell, and are related by hitherto unrecognized structural principles; we call these family members embedded isoreticular zeolite structures.},
  copyright = {© 2015 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},
  doi       = {10.1038/nature14575},
  file      = {Guo et al. - 2015 - A zeolite family with expanding structural complex.pdf:by-author/G/Guo/2015_Guo_74a.pdf:application/pdf;nature14575-s1.pdf:by-author/G/Guo/2015_Guo_74.pdf:application/pdf;Snapshot:by-author/G/Guo/2015_Guo_74.html:text/html},
  keywords  = {Materials Chemistry; Porous Materials},
  language  = {en},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://www.nature.com/nature/journal/v524/n7563/full/nature14575.html},
  urldate   = {2015-08-24},
}

@Article{Gupta2004,
  author    = {Anshuman Gupta and Deepak Gupta and Dheeraj Sanghi},
  title     = {Study and Implementation of Secure E-mail Service and setting up Certifying Authority},
  year      = {2004},
  abstract  = {In this new era heralded by a communication revolution, digital transactions are encroaching almost every service offered by modern industry. E-mail system is one of the foremost guiding star of this change. E-mails are now an integral part of our daily business. But E-mails travel over the network unencrypted thus making it impossible to us it for sending confidential information. Moreover there is no authenticity or non-repudiation guaranteed with the existing system. Thus it is an important area of concern.Thus a secure e-mail system is needed to allow people to send important and confidential information using e-mails and providing another step ahead in the communication revolution.},
  file      = {:by-author/G/Gupta/2004_Gupta.pdf:PDF},
  keywords  = {Computer Science (CS); Cryptography},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Gupta2010,
  author    = {Maya R. Gupta and Yihua Chen},
  journal   = {Foundations and Trends in Signal Processing},
  title     = {Theory and Use of the {EM} Algorithm},
  year      = {2010},
  pages     = {223–296},
  volume    = {4},
  abstract  = {This introduction to the expectation–maximization (EM) algorithm provides an intuitive and mathematically rigorous understanding of EM. Two of the most popular applications of EM are described in detail: estimating Gaussian mixture models (GMMs), and estimat- ing hidden Markov models (HMMs). EM solutions are also derived for learning an optimal mixture of fixed models, for estimating the parameters of a compound Dirichlet distribution, and for dis-entangling superimposed signals. Practical issues that arise in the use of EM are discussed, as well as variants of the algorithm that help deal with these challenges.},
  doi       = {10.1561/2000000034},
  file      = {:by-author/G/Gupta/2010_Gupta_223.pdf:PDF},
  keywords  = {Expectation Maximisation},
  owner     = {andrius},
  timestamp = {2012.11.27},
  creationdate = {2012-11-27T00:00:00},
}

@Article{Gupta2012a,
  author     = {Gupta, Sandeep K},
  journal    = {International Journal of Applied and Basic Medical Research},
  title      = {Use of {Bayesian} statistics in drug development: {Advantages} and challenges},
  year       = {2012},
  issn       = {2229-516X},
  pages      = {3--6},
  volume     = {2},
  abstract   = {Mainly, two statistical methodologies are applicable to the design and analysis of clinical trials: frequentist and Bayesian. Most traditional clinical trial designs are based on frequentist statistics. In frequentist statistics prior information is utilized formally only in the design of a clinical trial but not in the analysis of the data. On the other hand, Bayesian statistics provide a formal mathematical method for combining prior information with current information at the design stage, during the conduct of the trial, and at the analysis stage. It is easier to implement adaptive trial designs using Bayesian methods than frequentist methods. The Bayesian approach can also be applied for post-marketing surveillance purposes and in meta-analysis. The basic tenets of good trial design are same for both Bayesian and frequentist trials. It has been recommended that the type of analysis to be used (Bayesian or frequentist) should be chosen beforehand. Switching to an analysis method that produces a more favorable outcome after observing the data is not recommended.},
  doi        = {10.4103/2229-516X.96789},
  file       = {Gupta - 2012 - Use of Bayesian statistics in drug development Ad.pdf:by-author/G/Gupta/2012_Gupta_3.pdf:application/pdf},
  groups     = {sg/Clinical Trials},
  owner      = {saulius},
  pmcid      = {PMC3657986},
  pmid       = {23776799},
  shorttitle = {Use of {Bayesian} statistics in drug development},
  timestamp = {2015.12.14},
  creationdate = {2015-12-14T00:00:00},
  url        = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3657986/},
  urldate    = {2015-12-12},
}

@Article{Gupta2005,
  author    = {Gupta, S P and Kumaran, S},
  journal   = {Journal of enzyme inhibition and medicinal chemistry},
  title     = {A quantitative structure-activity relationship study on some aromatic/heterocyclic sulfonamides and their charged derivatives acting as carbonic anhydrase inhibitors.},
  year      = {2005},
  pages     = {251--9},
  volume    = {20},
  abstract  = {A quantitative structure-activity relationship (QSAR) study is made on a series of aromatic/heterocyclic sulfonamides and their charged derivatives acting as carbonic anhydrase (CA) inhibitors. These compounds were studied by Scozzafava et al. (J. Med. Chem. 2000; 43: 292) for the selective inhibition of CAs--sulfonamides generally do not discriminate between different CA isozymes and hence exhibit many undesirable side effects when used as drugs against a particular disease. In this communication, an attempt has been made to investigate the physicochemical and structural properties that can make them selective for a given CA isozyme. Based on in vitro data reported by Scozzafava et al. against two cytosolic isozymes and one membrane-bound isozyme, the QSAR study has shown that uncharged compounds cannot be made selective for cytosolic or membrane-bound isozyme since in both the cases the compounds appear to follow the same mechanism of inhibition. However, for the charged compounds the polarizability of the molecule seems to greatly favor the inhibition of the membrane-bound enzyme, and hence they can be made selective for this enzyme by enhancing their polarizability, which is found to play no role in the inhibition of cytosolic enzymes.},
  file      = {2005_Gupta_251.pdf:by-author/G/Gupta/2005_Gupta_251.pdf:PDF},
  groups    = {sg/inhibitors, sg/modelling},
  keywords  = {Carbonic Anhydrases},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Gupta2012,
  author    = {Yogesh K. Gupta and Lin Yang and Siu-Hong Chan and James C. Samuelson and Shuang-yong Xu and Aneel K. Aggarwal},
  journal   = {Journal of Molecular Biology},
  title     = {Structural Insights into the Assembly and Shape of Type III Restriction-Modification (R-M) EcoP15I Complex by Small-Angle X-ray Scattering},
  year      = {2012},
  issn      = {0022-2836},
  pages     = {261 - 268},
  volume    = {420},
  abstract  = {EcoP15I is the prototype of the Type III restriction enzyme family, composed of two modification (Mod) subunits to which two (or one) restriction (Res) subunits are then added. The Mod subunits are responsible for DNA recognition and methylation, while the Res subunits are responsible for ATP hydrolysis and cleavage. Despite extensive biochemical and genetic studies, there is still no structural information on Type III restriction enzymes. We present here small-angle X-ray scattering (SAXS) and analytical ultracentrifugation analysis of the EcoP15I holoenzyme and the Mod2 subcomplex. We show that the Mod2 subcomplex has a relatively compact shape with a radius of gyration (RG) of ∼37.4 Å and a maximal dimension of ∼ 110 Å. The holoenzyme adopts an elongated crescent shape with an RG of ∼ 65.3 Å and a maximal dimension of ∼218 Å. From reconstructed SAXS envelopes, we postulate that Mod2 is likely docked in the middle of the holoenzyme with a Res subunit at each end. We discuss the implications of our model for EcoP15I action, whereby the Res subunits may come together and form a “sliding clamp” around the DNA.},
  doi       = {10.1016/j.jmb.2012.04.026},
  file      = {2012_Gupta_preprint.pdf:by-author/G/Gupta/2012_Gupta_preprint.pdf:PDF;2012_Gupta_261.pdf:by-author/G/Gupta/2012_Gupta_261.pdf:PDF},
  keywords  = {EcoP15I; Type III Restriction Enzyme},
  owner     = {em},
  timestamp = {2013.01.04},
  creationdate = {2013-01-04T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/S0022283612003683},
}

@MastersThesis{Gurson2007,
  author    = {Gurson, Adam P.},
  school    = {College of William \& Mary in Virginia},
  title     = {Simplex Search Behavior in Nonlinear Optimisation},
  year      = {2007},
  file      = {:by-author/G/Gurson/2007_Gurson_bscthesis.pdf:PDF},
  keywords  = {Computer Science (CS); Minimisation; Simplex Method},
  owner     = {saulius},
  pages     = {bscthesis},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Manuscript{Gutmann2007,
  author    = {Peter Gutmann},
  title     = {A Cost Analysis of Windows Vista Content Protection},
  year      = {2007},
  keywords  = {Computer Science (CS); Windows-fallacies},
  month     = {January},
  url       = {https://www.cs.auckland.ac.nz/~pgut001/pubs/vista_cost.html},
  abstract  = {Windows Vista includes an extensive reworking of core OS elements in order to provide content protection for so-called "premium content", typically HD data from Blu-Ray and HD-DVD sources. Providing this protection incurs considerable costs in terms of system performance, system stability, technical support overhead, and hardware and software cost. These issues affect not only users of Vista but the entire PC industry, since the effects of the protection measures extend to cover all hardware and software that will ever come into contact with Vista, even if it's not used directly with Vista (for example hardware in a Macintosh computer or on a Linux server). This document analyses the cost involved in Vista's content protection, and the collateral damage that this incurs throughout the computer industry.},
  file      = {:by-author/G/Gutmann/2007_Gutmann.txt:},
  owner     = {saulius},
  timestamp = {2015.03.10},
  creationdate = {2015-03-10T00:00:00},
}

@Manual{Guzei2016,
  title     = {Notes on OLEX2},
  author    = {Ilia A. Guzei},
  year      = {2016},
  date      = {2016-09-08},
  file      = {Ilia_Guzei_notes_on_OLEX2.pdf:by-author/G/Guzei/2016_Guzei.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.16},
  creationdate = {2016-12-16T00:00:00},
  url       = {http://xray.chem.wisc.edu/Resources/Manuals/Ilia_Guzei_notes_on_OLEX2.pdf},
}

@Article{Guzei2014,
  author    = {Guzei, Ilia A.},
  journal   = {Journal of Applied Crystallography},
  title     = {An idealized molecular geometry library for refinement of poorly behaved molecular fragments with constraints},
  year      = {2014},
  issn      = {1600-5767},
  month     = {Mar},
  number    = {2},
  pages     = {806–809},
  volume    = {47},
  abstract  = {An idealized molecular geometry library with 40 geometries of molecules and ions optimized by density functional theory methods has been created. All geometries are accessible through a web site. The library entries are tailored for constrained (also known as rigid body) refinements of problematic small-molecule structures with the OLEX2 and SHELXL software packages. The library application is demonstrated with the refinement of a Pd complex, trans-Pd(dimethyl sulfoxide)(OH2)(trifluoroacetate)2, that co-crystallizes in a 2:1 ratio with a solvent molecule of ethyl acetate disordered over an inversion center. Alternative approaches to constrained refinements are discussed.},
  doi       = {10.1107/s1600576714004427},
  file      = {2014_Guzei_806.pdf:by-author/G/Guzei/2014_Guzei_806.pdf:PDF},
  groups    = {sg/Crystallography, am/Crystallography},
  owner     = {andrius},
  publisher = {International Union of Crystallography (IUCr)},
  timestamp = {2017.02.08},
  creationdate = {2017-02-08T00:00:00},
  url       = {http://dx.doi.org/10.1107/S1600576714004427},
}

@Manuscript{Guzzo2006,
  author    = {Cristiane R. Guzzo and Ronaldo A. P. Nagem and João A. R. G. Barbosa and Chuck S. Farah},
  title     = {The structure of Xanthomonas axonopodis pv. citri YaeQ reveals new compact protein fold built around a variation of the PD-(D/E)XK nuclease motif},
  year      = {2006},
  keywords  = {Crystal Structure; For Review; Manuscripts; PD (D/E)XK Superfamily; Protein Topology; Xanthomonas Axonopodis pv Citri; YaeQ},
  abstract  = {The YaeQ family of proteins are found in many Gram-negative and a few Gram-positive bacteria. We have determined the first structure of a member of the YaeQ family by X-ray crystallography. The YaeQ fold consists of a central helix surround by two curved beta sheets in which most of the central helix is hidden from the solvent. Comparisons with other structures indicate that YaeQ represents a new compact protein fold built around a variation of the PD-(D/E)XK nuclease motif found in type II endonucleases and enzymes involved in DNA replication, repair, and recombination. We present a comparative analysis that shows that catalytically important residues in the PD-(D/E)XK nuclease superfamily are spatially conserved in YaeQ and other highly conserved YaeQ residues may be poised to interact with nucleic acid structures. While specific YaeQ function is unknown, these results point towards a probable role in a specific process involving recognition and/or cleavage of nucleic acids.},
  file      = {:by-author/G/Guzzo/2006_Guzzo_manuscript.pdf:PDF},
  owner     = {saulius},
  pages     = {manuscript},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Gyohda1997,
  author    = {Gyohda, A. and Funayama, N. and Komano, T.},
  journal   = {Journal of bacteriology},
  title     = {Analysis of DNA inversions in the shufflon of plasmid R64.},
  year      = {1997},
  pages     = {1867--71},
  volume    = {179},
  abstract  = {The shufflon, a multiple DNA inversion system in the plasmid R64, consists of four DNA segments flanked and separated by seven 19-bp repeat sequences. Site-specific recombinations mediated by the rci product occur between each inverted repeat sequence, resulting in inversions of the four segments independently or in groups. The seven 19-bp repeat sequences are classified into four types (repeat-a, -b, -c, and -d), according to their 3-bp variable sequences. We individually cloned A, B, and C segments of the R64 shufflon and determined the in vivo inversion frequency of each segment. The inversion frequencies of three segments differed greatly. The inversion frequency declined in the following order: segments A, B, and C. Synthetic 19-mer oligonucleotides corresponding to both strands of repeat-a, -b, -c, and -d sequences were inserted into appropriate sites of pBR322. The rci-mediated DNA inversion occurred between two synthetic inverted repeats, indicating that the 19-bp inverted repeat sequences are the sole elements required in cis for the shufflon system. The inversion frequencies of DNA segments flanked by various sequences indicate that the four types of repeat sequences determine the inversion frequency of the four DNA segments of the R64 shufflon. Deletion of a DNA segment flanked by direct repeat sequences could not be detected.},
  file      = {:by-author/G/Gyohda/1997_Gyohda_1867.pdf:PDF},
  keywords  = {Antirestriction},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Ha2007,
  author    = {Ha, Taekjip},
  journal   = {Cell},
  title     = {Need for speed: mechanical regulation of a replicative helicase.},
  year      = {2007},
  pages     = {1249--50},
  volume    = {129},
  abstract  = {There is much debate about how helicases unwind DNA during DNA replication and how their activity is regulated. In this issue, Johnson et al. (2007) shed light on this conundrum using a single molecule approach to dissect the behavior of the T7 DNA helicase.},
  file      = {:by-author/H/Ha/2007_Ha_1249.pdf:PDF},
  keywords  = {{gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Webpage{Haack2008,
  author    = {Phil Haack},
  retrieved = {2009-02-07},
  title     = {Research Supports The Effectiveness of TDD},
  url       = {http://haacked.com/archive/2008/01/22/research-supports-the-effectiveness-of-tdd.aspx},
  month     = {January},
  year      = {2008},
  file      = {:by-author/H/Haack/2008_Haack.war:},
  keywords  = {Computer Science (CS); Test Driven Development},
  owner     = {saulius},
  timestamp = {2015.03.02},
  creationdate = {2015-03-02T00:00:00},
}

@Article{Haak2012,
  author    = {Haak, Laurel L. and Baker, David and Ginther, Donna K. and Gordon, Gregg J. and Probus, Matthew A. and Kannankutty, Nirmala and Weinberg, Bruce A.},
  journal   = {Science},
  title     = {Standards and Infrastructure for Innovation Data Exchange},
  year      = {2012},
  pages     = {196--197},
  volume    = {338},
  doi       = {10.1126/science.1221840},
  eprint    = {http://www.sciencemag.org/content/338/6104/196.full.pdf},
  file      = {2012_Haak_196.pdf:by-author/H/Haak/2012_Haak_196.pdf:PDF},
  keywords  = {Data Access Policy; Data Management},
  owner     = {saulius},
  timestamp = {2012.11.19},
  creationdate = {2012-11-19T00:00:00},
  url       = {http://www.sciencemag.org/content/338/6104/196.short},
}

@Article{Haas1970,
  author    = {Haas, D J and Rossmann, M G},
  journal   = {Acta crystallographica. Section B: Structural crystallography and crystal chemistry},
  title     = {Crystallographic studies on lactate dehydrogenase at-75 degrees C.},
  year      = {1970},
  pages     = {998--1004},
  volume    = {26},
  file      = {1970_Haas_998.pdf:by-author/H/Haas/1970_Haas_998.pdf:PDF},
  keywords  = {Strange Spacegroups; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Presentation{Hafner2014,
  author    = {J. Hafner},
  title     = {Foundations of Density-Functional Theory},
  year      = {2014},
  file      = {2014_Hafner_slides.pdf:by-author/H/Hafner/2014_Hafner_slides.pdf:PDF},
  keywords  = {Density Functional Theory (DFT); VASP},
  owner     = {saulius},
  timestamp = {2014.10.21},
  creationdate = {2014-10-21T00:00:00},
  url       = {https://www.vasp.at/vasp-workshop/slides/dft_introd.pdf},
}

@Webpage{Hahn2005,
  author    = {Stephen Hahn},
  retrieved = {2008-07-28},
  title     = {Distributed SCM requirements draft},
  url       = {http://mail.opensolaris.org/pipermail/tools-discuss/2005-December/000039.html},
  month     = {December},
  year      = {2005},
  file      = {:by-author/H/Hahn/2005_Hahn.war:},
  keywords  = {Computer Science (CS)},
  owner     = {saulius},
  timestamp = {2015.03.02},
  creationdate = {2015-03-02T00:00:00},
}

@Article{Haehnke2015,
  author    = {Hähnke, Volker D. and Bolton, Evan E. and Bryant, Stephen H.},
  journal   = {Journal of Cheminformatics},
  title     = {{PubChem} atom environments},
  year      = {2015},
  issn      = {1758-2946},
  pages     = {1--37},
  volume    = {7},
  abstract  = {Background Atom environments and fragments find wide-spread use in chemical information and cheminformatics. They are the basis of prediction models, an integral part in similarity searching, and employed in structure search techniques. Most of these methods were developed and evaluated on the relatively small sets of chemical structures available at the time. An analysis of fragment distributions representative of most known chemical structures was published in the 1970s using the Chemical Abstracts Service data system. More recently, advances in automated synthesis of chemicals allow millions of chemicals to be synthesized by a single organization. In addition, open chemical databases are readily available containing tens of millions of chemical structures from a multitude of data sources, including chemical vendors, patents, and the scientific literature, making it possible for scientists to readily access most known chemical structures. With this availability of information, one can now address interesting questions, such as: what chemical fragments are known today? How do these fragments compare to earlier studies? How unique are chemical fragments found in chemical structures? Results For our analysis, after hydrogen suppression, atoms were characterized by atomic number, formal charge, implicit hydrogen count, explicit degree (number of neighbors), valence (bond order sum), and aromaticity. Bonds were differentiated as single, double, triple or aromatic bonds. Atom environments were created in a circular manner focused on a central atom with radii from 0 (atom types) up to 3 (representative of ECFP\_6 fragments). In total, combining atom types and atom environments that include up to three spheres of nearest neighbors, our investigation identified 28,462,319 unique fragments in the 46 million structures found in the PubChem Compound database as of January 2013. We could identify several factors inflating the number of environments involving transition metals, with many seemingly due to erroneous interpretation of structures from patent data. Compared to fragmentation statistics published 40 years ago, the exponential growth in chemistry is mirrored in a nearly eightfold increase in the number of unique chemical fragments; however, this result is clearly an upper bound estimate as earlier studies employed structure sampling approaches and this study shows that a relatively high rate of atom fragments are found in only a single chemical structure (singletons). In addition, the percentage of singletons grows as the size of the chemical fragment is increased. Conclusions The observed growth of the numbers of unique fragments over time suggests that many chemically possible connections of atom types to larger fragments have yet to be explored by chemists. A dramatic drop in the relative rate of increase of atom environments from smaller to larger fragments shows that larger fragments mainly consist of diverse combinations of a limited subset of smaller fragments. This is further supported by the observed concomitant increase of singleton atom environments. Combined, these findings suggest that there is considerable opportunity for chemists to combine known fragments to novel chemical compounds. The comparison of PubChem to an older study of known chemical structures shows noticeable differences. The changes suggest advances in synthetic capabilities of chemists to combine atoms in new patterns. Log–log plots of fragment incidence show small numbers of fragments are found in many structures and that large numbers of fragments are found in very few structures, with nearly half being novel using the methods in this work. The relative decrease in the count of new fragments as a function of size further suggests considerable opportunity for more novel chemicals exists. Lastly, the differences in atom environment diversity between PubChem Substance and Compound showcase the effect of PubChem standardization protocols, but also indicate that a normalization procedure for atom types, functional groups, and tautomeric/resonance forms based on atom environments is possible. The complete sets of atom types and atom environments are supplied as supporting information. Graphical abstract},
  doi       = {10.1186/s13321-015-0076-4},
  file      = {Hähnke et al. - 2015 - PubChem atom environments.pdf:by-author/H/Hähnke/2015_Hähnke_1.pdf:application/pdf;Snapshot:by-author/H/Hähnke/2015_Hähnke_1.html:text/html},
  keywords  = {Computational Biology/Bioinformatics; Computer Applications in Chemistry; Documentation and Information in Chemistry; Fragment; Molecular Graph; PubChem; SMARTS; Standardization; Theoretical and Computational Chemistry},
  language  = {en},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://link.springer.com/article/10.1186/s13321-015-0076-4},
  urldate   = {2015-08-26},
}

@Article{Haile1984,
  author    = {Haile, J. M.},
  journal   = {The Journal of Chemical Physics},
  title     = {Reply to ‘‘Comment on Extensions of the molecular dynamics simulation method. II. Isothermal systems’’},
  year      = {1984},
  number    = {8},
  pages     = {3750--3751},
  volume    = {81},
  doi       = {http://dx.doi.org/10.1063/1.448096},
  file      = {1984_Haile_3750.pdf:by-author/H/Haile/1984_Haile_3750.pdf:PDF},
  groups    = {sg/Molecular dynamics},
  keywords  = {Molecular Dynamics (MD); Polemics; Thermostats},
  owner     = {saulius},
  timestamp = {2016.02.24},
  creationdate = {2016-02-24T00:00:00},
  url       = {http://scitation.aip.org/content/aip/journal/jcp/81/8/10.1063/1.448096},
}

@Article{Haile1983,
  author    = {Haile, J. M. and Gupta, S.},
  journal   = {The Journal of Chemical Physics},
  title     = {Extensions of the molecular dynamics simulation method. II. Isothermal systems},
  year      = {1983},
  number    = {6},
  pages     = {3067--3076},
  volume    = {79},
  abstract  = {In this paper we systematically develop two general classes of equations of motion for performing molecular dynamics simulations at constant temperature. One member of each class is found to be identical to one of the two commonly used methods for performing such simulations. Of those two, one, namely the momentum scaling procedure, is proven to have no effect on the static properties of the simulated system. In addition, we have tested the two methods via equilibrium molecular dynamics on the Lennard‐Jones fluid and find the resulting velocity autocorrelation functions and self‐diffusion coefficients to be in good agreement with those determined by the standard NVE molecular dynamics method.},
  doi       = {10.1063/1.446137},
  file      = {1983_Haile_3067.pdf:by-author/H/Haile/1983_Haile_3067.pdf:PDF},
  groups    = {sg/Molecular dynamics},
  keywords  = {Molecular Dynamics (MD); Thermostats},
  owner     = {saulius},
  timestamp = {2016.02.24},
  creationdate = {2016-02-24T00:00:00},
  url       = {http://scitation.aip.org/content/aip/journal/jcp/79/6/10.1063/1.446137},
}

@TechReport{Halderman2006,
  author      = {J. Alex Halderman and Edward W. Felten},
  institution = {Center for Information Technology Policy, Department of Computer Science, Princeton University},
  title       = {Lessons from the Sony CD DRM Episode},
  year        = {2006},
  abstract    = {In the fall of 2005, problems discovered in two Sony-BMG compact disc copy protection systems, XCP and MediaMax, triggered a public uproar that ultimately led to class-action litigation and the recall of millions of discs. We present an in-depth analysis of these technologies, including their design, im- plementation, and deployment. The systems are surprisingly complex and suffer from a diverse array of flaws that weaken their content protection and expose users to serious security and privacy risks. Their complexity, and their failure, makes them an interesting case study of digital rights management that carries valuable lessons for content companies, DRM vendors, policymakers, end users, and the security community.},
  file        = {:by-author/H/Halderman/2006_Halderman.pdf:PDF},
  keywords    = {Computer Science (CS); DRM},
  owner       = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@InProceedings{Halderman2008,
  author    = {J. Alex Halderman and Seth D. Schoen and Nadia Heninger and William Clarkson and William Paul and Joseph A. Calandrino and Ariel J. Feldman and Jacob Appelbaum and Edward W. Felten},
  booktitle = {Proc. 17th USENIX Security Symposium},
  title     = {Lest We Remember: Cold Boot Attacks on Encryption Keys},
  year      = {2008},
  month     = {July},
  abstract  = {Contrary to popular assumption, DRAMs used in most modern computers retain their contents for seconds to minutes after power is lost, even at operating temperatures and even if removed from a motherboard. Although DRAMs become less reliable when they are not refreshed, they are not immediately erased, and their contents persist sufficiently for malicious (or forensic) acquisition of usable full-system memory images. We show that this phenomenon limits the ability of an operating system to protect cryptographic key material from an attacker with physical access. We use cold reboots to mount attacks on popular disk encryption systems — BitLocker, FileVault, dm-crypt, and TrueCrypt — using no special devices or materials. We experimentally characterize the extent and predictability of memory remanence and report that remanence times can be increased dramatically with simple techniques. We offer new algorithms for finding cryptographic keys in memory images and for correcting errors caused by bit decay. Though we discuss several strategies for partially mitigating these risks, we know of no simple remedy that would eliminate them.},
  file      = {:by-author/H/Halderman/2008_Halderman.pdf:PDF},
  keywords  = {Computer Science (CS); Kriptografija},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
  url       = {http://citp.princeton.edu/memory},
}

@Article{Hale2012,
  author    = {Hale, Caryn R. and Majumdar, Sonali and Elmore, Joshua and Pfister, Neil and Compton, Mark and Olson, Sara and Resch, Alissa M. and Glover III, Claiborne V.C. and Graveley, Brenton R. and Terns, Rebecca M. and Terns, Michael P.},
  journal   = {Mol. Cell},
  title     = {Essential Features and Rational Design of CRISPR RNAs that Function with the Cas RAMP Module Complex to Cleave RNAs},
  year      = {2012},
  pages     = {292–302},
  volume    = {45},
  abstract  = {Small RNAs target invaders for silencing in the CRISPR-Cas pathways that protect bacteria and archaea from viruses and plasmids. The CRISPR RNAs (crRNAs) contain sequence elements acquired from invaders that guide CRISPR-associated (Cas) proteins back to the complementary invading DNA or RNA. Here, we have analyzed essential features of the crRNAs associated with the Cas RAMP module (Cmr) effector complex, which cleaves targeted RNAs. We show that Cmr crRNAs contain an 8 nucle- otide 50 sequence tag (also found on crRNAs associ- ated with other CRISPR-Cas pathways) that is critical for crRNA function and can be used to engineer crRNAs that direct cleavage of novel targets. We also present data that indicate that the Cmr complex cleaves an endogenous complementary RNA in Pyrococcus furiosus, providing direct in vivo evi- dence of RNA targeting by the CRISPR-Cas system. Our findings indicate that the CRISPR RNA-Cmr protein pathway may be exploited to cleave RNAs of interest.},
  doi       = {10.1016/j.molcel.2011.10.023},
  file      = {:by-author/H/Hale/2012_Hale_292.pdf:PDF},
  groups    = {sg/CRISPR-Cas},
  keywords  = {CRISPR; Cas Complex; Cmr Complex; RNA Cleavage},
  owner     = {em},
  timestamp = {2013.10.01},
  creationdate = {2013-10-01T00:00:00},
}

@Article{Halford2000,
  author    = {Halford, S. E. and Gowers, D. M. and Sessions, R. B.},
  journal   = {Nature structural biology},
  title     = {Two are better than one.},
  year      = {2000},
  pages     = {705--7},
  volume    = {7},
  file      = {:by-author/H/Halford/2000_Halford_705.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Halgren2004,
  author    = {Halgren, Thomas A. and Murphy, Robert B. and Friesner, Richard A. and Beard, Hege S. and Frye, Leah L. and Pollard, W. Thomas and Banks, Jay L.},
  journal   = {Journal of Medicinal Chemistry},
  title     = {Glide:  A New Approach for Rapid, Accurate Docking and Scoring. 2. Enrichment Factors in Database Screening},
  year      = {2004},
  pages     = {1750--1759},
  volume    = {47},
  abstract  = {Glide's ability to identify active compounds in a database screen is characterized by applying Glide to a diverse set of nine protein receptors. In many cases, two, or even three, protein sites are employed to probe the sensitivity of the results to the site geometry. To make the database screens as realistic as possible, the screens use sets of “druglike” decoy ligands that have been selected to be representative of what we believe is likely to be found in the compound collection of a pharmaceutical or biotechnology company. Results are presented for releases 1.8, 2.0, and 2.5 of Glide. The comparisons show that average measures for both “early” and “global” enrichment for Glide 2.5 are 3 times higher than for Glide 1.8 and more than 2 times higher than for Glide 2.0 because of better results for the least well-handled screens. This improvement in enrichment stems largely from the better balance of the more widely parametrized GlideScore 2.5 function and the inclusion of terms that penalize ligand−protein interactions that violate established principles of physical chemistry, particularly as it concerns the exposure to solvent of charged protein and ligand groups. Comparisons to results for the thymidine kinase and estrogen receptors published by Rognan and co-workers (J. Med. Chem. 2000, 43, 4759−4767) show that Glide 2.5 performs better than GOLD 1.1, FlexX 1.8, or DOCK 4.01.},
  doi       = {10.1021/jm030644s},
  eprint    = {http://pubs.acs.org/doi/pdf/10.1021/jm030644s},
  file      = {2004_Halgren_1750.pdf:by-author/H/Halgren/2004_Halgren_1750.pdf:PDF},
  owner     = {saulius},
  timestamp = {2013.04.01},
  creationdate = {2013-04-01T00:00:00},
  url       = {http://pubs.acs.org/doi/abs/10.1021/jm030644s},
}

@MastersThesis{Hall2010,
  author    = {Adam Hall},
  school    = {THE FACULTY OF GRADUATE STUDIES (Bioinformatics) THE UNIVERSITY OF BRITISH COLUMBIA (Vancouver)},
  title     = {Short-Read DNA Sequence Alignment with Custom Designed FPGA-based Hardware},
  year      = {2010},
  month     = {November},
  abstract  = {The alignment of short DNA read sequencing data to a human reference genome sequence has become a standard step in the analysis pipeline for short DNA read sequence data. As the rate at which short read DNA sequence data is being produced doubles every 5 months, analysis of this data in a computationally efficient way is becoming increasingly important. We demonstrate how we can exploit the ``embarrassingly parallel'' property of short read sequence alignment in custom-designed hardware in FPGA’s. Hardware is chosen, a system is designed, and this system is implemented. My FPGA-based hit finder was demonstrated to produce correct hit results. The performance of this single FPGA implementation was demonstrated to be 71,000 seed hits found per hour on a human genome sized reference sequence. The implementation was demonstrated to produce identical results to the hit finder stage of the MAQ aligner. We demonstrate that the price/performance of this sliding-window FPGA aligner (approximately ~355 seeds/hr/$) compares favorably to the price/performance of sliding-window software aligners (approximately ~67.5 seeds/hr/$ for MAQ). However, software aligners which are based on the superior Burrows-Wheeler alignment algorithm still have a significant price/performance advantage over the FPGA-based approach (approximately ~7,200 seeds/hr/$). We predict that as chips continue to increase in size due to Moore’s Law and computation is performed in high-density cloud-computing datacenters the FPGA-based approach will become preferable to current software aligners.},
  file      = {2010_Hall_masterthesis.pdf:by-author/H/Hall/2010_Hall_masterthesis.pdf:PDF},
  keywords  = {Custom Hardware; FPGA; NGS; New Generation Sequenceing; Sequence Alignment; VHDL; Verilog},
  owner     = {saulius},
  timestamp = {2016.10.03},
  creationdate = {2016-10-03T00:00:00},
  url       = {https://open.library.ubc.ca/cIRcle/collections/ubctheses/24/items/1.0071441},
}

@Article{Hall1991b,
  author           = {Hall, Sydney R.},
  journal          = {Journal of Chemical Information and Computer Sciences},
  title            = {The {STAR} file: a new format for electronic data transfer and archiving},
  year             = {1991},
  pages            = {326--333},
  volume           = {31},
  creationdate     = {2015-06-23T00:00:00},
  doi              = {10.1021/ci00002a020},
  file             = {:by-author/H/Hall/1991_Hall_326.pdf:PDF},
  keywords         = {CIF; Crystallography; Data Exchange; File Formats; STAR; Standards; X-ray},
  modificationdate = {2023-08-07T10:23:05},
  owner            = {andrius},
  timestamp        = {2015.06.23},
  url              = {http://dx.doi.org/10.1021/ci00002a020},
}

@Article{Hall1991,
  author           = {Hall, S. R. and Allen, F. H. and Brown, I. D.},
  journal          = {Acta Crystallographica Section A},
  title            = {The crystallographic information file ({CIF}): a new standard archive file for crystallography},
  year             = {1991},
  pages            = {655--685},
  volume           = {47},
  creationdate     = {2008-07-28T00:00:00},
  doi              = {10.1107/S010876739101067X},
  file             = {:by-author/H/Hall/1991_Hall_655.pdf:PDF},
  groups           = {sg/CIF, am/CIF},
  keywords         = {CIF; Crystallography; Data Exchange; File Formats; STAR; Standards; X-ray},
  modificationdate = {2023-08-07T10:23:05},
  owner            = {saulius},
  timestamp        = {2008.07.28},
  url              = {http://dx.doi.org/10.1107/S010876739101067X},
}

@Article{Hall1994,
  author           = {Hall, Sydney R. and Spadaccini, Nick},
  journal          = {Journal of Chemical Information and Computer Sciences},
  title            = {The {STAR} File: Detailed Specifications},
  year             = {1994},
  pages            = {505--508},
  volume           = {34},
  creationdate     = {2015-07-20T00:00:00},
  doi              = {10.1021/ci00019a005},
  file             = {:by-author/H/Hall/1994_Hall_505.pdf:PDF},
  groups           = {sg/CIF, am/CIF},
  keywords         = {CIF},
  modificationdate = {2023-08-07T10:23:05},
  owner            = {andrius},
  timestamp        = {2015.07.20},
  url              = {http://dx.doi.org/10.1021/ci00019a005},
}

@Article{Halmi2006,
  author    = {Halmi, Piia and Parkkila, Seppo and Honkaniemi, Jari},
  journal   = {Neurochemistry international},
  title     = {Expression of carbonic anhydrases II, IV, VII, VIII and XII in rat brain after kainic acid induced status epilepticus.},
  year      = {2006},
  pages     = {24--30},
  volume    = {48},
  abstract  = {Carbonic anhydrases (CAs) are important enzymes in the central nervous system (CNS), where they participate in regulating cerebrospinal fluid (CSF) secretion, blood-brain barrier and glial cell function. Using RT-PCR we found CA XII mRNA in rat and mouse brain. Cloning of rat CA XII revealed 94% homology with the mouse CA XII. To map the putative functional roles of different CAs, we studied the expression and localization of CA II, CA IV, CA VII, CA-related protein (CA-RP) VIII and CA XII mRNAs in rat brain after kainic acid induced epileptic seizures using Northern blot analysis and in situ hybridization. The expression of CA IV, CA VII and CA-RP VIII was somewhat similar: they were expressed in the cortex, hippocampus and midbrain structures and their expression did not change after the kainic acid treatment. The expression of CA II was concentrated in the white matter structures, which is in line with the preferential expression of CA II in the oligodendrocytes. High levels of CA II mRNA were also detected in the choroid plexus. Surprisingly, CA II was induced 3-12 h after seizures in the vulnerable CA1 region. CA XII was expressed in dentate granule cells, cortex and choroid plexus. Kainic acid stimulated CA XII expression throughout the cortical layer I. The observed hippocampal induction of CA II may indicate a pro-apoptotic and/or epileptogenic role of CA II after prolonged seizures. The physiological significance of the observed cortical induction of CA XII remains obscure. Cytosolic CA II is known to participate in CSF secretion, and the high expression of CA XII in the choroid plexus suggests an analogous role for this membrane-bound isozyme.},
  file      = {2006_Halmi_24.pdf:by-author/H/Halmi/2006_Halmi_24.pdf:PDF},
  groups    = {sg/medicine, sg/hCA2, sg/hCA4, sg/hCA7, sg/hCA8},
  keywords  = {Carbonic Anhydrases},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Hamdan2010,
  author    = {Hamdan, Samir M. and van Oijen, Antoine M.},
  journal   = {The Journal of biological chemistry},
  title     = {Timing, coordination, and rhythm: acrobatics at the DNA replication fork.},
  year      = {2010},
  pages     = {18979--83},
  volume    = {285},
  abstract  = {In DNA replication, the antiparallel nature of the parental duplex imposes certain constraints on the activity of the DNA polymerases that synthesize new DNA. The leading-strand polymerase advances in a continuous fashion, but the lagging-strand polymerase is forced to restart at short intervals. In several prokaryotic systems studied so far, this problem is solved by the formation of a loop in the lagging strand of the replication fork to reorient the lagging-strand DNA polymerase so that it advances in parallel with the leading-strand polymerase. The replication loop grows and shrinks during each cycle of Okazaki fragment synthesis. The timing of Okazaki fragment synthesis and loop formation is determined by a subtle interplay of enzymatic activities at the fork. Recent developments in single-molecule techniques have enabled the direct observation of these processes and have greatly contributed to a better understanding of the dynamic nature of the replication fork. Here, we will review recent experimental advances, present the current models, and discuss some of the exciting developments in the field.},
  file      = {:by-author/H/Hamdan/2010_Hamdan_18979.pdf:PDF},
  keywords  = {{gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Hamilton1835,
  author    = {William Rowan Hamilton},
  journal   = {Philosophical Transactions of the Royal Society},
  title     = {Second essay on a general method in dynamics},
  year      = {1835},
  pages     = {95--144},
  volume    = {part I},
  abstract  = {The former Essay* contained a general method for reducing all the most important problems of dynamics to the study of one characteristic function, one central or radical relation. It was remarked at the close of that Essay, that many eliminations required by this method in its first conception, might be avoided by a general transformation, introducing the time explicitly into a part S of the whole characteristic function V ; and it is now proposed to fix the attention chiefly on this part S, and to call it the Principal Function. The properties of this part or function S, which were noticed briefly in the former Essay, are now more fully set forth; and especially its uses in questions of perturbation, in which it dispenses with many laborious and circuitous processes, and enables us to express accurately the disturbed configuration of a system by the rules of undisturbed motion, if only the initial components of velocities be changed in a suitable manner. Another manner of extending rigorously to disturbed motion the rules of undisturbed, by the gradual variation of elements, in number double the number of coordinates or other marks of position of the system, which was first invented by Lagrange, and was afterwards improved by Poisson, is considered in this Second Essay under a form perhaps a little more general; and the general method of calculation which has already been applied to other analogous questions in optics and in dynamics by the author of the present Essay, is now applied to the integration of the equations which determine these elements. This general method is founded chiefly on a combination of the principles of variations with those of partial differentials, and may furnish, when it shall be matured by the labours of other analysts, a separate branch of algebra, which may be called perhaps the Calculus of Principal Functions; because, in all the chief applications of algebra to physics, and in a very extensive class of purely mathematical questions, it reduces the determination of many mutually connected functions to the search and study of one principal or central relation. When applied to the integration of the equations of varying elements, it suggests, as is now shown, the consideration of a certain Function of Elements, which may be variously chosen, and may either be rigorously determined, or at least approached to, with an indefinite accuracy, by a corollary of the general method. And to illustrate all these new general processes, but especially those which are connected with problems of perturbation, they are applied in this Essay to a very simple example, suggested by the motions of projectiles, the parabolic path being treated as the undisturbed. As a more important example, the problem of determining the motions of a ternary or multiple system, with any laws of attraction or repulsion, and with one predominant mass, which was touched on in the former Essay, is here resumed in a new way, by forming and integrating the differential equations of a new set of varying elements, entirely distinct in theory (though little differing in practice) from the elements conceived by Lagrange, and having this advantage, that the differentials of all the new elements for both the disturbed and disturbing masses may be expressed by the coefficients of one disturbing function.},
  file      = {:by-author/H/Hamilton/1835_Hamilton_95.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.05.02},
  creationdate = {2012-05-02T00:00:00},
}

@Article{Hamilton1834,
  author    = {William Rowan Hamilton},
  journal   = {Philosophical Transactions of the Royal Society},
  title     = {On a general method in dynamics},
  year      = {1834},
  pages     = {247--308},
  volume    = {part II},
  abstract  = {The theoretical development of the laws of motion of bodies is a problem of such interest and importance, that it has engaged the attention of all the most eminent mathematicians, since the invention of dynamics as a mathematical science by Galileo, and especially since the wonderful extension which was given to that science by Newton. Among the successors of those illustrious men, Lagrange has perhaps done more than any other analyst, to give extent and harmony to such deductive researches, by showing that the most varied consequences respecting the motions of systems of bodies may be derived from one radical formula; the beauty of the method so suiting the dignity of the results, as to make of his great work a kind of scientific poem. But the science of force, or of power acting by law in space and time, has undergone already another revolution, and has become already more dynamic, by having almost dismissed the conceptions of solidity and cohesion, and those other material ties, or geometrically imaginably conditions, which Lagrange so happily reasoned on, and by tending more and more to resolve all connexions and actions of bodies into attractions and repulsions of points: and while the science is advancing thus in one direction by the improvement of physical views, it may advance in another direction also by the invention of mathematical methods. And the method proposed in the present essay, for the deductive study of the motions of attracting or repelling systems, will perhaps be received with indulgence, as an attempt to assist in carrying forward so high an inquiry.},
  file      = {:by-author/H/Hamilton/1834_Hamilton_247.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.05.02},
  creationdate = {2012-05-02T00:00:00},
}

@Article{Hammarstroem2001,
  author    = {Hammarström, P and Owenius, R and Mårtensson, L G and Carlsson, U and Lindgren, M},
  journal   = {Biophysical journal},
  title     = {High-resolution probing of local conformational changes in proteins by the use of multiple labeling: unfolding and self-assembly of human carbonic anhydrase II monitored by spin, fluorescent, and chemical reactivity probes.},
  year      = {2001},
  pages     = {2867--85},
  volume    = {80},
  abstract  = {Two different spin labels, N-(1-oxyl-2,2,5,5-tetramethyl-3-pyrrolidinyl)iodoacetamide (IPSL) and (1-oxyl-2,2,5,5-tetramethylpyrroline-3-methyl) methanethiosulfonate (MTSSL), and two different fluorescent labels 5-((((2-iodoacetyl)amino)-ethyl)amino)naphtalene-1-sulfonic acid (IAEDANS) and 6-bromoacetyl-2-dimetylaminonaphtalene (BADAN), were attached to the introduced C79 in human carbonic anhydrase (HCA II) to probe local structural changes upon unfolding and aggregation. HCA II unfolds in a multi-step manner with an intermediate state populated between the native and unfolded states. The spin label IPSL and the fluorescent label IAEDANS reported on a substantial change in mobility and polarity at both unfolding transitions at a distance of 7.4-11.2 A from the backbone of position 79. The shorter and less flexible labels BADAN and MTSSL revealed less pronounced spectroscopic changes in the native-to-intermediate transition, 6.6-9.0 A from the backbone. At intermediate guanidine (Gu)-HCl concentrations the occurrence of soluble but irreversibly aggregated oligomeric protein was identified from refolding experiments. At approximately 1 M Gu-HCl the aggregation was found to be essentially complete. The size and structure of the aggregates could be varied by changing the protein concentration. EPR measurements and line-shape simulations together with fluorescence lifetime and anisotropy measurements provided a picture of the self-assembled protein as a disordered protein structure with a representation of both compact as well as dynamic and polar environments at the site of the molecular labels. This suggests that a partially folded intermediate of HCA II self-assembles by both local unfolding and intermolecular docking of the intermediates vicinal to position 79. The aggregates were determined to be 40-90 A in diameter depending on the experimental conditions and spectroscopic technique used.},
  file      = {2001_Hammarstrom_2867.pdf:by-author/H/Hammarström/2001_Hammarström_2867.pdf:PDF},
  groups    = {sg/hCA2},
  keywords  = {Carbonic Anhydrases},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Handa2000,
  author    = {Handa, N. and Ichige, A. and Kusano, K. and Kobayashi, I.},
  journal   = {Journal of bacteriology},
  title     = {Cellular responses to postsegregational killing by restriction-modification genes.},
  year      = {2000},
  pages     = {2218--29},
  volume    = {182},
  abstract  = {Plasmids that carry one of several type II restriction modification gene complexes are known to show increased stability. The underlying mechanism was proposed to be the lethal attack by restriction enzyme at chromosomal recognition sites in cells that had lost the restriction modification gene complex. In order to examine bacterial responses to this postsegregational cell killing, we analyzed the cellular processes following loss of the EcoRI restriction modification gene complex carried by a temperature-sensitive plasmid in an Escherichia coli strain that is wild type with respect to DNA repair. A shift to the nonpermissive temperature blocked plasmid replication, reduced the increase in viable cell counts and resulted in loss of cell viability. Many cells formed long filaments, some of which were multinucleated and others anucleated. In a mutant defective in RecBCD exonuclease/recombinase, these cell death symptoms were more severe and cleaved chromosomes accumulated. Growth inhibition was also more severe in recA, ruvAB, ruvC, recG, and recN mutants. The cells induced the SOS response in a RecBC-dependent manner. These observations strongly suggest that bacterial cells die as a result of chromosome cleavage after loss of a restriction modification gene complex and that the bacterial RecBCD/RecA machinery helps the cells to survive, at least to some extent, by repairing the cleaved chromosomes. These and previous results have led us to hypothesize that the RecBCD/Chi/RecA system serves to destroy restricted &quot;nonself&quot; DNA and repair restricted &quot;self&quot; DNA.},
  file      = {:by-author/H/Handa/2000_Handa_2218.pdf:PDF},
  keywords  = {TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Hang2004,
  author    = {Hang, Howard C. and Yu, Chong and Pratt, Matthew R. and Bertozzi, Carolyn R.},
  journal   = {Journal of the American Chemical Society},
  title     = {Probing glycosyltransferase activities with the Staudinger ligation.},
  year      = {2004},
  pages     = {6--7},
  volume    = {126},
  abstract  = {The development of rapid screening methods for probing glycosyltransferase activities is essential for advancing the field of glycobiology. While assays for specific glycosyltransferases exist, there is no generalizable method that can be applied across the enzyme superfamily. Herein we describe a novel glycosyltransferase assay that exploits their unnatural substrate tolerance and the unique chemical reactivity of the azide. We applied this &quot;azido-ELISA&quot; to the family of polypeptide alpha-N-acetylgalactosaminyltransferases (ppGalNAcTs), all of which were able to transfer N-azidoacetylgalactosamine (GalNAz) from the unnatural nucleotide sugar donor UDP-GalNAz. The azide was detected and quantified by Staudinger ligation with a phosphine probe in a microtiter plate format. This approach should be applicable to any glycosyltransferase or group-transfer enzyme that tolerates unnatural azido substrates.},
  file      = {:by-author/H/Hang/2004_Hang_6.pdf:PDF},
  keywords  = {Bioconjugation},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@Article{Hanke2012,
  author    = {Hanke, Maximilian and Arslan, Hasan K. and Bauer, Stella and Zybaylo, Olexandra and Christophis, Christof and Gliemann, Hartmut and Rosenhahn, Axel and Wöll, Christof},
  journal   = {Langmuir : the ACS journal of surfaces and colloids},
  title     = {The biocompatibility of metal-organic framework coatings: an investigation on the stability of SURMOFs with regard to water and selected cell culture media.},
  year      = {2012},
  pages     = {6877--84},
  volume    = {28},
  abstract  = {Highly porous thin films based on a [Cu(bdc)(2)](n) (bdc = benzene-1,4-dicarboxylic acid) metal-organic framework, MOF, grown using liquid-phase epitaxy (LPE) show remarkable stability in pure water as well as in artificial seawater. This opens the possibility to use these highly porous coatings for environmental and life science applications. Here we characterize in detail the stability of these SURMOF 2 thin films under aqueous and cell culture conditions. We find that the material degrades only very slowly in water and artificial seawater (ASW) whereas in typical cell culture media (PBS and DMEM) a rapid dissolution is observed. The release of Cu(2+) ions resulting from the dissolution of the SURMOF 2 in the liquids exhibits no adverse effect on the adhesion of fibroblasts, prototype eukaryotic cells, to the substrate and their subsequent proliferation, thus demonstrating the biocompatibility of SURMOF 2 surface coatings. Thus, the results are an important step toward application of these porous materials as a slow release matrix, for example, for pharmaceuticals and growth factors.},
  doi       = {10.1021/la300457z},
  file      = {:by-author/H/Hanke/2012_Hanke_6877.pdf:PDF},
  groups    = {sg/MOF, sg/MOFs, am/MOFs},
  keywords  = {Biocompatibility; Metal-Organic Frameworks (MOF)},
  owner     = {saulius},
  timestamp = {2013.01.05},
  creationdate = {2013-01-05T00:00:00},
}

@Presentation{Hans2004,
  author    = {Hans},
  title     = {Performance evaluation},
  year      = {2004},
  file      = {:by-author/H/Hans/2004_Hans.pdf:PDF},
  keywords  = {Computer Architecture; Computer Science (CS); Performance Comparison},
  month     = {October},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@TechReport{Hansen2006,
  author      = {Jacob Gorm Hansen},
  institution = {Department of Computer Science University of Copenhagen, Denmark},
  title       = {Blink: {3D} Display Multiplexing for Virtualized Applications},
  year        = {2006},
  abstract    = {For management and security reasons, Virtual Machines are increasingly being deployed on Desktop PC’s, but because existing VMM technologies are mostly targeted at servers, graphical performance is a stumbling block to many modern applications such as games, simulation, and video-conferencing. Existing high-performance display systems sacrifice safety and provide applications with direct hardware access, but the aim of our work is to build a display system with Virtual Machine quality safety and isolation, while retaining performance comparable to less safe “direct” approaches. We are developing Blink, a Display System for Virtual Machines, the core component of which is a JIT-compiler for extended OpenGL programs which execute safely inside the address space of the display server. Our results show that this model can lead to fewer context switches than traditional client/server approaches, can eliminate redundant copying and clearing of graphics buffers, and reduce the visible effects of scheduler timing variance.},
  file        = {:by-author/H/Hansen/2006_Hansen_techreport.pdf:PDF},
  keywords    = {Computer Graphics; Computer Science (CS)},
  owner       = {saulius},
  pages       = {techreport},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Hanser1996,
  author    = {Hanser, T. and Jauffret, P. and Kaufmann, G.},
  journal   = {Journal of Chemical Information and Modeling},
  title     = {A New Algorithm for Exhaustive Ring Perception in a Molecular Graph},
  year      = {1996},
  issn      = {1549-9596},
  pages     = {1146--1152},
  volume    = {36},
  doi       = {10.1021/ci960322f},
  file      = {1996_Hanser_1146.pdf:by-author/H/Hanser/1996_Hanser_1146.pdf:PDF},
  keywords  = {Ring Perception},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://pubs.acs.org/cgi-bin/doilookup/?10.1021/ci960322f},
}

@Article{Hanson2010,
  author    = {Hanson, Robert M.},
  journal   = {Journal of Applied Crystallography},
  title     = {{\it Jmol} {--} a paradigm shift in crystallographic visualization},
  year      = {2010},
  pages     = {1250--1260},
  volume    = {43},
  abstract  = {Recent advances in molecular and crystallographic visualization methods are allowing instructors unprecedented opportunities to enhance student learning using virtual models within a familiar web-browser context. In step with these advances, the latest versions of the Jmol molecular visualization applet offer capabilities that hold potential for revolutionizing the way students learn about symmetry, uncertainty and the overall enterprise of molecular structure determination.},
  doi       = {10.1107/S0021889810030256},
  file      = {2010_Hanson_1250.pdf:by-author/H/Hanson/2010_Hanson_1250.pdf:PDF},
  keywords  = {Algorithms; Crystallography; Jmol; Visualisation},
  owner     = {saulius},
  timestamp = {2013.04.19},
  creationdate = {2013-04-19T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0021889810030256},
}

@Webpage{Hanson2011,
  author    = {Robert M. Hanson and Erik F. Wyatt},
  retrieved = {2013-03-24},
  title     = {Interactive Visualization of Intermolecular Contacts},
  url       = {http://www.stolaf.edu/people/hansonr/jmol/contact/gordon.htm},
  year      = {2011},
  abstract  = {The visual depiction of protein-ligand interactions is often made difficult due to limitations inherent in popular programs such as PyMOL and VMD. Our goal in this project is to devise new and more effective ways of depicting interactions that will be vivid, concise, and -- most importantly -- simple enough to create that they could be generated easily by anyone wanting either a production-quality image or its underlying user-interactive model equivalent. We describe here a method that allows depiction of protein-ligand interactions in a variety of ways. The method is based on linear combinations of van der Waals surfaces (intersection, difference, and sum). Jmol implements the method in the contact command, to be introduced in Jmol version 12.2 later this summer.},
  file      = {:by-author/H/Hanson/2011_Hanson.odt:PDF},
  keywords  = {Algorithms; Crystallography; Jmol; Surfaces; Visualisation},
  owner     = {saulius},
  timestamp = {2013.03.24},
  creationdate = {2013-03-24T00:00:00},
}

@Article{Hanwell2012,
  author    = {Hanwell, Marcus and Curtis, Donald and Lonie, David and Vandermeersch, Tim and Zurek, Eva and Hutchison, Geoffrey},
  journal   = {Journal of Cheminformatics},
  title     = {Avogadro: an advanced semantic chemical editor, visualization, and analysis platform},
  year      = {2012},
  issn      = {1758-2946},
  pages     = {17},
  volume    = {4},
  abstract  = {BACKGROUND:The Avogadro project has developed an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible, high quality rendering, and a powerful plugin architecture. Typical uses include building molecular structures, formatting input files, and analyzing output of a wide variety of computational chemistry packages. By using the CML file format as its native document type, Avogadro seeks to enhance the semantic accessibility of chemical data types. RESULTS:The work presented here details the Avogadro library, which is a framework providing a code library and application programming interface (API) with three-dimensional visualization capabilities; and has direct applications to research and education in the fields of chemistry, physics, materials science, and biology. The Avogadro application provides a rich graphical interface using dynamically loaded plugins through the library itself. The application and library can each be extended by implementing a plugin module in C++ or Python to explore different visualization techniques, build/manipulate molecular structures, and interact with other programs. We describe some example extensions, one which uses a genetic algorithm to find stable crystal structures, and one which interfaces with the PackMol program to create packed, solvated structures for molecular dynamics simulations. The 1.0 release series of Avogadro is the main focus of the results discussed here. CONCLUSIONS:Avogadro offers a semantic chemical builder and platform for visualization and analysis. For users, it offers an easy-to-use builder, integrated support for downloading from common databases such as PubChem and the Protein Data Bank, extracting chemical data from a wide variety of formats, including computational chemistry output, and native, semantic support for the CML file format. For developers, it can be easily extended via a powerful plugin mechanism to support new features in organic chemistry, inorganic complexes, drug design, materials, biomolecules, and simulations. Avogadro is freely available under an open-source license from http://avogadro.openmolecules.net webcite.},
  doi       = {10.1186/1758-2946-4-17},
  file      = {2012_Hanwell_17.pdf:by-author/H/Hanwell/2012_Hanwell_17.pdf:PDF},
  owner     = {saulius},
  pubmedid  = {22889332},
  timestamp = {2013.09.19},
  creationdate = {2013-09-19T00:00:00},
  url       = {http://www.jcheminf.com/content},
}

@Article{Hao2001,
  author    = {Hao, Q},
  journal   = {Acta crystallographica. Section D, Biological crystallography},
  title     = {Phasing from an envelope.},
  year      = {2001},
  pages     = {1410--4},
  volume    = {57},
  file      = {2001_Hao_1410.pdf:by-author/H/Hao/2001_Hao_1410.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Haq2001,
  author    = {Haq, I. and O'Brien, R. and Lagunavicius, A. and Siksnys, V. and Ladbury, J. E.},
  journal   = {Biochemistry},
  title     = {Specific DNA recognition by the type II restriction endonuclease MunI: the effect of pH.},
  year      = {2001},
  pages     = {14960--7},
  volume    = {40},
  abstract  = {To investigate the effect of pH on sequence-specific binding, a thermodynamic characterization of the interaction of the protein MunI with a specific, and a nonspecific, oligonucleotide was performed. MunI is a type II restriction endonuclease which is able to bind specifically, but loses its enzymatic activity in the absence of magnesium ions. Comparison of the specific and nonspecific interactions at 10 and 25 degrees C shows that the latter is accompanied by a small change in enthalpy, and a negligible change in constant pressure heat capacity. On going through the pH range 5.75-9.0 at 25 degrees C, the affinity of specific complex formation is reduced by 20-fold. The interaction is accompanied by the protonation of groups assumed to be on the protein. Based on the simplest model that will fit the data, two distinct protonation events are observed. At low pH, two groups per protein molecule undergo protonation with a pK(a) of 6.0 and 6.9 in the free and bound forms, respectively. At high pH, a further independent protonation occurs involving two groups with pK(a) values of 8.9 and approximately 10.7 in the free and bound forms, respectively. The change in heat capacity ranges from -2.7 to -1.7 kJ mol(-1) K(-1) in going from pH 6.5 to 8.5. This range of variation of change in heat capacity can be accounted for by the effects of protonation of the interacting molecules. The change in heat capacity, calculated from surface area burial using a previously established relationship (1.15 kJ mol(-1) K(-1)), does not correlate well with the experimentally determined values.},
  file      = {:by-author/H/Haq/2001_Haq_14960.pdf:PDF},
  keywords  = {MunI; TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Harding2004,
  author    = {Marjorie M. Harding},
  journal   = {Acta Crystallographica Section D},
  title     = {The architecture of metal coordination groups in proteins},
  year      = {2004},
  pages     = {849--859},
  volume    = {D60},
  abstract  = {A set of tables is presented and a survey given of the architecture of metal coordination groups in a representative set of protein structures from the Protein Data Bank [Bernstein et al. (1977), J. Mol. Biol. 112, 535-542; Berman et al. (2000), Nucleic Acids Res. 28, 235-242]. The structures have been determined to a resolution of 2.5 Å or better; the metals considered are Ca, Mg, Mn, Fe, Cu, Zn, Na and K, with particular emphasis on Ca and Zn and the exclusion of haem groups and Fe/S clusters; the proteins are a representative set in which none has more than 30% sequence identity with any other. In them the metal is coordinated by several donor groups from different amino-acid residues in the protein chain and often also by water or other small molecules. The tables, for ~600 metal coordination groups, include information on the conformations of the protein chain in the region around the metal and reliability indicators. They illustrate the wide variety of coordination numbers, chelate-loop sizes and other properties and the different characteristics of different metals. They show that glycine has a particular significance in the position adjacent to a donor residue, especially in Ca coordination groups. They also show that metal coordination does not appear to lead to significant distortions of the torsion angles [varphi], [psi] from their normally allowed values. Very few metal coordination groups occur more than once in the representative set and when they do they are usually related in fold and function; they have similar but not necessarily identical conformations. However, individual chelate loops, for example Zn(-C-X-X'-C-), in which both cysteines are coordinated to Zn through S, and X and X' are any amino acids, are repeated frequently in many different and unrelated proteins. Not all chelate loops with the same composition have the same conformation, but for smaller loops there are usually one or two strongly preferred and well defined conformations. Quite frequently more than one metal coordination group is associated with one protein chain; these proteins are identified.},
  doi       = {10.1107/S0907444904004081},
  file      = {:by-author/H/Harding/2004_Harding_849.pdf:PDF},
  keywords  = {Metal Coordination Spheres},
  owner     = {antanas},
  timestamp = {2013.12.12},
  creationdate = {2013-12-12T00:00:00},
  url       = {http://scripts.iucr.org/cgi-bin/paper?S0907444904004081},
}

@Article{Harding2001,
  author    = {Harding, Majorie M.},
  journal   = {Acta Crystallographica Section D},
  title     = {Geometry of Metal-Ligand Interactions in Proteins},
  year      = {2001},
  pages     = {401--411},
  volume    = {57},
  abstract  = {The geometry of metal-ligand interactions in proteins is examined and compared with information for small-molecule complexes from the Cambridge Structural Database (CSD). The paper deals with the metals Ca, Mg, Mn, Fe, Cu, Zn and with metal-donor atom distances, coordination numbers and extent of distortion from ideal geometry (octahedral, tetrahedral etc.). It assesses the agreement between geometry found in all metalloprotein structures in the Protein Data Bank (PDB) determined at resolution [less-than or equal to] 1.6 Å with that predicted from the CSD for ligands which are analogues of amino-acid side chains in proteins [Harding (1999), Acta Cryst. D55, 1432-1443; Harding (2000), Acta Cryst. D56, 857-867]. The agreement is reasonably good for these structures but poorer for many determined at lower resolution (examined to 2.8 Å resolution). For metal-donor distances, the predictions from the CSD, with minor adjustments, provide good targets either for validation or for restraints in refinement of structures where only poorer resolution data is available. These target distances are tabulated and the use of restraints is recommended. Validation of angles or the use in refinement of restraints on angles at the metal atom is more difficult because of the inherent flexibility of these angles. A much simplified set of parameters for angle restraints with quite large standard deviations is provided. (Despite the flexibility of the angles, acceptable and preferred coordination numbers and shapes are well established and a summary table is provided.) An unusual and perhaps biochemically important feature of Zn coordination with carboxylate seen in the CSD examples is also clearly present in metalloprotein structures. With metals like Ca, carboxylate coordination is monodentate or bidentate (two M-O bonds of nearly equal length). In Zn carboxylates a continuous range between monodentate and bidentate coordination is found, with one Zn-O bond of normal length and another of any length between this and a van der Waals contact.},
  doi       = {10.1107/S0907444900019168},
  file      = {:by-author/H/Harding/2001_Harding_401.pdf:PDF},
  keywords  = {Grow Krystal; Metals; X-ray Crystallography},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444900019168},
}

@Article{Harding2000,
  author    = {Harding, Marjorie M.},
  journal   = {Acta Crystallographica Section D},
  title     = {The Geometry of Metal-Ligand Interactions Relevant to Proteins. {II}. {A}ngles at the Metal Atom, Additional Weak Metal-Donor Interactions},
  year      = {2000},
  pages     = {857--867},
  volume    = {56},
  abstract  = {Geometrical data which could be of relevance in the structure determination, structure refinement, assessment or understanding of metalloproteins have been extracted from the Cambridge Structural Database (CSD). The CSD contains crystallographic data from 'small-molecule' structures determined by X-ray or neutron diffraction to an accuracy and precision much better than that of most current protein structure determinations. Structures of Mg, Mn, Fe, Cu and Zn complexes with ligands whose donor atoms may be only N, O, S or Cl have been selected and analysed in terms of the geometry of the metal coordination group - octahedral, tetrahedral, tetragonal pyramidal etc. The r.m.s. deviation of all the interbond angles around the metal atom provides a measure, delta, of the deviation from ideal geometry. Average values of delta are tabulated for the different metals in each type of complex. For simple non-chelated complexes of Mn, Fe and Zn, distortions of up to 5 degrees in octahedral complexes and 10 degrees in tetrahedral complexes are found to be normal and seem likely to be a consequence of packing effects, ligand bulk or intramolecular effects. Substantially larger distortions are found for some other metals and geometries and are common for chelated complexes. Brief comments on six-, seven- and eight-coordinate Ca complexes are included. Tables are also presented showing that for four- and five-coordinate complexes of Zn and Cu it is quite common to find additional weakly coordinated ligands, usually with N or O donor atoms and with M.N,O distances longer than a normal bond length but shorter than a van der Waals contact, e.g. in the range 2.4-3.0 A for Zn and 2.6-3.0 A for Cu. Although the contributions to bond valency or bonding energy of such interactions may not be great, their effect on geometry can be considerable; they can, for example, cause much larger distortions of tetrahedral Zn complexes than indicated above.},
  doi       = {10.1107/S0907444900005849},
  file      = {:by-author/H/Harding/2000_Harding_857.pdf:PDF},
  keywords  = {Grow Krystal; Metals},
  owner     = {em},
  timestamp = {2012.11.28},
  creationdate = {2012-11-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444900005849},
}

@Article{Harding1999,
  author    = {Harding, Majorie M.},
  journal   = {Acta Crystallographica Section D},
  title     = {The Geometry of Metal-Ligand Interactions Relevant to Proteins},
  year      = {1999},
  pages     = {1432--1443},
  volume    = {55},
  abstract  = {Geometrical data which could be of relevance in the structure determination, structure refinement, assessment or understanding of metalloproteins have been extracted from the Cambridge Structural Database (CSD). The CSD contains crystallographic data from 'small-molecule' structures determined by X-ray or neutron diffraction to an accuracy much better than that of most current protein structure determinations. The structures selected have a crystallographic R factor &lt;/= 0.065 and contain Ca, Mg, Mn, Fe, Cu or Zn interacting with ligands which are analogues of the amino-acid side chains commonly found in proteins; they include carboxylate groups, alcohols, phenolates, thiolates, imidazole groups and also water molecules. For each pair, the mean metal-donor-atom distance, the sample standard deviation and the range of observed values are tabulated, using approximately 4500 observations in all. Where practicable, subsets with different coordination numbers and/or oxidation states are given. Also included are inter-bond angles at the ligand donor atom, the orientation of carboxylate and imidazole groups with respect to the metal-donor-atom bond and some other aspects of ligand geometry. Thus, for example, target distances and their standard deviations could be easily looked up for the validation of a metalloprotein structure or for use in restrained refinement with low-resolution data.},
  doi       = {10.1107/S0907444999007374},
  file      = {:by-author/H/Harding/1999_Harding_1432.pdf:PDF},
  keywords  = {Grow Krystal; Metals; X-ray Crystallography},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444999007374},
}

@Misc{Hardinger2012,
  author    = {Steve Hardinger},
  title     = {Enantiomers, diastereomers, and meso compounds 101},
  year      = {2012},
  file      = {enantiomers final - tutorial72.pdf:by-author/H/Hardinger/2012_Hardinger.pdf:application/pdf},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://www.chem.ucla.edu/harding/ec_tutorials/tutorial72.pdf},
  urldate   = {2015-08-28},
}

@Misc{Hardinger2010,
  author    = {Steve Hardinger},
  title     = {Stereochemistry tutorial : drawing enantiomers and diastereomers},
  year      = {2010},
  comment   = {http://www.chem.ucla.edu/harding/},
  file      = {draw_enant - draw_enant.pdf:by-author/H/Hardinger/2010_Hardinger.pdf:application/pdf},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://www.chem.ucla.edu/harding/tutorials/stereochem/draw_enant.pdf},
  urldate   = {2015-08-28},
}

@Article{Hariharan2005,
  author    = {Hariharan, Chithra and Reha-Krantz, Linda J.},
  journal   = {Biochemistry},
  title     = {Using 2-aminopurine fluorescence to detect bacteriophage T4 DNA polymerase-DNA complexes that are important for primer extension and proofreading reactions.},
  year      = {2005},
  pages     = {15674--84},
  volume    = {44},
  abstract  = {The fluorescence of the base analogue 2-aminopurine (2AP) was used to probe bacteriophage T4 DNA polymerase-induced conformational changes in the template strand produced during the nucleotide incorporation and proofreading reactions. 2AP fluorescence in DNA is quenched by 2AP interactions with neighboring bases, but T4 DNA polymerase binding to DNA substrates labeled with 2AP in the templating position produces large increases in fluorescence intensity. Fluorescence lifetime studies were performed to characterize the fluorescent complexes. Three fluorescence lifetime components were observed for unbound DNA substrates as reported previously, but T4 DNA polymerase binding modulated the amplitudes of these components and created a new, highly fluorescent 10.5 ns component. Experimental evidence for correlation of fluorescence lifetimes with functionally distinct complexes was obtained by forming complexes under different reaction conditions. T4 DNA polymerase complexes were formed with DNA substrates with matched and mismatched primer ends and with A+T- or G+C-rich primer-terminal regions. dTTP was added to binary complexes to form ternary DNA polymerase-DNA-nucleotide complexes. The effect of temperature on complex formation was studied, and complexes were formed with proofreading-defective T4 DNA polymerases. Complexes characterized by the 10.5 ns lifetime were demonstrated to be formed at the crossroads of the primer-extension and proofreading pathways.},
  file      = {:by-author/H/Hariharan/2005_Hariharan_15674.pdf:PDF},
  keywords  = {{gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Harlow1996,
  author           = {Harlow, R. L.},
  journal          = {Journal of Research of the National Institute of Standards and Technology},
  title            = {Troublesome crystal structures. Prevention, detection, and resolution},
  year             = {1996},
  issn             = {1044-677X},
  month            = {May},
  number           = {3},
  pages            = {327--339},
  volume           = {101},
  abstract         = {A large number of incorrect crystal structures is being published today. These structures are proving to be a particular problem to those of us who are interested in comparing structural moieties found in the databases in order to develop structure-property relationships. Problems can reside in the input data, e.g., wrong unit cell or low quality intensity data, or in the structural model, e.g., wrong space group or atom types. Many of the common mistakes are, however, relatively easy to detect and thus should be preventable; at the very least, suspicious structures can be flagged, if not by the authors then by the referees and, ultimately, the crystallographic databases. This article describes some of the more common mistakes and their effects on the resulting structures, lists a series of tests that can be used to detect incorrect structures, and makes a strong plea for the publication of higher quality structures.},
  comment          = {Describes consequences of the refinement in a space group which is too low:

"structure was refined in noncentrosymmetric space group Pca2_1 when it should have been refined in centrosymmetric Pcam (Pbcm). Not only are the thermal ellipsoids nonsensical, but the chemically-equivalent bond distances such as S(1)–C(1) and S(2–C(9) differ by 0.10 Å. These symptoms are caused by the high correlations between positional and thermal parameters of atoms in the two halves of the molecule which are actually related by a mirror plane in Pcam."},
  creationdate     = {2016-12-16T00:00:00},
  doi              = {10.6028/jres.101.034},
  file             = {1996_Harlow_327.pdf:by-author/H/Harlow/1996_Harlow_327.pdf:PDF},
  groups           = {sg/Crystallography, am/Crystallography, am/Data quality},
  keywords         = {Crystallography; Data Quality; Incorrectly Determined Spacegroup; Reported Symmetry Too Low},
  modificationdate = {2024-08-26T13:57:32},
  owner            = {andrius},
  publisher        = {National Institute of Standards and Technology (NIST)},
  timestamp        = {2016.12.16},
  url              = {http://dx.doi.org/10.6028/jres.101.034},
}

@InProceedings{Harmanani2003,
  author    = {Haidar Harmanani and Jean Hannouche and Nancy Khoury},
  booktitle = {Proceedings of the 12th IASTED International Conference Applied Simulation and Modelling},
  title     = {A Neural Networks Algorithm for the Minimum Coloring Problem Using FPGAs},
  year      = {2003},
  pages     = {152},
  abstract  = {This paper presents a hardware implementation to solve the graph coloring problem (chromatic number) for arbitrary graphs using the hopfield neural network model of computation. The graph coloring problem, an NP-hard problem, has important applications in many areas includ- ing time tabling and scheduling, frequency assignment, and register allocation. The proposed algorithm has a time complexity of for a neural network with vertices and colors. The algorithm was implemented using VHDL and downloaded on a Field Programmable Gate Array (FPGA) device. The algorithm was simulated and tested on various graphs, all yielding optimum solutions.},
  file      = {:by-author/H/Harmanani/2003_Harmanani_152.pdf:PDF},
  keywords  = {Combinatorial Optimization; Computer Architecture; Computer Science (CS); FPGA; Graph Coloring; Hardware; Neural Networks (NN)},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Harnad2004,
  author    = {Stevan Harnad and Tim Brody},
  journal   = {D-Lib Magazine},
  title     = {Comparing the Impact of Open Access (OA) vs. Non-OA Articles in the Same Journals},
  year      = {2004},
  issn      = {1082-9873},
  month     = {June},
  number    = {6},
  volume    = {10},
  abstract  = {The way to test the impact advantage of Open Access (OA) is not to compare the citation impact factors of OA and non-OA journals but to compare the citation counts of individual OA and non-OA articles appearing in the same (non-OA) journals. Such ongoing comparisons are revealing dramatic citation advantages for OA.},
  file      = {2004_Harnad.pdf:by-author/H/Harnad/2004_Harnad.pdf:PDF;2004_Harnad.odt:by-author/H/Harnad/2004_Harnad.odt:OpenDocument text},
  keywords  = {Article Impatc; Citation Counts; Open Access},
  owner     = {saulius},
  timestamp = {2016.10.16},
  creationdate = {2016-10-16T00:00:00},
  url       = {http://www.dlib.org/dlib/june04/harnad/06harnad.html},
}

@Article{Harnad2008,
  author    = {Harnad, Stevan and Brody, Tim and Vallières, François and Carr, Les and Hitchcock, Steve and Gingras, Yves and Oppenheim, Charles and Hajjem, Chawki and Hilf, Eberhard R.},
  journal   = {Serials Review},
  title     = {The Access/Impact Problem and the Green and Gold Roads to Open Access: An Update},
  year      = {2008},
  issn      = {1879-095X},
  month     = {Mar},
  number    = {1},
  pages     = {36--40},
  volume    = {34},
  abstract  = {The research access/impact problem arises because journal articles are not accessible to all of their would-be users; hence, they are losing potential research impact. The solution is to make all articles open access (OA, i.e., accessible online, free for all). OA articles have significantly higher citation impact than non-OA articles. There are two roads to OA: the “golden” road (publish your article in an OA journal) and the “green” road (publish your article in a non-OA journal but also self-archive it in an OA archive). About 10% of journals are gold, but over 90% are already green (i.e., they have given their authors the green light to self-archive); yet only about 10–20% of articles have been self-archived. To reach 100% OA, self-archiving needs to be mandated by researchers’ employers and funders, as they are now increasingly beginning to do},
  doi       = {10.1080/00987913.2008.10765150},
  file      = {2008_Harnad_36.pdf:by-author/H/Harnad/2008_Harnad_36.pdf:PDF},
  keywords  = {Article Impatc; Citation Counts; Open Access},
  owner     = {saulius},
  publisher = {Informa UK Limited},
  timestamp = {2016.10.16},
  creationdate = {2016-10-16T00:00:00},
  url       = {http://dx.doi.org/10.1080/00987913.2008.10765150},
}

@Article{Harner2003,
  author    = {E. James Harner and Harshinder Singh and Shenggiao Li and Jun Tan},
  title     = {Computational Challenges in Computing Nearest Neighbor Estimates of Entropy for Large Molecules},
  year      = {2003},
  abstract  = {Entropy is a statistical thermodynamic property of molecules; its evaluation is important for studying the properties of biological molecules (such as peptides, proteins, and DNA molecules) and chemical molecules. Entropy evaluation is also important in drug designs and for investigating the effect of toxins on human skin. The entropy of a molecule depends mainly on random fluctuations in its torsional (also called the rotational or dihedral) angles. The traditional approach assumed a multivariate normal distribution for the torsional angles of large molecules (Karplus and Kushik, Macromolecules, 1981). However, the assumption of normality is not valid in many situations, particularly when there are large fluctuations in the tor- sional angles. Demchuk and Singh (2001) introduced a circular probability approach to model- ing torsional angles in molecules and illustrated the modeling of the torsional angle of methanol using von Mises distributions. A bathtub shaped probability distribu- tion was derived for the potential energy of the methanol molecule. Singh et al. (2002) introduced a bivariate circular model, which is a natural torus version of the bivariate normal distribution to which it reduces when the fluctuations in the angles are small. The marginal distributions are symmetric and are either unimodal or bimodal. This model was used for modeling two angles of a pentapeptide. In general, the torsional angles can have arbitrary shapes and macromolecules have a large number of torsional angles, which are interdependent. Thus a nonparametric approach appears to be a natural choice for entropy estimation of large molecules. However, entropy evaluation using histogram and kernel density estimates also has problems in high dimensions. Estimates of entropy based on nearest neighbor distances between sample points (Kozachenko and Leonenko (1987)) and estimates of entropy based on k th nearest neighbor distances (Singh et al. (2003)) offer hope for estimating entropy for large molecules. However, evaluating nearest neighbor distances is computationally chal- lenging when the number of torsional angles is large and the data obtained using molecular dynamic simulations on the molecule is huge. We discuss computational approaches for obtaining estimates of entropy based on nearest neighbor distances. Our approaches use Rmpi to parallelize n2 and n ln n k th nearest neighbor algo- rithms, where n is the number of dynamic simulations. We illustrate this approach using data on torsional angles of some large molecules.},
  file      = {:by-author/H/Harner/2003_Harner.pdf:PDF},
  keywords  = {Entropy},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Manuscript{Har-Peled2001,
  author    = {Har-Peled, Sariel},
  title     = {A Practical Approach for Computing the Diameter of a Point Set},
  year      = {2001},
  keywords  = {Algorithms; Computer Science (CS); Set Diameter},
  abstract  = {We present an approximation algorithm for computing the diameter of a point-set in d-dimensions. The new algorithm is sensitive to the “hardness” of computing the diameter of the given input, and for most inputs it is able to compute the exact diameter extremely fast. The new algorithm is simple, robust, has good empirical performance, and can be implemented quickly. As such, it seems to be the algorithm of choice in practice for computing/approximating the diameter.},
  file      = {:by-author/H/Har-Peled/2001_Har-Peled.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@InCollection{Harries2008,
  author    = {Daniel Harries and Jörg Rösgen},
  booktitle = {Biophysical Tools for Biologists, Volume One: In Vitro Techniques},
  publisher = {Academic Press},
  title     = {A Practical Guide on How Osmolytes Modulate Macromolecular Properties},
  year      = {2008},
  chapter   = {chapter 22},
  editor    = {John J. Correia and H. William Detrich, III},
  pages     = {679--735},
  series    = {Methods in Cell Biology},
  volume    = {84},
  abstract  = {Osmolytes are a class of compounds ubiquitously used by living organisms to respond to cellular stress or to fine-tune molecular properties in the cell. These compounds are also highly useful in vitro. In this chapter, we give an overview of the possible uses of osmolytes in the laboratory, and how we can investigate and understand their modes of action. Experimental procedures are discussed with a specific emphasis on osmolyte-related aspects and on the theoretical aspects that are important to both introductory and more advanced interpretations of such experiments.},
  doi       = {10.1016/S0091-679X(07)84022-2},
  file      = {2008_Harries_679.pdf:by-author/H/Harries/2008_Harries_679.pdf:PDF},
  issn      = {0091-679X},
  keywords  = {Solution Theory; Staistical Mechanics},
  owner     = {saulius},
  timestamp = {2015.03.13},
  creationdate = {2015-03-13T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/S0091679X07840222},
}

@Article{Harris2005,
  author    = {Harris, Sarah A and Sands, Zara A and Laughton, Charles A},
  journal   = {Biophysical journal},
  title     = {Molecular dynamics simulations of duplex stretching reveal the importance of entropy in determining the biomechanical properties of DNA.},
  year      = {2005},
  pages     = {1684--91},
  volume    = {88},
  abstract  = {Advances in nanomanipulation techniques have made it possible to measure the response of an individual biomolecule to a force applied in the laboratory. Experiments that stretch a single molecule of duplex DNA have been difficult to interpret theoretically, particularly as the major changes in molecular structure caused by the force cannot be measured. In principle, computer simulation can calculate these conformational changes in atomic level detail, but to date such studies have failed to reproduce the experimental data due to the computational expense of the calculations. Here we show that a combination of molecular modeling and statistical physics can be used successfully to understand the stretching behavior of DNA. Our simulations provide new information about the dynamics of DNA denaturation under force in atomic level detail and also show the importance of entropy in determining biomechanical properties in general.},
  file      = {2005_Harris_1684.pdf:by-author/H/Harris/2005_Harris_1684.pdf:PDF;:by-author/H/Harris/2005_Harris_1684.war:WAR archive},
  groups    = {sg/applications},
  keywords  = {Poisson-Boltzmann eq; Protein Physics; Solvatation},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Manuscript{Harrison2002,
  author    = {N. M. Harrison},
  title     = {An Introduction to Density Functional Theory},
  year      = {2002},
  keywords  = {Density Functional Theory (DFT)},
  url       = {http://www.ch.ic.ac.uk/harrison/Teaching/DFT_NATO.pdf},
  file      = {2002_Harrison.pdf:by-author/H/Harrison/2002_Harrison.pdf:PDF},
  owner     = {saulius},
  timestamp = {2014.10.21},
  creationdate = {2014-10-21T00:00:00},
}

@Article{Harrison2016,
  author    = {Harrison, William T. A. and Simpson, Jim and Stoeckli-Evans, Helen and Tiekink, Edward R. T. and Van Meervelt, Luc and Weil, Matthias},
  journal   = {IUCrData},
  title     = {The birth of {IUCrData}},
  year      = {2016},
  issn      = {2414-3146},
  month     = {Jan},
  number    = {1},
  volume    = {1},
  doi       = {10.1107/s2414314615023172},
  file      = {:by-author/H/Harrison/2016_Harrison_e1.pdf:PDF},
  owner     = {andrius},
  publisher = {International Union of Crystallography (IUCr)},
  timestamp = {2016.02.17},
  creationdate = {2016-02-17T00:00:00},
  url       = {http://dx.doi.org/10.1107/S2414314615023172},
}

@Article{Harrison2010,
  author    = {William T. A. Harrison and Jim Simpson and Matthias Weil},
  journal   = {Acta Crystallographica Section E},
  title     = {Editorial},
  year      = {2010},
  pages     = {e1-e2},
  volume    = {66},
  doi       = {10.1107/S1600536809051757},
  file      = {:by-author/H/Harrison/2010_Harrison_e1.pdf:PDF},
  owner     = {andrius},
  timestamp = {2013.04.25},
  creationdate = {2013-04-25T00:00:00},
}

@Article{Hart2003,
  author    = {Hart},
  title     = {Robert Hart 1997: The Case for Patent Protection for Computer Program-Related Inventions},
  year      = {2003},
  abstract  = {Patent lawyers try to create the impression that the United States introduced software patents after a conscious, public-opinion based debate. One of the most outspoken pro software patent activists at the European Commission, Robert Hart, argued the case in 1997 by misrepresenting the positions of some major patent-critical voices as being pro software patent. Hart later co-authored an “independent study” at the order of the European Commission. Both use approximately the same methodology.},
  file      = {:by-author/H/Hart/2003_Hart.pdf:PDF},
  keywords  = {Patentai; Teise},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Hart2007,
  author    = {Hart, Gus L. W.},
  journal   = {Nat Mater},
  title     = {Where are nature's missing structures?},
  year      = {2007},
  issn      = {1476-1122},
  pages     = {941--945},
  volume    = {6},
  abstract  = {Our society’s environmental and economic progress depends on the development of high-performance materials such as lightweight alloys, high-energy-density battery materials, recyclable motor vehicle and building components, and energy-efficient lighting. Meeting these needs requires us to understand the central role of crystal structure in a material’s properties. Despite more than 50 years of progress in first-principles calculations, it is still impossible in most materials to infer ground-state properties purely from a knowledge of their atomic components—a situation described as ‘scandalous’ in the well-known essay by Maddox1. Many methods attempt to predict crystal structures and compound stability, but here I take a different tack—to infer the existence of structures on the basis of combinatorics and geometric simplicity2. The method identifies ‘least random’ structures, for which the energy is an extremum (maximum or minimum). Although the key to the generic nature of the approach is energy minimization, the extrema are found in a chemistry-independent way.},
  comment   = {10.1038/nmat2057},
  doi       = {10.1038/nmat2057},
  file      = {2007_Hart_941.pdf:by-author/H/Hart/2007_Hart_941.pdf:PDF},
  groups    = {sg/Crystal structure prediction},
  owner     = {saulius},
  publisher = {Nature Publishing Group},
  timestamp = {2015.06.09},
  creationdate = {2015-06-09T00:00:00},
  url       = {http://dx.doi.org/10.1038/nmat2057},
}

@Presentation{Hartig2009,
  author    = {Olaf Hartig},
  title     = {Querying Linked Data with SPARQL},
  year      = {2009},
  file      = {:./by-author/H/Hartig/2009_Hartig_slides.pdf:PDF},
  owner     = {antanas},
  timestamp = {2014.01.29},
  creationdate = {2014-01-29T00:00:00},
  url       = {http://www.slideshare.net/olafhartig/querying-linked-data-with-sparql},
}

@Presentation{Hartman-Baker2004,
  author       = {Rebecca Hartman-Baker},
  title        = {Using OpenMP},
  year         = {2004},
  organization = {Oak Ridge and National Laboratory},
  file         = {:by-author/H/Hartman-Baker/2004_Hartman-Baker.pdf:PDF},
  owner        = {saulius},
  timestamp = {2013.08.11},
  creationdate = {2013-08-11T00:00:00},
}

@Article{Hartmann1998a,
  author    = {Erich Hartmann},
  journal   = {The Visual Computer},
  title     = {A marching method for the triangulation of surfaces},
  year      = {1998},
  pages     = {95--108},
  volume    = {14},
  abstract  = {All surfaces that can be described by collections of equations, especially the parametric ones, can be treated uniformly as implicit surfaces. The idea of numerical implicitization makes this possible. We introduce a marching method for the triangulation of implicit surfaces. The method produces coherent nets of triangles, even for sets of intersecting surface patches.},
  file      = {1998_Hartmann_95.pdf:by-author/H/Hartmann/1998_Hartmann_95.pdf:PDF},
  keywords  = {Algorithms; Triangulation},
  owner     = {saulius},
  timestamp = {2014.10.21},
  creationdate = {2014-10-21T00:00:00},
  url       = {http://www.afhalifax.ca/magazine/wp-content/sciences/EmpilementDeDisques/delaunaycourbe/TriangulationImpliciteSurface/hartmann.pdf},
}

@Article{Hartmann1998,
  author    = {Michael Hartmann and Merz, Jr., Kenneth M. and Rudi van Eldik and Timothy Clark},
  journal   = {J. Mol. Model.},
  title     = {The Important Role of Active Site Water in the Catalytic Mechanism of Human Carbonic Anhydrase II - A Semiempirical MO Approach to the Hydration of CO$_2$},
  year      = {1998},
  pages     = {355--365},
  volume    = {4},
  abstract  = {The approach of CO2 to a series of active site model complexes of human carbonic anhydrase II (HCAII) and its catalytic hydration to bicarbonate anion have been investigated using semiempirical MO theory (AM1). The results show that direct nucleophilic attack of zinc-bound hydroxide to the substrate carbon occurs in each model system. Further rearrangement of the bicarbonate complex thus formed via a rotation-like movement of the bicarbonate ligand can only be found in active site model systems that include at least one additional water molecule. Further refinement of the model complex by adding a methanol molecule to mimic Thr-199 makes this process almost activationless. The formation of the final bicarbonate complex by an internal (intramolecular) proton transfer is only possible in the simplest of all model systems, namely {[Im3Zn(OH)]+·CO2}. The energy of activation for this process, however, is 36.8 kcal·mol–1 and thus too high for enzymatic catalysis. Therefore, we conclude that within the limitations of the model systems presented and the level of theory employed, the overall mechanism for the formation of the bicarbonate complex comprises an initial direct nucleophilic attack of zinc-bound hydroxide to carbon dioxide followed by a rotation-like rearrangement of the bicarbonate ligand via a penta-coordinate Zn2+ transition state structure, including the participation of an extra active site water molecule.},
  file      = {1998_Hartmann_355.pdf:by-author/H/Hartmann/1998_Hartmann_355.pdf:PDF},
  groups    = {sg/hCA2},
  keywords  = {Carbonic Anhydrases},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Hashimoto2005,
  author    = {Hashimoto, Hiroshi and Shimizu, Toshiyuki and Imasaki, Tsuyoshi and Kato, Matsuri and Shichijo, Naoki and Kita, Keiko and Sato, Mamoru},
  journal   = {The Journal of biological chemistry},
  title     = {Crystal structures of type II restriction endonuclease EcoO109I and its complex with cognate DNA.},
  year      = {2005},
  pages     = {5605--10},
  volume    = {280},
  abstract  = {EcoO109I is a type II restriction endonuclease that recognizes the DNA sequence of RGGNCCY. Here we describe the crystal structures of EcoO109I and its complex with DNA. A comparison of the two structures shows that the catalytic domain moves drastically to capture the DNA. One metal ion and two water molecules are observed near the active site of the DNA complex. The metal ion is a Lewis acid that stabilizes the pentavalent phosphorus atom in the transition state. One water molecule, activated by Lys-126, attacks the phosphorus atom in an S(N)2 mechanism, whereas the other water interacts with the 3'-leaving oxygen to donate a proton to the oxygen. EcoO109I is similar to EcoRI family enzymes in terms of its DNA cleavage pattern and folding topology of the common motif in the catalytic domain, but it differs in the manner of DNA recognition. Our findings propose a novel classification of the type II restriction endonucleases and lead to the suggestion that EcoO109I represents a new subclass of the EcoRI family.},
  file      = {:by-author/H/Hashimoto/2005_Hashimoto_5605.pdf:PDF;:by-author/H/Hashimoto/2004_Hashimoto_5605.pdf:PDF;2005_Hashimoto_5605manuscript.pdf:by-author/H/Hashimoto/2005_Hashimoto_5605manuscript.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Hassell2007,
  author    = {Hassell, Anne M. and An, Gang and Bledsoe, Randy K. and Bynum, Jane M. and Carter, 3rd, H. Luke and Deng, Su-Jun J. and Gampe, Robert T. and Grisard, Tamara E. and Madauss, Kevin P. and Nolte, Robert T. and Rocque, Warren J. and Wang, Liping and Weaver, Kurt L. and Williams, Shawn P. and Wisely, G. Bruce and Xu, Robert and Shewchuk, Lisa M.},
  journal   = {Acta crystallographica. Section D, Biological crystallography},
  title     = {Crystallization of protein-ligand complexes.},
  year      = {2007},
  pages     = {72--9},
  volume    = {63},
  abstract  = {Obtaining diffraction-quality crystals has long been a bottleneck in solving the three-dimensional structures of proteins. Often proteins may be stabilized when they are complexed with a substrate, nucleic acid, cofactor or small molecule. These ligands, on the other hand, have the potential to induce significant conformational changes to the protein and ab initio screening may be required to find a new crystal form. This paper presents an overview of strategies in the following areas for obtaining crystals of protein-ligand complexes: (i) co-expression of the protein with the ligands of interest, (ii) use of the ligands during protein purification, (iii) cocrystallization and (iv) soaks.},
  doi       = {10.1107/S0907444906047020},
  file      = {:by-author/H/Hassell/2007_Hassell_72.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Hastings2011,
  author    = {Janna Hastings and Leonid Chepelev and Egon Willighagen and Nico Adams and Christoph Steinbeck and Michel Dumontier},
  journal   = {PLoS ONE},
  title     = {The Chemical Information Ontology: Provenance and Disambiguation for Chemical Data on the Biological Semantic Web},
  year      = {2011},
  pages     = {e25513},
  volume    = {6},
  doi       = {10.1371/journal.pone.0025513},
  file      = {:by-author/H/Hastings/2011_Hastings_e25513.pdf:PDF},
  keywords  = {Chemical Ontologies; Computer Languages; Data Management; Ontologies; Semantics; Software},
  owner     = {saulius},
  timestamp = {2014.01.21},
  creationdate = {2014-01-21T00:00:00},
  url       = {http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0025513},
}

@Article{Hatch1985,
  author    = {Hatch, Dorian M. and Stokes, Harold T.},
  journal   = {Phys. Rev. B},
  title     = {Practical algorithm for identifying subgroups of space groups},
  year      = {1985},
  pages     = {2908--2912},
  volume    = {31},
  abstract  = {The problem of identifying subgroups G’ of a space group G with respect to a conventional listing is considered. The properties of space groups and subgroups are given in terms of an algebraic rather than a geometric description. In this algebraic description, G’ is equivalent to one of the standard listings through a similarity transformation consisting of a linear unimodular component and a translation. A general algorithm is presented to determine which standard listing corresponds to subgroup G’. The algorithm is applied to a specific example, a subgroup of D63d.},
  doi       = {10.1103/PhysRevB.31.2908},
  file      = {1985_Hatch_2908.pdf:by-author/H/Hatch/1985_Hatch_2908.pdf:PDF},
  issue     = {5},
  keywords  = {Algorithms; Spacegroups; Symmetry},
  numpages  = {0},
  owner     = {saulius},
  publisher = {American Physical Society},
  timestamp = {2015.06.15},
  creationdate = {2015-06-15T00:00:00},
  url       = {http://link.aps.org/doi/10.1103/PhysRevB.31.2908},
}

@Article{Haurwitz2010,
  author    = {Haurwitz, Rachel E. and Jinek, Martin and Wiedenheft, Blake and Zhou, Kaihong and Doudna, Jennifer A.},
  journal   = {Science (New York, N.Y.)},
  title     = {Sequence- and structure-specific RNA processing by a CRISPR endonuclease.},
  year      = {2010},
  pages     = {1355--8},
  volume    = {329},
  abstract  = {Many bacteria and archaea contain clustered regularly interspaced short palindromic repeats (CRISPRs) that confer resistance to invasive genetic elements. Central to this immune system is the production of CRISPR-derived RNAs (crRNAs) after transcription of the CRISPR locus. Here, we identify the endoribonuclease (Csy4) responsible for CRISPR transcript (pre-crRNA) processing in Pseudomonas aeruginosa. A 1.8 angstrom crystal structure of Csy4 bound to its cognate RNA reveals that Csy4 makes sequence-specific interactions in the major groove of the crRNA repeat stem-loop. Together with electrostatic contacts to the phosphate backbone, these enable Csy4 to bind selectively and cleave pre-crRNAs using phylogenetically conserved serine and histidine residues in the active site. The RNA recognition mechanism identified here explains sequence- and structure-specific processing by a large family of CRISPR-specific endoribonucleases.},
  file      = {:by-author/H/Haurwitz/2010_Haurwitz_1355.pdf:PDF},
  groups    = {sg/CRISPR-Cas},
  keywords  = {CRISPR},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Hausmann1973,
  author    = {Hausmann, R.},
  journal   = {Annual review of microbiology},
  title     = {The genetics of T-odd phages.},
  year      = {1973},
  pages     = {51--67},
  volume    = {27},
  file      = {:by-author/H/Hausmann/1973_Hausmann_51.pdf:PDF},
  keywords  = {{gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Hautier2011,
  author    = {Geoffroy Hautier and Chris Fischer and Virginie Ehrlacher and Anubhav Jain and Gerbrand Ceder},
  journal   = {Inorg. Chem.},
  title     = {Data Mined Ionic Substitutions for the Discovery of New Compounds},
  year      = {2011},
  pages     = {656--663},
  volume    = {50},
  abstract  = {The existence of new compounds is often postulated by solid state chemists by replacing an ion in the crystal structure of a known compound by a chemically similar ion. In this work, we present how this new compound discovery process through ionic substitutions can be formulated in a mathematical framework. We propose a probabilistic model assessing the likelihood for ionic species to substitute for each other while retaining the crystal structure. This model is trained on an experimental database of crystal structures, and can be used to quantitatively suggest novel compounds and their structures. The predictive power of the model is demonstrated using cross-validation on quaternary ionic compounds. The different substitution rules embedded in the model are analyzed and compared to some of the traditional rules used by solid state chemists to propose new compounds (e.g., ionic size).},
  doi       = {10.1021/ic102031h},
  file      = {2011_Hautier_656.pdf:by-author/H/Hautier/2011_Hautier_656.pdf:PDF},
  keywords  = {Density Functional Theory (DFT)},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Hautier2010,
  author    = {Geoffroy Hautier and Christopher C. Fischer and Anubhav Jain and Tim Mueller and Gerbrand Ceder},
  journal   = {Chem. Mater.},
  title     = {Finding Nature’s Missing Ternary Oxide Compounds Using Machine Learning and Density Functional Theory},
  year      = {2010},
  pages     = {3762--3767},
  volume    = {22},
  abstract  = {Finding new compounds and their crystal structures is an essential step to new materials discoveries. We demonstrate how this search can be accelerated using a combination of machine learning techniques and high-throughput ab initio computations. Using a probabilistic model built on an experimental crystal structure database, novel compositions that are most likely to form a compound, and their most-probable crystal structures, are identified and tested for stability by ab initio computations. We performed such a large-scale search for new ternary oxides, discovering 209 new compounds with a limited computational budget. A list of these predicted compounds is provided, and we discuss the chemistries in which high discovery rates can be expected.},
  doi       = {10.1021/cm100795d},
  file      = {2010_Hautier_3762.pdf:by-author/H/Hautier/2010_Hautier_3762.pdf:PDF},
  keywords  = {Density Functional Theory (DFT)},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Hawizy2011,
  author    = {Hawizy, Lezan and Jessop, David and Adams, Nico and Murray-Rust, Peter},
  journal   = {Journal of Cheminformatics},
  title     = {ChemicalTagger: A tool for semantic text-mining in chemistry},
  year      = {2011},
  issn      = {1758-2946},
  pages     = {17},
  volume    = {3},
  abstract  = {BACKGROUND:The primary method for scientific communication is in the form of published scientific articles and theses which use natural language combined with domain-specific terminology. As such, they contain free owing unstructured text. Given the usefulness of data extraction from unstructured literature, we aim to show how this can be achieved for the discipline of chemistry. The highly formulaic style of writing most chemists adopt make their contributions well suited to high-throughput Natural Language Processing (NLP) approaches.RESULTS:We have developed the ChemicalTagger parser as a medium-depth, phrase-based semantic NLP tool for the language of chemical experiments. Tagging is based on a modular architecture and uses a combination of OSCAR, domain-specific regex and English taggers to identify parts-of-speech. The ANTLR grammar is used to structure this into tree-based phrases. Using a metric that allows for overlapping annotations, we achieved machine-annotator agreements of 88.9% for phrase recognition and 91.9% for phrase-type identification (Action names).CONCLUSIONS:It is possible parse to chemical experimental text using rule-based techniques in conjunction with a formal grammar parser. ChemicalTagger has been deployed for over 10,000 patents and has identified solvents from their linguistic context with >99.5% precision.},
  doi       = {10.1186/1758-2946-3-17},
  file      = {2011_Hawizy_3\:17:by-author/H/Hawizy/2011_Hawizy_3\:17.pdf:PDF},
  keywords  = {Data Processing; Natural Language Processing},
  owner     = {saulius},
  pubmedid  = {21575201},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://www.jcheminf.com/content/3/1/17},
}

@Article{Hawkins1980,
  author    = {Donald T. Hawkins},
  journal   = {Acta Cryst. A},
  title     = {Crystallographic Literature: A Bibllometrie and Citation Analysis},
  year      = {1980},
  pages     = {475--482},
  volume    = {36},
  abstract  = {The literature of crystallography was studied by publication of journal articles on crystallography bibliometric analysis using the Lockheed DIALOG...},
  file      = {:by-author/H/Hawkins/1980_Hawkins_475.pdf:PDF},
  groups    = {sg/Bibliometrics},
  keywords  = {Bibliometry; Scientific Publications},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@InCollection{Hawthorne2011,
  author    = {James Hawthorne},
  booktitle = {The Continuum Companion to the Philosophy of Science},
  publisher = {Continuum},
  title     = {Bayesian Confirmation Theory},
  year      = {2011},
  pages     = {197--217},
  file      = {:by-author/H/Hawthorne/2011_Hawthorne_197.pdf:PDF},
  groups    = {sg/Bayesian},
  keywords  = {Bayesian Statistics},
  owner     = {saulius},
  timestamp = {2012.09.30},
  creationdate = {2012-09-30T00:00:00},
}

@Manuscript{Hawthorne1970,
  author      = {James Hawthorne},
  title       = {A Better Bayesian Convergence Theorem},
  year        = {1970},
  institution = {University of Oklahoma},
  keywords    = {Bayesian Statistics},
  abstract    = {Any inductive logic worthy of the name ought to supply a measure of evidential support that, as a reasonable amount of evidence accumulates, tends to indicate that false hypotheses are probably false and that true hypotheses are probably true. Is there an inductive logic that can be shown to possess this delightful property? I will argue that a proper construal of Bayesian confirmation provides just this kind of truth-value indicating measure. I aim to convince you of this by explicating a so-called Bayesian Convergence Theorem. The theorem will show that under some rather sensible conditions, if a hypothesis h is false, its Bayesian posterior probabilities will very probably approach the falsehood indicating value 0 as evidence accumulates; and as the posterior probabilities of false competitors fall, the posterior probability of the true hypothesis heads towards 1.},
  email       = {hawthorne@ou.edu},
  file        = {:by-author/H/Hawthorne/1970_Hawthorne.pdf:PDF},
  groups      = {sg/Bayesian},
  owner       = {saulius},
  timestamp = {2012.09.30},
  creationdate = {2012-09-30T00:00:00},
}

@Article{Hayes2008,
  author     = {Hayes, Brian},
  journal    = {Commun. ACM},
  title      = {Cloud Computing},
  year       = {2008},
  issn       = {0001-0782},
  pages      = {9--11},
  volume     = {51},
  address    = {New York, NY, USA},
  doi        = {10.1145/1364782.1364786},
  file       = {:by-author/H/Hayes/2008_Hayes_9.pdf:PDF},
  issue_date = {July 2008},
  owner      = {saulius},
  publisher  = {ACM},
  timestamp = {2012.10.03},
  creationdate = {2012-10-03T00:00:00},
  url        = {http://doi.acm.org/10.1145/1364782.1364786},
}

@Manuscript{Hazen2016,
  author    = {Robert Hazen},
  title     = {PROV301 (formerly UNIV301): Great Ideas in Science},
  year      = {2016},
  comment   = {Course project for non-science students},
  file      = {2016_Hazen.doc:by-author/H/Hazen/2016_Hazen.doc:Word},
  owner     = {saulius},
  timestamp = {2016.05.14},
  creationdate = {2016-05-14T00:00:00},
}

@Article{Hazen2007,
  author    = {Hazen, R. M. and Griffin, P. L. and Carothers, J. M. and Szostak, J. W.},
  journal   = {Proceedings of the National Academy of Sciences},
  title     = {Functional information and the emergence of biocomplexity},
  year      = {2007},
  issn      = {1091-6490},
  month     = {May},
  number    = {Supplement 1},
  pages     = {8574--8581},
  volume    = {104},
  abstract  = {Complex emergent systems of many interacting components, including complex biological systems, have the potential to perform quantifiable functions. Accordingly, we define “functional information,” I(Ex), as a measure of system complexity. For a given system and function, x (e.g., a folded RNA sequence that binds to GTP), and degree of function, Ex (e.g., the RNA–GTP binding energy), I(Ex) = −log2[F(Ex)], where F(Ex) is the fraction of all possible configurations of the system that possess a degree of function ≥ Ex. Functional information, which we illustrate with letter sequences, artificial life, and biopolymers, thus represents the probability that an arbitrary configuration of a system will achieve a specific function to a specified degree. In each case we observe evidence for several distinct solutions with different maximum degrees of function, features that lead to steps in plots of information versus degree of function.},
  doi       = {10.1073/pnas.0701744104},
  file      = {2007_Hazen_8574.pdf:by-author/H/Hazen/2007_Hazen_8574.pdf:PDF},
  keywords  = {Artificial Life; Complexity; Functional Information; Information Theory},
  owner     = {saulius},
  publisher = {Proceedings of the National Academy of Sciences},
  timestamp = {2016.04.26},
  creationdate = {2016-04-26T00:00:00},
  url       = {http://dx.doi.org/10.1073/pnas.0701744104},
}

@Article{Hazen2008,
  author    = {Hazen, R. M. and Papineau, D. and Bleeker, W. and Downs, R. T. and Ferry, J. M. and McCoy, T. J. and Sverjensky, D. A. and Yang, H.},
  journal   = {American Mineralogist},
  title     = {Mineral evolution},
  year      = {2008},
  pages     = {1693--1720},
  volume    = {93},
  file      = {:by-author/H/Hazen/2008_Hazen_1693.pdf:PDF},
  owner     = {saulius},
  timestamp = {2013.09.19},
  creationdate = {2013-09-19T00:00:00},
  url       = {http://www.geo.arizona.edu/xtal/group/pdf/AM93_1693.pdf},
}

@InBook{Hazen2000,
  author    = {Hazen, R.M. abd Downs, R.T. and Prewitt, C.T.},
  chapter   = {Principles of comparative crystal chemistry},
  editor    = {Robert M. Hazen and Robert T. Downs},
  pages     = {1--33},
  publisher = {Mineralogical Society of America, Washington DC},
  title     = {High-Temperature and High-Pressure Crystal Chemistry},
  year      = {2000},
  volume    = {41},
  abstract  = {The art and science of crystal chemistry lies in the interpretation of three-dimensional electron and nuclear density data from diffraction experiments in terms of interatomic bonding and forces. With the exception of meticulous high-resolution studies (e.g. Downs 1983, Downs et al. 1985, Zuo et al. 1999), these density data reveal little more than the possible atomic species and their distributions within the unit cell. Other parameterizations of crystal structures, including atomic radii, bond distances, packing indices, polyhedral representations, and distortion indices, are model-dependent. These secondary parameters have proven essential to understanding structural systematics, but they are all based on interpretations of the primary diffraction data.},
  file      = {:by-author/H/Hazen/2000_Hazen_1.pdf:PDF},
  journal   = {Reviews in Mineralogy and Geochemistry},
  owner     = {saulius},
  timestamp = {2013.09.19},
  creationdate = {2013-09-19T00:00:00},
  url       = {http://www.geo.arizona.edu/xtal/group/pdf/RIM41_1.pdf},
}

@InProceedings{He2006,
  author       = {Huahai He and Ambuj K. Singh},
  booktitle    = {Proceedings of the 22nd International Conference on Data Engineering (ICDE’06)},
  title        = {Closure-Tree: An Index Structure for Graph Queries},
  year         = {2006},
  organization = {The University of California and Santa Barbara},
  publisher    = {IEEE},
  abstract     = {Graphs have become popular for modeling structured data. As a result, graph queries are becoming common and graph indexing has come to play an essential role in query processing. We introduce the concept of a graph closure, a generalized graph that represents a number of graphs. Our indexing technique, called Closure-tree, orga- nizes graphs hierarchically where each node summarizes its descendants by a graph closure. Closure-tree can efficiently support both subgraph queries and similarity queries. Sub- graph queries find graphs that contain a specific subgraph, whereas similarity queries find graphs that are similar to a query graph. For subgraph queries, we propose a tech- nique called pseudo subgraph isomorphism which approxi- mates subgraph isomorphism with high accuracy. For sim- ilarity queries, we measure graph similarity through edit distance using heuristic graph mapping methods. We im- plement two kinds of similarity queries: K-NN query and range query. Our experiments on chemical compounds and synthetic graphs show that for subgraph queries, Closure- tree outperforms existing techniques by up to two orders of magnitude in terms of candidate answer set size and index size. For similarity queries, our experiments validate the quality and efficiency of the presented algorithms.},
  file         = {:by-author/H/He/2006_He.pdf:PDF},
  owner        = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{He2005,
  author    = {He, Molly M. and Smith, Annemarie Stroustrup and Oslob, Johan D. and Flanagan, William M. and Braisted, Andrew C. and Whitty, Adrian and Cancilla, Mark T. and Wang, Jun and Lugovskoy, Alexey A. and Yoburn, Josh C. and Fung, Amy D. and Farrington, Graham and Eldredge, John K. and Day, Eric S. and Cruz, Leslie A. and Cachero, Teresa G. and Miller, Stephan K. and Friedman, Jessica E. and Choong, Ingrid C. and Cunningham, Brian C.},
  journal   = {Science (New York, N.Y.)},
  title     = {Small-molecule inhibition of TNF-alpha.},
  year      = {2005},
  pages     = {1022--5},
  volume    = {310},
  abstract  = {We have identified a small-molecule inhibitor of tumor necrosis factor alpha (TNF-alpha) that promotes subunit disassembly of this trimeric cytokine family member. The compound inhibits TNF-alpha activity in biochemical and cell-based assays with median inhibitory concentrations of 22 and 4.6 micromolar, respectively. Formation of an intermediate complex between the compound and the intact trimer results in a 600-fold accelerated subunit dissociation rate that leads to trimer dissociation. A structure solved by x-ray crystallography reveals that a single compound molecule displaces a subunit of the trimer to form a complex with a dimer of TNF-alpha subunits.},
  file      = {:by-author/H/He/2005_He_1022.pdf:PDF},
  keywords  = {Drug Design; TNF Alpha Inhibitor},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Presentation{He2011,
  author    = {Yun (Helen) He},
  title     = {Introduction to OpenMP},
  year      = {2011},
  file      = {:by-author/H/He/2011_He.pdf:PDF},
  owner     = {saulius},
  timestamp = {2013.07.02},
  creationdate = {2013-07-02T00:00:00},
}

@Article{He2007,
  author    = {He, Yao and Yao, De-Qiang and Gu, Yuan-Xin and Lin, Zheng-Jiong and Zheng, Chao-De and Fan, Hai-Fu},
  journal   = {Acta crystallographica. Section D, Biological crystallography},
  title     = {OASIS and molecular-replacement model completion.},
  year      = {2007},
  pages     = {793--9},
  volume    = {63},
  abstract  = {A method of dual-space molecular-replacement model completion has been proposed which involves the programs ARP/wARP, REFMAC, OASIS and DM. OASIS is used in reciprocal space for phase refinement based on models built by ARP/wARP. For this purpose, the direct-method probability formula of breaking SAD/SIR phase ambiguities has been redefined. During the phase refinement, phi(h)('') in the expression phi(h) = phi(h)('') +/- |Delta phi(h)| is redefined as a reference phase calculated from a randomly selected 5% of the atoms in the current structure model, while |Delta phi(h)| is defined as the absolute difference between the phase of the current model and phi(h)(''). The probability formula P(+)(Delta phi(h)) = (1/2) + (1/2) tanh {sin |Delta phi(h)| x [Sigma (h('))m(h('))m(h - h('))kappa(h,h(')) sin(Phi'(3) + Delta phi(h'best) + Delta phi(h - h'best)) + chi sin delta(h)]} is then used to derive the sign of Delta phi(h). In this way the '0-2pi' phase problem is reduced to a 'plus or minus' sign problem. The redefinition implies that during the refinement phases close to the true values will probably be kept unchanged, while those distant from the true values will probably undergo a large shift. This is the desired property of phase refinement. The procedure has been tested using protein diffraction data without SAD/SIR signals. The results show that dual-space MR-model completion making use of OASIS is much more efficient than that without.},
  doi       = {10.1107/S0907444907023451},
  file      = {:by-author/H/He/2007_He_793.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Presentation{Heath2009,
  author       = {Tom Heath},
  title        = {An Introduction to Linked Data},
  year         = {2009},
  organization = {Platform Division, Talis Information Ltd},
  file         = {2009_Heath_slides.pdf:by-author/H/Heath/2009_Heath_slides.pdf:PDF},
  keywords     = {Data Access Policy; Data Management; Databases; Linked Data; RDF; Scientific Data Dissemination},
  owner        = {saulius},
  timestamp = {2013.12.30},
  creationdate = {2013-12-30T00:00:00},
  url          = {http://tomheath.com/slides/2009-02-austin-linkeddata-tutorial.pdf},
}

@Article{Hefter2005,
  author    = {Glenn Hefter},
  journal   = {Pure Appl. Chem.},
  title     = {Ion solvation in aqueous–organic mixtures},
  year      = {2005},
  pages     = {605--617},
  volume    = {77},
  abstract  = {The importance of ion solvation in determining the properties of electrolyte solutions in aqueous–organic solvent mixtures is discussed. Solubility measurements are shown to be particularly useful for determining the Gibbs energies of transfer of ions between solvents, which reflect differences in the overall solvation of the ions in different solvent mixtures. Solubility measurements can also be used to determine the other thermodynamic parameters of transfer, but such quantities are usually better obtained by more direct methods. The inadequacy of current theories of ion solvation to quantitatively account for the thermo- dynamics of ion transfer is discussed by reference to measurements on some simple model systems. Although donor/acceptor interactions can explain many of the observed effects between pure solvents, the situation is more complex in aqueous–organic mixtures because se- lective solvation and even solvent–solvent interactions may become significant. This is illus- trated by consideration of ion transfer from water to water + t-butanol solutions, where spectacular effects are observed in the enthalpies and entropies and especially in the heat capacities and volumes.},
  doi       = {10.1351/pac200577030605},
  file      = {2005_Hefter_605.pdf:by-author/H/Hefter/2005_Hefter_605.pdf:PDF},
  keywords  = {Ion Hydration; Protein Physics},
  owner     = {saulius},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
  url       = {http://iupac.org/publications/pac/77/3/0605/},
}

@Manuscript{Hehner2016,
  author    = {Eric C. R. Hehner and R. N. S. Horspool},
  title     = {A new representation of the rational numbers for fast easy arithmetic},
  year      = {2016},
  keywords  = {Computer Arithmetic; Computer Languages; Floating Point Numbers; Number Representation; Positional Systems; Rational Numbers},
  url       = {http://www.cs.toronto.edu/~hehner/ratno.pdf},
  file      = {2016_Hehner.pdf:by-author/H/Hehner/2016_Hehner.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.06.13},
  creationdate = {2016-06-13T00:00:00},
}

@Article{Heidelberg2000,
  author    = {Heidelberg, J F and Eisen, J A and Nelson, W C and Clayton, R A and Gwinn, M L and Dodson, R J and Haft, D H and Hickey, E K and Peterson, J D and Umayam, L and Gill, S R and Nelson, K E and Read, T D and Tettelin, H and Richardson, D and Ermolaeva, M D and Vamathevan, J and Bass, S and Qin, H and Dragoi, I and Sellers, P and McDonald, L and Utterback, T and Fleishmann, R D and Nierman, W C and White, O and Salzberg, S L and Smith, H O and Colwell, R R and Mekalanos, J J and Venter, J C and Fraser, C M},
  journal   = {Nature},
  title     = {DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae.},
  year      = {2000},
  pages     = {477--83},
  volume    = {406},
  abstract  = {Here we determine the complete genomic sequence of the gram negative, gamma-Proteobacterium Vibrio cholerae El Tor N16961 to be 4,033,460 base pairs (bp). The genome consists of two circular chromosomes of 2,961,146 bp and 1,072,314 bp that together encode 3,885 open reading frames. The vast majority of recognizable genes for essential cell functions (such as DNA replication, transcription, translation and cell-wall biosynthesis) and pathogenicity (for example, toxins, surface antigens and adhesins) are located on the large chromosome. In contrast, the small chromosome contains a larger fraction (59%) of hypothetical genes compared with the large chromosome (42%), and also contains many more genes that appear to have origins other than the gamma-Proteobacteria. The small chromosome also carries a gene capture system (the integron island) and host 'addiction' genes that are typically found on plasmids; thus, the small chromosome may have originally been a megaplasmid that was captured by an ancestral Vibrio species. The V. cholerae genomic sequence provides a starting point for understanding how a free-living, environmental organism emerged to become a significant human bacterial pathogen.},
  file      = {Heidelberg_2000_477.pdf:by-author/H/Heidelberg/2000_Heidelberg_477.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Heilemann2005,
  author    = {Heilemann, Mike and Margeat, Emmanuel and Kasper, Robert and Sauer, Markus and Tinnefeld, Philip},
  journal   = {Journal of the American Chemical Society},
  title     = {Carbocyanine dyes as efficient reversible single-molecule optical switch},
  year      = {2005},
  issn      = {0002-7863},
  pages     = {3801--3806},
  volume    = {127},
  abstract  = {We demonstrate that commercially available unmodified carbocyanine dyes such as Cy5 (usually excited at 633 nm) can be used as efficient reversible single-molecule optical switch, whose fluorescent state after apparent photobleaching can be restored at room temperature upon irradiation at shorter wavelengths. Ensemble photobleaching and recovery experiments of Cy5 in aqueous solution irradiating first at 633 nm, then at 337, 488, or 532 nm, demonstrate that restoration of absorption and fluorescence strongly depends on efficient oxygen removal and the addition of the triplet quencher -mercaptoethylamine. Single-molecule fluorescence experiments show that individual immobilized Cy5 molecules can be switched optically in milliseconds by applying alternating excitation at 633 and 488 nm between a fluorescent and nonfluorescent state up to 100 times with a reliability of 90\% at room temperature. Because of their intriguing performance, carbocyanine dyes volunteer as a simple alternative for ultrahigh-density optical data storage. Measurements on single donor/acceptor (tetramethylrhodamine/Cy5) labeled oligonucleotides point out that the described light-driven switching behavior imposes fundamental limitations on the use of carbocyanine dyes as energy transfer acceptors for the study of biological processes.},
  doi       = {10.1021/ja044686x},
  file      = {Heilemann et al. - 2005 - Carbocyanine Dyes as Efficient Reversible Single-M.pdf:by-author/H/Heilemann/2005_Heilemann_3801.pdf:application/pdf;ACS Full Text Snapshot:by-author/H/Heilemann/2005_Heilemann_3801.html:text/html},
  groups    = {sg/chemical},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://dx.doi.org/10.1021/ja044686x},
  urldate   = {2015-08-05},
}

@Article{Heinemann1992,
  author    = {Heinemann, U. and Alings, C. and Bansal, M.},
  journal   = {The EMBO journal},
  title     = {Double helix conformation, groove dimensions and ligand binding potential of a G/C stretch in B-DNA.},
  year      = {1992},
  pages     = {1931--9},
  volume    = {11},
  abstract  = {The self-complementary DNA fragment CCGGCGCCGG crystallizes in the rhombohedral space group R3 with unit cell parameters a = 54.07 A and c = 44.59 A. The structure has been determined by X-ray diffraction methods at 2.2 A resolution and refined to an R value of 16.7%. In the crystal, the decamer forms B-DNA double helices with characteristic groove dimensions: compared with B-DNA of random sequence, the minor groove is wide and deep and the major groove is rather shallow. Local base pair geometries and stacking patterns are within the range commonly observed in B-DNA crystal structures. The duplex bears no resemblance to A-form DNA as might have been expected for a sequence with only GC base pairs. The shallow major groove permits an unusual crystal packing pattern with several direct intermolecular hydrogen bonds between phosphate oxygens and cytosine amino groups. In addition, decameric duplexes form quasi-infinite double helices in the crystal by end-to-end stacking. The groove geometries and accessibilities of this molecule as observed in the crystal may be important for the mode of binding of both proteins and drug molecules to G/C stretches in DNA.},
  file      = {:by-author/H/Heinemann/1992_Heinemann_1931.pdf:PDF},
  keywords  = {Conformation; Readout; Struct},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Helal2016,
  author    = {Kazi Yasin Helal and Mateusz Maciejewski and Elisabet Gregori-Puigjané and Meir Glick and Anne Mai Wassermann},
  journal   = {Journal of Chemical Information and Modeling},
  title     = {Public Domain HTS Fingerprints: Design and Evaluation of Compound Bioactivity Profiles from PubChem’s Bioassay Repository},
  year      = {2016},
  note      = {PMID: 26898267},
  number    = {2},
  pages     = {390--398},
  volume    = {56},
  abstract  = {Molecular profiling efforts aim at characterizing the biological actions of small molecules by screening them in hundreds of different biochemical and/or cell-based assays. Together, these assays yield a rich data landscape of target-based and phenotypic effects of the tested compounds. However, submitting an entire compound library to a molecular profiling panel can easily become cost-prohibitive. Here, we make use of historical screening assays to create comprehensive bioactivity profiles for more than 300 000 small molecules. These bioactivity profiles, termed PubChem high-throughput screening fingerprints (PubChem HTSFPs), report small molecule activities in 243 different PubChem bioassays. Although the assays originate from originally independently pursued drug or probe discovery projects, we demonstrate their value as molecular signatures when used in combination. We use these PubChem HTSFPs as molecular descriptors in hit expansion experiments for 33 different targets and phenotypes, showing that, on average, they lead to 27 times as many hits in a set of 1000 chosen molecules as a random screening subset of the same size (average ROC score: 0.82). Moreover, we demonstrate that PubChem HTSFPs retrieve hits that are structurally diverse and distinct from active compounds retrieved by chemical similarity-based hit expansion methods. PubChem HTSFPs are made freely available for the chemical biology research community.},
  doi       = {10.1021/acs.jcim.5b00498},
  eprint    = {http://dx.doi.org/10.1021/acs.jcim.5b00498},
  file      = {2016_Helal_390.pdf:by-author/H/Helal/2016_Helal_390.pdf:PDF},
  keywords  = {Chemical Fingerprints},
  owner     = {saulius},
  timestamp = {2016.07.07},
  creationdate = {2016-07-07T00:00:00},
  url       = {http://dx.doi.org/10.1021/acs.jcim.5b00498},
}

@Article{Helliwell2016,
  author    = {John R. Helliwell},
  journal   = {Postępy Biochemii},
  title     = {Crystallographic raw data, education and refereeing},
  year      = {2016},
  number    = {3},
  pages     = {257--261},
  volume    = {62},
  abstract  = {This article provides an overview of the preservation of raw diffraction data, then addresses the impact on future plans in the education and training of our community with respect to raw diffraction data and its potential reuse, and, thirdly presents the issue of referee access to the underpinning diffraction data and coordinates, as well as the Protein Data Bank Validation Report, in the review process of structural biology articles submitted for publication. Overall I pay tribute to the scientific achievements of Alex Wlodawer, who is also an ardent advocate of the importance of experimental data.},
  file      = {2016_Helliwell_257.pdf:by-author/H/Helliwell/2016_Helliwell_257.pdf:PDF},
  keywords  = {Archiving of Raw Diffraction Data; Combined Training and Education in Biological and Chemical Crystallography; Education Initiatives for the Open Science Era; Neutron Macromolecular Crystallography; Refereeing of Articles Together With Diffraction Data and Coordinates; Synchrotron Radiation Macromolecular Crystallography},
  owner     = {saulius},
  timestamp = {2016.10.05},
  creationdate = {2016-10-05T00:00:00},
  url       = {http://www.postepybiochemii.pl/pdf/3_2016/257-261.pdf},
}

@Manuscript{Helliwell2013,
  author    = {John R. Helliwell},
  title     = {Open access and Evaluation by metrics: IUCr input to ICSU on the two related issues},
  year      = {2013},
  keywords  = {Data Access Policy; Data Management; IUCr; Open Access; Scientific Data Dissemination},
  url       = {http://www.icsti.org/IMG/pdf/ICSTI_input_to_ICSU_re_Open_Access_and_Metrics_JRH_BM_TT_JRHaa.pdf},
  file      = {2013_Helliwell_manuscript.pdf:by-author/H/Helliwell/2013_Helliwell_manuscript.pdf:PDF},
  owner     = {saulius},
  timestamp = {2013.12.30},
  creationdate = {2013-12-30T00:00:00},
}

@Presentation{Hemingway2008,
  author    = {Bruce Hemingway},
  title     = {Fixed-Point Arithmetic},
  year      = {2008},
  file      = {2008_Hemingway.pdf:by-author/H/Hemingway/2008_Hemingway.pdf:PDF},
  keywords  = {Computer Arithmetic; Computer Science (CS); Fixed Point Arithmetic; Real Number Representation},
  owner     = {saulius},
  timestamp = {2015.04.09},
  creationdate = {2015-04-09T00:00:00},
  url       = {http://courses.cs.washington.edu/courses/cse467/08au/pdfs/lectures/11-FixedPointArithmetic.pdf},
}

@Article{Henderson1990,
  author    = {Henderson, Richard},
  journal   = {Proceedings of the Royal Society of London. Series B: Biological Sciences},
  title     = {Cryo-Protection of Protein Crystals against Radiation Damage in Electron and X-Ray Diffraction},
  year      = {1990},
  pages     = {6--8},
  volume    = {241},
  abstract  = {By using the fading of electron diffraction patterns during electron irradiation of protein or other organic crystals as a benchmark to measure destruction of the crystalline atomic arrangement by ionizing radiation, calculations suggest that protein crystals in laboratory X-ray beams might last for about five years when the specimen is cooled to liquid nitrogen temperatures or below. It is suggested that all crystals should be equally stable to X-irradiation at this temperature, as they are to electron irradiation. The calculation, which depends on the assumption that electrons and X-rays are more or less equally damaging to the structure giving rise to the diffraction at very low temperature, supports experimental observations that X-ray diffraction from protein crystals seems to last indefinitely at liquid nitrogen temperatures, even in the most powerful beams available at synchrotron X-ray sources. An attempt is made to explain the relation between the present analysis and other ways of viewing radiation damage.},
  doi       = {10.1098/rspb.1990.0057},
  eprint    = {http://rspb.royalsocietypublishing.org/content/241/1300/6.full.pdf+html},
  file      = {1990_Henderson_6.pdf:by-author/H/Henderson/1990_Henderson_6.pdf:PDF},
  keywords  = {Cryo-cooling; Protein Crystallography; Radiation Damage; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2014.03.24},
  creationdate = {2014-03-24T00:00:00},
  url       = {http://rspb.royalsocietypublishing.org/content/241/1300/6.abstract},
}

@Article{Hendrickson1985,
  author    = {Wayne A. Hendrickson},
  journal   = {Methods in enzymology},
  title     = {Stereochemically Restrained Refinement of Macromolecular Structures},
  year      = {1985},
  pages     = {252--270},
  volume    = {115},
  doi       = {10.1016/0076-6879(85)15021-4},
  file      = {:by-author/H/Hendrickson/1985_Hendrickson_252.pdf:PDF},
  owner     = {andrius},
  timestamp = {2013.04.21},
  creationdate = {2013-04-21T00:00:00},
}

@Article{Hendrickson1979,
  author    = {Wayne A. Hendrickson},
  journal   = {Acta Crystallographica Section A},
  title     = {Transformations to Optimize the Superposition of Similar Structures},
  year      = {1979},
  pages     = {158--163},
  volume    = {35},
  abstract  = {A simple, efficient and general method is described for finding the linear orthogonal transformation to superpose two similar structures given by sets of equivalent points, usually atomic position vectors. Formulae are also given for extracting the independent variables of rotation from the resulting transformation matrix. In addition, general transformations are derived, both in the case of proper rotation and in the case of rotatory inversion, to convert to a molecular frame of reference based on the superposition axis of symmetry.},
  doi       = {10.1107/S0567739479000279},
  file      = {:by-author/H/Hendrickson/1979_Hendrickson_158.pdf:PDF},
  keywords  = {Algorithms; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://scripts.iucr.org/cgi-bin/paper?S0567739479000279},
}

@Article{Hendrickson1980,
  author    = {Wayne A. Hendrickson and John H. Konnert},
  journal   = {Biophys J.},
  title     = {Diffraction analysis of motion in proteins},
  year      = {1980},
  pages     = {645--647},
  volume    = {32},
  abstract  = {Analysis of the x-ray or neutron diffraction from crystals gives only an average picture of the contents of a crystallographic unit cell, the average being over a long time (usually many hours) and the entire lattice. However, this picture can rather accurately define not only the mean atomic positions but also the distribution of displacements from rest positions. These displacements may include components from three main sources: (a) thermal vibration, both of individual atoms and of rigid groups, (b) dynamic disordering among thermally accessible conformational states, and (c) static variations among the structures within different unit cells, either due to lattice imperfections or because of conformational heterogeneity that is frozen in at the experimental temperature. Thus the accumulated spoor of atomic motions is accessible to the diffraction experiment even though the dynamic pathways are not.},
  file      = {1980_Hendrickson_645.pdf:by-author/H/Hendrickson/1980_Hendrickson_645.pdf:PDF},
  owner     = {saulius},
  timestamp = {2013.04.01},
  creationdate = {2013-04-01T00:00:00},
}

@Article{Hendry1962,
  author    = {HENDRY, D. P. and PERRY, A. M.},
  journal   = {Journal of the experimental analysis of behavior},
  title     = {A simple flip-flop circuit.},
  year      = {1962},
  pages     = {442},
  volume    = {5},
  file      = {:by-author/H/HENDRY/1962_HENDRY_442.pdf:PDF},
  keywords  = {Electronics},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Henikoff1992,
  author    = {Henikoff, S. and Henikoff, J. G.},
  journal   = {Proceedings of the National Academy of Sciences of the United States of America},
  title     = {Amino acid substitution matrices from protein blocks.},
  year      = {1992},
  pages     = {10915--9},
  volume    = {89},
  abstract  = {Methods for alignment of protein sequences typically measure similarity by using a substitution matrix with scores for all possible exchanges of one amino acid with another. The most widely used matrices are based on the Dayhoff model of evolutionary rates. Using a different approach, we have derived substitution matrices from about 2000 blocks of aligned sequence segments characterizing more than 500 groups of related proteins. This led to marked improvements in alignments and in searches using queries from each of the groups.},
  file      = {:by-author/H/Henikoff/1992_Henikoff_10915.pdf:PDF},
  keywords  = {Bioinformatics},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@MastersThesis{Henrichs2009,
  author    = {Henrichs, M.R.},
  school    = {TU Delft, Faculty of Electrical Engineering, Mathematics and Computer Science, Department of Parallel and Distributed Systems},
  title     = {A Conceptual Framework for Constructing Distributed Object Libraries using Gellish},
  year      = {2009},
  abstract  = {This master's thesis describes the processes concerned with, and motivations behind the construction of a framework for building distributed object libraries using Gellish. This framework, together with the applications implemented with the goal of demonstrating and managing the capabilities of the distributed object library, is designed to provide users the capability of sharing and reusing information in a distributed fashion. Although a large number of ontology modeling languages exist, the problem of mapping knowledge from one modeling language onto another was placed outside the scope of this project, which resulted in Gellish being selected as the modeling language used to conceptualize the information stored at the distributed data stores. The need to classify ontology modeling languages, based on their subject and structure of conceptualization, resulted in the construction of the conceptualization graph. This graph is used to compare ontology modeling languages used within the building and construction industry, but also to motivate the aforementioned choice for Gellish as the modeling language used throughout the distributed object library. With the distributed object library framework and associated applications constructed, the final part of this thesis will conclude with the identification of limitations, based on tests performed with these applications, and present recommendations for improving the framework and applications where needed.},
  file      = {2009_Henrichs.pdf:by-author/H/Henrichs/2009_Henrichs.pdf:PDF},
  groups    = {sg/Gellish, sg/Conrolled vocabularies},
  keywords  = {Artificial Languages; Controlled Wocabulary; Gellish; Ontologies},
  owner     = {saulius},
  timestamp = {2016.02.23},
  creationdate = {2016-02-23T00:00:00},
  url       = {http://repository.tudelft.nl/view/ir/uuid%3A5724f667-fbe5-4b77-9688-c3d7bc9513c9/},
}

@Article{Heo2009,
  author    = {Heo, Muyoung and Kang, Louis and Shakhnovich, Eugene I.},
  journal   = {Proceedings of the National Academy of Sciences},
  title     = {Emergence of species in evolutionary “simulated annealing”},
  year      = {2009},
  pages     = {1869--1874},
  volume    = {106},
  abstract  = {Which factors govern the evolution of mutation rates and emergence of species? Here, we address this question by using a first principles model of life where population dynamics of asexual organisms is coupled to molecular properties and interactions of proteins encoded in their genomes. Simulating evolution of populations, we found that fitness increases in punctuated steps via epistatic events, leading to formation of stable and functionally interacting proteins. At low mutation rates, species form populations of organisms tightly localized in sequence space, whereas at higher mutation rates, species are lost without an apparent loss of fitness. However, when mutation rate was a selectable trait, the population initially maintained high mutation rate until a high fitness level was reached, after which organisms with low mutation rates are gradually selected, with the population eventually reaching mutation rates comparable with those of modern DNA-based organisms. This study shows that the fitness landscape of a biophysically realistic system is extremely complex, with huge number of local peaks rendering adaptation dynamics to be a glass-like process. On a more practical level, our results provide a rationale to experimental observations of the effect of mutation rate on fitness of populations of asexual organisms.},
  doi       = {10.1073/pnas.0809852106},
  eprint    = {http://www.pnas.org/content/106/6/1869.full.pdf+html},
  file      = {2009_Heo_1869.pdf:by-author/H/Heo/2009_Heo_1869.pdf:PDF},
  groups    = {sg/Molecular dynamics},
  keywords  = {Computer Simulations; Evolution},
  owner     = {saulius},
  timestamp = {2013.10.02},
  creationdate = {2013-10-02T00:00:00},
  url       = {http://www.pnas.org/content/106/6/1869.abstract},
}

@Article{Heo2008,
  author        = {Heo, M. and Kang, L. and Shakhnovich, E. I.},
  journal       = {Proceedings of the National Academy of Science - arXiv preprint},
  title         = {Emergence of species in evolutionary ``simulated annealing''},
  year          = {2008},
  pages         = {0810.1765},
  volume        = {106},
  abstract      = {Which factors govern the evolution of mutation rates and emergence of species? Here, we address this question using a first principles model of life where population dynamics of asexual organisms is coupled to molecular properties and interactions of proteins encoded in their genomes. Simulating evolution of populations, we found that fitness increases in punctuated steps via epistatic events, leading to formation of stable and functionally interacting proteins. At low mutation rates, species - populations of organisms with identical genotypes - form, while at higher mutation rates, species are lost through delocalization in sequence space without an apparent loss of fitness. However, when mutation rate was a selectable trait, the population initially maintained high mutation rate until a high fitness level is reached, after which organisms with low mutation rates are gradually selected, with the population eventually reaching mutation rates comparable to those of modern DNA-based organisms. These results provide microscopic insights into the dynamic fitness landscape of asexual populations of unicellular organisms.},
  adsnote       = {Provided by the SAO/NASA Astrophysics Data System},
  adsurl        = {http://adsabs.harvard.edu/abs/2009PNAS..106.1869H},
  archiveprefix = {arXiv},
  eprint        = {0810.1765},
  file          = {2008_Heo_0810.1765.pdf:by-author/H/Heo/2008_Heo_0810.1765.pdf:PDF},
  groups        = {sg/Molecular dynamics},
  keywords      = {Digital Life; Fitness Landscape; Molecular Evolution; Mutation Rates; Protein Interaction Networks},
  owner         = {saulius},
  primaryclass  = {q-bio.PE},
  timestamp = {2013.10.02},
  creationdate = {2013-10-02T00:00:00},
  url           = {http://arxiv.org/abs/0810.1765},
}

@Article{Hermann1998,
  author    = {Hermann, T and Auffinger, P and Westhof, E},
  journal   = {European biophysics journal : EBJ},
  title     = {Molecular dynamics investigations of hammerhead ribozyme RNA.},
  year      = {1998},
  pages     = {153--65},
  volume    = {27},
  abstract  = {The hammerhead ribozyme, a small catalytic RNA molecule, cleaves, in the presence of magnesium ions, a specific phosphodiester bond within its own backbone, leading to 23-cyclic phosphate and 5-OH extremities. In order to study the dynamical flexibility of the hammerhead RNA, we performed molecular dynamics simulations of the solvated crystal structure of an active hammerhead ribozyme, obtained after flash-freezing crystals soaked with magnesium. Because of a careful equilibration protocol and the use of the Ewald summation in calculating the electrostatic interactions, the RNA structure remained close to the crystal structure, as attested by a root-mean-square deviation below 2.5 A after 750 ps of simulation. All Watson-Crick base pairs were intact at the end of the simulations. The tertiary interactions, such as the sheared G.A pairs and the U-turn, important for the stabilisation of the three-dimensional RNA fold, were also retained. The results demonstrate that molecular dynamics simulations can be successfully used to investigate the dynamical behaviour of a ribozyme, thus, opening a road to study the role of transient structural changes involved in ribozyme catalysis.},
  file      = {Hermann_1998_153.pdf:by-author/H/Hermann/1998_Hermann_153.pdf:PDF},
  groups    = {sg/applications},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Hermite1854,
  author    = {C. Hermite},
  journal   = {Journal für die reine und angewandte Mathematik},
  title     = {Sur la théorie des formes quadratiques ternaires indéfinies},
  year      = {1854},
  pages     = {307--312},
  volume    = {47},
  file      = {1854_Hermite_307.pdf:by-author/H/Hermite/1854_Hermite_307.pdf:PDF},
  groups    = {sg/Cell reduction, sg/Probability theory, sg/Quadratic forms},
  keywords  = {Quadratic Forms; Reduction},
  owner     = {saulius},
  timestamp = {2016.04.13},
  creationdate = {2016-04-13T00:00:00},
  url       = {http://www.digizeitschriften.de/dms/img/?PID=GDZPPN002148455},
}

@Article{Hermite1854a,
  author    = {C. Hermite},
  journal   = {Journal für die reine und angewandte Mathematik},
  title     = {Sur la théorie des formes quadratiques. Premier mémoire},
  year      = {1854},
  pages     = {313--342},
  volume    = {47},
  file      = {1854_Hermite_313.pdf:by-author/H/Hermite/1854_Hermite_313.pdf:PDF},
  groups    = {sg/Cell reduction, sg/Probability theory, sg/Quadratic forms},
  keywords  = {Quadratic Forms; Reduction},
  owner     = {saulius},
  timestamp = {2016.04.13},
  creationdate = {2016-04-13T00:00:00},
  url       = {http://www.digizeitschriften.de/dms/img/?PID=GDZPPN002148463},
}

@Article{Hermite1854b,
  author    = {C. Hermite},
  journal   = {Journal für die reine und angewandte Mathematik},
  title     = {Sur la théorie des formes quadratiques. Second mémoire},
  year      = {1854},
  pages     = {343--368},
  volume    = {47},
  file      = {1854_Hermite_343.pdf:by-author/H/Hermite/1854_Hermite_343.pdf:PDF},
  groups    = {sg/Cell reduction, sg/Probability theory, sg/Quadratic forms},
  keywords  = {Quadratic Forms; Reduction},
  owner     = {saulius},
  timestamp = {2016.04.13},
  creationdate = {2016-04-13T00:00:00},
  url       = {http://www.digizeitschriften.de/dms/img/?PID=GDZPPN002148471},
}

@Article{Hermite1850,
  author    = {C. Hermite},
  journal   = {Journal für die reine und angewandte Mathematik},
  title     = {Sur la théorie des formes quadratiques ternaires},
  year      = {1850},
  pages     = {181--185},
  volume    = {40},
  file      = {1850_Hermite_181.pdf:by-author/H/Hermite/1850_Hermite_181.pdf:PDF},
  groups    = {sg/Cell reduction, sg/Probability theory, sg/Quadratic forms},
  keywords  = {Cell Reduction; Quadratic Forms; Reduction},
  owner     = {saulius},
  timestamp = {2016.04.13},
  creationdate = {2016-04-13T00:00:00},
  url       = {http://www.digizeitschriften.de/dms/img/?PID=GDZPPN002146789},
}

@Article{Hermo2005,
  author    = {Hermo, Louis and Chong, Dennis Lee and Moffatt, Pierre and Sly, William S and Waheed, Abdul and Smith, Charles E},
  journal   = {The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society},
  title     = {Region- and cell-specific differences in the distribution of carbonic anhydrases II, III, XII, and XIV in the adult rat epididymis.},
  year      = {2005},
  pages     = {699--713},
  volume    = {53},
  abstract  = {We employed RT-PCR followed by light microscope immunocytochemistry on St. Marie's- and Bouin's-fixed tissues to define the distribution of carbonic anhydrase (CA) isoforms in the male reproductive tract. The data revealed that CA II, III, IV, XII, and XIV were expressed in rat epididymis. Whereas CA III was found in principal cells of all epididymal regions, CA II was localized in narrow cells of the initial segment and principal cells of all regions. CA XII expression was most intense in the corpus and proximal cauda regions, where it appeared over the basolateral plasma membranes of principal cells. Narrow cells of the initial segment also revealed intense reactions, as did basal cells of the corpus and proximal cauda regions. Principal cells of the initial segment and proximal caput regions showed diffuse apical cytosolic reactions and occasional basolateral staining for CA XIV, whereas principal cells of distal regions showed more diffuse cytosolic reactions highlighting both apical and basal regions of the cell, with basal cells also being reactive. These data suggest subtle differences in cell type and subcellular- and region-specific distributions for CAs in their role of fine-tuning pH in the lumen, cell cytosol, and intervening intercellular spaces of the epididymis.},
  file      = {2005_Hermo_699.pdf:by-author/H/Hermo/2005_Hermo_699.pdf:PDF},
  groups    = {sg/medicine, sg/physiology, sg/hCA2, sg/hCA3, sg/hCA12, sg/hCA14, sg/MOFs, am/MOFs},
  keywords  = {CA14; Carbonic Anhydrases},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Herrera2004,
  author    = {Herrera},
  title     = {Ideology or Pragmatism in Elections},
  year      = {2005},
  abstract  = {We model electoral competition between two parties in a winner take all election. Parties choose strategically first their platforms and then their campain spending under aggregate uncer- tainty about voters’ preferences. In the unique Nash equilibrium larger elections are characterized by a higher participation rate. In equilibrium parties spend the same amounts for their campain, regardless of the relative advantage of one party among voters. More uncertainty over voters’ preferences implies lower campaign spending and more ideological parties: platforms diverge to approach the parties’ ideal points. If spending is limited parties are more pragmatic: platforms approach the median voter.},
  file      = {:by-author/H/Herrera/2005_Herrera.pdf:PDF},
  keywords  = {SocialSci},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Hester2016,
  author    = {Hester, James R.},
  journal   = {Data Science Journal},
  title     = {A Robust, Format-Agnostic Scientific Data Transfer Framework},
  year      = {2016},
  issn      = {1683-1470},
  month     = {Sep},
  volume    = {15},
  abstract  = {The olog approach of Spivak and Kent (PLoS ONE 7, 1 (2012) p e24274) is applied to the practical development of data transfer frameworks, yielding simple rules for construction and assessment of data transfer standards. The simplicity, extensibility and modularity of such descriptions allows discipline experts unfamiliar with complex ontological constructs or toolsets to synthesise multiple pre-existing standards, potentially including a variety of file formats, into a single overarching ontology. These ontologies nevertheless capture all scientifically-relevant prior knowledge, and when expressed in machine-readable form are sufficiently expressive to mediate translation between legacy and modern data formats. A format-independent programming interface informed by this ontology consists of six functions, of which only two handle data. Demonstration software implementing this interface is used to translate between two common diffraction image formats using such an ontology in place of an intermediate format.},
  doi       = {10.5334/dsj-2016-012},
  file      = {XML:by-author/H/Hester/2016_Hester_dsj-2016-012.xml:Text;2016_Hester_dsj-2016-012.pdf:by-author/H/Hester/2016_Hester_dsj-2016-012.pdf:PDF},
  keywords  = {Data Formats; Knowledge Representation; Metadata; Ontology},
  owner     = {saulius},
  publisher = {Ubiquity Press, Ltd.},
  timestamp = {2016.10.05},
  creationdate = {2016-10-05T00:00:00},
  url       = {http://dx.doi.org/10.5334/dsj-2016-012},
}

@Article{Hester2006,
  author           = {Hester, J. R.},
  journal          = {Journal of Applied Crystallography},
  title            = {A validating CIF parser: {\it PyCIFRW}},
  year             = {2006},
  pages            = {621--625},
  volume           = {39},
  creationdate     = {2008-07-28T00:00:00},
  doi              = {10.1107/S0021889806015627},
  file             = {wf5020.pdf:by-author/H/Hester/2006_Hester_621.pdf:PDF},
  groups           = {sg/CIF, am/CIF},
  keywords         = {CIF},
  modificationdate = {2023-08-07T10:23:05},
  owner            = {saulius},
  timestamp        = {2008.07.28},
  url              = {http://dx.doi.org/10.1107/S0021889806015627},
}

@Article{Hester1998,
  author           = {Hester, J. R. and Okamura, F. P.},
  journal          = {Journal of Applied Crystallography},
  title            = {CIF Applications. X. Automatic Construction of CIF Input Functions: {\it CifSieve}},
  year             = {1998},
  pages            = {965--968},
  volume           = {31},
  creationdate     = {2008-07-28T00:00:00},
  doi              = {10.1107/S0021889898008978},
  file             = {gl0560.pdf:by-author/H/Hester/1998_Hester_965.pdf:PDF},
  groups           = {sg/CIF, am/CIF},
  keywords         = {CIF},
  modificationdate = {2023-08-07T10:23:05},
  owner            = {saulius},
  timestamp        = {2008.07.28},
  url              = {http://dx.doi.org/10.1107/S0021889898008978},
}

@Article{Hewson2009,
  author    = {Paul Hewson},
  title     = {The Jeffreys Prior},
  year      = {2009},
  file      = {:by-author/H/Hewson/2009_Hewson.pdf:PDF},
  groups    = {sg/Bayesian},
  keywords  = {Bayesian Statistics; Mathematics},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Hickey2013,
  author    = {Steve Hickey and Caroline Chibelushi},
  title     = {Bayesian Clinical Trials for Orthomolecular Medicine},
  year      = {2013},
  pages     = {61--74},
  volume    = {28},
  file      = {Steve Hickey and Caroline Chibelushi - 2013 - Bayesian Clinical Trials for Orthomolecular Medici.pdf:by-author/H/Hickey/2013_Hickey_61.pdf:application/pdf},
  groups    = {sg/Clinical Trials},
  owner     = {saulius},
  timestamp = {2015.12.14},
  creationdate = {2015-12-14T00:00:00},
  url       = {https://www.csom.ca/wp-content/uploads/2013/06/Bayesian-Clinical-Trials-for-Orthomolecular-Medicine-28.2.pdf},
  urldate   = {2015-12-12},
}

@Article{Hickman2000,
  author    = {Hickman, A. B. and Li, Y. and Mathew, S. V. and May, E. W. and Craig, N. L. and Dyda, F.},
  journal   = {Molecular cell},
  title     = {Unexpected structural diversity in DNA recombination: the restriction endonuclease connection.},
  year      = {2000},
  pages     = {1025--34},
  volume    = {5},
  abstract  = {Transposition requires a coordinated series of DNA breakage and joining reactions. The Tn7 transposase contains two proteins: TnsA, which carries out DNA breakage at the 5' ends of the transposon, and TnsB, which carries out breakage and joining at the 3' ends of the transposon. TnsB is a member of the retroviral integrase superfamily whose hallmark is a conserved DDE motif. We report here the structure of TnsA at 2.4 A resolution. Surprisingly, the TnsA fold is that of a type II restriction endonuclease. Thus, Tn7 transposition involves a collaboration between polypeptides, one containing a DDE motif and one that does not. This result indicates that the range of biological processes that utilize restriction enzyme-like folds also includes DNA transposition.},
  file      = {:by-author/H/Hickman/2000_Hickman_1025.pdf:PDF},
  keywords  = {McrBC},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Misc{Hicks2015,
  author    = {Diana Hicks and Paul Wouters},
  title     = {The Leiden Manifesto for research metrics},
  year      = {2015},
  file      = {:by-author/H/Hicks/2015_Hicks.pdf:PDF},
  groups    = {sg/Bibliometrics},
  keywords  = {Impact Factor (IF); Quality of Research; Research Assessment},
  owner     = {saulius},
  timestamp = {2017.02.11},
  creationdate = {2017-02-11T00:00:00},
  url       = {http://www.nature.com/polopoly_fs/1.17351!/menu/main/topColumns/topLeftColumn/pdf/520429a.pdf},
}

@Manuscript{Hiebeler2011,
  author    = {David Hiebeler},
  title     = {MATLAB / R Reference},
  year      = {2011},
  url       = {http://www.math.umaine.edu/~hiebeler},
  file      = {:by-author/H/Hiebeler/2011_Hiebeler.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.09.30},
  creationdate = {2012-09-30T00:00:00},
}

@TechReport{Hilibrand1956,
  author      = {Jack Hilibrand},
  institution = {Research Laboratory of Electronics Massachusetts, Institute of Technology Cambridge, Massachusetts},
  title       = {Characterization of probability distributions for excess physical noises},
  year        = {1956},
  month       = {sep},
  abstract    = {Theoretical and experimental techniques are described for characterizing the probability distributions of certain excess physical noises by their moments. Theo- retical methods are presented for applying this "moments technique" in the time domain to random-pulse noise, and in the frequency domain to any random functions for which the moments exist. The frequency-domain technique is used for a theoretical study of the approach to a gaussian distribution of random-pulse noise that is subjected to severe band-limiting. In contrast, the departure from a gaussian distribution of random-pulse noise that is band-limited by RC cutoffs at low and high frequencies is examined by using the time-domain technique. It is found that the approach of noise distributions to gauss- ian is governed by the "memory" of the filter system rather than simply by its band- width. An experimental system is described for measuring the first four moments of noises in the 0.2 cps - 10 kc range. It is concluded that experimental measurements of moments are more desirable than direct probability density measurements when the goals are: (a) to categorize broadly the form of continuous noise distribution by a small number of parameters, and/or (b) when a minimum investment of time and equipment is desired. Measurements on 1/f noise in germanium diodes confirm (within experimental error) that the first probability distribution of this noise is gaussian in nature. Some effects of limited system bandwidth are illustrated by measurements on the distinctly non-gaussian "avalanche" noise in silicon junction diodes.},
  file        = {1956_Hilibrand_tr.pdf:by-author/H/Hilibrand/1956_Hilibrand_tr.pdf:PDF},
  owner       = {saulius},
  timestamp = {2012.09.18},
  creationdate = {2012-09-18T00:00:00},
}

@Article{Hill1980,
  author    = {Hill, Bruce M.},
  journal   = {Trabajos de Estadistica Y de Investigacion Operativa},
  title     = {On some statistical paradoxes and non-conglomerability},
  year      = {1980},
  issn      = {0041-0241},
  pages     = {39--66},
  volume    = {31},
  abstract  = {Summary Some statistical paradoxes arising from the use of non-conglomerable finitely additive distributions are discussed.},
  doi       = {10.1007/BF02888346},
  file      = {Hill - 1980 - On some statistical paradoxes and non-conglomerabi.pdf:by-author/H/Hill/1980_Hill_39.pdf:PDF;Snapshot:by-author/H/Hill/1980_Hill_39.html:URL},
  groups    = {sg/Bayesian},
  keywords  = {Conglomerability; Finite Additivity; General; Likelihood Principle; Statistics},
  language  = {en},
  owner     = {saulius},
  timestamp = {2015.12.07},
  creationdate = {2015-12-07T00:00:00},
  url       = {http://link.springer.com/article/10.1007/BF02888346},
  urldate   = {2015-12-07},
}

@TechReport{Hilse2006,
  author      = {Hans-Werner Hilse and Jochen Kothe},
  institution = {Research and Development Department of the Goettingen State and University Library (Niedersächsische Staats- und Universitäts-bibliothek Göttingen)},
  title       = {Implementing Persistent Identifiers},
  year        = {2006},
  abstract    = {Traditionally, organisations have relied on URL hyperlinks to provide interested parties with access to their digitised content via the internet. However, over time, more and more of these hyperlinks are ‘broken’. The URL relies on providing the specific location details for a document. When, for example, an organisation’s website is re-organised and its directories are renamed, the URL no longer provides a correct location path, thus rendering the documents effectively inaccessible to the end-user. In the mid 1990s, a number of schemes were developed that, rather than relying on the precise address of a document, introduced the idea of name spaces for recording the names and locations of documents. The identifiers for documents are registered centrally. When an end-user wishes to access a certain document, the identifier in his request is ‘resolved’, i.e. the correct document is retrieved, without the end-user needing to know the exact location of the document. This report describes a number of such schemes in detail. Key concepts introduced include Handles, Digital Object Identifiers (DOIs), Archival Resource Keys (ARKs), Persistent Uniform Resource Locators (PURLs), Uniform Resource Names (URNs), National Bibliography Numbers (NBNs), and the OpenURL. These schemes are described with examples and extensive references. The report emphasises that supporting persistent identification requires administrative effort and commitment. The systems presented support these administrative tasks but do not render them obsolete. All changes in location, ownership or metadata must be reflected in the name-space system – causing the organisations that run an identification system to incur costs. To assist organisations that wish to implement a persistent identification scheme, the report details questions that need to be addressed and offers possible strategies to tackle a number of scenarios. Organisations are strongly recommended to investigate collaboration with partners with existing schemes that have similar problems to solve and to choose the syntax for their persistent identifiers in such a way that they can be integrated into any of the schemes introduced in this report.},
  file        = {2006_Hilse.pdf:by-author/H/Hilse/2006_Hilse.pdf:PDF},
  isbn        = {90-6984-508-3},
  keywords    = {Data Citation; Data Management; Persistent Identifiers},
  owner       = {saulius},
  timestamp = {2016.10.25},
  creationdate = {2016-10-25T00:00:00},
  url         = {http://nbn-resolving.de/urn:nbn:de:gbv:7-isbn-90-6984-508-3-8},
}

@Article{Hilvo2005,
  author    = {Hilvo, Mika and Tolvanen, Martti and Clark, Amy and Shen, Bairong and Shah, Gul N and Waheed, Abdul and Halmi, Piia and Hänninen, Milla and Hämäläinen, Jonna M and Vihinen, Mauno and Sly, William S and Parkkila, Seppo},
  journal   = {The Biochemical journal},
  title     = {Characterization of CA XV, a new GPI-anchored form of carbonic anhydrase.},
  year      = {2005},
  pages     = {83--92},
  volume    = {392},
  abstract  = {The main function of CAs (carbonic anhydrases) is to participate in the regulation of acid-base balance. Although 12 active isoenzymes of this family had already been described, analyses of genomic databases suggested that there still exists another isoenzyme, CA XV. Sequence analyses were performed to identify those species that are likely to have an active form of this enzyme. Eight species had genomic sequences encoding CA XV, in which all the amino acid residues critical for CA activity are present. However, based on the sequence data, it was apparent that CA XV has become a non-processed pseudogene in humans and chimpanzees. RT-PCR (reverse transcriptase PCR) confirmed that humans do not express CA XV. In contrast, RT-PCR and in situ hybridization performed in mice showed positive expression in the kidney, brain and testis. A prediction of the mouse CA XV structure was performed. Phylogenetic analysis showed that mouse CA XV is related to CA IV. Therefore both of these enzymes were expressed in COS-7 cells and studied in parallel experiments. The results showed that CA XV shares several properties with CA IV, i.e. it is a glycosylated glycosylphosphatidylinositol-anchored membrane protein, and it binds CA inhibitor. The catalytic activity of CA XV is low, and the correct formation of disulphide bridges is important for the activity. Both specific and non-specific chaperones increase the production of active enzyme. The results suggest that CA XV is the first member of the alpha-CA gene family that is expressed in several species, but not in humans and chimpanzees.},
  file      = {2005_Hilvo_83.pdf:by-author/H/Hilvo/2005_Hilvo_83.pdf:PDF},
  groups    = {sg/hCA15},
  keywords  = {Carbonic Anhydrases},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Bitinaite2003,
  author    = {Kamini Hingorani-Varma and Jurate Bitinaite},
  journal   = {The Journal of Biological Chemistry},
  title     = {Kinetic Analysis of the Coordinated Interaction of {SgrAI} Restriction Endonuclease with Different {DNA} Targets},
  year      = {2003},
  pages     = {40392--40399},
  file      = {:by-author/B/Bitinaite/2003_Bitinaite_40392.pdf:PDF},
  keywords  = {Tetra; TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Hinsen2011,
  author    = {Hinsen, Konrad},
  journal   = {Procedia Computer Science},
  title     = {A data and code model for reproducible research and executable papers},
  year      = {2011},
  issn      = {1877-0509},
  pages     = {579--588},
  volume    = {4},
  abstract  = {This proposal describes how data, program code, and presentation can be stored together in a single file suitable for electronic publication and permitting the reproduction of computational results.. Universality, effciency, platformindependence, automated verifiability, and provenance tracking are the major design criteria. Existing and well-tested technology is used as much as possible, the two major building blocks being the Hierarchical Data Format for storage and the Java Virtual Machine for platform-independent code representation and secure execution.},
  doi       = {10.1016/j.procs.2011.04.061},
  file      = {2011_Hinsen_579.pdf:by-author/H/Hinsen/2011_Hinsen_579.pdf:PDF},
  groups    = {sg/Methods and tools},
  keywords  = {Executable Papers; Reproducible Research},
  owner     = {saulius},
  publisher = {Elsevier BV},
  timestamp = {2016.11.17},
  creationdate = {2016-11-17T00:00:00},
  url       = {http://dx.doi.org/10.1016/j.procs.2011.04.061},
}

@TechReport{Hinsen2007,
  author      = {Konrad Hinsen},
  institution = {Centre de Biophysique Mol\'{e}culaire (UPR 4301 CNRS) Rue Charles Sadron 45071 Orl\'{e}ans Cedex 2 France},
  title       = {The Molecular Modeling Toolkit: A New Approach to Molecular Simulations},
  year        = {2007},
  file        = {:by-author/H/Hinsen/2007_Hinsen.pdf:PDF},
  owner       = {saulius},
  timestamp = {2012.05.16},
  creationdate = {2012-05-16T00:00:00},
}

@Article{Hinton1987,
  author    = {Hinton, D. M. and Nossal, N. G.},
  journal   = {The Journal of biological chemistry},
  title     = {Bacteriophage T4 DNA primase-helicase. Characterization of oligomer synthesis by T4 61 protein alone and in conjunction with T4 41 protein.},
  year      = {1987},
  pages     = {10873--8},
  volume    = {262},
  abstract  = {The bacteriophage T4 41 and 61 proteins function as a primase-helicase which in vitro both unwinds double-stranded DNA and synthesizes the pentaribonucleotides used to initiate DNA synthesis on the lagging strand. We demonstrate that 61 protein alone possesses a weak DNA template-dependent oligomer synthesizing activity, whose products differ in size and nucleotide specificity from those made by the 61 and 41 proteins together. We have previously shown that the 61 and 41 proteins make primarily ribonucleotide pentamers of the sequence pppApC(pN)3, although some pentamers beginning with G were also detected on phi X174 single-stranded DNA. The pentamers pppApC(pN)3 have also been shown to initiate T4 DNA chains in vivo (Kurosawa, Y., and Okazaki, T. (1979) J. Mol. Biol. 135, 841-861). We now show that in contrast, the major products made by 61 protein alone on phi X174 DNA with [alpha-32P]CTP and the other three ribonucleoside triphosphates are not pentamers, but the dimers pppApC and pppGpC. In addition, minor amounts of products from 3 to approximately 45 nucleotides in length are also synthesized. Unlike the 61/41 protein reaction, 61 protein alone can substitute dATP or dGTP for ATP or GTP. Addition of 41 protein greatly stimulates oligomer synthesis, especially the synthesis of products made with ATP and CTP and products 5 nucleotides in length. Thus, both 61 and 41 proteins are needed to obtain efficient synthesis of the biologically relevant pentamers pppApC(pN)3. We demonstrate that the glucosylated hydroxymethylcytosines present in T4 DNA do not support the initiation of primer synthesis by the 61 protein on this template. With glycosylated hydroxymethyl T4 DNA, pppApC but not pppGpC oligomers are detected. If the T4 DNA is modified by hydroxymethylation but not glucosylation, pppApC and only a trace of pppGpC products are seen. In the accompanying paper (Nossal, N.G., and Hinton, D.M. (1987) J. Biol. Chem. 262, 10879-10885), we examine DNA synthesis primed by 61 protein in the absence of 41 protein.},
  file      = {:by-author/H/Hinton/1987_Hinton_10873.pdf:PDF},
  keywords  = {{gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Hinton1985,
  author    = {Hinton, D. M. and Nossal, N. G.},
  journal   = {The Journal of biological chemistry},
  title     = {Bacteriophage T4 DNA replication protein 61. Cloning of the gene and purification of the expressed protein.},
  year      = {1985},
  pages     = {12858--65},
  volume    = {260},
  abstract  = {In vitro, a bacteriophage T4 primase composed of T4 61 and 41 proteins, catalyzes the formation of pentaribonucleotides used to initiate DNA synthesis on single-stranded DNA. We have determined that cells containing a plasmid with the T4 DNA from 18.68 to 15.05 map units express an activity that substitutes for authentic 61 protein in vitro in catalyzing primer-dependent DNA synthesis with six other T4 DNA replication proteins. This result establishes that this region, genetically assigned to gene 61, is the structural gene for the priming protein. Cells containing a plasmid with gene 61 downstream of the strong phage lambda promoter PL and the antitermination site nutL produce 100-fold more 61 protein than T4-infected cells. We have developed an improved purification procedure which yields 100 mg of homogeneous, active protein from 178 g of these cells. In the plasmid, the T4 DNA downstream of gene 61 expresses a protein of 30,000 daltons. This protein may be the T4 DNA adenine methylase (dam) gene product, since Schlagman and Hattman (Schlagman, S. L. and Hattman, S. (1983) Gene 22, 139-156) have shown that this activity is expressed by plasmids containing T4 DNA from this region. In the PL, nutL vector, the expression of both the 30,000-dalton and 61 proteins is enhanced up to 20-fold by the presence of the phage lambda N protein, a transcription antitermination protein, suggesting that expression of the T4 DNA in the plasmid may be regulated transcriptionally. In addition, in both N+ and N- cells, the level of 61 protein, whose gene is proximal to PL on the plasmid, is lower than that of the product of the promoter distal 30,000-dalton protein gene. This result suggests that, at least in the plasmid construction, the expression of 61 protein may also be regulated after transcription.},
  file      = {:by-author/H/Hinton/1985_Hinton_12858.pdf:PDF},
  keywords  = {{gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Hinton1985a,
  author    = {Hinton, D. M. and Silver, L. L. and Nossal, N. G.},
  journal   = {The Journal of biological chemistry},
  title     = {Bacteriophage T4 DNA replication protein 41. Cloning of the gene and purification of the expressed protein.},
  year      = {1985},
  pages     = {12851--7},
  volume    = {260},
  abstract  = {The bacteriophage T4 primase, composed of the T4 proteins 41 and 61, synthesizes pentaribonucleotides used to prime DNA synthesis on single-stranded DNA in vitro. 41 protein is also a DNA helicase that opens DNA in the same direction as the growing replication fork. Previously, Mattson et al. (Mattson, T., Van Houwe, G., Bolle, A., Selzer, G., and Epstein, R. (1977) Mol. Gen. Genet. 154, 319-326) located part of gene 41 on a 3400-base pair EcoRI fragment of T4 DNA (map units 24.3 to 21.15). In this paper, we report the cloning of T4 DNA representing map units 24.3 to 20.06 in a multicopy plasmid vector. Extracts of cells containing this plasmid complement gene 41- extracts in a DNA synthesis assay, indicating that this region contains all the information necessary for the expression of active 41 protein. We located gene 41 more precisely between T4 map units 22.01 to 20.06 since our cloning of this region downstream of the strong lambda promoter PL results in the production of active 41 protein at a level 100-fold greater than after T4 infection. We have purified 133 mg of homogeneous 41 protein from 27 g of these cells. Like the 41 protein from T4 infected cells, the purified 41 protein in conjunction with the T4 gene 61 priming protein catalyzes primer formation (assayed by RNA primer-dependent DNA synthesis with T4 polymerase, the genes 44/62 and 45 polymerase accessory proteins, and the gene 32 helix-destabilizing protein) and is a helicase whose activity is stimulated by T4 61 protein.},
  file      = {:by-author/H/Hinton/1985_Hinton_12851.pdf:PDF},
  keywords  = {{gp41}; {gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Manuscript{Togo2015a,
  author    = {Yoyo Hinuma and Atsushi Togo and Hiroyuki Hayashi and Isao Tanaka},
  title     = {Choice of basis vectors for conventional unit cells revisited},
  year      = {2015},
  file      = {:by-author/T/Togo/2015_Togo.pdf:PDF},
  owner     = {andrius},
  timestamp = {2015.06.08},
  creationdate = {2015-06-08T00:00:00},
}

@InBook{Hirakawa2015,
  author    = {Kazutaka Hirakawa},
  chapter   = {2},
  editor    = {Zaheer Ul-Haq and Jeffry D. Madura},
  pages     = {27--70},
  publisher = {Bentham Science Publishers},
  title     = {Computational Chemistry for Photosensitizer Design and Investigation of DNA Damage},
  year      = {2015},
  series    = {Frontiers in Computational Chemistry},
  abstract  = {Computational chemistry can be used for the prediction of photochemical reactivity and the design of photosensitizers for cancer phototherapy. For example, the activity of a photosensitizer for DNA damage can be estimated from the calculation of the HOMO energy of the molecules. In general, DNA damage is mediated by the following two processes: 1) photo-induced electron transfer from the DNA base to the photoexcited photosensitizer and 2) base modification by singlet oxygen generation through photo- energy transfer from the photosensitizer to oxygen. The DNA-damaging activity of the photosensitizer through electron transfer is closely related to the HOMO energy level of the molecule. It has been demonstrated that the extent of DNA damage photosensitized by xanthone analogues is proportional to the energy gap between the HOMO level of the photosensitizer and that of guanine. In addition, computational chemistry can be used to investigate the mechanism of the chemopreventive effect on phototoxicity. Furthermore, the molecular orbital calculation is useful to design a photosensitizer in which the activity of singlet oxygen generation is controlled by DNA recognition. Singlet oxygen is an important reactive oxygen species to attack cancer. The control of singlet oxygen generation by DNA is necessary to achieve the tailor-made cancer photo-therapy. Several porphyrin photosensitizers have been designed on the basis of the molecular orbital calculation to control the activity of singlet oxygen generation.},
  booktitle = {Frontiers in Computational Chemistry},
  doi       = {10.2174/9781608059782115020004},
  file      = {:by-author/H/Hirakawa/2015_Hirakawa_27.pdf:pdf},
  owner     = {saulius},
  timestamp = {2015.10.09},
  creationdate = {2015-10-09T00:00:00},
  url       = {http://www.eurekaselect.com/128893/chapter/computational-chemistry-for-photosensitizer-design-and-investigation-of-dna-damag},
}

@Article{Hirao2012,
  author    = {Hirao, Ichiro and Kimoto, Michiko},
  journal   = {Proceedings of the Japan Academy, Series B},
  title     = {Unnatural base pair systems toward the expansion of the genetic alphabet in the central dogma},
  year      = {2012},
  issn      = {1349-2896},
  number    = {7},
  pages     = {345--367},
  volume    = {88},
  doi       = {10.2183/pjab.88.345},
  file      = {:by-author/H/Hirao/2012_Hirao_345.pdf:PDF},
  groups    = {am/Expanded genetic code},
  owner     = {andrius},
  publisher = {Japan Academy},
  timestamp = {2016.05.25},
  creationdate = {2016-05-25T00:00:00},
  url       = {http://dx.doi.org/10.2183/pjab.88.345},
}

@Article{Hirao2002,
  author    = {Hirao, Ichiro and Ohtsuki, Takashi and Fujiwara, Tsuyoshi and Mitsui, Tsuneo and Yokogawa, Tomoko and Okuni, Taeko and Nakayama, Hiroshi and Takio, Koji and Yabuki, Takashi and Kigawa, Takanori and et al.},
  journal   = {Nature Biotechnology},
  title     = {An unnatural base pair for incorporating amino acid analogs into proteins},
  year      = {2002},
  issn      = {1087-0156},
  month     = {Feb},
  number    = {2},
  pages     = {177--182},
  volume    = {20},
  doi       = {10.1038/nbt0202-177},
  file      = {:by-author/H/Hirao/2002_Hirao_177.pdf:PDF},
  groups    = {am/Expanded genetic code},
  owner     = {andrius},
  publisher = {Nature Publishing Group},
  timestamp = {2016.05.18},
  creationdate = {2016-05-18T00:00:00},
  url       = {http://dx.doi.org/10.1038/nbt0202-177},
}

@Article{Hirata1988,
  author    = {Fumio Hirata and Paul Redfern and Ronald M. Levy},
  journal   = {International Journal of Quantum Chemistry: Quantum Biology Symposium},
  title     = {Viewing the Born model for ion hydration through a microscope},
  year      = {1988},
  pages     = {179--190},
  volume    = {15},
  file      = {1988_Hirata_179.pdf:by-author/H/Hirata/1988_Hirata_179.pdf:PDF},
  keywords  = {Poisson-Boltzmann eq; Protein Physics; Solvatation},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Hirshfeld1977,
  author    = {Hirshfeld, F.L.},
  journal   = {Theoretica chimica acta},
  title     = {Bonded-atom fragments for describing molecular charge densities},
  year      = {1977},
  issn      = {0040-5744},
  pages     = {129--138},
  volume    = {44},
  doi       = {10.1007/BF00549096},
  file      = {:by-author/H/Hirshfeld/1977_Hirshfeld_129.pdf:PDF},
  keywords  = {Bonded Atoms; Dipole Moments; Electron Density; Hirshfeld Surface; Populations},
  language  = {English},
  owner     = {saulius},
  publisher = {Springer-Verlag},
  timestamp = {2014.08.11},
  creationdate = {2014-08-11T00:00:00},
  url       = {http://dx.doi.org/10.1007/BF00549096},
}

@Article{Hirshfeld1968,
  author    = {Hirshfeld, F. L.},
  journal   = {Acta Crystallographica Section A},
  title     = {Symmetry in the generation of trial structures},
  year      = {1968},
  pages     = {301--311},
  volume    = {24},
  abstract  = {In the generation of trial structures by the systematic variation of the position and orientation of a molecule of known dimensions, the ranges to be scanned by the positional and orientational parameters depend on the symmetry of the molecule and on the space group. The set of transformations of the crystal axes that leave invariant the coordinates of equivalent positions for a given space group defines a corresponding derivative symmetry, conforming to one of thirty distinct `Cheshire' groups. The direct product of this group with the molecular point group specifies the symmetry of the six-dimensional space of the trial-structure parameters. The asymmetric unit in this space is the region to be scanned by the several parameters.},
  doi       = {10.1107/S0567739468000501},
  file      = {1968_Hirshfeld_301.pdf:by-author/H/Hirshfeld/1968_Hirshfeld_301.pdf:PDF},
  keywords  = {Cheshire Groups; Spacegroups; Symmetry; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2014.05.08},
  creationdate = {2014-05-08T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0567739468000501},
}

@Article{Hizver2001,
  author    = {Hizver, J. and Rozenberg, H. and Frolow, F. and Rabinovich, D. and Shakked, Z.},
  journal   = {Proceedings of the National Academy of Sciences of the United States of America},
  title     = {DNA bending by an adenine--thymine tract and its role in gene regulation.},
  year      = {2001},
  pages     = {8490--5},
  volume    = {98},
  abstract  = {To gain insight into the structural basis of DNA bending by adenine-thymine tracts (A-tracts) and their role in DNA recognition by gene-regulatory proteins, we have determined the crystal structure of the high-affinity DNA target of the cancer-associated human papillomavirus E2 protein. The three independent B-DNA molecules of the crystal structure determined at 2.2-A resolution are examples of A-tract-containing helices where the global direction and magnitude of curvature are in accord with solution data, thereby providing insights, at the base pair level, into the mechanism of DNA bending by such sequence motifs. A comparative analysis of E2-DNA conformations with respect to other structural and biochemical studies demonstrates that (i) the A-tract structure of the core region, which is not contacted by the protein, is critical for the formation of the high-affinity sequence-specific protein-DNA complex, and (ii) differential binding affinity is regulated by the intrinsic structure and deformability encoded in the base sequence of the DNA target.},
  file      = {:by-author/H/Hizver/2001_Hizver_8490.pdf:PDF},
  keywords  = {Readout},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Hjaltason2002,
  author     = {Hjaltason, Gisli R. and Samet, Hanan},
  journal    = {The VLDB Journal},
  title      = {Speeding up construction of {PMR} quadtree-based spatial indexes},
  year       = {2002},
  issn       = {1066-8888},
  pages      = {109--137},
  volume     = {11},
  abstract   = {Spatial indexes, such as those based on the quadtree, are important in spatial databases for efficient execu- tion of queries involving spatial constraints, especially when the queries involve spatial joins. In this paper we present a number of techniques for speeding up the construction of quadtree-based spatial indexes, specifically the PMR quadtree, which can index arbitrary spatial data. We assume a quadtree implementation using the “linear quadtree”, a disk-resident representation that stores objects contained in the leaf nodes of the quadtree in a linear index (e.g., a B-tree) ordered based on a space-filling curve. We present two complementary tech- niques: an improved insertion algorithm and a bulk-loading method. The bulk-loading method can be extended to handle bulk-insertions into an existing PMR quadtree. We make some analytical observations about the I/O cost and CPU cost of our PMR quadtree bulk-loading algorithm, and conduct an exten- sive empirical study of the techniques presented in the paper. Our techniques are found to yield significant speedup com- pared to traditional quadtree building methods, even when the size of a main memory buffer is very small compared to the size of the resulting quadtrees.},
  doi        = {10.1007/s00778-002-0067-8},
  file       = {:by-author/H/Hjaltason/2002_Hjaltason_109.pdf:PDF},
  issue_date = {October 2002},
  keywords   = {Bulk Loading; I/O; Spatial Indexing},
  owner      = {saulius},
  publisher  = {Springer-Verlag New York, Inc.},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url        = {http://dx.doi.org/10.1007/s00778-002-0067-8},
}

@Article{Hjaltason1999,
  author      = {Hjaltason, G\'{\i}sli R. and Samet, Hanan},
  journal     = {ACM Transactions on Database Systems},
  title       = {Distance Browsing in Spatial Databases},
  year        = {1999},
  issn        = {0362-5915},
  pages       = {265--318},
  volume      = {24},
  abstract    = {We compare two different techniques for browsing through a collection of spatial objects stored in an R-tree spatial data structure on the basis of their distances from an arbitrary spatial query object. The conventional approach is one that makes use of a k -nearest neighbor algorithm where k is known prior to the invocation of the algorithm. Thus if m Ͼ k neighbors are needed, the k -nearest neighbor algorithm has to be reinvoked for m neighbors, thereby possibly performing some redundant computations. The second approach is incremental in the sense that having obtained the k nearest neighbors, the k ϩ 1 st neighbor can be obtained without having to calculate the k ϩ 1 nearest neighbors from scratch. The incremental approach is useful when processing complex queries where one of the conditions involves spatial proximity (e.g., the nearest city to Chicago with population greater than a million), in which case a query engine can make use of a pipelined strategy. We present a general incremental nearest neighbor algorithm that is applicable to a large class of hierarchical spatial data structures. This algorithm is adapted to the R-tree and its performance is compared to an existing k -nearest neighbor algorithm for R-trees [Roussopoulos et al. 1995]. Experiments show that the incremental nearest neighbor algorithm significantly outperforms the k -nearest neighbor algorithm for distance browsing queries in a spatial database that uses the R-tree as a spatial index. Moreover, the incremental nearest neighbor algorithm usually outperforms the k -nearest neighbor algorithm when applied to the k -nearest neighbor problem for the R-tree, although the improvement is not nearly as large as for distance browsing queries. In fact, we prove informally that at any step in its execution the incremental nearest neighbor algorithm is optimal with respect to the spatial data structure that is employed. Furthermore, based on some simplifying assumptions, we prove that in two dimensions the number of distance computations and leaf nodes accesses made by the algorithm for finding k neighbors is O (k1 k).},
  doi         = {10.1145/320248.320255},
  file        = {:by-author/H/Hjaltason/1999_Hjaltason_265.pdf:PDF},
  institution = {University of Maryland},
  owner       = {saulius},
  publisher   = {ACM},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url         = {http://doi.acm.org/10.1145/320248.320255},
}

@Manuscript{Hjaltason1998,
  author    = {Hjaltason, G\'{\i}sli R. and Samet, Hanan},
  title     = {Ranking in Spatial Databases},
  year      = {1998},
  file      = {:by-author/H/Hjaltason/1998_Hjaltason.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Presentation{Hjorth-Jensen2011,
  author       = {Morten Hjorth-Jensen},
  title        = {Parallel programming using MPI},
  year         = {2011},
  conference   = {NOTUR 2011},
  organization = {Department of Physics and Center of Mathematics for Applications, University of Oslo, N-0316 Oslo, Norway},
  file         = {:by-author/H/Hjorth-Jensen/2011_Hjorth-Jensen_slides.pdf:PDF},
  owner        = {saulius},
  pages        = {slides},
  timestamp = {2013.07.02},
  creationdate = {2013-07-02T00:00:00},
}

@Article{Ho2003,
  author    = {Ho, Bosco K. and Thomas, Annick and Brasseur, Robert},
  journal   = {Protein science : a publication of the Protein Society},
  title     = {Revisiting the Ramachandran plot: hard-sphere repulsion, electrostatics, and H-bonding in the alpha-helix.},
  year      = {2003},
  pages     = {2508--22},
  volume    = {12},
  abstract  = {What determines the shape of the allowed regions in the Ramachandran plot? Although Ramachandran explained these regions in terms of 1-4 hard-sphere repulsions, there are discrepancies with the data where, in particular, the alphaR, alphaL, and beta-strand regions are diagonal. The alphaR-region also varies along the alpha-helix where it is constrained at the center and the amino terminus but diffuse at the carboxyl terminus. By analyzing a high-resolution database of protein structures, we find that certain 1-4 hard-sphere repulsions in the standard steric map of Ramachandran do not affect the statistical distributions. By ignoring these steric clashes (NH(i+1) and O(i-1)C), we identify a revised set of steric clashes (CbetaO, O(i-1)N(i+1), CbetaN(i+1), O(i-1)Cbeta, and O(i-1)O) that produce a better match with the data. We also find that the strictly forbidden region in the Ramachandran plot is excluded by multiple steric clashes, whereas the outlier region is excluded by only one significant steric clash. However, steric clashes alone do not account for the diagonal regions. Using electrostatics to analyze the conformational dependence of specific interatomic interactions, we find that the diagonal shape of the alphaR and alphaL-regions also depends on the optimization of the NH(i+1) and O(i-1)C interactions, and the diagonal beta-strand region is due to the alignment of the CO and NH dipoles. Finally, we reproduce the variation of the Ramachandran plot along the alpha-helix in a simple model that uses only H-bonding constraints. This allows us to rationalize the difference between the amino terminus and the carboxyl terminus of the alpha-helix in terms of backbone entropy.},
  file      = {:by-author/H/Ho/2003_Ho_2508.pdf:PDF},
  keywords  = {Protein Structures; Ramachandran Map},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Hoare1969,
  author     = {Hoare, C. A. R.},
  journal    = {Commun. ACM},
  title      = {An Axiomatic Basis For Computer Programming},
  year       = {1969},
  issn       = {0001-0782},
  pages      = {576--580},
  volume     = {12},
  abstract   = {In this paper an attempt is made to explore the logical foundations of computer programming by use of techniques which were first applied in the study of geometry and have later been extended to other branches of mathematics. This involves the elucidation of sets of axioms and rules of inference which can be used in proofs of the properties of computer programs. Examples are given of such axioms and rules, and a formal proof of a simple theorem is displayed. Finally, it is argued that important advantage, both theoretical and practical, may follow from a pursuance of these topics.},
  address    = {New York, NY, USA},
  doi        = {10.1145/363235.363259},
  file       = {:by-author/H/Hoare/1969_Hoare_576.pdf:PDF},
  groups     = {sg/Correctness proofs},
  issue_date = {Oct. 1969},
  keywords   = {Computer Science (CS); Correctness Proofs},
  owner      = {saulius},
  publisher  = {ACM},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
  url        = {http://doi.acm.org/10.1145/363235.363259},
}

@InProceedings{Hoebarth2011,
  author    = {Sebastian Höbarth and Rene Mayrhofer and Upper Austria and University of Applied and Sciences Upper and Austria University and of Applied and Sciences and sebastian.hoebarth@fh-hagenberg.at rene.mayrhofer@fh-hagenberg.at},
  title     = {A framework for on-device privilege escalation exploit execution on Android},
  year      = {2011},
  abstract  = {context is associated with higher access privileges than the Exploits on mobile phones can be used for various reasons; a user providing the input, it can be exploited to achieve tem-},
  comment   = {A framework for on-device privilege escalation exploit execution on Android Sebastian Höbarth Rene Mayrhofer Upper Austria University of Applied Sciences Upper Austria University of Applied Sciences sebastian.hoebarth@fh-hagenberg.at rene.mayrhofer@fh-hagenberg.at ABSTRACT context is associated with higher access privileges than the Exploits on mobile phones can be used for various reasons; a user providing the input, it can be exploited to achieve tem- benign one may be to achieve system-level access on a device porary privilege escalation, forming a so-called buffer over- that was locked by the manufacturer or service provider (also flow exploit (cf. e.g. [3, 6]). Another common example is known as ‘jailbreaking’ or ‘rooting’), while potentially ma- missing input sanitization, which allows to open, read, write, licious reasons are manifold. Independently of the use case or execute files with higher privilege by exploiting a service however, a specific exploit is not sufficient to achieve the or function that is supposed to be limited to a certain path desired access rights. Typically, exploits provide temporary or type of files but fails to verify this accordingly. privilege escalation immediately after their execution. To The range of exploits that have already been published provide additional access to applications, permanent priv- for Android and other mobile phone platforms is manifold, ilege escalation is required – in the benign case, including and their specific attack vectors are significantly different. secure access control for the user to decide which (parts of) Therefore, it is difficult to unify the actual exploit codes applications are granted elevated access. In this paper, we into a common structure or a framework; it is often not present a framework that can use arbitrary temporary ex- even necessary, considering that exploit codes written in C ploits on Android devices to achieve permanent ‘root’ capa- are most typically very short (in the order of a few hundreds bilities for select (parts of) applications. of lines of code). However, the steps that need to be executed after an initial temporary privilege escalation was achieved are often similar. To progress from temporary to permanent 1. INTRODUCTION privilege escalation, the (mobile phone) system needs to be Current mobile phone platforms such as Android, iOS, or modified. This typically includes the installation of new Maemo/MeeGo all build on native code for their respective binaries that allow controlled elevation of access rights. kernels, libraries. User space utilities and services are there- A more typical approach for handling various exploits is fore often susceptible to typical programming errors such as therefore to collect them into a common framework for ex- buffer overflows or missing input sanitization. These errors ecuting as many exploits as possible and, upon the first typically lead to application crashes or malfunctions, but successful execution of any of these exploits, to install per- can sometimes allow the caller of the corresponding service manent means for system-level access within the temporary or function to cause unintended consequences. context returned by the exploit. Metasploit 1 is currently the One example for a common class of programming errors is most comprehensive framework for exploits and is widely a buffer overflow in native C code that allows user-provided used [7], but focuses on being executed on a standard desk- (often binary) input to be copied into a some allocated buffer top/laptop computer. At the time of this writing, there are (typically an array of bytes or characters) without validat- initial ports of Metasploit to iPhone and Nokia N900 and ex- ing the sizes of input and buffer. If this buffer is allocated perimental builds for Android, but all these require a mobile sufficiently close to some program memory that contains ad- phone on which the user already has system-level access (i.e. dresses to program code (such as function return addresses ‘root’ on Android or ‘jailbreak’ on iPhone). In contrast to or library function mappings), than a carefully crafted in- Metasploit, we focus on executing Android system exloits on put can overflow the boundaries of the buffer and overwrite the devices themselves, with the aim of achieving permanent these addresses with new program code contained in the user privilege escalation on a single device (independently of the input. This new program code will then be executed within benign or malicious use case after reaching system-level ac- the context of the running service or function and, if this cess). With the exception of a few closed-source Android ap- plications that bundle specific exploits with additional (but, between the applications, different) steps for advancing from temporary to permanent privilege escalation (most notably Permission to make digital or hard copies of all or part of this work for Visionary+ for the HTC Desire HD and z4root for multi- personal or classroom use is granted without fee provided that copies are ple Android devices), we are not aware of other publications not made or distributed for profit or commercial advantage and that copies on Android on-device system exploit execution frameworks. bear this notice and the full citation on the first page. To copy otherwise, to Other related work concerning Android exploits and exploit republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. prevention is discussed within the respective sections. IWSSI2011 12 June, 2011, San Francisco, US 1 . http://www.metasploit.com Third International Workshop on Security and Privacy in Spontaneous Interaction and Mobile Phone Use (IWSSI/SPMU) June 12, 2011, San Francisco, CA, USA},
  file      = {:by-author/H/Höbarth/2011_Höbarth.pdf:PDF},
  owner     = {saulius},
  timestamp = {2013.08.10},
  creationdate = {2013-08-10T00:00:00},
}

@TechReport{Hobbs2004,
  author      = {Jerry~R. Hobbs and Douglas~E. Appelt and John Bear and Mabry Tyson and David Magerman},
  institution = {Artificial Intelligence Center, SRI International, Menlo Park, California},
  title       = {Robust Processing of Real-World Natural-Language Texts},
  year        = {2004},
  file        = {:by-author/H/Hobbs/2004_Hobbs.war:},
  keywords    = {Computer Science (CS)},
  owner       = {saulius},
  timestamp = {2015.03.02},
  creationdate = {2015-03-02T00:00:00},
  url         = {http://www.isi.edu/~hobbs/robust/robust.html},
}

@Article{Hobbs1996,
  author    = {Hobbs, L. J. and Nossal, N. G.},
  journal   = {Journal of bacteriology},
  title     = {Either bacteriophage T4 RNase H or Escherichia coli DNA polymerase I is essential for phage replication.},
  year      = {1996},
  pages     = {6772--7},
  volume    = {178},
  abstract  = {Bacteriophage T4 rnh encodes an RNase H that removes ribopentamer primers from nascent DNA chains during synthesis by the T4 multienzyme replication system in vitro (H. C. Hollingsworth and N. G. Nossal, J. Biol. Chem. 266:1888-1897, 1991). This paper demonstrates that either T4 RNase HI or Escherichia coli DNA polymerase I (Pol I) is essential for phage replication. Wild-type T4 phage production was not diminished by the polA12 mutation, which disrupts coordination between the polymerase and the 5'-to-3' nuclease activities of E. coli DNA Pol I, or by an interruption in the gene for E. coli RNase HI. Deleting the C-terminal amino acids 118 to 305 from T4 RNase H reduced phage production to 47% of that of wild-type T4 on a wild-type E. coli host, 10% on an isogenic host defective in RNase H, and less than 0.1% on a polA12 host. The T4 rnh(delta118-305) mutant synthesized DNA at about half the rate of wild-type T4 in the polA12 host. More than 50% of pulse-labelled mutant DNA was in short chains characteristic of Okazaki fragments. Phage production was restored in the nonpermissive host by providing the T4 rnh gene on a plasmid. Thus, T4 RNase H was sufficient to sustain the high rate of T4 DNA synthesis, but E. coli RNase HI and the 5'-to-3' exonuclease of Pol I could substitute to some extent for the T4 enzyme. However, replication was less accurate in the absence of the T4 RNase H, as judged by the increased frequency of acriflavine-resistant mutations after infection of a wild-type host with the T4 rnh (delta118-305) mutant.},
  file      = {:by-author/H/Hobbs/1996_Hobbs_6772.pdf:PDF},
  keywords  = {{gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Presentation{Hodson2014,
  author    = {Simon Hodson},
  title     = {New Requirements for Dataset Metadata: a perspective from CODATA},
  year      = {2014},
  file      = {PPTX:by-author/H/Hodson/2014_Hodson_slides.pptx:OpenDocument presentation},
  keywords  = {CODATA; Data Management; Metadata},
  owner     = {saulius},
  timestamp = {2014.10.21},
  creationdate = {2014-10-21T00:00:00},
  url       = {http://www.eurocris.org/Uploads/Web%20pages/seminars/Seminar_2013/Session%206%20-%20Simon%20Hodson.pptx},
}

@Manuscript{Hoefler2009,
  author    = {Torsten Hoefler and Andrew Lumsdaine and Jack Dongarra},
  title     = {Towards Efficient MapReduce Using MPI},
  year      = {2009},
  file      = {:by-author/H/Hoefler/2009_Hoefler.pdf:PDF},
  groups    = {sg/SdaI},
  owner     = {saulius},
  timestamp = {2013.07.02},
  creationdate = {2013-07-02T00:00:00},
}

@Article{Hoeppner2012,
  author    = {Hoeppner, M .P. and Gardner, P. P. and Poole, A. M.},
  journal   = {PLoS Comput. Biol.},
  title     = {Comparative Analysis of RNA Families Reveals Distinct Repertoires for Each Domain of Life},
  year      = {2012},
  pages     = {e1002752},
  volume    = {8},
  abstract  = {The RNA world hypothesis, that RNA genomes and catalysts preceded DNA genomes and genetically-encoded protein catalysts, has been central to models for the early evolution of life on Earth. A key part of such models is continuity between the earliest stages in the evolution of life and the RNA repertoires of extant lineages. Some assessments seem consistent with a diverse RNA world, yet direct continuity between modern RNAs and an RNA world has not been demonstrated for the majority of RNA families, and, anecdotally, many RNA functions appear restricted in their distribution. Despite much discussion of the possible antiquity of RNA families, no systematic analyses of RNA family distribution have been performed. To chart the broad evolutionary history of known RNA families, we performed comparative genomic analysis of over 3 million RNA annotations spanning 1446 families from the Rfam 10 database. We report that 99% of known RNA families are restricted to a single domain of life, revealing discrete repertoires for each domain. For the 1% of RNA families/clans present in more than one domain, over half show evidence of horizontal gene transfer (HGT), and the rest show a vertical trace, indicating the presence of a complex protein synthesis machinery in the Last Universal Common Ancestor (LUCA) and consistent with the evolutionary history of the most ancient protein-coding genes. However, with limited interdomain transfer and few RNA families exhibiting demonstrable antiquity as predicted under RNA world continuity, our results indicate that the majority of modern cellular RNA repertoires have primarily evolved in a domain-specific manner.},
  doi       = {10.1371/journal.pcbi.1002752},
  file      = {:by-author/H/Hoeppner/2012_Hoeppner_e1002752.pdf:PDF},
  owner     = {saulius},
  timestamp = {2013.10.03},
  creationdate = {2013-10-03T00:00:00},
}

@Article{Hoesl2012,
  author    = {Hoesl, Michael Georg and Budisa, Nediljko},
  journal   = {Current Opinion in Biotechnology},
  title     = {Recent advances in genetic code engineering in Escherichia coli},
  year      = {2012},
  issn      = {0958-1669},
  month     = {Oct},
  number    = {5},
  pages     = {751–757},
  volume    = {23},
  doi       = {10.1016/j.copbio.2011.12.027},
  file      = {:by-author/H/Hoesl/2012_Hoesl_751.pdf:PDF},
  groups    = {am/Expanded genetic code},
  owner     = {andrius},
  publisher = {Elsevier BV},
  timestamp = {2016.04.29},
  creationdate = {2016-04-29T00:00:00},
  url       = {http://dx.doi.org/10.1016/j.copbio.2011.12.027},
}

@Manuscript{Hof1996,
  author    = {Markus Hof and Hanspeter Mössenböck and Peter Pirkelbauer},
  title     = {Zero-Overhead Exception Handling Using Metaprogramming},
  year      = {1996},
  file      = {:by-author/H/Hof/1996_Hof.ps.gz:PostScript;:by-author/H/Hof/1996_Hof.pdf:PDF},
  owner     = {saulius},
  timestamp = {2013.08.10},
  creationdate = {2013-08-10T00:00:00},
}

@Manuscript{Hoeffgen1994,
  author    = {Klaus-U. Höffgen and Hans-U. Simon and Van Horn, Kevin S.},
  title     = {Robust Trainability of Single Neurons},
  year      = {1994},
  abstract  = {It is well known that (McCulloch-Pitts) neurons are efficiently trainable to learn an unknown halfspace from examples, using linear-programming methods. We want to analyze how the learning performance degrades when the representational power of the neuron is overstrained, i.e., if more complex concepts than just halfspaces are allowed. We show that the problem of learning a probably almost optimal weight vector for a neuron is so difficult that the minimum error cannot even be approximated to within a constant factor in polynomial time (unless RP = NP); we obtain the same hardness result for several variants of this problem. We consider strengthen these negative results for neurons with binary weights 0 or 1. We also show that neither heuristical learning nor learning by sigmoidal neurons with a constant reject rate is efficiently possible (unless RP = NP).},
  comment   = {To appear in Journal of Computer and System Sciences},
  file      = {:by-author/H/Höffgen/1994_Höffgen.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.11.20},
  creationdate = {2012-11-20T00:00:00},
}

@Article{Hoffman1991,
  author    = {Hoffman, M},
  journal   = {Science (New York, N.Y.)},
  title     = {Brave new (RNA) world.},
  year      = {1991},
  pages     = {379},
  volume    = {254},
  file      = {1991_Hoffman_379.pdf:by-author/H/Hoffman/1991_Hoffman_379.pdf:PDF},
  keywords  = {RNA World; Ribozymes},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@TechReport{Hoffmann2003,
  author      = {Chris Hoffmann and Richard Gruet and Simon Brunning},
  institution = {vicorp.com and intraware.com},
  title       = {Python 2.1 Quick Reference},
  year        = {2003},
  file        = {:by-author/H/Hoffmann/2003_Hoffmann.pdf:PDF;:by-author/H/Hoffmann/2003_Hoffmann.ps:PostScript;:by-author/H/Hoffmann/2003_Hoffmann.txt:Text},
  owner       = {saulius},
  timestamp = {2015.02.25},
  creationdate = {2015-02-25T00:00:00},
}

@Lecture{Hoglinger2006,
  author    = {Höglinger, Christian},
  title     = {Conservative Garbage Collection for C},
  year      = {2006},
  file      = {:by-author/H/Höglinger/2006_Höglinger.pdf:PDF},
  groups    = {sg/Garbage collectors},
  keywords  = {C; Computer Science (CS); Conservative Garbage Colelctor; Garbage Collectors},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Hohenberg1964,
  author    = {Hohenberg, P. and Kohn, W.},
  journal   = {Phys. Rev.},
  title     = {Inhomogeneous Electron Gas},
  year      = {1964},
  pages     = {B864--B871},
  volume    = {136},
  doi       = {10.1103/PhysRev.136.B864},
  file      = {:by-author/H/Hohenberg/1964_Hohenberg_B864.pdf:PDF},
  issue     = {3B},
  keywords  = {Quantum Mechanics (QM)},
  owner     = {andrius},
  publisher = {American Physical Society},
  timestamp = {2014.04.14},
  creationdate = {2014-04-14T00:00:00},
}

@Presentation{Hol2011,
  author    = {Hol, Wim G.J.},
  title     = {Protein Crystallization, Crystal CryoProtection and Crystal Annealing},
  year      = {2011},
  file      = {2011_Hol_slides.pdf:by-author/H/Hol/2011_Hol_slides.pdf:PDF},
  owner     = {saulius},
  timestamp = {2013.11.06},
  creationdate = {2013-11-06T00:00:00},
  url       = {http://bstr521.biostr.washington.edu/PDF/CrystalGrowth11.pdf},
}

@Article{Holbrook2001,
  author    = {Holbrook, J. A. and Tsodikov, O. V. and Saecker, R. M. and Record, Jr, M. T.},
  journal   = {Journal of Molecular Biology},
  title     = {Specific and non-specific interactions of integration host factor with DNA: thermodynamic evidence for disruption of multiple IHF surface salt-bridges coupled to DNA binding.},
  year      = {2001},
  pages     = {379--401},
  volume    = {310},
  abstract  = {Site-specific DNA binding of architectural protein integration host factor (IHF) is involved in formation of functional multiprotein-DNA assemblies in Escherichia coli, while non-specific binding of IHF and other histone-like proteins serves to structure the nucleoid. Here, we report an isothermal titration calorimetry study of the thermodynamics of binding IHF to a 34 bp fragment composed entirely of the specific H' site from lambda-phage DNA. At low to moderate [K(+)] (60-100 mM), strong competition is observed between specific and non-specific binding as a result of a low specificity ratio (approximately 10(2)) and a very small non-specific site size. In this [K(+)] range, both specific and non-specific binding are enthalpy-driven, with large negative enthalpy, entropy and heat capacity changes and binding constants that are insensitive to [K(+)]. Above 100 mM K(+), only specific binding is observed, and both the binding constant and the magnitudes of enthalpy, entropy and heat capacity changes all decrease strongly with increasing [K(+)]. When interpreted in the context of the structure of the specific complex, the thermodynamics provide compelling evidence for a previously unrecognized design principle by which proteins that form extensive binding interfaces with nucleic acids control binding constants, binding site sizes and effects of temperature and ion concentrations on stability and specificity. We propose that up to 22 of the 23 IHF cationic side-chains that are located within 6 A of DNA phosphate oxygen atoms in the complex, are masked in the absence of DNA by pairing with anionic carboxylate groups in intramolecular salt-bridges (dehydrated ion-pairs). These salt-bridges increase in stability with increasing temperature and decreasing [K(+)]. To explain the unusual thermodynamics of IHF-DNA interactions, we propose that both specific and non-specific binding at low [K(+)] require disruption of salt-bridges (as many as 18 for specific binding) whereupon many of the unmasked charged groups hydrate and the cationic groups interact with DNA. From structural or thermodynamic parallels with IHF, we propose that large-scale coupling of disruption of protein salt-bridges to DNA binding is significant for other large-interface DNA wrapping proteins including the nucleosome, lac repressor core tetramer, RNA polymerase core protein, HU and SSB.},
  file      = {:by-author/H/Holbrook/2001_Holbrook_379.pdf:PDF},
  keywords  = {Jen Jacobson},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Holder2003,
  author    = {Mark Holder and Paul O. Lewis},
  journal   = {Nature Reviews Genetics},
  title     = {Phylogeny estimation: traditional and Bayesian approaches},
  year      = {2003},
  pages     = {275--283},
  volume    = {4},
  doi       = {10.1038/nrg1044},
  file      = {:by-author/H/Holder/2003_Holder_275.pdf:PDF},
  groups    = {sg/Bayesian},
  keywords  = {Bayesian Statistics; Bioinformatics; Parsimony; Phylogenetic Trees; Systematics},
  owner     = {saulius},
  timestamp = {2012.10.09},
  creationdate = {2012-10-09T00:00:00},
}

@Article{Holliday2005,
  author    = {Holliday, Gemma L. and Bartlett, Gail J. and Almonacid, Daniel E. and O'Boyle, Noel M. and Murray-Rust, Peter and Thornton, Janet M. and Mitchell, John B. O.},
  journal   = {Bioinformatics},
  title     = {MACiE: a database of enzyme reaction mechanisms},
  year      = {2005},
  pages     = {4315--4316},
  volume    = {21},
  abstract  = {Summary: MACiE (mechanism, annotation and classification in enzymes) is a publicly available web-based database, held in CMLReact (an XML application), that aims to help our understanding of the evolution of enzyme catalytic mechanisms and also to create a classification system which reflects the actual chemical mechanism (catalytic steps) of an enzyme reaction, not only the overall reaction.Availability: http://www-mitchell.ch.cam.ac.uk/macie/Contact: jbom1@cam.ac.uk},
  doi       = {10.1093/bioinformatics/bti693},
  eprint    = {http://bioinformatics.oxfordjournals.org/content/21/23/4315.full.pdf+html},
  file      = {2005_Holliday_4315.pdf:by-author/H/Holliday/2005_Holliday_4315.pdf:PDF},
  keywords  = {CML; Chemoinformatics; Crystallography; Data Formats; Data Management; X-ray Crystallography; XML},
  owner     = {saulius},
  timestamp = {2014.06.24},
  creationdate = {2014-06-24T00:00:00},
  url       = {http://bioinformatics.oxfordjournals.org/content/21/23/4315.abstract},
}

@Article{Holliday2006,
  author    = {Holliday, Gemma L. and Murray-Rust, Peter and Rzepa, Henry S.},
  journal   = {Journal of Chemical Information and Modeling},
  title     = {Chemical Markup, XML, and the World Wide Web. 6. CMLReact, an XML Vocabulary for Chemical Reactions},
  year      = {2006},
  pages     = {145--157},
  volume    = {46},
  abstract  = {A set of components (CMLReact) for managing chemical and biochemical reactions has been added to CML. These can be combined to support most of the strategies for the formal representation of reactions. The elements, attributes, and types are formally defined as XMLSchema components, and their semantics are developed. New syntax and semantics in CML are reported and illustrated with 10 examples.},
  doi       = {10.1021/ci0502698},
  eprint    = {http://pubs.acs.org/doi/pdf/10.1021/ci0502698},
  file      = {2006_Holliday_145.pdf:by-author/H/Holliday/2006_Holliday_145.pdf:PDF},
  keywords  = {CML; Chemoinformatics; Crystallography; Data Formats; Data Management; X-ray Crystallography; XML},
  owner     = {saulius},
  timestamp = {2014.06.24},
  creationdate = {2014-06-24T00:00:00},
  url       = {http://pubs.acs.org/doi/abs/10.1021/ci0502698},
}

@Article{Holm2000,
  author    = {Holm, L and Park, J},
  journal   = {Bioinformatics (Oxford, England)},
  title     = {DaliLite workbench for protein structure comparison.},
  year      = {2000},
  pages     = {566--7},
  volume    = {16},
  file      = {Holm_2000_566.pdf:by-author/H/Holm/2000_Holm_566.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Holm1998,
  author    = {Holm, L and Sander, C},
  journal   = {Proteins},
  title     = {Dictionary of recurrent domains in protein structures.},
  year      = {1998},
  pages     = {88--96},
  volume    = {33},
  abstract  = {The rapid growth in the number of experimentally determined three-dimensional protein structures has sharpened the need for comprehensive and up-to-date surveys of known structures. Classic work on protein structure classification has made it clear that a structural survey is best carried out at the level of domains, i.e., substructures that recur in evolution as functional units in different protein contexts. We present a method for automated domain identification from protein structure atomic coordinates based on quantitative measures of compactness and, as the new element, recurrence. Compactness criteria are used to recursively divide a protein into a series of successively smaller and smaller substructures. Recurrence criteria are used to select an optimal size level of these substructures, so that many of the chosen substructures are common to different proteins at a high level of statistical significance. The joint application of these criteria automatically yields consistent domain definitions between remote homologs, a result difficult to achieve using compactness criteria alone. The method is applied to a representative set of 1,137 sequence-unique protein families covering 6,500 known structures. Clustering of the resulting set of domains (substructures) yields 594 distinct fold classes (types of substructures). The Dali Domain Dictionary (http://www.embl-ebi.ac.uk/dali/) not only provides a global structural classification, but also a comprehensive description of families of protein sequences grouped around representative proteins of known structure. The classification will be continuously updated and can serve as a basis for improving our understanding of protein evolution and function and for evolving optimal strategies to complete the map of all natural protein structures.},
  file      = {Holm_1998_88.pdf:by-author/H/Holm/1998_Holm_88.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Holm1993,
  author    = {Holm, L. and Sander, C.},
  journal   = {J. Mol. Biol.},
  title     = {Protein structure comparison by alignment of distance matrices},
  year      = {1993},
  month     = {Sep},
  number    = {1},
  pages     = {123--38},
  volume    = {233},
  abstract  = {With a rapidly growing pool of known tertiary structures, the importance of protein structure comparison parallels that of sequence alignment. We have developed a novel algorithm (DALI) for optimal pairwise alignment of protein structures. The three-dimensional co-ordinates of each protein are used to calculate residue-residue (C alpha-C alpha) distance matrices. The distance matrices are first decomposed into elementary contact patterns, e.g. hexapeptide-hexapeptide submatrices. Then, similar contact patterns in the two matrices are paired and combined into larger consistent sets of pairs. A Monte Carlo procedure is used to optimize a similarity score defined in terms of equivalent intramolecular distances. Several alignments are optimized in parallel, leading to simultaneous detection of the best, second-best and so on solutions. The method allows sequence gaps of any length, reversal of chain direction and free topological connectivity of aligned segments. Sequential connectivity can be imposed as an option. The method is fully automatic and identifies structural resemblances and common structural cores accurately and sensitively, even in the presence of geometrical distortions. An all-against-all alignment of over 200 representative protein structures results in an objective classification of known three-dimensional folds in agreement with visual classifications. Unexpected topological similarities of biological interest have been detected, e.g. between the bacterial toxin colicin A and globins, and between the eukaryotic POU-specific DNA-binding domain and the bacterial lambda repressor},
  address   = {European Molecular Biology Laboratory, Heidelberg, Federal Republic of Germany},
  doi       = {10.1006/jmbi.1993.1489},
  file      = {1993_Holm_123.pdf:by-author/H/Holm/1993_Holm_123.pdf:PDF},
  keywords  = {Difference Distance Matrix; Protein Structure Comparison},
  owner     = {em},
  timestamp = {2016.06.16},
  creationdate = {2016-06-16T00:00:00},
  url       = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&dopt=abstract&list_uids=8377180},
}

@Webpage{Holub2003,
  author    = {Allen Holub},
  retrieved = {2009-02-07},
  title     = {Why getter and setter methods are evil: Make your code more maintainable by avoiding accessors},
  url       = {http://www.javaworld.com/article/2073723/core-java/why-getter-and-setter-methods-are-evil.html},
  year      = {2003},
  file      = {:by-author/H/Holub/2003_Holub_a.war:WAR;:by-author/H/Holub/2003_Holub.war:WAR},
  keywords  = {Computer Science (CS); Fragile-base-class-problem},
  owner     = {saulius},
  timestamp = {2015.03.02},
  creationdate = {2015-03-02T00:00:00},
}

@Webpage{Holub2003a,
  author    = {Allen Holub},
  retrieved = {2008-07-28},
  title     = {Why extends is evil: Improve your code by replacing concrete base classes with interfaces},
  url       = {http://www.javaworld.com/article/2073649/core-java/why-extends-is-evil.html},
  year      = {2003},
  abstract  = {Most good designers avoid implementation inheritance (the extends relationship) like the plague. As much as 80 percent of your code should be written entirely in terms of interfaces, not concrete base classes. The Gang of Four Design Patterns book, in fact, is largely about how to replace implementation inheritance with interface inheritance. This article describes why designers have such odd beliefs.},
  file      = {:by-author/H/Holub/2003_Holub_b.war:},
  keywords  = {Computer Science (CS); Fragile-base-class-problem},
  owner     = {saulius},
  timestamp = {2015.03.02},
  creationdate = {2015-03-02T00:00:00},
}

@Manuscript{Holub1997,
  author    = {Allen I. Holub},
  title     = {Compiler Design in C},
  year      = {1997},
  keywords  = {Compiler Design; Computer Science (CS)},
  file      = {:by-author/H/Holub/1997_Holub.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Holubova2004,
  author    = {Holubová, I. and Vejsadová, S. and Firman, K. and Weiserová, M.},
  journal   = {Biochemical and biophysical research communications},
  title     = {Cellular localization of Type I restriction-modification enzymes is family dependent.},
  year      = {2004},
  pages     = {375--80},
  volume    = {319},
  abstract  = {Cellular localization of Type I restriction-modification enzymes EcoKI, EcoAI, and EcoR124I-the most frequently studied representatives of IA, IB, and IC families-was analyzed by immunoblotting of subcellular fractions isolated from Escherichia coli strains harboring the corresponding hsd genes. EcoR124I shows characteristics similar to those of EcoKI. The complex enzymes are associated with the cytoplasmic membrane via DNA interaction as documented by the release of the Hsd subunits from the membrane into the soluble fraction following benzonase treatment. HsdR subunits of the membrane-bound enzymes EcoKI and EcoR124I are accessible, though to a different extent, at the external surface of cytoplasmic membrane as shown by trypsinization of intact spheroplasts. EcoAI strongly differs from EcoKI and EcoR124I, since neither benzonase nor trypsin affects its association with the cytoplasmic membrane. Possible reasons for such a different organization are discussed in relation of the control of the restriction-modification activities in vivo.},
  file      = {:by-author/H/Holubová/2004_Holubova_375.pdf:PDF},
  keywords  = {TypeI},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Holubova2000,
  author    = {Holubová, I. and Vejsadová, S. and Weiserová, M. and Firman, K.},
  journal   = {Biochemical and biophysical research communications},
  title     = {Localization of the type I restriction-modification enzyme EcoKI in the bacterial cell.},
  year      = {2000},
  pages     = {46--51},
  volume    = {270},
  abstract  = {To localise the type I restriction-modification (R-M) enzyme EcoKI within the bacterial cell, the Hsd subunits present in subcellular fractions were analysed using immunoblotting techniques. The endonuclease (ENase) as well as the methylase (MTase) were found to be associated with the cytoplasmic membrane. HsdR and HsdM subunits produced individually were soluble, cytoplasmic polypeptides and only became membrane-associated when coproduced with the insoluble HsdS subunit. The release of enzyme from the membrane fraction following benzonase treatment indicated a role for DNA in this interaction. Trypsinization of spheroplasts revealed that the HsdR subunit in the assembled ENase was accessible to protease, while HsdM and HsdS, in both ENase and MTase complexes, were fully protected against digestion. We postulate that the R-M enzyme EcoKI is associated with the cytoplasmic membrane in a manner that allows access of HsdR to the periplasmic space, while the MTase components are localised on the inner side of the plasma membrane.},
  file      = {:by-author/H/Holubová/2000_Holubova_46.pdf:PDF},
  keywords  = {TypeI},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@TechReport{Holzle1993,
  author      = {Urs Hölzle},
  institution = {Computer Systems Laboratory, Stanford University},
  title       = {A Fast Write Barrier for Generational Garbage Collectors},
  year        = {1993},
  abstract    = {Generational garbage collectors need to keep track of references from older to younger generations so that younger generations can be garbage-collected without inspecting every object in the older generation(s) [LH83], [Ung86]. The set of locations potentially containing pointers to newer objects is often called the remembered set [Ung86]. At every store, the system must ensure that the updated location is added to the remembered set if the store creates a reference from an older to a newer object. This mechanism is usually referred to as a write barrier or store check. For some stores, the compiler can know statically that no store check is necessary, for example, when storing an integer (assuming that integers are implemented as immediates rather than as real heap-allocated objects). However, in the general case, a store check must be executed for every store operation. Since stores are fairly frequent in non-functional languages, an efficient write barrier implementation is essential. The write barrier implementation described here reduces the write barrier overhead in the mutator to only two extra instructions per checked store.},
  file        = {:by-author/H/Hölzle/1993_Hölzle.pdf:PDF},
  groups      = {sg/Garbage collectors},
  keywords    = {Computer Science (CS); Garbage Collectors},
  owner       = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Honig1995,
  author    = {Honig, B and Nicholls, A},
  journal   = {Science (New York, N.Y.)},
  title     = {Classical electrostatics in biology and chemistry.},
  year      = {1995},
  pages     = {1144--9},
  volume    = {268},
  file      = {1995_Honig_1144.pdf:by-author/H/Honig/1995_Honig_1144.pdf:PDF},
  keywords  = {Poisson-Boltzmann eq; Protein Physics; Solvatation},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Hooft1996,
  author    = {Hooft, R W and Vriend, G and Sander, C and Abola, E E},
  journal   = {Nature},
  title     = {Errors in protein structures.},
  year      = {1996},
  pages     = {272},
  volume    = {381},
  file      = {1996_Hooft_272.pdf:by-author/H/Hooft/1996_Hooft_272.pdf:PDF;1996_Hooft_272.djvu:by-author/H/Hooft/1996_Hooft_272.djvu:DJVU},
  keywords  = {Data Quality; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Hooft1994,
  author    = {R. W. W. Hooft and C. Sander and G. Vriend},
  journal   = {Journal of Applied Crystallography},
  title     = {Reconstruction of Symmetry-Related Molecules from Protein Data Bank (PDB) Files},
  year      = {1994},
  pages     = {1006--1009},
  volume    = {27},
  abstract  = {Many natural proteins are active as multimers. Crystallographic protein databases, however, generally store only part of the native multimer, the asymmetric unit, along with symmetry information. As a result of inaccuracies in the data, it is not always possible to reconstruct the native multimer. Here, a set of methods is presented that are designed to cope with inconsistencies in symmetry information. Applications include the validation of Protein Data Bank entries and the automatic generation of symmetry contacts for inspection and analysis.},
  doi       = {10.1107/S0021889894007764},
  file      = {:by-author/H/Hooft/1994_Hooft_1006.pdf:PDF},
  keywords  = {Symmetry; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0021889894007764},
}

@Article{Hoover1985,
  author           = {Hoover, William G.},
  journal          = {Phys. Rev. A},
  title            = {Canonical dynamics: Equilibrium phase-space distributions},
  year             = {1985},
  month            = {Mar},
  pages            = {1695--1697},
  volume           = {31},
  comment          = {Cited in https://computecanada.github.io/molmodsim-md-theory-lesson-novice/reference.html.},
  creationdate     = {2016-02-24T00:00:00},
  doi              = {10.1103/PhysRevA.31.1695},
  file             = {1985_Hoover_1695.pdf:by-author/H/Hoover/1985_Hoover_1695.pdf:PDF},
  groups           = {sg/Molecular dynamics},
  issue            = {3},
  keywords         = {Molecular Dynamics (MD); Thermostats},
  modificationdate = {2023-01-29T18:15:05},
  numpages         = {0},
  owner            = {saulius},
  publisher        = {American Physical Society},
  timestamp        = {2016.02.24},
  url              = {http://link.aps.org/doi/10.1103/PhysRevA.31.1695},
}

@Article{Hoover1982,
  author    = {Hoover, William G. and Ladd, Anthony J. C. and Moran, Bill},
  journal   = {Phys. Rev. Lett.},
  title     = {High-Strain-Rate Plastic Flow Studied via Nonequilibrium Molecular Dynamics},
  year      = {1982},
  month     = {Jun},
  pages     = {1818--1820},
  volume    = {48},
  comment   = {Referenced by: (Nose1984) Nosé, S. A unified formulation of the constant temperature molecular dynamics methods The Journal of Chemical Physics, 1984, 81, 511-519 doi: 10.1063/1.447334},
  doi       = {10.1103/PhysRevLett.48.1818},
  file      = {1982_Hoover_1818.pdf:by-author/H/Hoover/1982_Hoover_1818.pdf:PDF},
  groups    = {sg/Molecular dynamics},
  issue     = {26},
  keywords  = {Molecular Dynamics (MD); Thermostats},
  numpages  = {0},
  owner     = {saulius},
  publisher = {American Physical Society},
  timestamp = {2016.02.24},
  creationdate = {2016-02-24T00:00:00},
  url       = {http://link.aps.org/doi/10.1103/PhysRevLett.48.1818},
}

@InBook{Hopcroft2007,
  author    = {Hopcroft},
  chapter   = {2},
  pages     = {8},
  title     = {Grammars},
  year      = {2007},
  file      = {:by-author/H/Hopcroft/2007_Hopcroft_8.pdf:PDF},
  keywords  = {Compiler Design; Computer Science (CS)},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Hopkins2014,
  author       = {Andrew L Hopkins and György M Keserü and Paul D Leeson and David C Rees and Charles H Reynolds},
  journal      = {Nat Rev Drug Discov},
  title        = {The role of ligand efficiency metrics in drug discovery.},
  year         = {2014},
  month        = {Feb},
  number       = {2},
  pages        = {105--121},
  volume       = {13},
  abstract     = {The judicious application of ligand or binding efficiency metrics, which quantify the molecular properties required to obtain binding affinity for a drug target, is gaining traction in the selection and optimization of fragments, hits and leads. Retrospective analysis of recently marketed oral drugs shows that they frequently have highly optimized ligand efficiency values for their targets. Optimizing ligand efficiency metrics based on both molecular mass and lipophilicity, when set in the context of the specific target, has the potential to ameliorate the inflation of these properties that has been observed in current medicinal chemistry practice, and to increase the quality of drug candidates.},
  creationdate = {2016-06-06T00:00:00},
  doi          = {10.1038/nrd4163},
  file         = {2014_Hopkins_105.pdf:by-author/H/Hopkins/2014_Hopkins_105.pdf:PDF},
  institution  = {Gfree Bio, 3805 Old Easton Road, Doylestown, Pennsylvania 18902, USA.},
  keywords     = {Administration; Administration /&/ Dosage/chemistry; Databases; Drug Discovery; Factual; Humans; Ligands; Methods; Molecular Structure; Molecular Weight (MW); Oral; Pharmaceutical Preparations; Physicochemical Processes; Protein Binding; Small Molecule Libraries; Structure-activity Relationship (SAR); Thermodynamics},
  language     = {eng},
  medline-pst  = {ppublish},
  owner        = {alexey},
  pii          = {nrd4163},
  pmid         = {24481311},
  timestamp    = {2016.06.06},
  url          = {http://dx.doi.org/10.1038/nrd4163},
}

@Article{Horn1987,
  author           = {Berthold K. P. Horn},
  journal          = {Journal of the Optical Society of America A},
  title            = {Closed-form solution of absolute orientation using unit quaternions},
  year             = {1987},
  pages            = {629--642},
  volume           = {4},
  comment          = {Cited in Babcock1994a (1994_Babcock_125.pdf).
"That is, the translation is just the difference of the right centroid and the scaled and rotated left centroid." Contradicts Chen2004?},
  creationdate     = {2012-05-16T00:00:00},
  doi              = {10.1364/JOSAA.4.000629},
  file             = {:by-author/H/Horn/1987_Horn_629.pdf:PDF;manuscript:by-author/H/Horn/1999_Horn_manuscript.pdf:PDF},
  groups           = {sg/Molecule superposion, sg/Superposition, sg/Bioinf. Algorithms},
  keywords         = {Algorithms; Quaternions; Structure Superposition},
  modificationdate = {2024-05-12T17:47:33},
  owner            = {saulius},
  timestamp        = {2012.05.16},
}

@Manual{Hornik2013,
  title     = {{movMF}: An {R} Package for Fitting Mixtures of {v}on {M}ises-{F}isher Distributions},
  author    = {Kurt Hornik and Bettina Grun},
  month     = {Sep.},
  year      = {2013},
  abstract  = {Finite mixtures of von Mises-Fisher distributions allow to apply model-based clustering methods to data which is of standardized length, i.e., all data points lie on the unit sphere. The R package movMF contains functionality to draw samples from finite mixtures of von Mises-Fisher distributions and to fit these models using the expectation-maximization al- gorithm for maximum likelihood estimation. Special features are the possibility to use sparse matrix representations for the input data, different variants of the expectation- maximization algorithm, different methods for determining the concentration parameters in the M-step and to impose constraints on the concentration parameters over the com- ponents. In this paper we describe the main fitting function of the package and illustrate its application. We also discuss how several numerical issues are resolved which occur for estimating the concentration parameters and for determining the normalizing constant of the von Mises-Fisher distribution.},
  file      = {:by-author/H/Hornik/2013_Hornik_manual.pdf:PDF},
  keywords  = {Expectation Maximisation; R},
  owner     = {andrius},
  timestamp = {2013.10.09},
  creationdate = {2013-10-09T00:00:00},
  url       = {http://cran.r-project.org/web/packages/movMF/vignettes/movMF.pdf},
}

@TechReport{Hors1991,
  author      = {Arnaud Le Hors and Colas Nahaboo},
  institution = {BULL Research FRANCE Sophia Antipolis},
  title       = {XPM: The X PixMap Format},
  year        = {1991},
  month       = {November},
  file        = {:by-author/H/Hors/1991_Hors.ps.gz:PostScript;:by-author/H/Hors/1991_Hors.pdf:PDF},
  owner       = {saulius},
  timestamp = {2015.02.27},
  creationdate = {2015-02-27T00:00:00},
}

@Article{Horsford1887,
  author    = {Horsford, E. A.},
  journal   = {Science (New York, N.Y.)},
  title     = {Volapuk.},
  year      = {1887},
  pages     = {10},
  volume    = {10},
  file      = {:by-author/H/Horsford/1887_Horsford_10.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Manuscript{Horton2004a,
  author    = {Horton},
  title     = {Effect of Backbone Sugar Pucker on DNA Base Flipping},
  year      = {2004},
  file      = {:by-author/H/Horton/2004_Horton_manuscript.pdf:PDF},
  owner     = {saulius},
  pages     = {manuscript},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Horton2012,
  author    = {Horton, John R. and Mabuchi, Megumu Yamada and Cohen-Karni, Devora and Zhang, Xing and Griggs, Rose M. and Samaranayake, Mala and Roberts, Richard J. and Zheng, Yu and Cheng, Xiaodong},
  journal   = {Nucleic Acids Res.},
  title     = {Structure and cleavage activity of the tetrameric MspJI DNA modification-dependent restriction endonuclease},
  year      = {2012},
  pages     = {9763–9773},
  volume    = {40},
  abstract  = {The MspJI modification-dependent restriction endonuclease recognizes 5-methylcytosine or 5-hydroxymethylcytosine in the context of CNN(G/ A) and cleaves both strands at fixed distances (N12/N16) away from the modified cytosine at the 30 -side. We determined the crystal structure of MspJI of Mycobacterium sp. JLS at 2.05-A reso- lution. Each protein monomer harbors two domains: an N-terminal DNA-binding domain and a C-terminal endonuclease. The N-terminal domain is structurally similar to that of the eukaryotic SET and RING-associated domain, which is known to bind to a hemi-methylated CpG dinucleotide. Four protein monomers are found in the crystallographic asym- metric unit. Analytical gel-filtration and ultracentri- fugation measurements confirm that the protein exists as a tetramer in solution. Two monomers form a back-to-back dimer mediated by their C-terminal endonuclease domains. Two back-to- back dimers interact to generate a tetramer with two double-stranded DNA cleavage modules. Each cleavage module contains two active sites facing each other, enabling double-strand DNA cuts. Biochemical, mutagenesis and structural character- ization suggest three different monomers of the tetramer may be involved respectively in binding the modified cytosine, making the first proximal N12 cleavage in the same strand and then the second distal N16 cleavage in the opposite strand. Both cleavage events require binding of at least a second recognition site either in cis or in trans.},
  doi       = {10.1093/nar/gks719},
  file      = {:by-author/H/Horton/2012_Horton_9763.pdf:PDF},
  keywords  = {Crystal Structure; Methyl-directed; MspJI; REase; Restriction Endonuclease (RE); Tetramer},
  owner     = {em},
  timestamp = {2013.10.28},
  creationdate = {2013-10-28T00:00:00},
}

@Article{Horton2004,
  author    = {Horton, John R. and Ratner, Gary and Banavali, Nilesh K. and Huang, Niu and Choi, Yongseok and Maier, Martin A. and Marquez, Victor E. and MacKerell, Jr, Alexander D. and Cheng, Xiaodong},
  journal   = {Nucleic acids research},
  title     = {Caught in the act: visualization of an intermediate in the DNA base-flipping pathway induced by HhaI methyltransferase.},
  year      = {2004},
  pages     = {3877--86},
  volume    = {32},
  abstract  = {Rotation of a DNA or RNA nucleotide out of the double helix and into a protein pocket ('base flipping') is a mechanistic feature common to some DNA/RNA-binding proteins. Here, we report the structure of HhaI methyltransferase in complex with DNA containing a south-constrained abasic carbocyclic sugar at the target site in the presence of the methyl donor byproduct AdoHcy. Unexpectedly, the locked south pseudosugar appears to be trapped in the middle of the flipping pathway via the DNA major groove, held in place primarily through Van der Waals contacts with a set of invariant amino acids. Molecular dynamics simulations indicate that the structural stabilization observed with the south-constrained pseudosugar will not occur with a north-constrained pseudosugar, which explains its lowered binding affinity. Moreover, comparison of structural transitions of the sugar and phosphodiester backbone observed during computational studies of base flipping in the M.HhaI-DNA-AdoHcy ternary complex indicate that the south-constrained pseudosugar induces a conformation on the phosphodiester backbone that corresponds to that of a discrete intermediate of the base-flipping pathway. As previous crystal structures of M.HhaI ternary complex with DNA displayed the flipped sugar moiety in the antipodal north conformation, we suggest that conversion of the sugar pucker from south to north beyond the middle of the pathway is an essential part of the mechanism through which flipping must proceed to reach its final destination. We also discuss the possibility of the south-constrained pseudosugar mimicking a transition state in the phosphodiester and sugar moieties that occurs during DNA base flipping in the presence of M.HhaI.},
  file      = {:by-author/H/Horton/2004_Horton_3877.pdf:PDF},
  keywords  = {HhaI},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Horton2006,
  author    = {Horton, John R. and Zhang, Xing and Maunus, Robert and Yang, Zhe and Wilson, Geoffrey G. and Roberts, Richard J. and Cheng, Xiaodong},
  journal   = {Nucleic acids research},
  title     = {DNA nicking by HinP1I endonuclease: bending, base flipping and minor groove expansion.},
  year      = {2006},
  pages     = {939--48},
  volume    = {34},
  abstract  = {HinP1I recognizes and cleaves the palindromic tetranucleotide sequence G downward arrowCGC in DNA. We report three structures of HinP1I-DNA complexes: in the presence of Ca(2+) (pre-reactive complex), in the absence of metal ion (binary complex) and in the presence of Mg(2+) (post-reactive complex). HinP1I forms a back-to-back dimer with two active sites and two DNA duplexes bound on the outer surfaces of the dimer facing away from each other. The 10 bp DNA duplexes undergo protein-induced distortions exhibiting features of A-, B- and Z-conformations: bending on one side (by intercalation of a phenylalanine side chain into the major groove), base flipping on the other side of the recognition site (by expanding the step rise distance of the local base pair to Z-form) and a local A-form conformation between the two central C:G base pairs of the recognition site (by binding of the N-terminal helix in the minor groove). In the pre- and post-reactive complexes, two metals (Ca(2+) or Mg(2+)) are found in the active site. The enzyme appears to cleave DNA sequentially, hydrolyzing first one DNA strand, as seen in the post-reactive complex in the crystalline state, and then the other, as supported by the observation that, in solution, a nicked DNA intermediate accumulates before linearization.},
  file      = {:by-author/H/Horton/2006_Horton_939.pdf:PDF},
  keywords  = {DNA Conf; TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Horton2001a,
  author    = {Nancy C. Horton and Lydia F. Dorner and John J. Perona},
  journal   = {Nature structural biology},
  title     = {Sequence selectivity and degeneracy of a restriction endonuclease mediated by {DNA} intercalation},
  year      = {2001},
  pages     = {42},
  file      = {:by-author/H/Horton/2001_Horton_42.pdf:PDF},
  keywords  = {Indirect; Readout},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Horton1998,
  author      = {N. C. Horton and K. J. Newberry and J. J. Perona},
  journal     = {Proc. Natl. Acad. Sci. U. S. A.},
  title       = {Metal ion-mediated substrate-assisted catalysis in type II restriction endonucleases.},
  year        = {1998},
  month       = {Nov},
  number      = {23},
  pages       = {13489--13494},
  volume      = {95},
  abstract    = {The 2.15-A resolution cocrystal structure of EcoRV endonuclease mutant T93A complexed with DNA and Ca2+ ions reveals two divalent metals bound in one of the active sites. One of these metals is ligated through an inner-sphere water molecule to the phosphate group located 3' to the scissile phosphate. A second inner-sphere water on this metal is positioned approximately in-line for attack on the scissile phosphate. This structure corroborates the observation that the pro-SP phosphoryl oxygen on the adjacent 3' phosphate cannot be modified without severe loss of catalytic efficiency. The structural equivalence of key groups, conserved in the active sites of EcoRV, EcoRI, PvuII, and BamHI endonucleases, suggests that ligation of a catalytic divalent metal ion to this phosphate may occur in many type II restriction enzymes. Together with previous cocrystal structures, these data allow construction of a detailed model for the pretransition state configuration in EcoRV. This model features three divalent metal ions per active site and invokes assistance in the bond-making step by a conserved lysine, which stabilizes the attacking hydroxide ion nucleophile.},
  file        = {1998_Horton_13489.pdf:by-author/H/Horton/1998_Horton_13489.pdf:PDF},
  institution = {Department of Chemistry and Interdepartmental Program in Biochemistry and Molecular Biology, University of California, Santa Barbara, CA 93106-9510, USA.},
  keywords    = {Animals; Deoxyribonucleases; Metals; Molecular Sequence Data; Protein Conformation; Substrate Specificity; Type II Site-Specific},
  owner       = {em},
  pmid        = {9811827},
  timestamp = {2011.06.10},
  creationdate = {2011-06-10T00:00:00},
}

@Article{Horton1998b,
  author    = {Horton, N. C. and Newberry, K. J. and Perona, J. J.},
  journal   = {Proceedings of the National Academy of Sciences of the United States of America},
  title     = {Metal ion-mediated substrate-assisted catalysis in type II restriction endonucleases.},
  year      = {1998},
  pages     = {13489--94},
  volume    = {95},
  abstract  = {The 2.15-A resolution cocrystal structure of EcoRV endonuclease mutant T93A complexed with DNA and Ca2+ ions reveals two divalent metals bound in one of the active sites. One of these metals is ligated through an inner-sphere water molecule to the phosphate group located 3' to the scissile phosphate. A second inner-sphere water on this metal is positioned approximately in-line for attack on the scissile phosphate. This structure corroborates the observation that the pro-SP phosphoryl oxygen on the adjacent 3' phosphate cannot be modified without severe loss of catalytic efficiency. The structural equivalence of key groups, conserved in the active sites of EcoRV, EcoRI, PvuII, and BamHI endonucleases, suggests that ligation of a catalytic divalent metal ion to this phosphate may occur in many type II restriction enzymes. Together with previous cocrystal structures, these data allow construction of a detailed model for the pretransition state configuration in EcoRV. This model features three divalent metal ions per active site and invokes assistance in the bond-making step by a conserved lysine, which stabilizes the attacking hydroxide ion nucleophile.},
  file      = {:by-author/H/Horton/1998_Horton_13489.pdf:PDF},
  keywords  = {Catalysis; TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Horton2001,
  author    = {N. C. Horton and J. J. Perona},
  journal   = {Nat. Struct. Biol.},
  title     = {Making the most of metal ions.},
  year      = {2001},
  month     = {Apr},
  number    = {4},
  pages     = {290--293},
  volume    = {8},
  doi       = {10.1038/86149},
  file      = {2001_Horton_42.pdf:by-author/H/Horton/2001_Horton_42.pdf:PDF},
  keywords  = {Amino Acid Sequence; Binding Sites; Calcium; Chemical; Crystallography; DNA; DNA Restriction Enzymes; DNA-Binding Proteins; Gene Conversion; Introns; Magnesium; Metals; Models; Water; X-Ray},
  owner     = {em},
  pii       = {86149},
  pmid      = {11276242},
  timestamp = {2011.06.10},
  creationdate = {2011-06-10T00:00:00},
  url       = {http://dx.doi.org/10.1038/86149},
}

@Article{Horton1998a,
  author      = {N. C. Horton and J. J. Perona},
  journal     = {J. Mol. Biol.},
  title       = {Role of protein-induced bending in the specificity of DNA recognition: crystal structure of EcoRV endonuclease complexed with d(AAAGAT) + d(ATCTT).},
  year        = {1998},
  month       = {Apr},
  number      = {4},
  pages       = {779--787},
  volume      = {277},
  abstract    = {The crystal structure of EcoRV endonuclease has been determined at 2. 1 A resolution complexed to two five-base-pair DNA duplexes each containing the cognate recognition half-site. The highly localized 50 degrees bend into the major groove seen at the center TA-step of the continuous GATATC site is preserved in this discontinuous DNA complex lacking the scissile phosphates. Thus, this crystal structure provides evidence that covalent constraints associated with a continuous target site are not essential to enzyme-induced DNA bending, even when these constraints are removed directly at the locus of the bend. The scissile phosphates are also absent in the crystal structure of EcoRV bound to the non-specific site TCGCGA, which shows a straight B-like conformation. We conclude that DNA bending by EcoRV is governed only by the sequence and is not influenced by the continuity of the phosphodiester backbone. Together with other data showing that cleavable non-cognate sites are bent, these results indicate that EcoRV bends non-cognate sites differing by one or two base-pairs from GATATC, but does not bend non-specific sites that are less similar. Structural and thermodynamic considerations suggest that the sequence-dependent energy cost of DNA bending is likely to play an important role in determining the specificity of EcoRV. This differential cost is manifested at the binding step for bent non-cognate sequences and at the catalytic step for unbent non-specific sequences.},
  doi         = {10.1006/jmbi.1998.1655},
  file        = {1998_Horton_13489.pdf:by-author/H/Horton/1998_Horton_13489.pdf:PDF},
  institution = {Department of Chemistry and Interdepartmental Program in Biochemistry and Molecular Biology, University of California at Santa Barbara, Santa Barbara, CA, 93106-9510, USA.},
  keywords    = {Base Sequence; Binding Sites; Crystallography; DNA; Deoxyribonucleases; Macromolecular Substances; Models; Molecular; Molecular Sequence Data; Nucleic Acid Conformation; Protein Conformation; Substrate Specificity; Type II Site-Specific; X-Ray},
  owner       = {em},
  pii         = {S0022-2836(98)91655-2},
  pmid        = {9545372},
  timestamp = {2011.06.10},
  creationdate = {2011-06-10T00:00:00},
  url         = {http://dx.doi.org/10.1006/jmbi.1998.1655},
}

@Article{Horvath2008,
  author    = {Horvath, Philippe and Romero, Dennis A. and Coûté-Monvoisin, Anne-Claire and Richards, Melissa and Deveau, Hélène and Moineau, Sylvain and Boyaval, Patrick and Fremaux, Christophe and Barrangou, Rodolphe},
  journal   = {Journal of bacteriology},
  title     = {Diversity, activity, and evolution of CRISPR loci in Streptococcus thermophilus.},
  year      = {2008},
  pages     = {1401--12},
  volume    = {190},
  abstract  = {Clustered regularly interspaced short palindromic repeats (CRISPR) are hypervariable loci widely distributed in prokaryotes that provide acquired immunity against foreign genetic elements. Here, we characterize a novel Streptococcus thermophilus locus, CRISPR3, and experimentally demonstrate its ability to integrate novel spacers in response to bacteriophage. Also, we analyze CRISPR diversity and activity across three distinct CRISPR loci in several S. thermophilus strains. We show that both CRISPR repeats and cas genes are locus specific and functionally coupled. A total of 124 strains were studied, and 109 unique spacer arrangements were observed across the three CRISPR loci. Overall, 3,626 spacers were analyzed, including 2,829 for CRISPR1 (782 unique), 173 for CRISPR2 (16 unique), and 624 for CRISPR3 (154 unique). Sequence analysis of the spacers revealed homology and identity to phage sequences (77%), plasmid sequences (16%), and S. thermophilus chromosomal sequences (7%). Polymorphisms were observed for the CRISPR repeats, CRISPR spacers, cas genes, CRISPR motif, locus architecture, and specific sequence content. Interestingly, CRISPR loci evolved both via polarized addition of novel spacers after exposure to foreign genetic elements and via internal deletion of spacers. We hypothesize that the level of diversity is correlated with relative CRISPR activity and propose that the activity is highest for CRISPR1, followed by CRISPR3, while CRISPR2 may be degenerate. Globally, the dynamic nature of CRISPR loci might prove valuable for typing and comparative analyses of strains and microbial populations. Also, CRISPRs provide critical insights into the relationships between prokaryotes and their environments, notably the coevolution of host and viral genomes.},
  file      = {:by-author/H/Horvath/2008_Horvath_1401.pdf:PDF},
  groups    = {sg/CRISPR-Cas},
  keywords  = {CRISPR},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Hoshino2016,
  author       = {Hoshino, M. and Khutia, A. and Xing, H. and Inokuma, Y. and Fujita, M.},
  journal      = {{IUCrJ}},
  title        = {The crystalline sponge method updated},
  year         = {2016},
  issn         = {2052-2525},
  number       = {2},
  pages        = {139--151},
  volume       = {3},
  abstract     = {Crystalline sponges are porous metal complexes that can absorb and orient common organic molecules in their pores and make them observable by conventional X-ray structure analysis (crystalline sponge method). In this study, all of the steps in the crystalline sponge method, including sponge crystal preparation, pore–solvent exchange, guest soaking, data collection and crystallographic analysis, are carefully examined and thoroughly optimized to provide reliable and meaningful chemical information as chemical crystallography. Major improvements in the method have been made in the guest-soaking and data-collection steps. In the soaking step, obtaining a high site occupancy of the guest is particularly important, and dominant parameters for guest soaking (e.g. temperature, time, concentration, solvents) therefore have to be optimized for every sample compound. When standard conditions do not work, a high-throughput method is useful for efficiently optimizing the soaking conditions. The X-ray experiments are also carefully re-examined. Significant improvement of the guest data quality is achieved by complete data collection at high angle regions. The appropriate disorder treatment of the most flexible {ZnI}2 portions of the host framework and refinement of the solvents filling the remaining void are also particularly important for obtaining better data quality. A benchmark test for the crystalline sponge method toward an achiral molecule is proposed with a guaiazulene guest, in which the guest structure (with ∼ 100\% site occupancy) is refined without applying any restraints or constraints. The obtained data quality with Rint = 0.0279 and R1 = 0.0379 is comparable with that of current conventional crystallographic analysis for small molecules. Another benchmark test for this method toward a chiral molecule is also proposed with a santonin guest. The crystallographic data obtained [Rint = 0.0421, R1 = 0.0312, Flack (Parsons) = −0.0071 (11)] represents the potential ability of this method for reliable absolute structure determination.},
  date         = {2016-03-01},
  doi          = {10.1107/S2052252515024379},
  file         = {Full Text PDF:by-author/H/Hoshino/2016_Hoshino_139.pdf:PDF;Snapshot:by-author/H/Hoshino/2016_Hoshino_139.html:URL},
  groups       = {sg/MOF, sg/MOFs, am/MOFs},
  journaltitle = {{IUCrJ}},
  keywords     = {Chemical Crystallography; Crystalline Sponge Method; Metal-Organic Frameworks (MOF); Porous Materials},
  langid       = {english},
  owner        = {saulius},
  rights       = {http://creativecommons.org/licenses/by/2.0/uk},
  shortjournal = {{IUCrJ}},
  timestamp = {2017.01.29},
  creationdate = {2017-01-29T00:00:00},
  url          = {http://scripts.iucr.org/cgi-bin/paper?de5035},
  urldate      = {2017-01-29},
}

@TechReport{Hosseini2004,
  author      = {Ali Hosseini},
  institution = {Helsingin yliopisto – helsingfors universitet},
  title       = {Continuous Queries Over Append-Only Databases},
  year        = {2004},
  file        = {:by-author/H/Hosseini/2004_Hosseini.pdf:PDF},
  keywords    = {Computer Science (CS); Databases; Organisation},
  owner       = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@InBook{HouseXXXX,
  author    = {House, Donald H.},
  chapter   = {14},
  pages     = {89--105},
  title     = {3D Computer Graphics: Spline Curves},
  file      = {:by-author/H/House/XXXX_House_89.pdf:PDF},
  owner     = {andrius},
  timestamp = {2012.07.13},
  creationdate = {2012-07-13T00:00:00},
  url       = {http://www.cs.clemson.edu/~dhouse/courses/405/notes/splines.pdf},
}

@Article{Hovmoller2002,
  author    = {Hovm{\"{o}}ller, Sven and Zhou, Tuping and Ohlson, Tomas},
  journal   = {Acta Crystallographica Section D},
  title     = {Conformations of amino acids in proteins},
  year      = {2002},
  pages     = {768--776},
  volume    = {58},
  doi       = {10.1107/S0907444902003359},
  file      = {gr2189.pdf:by-author/H/Hovmoller/2002_Hovmoller_768.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444902003359},
}

@Article{Howard1994,
  author     = {Howard, J B and Rees, D C},
  journal    = {Annual Review of Biochemistry},
  title      = {Nitrogenase: {A} nucleotide-dependent molecular switch},
  year       = {1994},
  issn       = {0066-4154, 1545-4509},
  pages      = {235--264},
  volume     = {63},
  doi        = {10.1146/annurev.bi.63.070194.001315},
  file       = {Nitrogenase\: A Nucleotide-Dependent Molecular Switch - HOWarb94.pdf:by-author/H/Howard/1994_Howard_235.pdf:application/pdf},
  groups     = {sg/biomolecular},
  language   = {en},
  owner      = {saulius},
  shorttitle = nitrogenase,
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url        = {http://www.annualreviews.org/doi/abs/10.1146/annurev.bi.63.070194.001315},
  urldate    = {2015-08-05},
}

@TechReport{Howson2015,
  author = {Howson, Ian},
  title  = {bulkem: an {R} package that quickly fits mixture models using the {EM} algorithm on {CUDA} hardware},
  year   = {2015},
  file   = {:by-author/H/Howson/2015_Howson.pdf:PDF},
  url    = {https://ianhowson.com/bulkem/bulkem.pdf},
  creationdate = {2021-07-02T14:29:20},
  modificationdate = {2022-12-24T18:32+02:00},
  owner      = {andrius},
}

@Article{Hrabal1996,
  author    = {Hrabal, R. and Komives, E. A. and Ni, F.},
  journal   = {Protein science : a publication of the Protein Society},
  title     = {Structural resiliency of an EGF-like subdomain bound to its target protein, thrombin.},
  year      = {1996},
  pages     = {195--203},
  volume    = {5},
  abstract  = {The thrombin-bound structures of native peptide fragments from the fifth EGF-like domain of thrombomodulin were determined by use of NMR and transferred NOE spectroscopy. The bound peptides assume an EGF-like structure of an antiparallel beta-sheet, a novel structural motif observed for a bound peptide in protein-peptide complexes. There is a remarkable structural resiliency of this structure motif manifested in its ability to accommodate a different number of residues within the disulfide loop. Docking experiments revealed that the key contacts with thrombin are hydrophobic interactions between the side chains of residues Ile 414 and Ile 424 of thrombomodulin and a hydrophobic pocket on the thrombin surface. Residues Leu 415, Phe 419, and Ile 420, which would have been buried in intact EGF-like domains, are unfavorably exposed in the complex of thrombin with the EGF-like thrombomodulin fragment, thus providing a rationale for the enhancement of binding affinity upon the deletion of Ile 420. The unique beta-sheet structures of the bound peptides are specified by the presence of disulfide bridges in the peptides because a corresponding linear thrombomodulin fragment folds into a sheet structure with a different backbone topology. The different bound conformations for the linear and the cyclized peptides indicate that side-chain interactions within a specific environment may dictate the folding of bound peptides in protein-peptide complexes.},
  file      = {:by-author/H/Hrabal/1996_Hrabal_195.pdf:PDF},
  keywords  = {Protein Subdomains},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Hsieh2000,
  author    = {Hsieh, P. C. and Xiao, J. P. and O'loane, D. and Xu, S. Y.},
  journal   = {Journal of bacteriology},
  title     = {Cloning, expression, and purification of a thermostable nonhomodimeric restriction enzyme, BslI.},
  year      = {2000},
  pages     = {949--55},
  volume    = {182},
  abstract  = {BslI is a thermostable type II restriction endonuclease with interrupted recognition sequence CCNNNNN/NNGG (/, cleavage position). The BslI restriction-modification system from Bacillus species was cloned and expressed in Escherichia coli. The system is encoded by three genes: the 2,739-bp BslI methylase gene (bslIM), the bslIRalpha gene, and the bslIRbeta gene. The alpha and beta subunits of BslI can be expressed independently in E. coli in the absence of BslI methylase (M.BslI) protection. BslI endonuclease activity can be reconstituted in vitro by mixing the two subunits together. Gel filtration chromatography and native polyacrylamide gel electrophoresis indicated that BslI forms heterodimers (alphabeta), heterotetramers (alpha(2)beta(2)), and possibly oligomers in solution. Two beta subunits can be cross-linked by a chemical cross-linking agent, indicating formation of heterotetramer BslI complex (alpha(2)beta(2)). In DNA mobility shift assays, neither subunit alone can bind DNA. DNA mobility shift activity was detected after mixing the two subunits together. Because of the symmetric recognition sequence of the BslI endonuclease, we propose that its active form is alpha(2)beta(2). M.BslI contains nine conserved motifs of N-4 cytosine DNA methylases within the beta group of aminomethyltransferase. Synthetic duplex deoxyoligonucleotides containing cytosine hemimethylated or fully methylated at N-4 in BslI sites in the first or second cytosine are resistant to BslI digestion. C-5 methylation of the second cytosine on both strands within the recognition sequence also renders the site refractory to BslI digestion. Two putative zinc fingers are found in the alpha subunit of BslI endonuclease.},
  file      = {:by-author/H/Hsieh/2000_Hsieh_949.pdf:PDF},
  keywords  = {TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@TechReport{Hsu2011,
  author      = {Aaron W. Hsu},
  institution = {Indiana University},
  title       = {Hygienic Literate Programming: Lessons from ChezWEB},
  year        = {2011},
  abstract    = {Literate programming systems are a class of domain specific languages designed to encourage writing programs specifically to be read as essays or books by humans instead of by machines. Systems like CWEB, WEB, and ChezWEB allow the user to associate arbitrary code bodies with a concise but natural language description. That description may then be referred to in other sec- tions of the program source, and the code body associ- ated with the description is substituted for the reference in the program source. Using Scheme macros, we de- scribe how this substitution is performed unhygienically. We then describe and implement an innovation unique to ChezWEB that extends the notion of code reordering to provide hygiene and referential transparency guaran- tees for section references and code substitutions in the system. Our implementation strategy serves as a design pattern for implementing other language forms for which the programmer desires similar hygienic guarantees.},
  file        = {:by-author/H/Hsu/2011_Hsu.pdf:PDF},
  keywords    = {Computer Languages; Computer Science (CS); Oregon Workshop; Scheme},
  owner       = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Presentation{Hsu2003,
  author    = {Tsan-sheng Hsu},
  title     = {Symbol Tables},
  year      = {2003},
  file      = {:by-author/H/Hsu/2003_Hsu_slides.pdf:PDF},
  keywords  = {Compiler Symbol Tables; Computer Science (CS)},
  owner     = {saulius},
  pages     = {slides},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Presentation{Hu2008,
  author    = {Hu},
  title     = {Mathematical Structures in Programming},
  year      = {2008},
  file      = {:by-author/H/Hu/2008_Hu_slides.pdf:PDF},
  owner     = {saulius},
  pages     = {slides},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Manuscript{Huaa,
  author    = {Gary Hin Hua and Hantao Zhang},
  title     = {Formal Semantics of VHDL for Verification of Circuit Designs},
  keywords  = {Automated Reasoning; Computer Science (CS); Cover Set Induction; Program Verification},
  file      = {:by-author/H/Hua/XXXX_Hua.dvi:DVI},
  owner     = {saulius},
  timestamp = {2015.03.03},
  creationdate = {2015-03-03T00:00:00},
}

@Manuscript{Huab,
  author    = {Xin Hua and Hantao Zhang},
  title     = {Axiomatic Semantics of a Hardware Specification Language},
  keywords  = {Automated Reasoning; Computer Science (CS); Cover Set Induction; Program Verification},
  file      = {:by-author/H/Hua/XXXX_Hua_a.dvi:DVI},
  owner     = {saulius},
  timestamp = {2015.03.03},
  creationdate = {2015-03-03T00:00:00},
}

@Manuscript{Hua,
  author    = {Zin Hua and Hantao Zhang},
  title     = {FRI: Failure-Resistant Induction in RRL},
  keywords  = {Automated Reasoning; Computer Science (CS); Cover Set Induction; Program Verification},
  file      = {:by-author/H/Hua/XXXX_Hua_b.dvi:DVI},
  owner     = {saulius},
  timestamp = {2015.03.03},
  creationdate = {2015-03-03T00:00:00},
}

@Article{Huai2000,
  author    = {Huai, Q and Colandene, J D and Chen, Y and Luo, F and Zhao, Y and Topal, M D and Ke, H},
  journal   = {The EMBO journal},
  title     = {Crystal structure of NaeI-an evolutionary bridge between DNA endonuclease and topoisomerase.},
  year      = {2000},
  pages     = {3110--8},
  volume    = {19},
  abstract  = {NAE:I is transformed from DNA endonuclease to DNA topoisomerase and recombinase by a single amino acid substitution. The crystal structure of NAE:I was solved at 2.3 A resolution and shows that NAE:I is a dimeric molecule with two domains per monomer. Each domain contains one potential DNA recognition motif corresponding to either endonuclease or topoisomerase activity. The N-terminal domain core folds like the other type II restriction endonucleases as well as lambda-exonuclease and the DNA repair enzymes MutH and Vsr, implying a common evolutionary origin and catalytic mechanism. The C-terminal domain contains a catabolite activator protein (CAP) motif present in many DNA-binding proteins, including the type IA and type II topoisomerases. Thus, the NAE:I structure implies that DNA processing enzymes evolved from a few common ancestors. NAE:I may be an evolutionary bridge between endonuclease and DNA processing enzymes.},
  file      = {Huai_2000_3110-NaeI_struct.pdf:by-author/H/Huai/2000_Huai_3110.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Huan2016,
  author    = {Huan, Tran Doan and Mannodi-Kanakkithodi, Arun and Kim, Chiho and Sharma, Vinit and Pilania, Ghanshyam and Ramprasad, Rampi},
  journal   = {Sci. Data},
  title     = {A polymer dataset for accelerated property prediction and design},
  year      = {2016},
  issn      = {2052-4463},
  month     = {Mar},
  pages     = {160012},
  volume    = {3},
  abstract  = {Emerging computation- and data-driven approaches are particularly useful for rationally designing materials with targeted properties. Generally, these approaches rely on identifying structure-property relationships by learning from a dataset of sufficiently large number of relevant materials. The learned information can then be used to predict the properties of materials not already in the dataset, thus accelerating the materials design. Herein, we develop a dataset of 1,073 polymers and related materials and make it available at http://khazana.uconn.edu/. This dataset is uniformly prepared using first-principles calculations with structures obtained either from other sources or by using structure search methods. Because the immediate target of this work is to assist the design of high dielectric constant polymers, it is initially designed to include the optimized structures, atomization energies, band gaps, and dielectric constants. It will be progressively expanded by accumulating new materials and including additional properties calculated for the optimized structures provided.},
  doi       = {10.1038/sdata.2016.12},
  file      = {:by-author/H/Huan/2016_Huan_160012.pdf:PDF},
  keywords  = {Citing COD},
  owner     = {andrius},
  publisher = {Nature Publishing Group},
  timestamp = {2016.03.07},
  creationdate = {2016-03-07T00:00:00},
  url       = {http://dx.doi.org/10.1038/sdata.2016.12},
}

@Article{Huan2015,
  author    = {Huan, Tran Doan and Mannodi-Kanakkithodi, Arun and Ramprasad, Rampi},
  journal   = {Physical Review B},
  title     = {Accelerated materials property predictions and design using motif-based fingerprints},
  year      = {2015},
  issn      = {1550-235X},
  month     = {Jul},
  number    = {1},
  pages     = {014106},
  volume    = {92},
  abstract  = {Data-driven approaches are particularly useful for computational materials discovery and design as they can be used for rapidly screening over a very large number of materials, thus suggesting lead candidates for further in-depth investigations. A central challenge of such approaches is to develop a numerical representation, often referred to as a fingerprint, of the materials. Inspired by recent developments in cheminformatics, we propose a class of hierarchical motif-based topological fingerprints for materials composed of elements such as C, O, H, N, F, etc., whose coordination preferences are well understood. We show that these fingerprints, when representing either molecules or crystals, may be effectively mapped onto a variety of properties using a similarity-based learning model and hence can be used to predict the relevant properties of a material, given that its fingerprint can be defined. Two simple machine-learning-based procedures are introduced to demonstrate that the learning model can be inverted to identify the desired fingerprints and then to reconstruct molecules which possess a set of targeted properties.},
  doi       = {10.1103/physrevb.92.014106},
  file      = {:by-author/H/Huan/2015_Huan_014106.pdf:PDF},
  keywords  = {Citing COD},
  owner     = {andrius},
  publisher = {American Physical Society (APS)},
  timestamp = {2016.03.08},
  creationdate = {2016-03-08T00:00:00},
  url       = {http://dx.doi.org/10.1103/PhysRevB.92.014106},
}

@Article{Huang2007,
  author    = {Huoqiang Huang and Xulin Pan and Ninghua Tan and, Guangzhi Zeng and Changjiu Ji},
  journal   = {European Journal of Medicinal Chemistry},
  title     = {3D-QSAR study of sulfonamide inhibitors of human carbonic anhydrase II},
  year      = {2007},
  pages     = {365--372},
  volume    = {42},
  abstract  = {3D-QSAR models of Comparative of Molecular Field Analysis (CoMFA) and Comparative of Molecular Similarity Indices Analysis (CoMSIA) of 61 potent carbonic anhydrase II (CAII) sulfonamide inhibitors were performed using two methods. The conventional ligand-based 3D-QSAR studies were performed based on the lower energy conformations employing database alignment rule. The receptor-based 3D-QSAR models were also derived using bioactive conformations obtained by docking compounds to the active sites of CAII. The receptor-based model gave q2 values of 0.623 and 0.562, r2 values of 0.986 and 0.987 for CoMFA and CoMSIA, respectively, which were much better than those of ligand-based model (q2 values of 0.532 and 0.466). The predictive ability of the models was validated using the test set of 10 compounds that were not included in the training set of 51 compounds. Results of CoMFA and CoMSIA suggested that heterocyclic sulfonamides are more active than aromatic sulfonamides, in the latter 1,3,5-triazole group substituting one hydrogen atom of the amido is favored and moderate groups in its 4- and 6-position are required. These results provided further understanding of the relationship between the structural features of CAII and its activities, which should be applicable to design and find new potential CAII inhibitors.},
  doi       = {10.1016/j.ejmech.2006.09.022},
  file      = {2007_Huang_365.pdf:by-author/H/Huang/2007_Huang_365.pdf:PDF},
  groups    = {sg/inhibitors, sg/modelling, sg/hCA2},
  keywords  = {Carbonic Anhydrases},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Huang2003,
  author    = {Niu Huang and Nilesh K. Banavali and MacKerell, Jr., Alexander D.},
  journal   = {PNAS},
  title     = {Protein-facilitated base flipping in DNA by cytosine-5-methyltransferase},
  year      = {2003},
  pages     = {68--73},
  volume    = {100},
  abstract  = {DNA methylation, various DNA repair mechanisms, and possibly early events in the opening of DNA as required for transcription and replication are initiated by flipping of a DNA base out of the DNA double helix. The energetics and structural mechanism of base flipping in the presence of the DNA-processing enzyme, cytosine 5-methyltransferase from HhaI (M.HhaI), were obtained through molecular dynamics based upon free-energy calculations. Free- energy profiles for base flipping show that, when in the closed conformation, M.HhaI lowers the free-energy barrier to flipping by 17 kcal͞mol and stabilizes the fully flipped state. Flipping is shown to occur via the major groove of the DNA. Structural analysis indicates that flipping is facilitated by destabilization of the DNA double-helical structure and substitution of DNA base-pairing and base-stacking interactions with DNA–protein interactions. The fully flipped state is stabilized by DNA–protein interactions that are enhanced upon binding of coenzyme. This study represents an atomic detail description of the mechanism by which a protein facilitates specific structural distortion in DNA.},
  doi       = {10.1073͞pnas.0135427100},
  file      = {2003_Huang_68.pdf:by-author/H/Huang/2003_Huang_68.pdf:PDF},
  groups    = {sg/applications},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Huang2006,
  author    = {Huang, Niu and Shoichet, Brian K. and Irwin, John J.},
  journal   = {Journal of Medicinal Chemistry},
  title     = {Benchmarking Sets for Molecular Docking},
  year      = {2006},
  pages     = {6789--6801},
  volume    = {49},
  abstract  = {Ligand enrichment among top-ranking hits is a key metric of molecular docking. To avoid bias, decoys should resemble ligands physically, so that enrichment is not simply a separation of gross features, yet be chemically distinct from them, so that they are unlikely to be binders. We have assembled a directory of useful decoys (DUD), with 2950 ligands for 40 different targets. Every ligand has 36 decoy molecules that are physically similar but topologically distinct, leading to a database of 98 266 compounds. For most targets, enrichment was at least half a log better with uncorrected databases such as the MDDR than with DUD, evidence of bias in the former. These calculations also allowed 40 × 40 cross-docking, where the enrichments of each ligand set could be compared for all 40 targets, enabling a specificity metric for the docking screens. DUD is freely available online as a benchmarking set for docking at http://blaster.docking.org/dud/.},
  doi       = {10.1021/jm0608356},
  eprint    = {http://pubs.acs.org/doi/pdf/10.1021/jm0608356},
  file      = {2006_Huang_6789-manuscript.pdf:by-author/H/Huang/2006_Huang_6789-manuscript.pdf:PDF;2006_Huang_6789.pdf:by-author/H/Huang/2006_Huang_6789.pdf:PDF},
  owner     = {saulius},
  timestamp = {2013.04.01},
  creationdate = {2013-04-01T00:00:00},
  url       = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3383317/},
}

@Article{Huang2014,
  author    = {Huang, P.-S. and Oberdorfer, G. and Xu, C. and Pei, X. Y. and Nannenga, B. L. and Rogers, J. M. and DiMaio, F. and Gonen, T. and Luisi, B. and Baker, D.},
  journal   = {Science},
  title     = {High thermodynamic stability of parametrically designed helical bundles},
  year      = {2014},
  issn      = {1095-9203},
  month     = {Oct},
  number    = {6208},
  pages     = {481–485},
  volume    = {346},
  abstract  = {We describe a procedure for designing proteins with backbones produced by varying the parameters in the Crick coiled coil–generating equations. Combinatorial design calculations identify low-energy sequences for alternative helix supercoil arrangements, and the helices in the lowest-energy arrangements are connected by loop building. We design an antiparallel monomeric untwisted three-helix bundle with 80-residue helices, an antiparallel monomeric right-handed four-helix bundle, and a pentameric parallel left-handed five-helix bundle. The designed proteins are extremely stable (extrapolated DG fold > 60 kilocalories per mole), and their crystal structures are close to those of the design models with nearly identical core packing between the helices. The approach enables the custom design of hyperstable proteins with fine-tuned geometries for a wide range of applications.},
  doi       = {10.1126/science.1257481},
  file      = {2014_Huang_481.pdf:by-author/H/Huang/2014_Huang_481.pdf:PDF},
  keywords  = {Bioinformatics; Protein Design},
  owner     = {saulius},
  publisher = {American Association for the Advancement of Science (AAAS)},
  timestamp = {2016.03.09},
  creationdate = {2016-03-09T00:00:00},
  url       = {http://dx.doi.org/10.1126/science.1257481},
}

@Article{Huang2012,
  author    = {Huang, Raven H.},
  journal   = {Structure},
  title     = {Cas Protein Cmr2 Full of Surprises},
  year      = {2012},
  pages     = {389--390},
  volume    = {20},
  abstract  = {The Cmr complex carries out target RNA degradation in organisms possessing the CRISPR-Cas system. In this issue of Structure, Cocozaki et al. present the crystal structure of Cmr2, providing insight into the architecture of the Cmr complex.},
  doi       = {10.1016/j.str.2012.02.007},
  file      = {:by-author/H/Huang/2012_Huang_389.pdf:PDF},
  groups    = {sg/CRISPR-Cas},
  keywords  = {CRISPR; Cas Complex; Cmr Complex; Cmr2; Cocozaki; Crystal Structure},
  owner     = {em},
  timestamp = {2013.10.01},
  creationdate = {2013-10-01T00:00:00},
}

@Presentation{Huang2009,
  author       = {Shao-Ching Huang},
  title        = {Parallel Computing and OpenMP Tutorial},
  year         = {2009},
  conference   = {Seminar at UCLA LONI},
  organization = {UCLA IDRE/ATS},
  file         = {:by-author/H/Huang/2009_Huang_slides.pdf:PDF},
  month        = {aug},
  owner        = {saulius},
  pages        = {slides},
  timestamp = {2013.07.02},
  creationdate = {2013-07-02T00:00:00},
}

@Article{Huber1986,
  author    = {Huber},
  journal   = {Journal de Physique},
  title     = {On Some Hexagonal and Pentagonal Nets},
  year      = {1986},
  pages     = {C3-173-C3-179},
  volume    = {47},
  abstract  = {The notions of lattice and motif (unit of pattern) which are fundamental for crystals also are valid in the field of quasi-crystals. The historical aspects of crystal theory show their respective importance, which are illustrated by two tesselations of non regular hexagons and pentagons.},
  doi       = {10.1051/jphyscol:1986317},
  file      = {:by-author/H/Huber/1986_Huber_C3.pdf:PDF},
  keywords  = {Quasicrystals},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
  url       = {http://dx.doi.org/10.1051/jphyscol:1986317},
}

@Article{Huber2020,
  author           = {Huber, Sebastiaan P. and Zoupanos, Spyros and Uhrin, Martin and Talirz, Leopold and Kahle, Leonid and Häuselmann, Rico and Gresch, Dominik and Müller, Tiziano and Yakutovich, Aliaksandr V. and Andersen, Casper W. and Ramirez, Francisco F. and Adorf, Carl S. and Gargiulo, Fernando and Kumbhar, Snehal and Passaro, Elsa and Johnston, Conrad and Merkys, Andrius and Cepellotti, Andrea and Mounet, Nicolas and Marzari, Nicola and Kozinsky, Boris and Pizzi, Giovanni},
  journal          = {Scientific Data},
  title            = {{AiiDA} 1.0, a scalable computational infrastructure for automated reproducible workflows and data provenance},
  year             = {2020},
  issn             = {2052-4463},
  month            = {Sep},
  number           = {1},
  pages            = {300},
  volume           = {7},
  creationdate     = {2021-05-24T05:04:37+0000},
  doi              = {10.1038/s41597-020-00638-4},
  file             = {:by-author/H/Huber/2020_Huber_300.pdf:PDF},
  keywords         = {AiiDA; Chemoinformatics; Computer Science (CS); Workflow Managers; Workflows},
  modificationdate = {2022-12-03T13:59:30},
  owner            = {andrius},
  publisher        = {Springer Science and Business Media LLC},
  timestamp        = {2021.05.24},
  url              = {https://doi.org/10.1038/s41597-020-00638-4},
}

@Webpage{Hudak-David1996,
  author    = {Ginny Hudak-David},
  retrieved = {2015-03-06},
  title     = {A Beginner's Guide to HTML},
  url       = {http://www.sv.vt.edu/classes/ESM4714/Assign/HTMLPrimerAll.html},
  year      = {1996},
  file      = {:by-author/H/Hudak-David/1996_Hudak-David.html:},
  keywords  = {Computer Science (CS); HTML; Languages},
  owner     = {saulius},
  timestamp = {2015.03.03},
  creationdate = {2015-03-03T00:00:00},
}

@Article{Hufflen2006,
  author    = {Jean-Michel Hufflen},
  journal   = {TUGboat},
  title     = {Names in BibTEX and MlBibTEX},
  year      = {2006},
  pages     = {243--253},
  volume    = {27},
  abstract  = {Within the bibliographical entries managed by BibTEX, the bibliography processor usually associated with LaTEX, person and organisation names are specified with a rough syntax, whose details are not very well known. Likewise, the features related to formatting names within bibliography styles are often viewed as ob- scure. We explain these points in detail, giving some cases difficult or impossible to handle with BibTEX. Then we show how these problems can be solved within MlBibTEX, our reimplementation of BibTEX focusing on multilingual features and using an extension of XSLT as the language for bibliography styles. Keywords BibTEX, MlBibTEX, Bibliographies, bibliography styles, specifying and formatting person names.},
  file      = {:by-author/H/Hufflen/2006_Hufflen_243.pdf:PDF},
  owner     = {saulius},
  timestamp = {2013.03.22},
  creationdate = {2013-03-22T00:00:00},
}

@Article{Hufflen2001,
  author    = {Jean-Michel Hufflen},
  title     = {{MLBIBTEX}: a New Implementation of {BIBTEX}},
  year      = {2001},
  pages     = {74--94},
  file      = {:by-author/H/Hufflen/2001_Hufflen_74.pdf:PDF},
  keywords  = {Bibtex; Computer Science (CS)},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Hug2012,
  author     = {Hug, E. and Thibault, S. and Chateigner, D. and Maunoury, L.},
  journal    = {Surface and Coatings Technology},
  title      = {Nitriding aluminum alloys by {N}-multicharged ions implantation: correlation between surface strengthening and microstructure modifications},
  year       = {2012},
  pages      = {5028--5035},
  volume     = {206},
  file       = {[PDF] from researchgate.net:by-author/H/Hug/2012_Hug_5028.pdf:application/pdf;Snapshot:by-author/H/Hug/2012_Hug_5028.html:text/html},
  groups     = {sg/JAC2009},
  owner      = {saulius},
  shorttitle = {Nitriding aluminum alloys by {N}-multicharged ions implantation},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url        = {http://www.sciencedirect.com/science/article/pii/S0257897212003271},
  urldate    = {2015-08-31},
}

@TechReport{Huisman2014,
  author      = {Huisman, Marieke and Ahrendt, Wolfgang and Bruns, Daniel and Hentschel, Martin},
  institution = {Institut für Theoretische Informatik (ITI)},
  title       = {Formal Specification with JML},
  year        = {2014},
  number      = {2014,10},
  abstract    = {This text is a general, self contained, and tool independent introduction into the Java Modeling Language, JML. It is a preview of a chapter planned to appear in a book about the KeY approach and tool to the verification of Java software. JML is the dominating starting point of KeY style Java verification. However, this paper does not in any way depend on any tool nor verification methodology. Other chapters in this book talk about the usage of JML in KeY style verification. Here, we only refer to KeY in very few places, without relying on it. This introduction is written for all readers with an interest in formal specification of software in general, and anyone who wants to learn about the JML approach to specification in particular. The authors appreciate any comments or questions that help to improve the text.},
  doi         = {10.5445/IR/1000041881},
  file        = {2014_Huisman.pdf:by-author/H/Huisman/2014_Huisman.pdf:PDF},
  issn        = {2190-4782},
  keywords    = {Computer Science (CS); JML; Java; Java Modeling Language; Program Verification},
  kitopenid   = {1000041881},
  language    = {English},
  owner       = {saulius},
  timestamp = {2016.12.13},
  creationdate = {2016-12-13T00:00:00},
  url         = {https://publikationen.bibliothek.kit.edu/1000041881/3143677},
  urn         = {urn:nbn:de:swb:90-418817},
}

@Presentation{Hulme2006,
  author       = {Alison N. Hulme},
  title        = {Chemical Biology Approaches to Tagging and Imaging in Biological Systems},
  year         = {2006},
  organization = {The University of Edinburgh},
  file         = {:by-author/H/Hulme/2006_Hulme.ppt:PPT},
  keywords     = {Bioconjugation},
  month        = {September},
  owner        = {saulius},
  timestamp = {2015.03.03},
  creationdate = {2015-03-03T00:00:00},
}

@Article{Hummelshoej2012,
  author    = {Hummelshøj, Jens S. and Abild-Pedersen, Frank and Studt, Felix and Bligaard, Thomas and Nørskov, Jens K.},
  journal   = {Angewandte Chemie International Edition},
  title     = {CatApp: A Web Application for Surface Chemistry and Heterogeneous Catalysis},
  year      = {2012},
  issn      = {1521-3773},
  pages     = {272--274},
  volume    = {51},
  doi       = {10.1002/anie.201107947},
  file      = {:by-author/H/Hummelshoej/2012_Hummelshoej_272.pdf:PDF},
  keywords  = {Heterogeneous Catalysis; Surface Chemistry; Web Applications},
  owner     = {saulius},
  publisher = {WILEY-VCH Verlag},
  timestamp = {2015.06.08},
  creationdate = {2015-06-08T00:00:00},
  url       = {http://dx.doi.org/10.1002/anie.201107947},
}

@Article{Hummer1997,
  author    = {Gerhard Hummer and Lawrence R. Pratt and Angel E. García},
  journal   = {J. Chem. Phys},
  title     = {Ion Sizes and Finite-Size Corrections for Ionic-Solvation Free Energies},
  year      = {1997},
  pages     = {9275},
  volume    = {107},
  abstract  = {Free energies of ionic solvation calculated from computer simulations exhibit a strong system size dependence. We perform a finite-size analysis based on a dielectric-continuum model with periodic boundary conditions. That analysis results in an estimate of the Born ion size. Remarkably, the finite-size correction applies to systems with only eight water molecules hydrating a sodium ion and results in an estimate of the Born radius of sodium that agrees with the experimental value.},
  doi       = {10.1063/1.475219},
  file      = {1997_Hummer_1.pdf:by-author/H/Hummer/1997_Hummer_1.pdf:PDF},
  keywords  = {Poisson-Boltzmann eq; Protein Physics; Solvatation},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Hummer1996,
  author    = {Gerhard Hummer and Lawrence R. Pratt and Angel E. García},
  journal   = {J. Phys. Chem.},
  title     = {Free Energy of Ionic Hydration},
  year      = {1996},
  pages     = {1206--1215},
  volume    = {100},
  abstract  = {The hydration free energies of ions exhibit an approximately quadratic dependence on the ionic charge, as predicted by the Born model. We analyze this behavior using second-order perturbation theory. The average and the fluctuation of the electrostatic potential at charge sites appear as the first coefficients in a Taylor expansion of the free energy of charging. Combining the data from different charge states (e.g., charged and uncharged) allows calculation of free-energy profiles as a function of the ionic charge. The first two Taylor coefficients of the free-energy profiles can be computed accurately from equilibrium simulations, but they are affected by a strong system-size dependence. We apply corrections for these finite-size effects by using Ewald lattice summation and adding the self-interactions consistently. An analogous procedure is used for the reaction-field electrostatics. Results are presented for a model ion with methane-like Lennard-Jones parameters in simple point charge water. We find two very closely quadratic regimes with different parameters for positive and negative ions. We also studied the hydration free energy of potassium, calcium, fluoride, chloride, and bromide ions. We find negative ions to be solvated more strongly (as measured by hydration free energies) compared to positive ions of equal size, in agreement with experimental data. We ascribe this preference of negative ions to their strong interactions with water hydrogens, which can penetrate the ionic van der Waals shell without direct energetic penalty in the models used. In addition, we consistently find a positive electrostatic potential at the center of uncharged Lennard-Jones particles in water, which also favors negative ions. Regarding the effects of a finite system size, we show that even using only 16 water molecules it is possible to calculate accurately the hydration free energy of sodium, if self-interactions are considered},
  file      = {1996_Hummer_1206.pdf:by-author/H/Hummer/1996_Hummer_1206.pdf:PDF},
  keywords  = {Poisson-Boltzmann eq; Protein Physics; Solvatation},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Hummer1991,
  author    = {Hümmer, K. and Schwegle, W. and Weckert, E.},
  journal   = {Acta Crystallographica. Section A, Foundations of Crystallography},
  title     = {A Feasibility Study of Experimental Triplet-phase Determination in Small Proteins},
  year      = {1991},
  pages     = {60--2},
  volume    = {47 ( Pt 1)},
  abstract  = {It is shown for the first time that the measurement of triplet phases of three-beam cases where strong structure factors are involved is possible in small protein structures, for example myoglobin. The exploitation of the triplet phase from the interference profile is not affected as long as the structure factors of unavoidable overlapping three-beam cases are small.},
  doi       = {10.1107/S0108767390013150},
  file      = {:by-author/H/Hümmer/1991_Hümmer_60.pdf:PDF},
  keywords  = {Direct Methods; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0108767390013150},
}

@InProceedings{Humphreys2001,
  author    = {Humphreys, Greg and Eldridge, Matthew and Buck, Ian and Stoll, Gordan and Everett, Matthew and Hanrahan, Pat},
  booktitle = {Proceedings of the 28th annual conference on Computer graphics and interactive techniques},
  title     = {{WireGL}: A Scalable Graphics System for Clusters},
  year      = {2001},
  address   = {New York, NY, USA},
  pages     = {129--140},
  publisher = {ACM},
  series    = {SIGGRAPH '01},
  abstract  = {We describe WireGL, a system for scalable interactive rendering on a cluster of workstations. WireGL provides the familiar OpenGL API to each node in a cluster, virtualizing multiple graphics accel- erators into a sort-first parallel renderer with a parallel interface. We also describe techniques for reassembling an output image from a set of tiles distributed over a cluster. Using flexible display man- agement, WireGL can drive a variety of output devices, from stan- dalone displays to tiled display walls. By combining the power of virtual graphics, the familiarity and ordered semantics of OpenGL, and the scalability of clusters, we are able to create time-varying visualizations that sustain rendering performance over 70,000,000 triangles per second at interactive refresh rates using 16 compute nodes and 16 rendering nodes.},
  doi       = {10.1145/383259.383272},
  file      = {:by-author/H/Humphreys/2001_Humphreys_129.pdf:PDF},
  isbn      = {1-58113-374-X},
  keywords  = {Computer Graphics; Computer Science (CS)},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
  url       = {http://doi.acm.org/10.1145/383259.383272},
}

@Article{Hundt2006,
  author    = {Hundt, R. and Sch{\"{o}}n, J. C. and Jansen, M.},
  journal   = {Journal of Applied Crystallography},
  title     = {{CMPZ} -- an algorithm for the efficient comparison of periodic structures},
  year      = {2006},
  pages     = {6--16},
  volume    = {39},
  abstract  = {The systematic comparison of the atomic structure of solid compounds has become an important task in crystallography, chemistry, physics and materials science, in particular in the context of structure prediction and structure determination of crystalline solids. In this work, an efficient and robust algorithm for the comparison of periodic structures is presented, which is based on the mapping of the point patterns of the two structures into each other. This algorithm has been implemented as the module {\it CMPZ} in the structure visualization and analysis program {\it KPLOT}.},
  doi       = {10.1107/S0021889805032450},
  file      = {:by-author/H/Hundt/2006_Hundt_6.pdf:PDF},
  owner     = {andrius},
  timestamp = {2015.05.27},
  creationdate = {2015-05-27T00:00:00},
}

@Article{Hung1999,
  author    = {Hung, L. W. and Kohmura, M. and Ariyoshi, Y. and Kim, S. H.},
  journal   = {Journal of Molecular Biology},
  title     = {Structural differences in D and L-monellin in the crystals of racemic mixture.},
  year      = {1999},
  pages     = {311--21},
  volume    = {285},
  abstract  = {The racemic mixture of synthetic d and l-monellin has been crystallized, and its structure has been determined by X-ray crystallography at 1.9 A resolution. The crystal structure consists of two d and two l-monellin molecules in the P1 unit cell with a pseudo-centrosymmetrical arrangement. The final structure reveals small but significant structural differences between d and l-monellin in the same crystal. Possible reasons for these differences and their implications are discussed.},
  file      = {:by-author/H/Hung/1999_Hung_311.pdf:PDF},
  keywords  = {Crazy Spacegroups; Structures},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@Article{Hunt2003,
  author    = {Hunt, John F. and Deisenhofer, Johann},
  journal   = {Acta Crystallographica Section D},
  title     = {Ping-pong cross-validation in real space: a method for increasing the phasing power of a partial model without risk of model bias},
  year      = {2003},
  pages     = {214--224},
  volume    = {59},
  doi       = {10.1107/S0907444902018930},
  file      = {gr2264.pdf:by-author/H/Hunt/2003_Hunt_214.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444902018930},
}

@Article{Hunter2005,
  author    = {Hunter, Ryan C and Beveridge, Terry J},
  journal   = {Applied and environmental microbiology},
  title     = {Application of a pH-sensitive fluoroprobe (C-SNARF-4) for pH microenvironment analysis in Pseudomonas aeruginosa biofilms.},
  year      = {2005},
  pages     = {2501--10},
  volume    = {71},
  abstract  = {An important feature of microbial biofilms is the development of four-dimensional physical and chemical gradients in space and time. There is need for novel approaches to probe these so-called microenvironments to determine their effect on biofilm-specific processes. In this study, we describe the use of seminaphthorhodafluor-4F 5-(and-6) carboxylic acid (C-SNARF-4) for pH microenvironment analysis in Pseudomonas aeruginosa biofilms. C-SNARF-4 is a fluorescent ratiometric probe that allows pH quantification independent of probe concentration and/or laser intensity. By confocal scanning laser microscopy, C-SNARF-4 revealed pH heterogeneity throughout the biofilm in both the x,y and x,z planes, with values ranging from pH 5.6 (within the biofilm) to pH 7.0 (bulk fluid). pH values were typically remarkably different than those just a few micrometers away. Although this probe has been successfully used in a number of eukaryotic systems, problems have been reported which describe spectral emission changes as a result of macromolecular interactions with the fluorophore. To assess how the biofilm environment may influence fluorescent properties of the dye, fluorescence of C-SNARF-4 was quantified via spectrofluorometry while the probe was suspended in various concentrations of representative biofilm matrix components (i.e., proteins, polysaccharides, and bacterial cells) and growth medium. Surprisingly, our data demonstrate that few changes in emission spectra occur as a result of matrix interactions below pH 7. These studies suggest that C-SNARF-4 can be used as a reliable indicator of pH microenvironments, which may help elucidate their influence on the medical and geobiological roles of natural biofilms.},
  file      = {2005_Hunter_2501.pdf:by-author/H/Hunter/2005_Hunter_2501.pdf:PDF},
  keywords  = {{pH} Sensitive DNA Base Analogues},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@PhdThesis{Huper2002,
  author    = {Knut Hüper},
  school    = {Fakultät für Mathematik und Informatik der Bayerischen Julius-Maximilians-Universität Würzburg},
  title     = {A Calculus Approach to Matrix Eigenvalue Algorithms},
  year      = {2002},
  file      = {:by-author/H/Hüper/2002_Hüper.pdf:PDF},
  owner     = {saulius},
  timestamp = {2011.12.13},
  creationdate = {2011-12-13T00:00:00},
}

@Article{Huse2002,
  author    = {Huse, Morgan and Kuriyan, John},
  journal   = {Cell},
  title     = {The conformational plasticity of protein kinases},
  year      = {2002},
  issn      = {0092-8674},
  pages     = {275--282},
  volume    = {109},
  abstract  = {Protein kinases operate in a large number of distinct signaling pathways, where the tight regulation of their catalytic activity is crucial to the development and maintenance of eukaryotic organisms. The catalytic domains of different kinases adopt strikingly similar structures when they are active. By contrast, crystal structures of inactive kinases have revealed a remarkable plasticity in the kinase domain that allows the adoption of distinct conformations in response to interactions with specific regulatory domains or proteins.},
  doi       = {10.1016/S0092-8674(02)00741-9},
  file      = {ScienceDirect Full Text PDF:by-author/H/Huse/2002_Huse_275.pdf:application/pdf;ScienceDirect Snapshot:by-author/H/Huse/2002_Huse_275.html:text/html},
  groups    = {sg/biomolecular},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/S0092867402007419},
  urldate   = {2015-08-05},
}

@TechReport{Hutton2004,
  author      = {Graham Hutton and Joel Wright},
  institution = {School of Computer Science and IT, University of Nottingham, United Kingdom},
  title       = {Compiling Exceptions Correctly},
  year        = {2004},
  abstract    = {Exceptions are an important feature of modern programming languages, but their compilation has traditionally been viewed as an ad- vanced topic. In this article we show that the basic method of compiling exceptions using stack unwinding can be explained and verified both sim- ply and precisely, using elementary functional programming techniques. In particular, we develop a compiler for a small language with exceptions, together with a proof of its correctness.},
  file        = {:by-author/H/Hutton/2004_Hutton.pdf:PDF},
  keywords    = {Computer Science (CS); Exception Handling},
  owner       = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Huxley1952,
  author    = {Huxley, H. E. and Kendrew, J. C.},
  journal   = {Nature},
  title     = {Extractability of the Lotmar-Picken material from dried muscle.},
  year      = {1952},
  pages     = {882},
  volume    = {170},
  file      = {:by-author/H/Huxley/1952_Huxley_882.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.11.21},
  creationdate = {2012-11-21T00:00:00},
  url       = {http://www.nature.com/nature/focus/crick/pdf/crick170.pdf},
}

@Article{Iancu2006,
  author    = {Iancu, Violeta and Deshpande, Aparna and Hla, Saw-Wai},
  journal   = {Nano Letters},
  title     = {Manipulating kondo temperature via single molecule switching},
  year      = {2006},
  issn      = {1530-6984},
  pages     = {820--823},
  volume    = {6},
  abstract  = {Two conformations of isolated single TBrPP?Co molecules on a Cu(111) surface are switched by applying +2.2 V voltage pulses from a scanning tunneling microscope tip at 4.6 K. The TBrPP?Co has a spin-active cobalt atom caged at its center, and the interaction between the spin of this cobalt atom and free electrons from the Cu(111) substrate can cause a Kondo resonance. Tunneling spectroscopy data reveal that switching from the saddle to a planar molecular conformation enhances spin?electron coupling, which increases the associated Kondo temperature from 130 to 170 K. This result demonstrates that the Kondo temperature can be manipulated just by changing molecular conformation without altering chemical composition of the molecule.},
  doi       = {10.1021/nl0601886},
  file      = {ACS Full Text PDF w/ Links:by-author/I/Iancu/2006_Iancu_820.pdf:application/pdf;ACS Full Text Snapshot:by-author/I/Iancu/2006_Iancu_820.html:text/html},
  groups    = {sg/chemical},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://dx.doi.org/10.1021/nl0601886},
  urldate   = {2015-08-21},
}

@Article{Ibrahim2012,
  author     = {Ibrahim, Joseph G. and Chen, Ming-Hui and Chu, Haitao},
  journal    = {BMC Medical Research Methodology},
  title      = {Bayesian methods in clinical trials: a {Bayesian} analysis of {ECOG} trials {E}1684 and {E}1690},
  year       = {2012},
  issn       = {1471-2288},
  pages      = {183},
  volume     = {12},
  abstract   = {E1684 was the pivotal adjuvant melanoma trial for establishment of high-dose interferon (IFN) as effective therapy of high-risk melanoma patients. E1690 was an intriguing effort to corroborate E1684, and the differences between the outcomes of these trials have embroiled the field in controversy over the past several years. The analyses of E1684 and E1690 were carried out separately when the results were published, and there were no further analyses trying to perform a single analysis of the combined trials.},
  copyright  = {2012 Ibrahim et al.; licensee BioMed Central Ltd.},
  doi        = {10.1186/1471-2288-12-183},
  file       = {Ibrahim et al. - 2012 - Bayesian methods in clinical trials a Bayesian an.pdf:by-author/I/Ibrahim/2012_Ibrahim_183.pdf:PDF;Snapshot:by-author/I/Ibrahim/2012_Ibrahim_183.html:URL},
  groups     = {sg/Clinical Trials},
  keywords   = {Cure Rate Model; Historical Data; Posterior Distribution; Prior Distribution},
  language   = {en},
  owner      = {saulius},
  pmid       = {23194570},
  shorttitle = {Bayesian methods in clinical trials},
  timestamp = {2015.12.14},
  creationdate = {2015-12-14T00:00:00},
  url        = {http://www.biomedcentral.com/1471-2288/12/183/abstract},
  urldate    = {2015-12-12},
}

@Booklet{ICDD2004,
  title     = {PDF-4+ 2014: an Electron Diffraction Database},
  author    = {ICDD},
  year      = {2004},
  file      = {:by-author/I/ICDD/2014_ICDD.pdf:PDF},
  owner     = {saulius},
  timestamp = {2015.06.12},
  creationdate = {2015-06-12T00:00:00},
}

@TechReport{ICSD2014,
  author      = {ICSD},
  institution = {FIZ Karlsrue},
  title       = {A Focus on Crystallography: Modern crystallography – creation and development of crystal structure databases using the Inorganic Crystal Structure Database (ICSD) as an example},
  year        = {2014},
  abstract    = {About one hundred years ago, Max von Laue discovered the diffrac- tion of X-rays by crystals. This won him the Nobel Prize in Physics in 1914. At almost the same time William Henry Bragg and his son, William Lawrence Bragg, recognized that X-rays could be used to identify crystal structures and were awarded the Nobel Prize in Physics in 1915. Sabine Brünger-Weilandt President & CEO of FIZ Karlsruhe Today, 100 years later, these ground-breaking discoveries are honored and remembered on the occasion of the International Year of Crystallography. Over the years, crystallography has steadily evolved into one of the most basic and most important sciences of our times, which is reflected, among other things, in more than twenty Nobel Prizes based on a crystallographic background.},
  comment     = {Original name: Kristallografie-2014_1077681.pdf},
  file        = {:by-author/I/ICSD/2014_ICSD.pdf:PDF},
  keywords    = {Data Management; Databases; History; History of Science; ICSD; X-ray Crystallography},
  owner       = {saulius},
  timestamp = {2015.03.30},
  creationdate = {2015-03-30T00:00:00},
}

@Manual{ICSD2008,
  title        = {Inorganic Crystal Structure Database: Scientific Manual},
  author       = {ICSD},
  organization = {ICSD},
  year         = {2008},
  comment      = {contact: crysdata@fiz-karlsruhe.de},
  file         = {:by-author/I/ICSD/2008_ICSD.pdf:pdf},
  owner        = {saulius},
  timestamp = {2015.10.09},
  creationdate = {2015-10-09T00:00:00},
  url          = {http://www.nist.gov/srd/upload/09-0303-sci_man_ICSD_v1.pdf},
}

@TechReport{ICSTI2005,
  author      = {{ICSTI} and {IUCr}},
  institution = {ICSTI; IUCr},
  title       = {ICSTI-IUCr study on the long-term availability of the digital records of science},
  year        = {2005},
  file        = {:by-author/i/iucr-icsti/2005_iucr-icsti.pdf:PDF},
  keywords    = {Data Management; Preservation},
  owner       = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Booklet{ICSU2011,
  title     = {Interim Report to the ICSU Committee on Scientific Planning and Review},
  author    = {ICSU},
  year      = {2011},
  file      = {:by-author/I/ICSU/2011_ICSU.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.09.18},
  creationdate = {2012-09-18T00:00:00},
}

@Article{Iengar2006,
  author    = {Iengar, Prathima and Joshi, N. V. and Balaram, Padmanabhan},
  journal   = {Structure (London, England : 1993)},
  title     = {Conformational and sequence signatures in beta helix proteins.},
  year      = {2006},
  pages     = {529--42},
  volume    = {14},
  abstract  = {beta helix proteins are characterized by a repetitive fold, in which the repeating unit is a beta-helical coil formed by three strand segments linked by three loop segments. Using a data set of left- and right-handed beta helix proteins, we have examined conformational features at equivalent positions in successive coils. This has provided insights into the conformational rules that the proteins employ to fold into beta helices. Left-handed beta helices attain their equilateral prism fold by incorporating &quot;corners&quot; with the conformational sequence P(II)-P(II)-alpha(L)-P(II), which imposes sequence restrictions, resulting in the first and third P(II) residues often being G and a small, uncharged residue (V, A, S, T, C), respectively. Right-handed beta helices feature mid-sized loops (4, 5, or 6 residues) of conserved conformation, but not of conserved sequence; they also display an alpha-helical residue at the C-terminal end of L2 loops. Backbone conformational parameters (phi,psi) that permit the formation of continuous, loopless beta helices (Perutz nanotubes) have also been investigated.},
  file      = {:by-author/I/Iengar/2006_Iengar_529.pdf:PDF},
  keywords  = {Beta Helices; Protein Structures},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Manuscript{Ierusalimschy2014,
  author    = {Roberto Ierusalimschy and Luiz Henrique de Figueiredo and Waldemar Celes},
  title     = {The Implementation of Lua 5.0},
  year      = {2014},
  keywords  = {Compiler Construction; Computer Languages; Lua; Lua 5.0; Programming Languages; Runtime Implementation; Runtimes; Stack Machines; Tagged Pointers},
  url       = {http://www.lua.org/doc/jucs05.pdf},
  file      = {2014_Ierusalimschy.pdf:by-author/I/Ierusalimschy/2014_Ierusalimschy.pdf:PDF},
  note      = {The year 2014 is the download year; publication year was not specified.},
  owner     = {saulius},
  timestamp = {2014.10.21},
  creationdate = {2014-10-21T00:00:00},
}

@Manuscript{Ihaka2009,
  author    = {Ross Ihaka},
  title     = {Customizing {S}weave to Produce Better Looking {LaTeX} Output},
  year      = {2009},
  keywords  = {Latex; R},
  file      = {:by-author/I/Ihaka/2009_Ihaka.pdf:PDF},
  owner     = {andrius},
  timestamp = {2013.03.08},
  creationdate = {2013-03-08T00:00:00},
}

@Presentation{Ihaka2003,
  author       = {Ross Ihaka},
  title        = {Directions For R Graphics Development},
  year         = {2003},
  organization = {The R Foundation \& University of Auckland},
  email        = {ihaka@stat.auckland.ac.nz},
  file         = {:by-author/I/Ihaka/2003_Ihaka_slides.pdf:PDF},
  keywords     = {Computer Graphics},
  owner        = {saulius},
  pages        = {slides},
  timestamp = {2012.09.30},
  creationdate = {2012-09-30T00:00:00},
}

@Article{Ikeda1997,
  author     = {Ikeda, Atsushi and Shinkai, Seiji},
  journal    = {Chemical Reviews},
  title      = {Novel cavity design using calix[n]arene skeletons:  toward molecular recognition and metal binding},
  year       = {1997},
  issn       = {0009-2665},
  pages      = {1713--1734},
  volume     = {97},
  doi        = {10.1021/cr960385x},
  file       = {Ikeda and Shinkai - 1997 - Novel Cavity Design Using Calix[n]arene Skeletons.pdf:by-author/I/Ikeda/1997_Ikeda_1713.pdf:application/pdf;ACS Full Text Snapshot:by-author/I/Ikeda/1997_Ikeda_1713.html:text/html},
  groups     = {sg/chemical},
  owner      = {saulius},
  shorttitle = {Novel cavity design using calix[n]arene skeletons},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url        = {http://dx.doi.org/10.1021/cr960385x},
  urldate    = {2015-08-05},
}

@Article{Ikeda2003,
  author    = {Ikeda, M. and Nakagawa, S.},
  journal   = {Applied Microbiology and Biotechnology},
  title     = {The Corynebacterium glutamicum genome: features and impacts on biotechnological processes},
  year      = {2003},
  pages     = {99--109},
  volume    = {62},
  abstract  = {Abstract Corynebacterium glutamicum has played a principal role in the progress of the amino acid fermen- tation industry. The complete genome sequence of the representative wild-type strain of C. glutamicum, ATCC 13032, has been determined and analyzed to improve our understanding of the molecular biology and physiology of this organism, and to advance the development of more efficient production strains. Genome annotation has helped in elucidation of the gene repertoire defining a desired pathway, which is accelerating pathway engi- neering. Post genome technologies such as DNA arrays and proteomics are currently undergoing rapid develop- ment in C. glutamicum. Such progress has already exposed new regulatory networks and functions that had so far been unidentified in this microbe. The next goal of these studies is to integrate the fruits of genomics into strain development technology. A novel methodology that merges genomics with classical strain improvement has been developed and applied for the reconstruction of classically derived production strains. How can traditional fermentation benefit from the C. glutamicum genomic data? The path from genomics to biotechnological processes is presented.},
  doi       = {10.1007/s00253-003-1328-1},
  file      = {:by-author/I/Ikeda/2003_Ikeda_99.pdf:PDF},
  keywords  = {CglI; Restriction Endonuclease (RE)},
  owner     = {em},
  timestamp = {2014.05.22},
  creationdate = {2014-05-22T00:00:00},
}

@Article{Ilies2004,
  author    = {Ilies, Marc A and Masereel, Bernard and Rolin, Stéphanie and Scozzafava, Andrea and Câmpeanu, Gheorghe and Cîmpeanu, Valentin and Supuran, Claudiu T},
  journal   = {Bioorganic \&amp; medicinal chemistry},
  title     = {Carbonic anhydrase inhibitors: aromatic and heterocyclic sulfonamides incorporating adamantyl moieties with strong anticonvulsant activity.},
  year      = {2004},
  pages     = {2717--26},
  volume    = {12},
  file      = {2004_Ilies_2717.pdf:by-author/I/Ilies/2004_Ilies_2717.pdf:PDF},
  groups    = {sg/inhibitors},
  keywords  = {Carbonic Anhydrases},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Immirzi2009,
  author    = {Immirzi, Attilio},
  journal   = {Journal of Applied Crystallography},
  title     = {Constraints and restraints in crystal structure analysis},
  year      = {2009},
  month     = {Apr},
  number    = {2},
  pages     = {362--364},
  volume    = {42},
  abstract  = {The widely used restraint-based approach to structural analysis using diffraction data is critiqued. The convenience of using rigid constraints, through the use of internal coordinates, is discussed.},
  doi       = {10.1107/S0021889808044142},
  file      = {2009_Immirzi_362.pdf:by-author/I/Immirzi/2009_Immirzi_362.pdf:PDF},
  keywords  = {Constraints; Crystal Structure Analysis; Restraints},
  owner     = {saulius},
  timestamp = {2016.01.22},
  creationdate = {2016-01-22T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0021889808044142},
}

@Article{Incardona2009,
  author    = {Incardona, Marie-Fran{\c{c}}oise and Bourenkov, Gleb P. and Levik, Karl and Pieritz, Romeu A. and Popov, Alexander N. and Svensson, Olof},
  journal   = {Journal of Synchrotron Radiation},
  title     = {{\it EDNA}: a framework for plugin-based applications applied to X-ray experiment online data analysis},
  year      = {2009},
  pages     = {872--879},
  volume    = {16},
  abstract  = {EDNA is a framework for developing plugin-based applications especially for online data analysis in the X-ray experiments field. This article describes the features provided by the EDNA framework to ease the development of extensible scientific applications. This framework includes a plugins class hierarchy, configuration and application facilities, a mechanism to generate data classes and a testing framework. These utilities allow rapid development and integration in which robustness and quality play a fundamental role. A first prototype, designed for macromolecular crystallography experiments and tested at several synchrotrons, is presented.},
  doi       = {10.1107/S0909049509036681},
  file      = {wa5014.pdf:by-author/I/Incardona/2009_Incardona_872.pdf:PDF;:by-author/I/Incardona/2009_Incardona_872/MXv2i_Displacers.png:PNG image;:by-author/I/Incardona/2009_Incardona_872/MXv2i_Detector.png:PNG image;:by-author/I/Incardona/2009_Incardona_872/MXv2.eap:Text},
  keywords  = {Data Processing; Data Processing Pipelines; Diffraction Data Processing; Image Processing; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0909049509036681},
}

@Article{Innocenti2005,
  author    = {Innocenti, Alessio and Firnges, Michael A and Antel, Jochen and Wurl, Michael and Scozzafava, Andrea and Supuran, Claudiu T},
  journal   = {Bioorganic \&amp; medicinal chemistry letters},
  title     = {Carbonic anhydrase inhibitors. Inhibition of the membrane-bound human and bovine isozymes IV with sulfonamides.},
  year      = {2005},
  pages     = {1149--54},
  volume    = {15},
  doi       = {10.1016/j.bmcl.2004.12.009},
  file      = {2005_Innocenti_1149.pdf:by-author/I/Innocenti/2005_Innocenti_1149.pdf:PDF},
  groups    = {sg/inhibitors, sg/hCA4},
  keywords  = {Carbonic Anhydrases},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Innocenti2005a,
  author    = {Innocenti, Alessio and Villar, Raquel and Martinez-Merino, Victor and Gil, María J and Scozzafava, Andrea and Vullo, Daniela and Supuran, Claudiu T},
  journal   = {Bioorganic \&amp; medicinal chemistry letters},
  title     = {Carbonic anhydrase inhibitors: inhibition of cytosolic/tumor-associated carbonic anhydrase isozymes I, II, and IX with benzo[b]thiophene 1,1-dioxide sulfonamides.},
  year      = {2005},
  pages     = {4872--6},
  volume    = {15},
  doi       = {10.1016/j.bmcl.2005.04.078},
  file      = {2005_Innocenti_4872.pdf:by-author/I/Innocenti/2005_Innocenti_4872.pdf:PDF},
  groups    = {sg/inhibitors, sg/hCA1, sg/hCA2, sg/hCA9},
  keywords  = {Carbonic Anhydrases},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Inokuma2010,
  author    = {Inokuma, Yasuhide and Arai, Tatsuhiko and Fujita, Makoto},
  journal   = {Nature Chem},
  title     = {Networked molecular cages as crystalline sponges for fullerenes and other guests},
  year      = {2010},
  issn      = {1755-4349},
  month     = {Jul},
  number    = {9},
  pages     = {780--783},
  volume    = {2},
  doi       = {10.1038/nchem.742},
  file      = {2010_Inokuma_780.pdf:by-author/I/Inokuma/2010_Inokuma_780.pdf:PDF},
  groups    = {sg/Crystal sponges, sg/Crystallisation, sg/MOF, sg/MOFs, am/MOFs},
  keywords  = {Chemical Crystalography; Crystallography; Porous Materials; X-ray Crystallography},
  owner     = {saulius},
  publisher = {Nature Publishing Group},
  timestamp = {2016.05.14},
  creationdate = {2016-05-14T00:00:00},
  url       = {http://dx.doi.org/10.1038/nchem.742},
}

@Article{Inokuma2016,
  author    = {Inokuma, Yasuhide and Matsumura, Kazuki and Yoshioka, Shota and Fujita, Makoto},
  journal   = {Chemistry - An Asian Journal},
  title     = {Finding a New Crystalline Sponge from a Crystallographic Database},
  year      = {2016},
  issn      = {1861-4728},
  month     = {Dec},
  abstract  = {Empirical searching conditions were adopted to identify suitable candidates from the Cambridge Structural Database (CSD) for crystalline sponge hosts for X-ray crystallographic analysis of incoming guest compounds. After optimization of the solvent and soaking conditions, one of the candidates was used as a crystalline sponge for the structure determination of an aromatic guest.},
  doi       = {10.1002/asia.201601551},
  file      = {2016_Inokuma.pdf:by-author/I/Inokuma/2016_Inokuma.pdf:PDF},
  groups    = {sg/MOF, sg/MOFs, am/MOFs},
  keywords  = {Metal-Organic Frameworks (MOF)},
  owner     = {saulius},
  publisher = {Wiley-Blackwell},
  timestamp = {2016.12.27},
  creationdate = {2016-12-27T00:00:00},
  url       = {http://dx.doi.org/10.1002/asia.201601551},
}

@Article{Inokuma2014,
  author    = {Inokuma, Yasuhide and Yoshioka, Shota and Ariyoshi, Junko and Arai, Tatsuhiko and Fujita, Makoto},
  journal   = {Nat. Protocols},
  title     = {Preparation and guest-uptake protocol for a porous complex useful for 'crystal-free' crystallography},
  year      = {2014},
  issn      = {1754-2189},
  month     = feb,
  number    = {2},
  pages     = {246--252},
  volume    = {9},
  abstract  = {We recently reported a new method for single-crystal X-ray diffraction (SCD) analysis that does not require the crystallization of the target compound. In this 'crystal-free' crystallography, a tiny crystal of a porous complex is soaked in the solution of the target guest. The guest molecules are absorbed and oriented in the crystal pores and can be analyzed by X-ray diffraction. We describe here a detailed synthetic protocol for the preparation of uniform single crystals of the porous host complex and for the subsequent guest uptake. The protocol describes our most versatile porous complex, which is prepared from commercially available ZnI2 and 2,4,6-tri(4-pyridyl)-1,3,5-triazine. The host complex has large pores with a cross-section of 8 × 5 Å2. Single crystals of the complex are grown from layered solutions of the two components. The pores of the as-synthesized complex are filled with nitrobenzene, which is replaced with the inert solvent cyclohexane. This solvent exchange is essential for the rapid and effective inclusion of target compounds. The most crucial and delicate step is the selection of high-quality single crystals from the mixture of crystals of various shapes and sizes. We suggest using the facial indices of the single crystals as a criterion for crystal selection. Single-crystal samples for X-ray analysis can be prepared by immersing the selected crystals in a cyclohexane/dichloromethane solution of target compound. After a very slow evaporation of the solvent, typically over 2 d, the final crystal can be picked and directly subjected to SCD analysis. The protocol can be completed within ∼16 d.},
  file      = {2014_Inokuma_246.pdf:by-author/I/Inokuma/2014_Inokuma_246.pdf:PDF},
  groups    = {sg/Crystal sponges, sg/Crystallisation, sg/MOF, sg/MOFs, am/MOFs},
  keywords  = {Chemical Crystalography; Crystallography; Porous Materials; X-ray Crystallography},
  owner     = {saulius},
  publisher = {Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},
  timestamp = {2016.05.14},
  creationdate = {2016-05-14T00:00:00},
  url       = {http://dx.doi.org/10.1038/nprot.2014.007},
}

@Article{Inokuma2013,
  author    = {Inokuma, Yasuhide and Yoshioka, Shota and Ariyoshi, Junko and Arai, Tatsuhiko and Hitora, Yuki and Takada, Kentaro and Matsunaga, Shigeki and Rissanen, Kari and Fujita, Makoto},
  journal   = {Nature},
  title     = {X-ray analysis on the nanogram to microgram scale using porous complexes},
  year      = {2013},
  issn      = {0028-0836},
  pages     = {461--466},
  volume    = {495},
  abstract  = {X-ray single-crystal diffraction (SCD) analysis has the intrinsic limitation that the target molecules must be obtained as single crystals. Here we report a protocol for SCD analysis that does not require the crystallization of the sample. In our method, tiny crystals of porous complexes are soaked in a solution of the target, such that the complexes can absorb the target molecules. Crystallographic analysis clearly determines the absorbed guest structures along with the host frameworks. Because the SCD analysis is carried out on only one tiny crystal of the complex, the required sample mass is of the nanogram–microgram order. We demonstrate that as little as about 80 nanograms of a sample is enough for the SCD analysis. In combination with high-performance liquid chromatography, our protocol allows the direct characterization of multiple fractions, establishing a prototypical means of liquid chromatography SCD analysis. Furthermore, we unambiguously determined the structure of a scarce marine natural product using only 5 micrograms of the compound.},
  comment   = {10.1038/nature11990},
  file      = {2013_Inokuma_461.pdf:by-author/I/Inokuma/2013_Inokuma_461.pdf:PDF;2013_Inokuma_461-suppl.pdf:by-author/I/Inokuma/2013_Inokuma_461-suppl.pdf:PDF},
  groups    = {sg/Crystal sponges, sg/Crystallisation, sg/Small molecule, sg/MOF, sg/MOFs, am/MOFs},
  keywords  = {Chemical Crystalography; Crystallography; Porous Materials; X-ray Crystallography},
  owner     = {saulius},
  publisher = {Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},
  timestamp = {2013.04.03},
  creationdate = {2013-04-03T00:00:00},
  url       = {http://dx.doi.org/10.1038/nature11990},
}

@Webpage{FritzHaberInstitute2016,
  author    = {Fritz Haber Institute},
  retrieved = {2016-01-13},
  title     = {Towards a Common Format for Computational Materials Science Data},
  url       = {http://th.fhi-berlin.mpg.de/meetings/FCMSD2016/},
  year      = {2016},
  file      = {:by-author/F/FritzHaberInstitute/2016_FritzHaberInstitute.pdf:PDF},
  owner     = {andrius},
  timestamp = {2016.01.13},
  creationdate = {2016-01-13T00:00:00},
}

@Article{Interthal2001,
  author    = {Heidrun Interthal and Jeffrey J. Pouliot and James J. Champoux},
  journal   = {PNAS},
  title     = {The tyrosyl-DNA phosphodiesterase Tdp1 is a member of the phospholipase D superfamily},
  year      = {2001},
  pages     = {12009--12014},
  volume    = {98},
  abstract  = {The phospholipase D (PLD) superfamily is a diverse group of proteins that includes enzymes involved in phospholipid metabolism, a bacterial toxin, poxvirus envelope proteins, and bacterial nucleases. Based on sequence comparisons, we show here that the tyrosyl-DNA phosphodiesterase (Tdp1) that has been implicated in the repair of topoisomerase I covalent complexes with DNA contains two unusual HKD signature motifs that place the enzyme in a distinct class within the PLD superfamily. Mutagenesis studies with the human enzyme in which the invariant histidines and lysines of the HKD motifs are changed confirm that these highly conserved residues are essential for Tdp1 activity. Furthermore, we show that, like other members of the family for which it has been examined, the reaction involves the formation of an intermediate in which the cleaved substrate is covalently linked to the enzyme. These results reveal that the hydrolytic reaction catalyzed by Tdp1 occurs by the phosphoryl transfer chemistry that is common to all members of the PLD superfamily.},
  doi       = {10.1073/pnas.211429198},
  file      = {2001_Interthal_12009.pdf:by-author/I/Interthal/2001_Interthal_12009.pdf:PDF},
  keywords  = {Phospholipase D Superfamily; Tdp1; Tyrosyl DNA Phosphodiesterase},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Presentation{Invitrogen2006,
  author    = {Invitrogen},
  title     = {Gateway® Cloning},
  year      = {2006},
  file      = {:by-author/I/Invitrogen/2006_Invitrogen_slides.pdf:PDF},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Ioannidis2009,
  author    = {Ioannidis, John P A and Allison, David B and Ball, Catherine A and Coulibaly, Issa and Cui, Xiangqin and Culhane, Aedin C and Falchi, Mario and Furlanello, Cesare and Game, Laurence and Jurman, Giuseppe and Mangion, Jon and Mehta, Tapan and Nitzberg, Michael and Page, Grier P and Petretto, Enrico and van Noort, Vera},
  journal   = {Nat Genet},
  title     = {Repeatability of published microarray gene expression analyses},
  year      = {2009},
  issn      = {1061-4036},
  month     = feb,
  note      = {The paper demonstrates that >50% of all microaray data are not reproducible.},
  number    = {2},
  pages     = {149--155},
  volume    = {41},
  abstract  = {Given the complexity of microarray-based gene expression studies, guidelines encourage transparent design and public data availability. Several journals require public data deposition and several public databases exist. However, not all data are publicly available, and even when available, it is unknown whether the published results are reproducible by independent scientists. Here we evaluated the replication of data analyses in 18 articles on microarray-based gene expression profiling published in Nature Genetics in 2005–2006. One table or figure from each article was independently evaluated by two teams of analysts. We reproduced two analyses in principle and six partially or with some discrepancies; ten could not be reproduced. The main reason for failure to reproduce was data unavailability, and discrepancies were mostly due to incomplete data annotation or specification of data processing and analysis. Repeatability of published microarray studies is apparently limited. More strict publication rules enforcing public data availability and explicit description of data processing and analysis should be considered.},
  comment   = {10.1038/ng.295},
  file      = {2009_Ioannidis_149.pdf:by-author/I/Ioannidis/2009_Ioannidis_149.pdf:PDF},
  keywords  = {Data Management; Reproducible Research},
  owner     = {saulius},
  publisher = {Nature Publishing Group},
  timestamp = {2015.06.12},
  creationdate = {2015-06-12T00:00:00},
  url       = {http://dx.doi.org/10.1038/ng.295},
}

@Manuscript{Iriyama2008,
  author    = {Satoshi Iriyama and Masanori Ohya and Igor Volovich},
  title     = {Generalized Quantum Turing Machine and its Application to the {SAT} Chaos Algorithm},
  year      = {2008},
  keywords  = {Quantum Computing},
  abstract  = {Ohya and Volovich have proposed a new quantum computation model with chaotic amplification to solve the SAT problem, which went beyond usual quantum algorithm. In this paper, we generalize quantum Turing machine, and we show in this general quantum Turing machine (GQTM) that we can treat the Ohya-Volovich (OV) SAT algorithm.},
  file      = {:by-author/I/Iriyama/2008_Iriyama_1.pdf:PDF},
  owner     = {andrius},
  pages     = {1--19},
  timestamp = {2012.05.07},
  creationdate = {2012-05-07T00:00:00},
}

@Presentation{Irony2009,
  author    = {Irony, Telba},
  title     = {Planning and Analyzing a Flexible Bayesian Clinical Trial},
  year      = {2009},
  file      = {2009_Irony.pdf:by-author/I/Irony/2009_Irony.pdf:PDF},
  groups    = {sg/Clinical Trials},
  owner     = {saulius},
  timestamp = {2015.12.14},
  creationdate = {2015-12-14T00:00:00},
  url       = {http://www.advamedmtli.org/download/File/Statistics_April_2009/Irony_TelbaBayes.pdf},
  urldate   = {2015-12-12},
}

@Article{Irwin2009,
  author    = {Irwin, John J},
  journal   = {Nat Chem Biol},
  title     = {Staring off into chemical space},
  year      = {2009},
  issn      = {1552-4450},
  pages     = {536--537},
  volume    = {5},
  abstract  = {Chemical space is so enormous that it is hard to look at. This is a problem for medicinal chemists and chemical biologists who seek new molecules for their biological targets.},
  comment   = {10.1038/nchembio0809-536},
  file      = {2009_Irwin_536.pdf:by-author/I/Irwin/2009_Irwin_536.pdf:PDF},
  owner     = {saulius},
  publisher = {Nature Publishing Group},
  timestamp = {2013.04.01},
  creationdate = {2013-04-01T00:00:00},
  url       = {http://dx.doi.org/10.1038/nchembio0809-536},
}

@Article{Isaacs1978,
  author    = {Isaacs, N. W. and Agarwal, R. C.},
  journal   = {Acta Crystallographica Section A},
  title     = {Experience with fast Fourier least squares in the refinement of the crystal structure of rhombohedral 2-zinc insulin at 1.5 {\AA} resolution},
  year      = {1978},
  pages     = {782--791},
  volume    = {34},
  abstract  = {The newly developed fast Fourier least-squares algorithm [Agarwal (1978). Acta Cryst. A34, 791-809] has been used to refine the structure of rhombohedral 2-Zn pig insulin at a resolution of 1.5 Å. The CPU time required for each cycle of refinement was about 3 min on an IBM 370/168 computer. After 67 cycles of refinement the conventional R factor was 0.113 for 11 890 terms. The procedure used in the refinement is described and an analysis of the results presented. From the experience learned in this refinement a procedure is suggested which should provide faster convergence and require considerably fewer refinement cycles.},
  doi       = {10.1107/S0567739478001606},
  file      = {1978_Isaacs_782.pdf:by-author/I/Isaacs/1978_Isaacs_782.pdf:PDF},
  keywords  = {Algorithms; Protein Crystallography; Structure Refinement; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2013.03.25},
  creationdate = {2013-03-25T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0567739478001606},
}

@Article{Ishikawa2010,
  author    = {Ishikawa, Ken and Fukuda, Eri and Kobayashi, Ichizo},
  journal   = {DNA research : an international journal for rapid publication of reports on genes and genomes},
  title     = {Conflicts targeting epigenetic systems and their resolution by cell death: novel concepts for methyl-specific and other restriction systems.},
  year      = {2010},
  pages     = {325--42},
  volume    = {17},
  abstract  = {Epigenetic modification of genomic DNA by methylation is important for defining the epigenome and the transcriptome in eukaryotes as well as in prokaryotes. In prokaryotes, the DNA methyltransferase genes often vary, are mobile, and are paired with the gene for a restriction enzyme. Decrease in a certain epigenetic methylation may lead to chromosome cleavage by the partner restriction enzyme, leading to eventual cell death. Thus, the pairing of a DNA methyltransferase and a restriction enzyme forces an epigenetic state to be maintained within the genome. Although restriction enzymes were originally discovered for their ability to attack invading DNAs, it may be understood because such DNAs show deviation from this epigenetic status. DNAs with epigenetic methylation, by a methyltransferase linked or unlinked with a restriction enzyme, can also be the target of DNases, such as McrBC of Escherichia coli, which was discovered because of its methyl-specific restriction. McrBC responds to specific genome methylation systems by killing the host bacterial cell through chromosome cleavage. Evolutionary and genomic analysis of McrBC homologues revealed their mobility and wide distribution in prokaryotes similar to restriction-modification systems. These findings support the hypothesis that this family of methyl-specific DNases evolved as mobile elements competing with specific genome methylation systems through host killing. These restriction systems clearly demonstrate the presence of conflicts between epigenetic systems.},
  file      = {:by-author/I/Ishikawa/2010_Ishikawa_325.pdf:PDF},
  keywords  = {McrBC},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Ishikawa2005,
  author    = {Ishikawa, Ken and Watanabe, Miki and Kuroita, Toshihiro and Uchiyama, Ikuo and Bujnicki, Janusz M. and Kawakami, Bunsei and Tanokura, Masaru and Kobayashi, Ichizo},
  journal   = {Nucleic acids research},
  title     = {Discovery of a novel restriction endonuclease by genome comparison and application of a wheat-germ-based cell-free translation assay: PabI (5'-GTA/C) from the hyperthermophilic archaeon Pyrococcus abyssi.},
  year      = {2005},
  pages     = {e112},
  volume    = {33},
  abstract  = {To search for restriction endonucleases, we used a novel plant-based cell-free translation procedure that bypasses the toxicity of these enzymes. To identify candidate genes, the related genomes of the hyperthermophilic archaea Pyrococcus abyssi and Pyrococcus horikoshii were compared. In line with the selfish mobile gene hypothesis for restriction-modification systems, apparent genome rearrangement around putative restriction genes served as a selecting criterion. Several candidate restriction genes were identified and then amplified in such a way that they were removed from their own translation signal. During their cloning into a plasmid, the genes became connected with a plant translation signal. After in vitro transcription by T7 RNA polymerase, the mRNAs were separated from the template DNA and translated in a wheat-germ-based cell-free protein synthesis system. The resulting solution could be directly assayed for restriction activity. We identified two deoxyribonucleases. The novel enzyme was denoted as PabI, purified and found to recognize 5'-GTAC and leave a 3'-TA overhang (5'-GTA/C), a novel restriction enzyme-generated terminus. PabI is active up to 90 degrees C and optimally active at a pH of around 6 and in NaCl concentrations ranging from 100 to 200 mM. We predict that it has a novel 3D structure.},
  file      = {:by-author/I/Ishikawa/2005_Ishikawa_e112.pdf:PDF},
  keywords  = {Evolution; TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Ishmael2002,
  author    = {Ishmael, Faoud T. and Alley, Stephen C. and Benkovic, Stephen J.},
  journal   = {The Journal of biological chemistry},
  title     = {Assembly of the bacteriophage T4 helicase: architecture and stoichiometry of the gp41-gp59 complex.},
  year      = {2002},
  pages     = {20555--62},
  volume    = {277},
  abstract  = {The bacteriophage T4 59 protein (gp59) plays an essential role in recombination and replication by mediating the assembly of the gene 41 helicase (gp41) onto DNA. gp59 is required to displace the gp32 single-stranded binding protein on the lagging strand to expose a site for helicase binding. To gain a better understanding of the mechanism of helicase assembly, the architecture and stoichiometry of the gp41-gp59 complex were investigated. Both the N and C termini of gp41 were found to lie close to or in the gp41-gp41 subunit interface and interact with gp59. The site of interaction of gp41 on gp59 is proximal to Cys-215 of gp59. Binding of gp41 to gp59 stimulates a conformational change in the protein resulting in hexamer formation of gp59, and gp59 likewise stimulates oligomer formation of gp41. The gp59 subunits in this complex are arranged in a head to head orientation, such that Cys-42 of one subunit is in close proximity to Cys-42 on an adjacent subunit, and Cys-215 on one subunit is close to Cys-215 on a neighboring subunit. As the helicase is loaded onto DNA, a conformational change in the gp41-gp59 complex occurs, which may serve to displace gp32 from the lagging strand and load the hexameric helicase in its place.},
  file      = {:by-author/I/Ishmael/2002_Ishmael_20555.pdf:PDF},
  keywords  = {{gp41}; {gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Ishmael2001,
  author    = {Ishmael, F. T. and Alley, S. C. and Benkovic, S. J.},
  journal   = {The Journal of biological chemistry},
  title     = {Identification and mapping of protein-protein interactions between gp32 and gp59 by cross-linking.},
  year      = {2001},
  pages     = {25236--42},
  volume    = {276},
  abstract  = {The bacteriophage T4 59 protein (gp59) plays a vital role in recombination and replication by promoting the assembly of the gene 41 helicase (gp41) onto DNA, thus enabling replication as well as strand exchange in recombination. Loading of the helicase onto gp32 (the T4 single strand binding protein)-coated single-stranded DNA requires gp59 to remove gp32 and replace it with gp41. Cross-linking studies between gp32 and gp59 reveal an interaction between Cys-166 of gp32 and Cys-42 of gp59. Since Cys-166 lies in the DNA binding core domain of gp32, this interaction may affect the association of gp32 with DNA. In the presence of gp32 or DNA, gp59 is capable of forming a multimer consisting of at least five gp59 subunits. Kinetics studies suggest that gp59 and gp41 exist in a one-to-one ratio, predicting that gp59 is capable of forming a hexamer (Raney, K. D., Carver, T. E., and Benkovic, S. J. (1996) J. Biol. Chem. 271, 14074-14081). The C-terminal A-domain of gp32 is needed for gp59 oligomer formation. Cross-linking has established that gp59 can interact with gp32-A (a truncated form of gp32 lacking the A-domain) but cannot form higher species. The results support a model in which gp59 binds to gp32 on a replication fork, destabilizing the gp32-single-stranded DNA interaction concomitant with the oligomerization of gp59 that results in a switching of gp41 for gp32 at the replication fork.},
  file      = {:by-author/I/Ishmael/2001_Ishmael_25236.pdf:PDF},
  keywords  = {{gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@TechReport{Isloor1980,
  author      = {Isloor, Sreekaanth S. and T. Anthony Marsland},
  institution = {University of Alberta},
  title       = {The Deadlock Problem: An Overview},
  year        = {1980},
  file        = {:by-author/I/Isloor/1980_Isloor.pdf:PDF},
  keywords    = {Computer Science (CS); Deadlock},
  owner       = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Standard{ISO2007,
  institution  = {WG14/N1256},
  organization = {ISO/IEC},
  title        = {Programming languages — C. Committee Draft — Septermber 7, 2007 ISO/IEC 9899:TC3},
  author       = {ISO},
  year         = {2007},
  file         = {:by-author/I/ISO/2007_ISO.pdf:PDF},
  groups       = {sg/C++},
  keywords     = {C; Computer Science (CS); Programming Languages; Standards},
  owner        = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Israelachvili1996,
  author    = {Israelachvili, J and Wennerström, H},
  journal   = {Nature},
  title     = {Role of hydration and water structure in biological and colloidal interactions.},
  year      = {1996},
  pages     = {219--225},
  volume    = {379},
  abstract  = {The conventional explanation of why hydrophilic surfaces and macromolecules remain well separated in water is that they experience a monotonically repulsive hydration force owing to structuring of water molecules at the surfaces. A consideration of recent experimental and theoretical results suggests an alternative interpretation in which hydration forces are either attractive or oscillatory, and where repulsions have a totally different origin. Further experiments are needed to distinguish between these possibilities.},
  file      = {1996_Israelachvili_219.pdf:by-author/I/Israelachvili/1996_Israelachvili_219.pdf:PDF;1996_Israelachvili_219.djvu:by-author/I/Israelachvili/1996_Israelachvili_219.djvu:Djvu},
  keywords  = {Protein Structures},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Issac2002,
  author    = {Issac, Roy and Chmielewski, Jean},
  journal   = {Journal of the American Chemical Society},
  title     = {Approaching exponential growth with a self-replicating peptide.},
  year      = {2002},
  pages     = {6808--9},
  volume    = {124},
  abstract  = {Self-replicating peptide systems hold great promise for a wide range of technological applications, as well as to address fundamental questions pertaining to the molecular origins of life. The development of self-replicating compounds capable of high efficiency, however, has remained elusive. Here we disclose a successful strategy whereby modulation of coiled-coil stability results in remarkable catalytic efficiency for self-replication. By shortening the peptide to the minimum length necessary for coiled-coil formation a highly efficient self-replicating system was obtained due to very low background reaction rates, bringing the efficiency close to naturally occurring enzymes.},
  file      = {2002_Issac_6808.pdf:by-author/I/Issac/2002_Issac_6808.pdf:PDF},
  keywords  = {Chemical Prebiotic; Evolution},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Webpage{IUCr2011,
  author    = {IUCr},
  retrieved = {2011-06-24},
  title     = {Publication standards for crystal structures},
  url       = {http://www.iucr.org/home/leading-article/2011/2011-06-02},
  year      = {2011},
  file      = {:by-author/I/IUCr/2011_IUCr.odt:},
  keywords  = {Data-publication; Publication Standards for Crystal Structures; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2015.03.03},
  creationdate = {2015-03-03T00:00:00},
}

@Manual{IUCr2003,
  title        = {Sample Paper Using the IUCr LaTeX Macro Package},
  author       = {IUCr},
  organization = {IUCr},
  year         = {2003},
  file         = {:by-author/I/IUCr/2003_IUCr.pdf:PDF},
  keywords     = {Documentation; IUCr Paper; LaTeX Template},
  owner        = {antanas},
  timestamp = {2014.07.02},
  creationdate = {2014-07-02T00:00:00},
  url          = {http://www.iucr.org/__data/assets/pdf_file/0007/27097/documentation.pdf},
}

@MastersThesis{Ive2003,
  author    = {Anders Ive},
  school    = {Department of Computer Science, Lund Institute of Technology, Lund University},
  title     = {Towards an embedded real-time Java virtual machine},
  year      = {2003},
  file      = {2003_Ive.pdf:by-author/I/Ive/2003_Ive.pdf:PDF},
  groups    = {sg/Garbage collectors, sg/Java},
  keywords  = {Computer Science (CS); Garbage Collectors; Java},
  owner     = {saulius},
  timestamp = {2015.12.16},
  creationdate = {2015-12-16T00:00:00},
  url       = {http://fileadmin.cs.lth.se/sde/publications/theses/2003-AndersIve-Lic.pdf},
}

@Article{Iwase1999,
  author    = {Iwase, Kazuhiko and Hirono, Shuichi},
  journal   = {Journal of Computer-Aided Molecular Design},
  title     = {Estimation of active conformations of drugs by a new molecular superposing procedure},
  year      = {1999},
  issn      = {0920-654X},
  pages     = {499--512},
  volume    = {13},
  abstract  = {We have developed a new program, SUPERPOSE, to superpose two molecules based on the physicochemical properties of functional atoms within individual molecules. SUPERPOSE treats a pseudo-molecule consisting of functional atoms instead of a real molecule. Four types of physicochemical properties – hydrophobicity, presence of a hydrogen-bonding donor, presence of a hydrogen-bonding acceptor and presence of a hydrogen-bonding donor/acceptor – were supposed and a score was given to each overlap. When functional atoms with the same physicochemical properties were overlapped, points were added to the score, and when the functional atoms with different physicochemical properties were overlapped, points were subtracted. We applied SUPERPOSE to 12 pairs of 24 enzyme inhibitors and found that the best scored overlay for each inhibitor pair could successfully reproduce the superposition obtained from X-ray crystallography. Next, we applied SUPERPOSE to estimate the active conformations of the thrombin inhibitors MQPA, 4-TAPAP and NAPAP. Superpositions of conformers sampled by the high-temperature molecular dynamics calculation with respect to the three inhibitors were performed, and 13 sets of conformers having the best common overlay to the three inhibitors were selected. One among 13 sets was consistent with the superposition of the active conformations derived from the X-ray crystallography of the thrombin–inhibitor complexes.},
  file      = {1999_Iwase_499.pdf:by-author/I/Iwase/1999_Iwase_499.pdf:PDF},
  groups    = {sg/Molecule superposion, sg/Superposition, sg/Bioinf. Algorithms},
  issue     = {5},
  keywords  = {Algorithms; Structure Superposition},
  owner     = {saulius},
  publisher = {Springer Netherlands},
  timestamp = {2012.05.16},
  creationdate = {2012-05-16T00:00:00},
  url       = {http://dx.doi.org/10.1023/A:1008011422113},
}

@InProceedings{Iwerks2004,
  author    = {Iwerks, Glenn S. and Samet, Hanan and Smith, Kenneth P.},
  booktitle = {Proceedings of the Thirtieth international conference on Very large data bases - Volume 30},
  title     = {Maintenance of Spatial Semijoin Queries on Moving Points},
  year      = {2004},
  pages     = {828--839},
  publisher = {VLDB Endowment},
  abstract  = {In this paper, we address the maintenance of spa- tial semijoin queries over continuously moving points, where points are modeled as linear func- tions of time. This is analogous to the main- tenance of a materialized view except, as time advances, the query result may change indepen- dently of updates. As in a materialized view, we assume there is no prior knowledge of updates be- fore they occur. We present a new approach, con- tinuous fuzzy sets (CFS), to maintain continuous spatial semijoins efficiently. CFS is compared ex- perimentally to a simple scaling of previous work. The result is significantly better performance of CFS compared to previous work by up to an order of magnitude in some cases.},
  file      = {:by-author/I/Iwerks/2004_Iwerks_828.pdf:PDF},
  isbn      = {0-12-088469-0},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{JackLee2012,
  author    = {Jack Lee, J. and Chu, Caleb T.},
  journal   = {Statistics in Medicine},
  title     = {Bayesian clinical trials in action},
  year      = {2012},
  issn      = {1097-0258},
  pages     = {2955--2972},
  volume    = {31},
  abstract  = {Although the frequentist paradigm has been the predominant approach to clinical trial design since the 1940s, it has several notable limitations. Advancements in computational algorithms and computer hardware have greatly enhanced the alternative Bayesian paradigm. Compared with its frequentist counterpart, the Bayesian framework has several unique advantages, and its incorporation into clinical trial design is occurring more frequently. Using an extensive literature review to assess how Bayesian methods are used in clinical trials, we find them most commonly used for dose finding, efficacy monitoring, toxicity monitoring, diagnosis/decision making, and studying pharmacokinetics/pharmacodynamics. The additional infrastructure required for implementing Bayesian methods in clinical trials may include specialized software programs to run the study design, simulation and analysis, and web-based applications, all of which are particularly useful for timely data entry and analysis. Trial success requires not only the development of proper tools but also timely and accurate execution of data entry, quality control, adaptive randomization, and Bayesian computation. The relative merit of the Bayesian and frequentist approaches continues to be the subject of debate in statistics. However, more evidence can be found showing the convergence of the two camps, at least at the practical level. Ultimately, better clinical trial methods lead to more efficient designs, lower sample sizes, more accurate conclusions, and better outcomes for patients enrolled in the trials. Bayesian methods offer attractive alternatives for better trials. More Bayesian trials should be designed and conducted to refine the approach and demonstrate their real benefit in action. Copyright © 2012 John Wiley \& Sons, Ltd.},
  doi       = {10.1002/sim.5404},
  file      = {Jack Lee and Chu - 2012 - Bayesian clinical trials in action.pdf:by-author/J/JackLee/2012_JackLee_2955.pdf:PDF;Snapshot:by-author/J/JackLee/2012_JackLee_2955.html:URL},
  groups    = {sg/Clinical Trials},
  keywords  = {Adaptive Trial Design; Bayesian Paradigm; Clinical Trial Conduct; Frequentist Paradigm; Trial Efficiency; Trial Ethics},
  language  = {en},
  owner     = {saulius},
  timestamp = {2015.12.14},
  creationdate = {2015-12-14T00:00:00},
  url       = {http://onlinelibrary.wiley.com/doi/10.1002/sim.5404/abstract},
  urldate   = {2015-12-12},
}

@Article{Jacox2003,
  author    = {Jacox, Edwin H. and Samet, Hanan},
  journal   = {ACM Transactions on Database Systems},
  title     = {Iterative Spatial Join},
  year      = {2003},
  issn      = {0362-5915},
  pages     = {230--256},
  volume    = {28},
  abstract  = {The key issue in performing spatial joins is finding the pairs of intersecting rectangles. For unindexed data sets, this is usually resolved by partitioning the data and then performing a plane sweep on the individual partitions. The resulting join can be viewed as a two-step process where the partition corresponds to a hash-based join while the plane-sweep corresponds to a sort-merge join. In this article, we look at extending the idea of the sort-merge join for one-dimensional data to multiple dimensions and introduce the Iterative Spatial Join. As with the sort-merge join, the Iterative Spatial Join is best suited to cases where the data is already sorted. However, as we show in the experiments, the Iterative Spatial Join performs well when internal memory is limited, compared to the partitioning methods. This suggests that the Iterative Spatial Join would be useful for very large data sets or in situations where internal memory is a shared resource and is therefore limited, such as with today's database engines which share internal memory amongst several queries. Furthermore, the performance of the Iterative Spatial Join is predictable and has no parameters which need to be tuned, unlike other algorithms. The Iterative Spatial Join is based on a plane sweep algorithm, which requires the entire data set to fit in internal memory. When internal memory overflows, the Iterative Spatial Join simply makes additional passes on the data, thereby exhibiting only a gradual performance degradation. To demonstrate the use and efficacy of the Iterative Spatial Join, we first examine and analyze current approaches to performing spatial joins, and then give a detailed analysis of the Iterative Spatial Join as well as present the results of extensive testing of the algorithm, including a comparison with partitioning-based spatial join methods. These tests show that the Iterative Spatial Join overcomes the performance limitations of the other algorithms for data sets of all sizes as well as differing amounts of internal memory.},
  doi       = {10.1145/937598.937600},
  file      = {:by-author/J/Jacox/2003_Jacox_230.pdf:PDF},
  owner     = {saulius},
  publisher = {ACM},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://doi.acm.org/10.1145/937598.937600},
}

@Article{Jacques2012,
  author    = {Jacques, David A. and Mitchell Guss, J. and Svergun, Dmitri I. and Trewhella, Jill},
  journal   = {Acta Crystallographica Section D Biological Crystallography},
  title     = {Publication guidelines for structural modelling of small-angle scattering data from biomolecules in solution},
  year      = {2012},
  pages     = {620–626},
  volume    = {D68},
  abstract  = {Small-angle scattering is becoming a mainstream technique for structural molecular biology. As such, it is important to establish guidelines for publication that will ensure that there is adequate reporting of the data and its treatment so that reviewers and readers can independently assess the quality of the data and the basis for any interpretations presented. This article presents a set of preliminary guidelines that emerged after consultation with the IUCr Commission on Small-Angle Scattering and other experts in the field and discusses the rationale for their application. At the 2011 Congress of the IUCr in Madrid, the Commission on Journals agreed to adopt these preliminary guidelines for the presentation of biomolecular structures from small-angle scattering data in IUCr publications. Here, these guidelines are outlined and the reasons for standardizing the way in which small-angle scattering data are presented.},
  doi       = {10.1107/S0907444912012073},
  file      = {:by-author/J/Jacques/2012_Jacques_620.pdf:PDF},
  keywords  = {Quality; SAXS; Validation},
  owner     = {em},
  timestamp = {2013.06.28},
  creationdate = {2013-06-28T00:00:00},
}

@Article{Jahn1937,
  author    = {H. A. Jahn and E. Teller},
  journal   = {Proc. R. Soc. Lond.},
  title     = {Stability of Polyatomic Molecules in Degenerate Electronic States. {I}. Orbital Degeneracy},
  year      = {1937},
  pages     = {220--235},
  volume    = {161},
  doi       = {10.1098/rspa.1937.0142},
  file      = {:by-author/J/Jahn/1937_Jahn_220.pdf:PDF},
  keywords  = {Metal Coordination},
  owner     = {andrius},
  timestamp = {2014.08.26},
  creationdate = {2014-08-26T00:00:00},
}

@Article{Jahren2014,
  author    = {Jahren, A. Hope and Bostic, Joshua N. and Davy, Brenda M.},
  journal   = {Journal of Analytical Atomic Spectrometry},
  title     = {The potential for a carbon stable isotope biomarker of dietary sugar intake},
  year      = {2014},
  issn      = {1364-5544},
  pages     = {795--816},
  volume    = {29},
  abstract  = {Added sugar is sweetener added to foods during processing or preparation that offers no health benefits to the consumer. The mean U.S. intake of added sugar is ≈16\% of total calories; at the highest level of consumption, this value exceeds 35\%. In addition, 78\% of added sugar typically consumed is refined from C4 plants (e.g., corn and sugar cane) and it follows that the δ13C value of these sweeteners is conspicuously high compared to carbohydrates derived from C3 plants. We first suggested in 2006 the potential for the δ13C of human tissues to indicate corn- and cane-sugar intake for use in a clinical setting. At present, self-reported dietary assessment methods are commonly used to measure added sugar intake, but are subject to underreporting, particularly for sugar-rich foods. If a carbon isotope technique could produce a quantitative indicator of dietary sugar intake, it would be invaluable to the prevention and clinical treatment of chronic diseases associated with excess sugar consumption. Research to date has focused upon testing the correlation between diet as characterized either by bulk food δ13C value or by food composition (e.g., added sugar intake quartile) and the δ13C values of human tissues. Analysis of hair, nail and red blood cells in modern humans with known diet has revealed associations between the δ13C value of bulk diet and the δ13C value of these tissues. With respect to added sugar, the δ13C values of blood serum and fingerstick blood have both been shown to be associated with added sugar intake, even after adjustment for meat intake. Researchers have attempted to isolate specific compounds in blood that are uniquely derived from dietary carbohydrates, such as direct endogenous carbohydrate sources (blood glucose) and specific non-essential amino acids (red blood cell alanine), and have seen strong correlations with added sugar intake. Recognized dietary confounders such as meat/animal products have been addressed using statistical adjustments and a dual-isotope analytical approach that invokes δ15N as a correction factor. Further controlled feeding studies and epidemiological surveys complete with Institutional Review Board approval are needed to establish the sensitivity of δ13C tissue assay as an objective biomarker for added sugar intake.},
  doi       = {10.1039/C3JA50339A},
  file      = {Jahren et al. - 2014 - The potential for a carbon stable isotope biomarke.pdf:by-author/J/Jahren/2014_Jahren_795.pdf:application/pdf;Snapshot:by-author/J/Jahren/2014_Jahren_795.html:text/html},
  language  = {en},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://pubs.rsc.org/en/content/articlelanding/2014/ja/c3ja50339a},
  urldate   = {2015-10-02},
}

@Article{Jain2011,
  author    = {Anubhav Jain and Geoffroy Hautier and Charles J. Moore and Shyue Ping Ong and Christopher C. Fischer and Tim Mueller and Kristin A. Persson and Gerbrand Ceder},
  journal   = {Computational Materials Science},
  title     = {A High-throughput Infrastructure for Density Functional Theory Calculations},
  year      = {2011},
  issn      = {0927-0256},
  pages     = {2295--2310},
  volume    = {50},
  abstract  = {The use of high-throughput density functional theory (DFT) calculations to screen for new materials and conduct fundamental research presents an exciting opportunity for materials science and materials innovation. High-throughput DFT typically involves computations on hundreds, thousands, or tens of thousands of compounds, and such a change of scale requires new calculation and data management methodologies. In this article, we describe aspects of the necessary data infrastructure for such projects to handle data generation and data analysis in a scalable way. We discuss the problem of accurately computing properties of compounds across diverse chemical spaces with a single exchange correlation functional, and demonstrate that errors in the generalized gradient approximation are highly dependent on chemical environment.},
  doi       = {10.1016/j.commatsci.2011.02.023},
  file      = {:by-author/J/Jain/2011_Jain_2295.pdf:PDF},
  keywords  = {Density Functional Theory (DFT)},
  owner     = {saulius},
  timestamp = {2012.05.02},
  creationdate = {2012-05-02T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/S0927025611001133},
}

@Article{Jain2013,
  author    = {Jain, Anubhav and Ong, Shyue Ping and Hautier, Geoffroy and Chen, Wei and Richards, William Davidson and Dacek, Stephen and Cholia, Shreyas and Gunter, Dan and Skinner, David and Ceder, Gerbrand and Persson, Kristin A.},
  journal   = {APL Materials},
  title     = {Commentary: The Materials Project: A materials genome approach to accelerating materials innovation},
  year      = {2013},
  number    = {1},
  pages     = {011002},
  volume    = {1},
  doi       = {10.1063/1.4812323},
  file      = {:by-author/J/Jain/2013_Jain_011002.pdf:PDF},
  keywords  = {Density Functional Theory (DFT)},
  owner     = {andrius},
  timestamp = {2015.07.31},
  creationdate = {2015-07-31T00:00:00},
  url       = {http://scitation.aip.org/content/aip/journal/aplmater/1/1/10.1063/1.4812323},
}

@Article{Jain1996,
  author    = {Anil K. Jain and Yu Zhong},
  journal   = {Pattern Recognition},
  title     = {Page segmentation using texture analysis},
  year      = {1996},
  issn      = {0031-3203},
  number    = {5},
  pages     = {743--770},
  volume    = {29},
  abstract  = {We propose a new texture-based language-free page segmentation algorithm which automatically extracts the text, halftone, and line-drawing regions from input greyscale document images. This approach utilizes a neural network to train a set of masks which is optimal for discriminating the three main texture classes in the page segmentation problem: halftone, background, and text and line-drawing regions. The text and line-drawing regions are further discriminated based on connectivity analysis. We have applied the algorithm to successfully segment English and Chinese document images. We also demonstrate that the masks can perform language separation (English/Chinese) when appropriately trained.},
  doi       = {http://dx.doi.org/10.1016/0031-3203(95)00131-X},
  file      = {1996_Jain_743.pdf:by-author/J/Jain/1996_Jain_743.pdf:PDF},
  keywords  = {Document Analysis; Image Segmentation; OCR; Text Segmentation},
  owner     = {saulius},
  timestamp = {2016.02.05},
  creationdate = {2016-02-05T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/003132039500131X},
}

@InCollection{Jain2015,
  author    = {Swati Jain and David C. Richardson and Jane S. Richardson},
  booktitle = {Methods in Enzymology},
  publisher = {Academic Press},
  title     = {Computational Methods for {RNA} Structure Validation and Improvement},
  year      = {2015},
  series    = {Methods in Enzymology},
  abstract  = {Abstract With increasing recognition of the roles \{RNA\} molecules and RNA/protein complexes play in an unexpected variety of biological processes, understanding of \{RNA\} structure–function relationships is of high current importance. To make clean biological interpretations from three-dimensional structures, it is imperative to have high-quality, accurate \{RNA\} crystal structures available, and the community has thoroughly embraced that goal. However, due to the many degrees of freedom inherent in \{RNA\} structure (especially for the backbone), it is a significant challenge to succeed in building accurate experimental models for \{RNA\} structures. This chapter describes the tools and techniques our research group and our collaborators have developed over the years to help \{RNA\} structural biologists both evaluate and achieve better accuracy. Expert analysis of large, high-resolution, quality-conscious \{RNA\} datasets provides the fundamental information that enables automated methods for robust and efficient error diagnosis in validating \{RNA\} structures at all resolutions. The even more crucial goal of correcting the diagnosed outliers has steadily developed toward highly effective, computationally based techniques. Automation enables solving complex issues in large \{RNA\} structures, but cannot circumvent the need for thoughtful examination of local details, and so we also provide some guidance for interpreting and acting on the results of current structure validation for RNA.},
  doi       = {http://dx.doi.org/10.1016/bs.mie.2015.01.007},
  file      = {:by-author/J/Jain/2015_Jain.pdf:PDF},
  groups    = {sg/JAC2009},
  issn      = {0076-6879},
  keywords  = {Crystallography; RNA},
  owner     = {saulius},
  timestamp = {2015.04.08},
  creationdate = {2015-04-08T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/S0076687915000208},
}

@Article{Jaki2004,
  author    = {Jaki},
  title     = {A Late Awakening to Gödel in Physics},
  year      = {2004},
  file      = {:by-author/J/Jaki/2004_Jaki.pdf:PDF},
  keywords  = {Goedel's Theorem},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@PhdThesis{Jakubauskas2007,
  author    = {Jakubauskas},
  school    = {Vilniaus Universitetas, Biotechnologijos Institutas},
  title     = {II Tipo Restrikcijos Endonukleazių Domeninės Struktūros Tyrimas},
  year      = {2007},
  file      = {:by-author/J/Jakubauskas/2007_Jakubauskas_phdthesis.pdf:PDF},
  keywords  = {Manuscripts},
  owner     = {saulius},
  pages     = {phdthesis},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{James2014,
  author       = {James, S. L.},
  journal      = {{IUCrJ}},
  title        = {Tackling a difficult question: how do crystals of coordination polymers form?},
  year         = {2014},
  issn         = {2052-2525},
  number       = {5},
  pages        = {263--264},
  volume       = {1},
  date         = {2014-09-01},
  doi          = {10.1107/S2052252514018624},
  file         = {Full Text PDF:by-author/J/James/2014_James_263.pdf:PDF;Snapshot:by-author/J/James/2014_James_263.html:URL},
  groups       = {sg/MOF, sg/MOFs, am/MOFs},
  journaltitle = {{IUCrJ}},
  keywords     = {Coordination Polymers; Crystallization; Metal-Organic Frameworks (MOF); Ring-opening Polymerization},
  langid       = {english},
  owner        = {saulius},
  rights       = {http://creativecommons.org/licenses/by/2.0/uk},
  shortjournal = {{IUCrJ}},
  shorttitle   = {Tackling a difficult question},
  timestamp = {2017.01.29},
  creationdate = {2017-01-29T00:00:00},
  url          = {http://scripts.iucr.org/cgi-bin/paper?hi0134},
  urldate      = {2017-01-29},
}

@Manuscript{Jamrog2002,
  author    = {Jamrog, Diane C. and Phillips, Jr., George N. and Richard A. Tapia and Yin Zhang},
  title     = {A global optimisation method for the molecular replacement problem in {X}-ray crystallography},
  year      = {2002},
  keywords  = {Molecular Replacement; X-ray Crystallography},
  file      = {:by-author/J/Jamrog/2002_Jamrog.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.09.18},
  creationdate = {2012-09-18T00:00:00},
}

@Manuscript{Jamrog2003a,
  author    = {Diane C. Jamrog and Phillips, Jr., George N. and Yin Zhang},
  title     = {On the Equivalence Between a Commonly Used Correlation Coefficient and a Least Squares Function},
  year      = {2003},
  keywords  = {Correlation Coefficient; Molecular Replacement; R-factor; X-ray Crystallography},
  url       = {http://www.caam.rice.edu/tech_reports/2003/TR03-02.pdf},
  file      = {:by-author/J/Jamrog/2003_Jamrog.pdf:PDF},
  owner     = {saulius},
  timestamp = {2014.03.24},
  creationdate = {2014-03-24T00:00:00},
}

@Article{Jamrog2003,
  author    = {Jamrog, Diane C. and Zhang, Yin and Phillips, Jr, George N.},
  journal   = {Acta Crystallographica Section D},
  title     = {{\it SOMoRe}: a multi-dimensional search and optimization approach to molecular replacement},
  year      = {2003},
  pages     = {304--314},
  volume    = {59},
  doi       = {10.1107/S0907444902021935},
  file      = {gr2306.pdf:by-author/J/Jamrog/2003_Jamrog_304.pdf:PDF},
  keywords  = {Correlation Coefficient; Molecular Replacement; R-factor; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444902021935},
}

@Article{Jancarik2004,
  author    = {Jancarik, Jarmila and Pufan, Ramona and Hong, Connie and Kim, Sung Hou and Kim, Rosalind},
  journal   = {Acta crystallographica. Section D, Biological crystallography},
  title     = {Optimum solubility (OS) screening: an efficient method to optimize buffer conditions for homogeneity and crystallization of proteins.},
  year      = {2004},
  pages     = {1670--3},
  volume    = {60},
  abstract  = {One of the most critical steps in the preparation of protein samples for structural studies by X-ray crystallography is to obtain biochemically pure and conformationally homogenous protein samples. Very often, the purified sample does not meet these qualifications and therefore does not crystallize. A screening method, Optimum Solubility Screen, has been developed that consists of two steps. The first step selects a better buffer than that used during purification. 24 different buffers ranging from pH 3 to pH 10 are screened using a vapor-diffusion method and very small amounts of protein. The solubility of the protein is first determined by visual examination using a light microscope and those drops that remain clear after 24 h are further evaluated using dynamic light scattering. If the results from the first step are still not satisfactory, a second step explores a variety of chemical additives in order to improve the monodispersity of the protein sample. In 64% of the cases, crystallization was successful from proteins that had initially shown high levels of aggregation. This screen can be configured to perform in an automated high-throughput mode and can be expanded for additional buffers and additives.},
  file      = {:by-author/J/Jancarik/2004_Jancarik_1670.pdf:PDF},
  keywords  = {Grow Krystal},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Janner1980,
  author    = {Janner, A. and Janssen, T.},
  journal   = {Acta Crystallographica Section A},
  title     = {Symmetry of incommensurate crystal phases. I. Commensurate basic structures},
  year      = {1980},
  pages     = {399--408},
  volume    = {36},
  abstract  = {The superspace-group approach [Janner & Janssen (1977), Phys. Rev. B, 15, 643-658] is used to solve the symmetry problem of incommensurate crystal phases in the case of displacive- and occupation-wave modulation. Generalization is given to cover magnetic modulation as well. The symmetry conditions imposed by the superspace group on the crystal structure are derived and applied to the following incommensurate crystals, whose structures have been discussed in the literature independently from the present point of view: K2SeO4, 2H-TaSe2, NaNO2 and Cr. The superspace groups describing the symmetry of these compounds are indicated and the structural implications of the corresponding symmetry elements discussed.},
  doi       = {10.1107/S0567739480000885},
  file      = {:by-author/J/Janner/1980_Janner_399.pdf:PDF},
  keywords  = {Modulated Structures},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0567739480000885},
}

@Article{Janner1980a,
  author    = {Janner, A. and Janssen, T.},
  journal   = {Acta Crystallographica Section A},
  title     = {Symmetry of incommensurate crystal phases. II. Incommensurate basic structure},
  year      = {1980},
  pages     = {408},
  volume    = {36},
  abstract  = {In this second part [part I: Acta Cryst. (1980), A36, 399-408] the superspace-group approach is formulated for a class of crystals (called composite crystals) which involve a basic structure composed of subsystems, each one having three-dimensional space-group symmetry, but being mutually incommensurate. By taking into account the interaction among these subsystems, or other second-order effects, one is led to the actual structure, which very often is modulated, and in any case incommensurate. Neither the basic structure nor the actual one has a three-dimensional space-group symmetry but both allow a superspace-group characterization of their symmetry properties. The aim of the present paper is to show how these concepts apply in practice. Accordingly, two composite crystals, extensively studied in the literature, are considered from the present point of view: the organic compound (TTF)7I5 - x, i.e. C42H28S28.I5 - x, and the polymercury cation compound Hg3 - [delta]AsF6. The regularities found in these two compounds are interpreted and fit naturally with the corresponding superspace-symmetry groups.},
  doi       = {10.1107/S0567739480000897},
  file      = {:by-author/J/Janner/1980_Janner_408.pdf:PDF},
  keywords  = {Modulated Structures},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0567739480000897},
}

@Article{Janner1983,
  author    = {Janner, A. and Janssen, T. and de Wolff, P. M.},
  journal   = {Acta Crystallographica Section A},
  title     = {Bravais classes for incommensurate crystal phases},
  year      = {1983},
  pages     = {658--666},
  volume    = {39},
  doi       = {10.1107/S0108767383001348},
  file      = {1983_Janner_658.pdf:by-author/J/Janner/1983_Janner_658.pdf:PDF},
  keywords  = {Aperiodic Crystal; Incommensurate Crystals; Symmetry},
  owner     = {saulius},
  timestamp = {2014.10.21},
  creationdate = {2014-10-21T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0108767383001348},
}

@Article{Janot1993,
  author    = {Christian Janot},
  journal   = {Journal of Non-Crystalline Solids},
  title     = {The structure of quasicrystals. Part II Section 9. Quasicrystals},
  year      = {1993},
  pages     = {852--864},
  volume    = {156–158},
  doi       = {10.1016/0022-3093(93)90085-C},
  file      = {:by-author/J/Janot/1993_Janot_852.pdf:PDF},
  owner     = {saulius},
  timestamp = {2015.10.09},
  creationdate = {2015-10-09T00:00:00},
}

@Article{Janowski2007,
  author    = {Janowski, Bethany A and Younger, Scott T and Hardy, Daniel B and Ram, Rosalyn and Huffman, Kenneth E and Corey, David R},
  journal   = {Nat Chem Biol},
  title     = {Activating gene expression in mammalian cells with promoter-targeted duplex RNAs},
  year      = {2007},
  issn      = {1552-4450},
  month     = {Jan},
  number    = {3},
  pages     = {166–173},
  volume    = {3},
  doi       = {10.1038/nchembio860},
  file      = {2007_Janowski_166.pdf:by-author/J/Janowski/2007_Janowski_166.pdf:PDF},
  groups    = {am/RNA activation},
  owner     = {andrius},
  publisher = {Nature Publishing Group},
  timestamp = {2016.09.02},
  creationdate = {2016-09-02T00:00:00},
}

@Article{Janscak1996,
  author    = {Janscak, P. and Abadjieva, A. and Firman, K.},
  journal   = {Journal of molecular biology},
  title     = {The type I restriction endonuclease R.EcoR124I: over-production and biochemical properties.},
  year      = {1996},
  pages     = {977--91},
  volume    = {257},
  abstract  = {In this paper we describe a two-plasmid system which allows over-production of the R.EcoR124I restriction endonuclease. The endonuclease has been purified to homogeneity in milligram amounts and has been shown to be fully active for both restriction and modification. Unexpectedly, the enzyme was found to require only ATP and Mg2+ for ATPase activity and DNA cleavage; S-adenosyl methionine (SAM), which has been described as a cofactor of type I restriction enzymes, is not required by R.EcoR124I. However, SAM was found to stimulate the rate of ATPase activity and DNA cleavage. This may occur through an increase in specific DNA binding by R.EcoR124I in the presence of SAM, as indicated by our surface plasmon resonance experiments. These functional differences from the well described R.EcoKI restriction endonuclease are reflected in a possible structural difference between the two enzymes, namely that the stoichiometry of R.EcoR124I appears to be R1M2S1 while that of R.EcoKI is R2M2S1. Supercoiled DNA with one or two SR124I recognition sites is cleaved by the same mechanism inferring co-operation between specifically bound and excess enzymes. Nicked-circle DNA is an intermediate of cleavage reaction. Cleavage of DNA was inhibited by an increased degree of negative supercoiling, which may reflect an increased difficulty for the enzyme to translocate the DNA. Hemi-methylated DNA was the preferred substrate for methylation.},
  file      = {:by-author/J/Janscak/1996_Janscak_977.pdf:PDF},
  keywords  = {TypeI},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Janscak1998,
  author    = {Janscak, P. and Bickle, T. A.},
  journal   = {Journal of molecular biology},
  title     = {The DNA recognition subunit of the type IB restriction-modification enzyme EcoAI tolerates circular permutions of its polypeptide chain.},
  year      = {1998},
  pages     = {937--48},
  volume    = {284},
  abstract  = {The DNA specificity subunit (HsdS) of type I restriction-modification enzymes is composed of two independent target recognition domains and several regions whose amino acid sequence is conserved within an enzyme family. The conserved regions participate in intersubunit interactions with two modification subunits (HsdM) and two restriction subunits (HsdR) to form the complete endonuclease. It has been proposed that the domains of the HsdS subunit have a circular organisation providing the required symmetry for their interaction with the other subunits and with the bipartite DNA target. To test this model, we circularly permuted the HsdS subunit of the type IB R-M enzyme EcoAI at the DNA level by direct linkage of codons for original termini and introduction of new termini elsewhere along the N-terminal and central conserved regions. By analysing the activity of mutant enzymes, two circularly permuted variants of HsdS that had termini located at equivalent positions in the N-terminal and central repeats, respectively, were found to fold into a functional DNA recognition subunit with wild-type specificity, suggesting a close proximity of the N and C termini in the native protein. The wild-type HsdS subunit was purified to homogeneity and shown to form a stable trimeric complex with HsdM, M2S1, which was fully active as a DNA methyltransferase. Gel electrophoretic mobility shift assays revealed that the HsdS protein alone was not able to form a specific complex with a 30-mer oligoduplex containing a single EcoAI recognition site. However, addition of stoichiometric amounts of HsdM to HsdS led to efficient specific DNA binding. Our data provide evidence for the circular organisation of domains of the HsdS subunit. In addition, they suggest a possible role of HsdM subunits in the formation of this structure.},
  file      = {:by-author/J/Janscak/1998_Janscak_937.pdf:PDF},
  keywords  = {TypeI},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Janscak1999,
  author    = {Pavel Janscak and Maria P. MacWilliams and Ursula Sandmeier and Valakunja Nagaraja and Thomas A. Bickle},
  journal   = {The EMBO Journal},
  title     = {DNA translocation blockage, a general mechanism of cleavage site selection by type {I} restriction enzymes},
  year      = {1999},
  pages     = {2638a},
  file      = {:by-author/J/Janscak/1999_Janscak_2638a.pdf:PDF},
  keywords  = {TypeI},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Janscak1999a,
  author    = {Janscak, P. and Sandmeier, U. and Bickle, T. A.},
  journal   = {Nucleic acids research},
  title     = {Single amino acid substitutions in the HsdR subunit of the type IB restriction enzyme EcoAI uncouple the DNA translocation and DNA cleavage activities of the enzyme.},
  year      = {1999},
  pages     = {2638--43},
  volume    = {27},
  abstract  = {Type I restriction enzymes bind to specific DNA sequences but subsequently translocate non-specific DNA past the complex in a reaction coupled to ATP hydrolysis and cleave DNA at any barrier that can halt the translocation process. The restriction subunit of these enzymes, HsdR, contains a cluster of seven amino acid sequence motifs typical of helicase superfamily II, that are believed to be relevant to the ATP-dependent DNA translocation. Alignment of all available HsdR sequences reveals an additional conserved region at the protein N-terminus with a consensus sequence reminiscent of the P-D.(D/E)-X-K catalytic motif of many type II restriction enzymes. To investigate the role of these conserved residues, we have produced mutants of the type IB restriction enzyme Eco AI. We have found that single alanine substitutions at Asp-61, Glu-76 and Lys-78 residues of the HsdR subunit abolished the enzyme's restriction activity but had no effect on its ATPase and DNA translocation activities, suggesting that these residues are part of the active site for DNA cleavage.},
  file      = {:by-author/J/Janscak/1999_Janscak_2638.pdf:PDF},
  keywords  = {TypeI},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Janscak2001,
  author    = {Janscak, P. and Sandmeier, U. and Szczelkun, M. D. and Bickle, T. A.},
  journal   = {Journal of molecular biology},
  title     = {Subunit assembly and mode of DNA cleavage of the type III restriction endonucleases EcoP1I and EcoP15I.},
  year      = {2001},
  pages     = {417--31},
  volume    = {306},
  abstract  = {DNA cleavage by type III restriction endonucleases requires two inversely oriented asymmetric recognition sequences and results from ATP-dependent DNA translocation and collision of two enzyme molecules. Here, we characterized the structure and mode of action of the related EcoP1I and EcoP15I enzymes. Analytical ultracentrifugation and gel quantification revealed a common Res(2)Mod(2) subunit stoichiometry. Single alanine substitutions in the putative nuclease active site of ResP1 and ResP15 abolished DNA but not ATP hydrolysis, whilst a substitution in helicase motif VI abolished both activities. Positively supercoiled DNA substrates containing a pair of inversely oriented recognition sites were cleaved inefficiently, whereas the corresponding relaxed and negatively supercoiled substrates were cleaved efficiently, suggesting that DNA overtwisting impedes the convergence of the translocating enzymes. EcoP1I and EcoP15I could co-operate in DNA cleavage on circular substrate containing several EcoP1I sites inversely oriented to a single EcoP15I site; cleavage occurred predominantly at the EcoP15I site. EcoP15I alone showed nicking activity on these molecules, cutting exclusively the top DNA strand at its recognition site. This activity was dependent on enzyme concentration and local DNA sequence. The EcoP1I nuclease mutant greatly stimulated the EcoP15I nicking activity, while the EcoP1I motif VI mutant did not. Moreover, combining an EcoP15I nuclease mutant with wild-type EcoP1I resulted in cutting the bottom DNA strand at the EcoP15I site. These data suggest that double-strand breaks result from top strand cleavage by a Res subunit proximal to the site of cleavage, whilst bottom strand cleavage is catalysed by a Res subunit supplied in trans by the distal endonuclease in the collision complex.},
  file      = {:by-author/J/Janscak/2001_Janscak_417.pdf:PDF},
  keywords  = {TypeIII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Janscak2000,
  author    = {Janscak, P. and Weiserova, M. and Hubacek, J. and Holubova, I. and Dutta, C. F. and Firman, K.},
  journal   = {FEMS microbiology letters},
  title     = {Two temperature-sensitive mutations in the DNA binding subunit of EcoKI with differing properties.},
  year      = {2000},
  pages     = {99--104},
  volume    = {182},
  abstract  = {Two temperature-sensitive mutations in the hsdS gene, which encodes the DNA specificity subunit of the type IA restriction-modification system EcoKI, designated Sts1 (Ser(340)Phe) and Sts2 (Ala(204)Thr) had a different impact on restriction-modification functions in vitro and in vivo. The enzyme activities of the Sts1 mutant were temperature-sensitive in vitro and were reduced even at 30 degrees C (permissive temperature). Gel retardation assays revealed that the Sts1 mutant had significantly decreased DNA binding, which was temperature-sensitive. In contrast the Sts2 mutant did not show differences from the wild-type enzyme even at 42 degrees C. Unlike the HsdSts1 subunit, the HsdSts2 subunit was not able to compete with the wild-type subunit in assembly of the restriction enzyme in vivo, suggesting that the Sts2 mutation affects subunit assembly. Thus, it appears that these two mutations map two important regions in HsdS subunit responsible for DNA-protein and protein-protein interactions, respectively.},
  file      = {:by-author/J/Janscak/2000_Janscak_99.pdf:PDF},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Janssen2014,
  author    = {Janssen, Ted},
  journal   = {Symmetry},
  title     = {Development of Symmetry Concepts for Aperiodic Crystals},
  year      = {2014},
  issn      = {2073-8994},
  pages     = {171--188},
  volume    = {6},
  abstract  = {An overview is given of the use of symmetry considerations for aperiodic crystals. Superspace groups were introduced in the seventies for the description of incommensurate modulated phases with one modulation vector. Later, these groups were also used for quasi-periodic crystals of arbitrary rank. Further extensions use time reversal and time translation operations on magnetic and electrodynamic systems. An alternative description of magnetic structures to that with symmetry groups, the Shubnikov groups, is using representations of space groups. The same can be done for aperiodic crystals. A discussion of the relation between the two approaches is given. Representations of space groups and superspace groups play a role in the study of physical properties. These, and generalizations of them, are discussed for aperiodic crystals. They are used, in particular, for the characterization of phase transitions between aperiodic crystal phases.},
  doi       = {10.3390/sym6020171},
  file      = {2014_Janssen_171.pdf:by-author/J/Janssen/2014_Janssen_171.pdf:PDF},
  keywords  = {Speriodic Crystals; Symmetry},
  owner     = {saulius},
  timestamp = {2014.10.21},
  creationdate = {2014-10-21T00:00:00},
  url       = {http://www.mdpi.com/2073-8994/6/2/171},
}

@Article{Janthon2013,
  author    = {Patanachai Janthon and Sergey M. Kozlov and Francesc Viñes and Jumras Limtrakul and Francesc Illas},
  journal   = {Journal of Chemical Theory and Computation},
  title     = {Establishing the Accuracy of Broadly Used Density Functionals in Describing Bulk Properties of Transition Metals},
  year      = {2013},
  pages     = {1631--1640},
  volume    = {9},
  abstract  = {The performance of various commonly used density functionals is established by comparing calculated values of atomic structure data, cohesive energies, and bulk moduli of all transition metals to available experimental data. The functionals explored are the Ceperley–Alder (CA), Vosko–Wilk–Nussair (VWN) implementation of the Local Density Approximation (LDA); the Perdew–Wang (PW91) and Perdew–Burke–Ernzerhof (PBE) forms of the Generalized Gradient Approximation (GGA), and the RPBE and PBEsol modifications of PBE, aimed at better describing adsorption energies and bulk solid lattice properties, respectively. The present systematic study shows that PW91 and PBE consistently provide the smallest differences between the calculated and experimental values. Additional calculations of the (111) surface energy of several face centered cubic (fcc) transition metals reveal that LDA produces the most accurate results, while all other functionals significantly underestimate the experimental values. RPBE severely underestimates surface energy, which may be the origin for the reduced surface chemical activity and the better performance of RPBE describing adsorption energies.},
  doi       = {10.1021/ct3010326},
  file      = {:by-author/J/Janthon/2013_Janthon_manuscript.pdf:PDF;2013_Janthon_1631.pdf:by-author/J/Janthon/2013_Janthon_1631.pdf:PDF},
  keywords  = {Density Functional Theory (DFT)},
  owner     = {saulius},
  timestamp = {2013.03.22},
  creationdate = {2013-03-22T00:00:00},
}

@Article{Jaskolski2007,
  author    = {Jaskolski, Mariusz and Gilski, Miroslaw and Dauter, Zbigniew and Wlodawer, Alexander},
  journal   = {Acta crystallographica. Section D, Biological crystallography},
  title     = {Stereochemical restraints revisited: how accurate are refinement targets and how much should protein structures be allowed to deviate from them?},
  year      = {2007},
  pages     = {611--20},
  volume    = {63},
  abstract  = {The Protein Data Bank and Cambridge Structural Database were analyzed with the aim of verifying whether the restraints that are most commonly used for protein structure refinement are still appropriate 15 years after their introduction. From an analysis of selected main-chain parameters in well ordered fragments of ten highest resolution protein structures, it was concluded that some of the currently used geometrical target values should be adjusted somewhat (the C-N bond and the N-C(alpha)-C angle) or applied with less emphasis (peptide planarity). It was also found that the weighting of stereochemical information in medium-resolution refinements is often overemphasized at the cost of the experimental information in the diffraction data. A correctly set balance will be reflected in root-mean-square deviations from ideal bond lengths in the range 0.015-0.020 A for structures refined to R factors of 0.15-0.20. At ultrahigh resolution, however, the diffraction terms should be allowed to dominate, with even higher acceptable deviations from idealized standards in the well defined fragments of the protein. It is postulated that modern refinement programs should accommodate variable restraint weights that are dependent on the occupancies and B factors of the atoms involved.},
  file      = {:by-author/J/Jaskolski/2007_Jaskolski_611.pdf:PDF},
  keywords  = {Restrains; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2012.05.02},
  creationdate = {2012-05-02T00:00:00},
}

@Manuscript{Jay1998,
  author    = {C.B. Jay and P.A. Steckler},
  title     = {Polymorphism over nested regular arrays: theory and implementation in FISh},
  year      = {1998},
  keywords  = {Arrays; Compilers; Computer Science (CS); FISh; Polymorphism; Programming Languages},
  month     = {May},
  abstract  = {FISh is a higher-order, polymorphic language for array programming that sup- ports both functional and imperative styles, in the manner of an Algol-like language Rey81, OT97]. Polymorphic array programs can act on arrays with entries of di erent types, such as integers, oats, or even other arrays. Since these di erent types all have di erent storage requirements, it is usual to box the data, i.e. arrays contain pointers to their entries. This is a signi cant overhead (see, e.g. Sha97]), so that a variety of techniques have been developed to unbox data using type information. This works very smoothly for types that represent atomic values HM95], here called datum types, but for nested arrays one needs to know the length, or size of the array. This suggests using dependent types, in which list types},
  file      = {:by-author/J/Jay/1998_Jay.ps.gz:PostScript;:by-author/J/Jay/1998_Jay.pdf:PDF},
  owner     = {saulius},
  timestamp = {2015.02.27},
  creationdate = {2015-02-27T00:00:00},
}

@Article{Jayaram1989,
  author    = {B. Jayaram and Richard Fine and Kim Sharp and Barry Honig},
  journal   = {J. Phys. Chem.},
  title     = {Free energy calculations of ion hydratation: an analysis of the Born model in terms of microscopic simulations},
  year      = {1989},
  pages     = {4320--4327},
  abstract  = {The free energy perturbation technique is used in conjunction with Monte Carlo simulations to calculate the electrostatic contribution to the hydration free energy of a hypothetical cation whose charge varies in the range 0-3 au. The results are used to examine the validity of the continuum (Born) treatment of ion hydration. Saturation of the orientational polarizability of the water dipoles begins to become significant at values of the ionic charge of about +0.?5, a considerably higher value than predicted from a Langevin analysis. Moreover, due to the opposing effect of electrostriction on the dielectric response, the continuum prediction of a quadratic charge dependence of the hydration free energy is reproduced for values of the ionic charge up to approximately +1.1. These results suggest that dielectric saturation is insignificant for monovalent cations. Above charges of 1.1 the first solvation shell becomes fully saturated while the remaining water molecules continue to respond quadratically with increasing charge. It is argued that to within a few percent the assumptions of the Born model (without corrections for dielectric saturation) can be justified in terms of microscopic simulations.},
  file      = {1989_Jayaram_4320.pdf:by-author/J/Jayaram/1989_Jayaram_4320.pdf:PDF},
  keywords  = {Poisson-Boltzmann eq; Protein Physics; Solvatation},
  owner     = {saulius},
  timestamp = {2012.11.20},
  creationdate = {2012-11-20T00:00:00},
}

@Article{Jayaram1998,
  author    = {B. Jayaram and Y. Liu and D. L. Beveridge},
  journal   = {Journal of Chemical Physics},
  title     = {A modification of the generalized Born theory for improved estimates of solvation energies and p K shifts},
  year      = {1998},
  pages     = {1465--1471},
  volume    = {109},
  file      = {1998_Jayaram_1465.pdf:by-author/J/Jayaram/1998_Jayaram_1465.pdf:PDF},
  keywords  = {PKa; Protein Physics},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Jaynes1968b,
  author    = {Jaynes, E.T.},
  journal   = {Systems Science and Cybernetics, IEEE Transactions on},
  title     = {Prior Probabilities},
  year      = {1968},
  issn      = {0536-1567},
  pages     = {227 -241},
  volume    = {4},
  abstract  = {In decision theory, mathematical analysis shows that once the sampling distribution, loss function, and sample are specified, the only remaining basis for a choice among different admissible decisions lies in the prior probabilities. Therefore, the logical foundations of decision theory cannot be put in fully satisfactory form until the old problem of arbitrariness (sometimes called "subjectiveness") in assigning prior probabilities is resolved. The principle of maximum entropy represents one step in this direction. Its use is illustrated, and a correspondence property between maximum-entropy probabilities and frequencies is demonstrated. The consistency of this principle with the principles of conventional "direct probability" analysis is illustrated by showing that many known results may be derived by either method. However, an ambiguity remains in setting up a prior on a continuous parameter space because the results lack invariance under a change of parameters; thus a further principle is needed. It is shown that in many problems, including some of the most important in practice, this ambiguity can be removed by applying methods of group theoretical reasoning which have long been used in theoretical physics. By finding the group of transformations on the parameter space which convert the problem into an equivalent one, a basic desideratum of consistency can be stated in the form of functional equations which impose conditions on, and in some cases fully determine, an "invariant measure" on the parameter space.},
  doi       = {10.1109/TSSC.1968.300117},
  file      = {1968_Jaynes_227.pdf:by-author/J/Jaynes/1968_Jaynes_227.pdf:PDF},
  groups    = {sg/Bayesian},
  keywords  = {Bayesian Statistics},
  owner     = {saulius},
  timestamp = {2012.10.04},
  creationdate = {2012-10-04T00:00:00},
}

@InProceedings{Jaynes1980e,
  author    = {Edwin T. Jaynes},
  booktitle = {Foundations of Radiation Theory and Quantum Electrodynamics},
  title     = {Quantum Beats},
  year      = {1980},
  editor    = {A. O. Barut},
  pages     = {37},
  publisher = {Plenum Press, New York},
  file      = {:./by-author/J/Jaynes/1980_Jaynes_37.pdf:PDF},
  groups    = {sg/Bayesian},
  owner     = {saulius},
  timestamp = {2012.10.05},
  creationdate = {2012-10-05T00:00:00},
  url       = {http://bayes.wustl.edu/etj/articles/quantum.beats.pdf},
}

@InProceedings{Jaynes1985b,
  author    = {Edwin T. Jaynes},
  booktitle = {Bayesian Statistics 2},
  title     = {Highly Informative Priors},
  year      = {1985},
  editor    = {J. M. Bernardo and M. H. deGroot and D. V. Lindley and A. F. M. Smith},
  pages     = {329},
  publisher = {Elsevier, Amsterdam},
  abstract  = {After discussing the role of prior information in statistical inference, histori- cally and in current problems, we analyze the problem of seasonal adjustment in economics. Litterman (1980) has shown how informative priors for autoregressive coe cients can improve economic forecasts. We nd that in seasonal adjustment informative priors can have a much greater e ect on our conclusions. In our model, even the dimensionality of the joint posterior distribution of the irregulars depends on prior information about the seasonal component; and some functions of the ir- regulars can be determined more accurately than in sampling theory.},
  file      = {:./by-author/J/Jaynes/1985_Jaynes_329.pdf:PDF},
  groups    = {sg/Bayesian},
  keywords  = {Bayesian Statistics},
  owner     = {saulius},
  timestamp = {2012.10.05},
  creationdate = {2012-10-05T00:00:00},
  url       = {http://bayes.wustl.edu/etj/articles/highly.informative.priors.pdf},
}

@InProceedings{Jaynes1980b,
  author    = {Edwin T. Jaynes},
  booktitle = {Bayesian Statistics},
  title     = {What is the Question?},
  year      = {1980},
  editor    = {J. M. Bernardo and M. H. deGroot and D. V. Lindly and A. F. M. Smith},
  pages     = {618},
  publisher = {Valencia Univ. Press, Valencia},
  file      = {:./by-author/J/Jaynes/1980_Jaynes_618.pdf:PDF},
  groups    = {sg/Bayesian},
  journal   = {Bayesian Statistics},
  owner     = {saulius},
  timestamp = {2012.10.05},
  creationdate = {2012-10-05T00:00:00},
  url       = {http://bayes.wustl.edu/etj/articles/what.question.pdf},
}

@InProceedings{Jaynes1963b,
  author    = {Edwin T. Jaynes},
  booktitle = {Engineering Uses of Random Function Theory and Probability},
  title     = {New Engineering Applications of Information Theory},
  year      = {1963},
  editor    = {J. Bogdanoff and F. Kozin},
  pages     = {163--203},
  publisher = {Wiley, New York},
  file      = {:./by-author/J/Jaynes/1963_Jaynes_163.pdf:PDF},
  groups    = {sg/Bayesian},
  keywords  = {Bayesian Statistics},
  owner     = {saulius},
  timestamp = {2012.10.05},
  creationdate = {2012-10-05T00:00:00},
  url       = {http://bayes.wustl.edu/etj/articles/new.eng.app.pdf},
}

@InProceedings{Jaynes1967,
  author    = {Edwin T. Jaynes},
  booktitle = {Delaware Seminar in the Foundations of Physics},
  title     = {Foundations of Probability Theory and Statistical Mechanics},
  year      = {1967},
  editor    = {M. Bunge},
  pages     = {77},
  publisher = {Springer-Verlag, Berlin},
  file      = {:./by-author/J/Jaynes/1967_Jaynes_77.pdf:PDF},
  groups    = {sg/Bayesian},
  keywords  = {Bayesian Statistics; Statistical Mechanics},
  owner     = {saulius},
  timestamp = {2012.10.05},
  creationdate = {2012-10-05T00:00:00},
  url       = {http://bayes.wustl.edu/etj/articles/foundations.of.prob.st.pdf},
}

@InProceedings{Jaynes1992,
  author    = {Edwin T. Jaynes},
  booktitle = {Maximum-Entropy and Bayesian Methods},
  title     = {The {G}ibbs paradox},
  year      = {1992},
  editor    = {G. Erickson and P. Neudorfer and C. R. Smith},
  pages     = {1},
  publisher = {Kluwer, Dordrecht},
  file      = {:./by-author/J/Jaynes/1992_Jaynes_1.pdf:PDF},
  groups    = {sg/Bayesian},
  keywords  = {Bayesian Statistics},
  owner     = {saulius},
  timestamp = {2012.10.05},
  creationdate = {2012-10-05T00:00:00},
  url       = {http://bayes.wustl.edu/etj/articles/gibbs.paradox.pdf},
}

@InProceedings{Jaynes1988,
  author    = {Edwin T. Jaynes},
  booktitle = {Maximum-Entropy and Bayesian Methods in Science and Engineering},
  title     = {The evolution of {C}arnot's principle},
  year      = {1988},
  editor    = {G. J. Erickson and C. R. Smith},
  pages     = {267},
  publisher = {Kluwer, Dordrecht},
  abstract  = {We trace the development of the technical ideas showing that the Second Law of Ther- modynamics became, over a Century ago, a general principle of reasoning, applicable to scienti c inference in other elds than thermodynamics. Both the logic and the procedure of our present maximum entropy applications are easily recognized in the methods for predicting equilibrium con- ditions introduced by Gibbs in 1875. Chemical thermodynamics has been based on them ever since. What is new in this eld is not the method, but the recognition of its generality.},
  file      = {:./by-author/J/Jaynes/1988_Jaynes_267.pdf:PDF},
  groups    = {sg/Bayesian},
  keywords  = {Bayesian Statistics},
  owner     = {saulius},
  timestamp = {2012.10.05},
  creationdate = {2012-10-05T00:00:00},
  url       = {http://bayes.wustl.edu/etj/articles/ccarnot.pdf},
}

@InProceedings{Jaynes1988a,
  author    = {Edwin T. Jaynes},
  booktitle = {Maximum-Entropy and Bayesian Methods in Science and Engineering},
  title     = {The Relation of Bayesian and Maximum Entropy Methods},
  year      = {1988},
  editor    = {G. J. Erickson and C. R. Smith},
  pages     = {25},
  publisher = {Kluwer, Dordrecht},
  abstract  = {Further progress in scientific inference must, in our view, come from some kinde of unification of our present principles. As a prerequisite for thies, we note briefly the great conceptual diferences, and the equally great mathematical similarities, of Bayesian and Maximumm Entropy methods.},
  file      = {:./by-author/J/Jaynes/1988_Jaynes_25.pdf:PDF},
  groups    = {sg/Bayesian},
  keywords  = {Bayesian Statistics; MaxEnt; Maximum Entropy},
  owner     = {saulius},
  timestamp = {2012.10.05},
  creationdate = {2012-10-05T00:00:00},
  url       = {http://bayes.wustl.edu/etj/articles/relationship.pdf},
}

@InProceedings{Jaynes1988b,
  author    = {Edwin T. Jaynes},
  booktitle = {Maximum-Entropy and Bayesian Methods in Science and Engineering},
  title     = {Detection of Extra-Solar-System Planets},
  year      = {1988},
  editor    = {G. J. Erickson and C. R. Smith},
  pages     = {147},
  publisher = {Kluwer, Dordrecht},
  abstract  = {aStimulated by a proposal of Wm. Hayden Smith and co workers to detect planets on nearby stars by high resolution imaging, we speculate on the appropriate data analysis method, making use of probability theory to perform the optimal deconvolution of the point spread function. In this preliminary study, we seek to understand what probability theory has to say about the fundamental problem, by analyzing a simple one dimensional version. The necessary theoretical principles are developed in the thesis of G. L. Bretthorst (Washington University, May 1987) and in Bretthorst (1988). Our main message is this: once one is committed to using a computer to analyze the data, the high resolution imaging problem is completely changed. What one has tried to do in the past by fancy optical and mechanical engineering feats (apodizing, image stabilizing) can be done far better, and at a small fraction of the cost, by the computer.},
  file      = {:./by-author/J/Jaynes/1988_Jaynes_147.pdf:PDF},
  groups    = {sg/Bayesian},
  keywords  = {Bayesian Statistics; MaxEnt; Maximum Entropy},
  owner     = {saulius},
  timestamp = {2012.10.05},
  creationdate = {2012-10-05T00:00:00},
  url       = {http://bayes.wustl.edu/etj/articles/cplanets.pdf},
}

@InProceedings{Jaynes1988c,
  author    = {Edwin T. Jaynes},
  booktitle = {Maximum-Entropy and Bayesian Methods in Science and Engineering},
  title     = {How Does the Brain Do Plausible Reasoning?},
  year      = {1988},
  editor    = {G. J. Erickson and C. R. Smith},
  pages     = {1},
  publisher = {Kluwer, Dordrecht},
  abstract  = {We start from the observation that the human brain does plausible reasoning in a fairly definite way. It is shown that there is only as single set of rules for doing this which is consistent and in qualitative correspondence with common sense. These rules are simply the equations of probability theory, and they can be deduced without any reference to frequencies. W conclude that the method of maximum--entropy inference and the use of Bayes' theorem are statistical techniques fully as valid as any based on the frequency interpretation of probability. Their introduction enables us to broaden the scope of statistical inference so that it includes both communication theory and thermodynamics as special cases. The program of statistical inference is thus formulated in a new way. We regard the general problem of statistical inference as that of devising new consistent principles by which we can translate "raw" information into numerical values of probabilities, so that the Laplace--Bayes model is enabled to operate on more and more diferent kinds of information. That there must exist many such principles, as yet undiscovered, is shown by the simple fact that our brains do this every day.},
  file      = {:./by-author/J/Jaynes/1988_Jaynes_1.pdf:PDF},
  groups    = {sg/Bayesian},
  owner     = {saulius},
  timestamp = {2012.10.05},
  creationdate = {2012-10-05T00:00:00},
  url       = {http://bayes.wustl.edu/etj/articles/brain.pdf},
}

@InProceedings{Jaynes1963a,
  author    = {Edwin T. Jaynes},
  booktitle = {Statistical Physics},
  title     = {Information Theory and Statistical Mechanics},
  year      = {1963},
  editor    = {K. Ford},
  pages     = {181--218},
  publisher = {Benjamin, New York},
  file      = {:./by-author/J/Jaynes/1963_Jaynes_181.pdf:PDF},
  groups    = {sg/Bayesian},
  keywords  = {Bayesian Statistics; Statistical Mechanics},
  owner     = {saulius},
  timestamp = {2012.10.05},
  creationdate = {2012-10-05T00:00:00},
  url       = {http://bayes.wustl.edu/etj/articles/brandeis.pdf},
}

@InProceedings{Jaynes1990a,
  author    = {Edwin T. Jaynes},
  booktitle = {Maximum-Entropy and Bayesian Methods},
  title     = {Probability theory as logic},
  year      = {1990},
  editor    = {P. F. Fougère},
  pages     = {1},
  publisher = {Kluwer, Dordrecht},
  abstract  = {At the 1988 workshop we called attention to the Mind Projection Fallacy" which is present in all elds that use probability. Here we give a more complete discussion showing why probabilities need not correspond to physical causal in uences, or propensities" a ecting mass phenomena. Probability theory is far more useful if we recognize that probabilities express fundamentally logical inferences pertaining to individual cases. We note several examples of the di erence this makes in real applications.},
  file      = {:./by-author/J/Jaynes/1990_Jaynes_1.pdf:PDF},
  groups    = {sg/Bayesian},
  keywords  = {Bayesian Statistics},
  owner     = {saulius},
  timestamp = {2012.10.05},
  creationdate = {2012-10-05T00:00:00},
  url       = {http://bayes.wustl.edu/etj/articles/prob.as.logic.pdf},
}

@InProceedings{Jaynes1986a,
  author    = {Edwin T. Jaynes},
  booktitle = {Bayesian Inference and Decision Techniques with Applications: Essays in Honor of Bruno de Finetti},
  title     = {Some Applications and Extensions of the de Finetti Representation Theorem},
  year      = {1986},
  editor    = {P. K. Goel and A. Zellner},
  pages     = {31},
  publisher = {North-Holland, Amsterdam},
  abstract  = {The de Finetti representation, when extended by a trivial modification to cover finite as well as infinite exchangeable sequences, becomes a powerful analytical tool for dealing with real statistical problems.},
  file      = {:./by-author/J/Jaynes/1986_Jaynes_31.pdf:PDF},
  groups    = {sg/Bayesian},
  keywords  = {Bayesian Statistics},
  owner     = {saulius},
  timestamp = {2012.10.05},
  creationdate = {2012-10-05T00:00:00},
  url       = {http://bayes.wustl.edu/etj/articles/applications.pdf},
}

@InBook{Jaynes1993,
  author    = {Edwin T. Jaynes},
  chapter   = {A backward look to the future},
  editor    = {Grandy, Jr., W. T. and P. W. Milonni},
  pages     = {261--275},
  publisher = {Cambridge Univ. Press, Cambridge, England},
  title     = {Physics and Probability},
  year      = {1993},
  abstract  = {We survey briefly some fifty years of thinking about physics and probability with the aim of explaining: (1) What I did not know then, but know now; (2) What I have been trying to accomplish in science and education, and to what extent these e orts have succeeded; (3) What remains un nished, but where I think the greatest future opportunities lie; and (4) What personal and professional advice I can now give to young people (and wish someone had given me fifty years ago).},
  file      = {:./by-author/J/Jaynes/1993_Jaynes_261.pdf:PDF},
  groups    = {sg/Bayesian},
  keywords  = {Bayesian Statistics},
  owner     = {saulius},
  timestamp = {2012.10.05},
  creationdate = {2012-10-05T00:00:00},
  url       = {http://bayes.wustl.edu/etj/articles/backward.look.pdf},
}

@InProceedings{Jaynes1991b,
  author    = {Edwin T. Jaynes},
  booktitle = {Maximum Entropy and Bayesian Methods},
  title     = {Notes On Present Status And Future Prospects},
  year      = {1991},
  editor    = {Grandy, Jr., W. T. and L. H. Schick},
  pages     = {1},
  publisher = {Kluwer, Dordrecht},
  file      = {:./by-author/J/Jaynes/1991_Jaynes_1.pdf:PDF},
  groups    = {sg/Bayesian},
  owner     = {saulius},
  timestamp = {2012.10.05},
  creationdate = {2012-10-05T00:00:00},
  url       = {http://bayes.wustl.edu/etj/articles/present.status.pdf},
}

@InProceedings{Jaynes1985c,
  author    = {Edwin T. Jaynes},
  booktitle = {Complex Systems - Operational Approaches},
  title     = {Macroscopic Prediction},
  year      = {1985},
  editor    = {H. Haken},
  pages     = {254},
  publisher = {Springer-Verlag, Berlin},
  file      = {:./by-author/J/Jaynes/1985_Jaynes_254.pdf:PDF},
  groups    = {sg/Bayesian},
  keywords  = {Bayesian Statistics},
  owner     = {saulius},
  timestamp = {2012.10.05},
  creationdate = {2012-10-05T00:00:00},
  url       = {http://bayes.wustl.edu/etj/articles/macroscopic.prediction.pdf},
}

@InProceedings{Jaynes1976,
  author    = {Edwin T. Jaynes},
  booktitle = {Foundations of Probability Theory, Statistical Inference, and Statistical Theories of Science},
  title     = {Confidence Intervals vs Bayesian Intervals},
  year      = {1976},
  editor    = {W. L. Harper and C. A. Hooker},
  pages     = {175--257},
  publisher = {D. Reidel, Dordrecht},
  volume    = {II},
  abstract  = {For many years, statistics textbooks have followed this 'canonical' procedure: (1) the reader is warned not to use the discredited methods of Bayes and Laplace, (2) an orthodox method is extolled as superior and applied to a few simple problems, (3) the corresponding Bayesian solutions are {\em not} worked out or described in any way. The net result is that no evidence whatsoever is offered to substantiate claim of superiority of the orthodox method. To correct this situation we exhibit the Bayesian and orthodox solutions to six common statistcal problems involving confidence intervals (including significance tests based on the same reasoning). In every case, we find that the sutuation is exactely the opposite; i.e., the Bayesian method is easier to apply and yields the same or better results. Indeed, the orthodox results are satisfactory only when they agree closely (or exactely) with the Bayesian results. No contrary example has yet been produced. By a refinement of the orthodox statistitian's own criterion of performance, the best confidence interval for any location or scale parameter is proved to be the Bayesian posterior probability interval. In the cases of point estimation and hypothesis testing, similar proofs have long been known. We conclude that the orthodox claims of superiority are totally unjustified; today, the original statistical method of Bayes and Laplace stands in a position of proven superiority in actual performance, that places them beyond the reach of mere ideological or philosophical attacks. It is the continued teaching and use of orthodox methods that is in need of justification and defence.},
  file      = {:./by-author/J/Jaynes/1976_Jaynes_175.pdf:PDF},
  groups    = {sg/Bayesian},
  keywords  = {Bayesian Statistics; Criticism; Frequentist Statistics},
  owner     = {saulius},
  timestamp = {2012.10.05},
  creationdate = {2012-10-05T00:00:00},
  url       = {http://bayes.wustl.edu/etj/articles/confidence.pdf},
}

@InProceedings{Jaynes1991a,
  author    = {Edwin T. Jaynes},
  booktitle = {The Electron},
  title     = {Scattering of light by free electrons as a test of quantum theory},
  year      = {1991},
  editor    = {D. Hestenes and A. Weingartshofer},
  pages     = {1--19},
  publisher = {Kluwer, Dordrecht},
  file      = {:./by-author/J/Jaynes/1991_Jaynes_1a.pdf:PDF},
  groups    = {sg/Bayesian},
  keywords  = {Electrodynamics; Electron; Quantum Electrodynamics; Quantum Mechanics (QM)},
  owner     = {saulius},
  timestamp = {2012.10.05},
  creationdate = {2012-10-05T00:00:00},
  url       = {http://bayes.wustl.edu/etj/articles/scattering.by.free.pdf},
}

@InProceedings{Jaynes1978c,
  author    = {Edwin T. Jaynes},
  booktitle = {Novel Sources of Coherent Radiation},
  title     = {Ancient History of Free Electron Devices},
  year      = {1978},
  editor    = {S. F. Jacob and M. Scully and Sargent, III, M.},
  pages     = {1},
  publisher = {Addison-Wesley, Reading, MA},
  file      = {:./by-author/J/Jaynes/1978_Jaynes_1.pdf:PDF},
  groups    = {sg/Bayesian},
  owner     = {saulius},
  timestamp = {2012.10.05},
  creationdate = {2012-10-05T00:00:00},
  url       = {http://bayes.wustl.edu/etj/articles/history.pdf},
}

@InProceedings{Jaynes1986b,
  author    = {Edwin T. Jaynes},
  booktitle = {Maximum-Entropy and Bayesian Methods in Applied Statistics},
  title     = {Monkeys, Kangaroos and N},
  year      = {1986},
  editor    = {J. H. Justice},
  pages     = {26},
  publisher = {Cambridge Univ. Press, Cambridge},
  abstract  = {We examine some points of the rationale underlying the choice of priors for MAXENT image reconstruction. The original combinatorial (monkey) and exchangeability (kangaroo) approaches each contains important truth. Yet each also represents in a sense an extreme position which ignores the truth in the other. The models of W. E. Johnson, I.~J.~Good, and S. Zabell provide a continuous interpolation between them, in which the monkeys' entropy factor is always present in the prior, but becomes increasingly levelled out and disappears in the limit. However, it appears that the class of interpolated priors is still too narrow. A fully satisfactory prior for image reconstruction, which expresses all our prior information, needs to be able to express the common sense judgment that correlations vary with the distance between pixels. To do this, we must go outside the class of exchangeable priors, perhaps into an altogether deeper hypothesis space.},
  file      = {:./by-author/J/Jaynes/1986_Jaynes_26.pdf:PDF},
  groups    = {sg/Bayesian},
  keywords  = {Bayesian Statistics; MaxEnt; Maximum Entropy},
  owner     = {saulius},
  timestamp = {2012.10.05},
  creationdate = {2012-10-05T00:00:00},
  url       = {http://bayes.wustl.edu/etj/articles/cmonkeys.pdf},
}

@InProceedings{Jaynes1986c,
  author    = {Edwin T. Jaynes},
  booktitle = {Maximum-Entropy and Bayesian Methods in Applied Statistics},
  title     = {Bayesian Methods: General Background},
  year      = {1986},
  editor    = {J. H. Justice},
  pages     = {1},
  publisher = {Cambridge Univ. Press, Cambridge},
  file      = {:./by-author/J/Jaynes/1986_Jaynes_1.pdf:PDF},
  groups    = {sg/Bayesian},
  owner     = {saulius},
  timestamp = {2012.10.05},
  creationdate = {2012-10-05T00:00:00},
  url       = {http://bayes.wustl.edu/etj/articles/general.background.pdf},
}

@InProceedings{Jaynes1979a,
  author    = {Edwin T. Jaynes},
  booktitle = {The Maximum Entropy Formalism},
  title     = {Where do we Stand on Maximum Entropy?},
  year      = {1979},
  editor    = {R. D. Levine and M. Tribus},
  pages     = {15manuscript},
  publisher = {M. I. T. Press, Cambridge, MA},
  file      = {:./by-author/J/Jaynes/1979_Jaynes_15manuscript.pdf:PDF},
  groups    = {sg/Bayesian},
  owner     = {saulius},
  timestamp = {2012.10.05},
  creationdate = {2012-10-05T00:00:00},
  url       = {http://bayes.wustl.edu/etj/articles/stand.on.entropy.pdf},
}

@InProceedings{Jaynes1978a,
  author    = {Edwin T. Jaynes},
  booktitle = {Coherence and Quantum Optics},
  title     = {Electrodynamics Today},
  year      = {1978},
  editor    = {L. Mandel and E. Wolf},
  pages     = {495manuscript},
  publisher = {Plenum Press, New York},
  volume    = {IV},
  file      = {:./by-author/J/Jaynes/1978_Jaynes_495manuscript.pdf:PDF},
  groups    = {sg/Bayesian},
  owner     = {saulius},
  timestamp = {2012.10.05},
  creationdate = {2012-10-05T00:00:00},
  url       = {http://bayes.wustl.edu/etj/articles/electrodynamics.today.pdf},
}

@InProceedings{Jaynes1966,
  author    = {Edwin T. Jaynes},
  booktitle = {Proceedings of the Second Rochester Conference on Coherence and Quantum Optics},
  title     = {Is QED Necessary},
  year      = {1966},
  editor    = {L. Mandel and E. Wolf},
  pages     = {21},
  publisher = {Plenum, New York},
  file      = {:./by-author/J/Jaynes/1966_Jaynes_21.pdf:PDF},
  groups    = {sg/Bayesian},
  owner     = {saulius},
  timestamp = {2012.10.05},
  creationdate = {2012-10-05T00:00:00},
  url       = {http://bayes.wustl.edu/etj/articles/is.qed.necessary.pdf},
}

@InProceedings{Jaynes1986,
  author    = {Edwin T. Jaynes},
  booktitle = {Frontiers of Nonequilibrium Statistical Physics},
  title     = {Predictive Statistical Mechanics},
  year      = {1986},
  editor    = {G. T. Moore and M. O. Scully},
  pages     = {33},
  publisher = {Plenum Press, New York},
  file      = {:./by-author/J/Jaynes/1986_Jaynes_33.pdf:PDF},
  groups    = {sg/Bayesian},
  keywords  = {Bayesian Statistics; Quantum Mechanics (QM); Statistical Mechanics},
  owner     = {saulius},
  timestamp = {2012.10.05},
  creationdate = {2012-10-05T00:00:00},
  url       = {http://bayes.wustl.edu/etj/articles/predictive.pdf},
}

@InProceedings{Jaynes1979,
  author    = {Edwin T. Jaynes},
  booktitle = {E. T. Jaynes: Papers on Probability, Statistics and Statistical Physics},
  title     = {Concentration of Distributions at Entropy Maxima},
  year      = {1979},
  editor    = {R. D. Rosenkrantz},
  pages     = {315manuscript},
  publisher = {D. Reidel, Dordrecht},
  file      = {:./by-author/J/Jaynes/1979_Jaynes_315manuscript.pdf:PDF},
  groups    = {sg/Bayesian},
  owner     = {saulius},
  timestamp = {2012.10.05},
  creationdate = {2012-10-05T00:00:00},
  url       = {http://bayes.wustl.edu/etj/articles/entropy.concentration.pdf},
}

@InProceedings{Jaynes1989,
  author    = {Edwin T. Jaynes},
  booktitle = {Maximum-Entropy and Bayesian Methods},
  title     = {Clearing up mysteries -- the original goal},
  year      = {1989},
  editor    = {J. Skilling},
  pages     = {1},
  publisher = {Kluwer, Dordrecht},
  abstract  = {We show how the character of a scienti c theory depends on one's attitude toward proba- bility. Many circumstances seem mysterious or paradoxical to one who thinks that probabilities are real physical properties existing in Nature. But when we adopt the Bayesian Inference" viewpoint of Harold Je reys, paradoxes often become simple platitudes and we have a more powerful tool for useful calculations. This is illustrated by three examples from widely di erent elds: di usion in kinetic theory, the Einstein Podolsky Rosen EPR paradox in quantum theory, and the second law of thermodynamics in biology.},
  file      = {:./by-author/J/Jaynes/1989_Jaynes_1.pdf:PDF},
  groups    = {sg/Bayesian},
  keywords  = {Bayesian Statistics},
  owner     = {saulius},
  timestamp = {2012.10.05},
  creationdate = {2012-10-05T00:00:00},
  url       = {http://bayes.wustl.edu/etj/articles/cmystery.pdf},
}

@InProceedings{Jaynes1987a,
  author    = {Edwin T. Jaynes},
  booktitle = {Maximum Entropy and Bayesian Spectral Analysis and Estimation Problems},
  title     = {Bayesian Spectrum and Chirp Analysis},
  year      = {1987},
  editor    = {C. R. Smith and G. J. Erickson},
  pages     = {1},
  publisher = {D. Reidel, Dordrecht},
  file      = {:./by-author/J/Jaynes/1987_Jaynes_1.pdf:PDF},
  groups    = {sg/Bayesian},
  keywords  = {Bayesian Statistics; MaxEnt; Maximum Entropy},
  owner     = {saulius},
  timestamp = {2012.10.05},
  creationdate = {2012-10-05T00:00:00},
  url       = {http://bayes.wustl.edu/etj/articles/cchirp.pdf},
}

@InProceedings{Jaynes1985,
  author    = {Edwin T. Jaynes},
  booktitle = {Maximum-Entropy and Bayesian Methods in Inverse Problems},
  title     = {Entropy and Search-Theory},
  year      = {1985},
  editor    = {C. R. Smith and Grandy, Jr., W. T.},
  pages     = {443},
  publisher = {D. Reidel, Dordrecht},
  file      = {:./by-author/J/Jaynes/1985_Jaynes_443.pdf:PDF},
  groups    = {sg/Bayesian},
  keywords  = {Bayesian Statistics; Entropy},
  owner     = {saulius},
  timestamp = {2012.10.05},
  creationdate = {2012-10-05T00:00:00},
  url       = {http://bayes.wustl.edu/etj/articles/search.pdf},
}

@InProceedings{Jaynes1985a,
  author    = {Edwin T. Jaynes},
  booktitle = {Maximum-Entropy and Bayesian Methods in Inverse Problems},
  title     = {Inferential scattering},
  year      = {1985},
  editor    = {C. R. Smith and Grandy, Jr., W. T.},
  pages     = {377},
  publisher = {D. Reidel, Dordrecht},
  abstract  = {Some diffcult conceptual problems that have plagued Statistical Mechanics from the start, are explained by reference to a very simple experiment, which also explains why the MAXENT formalism gives reliable predictions. Then some of the inner workings of MAXENT are revealed by a general perturbation theorem, showing how a prediction is modi ed by adding a new constraint. It is illustrated by the example of Rayleigh scattering in acoustics. Here it appears rather like Schwinger's Source Theory in that multiple scattered waves of arbitrarily high order appear already in the rst order of the MAXENT perturbation scheme. The result holds in much more general problems of inferential scattering" in which any statistical inference is modi ed by new information.},
  file      = {:./by-author/J/Jaynes/1985_Jaynes_377.pdf:PDF},
  groups    = {sg/Bayesian},
  keywords  = {Bayesian Statistics},
  owner     = {saulius},
  timestamp = {2012.10.05},
  creationdate = {2012-10-05T00:00:00},
  url       = {http://bayes.wustl.edu/etj/articles/cinfscat.pdf},
}

@InProceedings{Jaynes1985d,
  author    = {Edwin T. Jaynes},
  booktitle = {Maximum-Entropy and Bayesian Methods in Inverse Problems},
  title     = {Where do we go from Here?},
  year      = {1985},
  editor    = {C. R. Smith and Grandy, Jr., W. T.},
  pages     = {21},
  publisher = {D. Reidel, Dordrecht},
  file      = {:./by-author/J/Jaynes/1985_Jaynes_21.pdf:PDF},
  groups    = {sg/Bayesian},
  keywords  = {Bayesian Statistics},
  owner     = {saulius},
  timestamp = {2012.10.05},
  creationdate = {2012-10-05T00:00:00},
  url       = {http://bayes.wustl.edu/etj/articles/fromhere.pdf},
}

@InProceedings{Jaynes1960,
  author    = {Edwin T. Jaynes},
  booktitle = {Quantum Electronics},
  title     = {The Maser as a Parametric Amplifier},
  year      = {1960},
  editor    = {C. H. Townes},
  pages     = {287--292},
  publisher = {Columbia Univ. Press, New York},
  file      = {:./by-author/J/Jaynes/1960_Jaynes_287.pdf:PDF},
  groups    = {sg/Bayesian},
  owner     = {saulius},
  timestamp = {2012.10.05},
  creationdate = {2012-10-05T00:00:00},
  url       = {http://bayes.wustl.edu/etj/articles/parametric.amplifier.pdf},
}

@InProceedings{Jaynes1980,
  author    = {Edwin T. Jaynes},
  booktitle = {Bayesian Analysis in Econometrics and Statistics},
  title     = {Reply to Dawid, Stone, and Zidek},
  year      = {1980},
  editor    = {A. Zellner},
  pages     = {83--87},
  publisher = {North-Holland Amsterdam},
  file      = {:./by-author/J/Jaynes/1980_Jaynes_83.pdf:PDF},
  groups    = {sg/Bayesian},
  owner     = {saulius},
  timestamp = {2012.10.05},
  creationdate = {2012-10-05T00:00:00},
  url       = {http://bayes.wustl.edu/etj/articles/reply.to.dawid.pdf},
}

@InProceedings{Jaynes1980d,
  author    = {Edwin T. Jaynes},
  booktitle = {Bayesian Analysis in Econometrics and Statistics},
  title     = {Marginalization and Prior Probabilities},
  year      = {1980},
  editor    = {A. Zellner},
  pages     = {43},
  publisher = {North-Holland, Amsterdam},
  file      = {:./by-author/J/Jaynes/1980_Jaynes_43.pdf:PDF},
  groups    = {sg/Bayesian},
  owner     = {saulius},
  timestamp = {2012.10.05},
  creationdate = {2012-10-05T00:00:00},
  url       = {http://bayes.wustl.edu/etj/articles/margin.pdf},
}

@InBook{Jaynes1990,
  author    = {Edwin T. Jaynes},
  chapter   = {Probability in quantum theory},
  editor    = {W. H. Zurek},
  pages     = {381},
  publisher = {Addison-Wesley, Redwood City, CA},
  title     = {Complexity, Entropy, and the Physics of Information},
  year      = {1990},
  abstract  = {For some sixty years it has appeared to many physicists that probability plays a fundamentally di erent role in quantum theory than it does in statistical mechanics and analysis of measurement errors. It is a commonly heard statement that probabilities calculated within a pure state have a di erent character than the probabilities with which di erent pure states appear in a mixture, or density matrix. As Pauli put it, the former represents Eine prinzipielle Unbestimmtheit, nicht nur Unbekanntheit". But this viewpoint leads to so many paradoxes and mysteries that we explore the consequences of the uni ed view, that all probability signi es only incomplete human information. We examine in detail only one of the issues this raises: the reality of zero point energy.},
  file      = {:./by-author/J/Jaynes/1990_Jaynes_381.pdf:PDF},
  groups    = {sg/Bayesian},
  keywords  = {Bayesian Statistics; Entropy},
  owner     = {saulius},
  timestamp = {2012.10.05},
  creationdate = {2012-10-05T00:00:00},
  url       = {http://bayes.wustl.edu/etj/articles/prob.in.qm.pdf},
}

@Article{Jaynes2003,
  author    = {Edwin T. Jaynes},
  journal   = {Am. J. Phys.},
  title     = {Note on thermal heating efficiency},
  year      = {2003},
  pages     = {180--183},
  volume    = {71},
  abstract  = {Kelvin showed the maximum efficiency with which heat can be converted into work; but there is a dual theorem about the maximum efficiency with which heat at one temperature can be converted into heat at another temperature. It has some surprising implications, in particular that the efficiency with which we heat our buildings could in principle be improved by a large factor. This long known, but still little known, fact is of current pedagogical interest and practical importance.},
  doi       = {10.1119/1.1508446},
  file      = {:./by-author/J/Jaynes/2003_Jaynes_180.pdf:PDF},
  groups    = {sg/Bayesian},
  keywords  = {Thermodynamics},
  owner     = {saulius},
  timestamp = {2012.10.05},
  creationdate = {2012-10-05T00:00:00},
  url       = {http://bayes.wustl.edu/etj/articles/AJP00180.pdf},
}

@Article{Jaynes1991,
  author    = {Edwin T. Jaynes},
  journal   = {Computers and Mathematics with Applications},
  title     = {Commentary on Two Articles by C.A. Los},
  year      = {1991},
  pages     = {manuscript},
  abstract  = {Recently, C. A. Los has recommended that all previous methods for estimating linear relations from data with unknown errors be scrapped, and proposes to find an `exact objective mathematical solution' that depends only on the data. We discuss this with the conclusions that (1) his criticisms of previous methods, while overly severe, make some important points worth noting; (2) however, his solution ignores relevant information and does not exist except in very special cases; (3) the Los solution, when it exists, may be characterized as the one which would be correct if we had an infinite amount of data which led to the same data correlation matrix; (4) methods for dealing with the problem which are optimal in all cases have been known for 20 years},
  file      = {:./by-author/J/Jaynes/1991_Jaynes_manuscript.pdf:PDF},
  groups    = {sg/Bayesian},
  keywords  = {Bayesian Statistics},
  owner     = {saulius},
  timestamp = {2012.10.05},
  creationdate = {2012-10-05T00:00:00},
  url       = {http://bayes.wustl.edu/etj/articles/commentary.on.los.pdf},
}

@Article{Jaynes1987,
  author    = {Edwin T. Jaynes},
  journal   = {Contemp. Phys.},
  title     = {Comments on a Review by P.W. Atkins},
  year      = {1987},
  pages     = {501},
  volume    = {28},
  file      = {:./by-author/J/Jaynes/1987_Jaynes_501.pdf:PDF},
  groups    = {sg/Bayesian},
  owner     = {saulius},
  timestamp = {2012.10.05},
  creationdate = {2012-10-05T00:00:00},
  url       = {http://bayes.wustl.edu/etj/articles/review.by.atkins.pdf},
}

@Article{Jaynes1985e,
  author    = {Edwin T. Jaynes},
  journal   = {Synthese},
  title     = {Some Random Observations},
  year      = {1985},
  pages     = {115--138},
  volume    = {63},
  abstract  = {Of course, the rationale of PME is so different from what has been taught in ldquoorthodoxrdquo statistics courses for fifty years, that it causes conceptual hangups for many with conventional training. But beginning students have no difficulty with it, for it is just a mathematical model of the natural, common sense way in which anybody does conduct his inferences in problems of everyday life. The difficulties that seem so prominent in the literature today are, therefore, only transient phenomena that will disappear automatically in time. Indeed, this revolution in our attitude toward inference is already an accomplished fact among those concerned with a few specialized applications; with a little familarity in its use its advantages are apparent and it no longer seems strange. It is the idea that inference was once thought to be tied to frequencies in random experiments, that will seem strange to future generations.},
  doi       = {10.1007/BF00485957},
  file      = {:./by-author/J/Jaynes/1985_Jaynes_115.pdf:PDF},
  groups    = {sg/Bayesian},
  keywords  = {Bayesian Statistics; MaxEnt; Maximum Entropy},
  owner     = {saulius},
  timestamp = {2012.10.05},
  creationdate = {2012-10-05T00:00:00},
  url       = {http://bayes.wustl.edu/etj/articles/random.pdf},
}

@Article{Jaynes1984,
  author    = {Edwin T. Jaynes},
  journal   = {SIAM-AMS Proceedings},
  title     = {Prior information and ambiguity in inverse problems},
  year      = {1984},
  pages     = {151},
  abstract  = {Mathematically ill-posed problems, asking us to invert a singular or neraly singular operator, appear constantly in applications. Many attempts have been made to deal with such problems by inventing ad hoc algorithms which imitate the direct mathematical invertion that one would like to carry out. But if we view these as problems of inference rather than inversion there is a formal Decission Theory that, by taking into account prior information and value judgments about the purpose of th einversion, can often guide us without ad hockery to an algorithm that is unique, numerically stable, and demonstrably optimal by some rather basic criteria of rational choice. The method is illustrated by two simple examples, inversion of an integral equation in which the instbility is resolved by prior information about the class of probable solutions; and inversion of a singular matrix (image reconstruction) in which the ambiguity is resolved by entropy factors; i.e., prior information about multiplicity.},
  booktitle = {Inverse Problems [SIAM-AMS Proceedings]},
  file      = {:./by-author/J/Jaynes/1984_Jaynes_151.pdf:PDF},
  groups    = {sg/Bayesian},
  owner     = {saulius},
  timestamp = {2012.10.05},
  creationdate = {2012-10-05T00:00:00},
  url       = {http://bayes.wustl.edu/etj/articles/ambiguity.pdf},
}

@Article{Jaynes1984a,
  author    = {Edwin T. Jaynes},
  journal   = {Epistemologia},
  title     = {The Intuitive Inadequacy of Classical Statistics},
  year      = {1984},
  pages     = {43--74},
  volume    = {7},
  file      = {1984_Jaynes_43.pdf:by-author/J/Jaynes/1984_Jaynes_43.pdf:PDF},
  groups    = {sg/Bayesian},
  owner     = {saulius},
  timestamp = {2012.10.05},
  creationdate = {2012-10-05T00:00:00},
  url       = {http://bayes.wustl.edu/etj/articles/inadequacy.pdf},
}

@Article{Jaynes1982,
  author    = {Edwin T. Jaynes},
  journal   = {Proceedings of the IEEE},
  title     = {On the Rationale of Maximum-Entropy Methods},
  year      = {1982},
  pages     = {939--952},
  volume    = {70},
  abstract  = {We discuss the relations between maximum-entropy (MAXENT) and other methods of spectral analysis such as the Schuster, Blackman-Tukey, maximum-likelihood, Bayesian, and Autoregressive (AR, ARMA, or ARIMA) models, emphasizing that they are not in conflict, but rather are appropriate in different problems. We conclude that: 1) "Orthodox" sampling theory methods are useful in problems where we have a known model (sampling distribution) for the properties of the noise, but no appreciable prior information about the quantities being estimated. 2) MAXENT is optimal in problems where we have prior information about multiplicities, but no noise. 3) The full Bayesian solution includes both of these as special cases and is needed in problems where we have both prior information and noise. 4) AR models are in one sense a special case of MAXENT, but in another sense they are ubiquitous in all spectral analysis problems with discrete time series. 5) Empirical methods such as Blackman-Tukey, which do not invoke even a likelihood function, are useful in the preliminary, exploratory phase of a problem where our knowledge is sufficient to permit intuitive judgments about how to organize a calculation (smoothing, decimation, windows, prewhitening, padding with zeroes, etc.) but insufficient to set up a quantitative model which would do the proper things for us automatically and optimally.},
  file      = {:./by-author/J/Jaynes/1982_Jaynes_939.pdf:PDF},
  groups    = {sg/Bayesian},
  owner     = {saulius},
  timestamp = {2012.10.05},
  creationdate = {2012-10-05T00:00:00},
  url       = {http://bayes.wustl.edu/etj/articles/rational.pdf},
}

@Article{Jaynes1980a,
  author    = {Edwin T. Jaynes},
  journal   = {J. Acoust. Soc. Am.},
  title     = {Kramers-Kronig Relationship between Ultrasonic Attenuation and Phase Velocity},
  year      = {1980},
  pages     = {696--701},
  volume    = {69},
  abstract  = {Kramers--Kronig relations linking the attenuation and dispersion are presented for a linear acoustic system. These expressions are used as a starting point to derive approximate, nearly local expressions relating the ultrasonic attenuation at a specific frequency to the local frequency derivative of the phase velocity (i.e. dispersion). The validity of these approximate relationships is demonstrate in several acoustic systems exhibiting different physical properties.},
  file      = {:./by-author/J/Jaynes/1980_Jaynes_696.pdf:PDF},
  groups    = {sg/Bayesian},
  owner     = {saulius},
  timestamp = {2012.10.05},
  creationdate = {2012-10-05T00:00:00},
  url       = {http://bayes.wustl.edu/etj/articles/kramers-kronig.pdf},
}

@Article{Jaynes1980c,
  author    = {Edwin T. Jaynes},
  journal   = {Ann. Rev. Phys. Chem.},
  title     = {The Minimum Entropy Production Principle},
  year      = {1980},
  pages     = {579--601},
  volume    = {31},
  abstract  = {It seems intuitively reasonable that Gibbs' variational principle de­ termining the conditions of heterogeneous equilibrium can be gener­ alized to nonequilibrium conditions. That is, a nonequilibriurn steady state should be the one that makes some kind of generalized-entropy production stationary; and even in the presence of irreversible fluxes, the condition for migrational equilibrium should still be the equality of some generalized chemical potentials. We summarize progress to date toward this goal, reviewing (a) the early history, (b) work of Onsager and first attempts at generalization, (c) the new direction the field took after 1967 with the work of Tykodi and Mitchell, and (d) the present situation and prospects. Our conclu­ sion will be, briefly, that the o utlook is good in that the basic principles are believed known; but we do not yet now whether they can be reduced to simple rules immediately useful in practice, in the way that the Gibbs phase rule is useful. For this, we need more experience in the technique of applying them to particular cases, and more data to test some conjectures.},
  doi       = {10.1146/annurev.pc.31.100180.003051},
  file      = {1980_Jaynes_579a.pdf:by-author/J/Jaynes/1980_Jaynes_579a.pdf:PDF;1980_Jaynes_579.pdf:by-author/J/Jaynes/1980_Jaynes_579.pdf:PDF},
  groups    = {sg/Bayesian},
  owner     = {saulius},
  timestamp = {2012.10.05},
  creationdate = {2012-10-05T00:00:00},
  url       = {http://bayes.wustl.edu/etj/articles/min.ent.prod.pdf},
}

@Article{Jaynes1980f,
  author    = {Edwin T. Jaynes},
  journal   = {J. Opt. Soc. Am.},
  title     = {Phase-Sensitive Optical Amplifier},
  year      = {1980},
  pages     = {263--267},
  volume    = {70},
  abstract  = {The application of Armstrong’s super-regenerative principle to a laser amplifier shows that it is possible to control the phase of even a low-gain He-Ne laser amplifier by injecting as few as four or five photons just after the laser is turned on and while it goes through threshold. Estimation of the uncertainties in determining the level of the injected signal and the phase of the laser output indicates that measurements approaching the limit ΔnΔø≅½ may be possible.},
  doi       = {10.1364/JOSA.70.000263},
  file      = {:./by-author/J/Jaynes/1980_Jaynes_263.pdf:PDF},
  groups    = {sg/Bayesian},
  owner     = {saulius},
  timestamp = {2012.10.05},
  creationdate = {2012-10-05T00:00:00},
  url       = {http://bayes.wustl.edu/etj/articles/optical.amplifier.pdf},
}

@Manuscript{Jaynes1978,
  author    = {Edwin T. Jaynes},
  title     = {Marginalization and Prior Probabilities},
  year      = {1978},
  keywords  = {Bayesian Statistics},
  url       = {http://bayes.wustl.edu/etj/articles/margin.pdf},
  file      = {:./by-author/J/Jaynes/1978_Jaynes_manuscript.pdf:PDF},
  groups    = {sg/Bayesian},
  owner     = {saulius},
  pages     = {manuscript},
  timestamp = {2012.10.05},
  creationdate = {2012-10-05T00:00:00},
}

@Article{Jaynes1973,
  author    = {Edwin T. Jaynes},
  journal   = {Foundations of Physics},
  title     = {The Well-Posed Problem},
  year      = {1973},
  pages     = {477--493},
  volume    = {3},
  abstract  = {Many statistical problems, including some of the most important for physical ap- plications, have long been regarded as underdetermined from the standpoint of a strict frequency de nition of probability yet they may appear well posed or even overdetermined by the principles of maximum entropy and transformation groups. Furthermore, the distributions found by these methods turn out to have a de nite frequency correspondence the distribution obtained by invariance under a transformation group is by far the most likely to be observed experimentally, in the sense that it requires by far the least "skill." These properties are illustrated by analyzing the famous Bertrand paradox. On the viewpoint advocated here, Bertrand's prob- lem turns out to be well posed after all, and the unique solution has been veri ed experimentally. We conclude that probability theory has a wider range of useful applications than would be supposed from the standpoint of the usual frequency de nitions.},
  file      = {:./by-author/J/Jaynes/1973_Jaynes_477.pdf:PDF},
  groups    = {sg/Bayesian},
  keywords  = {Bayesian Statistics},
  owner     = {saulius},
  timestamp = {2012.10.05},
  creationdate = {2012-10-05T00:00:00},
  url       = {http://bayes.wustl.edu/etj/articles/well.pdf},
}

@Article{Jaynes1971,
  author    = {Edwin T. Jaynes},
  journal   = {Physical Review A},
  title     = {Violation of Boltzmann's H-Theorem in Real Gases},
  year      = {1971},
  pages     = {747},
  volume    = {4},
  abstract  = {The well-known variational (maximum-entropy) property of the Maxwellian velocity distribution is used to shed some light on the range of validity of the Boltzmann transport equation. It permits a characterisation of the initial states for which Boltzman {\em H} theorem is vialoated. In particular, it is shown that: (a) Any monoatomic system for which the equilibrium potential energy exceds the minimum possible value possesses a continuum of initial states for which the approach to equilibrium takes place through an increase, rather than a decrease, in Boltzmann's {\em H}. (b) If the initial distribution of particles is spatially homogenous and Maxwellian, the approach to equilibrium will take place through an increase (decrease) in the Boltzmann {\em H}, according as the innitial potential energy is less (greater) than the equilibrium value. (c) A necessary condition for the {\em H}-theorem-viaolating phenomenon is that the approach to equilibrium takes place through a conversion of kinetic energy into potential energy; a sufficient condition requires also that the initial velocity distribution be sufficiently close to Maxwellian. (d) These {\em H}-theorem-violating conditions are readily attained experimentally; for example, the free expansion of oxygen gas at 160$^\circ$K and 45-atm pressure produces an experimentally realisable violation of the Boltzmann {\em H} theorem.},
  file      = {:./by-author/J/Jaynes/1971_Jaynes_747.pdf:PDF},
  groups    = {sg/Bayesian},
  keywords  = {Entropy; Statistical Mechanics},
  owner     = {saulius},
  timestamp = {2012.10.05},
  creationdate = {2012-10-05T00:00:00},
  url       = {http://bayes.wustl.edu/etj/articles/violation.pdf},
}

@Article{Jaynes1968,
  author    = {Edwin T. Jaynes},
  journal   = {Popular Electronics},
  title     = {You CAN Parallel Storage Batteries},
  year      = {1968},
  pages     = {86},
  volume    = {33},
  file      = {:./by-author/J/Jaynes/1968_Jaynes_86.pdf:PDF},
  groups    = {sg/Bayesian},
  keywords  = {Electronics},
  owner     = {saulius},
  timestamp = {2012.10.05},
  creationdate = {2012-10-05T00:00:00},
  url       = {http://bayes.wustl.edu/etj/articles/parallel.batteries.pdf},
}

@Article{Jaynes1968a,
  author    = {Edwin T. Jaynes},
  journal   = {IEEE Transactions On Systems Science and Cybernetics},
  title     = {Prior Probabilities},
  year      = {1968},
  pages     = {227--241},
  volume    = {4},
  abstract  = {In decision theory, mathematical analysis shows that once the sampling distributions, loss function, and sample are specified, the only remaining basis for a choice among different admissible decisions lies in the prior probabilities. Therefore, the logical foundations of decision theory cannot be put in fully satisfactory form until the old problem of arbitrariness (sometimes called "subjectiveness") in assigning prior probabilities is resolved. The principle of maximum entropy represents one step in this direction. Its use is illustrated, and a correspondence property between maximum-entropy probabilities and frequencies is demonstrated. The consistency of this principle with the principles of conventional "direct probability" analysis is illustrated by showing that many known results may be derived by either method. However, an ambiguity remains in setting up a prior on a continuous parameter space because the results lack invariance under a change of parameter thus a further principle is needed. It is shown that in many problems, including some of the most important in practice, this ambiguity can be removed by applying methods of group theoretical reasoning which have long been used in theoretical physics. By nding the group of transformations on the parameter space which converts the problem into an equivalent one, a basic desideratum of consistency can be stated in the form of functional equations which impose conditions on, and in some cases fully determine, and "invariant measure" on the parameter space. The method is illustrated for the case of location and scale parameters, rate constants, and in Bernoulli trials with unknown probability of success. In realistic problems, both the transformation group analysis and the principle of maximum entropy are needed to determine the prior. The distributions thus found are uniquely determined by the prior information, independently of the choice of parameters. In a certain class of problems, therefore, the prior distributions may now be claimed to be fully as "objective" as the sampling distributions.},
  file      = {:./by-author/J/Jaynes/1968_Jaynes_227reprint.pdf:PDF},
  groups    = {sg/Bayesian},
  keywords  = {Bayesian Statistics},
  owner     = {saulius},
  timestamp = {2012.10.05},
  creationdate = {2012-10-05T00:00:00},
  url       = {http://bayes.wustl.edu/etj/articles/prior.pdf},
}

@Article{Jaynes1965,
  author    = {Edwin T. Jaynes},
  journal   = {Am. J. Phys.},
  title     = {Gibbs vs Boltzmann Entropies},
  year      = {1965},
  pages     = {391--398},
  volume    = {33},
  abstract  = {The status of the Gibbs and Boltzmann expressions for entropy has been a matter of someconfusion in the literature. We show that: (1) the Gibbs H function yields the correct entropyas defined in phenomenological thermodynamics; (2) the Boltzmann H yields an "entropy" that is in error by a nonnegligible amount whenever interparticle forces affect thermodynamicproperties; (3) Boltzmann's other interpretation of entropy, S = k log W, is consistent with the Gibbs H, and derivable from it; (4) the Boltzmann H theorem does not constitute a demonstration of the second law for dilute gases; (5) the dynamical invariance of the Gibbs H givesa simple proof of the second law for arbitrary interparticle forces; (6) the second law is a specialcase of a general requirement for any macroscopic process to be experimentally reproducible. Finally, the "anthropomorphic" nature of entropy, on both the statistical and phenomenologicallevels, is stressed.},
  file      = {:./by-author/J/Jaynes/1965_Jaynes_391.pdf:PDF},
  groups    = {sg/Bayesian},
  owner     = {saulius},
  timestamp = {2012.10.05},
  creationdate = {2012-10-05T00:00:00},
  url       = {http://bayes.wustl.edu/etj/articles/gibbs.vs.boltzmann.pdf},
}

@Article{Jaynes1963,
  author    = {Edwin T. Jaynes},
  journal   = {Science},
  title     = {Comments on an article by Ulric Neisser},
  year      = {1963},
  pages     = {216},
  volume    = {140},
  file      = {:./by-author/J/Jaynes/1963_Jaynes_216.pdf:PDF},
  groups    = {sg/Bayesian},
  keywords  = {Artificial Inteligence; Bayesian Statistics; Computation Theory; Criticism},
  owner     = {saulius},
  timestamp = {2012.10.05},
  creationdate = {2012-10-05T00:00:00},
  url       = {http://bayes.wustl.edu/etj/articles/comment.on.neisser.pdf},
}

@Article{Jaynes1959,
  author    = {Edwin T. Jaynes},
  journal   = {IRE Trans. on Information Theory},
  title     = {Note on Unique Decipherability},
  year      = {1959},
  pages     = {98--102},
  volume    = {IT-5},
  file      = {:./by-author/J/Jaynes/1959_Jaynes_98.pdf:PDF},
  groups    = {sg/Bayesian},
  owner     = {saulius},
  timestamp = {2012.10.05},
  creationdate = {2012-10-05T00:00:00},
  url       = {http://bayes.wustl.edu/etj/articles/unique.dicipherability.pdf},
}

@Article{Jaynes1958,
  author    = {Edwin T. Jaynes},
  journal   = {Am. J. Phys.},
  title     = {Relativistic Clock Experiments},
  year      = {1958},
  pages     = {197},
  volume    = {26},
  file      = {:./by-author/J/Jaynes/1958_Jaynes_197.pdf:PDF},
  groups    = {sg/Bayesian},
  owner     = {saulius},
  timestamp = {2012.10.05},
  creationdate = {2012-10-05T00:00:00},
  url       = {http://bayes.wustl.edu/etj/articles/realativistic.clock.pdf},
}

@Article{Jaynes1957,
  author    = {Jaynes, E. T.},
  journal   = {Phys. Rev.},
  title     = {Information Theory and Statistical Mechanics},
  year      = {1957},
  pages     = {620--630},
  volume    = {106},
  abstract  = {Information theory provides a constructive criterion for setting up probability distributions on the basis of partial knowledge, and leads to a type of statistical inference which is called the maximum-entropy estimate. It is the least biased estimate possible on the given information; i.e., it is maximally noncommittal with regard to missing information. If one considers statistical mechanics as a form of statistical inference rather than as a physical theory, it is found that the usual computational rules, starting with the determination of the partition function, are an immediate consequence of the maximum-entropy principle. In the resulting "subjective statistical mechanics," the usual rules are thus justified independently of any physical argument, and in particular independently of experimental verification; whether or not the results agree with experiment, they still represent the best estimates that could have been made on the basis of the information available. It is concluded that statistical mechanics need not be regarded as a physical theory dependent for its validity on the truth of additional assumptions not contained in the laws of mechanics (such as ergodicity, metric transitivity, equal a priori probabilities, etc.). Furthermore, it is possible to maintain a sharp distinction between its physical and statistical aspects. The former consists only of the correct enumeration of the states of a system and their properties; the latter is a straightforward example of statistical inference.nce.},
  doi       = {10.1103/PhysRev.106.620},
  file      = {1957_Jaynes_620.pdf:by-author/J/Jaynes/1957_Jaynes_620.pdf:PDF},
  groups    = {sg/Bayesian},
  issue     = {4},
  keywords  = {Bayesian Statistics},
  owner     = {saulius},
  publisher = {American Physical Society},
  timestamp = {2012.10.04},
  creationdate = {2012-10-04T00:00:00},
  url       = {http://link.aps.org/doi/10.1103/PhysRev.106.620},
}

@Article{Jaynes1957a,
  author    = {Jaynes, E. T.},
  journal   = {Phys. Rev.},
  title     = {Information Theory and Statistical Mechanics. II},
  year      = {1957},
  pages     = {171--190},
  volume    = {108},
  abstract  = {Treatment of the predictive aspect of statistical mechanics as a form of statistical inference is extended to the density-matrix formalism and applied to a discussion of the relation between irreversibility and information loss. A principle of "statistical complementarity" is pointed out, according to which the empirically verifiable probabilities of statistical mechanics necessarily correspond to incomplete predictions. A preliminary discussion is given of the second law of thermodynamics and of a certain class of irreversible processes, in an approximation equivalent to that of the semiclassical theory of radiation. It is shown that a density matrix does not in general contain all the information about a system that is relevant for predicting its behavior. In the case of a system perturbed by random fluctuating fields, the density matrix cannot satisfy any differential equation because ρ̇(t) does not depend only on ρ(t), but also on past conditions The rigorous theory involves stochastic equations in the type ρ(t)=G(t, 0)ρ(0), where the operator G is a functional of conditions during the entire interval (0→t). Therefore a general theory of irreversible processes cannot be based on differential rate equations corresponding to time-proportional transition probabilities. However, such equations often represent useful approximations.},
  doi       = {10.1103/PhysRev.108.171},
  file      = {1957_Jaynes_171.pdf:by-author/J/Jaynes/1957_Jaynes_171.pdf:PDF},
  groups    = {sg/Bayesian},
  issue     = {2},
  keywords  = {Bayesian Statistics},
  owner     = {saulius},
  publisher = {American Physical Society},
  timestamp = {2012.10.04},
  creationdate = {2012-10-04T00:00:00},
  url       = {http://link.aps.org/doi/10.1103/PhysRev.108.171},
}

@Article{Jaynes1955,
  author    = {Edwin T. Jaynes},
  journal   = {The Physical Review},
  title     = {Matrix Treatment of Nuclear Induction},
  year      = {1955},
  pages     = {1099--1105},
  volume    = {98},
  abstract  = {By use of matrix notation, solutions of the Bloch equations may be kept in simple, manageable form even in case of applied fields that are complicated functions of time. Effects that from the usual standpoint are grosly nonlinear appear as linear relations between matrices, of the same form the one encounters in simple radioactive decay problems. A general property of transients in the case of an arbitrary repetitive applied signal is established, and formalism is set up in terms of which a large class of special problems may be solved.},
  file      = {:./by-author/J/Jaynes/1955_Jaynes_1099.pdf:PDF},
  groups    = {sg/Bayesian},
  owner     = {saulius},
  timestamp = {2012.10.05},
  creationdate = {2012-10-05T00:00:00},
  url       = {http://bayes.wustl.edu/etj/articles/matrix.treatment.pdf},
}

@Article{Jaynes1950,
  author    = {Edwin T. Jaynes},
  journal   = {The Physical Review},
  title     = {Displacement of Oxygen in BaTiO3},
  year      = {1950},
  pages     = {1008--1009},
  volume    = {79},
  file      = {:./by-author/J/Jaynes/1950_Jaynes_1008.pdf:PDF},
  groups    = {sg/Bayesian},
  owner     = {saulius},
  timestamp = {2012.10.05},
  creationdate = {2012-10-05T00:00:00},
  url       = {http://bayes.wustl.edu/etj/articles/displacement.pdf},
}

@TechReport{Jaynes1954,
  author      = {Edwin T. Jaynes and Arnold Bloom},
  institution = {Varian Associates},
  title       = {Matrix Treatment of Nuclear Induction},
  year        = {1954},
  file        = {:./by-author/J/Jaynes/1954_Jaynes_tr.pdf:PDF},
  groups      = {sg/Bayesian},
  owner       = {saulius},
  pages       = {tr},
  timestamp = {2012.10.05},
  creationdate = {2012-10-05T00:00:00},
  url         = {http://bayes.wustl.edu/etj/articles/matrix.treatment.varian.pdf},
}

@TechReport{Jefferys1991,
  author      = {William H. Jefferys and James O. Berger},
  institution = {Department of Statistics, Purdue University},
  title       = {Sharpening Ockham's Razor On a Bayesian Strop},
  year        = {1991},
  abstract    = {Ockham's Razor, an established principle used every day in science, has deep connections with Bayesian reasoning, which traces directly back to Sir Harold Jeffreys' pioneering work on statistics during the 1920s and 30s. In this paper we shall explore the connection between Ockham's Razor and Bayesian statistics, and present an objective quantification of Ockham's Razor. Postscript File (394kB)},
  file        = {:by-author/J/Jefferys/1991_Jefferys_tr91-44.ps:PDF},
  groups      = {sg/Bayesian},
  keywords    = {Bayesian Statistics; Ockham's Razor},
  owner       = {saulius},
  pages       = {tr91-44},
  timestamp = {2012.11.24},
  creationdate = {2012-11-24T00:00:00},
  url         = {http://www.stat.duke.edu/~berger/papers/ockham.ps},
}

@Article{Jeffrey1979,
  author    = {George A. Jeffrey and John H. Yates},
  journal   = {Carbohydrate Research},
  title     = {Stereographic representation of the {Cremer-Pople} ring-puckering parameters for pyranoid rings},
  year      = {1979},
  pages     = {319--322},
  volume    = {74},
  doi       = {10.1016/S0008-6215(00)84786-2},
  file      = {:by-author/J/Jeffrey/1979_Jeffrey_319.pdf:PDF},
  keywords  = {Cremer & Pople Parameters},
  owner     = {andrius},
  timestamp = {2014.03.03},
  creationdate = {2014-03-03T00:00:00},
}

@Article{Jelesarov2008,
  author    = {I. Jelesarov and A. Karshikoff},
  journal   = {Biotechnology \& Biotechnological Equipment},
  title     = {Meet to fold: the peculiar folding of oligomeric protens},
  year      = {2008},
  pages     = {598--605},
  volume    = {22},
  abstract  = {Oligomeric proteins have been created as an evolutionary solution to fulfill specific cellular tasks, trading off functional and molecular requirements such as domain organization, molecular economy, minimization of the size of structural genes, reducing the costs for elimination of misfolded polypeptide chains, cooperativity, tight control, etc. Oligomers are also a challenging experimental object to test our concepts of the sequence-structure-energy-function relationships in proteins. In this paper, we briefly discuss the evolutionary aspects of the appearance of oligomers, and present with a few selected examples the current state of affairs in understanding the folding of small oligomeric proteins.},
  file      = {2008_Jelesarov_598.pdf:by-author/J/Jelesarov/2008_Jelesarov_598.pdf:PDF},
  keywords  = {Folding Kinetics; Folding Mechanism; Noncovalent Interactions; Protein Folding; Protein Physics; Protein Stability},
  owner     = {saulius},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
  url       = {http://www.diagnosisp.com/dp/journals/view_article.php?journal_id=1&archive=0&issue_id=17&article_id=470},
}

@Article{Jelsch2000,
  author    = {Jelsch, C. and Teeter, M. M. and Lamzin, V. and Pichon-Pesme, V. and Blessing, R. H. and Lecomte, C.},
  journal   = {Proceedings of the National Academy of Sciences of the United States of America},
  title     = {Accurate protein crystallography at ultra-high resolution: valence electron distribution in crambin.},
  year      = {2000},
  pages     = {3171--6},
  volume    = {97},
  abstract  = {The charge density distribution of a protein has been refined experimentally. Diffraction data for a crambin crystal were measured to ultra-high resolution (0.54 A) at low temperature by using short-wavelength synchrotron radiation. The crystal structure was refined with a model for charged, nonspherical, multipolar atoms to accurately describe the molecular electron density distribution. The refined parameters agree within 25% with our transferable electron density library derived from accurate single crystal diffraction analyses of several amino acids and small peptides. The resulting electron density maps of redistributed valence electrons (deformation maps) compare quantitatively well with a high-level quantum mechanical calculation performed on a monopeptide. This study provides validation for experimentally derived parameters and a window into charge density analysis of biological macromolecules.},
  file      = {:by-author/J/Jeltsch/2000_Jelsch_3171.pdf:PDF},
  owner     = {saulius},
  timestamp = {2013.02.12},
  creationdate = {2013-02-12T00:00:00},
}

@Article{Jeltsch2003,
  author    = {Jeltsch, Albert},
  journal   = {Gene},
  title     = {Maintenance of species identity and controlling speciation of bacteria: a new function for restriction/modification systems?},
  year      = {2003},
  pages     = {13--6},
  volume    = {317},
  abstract  = {Bacteria frequently exchange DNA among each other by horizontal gene transfer. However, maintenance of species identity and in particular speciation requires a certain barrier against an unregulated uptake of foreign DNA. Here it is suggested that formation of such a barrier is one important biological function of restriction/modification systems, in addition to the classical function of protection of bacteria against bacteriophage infection. This model explains the extreme variability and wide distribution of restriction/modification systems among prokaryotes, the prevalence of RM-systems in pathogenic bacteria and the existence of several RM-systems in single bacterial strains.},
  file      = {:by-author/J/Jeltsch/2003_Jeltsch_13.pdf:PDF},
  keywords  = {Evolution},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Jeltsch1995a,
  author      = {A. Jeltsch and M. Kröger and A. Pingoud},
  journal     = {Gene},
  title       = {Evidence for an evolutionary relationship among type-II restriction endonucleases.},
  year        = {1995},
  month       = {Jul},
  number      = {1},
  pages       = {7--16},
  volume      = {160},
  abstract    = {Type-II restriction-modification (R-M) systems comprise two enzymes, a DNA methyltransferase (MTase) and a restriction endonuclease (ENase), each of which specifically interact with the same 4-8 bp sequence. All type-II MTases share several amino acid (aa) sequence motifs, which makes an evolutionary relatedness among these enzymes probable. The type-II ENases, in contrast, except for some homologous isoschizomers, do not share significant aa sequence similarity. Therefore, ENases in general have been considered unrelated. Here we show that in addition to the analysis of the genotype (aa sequence), a comparison of the phenotype (recognition sequence) of these enzymes can provide independent information regarding evolutionary relationships, and thereby, help to analyze the significance of weak aa sequence similarities. Multistep Monte-Carlo analyses were employed to demonstrate that the recognition sequences of those ENases, which were found to be related by a progressive multiple aa sequence alignment, are more similar to each other than would be expected by chance. This analysis supports the notion that not only type-II MTases, but also type-II ENases did not arise independently in evolution, but rather evolved from one or a few primordial DNA-modifying and DNA-cleaving enzymes, respectively.},
  doi         = {10.1016/0378-1119(95)00181-5},
  file        = {1995_Jeltsch_7.pdf:by-author/J/Jeltsch/1995_Jeltsch_7.pdf:PDF},
  institution = {Institut für Biochemie, Justus-Liebig-Universität, Giessen, Germany.},
  keywords    = {Amino Acid; Amino Acid Sequence; Bacteria; Base Composition; Biological Evolution; Deoxyribonucleases; Enzymology/genetics; Genetics/metabolism; Genotype; Monte Carlo Method; Phenotype; Phylogeny; Sequence Homology; Substrate Specificity; Type II Site-Specific},
  language    = {eng},
  medline-pst = {ppublish},
  owner       = {em},
  pii         = {0378-1119(95)00181-5},
  pmid        = {7628720},
  timestamp = {2016.06.16},
  creationdate = {2016-06-16T00:00:00},
}

@Article{Jeltsch1995,
  author    = {Albert Jeltsch and Milda Pleckaityte and Ursel Selent and Heiner Wolfes and Virginius Siksnys and Alfred Pingoud},
  journal   = {Gene},
  title     = {Evidence for substrate-assisted catalysis in the {DNA} cleavage of several restriction endonucleases},
  year      = {1995},
  pages     = {157},
  doi       = {10.1016/0378-1119(94)00617-2},
  file      = {:by-author/J/Jeltch/1995_Jeltch_157.pdf:PDF},
  keywords  = {Catalyse; TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Manuscript{Jen-Jacobson2004,
  author    = {Linda Jen-Jacobson},
  title     = {Protein-DNA recognition complexes: Conservation of structure and binding energy in the transition state},
  year      = {2004},
  keywords  = {Jen-Jacobson},
  file      = {:by-author/J/Jen-Jacobson/2004_Jen-Jacobson.doc:DOC},
  owner     = {saulius},
  timestamp = {2015.02.28},
  creationdate = {2015-02-28T00:00:00},
}

@Article{Jen-Jacobson2000,
  author    = {Jen-Jacobson, L. and Engler, L. E. and Jacobson, L. A.},
  journal   = {Structure (London, England : 1993)},
  title     = {Structural and thermodynamic strategies for site-specific DNA binding proteins.},
  year      = {2000},
  pages     = {1015--23},
  volume    = {8},
  file      = {:by-author/J/Jen-Jacobson/2000_Jen-Jacobson_1015.pdf:PDF},
  keywords  = {Jen Jacobson},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Jen-Jacobson2000a,
  author      = {L. Jen-Jacobson and L. E. Engler and L. A. Jacobson},
  journal     = {Structure},
  title       = {Structural and thermodynamic strategies for site-specific DNA binding proteins.},
  year        = {2000},
  month       = {Oct},
  number      = {10},
  pages       = {1015--1023},
  volume      = {8},
  abstract    = {Site-specific protein-DNA complexes vary greatly in structural properties and in the thermodynamic strategy for achieving an appropriate binding free energy. A better understanding of the structural and energetic engineering principles might lead to rational methods for modification or design of such proteins.A novel analysis of ten site-specific protein-DNA complexes reveals a striking correspondence between the degree of imposed DNA distortion and the thermodynamic parameters of each system. For complexes with relatively undistorted DNA, favorable enthalpy change drives unfavorable entropy change, whereas for complexes with highly distorted DNA, unfavorable DeltaH degrees is driven by favorable DeltaS degrees. We show for the first time that protein-DNA associations have isothermal enthalpy-entropy compensation, distinct from temperature-dependent compensation, so DeltaH degrees and DeltaS degrees do not vary independently. All complexes have favorable DeltaH degrees from direct protein-DNA recognition interactions and favorable DeltaS degrees from water release. Systems that strongly distort the DNA nevertheless have net unfavorable DeltaH degrees as the result of molecular strain, primarily associated with the base pair destacking. These systems have little coupled protein folding and the strained interface suffers less immobilization, so DeltaS degrees is net favorable. By contrast, systems with little DNA distortion have net favorable DeltaH degrees, which must be counterbalanced by net unfavorable DeltaS degrees, derived from loss of vibrational entropy (a result of isothermal enthalpy-entropy compensation) and from coupling between DNA binding and protein folding.Isothermal enthalpy-entropy compensation implies that a structurally optimal, unstrained fit is achieved only at the cost of entropically unfavorable immobilization, whereas an enthalpically weaker, strained interface entails smaller entropic penalties.},
  file        = {2000_Jen-Jacobson_1015.pdf:by-author/J/Jen-Jacobson/2000_Jen-Jacobson_1015.pdf:PDF},
  institution = {Department of Biological Sciences University of Pittsburgh, Pittsburgh, PA 15260, USA. ljen@pitt.edu},
  keywords    = {Binding Sites; Chemistry/metabolism; DNA; DNA-Binding Proteins; Entropy; Models; Molecular; Nucleic Acid Conformation; Protein Binding; Protein Conformation; Protein Engineering; Structure-activity Relationship (SAR); Substrate Specificity; Temperature; Transcription Factors},
  language    = {eng},
  medline-pst = {ppublish},
  owner       = {em},
  pii         = {S0969212600005013},
  pmid        = {11080623},
  timestamp = {2011.06.14},
  creationdate = {2011-06-14T00:00:00},
}

@Article{Jenkins1996,
  author    = {A. D. Jenkins and P. Kratochvíl and R. F. T. Stepto and U. W. Suter},
  journal   = {Pure Appl. Chem.},
  title     = {Glossary Of Basic Terms In Polymer Science},
  year      = {1996},
  pages     = {1591–1595},
  file      = {:by-author/J/Jenkins/1996_Jenkins_1591.pdf:PDF},
  owner     = {andrius},
  timestamp = {2012.06.12},
  creationdate = {2012-06-12T00:00:00},
}

@Article{Jenkins1970,
  author    = {M. A. Jenkins and J. F. Traub},
  journal   = {SIAM Journal on Numerical Analysis},
  title     = {A Three-Stage Algorithm for Real Polynomials Using Quadratic Iteration},
  year      = {1970},
  issn      = {00361429},
  number    = {4},
  pages     = {545--566},
  volume    = {7},
  abstract  = {We introduce a new three-stage process for calculating the zeros of a polynomial with real coefficients. The algorithm finds either a linear or quadratic factor, working completely in real arithmetic. In the third stage the algorithm uses one of two variable-shift iterations corresponding to the linear or quadratic case. The iteration for a linear factor is a real arithmetic version of the third stage of the algorithm for complex polynomials which we studied in an earlier paper. A new variable-shift iteration is introduced in this paper which is suitable for quadratic factors. If the complex algorithm and the new real algorithm are applied to the same real polynomial, then the real algorithm is about four times as fast. We prove that the mathematical algorithm always converges and show that the rate of convergence of the third stage is faster than second order. The problem and algorithm may be recast into matrix form. The third stage is a quadratic form of shifted inverse powering and a quadratic form of generalized Rayleigh iteration. The results of extensive testing are summarized. For an ALGOL W program run on an IBM 360/67 we found that for polynomials ranging in degree from 20 to 50, the time required to calculate all zeros averaged 2n<sup>2</sup> milliseconds. An ALGOL 60 implementation of the algorithm and a program which calculates a posteriori bounds on the zeros may be found in Jenkins' 1969 Stanford dissertation [2].},
  file      = {:by-author/J/Jenkins/1970_Jenkins_545.pdf:PDF},
  groups    = {am/Numerical sg/methods},
  owner     = {andrius},
  publisher = {Society for Industrial and Applied Mathematics},
  timestamp = {2016.03.22},
  creationdate = {2016-03-22T00:00:00},
  url       = {http://www.jstor.org/stable/2949376},
}

@Article{Jensen1999,
  author    = {C. S. Jensen and R. T. Snodgrass},
  journal   = {IEEE Transactions on Knowledge and Data Engineering},
  title     = {Temporal data management},
  year      = {1999},
  issn      = {1041-4347},
  month     = {Jan},
  number    = {1},
  pages     = {36--44},
  volume    = {11},
  abstract  = {A wide range of database applications manage time-varying information. Existing database technology currently provides little support for managing such data. The research area of temporal databases has made important contributions in characterizing the semantics of such information and in providing expressive and efficient means to model, store, and query temporal data. This paper introduces the reader to temporal data management, surveys stale-of-the-art solutions to challenging aspects of temporal data management, and points to research directions},
  doi       = {10.1109/69.755613},
  file      = {1999_Jensen_36.pdf:by-author/J/Jensen/1999_Jensen_36.pdf:PDF},
  keywords  = {Computer Science (CS); Data Management; Data Models; Query Processing; Temporal Databases},
  owner     = {saulius},
  timestamp = {2016.11.21},
  creationdate = {2016-11-21T00:00:00},
  url       = {http://ieeexplore.ieee.org/document/755613/},
}

@TechReport{Jensen1997,
  author      = {Christian S. Jensen and Richard T. Snodgrass},
  institution = {TimeCenter},
  title       = {Temporal Data Management},
  year        = {1997},
  month       = {June},
  number      = {TR-17},
  abstract    = {A wide range of database applications manage time-varying information. Existing database technology currently provides little support for managing such data. The research area of temporal databases has made important con- tributions in characterizing the semantics of such information and in providing expressive and efficient means to model, store, and query temporal data. This paper introduces the reader to temporal data management, surveys state-of-the-art solutions to challenging aspects of temporal data management, and points to research directions.},
  comment     = {Cited by Rauber2016a in this revision.},
  file        = {1997_Jensen_TR-17.pdf:by-author/J/Jensen/1997_Jensen_TR-17.pdf:PDF},
  keywords    = {Computer Science (CS); Data Management; Reproducible Research; Temporal Databases},
  owner       = {saulius},
  timestamp = {2016.11.21},
  creationdate = {2016-11-21T00:00:00},
  url         = {http://timecenter.cs.aau.dk/TimeCenterPublications/TR-17.pdf},
}

@Article{Jeong2003,
  author    = {Chan-Seok Jeong and Yongjin Song},
  journal   = {Trends in Mathematic},
  title     = {Two multiplications in infinite braid-permutation group},
  year      = {2003},
  pages     = {79–86},
  volume    = {6},
  file      = {2003_Jeong_79.pdf:by-author/J/Jeong/2003_Jeong_79–86.pdf:PDF},
  keywords  = {Braid Groups; Mathematics},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@InProceedings{Jermaine2001,
  author    = {Jermaine, Christopher and Omiecinksi, Edward and Yee, Wai Gen},
  booktitle = {Proceedings of the 9th ACM international symposium on Advances in geographic information systems},
  title     = {Maintaining a Large Spatial Database With {T2SM}},
  year      = {2001},
  address   = {New York, NY, USA},
  pages     = {76--81},
  publisher = {ACM},
  series    = {GIS '01},
  abstract  = {Large, spatial databases may be required to prosses both intense query and intense update loads. For example, a data warehouse which contains spatial data may be required to answer difficult, analytical queries at the same time as it accepts massive amounts of new data, and any downtime to merge new data into existing data organizations may be unacceptable. Traditional, incremental spatial access methods (like the popular R-tree and its variants) may be unacceptable for use in such an environment since they support relatively slow update rates, and may lead to a relatively poor global data organization resulting in slow query evaluation. In this paper, we present the details T2SM, which is an instantiation of the linear file template, for use with spatial data. in T2SM, data are organized as a set of ongoing, external memory sorts based on the STR algorithm. T2SM exhibits query performance similar to (and sometimes superior to) a bulk-loaded R-Tree, but at the same time is truly incremental and can maintain exceptional update rates.},
  doi       = {10.1145/512161.512179},
  file      = {:by-author/J/Jermaine/2001_Jermaine_76.pdf:PDF},
  isbn      = {1-58113-443-6},
  location  = {Atlanta, Georgia, USA},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://doi.acm.org/10.1145/512161.512179},
}

@Article{Jewett2003,
  author    = {Jewett, Andrew I. and Huang, Conrad C. and Ferrin, Thomas E.},
  journal   = {Bioinformatics},
  title     = {MINRMS: an efficient algorithm for determining protein structure similarity using root-mean-squared-distance},
  year      = {2003},
  pages     = {625--634},
  volume    = {19},
  abstract  = {Motivation: Existing algorithms for automated protein structure alignment generate contradictory results and are difficult to interpret. An algorithm which can provide a context for interpreting the alignment and uses a simple method to characterize protein structure similarity is needed.Results: We describe a heuristic for limiting the search space for structure alignment comparisons between two proteins, and an algorithm for finding minimal root-mean-squared-distance (RMSD) alignments as a function of the number of matching residue pairs within this limited search space. Our alignment algorithm uses coordinates of alpha-carbon atoms to represent each amino acid residue and requires a total computation time of O(m3 n2), where m and n denote the lengths of the protein sequences. This makes our method fast enough for comparisons of moderate-size proteins (fewer than ∼800 residues) on current workstation-class computers and therefore addresses the need for a systematic analysis of multiple plausible shape similarities between two proteins using a widely accepted comparison metric.Availability: See http://www.cgl.ucsf.edu/Research/minrmsContact: tef@cgl.ucsf.edu},
  doi       = {10.1093/bioinformatics/btg035},
  eprint    = {http://bioinformatics.oxfordjournals.org/content/19/5/625.full.pdf+html},
  file      = {2003_Jewett_625.pdf:by-author/J/Jewett/2003_Jewett_625.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.12.02},
  creationdate = {2012-12-02T00:00:00},
  url       = {http://bioinformatics.oxfordjournals.org/content/19/5/625.abstract},
}

@Article{Jezewska1998,
  author    = {Jezewska, M. J. and Rajendran, S. and Bujalowski, W.},
  journal   = {Biochemistry},
  title     = {Complex of Escherichia coli primary replicative helicase DnaB protein with a replication fork: recognition and structure.},
  year      = {1998},
  pages     = {3116--36},
  volume    = {37},
  abstract  = {Interactions of the Escherichia coli replicative helicase DnaB protein, with DNA replication fork substrates, have been studied using rigorous fluorescence titration, fluorescence energy transfer, and analytical ultracentrifugation methods. DnaB binds the 5' single-arm fork, the 3' single-arm fork, and the two-arm fork with stoichiometries of 1, 1, and 2 DnaB hexamers per fork, independent of the length of the duplex part of the fork. Within the structurally heterogeneous binding site, the helicase accesses most of the 20 nucleotide residues of an arm. The dsDNA of the fork does not contribute to the affinity; however, it affects the positioning of the enzyme on the 5' or 3' arm. Fluorescence energy transfer experiments provide direct evidence that the DnaB helicase binds the 5' arm of the fork in a single orientation, with respect to the duplex part of the fork. The 33-kDa domains of the hexamer face the dsDNA, while the small 12-kDa domains face the 5' end of the arm. In the complex with the 3' arm, the helicase is bound in an opposite orientation when compared to the 5' arm. This is the first determination of the strict, single orientation of a helicase in the complex with a replication fork. The 3' arm accommodates a DnaB hexamer, while another hexamer is associated with the 5' arm. The complex of two DnaB hexamers bound in opposite orientations with each arm of the fork may play an important role during bidirectional replication of the E. coli DNA.},
  file      = {:by-author/J/Jezewska/1998_Jezewska_3116.pdf:PDF},
  keywords  = {Ecoli; {gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Jezewska1997,
  author    = {Jezewska, M. J. and Rajendran, S. and Bujalowski, W.},
  journal   = {Biochemistry},
  title     = {Strand specificity in the interactions of Escherichia coli primary replicative helicase DnaB protein with a replication fork.},
  year      = {1997},
  pages     = {10320--6},
  volume    = {36},
  abstract  = {The interactions of the Escherichia coli primary replicative helicase DnaB protein, with synthetic DNA replication fork substrates, having either a single arm or both arms, have been studied using the thermodynamically rigorous fluorescence titration techniques. This approach allows us to obtain absolute stoichiometries of the formed complexes and interaction parameters without any assumptions about the relationship between the observed signal (fluorescence) and the degree of binding. Subsequently, the formation of the complexes, with different replication fork substrates, has also been characterized using the sedimentation velocity technique. To our knowledge, this is the first quantitative characterization of interactions of a hexameric helicase with replication fork substrates. In the presence of the ATP nonhydrolyzable analog, AMP-PNP, the E. coli DnaB helicase preferentially binds to the 5' arm of the single-arm fork substrate with an intrinsic affinity 6-fold higher than its affinity for the 3' arm. ATP hydrolysis is not necessary for formation of the helicase-fork complex. The asymmetric interactions are consistent with the 5' --&gt; 3' directionality of the helicase activity of the DnaB protein and most probably reflects a preferential 5' --&gt; 3' polarity in the helicase binding to ssDNA, with respect to the ssDNA backbone. The double-stranded part of the fork contributes little to the free energy of binding. The data indicate a rather passive role of the duplex part of the fork in the binding of the helicase. This role seems to be limited to impose steric hindrance in the formation of nonproductive complexes of the enzyme with the fork. Quantitative analysis of binding of the helicase to the two-arm fork substrate shows that two DnaB hexamers can bind to the fork, with each single hexamer associated with a single arm of the fork. In this complex, the intrinsic affinity of the DnaB hexamer for the 5' arm in a two-arm fork is not affected by the presence of the 3' arm. Moreover, the results show that the 3' arm is in a conformation which makes it easily available for the binding of the next DnaB hexamer. Because of the large size of the DnaB hexamer, the data indicate that the 3' arm is separated from the 5' arm. The separation of both arms must be to such an extent that the 3' arm can bind an additional large DnaB hexamer. These results reveal that the 3' arm is not engaged in thermodynamically stable interactions with the helicase hexamer, when it is bound in its stationary complex to the 5' arm of the fork. The significance of the these results for a mechanistic model of the hexameric DnaB helicase action is discussed.},
  file      = {:by-author/J/Jezewska/1997_Jezewska_10320.pdf:PDF},
  keywords  = {Ecoli; {gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@PhdThesis{Jia2012,
  author    = {Jia, Lin},
  school    = {Massachusetts Institute of Technology},
  title     = {Impact of morphology and scale on the physical properties of periodic/quasiperiodic micro-and nano-structures},
  year      = {2012},
  file      = {[PDF] from 18.7.29.232:by-author/J/Jia/2012_Jia.pdf:PDF;Snapshot:by-author/J/Jia/2012_Jia.html:URL},
  groups    = {sg/JAC2009},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://18.7.29.232/handle/1721.1/75844},
  urldate   = {2015-08-31},
}

@Article{Jiang2014,
  author       = {Jiang, J.-J. and He, J.-R. and Lü, X.-Q. and Wang, D.-W. and Li, G.-B. and Su, C.-Y.},
  journal      = {{IUCrJ}},
  title        = {Structural disorder and transformation in crystal growth: direct observation of ring-opening isomerization in a metal–organic solid solution},
  year         = {2014},
  issn         = {2052-2525},
  number       = {5},
  pages        = {318--327},
  volume       = {1},
  abstract     = {A rare example is reported in which discrete Ag2L2 ring and ({AgL})∞ chain motifs [L = N,N′-bis(3-imidazol-1-yl-propyl)-pyromellitic diimide] co-crystallize in the same crystal lattice with varying ratios and degrees of disorder. Crystal structures obtained from representative crystals reveal compatible packing arrangements of the cyclic and polymeric isomers within the crystal lattice, which enables them to co-exist within a crystalline solid solution. A feasible pathway for transformation between the isomers is suggested via facile rotation of the coordinating imidazolyl groups. This chemical system could provide a chance for direct observation of ring-opening isomerization at the crystal surface. Mass spectrometry and 1H {NMR} titration show a dynamic equilibrium between cyclic and oligomeric species in solution, and a potential crystallization process is suggested involving alignment of precursors directed by aromatic stacking interactions between pyromellitic diimide units, followed by ring-opening isomerization at the interface between the solid and the solution. Both cyclic and oligomeric species can act as precursors, with interconversion between them being facile due to a low energy barrier for rotation of the imidazole rings. Thermogravimetric analysis and variable-temperature powder X-ray diffraction indicate a transition to a different crystalline phase around 120°C, which is associated with loss of solvent from the crystal lattice.},
  date         = {2014-09-01},
  doi          = {10.1107/S2052252514015966},
  file         = {Full Text PDF:by-author/J/Jiang/2014_Jiang_318.pdf:PDF;Snapshot:by-author/J/Jiang/2014_Jiang_318.html:URL},
  groups       = {sg/MOF, sg/MOFs, am/MOFs},
  journaltitle = {{IUCrJ}},
  langid       = {english},
  owner        = {saulius},
  rights       = {http://creativecommons.org/licenses/by/2.0/uk},
  shortjournal = {{IUCrJ}},
  shorttitle   = {Structural disorder and transformation in crystal growth},
  timestamp = {2017.01.29},
  creationdate = {2017-01-29T00:00:00},
  url          = {http://scripts.iucr.org/cgi-bin/paper?bi5033},
  urldate      = {2017-01-29},
}

@Article{Jiao2014,
  author    = {Jiao, Alan L and Slack, Frank J},
  journal   = {Epigenetics},
  title     = {{RNA}-mediated gene activation},
  year      = {2014},
  issn      = {1559-2308},
  month     = {Jan},
  number    = {1},
  pages     = {27–36},
  volume    = {9},
  doi       = {10.4161/epi.26942},
  file      = {2014_Jiao_27.pdf:by-author/J/Jiao/2014_Jiao_27.pdf:PDF},
  groups    = {am/RNA activation},
  owner     = {andrius},
  publisher = {Informa UK Limited},
  timestamp = {2016.08.30},
  creationdate = {2016-08-30T00:00:00},
}

@Manuscript{Jibaja2011,
  author    = {Jibaja, Ivan and Stephen M. Blackburn and Mohammad R. Haghighat and Kathryn S. McKinley},
  title     = {Deferred Gratification: Engineering for High Performance Garbage Collection from the Get Go},
  year      = {2011},
  keywords  = {Computer Science (CS); Garbage Collectors; Heap; Memory Management; PHP; Scripting Languages; Strict Garbage Collector},
  abstract  = {Implementing a new programming language system is a daunting task. A common trap is to punt on the design and engineering of exact garbage collection and instead opt for reference counting or conservative garbage collection (GC). For example, AppleScriptTM , Perl, Python, and PHP implementers chose reference counting (RC) and Ruby chose conservative GC. Although easier to get working, reference counting has terrible performance and conser- vative GC is inflexible and performs poorly when allocation rates are high. However, high performance GC is central to performance for managed languages and only becoming more critical due to relatively lower memory bandwidth and higher memory latency of modern architectures. Unfortunately, retrofitting support for high performance collectors later is a formidable software engineering task due to their exact nature. Whether they realize it or not, imple- menters have three routes: (1) forge ahead with reference counting or conservative GC, and worry about the consequences later; (2) build the language on top of an existing managed runtime with ex- act GC, and tune the GC to scripting language workloads; or (3) engineer exact GC from the ground up and enjoy the correctness and performance benefits sooner rather than later. We explore this conundrum using PHP, the most popular server side scripting language. PHP implements reference counting, mir- roring scripting languages before it. Because reference counting is incomplete, the implementors must (a) also implement tracing to detect cyclic garbage, or (b) prohibit cyclic data structures, or (c) never reclaim cyclic garbage. PHP chose (a), AppleScript chose (b), and Perl chose (c). We characterize the memory behavior of five typical PHP programs to determine whether their implementa- tion choice was a good one in light of the growing demand for high performance PHP. The memory behavior of these PHP programs is similar to other managed languages, such as JavaTM —they allocate many short lived objects, a large variety of object sizes, and the av- erage allocated object size is small. These characteristics suggest copying generational GC will attain high performance. Language implementers who are serious about correctness and performance need to understand deferred gratification: paying the software engineering cost of exact GC up front will deliver correct- ness and memory system performance later.},
  file      = {:by-author/J/Jibaja/2011_Jibaja.pdf:PDF},
  groups    = {sg/Garbage collectors},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Manuscript{Jin2010,
  author    = {Jin, Haoqiang and Jespersen, Dennis and Mehrotra, Piyush and Biswas, Rupak and Lei Huang and Barbara Chapman},
  title     = {High Performance Computing Using MPI and OpenMP on Multi-core Parallel Systems},
  year      = {2010},
  abstract  = {The rapidly increasing number of cores in modern microprocessors is pushing the cur- rent high performance computing (HPC) systems into the petascale and exascale era. The hybrid nature of these systems—distributed memory across nodes and shared memory with non-uniform memory access within each node—poses a challenge to application developers. In this paper, we study a hybrid approach to programming such systems – a combination of two traditional programming models, MPI and OpenMP. We present the performance of standard benchmarks from the multi-zone NAS Parallel Benchmarks and two full applications using this approach on several multi-core based systems including an SGI Altix 4700, an IBM p575+ and an SGI Altix ICE 8200EX. We also present new data locality extensions to OpenMP to better match the hierarchical memory structure of multi-core architectures.},
  file      = {:by-author/J/Jin/2010_Jin.pdf:PDF},
  owner     = {saulius},
  timestamp = {2013.07.02},
  creationdate = {2013-07-02T00:00:00},
}

@Article{Jindrova2005,
  author    = {Jindrova, Eva and Schmid-Nuoffer, Stefanie and Hamburger, Fabienne and Janscak, Pavel and Bickle, Thomas A.},
  journal   = {Nucleic acids research},
  title     = {On the DNA cleavage mechanism of Type I restriction enzymes.},
  year      = {2005},
  pages     = {1760--6},
  volume    = {33},
  abstract  = {Although the DNA cleavage mechanism of Type I restriction-modification enzymes has been extensively studied, the mode of cleavage remains elusive. In this work, DNA ends produced by EcoKI, EcoAI and EcoR124I, members of the Type IA, IB and IC families, respectively, have been characterized by cloning and sequencing restriction products from the reactions with a plasmid DNA substrate containing a single recognition site for each enzyme. Here, we show that all three enzymes cut this substrate randomly with no preference for a particular base composition surrounding the cleavage site, producing both 5'- and 3'-overhangs of varying lengths. EcoAI preferentially generated 3'-overhangs of 2-3 nt, whereas EcoKI and EcoR124I displayed some preference for the formation of 5'-overhangs of a length of approximately 6-7 and 3-5 nt, respectively. A mutant EcoAI endonuclease assembled from wild-type and nuclease-deficient restriction subunits generated a high proportion of nicked circular DNA, whereas the wild-type enzyme catalyzed efficient cleavage of both DNA strands. We conclude that Type I restriction enzymes require two restriction subunits to introduce DNA double-strand breaks, each providing one catalytic center for phosphodiester bond hydrolysis. Possible models for DNA cleavage are discussed.},
  file      = {:by-author/J/Jindrova/2005_Jindrova_1760.pdf:PDF},
  keywords  = {TypeI},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Jindrova2005a,
  author    = {Eva Jindrova and Stefanie Schmid-Nuoffer and Fabienne Hamburger and Pavel Janscak and Thomas A. Bickle},
  journal   = {Nucleic Acids Research},
  title     = {On the {DNA} cleavage mechanism of Type {I} restriction enzymes},
  year      = {2005},
  pages     = {1760a},
  file      = {:by-author/J/Jindrova/2005_Jindrova_1760a.pdf:PDF},
  keywords  = {TypeI},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Jinek2014,
  author    = {Jinek, Martin and Jiang, Fuguo and Taylor, David W. and Sternberg, Samuel H. and Kaya, Emine and Ma, Enbo and Anders, Carolin and Hauer, Michael and Zhou, Kaihong and Lin, Steven and Kaplan, Matias and Iavarone, Anthony T. and Charpentier, Emmanuelle and Nogales, Eva and Doudna, Jennifer A.},
  journal   = {Science},
  title     = {Structures of Cas9 Endonucleases Reveal RNA-Mediated Conformational Activation},
  year      = {2014},
  pages     = {1247997},
  abstract  = {Type II CRISPR-Cas systems use an RNA-guided DNA endonuclease, Cas9, to generate double-strand breaks in invasive DNA during an adaptive bacterial immune response. Cas9 has been harnessed as a powerful tool for genome editing and gene regulation in many eukaryotic organisms. Here, we report 2.6 and 2.2 Å resolution crystal structures of two major Cas9 enzymes subtypes, revealing the structural core shared by all Cas9 family members. The architectures of Cas9 enzymes define nucleic acid binding clefts, and single-particle electron microscopy reconstructions show that the two structural lobes harboring these clefts undergo guide RNA-induced reorientation to form a central channel where DNA substrates are bound. The observation that extensive structural rearrangements occur before target DNA duplex binding implicates guide RNA loading as a key step in Cas9 activation.},
  doi       = {10.1126/science.1247997},
  eprint    = {http://www.sciencemag.org/content/early/2014/02/05/science.1247997.full.pdf},
  file      = {2014_Jinek_1247997.pdf:by-author/J/Jinek/2014_Jinek_1247997.pdf:PDF},
  groups    = {sg/CRISPR-Cas},
  keywords  = {CRISPR; Cas9; Protein Structure; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2014.02.12},
  creationdate = {2014-02-12T00:00:00},
  url       = {http://www.sciencemag.org/content/early/2014/02/05/science.1247997.abstract},
}

@Article{Jing2004,
  author    = {Jing, Debra and Beechem, Joseph M. and Patton, Wayne F.},
  journal   = {Electrophoresis},
  title     = {The utility of a two-color fluorescence electrophoretic mobility shift assay procedure for the analysis of DNA replication complexes.},
  year      = {2004},
  pages     = {2439--46},
  volume    = {25},
  abstract  = {Protein-DNA and protein-protein interactions play essential roles in many biologic processes such as transcription, replication, recombination, and DNA repair. One of the most popular approaches to investigate specific protein-nucleic acid interactions is the electrophoretic mobility shift assay (EMSA). We have developed a new nonradioactive method to detect both nucleotides and protein in EMSA. Nucleic acids are detected with SYBR Green EMSA dye, while proteins are subsequently detected with SYPRO Ruby EMSA dye. All fluorescent staining steps are performed after the entire gel-shift experiment is completed, so there is no need to prelabel either the nucleic acids or the protein. The two-color fluorescence dye staining procedure is fast, simple, and allows independent quantitative determination of either free or bound nucleic acids and protein. The interactions between lac repressor-operator, and among the T4 primase-helicase, primase-DNA, helicase-DNA, and within T4 [ssDNA-primase-helicase6] primosome, were used to demonstrate the advantages of this two-color fluorescence detection EMSA method.},
  file      = {:by-author/J/Jing/2004_Jing_2439.pdf:PDF},
  keywords  = {Gel; {gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Jing1999a,
  author    = {Jing, D. H. and Dong, F. and Latham, G. J. and von Hippel, P. H.},
  journal   = {The Journal of biological chemistry},
  title     = {Interactions of bacteriophage T4-coded primase (gp61) with the T4 replication helicase (gp41) and DNA in primosome formation.},
  year      = {1999},
  pages     = {27287--98},
  volume    = {274},
  abstract  = {One primase (gp61) and six helicase (gp41) subunits interact to form the bacteriophage T4-coded primosome at the DNA replication fork. In order to map some of the detailed interactions of the primase within the primosome, we have constructed and characterized variants of the gp61 primase that carry kinase tags at either the N or the C terminus of the polypeptide chain. These tagged gp61 constructs have been probed using several analytical methods. Proteolytic digestion and protein kinase protection experiments show that specific interactions with single-stranded DNA and the T4 helicase hexamer significantly protect both the N- and the C-terminal regions of the T4 primase polypeptide chain against modification by these procedures and that this protection becomes more pronounced when the primase is assembled within the complete ternary primosome complex. Additional discrete sites of both protection and apparent hypersensitivity along the gp61 polypeptide chain have also been mapped by proteolytic footprinting reactions for the binary helicase-primase complex and in the three component primosome. These studies provide a detailed map of a number of gp61 contact positions within the primosome and reveal interactions that may be important in the structure and function of this central component of the T4 DNA replication complex.},
  file      = {:by-author/J/Jing/1999_Jing_27287.pdf:PDF},
  keywords  = {Gel; {gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Jing-Qi2014,
  author    = {Jing-Qi, Yang and Shao-Xian, Li and Hong-Wei, Zhao and Jian-Bing, Zhang and Na, Yang and Dan-Dan, Jing and Chen-Yang, Wang and Jia-Guang, Han},
  title     = {Terahertz study of {L}-asparagine and its monohydrate},
  year      = {2014},
  file      = {[PDF] from iphy.ac.cn:by-author/J/Jing-Qi/2014_Jing-Qi.pdf:application/pdf},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://wulixb.iphy.ac.cn/EN/article/downloadArticleFile.do?attachType=PDF&id=60071},
  urldate   = {2015-08-31},
}

@Article{Joachim2000,
  author    = {Joachim, C. and Gimzewski, J. K. and Aviram, A.},
  journal   = {Nature},
  title     = {Electronics using hybrid-molecular and mono-molecular devices},
  year      = {2000},
  issn      = {0028-0836},
  pages     = {541--548},
  volume    = {408},
  abstract  = {The semiconductor industry has seen a remarkable miniaturization trend, driven by many scientific and technological innovations. But if this trend is to continue, and provide ever faster and cheaper computers, the size of microelectronic circuit components will soon need to reach the scale of atoms or molecules—a goal that will require conceptually new device structures. The idea that a few molecules, or even a single molecule, could be embedded between electrodes and perform the basic functions of digital electronics—rectification, amplification and storage—was first put forward in the mid-1970s. The concept is now realized for individual components, but the economic fabrication of complete circuits at the molecular level remains challenging because of the difficulty of connecting molecules to one another. A possible solution to this problem is ‘mono-molecular’ electronics, in which a single molecule will integrate the elementary functions and interconnections required for computation.},
  copyright = {© 2000 Nature Publishing Group},
  doi       = {10.1038/35046000},
  file      = {Full Text PDF:by-author/J/Joachim/2000_Joachim_541.pdf:application/pdf;Snapshot:by-author/J/Joachim/2000_Joachim_541.html:text/html},
  groups    = {sg/chemical, sg/electronics},
  language  = {en},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://www.nature.com/nature/journal/v408/n6812/full/408541a0.html},
  urldate   = {2015-08-05},
}

@Article{Jogl2001,
  author    = {Jogl, Gerwald and Tao, Xiao and Xu, Yingwu and Tong, Liang},
  journal   = {Acta Crystallographica Section D},
  title     = {{\it COMO}: a program for combined molecular replacement},
  year      = {2001},
  pages     = {1127--1134},
  volume    = {57},
  doi       = {10.1107/S0907444901006783},
  file      = {gr2149.pdf:by-author/J/Jogl/2001_Jogl_1127.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444901006783},
}

@Article{Johnson1984,
  author    = {David S. Johnson},
  journal   = {J. Algorithms},
  title     = {The NP-Completeness Column: An Ongoing Guide},
  year      = {1984},
  pages     = {433--447},
  abstract  = {This is the twelfth edition of a quarterly column that provides continuing coverage of new developments in the theory of NP-completeness. The presentation is modeled on that used by M. R. Garey and myself in our book ‘‘Computers and Intractability: A Guide to the Theory of NP-Completeness,’’ W. H. Freeman & Co., New York, 1979 (hereinafter referred to as ‘‘[G&J]’’; previous columns will be referred to by their dates). A back- ground equivalent to that provided by [G&J] is assumed, and, when appropriate, cross- references will be given to that book and the list of problems (NP-complete and harder) presented there. Readers who have results they would like mentioned (NP-hardness, PSPACE-hardness, polynomial-time-solvability, etc.), or open problems they would like publicized, should send them to David S. Johnson, Room 2C-355, AT&T Bell Laborato- ries, Murray Hill, NJ 07974 (CSNET address: dsj.rabbit.btl@csnet-relay). Please include details, or at least sketches, of any new proofs (full papers are preferred). If the results are unpublished, please state explicitly that you would like them to be mentioned in the col- umn. Comments and corrections are also welcome. For more details on the nature of the column and the form of desired submissions, see the December 1981 issue of this Journal.},
  file      = {1984_Johnson_433.pdf:by-author/J/Johnson/1984_Johnson_433.pdf:PDF},
  keywords  = {Computer Science (CS); Turing Machines},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Johnson2007,
  author    = {Johnson, Daniel S. and Bai, Lu and Smith, Benjamin Y. and Patel, Smita S. and Wang, Michelle D.},
  journal   = {Cell},
  title     = {Single-molecule studies reveal dynamics of DNA unwinding by the ring-shaped T7 helicase.},
  year      = {2007},
  pages     = {1299--309},
  volume    = {129},
  abstract  = {Helicases are molecular motors that separate DNA strands for efficient replication of genomes. We probed the kinetics of individual ring-shaped T7 helicase molecules as they unwound double-stranded DNA (dsDNA) or translocated on single-stranded DNA (ssDNA). A distinctive DNA sequence dependence was observed in the unwinding rate that correlated with the local DNA unzipping energy landscape. The unwinding rate increased approximately 10-fold (approaching the ssDNA translocation rate) when a destabilizing force on the DNA fork junction was increased from 5 to 11 pN. These observations reveal a fundamental difference between the mechanisms of ring-shaped and nonring-shaped helicases. The observed force-velocity and sequence dependence are not consistent with a simple passive unwinding model. However, an active unwinding model fully supports the data even though the helicase on its own does not unwind at its optimal rate. This work offers insights into possible ways helicase activity is enhanced by associated proteins.},
  file      = {:by-author/J/Johnson/2007_Johnson_1299.pdf:PDF},
  keywords  = {T7; {gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Johnson2009,
  author    = {Mark Johnson and Sharon Goldwater},
  journal   = {Human Language Technologies: The 2009 Annual Conference of the North American Chapter of the ACL},
  title     = {Improving nonparameteric Bayesian inference: experiments on unsupervised word segmentation with adaptor grammars},
  year      = {2009},
  pages     = {317--325},
  abstract  = {One of the reasons nonparametric Bayesian inference is attracting attention in computa- tional linguistics is because it provides a principled way of learning the units of generalization together with their probabilities. Adaptor grammars are a framework for defining a variety of hierarchical nonparametric Bayesian models. This paper investigates some of the choices that arise in formulating adaptor grammars and associated inference procedures, and shows that they can have a dramatic impact on performance in an unsupervised word segmentation task. With appro- priate adaptor grammars and inference proce- dures we achieve an 87% word token f-score on the standard Brent version of the Bernstein- Ratner corpus, which is an error reduction of over 35% over the best previously reported results for this corpus.},
  file      = {:by-author/J/Johnson/2009_Johnson_317.pdf:PDF},
  groups    = {sg/Bayesian},
  keywords  = {Bayesian Statistics},
  owner     = {saulius},
  timestamp = {2012.09.30},
  creationdate = {2012-09-30T00:00:00},
}

@Presentation{Johnson2015,
  author    = {Natalie Johnson},
  title     = {X-ray Origins; Protection or Paranoia?},
  year      = {2015},
  school    = {Newcastle University},
  file      = {2015_Johnson_slides.pdf:by-author/J/Johnson/2015_Johnson_slides.pdf:PDF},
  groups    = {sg/Data Management},
  keywords  = {Data Management; Fraud Prevention; Image Formats; Scientific Fraud; X-ray Data Processing},
  owner     = {saulius},
  timestamp = {2015.11.11},
  creationdate = {2015-11-11T00:00:00},
  url       = {http://www.iucr.org/__data/assets/pdf_file/0015/114126/05_Johnson.pdf},
}

@Manuscript{Johnson2003,
  author    = {Stephen C. Johnson},
  title     = {{YACC} -- {Y}et {A}nother {C}ompiler-{C}ompiler},
  year      = {2003},
  keywords  = {Compiler Generator; Compiler-compiler; Computer Science (CS); Programming Languages; YACC},
  url       = {http://www.tom-yam.or.jp/2238/ref/yacc.pdf},
  abstract  = {Computer program input generally has some structure; in fact, every computer program which does input can be thought of as defining an ‘‘input language" which it accepts. The input languages may be as complex as a programming language, or as simple as a sequence of numbers. Unfortunately, standard input facilities are restricted, difficult to use and change, and do not completely check their inputs for validity. Yacc provides a general tool for controlling the input to a computer program. The Yacc user describes the structures of his input, together with code which is to be invoked when each such structure is recognized. Yacc turns such a specification into a subroutine which may be invoked to handle the input process; frequently, it is convenient and appropriate to have most of the flow of control in the user's application handled by this subroutine.},
  file      = {2003_Johnson.pdf:by-author/J/Johnson/2003_Johnson.pdf:PDF},
  owner     = {saulius},
  timestamp = {2015.11.23},
  creationdate = {2015-11-23T00:00:00},
}

@Article{Johnson2000,
  author    = {Johnson, S. K. and Bhattacharyya, S. and Griep, M. A.},
  journal   = {Biochemistry},
  title     = {DnaB helicase stimulates primer synthesis activity on short oligonucleotide templates.},
  year      = {2000},
  pages     = {736--44},
  volume    = {39},
  abstract  = {DnaB helicase stimulated the second-order RNA primer synthesis activity of primase by over 5000-fold on DNA templates that were 23 nucleotides long. This template length is the same as the DnaB helicase thermodynamic binding site size [Jezewska, M. J., and Bujalowski, W. (1996) Biochemistry 35, 2117-2128]. This phenomenal stimulation was achieved by increasing the template affinity of primase by over 300-fold and increasing the catalytic rate by over 15-fold. It was necessary to determine the optimal amount of DnaB helicase to achieve this stimulation because helicase stimulation was cooperative at low concentration and inhibitory at high helicase concentration. The cooperative stimulation at low concentration indicated the presence of a time-dependent assembly step that preceded the active state. Besides stimulating primase activity, DnaB helicase also prevented primase from synthesizing RNA primers that were longer than the template sequence. In the absence of DnaB helicase, the majority of primers synthesized by primase were longer than the template and were named "overlong primers" [Swart, J. R., and Griep, M. A. (1995) Biochemistry 34, 16097-16106]. In contrast, the helicase-stimulated RNA primers were from 10 to 14 nucleotides in length with the 12-mer representing the majority of the total RNA primers produced. It was shown that DnaB helicase stabilized the open or single-stranded conformation of the template, which favored the synthesis of the template-length-dependent primers. In contrast, when primase acted alone, it stabilized the 3'-end hairpin conformation of the template so that the template's 3'-hydroxyl served as a "DNA primer" from which primase elongated to create the overlong primers.},
  file      = {:by-author/J/Johnson/2000_Johnson_736.pdf:PDF},
  keywords  = {Ecoli; {gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Johnston2001,
  author    = {Johnston, W K and Unrau, P J and Lawrence, M S and Glasner, M E and Bartel, D P},
  journal   = {Science (New York, N.Y.)},
  title     = {RNA-catalyzed RNA polymerization: accurate and general RNA-templated primer extension.},
  year      = {2001},
  pages     = {1319--25},
  volume    = {292},
  file      = {2001_Johnston_1319.pdf:by-author/J/Johnston/2001_Johnston_1319.pdf:PDF},
  keywords  = {Ribozymes},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Jones2001,
  author    = {Jones, C. E. and Mueser, T. C. and Dudas, K. C. and Kreuzer, K. N. and Nossal, N. G.},
  journal   = {Proceedings of the National Academy of Sciences of the United States of America},
  title     = {Bacteriophage T4 gene 41 helicase and gene 59 helicase-loading protein: a versatile couple with roles in replication and recombination.},
  year      = {2001},
  pages     = {8312--8},
  volume    = {98},
  abstract  = {Bacteriophage T4 uses two modes of replication initiation: origin-dependent replication early in infection and recombination-dependent replication at later times. The same relatively simple complex of T4 replication proteins is responsible for both modes of DNA synthesis. Thus the mechanism for loading the T4 41 helicase must be versatile enough to allow it to be loaded on R loops created by transcription at several origins, on D loops created by recombination, and on stalled replication forks. T4 59 helicase-loading protein is a small, basic, almost completely alpha-helical protein whose N-terminal domain has structural similarity to high mobility group family proteins. In this paper we review recent evidence that 59 protein recognizes specific structures rather than specific sequences. It binds and loads the helicase on replication forks and on three- and four-stranded (Holliday junction) recombination structures, without sequence specificity. We summarize our experiments showing that purified T4 enzymes catalyze complete unidirectional replication of a plasmid containing the T4 ori(uvsY) origin, with a preformed R loop at the position of the R loop identified at this origin in vivo. This replication depends on the 41 helicase and is strongly stimulated by 59 protein. Moreover, the helicase-loading protein helps to coordinate leading and lagging strand synthesis by blocking replication on the ori(uvsY) R loop plasmid until the helicase is loaded. The T4 enzymes also can replicate plasmids with R loops that do not have a T4 origin sequence, but only if the R loops are within an easily unwound DNA sequence.},
  file      = {:by-author/J/Jones/2001_Jones_8312.pdf:PDF},
  keywords  = {Struktur; {gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Jones2000,
  author    = {Jones, C. E. and Mueser, T. C. and Nossal, N. G.},
  journal   = {The Journal of biological chemistry},
  title     = {Interaction of the bacteriophage T4 gene 59 helicase loading protein and gene 41 helicase with each other and with fork, flap, and cruciform DNA.},
  year      = {2000},
  pages     = {27145--54},
  volume    = {275},
  abstract  = {Bacteriophage T4 gene 59 helicase loading protein accelerates the loading of T4 gene 41 DNA helicase and is required for recombination-dependent DNA replication late in T4 phage infection. The crystal structure of 59 protein revealed a two-domain alpha-helical protein, whose N-terminal domain has strong structural similarity to the DNA binding domain of high mobility group family proteins (Mueser, T. C., Jones, C. E., Nossal, N. G., and Hyde, C. C. (2000) J. Mol. Biol. 296, 597-612). We have previously shown that 59 protein binds preferentially to fork DNA. Here we show that 59 protein binds to completely duplex forks but cannot load the helicase unless there is a single-stranded gap of more than 5 nucleotides on the fork arm corresponding to the lagging strand template. Consistent with the roles of these proteins in recombination, we find that 59 protein binds to and stimulates 41 helicase activity on Holliday junction DNA, and on a substrate that resembles a strand invasion structure. 59 protein forms a stable complex with wild type 41 helicase and fork DNA in the presence of adenosine 5'-O-(thiotriphosphate). The unwinding activity of 41 helicase missing 20 C-terminal amino acids is not stimulated by 59 protein, and it does not form a complex with 59 protein on fork DNA.},
  file      = {:by-author/J/Jones/2000_Jones_27145.pdf:PDF},
  keywords  = {Gel; {gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@InProceedings{Jones1976,
  author    = {Jones, Daniel E.},
  booktitle = {Proceedings of the 14th annual Southeast regional conference},
  title     = {Structured programming and FORTRAN},
  year      = {1976},
  address   = {New York, NY, USA},
  pages     = {1--6},
  publisher = {ACM},
  series    = {ACM-SE 14},
  acmid     = {503563},
  doi       = {10.1145/503561.503563},
  file      = {1976_Jones_1.pdf:by-author/J/Jones/1976_Jones_1.pdf:PDF},
  keywords  = {Algorithms; Programming Languages; Structured Programming},
  location  = {Birmingham, Alabama},
  numpages  = {6},
  owner     = {saulius},
  timestamp = {2012.05.17},
  creationdate = {2012-05-17T00:00:00},
  url       = {http://doi.acm.org/10.1145/503561.503563},
}

@Article{Jones2001a,
  author    = {Jones, David T.},
  journal   = {Acta Crystallographica Section D},
  title     = {Evaluating the potential of using fold-recognition models for molecular replacement},
  year      = {2001},
  pages     = {1428--1434},
  volume    = {57},
  doi       = {10.1107/S0907444901013403},
  file      = {ba5016.pdf:by-author/J/Jones/2001_Jones_1428.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444901013403},
}

@TechReport{Jones1997,
  author      = {Richard W. M. Jones and Paul H. J. Kelly},
  institution = {Department of Computing, Imperial College of Science, Technology and Medicine, 180 Queen's Gate, London SW7 2BZ},
  title       = {Backwards-compatible bounds checking for arrays and pointers in C},
  year        = {1997},
  abstract    = {This paper presents a new approach to enforcing array bounds and pointer checking in the C language. Check- ing is rigorous in the sense that the result of pointer arithmetic must refer to the same object as the orig- inal pointer (this object is sometimes called the 'in- tended referent'). The novel aspect of this work is that checked code can inter-operate without restriction with unchecked code, without interface problems, with some e ective checking, and without false alarms. This \backwards compatibility" property allows the overheads of checking to be con ned to suspect modules, and also facilitates the use of libraries for which source code is not available. The paper describes the scheme, its pro- totype implementation (as an extension to the GNU C compiler), presents experimental results to evaluate its e ectiveness, and discusses performance issues and the e ectiveness of some simple optimisations.},
  file        = {:by-author/J/Jones/1997_Jones.ps.gz:PostScript;:by-author/J/Jones/1997_Jones.pdf:PDF},
  owner       = {saulius},
  timestamp = {2015.02.27},
  creationdate = {2015-02-27T00:00:00},
}

@Article{Jones2003,
  author    = {Jones, Susan and Barker, Jonathan A and Nobeli, Irene and Thornton, Janet M},
  journal   = {Nucleic Acids Res},
  title     = {Using structural motif templates to identify proteins with DNA binding function},
  year      = {2003},
  month     = {Jun},
  number    = {11},
  pages     = {2811--23},
  volume    = {31},
  abstract  = {This work describes a method for predicting DNA binding function from structure using 3-dimensional templates. Proteins that bind DNA using small contiguous helix-turn-helix (HTH) motifs comprise a significant number of all DNA-binding proteins. A structural template library of seven HTH motifs has been created from non-homologous DNA-binding proteins in the Protein Data Bank. The templates were used to scan complete protein structures using an algorithm that calculated the root mean squared deviation (rmsd) for the optimal superposition of each template on each structure, based on C(alpha) backbone coordinates. Distributions of rmsd values for known HTH-containing proteins (true hits) and non-HTH proteins (false hits) were calculated. A threshold value of 1.6 A rmsd was selected that gave a true hit rate of 88.4% and a false positive rate of 0.7%. The false positive rate was further reduced to 0.5% by introducing an accessible surface area threshold value of 990 A2 per HTH motif. The template library and the validated thresholds were used to make predictions for target proteins from a structural genomics project},
  address   = {EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. suej@ebi.ac.uk},
  doi       = {10.1093/nar/gkg386},
  file      = {2003_Jones_2811.pdf:by-author/J/Jones/2003_Jones_2811.pdf:PDF},
  keywords  = {DNA-binding; Protein Structure},
  owner     = {em},
  timestamp = {2016.06.16},
  creationdate = {2016-06-16T00:00:00},
  url       = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&dopt=abstract&list_uids=12771208},
}

@Article{Jones2001b,
  author      = {Jones, S. and Daley, D. T. and Luscombe, N. M. and Berman, H. M. and Thornton, J. M.},
  journal     = {Nucleic Acids Res},
  title       = {Protein-RNA interactions: a structural analysis.},
  year        = {2001},
  pages       = {943--954},
  volume      = {29},
  abstract    = {A detailed computational analysis of 32 protein-RNA complexes is presented. A number of physical and chemical properties of the intermolecular interfaces are calculated and compared with those observed in protein-double-stranded DNA and protein-single-stranded DNA complexes. The interface properties of the protein-RNA complexes reveal the diverse nature of the binding sites. van der Waals contacts played a more prevalent role than hydrogen bond contacts, and preferential binding to guanine and uracil was observed. The positively charged residue, arginine, and the single aromatic residues, phenylalanine and tyrosine, all played key roles in the RNA binding sites. A comparison between protein-RNA and protein-DNA complexes showed that whilst base and backbone contacts (both hydrogen bonding and van der Waals) were observed with equal frequency in the protein-RNA complexes, backbone contacts were more dominant in the protein-DNA complexes. Although similar modes of secondary structure interactions have been observed in RNA and DNA binding proteins, the current analysis emphasises the differences that exist between the two types of nucleic acid binding protein at the atomic contact level.},
  doi         = {10.1093/nar/29.4.943},
  file        = {2001_Jones_943.pdf:by-author/J/Jones/2001_Jones_943.pdf:PDF},
  institution = {Biomolecular Structure and Modelling Unit, Department of Biochemistry and Molecular Biology, University College, Gower Street, London WC1E 6BT, UK.},
  keywords    = {Base Pairing; Binding Sites; Chemistry/classification/metabolism; Chemistry/genetics/metabolism; Computational Biology; DNA; Databases as Topic; Guanine; Hydrogen Bonding; Internet; Metabolism; Models; Molecular; Protein Binding; Protein Structure; RNA; RNA-Binding Proteins; Secondary; Uracil},
  language    = {eng},
  medline-pst = {ppublish},
  owner       = {saulius},
  pmid        = {11160927},
  timestamp = {2012.09.16},
  creationdate = {2012-09-16T00:00:00},
  url         = {http://nar.oxfordjournals.org/content/29/4/943.abstract},
}

@Article{Jones1999a,
  author    = {Jones, S and van Heyningen, P and Berman, H M and Thornton, J M},
  journal   = {J Mol Biol},
  title     = {Protein-DNA interactions: A structural analysis},
  year      = {1999},
  month     = {Apr},
  number    = {5},
  pages     = {877--96},
  volume    = {287},
  abstract  = {A detailed analysis of the DNA-binding sites of 26 proteins is presented using data from the Nucleic Acid Database (NDB) and the Protein Data Bank (PDB). Chemical and physical properties of the protein-DNA interface, such as polarity, size, shape, and packing, were analysed. The DNA-binding sites shared common features, comprising many discontinuous sequence segments forming hydrophilic surfaces capable of direct and water-mediated hydrogen bonds. These interface sites were compared to those of protein-protein binding sites, revealing them to be more polar, with many more intermolecular hydrogen bonds and buried water molecules than the protein-protein interface sites. By looking at the number and positioning of protein residue-DNA base interactions in a series of interaction footprints, three modes of DNA binding were identified (single-headed, double-headed and enveloping). Six of the eight enzymes in the data set bound in the enveloping mode, with the protein presenting a large interface area effectively wrapped around the DNA.A comparison of structural parameters of the DNA revealed that some values for the bound DNA (including twist, slide and roll) were intermediate of those observed for the unbound B-DNA and A-DNA. The distortion of bound DNA was evaluated by calculating a root-mean-square deviation on fitting to a canonical B-DNA structure. Major distortions were commonly caused by specific kinks in the DNA sequence, some resulting in the overall bending of the helix. The helix bending affected the dimensions of the grooves in the DNA, allowing the binding of protein elements that would otherwise be unable to make contact. From this structural analysis a preliminary set of rules that govern the bending of the DNA in protein-DNA complexes, are proposed},
  address   = {Biomolecular Structure and Modelling Unit, Department of Biochemistry and Molecular Biology, University College, Gower Street, London, WC1E 6BT, England.sue@biochem.ucl.ac.uk},
  doi       = {10.1006/jmbi.1999.2659},
  file      = {1999_Jones_877.pdf:by-author/J/Jones/1999_Jones_877.pdf:PDF},
  groups    = {sg/Garbage collectors},
  owner     = {em},
  timestamp = {2016.06.16},
  creationdate = {2016-06-16T00:00:00},
  url       = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&dopt=abstract&list_uids=10222198},
}

@Article{Jones2000a,
  author    = {Jessica M. Jones and Hiroshi Nakai},
  journal   = {Molecular Microbiology},
  title     = {{PriA} and phage {T4} gp59: factors that promote {DNA} replication on forked {DNA} substrates},
  year      = {2000},
  month     = {jan},
  number    = {3},
  pages     = {519--527},
  volume    = {37},
  doi       = {10.1046/j.1365-2958.2000.01888.x},
  file      = {:by-author/J/Jones/2000_Jones_519.pdf:PDF},
  keywords  = {{gp41} Helicase},
  owner     = {em},
  publisher = {Wiley},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Manuscript{Jones1999,
  author    = {Simon Peyton Jones and Norman Ramsey and Fermin Reig},
  title     = {C--: a portable assembly language that supports garbage collection},
  year      = {1999},
  abstract  = {For a compiler writer, generating good machine code for a variety of platforms is hard work. One might try to reuse a retargetable code generator, but code generators are complex and di cult to use, and they limit one's choice of implementation language. One might try to use C as a portable assembly language, but C limits the compiler writer's exibility and the performance of the resulting code. The wide use of C, despite these drawbacks, argues for a portable assembly lan- guage. C-- is a new language designed expressly for this purpose. The use of a portable assembly language introduces new problems in the sup- port of such high-level run-time services as garbage collection, exception handling, concurrency, pro ling, and debugging. We address these prob- lems by combining the C-- language with a C-- run-time interface. The combination is designed to allow the compiler writer a choice of source- language semantics and implementation techniques, while still providing good performan},
  file      = {:by-author/J/Jones/1999_Jones.ps.gz:PostScript;:by-author/J/Jones/1999_Jones.pdf:PDF},
  groups    = {sg/Garbage collectors},
  owner     = {saulius},
  timestamp = {2015.02.27},
  creationdate = {2015-02-27T00:00:00},
}

@Article{Jones1996,
  author           = {Jones, T. A. and Kleywegt, G. J. and Brunger, A. T.},
  journal          = {Nature},
  title            = {Storing diffraction data},
  year             = {1996},
  pages            = {18--19},
  volume           = {383},
  creationdate     = {2008-07-28T00:00:00},
  file             = {1996_Jones_18.pdf:by-author/J/Jones/1996_Jones_18.pdf:PDF;:by-author/J/Jones/1996_Jones_18.djvu:Djvu},
  keywords         = {Data Quality; X-ray Crystallography},
  modificationdate = {2024-08-15T18:45:02},
  owner            = {saulius},
  timestamp        = {2008.07.28},
}

@Article{Jones1991,
  author    = {Jones, T A and Zou, J Y and Cowan, S W},
  journal   = {Acta Crystallogr A},
  title     = {Improved methods for building protein models in electron density maps and the location of errors in these models},
  year      = {1991},
  month     = {Mar},
  pages     = {110--9},
  volume    = {47 ( Pt 2)},
  abstract  = {Map interpretation remains a critical step in solving the structure of a macromolecule. Errors introduced at this early stage may persist throughout crystallographic refinement and result in an incorrect structure. The normally quoted crystallographic residual is often a poor description for the quality of the model. Strategies and tools are described that help to alleviate this problem. These simplify the model-building process, quantify the goodness of fit of the model on a per-residue basis and locate possible errors in peptide and side-chain conformations},
  address   = {Department of Molecular Biology, BMC, Uppsala, Sweden},
  doi       = {10.1107/S0108767390010224},
  file      = {1991_Jones_110.pdf:by-author/J/Jones/1991_Jones_110.pdf:PDF},
  keywords  = {Map Interpretation; X-ray Crystallography},
  owner     = {em},
  timestamp = {2016.06.16},
  creationdate = {2016-06-16T00:00:00},
  url       = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&dopt=abstract&list_uids=2025413},
}

@Article{Jones1991a,
  author    = {Jones, T. A. and Zou, J. Y. and Cowan, S. W. and Kjeldgaard, M.},
  journal   = {Acta crystallographica. Section A, Foundations of crystallography},
  title     = {Improved methods for building protein models in electron density maps and the location of errors in these models.},
  year      = {1991},
  pages     = {110--119},
  volume    = {47 ( Pt 2)},
  abstract  = {Map interpretation remains a critical step in solving the structure of a macromolecule. Errors introduced at this early stage may persist throughout crystallographic refinement and result in an incorrect structure. The normally quoted crystallographic residual is often a poor description for the quality of the model. Strategies and tools are described that help to alleviate this problem. These simplify the model-building process, quantify the goodness of fit of the model on a per-residue basis and locate possible errors in peptide and side-chain conformations.},
  doi       = {10.1107/S0108767390010224},
  file      = {:by-author/J/Jones/1991_Jones_110a.pdf:pdf},
  keywords  = {Validation},
  owner     = {saulius},
  pubmed    = {2025413},
  timestamp = {2016.12.12},
  creationdate = {2016-12-12T00:00:00},
  url       = {http://scripts.iucr.org/cgi-bin/paper?bu0242},
}

@Article{Jones1997a,
  author    = {Jones, T.A. and Kjeldgaard, M.},
  journal   = {Macromolecular Crystallography Part B},
  title     = {[10] Electron-density map interpretation},
  year      = {1997},
  issn      = {0076-6879},
  pages     = {173--208},
  volume    = {277},
  abstract  = {Any errors that occur in a crystallographic project usually will be found before publication. Often, if an error has been made, the project will stall and there will be no publication. Introducing a serious error in a model can be different. This chapter discusses the kinds of error that might be made and why these errors are made. It discusses some of the features of the crystallographic model-building program O. Real errors in models occur with frequencies that are, fortunately, inversely proportional to the seriousness of the error. Building a molecular model from electron density is a complicated process. During the interpretation of an electron-density map, the basic function of the molecular graphics program is to assist the scientist in imagining, and then remembering, the three-dimensional folding and features of the structure. Thus, it is important to be able to change the model quickly and not to be interrupted by the details of operating a computer program. To facilitate the rapid building and rebuilding of molecular models, O incorporates autobuild options, allowing the user to create a molecular structure quickly from a rough three-dimensional sketch. This has the drawback of possibly making it even easier to build a wrong structure.},
  doi       = {10.1016/s0076-6879(97)77012-5},
  file      = {:by-author/J/Jones/1997_Jones_173.pdf:pdf},
  isbn      = {http://id.crossref.org/isbn/9780121821784},
  keywords  = {Validation},
  owner     = {saulius},
  publisher = {Elsevier BV},
  pubmed    = {18488310},
  timestamp = {2016.12.12},
  creationdate = {2016-12-12T00:00:00},
  url       = {http://dx.doi.org/10.1016/S0076-6879(97)77012-5},
}

@Article{Jong2013,
  author    = {de Jong, Wibe and Walker, Andrew and Hanwell, Marcus},
  journal   = {Journal of Cheminformatics},
  title     = {From data to analysis: linking NWChem and Avogadro with the syntax and semantics of Chemical Markup Language},
  year      = {2013},
  issn      = {1758-2946},
  pages     = {25},
  volume    = {5},
  abstract  = {BACKGROUND:Multidisciplinary integrated research requires the ability to couple thediverse sets of data obtained from a range of complex experiments andcomputer simulations. Integrating data requires semantically richinformation. In this paper an end-to-end use of semantically rich data incomputational chemistry is demonstrated utilizing the Chemical MarkupLanguage (CML) framework. Semantically rich data is generated by the NWChemcomputational chemistry software with the FoX library and utilized by theAvogadro molecular editor for analysis and visualization. RESULTS:The NWChem computational chemistry software has been modified and coupled tothe FoX library to write CML compliant XML data files. The FoX library wasexpanded to represent the lexical input files and molecular orbitals used bythe computational chemistry software. Draft dictionary entries and a formatfor molecular orbitals within CML CompChem were developed. The Avogadroapplication was extended to read in CML data, and display molecular geometryand electronic structure in the GUI allowing for an end-to-end solutionwhere Avogadro can create input structures, generate input files, NWChem canrun the calculation and Avogadro can then read in and analyse the CML outputproduced. The developments outlined in this paper will be made available infuture releases of NWChem, FoX, and Avogadro. CONCLUSIONS:The production of CML compliant XML files for computational chemistrysoftware such as NWChem can be accomplished relatively easily using the FoXlibrary. The CML data can be read in by a newly developed reader in Avogadroand analysed or visualized in various ways. A community-based effort isneeded to further develop the CML CompChem convention and dictionary. Thiswill enable the long-term goal of allowing a researcher to run simple"Google-style" searches of chemistry and physics and have theresults of computational calculations returned in a comprehensible formalongside articles from the published literature.},
  doi       = {10.1186/1758-2946-5-25},
  file      = {2013_Jong_25.pdf:by-author/J/Jong/2013_Jong_25.pdf:PDF},
  keywords  = {Avogadro; CML; Chemical Markup Language; Computational Chemistry; Data Management; FoX; NWChem},
  owner     = {saulius},
  pubmedid  = {23705910},
  timestamp = {2013.09.15},
  creationdate = {2013-09-15T00:00:00},
  url       = {http://www.jcheminf.com/content/5/1/25},
}

@Article{Joosten2009,
  author    = {Joosten, Robbie P. and Salzemann, Jean and Bloch, Vincent and Stockinger, Heinz and Berglund, Ann-Charlott and Blanchet, Christophe and Bongcam-Rudloff, Erik and Combet, Christophe and Da Costa, Ana L. and Deleage, Gilbert and Diarena, Matteo and Fabbretti, Roberto and Fettahi, G{\'{e}}raldine and Flegel, Volker and Gisel, Andreas and Kasam, Vinod and Kervinen, Timo and Korpelainen, Eija and Mattila, Kimmo and Pagni, Marco and Reichstadt, Matthieu and Breton, Vincent and Tickle, Ian J. and Vriend, Gert},
  journal   = {Journal of Applied Crystallography},
  title     = {PDB_REDO: automated re-refinement of X-ray structure models in the PDB},
  year      = {2009},
  pages     = {376--384},
  volume    = {42},
  doi       = {10.1107/S0021889809008784},
  file      = {he5437.pdf:by-author/J/Joosten/2009_Joosten_376.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0021889809008784},
}

@InProceedings{Jordan2013a,
  author    = {Jordan, Alexander and Brandner, Florian and Schoeberl, Martin},
  booktitle = {Proceedings of the 21st International Conference on Real-Time Networks and Systems},
  title     = {Static Analysis of Worst-case Stack Cache Behavior},
  year      = {2013},
  address   = {New York, NY, USA},
  pages     = {55--64},
  publisher = {ACM},
  series    = {RTNS '13},
  abstract  = {Utilizing a stack cache in a real-time system can aid predictability by avoiding interference that heap memory traffic causes on the data cache. While loads and stores are guaranteed cache hits, explicit operations are responsible for managing the stack cache. The behavior of these operations can be analyzed statically. We present algorithms that derive worst-case bounds on the latency-inducing operations of the stack cache. Their results can be used by a static WCET tool. By breaking the analysis down into subproblems that solve intra-procedural data-flow analysis and path searches on the call-graph, the worst-case bounds can be efficiently yet precisely determined. Our evaluation using the MiBench benchmark suite shows that only 37% and 21% of potential stack cache operations actually store to and load from memory, respectively. Analysis times are modest, on average running between 0.46s and 1.30s per benchmark, depending on the size of the stack cache.},
  acmid     = {2516828},
  doi       = {10.1145/2516821.2516828},
  file      = {2013_Jordan_55.pdf:by-author/J/Jordan/2013_Jordan_55.pdf:PDF},
  groups    = {sg/Compiler construction, sg/Stack machines},
  isbn      = {978-1-4503-2058-0},
  keywords  = {Program Analysis; Real-time Systems; Stack Cache},
  location  = {Sophia Antipolis, France},
  numpages  = {10},
  owner     = {saulius},
  timestamp = {2015.12.16},
  creationdate = {2015-12-16T00:00:00},
  url       = {http://doi.acm.org/10.1145/2516821.2516828},
}

@Article{Jordan2013,
  author    = {Jordan, Andrew N.},
  journal   = {Nature},
  title     = {Quantum physics: Watching the wavefunction collapse},
  year      = {2013},
  issn      = {0028-0836},
  pages     = {177--178},
  volume    = {502},
  abstract  = {The continuous random path of a superconducting system's quantum state has been tracked as the state changes during measurement. The results open the possibility of steering quantum systems into a desired state.},
  doi       = {10.1038/502177a},
  file      = {2013_Jordan_177.pdf:by-author/J/Jordan/2013_Jordan_177.pdf:PDF},
  keywords  = {Quantum Mechanics (QM); Wavefunction Collapse},
  owner     = {saulius},
  publisher = {Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},
  timestamp = {2013.10.18},
  creationdate = {2013-10-18T00:00:00},
  url       = {http://dx.doi.org/10.1038/502177a},
}

@Article{Jore2011,
  author    = {Jore, Matthijs M. and Lundgren, Magnus and van Duijn, Esther and Bultema, Jelle B. and Westra, Edze R. and Waghmare, Sakharam P. and Wiedenheft, Blake and Pul, Ümit and Wurm, Reinhild and Wagner, Rolf and Beijer, Marieke R. and Barendregt, Arjan and Zhou, Kaihong and Snijders, Ambrosius P. L. and Dickman, Mark J. and Doudna, Jennifer A. and Boekema, Egbert J. and Heck, Albert J. R. and van der Oost, John and Brouns, Stan J. J.},
  journal   = {Nature structural \& molecular biology},
  title     = {Structural basis for {CRISPR} {RNA}-guided {DNA} recognition by Cascade},
  year      = {2011},
  pages     = {1545--9993},
  doi       = {10.1038/nsmb.2019},
  file      = {:by-author/J/Jore/2011_Jore_Brouns_NSMB_Cascade.pdf:PDF},
  groups    = {sg/CRISPR-Cas},
  keywords  = {CRISPR},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Jorgensen2000,
  author      = {Jorgensen, William L.},
  journal     = {Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta)},
  title       = {Perspective on "Equation of state calculations by fast computing machines"},
  year        = {2000},
  issn        = {1432-881X},
  pages       = {225--227},
  volume      = {103},
  abstract    = {An overview is given of the paper by Metropolis et al. that has formed the basis for Monte Carlo statistical mechanics simulations of atomic and molecular systems.},
  affiliation = {Department of Chemistry, Yale University, New Haven, CT 06520–8107, USA US},
  doi         = {10.1007/s002149900053},
  file        = {2000_Jorgensen_225.pdf:by-author/J/Jorgensen/2000_Jorgensen_225.pdf:PDF},
  groups      = {sg/Molecular dynamics},
  issue       = {3},
  keywords    = {Molecular Dynamics (MD); Monte Carlo},
  owner       = {saulius},
  publisher   = {Springer Berlin / Heidelberg},
  timestamp = {2011.10.21},
  creationdate = {2011-10-21T00:00:00},
  url         = {http://dx.doi.org/10.1007/s002149900053},
}

@TechReport{JOSES2000,
  author      = {JOSES},
  institution = {The JOSES Consortium},
  title       = {Tuned Dynamic Real-Time Garbage Collector},
  year        = {2000},
  file        = {:by-author/J/JOSES/2001_JOSES.pdf:PDF},
  groups      = {sg/Garbage collectors},
  keywords    = {Computer Science (CS); Garbage Collectors},
  owner       = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Joshi2006,
  author    = {Joshi, Hemant K. and Etzkorn, Christopher and Chatwell, Lorentz and Bitinaite, Jurate and Horton, Nancy C.},
  journal   = {The Journal of biological chemistry},
  title     = {Alteration of sequence specificity of the type II restriction endonuclease HincII through an indirect readout mechanism.},
  year      = {2006},
  pages     = {23852--69},
  volume    = {281},
  abstract  = {The functional and structural consequences of a mutation of the DNA intercalating residue of HincII, Q138F, are presented. Modeling has suggested that the DNA intercalation by Gln-138 results in DNA distortions potentially used by HincII in indirect readout of its cognate DNA, GTYRAC (Y = C or T, R = A or G) (Horton, N. C., Dorner, L. F., and Perona, J. J. (2002) Nat. Struct. Biol. 9, 42-47). Kinetic data presented here indicate that the mutation of glutamine 138 to phenylalanine (Q138F) results in a change in sequence specificity at the center two base pairs of the cognate recognition site. We show that the preference of HincII for cutting, but not binding, the three cognate sites differing in the center two base pairs has been altered by the mutation Q138F. Five new crystal structures are presented including Q138F HincII bound to GTTAAC and GTCGAC both with and without Ca2+ as well as the structure of wild type HincII bound to GTTAAC. The Q138F HincII/DNA structures show conformational changes in the protein, bound DNA, and at the protein-DNA interface, consistent with the formation of adaptive complexes. Analysis of these structures and the effect of Ca2+ binding on the protein-DNA interface illuminates the origin of the altered specificity by the mutation Q138F in the HincII enzyme.},
  file      = {:by-author/J/Joshi/2006_Joshi_23852.pdf:PDF},
  keywords  = {DNA Conf; Indirect; Readout; TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Joshi2006a,
  author      = {Hemant K Joshi and Christopher Etzkorn and Lorentz Chatwell and Jurate Bitinaite and Nancy C Horton},
  journal     = {J Biol Chem},
  title       = {Alteration of sequence specificity of the type II restriction endonuclease HincII through an indirect readout mechanism.},
  year        = {2006},
  month       = {Aug},
  number      = {33},
  pages       = {23852--23869},
  volume      = {281},
  abstract    = {The functional and structural consequences of a mutation of the DNA intercalating residue of HincII, Q138F, are presented. Modeling has suggested that the DNA intercalation by Gln-138 results in DNA distortions potentially used by HincII in indirect readout of its cognate DNA, GTYRAC (Y = C or T, R = A or G) (Horton, N. C., Dorner, L. F., and Perona, J. J. (2002) Nat. Struct. Biol. 9, 42-47). Kinetic data presented here indicate that the mutation of glutamine 138 to phenylalanine (Q138F) results in a change in sequence specificity at the center two base pairs of the cognate recognition site. We show that the preference of HincII for cutting, but not binding, the three cognate sites differing in the center two base pairs has been altered by the mutation Q138F. Five new crystal structures are presented including Q138F HincII bound to GTTAAC and GTCGAC both with and without Ca2+ as well as the structure of wild type HincII bound to GTTAAC. The Q138F HincII/DNA structures show conformational changes in the protein, bound DNA, and at the protein-DNA interface, consistent with the formation of adaptive complexes. Analysis of these structures and the effect of Ca2+ binding on the protein-DNA interface illuminates the origin of the altered specificity by the mutation Q138F in the HincII enzyme.},
  doi         = {10.1074/jbc.M512339200},
  file        = {2006_Joshi_23852.pdf:by-author/J/Joshi/2006_Joshi_23852.pdf:PDF},
  institution = {Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, Arizona 85721, USA.},
  keywords    = {Amino Acid Substitution; Bacterial; Bacterial Proteins; Base Sequence; Calcium; Crystallography; DNA; Deoxyribonucleases; Glutamine; Haemophilus Influenzae; Hydrolysis; Intercalating Agents; Kinetics; Mutagenesis; Nucleic Acid Conformation; Phenylalanine; Protein Binding; Site-Directed; Substrate Specificity; Type II Site-Specific; X-Ray},
  owner       = {em},
  pii         = {M512339200},
  pmid        = {16675462},
  timestamp = {2011.06.10},
  creationdate = {2011-06-10T00:00:00},
  url         = {http://dx.doi.org/10.1074/jbc.M512339200},
}

@Manuscript{Joyce2008,
  author    = {Joyce},
  title     = {A First Principles Theory of Nuclear Magnetic Resonance J-Coupling in solid-state systems.},
  year      = {2008},
  keywords  = {NMR},
  file      = {:by-author/J/Joyce/2008_Joyce_manuscript.pdf:PDF},
  owner     = {saulius},
  pages     = {manuscript},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Joyce2000,
  author    = {Gerald F. Joyce},
  journal   = {Science},
  title     = {Ribozyme Evolution at the Crossroads},
  year      = {2000},
  pages     = {401--402},
  volume    = {289},
  doi       = {10.1126/science.289.5478.401},
  file      = {:by-author/J/Joyce/2000_Joyce_401.war:},
  keywords  = {Ribozymes},
  owner     = {saulius},
  timestamp = {2015.03.02},
  creationdate = {2015-03-02T00:00:00},
}

@Article{Juers2004,
  author    = {Juers, Douglas H. and Matthews, Brian W.},
  journal   = {Acta Crystallographica Section D},
  title     = {The role of solvent transport in cryo-annealing of macromolecular crystals},
  year      = {2004},
  pages     = {412--421},
  volume    = {60},
  doi       = {10.1107/S0907444903027938},
  file      = {fw5003.pdf:by-author/J/Juers/2004_Juers_412.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444903027938},
}

@Article{Juers2001,
  author           = {Douglas H. Juers and Brian W. Matthews},
  journal          = {Journal of Molecular Biology},
  title            = {Reversible lattice repacking illustrates the temperature dependence of macromolecular interactions},
  year             = {2001},
  issn             = {0022-2836},
  pages            = {851--862},
  volume           = {311},
  abstract         = {Flash-freezing, which has become routine in macromolecular X-ray crystallography, causes the crystal to contract substantially. In the case of Escherichia coli β-galactosidase the changes are reversible and are shown to be due to lattice repacking. On cooling, the area of the protein surface involved in lattice contacts increases by 50%. There are substantial alterations in intermolecular contacts, these changes being dominated by the long, polar side-chains. For entropic reasons such side-chains, as well as surface solvent molecules, tend to be somewhat disordered at room temperature but can form extensive hydrogen-bonded networks on cooling. Low-temperature density measurements suggest that, at least in some cases, the beneficial effect of cryosolvents may be due to a density increase on vitrification which reduces the volume of bulk solvent that needs to be expelled from the crystal. Analysis of β-galactosidase and several other proteins suggests that both intramolecular and intermolecular contact interfaces can be perturbed by cryocooling but that the changes tend to be more dramatic in the latter case. The temperature-dependence of the intermolecular interactions suggests that caution may be necessary in interpreting protein-protein and protein-nucleic acid interactions based on low-temperature crystal structures.},
  creationdate     = {2013-03-25T00:00:00},
  doi              = {10.1006/jmbi.2001.4891},
  file             = {2001_Juers_851.pdf:by-author/J/Juers/2001_Juers_851.pdf:PDF},
  keywords         = {Contraction; Cryo Cooling; Macromolecular Interactions; Protein Crystallography; Vitrification; X-ray Crystallography; β-galactosidase},
  modificationdate = {2023-05-02T10:19:00},
  owner            = {saulius},
  timestamp        = {2013.03.25},
  url              = {http://www.sciencedirect.com/science/article/pii/S0022283601948910},
}

@Article{Juhas2010a,
  author    = {Juhas, Pavol and Granlund, Luke and Gujarathi, Saurabh R. and Duxbury, Phillip M. and Billinge, Simon JL},
  journal   = {Journal of Applied Crystallography},
  title     = {Crystal structure solution from experimentally determined atomic pair distribution functions},
  year      = {2010},
  pages     = {623--629},
  volume    = {43},
  file      = {[PDF] from arxiv.org:by-author/J/Juhas/2010_Juhas_623.pdf:application/pdf},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://scripts.iucr.org/cgi-bin/paper?wf5062},
  urldate   = {2015-08-31},
}

@Article{Juhas2010,
  author    = {Juhás, P. and Granlund, L. and Gujarathi, S. R. and Duxbury, P. M. and Billinge, S. J. L.},
  journal   = {Journal of Applied Crystallography},
  title     = {Crystal structure solution from experimentally determined atomic pair distribution functions},
  year      = {2010},
  pages     = {623--629},
  volume    = {43},
  abstract  = {An extension of the Liga algorithm for structure solution from atomic pair distribution functions (PDFs), to handle periodic crystal structures with multiple elements in the unit cell, is described. The procedure is performed in three separate steps. First, pair distances are extracted from the experimental PDF. In the second step the Liga algorithm is used to find unit-cell sites consistent with these pair distances. Finally, the atom species are assigned over the cell sites by minimizing the overlap of their empirical atomic radii. The procedure has been demonstrated on synchrotron X-ray PDF data from 16 test samples. The structure solution was successful for 14 samples, including cases with enlarged supercells. The algorithm success rate and the reasons for the failed cases are discussed, together with enhancements that should improve its convergence and usability.},
  doi       = {10.1107/S002188981000988X},
  file      = {:by-author/J/Juhás/2010_Juhás_623.pdf:PDF},
  keywords  = {COD Citations; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
  url       = {http://dx.doi.org/10.1107/S002188981000988X},
}

@Article{Jung1997,
  author    = {Jung, Ok-Sang and Jo, Du Hwan and Lee, Young-A and Conklin, Brenda J. and Pierpont, Cortlandt G.},
  journal   = {Inorganic Chemistry},
  title     = {Bistability and molecular switching for semiquinone and catechol complexes of cobalt. studies on redox isomerism for the bis(pyridine) ether series {Co}(py2X)(3,6-{DBQ})2, {X} = {O}, {S}, {Se}, and {Te}},
  year      = {1997},
  issn      = {0020-1669},
  pages     = {19--24},
  volume    = {36},
  abstract  = {Intramolecular electron transfer between CoII(SQ) and CoIII(Cat) species has been investigated for the series of complexes Co(py2X)(3,6-DBQ)2, where 3,6-DBQ are semiquinonate and catecholate forms of 3,6-di-tert-butyl-1,2-benzoquinone and py2X is bis(pyridine) ether and its heteroatomic analogs with X = S, Se, and Te. Transition temperature for Co(III)/Co(II) redox isomerism decreases in steps of approximately 30 K in toluene solution and in steps of 80 K in the solid state for the complexes with X = S, Se, Te. This appears to be primarily associated with an entropy increase that results from low-energy shifts in vibrational modes with increasing heteroatomic mass. Complexes containing py2O have been isolated at room temperature in two charge distributions, CoII(py2O)(3,6-DBSQ)2 and CoIII(py2O)(3,6-DBSQ)(3,6-DBCat). Crystallographic characterization on both forms of the complex [CoII(py2O)(3,6-DBSQ)2, monoclinic, P21/c, a = 11.0280(2) Å, b = 30.2750(9) Å, c = 12.1120(2) Å, ? = 113.490(2)°, V = 3708.7(1) Å3, Z = 4, R = 0.056; CoIII(py2O)(3,6-DBSQ)(3,6-DBCat), monoclinic, P21/n, a = 9.882(3) Å, b = 20.915(5) Å, c = 17.579(4) Å, ? = 91.57(2)°, V = 3632(2) Å3, Z = 4, R = 0.054] has shown that the py2O ligand adopts a planar structure for the Co(II) isomer that shifts to a folded, nonplanar structure with the smaller Co(III) ion. This structural change is responsible for hysteresis in the Co(III) ? Co(II) and Co(II) ? Co(III) electron transfer steps in the solid state. Optically induced shifts in charge distribution have been investigated using a low-energy polychromatic light source.},
  doi       = {10.1021/ic961214d},
  file      = {Jung et al. - 1997 - Bistability and Molecular Switching for Semiquinon.pdf:by-author/J/Jung/1997_Jung_19.pdf:application/pdf;ACS Full Text Snapshot:by-author/J/Jung/1997_Jung_19.html:text/html},
  groups    = {sg/chemical},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://dx.doi.org/10.1021/ic961214d},
  urldate   = {2015-08-21},
}

@Article{Jung2011,
  author    = {Jung, Suhyun and Kim, Youngmee and Kim, Sung-Jin and Kwon, Tae-Hwan and Huh, Seong and Park, Seongsoon},
  journal   = {Chemical communications (Cambridge, England)},
  title     = {Bio-functionalization of metal-organic frameworks by covalent protein conjugation.},
  year      = {2011},
  pages     = {2904--6},
  volume    = {47},
  abstract  = {Bioconjugation of functional proteins onto metal-organic frameworks (MOFs) has been achieved using activation of pendent linking groups of the organic linkers on the surface of MOFs. Fluorescent microscopy revealed successful conjugation of an enhanced fluorescent protein onto MOFs. In addition, Candida-antarctica-lipase-B-conjugated MOFs showed no loss of enantioselectivity and activity in transesterification of (±)-1-phenylethanol.},
  doi       = {10.1039/C0CC03288C},
  file      = {:by-author/J/Jung/2011_Jung_2904.pdf:PDF},
  groups    = {sg/MOF, sg/MOFs, am/MOFs},
  keywords  = {Bioconjugation; Metal-Organic Frameworks (MOF); Proteins},
  owner     = {saulius},
  timestamp = {2013.01.05},
  creationdate = {2013-01-05T00:00:00},
}

@Article{Jurenaite-Urbanaviciene2001,
  author    = {Jurenaite-Urbanaviciene, S. and Kazlauskiene, R. and Urbelyte, V. and Maneliene, Z. and Petrusyte, M. and Lubys, A. and Janulaitis, A.},
  journal   = {Nucleic acids research},
  title     = {Characterization of BseMII, a new type IV restriction-modification system, which recognizes the pentanucleotide sequence 5'-CTCAG(N)(10/8)/.},
  year      = {2001},
  pages     = {895--903},
  volume    = {29},
  abstract  = {We report the properties of the new BseMII restriction and modification enzymes from Bacillus stearothermophilus Isl 15-111, which recognize the 5'-CTCAG sequence, and the nucleotide sequence of the genes encoding them. The restriction endonuclease R.BseMII makes a staggered cut at the tenth base pair downstream of the recognition sequence on the upper strand, producing a two base 3'-protruding end. Magnesium ions and S:-adenosyl-L-methionine (AdoMet) are required for cleavage. S:-adenosylhomocysteine and sinefungin can replace AdoMet in the cleavage reaction. The BseMII methyltransferase modifies unique adenine residues in both strands of the target sequence 5'-CTCAG-3'/5'-CTGAG-3'. Monomeric R.BseMII in addition to endonucleolytic activity also possesses methyltransferase activity that modifies the A base only within the 5'-CTCAG strand of the target duplex. The deduced amino acid sequence of the restriction endonuclease contains conserved motifs of DNA N6-adenine methylases involved in S-adenosyl-L-methionine binding and catalysis. According to its structure and enzymatic properties, R.BseMII may be regarded as a representative of the type IV restriction endonucleases.},
  file      = {:by-author/J/Jurenaite-Urbanaviciene/2001_Jurenaite-Urbanaviciene_895.pdf:PDF},
  keywords  = {McrBC},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Jurenaite-Urbanaviciene2007,
  author    = {Jurenaite-Urbanaviciene, Sonata and Serksnaite, Jurgita and Kriukiene, Edita and Giedriene, Jolanta and Venclovas, Ceslovas and Lubys, Arvydas},
  journal   = {Proceedings of the National Academy of Sciences of the United States of America},
  title     = {Generation of DNA cleavage specificities of type II restriction endonucleases by reassortment of target recognition domains.},
  year      = {2007},
  number    = {25},
  pages     = {10358--10363},
  volume    = {104},
  abstract  = {Type II restriction endonucleases (REases) cleave double-stranded DNA at specific sites within or close to their recognition sequences. Shortly after their discovery in 1970, REases have become one of the primary tools in molecular biology. However, the list of available specificities of type II REases is relatively short despite the extensive search for them in natural sources and multiple attempts to artificially change their specificity. In this study, we examined the possibility of generating cleavage specificities of REases by swapping putative target recognition domains (TRDs) between the type IIB enzymes AloI, PpiI, and TstI. Our results demonstrate that individual TRDs recognize distinct parts of the bipartite DNA targets of these enzymes and are interchangeable. Based on these properties, we engineered a functional type IIB REase having previously undescribed DNA specificity. Our study suggests that the TRD-swapping approach may be used as a general technique for the generation of type II enzymes with predetermined specificities.},
  doi       = {10.1073/pnas.0610365104},
  file      = {:by-author/J/Jurenaite-Urbanaviciene/2007_Jurenaite-Urbanaviciene_10358.pdf:PDF},
  groups    = {sg/TstI},
  keywords  = {IIB; TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Presentation{Jurgutis2013,
  author       = {Marijus Jurgutis},
  title        = {Nacionalinis mokslo tyrimų duomenų skaitmeninis archyvas},
  year         = {2013},
  conference   = {Kompiuterininkų dienos KoDi2011},
  organization = {Vilniaus Universitetas},
  comment      = {Finansavimo nuoroda: http://www.esparama.lt/kvietimas?id=090bdd53800ff10c},
  file         = {:by-author/J/Jurgutis/2012_Jurgutis_slides.pdf:PDF},
  keywords     = {Data Access Policy; Data Management; Databases; MIDAS; Scientific Data Dissemination},
  owner        = {saulius},
  timestamp = {2013.04.16},
  creationdate = {2013-04-16T00:00:00},
  url          = {ftp://ftp.science.mii.lt/pub/KoDi2011/Mokslines_kompiuterininku_konf_pranesimai/2_Jurgutis.pdf},
}

@Presentation{Jorgensen2006,
  author       = {Jørgensen},
  title        = {Electrospray Ionization Mass Spectrometry},
  year         = {2006},
  organization = {Institut for Biokemi og Molekylær Biologi},
  school       = {Syddansk Universitet},
  file         = {:by-author/J/Jørgensen/2006_Jørgensen_slides.pdf:PDF},
  owner        = {saulius},
  pages        = {slides},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Kvrivy1976,
  author    = {K{\v{r}}iv{\'{y}}, I. and Gruber, B.},
  journal   = {Acta Crystallographica Section A},
  title     = {A unified algorithm for determining the reduced (Niggli) cell},
  year      = {1976},
  pages     = {297--298},
  volume    = {32},
  abstract  = {An algorithm is proposed which enables one, starting from an arbitrary primitive cell of a three-dimensional Bravais lattice, to reach the Niggli form requisite for the lattice type determination.},
  doi       = {10.1107/S0567739476000636},
  file      = {:by-author/K/Krivy/1976_Krivy_297.pdf:PDF},
  keywords  = {Algorithms; Niggli Cell; Reduced Cell; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2014.03.27},
  creationdate = {2014-03-27T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0567739476000636},
}

@Article{Ka1996,
  author    = {Ka},
  title     = {The Binding Energy of HIV-1 Protease Inhibitor},
  year      = {1996},
  pages     = {19},
  file      = {:by-author/K/Ka/1996_Ka_19.pdf:PDF},
  keywords  = {Protein Ligand Complexes},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Manual{Kabsch2016,
  title        = {XDS Manual},
  author       = {Wolfgang Kabsch},
  organization = {MPI for Medical Research, Heidelberg},
  year         = {2016},
  file         = {2016_Kabsch_XDS-manual.pdf:by-author/K/Kabsch/2016_Kabsch_XDS-manual.pdf:PDF;2016_Kabsch_XDS-manual.odt:by-author/K/Kabsch/2016_Kabsch_XDS-manual.odt:OpenDocument text},
  keywords     = {Data Reduction; Reflection Integration; Software; X-ray Crystallography; XDS},
  owner        = {saulius},
  timestamp = {2016.12.21},
  creationdate = {2016-12-21T00:00:00},
  url          = {http://xds.mpimf-heidelberg.mpg.de/},
}

@Article{Kabsch2010,
  author    = {Kabsch, Wolfgang},
  journal   = {Acta Crystallographica Section D},
  title     = {XDS},
  year      = {2010},
  pages     = {125–132},
  volume    = {D66},
  doi       = {10.1107/S0907444909047337},
  file      = {:by-author/K/Kabsch/2010_Kabsch_125.pdf:PDF},
  keywords  = {Crystal Structure; Data Processing; Integration; XDS},
  owner     = {em},
  timestamp = {2013.10.02},
  creationdate = {2013-10-02T00:00:00},
}

@Article{Kabsch1978,
  author    = {Wolfgang Kabsch},
  journal   = {Acta Crystallographica Section A},
  title     = {A discussion of the solution for the best rotation to relate two sets of vectors},
  year      = {1978},
  pages     = {827--828},
  volume    = {34},
  abstract  = {A method is discussed for obtaining the best proper rotation to relate two sets of vectors.},
  doi       = {10.1107/S0567739478001680},
  file      = {:by-author/K/Kabsch/1978_Kabsch_827.pdf:PDF},
  groups    = {sg/Molecule superposion, sg/Superposition, sg/Bioinf. Algorithms},
  keywords  = {Algorithms; Structure Superposition; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://scripts.iucr.org/cgi-bin/paper?a15629},
}

@Article{Kabsch1976,
  author    = {Wolfgang Kabsch},
  journal   = {Acta Crystallographica Section A},
  title     = {A solution for best rotation to relate two sets of vectors},
  year      = {1976},
  pages     = {922--923},
  volume    = {32},
  abstract  = {A simple procedure is derived which determines a best rotation of a given vector set into a second vector set by minimizing the weighted sum of squared deviations. The method is generalized for any given metric constraint on the transformation.},
  doi       = {10.1107/S0567739476001873},
  file      = {:by-author/K/Kabsch/1976_Kabsch_922.pdf:PDF},
  groups    = {sg/Molecule superposion, sg/Superposition, sg/Bioinf. Algorithms},
  keywords  = {Algorithms; Structure Superposition; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://scripts.iucr.org/cgi-bin/paper?S0567739476001873},
}

@Article{Kachalova2008,
  author     = {Galina S. Kachalova and Eugeny A. Rogulin and Alfiya K. Yunusova and Rimma I. Artyukh and Tatyana A. Perevyazova and Nickolay I. Matvienko and Ludmila A. Zheleznaya and Hans D. Bartunik},
  journal    = {Journal of molecular biology},
  title      = {Structural Analysis of the Heterodimeric Type IIS Restriction Endonuclease R.BspD6I Acting as a Complex between a Monomeric Site-specific Nickase and a Catalytic Subunit},
  year       = {2008},
  pages      = {489--502},
  volume     = {384},
  abstract   = {The heterodimeric restriction endonuclease R.BspD6I from Bacillus species D6 recognizes a pseudosymmetric sequence and cuts both DNA strands outside the recognition sequence. The large subunit, Nt.BspD6I, acts as a type IIS site-specific monomeric nicking endonuclease. The isolated small subunit, ss.BspD6I, does not bind DNA and is not catalytically active. We solved the crystal structures of Nt.BspD6I and ss.BspD6I at high resolution. Nt.BspD6I consists of three domains, two of which exhibit structural similarity to the recognition and cleavage domains of FokI. ss.BspD6I has a fold similar to that of the cleavage domain of Nt.BspD6I, each containing a PD-(D/E)XK motif and a histidine as an additional putative catalytic residue. In contrast to the DNA-bound FokI structure, in which the cleavage domain is rotated away from the DNA, the crystal structure of Nt.BspD6I shows the recognition and cleavage domains in favorable orientations for interactions with DNA. Docking models of complexes of Nt.BspD6I and R.BspD6I with cognate DNA were constructed on the basis of structural similarity to individual domains of FokI, R.BpuJI and HindIII. A three-helix bundle forming an interdomain linker in Nt.BspD6I acts as a rigid spacer adjusting the orientations of the spatially separated domains to match the distance between the recognition and cleavage sites accurately.},
  doi        = {10.1016/j.jmb.2008.09.033},
  file       = {Bsp_struktura_2008.pdf:by-author/K/Kachalova/2008_Kachalova_489.pdf:PDF},
  keywords   = {FokI; Nicking Endonuclease; Protein-DNA Complex; Restriction Enzyme; X Ray Crystal Structure},
  owner      = {saulius},
  publishers = {Elsevier Ltd},
  timestamp = {2011.12.07},
  creationdate = {2011-12-07T00:00:00},
}

@Article{Kaduk2002,
  author    = {Kaduk, James A},
  journal   = {Acta crystallographica. Section B, Structural science},
  title     = {Use of the Inorganic Crystal Structure Database as a problem solving tool.},
  year      = {2002},
  pages     = {370--9},
  volume    = {58},
  file      = {2002_Kaduk_370.pdf:by-author/K/Kaduk/2002_Kaduk_370.pdf:PDF},
  keywords  = {For COD Deposition; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Kadyrov2002,
  author    = {Kadyrov, Farid A. and Drake, John W.},
  journal   = {Nucleic acids research},
  title     = {Characterization of DNA synthesis catalyzed by bacteriophage T4 replication complexes reconstituted on synthetic circular substrates.},
  year      = {2002},
  pages     = {4387--97},
  volume    = {30},
  abstract  = {Replication complexes were reconstituted using the eight purified bacteriophage T4 replication proteins and synthetic circular 70-, 120- or 240-nt DNA substrates annealed to a leading-strand primer. To differentiate leading strands from lagging strands, the circular parts of the substrates lacked dCMP; thus, no dCTP was required for leading-strand synthesis and no dGTP for lagging-strand synthesis. The size of the substrates was crucial, the longer substrates supporting much more DNA synthesis. Leading and lagging strands were synthesized in a coupled manner. Specifically targeting leading-strand synthesis by decreasing the concentration of dGTP decreased the rate of extension of leading strands. However, blocking lagging-strand synthesis by lowering the dCTP concentration, by omitting dCTP altogether, by adding ddCTP, or with a single abasic site had no immediate effect on the rate of extension of leading strands.},
  file      = {:by-author/K/Kadyrov/2002_Kadyrov_4387.pdf:PDF},
  keywords  = {Replisoma; {gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Kadyrov2001a,
  author    = {Kadyrov, F. A. and Drake, J. W.},
  journal   = {The Journal of biological chemistry},
  title     = {Conditional coupling of leading-strand and lagging-strand DNA synthesis at bacteriophage T4 replication forks.},
  year      = {2001},
  pages     = {29559--66},
  volume    = {276},
  abstract  = {Eight proteins encoded by bacteriophage T4 are required for the replicative synthesis of the leading and lagging strands of T4 DNA. We show here that active T4 replication forks, which catalyze the coordinated synthesis of leading and lagging strands, remain stable in the face of dilution provided that the gp44/62 clamp loader, the gp45 sliding clamp, and the gp32 ssDNA-binding protein are present at sufficient levels after dilution. If any of these accessory proteins is omitted from the dilution mixture, uncoordinated DNA synthesis occurs, and/or large Okazaki fragments are formed. Thus, the accessory proteins must be recruited from solution for each round of initiation of lagging-strand synthesis. A modified bacteriophage T7 DNA polymerase (Sequenase) can replace the T4 DNA polymerase for leading-strand synthesis but not for well coordinated lagging-strand synthesis. Although T4 DNA polymerase has been reported to self-associate, gel-exclusion chromatography displays it as a monomer in solution in the absence of DNA. It forms no stable holoenzyme complex in solution with the accessory proteins or with the gp41-gp61 helicase-primase. Instead, template DNA is required for the assembly of the T4 replication complex, which then catalyzes coordinated synthesis of leading and lagging strands in a conditionally coupled manner.},
  file      = {:by-author/K/Kadyrov/2001_Kadyrov_29559.pdf:PDF},
  keywords  = {{gp41}; {gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Kagaya1999,
  author      = {Y. Kagaya and K. Ohmiya and T. Hattori},
  journal     = {Nucleic Acids Res},
  title       = {RAV1, a novel DNA-binding protein, binds to bipartite recognition sequence through two distinct DNA-binding domains uniquely found in higher plants.},
  year        = {1999},
  pages       = {470--478},
  volume      = {27},
  abstract    = {We have cloned and characterized two novel DNA binding proteins designated RAV1 and RAV2 from Arabidopsis thaliana. RAV1 and RAV2 contain two distinct amino acid sequence domains found only in higher plant species. The N-terminal regions of RAV1 and RAV2 are homologous to the AP2 DNA-binding domain present in a family of transcription factors represented by the Arabidopsis APETALA2 and tobacco EREBP proteins, while the C-terminal region exhibits homology to the highly conserved C-terminal domain, designated B3, of VP1/ABI3 transcription factors. Binding site selection assays using a recombinant glutathione S-transferase fusion protein have revealed that RAV1 binds specifically to bipartite recognition sequences composed of two unrelated motifs, 5'-CAACA-3' and 5'-CACCTG-3', separated by various spacings in two different relative orientations. Analyses using various deletion derivatives of the RAV1 fusion protein show that the AP2 and B3-like domains of RAV1 bind autonomously to the CAACA and CACCTG motifs, respectively, and together achieve a high affinity and specificity of binding. From these results, we suggest that the AP2 and B3-like domains of RAV1 are connected by a highly flexible structure enabling the two domains to bind to the CAACA and CACCTG motifs in various spacings and orientations.},
  file        = {:by-author/K/Kagaya/1999_Kagaya_470.pdf:PDF},
  institution = {Center for Molecular Biology and Genetics and Department of Bioresources, School of Bioresources, Mie University, 1515 Kamihama-cho, Tsu 514-8507, Japan.},
  keywords    = {Amino Acid; Amino Acid Sequence; Angiosperms; Arabidopsis; Arabidopsis Proteins; B3; Binding Sites; DNA-Binding Proteins; Genetics; Genetics/metabolism; Molecular Sequence Data; Plant Proteins; Protein Binding; Protein Conformation; RAV1; Sequence Homology; Trans-Activators; Transcription Factor AP-2; Transcription Factors},
  language    = {eng},
  medline-pst = {ppublish},
  owner       = {em},
  pii         = {gkc132},
  pmid        = {9862967},
  timestamp = {2013.09.04},
  creationdate = {2013-09-04T00:00:00},
}

@Manuscript{Kahan2006,
  author    = {William Kahan},
  title     = {How Futile are Mindless Assessments of Roundoff in Floating-Point Computation ?},
  year      = {2006},
  keywords  = {Computer Science (CS); Floating Point Arithmetics},
  month     = {jan},
  url       = {http://www.cs.berkeley.edu/~wkahan/Mindless.pdf},
  abstract  = {Redesigning computers costs less than retraining people, so it behooves us to adapt computers to the way people have evolved rather than try to adapt people to the way computers have evolved. As the population of computer programmers has grown, proficiency in rounding-error analysis has dwindled. To compensate, better diagnostic aids should be incorporated into hardware, into program development environments, and into programming languages; but this is not happening. Schemes to assist roundoff analysis are beset by failure modes; no scheme is foolproof; only two or three are worth trying. Alas, these few rely upon hardware features built into IEEE Standard 754 for binary floating-point but now atrophying for lack of adequate linguistic support. Here extensive analyses of the genesis of embarrassment due to roundoff, and of the failure modes of all schemes devised so far to avert it, point clearly to what needs doing next.},
  file      = {:by-author/K/Kahan/2006_Kahan.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.09.27},
  creationdate = {2012-09-27T00:00:00},
}

@Article{Kahle1989,
  author    = {Kahle, B.A. and Hillis, W.D.},
  journal   = {IEEE Trans. Syst., Man, Cybern.},
  title     = {The Connection Machine model CM-1 architecture},
  year      = {1989},
  issn      = {0018-9472},
  number    = {4},
  pages     = {707--713},
  volume    = {19},
  doi       = {10.1109/21.35335},
  file      = {1989_Kahle_707.pdf:by-author/K/Kahle/1989_Kahle_707.pdf:PDF},
  groups    = {sg/Connection Machine},
  keywords  = {Computer Architecture; Computer Science (CS); Computing History; Hardware; Lisp; Parallel Computations; Star Lisp; Supercomputers},
  owner     = {saulius},
  publisher = {Institute of Electrical \& Electronics Engineers (IEEE)},
  timestamp = {2016.06.16},
  creationdate = {2016-06-16T00:00:00},
  url       = {http://dx.doi.org/10.1109/21.35335},
}

@Article{Kahn1962,
  author    = {Kahn, A. B.},
  journal   = {Communications of the ACM},
  title     = {Topological sorting of large networks},
  year      = {1962},
  issn      = {0001-0782},
  month     = {Nov},
  number    = {11},
  pages     = {558–562},
  volume    = {5},
  doi       = {10.1145/368996.369025},
  file      = {:by-author/K/Kahn/1989_Kahn_185.pdf:PDF},
  owner     = {andrius},
  publisher = {Association for Computing Machinery (ACM)},
  timestamp = {2016.02.23},
  creationdate = {2016-02-23T00:00:00},
  url       = {http://dx.doi.org/10.1145/368996.369025},
}

@Article{Kahn1989,
  author    = {Peter C. Kahn},
  journal   = {Computers \& Chemistry},
  title     = {Defining the Axis of a Helix},
  year      = {1989},
  pages     = {185--189},
  volume    = {13},
  abstract  = {A simple method for finding the axis of a helix is presented. Although described in terms of protein alpha helices, the method is generally applicable to helices whose defining units are more or less regularly spaced. Absolute mathematical regularity of the helical parameters is not required. The procedure can be applied at several levels of rigor. At its simplest it involves simple vector operations only and yields two points that define the axis along with the axis direction cosines. No regression analysis is needed. The minimum length helix required for the algorithm is four residues, which define an axis segment between residues 2 and 3. In its more rigorous form the algorithm scans along the chain one residue at a time, yielding a set of axis segments to which a linear least squares regression fits the axis. Non-linear, iterative procedures are not necessary. For each consecutive set of four residues the pitch, radius, rise per residue, rotation per residue about the axis and number of residues per turn are also obtained. Methods are also outlined for distinguishing between smoothly curved and sharply kinked helices and for extracting from these structures the radius of curvature and the location and angle of the kink.},
  doi       = {10.1016/0097-8485(89)85005-3},
  file      = {:by-author/K/Kahn/1989_Kahn_185.pdf:PDF},
  keywords  = {Helical Parameters; Protein Bioinformatics},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/0097848589850053},
}

@Article{Kaindl1997,
  author           = {Kaindl, K. and Steipe, B.},
  journal          = {Acta Crystallographica Section A},
  title            = {Metric properties of the root-mean-square deviation of vector sets},
  year             = {1997},
  pages            = {809},
  volume           = {53},
  abstract         = {A proof is given that the root-mean-square deviation between more than two vector sets after optimal superposition induces a metric.},
  comment          = {From Steipe2002: A previous communication to this effect (Kaindl & Steipe, 1997) contains a technical error that invalidates the proof that the RMSD opt is a metric (see Steipe, 2002, for an Erratum). "After optimal superposition, the vector set centroids coincide." Contradicts Chen2004?},
  creationdate     = {2013-03-22T00:00:00},
  doi              = {10.1107/S0108767397010325},
  file             = {1997_Kaindl_809.pdf:by-author/K/Kaindl/1997_Kaindl_809.pdf:PDF},
  groups           = {sg/Molecule superposion, sg/Superposition, sg/Bioinf. Algorithms},
  keywords         = {Algorithms; Proof; RMSD; Structure Superposition},
  modificationdate = {2024-05-12T19:22:44},
  owner            = {saulius},
  timestamp        = {2013.03.22},
  url              = {http://dx.doi.org/10.1107/S0108767397010325},
}

@Presentation{Kaiser2010,
  author    = {Timothy H. Kaiser},
  title     = {OpenMP an Overview},
  year      = {2010},
  school    = {School of Mines, Colorado},
  file      = {:by-author/K/Kaiser/2010_Kaiser.pdf:PDF},
  owner     = {saulius},
  timestamp = {2013.07.02},
  creationdate = {2013-07-02T00:00:00},
}

@Article{Kalantari2015,
  author    = {Kalantari, Roya and Chiang, Cheng-Ming and Corey, David R.},
  journal   = {Nucleic Acids Research},
  title     = {Regulation of mammalian transcription and splicing by Nuclear RNAi},
  year      = {2015},
  issn      = {1362-4962},
  month     = {Nov},
  number    = {2},
  pages     = {524–537},
  volume    = {44},
  doi       = {10.1093/nar/gkv1305},
  file      = {:by-author/K/Kalantari/2015_Kalantari_524.pdf:PDF},
  groups    = {am/RNA activation},
  owner     = {andrius},
  publisher = {Oxford University Press (OUP)},
  timestamp = {2016.09.10},
  creationdate = {2016-09-10T00:00:00},
  url       = {http://dx.doi.org/10.1093/nar/gkv1305},
}

@Article{Kalas2010,
  author    = {Matúš Kalaš and Puntervoll, P. and Joseph, A. and Bartaseviciute, E. and Topfer, A. and Venkataraman, P. and Pettifer, S. and Bryne, J. C. and Ison, J. and Blanchet, C. and Kristoffer Rapacki and Inge Jonassen},
  journal   = {Bioinformatics},
  title     = {BioXSD: the common data-exchange format for everyday bioinformatics web services},
  year      = {2010},
  issn      = {1460-2059},
  month     = {Sep},
  number    = {18},
  pages     = {i540--i546},
  volume    = {26},
  doi       = {10.1093/bioinformatics/btq391},
  file      = {2010_Kalas_i540.pdf:by-author/K/Kalaš/2010_Kalaš_i540.pdf:PDF;XML Schema:by-author/K/Kalaš/2010_Kalaš_i540.0.xsd:XML},
  owner     = {saulius},
  publisher = {Oxford University Press (OUP)},
  timestamp = {2017.04.02},
  creationdate = {2017-04-02T00:00:00},
  url       = {http://dx.doi.org/10.1093/bioinformatics/btq391},
}

@Article{Kalinowski2003,
  author    = {Kalinowski, Jorn and Bathe, Brigitte and Bartels, Daniela and Bischoff, Nicole and Bott, Michael and Burkovski, Andreas and Dusch, Nicole and Eggeling, Lothar and Eikmanns,Bernhard J. and Gaigalat. Lars and Goesmann, Alexander and Hartmann, Michael and Huthmacher, Klaus and Kramer, Reinhard and Linke, Burkhard and McHardy, Alice C. and Meyer, Folker and Mockel, Bettina and Pfefferle, Walter and Puhler, Alfred and Rey, Daniel and Ruckert, Christian Ruckert and Rupp, Oliver and Sahm, Hermann and Wendisch, Volker F. and Wiegrabe, Iris and Tauch, Andreas},
  journal   = {Journal of Biotechnology},
  title     = {The complete Corynebacterium glutamicum ATCC 13032 genome sequence and its impact on the production of L-aspartate-derived amino acids and vitamins},
  year      = {2003},
  pages     = {5--25},
  volume    = {104},
  doi       = {10.1016/S0168-1656(03)00154-8},
  file      = {:by-author/K/Kalinowski/2003_Kalinowski_5.pdf:PDF},
  keywords  = {CglI; Restriction Endonuclease (RE)},
  owner     = {em},
  timestamp = {2014.05.22},
  creationdate = {2014-05-22T00:00:00},
}

@Article{Kaellberg2012,
  author    = {Morten Källberg and Haipeng Wang and Sheng Wang and Jian Peng and Zhiyong Wang and Hui Lu and Jinbo Xu},
  journal   = {Nature Protocols},
  title     = {Template-based protein structure modeling using the {RaptorX} web server},
  year      = {2012},
  pages     = {1511--1522},
  volume    = {7},
  comment   = {A key challenge of modern biology is to uncover the functional role of the protein entities that compose cellular proteomes. To this end, the availability of reliable three-dimensional atomic models of proteins is often crucial. This protocol presents a community-wide web-based method using RaptorX (http://raptorx.uchicago.edu/) for protein secondary structure prediction, template-based tertiary structure modeling, alignment quality assessment and sophisticated probabilistic alignment sampling. RaptorX distinguishes itself from other servers by the quality of the alignment between a target sequence and one or multiple distantly related template proteins (especially those with sparse sequence profiles) and by a novel nonlinear scoring function and a probabilistic-consistency algorithm. Consequently, RaptorX delivers high-quality structural models for many targets with only remote templates. At present, it takes RaptorX ~35 min to finish processing a sequence of 200 amino acids. Since its official release in August 2011, RaptorX has processed ~6,000 sequences submitted by ~1,600 users from around the world.},
  doi       = {10.1038/nprot.2012.085},
  file      = {:by-author/K/Källberg/2012_Källberg_1511.pdf:PDF},
  keywords  = {Proteins; Structure Prediction},
  owner     = {andrius},
  timestamp = {2013.12.05},
  creationdate = {2013-12-05T00:00:00},
}

@Article{Kamaeva1968,
  author    = {Kamaeva, I. G. and Serebrennikov, V. V.},
  journal   = {Journal of Structural Chemistry},
  title     = {A program for indexing x-ray diffraction patterns of polycrystalline substances with low symmetry},
  year      = {1968},
  issn      = {1573-8779},
  number    = {4},
  pages     = {625--626},
  volume    = {9},
  abstract  = {The aim of the present work was to compile a program for calculating lattice parameters from powder dia- grams for substances belonging to the m0noclinic and triclinic systems, using Ito's method [1] with subsequent refinement of the parameters by least squares refinement (LSR).},
  doi       = {10.1007/BF00738582},
  file      = {1968_Kamaeva_625.pdf:by-author/K/Kamaeva/1968_Kamaeva_625.pdf:PDF},
  groups    = {sg/Indexing, sg/Bioinf. Algorithms},
  owner     = {saulius},
  timestamp = {2016.04.12},
  creationdate = {2016-04-12T00:00:00},
  url       = {http://dx.doi.org/10.1007/BF00738582},
}

@Manuscript{Kaminsky2004,
  author    = {Kaminsky, Dan},
  title     = {{MD5} To Be Considered Harmful Someday},
  year      = {2004},
  keywords  = {Computer Science (CS); Cryptography},
  abstract  = {Joux and Wang’s multicollision attack has yielded collisions for several one-way hash algorithms. Of these, MD5 is the most problematic due to its heavy deployment, but there exists a perception that the flaws identified have no applied implications. We show that the appendability of Merkle-Damgard allows us to add any payload to the proof-of-concept hashes released by Wang et al. We then demonstrate a tool, Stripwire, that uses this capability to create two files – one which executes an arbitrary sequence of commands, the other which hides those commands with the strength of AES – both with the same MD5 hash. We show how this affects file-oriented system auditors such as Tripwire, but point out that the failure is nowhere near as catastrophic as it appears at first glance. We examine how this failure affects HMAC and Digital Signatures within Digital Rights Management (DRM) systems, and how the full attack expands into an unusual pseudo- steganographic strikeback methodology against peer to peer networks.},
  file      = {:by-author/K/Kaminsky/2004_Kaminsky.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Kaminsky2015,
  author    = {Werner Kaminsky and Trevor Snyder and Jennifer Stone-Sundberg and Peter Moeck},
  journal   = {Z. Kristallogr.},
  title     = {3D printing of representation surfaces from tensor data of KH2PO4 and low-quartz utilizing the WinTensor software},
  year      = {2015},
  pages     = {651–656},
  volume    = {230},
  doi       = {10.1515/zkri-2014-1826},
  file      = {2015_Kaminsky.pdf:by-author/K/Kaminsky/2015_Kaminsky.pdf:PDF},
  keywords  = {3D Printing; Crystallography; Teaching},
  owner     = {saulius},
  timestamp = {2015.05.08},
  creationdate = {2015-05-08T00:00:00},
}

@Manuscript{Kamisetty2010,
  author    = {Hetunandan Kamisetty and Arvind Ramanathan and Chris Bailey-Kellogg and Christopher James Langmead},
  title     = {Accounting for Conformational Entropy in Predicting Binding Free Energies of Protein-protein Interactions},
  year      = {2010},
  keywords  = {Entropy; Goblin; Protein-protein Interactions},
  url       = {http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.361.2189},
  file      = {PDF:by-author/K/Kamisetty/2010_Kamisetty_manuscript.pdf:PDF},
  owner     = {saulius},
  timestamp = {2015.08.06},
  creationdate = {2015-08-06T00:00:00},
}

@Manuscript{Kamisetty2010a,
  author    = {Hetunandan Kamisetty and Arvind Ramanathan and Chris Bailey-Kellogg and Christopher James Langmead},
  title     = {Accounting for Conformational Entropy in Predicting Binding Free Energies of Protein-protein Interactions},
  year      = {2010},
  keywords  = {Mutation; Prediction; Probabilistic Graphical Models; Protein Complex; Thermodynamics; Variational Inference},
  url       = {http://www.cs.cmu.edu/ hetu/pubs/goblin.pdf},
  abstract  = {Protein-protein interactions are governed by the change in free energy upon binding, ∆G=∆H − T ∆S. These interactions are often marginally stable, so one must examine the balance between the change in enthalpy, ∆H, and the change in entropy, ∆S, when inves- tigating known complexes, characterizing the effects of mutations, or designing optimized variants. In order to perform a large-scale study into the contribution of conformational en- tropy to binding free energy, we developed a technique called GOBLIN (Graphical mOdel for BiomoLecular INteractions) that performs physics-based free energy calculations for protein-protein complexes under both side-chain and backbone flexibility. GOBLIN uses a probabilistic graphical model that exploits conditional independencies in the Boltzmann distribution and employs variational inference techniques that approximate the free energy of binding in only a few minutes. We examined the role of conformational entropy on a benchmark set of more than 700 mutants in eight large, well-studied complexes. Our find- ings suggest that conformational entropy is important in protein-protein interactions—the root mean square error (RMSE) between calculated and experimentally measured ∆∆Gs decreases by 12% when explicit entropic contributions were incorporated. GOBLIN mod- els all atoms of the protein complex and detects changes to the binding entropy along the interface as well as positions distal to the binding interface. Our results also suggest that a variational approach to entropy calculations may be quantitatively more accurate than the knowledge-based approaches used by the well-known programs F OLD X and R OSETTA — GOBLIN ’s RMSEs are 10% and 36% lower than these programs, respectively.},
  file      = {goblin.pdf:by-author/K/Kamisetty/2010_Kamisetty.pdf:PDF},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  urldate   = {2015-07-18},
}

@Article{Kantardjiev2011,
  author    = {A. Kantardijev and B. Atanasov},
  title     = {pH-Dependent Protein Electrostatics – Hydrogen Bond Networks Perspective},
  year      = {2011},
  pages     = {155},
  file      = {:by-author/K/Kantardjiev/2011_Kantardjiev_155.pdf:PDF},
  keywords  = {Noncovalent Interactions; Protein Physics},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Kantardjieff2010a,
  author    = {Kantardjieff, Katherine},
  journal   = {Journal of Applied Crystallography},
  title     = {Pushing the boundaries of technology to educate and train the next generation of crystallographers},
  year      = {2010},
  pages     = {1276--1282},
  volume    = {43},
  abstract  = {This article describes the evolution of educational technologies, moving from the Web 1.0 to the current Web 3.0 decade, with the aim of stimulating discussion and inspiring innovative and effective crystallography education in the Web 3.0 decade. In the last 15 years, academic crystallography has largely migrated from a research specialty to a technique employed by a broad user community. This has led to the growth of and dependence on independently funded workshops and summer schools, as well as other non-traditional curricular resources for crystallography instruction, such as web pages and online courses, which allow crystallography to be self-taught. In fact, informal courses and e-learning constitute 70{--}80% of all learning today, and students expect on-demand learning. Implementing modern web technologies with sound pedagogy requires skilful integration of relevant, often disparate, resources into useful and usable frameworks, enabling learners to interact, explore new situations, and use scientific reasoning skills such as hypothesis testing and model-based reasoning. The evident disproportion in implementing contemporary technologies into our global crystallography education resources requires that we shift our focus from simply imparting subject knowledge by posting largely text-based content to empowering students with the fundamental processes and skills needed for on-demand learning and practice in crystallography.},
  doi       = {10.1107/S0021889810027494},
  file      = {2010_Kantardjieff_1276.pdf:by-author/K/Kantardjieff/2010_Kantardjieff_1276.pdf:PDF},
  keywords  = {Crystallographic Education; Cyberinfrastructure; E-learning; Educational Technology; Web 2.0; Web 3.0},
  owner     = {saulius},
  timestamp = {2015.04.03},
  creationdate = {2015-04-03T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0021889810027494},
}

@Article{Kantardjieff2010b,
  author    = {Kantardjieff, Katherine A. and Kaysser-Pyzalla, Anke R. and Spadon, Paola},
  journal   = {Journal of Applied Crystallography},
  title     = {Crystallography education and training for the 21st century},
  year      = {2010},
  pages     = {1137--1138},
  volume    = {43},
  doi       = {10.1107/S0021889810034357},
  file      = {2010_Kantardjieff_1137.pdf:by-author/K/Kantardjieff/2010_Kantardjieff_1137.pdf:PDF},
  keywords  = {Crystallographic Education; Editorial},
  owner     = {saulius},
  timestamp = {2015.04.03},
  creationdate = {2015-04-03T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0021889810034357},
}

@Article{Kantardjieff2010,
  author    = {Kantardjieff, Katherine A. and Lind, Cora and Ng, Joseph and Santarsiero, Bernard D.},
  journal   = {Journal of Applied Crystallography},
  title     = {Efforts to enhance coverage of crystallography in United States secondary education},
  year      = {2010},
  pages     = {1181--1188},
  volume    = {43},
  abstract  = {Because crystallography has often been regarded as an `experts only' science, requiring advanced mathematics and physics, it has been eliminated from many science curricula. In the United States, high school is a critical time when students are exposed to science at a more significant level, preparing them for university, and it is when they make career choices. A contemporary secondary science teaching credential must qualify teachers to present topics in substantive ways, to attract talented and enthusiastic young people to science, and to develop scientific literacy in the future workforce. Education and training policies put forward by the United States National Committee for Crystallography and the American Crystallographic Association recommend that molecular structure awareness should begin in K-12 (kindergarten through 12th grade) education as a core component for implementing established national science standards. Furthermore, many contexts exist in which crystallography can be incorporated into secondary education with minimal disruption. Following these guidelines, preparation of secondary teachers should include professional development in crystallography, providing them with knowledge (fundamental and practical), learning units, tools and modern examples to incorporate into their curricula. This article describes activities whose objective is to enhance secondary education by raising crystallography awareness through workshops, summer schools, student/teacher research internships and remote-enabling technologies.},
  doi       = {10.1107/S0021889810034333},
  file      = {2010_Kantardjieff_1181.pdf:by-author/K/Kantardjieff/2010_Kantardjieff_1181.pdf:PDF},
  keywords  = {Crystallographic Education; Education Policies; Outreach; Science Content Standards; Secondary Education},
  owner     = {saulius},
  timestamp = {2015.04.03},
  creationdate = {2015-04-03T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0021889810034333},
}

@InProceedings{Kantere2007,
  author    = {Kantere, Verena and Sellis, Timos},
  booktitle = {Proceedings of the 15th annual ACM international symposium on Advances in geographic information systems},
  title     = {Handling spatial data in distributed environments},
  year      = {2007},
  address   = {New York, NY, USA},
  pages     = {3:1-3:8},
  publisher = {ACM},
  series    = {GIS '07},
  abstract  = {Handling spatial data in distributed environments is an intriguing issue. We consider autonomous sites of an overlay network that are bound to specific spatial information. We assume that each site has partial knowledge of the overlay. Actually, the sites are aware of and can communicate with some other sites, according to the spatial data to which they are bound to. We are interested in routing queries about spatial data in such overlays, solely by exploiting local knowledge on sites, i.e. based on locality and directionality in space. For such a system, we explore the parameters that can make search for any spatial information realizable and efficient. In this work we focus on the management of grid-partitioned space. In such a system there is a necessity for a mechanism that provides even knowledge of space to each site of the overlay. We investigate two different ways to define the directions of grid knowledge on each site and we propose a new distance metric. Moreover, we consider a new locality function that is specifically constructed in order to achieve even knowledge of space towards all directions. Furthermore, we present an experimental study that evaluates the theoretical propositions and verifies the theoretical results.},
  articleno = {3},
  doi       = {10.1145/1341012.1341017},
  file      = {:by-author/K/Kantere/2007_Kantere_3\:1.pdf:PDF},
  isbn      = {978-1-59593-914-2},
  location  = {Seattle, Washington},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://doi.acm.org/10.1145/1341012.1341017},
}

@InBook{Kantor2006,
  author    = {Reuben Kantor},
  pages     = {B-26},
  title     = {Constructing a Basic Arithmetic Logic Unit},
  year      = {2006},
  file      = {:by-author/K/Kantor/2006_Kantor_B.pdf:PDF},
  keywords  = {ALU; CPU Design; Computer Science (CS); Electronics},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Kaplan2002,
  author    = {Kaplan, Daniel L. and O'Donnell, Mike},
  journal   = {Molecular cell},
  title     = {DnaB drives DNA branch migration and dislodges proteins while encircling two DNA strands.},
  year      = {2002},
  pages     = {647--57},
  volume    = {10},
  abstract  = {DnaB is a ring-shaped, hexameric helicase that unwinds the E. coli DNA replication fork while encircling one DNA strand. This report demonstrates that DnaB can also encircle both DNA strands and then actively translocate along the duplex. With two strands positioned inside its central channel, DnaB translocates with sufficient force to displace proteins tightly bound to DNA with no resultant DNA unwinding. Thus, DnaB may clear proteins from chromosomal DNA. Furthermore, while encircling two DNA strands, DnaB can drive branch migration of a synthetic Holliday junction with heterologous duplex arms, suggesting that DnaB may be directly involved in DNA recombination in vivo. DnaB binds to just one DNA strand during branch migration. T7 phage gp4 protein also drives DNA branch migration, suggesting this activity generalizes to other ring-shaped helicases.},
  file      = {:by-author/K/Kaplan/2002_Kaplan_647.pdf:PDF},
  keywords  = {T7; {gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Presentation{Kappenstein2011,
  author    = {Charles Kappenstein},
  title     = {Powder X-ray Diffraction. II -- Diffraction},
  year      = {2011},
  file      = {2011_Kappenstein_slides.pdf:by-author/K/Kappenstein/2011_Kappenstein_slides.pdf:PDF},
  keywords  = {Diffraction Peak Multiplicities; Intensity Calculation; Powder Diffraction},
  owner     = {saulius},
  timestamp = {2014.09.16},
  creationdate = {2014-09-16T00:00:00},
  url       = {http://www.gsc.dicp.ac.cn/down/jx/2011/2011.5.23/2-Diffraction-A.pdf},
}

@Article{Kappes2015,
  author    = {Kappes, Branden B. and Ciobanu, Cristian V.},
  journal   = {Materials and Manufacturing Processes},
  title     = {Materials screening through {GPU} accelerated topological mapping},
  year      = {2015},
  pages     = {529--537},
  volume    = {30},
  file      = {Kappes and Ciobanu - 2015 - Materials Screening Through GPU Accelerated Topolo.pdf:by-author/K/Kappes/2015_Kappes_529.pdf:application/pdf;Snapshot:by-author/K/Kappes/2015_Kappes_529b.html:text/html;Snapshot:by-author/K/Kappes/2015_Kappes_529a.html:text/html;Snapshot:by-author/K/Kappes/2015_Kappes_529.html:text/html},
  groups    = {sg/JAC2009, sg/NAR2012},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://www.tandfonline.com/doi/abs/10.1080/10426914.2014.984215},
  urldate   = {2015-08-31},
}

@Manuscript{Kapur,
  author    = {Deepak Kapur and Hantao Zhang},
  title     = {Automatic Induction: Explicit vs. Inductionless},
  keywords  = {Automated Reasoning; Computer Science (CS); Cover Set Induction; Program Verification},
  file      = {:by-author/K/Kapur/XXXX_Kapur.dvi:},
  owner     = {saulius},
  timestamp = {2015.03.03},
  creationdate = {2015-03-03T00:00:00},
}

@Manuscript{Kapura,
  author    = {Deepak Kapur and Hantao Zhang},
  title     = {An Overview of Rewrite Rule Laboratory (RRL)},
  keywords  = {Automated Reasoning; Computer Science (CS); Cover Set Induction; Program Verification; RRL},
  file      = {:by-author/K/Kapur/XXXX_Kapur_a.dvi:DVI},
  owner     = {saulius},
  timestamp = {2015.03.03},
  creationdate = {2015-03-03T00:00:00},
}

@Article{Karaman2015,
  author    = {Rafik Karaman},
  journal   = {Frontiers in Computational Chemistry},
  title     = {From Conventional Prodrugs to Prodrugs Designed by Molecular Orbital Methods},
  year      = {2015},
  pages     = {187--249},
  volume    = {2},
  booktitle = {Frontiers in Computational Chemistry},
  doi       = {10.2174/9781608059782115020007},
  file      = {:by-author/K/Karaman/2015_Karaman_187.pdf:PDF},
  isbn      = {978-1-60805-979-9},
  language  = {English},
  owner     = {saulius},
  series    = {Frontiers in Computational Chemistry},
  timestamp = {2015.10.09},
  creationdate = {2015-10-09T00:00:00},
  url       = {http://dx.doi.org/10.2174/9781608059782115020007},
  urldate   = {2015-09-07},
}

@InProceedings{Kareiva2017,
  author           = {Kareiva, Aivaras and Laurik{\.{e}}nas, Andrius and Barkauskas, Jurgis},
  booktitle        = {7th Forum on New Materials - Part B},
  title            = {Synthesis and Characterization of Lanthanide Metal-Organic Frameworks with Perfluorinated Linkers},
  year             = {2017},
  month            = {1},
  pages            = {70--74},
  publisher        = {Trans Tech Publications},
  series           = {Advances in Science and Technology},
  volume           = {98},
  abstract         = {In this study, lanthanide elements (Ln3+) and 2,3,5,6-tetrafluoro-1,4-benzenedicarboxylic acid (TFBDC) based metal-organic frameworks (MOFs) were synthesized by precipitation and diffusion-controlled precipitation methods. Powders insoluble in aqueous media and polar solvents were obtained. The microstructure and properties of Ln3+ MOFs were evaluated and discussed. X-ray diffraction (XRD) analysis, infrared (FTIR) spectroscopy, scanning electron microscopy (SEM) and fluorescence spectroscopy (FLS) were carried out to characterize Ln3+ MOF's crystallinity, the microstructure, chemical composition and optical properties.},
  creationdate     = {2017-02-11T00:00:00},
  doi              = {10.4028/www.scientific.net/AST.98.70},
  file             = {2017_Kareiva_70.pdf:by-author/K/Kareiva/2017_Kareiva_70.pdf:PDF},
  groups           = {sg/MOF, sg/MOFs, am/MOFs},
  keywords         = {2,3,5,6-Tetrafluoro-1,4-Benzenedicarboxylic Acid; Lanthanide; Metal-Organic Framework},
  modificationdate = {2024-11-14T15:18:49},
  owner            = {saulius},
  timestamp        = {2017.02.11},
}

@Article{Karimaeki1992,
  author    = {Veikko Karimäki},
  journal   = {Computer Physics Communications},
  title     = {Fast code to fit circular arcs},
  year      = {1992},
  pages     = {133--141},
  volume    = {69},
  abstract  = {We present a fast code to fit circular arcs to measured points. Our algorithm is based on an explicit solution of a non-linear least-squares problem to fit the circle curvature, direction and position parameters. The code includes error estimation of the circle parameters as well as the transformation of parameters and error matrix to another point of reference. The formalism is valid for any arc length up to a full circle.},
  file      = {1992_Karimäki_133.pdf:by-author/K/Karimäki/1992_Karimäki_133.pdf:PDF},
  groups    = {sg/Arc fitting, sg/Bioinf. Algorithms},
  keywords  = {Algorithms; Arc Fitting},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Karipides1993,
  author    = {Karipides, A. and White, C.},
  journal   = {Acta Crystallographica Section C},
  title     = {Structure of diaquatetrakis({$\mu$}-2,6-difluorobenzoato-{$\kappa$}{\it O}:{$\kappa$}{\it O}')dicopper(II)},
  year      = {1993},
  pages     = {1920--1923},
  volume    = {49},
  doi       = {10.1107/S0108270193004214},
  file      = {:by-author/K/Karipides/1993_Karipides_1920.pdf:PDF},
  owner     = {antanas},
  timestamp = {2013.04.11},
  creationdate = {2013-04-11T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0108270193004214},
}

@Article{Karki2007,
  author    = {Karki, Shyam and Fábián, László and Friščić, Tomislav and Jones, William},
  journal   = {Organic Letters},
  title     = {Powder X-ray Diffraction as an Emerging Method to Structurally Characterize Organic Solids},
  year      = {2007},
  pages     = {3133--3136},
  volume    = {9},
  abstract  = {The current level of laboratory instrumentation and computational resources allows X-ray powder diffraction to be implemented into the toolbox of organic chemists, providing a means for rapid (i.e., within a day) structural characterization of organic solids, without the need for single crystals. We illustrate such use of powder diffraction using two case studies of molecular cocrystals of trifluoroacetic acid and malonic acid, involving theobromine, a model active pharmaceutical ingredient. We also report on a previously unobserved conformation of malonic acid in the solid state.},
  doi       = {10.1021/ol071329t},
  eprint    = {http://pubs.acs.org/doi/pdf/10.1021/ol071329t},
  file      = {2007_Karki_3133.pdf:by-author/K/Karki/2007_Karki_3133.pdf:PDF},
  keywords  = {Powder Diffraction},
  owner     = {saulius},
  timestamp = {2012.05.17},
  creationdate = {2012-05-17T00:00:00},
  url       = {http://pubs.acs.org/doi/abs/10.1021/ol071329t},
}

@Article{Karney2007,
  author    = {Karney, Charles F. F.},
  journal   = {Journal of molecular graphics \& modelling},
  title     = {Quaternions in molecular modeling.},
  year      = {2007},
  pages     = {595--604},
  volume    = {25},
  abstract  = {Quaternions are an important tool to describe the orientation of a molecule. This paper considers the use of quaternions in matching two conformations of a molecule, in interpolating rotations, in performing statistics on orientational data, in the random sampling of rotations, and in establishing grids in orientation space. These examples show that many of the rotational problems that arise in molecular modeling may be handled simply and efficiently using quaternions.},
  doi       = {10.1016/j.jmgm.2006.04.002},
  file      = {manuscript:by-author/K/Karney/2006_Karney_manuscript.pdf:PDF;:by-author/K/Karney/2007_Karney_595.pdf:PDF},
  groups    = {sg/Molecule superposion, sg/Superposition, sg/Bioinf. Algorithms},
  keywords  = {Quaternions; Structure Superposition},
  owner     = {saulius},
  timestamp = {2012.05.15},
  creationdate = {2012-05-15T00:00:00},
}

@Article{Karplus2003,
  author    = {Karplus, Martin},
  journal   = {Biopolymers},
  title     = {Molecular dynamics of biological macromolecules: A brief history and perspective},
  year      = {2003},
  issn      = {1097-0282},
  pages     = {350--358},
  volume    = {68},
  abstract  = {A description of the origin of my interest in and the development of molecular dynamics simulations of biomolecules is presented with a historical overview, including the role of my interactions with Shneior Lifson and his group in Israel. Some early applications of the methodology by members of my group are summarized, followed by a description of examples of recent applications and some discussion of possible future directions. © 2003 Wiley Periodicals, Inc. Biopolymers: 350–358, 2003},
  doi       = {10.1002/bip.10266},
  file      = {2003_Karplus_350.pdf:by-author/K/Karplus/2003_Karplus_350.pdf:PDF},
  groups    = {sg/Molecular dynamics},
  keywords  = {Channels; Conformational Change; Molecular Dynamics Simulations; NMR; Proteins; Trajectory Calculations},
  owner     = {saulius},
  publisher = {Wiley Subscription Services, Inc., A Wiley Company},
  timestamp = {2013.04.01},
  creationdate = {2013-04-01T00:00:00},
  url       = {http://dx.doi.org/10.1002/bip.10266},
}

@Article{Karplus2012,
  author    = {Karplus, P. Andrew and Diederichs, Kay},
  journal   = {Science},
  title     = {Linking Crystallographic Model and Data Quality},
  year      = {2012},
  pages     = {1030--1033},
  volume    = {336},
  abstract  = {In macromolecular x-ray crystallography, refinement R values measure the agreement between observed and calculated data. Analogously, Rmerge values reporting on the agreement between multiple measurements of a given reflection are used to assess data quality. Here, we show that despite their widespread use, Rmerge values are poorly suited for determining the high-resolution limit and that current standard protocols discard much useful data. We introduce a statistic that estimates the correlation of an observed data set with the underlying (not measurable) true signal; this quantity, CC*, provides a single statistically valid guide for deciding which data are useful. CC* also can be used to assess model and data quality on the same scale, and this reveals when data quality is limiting model improvement.},
  doi       = {10.1126/science.1218231},
  eprint    = {http://www.sciencemag.org/content/336/6084/1030.full.pdf},
  file      = {2012_Karplus_1030.pdf:by-author/K/Karplus/2012_Karplus_1030.pdf:PDF},
  keywords  = {Data Quality; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2014.03.24},
  creationdate = {2014-03-24T00:00:00},
  url       = {http://www.sciencemag.org/content/336/6084/1030.abstract},
}

@Article{Karshikoff2008,
  author    = {A. Karshikoff and I. Jelesarov},
  journal   = {Biotechnology \& Biotechnological Equipment},
  title     = {Salt bridges and conformational flexibility: effect on protein stability},
  year      = {2008},
  pages     = {606--611},
  volume    = {22},
  abstract  = {Salt bridges are believed to have an important role in stabilisation of native protein structure. The assessment of their contribution to the electrostatic term of the free energy is a yet unsolved task. One can point out a number of reasons: beginning with conceptual issues, such as the complex nature of the interplay between the different types of non-covalent interactions and going to details, such as the interactions of the participating groups with their environments. Here we focus on the interplay between electrostatic interactions the functional groups forming salt bridges are involved in and the conformational flexibility of the protein molecule. We show that the connection between these two factors appears to be one of the keys for a better understanding of the forces determining stability of proteins.},
  file      = {2008_Karshikoff_606.pdf:by-author/K/Karshikoff/2008_Karshikoff_606.pdf:PDF},
  keywords  = {Electrostatic Interactions; Modelling; Noncovalent Interactions; Protein Physics; Proteins; Salt Bridges; Stability},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://www.diagnosisp.com/dp/journals/view_article.php?journal_id=1&archive=0&issue_id=17&article_id=471},
}

@Presentation{Karvelis2015,
  author    = {Tautvydas Karvelis},
  title     = {Netipinės CRISPR-Cas sistemų funkcijos},
  year      = {2015},
  file      = {2015_Karvelis_slides.pdf:by-author/K/Karvelis/2015_Karvelis_slides.pdf:PDF},
  groups    = {sg/CRISPR-Cas},
  keywords  = {CRISPR; Cas; Overview},
  owner     = {saulius},
  timestamp = {2015.10.16},
  creationdate = {2015-10-16T00:00:00},
}

@Article{Karvelis2013,
  author    = {Karvelis, Tautvydas and Gasiunas, Giedrius and Miksys, Algirdas and Barrangou, Rodolphe and Horvath, Philippe and Siksnys, Virginijus},
  journal   = {RNA Biology},
  title     = {crRNA and tracrRNA guide Cas9-mediated DNA interference in Streptococcus thermophilus},
  year      = {2013},
  pages     = {841–851},
  volume    = {10},
  abstract  = {The Cas9-crRNA complex of the Streptococcus thermophilus DGCC7710 CRISPR3-Cas system functions as an RNA-guided endonuclease with crRNA-directed target sequence recognition and protein-mediated DNA cleavage. We show here that an additional RNA molecule, tracrRNA (trans-activating CRISPR RNA), co-purifies with the Cas9 protein isolated from the heterologous E. coli strain carrying the S. thermophilus DGCC7710 CRISPR3-Cas system. We provide experimental evidence that tracrRNA is required for Cas9-mediated DNA interference both in vitro and in vivo. We show that Cas9 specifically promotes duplex formation between the precursor crRNA (pre-crRNA) transcript and tracrRNA, in vitro. Furthermore, the housekeeping RNase III contributes to primary pre-crRNA-tracrRNA duplex cleavage for mature crRNA biogenesis. RNase III, however, is not required in the processing of a short pre-crRNA transcribed from a minimal CRISPR array containing a single spacer. Finally, we show that an in vitro-assembled ternary Cas9-crRNA-tracrRNA complex cleaves DNA. This study further specifies the molecular basis for crRNA-based re-programming of Cas9 to specifically cleave any target DNA sequence for precise genome surgery. The processes for crRNA maturation and effector complex assembly established here will contribute to the further development of the Cas9 re-programmable system for genome editing applications.},
  doi       = {10.4161/rna.24203},
  file      = {:by-author/K/Karvelis/2013_Karvelis_841.pdf:PDF},
  groups    = {sg/CRISPR-Cas},
  keywords  = {CRISPR; Cas9; CrRNA; DNA Silencing; Type II CRISPR-Cas Systems},
  owner     = {em},
  timestamp = {2014.05.26},
  creationdate = {2014-05-26T00:00:00},
}

@Manuscript{Kasar2013,
  author    = {T Kasar and P. Barlas and S. Adam and C. Chatelain† and T. Paquet},
  title     = {Learning to Detect Tables in Scanned Document Images using Line Information},
  year      = {2013},
  keywords  = {Data Management; OCR},
  url       = {http://clement.chatelain.free.fr/publications/kasar_icdar2013.pdf},
  file      = {:by-author/K/Kasar/2013_Kasar.pdf:PDF},
  groups    = {sg/Text segmentation},
  owner     = {saulius},
  timestamp = {2014.11.06},
  creationdate = {2014-11-06T00:00:00},
}

@Article{Kasarjian2004,
  author    = {Kasarjian, Julie K. A. and Hidaka, Masumi and Horiuchi, Takashi and Iida, Masatake and Ryu, Junichi},
  journal   = {Nucleic acids research},
  title     = {The recognition and modification sites for the bacterial type I restriction systems KpnAI, StySEAI, StySENI and StySGI.},
  year      = {2004},
  pages     = {e82},
  volume    = {32},
  abstract  = {Using an in vivo plasmid transformation method, we have determined the DNA sequences recognized by the KpnAI, StySEAI, StySENI and StySGI R-M systems from Klebsiella oxytoca strain M5a1, Salmonella eastbourne, Salmonella enteritidis and Salmonella gelsenkirchen, respectively. These type I restriction-modification systems were originally identified using traditional phage assay, and described here is the plasmid transformation test and computer program used to determine their DNA recognition sequences. For this test, we constructed two sets of plasmids, pL and pE, that contain phage lambda and Escherichia coli K-12 chromosomal DNA fragments, respectively. Further, using the methylation sensitivities of various known type II restriction enzymes, we identified the target adenines for methylation (listed in bold italics below as A or T in case of the complementary strand). The recognition sequence and methylation sites are GAA(6N)TGCC (KpnAI), ACA(6N)TYCA (StySEAI), CGA(6N)TACC (StySENI) and TAAC(7N)RTCG (StySGI). These DNA recognition sequences all have a typical type I bipartite pattern and represent three novel specificities and one isoschizomer (StySENI). For confirmation, oligonucleotides containing each of the predicted sequences were synthesized, cloned into plasmid pMECA and transformed into each strain, resulting in a large reduction in efficiency of transformation (EOT).},
  file      = {:by-author/K/Kasarjian/2004_Kasarjian_e82.pdf:PDF},
  keywords  = {TypeI},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Manuscript{Kass2011,
  author    = {Robert E. Kass},
  title     = {Statistical Inference: The Big Picture},
  year      = {2011},
  language  = {English},
  url       = {http://arxiv.org/pdf/1106.2895v2.pdf},
  abstract  = {Statistics has moved beyond the frequentist-Bayesian con- troversies of the past. Where does this leave our ability to interpret results? I suggest that a philosophy compatible with statistical practice, labeled here statistical pragmatism, serves as a foundation for inference. Statistical pragmatism is inclusive and emphasizes the assump- tions that connect statistical models with observed data. I argue that introductory courses often mischaracterize the process of statistical inference and I propose an alternative “big picture” depiction.},
  file      = {Robert E. Kass - 2011 - Statistical Inference The Big Picture.pdf:by-author/K/Kass/2011_Kass_1.pdf:application/pdf},
  groups    = {sg/Inference theory, sg/Statistical inference, sg/Bayesian},
  number    = {1},
  owner     = {saulius},
  pages     = {1--9},
  timestamp = {2015.12.13},
  creationdate = {2015-12-13T00:00:00},
  urldate   = {2015-12-13},
  volume    = {26},
}

@Article{Kass1995,
  author    = {Kass, Robert E. and Raftery, Adrian E.},
  journal   = {Journal of the American Statistical Association},
  title     = {Bayes Factors},
  year      = {1995},
  issn      = {1537-274X},
  month     = {Jun},
  number    = {430},
  pages     = {773–795},
  volume    = {90},
  doi       = {10.1080/01621459.1995.10476572},
  file      = {1995_Kass_773.pdf:by-author/K/Kass/1995_Kass_773.pdf:PDF},
  owner     = {andrius},
  publisher = {Informa UK Limited},
  timestamp = {2017.04.14},
  creationdate = {2017-04-14T00:00:00},
  url       = {http://dx.doi.org/10.1080/01621459.1995.10476572},
}

@Presentation{Kataria2008,
  author    = {Puneet Kataria},
  title     = {Parallel quicksort implementation using MPI and pthreads},
  year      = {2008},
  file      = {:by-author/K/Kataria/2008_Kataria_slides.pdf:PDF},
  owner     = {saulius},
  pages     = {slides},
  timestamp = {2013.07.02},
  creationdate = {2013-07-02T00:00:00},
}

@InProceedings{Katayama1997,
  author    = {Katayama, Norio and Satoh, Shin'ichi},
  booktitle = {Proceedings of the 1997 ACM SIGMOD international conference on Management of data},
  title     = {The SR-tree: an index structure for high-dimensional nearest neighbor queries},
  year      = {1997},
  pages     = {369--380},
  publisher = {ACM},
  abstract  = {Recently, similarity queries on feature vectors have been widely used to perform content-based retrieval of images. To apply this technique to large databases, it is required to develop multidimensional index structures supporting nearest neighbor queries efficiently. The SS-tree had been proposed for this purpose and is known to outperform other index structures such as the R*-tree and the K-D-B-tree. One of its most important features is that it employs bounding spheres rather than bounding rectangles for the shape of regions. However, we demonstrate in this paper that bounding spheres occupy much larger volume than bounding rectangles with high-dimensional data and that this reduces search efficiency. To overcome this drawback, we propose a new index structure called the SR-tree (Sphere/Rectangle-tree) which integrates bounding spheres and bounding rectangles. A region of the SR-tree is specified by the intersection of a bounding sphere and a bounding rectangle. Incorporating bounding rectangles permits neighborhoods to be partitioned into smaller regions than the SS-tree and improves the disjointness among regions. This enhances the performance on nearest neighbor queries especially for high-dimensional and non-uniform data which can be practical in actual image/video similarity indexing. We include the performance test results the verify this advantage of the SR-tree and show that the SR-tree outperforms both the SS-tree and the R*-tree.},
  doi       = {10.1145/253260.253347},
  file      = {:by-author/K/Katayama/1997_Katayama_369.pdf:PDF},
  isbn      = {0-89791-911-4},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://doi.acm.org/10.1145/253260.253347},
}

@Presentation{Katchabaw2014,
  author       = {Michael Katchabaw and Mark Daley},
  title        = {Abort, Retry, Fail: Why Computer Science is an Essential Part of Every Science Education},
  year         = {2014},
  organization = {Department of Computer Science},
  school       = {The University of Western Ontario},
  file         = {2014_Katchabaw.pdf:by-author/K/Katchabaw/2014_Katchabaw.pdf:PDF},
  keywords     = {Computer Science (CS); Teaching},
  owner        = {saulius},
  timestamp = {2015.06.12},
  creationdate = {2015-06-12T00:00:00},
  url          = {http://ir.lib.uwo.ca/wcse/WCSEEleven/Wed_July_6/4/},
}

@Article{Katchabaw2011,
  author     = {Katchabaw, Michael and Daley, Mark},
  journal    = {The Western Conference on Science Education},
  title      = {Abort, retry, fail? why computer science is an essential part of every science education},
  year       = {2011},
  file       = {Katchabaw and Daley - 2011 - Abort, Retry, Fail Why Comp. Sci. is an Essential Part of Science Education.pdf:by-author/K/Katchabaw/2011_Katchabaw.pdf:application/pdf;Scholarship@Western - The Western Conference on Science Education\: Abort, Retry, Fail? Why Computer Science is an Essential Part of Every Science Education:by-author/K/Katchabaw/2011_Katchabaw.html:text/html},
  owner      = {saulius},
  shorttitle = {Abort, retry, fail?},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url        = {http://ir.lib.uwo.ca/wcse/WCSEEleven/Wed_July_6/4},
}

@Article{Katiliene2003,
  author    = {Katiliene, Zivile and Katilius, Evaldas and Woodbury, Neal W},
  journal   = {Biophysical journal},
  title     = {Single molecule detection of DNA looping by NgoMIV restriction endonuclease.},
  year      = {2003},
  pages     = {4053--61},
  volume    = {84},
  abstract  = {Single molecule fluorescence resonance energy transfer (FRET) and fluorescence correlation spectroscopy were used to investigate DNA looping by NgoMIV restriction endonuclease. Using a linear double-stranded DNA (dsDNA) molecule labeled with a fluorescence donor molecule, Cy3, and fluorescence acceptor molecule, Cy5, and by varying the concentration of NgoMIV endonuclease from 0 to 3 x 10(-6) M, it was possible to detect and determine diffusion properties of looped DNA/protein complexes. FRET efficiency distributions revealed a subpopulation of complexes with an energy transfer efficiency of 30%, which appeared upon addition of enzyme in the picomolar to nanomolar concentration range (using 10(-11) M dsDNA). The concentration dependence, fluorescence burst size analysis, and fluorescence correlation analysis were all consistent with this subpopulation arising from a sequence specific interaction between an individual enzyme and a DNA molecule. A 30% FRET efficiency corresponds to a distance of approximately 65 A, which correlates well with the distance between the ends of the dsDNA molecule when bound to NgoMIV according to the crystal structure of this complex. Formation of the looped complexes was also evident in measurements of the diffusion times of freely diffusing DNA molecules with and without NgoMIV. At very high protein concentrations compared to the DNA concentration, FRET and fluorescence correlation spectroscopy results revealed the formation of larger DNA/protein complexes.},
  file      = {Katiliene_2003_4053-Single_mol_detection_NgoMIV.pdf:by-author/K/Katiliene/2003_Katiliene_4053.pdf:PDF},
  groups    = {sg/NgoMIV},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Kato1990,
  author    = {Katsuo Kato and Mitsuko Onoda},
  journal   = {Acta Cryst. A},
  title     = {Strukturverfeinerung des Kompositkristalls im mehrdimensionalen Raum: Kommensurabler Komposit-kristall},
  year      = {1990},
  pages     = {55--56},
  volume    = {47},
  abstract  = {The superspace-group approach formulated for incom- mensurate composite crystals by Janner & Janssen [Acta Cryst. (1980), A36, 408-415] is applicable to the structure refinement of commensurate composite crystals, if the number and the coordinates of summation points in the structure-factor formula are determined through an algorithm given in the text.},
  file      = {:by-author/K/Kato/1990_Kato_55.pdf:PDF},
  keywords  = {Modulated Structures},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Kato2003,
  author    = {Kato, Masato and Ito, Takuhiro and Wagner, Gerhard and Richardson, Charles C. and Ellenberger, Tom},
  journal   = {Molecular cell},
  title     = {Modular architecture of the bacteriophage T7 primase couples RNA primer synthesis to DNA synthesis.},
  year      = {2003},
  pages     = {1349--60},
  volume    = {11},
  abstract  = {DNA primases are template-dependent RNA polymerases that synthesize oligoribonucleotide primers that can be extended by DNA polymerase. The bacterial primases consist of zinc binding and RNA polymerase domains that polymerize ribonucleotides at templating sequences of single-stranded DNA. We report a crystal structure of bacteriophage T7 primase that reveals its two domains and the presence of two Mg(2+) ions bound to the active site. NMR and biochemical data show that the two domains remain separated until the primase binds to DNA and nucleotide. The zinc binding domain alone can stimulate primer extension by T7 DNA polymerase. These findings suggest that the zinc binding domain couples primer synthesis with primer utilization by securing the DNA template in the primase active site and then delivering the primed DNA template to DNA polymerase. The modular architecture of the primase and a similar mechanism of priming DNA synthesis are likely to apply broadly to prokaryotic primases.},
  file      = {:by-author/K/Kato/2003_Kato_1349.pdf:PDF},
  keywords  = {T7; {gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Kato1991,
  author    = {Kato, N.},
  journal   = {Acta Crystallographica Section A},
  title     = {A foundation for the statistical dynamical theory of diffraction},
  year      = {1991},
  pages     = {1--11},
  volume    = {47},
  abstract  = {The statistical dynamical theory [Kato (1980). Acta Cryst. A36, 763-769] is reformulated on a sounder basis. The starting wave equation is free from the so-called Takagi-Taupin (T-T) approximation. Functional calculus, an operational technique and the concept of the Green function are used as mathematical tools. Integro-differential equations are derived for the coherent (averaged) wave field and the energy flow vector of the incoherent intensity field. The formulae are exact except for assuming a model in which the fluctuation of the lattice phase is a set of Gaussian random variables defined in three-dimensional space. The general framework of the previous theory is justified within the T-T approximation. In general, however, new terms must be added and some terms have to be revised by introducing a Green function matrix. The theory may be used as a starting point when any approximate theory is developed for practical purposes.},
  doi       = {10.1107/S0108767390008790},
  file      = {:by-author/K/Kato/1991_Kato_1.pdf:PDF},
  keywords  = {Dynamic Theory; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0108767390008790},
}

@Webpage{Kauffman2003,
  author    = {Leah Kauffman},
  retrieved = {2015-03-06},
  title     = {When DNA Flips Out},
  url       = {http://www.psc.edu/science/2003/mackerell/when_dna_flips_out.html},
  year      = {2003},
  file      = {:by-author/K/Kauffman/2003_Kauffman.pdf:},
  keywords  = {MTases},
  owner     = {saulius},
  timestamp = {2015.03.03},
  creationdate = {2015-03-03T00:00:00},
}

@Webpage{Kauffman2003a,
  author    = {Leah Kauffman},
  retrieved = {2008-07-28},
  title     = {The First Step-by-step Picture of how DNA Opens up to Interact with an Enzyme},
  url       = {http://www.psc.edu/science/2003/mackerell/when_dna_flips_out.html},
  year      = {2003},
  file      = {:by-author/K/Kauffman/2003_Kauffman.war:},
  keywords  = {MTases},
  owner     = {saulius},
  timestamp = {2015.03.02},
  creationdate = {2015-03-02T00:00:00},
}

@Manuscript{Kaulakys2007,
  author    = {Kaulakys, Vygintas},
  title     = {Keletas faktų apie Lietuvos mokslą ir studijas},
  year      = {2007},
  keywords  = {Lietuva},
  file      = {:by-author/K/Kaulakys/2007_Kaulakys.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Kaunisto2002,
  author    = {Kaunisto, Kari and Parkkila, Seppo and Rajaniemi, Hannu and Waheed, Abdul and Grubb, Jeffrey and Sly, William S},
  journal   = {Kidney international},
  title     = {Carbonic anhydrase XIV: luminal expression suggests key role in renal acidification.},
  year      = {2002},
  pages     = {2111--8},
  volume    = {61},
  file      = {2002_Kaunisto_2111.pdf:by-author/K/Kaunisto/2002_Kaunisto_2111.pdf:PDF},
  groups    = {sg/physical sg/methods, sg/physiology, sg/hCA14},
  keywords  = {CA14; Carbonic Anhydrases},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Kaur2002,
  author    = {Kaur, Indu Pal and Smitha, R and Aggarwal, Deepika and Kapil, Mona},
  journal   = {International journal of pharmaceutics},
  title     = {Acetazolamide: future perspective in topical glaucoma therapeutics.},
  year      = {2002},
  pages     = {1--14},
  volume    = {248},
  abstract  = {Through this review it is contemplated that acetazolamide (ACZ), an age-old treatment for glaucoma with a myriad of side effects and inadequate topical effectiveness, may be formulated into a topically effective agent by utilizing various newer formulation approaches of ocular drug delivery. Even though it has a poor solubility and penetration power, various studies mentioned in the review indicate that it is possible to successfully formulate topically effective ACZ by using: (i) high concentration of the drug, (ii) surfactant gel preparations of ACZ, (iii) ACZ loaded into liposomes, (iv) cyclodextrins to increase the solubility and hence bioavailability of ACZ, and (v) viscolyzers and other polymers either alone or in combination with cyclodextrins. With the advent of newer topical carbonic anhydrase inhibitors (CAIs) like dorzolamide and brinzolamide, a localized effect with fewer side effects is expected. But whenever absorbed systemically, a similar range of adverse effects (attributable to sulphonamides) may occur upon use. Furthermore, oral ACZ is reported to be more physiologically effective than 2% dorzolamide hydrochloride administered topically, even though in isolated tissues dorzolamide appears to be the most active as it shows the lowest IC(50) values for CA-II and CA-IV [M.F. Surgue, J. Ocular Pharmacol. Ther. 12 (1996) 363-376]. Hence, there exists considerable scope for the development of more/equally effective and inexpensive topically effective formulations of ACZ. The use of various formulation technologies discussed in this review can provide a fresh impetus to research in this area.},
  file      = {2002_Kaur_1.pdf:by-author/K/Kaur/2002_Kaur_1.pdf:PDF},
  groups    = {sg/inhibitors, sg/medicine},
  keywords  = {Carbonic Anhydrases},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Kaus-Drobek2007,
  author    = {Kaus-Drobek, Magdalena and Czapinska, Honorata and Sokołowska, Monika and Tamulaitis, Gintautas and Szczepanowski, Roman H. and Urbanke, Claus and Siksnys, Virginijus and Bochtler, Matthias},
  journal   = {Nucleic acids research},
  title     = {Restriction endonuclease MvaI is a monomer that recognizes its target sequence asymmetrically.},
  year      = {2007},
  pages     = {2035--46},
  volume    = {35},
  abstract  = {Restriction endonuclease MvaI recognizes the sequence CC/WGG (W stands for A or T, '/' designates the cleavage site) and generates products with single nucleotide 5'-overhangs. The enzyme has been noted for its tolerance towards DNA modifications. Here, we report a biochemical characterization and crystal structures of MvaI in an apo-form and in a complex with target DNA at 1.5 A resolution. Our results show that MvaI is a monomer and recognizes its pseudosymmetric target sequence asymmetrically. The enzyme consists of two lobes. The catalytic lobe anchors the active site residues Glu36, Asp50, Glu55 and Lys57 and contacts the bases from the minor grove side. The recognition lobe mediates all major grove interactions with the bases. The enzyme in the crystal is bound to the strand with T at the center of the recognition sequence. The crystal structure with calcium ions and DNA mimics the prereactive state. MvaI shows structural similarities to BcnI, which cleaves the related sequence CC/SGG and to MutH enzyme, which is a component of the DNA repair machinery, and nicks one DNA strand instead of making a double-strand break.},
  file      = {:by-author/K/Kaus-Drobek/2007_Kaus-Drobek_2035.pdf:PDF},
  keywords  = {Struct; TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@InCollection{Kauzmann1959,
  author    = {W. Kauzmann},
  publisher = {Academic Press},
  title     = {Some Factors in the Interpretation of Protein Denaturation1},
  year      = {1959},
  editor    = {C. B. Anfinsen and M. L. Anson and Kenneth Bailey and John T. Edsall},
  pages     = {1 - 63},
  series    = {Advances in Protein Chemistry},
  volume    = {14},
  abstract  = {This chapter explores that the changes that take place in the protein molecules during denaturation constitute one of the most interesting and complex classes of reactions that can be found either in nature or in the laboratory. These reactions are important because of the information they can provide about the more intimate details of protein structure and function. They are also significant because they challenge the chemist with a difficult area for the application of chemical principles. The chapter reviews that the denaturation is a process in which the spatial arrangement of the polypeptide chains within the molecule is changed from that typical of the native protein to a more disordered arrangement. The chapter also discusses the classification of protein structures: primary, secondary, and tertiary structures. The primary structure is that expressed by the structural chemical formula and depends entirely on the chemical valence bonds that the classical organic chemist would write down for the protein molecule. The secondary structure is the configuration of the polypeptide chain that results from the satisfaction of the hydrogen bonding potential between the peptide N-H and C=O groups. The tertiary structure is the pattern according to which the secondary structures are packed together within the native protein molecule. The term “denaturation” as used in this chapter is indented to include changes in both the secondary and tertiary structures.},
  doi       = {10.1016/S0065-3233(08)60608-7},
  file      = {1959_Kauzmann_1.pdf:by-author/K/Kauzmann/1959_Kauzmann_1.pdf:PDF},
  issn      = {0065-3233},
  keywords  = {Hydrophobic Effect; Protein Folding; Thermodicanic Hypothesis},
  owner     = {saulius},
  timestamp = {2015.03.13},
  creationdate = {2015-03-13T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/S0065323308606087},
}

@Article{Kavraki2007,
  author           = {Kavraki, Lydia E.},
  title            = {Molecular distance measures},
  year             = {2007},
  pages            = {m11608},
  creationdate     = {2012-05-15T00:00:00},
  file             = {:by-author/K/Kavraki/2007_Kavraki_m11608.pdf:PDF},
  groups           = {sg/Molecule superposion, sg/Superposition, sg/Bioinf. Algorithms},
  keywords         = {Structure Superposition},
  modificationdate = {2024-05-12T16:46:57},
  owner            = {saulius},
  timestamp        = {2012.05.15},
}

@InProceedings{Kazemi2007,
  author    = {Kazemi, Leyla and Shahabi, Cyrus and Sharifzadeh, Mehdi and Vincent, Luc},
  booktitle = {Proceedings of the 15th annual ACM international symposium on Advances in geographic information systems},
  title     = {Optimal Traversal and Planning in Road and Networks with and Navigational Constraints},
  year      = {2007},
  address   = {New York, NY, USA},
  pages     = {19:1-19:8},
  publisher = {ACM},
  series    = {GIS '07},
  abstract  = {A frequent query in geospatial planning and decision making domains (e.g., emergency response, data acquisition, street cleaning), is to find an optimal traversal plan (OTP) that traverses an entire area (e.g., a city) by navigating through all its streets. The optimality is defined in terms of the time it takes to complete the traversal. This time depends on the number of times each street segment is traversed as well as the navigation time such as the time spent on changing direction at each intersection. While the problem roots in the classic problems of graph theory, real-world geospatial constraints of road network introduce new application-specific challenges. In this paper, we propose two algorithms to find OTP of a directed road network. Our greedy algorithm employs a classic graph traversal algorithm. During the traversal, it utilizes a set of heuristics at each intersection to minimize the total travel time. Our near-optimal algorithm, however, reduces an OTP problem to an Asymmetric Traveling Salesman Problem (ATSP) by extracting the dual graph of the original network in which each edge is represented by a graph node. Using an approximate solution for ATSP, our algorithm finds a near optimal answer. Our experiments using real-world road networks verify that our near-optimal algorithm outperforms the greedy algorithm in terms of the overall cost of its generated traversal by a factor of two, while its complexity is tolerable in real-world cases.},
  articleno = {19},
  doi       = {10.1145/1341012.1341038},
  file      = {:by-author/K/Kazemi/2007_Kazemi_19\:1.pdf:PDF},
  isbn      = {978-1-59593-914-2},
  location  = {Seattle, Washington},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://doi.acm.org/10.1145/1341012.1341038},
}

@Article{Kazrani2014,
  author       = {Asgar Abbas Kazrani and Monika Kowalska and Honorata Czapinska and Matthias Bochtler},
  journal      = {Nucleic Acids Res},
  title        = {Crystal structure of the 5hmC specific endonuclease PvuRts1I.},
  year         = {2014},
  month        = {May},
  number       = {9},
  pages        = {5929--5936},
  volume       = {42},
  abstract     = {PvuRts1I is a prototype for a larger family of restriction endonucleases that cleave DNA containing 5-hydroxymethylcytosine (5hmC) or 5-glucosylhydroxymethylcytosine (5ghmC), but not 5-methylcytosine (5mC) or cytosine. Here, we report a crystal structure of the enzyme at 2.35 Å resolution. Although the protein has been crystallized in the absence of DNA, the structure is very informative. It shows that PvuRts1I consists of an N-terminal, atypical PD-(D/E)XK catalytic domain and a C-terminal SRA domain that might accommodate a flipped 5hmC or 5ghmC base. Changes to predicted catalytic residues of the PD-(D/E)XK domain or to the putative pocket for a flipped base abolish catalytic activity. Surprisingly, fluorescence changes indicative of base flipping are not observed when PvuRts1I is added to DNA substrates containing pyrrolocytosine in place of 5hmC (5ghmC). Despite this caveat, the structure suggests a model for PvuRts1I activity and presents opportunities for protein engineering to alter the enzyme properties for biotechnological applications.},
  creationdate = {2016-06-16T00:00:00},
  doi          = {10.1093/nar/gku186},
  file         = {:by-author/K/Kazrani/2014_Kazrani_1.pdf:PDF},
  institution  = {International Institute of Molecular and Cell Biology, Trojdena 4, 02109 Warsaw, Poland Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02106 Warsaw, Poland mbochtler@iimcb.gov.pl.},
  keywords     = {Amino Acid Sequence; Amino Acid Substitution; Analogs /&/ Derivatives/chemistry; Bacterial Proteins; Bacteriophage T4; Catalytic Domain; Chemistry; Chemistry/genetics; Crystal Structure; Crystallography; Cytosine; DNA; DNA Restriction Enzymes; Enzymology; Genetics; Methyl-directed; Models; Molecular; Molecular Sequence Data; Mutagenesis; Protein Binding; Protein Structure; Proteus Vulgaris; Restriction Endonuclease (RE); Secondary; Site-Directed; Substrate Specificity; Viral; X-Ray},
  language     = {eng},
  medline-pst  = {ppublish},
  owner        = {em},
  pii          = {gku186},
  pmid         = {24634440},
  timestamp    = {2016.06.16},
  url          = {http://dx.doi.org/10.1093/nar/gku186},
}

@Article{Kearsley1989,
  author    = {S. K. Kearsley},
  journal   = {Acta Crystallographica Section A},
  title     = {On the orthogonal transformation used for structural comparisons},
  year      = {1989},
  pages     = {208--210},
  volume    = {45},
  abstract  = {Rotation matrices that minimize or maximize the sum of the squared distances between corresponding atoms for two structures are found using a constrained least-squares procedure solved analytically as an eigenvalue problem in quaternion parameters.},
  doi       = {10.1107/S0108767388010128},
  file      = {:by-author/K/Kearsley/1989_Kearsley_208.pdf:PDF},
  owner     = {saulius},
  timestamp = {2011.12.21},
  creationdate = {2011-12-21T00:00:00},
  url       = {http://scripts.iucr.org/cgi-bin/paper?S0108767388010128},
}

@Article{Keatch2005,
  author    = {Keatch, S. A. and Leonard, P. G. and Ladbury, J. E. and Dryden, D. T. F.},
  journal   = {Nucleic acids research},
  title     = {StpA protein from Escherichia coli condenses supercoiled DNA in preference to linear DNA and protects it from digestion by DNase I and EcoKI.},
  year      = {2005},
  pages     = {6540--6},
  volume    = {33},
  abstract  = {The nucleoid-associated protein, StpA, of Escherichia coli binds non-specifically to double-stranded DNA (dsDNA) and apparently forms bridges between adjacent segments of the DNA. Such a coating of protein on the DNA would be expected to hinder the action of nucleases. We demonstrate that StpA binding hinders dsDNA cleavage by both the non-specific endonuclease, DNase I, and by the site-specific type I restriction endonuclease, EcoKI. It requires approximately one StpA molecule per 250-300 bp of supercoiled DNA and approximately one StpA molecule per 60-100 bp on linear DNA for strong inhibition of the nucleases. These results support the role of StpA as a nucleoid-structuring protein which binds DNA segments together. The inhibition of EcoKI, which cleaves DNA at a site remote from its initial target sequence after extensive DNA translocation driven by ATP hydrolysis, suggests that these enzymes would be unable to function on chromosomal DNA even during times of DNA damage when potentially lethal, unmodified target sites occur on the chromosome. This supports a role for nucleoid-associated proteins in restriction alleviation during times of cell stress.},
  file      = {:by-author/K/Keatch/2005_Keatch_6540.pdf:PDF},
  keywords  = {TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Keatch2004,
  author    = {Keatch, Steven A. and Su, Tsueu-Ju and Dryden, David T. F.},
  journal   = {Nucleic acids research},
  title     = {Alleviation of restriction by DNA condensation and non-specific DNA binding ligands.},
  year      = {2004},
  pages     = {5841--50},
  volume    = {32},
  abstract  = {During conditions of cell stress, the type I restriction and modification enzymes of bacteria show reduced, but not zero, levels of restriction of unmethylated foreign DNA. In such conditions, chemically identical unmethylated recognition sequences also occur on the chromosome of the host but restriction alleviation prevents the enzymes from destroying the host DNA. How is this distinction between chemically identical DNA molecules achieved? For some, but not all, type I restriction enzymes, alleviation is partially due to proteolytic degradation of a subunit of the enzyme. We identify that the additional alleviation factor is attributable to the structural difference between foreign DNA entering the cell as a random coil and host DNA, which exists in a condensed nucleoid structure coated with many non-specific ligands. The type I restriction enzyme is able to destroy the 'naked' DNA using a complex reaction linked to DNA translocation, but this essential translocation process is inhibited by DNA condensation and the presence of non-specific ligands bound along the DNA.},
  file      = {:by-author/K/Keatch/2004_Keatch_5841.pdf:PDF},
  keywords  = {Antirestriction},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Keck2000,
  author    = {Keck, J. L. and Roche, D. D. and Lynch, A. S. and Berger, J. M.},
  journal   = {Science (New York, N.Y.)},
  title     = {Structure of the RNA polymerase domain of E. coli primase.},
  year      = {2000},
  pages     = {2482--6},
  volume    = {287},
  abstract  = {All cellular organisms use specialized RNA polymerases called "primases" to synthesize RNA primers for the initiation of DNA replication. The high-resolution crystal structure of a primase, comprising the catalytic core of the Escherichia coli DnaG protein, was determined. The core structure contains an active-site architecture that is unrelated to other DNA or RNA polymerase palm folds, but is instead related to the "toprim" fold. On the basis of the structure, it is likely that DnaG binds nucleic acid in a groove clustered with invariant residues and that DnaG is positioned within the replisome to accept single-stranded DNA directly from the replicative helicase.},
  file      = {:by-author/K/Keck/2000_Keck_2482.pdf:PDF},
  keywords  = {Ecoli; {gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Keegan2007,
  author    = {Keegan, Ronan M. and Winn, Martyn D.},
  journal   = {Acta crystallographica. Section D, Biological crystallography},
  title     = {Automated search-model discovery and preparation for structure solution by molecular replacement.},
  year      = {2007},
  pages     = {447--57},
  volume    = {63},
  abstract  = {A novel automation pipeline for macromolecular structure solution by molecular replacement is described. There is a special emphasis on the discovery and preparation of a large number of search models, all of which can be passed to the core molecular-replacement programs. For routine molecular-replacement problems, the pipeline automates what a crystallographer might do and its value is simply one of convenience. For more difficult cases, the pipeline aims to discover the particular template structure and model edits required to produce a viable search model and may succeed in finding an efficacious combination that would be missed otherwise. The pipeline is described in detail and a number of examples are given. The examples are chosen to illustrate successes in real crystallography problems and also particular features of the pipeline. It is concluded that exploring a range of search models automatically can be valuable in many cases.},
  doi       = {10.1107/S0907444907002661},
  file      = {:by-author/K/Keegan/2007_Keegan_447.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Lecture{Keeler1999,
  author    = {James Keeler},
  title     = {Introduction to quantum mechanics},
  year      = {1999},
  school    = {University of Cambridge},
  file      = {:by-author/K/Keeler/1999_Keeler.pdf:PDF},
  keywords  = {Quantum Mechanics (QM)},
  owner     = {andrius},
  timestamp = {2014.04.22},
  creationdate = {2014-04-22T00:00:00},
  url       = {http://www-keeler.ch.cam.ac.uk/lectures/quant_a4.pdf},
}

@TechReport{Keep2011,
  author      = {Andrew W. Keep and R. Kent Dybvig},
  institution = {Indiana University},
  title       = {Ftypes: Structured foreign types},
  year        = {2011},
  abstract    = {High-level programming languages, like Scheme, typically repre- sent data in ways that differ from the host platform to support consistent behavior across platforms and automatic storage man- agement, i.e., garbage collection. While crucial to the program- ming model, differences in data representation can complicate in- teraction with foreign programs and libraries that employ machine- dependent data structures that do not readily support garbage col- lection. To bridge this gap, many high-level languages feature for- eign function interfaces that include some ability to interact with foreign data, though they often do not provide complete control over the structure of foreign data, are not always fully integrated into the language and run-time system, and are often not as effi- cient as possible. This paper describes a Scheme syntactic abstrac- tion for describing foreign data, a set of operators for interacting with that data, and an implementation that together provide a com- plete, well integrated, and efficient solution for handling structured data outside the Scheme heap.},
  file        = {:by-author/K/Keep/2011_Keep.pdf:PDF},
  groups      = {sg/Garbage collectors},
  keywords    = {Computer Languages; Computer Science (CS); Data Presentation; Data Types; FFI; Foreighn Function Interface; Oregon Workshop; Scheme},
  owner       = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Kehl1958,
  author    = {Kehl, W. L. and Jeffrey, G. A.},
  journal   = {Acta Crystallographica},
  title     = {The structure of 4-methyl-1,2-dithia-4-cyclopentene-3-thione},
  year      = {1958},
  pages     = {813--819},
  volume    = {11},
  abstract  = {The compound 4-methyl-l,2-dithia-4-eyclopentene-3-thione is a member of a large class of com- pounds of a general type which have been obtained from reactions of olefins and sulfur. The crystal structure was solved for the well-resolved c-axis projection by the Harker-Kasper inequalities method, and was refined first by difference syntheses on the (hk0) data, and then by least-squares and differential syntheses on the 680 observed (hkl) reflections. The two three-dimensional refine- ments gave results differing by as much as 0.09 ~ in the position of one of the carbon atoms, and the differential synthesis method gave the atomic parameters which are more consistent with a planar molecule and with chemical theory. The observed bond lengths indicate that the five- membered ring has some aromatic character, since within the ring the two C-S bonds are shorter than single bonds, while the two C-C bonds are intermediate in length between single and double bonds. This g-bonding does not, however, appear to include the S-S link which has a normal single bond length. The molecules lie in planes inclined at approximately 25 ° to the (001) plane.},
  doi       = {10.1107/S0365110X58002279},
  file      = {:by-author/K/Kehl/1958_Kehl_813.pdf:PDF},
  keywords  = {For COD Deposition; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0365110X58002279},
}

@InProceedings{Keijzer2013,
  author    = {Keijzer, Maarten},
  booktitle = {Proceedings of the 15th Annual Conference Companion on Genetic and Evolutionary Computation},
  title     = {Push-forth: A Light-weight, Strongly-typed, Stack-based Genetic Programming Language},
  year      = {2013},
  address   = {New York, NY, USA},
  pages     = {1635--1640},
  publisher = {ACM},
  series    = {GECCO '13 Companion},
  abstract  = {This paper defines the push-forth language, a recombination of Push [3] and Joy [7], borrowing type-safety considerations from Alp [2]. Push-forth is stack-based, strongly typed and easy to extend. The concept of an Evolutionary Development Environment is presented, and some informal experiments are described to illustrate the utility of such an environment.},
  acmid     = {2482742},
  doi       = {10.1145/2464576.2482742},
  file      = {2013_Keijzer_1635.pdf:by-author/K/Keijzer/2013_Keijzer_1635.pdf:PDF},
  isbn      = {978-1-4503-1964-5},
  keywords  = {Evolutionary Development Environment; Forth; Functional Programming; Genetic Programming; Joy; Programming Languages; Push},
  location  = {Amsterdam, The Netherlands},
  numpages  = {6},
  owner     = {saulius},
  timestamp = {2015.03.11},
  creationdate = {2015-03-11T00:00:00},
  url       = {http://doi.acm.org/10.1145/2464576.2482742},
}

@Article{Keith2010,
  author    = {Keith, J. Brandon and McClurg, Richard B.},
  journal   = {Acta crystallographica. Section A, Foundations of crystallography},
  title     = {Molecular crystal global phase diagrams. III. Sufficient parameter space determination.},
  year      = {2010},
  pages     = {50--63},
  volume    = {66},
  abstract  = {In previous parts of this series [Mettes et al. (2004). Acta Cryst. A60, 621-636; McClurg &amp; Keith (2010). Acta Cryst. A66, 38-49] a method for constructing global phase diagrams (GPDs) for molecular crystals was developed and the method was applied to single-component ordered crystal structures of tetrahedral molecules. GPDs are useful for visualizing what types of crystal structures a given molecule may assume depending on molecular form/interaction. Their construction uses group-theoretical methods which enumerate all possible symmetry breakings during a statistical mechanical high-to-low temperature search. In this work these results are expanded upon by outlining a method to determine a sufficiently rich parameter space to represent the experimentally observed crystal structures in a data set derived from the Cambridge Structural Database. This is significant because previous work (Mettes et al., 2004) did not specify the number of parameters needed for GPDs. Although there are suggestions in the literature that thousands of parameters are required to adequately describe tetrahedral molecule intermolecular potentials, it is found that 15 parameters are sufficient to represent the structures of the test data. The origin of this difference and its implications for determining GPD parameter values from a more detailed intermolecular potential and for interpreting GPD parameter values are discussed.},
  file      = {:by-author/K/Keith/2010_Keith_50.pdf:PDF},
  keywords  = {COD Citations; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Presentation{Keld2010,
  author    = {Keld},
  title     = {How to Get Good Performance by Using OpenMP},
  year      = {2010},
  file      = {:by-author/K/Keld/2010_Keld_slides.pdf:PDF},
  owner     = {saulius},
  pages     = {slides},
  timestamp = {2013.07.02},
  creationdate = {2013-07-02T00:00:00},
}

@Manuscript{Keller2013,
  author           = {Peter A. Keller},
  title            = {A lexical analyser for {STAR/CIF/mmCIF} data},
  year             = {2013},
  institution      = {Global Phasing Ltd., Cambridge, UK},
  keywords         = {CIF},
  month            = {Sep},
  url              = {http://www.globalphasing.com/startools/StarTools_article.pdf},
  creationdate     = {2015-07-31T00:00:00},
  file             = {:by-author/K/Keller/2013_Keller.pdf:PDF},
  modificationdate = {2023-08-07T10:23:05},
  owner            = {andrius},
  timestamp        = {2015.07.31},
}

@Article{Keller2006,
  author    = {Keller, Sascha and Pojer, Florence and Heide, Lutz and Lawson, David M.},
  journal   = {Acta crystallographica. Section D, Biological crystallography},
  title     = {Molecular replacement in the 'twilight zone': structure determination of the non-haem iron oxygenase NovR from Streptomyces spheroides through repeated density modification of a poor molecular-replacement solution.},
  year      = {2006},
  pages     = {1564--70},
  volume    = {62},
  abstract  = {Crystals of recombinant NovR (subunit MW = 29 924 Da; 270 amino acids), a non-haem iron oxygenase from Streptomyces spheroides, were grown by vapour diffusion. The protein crystallized in space group C2, with unit-cell parameters a = 86.69, b = 139.38, c = 100.82 A, beta = 101.18 degrees . Native data were collected to a resolution of 2.1 A from a single crystal at a synchrotron and a molecular-replacement solution was obtained using the program AMoRe. The starting phase information was very poor and did not permit model building. Phases were subsequently improved using a combination of fourfold averaging and very gradual phase extension in the program DM to yield an interpretable map. NovR belongs to a novel class of non-haem iron oxygenases that share sequence similarity with class II aldolases. It is predicted to perform two consecutive oxidative decarboxylation steps in the biosynthesis of the prenylated hydroxybenzoic acid moiety of the aminocoumarin antibiotic novobiocin.},
  doi       = {10.1107/S0907444906040169},
  file      = {:by-author/K/Keller/2006_Keller_1564.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Kelley1999,
  author    = {Kelley, S O and Barton, J K},
  journal   = {Science (New York, N.Y.)},
  title     = {Electron transfer between bases in double helical DNA.},
  year      = {1999},
  pages     = {375--81},
  volume    = {283},
  file      = {1999_Kelley_375.pdf:by-author/K/Kelley/1999_Kelley_375.pdf:PDF},
  keywords  = {Stacking},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Kelly2007,
  author    = {Casey P. Kelly and Christopher J. Cramer and Donald G. Truhlar},
  journal   = {J. Phys. Chem.},
  title     = {Single-Ion Solvation Free Energies and the Normal Hydrogen Electrode Potential in Methanol, Acetonitrile, and Dimethyl Sulfoxide},
  year      = {2007},
  pages     = {408--422},
  volume    = {111},
  abstract  = {The division of thermodynamic solvation free energies of electrolytes into contributions from individual ionic constituents is conventionally accomplished by using the single-ion solvation free energy of one reference ion, conventionally the proton, to set the single-ion scales. Thus, the determination of the free energy of solvation of the proton in various solvents is a fundamental issue of central importance in solution chemistry. In the present article, relative solvation free energies of ions and ion−solvent clusters in methanol, acetonitrile, and dimethyl sulfoxide (DMSO) have been determined using a combination of experimental and theoretical gas-phase free energies of formation, solution-phase reduction potentials and acid dissociation constants, and gas-phase clustering free energies. Applying the cluster pair approximation to differences between these relative solvation free energies leads to values of −263.5, −260.2, and −273.3 kcal/mol for the absolute solvation free energy of the proton in methanol, acetonitrile, and DMSO, respectively. The final absolute proton solvation free energies are used to assign absolute values for the normal hydrogen electrode potential and the solvation free energies of other single ions in the solvents mentioned above.},
  doi       = {10.1021/jp065403l},
  file      = {2007_Kelly_408.pdf:by-author/K/Kelly/2007_Kelly_408.pdf:PDF},
  keywords  = {Ion Hydration; Protein Physics},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Kelly1970,
  author    = {Kelly, Jr., Thomas J. and Smith, Hamilton O.},
  journal   = {Journal of Molecular Biology},
  title     = {A restriction enzyme from Hemophilus influenzae. II. Base Sequence of the Recognition Site},
  year      = {1970},
  issn      = {0022-2836},
  month     = {Jul},
  number    = {2},
  pages     = {393--409},
  volume    = {51},
  abstract  = {Hemphilus influenzae strain Rd contains an enzyme, endonuclease R, which specifically degrades foreign DNA. With phage T7 DNA as substrate the endonuclease introduces a limited number (about 40) double-strand breaks (5'-phosphoryl, 3'-hydroxyl). The limit product has an average length of about 1000 nucleotide pairs and contains no single-strand breaks. We have explored the nucleotide sequences at the 5'-ends of the limit product by labeling the 5'- phosphoryl groups (using polynucleotide kinase) and characterizing the labeled fragments released by various nucleases. Two classes of 5'-terminal sequences were obtained: pApApCpNp ... (60%) and pGpApCpNp ... (40%), where N indicates that the base in the 4th position is not unique. The dinucleoside monophosphates at the 3'-ends were isolated after micrococcal nuclease digestion of the limit product and identified as TpT(6O%) and TpC (40%). We conclude that endonuclease R of H. influenzae recognizes the following specific nucleotide sequence:
 5' ... pGpTpPy|pPupApCp... 3'
 3' ... pCpApPup|PypTpGp ... 5'
The implications of the twofold rotational symmetry of this sequence are discussed.},
  doi       = {10.1016/0022-2836(70)90150-6},
  file      = {1970_Kelly_393.pdf:by-author/K/Kelly/1970_Kelly_393.pdf:PDF},
  keywords  = {HindII; History; Recognition Model; Restriction Endonucleases (REases)},
  owner     = {saulius},
  pmid      = {5312501},
  publisher = {Elsevier BV},
  pubmedurl = {https://www.ncbi.nlm.nih.gov/pubmed/5312501},
  timestamp = {2016.12.04},
  creationdate = {2016-12-04T00:00:00},
  url       = {http://dx.doi.org/10.1016/0022-2836(70)90150-6},
}

@Article{Kelly1965,
  author    = {Kenneth L. Kelly},
  journal   = {Color Engineering},
  title     = {Twenty-two colors of maximum contrast},
  year      = {1965},
  pages     = {26--27},
  volume    = {3},
  file      = {:by-author/K/Kelly/1965_Kelly_26.pdf:PDF},
  owner     = {andrius},
  timestamp = {2016.04.15},
  creationdate = {2016-04-15T00:00:00},
  url       = {http://www.iscc.org/pdf/PC54_1724_001.pdf},
}

@Article{Kendrew1961,
  author    = {Kendrew, J. C.},
  journal   = {Scientific American},
  title     = {The Three-Dimensional Structure of a Protein Molecule},
  year      = {1961},
  pages     = {96--110},
  volume    = {205},
  doi       = {10.1038/scientificamerican1261-96},
  file      = {:by-author/K/Kendrew/1961_Kendrew_96.pdf:PDF},
  owner     = {andrius},
  timestamp = {2013.05.06},
  creationdate = {2013-05-06T00:00:00},
}

@Article{KenKnight1984,
  author    = {C. E. KenKnight},
  journal   = {Acta Crystallographica Section A},
  title     = {Comparison of Methods of Matching Protein Structures},
  year      = {1984},
  pages     = {708--712},
  volume    = {40},
  abstract  = {Two fast methods of superposing two sets of atomic coordinates by least-squares refinement are described and related to two earlier fast methods. A Newton method is applied to rotations of a 3 x 3 outer product matrix used previously by Ferro & Hermans [Acta Cryst. (1977), A33, 345-347] and by McLachlan [Acta Cryst. (1972), A28, 656-657]. Three of the methods work better if one molecule has its inertial matrix aligned with xyz. A Newton-Gauss method that rotates the coordinates can converge rapidly after a rough orientation using three strategic atoms. The average superposition takes about 0.003 s on a Cyber 175 with the best method, rotations about the xyz axes in turn. Experience with reliability is reported for large residuals.},
  doi       = {10.1107/S010876738400146X},
  file      = {:by-author/K/KenKnight/1984_KenKnight_708.pdf:PDF},
  owner     = {saulius},
  timestamp = {2011.12.21},
  creationdate = {2011-12-21T00:00:00},
}

@Article{Kennard1967,
  author    = {Kennard, O. and Speakman, J. C. and Donnay, J. D. H.},
  journal   = {Acta Crystallographica},
  title     = {Primary crystallographic data},
  year      = {1967},
  pages     = {445--449},
  volume    = {22},
  abstract  = {A report containing a list of recommendations on the presentation of crystallographic data in primary publications relating particularly to single-crystal work. The more important items of information are discussed in detail with examples. Numerical values of certain constants in common use are recorded.},
  doi       = {10.1107/S0365110X67000945},
  file      = {:by-author/K/Kennard/1967_Kennard_445.pdf:PDF},
  keywords  = {Databases},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0365110X67000945},
}

@TechReport{Kenney1999,
  author      = {J. F. Kenney},
  institution = {Joint Institute of the Physics of the Earth, Russian Academy of Sciences; Gas Resources Corporation, 11811 North Freeway, fl. 5, Houston, TX 77060, U.S.A.; JFK@alum.MIT.edu},
  title       = {The Evolution of Multicomponent Systems at High Pressures: II. The Alder-Wainwright, High-Density, Gas-Solid Phase Transition of the Hard-Sphere Fluid},
  year        = {1999},
  abstract    = {The thermodynamic stability of the hard-sphere gas has been examined, using the formalism of scaled particle theory [SPT], and by applying explicitly the conditions of stability required by both the second and third laws of thermodynamics.  The temperature and volume limits to the validity of SPT have also been examined.  It is demonstrated that scaled particle theory predicts absolute limits to the stability of the fluid phase of the hard-sphere system, at all temperatures within its range of validity.  Because scaled particle theory describes fluids equally well as dilute gases or dense liquids, the limits set upon the system stability by SPT must represent limits for the existence of the fluid phase and transition to the solid.  The reduced density at the stability limits determined by SPT is shown to agree exactly with those of that estimated for the Alder-Wainwright, supercritical, high-density gas-solid phase transition in a hard-sphere system, at a specific temperature, and closely over a range of more than 1,000K.  The temperature dependence of the gas-solid phase stability limits has been examined over the range 0.01K-10,000K.  It is further shown that SPT describes correctly the variation of the entropy of a hard-core fluid at low temperatures, requiring its entropy to vanish as T → 0 by undergoing a gas-solid phase transition at finite temperature and all pressures.},
  file        = {:by-author/K/Kenney/1999_Kenney.odt:},
  groups      = {sg/Molecular dynamics},
  keywords    = {Hard-spheres; Molecular-dynamics},
  owner       = {saulius},
  timestamp = {2015.03.03},
  creationdate = {2015-03-03T00:00:00},
}

@Manuscript{Keown1992,
  author    = {Keown, Jr., William F. and Philip Koopman and Aaron Collins},
  title     = {Performance of the {HARRIS} {RTX} 2000 Stack Architecture versus the {S}un 4 {SPARC} and the {S}un 3 M68020 Architectures},
  year      = {1992},
  keywords  = {Computer Architecture; Computer Science (CS); Performance Comparison},
  file      = {:by-author/K/Keown/1992_Keown.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Manuscript{Kerl2009,
  author    = {John Kerl},
  title     = {The Metropolis-Hastings algorithm by example},
  year      = {2009},
  keywords  = {Metropolis Hastings; Monte Carlo},
  file      = {:by-author/K/Kerl/2009_Kerl.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.10.04},
  creationdate = {2012-10-04T00:00:00},
}

@Presentation{Kerman2011,
  author    = {Jouni Kerman},
  title     = {Bayesian modeling in clinical trials: from early development to Phase {III}},
  year      = {2011},
  address   = {Stockholm},
  file      = {Jouni Kerman - 2011 - Bayesian modeling in clinical trials from early d.pdf:by-author/K/Kerman/2011_Kerman.pdf:PDF},
  groups    = {sg/Clinical Trials},
  owner     = {saulius},
  timestamp = {2015.12.14},
  creationdate = {2015-12-14T00:00:00},
  url       = {http://statistikframjandet.se/fms/wp-content/uploads/archive/2011/conferences/model_based_drug_development/Kerman.pdf},
  urldate   = {2015-12-12},
}

@TechReport{Kernighan1991a,
  author      = {Brian W. Kernighan},
  institution = {AT\&T Bell Laboratories},
  title       = {PIC -- A Graphics Language for Typesetting: User Manual},
  year        = {1991},
  month       = {May},
  file        = {:by-author/K/Kernighan/1991_Kernighan.pdf:PDF;:by-author/K/Kernighan/1991_Kernighan.ps:PostScript;:by-author/K/Kernighan/1991_Kernighan_tr116.ps.gz:PDF},
  keywords    = {Computer Science (CS); Groff; Manual; Nroff; Troff; Typesetting; Unix},
  owner       = {saulius},
  pages       = {tr116.ps.gz},
  timestamp = {2012.11.20},
  creationdate = {2012-11-20T00:00:00},
  url         = {http://cm.bell-labs.com/cm/cs/cstr/116.ps.gz},
}

@TechReport{Kernighan1982,
  author      = {Brian W. Kernighan},
  institution = {AT\&T Bell Laboratories},
  title       = {A Typesetter-independent TROFF},
  year        = {1982},
  month       = {March},
  file        = {:by-author/K/Kernighan/1982_Kernighan_tr97.ps.gz:PDF},
  keywords    = {Groff; Manual; Nroff; Troff; Typesetting; Unix},
  owner       = {saulius},
  pages       = {tr97.ps.gz},
  timestamp = {2012.11.20},
  creationdate = {2012-11-20T00:00:00},
  url         = {http://cm.bell-labs.com/cm/cs/cstr/97.ps.gz},
}

@TechReport{Kernighan1981,
  author      = {Brian W. Kernighan},
  institution = {AT\&T Bell Laboratories, Murray Hill, New Jersey 07974},
  title       = {Why Pascal is Not My Favorite Programming Language},
  year        = {1981},
  abstract    = {The programming language Pascal has become the dominant language of instruction in computer science education. It has also strongly influenced lan- guages developed subsequently, in particular Ada. Pascal was originally intended primarily as a teaching language, but it has been more and more often recommended as a language for serious programming as well, for example, for system programming tasks and even operating systems. Pascal, at least in its standard form, is just plain not suitable for serious programming. This paper discusses my personal discovery of some of the reasons why.},
  file        = {:by-author/K/Kernighan/1981_Kernighan.ps.gz:PostScript;:by-author/K/Kernighan/1981_Kernighan.pdf:PDF},
  owner       = {saulius},
  timestamp = {2015.02.27},
  creationdate = {2015-02-27T00:00:00},
}

@Manual{Kernighan1978a,
  title     = {A TROFF Tutorial},
  author    = {Brian W. Kernighan},
  month     = {August},
  year      = {1978},
  abstract  = {troff is a text-formatting program for driving the Graphic Systems phototypesetter on the UNIX† and GCOS operating systems. This device is capable of producing high quality text; this paper is an example of troff output. The phototypesetter itself normally runs with four fonts, containing roman, italic and bold letters (as on this page), a full greek alphabet, and a substantial number of spe- cial characters and mathematical symbols. Characters can be printed in a range of sizes, and placed anywhere on the page. troff allows the user full control over fonts, sizes, and character positions, as well as the usual features of a formatter — right-margin justification, automatic hyphenation, page titling and numbering, and so on. It also provides macros, arithmetic variables and operations, and conditional testing, for complicated formatting tasks. This document is an introduction to the most basic use of troff. It presents just enough information to enable the user to do simple formatting tasks like making view- graphs, and to make incremental changes to existing packages of troff commands. In most respects, the UNIX formatter nroff is identical to troff, so this document also serves as a tutorial on nroff.},
  file      = {:by-author/K/Kernighan/1978_Kernighan.ps:PostScript;:by-author/K/Kernighan/1978_Kernighan.pdf:PDF},
  keywords  = {Computer Science (CS); Groff; Nroff; Roff; Text Formatting; Troff; Typesetting; Unix},
  owner     = {saulius},
  timestamp = {2015.02.27},
  creationdate = {2015-02-27T00:00:00},
}

@Manual{Kernighan1978,
  title     = {Typesetting Mathematics — User’s Guide (Second Edition)},
  author    = {Brian W. Kernighan and Lorinda L. Cherry},
  month     = {August},
  year      = {1978},
  abstract  = {This is the user’s guide for a system for typesetting mathematics, using the phototypesetters on the UNIX† and GCOS operating systems.},
  file      = {:by-author/K/Kernighan/1978_Kernighan_a.ps:PostScript;:by-author/K/Kernighan/1978_Kernighan_a.pdf:PDF},
  keywords  = {Computer Science (CS); Eqn; Groff; Roff; Troff; Typesetting; Unix},
  owner     = {saulius},
  timestamp = {2015.02.27},
  creationdate = {2015-02-27T00:00:00},
}

@Manuscript{Kernighan1975,
  author    = {Brian W. Kernighan and Lorinda L. Cherry},
  title     = {A System for Typesetting Mathematics},
  year      = {1975},
  keywords  = {Computer Science (CS); Eqn; Groff; Roff; Troff; Typesetting; Unix},
  month     = {March},
  abstract  = {This paper describes the design and implementation of a system for typesetting mathematics. The language has been designed to be easy to learn and to use by people (for example, secretaries and mathematical typists) who know neither mathematics nor typesetting. Experience indicates that the language can be learned in an hour or so, for it has few rules and fewer exceptions. For typical expressions, the size and font changes, positioning, line drawing, and the like necessary to print according to mathematical conventions are all done automatically.},
  file      = {:by-author/K/Kernighan/1975_Kernighan.ps:PostScript;:by-author/K/Kernighan/1975_Kernighan.pdf:PDF},
  journal   = {CACM},
  owner     = {saulius},
  timestamp = {2015.02.27},
  creationdate = {2015-02-27T00:00:00},
}

@Article{Kerppola1991,
  author    = {Kerppola, T. K. and Curran, T.},
  journal   = {Science (New York, N.Y.)},
  title     = {DNA bending by Fos and Jun: the flexible hinge model.},
  year      = {1991},
  pages     = {1210--4},
  volume    = {254},
  abstract  = {DNA bending is essential for the assembly of multiprotein complexes that contact several DNA sequence elements. An approach based on phasing analysis was developed that allows determination of both the directed DNA bend angle and the orientation of DNA bending. This technique has been applied to the analysis of DNA bending by the transcription regulatory proteins Fos and Jun. Complexes that contained different combinations of full-length and truncated Fos and Jun induced DNA bends of different magnitudes and orientations. The DNA bends induced by the individual proteins were determined on the basis of a quantitative model for DNA bending by dimeric complexes. This information was used to visualize the consequences of DNA bending by Fos and Jun for the structures of Fos-Jun-DNA and Jun-DNA complexes.},
  file      = {:by-author/K/Kerppola/1991_Kerppola_1210.pdf:PDF},
  keywords  = {DNA Protein; Readout},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Kerr2003,
  author    = {Kerr, Iain D and Wadsworth, Ross I M and Cubeddu, Liza and Blankenfeldt, Wulf and Naismith, James H and White, Malcolm F},
  journal   = {The EMBO journal},
  title     = {Insights into ssDNA recognition by the OB fold from a structural and thermodynamic study of Sulfolobus SSB protein.},
  year      = {2003},
  pages     = {2561--70},
  volume    = {22},
  abstract  = {Information processing pathways such as DNA replication are conserved in eukaryotes and archaea and are significantly different from those found in bacteria. Single-stranded DNA-binding (SSB) proteins (or replication protein A, RPA, in eukaryotes) play a central role in many of these pathways. However, whilst euryarchaea have a eukaryotic-type RPA homologue, crenarchaeal SSB proteins appear much more similar to the bacterial proteins, with a single OB fold for DNA binding and a flexible C-terminal tail that is implicated in protein-protein interactions. We have determined the crystal structure of the SSB protein from the crenarchaeote Sulfolobus solfataricus to 1.26 A. The structure shows a striking and unexpected similarity to the DNA-binding domains of human RPA, providing confirmation of the close relationship between archaea and eukaryotes. The high resolution of the structure, together with thermodynamic and mutational studies of DNA binding, allow us to propose a molecular basis for DNA binding and define the features required for eukaryotic and archaeal OB folds.},
  file      = {Kerr_2003_2561.pdf:by-author/K/Kerr/2003_Kerr_2561.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Kesminiene2001,
  author    = {Kesminiene, A. and Maneliene, Z. and Vitkute, J. and Petrusyte, M. and Janulaitis, A.},
  journal   = {Nucleic acids research},
  title     = {A unique type II restriction endonuclease FspAI, that recognizes the octanucleotide sequence 5'-RTGC/GCAY-3'.},
  year      = {2001},
  pages     = {E120},
  volume    = {29},
  abstract  = {A new type II restriction endonuclease designated FspAI has been partially purified from a Flexibacter species Tv-m21K. FspAI recognizes the octanucleotide sequence 5'-RTGC/GCAY-3' and cleaves it in the center generating blunt-ended DNA fragments.},
  file      = {:by-author/K/Kesminiene/2001_Kesminiene_e120.pdf:PDF},
  keywords  = {TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Kessler2012,
  author    = {Mathieu Kessler and José Pérez},
  journal   = {Journal of Mathematical Chemistry},
  title     = {Equivalence Properties of the {C}remer \& {P}ople Puckering Coordinates for {N}-membered Rings},
  year      = {2012},
  pages     = {187--209},
  volume    = {50},
  doi       = {10.1007/s10910-011-9905-5},
  file      = {:by-author/K/Kessler/2012_Kessler_187.pdf:PDF},
  owner     = {andrius},
  timestamp = {2012.08.12},
  creationdate = {2012-08-12T00:00:00},
}

@Article{Khalifah2003,
  author    = {Khalifah, Raja G},
  journal   = {Biophysical chemistry},
  title     = {Reflections on Edsall's carbonic anhydrase: paradoxes of an ultra fast enzyme.},
  year      = {2003},
  pages     = {159--70},
  volume    = {100},
  abstract  = {John Edsall's investigations of human erythrocyte carbonic anhydrase, a zinc metalloenzyme that powerfully catalyzes the reversible hydration of carbon dioxide, highlighted a conundrum regarding the correct hydration product. The measured kinetic parameters could not be reconciled with the choice of carbonic acid, since its bimolecular recombination rate with enzyme would exceed the diffusion limit. The alternate choice of bicarbonate obviated the recombination rate problem but required that the active site deprotonation exceed the diffusion-limited maximum rate by an even greater extent. This paradox was resolved in favor of bicarbonate when the unsuspected role of buffer species indirectly deprotonating the enzyme was finally proposed, spurring numerous investigations to verify the hypothesis. Edsall's laboratory also reported the accidental discovery of the first competitive inhibitor, imidazole. This opened new avenues to understanding the binding of the CO(2) substrate and stimulated many investigations on this inhibitor. Paramagnetic NMR and crystallographic studies demonstrated that the only other known competitive inhibitor, phenol, apparently shared this unusual binding site. Despite enormous progress since Edsall's retirement, particularly the use of site-directed mutagenesis approaches, the precise interactions of carbon dioxide and bicarbonate with specific active site moieties remain as elusive today as when Edsall first considered these questions.},
  file      = {2003_Khalifah_159.pdf:by-author/K/Khalifah/2003_Khalifah_159.pdf:PDF},
  groups    = {sg/physical sg/methods, sg/physiology},
  keywords  = {Carbonic Anhydrases},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Manuscript{Khan1997,
  author    = {Fitratullah Khan and Sohail Anwar},
  title     = {Design and Construction of a PC-Based Stack Machine Simulator for Undergraduate Computer Science \& Engineering Courses},
  year      = {1997},
  keywords  = {Computer Architecture; Computer Science (CS); Hardware},
  abstract  = {A senior level compiler design course in an undergraduate computer science and engineering program usually deals with teaching the students the basics of compiler construction. A thorough understanding of the grammar of a formal language and a compiler designed for it can only be truly obtained by writing a working compiler for the language. A semester long feat of constructing the lexical, syntactic, semantic, and code generation phases of a compiler exposes the students to the inner workings of the compiler. The final phase of testing the integrity and effectiveness of the constructed compiler is both important and rewarding for a student. Furthermore, since the impetus of such an undergraduate course is to deal with the issues of compiler construction rather than intricacies of different machines, it is instructive to generate the code for a simple stack machine, incorporating a hardware stack, rather than dealing with a register-based machine such as a microcomputer. However, the educational institutions have the latter as a well established computing platform. Therefore, for testing a constructed compiler for a stack machine, it is feasible to make a microcomputer-based stack machine simulator. This paper presents the working design of a PC-based stack machine simulator developed by the authors for use in an undergraduate computer science and engineering course in compiler design. This paper begins by putting forward the architecture of the virtual stack machine for which the simulator is designed and constructed. The stack machine’s instruction set is explained and then followed by a discussion of its encoding scheme. The main data structures and the different stages of the simulator are elaborated upon, culminating in a description of the salient features of the simulator that make it an effective tool in a compiler construction course. This includes the simulator’s different analytical features such as measuring space-time complexity to analyze the effectiveness of a compiled code.},
  file      = {:by-author/K/Khan/1997_Khan_manuscript.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Khuzestani2013,
  author    = {Khuzestani, Reza Bashiri and Souri, Bubak},
  journal   = {Journal of Environmental Sciences},
  title     = {Evaluation of heavy metal contamination hazards in nuisance dust particles, in kurdistan province, western iran},
  year      = {2013},
  pages     = {1346--1354},
  volume    = {25},
  file      = {[PDF] from jesc.ac.cn:by-author/K/Khuzestani/2013_Khuzestani_1346.pdf:application/pdf;Snapshot:by-author/K/Khuzestani/2013_Khuzestani_1346.html:text/html},
  groups    = {sg/JAC2009},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/S1001074212601478},
  urldate   = {2015-08-31},
}

@Manuscript{Kienzle2001,
  author    = {Jörg Kienzle and Alexander Romanovsky},
  title     = {Implementing Exceptions in Open Multithreaded Transactions Based On Ada 95 Exceptions},
  year      = {2001},
  keywords  = {Ada 95; Computer Science (CS); Exception Handling; Open Multithreaded Transactions},
  abstract  = {This position paper shows how Ada 95 exceptions have been used in a prototype implementation of a transaction support in order to provide more elaborate exception han- dling. The paper summarizes the open multithreaded trans- action model, which is a transaction model suitable for concurrent programming languages, reviews in detail its elaborate exception handling features, and analyzes the exception mechanism provided by the Ada 95 programming language. Different interfaces to the transaction support for the application programmer are presented, and the problems encountered during implementation of the proto- type with respect to exception handling are discussed.},
  file      = {:by-author/K/Kienzle/2001_Kienzle.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Manuscript{Kieu2004,
  author    = {Tien D. Kieu},
  title     = {Quantum Algorithm for {H}ilbert’s Tenth Problem},
  year      = {2004},
  keywords  = {Computer Science (CS); Quantum Computers},
  file      = {:by-author/K/Kieu/2004_Kieu_0110136v3.pdf:PDF},
  owner     = {saulius},
  pages     = {0110136v3},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Presentation{Kikhney2014,
  author       = {Kikhney, Alexey G.},
  title        = {Data reduction and processing},
  year         = {2014},
  organization = {EMBL, DESY},
  file         = {:by-author/K/Kikhney/2014_Kikhney.pdf:PDF},
  keywords     = {Aggregation; Data Processing; Data Reduction; Guinier; Kratky; Molecular Weight (MW); Porod; SAXS},
  owner        = {em},
  timestamp = {2014.05.26},
  creationdate = {2014-05-26T00:00:00},
}

@Article{Killean1967,
  author    = {Killean, R. C. G.},
  journal   = {Acta Crystallographica},
  title     = {Linear programming and the refinement of structures},
  year      = {1967},
  pages     = {905--907},
  volume    = {23},
  doi       = {10.1107/s0365110x67004025},
  file      = {:by-author/K/Killean/1967_Killean_905.pdf:PDF},
  owner     = {saulius},
  timestamp = {2014.11.06},
  creationdate = {2014-11-06T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0365110X67004025},
}

@Article{Kim2007,
  author    = {Chae Un Kim and Quan Hao and Sol M Gruner},
  journal   = {Acta Crystallographica Section D},
  title     = {High-pressure cryocooling for capillary sample cryoprotection and diffraction phasing at long wavelengths},
  year      = {2007},
  pages     = {653--659},
  volume    = {63},
  abstract  = {Crystal cryocooling is usually employed to reduce radiation damage during X-ray crystallography. Recently, a high-pressure cryocooling method has been developed which results in excellent diffraction-quality crystals without the use of penetrative cryoprotectants. Three new developments of the method are presented here: (i) Xe-He high-pressure cryocooling for Xe SAD phasing, (ii) native sulfur SAD phasing and (iii) successful cryopreservation of crystals in thick-walled capillaries without additional cryoprotectants other than the native mother liquor. These developments may be useful for structural solution of proteins without the need for selenomethionine incorporation and for high-throughput protein crystallography.},
  doi       = {10.1107/S0907444907011924},
  file      = {:by-author/K/Kim/2007_Kim_653.pdf:PDF},
  owner     = {saulius},
  timestamp = {2011.12.16},
  creationdate = {2011-12-16T00:00:00},
}

@Article{Kim2001,
  author    = {Kim, C Y and Chandra, P P and Jain, A and Christianson, D W},
  journal   = {Journal of the American Chemical Society},
  title     = {Fluoroaromatic-fluoroaromatic interactions between inhibitors bound in the crystal lattice of human carbonic anhydrase II.},
  year      = {2001},
  pages     = {9620--7},
  volume    = {123},
  abstract  = {Intermolecular interactions of eleven different fluoroaromatic inhibitors are probed within the scaffolding of the crystal lattice of Phe-131--&gt;Val carbonic anhydrase II. The degree and pattern of fluorine substitution on the inhibitor benzyl ring modulate its size, shape, and electronic character. In turn, these properties affect the geometry of intermolecular interactions between the fluoroaromatic rings of two different inhibitor molecules bound in the crystal lattice, as determined by X-ray crystallography. Depending on the degree and pattern of fluorine substitution, we observe a face-to-face (aromatic-aromatic) interaction, an atom-to-face (carbonyl-aromatic) interaction, or no interaction at all. These interaction geometries are analyzed with regard to van der Waals, electrostatic, and possible charge-transfer effects. For the aromatic-aromatic interactions investigated in this study, with aromatic ring quadrupoles specifically "tuned" by the degree and pattern of fluorination, the structural results suggest that London forces and charge-transfer complexation dominate over weakly polar electrostatic interactions in the association of aromatic ring pairs.},
  file      = {2001_Kim_9620.pdf:by-author/K/Kim/2001_Kim_9620.pdf:PDF},
  groups    = {sg/inhibitors, sg/physical sg/methods, sg/hCA2},
  keywords  = {Carbonic Anhydrases; Inhibitors},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Kim2005,
  author    = {Kim, Jeong-Sun and DeGiovanni, Andy and Jancarik, Jaru and Adams, Paul D. and Yokota, Hisao and Kim, Rosalind and Kim, Sung-Hou},
  journal   = {Proceedings of the National Academy of Sciences of the United States of America},
  title     = {Crystal structure of DNA sequence specificity subunit of a type I restriction-modification enzyme and its functional implications.},
  year      = {2005},
  pages     = {3248--53},
  volume    = {102},
  abstract  = {Type I restriction-modification enzymes are differentiated from type II and type III enzymes by their recognition of two specific dsDNA sequences separated by a given spacer and cleaving DNA randomly away from the recognition sites. They are oligomeric proteins formed by three subunits: a specificity subunit, a methylation subunit, and a restriction subunit. We solved the crystal structure of a specificity subunit from Methanococcus jannaschii at 2.4-A resolution. Two highly conserved regions (CRs) in the middle and at the C terminus form a coiled-coil of long antiparallel alpha-helices. Two target recognition domains form globular structures with almost identical topologies and two separate DNA binding clefts with a modeled DNA helix axis positioned across the CR helices. The structure suggests that the coiled-coil CRs act as a molecular ruler for the separation between two recognized DNA sequences. Furthermore, the relative orientation of the two DNA binding clefts suggests kinking of bound dsDNA and exposing of target adenines from the recognized DNA sequences.},
  file      = {:by-author/K/Kim/2005_Kim_3248.pdf:PDF},
  keywords  = {TypeI},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Kim2000,
  author    = {Kim, S. S. and Tam, J. K. and Wang, A. F. and Hegde, R. S.},
  journal   = {The Journal of biological chemistry},
  title     = {The structural basis of DNA target discrimination by papillomavirus E2 proteins.},
  year      = {2000},
  pages     = {31245--54},
  volume    = {275},
  abstract  = {The papillomavirus E2 proteins regulate the transcription of all papillomavirus genes and are necessary for viral DNA replication. Disruption of the E2 gene is commonly associated with malignancy in cervical carcinoma, indicating that E2 has a role in regulating tumor progression. Although the E2 proteins from all characterized papillomaviruses bind specifically to the same 12-base pair DNA sequence, the cancer-associated human papillomavirus E2 proteins display a unique ability to detect DNA flexibility and intrinsic curvature. To understand the structural basis for this phenomenon, we have determined the crystal structures of the human papillomavirus-18 E2 DNA-binding domain and its complexes with high and low affinity binding sites. The E2 protein is a dimeric beta-barrel and the E2-DNA interaction is accompanied by a large deformation of the DNA as it conforms to the E2 surface. DNA conformation and E2-DNA contacts are similar in both high and low affinity complexes. The differences in affinity correlate with the flexibility of the DNA sequence. Preferences of E2 proteins from different papillomavirus strains for flexible or prevent DNA targets correlate with the distribution of positive charge on their DNA interaction surfaces, suggesting a role for electrostatic forces in the recognition of DNA deformability.},
  file      = {:by-author/K/Kim/2000_Kim_31245.pdf:PDF},
  keywords  = {DNA Protein; Readout},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Kim2000a,
  author    = {Kim, Yoon-Ho and Yu, Rong and Kulik, Sergei P. and Shih, Yanhua and Scully, Marlan O.},
  journal   = {Phys. Rev. Lett.},
  title     = {Delayed ``Choice'' Quantum Eraser},
  year      = {2000},
  pages     = {1--5},
  volume    = {84},
  abstract  = {We report a delayed “choice” quantum eraser experiment of the type proposed by Scully and Drühl (where the “choice” is made randomly by a photon at a beam splitter). The experimental results demonstrate the possibility of delayed determination of particlelike or wavelike behavior via quantum entanglement. The which-path or both-path information of a quantum can be marked or erased by its entangled twin even after the registration of the quantum.},
  doi       = {10.1103/PhysRevLett.84.1},
  file      = {2000_Kim_1.pdf:by-author/K/Kim/2000_Kim_1.pdf:PDF;2000_Kim_1-arXiv-manuscript.pdf:by-author/K/Kim/2000_Kim_1-arXiv-manuscript.pdf:PDF},
  issue     = {1},
  keywords  = {Delayed Coice Experiments; Quantum Mechanics (QM); Wave Particle Duality},
  owner     = {saulius},
  publisher = {American Physical Society},
  timestamp = {2012.11.02},
  creationdate = {2012-11-02T00:00:00},
  url       = {http://link.aps.org/doi/10.1103/PhysRevLett.84.1},
}

@Article{Kinch2005,
  author    = {Kinch, Lisa N. and Ginalski, Krzysztof and Rychlewski, Leszek and Grishin, Nick V.},
  journal   = {Nucleic acids research},
  title     = {Identification of novel restriction endonuclease-like fold families among hypothetical proteins.},
  year      = {2005},
  pages     = {3598--605},
  volume    = {33},
  abstract  = {Restriction endonucleases and other nucleic acid cleaving enzymes form a large and extremely diverse superfamily that display little sequence similarity despite retaining a common core fold responsible for cleavage. The lack of significant sequence similarity between protein families makes homology inference a challenging task and hinders new family identification with traditional sequence-based approaches. Using the consensus fold recognition method Meta-BASIC that combines sequence profiles with predicted protein secondary structure, we identify nine new restriction endonuclease-like fold families among previously uncharacterized proteins and predict these proteins to cleave nucleic acid substrates. Application of transitive searches combined with gene neighborhood analysis allow us to confidently link these unknown families to a number of known restriction endonuclease-like structures and thus assign folds to the uncharacterized proteins. Finally, our method identifies a novel restriction endonuclease-like domain in the C-terminus of RecC that is not detected with structure-based searches of the existing PDB database.},
  file      = {:by-author/K/Kinch/2005_Kinch_3598.pdf:PDF},
  keywords  = {TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Manuscript{King2000,
  author    = {Chad King},
  title     = {Abort, retry, fail: protection for software-related inventions in the wake of state street bank \& trust co. v. signature financial group, inc.},
  year      = {2000},
  keywords  = {Patentai; Teise},
  month     = {May},
  file      = {:by-author/K/King/2000_King.doc:DOC},
  owner     = {saulius},
  timestamp = {2015.02.28},
  creationdate = {2015-02-28T00:00:00},
}

@Article{King1995,
  author    = {Gary King},
  journal   = {PS: Political Science and Politics},
  title     = {Replication, Replication},
  year      = {1995},
  pages     = {444--452},
  volume    = {28},
  file      = {:by-author/K/King/1995_King_444.pdf:PDF},
  keywords  = {Data Management},
  owner     = {saulius},
  timestamp = {2012.04.09},
  creationdate = {2012-04-09T00:00:00},
  url       = {http://www.jstor.org/stable/420301},
}

@Article{King2000a,
  author    = {King, G. F. and Shih, Y. L. and Maciejewski, M. W. and Bains, N. P. and Pan, B. and Rowland, S. L. and Mullen, G. P. and Rothfield, L. I.},
  journal   = {Nature structural biology},
  title     = {Structural basis for the topological specificity function of MinE.},
  year      = {2000},
  pages     = {1013--7},
  volume    = {7},
  abstract  = {Correct positioning of the division septum in Escherichia coli depends on the coordinated action of the MinC, MinD and MinE proteins. Topological specificity is conferred on the MinCD division inhibitor by MinE, which counters MinCD activity only in the vicinity of the preferred midcell division site. Here we report the structure of the homodimeric topological specificity domain of Escherichia coli MinE and show that it forms a novel alphabeta sandwich. Structure-directed mutagenesis of conserved surface residues has enabled us to identify a spatially restricted site on the surface of the protein that is critical for the topological specificity function of MinE.},
  file      = {:by-author/K/King/2000_King_1013.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{King2013,
  author    = {King, Gordon J. and Chanson, Aurélie H. and McCallum, Emily J. and Ohme-Takagi, Masaru and Byriel, Karl and Hill, Justine M. and Martin, Jennifer L. and Mylne, Joshua S.},
  journal   = {THE JOURNAL OF BIOLOGICAL CHEMISTRY},
  title     = {The Arabidopsis B3 Domain Protein VERNALIZATION1 (VRN1) Is Involved in Processes Essential for Development, with Structural and Mutational Studies Revealing Its DNA-binding Surface},
  year      = {2013},
  pages     = {3198 –3207},
  volume    = {288},
  abstract  = {The B3 DNA-binding domain is a plant-specific domain found throughout the plant kingdom from the alga Chlamy- domonas to grasses and flowering plants. Over 100 B3 domain- containing proteins are found in the model plant Arabidopsis thaliana, and one of these is critical for accelerating flowering in response to prolonged cold treatment, an epigenetic process called vernalization. Despite the specific phenotype of genetic vrn1 mutants, the VERNALIZATION1 (VRN1) protein localizes throughout the nucleus and shows sequence-nonspecific bind- ing in vitro. In this work, we used a dominant repressor tag that overcomes genetic redundancy to show that VRN1 is involved in processes beyond vernalization that are essential for Arabidop- sis development. To understand its sequence-nonspecific bind- ing, we crystallized VRN1(208 –341) and solved its crystal struc- ture to 1.6 Å resolution using selenium/single-wavelength anomalous diffraction methods. The crystallized construct comprises the second VRN1 B3 domain and a preceding region conserved among VRN1 orthologs but absent in other B3 domains. We established the DNA-binding face using NMR and then mutated positively charged residues on this surface with a series of 16 Ala and Glu substitutions, ensuring that the protein fold was not disturbed using heteronuclear single quantum cor- relation NMR spectra. The triple mutant R249E/R289E/R296E was almost completely incapable of DNA binding in vitro. Thus, we have revealed that although VRN1 is sequence-nonspecific in DNA binding, it has a defined DNA-binding surface.},
  doi       = {10.1074/jbc.M112.438572},
  file      = {:by-author/K/King/2013_King_3198.pdf:PDF},
  keywords  = {B3; Pseudobarrel; Structure; VRN1},
  owner     = {em},
  timestamp = {2013.09.04},
  creationdate = {2013-09-04T00:00:00},
  url       = {http://www.jbc.org/content/suppl/2012/12/19/M112.438572.DC1.html},
}

@Article{King1976,
  author     = {King, James C.},
  journal    = {Commun. ACM},
  title      = {Symbolic Execution and Program Testing},
  year       = {1976},
  issn       = {0001-0782},
  month      = jul,
  number     = {7},
  pages      = {385--394},
  volume     = {19},
  acmid      = {360252},
  address    = {New York, NY, USA},
  doi        = {10.1145/360248.360252},
  file       = {1976_King_385.pdf:by-author/K/King/1976_King_385.pdf:PDF},
  groups     = {sg/Correctness proofs},
  issue_date = {July 1976},
  keywords   = {Correctness Proofs; Program Debugging; Program Proving; Program Testing; Program Verification; Symbolic Execution; Symbolic Interpretation},
  numpages   = {10},
  owner      = {saulius},
  publisher  = {ACM},
  timestamp = {2016.11.25},
  creationdate = {2016-11-25T00:00:00},
  url        = {http://doi.acm.org/10.1145/360248.360252},
}

@Article{Kirillova2007,
  author    = {Kirillova, Olga and Chruszcz, Maksymilian and Shumilin, Igor A. and Skarina, Tatiana and Gorodichtchenskaia, Elena and Cymborowski, Marcin and Savchenko, Alexei and Edwards, Aled and Minor, Wladek},
  journal   = {Acta crystallographica. Section D, Biological crystallography},
  title     = {An extremely SAD case: structure of a putative redox-enzyme maturation protein from Archaeoglobus fulgidus at 3.4 A resolution.},
  year      = {2007},
  pages     = {348--54},
  volume    = {63},
  abstract  = {This paper describes the crystal structure of AF0173, a putative redox-enzyme maturation protein (REMP) from Archaeoglobus fulgidus. The REMPs serve as chaperones in the maturation of extracytoplasmic oxidoreductases in archaea and bacteria. The all-helical subunits of AF0173 form a dimer arising from the interaction of residues located in a funnel-shaped cavity on one subunit surface with an uncut expression tag from the other subunit. This cavity is likely to represent a binding site for the twin-arginine motif that interacts with REMPs. The conservation of the overall fold in AF0173 and bacterial REMPs as well as the presence of conserved residues in their putative binding sites indicates that REMPs act in a similar manner in archaea and bacteria despite their limited sequence similarity. A model of the binding of the twin-arginine motif by AF0173 is suggested. The solution of the AF0173 structure by the single anomalous dispersion method represents an extreme case of SAD structure determination: low resolution (3.4 A), the absence of NCS and the presence of only two anomalously scattering atoms in the asymmetric unit. An unusually high solvent content (73%) turned out to be important for the success of the density-modification procedures.},
  doi       = {10.1107/S0907444906055065},
  file      = {:by-author/K/Kirillova/2007_Kirillova_348.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Kirklin2015,
  author    = {Kirklin, Scott and Saal, James E and Meredig, Bryce and Thompson, Alex and Doak, Jeff W and Aykol, Muratahan and Rühl, Stephan and Wolverton, Chris},
  journal   = {npj Computational Materials},
  title     = {The {Open Quantum Materials Database (OQMD)}: Assessing the Accuracy of {DFT} Formation Energies},
  year      = {2015},
  issn      = {2057-3960},
  month     = {Dec},
  number    = {1},
  pages     = {15010},
  volume    = {1},
  doi       = {10.1038/npjcompumats.2015.10},
  file      = {:by-author/K/Kirklin/2015_Kirklin_15010.pdf:PDF;:by-author/K/Kirklin/2015_Kirklin_preprint.pdf:PDF},
  groups    = {am/OQMD},
  owner     = {andrius},
  publisher = {Springer Nature},
  timestamp = {2015.07.13},
  creationdate = {2015-07-13T00:00:00},
  url       = {http://dx.doi.org/10.1038/npjcompumats.2015.10},
}

@Article{Kirkwood1951,
  author    = {Kirkwood, John G. and Buff, Frank P.},
  journal   = {The Journal of Chemical Physics},
  title     = {The Statistical Mechanical Theory of Solutions. I},
  year      = {1951},
  pages     = {774--777},
  volume    = {19},
  abstract  = {A general statistical mechanical theory of solutions is developed with the aid of the theory of composition fluctuations in the grand canonical ensemble. It is shown that the derivatives of the chemical potentials and osmotic pressure with respect to concentrations, the partial molar volumes, and compressibility may be expressed in terms of integrals of the radial distribution functions of the several types of molecular pairs present in the solution. Explicit coefficients of a q‐fraction expansion of the thermodynamic variables are presented in a detailed treatment of the two‐component system.},
  doi       = {10.1063/1.1748352},
  file      = {1951_Kirkwood_774.pdf:by-author/K/Kirkwood/1951_Kirkwood_774.pdf:PDF},
  keywords  = {Statistical Mechanics; Theory of Solutions},
  owner     = {saulius},
  timestamp = {2015.03.13},
  creationdate = {2015-03-13T00:00:00},
  url       = {http://scitation.aip.org/content/aip/journal/jcp/19/6/10.1063/1.1748352},
}

@Article{Kiser2009,
  author    = {Kiser, Philip D. and Lorimer, George H. and Palczewski, Krzysztof},
  journal   = {Acta Crystallographica Section F},
  title     = {Use of thallium to identify monovalent cation binding sites in GroEL},
  year      = {2009},
  pages     = {967–971},
  volume    = {F65},
  abstract  = {GroEL is a bacterial chaperone protein that assembles into a homotetradeca- meric complex exhibiting D7 symmetry and utilizes the co-chaperone protein GroES and ATP hydrolysis to assist in the proper folding of a variety of cytosolic proteins. GroEL utilizes two metal cofactors, Mg2+ and K+, to bind and hydrolyze ATP. A K+-binding site has been proposed to be located next to the nucleotide-binding site, but the available structural data do not firmly support this conclusion. Moreover, more than one functionally significant K+-binding site may exist within GroEL. Because K+ has important and complex effects on GroEL activity and is involved in both positive (intra-ring) and negative (inter- ring) cooperativity for ATP hydrolysis, it is important to determine the exact location of these cation-binding site(s) within GroEL. In this study, the K+ mimetic Tl+ was incorporated into GroEL crystals, a moderately redundant ̊ 3.94 A resolution X-ray diffraction data set was collected from a single crystal and the strong anomalous scattering signal from the thallium ion was used to identify monovalent cation-binding sites. The results confirmed the previously proposed placement of K+ next to the nucleotide-binding site and also identified additional binding sites that may be important for GroEL function and co- operativity. These findings also demonstrate the general usefulness of Tl+ for the identification of monovalent cation-binding sites in protein crystal structures, even when the quality and resolution of the diffraction data are relatively low.},
  doi       = {10.1107/S1744309109032928},
  file      = {:by-author/K/Kiser/2009_Kiser_967.pdf:PDF},
  keywords  = {ATPase; GroEL; Heavy Atoms Derivative; Metal Binding; Potassium; Protein Crystallization; Thallium},
  owner     = {em},
  timestamp = {2014.05.22},
  creationdate = {2014-05-22T00:00:00},
}

@Article{Kisonaite2014,
  author      = {Miglė Kišonaitė and Asta Zubrienė and Edita Capkauskaitė and Alexey Smirnov and Joana Smirnovienė and Visvaldas Kairys and Vilma Michailovienė and Elena Manakova and Saulius Gražulis and Daumantas Matulis},
  journal     = {PLoS One},
  title       = {Intrinsic Thermodynamics and Structure Correlation of Benzenesulfonamides with a Pyrimidine Moiety Binding to Carbonic Anhydrases I, II, VII, XII, and XIII.},
  year        = {2014},
  pages       = {e114106},
  volume      = {9},
  abstract    = {The early stage of drug discovery is often based on selecting the highest affinity lead compound. To this end the structural and energetic characterization of the binding reaction is important. The binding energetics can be resolved into enthalpic and entropic contributions to the binding Gibbs free energy. Most compound binding reactions are coupled to the absorption or release of protons by the protein or the compound. A distinction between the observed and intrinsic parameters of the binding energetics requires the dissection of the protonation/deprotonation processes. Since only the intrinsic parameters can be correlated with molecular structural perturbations associated with complex formation, it is these parameters that are required for rational drug design. Carbonic anhydrase (CA) isoforms are important therapeutic targets to treat a range of disorders including glaucoma, obesity, epilepsy, and cancer. For effective treatment isoform-specific inhibitors are needed. In this work we investigated the binding and protonation energetics of sixteen [(2-pyrimidinylthio)acetyl]benzenesulfonamide CA inhibitors using isothermal titration calorimetry and fluorescent thermal shift assay. The compounds were built by combining four sulfonamide headgroups with four tailgroups yielding 16 compounds. Their intrinsic binding thermodynamics showed the limitations of the functional group energetic additivity approach used in fragment-based drug design, especially at the level of enthalpies and entropies of binding. Combined with high resolution crystal structural data correlations were drawn between the chemical functional groups on selected inhibitors and intrinsic thermodynamic parameters of CA-inhibitor complex formation.},
  doi         = {10.1371/journal.pone.0114106},
  file        = {2014_Kišonaitė_1.pdf:by-author/K/Kišonaitė/2014_Kišonaitė_1.pdf:PDF},
  groups      = {sg/inhibitors, sg/intrinsic parameters, sg/thermodynamics},
  institution = {Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Graičiūno 8, Vilnius, LT-02241, Lithuania.},
  language    = {eng},
  medline-pst = {epublish},
  owner       = {alexey},
  pii         = {PONE-D-14-37834},
  pmid        = {25493428},
  timestamp = {2015.01.09},
  creationdate = {2015-01-09T00:00:00},
  url         = {http://dx.doi.org/10.1371/journal.pone.0114106},
}

@Article{Kissinger2001,
  author    = {Kissinger, C R and Gehlhaar, D K and Smith, B A and Bouzida, D},
  journal   = {Acta crystallographica. Section D, Biological crystallography},
  title     = {Molecular replacement by evolutionary search.},
  year      = {2001},
  pages     = {1474--9},
  volume    = {57},
  file      = {2001_Kissinger_1474.pdf:by-author/K/Kissinger/2001_Kissinger_1474.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Kitagawa2016,
  author       = {Kitagawa, H. and Ohtsu, H. and Cruz-Cabeza, A. J. and Kawano, M.},
  journal      = {{IUCrJ}},
  title        = {Isolation and evolution of labile sulfur allotropes via kinetic encapsulation in interactive porous networks},
  year         = {2016},
  issn         = {2052-2525},
  number       = {4},
  pages        = {232--236},
  volume       = {3},
  abstract     = {The isolation and characterization of small sulfur allotropes have long remained unachievable because of their extreme lability. This study reports the first direct observation of disulfur (S2) with X-ray crystallography. Sulfur gas was kinetically trapped and frozen into the pores of two Cu-based porous coordination networks containing interactive iodide sites. Stabilization of S2 was achieved either through physisorption or chemisorption on iodide anions. One of the networks displayed shape selectivity for linear molecules only, therefore S2 was trapped and remained stable within the material at room temperature and higher. In the second network, however, the S2 molecules reacted further to produce bent-S3 species as the temperature was increased. Following the thermal evolution of the S2 species in this network using X-ray diffraction and Raman spectroscopy unveiled the generation of a new reaction intermediate never observed before, the cyclo-tri­sulfur dication (cyclo-S32+). It is envisaged that kinetic guest trapping in interactive crystalline porous networks will be a promising method to investigate transient chemical species.},
  date         = {2016-07-01},
  doi          = {10.1107/S2052252516008423},
  file         = {Full Text PDF:by-author/K/Kitagawa/2016_Kitagawa_232.pdf:PDF;Snapshot:by-author/K/Kitagawa/2016_Kitagawa_232.html:URL},
  groups       = {sg/MOF, sg/MOFs, am/MOFs},
  journaltitle = {{IUCrJ}},
  keywords     = {Allotropes; Coordination Polymers; Kinetic Trapping; Metal-Organic Frameworks (MOF); Porous Coordination Networks; Sulfur; Transient Chemical Species; X-ray Diffraction},
  langid       = {english},
  owner        = {saulius},
  rights       = {http://creativecommons.org/licenses/by/2.0/uk},
  shortjournal = {{IUCrJ}},
  timestamp = {2017.01.29},
  creationdate = {2017-01-29T00:00:00},
  url          = {http://scripts.iucr.org/cgi-bin/paper?ed5008},
  urldate      = {2017-01-29},
}

@Article{Kitani1985,
  author    = {Kitani, T. and Yoda, K. and Ogawa, T. and Okazaki, T.},
  journal   = {Journal of molecular biology},
  title     = {Evidence that discontinuous DNA replication in Escherichia coli is primed by approximately 10 to 12 residues of RNA starting with a purine.},
  year      = {1985},
  pages     = {45--52},
  volume    = {184},
  abstract  = {Intact primer RNA for discontinuous DNA replication of Escherichia coli has been detected by specific labeling in vitro of its 5'-terminal tri- (or di-) phosphate group with vaccinia guanylyltransferase and [alpha-32P]GTP. A mutant defective either in RNase H or in both RNase H and DNA polymerase I accumulated about 10 or 30 times more intact primer RNA, respectively, than wild-type cells. The primers started with purine in an A to G ratio of 5 and the most abundant 5'-terminal dinucleotide sequence was (p)ppA-Pu. The chain length of the intact primer RNA was approximately 10 to 12 nucleotide residues. The structural properties of the E. coli primer RNa resemble those of the eukaryotic primer RNA.},
  file      = {:by-author/K/Kitani/1985_Kitani_45.pdf:PDF},
  keywords  = {Ecoli; {gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Kivelae2005,
  author    = {Kivelä, Antti-J and Kivelä, Jyrki and Saarnio, Juha and Parkkila, Seppo},
  journal   = {World journal of gastroenterology : WJG},
  title     = {Carbonic anhydrases in normal gastrointestinal tract and gastrointestinal tumours.},
  year      = {2005},
  pages     = {155--63},
  volume    = {11},
  abstract  = {Carbonic anhydrases (CAs) catalyse the hydration of CO2 to bicarbonate at physiological pH. This chemical interconversion is crucial since HCO3- is the substrate for several biosynthetic reactions. This review is focused on the distribution and role of CA isoenzymes in both normal and pathological gastrointestinal (GI) tract tissues. It has been known for many years that CAs are widely present in the GI tract and play important roles in several physiological functions such as production of saliva, gastric acid, bile, and pancreatic juice as well as in absorption of salt and water in intestine. New information suggests that these enzymes participate in several processes that were not envisioned earlier. Especially, the recent reports on plasma membrane-bound isoenzymes IX and XII have raised considerable interest since they were reported to participate in cancer invasion and spread. They are induced by tumour hypoxia and may also play a role in von Hippel-Lindau (VHL)-mediated carcinogenesis.},
  file      = {2005_Kivela_155.pdf:by-author/K/Kivelä/2005_Kivelä_155.pdf:PDF},
  groups    = {sg/cancer, sg/medicine},
  keywords  = {Carbonic Anhydrases},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@PhdThesis{Kivela2004,
  author    = {Hanna Kivelä},
  school    = {University of Helsinki},
  title     = {Marine icosahedral membrane-containing dsDNA bacteriophage PM2: virion structure and host cell penetration},
  year      = {2004},
  file      = {:by-author/K/Kivelä/2004_Kivelä_phdthesis.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@InBook{Klebe1994,
  author    = {Klebe, Gerhard},
  chapter   = {13},
  editor    = {Biirgi, H.B. and Dunitz, J.D.},
  pages     = {543–603},
  publisher = {Wiley-Blackwell},
  title     = {Structure Correlation and Ligand/Receptor Interactions},
  year      = {1994},
  isbn      = {http://id.crossref.org/isbn/9783527290420},
  volume    = {2},
  doi       = {10.1002/9783527616091.ch13},
  file      = {1994_Klebe_543.pdf:by-author/K/Klebe/1994_Klebe_543.pdf:PDF},
  groups    = {sg/Crystallography, am/Crystallography},
  journal   = {Structure Correlation},
  owner     = {andrius},
  timestamp = {2016.12.21},
  creationdate = {2016-12-21T00:00:00},
  url       = {http://dx.doi.org/10.1002/9783527616091.ch13},
}

@Article{Klebe2015,
  author    = {Klebe, Gerhard},
  journal   = {Nat. Rev. Drug Discov.},
  title     = {Applying thermodynamic profiling in lead finding and optimization},
  year      = {2015},
  issn      = {1474-1776},
  pages     = {95--110},
  volume    = {14},
  abstract  = {Small-molecule drug discovery involves the optimization of various physicochemical properties of a ligand, particularly its binding affinity for its target receptor (or receptors). In recent years, there has been growing interest in using thermodynamic profiling of ligand-receptor interactions in order to select and optimize those ligands that might be most likely to become drug candidates with desirable physicochemical properties. The thermodynamics of binding is influenced by multiple factors, including hydrogen bonding and hydrophobic interactions, desolvation, residual mobility, dynamics and the local water structure. This article discusses key issues in understanding the effects of these factors and applying this knowledge in drug discovery.},
  file      = {2015_Klebe_95.pdf:by-author/K/Klebe/2015_Klebe_95.pdf:PDF;:by-author/K/Klebe/2015_Klebe_95_supplements/nrd4486-s1.pdf:PDF;:by-author/K/Klebe/2015_Klebe_95_supplements/nrd4486-s2.pdf:PDF;:by-author/K/Klebe/2015_Klebe_95_supplements/nrd4486-s3.pdf:PDF},
  keywords  = {Drug Design; Thermodynamics},
  owner     = {saulius},
  publisher = {Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},
  timestamp = {2015.07.01},
  creationdate = {2015-07-01T00:00:00},
  url       = {http://dx.doi.org/10.1038/nrd4486},
}

@Article{Klebe1994a,
  author    = {Klebe, Gerhard and Mietzner, Thomas},
  journal   = {Journal of Computer-Aided Molecular Design},
  title     = {A fast and efficient method to generate biologically relevant conformations},
  year      = {1994},
  issn      = {1573-4951},
  month     = {Oct},
  number    = {5},
  pages     = {583–606},
  volume    = {8},
  doi       = {10.1007/bf00123667},
  file      = {1994_Klebe_583.pdf:by-author/K/Klebe/1994_Klebe_583.pdf:PDF},
  groups    = {sg/Crystallography, am/Crystallography},
  owner     = {andrius},
  publisher = {Springer Nature},
  timestamp = {2016.12.22},
  creationdate = {2016-12-22T00:00:00},
  url       = {http://dx.doi.org/10.1007/bf00123667},
}

@Article{Kleene1958,
  author    = {S. C. Kleene},
  journal   = {ICM},
  title     = {Mathematical Logic: Constructive and Non-Constructive Operations},
  year      = {1958},
  pages     = {137},
  file      = {:by-author/K/Kleene/1958_Kleene_137.pdf:PDF},
  owner     = {saulius},
  timestamp = {2015.02.17},
  creationdate = {2015-02-17T00:00:00},
  url       = {http://www.mathunion.org/ICM/ICM1958/Main/icm1958.0137.0153.ocr.pdf},
}

@Lecture{Klein1998,
  author    = {Joshua P. Klein and Thomas H. Leete and Harvey Rubin},
  title     = {A Biomolecular Implementation of Logically Reversible Computation With Minimal Energy Dissipation},
  year      = {1998},
  school    = {University of Pennsylvania, School of Medicine, 536 Johnson Pavilion, Phialdelphia PA 19104, Fax: 215 662-7842},
  file      = {:by-author/K/Klein/1998_Klein.pdf:PDF},
  keywords  = {Computer Architecture; Computer Science (CS); DNA Based Computing},
  month     = {June},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Presentation{Kleywegt2010,
  author           = {Gerard J. Kleywegt},
  title            = {Applied common sense},
  year             = {2010},
  creationdate     = {2012-11-09T00:00:00},
  file             = {:by-author/K/Kleywegt/2010_Kleywegt_slides.pdf:PDF},
  keywords         = {SAXS},
  modificationdate = {2024-08-15T18:43:59},
  owner            = {em},
  timestamp        = {2012.11.09},
}

@Article{Kleywegt2007,
  author    = {Kleywegt, Gerard J.},
  journal   = {Acta crystallographica. Section D, Biological crystallography},
  title     = {Crystallographic refinement of ligand complexes},
  year      = {2007},
  pages     = {94--100},
  volume    = {63},
  abstract  = {Model building and refinement of complexes between biomacromolecules and small molecules requires sensible starting coordinates as well as the specification of restraint sets for all but the most common non-macromolecular entities. Here, it is described why this is necessary, how it can be accomplished and what pitfalls need to be avoided in order to produce chemically plausible models of the low-molecular-weight entities. A number of programs, servers, databases and other resources that can be of assistance in the process are also discussed.},
  doi       = {10.1107/S0907444906022657},
  file      = {:by-author/K/Kleywegt/2007_Kleywegt_94.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Kleywegt2000,
  author    = {Kleywegt, Gerard J.},
  journal   = {Acta Crystallographica Section D},
  title     = {Validation of protein crystal structures},
  year      = {2000},
  pages     = {249--265},
  volume    = {56},
  file      = {:by-author/K/Kleywegt/2000_Kleywegt_249.pdf:PDF},
  owner     = {andrius},
  timestamp = {2012.06.07},
  creationdate = {2012-06-07T00:00:00},
}

@Article{Kleywegt1996d,
  author    = {Kleywegt, G. J.},
  journal   = {Acta crystallographica. Section D, Biological crystallography},
  title     = {Use of non-crystallographic symmetry in protein structure refinement.},
  year      = {1996},
  number    = {Pt 4},
  pages     = {842--857},
  volume    = {52},
  abstract  = {Several methods to assess the (dis)similarity of protein structures objectively are described, some of which, when applied to non-crystallographically related protein models, are able to discriminate between significant differences and 'random noise'. Some of these methods have been used to investigate a sample of several hundred protein structures which have been solved by means of X-ray crystallography in order to investigate the extent to which non-crystallographically related protein models differ from one another. It is shown that the extent of such differences is largely dependent on the resolution of the data used for the determination and refinement of the structure and, measured by some statistics, even varies essentially linearly with the resolution. The implications of these findings for the strategies used to refine structures with non-crystallographic symmetry, in particular at low resolution, are discussed. Finally, two examples are given of recent structure determinations from this laboratory in which the presence (and employment) of non-crystallographic symmetry was crucial to the solution and refinement of the structure.},
  doi       = {10.1107/S0907444995016477},
  file      = {:by-author/K/Kleywegt/1996_Kleywegt_842.pdf:pdf},
  keywords  = {Validation},
  owner     = {saulius},
  pii       = {S0907444995016477},
  pubmed    = {15299650},
  timestamp = {2016.12.12},
  creationdate = {2016-12-12T00:00:00},
}

@Article{Kleywegt1996,
  author           = {Gerard J. Kleywegt and Axel T. Brünger},
  journal          = {Structure},
  title            = {Checking your imagination: applications of the free {R} value},
  year             = {1996},
  issn             = {0969-2126},
  number           = {8},
  pages            = {897--904},
  volume           = {4},
  abstract         = {In 1990, Brändén and Jones [1] suggested that the process of electron-density map interpretation involves a degree of subjectivity on the part of the crystallographer. In the worst case, serious errors may be introduced into a model. In particular, their commentary stimulated the development of many different approaches for assessing the quality of protein crystal structures. Many of these methods validate models using statistical surveys of high-resolution X-ray structures (either of small molecules or of macromolecules) from which expected values or ranges of values are calculated for structural features. However, without the use of experimental diffraction data, one can never be sure whether a statistical ‘outlier’ (for example, in a Ramachandran plot) represents an error in the model or a genuine feature of the crystal structure [2], and the distinction between the two is obviously important. The ambiguity can only be resolved if the diffraction data is used in the quality assessment. Therefore, methods to assess if the model is an accurate representation of the experimental data must rely on statistics that involve both the diffraction data and the atomic model. Furthermore, few statistical surveys have been performed for macromolecular structures other than proteins, such as RNA, which means that knowledge-based rules are not available for the latter.},
  creationdate     = {2016-12-08T00:00:00},
  doi              = {10.1016/S0969-2126(96)00097-4},
  file             = {1996_Kleywegt_897.pdf:by-author/K/Kleywegt/1996_Kleywegt_897.pdf:PDF},
  keywords         = {Crystallography; Rfree; Validation; X-ray Crystallography},
  modificationdate = {2024-08-15T18:46:58},
  owner            = {saulius},
  timestamp        = {2016.12.08},
  url              = {http://www.sciencedirect.com/science/article/pii/S0969212696000974},
}

@Article{Kleywegt2007a,
  author           = {Kleywegt, Gerard J. and Harris, Mark R.},
  journal          = {Acta Crystallographica Section D},
  title            = {{ValLigURL}: a server for ligand-structure comparison and validation},
  year             = {2007},
  pages            = {935--938},
  volume           = {63},
  creationdate     = {2012-06-01T00:00:00},
  doi              = {10.1107/S090744490703315X},
  file             = {:by-author/K/Kleywegt/2007_Kleywegt_935.pdf:PDF},
  modificationdate = {2024-08-15T18:45:35},
  owner            = {andrius},
  timestamp        = {2012.06.01},
  url              = {http://scripts.iucr.org/cgi-bin/paper?S090744490703315X},
}

@Article{Kleywegt2004,
  author           = {Kleywegt, Gerard J. and Harris, Mark R. and Zou, Jin-yu and Taylor, Thomas C. and W{\"{a}}hlby, Anders and Jones, T. Alwyn},
  journal          = {Acta Crystallographica Section D},
  title            = {The {U}ppsala electron-density server},
  year             = {2004},
  pages            = {2240--2249},
  volume           = {60},
  creationdate     = {2008-07-28T00:00:00},
  doi              = {10.1107/S0907444904013253},
  file             = {ba5061.pdf:by-author/K/Kleywegt/2004_Kleywegt_2240.pdf:PDF},
  modificationdate = {2024-08-15T18:44:55},
  owner            = {saulius},
  timestamp        = {2008.07.28},
  url              = {http://dx.doi.org/10.1107/S0907444904013253},
}

@Article{Kleywegt2003,
  author           = {Gerard J. Kleywegt and Kim Henrick and Eleanor J. Dodson and van Aalten, Daan M. F.},
  journal          = {Structure},
  title            = {Pound-wise but penny-foolish: how well do micromolecules fare in macromolecular refinement?},
  year             = {2003},
  pages            = {1051--1059},
  volume           = {11},
  abstract         = {For the refinement of protein and nucleic acid structures, high-quality geometric restraint libraries are available. Unfortunately, for other compounds, such as physiological ligands, lead compounds, substrate analogs, etc., the situation is not as favorable. As a result, the structures of small molecules found in complexes with biomacromolecules are often less reliable than those of the surrounding amino or nucleic acids. Here, we briefly review the use of geometric restraints in structure refinement (be it against X-ray crystallographic or NMR-derived data) and simulation. In addition, we discuss methods to generate both restraint libraries and (idealized) coordinates for small molecules and provide some practical advice.},
  creationdate     = {2013-04-21T00:00:00},
  doi              = {10.1016/S0969-2126(03)00186-2},
  file             = {:by-author/K/Kleywegt/2003_Kleywegt_1051.pdf:PDF},
  modificationdate = {2024-08-15T18:46:09},
  owner            = {andrius},
  timestamp        = {2013.04.21},
}

@Article{Kleywegt1996c,
  author    = {Kleywegt, G. J. and Hoier, H. and Jones, T. A.},
  journal   = {Acta Crystallographica Section D},
  title     = {A re-evaluation of the crystal structure of chloromuconate cycloisomerase},
  year      = {1996},
  month     = {Jul},
  number    = {4},
  pages     = {858--863},
  volume    = {52},
  abstract  = {It is shown here that the reported 3{\AA} crystal structure of chloromuconate cycloisomerase from {\it Alcaligenes eutrophus} [Hoier, Schl{\"{o}}mann, Hammer, Glusker, Carrell, Goldman, Stezowski & Heinemann (1994). {\it Acta Cryst.} D{\bf 50}, 75{--}84] was refined in the incorrect space group {\it I}4. In addition, a stretch of about 25 residues near the N-terminus is out-of-register with the density in the original structure. From the coordinates and structure factors deposited in the Protein Data Bank (PDB), it was possible to determine the correct space group to be {\it I}422. The structure was then re-refined, using the original data reduced to {\it I}422, to a crystallographic free {\it R} factor of 0.264 at 3{\AA} resolution (conventional {\it R} factor 0.189). With conservative refinement and rebuilding methods, the errors in the chain tracing could be identified and remedied. Since the two molecules per asymmetric unit in the original structure are actually related by crystallographic symmetry, the observed differences between them are artefacts. In particular, the differences between, and peculiarities of the metal-binding sites are unreal. This case shows the dangers of crystallographic refinement in cases with unfavourable data-to-parameter ratios, and the importance of reducing the number of parameters in such cases to prevent gross errors (for instance, by using NCS constraints). It also demonstrates how the evaluation and monitoring of model quality during the entire refinement and rebuilding process can be used to detect and remedy serious errors. Finally, it presents a strong case in favour of depositing not only model coordinates, but also experimental data (preferably, both merged and unmerged data).},
  doi       = {10.1107/S0907444995008936},
  file      = {1996_Kleywegt_858.pdf:by-author/K/Kleywegt/1996_Kleywegt_858.pdf:PDF},
  keywords  = {I4; I422; Incorrect Spacegroup; Validation; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2016.12.09},
  creationdate = {2016-12-09T00:00:00},
  url       = {https://doi.org/10.1107/S0907444995008936},
}

@Article{Kleywegt2002,
  author           = {Kleywegt, Gerard J. and Jones, T. Alwyn},
  journal          = {Structure (London, England : 1993)},
  title            = {Homo crystallographicus--quo vadis?},
  year             = {2002},
  number           = {4},
  pages            = {465--472},
  volume           = {10},
  abstract         = {As macromolecular crystal structures are determined and refined in an increasingly automated fashion, careful assessment of the reliability and quality of the resulting models becomes increasingly important. Here, we analyze various issues related to the reliability and quality of macromolecular crystal structures deposited between 1991 and 2000. We find that the average resolution at which these structures are determined is essentially constant. In line with this observation, the average quality as measured by Ramachandran analysis does not improve as a function of time. On the other hand, an observed decrease of the average discrepancy between free and conventional R values suggests that the fit of model and data is improving. Finally, we present a surprising correlation between the tendency of crystallographers to deposit their experimental data and the free R values of their models.},
  creationdate     = {2016-12-11T00:00:00},
  doi              = {10.1016/S0969-2126(02)00743-8},
  file             = {:by-author/K/Kleywegt/2002_Kleywegt_465.pdf:pdf},
  keywords         = {Black Box Software; Structure Refinement; Validation; X-ray Crystallography},
  modificationdate = {2024-08-15T16:58:29},
  owner            = {saulius},
  pii              = {S0969212602007438},
  pubmed           = {11937051},
  timestamp        = {2016.12.11},
}

@Article{Kleywegt1998,
  author           = {Kleywegt, Gerard J. and Jones, T. Alwyn},
  journal          = {Acta Crystallographica Section D},
  title            = {Databases in protein crystallography},
  year             = {1998},
  pages            = {1119--1131},
  volume           = {D54},
  creationdate     = {2012-05-14T00:00:00},
  doi              = {10.1107/S0907444998007100},
  file             = {:by-author/K/Kleywegt/1998_Kleywegt_1119.pdf:PDF},
  keywords         = {X-ray Crystallography},
  modificationdate = {2024-08-15T18:45:11},
  owner            = {andrius},
  timestamp        = {2012.05.14},
  url              = {http://scripts.iucr.org/cgi-bin/paper?S0907444998007100},
}

@Article{Kleywegt1996a,
  author           = {Gerard J. Kleywegt and T. Alwyn Jones},
  journal          = {Structure},
  title            = {{P}hi/{P}si-chology: {R}amachandran revisited},
  year             = {1996},
  issn             = {0969-2126},
  number           = {12},
  pages            = {1395--1400},
  volume           = {4},
  abstract         = {The errors that can be introduced into a protein model during model building and refinement vary tremendously in their importance and severity [1] and [2]. At one extreme, the mainchain may be totally incorrectly traced in the experimental map, or the molecular replacement solution may be wrong. Minor errors may include an incorrect peptide orientation, or misplaced or excessive water molecules. The reasons why errors creep into models are many, but for a structure built into an experimental map, the main ones are limited resolution and poorly phased diffraction data. Other things being equal, the resolution of the diffraction data should be the ultimate variable that determines the accuracy of a structural investigation. Inevitably, life is more complicated, and a successful structural investigation is often a learning experience for the people involved.},
  creationdate     = {2016-12-08T00:00:00},
  doi              = {http://dx.doi.org/10.1016/S0969-2126(96)00147-5},
  file             = {1996_Kleywegt_1395.pdf:by-author/K/Kleywegt/1996_Kleywegt_1395.pdf:PDF},
  keywords         = {Ramachandran Plot; Validation; X-ray Crystallography},
  modificationdate = {2024-08-15T18:46:51},
  owner            = {saulius},
  timestamp        = {2016.12.08},
  url              = {http://www.sciencedirect.com/science/article/pii/S0969212696001475},
}

@Article{Kleywegt1996b,
  author           = {Kleywegt, G. J. and Jones, T. A.},
  journal          = {Acta Crystallographica Section D},
  title            = {Efficient rebuilding of protein structures},
  year             = {1996},
  month            = {Jul},
  number           = {4},
  pages            = {829--832},
  volume           = {52},
  abstract         = {A computer program, called {\it OOPS}, is described which facilitates and speeds up the process of rebuilding a protein structure inside its electron density and reduces the chances of local errors persevering throughout the crystallographic protein structure determination process. The program uses a set of criteria to judge how reasonable each protein residue is and it generates macros for the macromolecular crystallographic model-building program {\it O} [Jones, Zou, Cowan & Kjeldgaard (1991). {\it Acta Cryst.} A{\bf 47}, 110{--}119] which, when executed, will take the crystallographer on a journey along all suspect residues.},
  creationdate     = {2016-12-09T00:00:00},
  doi              = {10.1107/S0907444996001783},
  file             = {1996_Kleywegt_829.pdf:by-author/K/Kleywegt/1996_Kleywegt_829.pdf:PDF},
  keywords         = {Validation; X-ray Crystallography},
  modificationdate = {2024-08-15T18:47:03},
  owner            = {saulius},
  timestamp        = {2016.12.09},
  url              = {https://doi.org/10.1107/S0907444996001783},
}

@Article{Kleywegt1995,
  author    = {Gerard J. Kleywegt and T. Alwyn Jones},
  journal   = {Structure},
  title     = {Where freedom is given, liberties are taken},
  year      = {1995},
  pages     = {535--540},
  volume    = {3},
  doi       = {10.1016/S0969-2126(01)00187-3},
  file      = {:by-author/K/Kleywegt/1995_Kleywegt_535.pdf:PDF},
  keywords  = {X-ray Crystallography},
  owner     = {andrius},
  timestamp = {2013.01.20},
  creationdate = {2013-01-20T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/S0969212601001873},
}

@Article{Klimasauskas1995,
  author    = {Klimasauskas, S. and Roberts, R. J.},
  journal   = {Nucleic acids research},
  title     = {M.HhaI binds tightly to substrates containing mismatches at the target base.},
  year      = {1995},
  pages     = {1388--95},
  volume    = {23},
  abstract  = {The (cytosine-5) DNA methyltransferase M.HhaI causes its target cytosine base to be flipped completely out of the DNA helix upon binding. We have investigated the effects of replacing the target cytosine by other, mismatched bases, including adenine, guanine, thymine and uracil. We find that M.HhaI binds more tightly to such mismatched substrates and can even transfer a methyl group to uracil if a G:U mismatch is present. Other mismatched substrates in which the orphan guanine is changed exhibit similar behavior. Overall, the affinity of DNA binding correlates inversely with the stability of the target base pair, while the nature of the target base appears irrelevant for complex formation. The presence of a cofactor analog. S-adenosyl-L-homocysteine, greatly enhances the selectivity of the methyltransferase for cytosine at the target site. We propose that the DNA methyltransferases have evolved from mismatch binding proteins and that base flipping was, and still is, a key element in many DNA-enzyme interactions.},
  file      = {:by-author/K/Klimasauskas/1995_Klimasauskas_1388.pdf:PDF},
  keywords  = {HhaI},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Klimasauskas1998,
  author    = {Klimasauskas, S. and Szyperski, T. and Serva, S. and Wüthrich, K.},
  journal   = {The EMBO journal},
  title     = {Dynamic modes of the flipped-out cytosine during HhaI methyltransferase-DNA interactions in solution.},
  year      = {1998},
  pages     = {317--24},
  volume    = {17},
  abstract  = {Flipping of a nucleotide out of a B-DNA helix into the active site of an enzyme has been observed for the HhaI and HaeIII cytosine-5 methyltransferases (M.HhaI and M.HaeIII) and for numerous DNA repair enzymes. Here we studied the base flipping motions in the binary M. HhaI-DNA and the ternary M.HhaI-DNA-cofactor systems in solution. Two 5-fluorocytosines were introduced into the DNA in the places of the target cytosine and, as an internal control, a cytosine positioned two nucleotides upstream of the recognition sequence 5'-GCGC-3'. The 19F NMR spectra combined with gel mobility data show that interaction with the enzyme induces partition of the target base among three states, i.e. stacked in the B-DNA, an ensemble of flipped-out forms and the flipped-out form locked in the enzyme active site. Addition of the cofactor analogue S-adenosyl-L-homocysteine greatly enhances the trapping of the target cytosine in the catalytic site. Distinct dynamic modes of the target cytosine have thus been identified along the reaction pathway, which includes novel base-flipping intermediates that were not observed in previous X-ray structures. The new data indicate that flipping of the target base out of the DNA helix is not dependent on binding of the cytosine in the catalytic pocket of M.HhaI, and suggest an active role of the enzyme in the opening of the DNA duplex.},
  file      = {:by-author/K/Klimasauskas/1998_Klimasauskas_317.pdf:PDF},
  keywords  = {HhaI},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Kneller2011,
  author           = {Kneller, Gerald R.},
  journal          = {Journal of computational chemistry},
  title            = {Comment on "{F}ast determination of the optimal rotational matrix for macromolecular superpositions" [J. Comp. Chem. 31, 1561 (2010)].},
  year             = {2011},
  issn             = {1096-987X},
  month            = nov,
  number           = {1},
  pages            = {183--184},
  volume           = {32},
  abstract         = {Recently Liu et al. published a fast algorithm to solve the eigenvector problem arising in the quaternion-based method for the rotational superposition of molecular structures (J Comput Chem 2010, 31, 1561.). In this Comment, it is shown that the construction of the 4 × 4 matrix to be diagonalized—and not the diagonalization itself—represents the dominating part of the computational effort for the quaternion-based solution of the rotational superposition problem if molecules with more than about 100 atoms are considered.},
  comment          = {Author reply: pp. 185-186},
  creationdate     = {2012-05-15T00:00:00},
  doi              = {10.1002/jcc.21607},
  file             = {:by-author/K/Kneller/2011_Kneller_183.pdf:PDF},
  groups           = {sg/Molecule superposion, sg/Superposition, sg/Bioinf. Algorithms},
  keywords         = {Structure Superposition},
  modificationdate = {2024-05-12T16:35:35},
  owner            = {saulius},
  publisher        = {Wiley},
  timestamp        = {2012.05.15},
}

@Article{Kneller2008,
  author           = {Gerald R. Kneller},
  journal          = {The Journal Of Chemical Physics},
  title            = {{E}ckart axis conditions, {G}auss’ principle of least constraint, and the optimal superposition of molecular structures},
  year             = {2008},
  pages            = {194101},
  volume           = {128},
  abstract         = {The relation of the Eckart axis conditions for polyatomic vibrating molecules to the problem of optimal superposition of molecular structures has been pointed out recently [J. Chem. Phys. 122, 224105 2005]. Here, it is shown that both problems are intimately related to Gauss’ principle of least constraint, for which a concise derivation is presented. In the context of this article, Gauss’ principle leads to a rotational superposition problem of the unconstrained atomic displacements and the corresponding displacements due to a molecular rigid-body motion. The Eckart axis conditions appear here as necessary conditions for a minimum of the constraint function. The importance of Eckart’s problem for extracting the internal motions of macromolecules from simulated molecular dynamics trajectories is pointed out, and it is shown how the case of coarse-grained sampled trajectories can be treated.},
  creationdate     = {2012-05-15T00:00:00},
  doi              = {10.1063/1.2902290},
  file             = {:by-author/K/Kneller/2008_Kneller_194101.pdf:PDF},
  groups           = {sg/Molecule superposion, sg/Superposition, sg/Bioinf. Algorithms},
  keywords         = {Structure Superposition},
  modificationdate = {2024-05-12T16:46:47},
  owner            = {saulius},
  timestamp        = {2012.05.15},
}

@Article{Knobloch1995,
  author    = {Knobloch, Harald and Orendi, Horst and Büchel, Michael and Seki, Takahiro and Ito, Shinzaburo and Knoll, Wolfgang},
  journal   = {Journal of Applied Physics},
  title     = {Photochromic command surface induced switching of liquid crystal optical waveguide structures},
  year      = {1995},
  issn      = {0021-8979, 1089-7550},
  pages     = {481--487},
  volume    = {77},
  abstract  = {We report on optical waveguidestructures containing a thin liquid crystal(LC)film held between two photochromic command surfaces. The command surfaces consist of three monomolecular layers of a polymer with azobenzene side chains deposited according to the Langmuir–Blodgett–Kuhn technique. When exposed to light of appropriate wavelength, the command surfaces undergo a trans↔cis photoisomerization process that induces a reversible change in the liquid crystalline orientation. Such an orientation change of the LC alters the optical properties of the optical waveguide. We present experiments on the dynamics of the LC orientation process. The transition is shown to be continuous, with the degree of orientation dependent on the ratio of the cis‐trans chromophore concentration ratio in the command surface.},
  doi       = {10.1063/1.359028},
  file      = {Knobloch et al. - 1995 - Photochromic command surface induced switching of .pdf:by-author/K/Knobloch/1995_Knobloch_481.pdf:application/pdf;Snapshot:by-author/K/Knobloch/1995_Knobloch_481.html:text/html},
  groups    = {sg/chemical},
  keywords  = {Liquid Crystal Structure; Liquid Crystals; Liquid Surface Structure; Liquid Surfaces; Optical Waveguides},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://scitation.aip.org/content/aip/journal/jap/77/2/10.1063/1.359028},
  urldate   = {2015-08-21},
}

@Article{Knorr2011,
  author    = {Knorr},
  title     = {Quantitative X-Ray Mineralogy of Iron Ore and Scales},
  year      = {2011},
  pages     = {1},
  file      = {:by-author/K/Knorr/2011_Knorr_1.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.05.02},
  creationdate = {2012-05-02T00:00:00},
}

@InProceedings{Knorr2001,
  author    = {Knorr, Edwin M. and Ng, Raymond T. and Zamar, Ruben H.},
  booktitle = {Proceedings of the seventh ACM SIGKDD international conference on Knowledge discovery and data mining},
  title     = {Robust Space Transformations for Distance-based Operations},
  year      = {2001},
  pages     = {126--135},
  publisher = {ACM},
  abstract  = {For many KDD operations, such as nearest neighbor search, distance-based clustering, and outlier detection, there is an underlying k-D data space in which each tuple/object is represented as a point in the space. In the presence of differing scales, variability, correlation, and/or outliers, we may get unintuitive results if an inappropriate space is used.The fundamental question that this paper addresses is: "What then is an appropriate space?" We propose using a robust space transformation called the Donoho-Stahel estimator. In the first half of the paper, we show the key properties of the estimator. Of particular importance to KDD applications involving databases is the stability property, which says that in spite of frequent updates, the estimator does not: (a) change much, (b) lose its usefulness, or (c) require re-computation. In the second half, we focus on the computation of the estimator for high-dimensional databases. We develop randomized algorithms and evaluate how well they perform empirically. The novel algorithm we develop called the Hybrid-random algorithm is, in most cases, at least an order of magnitude faster than the Fixed-angle and Subsampling algorithms.},
  doi       = {10.1145/502512.502532},
  file      = {:by-author/K/Knorr/2001_Knorr_126.pdf:PDF},
  isbn      = {1-58113-391-X},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://doi.acm.org/10.1145/502512.502532},
}

@Article{Knorr,
  author    = {Knorr, K. and Yang, N.},
  title     = {Quantitative {X}-ray mineralogy of iron ore and scales},
  file      = {[PDF] from researchgate.net:by-author/K/Knorr/XXXX_Knorr.pdf:application/pdf},
  groups    = {sg/JAC2009},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://www.researchgate.net/profile/Karsten_Knorr/publication/229812188_Quantitative_X-Ray_Mineralogy_of_Iron_Ore_and_Scales/links/0c9605211f944e8f47000000.pdf},
  urldate   = {2015-08-31},
}

@Article{Knox2011,
  author    = {Knox, Craig and Law, Vivian and Jewison, Timothy and Liu, Philip and Ly, Son and Frolkis, Alex and Pon, Allison and Banco, Kelly and Mak, Christine and Neveu, Vanessa and Djoumbou, Yannick and Eisner, Roman and Guo, An Chi and Wishart, David S.},
  journal   = {Nucleic Acids Research},
  title     = {DrugBank 3.0: a comprehensive resource for ‘Omics’ research on drugs},
  year      = {2011},
  pages     = {D1035-D1041},
  volume    = {39},
  abstract  = {DrugBank (http://www.drugbank.ca) is a richly annotated database of drug and drug target information. It contains extensive data on the nomenclature, ontology, chemistry, structure, function, action, pharmacology, pharmacokinetics, metabolism and pharmaceutical properties of both small molecule and large molecule (biotech) drugs. It also contains comprehensive information on the target diseases, proteins, genes and organisms on which these drugs act. First released in 2006, DrugBank has become widely used by pharmacists, medicinal chemists, pharmaceutical researchers, clinicians, educators and the general public. Since its last update in 2008, DrugBank has been greatly expanded through the addition of new drugs, new targets and the inclusion of more than 40 new data fields per drug entry (a 40% increase in data ‘depth’). These data field additions include illustrated drug-action pathways, drug transporter data, drug metabolite data, pharmacogenomic data, adverse drug response data, ADMET data, pharmacokinetic data, computed property data and chemical classification data. DrugBank 3.0 also offers expanded database links, improved search tools for drug–drug and food–drug interaction, new resources for querying and viewing drug pathways and hundreds of new drug entries with detailed patent, pricing and manufacturer data. These additions have been complemented by enhancements to the quality and quantity of existing data, particularly with regard to drug target, drug description and drug action data. DrugBank 3.0 represents the result of 2 years of manual annotation work aimed at making the database much more useful for a wide range of ‘omics’ (i.e. pharmacogenomic, pharmacoproteomic, pharmacometabolomic and even pharmacoeconomic) applications.},
  doi       = {10.1093/nar/gkq1126},
  eprint    = {http://nar.oxfordjournals.org/content/39/suppl_1/D1035.full.pdf+html},
  file      = {:by-author/K/Knox/2011_Knox_D1091.pdf:PDF},
  keywords  = {DrugBank},
  owner     = {antanas},
  timestamp = {2014.07.02},
  creationdate = {2014-07-02T00:00:00},
  url       = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013709/},
}

@Article{Knuth1974,
  author     = {Knuth, Donald E.},
  journal    = {ACM Comput. Surv.},
  title      = {Structured Programming with go to Statements},
  year       = {1974},
  issn       = {0360-0300},
  pages      = {261--301},
  volume     = {6},
  address    = {New York, NY, USA},
  doi        = {10.1145/356635.356640},
  file       = {:by-author/K/Knuth/1974_Knuth_261.pdf:PDF},
  issue_date = {Dec. 1974},
  keywords   = {Computer Science (CS); Structured Programming},
  owner      = {saulius},
  publisher  = {ACM},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
  url        = {http://doi.acm.org/10.1145/356635.356640},
}

@Article{Kocbach2009,
  author    = {Ladislav Kocbach and Suhail Lubbad},
  journal   = {Physics Education},
  title     = {Geometrical simplification of the dipole-dipole interaction formula},
  year      = {2009},
  pages     = {345--351},
  volume    = {45},
  abstract  = {Many students meet quite early this dipole-dipole potential energy when they are taught electrostatics or magnetostatics, and it is also a very popular formula, featured in the encyclopedias. We show that by a simple rewriting of the formula it becomes apparent that for example, by reorienting the two dipoles, their attraction can become exactly twice as large. The physical facts are naturally known, but the presented transformation seems to underline the geometrical features in a rather unexpected way. The consequence of the discussed features is the so called magic angle which appears in many applications. The present discussion also contributes to an easier introduction of this feature. We also discuss a possibility for designing educational toys and try to suggest why this formula has not been written down frequently before this work. Similar transformation is possible for the field of a single dipole, there it seems to be observed earlier, but also in this case we could not find any published detailed discussion.},
  file      = {2009_Kocbach_manuscript.pdf:by-author/K/Kocbach/2009_Kocbach_345.pdf:PDF},
  owner     = {saulius},
  timestamp = {2011.12.13},
  creationdate = {2011-12-13T00:00:00},
}

@InProceedings{Koch1999,
  author       = {Stefan Koch},
  booktitle    = {Proceedings of the Fifth Americas Conference on Information Systems (AMCIS 1999)},
  title        = {Using Weakest Precondition for Software Process Model Reuse},
  year         = {1999},
  organization = {Department for Applied Computer Science, University of Economics and Business Administration, Vienna, Austria, e-mail: stefan.koch@wu-wien.ac.at},
  pages        = {741--743},
  abstract     = {This paper describes a method to determine the possibility of combining two or more process models using an approach similar to the proof of (partial) correct- ness of algorithms by determining the weakest precon- dition and postcondition. This method also allows the analysis of process models with regard to their semantic correctness. The approach is described and demonstrated on an example process.},
  file         = {:by-author/K/Koch/1999_Koch_741.pdf:PDF},
  keywords     = {Computer Science (CS); Program Verification; Weakest Preconditions},
  owner        = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@InProceedings{Kocher1999,
  author    = {Kocher, Paul C.},
  booktitle = {Proceedings of the 16th Annual International Cryptology Conference on Advances in Cryptology},
  title     = {Timing Attacks on Implementations of {D}iffie-{H}ellman, {RSA}, {DSS}, and Other Systems},
  year      = {1996},
  address   = {London, UK, UK},
  pages     = {104--113},
  publisher = {Springer-Verlag},
  series    = {CRYPTO '96},
  abstract  = {By carefully measuring the amount of time required to perform private key operalions, attackers may be able to find fixed Diffie-Hellman exponents, factor RSA keys, and break other cryptosystems. Against, a valnerable system, the attack is computationally inexpensive and often requires only known ciphertext. Actual systems are potentially at risk, including cryptographic tokens, network-based cryptosystems, and other applications where attackers can make reasonably accurate timing measurements. Techniques for preventing the attack for RSA and Diffie-Hellman are presented. Some cryptosystems will need to be revised to protect against the attack, and new protocols and algorithms may need to incorporate measures to prevenl timing attacks.},
  file      = {:by-author/K/Kocher/1996_Kocher_104.pdf:PDF},
  isbn      = {3-540-61512-1},
  keywords  = {Computer Science (CS); Cryptography},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
  url       = {http://dl.acm.org/citation.cfm?id=646761.706156},
}

@InBook{Koehl2006,
  author      = {Patrice Koehl},
  chapter     = {1},
  editor      = {Kenny B. Lipkowitz and Thomas R. Cundari and Valerie J. Gillet},
  pages       = {1--55},
  publisher   = {Wiley-VCH, John Wiley \& Sons, Inc.},
  title       = {Protein Structure Classification},
  year        = {2006},
  note        = {Found via http://en.wikipedia.org/wiki/Structural_Classification_of_Proteins_database (2015-03-10)},
  volume      = {22},
  abstract    = {The molecular basis of life rests on the activity of large biological macro- molecules, including nucleic acids (DNA and RNA), carbohydrates, lipids, and proteins. Although each plays an essential role in life, there is something spe- cial about proteins, as they are the lead performers of cellular functions. As a response, structural molecular biology has emerged as a new line of experi- mental research focused on revealing the structure of these bio-molecules. This branch of biology has recently experienced a major uplift through the development of high-throughput structural studies aimed at developing a com- prehensive view of the protein structure universe. Although these studies are generating a wealth of information that are stored into protein structure data- bases, the key to their success lies in our ability to organize and analyze the information contained in those databases, and to integrate that information with other efforts aimed at solving the mysteries behind cell functions. In this survey, the first step behind any such organization scheme, namely the classification of protein structures, is described. The properties of protein structures, with special attention to their geometry, are reviewed. Computer methods for the automatic comparison and classification of these structures are then reviewed along with the existing classifications of protein structures and their applications in biology, with a special focus on computational biology. The chapter concludes the review with a discussion of the future of these classifications.},
  booktitle   = {Reviews in Computational Chemistry},
  doi         = {10.1002/0471780367},
  file        = {:by-author/K/Koehl/2006_Koehl_1.pdf:PDF},
  institution = {Department of Computer Science and Genome Center, University of California, Davis, California},
  isbn-10     = {0471779385},
  isbn-online = {9780471780366},
  isbn-print  = {9780471779384},
  owner       = {saulius},
  timestamp = {2012.11.20},
  creationdate = {2012-11-20T00:00:00},
  url         = {http://media.wiley.com/product_data/excerpt/85/04717793/0471779385.pdf},
}

@Article{Koehl1999,
  author    = {Patrice Koehl and Michael Levitt},
  journal   = {PNAS},
  title     = {Structure-based conformational preferences of amino acids},
  year      = {1999},
  pages     = {12524--12529},
  abstract  = {Proteins can be very tolerant to amino acid substitution, even within their core. Understanding the factors responsible for this behavior is of critical importance for protein engineering and design. Mutations in proteins have been quantified in terms of the changes in stability they induce. For example, guest residues in specific secondary struc- tures have been used as probes of conformational preferences of amino acids, yielding propensity scales. Predicting these amino acid propensities would be a good test of any new potential energy functions used to mimic protein stability. We have recently developed a protein design procedure that optimizes whole sequences for a given target conformation based on the knowledge of the template backbone and on a semiempirical potential energy function. This energy function is purely physical, including steric interactions based on a Lennard-Jones potential, electrostatics based on a Coulomb potential, and hydrophobicity in the form of an environment free energy based on accessible surface area and interatomic contact areas. Sequences designed by this procedure for 10 different proteins were analyzed to extract conformational preferences for amino acids. The resulting structure-based propensity scales show significant agreements with experimental propensity scale values, both for ␣-helices and ␤-sheets. These results indicate that amino acid confor- mational preferences are a natural consequence of the potential energy we use. This confirms the accuracy of our potential and indicates that such preferences should not be added as a design criterion.},
  file      = {1999_Koehl_12524.pdf:by-author/K/Koehl/1999_Koehl_12524.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.11.20},
  creationdate = {2012-11-20T00:00:00},
}

@Presentation{Koenig2002,
  author       = {Andrew Koenig},
  title        = {Notes from a polyglot outsider},
  year         = {2002},
  organization = {AT\&T Shannon Laboratory, ark@research.att.com},
  file         = {:by-author/K/Koenig/2002_Koenig_slides.pdf:PDF},
  keywords     = {Computer Science (CS); Programming Languages; Python},
  owner        = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Presentation{Kohlbacher2011,
  author    = {Oliver Kohlbacher},
  title     = {Drug Design 2},
  year      = {2011},
  lecture   = {3. 2D Similarity -- Part I},
  file      = {2011_Kohlbacher_BIOINF4372slides.pdf:by-author/K/Kohlbacher/2011_Kohlbacher_BIOINF4372slides.pdf:PDF},
  keywords  = {Algorithms; Chemical Database Search; Chemoinformatics; Drug Design; Molecule Identity; Molecule Similarity; Morgan Algorithm},
  owner     = {saulius},
  timestamp = {2014.10.20},
  creationdate = {2014-10-20T00:00:00},
  url       = {https://abi.inf.uni-tuebingen.de/Teaching/Old/ws-2011-12/DD2/Slides/DD2_WS11_03_2D_Similiarity_I_3up.pdf},
}

@Article{Kohn1998,
  author    = {Walter Kohn},
  journal   = {Chemistry},
  title     = {Electronic Structure of Matter -- Wave functions and Density Functionals},
  year      = {1998},
  note      = {Nobel Lecture, January 28, 1999},
  pages     = {213},
  file      = {:by-author/K/Kohn/1998_Kohn_213.pdf:PDF},
  owner     = {saulius},
  timestamp = {2014.03.23},
  creationdate = {2014-03-23T00:00:00},
}

@Article{Kolb2001,
  author    = {Kolb, Hartmuth C. and Finn, M. G. and Sharpless, K. Barry},
  journal   = {Angewandte Chemie (International ed. in English)},
  title     = {Click Chemistry: Diverse Chemical Function from a Few Good Reactions.},
  year      = {2001},
  pages     = {2004--2021},
  volume    = {40},
  abstract  = {Examination of nature's favorite molecules reveals a striking preference for making carbon-heteroatom bonds over carbon-carbon bonds-surely no surprise given that carbon dioxide is nature's starting material and that most reactions are performed in water. Nucleic acids, proteins, and polysaccharides are condensation polymers of small subunits stitched together by carbon-heteroatom bonds. Even the 35 or so building blocks from which these crucial molecules are made each contain, at most, six contiguous C-C bonds, except for the three aromatic amino acids. Taking our cue from nature's approach, we address here the development of a set of powerful, highly reliable, and selective reactions for the rapid synthesis of useful new compounds and combinatorial libraries through heteroatom links (C-X-C), an approach we call &quot;click chemistry&quot;. Click chemistry is at once defined, enabled, and constrained by a handful of nearly perfect &quot;spring-loaded&quot; reactions. The stringent criteria for a process to earn click chemistry status are described along with examples of the molecular frameworks that are easily made using this spartan, but powerful, synthetic strategy.},
  file      = {:by-author/K/Kolb/2001_Kolb_2004.pdf:PDF},
  keywords  = {Click Chemistry},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@Manuscript{Kolb2009,
  author       = {Ute Kolb and Tatiana Gorelik and Enrico Mugnaioli},
  title        = {Automated diffraction tomography combined with electron precession: a new tool for ab initio nanostructure analysis},
  year         = {2009},
  organization = {Institut für Physikalische Chemie, Johannes Gutenberg-Universität Mainz, Welderweg 11, D-55099 Mainz, Germany},
  file         = {:by-author/K/Kolb/2009_Kolb.pdf:PDF},
  owner        = {saulius},
  timestamp = {2014.03.23},
  creationdate = {2014-03-23T00:00:00},
}

@Article{Kolodner2000,
  author    = {Kolodner, R. D.},
  journal   = {Nature},
  title     = {Guarding against mutation},
  year      = {2000},
  pages     = {687, 689},
  volume    = {407},
  doi       = {10.1038/35037701},
  file      = {:by-author/K/Kolodner/2000_Kolodner_687.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Komori2000,
  author    = {Komori, Kayoko and Sakae, Shinzi and Daiyasu, Hiromi and Toh, Hiroyuki and Morikawa, Kosuke and Shinagawa, Hideo and Ishino, Yoshizumi},
  journal   = {J. Biol. Chem.},
  title     = {Mutational Analysis of the Pyrococcus furiosusHolliday Junction Resolvase Hjc Revealed Functionally Important Residues for Dimer Formation, Junction DNA Binding, and Cleavage Activities},
  year      = {2000},
  pages     = {40385--40391},
  volume    = {275},
  abstract  = {The Holliday junction cleavage protein, Hjc resolvase of Pyrococcus furiosus, is the first Holliday junction resolvase to be discovered in Archaea. Although the archaeal resolvase shares certain biochemical properties with other non-archaeal junction resolvases, no amino acid sequence similarity has been identified. To investigate the structure-function relationship of this new Holliday junction resolvase, we constructed a series of mutanthjc genes using site-directed mutagenesis targeted at the residues conserved among the archaeal orthologs. The products of these mutant genes were purified to homogeneity. With analysis of the activity of the mutant proteins to bind and cleave synthetic Holliday junctions, one acidic residue, Glu-9, and two basic residues, Arg-10 and Arg-25, were found to play critical roles in enzyme action. This is in addition to the three conserved residues, Asp-33, Glu-46, and Lys-48, which are also conserved in the motif found in the type II restriction endonuclease family proteins. Two aromatic residues, Phe-68 and Phe-72, are important for the formation of the homodimer probably through hydrophobic interactions. The results of these studies have provided insights into the structure-function relationships of the archaeal Holliday junction resolvase as well as the universality and diversity of the Holliday junction cleavage reaction.},
  doi       = {10.1074/jbc.M006294200},
  file      = {2000_Komori_40385.pdf:by-author/K/Komori/2000_Komori_40385.pdf:PDF},
  keywords  = {Holliday Junction Resolvase},
  owner     = {em},
  timestamp = {2013.01.03},
  creationdate = {2013-01-03T00:00:00},
}

@InProceedings{Konagurthu2014,
  author           = {Arun S. Konagurthu and Parthan Kasarapu and Lloyd Allison and James H. Collier and Arthur M. Lesk},
  booktitle        = {Research in Computational Molecular Biology},
  title            = {On sufficient statistics of least-squares superposition of vector sets},
  year             = {2014},
  editor           = {Sharan, Roded},
  pages            = {144--159},
  publisher        = {Springer International Publishing},
  series           = {Lecture Notes in Computer Science},
  volume           = {8394},
  abstract         = {Superposition by orthogonal transformation of vector sets by minimizing the least-squares error is a fundamental task in many areas of science, notably in structural molecular biology. Its widespread use for structural analyses is facilitated by exact solutions of this problem, computable in linear time. However, in several of these analyses it is common to invoke this superposition routine a very large number of times, often operating (through addition or deletion) on previously superposed vector sets. This paper derives a set of sufficient statistics for the least-squares orthogonal transformation problem. These sufficient statistics are additive. This property allows for the superposition parameters (rotation, translation, and root mean square deviation) to be computable as constant time updates from the statistics of partial solutions. We demonstrate that this results in a massive speed up in the computational effort, when compared to the method that recomputes superpositions ab initio. Among others, protein structural alignment algorithms stand to benefit from our results.},
  creationdate     = {2016-01-06T00:00:00},
  doi              = {10.1007/978-3-319-05269-4_11},
  file             = {:by-author/K/Konagurthu/2014_Konagurthu_144.pdf:PDF},
  keywords         = {RMSD; Rotational Superposition; Structure Superposition; Superposition},
  modificationdate = {2024-05-12T11:35:58},
  owner            = {antanas},
  timestamp        = {2016.01.06},
  url              = {http://link.springer.com/chapter/10.1007%2F978-3-319-05269-4_11},
}

@Presentation{Konarev2010,
  author    = {Konarev},
  title     = {Rigid body refinement tutorial ({MASSHA} case)},
  year      = {2010},
  file      = {:by-author/K/Konarev/2010_Konarev_slides.pdf:PDF},
  keywords  = {SAXS},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Presentation{Konarev2010a,
  author    = {Konarev},
  title     = {Data reduction and processing tutorial},
  year      = {2010},
  file      = {:by-author/K/Konarev/2010_Konarev_slides3.pdf:PDF},
  keywords  = {SAXS},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Presentation{Konarev2010b,
  author    = {Konarev},
  title     = {Analysis of mixtures tutorial},
  year      = {2010},
  file      = {:by-author/K/Konarev/2010_Konarev_slides2.pdf:PDF},
  keywords  = {SAXS},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Konarev2001,
  author    = {P. V. Konarev and M. V. Petoukhov and D. I. Svergun},
  journal   = {Journal of Applied Crystallography},
  title     = {{MASSHA} – a graphics system for rigid-body modelling of macromolecular complexes against solution scattering data},
  year      = {2001},
  number    = {34},
  pages     = {527--532},
  file      = {:by-author/K/Konarev/2001_Konarev_527.pdf:PDF},
  keywords  = {MASSHA; SAXS},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Konarev2006,
  author    = {Petr V. Konarev and Maxim V. Petoukhov and Vladimir V. Volkov and Dmitri I. Svergun},
  journal   = {Journal of Applied Crystallography},
  title     = {{ATSAS} 2.1, a program package for small-angle scattering data analysis},
  year      = {2006},
  pages     = {277--286},
  volume    = {39},
  file      = {:by-author/K/Konarev/2006_Konarev_277.pdf:PDF},
  keywords  = {ATSAS; DAMAVER; SAXS},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Konarev2003,
  author    = {Petr V. Konarev and Vladimir V. Volkov and Anna V. Sokolova and Michel H. J. Koch and Dmitri I. Svergun},
  journal   = {Journal of Applied Crystallography},
  title     = {{PRIMUS}: a {Windows} {PC}-based system for small-angle scattering data analysis},
  year      = {2003},
  pages     = {1277--1282},
  volume    = {36},
  file      = {:by-author/K/Konarev/2003_Konarev_1277.pdf:PDF},
  keywords  = {PRIMUS; SAXS},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Manuscript{Kong1991,
  author    = {Kong, Xianshu and Everett, Hazel and Toussaint, Godfried},
  title     = {The Graham Scan Triangulates Simple Polygons},
  year      = {1991},
  file      = {:by-author/K/Kong/1991_Kong.pdf:PDF;:by-author/K/Kong/1991_Kong.ps.gz:PostScript},
  owner     = {saulius},
  publisher = {IEEE},
  timestamp = {2013.08.10},
  creationdate = {2013-08-10T00:00:00},
}

@Article{Konnert1976,
  author    = {John H. Konnert},
  journal   = {Acta Crystallographica A},
  title     = {A Restrained-Parameter Structure-Factor Least-Squares Refinement Procedure for Large Asymmetric Units},
  year      = {1976},
  pages     = {614--617},
  volume    = {32},
  abstract  = {A rapidly converging method for refining approximate atomic models is presented. It combines the conditional structure-factor least-squares procedure described by Waser [Acta Cryst. (1963). 16, 1091- 1094] with the conjugate gradient method for solving linear systems [Hestenes & Stiefel, J. Res. Natl. Bur. Stand. (1952). 49, 409-436]. The method allows simultaneous variation of all of the structural parameters, although less than 1% of the derivative matrix need be calculated and stored for large systems and less than ~ t h of the diffraction data accessible with Cu radiation need be used. Applications involving a 240 atom mineral and an 812 atom protein are mentioned.},
  doi       = {10.1107/S0567739476001289},
  file      = {:by-author/K/Konnert/1976_Konnert_614.pdf:PDF},
  owner     = {andrius},
  timestamp = {2013.04.26},
  creationdate = {2013-04-26T00:00:00},
}

@Article{Koonin2009,
  author    = {Eugene V Koonin},
  journal   = {Nucleic Acids Research},
  title     = {SURVEY AND SUMMARY Darwinian evolution in the light of genomics},
  year      = {2009},
  pages     = {1011--1034},
  volume    = {37},
  abstract  = {Comparative genomics and systems biology offer unprecedented opportunities for testing central tenets of evolutionary biology formulated by Darwin in the Origin of Species in 1859 and expanded in the Modern Synthesis 100 years later. Evolutionary-genomic studies show that natural selection is only one of the forces that shape genome evolution and is not quantitatively dominant, whereas non-adaptive processes are much more prominent than previously suspected. Major contributions of horizontal gene transfer and diverse selfish genetic elements to genome evolution undermine the Tree of Life concept. An adequate depiction of evolution requires the more complex concept of a network or ‘forest’ of life. There is no consistent tendency of evolution towards increased genomic complexity, and when complexity increases, this appears to be a non-adaptive consequence of evolution under weak purifying selection rather than an adaptation. Several universals of genome evolution were discovered including the invariant distributions of evolutionary rates among orthologous genes from diverse genomes and of paralogous gene family sizes, and the negative correlation between gene expression level and sequence evolution rate. Simple, non-adaptive models of evolution explain some of these universals, suggesting that a new synthesis of evolutionary biology might become feasible in a not so remote future.},
  doi       = {10.1093/nar/gkp089},
  file      = {2009_Koonin_1011.pdf:by-author/K/Koonin/2009_Koonin_1011.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.07.17},
  creationdate = {2012-07-17T00:00:00},
  url       = {http://nar.oxfordjournals.org/content/37/4/1011},
}

@Manuscript{Koopman1997,
  author       = {Koopman, Jr., Philip},
  title        = {A Preliminary Exploration of Optimized Stack Code Generation},
  year         = {1997},
  keywords     = {Code Generation; Compiler Design; Computer Science (CS)},
  abstract     = {This paper presents an experimental code generator that performs intra-block stack scheduling for a stack-based execution model. For small test programs, 91% to 100% of redundant local variable accesses were eliminated using this compiler. Com- piled intra-block stack scheduling and hand-per- formed global stack scheduling show that significant opportunities exist to keep temporary variable values on the expression evaluation stack when compiling conventional languages.},
  conference   = {1992 Rochester Forth Conference},
  file         = {:by-author/K/Koopman/1997_Koopman_preprint.pdf:PDF},
  organisation = {United Technologies Research Center 411 Silver Lane M/S 48 East Hartford, CT 06108 koopman@utrcgw.utc.com},
  owner        = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Koopman1990,
  author    = {Koopman, Phillip Jr.},
  title     = {Architectural Opportunities for Future Stack Engines},
  year      = {1990},
  pages     = {79},
  abstract  = {The next generation of stack computer designs must address the changing realities of the marketplace. Embedded real time control will become the primary application area, forcing design tradeoffs that are different from those made by other processors/ Important issues that must be addressed by stack computer designers include: support for the C programming language, living with memory bandwidth limitations, and making the best possible use of large number of translators.},
  file      = {:by-author/K/Koopman/1990_Koopman_79.pdf:PDF},
  keywords  = {Computer Architecture; Computer Science (CS); Hardware},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Koopman1990a,
  author    = {Koopman, Phillip Jr.},
  journal   = {Forth Dimensions},
  title     = {Design Tradeoffs in Stack Computers - a Personal Experience},
  year      = {1990},
  pages     = {5},
  volume    = {11},
  file      = {:by-author/K/Koopman/1990_Koopman_5.pdf:PDF},
  keywords  = {Computer Architecture; Computer Science (CS); Hardware},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Korndoerfer2000,
  author           = {Ingo P. Korndörfer and Jeffrey Salerno and Debra Jing and Brian W. Matthews},
  journal          = {Acta Crystallographica Section D},
  title            = {Crystallization and preliminary {X}-ray analysis of a bacteriophage {T4} primase fragment},
  year             = {2000},
  pages            = {95--97},
  volume           = {56},
  abstract         = {The primase from bacteriophage T4 is a single-stranded DNA-dependent RNA polymerase that is one of the seven proteins that constitute the DNA-replication machinery of bacteriophage T4. In an attempt to crystallize the protein, a number of variants were generated. One such construct, which includes the C-terminal region (residues 196-340), gave four different crystal forms which diffract in the 3.5-6.0 Å resolution range.},
  creationdate     = {2011-12-13T00:00:00},
  doi              = {10.1107/S0907444999014225},
  file             = {:by-author/K/Korndörfer/2000_Korndörfer_95.pdf:PDF},
  modificationdate = {2023-05-02T10:19:55},
  owner            = {saulius},
  timestamp        = {2011.12.13},
}

@Article{Kosinski2005,
  author    = {Jan Kosinski and Marcin Feder and Janusz M. Bujnicki},
  journal   = {BMC Bioinformatics},
  title     = {The PD-(D/E)XK superfamily revisited: identification of new members among proteins involved in DNA metabolism and functional predictions for domains of (hitherto) unknown function},
  year      = {2005},
  pages     = {6:172},
  abstract  = {Background The PD-(D/E)XK nuclease superfamily, initially identified in type II restriction endonucleases and later in many enzymes involved in DNA recombination and repair, is one of the most challenging targets for protein sequence analysis and structure prediction. Typically, the sequence similarity between these proteins is so low, that most of the relationships between known members of the PD-(D/E)XK superfamily were identified only after the corresponding structures were determined experimentally. Thus, it is tempting to speculate that among the uncharacterized protein families, there are potential nucleases that remain to be discovered, but their identification requires more sensitive tools than traditional PSI-BLAST searches. Results The low degree of amino acid conservation hampers the possibility of identification of new members of the PD-(D/E)XK superfamily based solely on sequence comparisons to known members. Therefore, we used a recently developed method HHsearch for sensitive detection of remote similarities between protein families represented as profile Hidden Markov Models enhanced by secondary structure. We carried out a comparison of known families of PD-(D/E)XK nucleases to the database comprising the COG and PFAM profiles corresponding to both functionally characterized as well as uncharacterized protein families to detect significant similarities. The initial candidates for new nucleases were subsequently verified by sequence-structure threading, comparative modeling, and identification of potential active site residues. Conclusion In this article, we report identification of the PD-(D/E)XK nuclease domain in numerous proteins implicated in interactions with DNA but with unknown structure and mechanism of action (such as putative recombinase RmuC, DNA competence factor CoiA, a DNA-binding protein SfsA, a large human protein predicted to be a DNA repair enzyme, predicted archaeal transcription regulators, and the head completion protein of phage T4) and in proteins for which no function was assigned to date (such as YhcG, various phage proteins, novel candidates for restriction enzymes). Our results contributes to the reduction of "white spaces" on the sequence-structure-function map of the protein universe and will help to jump-start the experimental characterization of new nucleases, of which many may be of importance for the complete understanding of mechanisms that govern the evolution and stability of the genome.},
  doi       = {10.1186/1471-2105-6-172},
  file      = {:by-author/K/Kosinski/2005_Kosinski_1471.pdf:PDF},
  keywords  = {Bioinformatics; PD (D/E)XK; Restriction Endonucleases (REases)},
  owner     = {saulius},
  timestamp = {2012.11.20},
  creationdate = {2012-11-20T00:00:00},
}

@InProceedings{Kothuri2002,
  author    = {Kothuri, Ravi Kanth V and Ravada, Siva and Abugov, Daniel},
  booktitle = {Proceedings of the 2002 ACM SIGMOD international conference on Management of data},
  title     = {Quadtree And R-tree Indexes in Oracle Spatial: A Comparison Using GIS Data},
  year      = {2002},
  pages     = {546--557},
  publisher = {ACM},
  abstract  = {Spatial indexing has been one of the active focus areas in recent database research. Several variants of Quadtree and R-tree indexes have been proposed in database literature. In this paper, we first describe briefly our implementation of Quadtree and R-tree index structures and related optimizations in Oracle Spatial. We then examine the relative merits of two structures as implemented in Oracle Spatial and compare their performance for different types of queries and other operations. Finally, we summarize experiences with these different structures in indexing large GIS datasets in Oracle Spatial.},
  doi       = {10.1145/564691.564755},
  file      = {:by-author/K/Kothuri/2002_Kothuri_546.pdf:PDF},
  isbn      = {1-58113-497-5},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://doi.acm.org/10.1145/564691.564755},
}

@Article{Kovacs2002,
  author    = {Kovacs, Julio A. and Wriggers, Willy},
  journal   = {Acta crystallographica. Section D, Biological crystallography},
  title     = {Fast rotational matching.},
  year      = {2002},
  pages     = {1282--6},
  volume    = {58},
  abstract  = {A computationally efficient method is presented - 'fast rotational matching' or FRM - that significantly accelerates the search of the three rotational degrees of freedom (DOF) in biomolecular matching problems. This method uses a suitable parametrization of the three-dimensional rotation group along with spherical harmonics, which allows efficient computation of the Fourier Transform of the rotational correlation function. Previous methods have used Fourier techniques only for two of the rotational DOFs, leaving the remaining angle to be determined by an exhaustive search. Here for the first time a formulation is presented that makes it possible to Fourier transform all three rotational DOFs, resulting in notable improvements in speed. Applications to the docking of atomic structures into electron-microscopy maps and the molecular-replacement problem in X-ray crystallography are considered.},
  file      = {2002_Kovacs_1282.pdf:by-author/K/Kovacs/2002_Kovacs_1282.pdf:PDF},
  keywords  = {Algorithms; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2012.05.15},
  creationdate = {2012-05-15T00:00:00},
}

@Article{Kovalevski2001,
  author     = {Kovalevski, V. V and Buseck, Peter R and Cowley, J. M},
  journal    = {Carbon},
  title      = {Comparison of carbon in shungite rocks to other natural carbons: {An} {X}-ray and {TEM} study},
  year       = {2001},
  issn       = {0008-6223},
  pages      = {243--256},
  volume     = {39},
  abstract   = {The shungites of Karelia (Russia) form a large, diverse group of black Precambrian rocks, all of which contain an intriguing type of poorly crystalline carbon. Wide differences of opinion exist about its structural state and its relation to carbon from other geological environments and origins. We used a variety of measurement techniques to determine the structural features of the carbon in shungite samples and to relate them to other natural sources of carbon. Although there is a wide range of types of shungite rocks, it appears as if the structure of their carbon is similar throughout in respect to high-resolution transmission electron microscopy (HRTEM) images, and electron and X-ray diffraction patterns. Other samples whose carbon is indistinguishable using these techniques include those from the Erickson gold mine (Canada), the Sovetskaya gold mine (Russia), and the Sudbury impact structure (Ontario). Carbon samples from different localities of the Shunga district are characterized by containing curved layers, similar to samples from natural and synthetic cokes. The HRTEM images and nanodiffraction patterns of shungites suggest that some 3-dimensional closed shells occur but, more commonly, there are fractions of such shells or regions of structure that are highly disordered into bent stacks of graphene layers.},
  doi        = {10.1016/S0008-6223(00)00120-2},
  file       = {ScienceDirect Full Text PDF:by-author/K/Kovalevski/2001_Kovalevski_243.pdf:application/pdf;ScienceDirect Snapshot:by-author/K/Kovalevski/2001_Kovalevski_243.html:text/html},
  keywords   = {Amorphous Carbon; Microstructure; Transmission Electron Microscopy (TEM); X-ray Diffraction},
  owner      = {saulius},
  shorttitle = {Comparison of carbon in shungite rocks to other natural carbons},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url        = {http://www.sciencedirect.com/science/article/pii/S0008622300001202},
  urldate    = {2015-07-06},
}

@Article{Kovalevsky2010,
  author    = {Kovalevsky, Andrey and Fisher, Zoe and Johnson, Hannah and Mustyakimov, Marat and Waltman, Mary Jo and Langan, Paul},
  journal   = {Acta Crystallographica Section D},
  title     = {Macromolecular neutron crystallography at the Protein Crystallography Station (PCS)},
  year      = {2010},
  pages     = {1206–1212},
  volume    = {66},
  abstract  = {The Protein Crystallography Station (PCS) at Los Alamos Neutron Science Center is a high-performance beamline that forms the core of a capability for neutron macromolecular structure and function determination. Neutron diffraction is a powerful technique for locating H atoms and can therefore provide unique information about how biological macro- molecules function and interact with each other and smaller molecules. Users of the PCS have access to neutron beam time, deuteration facilities, the expression of proteins and the synthesis of substrates with stable isotopes and also support for data reduction and structure analysis. The beamline exploits the pulsed nature of spallation neutrons and a large electronic detector in order to collect wavelength-resolved Laue patterns using all available neutrons in the white beam. The PCS user facility is described and highlights from the user program are presented.},
  doi       = {10.1107/S0907444910027198},
  file      = {:by-author/K/Kovalevsky/2010_Kovalevsky_1206.pdf:PDF},
  keywords  = {Neutron Crystallography; Neutron Diffraction; Protein Crystallization},
  owner     = {em},
  timestamp = {2014.02.13},
  creationdate = {2014-02-13T00:00:00},
}

@Article{Kovall1998,
  author           = {Kovall, R. A. and Matthews, B. W.},
  journal          = {Proceedings of the National Academy of Sciences of the United States of America},
  title            = {Structural, functional, and evolutionary relationships between lambda-exonuclease and the type {II} restriction endonucleases},
  year             = {1998},
  pages            = {7893--7},
  volume           = {95},
  abstract         = {lambda-exonuclease participates in DNA recombination and repair. It binds a free end of double-stranded DNA and degrades one strand in the 5' to 3' direction. The primary sequence does not appear to be related to any other protein, but the crystal structure shows part of lambda-exonuclease to be similar to the type II restriction endonucleases PvuII and EcoRV. There is also a weaker correspondence with EcoRI, BamHI, and Cfr10I. The structure comparisons not only suggest that these enzymes all share a similar catalytic mechanism and a common structural ancestor but also provide strong evidence that the toroidal structure of lambda-exonuclease encircles its DNA substrate during hydrolysis.},
  creationdate     = {2008-07-28T00:00:00},
  file             = {Kovall_1998_7893-RE_struct_funct.pdf:by-author/K/Kovall/1998_Kovall_7893.pdf:PDF},
  groups           = {sg/Cfr10I},
  modificationdate = {2023-05-02T10:18:30},
  owner            = {saulius},
  timestamp        = {2008.07.28},
}

@Article{Kowalski2010,
  author    = {L. Kowalski},
  journal   = {Physics Letters A},
  title     = {Comment on “Piezonuclear decay of thorium” [Phys. Lett. A 373 (2009) 1956]},
  year      = {2010},
  pages     = {696--697},
  volume    = {374},
  abstract  = {Cardone et al. [F. Cardone, R. Mignani, A. Petrucci, Phys. Lett. A 373 (2009) 1956] claim that cavitation speeds up radioactive decay of 228Th dissolved in water. The experimental evidence they presented was criticized by Ericsson et al. [G. Ericsson, S. Pomp, H. Sjöstrand, E. Traneus, Phys. Lett. A 373 (2009) 3795]. This Comment focuses on a presumably-ignored trivial effect that might be responsible for the reported experimental results. It also contains suggestions for improving the quality of future investigations.},
  doi       = {10.1016/j.physleta.2009.11.056},
  file      = {:by-author/K/Kowalski/2010_Kowalski_696.pdf:PDF},
  keywords  = {Physics; Radioactive Decay},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/S0375960109014893},
}

@Article{Kozin2001,
  author    = {Kozin, M. B. and Svergun, D. I.},
  journal   = {Journal of Applied Crystallography},
  title     = {Automated matching of high- and low-resolution structural models},
  year      = {2001},
  pages     = {33--41},
  volume    = {34},
  abstract  = {A method is presented for automated best-matching alignment of three-dimensional models represented by ensembles of points. A normalized spatial discrepancy (NSD) is introduced as a proximity measure between three-dimensional objects. Starting from an inertia-axes alignment, the algorithm minimizes the NSD; the final value of the NSD provides a quantitative estimate of similarity between the objects. The method is implemented in a computer program. Simulations have been performed to test its performance on model structures with specified numbers of points ranging from a few to a few thousand. The method can be used for comparative analysis of structural models obtained by different methods, e.g. of high-resolution crystallographic atomic structures and low-resolution models from solution scattering or electron microscopy.},
  doi       = {10.1107/S0021889800014126},
  file      = {2001_Kozin_33.pdf:by-author/K/Kozin/2001_Kozin_33.pdf:PDF},
  keywords  = {SAXS; SUPCOMB},
  owner     = {em},
  timestamp = {2013.01.02},
  creationdate = {2013-01-02T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0021889800014126},
}

@Webpage{Kozlowski2007,
  author    = {Łukasz Kozłowski},
  retrieved = {2015-03-04},
  title     = {Theoretical basis of isoelectric point calculation, i.e. how to calculate isoelectric point of protein},
  url       = {http://www.isoelectric.ovh.org/files/isoelectric-point-theory.html},
  year      = {2007},
  file      = {:by-author/K/Kozłowski/2007_Kozłowski.war:WAR},
  keywords  = {Isoelectric-point; Protein-physics},
  owner     = {saulius},
  timestamp = {2015.03.02},
  creationdate = {2015-03-02T00:00:00},
}

@Book{Krafzig2004,
  author    = {Dirk Krafzig and Karl Banke and Dirk Slama},
  publisher = {Prentice Hall},
  title     = {Enterprise SOA: Service-Oriented Architecture Best Practices},
  year      = {2004},
  isbn      = {978-0-13-146575-6},
  file      = {:by-author/K/Krafzig/2004_Krafzig.doc:DOC},
  isbn10    = {0-13-146575-9},
  keywords  = {Computer Science (CS); Service-oriented-architecture},
  owner     = {saulius},
  timestamp = {2015.02.28},
  creationdate = {2015-02-28T00:00:00},
}

@Article{Kraulis1991,
  author    = {Kraulis, PJ},
  journal   = {J Appl Cryst},
  title     = {Molscript - a program to produce both detailed and schematic plots of protein structures},
  year      = {1991},
  pages     = {946--950},
  volume    = {24},
  doi       = {10.1107/S0021889891004399},
  file      = {1991_Kraulis_946.pdf:by-author/K/Kraulis/1991_Kraulis_946.pdf:PDF},
  keywords  = {Molecular Graphics; Molscript},
  owner     = {em},
  timestamp = {2016.06.16},
  creationdate = {2016-06-16T00:00:00},
}

@Manuscript{Krauss2000,
  author      = {Stefan Krauß and Laura Martignon and Ulrich Hoffrage},
  title       = {Simplifying Bayesian Inference},
  year        = {2000},
  institution = {Max Planck Institute For Human Development},
  keywords    = {Bayesian Statistics; Unaided Human Reasoning},
  abstract    = {Probability theory can be used to model inference under uncertainty. The particular way in which Bayes’formula is stated, which is of only minor importance in standard probability textbooks, becomes central in this context. When events can be interpreted as evidences and hypotheses, Bayes’formula allows one to update one’s belief in a hypothesis in light of new data.},
  file        = {:by-author/K/Krauß/2000_Krauß.pdf:PDF},
  groups      = {sg/Bayesian},
  owner       = {saulius},
  timestamp = {2012.09.30},
  creationdate = {2012-09-30T00:00:00},
}

@Article{Krenkel2003,
  author    = {Germán Krenkel and Eduardo A. Castro},
  journal   = {Molecular Medicinal Chemistry},
  title     = {Optimized Calculation on the Inhibition of Carbonic Anhydrase Isozymes I and II by some Phenyl and Pyridyl Substituted Sulfanilamide Schiff’s Bases},
  year      = {2003},
  pages     = {13--20},
  abstract  = {Previous linear calculations on the inhibition of carbonic anhydrase isozymes I and II by some phenyl and pyridyl substituted sulfanilamide Schiff’s bases are improved resorting to high-order fitting polynomials. Statistical parameters associated with the regression equations show a better predictive power for these new equations, which reveal the need to employ more general analytical fitting equations when dealing with this sort of Quantitative Structure Activity Relationships.},
  file      = {2003_Krenkel_13.pdf:by-author/K/Krenkel/2003_Krenkel_13.pdf:PDF},
  groups    = {sg/inhibitors, sg/hCA1, sg/hCA2},
  keywords  = {Carbonic Anhydrase Isozymes; Carbonic Anhydrases; Phenyl and Pyridyl Substituted; QSAR Theory; Schiff's Bases; Sulfanilamide},
  owner     = {saulius},
  timestamp = {2012.11.20},
  creationdate = {2012-11-20T00:00:00},
}

@Article{Kreuzer2000,
  author    = {Kreuzer, K. N.},
  journal   = {Trends in biochemical sciences},
  title     = {Recombination-dependent DNA replication in phage T4.},
  year      = {2000},
  pages     = {165--73},
  volume    = {25},
  abstract  = {Studies in the 1960s implied that bacteriophage T4 tightly couples DNA replication to genetic recombination. This contradicted the prevailing wisdom of the time, which staunchly supported recombination as a simple cut-and-paste process. More-recent investigations have shown how recombination triggers DNA synthesis and why the coupling of these two processes is important. Results from T4 were instrumental in our understanding of many important replication and recombination proteins, including the newly recognized replication/recombination mediator proteins. Recombination-dependent DNA replication is crucial to the T4 life cycle as it is the major mode of DNA replication and is also central to the repair of DNA breaks and other damage.},
  file      = {:by-author/K/Kreuzer/2000_Kreuzer_165.pdf:PDF},
  keywords  = {{gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Kreuzer2010,
  author    = {Kreuzer, Kenneth N. and Brister, J. Rodney},
  journal   = {Virology journal},
  title     = {Initiation of bacteriophage T4 DNA replication and replication fork dynamics: a review in the Virology Journal series on bacteriophage T4 and its relatives.},
  year      = {2010},
  pages     = {358},
  volume    = {7},
  abstract  = {Bacteriophage T4 initiates DNA replication from specialized structures that form in its genome. Immediately after infection, RNA-DNA hybrids (R-loops) occur on (at least some) replication origins, with the annealed RNA serving as a primer for leading-strand synthesis in one direction. As the infection progresses, replication initiation becomes dependent on recombination proteins in a process called recombination-dependent replication (RDR). RDR occurs when the replication machinery is assembled onto D-loop recombination intermediates, and in this case, the invading 3' DNA end is used as a primer for leading strand synthesis. Over the last 15 years, these two modes of T4 DNA replication initiation have been studied in vivo using a variety of approaches, including replication of plasmids with segments of the T4 genome, analysis of replication intermediates by two-dimensional gel electrophoresis, and genomic approaches that measure DNA copy number as the infection progresses. In addition, biochemical approaches have reconstituted replication from origin R-loop structures and have clarified some detailed roles of both replication and recombination proteins in the process of RDR and related pathways. We will also discuss the parallels between T4 DNA replication modes and similar events in cellular and eukaryotic organelle DNA replication, and close with some current questions of interest concerning the mechanisms of replication, recombination and repair in phage T4.},
  file      = {:by-author/K/Kreuzer/2010_Kreuzer_358.pdf:PDF},
  keywords  = {{gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@InProceedings{Kriegel2004,
  author    = {Kriegel, Hans-Peter and Kunath, Peter and Pfeifle, Martin and Renz, Matthias},
  booktitle = {Proceedings of the 12th annual ACM international workshop on Geographic information systems},
  title     = {Object-Relational Management of Complex Geographical Objects},
  year      = {2004},
  pages     = {109--117},
  publisher = {ACM},
  abstract  = {Modern database applications including computer-aided design, multimedia information systems, medical imaging, molecular biology, or geographical information systems impose new requirements on the effective and efficient management of spatial data. Particular problems arise from the need of high resolutions for large spatial objects and from the design goal to use general purpose database management systems in order to guarantee industrial-strength. In the past two decades, various stand-alone spatial index structures have been proposed but their integration into fully-fledged database systems is problematic. Most of these approaches are based on the decomposition of spatial objects leading to replicating index structures. In contrast to common black-and-white decompositions which suffer from the lack of intermediate solutions, we introduce gray intervals which are stored in a spatial index. Additionally, we store the exact information of these gray intervals in a compressed way. These gray intervals are created by using a cost-based decompositioning algorithm which takes the access probability and the decompression cost of them into account. Furthermore, we exploit statistical information of the database objects to find a cost-optimal decomposition of the query objects. The experimental evaluation on the SEQUOIA benchmark test points out that our new concept outperforms the Relational Interval Tree by more than one order of magnitude with respect to overall query response time.},
  doi       = {10.1145/1032222.1032240},
  file      = {:by-author/K/Kriegel/2004_Kriegel_109.pdf:PDF},
  isbn      = {1-58113-979-9},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://doi.acm.org/10.1145/1032222.1032240},
}

@Article{Kriminski2002,
  author    = {Kriminski, S. and Caylor, C. L. and Nonato, M. C. and Finkelstein, K. D. and Thorne, R. E.},
  journal   = {Acta Crystallographica Section D},
  title     = {Flash-cooling and annealing of protein crystals},
  year      = {2002},
  pages     = {459--471},
  volume    = {58},
  doi       = {10.1107/S0907444902000112},
  file      = {en0056.pdf:by-author/K/Kriminski/2002_Kriminski_459.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444902000112},
}

@Article{Kriminski2003,
  author    = {Kriminski, S. and Kazmierczak, M. and Thorne, R. E.},
  journal   = {Acta Crystallographica Section D},
  title     = {Heat transfer from protein crystals: implications for flash-cooling and X-ray beam heating},
  year      = {2003},
  pages     = {697--708},
  volume    = {59},
  doi       = {10.1107/S0907444903002713},
  file      = {en0073.pdf:by-author/K/Kriminski/2003_Kriminski_697.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444903002713},
}

@Article{Krisch1971,
  author    = {Krisch, H. M. and Shah, D. B. and Berger, H.},
  journal   = {Journal of virology},
  title     = {Replication and recombination in ligase-deficient rII bacteriophage T4D.},
  year      = {1971},
  pages     = {491--8},
  volume    = {7},
  abstract  = {Deoxyribonucleic acid replication and genetic recombination were investigated after infection of Escherichia coli with ligase-deficient rII bacteriophage T4D. The major observations are: (i) deoxyribonucleic acid synthesis is discontinuous, (ii) the discontinuities are more slowly repaired than in wild-type infection, (iii) host ligase is required for viability, and (iv) genetic recombination is increased.},
  file      = {:by-author/K/Krisch/1971_Krisch_491.pdf:PDF},
  keywords  = {{gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Krishnamurthy2008,
  author    = {Krishnamurthy, Vijay M and Kaufman, George K and Urbach, Adam R and Gitlin, Irina and Gudiksen, Katherine L and Weibel, Douglas B and Whitesides, George M},
  journal   = {Chemical reviews},
  title     = {Carbonic anhydrase as a model for biophysical and physical-organic studies of proteins and protein-ligand binding.},
  year      = {2008},
  pages     = {946--1051},
  volume    = {108},
  file      = {2008_Krishnamurthy_946.pdf:by-author/K/Krishnamurthy/2008_Krishnamurthy_946.pdf:PDF},
  groups    = {sg/inhibitors, sg/modelling, sg/physical sg/methods},
  keywords  = {Binding; Carbonic Anhydrases},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@TechReport{Krishnan2004,
  author      = {Manojkumar Krishnan and Jarek Nieplocha},
  institution = {Computational Sciences \& Mathematics, Pacific Northwest National Laboratory, {Manojkumar.Krishnan, Jarek.Nieplocha}@pnl.gov},
  title       = {SRUMMA: A Matrix Multiplication Algorithm Suitable for Clusters and Scalable Shared Memory Systems},
  year        = {2004},
  abstract    = {This paper describes a novel parallel algorithm that implements a dense matrix multiplication operation with algorithmic efficiency equivalent to that of Cannon’s algorithm. It is suitable for clusters and scalable shared memory systems. The current approach differs from the other parallel matrix multiplication algorithms by the explicit use of shared memory and remote memory access (RMA) communication rather than message passing. The experimental results on clusters (IBM SP, Linux-Myrinet) and shared memory systems (SGI Altix, Cray X1) demonstrate consistent performance advantages over pdgemm from the ScaLAPACK/PBBLAS suite, the leading implementation of the parallel matrix multiplication algorithms used today. In the best case on the SGI Altix, the new algorithm performs 20 times better than pdgemm for a matrix size of 1000 on 128 processors. The impact of zero-copy nonblocking RMA communications and shared memory communication on matrix multiplication performance on clusters are investigated.},
  file        = {:by-author/K/Krishnan/2004_Krishnan.pdf:PDF},
  keywords    = {Computer Science (CS); Matrix Multiplication},
  owner       = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Krissinel2004,
  author    = {Krissinel, E. and Henrick, K.},
  journal   = {Acta Crystallographica Section D},
  title     = {Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions},
  year      = {2004},
  pages     = {2256--2268},
  volume    = {60},
  doi       = {10.1107/S0907444904026460},
  file      = {ba5056.pdf:by-author/K/Krissinel/2004_Krissinel_2256.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444904026460},
}

@Article{Krissinel2004a,
  author    = {Krissinel, E. B. and Winn, M. D. and Ballard, C. C. and Ashton, A. W. and Patel, P. and Potterton, E. A. and McNicholas, S. J. and Cowtan, K. D. and Emsley, P.},
  journal   = {Acta Crystallographica Section D},
  title     = {The new {\it CCP}4 Coordinate Library as a toolkit for the design of coordinate-related applications in protein crystallography},
  year      = {2004},
  pages     = {2250--2255},
  volume    = {60},
  doi       = {10.1107/S0907444904027167},
  file      = {ba5055.pdf:by-author/K/Krissinel/2004_Krissinel_2250.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444904027167},
}

@Article{Kritzer2005,
  author    = {Kritzer, Joshua A. and Tirado-Rives, Julian and Hart, Scott A. and Lear, James D. and Jorgensen, William L. and Schepartz, Alanna},
  journal   = {Journal of the American Chemical Society},
  title     = {Relationship between side chain structure and 14-helix stability of beta3-peptides in water.},
  year      = {2005},
  pages     = {167--78},
  volume    = {127},
  abstract  = {Folded polymers are used in Nature for virtually every vital process. Nonnatural folded polymers, or foldamers, have the potential for similar versatility, and the design and refinement of such molecules is of considerable current interest. Here we report a complete and systematic analysis of the relationship between side chain structure and the 14-helicity of a well-studied class of foldamers, beta(3)-peptides, in water. Our experimental results (1) verify the importance of macrodipole stabilization for maintaining 14-helix structure, (2) provide comprehensive evidence that beta(3)-amino acids branched at the first side chain carbon are 14-helix-stabilizing, (3) suggest a novel role for side chain hydrogen bonding as an additional stabilizing force in beta(3)-peptides containing beta(3)-homoserine or beta(3)-homothreonine, and (4) demonstrate that diverse functionality can be incorporated into a stable 14-helix. Gas- and solution-phase calculations and Monte Carlo simulations recapitulate the experimental trends only in the context of oligomers, yielding insight into the mechanisms behind 14-helix folding. The 14-helix propensities of beta(3)-amino acids differ starkly from the alpha-helix propensities of analogous alpha-amino acids. This contrast informs current models for alpha-helix folding, and suggests that 14-helix folding is governed by different biophysical forces than is alpha-helix folding. The ability to modulate 14-helix structure through side chain choice will assist rational design of 14-helical beta-peptide ligands for macromolecular targets.},
  file      = {:by-author/K/Kritzer/2005_Kritzer_167.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@InProceedings{Kroah-Hartman2003,
  author       = {Greg Kroah-Hartman},
  booktitle    = {Proceedings of the Linux Symposium},
  title        = {udev – A Userspace Implementation of devfs},
  year         = {2003},
  organization = {IBM Corp., Linux Technology Center, greg@kroah.com, gregkh@us.ibm.com},
  file         = {:by-author/K/Kroah-Hartman/2003_Kroah-Hartman.pdf:PDF},
  keywords     = {Computer Science (CS); Linux; Operating Systems},
  owner        = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Kroon-Batenburg2014,
  author     = {Kroon-Batenburg, Loes M. J. and Helliwell, John R.},
  journal    = {Acta Crystallographica Section D: Biological Crystallography},
  title      = {Experiences with making diffraction image data available: what metadata do we need to archive?},
  year       = {2014},
  issn       = {0907-4449},
  pages      = {2502--2509},
  volume     = {70},
  abstract   = {A local raw ‘diffraction data images’ archive was made available and some data sets were retrieved and reprocessed, which led to analysis of the anomalous difference densities of two partially occupied Cl atoms in cisplatin as well as a re-evaluation of the resolution cutoff in these diffraction data. General questions on storing raw data are discussed. It is also demonstrated that often one needs unambiguous prior knowledge to read the (binary) detector format and the setup of goniometer geometries., Recently, the IUCr (International Union of Crystallography) initiated the formation of a Diffraction Data Deposition Working Group with the aim of developing standards for the representation of raw diffraction data associated with the publication of structural papers. Archiving of raw data serves several goals: to improve the record of science, to verify the reproducibility and to allow detailed checks of scientific data, safeguarding against fraud and to allow reanalysis with future improved techniques. A means of studying this issue is to submit exemplar publications with associated raw data and metadata. In a recent study of the binding of cisplatin and carboplatin to histidine in lysozyme crystals under several conditions, the possible effects of the equipment and X-ray diffraction data-processing software on the occupancies and B factors of the bound Pt compounds were compared. Initially, 35.3 GB of data were transferred from Manchester to Utrecht to be processed with EVAL. A detailed description and discussion of the availability of metadata was published in a paper that was linked to a local raw data archive at Utrecht University and also mirrored at the TARDIS raw diffraction data archive in Australia. By making these raw diffraction data sets available with the article, it is possible for the diffraction community to make their own evaluation. This led to one of the authors of XDS (K. Diederichs) to re-integrate the data from crystals that supposedly solely contained bound carboplatin, resulting in the analysis of partially occupied chlorine anomalous electron densities near the Pt-binding sites and the use of several criteria to more carefully assess the diffraction resolution limit. General arguments for archiving raw data, the possibilities of doing so and the requirement of resources are discussed. The problems associated with a partially unknown experimental setup, which preferably should be available as metadata, is discussed. Current thoughts on data compression are summarized, which could be a solution especially for pixel-device data sets with fine slicing that may otherwise present an unmanageable amount of data.},
  doi        = {10.1107/S1399004713029817},
  file       = {Kroon-Batenburg and Helliwell - 2014 - Experiences with making diffraction image data ava.pdf:by-author/K/Kroon-Batenburg/2014_Kroon-Batenburg_2502.pdf:application/pdf},
  owner      = {saulius},
  pmcid      = {PMC4187998},
  pmid       = {25286836},
  shorttitle = {Experiences with making diffraction image data available},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url        = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4187998/},
  urldate    = {2015-08-28},
}

@Article{Kroon-Batenburg2017,
  author    = {Kroon-Batenburg, Loes M. J. and Helliwell, John R. and McMahon, Brian and Terwilliger, Thomas C.},
  journal   = {IUCrJ},
  title     = {Raw diffraction data preservation and reuse: overview, update on practicalities and metadata requirements},
  year      = {2017},
  issn      = {2052-2525},
  month     = {Jan},
  number    = {1},
  pages     = {87--99},
  volume    = {4},
  doi       = {10.1107/s2052252516018315},
  file      = {:by-author/K/Kroon-Batenburg/2017_Kroon-Batenburg_87.pdf:PDF},
  publisher = {International Union of Crystallography (IUCr)},
  timestamp = {2021.09.09},
  creationdate = {2021-09-09T00:00:00},
  url       = {https://doi.org/10.1107/S2052252516018315},
}

@Article{Krueger2009,
  author    = {Krueger, Andrew T. and Kool, Eric T.},
  journal   = {Chemistry \& Biology},
  title     = {Redesigning the Architecture of the Base Pair: Toward Biochemical and Biological Function of New Genetic Sets},
  year      = {2009},
  issn      = {1074-5521},
  month     = {Mar},
  number    = {3},
  pages     = {242–248},
  volume    = {16},
  doi       = {10.1016/j.chembiol.2008.12.004},
  file      = {:by-author/K/Krueger/2009_Krueger_242.pdf:PDF},
  groups    = {am/Expanded genetic code},
  owner     = {andrius},
  publisher = {Elsevier BV},
  timestamp = {2016.05.02},
  creationdate = {2016-05-02T00:00:00},
  url       = {http://dx.doi.org/10.1016/j.chembiol.2008.12.004},
}

@Article{Krueger2007,
  author    = {Krueger, Andrew T and Kool, Eric T},
  journal   = {Current opinion in chemical biology},
  title     = {Model systems for understanding DNA base pairing.},
  year      = {2007},
  pages     = {588--94},
  volume    = {11},
  abstract  = {The fact that nucleic acid bases recognize each other to form pairs is a canonical part of the dogma of biology. However, they do not recognize each other well enough in water to account for the selectivity and efficiency that is needed in the transmission of biological information through a cell. Thus proteins assist in this recognition in multiple ways, and recent data suggest that these mechanisms of recognition can vary widely with context. To probe how the chemical differences of the four nucleobases are defined in various biological contexts, chemists and biochemists have developed modified versions that differ in their polarity, shape, size, and functional groups. This brief review covers recent advances in this field of research.},
  file      = {2007_Krueger_588.pdf:by-author/K/Krueger/2007_Krueger_588.pdf:PDF},
  keywords  = {DNA Bases},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Krueger1995,
  author    = {Krüger, T. and Wild, C. and Noyer-Weidner, M.},
  journal   = {The EMBO journal},
  title     = {McrB: a prokaryotic protein specifically recognizing DNA containing modified cytosine residues.},
  year      = {1995},
  pages     = {2661--9},
  volume    = {14},
  abstract  = {Restriction of DNA by the Escherichia coli K-12 McrBC restriction endonuclease, which consists of the two subunits McrB and McrC, depends on the presence of modified cytosine residues in a special constellation. From previous work by others it was known that restriction of 5-methylcytosine-containing DNA requires two methylated 5'-PuC sites separated by approximately 40-80 non-defined base pairs. Here we show that binding of the McrBC nuclease is mediated exclusively by the McrB subunit. McrB has a low affinity for non-methylated DNA, with which it forms low molecular weight complexes. The affinity for DNA is significantly increased, with variations depending on the sequence context, by hemi- or fully methylated 5'-PuC sites. Binding to such substrates yields high molecular weight complexes, presumably involving several McrB molecules. Methylation at unique 5'-PuC sites can be sufficient to stimulate DNA binding by McrB. As such substrates are not cleaved by the nuclease, restriction apparently requires the coordinated interaction of molecules bound to neighbouring 5'-PumC sites. The binding properties of McrB exhibit some similarities to recently identified eukaryotic proteins interacting in a non-sequence-specific manner with DNA containing methylated 5'-CpG sequences and might point to a common molecular origin of these proteins. In addition to DNA, McrB also binds GTP, an essential cofactor in DNA restriction by McrBC. McrC neither binds to DNA nor modulates the DNA binding potential of McrB. As McrC is essential for restriction it appears to predominantly function in catalysis.},
  file      = {:by-author/K/Krüger/1995_Krüger_2661.pdf:PDF},
  keywords  = {McrBC},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Ku2007,
  author    = {Ku, Shao-Yang and Smith, G. David and Howell, P. Lynne},
  journal   = {Acta crystallographica. Section D, Biological crystallography},
  title     = {ADP-2Ho as a phasing tool for nucleotide-containing proteins.},
  year      = {2007},
  pages     = {493--9},
  volume    = {63},
  abstract  = {Trivalent holmium ions were shown to isomorphously replace magnesium ions to form an ADP-2Ho complex in the nucleotide-binding domain of Bacillus subtilis 5-methylthioribose (MTR) kinase. This nucleotide-holmium complex provided sufficient phasing power to allow SAD and SIRAS phasing of this previously unknown structure using the L(III) absorption edge of holmium. The structure of ADP-2Ho reveals that the two Ho ions are approximately 4 A apart and are likely to share their ligands: the phosphoryl O atoms of ADP and a water molecule. The structure determination of MTR kinase using data collected using Cu Kalpha X-radiation was also attempted. Although the heavy-atom substructure determination was successful, interpretation of the map was more challenging. The isomorphous substitution of holmium for magnesium in the MTR kinase-nucleotide complex suggests that this could be a useful phasing tool for other metal-dependent nucleotide-containing proteins.},
  doi       = {10.1107/S0907444907006592},
  file      = {:by-author/K/Ku/2007_Ku_493.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@InProceedings{Kuan2007,
  author    = {George Kuan and David MacQueen},
  booktitle = {ML’07},
  title     = {Efficient ML Type Inference Using Ranked Type Variables},
  year      = {2007},
  abstract  = {The Damas-Milner type inference algorithm (commonly known as algorithm W) is at the core of all ML type checkers. Although the algorithm is known to have poor worst-case behavior [8], in prac- tice well-engineered type checkers will run in approximately linear time. To achieve this efficiency, implementations need to improve on algorithm W’s method of scanning the complete type environ- ment to determine whether a type variable can be generalized at a let binding. Following a suggestion of Damas, most ML type checkers use an alternative method based on ranking unification variables to track their position in the type environment. Here we formalize two such ranking systems, one based on lambda depth (used in the SML/NJ compiler), and the other based on let depth (used in OCaml, for instance). Each of these systems is formalized both with and without the value restriction, and they are proved correct relative to the classic algorithm W. Our formal- izations of the various algorithms use simple abstract machines that are similar to those derived from small-step evaluation semantics.},
  file      = {2007_Kuan_ML_ACM_conf_proceedings_3--Efficient_type_inference_using_ranked_type_variables.pdf:by-author/K/Kuan/2007_Kuan.pdf:PDF},
  keywords  = {Computer Science (CS); Type Systems},
  owner     = {saulius},
  timestamp = {2012.11.20},
  creationdate = {2012-11-20T00:00:00},
}

@Manuscript{Kuckert2005,
  author    = {Kuckert},
  title     = {Mathematische Grundlagen der Quantenmechanik},
  year      = {2005},
  keywords  = {Quantum Mechanics (QM)},
  abstract  = {Dieses Skript ist auf der Grundlage der beiden Vorlesungen entstanden, die ich im Herbsttrimester 2001 in Amsterdam und im Wintersemester 2002/2003 in Hamburg gehalten habe. Das eine oder andere wurde korrigiert, ergänzt oder weggelassen. Dieser Kurs ergänzt die einführenden Vorlesungen zur Quantenmechanik und das Studium der grundst ändigen Lehrbücher, wo erste Grundlagen, Rechentechniken und Rechnungen erlernt werden. Das Motivieren von Rechnungen und das Auswerten von Rechenresultaten erfordert jedoch Vertrautheit mit dem allgemeinen mathematischen Rahmen und seinen Fallstricken, und die werden hier ergänzt. Es wird hier im Gegensatz zu den Kursvorlesungen nicht historisch vorgegangen, sondern gleich mit dem mathematischen Formalismus begonnen.},
  file      = {:by-author/K/Kuckert/2005_Kuckert.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.09.26},
  creationdate = {2012-09-26T00:00:00},
}

@Article{Kudlicki2007,
  author    = {Kudlicki, Andrzej and Rowicka, Maga and Otwinowski, Zbyszek},
  journal   = {Acta crystallographica. Section A, Foundations of crystallography},
  title     = {The crystallographic fast Fourier transform. Recursive symmetry reduction.},
  year      = {2007},
  pages     = {465--80},
  volume    = {63},
  abstract  = {Algorithms are presented for maximally efficient computation of the crystallographic fast Fourier transform (FFT). The approach is applicable to all 230 space groups and allows reduction of both the computation time and the memory usage by a factor equal to the number of symmetry operators. The central idea is a recursive reduction of the problem to a series of transforms on grids with no special points. The maximally efficient FFT for such grids has been described in previous papers by the same authors. The interaction between the grid size factorization and the symmetry operators and its influence on the algorithm design are discussed},
  doi       = {10.1107/S0108767307047411},
  file      = {2007_Kudlicki_465.pdf:by-author/K/Kudlicki/2007_Kudlicki_465.pdf:PDF},
  keywords  = {Algorithms; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Kuenzi1979,
  author    = {N. J. Kuenzi and Bob Prielipp},
  journal   = {Topics for Teachers Series},
  title     = {Cryptarithms and other arithmetical pastimes},
  year      = {1979},
  month     = {May},
  number    = {1},
  file      = {:by-author/K/Kuenzi/1979_Kuenzi.pdf:PDF},
  keywords  = {Alphametics; Computer Science (CS)},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Manuscript{Kuhn1997,
  author    = {Markus Kuhn},
  title     = {The {TrustNo} 1 Cryptoprocessor Concept},
  year      = {1997},
  keywords  = {Computer Science (CS); Cryptography},
  abstract  = {Cryptoprocessors feature an on-chip block cipher hardware between the cache and the bus interface. Code and data are decrypted on-the-fly while be- ing fetched from RAM and are encrypted while being written into RAM. Even someone with full physical access to the printed circuit board cannot observe the executed cleartext software and its data structures. Cryptoprocessors have been used for many years as microcontrollers in security sensitive applications like financial transaction terminals. This paper explores the hardware, firmware, operating system, and key management mechanisms necessary in order to apply the cryptoprocessor concept in multitasking operating system workstations.},
  file      = {:by-author/K/Kuhn/1997_Kuhn.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@TechReport{Kuhn2003,
  author      = {Markus G. Kuhn},
  institution = {Computer Laboratory, University of Cambridge},
  title       = {Compromising emanations: eavesdropping risks of computer displays},
  year        = {2003},
  month       = {December},
  file        = {:by-author/K/Kuhn/2003_Kuhn_techreport.pdf:PDF},
  keywords    = {Computer Science (CS); Security},
  owner       = {saulius},
  pages       = {techreport},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@InProceedings{Kuhn2002,
  author      = {Markus G. Kuhn},
  booktitle   = {Proceedings 2002 IEEE Symposium on Security and Privacy},
  title       = {Optical Time-Domain Eavesdropping Risks of CRT Displays},
  year        = {2002},
  month       = {May},
  pages       = {3--18},
  abstract    = {A new eavesdropping technique can be used to read cathode-ray tube (CRT) displays at a distance. The inten- sity of the light emitted by a raster-scan screen as a func- tion of time corresponds to the video signal convolved with the impulse response of the phosphors. Experiments with a typical personal computer color monitor show that enough high-frequency content remains in the emitted light to per- mit the reconstruction of readable text by deconvolving the signal received with a fast photosensor. These optical com- promising emanations can be received even after diffuse re- flection from a wall. Shot noise from background light is the critical performance factor. In a sufficiently dark environ- ment and with a large enough sensor aperture, practically significant reception distances are possible. This informa- tion security risk should be considered in applications with high confidentiality requirements, especially in those that already require “TEMPEST”-shielded equipment designed to minimize radio-frequency emission-security concerns.},
  file        = {:by-author/K/Kuhn/2002_Kuhn_3.pdf:PDF},
  institution = {University of Cambridge, Computer Laboratory, JJ Thomson Avenue, Cambridge CB3 0FD, UK, mgk25@cl.cam.ac.uk},
  keywords    = {Computer Science (CS); Security},
  owner       = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Kuhn2007,
  author    = {Kuhn, Stefan and Helmus, Tobias and Lancashire, Robert J. and Murray-Rust, Peter and Rzepa, Henry S. and Steinbeck, Christoph and Willighagen, Egon L.},
  journal   = {Journal of Chemical Information and Modeling},
  title     = {Chemical Markup, XML, and the World Wide Web. 7. CMLSpect, an XML Vocabulary for Spectral Data},
  year      = {2007},
  pages     = {2015--2034},
  volume    = {47},
  abstract  = {CMLSpect is an extension of Chemical Markup Language (CML) for managing spectral and other analytical data. It is designed to be flexible enough to contain a wide variety of spectral data. The paper describes the CMLElements used and gives practical examples for common types of spectra. In addition it demonstrates how different views of the data can be expressed and what problems still exist.},
  doi       = {10.1021/ci600531a},
  eprint    = {http://pubs.acs.org/doi/pdf/10.1021/ci600531a},
  file      = {2007_Kuhn_2015.pdf:by-author/K/Kuhn/2007_Kuhn_2015.pdf:PDF},
  keywords  = {CML; Chemoinformatics; Crystallography; Data Formats; Data Management; X-ray Crystallography; XML},
  owner     = {saulius},
  timestamp = {2014.06.24},
  creationdate = {2014-06-24T00:00:00},
  url       = {http://pubs.acs.org/doi/abs/10.1021/ci600531a},
}

@Article{Kuijpers2004,
  author    = {Kuijpers, Brian H. M. and Groothuys, Stan and Keereweer, A. Bram R. and Quaedflieg, Peter J. L. M. and Blaauw, Richard H. and van Delft, Floris L. and Rutjes, Floris P. J. T.},
  journal   = {Organic letters},
  title     = {Expedient synthesis of triazole-linked glycosyl amino acids and peptides.},
  year      = {2004},
  pages     = {3123--6},
  volume    = {6},
  abstract  = {[structure: see text] An expedient, high-yielding synthesis of two types of triazole-linked glycopeptides is described. These novel and stable glycopeptide mimics were prepared via Cu(I)-catalyzed [3 + 2] cycloaddition of either azide-functionalized glycosides and acetylenic amino acids or acetylenic glycosides and azide-containing amino acids.},
  file      = {:by-author/K/Kuijpers/2004_Kuijpers_3123.pdf:PDF},
  keywords  = {Bioconjugation},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@Article{Kulik1996,
  author    = {Kulik, E. M. and Bickle, T. A.},
  journal   = {Journal of molecular biology},
  title     = {Regulation of the activity of the type IC EcoR124I restriction enzyme.},
  year      = {1996},
  pages     = {891--906},
  volume    = {264},
  abstract  = {Restriction-modification (R-M) systems must regulate the expression of their genes so that the chromosomal genome is modified at all times by the methyltransferase to protect the host cell from the potential lethal action of the cognate restriction endonuclease. Since type I R-M systems can be transferred to non-modified Escherichia coli cells by conjugation or transformation without killing the recipient, they must have some means to regulate their restriction activity upon entering a new host cell to avoid restriction of unprotected host DNA and cell death. This is especially true for EcoR124I, a type IC family member, which is coded for by a conjugative plasmid. Control of EcoR124I restriction activity is most likely at the post-translational level as the transfer of the EcoR124I system into a recipient cell that already expressed the HsdR subunit of this system was not a lethal event. Additionally, the kinetics of restriction activity upon transfer of the genes coding for the EcoR124I RM system to a recipient cell are the same, irrespective of the modification state of the recipient cell or the presence or absence of the EcoR124I HsdR subunit in the new host cells. The mechanism controlling the restriction activity of a type IC R-M system upon transfer to a new host cell is different from that controlling the chromosomally coded type IA and IB R-M systems. The previously discovered hsdC mutant, which affects the establishment of the type IA system EcoKI, was shown to affect the establishment of the type IB system EcoAI, but to have no influence on EcoR124I.},
  file      = {:by-author/K/Kulik/1996_Kulik_891.pdf:PDF},
  keywords  = {TypeI},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Kulkarni2012,
  author          = {Krishna Kulkarni and Jan-Eike Michels},
  journal         = j-SIGMOD,
  title           = {Temporal features in {SQL:2011}},
  year            = {2012},
  issn            = {0163-5808 (print), 1943-5835 (electronic)},
  month           = sep,
  number          = {3},
  pages           = {34--43},
  volume          = {41},
  abstract        = {SQL:2011 was published in December of 2011, replacing SQL:2008 as the most recent revision of the SQL standard. This paper covers the most important new functionality that is part of SQL:2011: the ability to create and manipulate temporal tables.},
  acknowledgement = ack-nhfb,
  bibdate         = {Mon Oct 22 10:52:52 MDT 2012},
  bibsource       = {http://portal.acm.org/; http://www.math.utah.edu/pub/tex/bib/sigmod.bib},
  coden           = {SRECD8},
  doi             = {http://dx.doi.org/10.1145/2380776.2380786},
  file            = {2012_Kulkarni_34.pdf:by-author/K/Kulkarni/2012_Kulkarni_34.pdf:PDF},
  fjournal        = {SIGMOD Record (ACM Special Interest Group on Management of Data)},
  issn-l          = {0163-5808},
  journal-url     = {http://portal.acm.org/browse_dl.cfm?idx=J689},
  keywords        = {Computer Science (CS); Data Versioning; SQL; SQL 2011; SQL Standard; Temporal Features},
  owner           = {saulius},
  timestamp = {2016.11.17},
  creationdate = {2016-11-17T00:00:00},
}

@Article{Kulys2009,
  author       = {Kulys, Juozas and Dapkunas, Zilvinas and Stupak, Robert},
  journal      = {Applied Biochemistry and Biotechnology},
  title        = {Intensification of Biocatalytical Processes by Synergistic Substrate Conversion. Fungal Peroxidase Catalyzed N-Hydroxy Derivative Oxidation in Presence of 10-Propyl Sulfonic Acid Phenoxazine},
  year         = {2009},
  issn         = {0273-2289},
  pages        = {445--456},
  volume       = {158},
  abstract     = {Many industrial pollutants, xenobiotics, and industry-important compounds are known to be oxidized by peroxidases. It has been shown that highly efficient peroxidase substrates are able to enhance the oxidation of low reactive substrate by acting as mediators. To explore this effect, the oxidation of two N-hydroxy derivatives, i.e., N-hydroxy-N-phenyl-acetamide (HPA) and N-hydroxy-N-phenyl-carbamic acid methyl ester (HPCM) catalyzed by recombinant Coprinus cinereus (rCiP) peroxidase has been studied in presence of efficient substrate 3-(4a,10a-dihydro-phenoxazin-10-yl)-propane-1-sulfonic acid (PPSA) at pH 8.5. The bimolecular constant of PPSA cation radical reaction with HPA was estimated to be (2.5 ± 0.2)·107 M−1 s−1 and for HPCM was even higher. The kinetic measurements show that rCiP-catalyzed oxidation of HPA and HPCM can increase up to 33,000 times and 5,500 times in the presence of equivalent concentration of high reactive substrate PPSA. The mathematical model of synergistic rCiP-catalyzed HPA–PPSA and HPCM–PPSA oxidation was proposed. Experimentally obtained rate constants were in good agreement with those calculated from the model confirming the synergistic scheme of the substrate oxidation. In order to explain the different reactivity of substrates, the docking of substrates in the active site of the enzyme was calculated. Molecular dynamic calculations show that the enzyme–substrate complexes are structurally stable. The high reactive PPSA exhibited higher affinity to enzyme active site than HPA and HPCM. Furthermore, the orientation of HPA and HPCM was not favorable for proton transfer to the distal histidine, and different substrate reactivity was explained by these diversities.},
  creationdate = {2013-10-20T00:00:00},
  doi          = {10.1007/s12010-008-8415-9},
  file         = {2009_Kulys_445.pdf:by-author/K/Kulys/2009_Kulys_445.pdf:PDF},
  keywords     = {3-(4a, 10a-dihydro-phenoxazin-10-yl)-propane-1-sulfonic Acid; Coprinus Cinereus Peroxidase; Docking Modeling; Kinetics; Molecular Dynamics (MD); N-hydroxy Derivative; PPSA; Synergistic},
  language     = {English},
  owner        = {saulius},
  publisher    = {Humana Press Inc},
  timestamp    = {2013.10.20},
  url          = {http://dx.doi.org/10.1007/s12010-008-8415-9},
}

@Article{Kumar2015,
  author    = {Kumar, Anup and Chhatwal, Megha and Gupta, Rinkoo D. and Awasthi, Satish Kumar},
  journal   = {RSC Adv.},
  title     = {Chemically-driven “molecular logic circuit” based on osmium chromophore with a resettable multiple readout},
  year      = {2015},
  issn      = {2046-2069},
  pages     = {5217–5220},
  volume    = {5},
  doi       = {10.1039/c4ra14269a},
  file      = {:by-author/K/Kumar/2015_Kumar_5217.pdf:PDF},
  owner     = {saulius},
  publisher = {Royal Society of Chemistry (RSC)},
  timestamp = {2015.02.25},
  creationdate = {2015-02-25T00:00:00},
  url       = {http://dx.doi.org/10.1039/C4RA14269A},
}

@Article{Kumar2014,
  author     = {Kumar, Prasun and Kailasam, Senthilkumar and Chakraborty, Shaunak and Bansal, Manju},
  journal    = {Applied Crystallography},
  title      = {{MolBridge}: a program for identifying nonbonded interactions in small molecules and biomolecular structures},
  year       = {2014},
  number     = {5},
  volume     = {47},
  file       = {[PDF] from researchgate.net:by-author/K/Kumar/2014_Kumar.pdf:application/pdf;Snapshot:by-author/K/Kumar/2014_Kumar.html:text/html},
  groups     = {sg/NAR2012},
  owner      = {saulius},
  shorttitle = {MolBridge},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url        = {http://journals.iucr.org/j/issues/2014/05/00/he5663/he5663bdy.html},
  urldate    = {2015-08-31},
}

@Article{Kumar1994,
  author    = {Kumar, S. and Cheng, X. and Klimasauskas, S. and Mi, S. and Posfai, J. and Roberts, R. J. and Wilson, G. G.},
  journal   = {Nucleic acids research},
  title     = {The DNA (cytosine-5) methyltransferases.},
  year      = {1994},
  pages     = {1--10},
  volume    = {22},
  abstract  = {The m5C-MTases form a closely-knit family of enzymes in which common amino acid sequence motifs almost certainly translate into common structural and functional elements. These common elements are located predominantly in a single structural domain that performs the chemistry of the reaction. Sequence-specific DNA recognition is accomplished by a separate domain that contains recognition elements not seen in other structures. This, combined with the novel and unexpected mechanistic feature of trapping a base out of the DNA helix, makes the m5C-MTases an intriguing class of enzymes for further study. The reaction pathway has suddenly become more complicated because of the base-flipping and much remains to be learned about the DNA recognition elements in the family members for which structural information is not yet available.},
  file      = {:by-author/K/Kumar/1994_Kumar_1.pdf:PDF},
  keywords  = {MTases},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Manuscript{Kumar2001,
  author    = {V. Kumar},
  title     = {The Theorems of Euler and Chasles},
  year      = {2001},
  file      = {:by-author/K/Kumar/2001_Kumar.pdf:PDF},
  owner     = {saulius},
  timestamp = {2013.03.22},
  creationdate = {2013-03-22T00:00:00},
}

@Article{Kummola2005,
  author    = {Kummola, Laura and Hämäläinen, Jonna M and Kivelä, Jyrki and Kivelä, Antti J and Saarnio, Juha and Karttunen, Tuomo and Parkkila, Seppo},
  journal   = {BMC cancer},
  title     = {Expression of a novel carbonic anhydrase, CA XIII, in normal and neoplastic colorectal mucosa.},
  year      = {2005},
  pages     = {41},
  volume    = {5},
  file      = {2005_Kummola_41.pdf:by-author/K/Kummola/2005_Kummola_41.pdf:PDF},
  groups    = {sg/cancer, sg/medicine, sg/hCA13},
  keywords  = {Carbonic Anhydrases},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Kuncak2011,
  author    = {Viktor Kuncak and Patrick Lam and Karen Zee and Martin~C. Rinard},
  journal   = {IEEE Transactions on Software Engineering},
  title     = {Modular Pluggable Analyses for Data Structure Consistency},
  year      = {2011},
  abstract  = {Hob is a program analysis system that enables the focused application of multiple analyses to different modules in the same program. In our approach, each module encapsulates one or more data structures and uses membership in abstract sets to characterize how objects participate in data structures. Each analysis verifies that the implementation of the module 1) preserves important internal data structure consistency prop- erties and 2) correctly implements a set algebra interface that characterizes the effects of operations on the data structure. Collectively, the analyses use the set algebra to 1) characterize how objects participate in multiple data structures and to 2) enable the inter-analysis communication required to verify properties that depend on multiple modules analyzed by different analyses. We implemented our system and deployed several pluggable analyses, including a flag analysis for modules in which abstract set membership is determined by a flag field in each object, a PALE shape analysis plugin, and a theorem proving plugin for analyzing arbitrarily complicated data structures. Our experience shows that our system can effectively 1) verify the consistency of data structures encapsulated within a single module and 2) combine analysis results from different analysis plugins to verify properties involving objects shared by multiple modules analyzed by different analyses.},
  file      = {:by-author/K/Kuncak/2011_Kuncak.pdf:PDF},
  groups    = {sg/Correctness proofs},
  keywords  = {Computer Science (CS); Correctness Proofs; Data Structure; Formal Methods; Invariant; Program Analysis; Program Verification; Programming Language Design; Shape Analysis},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@InProceedings{Kunkle2007,
  author    = {Daniel Kunkle and Gene Cooperman},
  booktitle = {ISSAC’07},
  title     = {Twenty-Six Moves Suffice for Rubik’s Cube},
  year      = {2007},
  file      = {rubik.dvi - rubik.pdf:by-author/K/Kunkle/2007_Kunkle.pdf:application/pdf},
  journal   = {ISSAC},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://www.ccs.neu.edu/home/gene/papers/rubik.pdf},
  urldate   = {2015-10-13},
}

@TechReport{Kunze2008,
  author           = {J. Kunze and R. Rodgers},
  institution      = {California Digital Library; US National Library of Medicine},
  title            = {The ARK Identifier Scheme},
  year             = {2008},
  month            = {May},
  comment          = {Cite by Rauber2016a in the citation examples.},
  creationdate     = {2016-11-21T00:00:00},
  file             = {2008_Kunze.pdf:by-author/K/Kunze/2008_Kunze.pdf:PDF},
  keywords         = {Computer Science (CS); Data Citation; Persistent Identifiers; Reproducible Research},
  modificationdate = {2023-01-03T09:16:29},
  owner            = {saulius},
  timestamp        = {2016.11.21},
  url              = {http://www.cdlib.org/services/uc3/arkspec.pdf},
}

@Article{Kuperberg2005,
  author    = {Kuperberg},
  title     = {A concise introduction to quantum probability, quantum mechanics, and quantum computation},
  year      = {2005},
  file      = {:by-author/K/Kuperberg/2005_Kuperberg.pdf:PDF},
  keywords  = {Quantum Mechanics (QM)},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Kupriyanova2000,
  author    = {Kupriyanova, N S and Kirilenko, P M and Netchvolodov, K K and Ryskov, A P},
  journal   = {Biochemical and biophysical research communications},
  title     = {Preferential cleavage sites for Sau3A restriction endonuclease in human ribosomal DNA.},
  year      = {2000},
  pages     = {11--5},
  volume    = {274},
  abstract  = {Previous studies of cloned ribosomal DNA (rDNA) variants isolated from the cosmid library of human chromosome 13 have revealed some disproportion in representativity of different rDNA regions (N. S. Kupriyanova, K. K. Netchvolodov, P. M. Kirilenko, B. I. Kapanadze, N. K. Yankovsky, and A. P. Ryskov, Mol. Biol. 30, 51-60, 1996). Here we show nonrandom cleavage of human rDNA with Sau3A or its isoshizomer MboI under mild hydrolysis conditions. The hypersensitive cleavage sites were found to be located in the ribosomal intergenic spacer (rIGS), especially in the regions of about 5-5.5 and 11 kb upstream of the rRNA transcription start point. This finding is based on sequencing mapping of the rDNA insert ends in randomly selected cosmid clones of human chromosome 13 and on the data of digestion kinetics of cloned and noncloned human genomic rDNA with Sau3A and MboI. The results show that a methylation status and superhelicity state of the rIGS have no effect on cleavage site sensitivity. It is interesting that all primary cleavage sites are adjacent to or entering into Alu or Psi cdc 27 retroposons of the rIGS suggesting a possible role of neighboring sequences in nuclease accessibility. The results explain nonequal representation of rDNA sequences in the human genomic DNA library used for this study.},
  file      = {Kupriyanova_2000_11.pdf:by-author/K/Kupriyanova/2000_Kupriyanova_11.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Kuzmanic2011,
  author           = {Kuzmanic, Antonija and Kruschel, Daniela and van Gunsteren, Wilfred F. and Pannu, Navraj S. and Zagrovic, Bojan},
  journal          = {Journal of Molecular Biology},
  title            = {Dynamics May Significantly Influence the Estimation of Interatomic Distances in Biomolecular X-ray Structures},
  year             = {2011},
  issn             = {0022-2836},
  month            = {Aug},
  number           = {1},
  pages            = {286–297},
  volume           = {411},
  abstract         = {Atomic positions obtained by X-ray crystallography are time and space averages over many molecules in the crystal. Importantly, interatomic distances, calculated between such average positions and frequently used in structural and mechanistic analyses, can be substantially different from the more appropriate time-average and ensemble-average interatomic distances. Using crystallographic B-factors, one can deduce corrections, which have so far been applied exclusively to small molecules, to obtain correct average distances as a function of the type of atomic motion. Here, using 4774 high-quality protein X-ray structures, we study the significance of such corrections for different types of atomic motion. Importantly, we show that for distances shorter than 5 Å, corrections greater than 0.5 Å may apply, especially for noncorrelated or anticorrelated motion. For example, 14% of the studied structures have at least one pair of atoms with a correction of ≥ 0.5 Å in the case of noncorrelated motion. Using molecular dynamics simulations of villin headpiece, ubiquitin, and SH3 domain unit cells, we demonstrate that the majority of average interatomic distances in these proteins agree with noncorrelated corrections, suggesting that such deviations may be truly relevant. Importantly, we demonstrate that the corrections do not significantly affect stereochemistry and the overall quality of final refined X-ray structures, but can provide marked improvements in starting unrefined models obtained from low-resolution X-ray data. Finally, we illustrate the potential mechanistic and biological significance of the calculated corrections for KcsA ion channel and show that they provide indirect evidence that motions in its selectivity filter are highly correlated.},
  creationdate     = {2017-01-19T00:00:00},
  doi              = {10.1016/j.jmb.2011.05.033},
  file             = {2011_Kuzmanic_286.pdf:by-author/K/Kuzmanic/2011_Kuzmanic_286.pdf:PDF},
  groups           = {sg/Crystallography, am/Crystallography},
  keywords         = {B-factor; Crystallography; Protein Crystallography; Structural Biology; Thermal Displacement Parameters},
  modificationdate = {2024-03-14T11:25:17},
  owner            = {andrius},
  publisher        = {Elsevier BV},
  timestamp        = {2017.01.19},
  url              = {http://dx.doi.org/10.1016/j.jmb.2011.05.033},
}

@Article{Kwiecinska2007,
  author    = {Kwiecinska, Barbara and Pusz, Slawomira and Krzesinska, Marta and Pilawa, Barbara},
  journal   = {International Journal of Coal Geology},
  title     = {Physical properties of shungite},
  year      = {2007},
  issn      = {0166-5162},
  pages     = {455--461},
  volume    = {71},
  abstract  = {This paper presents the results of physical parameters such as bulk porosity, true density, optical reflectance, dynamic elastic moduli, X-ray diffractograms and EPR spectra, determined for shungite. All shungite samples studied are considerably denser materials than anthracite — high rank coal with similar carbon content. Bright shungites were porous with the very dense matrix, while the dull shungite is compact, almost non-porous material. Elastic moduli of the dull shungite are generally higher than those of bright shungites and anthracite. All shungites studied (including anthracite) exhibit the directional dependence of elasticity. The maximum reflectance values of bright shungites are higher than those for dull shungite and anthracite. That corresponds with the denser matrix of these samples and suggests the greatest ordering of graphene layers in the case of bright shungites and also suggests some similarity to meta-anthracite from Paleozoic basins. Reflectance anisotropy of shungites studied are generally lower than that of anthracite. Ordering of graphene layers in bright shungite, as a high rank coal variety, is obvious, but lower anisotropy than that of anthracite is a surprise. X-ray studies confirm a high density of bright shungite. Interplanar distances dhkl of the shungite (d002 = 3.48 Å) are closer to those of anthracite (d002 = 3.52 Å) than to those of graphite (d002 = 3.35 Å). All results described here show the differences in molecular structure and degree of graphitisation of carbonaceous matter in bright, semi-bright and dull varieties of shungite. Our data could play a key role in production of materials composed of carbon nanoparticles.},
  doi       = {10.1016/j.coal.2006.05.008},
  file      = {ScienceDirect Full Text PDF:by-author/K/Kwiecinska/2007_Kwiecinska_455.pdf:application/pdf;ScienceDirect Snapshot:by-author/K/Kwiecinska/2007_Kwiecinska_455.html:text/html},
  keywords  = {Dynamic Elastic Modulus; EPR Spectrum; Optical Reflectance; Shungite; True Density; X-ray Measurements},
  owner     = {saulius},
  series    = {{ICCP} 2005 {Selected} papers presented at the 57th {Annual} {Meeting} of the {International} {Committee} for {Coal} and {Organic} {Petrology}, {Patras}, {Greece}},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/S0166516206001273},
  urldate   = {2015-07-06},
}

@InProceedings{Kwon2013,
  author    = {Kwon, Albert and Dhawan, Udit and Smith, Jonathan M. and Knight,Jr., Thomas F. and DeHon, Andre},
  booktitle = {Proceedings of the 2013 ACM SIGSAC Conference on Computer \&\#38; Communications Security},
  title     = {Low-fat Pointers: Compact Encoding and Efficient Gate-level Implementation of Fat Pointers for Spatial Safety and Capability-based Security},
  year      = {2013},
  address   = {New York, NY, USA},
  pages     = {721--732},
  publisher = {ACM},
  series    = {CCS '13},
  abstract  = {Referencing outside the bounds of an array or buffer is a common source of bugs and security vulnerabilities in today's software. We can enforce spatial safety and eliminate these violations by inseparably associating bounds with every pointer (fat pointer) and checking these bounds on every memory access. By further adding hardware-managed tags to the pointer, we make them unforgeable. This, in turn, allows the pointers to be used as capabilities to facilitate fine-grained access control and fast security domain crossing. Dedicated checking hardware runs in parallel with the processor's normal datapath so that the checks do not slow down processor operation (0% runtime overhead). To achieve the safety of fat pointers without increasing program state, we compactly encode approximate base and bound pointers along with exact address pointers for a 46b address space into one 64-bit word with a worst-case memory overhead of 3%. We develop gate-level implementations of the logic for updating and validating these compact fat pointers and show that the hardware requirements are low and the critical paths for common operations are smaller than processor ALU operations. Specifically, we show that the fat-pointer check and update operations can run in a 4 ns clock cycle on a Virtex 6 (40nm) implementation while only using 1100 6-LUTs or about the area of a double-precision, floating-point adder.},
  acmid     = {2516713},
  doi       = {10.1145/2508859.2516713},
  file      = {2013_Kwon_721.pdf:by-author/K/Kwon/2013_Kwon_721.pdf:PDF},
  isbn      = {978-1-4503-2477-9},
  keywords  = {Capabilities; Compiler Design; Computer Science (CS); Fat Pointer; Memory Safety; Processor; Security; Spatial Confinement},
  location  = {Berlin, Germany},
  numpages  = {12},
  owner     = {saulius},
  timestamp = {2016.10.05},
  creationdate = {2016-10-05T00:00:00},
  url       = {http://doi.acm.org/10.1145/2508859.2516713},
}

@Article{Kylloenen2003,
  author    = {Kyllönen, Matti S and Parkkila, Seppo and Rajaniemi, Hannu and Waheed, Abdul and Grubb, Jeffrey H and Shah, Gul N and Sly, William S and Kaunisto, Kari},
  journal   = {The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society},
  title     = {Localization of carbonic anhydrase XII to the basolateral membrane of H+-secreting cells of mouse and rat kidney.},
  year      = {2003},
  pages     = {1217--24},
  volume    = {51},
  abstract  = {Membrane-associated carbonic anhydrase (CA) has a crucial role in renal HCO(3)(-) absorption. CA activity has been localized to both luminal and basolateral membranes of the tubule epithelial cells. CA XII is a transmembrane isoenzyme that has been demonstrated in the basolateral plasma membrane of human renal, intestinal, and reproductive epithelia. The present study was designed to demonstrate the distribution of CA XII expression in the rodent kidney. A new polyclonal antibody to recombinant mouse CA XII was used in both Western blotting and immunohistochemistry. Western blotting analysis revealed a 40-45-kD polypeptide in CA XII-expressing CHO cells and isolated membranes of mouse and rat kidney. Immunofluorescence staining localized CA XII in the basolateral plasma membranes of S1 and S2 proximal tubule segments. Abundant basolateral staining of CA XII was seen in a subpopulation of cells in both cortical and medullary collecting ducts. Double immunofluorescence staining identified these cells as H(+)-secreting type A intercalated cells. The localization of CA XII in the peritubular space of proximal tubules suggests that it may play a role in renal HCO(3)(-) absorption, whereas the function of CA XII in the type A intercalated cells needs further investigation.},
  file      = {2003_Kyllönen_1217.pdf:by-author/K/Kyllönen/2003_Kyllönen_1217.pdf:PDF},
  groups    = {sg/hCA12},
  keywords  = {CA14},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Presentation{Kypraios2011,
  author    = {Theo Kypraios},
  title     = {A Gentle Tutorial in Bayesian Statistics},
  year      = {2011},
  file      = {2011_Kypraios.pdf:by-author/K/Kypraios/2011_Kypraios.pdf:PDF},
  groups    = {sg/Clinical Trials},
  owner     = {saulius},
  timestamp = {2015.12.14},
  creationdate = {2015-12-14T00:00:00},
  url       = {https://www.maths.nottingham.ac.uk/personal/tk/files/talks/nott_radiology_01_11.pdf},
  urldate   = {2015-12-12},
}

@Article{Levy1999,
  author    = {L{\'{e}}vy, D. and Barbier, J.},
  journal   = {Acta Crystallographica Section C},
  title     = {Normal and inverse garnets: Ca${\sb 3}$Fe${\sb 2}$Ge${\sb 3}$O${\sb 12}$, Ca${\sb 3}$Y${\sb 2}$Ge${\sb 3}$O${\sb 12}$ and Mg${\sb 3}$Y${\sb 2}$Ge${\sb 3}$O${\sb 12}$},
  year      = {1999},
  pages     = {1611--1614},
  volume    = {55},
  abstract  = {The structures of three garnets, namely, tricalcium diiron(III) trigermanium dodecaoxide, tricalcium diyttrium trigermanium dodecaoxide and trimagnesium diyttrium trigermanium dodecaoxide, have been determined by X-ray diffraction using flux-grown single crystals. The cation distributions correspond to a normal garnet structure for Ca${\sb 3}$Fe${\sb 2}$Ge${\sb 3}$O${\sb 12}$ and Ca${\sb 3}$Y${\sb 2}$Ge${\sb 3}$O${\sb 12}$, and to an inverse garnet structure for Mg${\sb 3}$Y${\sb 2}$Ge${\sb 3}$O${\sb 12}$},
  doi       = {10.1107/S0108270199007854},
  file      = {:by-author/L/Levy/1999_Levy_1611.pdf:PDF},
  keywords  = {For COD Deposition; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0108270199007854},
}

@Manuscript{Laakkonen2001,
  author    = {Ari Laakkonen},
  title     = {The EPO leads the way, but where to},
  year      = {2001},
  keywords  = {Patentai; Teise},
  file      = {:by-author/L/Laakkonen/2001_Laakkonen.doc:DOC},
  owner     = {saulius},
  timestamp = {2015.02.28},
  creationdate = {2015-02-28T00:00:00},
}

@Article{Ladbury2010,
  author       = {John E Ladbury and Gerhard Klebe and Ernesto Freire},
  journal      = {Nat Rev Drug Discov},
  title        = {Adding calorimetric data to decision making in lead discovery: a hot tip.},
  year         = {2010},
  month        = {Jan},
  number       = {1},
  pages        = {23--27},
  volume       = {9},
  abstract     = {Recognition of the limitations of high-throughput screening approaches in the discovery of candidate drugs has reawakened interest in structure-based and other rational design methods. Here, we describe how isothermal titration calorimetry can be used to obtain thermodynamic data on the binding of compounds to protein targets. We propose that these data--particularly the change in enthalpy--could provide a valuable, complementary addition to established tools for selecting compounds in lead discovery and for aiding lead optimization.},
  creationdate = {2016-06-06T00:00:00},
  doi          = {10.1038/nrd3054},
  file         = {2010_Ladbury_23.pdf:by-author/L/Ladbury/2010_Ladbury_23.pdf:PDF},
  institution  = {University of Texas, M. D. Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA. jeladbury@mdanderson.org},
  keywords     = {Calorimetry; Decision Making; Drug Design; Drug Discovery; Drug Industry; Methods; Protein Binding; Thermodynamics},
  language     = {eng},
  medline-pst  = {ppublish},
  owner        = {alexey},
  pii          = {nrd3054},
  pmid         = {19960014},
  timestamp    = {2016.06.06},
  url          = {http://dx.doi.org/10.1038/nrd3054},
}

@Article{Ladenstein2008,
  author    = {Rudolf Ladenstein},
  journal   = {Biotechnology \& Biotechnological Equipment},
  title     = {Heat capacity, configurational entropy, and the role of ionic interactions in protein thermostability},
  year      = {2008},
  pages     = {612--619},
  volume    = {22},
  abstract  = {Molecular dynamics simulation of solvated proteins at different temperatures can provide valuable descriptions of their global dynamics and their local fluctuations that can deepen our understanding of the molecular basis of protein thermostability. In this work a comparison of the dynamical behavior of homologous glutamate dehydrogenase domains from the hyperthermophilic bacterium Thermotoga maritima and the mesophilic bacterium Clostridium symbiosum as well as a molecular dynamics simulation study of a short polypeptide designed to fold into a trimeric coiled coil are reviewed with particular emphasis on the contribution of ion pairs and ionic networks to the conformational stability of the proteins. By considering the solvated proteins in their dynamic context thermodynamic properties such as electrostatic free energy differences, heat capacity and configurational entropy were calculated and suggested a new way of understanding protein thermostability on the basis of energetic fluctuations and accessible states. It appeared that a larger number of accessible degrees of freedom seems to accommodate the disorder caused by increased thermal motion.},
  file      = {2008_Ladenstein_612.pdf:by-author/L/Ladenstein/2008_Ladenstein_612.pdf:PDF},
  keywords  = {Heat Capacity; Ionic Networks; Molecular Dynamics (MD); Noncovalent-interactions; Protein Motions; Protein Thermostability; Protein-physics},
  owner     = {saulius},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
  url       = {http://www.diagnosisp.com/dp/journals/view_article.php?journal_id=1&archive=0&issue_id=17&article_id=472},
}

@Article{Laemmly1970,
  author    = {Laemmly, U. K.},
  journal   = {Nature},
  title     = {Cleavage of Structural Proteins during the Assembly of the Head of Bacteriophage {T4}},
  year      = {1970},
  pages     = {680--685},
  volume    = {227},
  abstract  = {Using an improved method of gel electrophoresis, many hitherto unknown proteins have been found in bacteriophage T4 and some of these have been identified with specific gene products. Four major components of the head are cleaved during the process of assembly, apparently after the precursor proteins have assembled into some large intermediate structure.},
  doi       = {10.1038/227680a0},
  file      = {:by-author/L/Laemmly/1970_Laemmly_680.pdf:PDF},
  keywords  = {Bacteriophages; Phage T4; SDS Electrophoresis},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@InBook{Lafuente2015,
  author    = {Lafuente, B. and Downs, R. T. and Yang, H. and Stone, N.},
  chapter   = {The power of databases: the RRUFF project},
  editor    = {T. Armbruster and R. M. Danisi},
  pages     = {1--30},
  publisher = {W. De Gruyter},
  title     = {Highlights in Mineralogical Crystallography},
  year      = {2015},
  file      = {2015_Lafuente_1.pdf:by-author/L/Lafuente/2015_Lafuente_1.pdf:PDF},
  keywords  = {Mineral Identification; Mineralogy; Raman Specroscopy},
  owner     = {saulius},
  timestamp = {2016.11.06},
  creationdate = {2016-11-06T00:00:00},
  url       = {http://rruff.info/about/downloads/HMC1-30.pdf},
}

@Article{Lagarias1998,
  author    = {Jeffrey C. Lagarias and James A. Reeds adn Margaret H. Wright and Paul E. Wright},
  journal   = {Siam J. Optim.},
  title     = {Convergence Properties of The {N}elder-{M}ead Simplex Method in Low Dimensions},
  year      = {1998},
  pages     = {112--147},
  file      = {:by-author/L/Lagarias/1998_Lagarias_112.pdf:PDF},
  keywords  = {Computer Science (CS); Minimisation; Simplex Method},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Lagarias2011,
  author    = {Jeffrey C. Lagarias and Bjorn Poonen and Margaret H. Wright},
  title     = {Convergence of the restricted Nelder–Mead algorithm in two dimensions},
  year      = {2011},
  file      = {:by-author/L/Lagarias/2011_Lagarias.pdf:PDF},
  keywords  = {Computer Science (CS); Minimisation; Simplex Method},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Lagunavicius1997,
  author    = {Lagunavicius, A. and Grazulis, S. and Balciunaite, E. and Vainius, D. and Siksnys, V.},
  journal   = {Biochemistry},
  title     = {DNA binding specificity of MunI restriction endonuclease is controlled by pH and calcium ions: involvement of active site carboxylate residues.},
  year      = {1997},
  pages     = {11093--9},
  volume    = {36},
  abstract  = {Gel shift analysis reveals [Lagunavicius, A., &amp; Siksnys, V. (1997) Biochemistry 36 (preceding paper in this issue)] that at pH 8.3 in the absence of Mg2+, MunI restriction endonuclease exhibits little DNA binding specificity, as compared with the D83A and E98A mutants of MunI. This suggests that charged carboxylate residue(s) influence the DNA binding specificity of MunI. In our efforts to establish the determinants of MunI binding specificity, we investigated the possible role of the ionic milieu, and we found that lowering pH or elevating Ca2+ levels per se induces specific DNA recognition by WT MunI. In contrast to the binding experiments at pH 8.3, gel shift analysis at pH 6.5 indicated tight sequence-specific binding of WT MunI in the absence of Mg2+, suggesting that protonation of active site carboxylate residue(s) which manifest anomalously high pKa value(s) control binding specificity. Interestingly, Ca2+ ion concentrations, which did not support DNA cleavage by MunI also induced DNA binding specificity in WT MunI at pH 8.3. To explore possible structural changes upon DNA binding, we then used a limited proteolysis technique. Trypsin cleavage of MunI-DNA complexes indicated that in the presence of cognate DNA the MunI restriction endonuclease became resistant to proteolytic cleavage, suggesting that binding of specific DNA induced a structural change. CD measurements confirmed this observation, suggesting minor secondary structural differences between complexes of MunI with cognate and noncognate DNA. These results therefore suggest that binding of MunI to its recognition sequence triggers a conformational transition that correctly juxtaposes active site carboxylate residues, which then chelate Mg2+ ions. In the absence of Mg2+ ions, at pH 8.3, conditions in which carboxylate groups would be expected to be completely ionized, electrostatic repulsion between charged carboxylates and phosphate oxygens is enhanced such as to interfere with specific DNA binding. Elimination of such repulsive constraints by replacement of carboxylate residues, by lowering pH, or by metal ion binding, then promotes MunI binding specificity.},
  file      = {:by-author/L/Lagunavicius/1997_Lagunavicius_11093.pdf:PDF},
  keywords  = {MunI; TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Lagunavicius2003,
  author    = {Lagunavicius, Arunas and Sasnauskas, Giedrius and Halford, Stephen E and Siksnys, Virginijus},
  journal   = {Journal of molecular biology},
  title     = {The metal-independent type IIs restriction enzyme BfiI is a dimer that binds two DNA sites but has only one catalytic centre.},
  year      = {2003},
  pages     = {1051--64},
  volume    = {326},
  abstract  = {BfiI is a novel type IIs restriction endonuclease that, unlike all other restriction enzymes characterised to date, cleaves DNA in the absence of Mg(2+). The amino acid sequence of the N-terminal part of BfiI has some similarities to Nuc of Salmonella typhimurium, an EDTA-resistant nuclease akin to phospholipase D. The dimeric form of Nuc contains a single active site composed of residues from both subunits. To examine the roles of the amino acid residues of BfiI that align with the catalytic residues in Nuc, a set of alanine replacement mutants was generated by site-directed mutagenesis. The mutationally altered forms of BfiI were all catalytically inactive but were still able to bind DNA specifically. The active site of BfiI is thus likely to be similar to that of Nuc. BfiI was also found by gel-filtration to be a dimer in solution. Both gel-shift and pull-down assays indicated that the dimeric form of BfiI binds two copies of its recognition sequence. In reactions on plasmids with either one or two copies of its recognition sequence, BfiI cleaved the DNA with two sites more rapidly than that with one site. Yet, when bound to two copies of its recognition sequence, the BfiI dimer cleaved only one phosphodiester bond at a time. The dimer thus seems to contain two DNA-binding domains but only one active site.},
  file      = {Lagunavicius_2003_1051-bfiI_is_a_dimer.pdf:by-author/L/Lagunavicius/2003_Lagunavicius_1051.pdf:PDF},
  keywords  = {BfiI; TypeII},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Lagunavicius1997a,
  author    = {Lagunavicius, A. and Siksnys, V.},
  journal   = {Biochemistry},
  title     = {Site-directed mutagenesis of putative active site residues of MunI restriction endonuclease: replacement of catalytically essential carboxylate residues triggers DNA binding specificity.},
  year      = {1997},
  pages     = {11086--92},
  volume    = {36},
  abstract  = {Mapping of the conserved sequence regions in the restriction endonucleases MunI (C/AATTG) and EcoRI (G/AATTC) to the known X-ray structure of EcoRI allowed us to identify the sequence motif 82PDX14EXK as the putative catalytic/Mg2+ ion binding site of MunI [Siksnys, V., Zareckaja, N., Vaisvila, R., Timinskas, A., Stakenas, P., Butkus, V., &amp; Janulaitis, A. Gene (1994) 142, 1-8]. Site-directed mutagenesis was then used to test whether amino acids P82, D83, E98, and K100 were important for the catalytic activity of MunI. Mutation P82A generated only a marginal effect on the cleavage properties of the enzyme. Investigation of the cleavage properties of the D83, E98, and K100 substitution mutants, however, in vivo and in vitro, revealed either an absence of catalytic activity or markedly reduced catalytic activity. Interestingly, the deleterious effect of the E98Q replacement in vitro was partially overcome by replacement of the metal cofactor used. Though the catalytic activity of the E98Q mutant was only 0.4% of WT under standard conditions (in the presence of Mg2+ ions), the mutant exhibited 40% of WT catalytic activity in buffer supplemented with Mn2+ ions. Further, the DNA binding properties of these substitution mutants were analyzed using the gel shift assay technique. In the absence of Mg2+ ions, WT MunI bound both cognate DNA and noncognate sequences with similar low affinities. The D83A and E98A mutants, in contrast, in the absence of Mg2+ ions, exhibited significant specificity of binding to cognate DNA, suggesting that the substitutions made can simulate the effect of the Mg2+ ion in conferring specificity to the MunI restriction enzyme.},
  file      = {:by-author/L/Lagunavicius/1997_Lagunavicius_11086.pdf:PDF},
  keywords  = {MunI; TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Presentation{Laibinis2016,
  author    = {Linas Laibinis},
  title     = {Interaktyvios automatizuotos matematinių įrodymų sistemos},
  year      = {2016},
  school    = {Vilniaus Universitetas, Matematikos Informatikos Fakultetas},
  file      = {2016_Laibinis.pdf:by-author/L/Laibinis/2016_Laibinis.pdf:PDF},
  keywords  = {HOL; Isabella; Mathematics; Programų Teisingumo įrodymai},
  owner     = {saulius},
  timestamp = {2016.11.17},
  creationdate = {2016-11-17T00:00:00},
}

@PhdThesis{Laibinis2000,
  author    = {Linas Laibinis},
  school    = {Turku Center for Computer Science},
  title     = {Mechanised Formal Reasining about Modular Programs},
  year      = {2000},
  month     = {April},
  file      = {2000_Laibinis_phdhesis.pdf:by-author/L/Laibinis/2000_Laibinis_phdhesis.pdf:PDF},
  keywords  = {Computer Science (CS); Formal Reasoning; Program Correctness Proofs; Program Verification},
  owner     = {saulius},
  timestamp = {2016.11.25},
  creationdate = {2016-11-25T00:00:00},
  url       = {http://users.abo.fi/llaibini/Thesis.pdf},
}

@Article{Laine2007,
  author    = {Laine, Christine and Goodman, Steven N. and Griswold, Michael E. and Sox, Harold C.},
  journal   = {Annals of Internal Medicine},
  title     = {Reproducible Research: Moving toward Research the Public Can Really Trust},
  year      = {2007},
  pages     = {450--453},
  volume    = {146},
  abstract  = {A community of scientists arrives at the truth by independently verifying new observations. In this time-honored process, journals serve 2 principal functions: evaluative and editorial. In their evaluative function, they winnow out research that is unlikely to stand up to independent verification; this task is accomplished by peer review. In their editorial function, they try to ensure transparent (by which we mean clear, complete, and unambiguous) and objective descriptions of the research. Both the evaluative and editorial functions go largely unnoticed by the public—the former only draws public attention when a journal publishes fraudulent research. However, both play a critical role in the progress of science. This paper is about both functions. We describe the evaluative processes we use and announce a new policy to help the scientific community evaluate, and build upon, the research findings that we publish.},
  eprint    = {http://www.annals.org/content/146/6/450.full.pdf+html},
  file      = {:by-author/L/Laine/2007_Laine_450.pdf:PDF},
  keywords  = {Data Management},
  owner     = {saulius},
  timestamp = {2012.04.09},
  creationdate = {2012-04-09T00:00:00},
  url       = {http://www.annals.org/content/146/6/450.abstract},
}

@Article{Laitaoja2013,
  author    = {Mikko Laitaoja and Jarkko Valjakka and Janne Janis},
  journal   = {Inorganic Chemistry},
  title     = {Zinc Coordination Spheres in Protein Structures},
  year      = {2013},
  pages     = {10983--10991},
  volume    = {52},
  abstract  = {A statistical analysis in terms of zinc coordinating amino acids, metal-to-ligand bond lengths, coordination number, and structural classification was performed, revealing coordination spheres from classical tetrahedral cysteine/histidine binding sites to more complex binuclear sites with carboxylated lysine residues. According to the results, coordination spheres of hundreds of crystal structures in the PDB could be misinterpreted due to symmetry-related molecules or missing electron densities for ligands.},
  doi       = {10.1021/ic401072d},
  file      = {:./by-author/L/Laitaoja/2013_Laitaoja_10983.pdf:PDF},
  owner     = {antanas},
  timestamp = {2014.01.15},
  creationdate = {2014-01-15T00:00:00},
  url       = {http://pubs.acs.org/doi/abs/10.1021/ic401072d},
}

@Article{Lajoie2013,
  author    = {Lajoie, M. J. and Kosuri, S. and Mosberg, J. A. and Gregg, C. J. and Zhang, D. and Church, G. M.},
  journal   = {Science},
  title     = {Probing the Limits of Genetic Recoding in Essential Genes},
  year      = {2013},
  issn      = {1095-9203},
  month     = {Oct},
  number    = {6156},
  pages     = {361--363},
  volume    = {342},
  doi       = {10.1126/science.1241460},
  file      = {:by-author/L/Lajoie/2013_Lajoie_361.pdf:PDF},
  groups    = {am/Expanded genetic code},
  owner     = {andrius},
  publisher = {American Association for the Advancement of Science (AAAS)},
  timestamp = {2016.05.17},
  creationdate = {2016-05-17T00:00:00},
  url       = {http://dx.doi.org/10.1126/science.1241460},
}

@Article{Lakkis1996,
  author    = {Lakkis, M M and Bergenhem, N C and Tashian, R E},
  journal   = {Biochemical and biophysical research communications},
  title     = {Expression of mouse carbonic anhydrase VII in E. coli and demonstration of its CO2 hydrase activity.},
  year      = {1996},
  pages     = {268--72},
  volume    = {226},
  abstract  = {The alpha-carbonic anhydrase (alpha-CA) gene family in mammals encodes 10 CA or CA-like proteins (CA I-CA X). Although the gene for human CA VII has been cloned and characterized, the corresponding protein has not previously been purified, and hence, the CO2 hydrase activity of its product has not as yet been demonstrated. In this study, we have cloned the mouse CA VII cDNA in an E. coli, glutathione-S-transferase (GST) expression vector. The CO2 hydrase activity of the expressed protein is about 4% that of the high-activity CAII isozyme, demonstrating that this evolutionarily highly conserved protein is a catalytically active member of this CA gene family.},
  file      = {1996_Lakkis_268.pdf:by-author/L/Lakkis/1996_Lakkis_268.pdf:PDF},
  groups    = {sg/hCA7},
  keywords  = {Carbonic Anhydrases},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Presentation{Lam2008,
  author    = {Lam, Patrick},
  title     = {MCMC Methods: Gibbs Sampling and the Metropolis-Hastings Algorithm},
  year      = {2008},
  file      = {:by-author/L/Lam/2008_Lam_slides.pdf:PDF},
  keywords  = {Metropolis Hastings; Monte Carlo},
  owner     = {saulius},
  pages     = {slides},
  timestamp = {2012.10.04},
  creationdate = {2012-10-04T00:00:00},
}

@Manuscript{Lam2011,
  author    = {Patrick Lam and Viktor Kuncak and Martin Rinard},
  title     = {Hob: A Tool for Verifying Data Structure Consistency},
  year      = {2011},
  keywords  = {Computer Science (CS); Correctness Proofs},
  abstract  = {This tool demonstration presents Hob, a system for verifying data structure con- sistency for programs written in a general-purpose programming language. Our tool enables the focused application of multiple communicating static analyses to different modules in the same program. Using our tool throughout the program development process, we have successfully identified several bugs in both specifications and implementations of programs.},
  file      = {:by-author/L/Lam/2011_Lam.pdf:PDF},
  groups    = {sg/Correctness proofs},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Lamers2000,
  author    = {Lamers, M. H. and Perrakis, A. and Enzlin, J. H. and Winterwerp, H. H. and de Wind, N. and Sixma, T. K.},
  journal   = {Nature},
  title     = {The crystal structure of DNA mismatch repair protein MutS binding to a G x T mismatch.},
  year      = {2000},
  pages     = {711--7},
  volume    = {407},
  abstract  = {DNA mismatch repair ensures genomic integrity on DNA replication. Recognition of a DNA mismatch by a dimeric MutS protein initiates a cascade of reactions and results in repair of the newly synthesized strand; however, details of the molecular mechanism remain controversial. Here we present the crystal structure at 2.2 A of MutS from Escherichia coli bound to a G x T mismatch. The two MutS monomers have different conformations and form a heterodimer at the structural level. Only one monomer recognizes the mismatch specifically and has ADP bound. Mismatch recognition occurs by extensive minor groove interactions causing unusual base pairing and kinking of the DNA. Nonspecific major groove DNA-binding domains from both monomers embrace the DNA in a clamp-like structure. The interleaved nucleotide-binding sites are located far from the DNA. Mutations in human MutS alpha (MSH2/MSH6) that lead to hereditary predisposition for cancer, such as hereditary non-polyposis colorectal cancer, can be mapped to this crystal structure.},
  file      = {:by-author/L/Lamers/2000_Lamers_711.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{LammertsvanBueren2010,
  author    = {Lammerts van Bueren, Alicia and Albert Ard{\`{e}}vol and Fayers-Kerr, Jennifer and Luo, Bo and Zhang, Yongmin and Sollogoub, Matthieu and Bl{\'{e}}riot, Yves and Rovira, Carme and Davies, Gideon J},
  journal   = {Journal of the American Chemical Society},
  title     = {Analysis of the Reaction Coordinate of \alpha-l-Fucosidases: A Combined Structural and Quantum Mechanical Approach},
  year      = {2010},
  pages     = {1804--1806},
  volume    = {132},
  abstract  = {The enzymatic hydrolysis of α-l-fucosides is of importance in cancer, bacterial infections, and fucosidosis, a neurodegenerative lysosomal storage disorder. Here we show a series of snapshots along the reaction coordinate of a glycoside hydrolase family GH29 α-l-fucosidase unveiling a Michaelis (ES) complex in a 1C4 (chair) conformation and a covalent glycosyl-enzyme intermediate in 3S1 (skew-boat). First principles metadynamics simulations on isolated α-l-fucose strongly support a 1C4↔3H4↔3S1 conformational itinerary for the glycosylation step of the reaction mechanism and indicate a strong “preactivation” of the 1C4 complex to nucleophilic attack as reflected by free energy, C1−O1/O5−C1 bond length elongation/reduction, C1−O1 bond orientation, and positive charge development around the anomeric carbon. Analysis of an imino sugar inhibitor is consistent with tight binding of a chair-conformed charged species.},
  doi       = {10.1021/ja908908q},
  eprint    = {http://pubs.acs.org/doi/pdf/10.1021/ja908908q},
  file      = {:by-author/L/LammertsvanBueren/2010_LammertsvanBueren_1804.pdf:PDF},
  keywords  = {Cremer & Pople Parameters},
  owner     = {andrius},
  timestamp = {2014.08.15},
  creationdate = {2014-08-15T00:00:00},
  url       = {http://pubs.acs.org/doi/abs/10.1021/ja908908q},
}

@Manuscript{Lamport2003,
  author    = {Leslie Lamport},
  title     = {The Future of Computing: Logic or Biology},
  year      = {2003},
  file      = {:by-author/L/Lamport/2003_Lamport.ps:PostScript;:by-author/L/Lamport/2003_Lamport.pdf:PDF},
  owner     = {saulius},
  timestamp = {2013.08.10},
  creationdate = {2013-08-10T00:00:00},
}

@Article{Lander1966,
  author    = {Lander, L. J. and Parkin, T. R.},
  journal   = {Bulletin of the American Mathematical Society},
  title     = {Counterexample to Euler's conjecture on sums of like powers},
  year      = {1966},
  pages     = {1079--1079},
  volume    = {72},
  file      = {:./by-author/L/Lander/1966_Lander_1079.pdf:PDF},
  keywords  = {Euler's Conjecture; Publication; Shortest},
  owner     = {antanas},
  timestamp = {2015.04.16},
  creationdate = {2015-04-16T00:00:00},
  url       = {http://www.ams.org/journals/bull/1966-72-06/S0002-9904-1966-11654-3/S0002-9904-1966-11654-3.pdf},
}

@Article{Landis2012,
  author    = {Landis, D.D. and Hummelshøj, J.S. and Nestorov, S. and Greeley, J. and Dułak, M. and Bligaard, T. and Nørskov, J.K. and Jacobsen, K.W.},
  journal   = {Computing in Science Engineering},
  title     = {The Computational Materials Repository},
  year      = {2012},
  issn      = {1521-9615},
  pages     = {51--57},
  volume    = {14},
  abstract  = {The possibilities for designing new materials based on quantum physics calculations are rapidly growing, but these design efforts lead to a significant increase in the amount of computational data created. The Computational Materials Repository (CMR) addresses this data challenge and provides a software infrastructure that supports the collection, storage, retrieval, analysis, and sharing of data produced by many electronic-structure simulators.},
  doi       = {10.1109/MCSE.2012.16},
  file      = {2012_Landis_51.pdf:by-author/L/Landis/2012_Landis_51.pdf:PDF},
  keywords  = {Data Management; Databases},
  owner     = {saulius},
  timestamp = {2013.09.08},
  creationdate = {2013-09-08T00:00:00},
}

@Presentation{Landrum2012,
  author    = {Gregory Landrum},
  title     = {Fingerprints in the {RDKit}},
  year      = {2012},
  file      = {:by-author/L/Landrum/2012_Landrum.pdf:PDF},
  owner     = {saulius},
  timestamp = {2014.03.23},
  creationdate = {2014-03-23T00:00:00},
}

@Article{Landry2007,
  author    = {Landry},
  title     = {From Book Covers to Domain Names: Searching for the True Meaning of the Cliffs Notes Temporal Test for Parody},
  year      = {2007},
  pages     = {19},
  file      = {:by-author/L/Landry/2007_Landry_19.pdf:PDF},
  keywords  = {Teise},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@TechReport{Lane2014,
  author      = {Jo Ann Lane and Supannika Koolmanojwong and Barry Boehm},
  institution = {University of Southern California},
  title       = {Affordable Systems: Balancing the Capability, Schedule, Flexibility, and Technical Debt Tradespace},
  year        = {2014},
  file        = {2014_Lane_tr502.pdf:by-author/L/Lane/2014_Lane_tr502.pdf:PDF},
  keywords    = {Computer Science (CS); Software Cost Estimation},
  owner       = {saulius},
  timestamp = {2015.11.22},
  creationdate = {2015-11-22T00:00:00},
  url         = {http://csse.usc.edu/TECHRPTS/2014/reports/usc-csse-2014-502.pdf},
}

@TechReport{Lane2012,
  author      = {Jo Ann Lane and Supannika Koolmanojwong and Barry Boehm},
  institution = {University of Southern California},
  title       = {Affordable Systems: Balancing the Capability, Schedule, Flexibility, and Technical Debt Tradespace},
  year        = {2012},
  type        = {techreport},
  abstract    = {With the increasing demands for affordable system capabilities that can be provided quickly to the user community, developers must explore a variety of options for identifying “satisficing” solutions. The system capability affordability tradespace must balance expedited systems engineering to reduce schedule and cost, encourage flexibility in architecture decisions to support future evolution of the system, and minimize technical debt that either results in later rework or adversely impacts future options. This paper shows how the University of Southern California (USC) Center for Systems and Software Engineering (CSSE) software and systems engineering cost models can be used in the analysis of this tradespace to show the range of options and the resulting consequences.},
  file        = {Jo Ann Lane et al. - 2012 - Affordable Systems Balancing the Capability, Sche.pdf:by-author/L/Lane/2012_Lane.pdf:application/pdf},
  keywords    = {Computer Science (CS); Project Management; Software Engineering; Technical Debt},
  language    = {English},
  owner       = {saulius},
  timestamp = {2016.01.20},
  creationdate = {2016-01-20T00:00:00},
  url         = {http://csse.usc.edu/TECHRPTS/2014/reports/usc-csse-2014-502.pdf},
  urldate     = {2015-11-22},
}

@Manuscript{Lang2000,
  author    = {Johannes Lang},
  title     = {Patent protection for e-commerce methods in Europe},
  year      = {2000},
  keywords  = {Patentai; Teise},
  file      = {:by-author/L/Lang/2000_Lang.doc:DOC},
  owner     = {saulius},
  timestamp = {2015.02.28},
  creationdate = {2015-02-28T00:00:00},
}

@Article{Lange1989,
  author    = {Lange, Kenneth L. and Little, Roderick J. A. and Taylor, Jeremy M. G.},
  journal   = {Journal of the American Statistical Association},
  title     = {Robust Statistical Modeling Using the t Distribution},
  year      = {1989},
  issn      = {0162-1459},
  month     = {Dec},
  number    = {408},
  pages     = {881},
  volume    = {84},
  doi       = {10.2307/2290063},
  file      = {1989_Lange_881.pdf:by-author/L/Lange/1989_Lange_881.pdf:PDF},
  groups    = {am/Student's t},
  owner     = {andrius},
  publisher = {JSTOR},
  timestamp = {2016.12.08},
  creationdate = {2016-12-08T00:00:00},
  url       = {http://dx.doi.org/10.2307/2290063},
}

@Article{Langer2012,
  author    = {Langer, Gerrit G. and Evrard, Guillaume X. and Carolan, Ciaran G. and Lamzin, Victor S.},
  journal   = {Journal of molecular biology},
  title     = {Fragmentation-tree density representation for crystallographic modelling of bound ligands.},
  year      = {2012},
  pages     = {211--22},
  volume    = {419},
  abstract  = {The identification and modelling of ligands into macromolecular models is important for understanding molecule's function and for designing inhibitors to modulate its activities. We describe new algorithms for the automated building of ligands into electron density maps in crystal structure determination. Location of the ligand-binding site is achieved by matching numerical shape features describing the ligand to those of density clusters using a &quot;fragmentation-tree&quot; density representation. The ligand molecule is built using two distinct algorithms exploiting free atoms with inter-atomic connectivity and Metropolis-based optimisation of the conformational state of the ligand, producing an ensemble of structures from which the final model is derived. The method was validated on several thousand entries from the Protein Data Bank. In the majority of cases, the ligand-binding site could be correctly located and the ligand model built with a coordinate accuracy of better than 1 Å. We anticipate that the method will be of routine use to anyone modelling ligands, lead compounds or even compound fragments as part of protein functional analyses or drug design efforts.},
  file      = {:by-author/L/Langer/2012_Langer_211.pdf:PDF},
  keywords  = {Grow Krystal},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Langer1981,
  author    = {Langer, P. J. and Shanabruch, W. G. and Walker, G. C.},
  journal   = {Journal of bacteriology},
  title     = {Functional organization of plasmid pKM101.},
  year      = {1981},
  pages     = {1310--6},
  volume    = {145},
  abstract  = {Tn5 insertion mutants and in vitro-generated deletion mutants of the mutagenesis-enhancing plasmid pKM101 have been used to identify several genetic regions on the pKM101 map. In clockwise order on the pKM101 map are: (i) the bla gene, coding for a beta-lactamase; (ii) the Slo region, responsible for retarding cell growth on minimal medium; (iii) the tra genes, enabling pKM101 to transfer conjugally; (iv) sensitivity to IKe phage (this function[s] maps within the tra region); (v) the muc gene(s), responsible for enhancing ultraviolet light and chemically induced mutagenesis in the cell; and (vi) the Rep region, essential for plasmid replication. The muc gene(s) and the Rep region are contained in a deoxyribonucleic acid region bounded by inverted repeated sequences.},
  file      = {:by-author/L/Langer/1981_Langer_1310.pdf:PDF},
  keywords  = {Antirestriction},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Langhans2009,
  author    = {Langhans, Mark T. and Palladino, Michael J.},
  journal   = {Current issues in molecular biology},
  title     = {Cleavage of mispaired heteroduplex DNA substrates by numerous restriction enzymes.},
  year      = {2009},
  pages     = {1--12},
  volume    = {11},
  abstract  = {The utility of restriction endonucleases as a tool in molecular biology is in large part due to the high degree of specificity with which they cleave well-characterized DNA recognition sequences. The specificity of restriction endonucleases is not absolute, yet many commonly used assays of biological phenomena and contemporary molecular biology techniques rely on the premise that restriction enzymes will cleave only perfect cognate recognition sites. In vitro, mispaired heteroduplex DNAs are commonly formed, especially subsequent to polymerase chain reaction amplification. We investigated a panel of restriction endonucleases to determine their ability to cleave mispaired heteroduplex DNA substrates. Two straightforward, non-radioactive assays are used to evaluate mispaired heteroduplex DNA cleavage: a PCR amplification method and an oligonucleotide-based assay. These assays demonstrated that most restriction endonucleases are capable of site-specific double-strand cleavage with heteroduplex mispaired DNA substrates, however, certain mispaired substrates do effectively abrogate cleavage to undetectable levels. These data are consistent with mispaired substrate cleavage previously reported for Eco RI and, importantly, extend our knowledge of mispaired heteroduplex substrate cleavage to 13 additional enzymes.},
  file      = {:by-author/L/Langhans/2009_Langhans_1.pdf:PDF},
  keywords  = {Catalysis; TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Langley1991,
  author    = {Richard B. Langley},
  journal   = {GPS World},
  title     = {The Mathematics of {GPS}},
  year      = {1991},
  file      = {:by-author/L/Langley/1991_Langley.pdf:PDF},
  keywords  = {Algorithms; GPS},
  owner     = {saulius},
  timestamp = {2014.11.06},
  creationdate = {2014-11-06T00:00:00},
  url       = {http://gauss.gge.unb.ca/gpsworld/EarlyInnovationColumns/Innov.1991.07-08.pdf},
}

@Article{Langmuir1919,
  author    = {Langmuir, Irving},
  journal   = {Journal of the American Chemical Society},
  title     = {The arrangement of electrons in atoms and molecules},
  year      = {1919},
  pages     = {868--934},
  volume    = {41},
  doi       = {10.1021/ja02227a002},
  file      = {1919_Langmuir_868.pdf:by-author/L/Langmuir/1919_Langmuir_868.pdf:PDF},
  keywords  = {Chemical Bond; Electronic Structure},
  owner     = {saulius},
  timestamp = {2014.04.16},
  creationdate = {2014-04-16T00:00:00},
}

@Article{Lanio1998,
  author    = {Lanio, T. and Jeltsch, A. and Pingoud, A.},
  journal   = {Journal of molecular biology},
  title     = {Towards the design of rare cutting restriction endonucleases: using directed evolution to generate variants of EcoRV differing in their substrate specificity by two orders of magnitude.},
  year      = {1998},
  pages     = {59--69},
  volume    = {283},
  abstract  = {The restriction endonuclease EcoRV cleaves DNA highly specifically within GATATC sequences. In order to create EcoRV variants that have an extended recognition site we have employed a semi-rational random mutagenesis/selection procedure. Twenty-two amino acid residues were subjected to random mutagenesis and about 500 EcoRV variants representing three generations of mutants were screened. Among these some highly active variants that strongly prefer AT-flanked cleavage sites (e.g. S183A/Q224R, T93S/I103F/S183A/T222S or N97T/S183A/T222S) and others that prefer GC flanks (e.g. K104N/A181T) were identified. As wild-type EcoRV does not discriminate between these cleavage sites, the generation of these variants represents a significant first step towards redesigning EcoRV to become an 8 or 10 bp cutter. Such enzymes, only very rarely found in nature, could be extremely helpful for the manipulation of large DNA fragments.},
  file      = {:by-author/L/Lanio/1998_Lanio_59.pdf:PDF},
  keywords  = {Design; Restriction Endonuclease (RE); Specificity},
  owner     = {em},
  timestamp = {2013.09.19},
  creationdate = {2013-09-19T00:00:00},
}

@Article{Lanskikh2011,
  author    = {Lanskikh, M. A. and Belova, Yu. M. and Tamm, N. B. and Chang, K. and Kemnitz, E. and Troyanov, S. I.},
  journal   = {Crystallography Reports},
  title     = {Crystal and molecular structures of trifluoromethyl derivatives of fullerenes C76 and C82},
  year      = {2011},
  issn      = {1562-689X},
  month     = {Nov},
  number    = {6},
  pages     = {1047--1053},
  volume    = {56},
  abstract  = {Trifluoromethyl derivatives of C 76 and C 82 were synthesized by the reaction of a mixture of higher fullerenes with trifluoroiodomethane followed by the separation by highperformance liquid chromatography. The crystal and molecular structures of C 76 (CF 3) 16 (two isomers) and crystal solvates of C 76 (CF 3) 18, C 82 (CF 3) 16, and C 82 (CF 3) 18 were determined by singlecrystal Xray diffraction using synchrotron radiation. The addition patterns of CF 3 groups in the C 76 (CF 3) 14-18 and C 82 (CF 3) 16-18 molecules are discussed.},
  doi       = {10.1134/s1063774511050178},
  file      = {2011_Lanskikh_1047.pdf:by-author/L/Lanskikh/2011_Lanskikh_1047.pdf:PDF},
  keywords  = {For COD Deposition; X-ray Crystallography},
  owner     = {saulius},
  publisher = {Pleiades Publishing Ltd},
  timestamp = {2016.10.03},
  creationdate = {2016-10-03T00:00:00},
  url       = {http://dx.doi.org/10.1134/S1063774511050178},
}

@Article{Lapkouski2009,
  author    = {Lapkouski, Mikalai and Panjikar, Santosh and Janscak, Pavel and Smatanova, Ivana Kuta and Carey, Jannette and Ettrich, Rüdiger and Csefalvay, Eva},
  journal   = {Nature structural \&amp; molecular biology},
  title     = {Structure of the motor subunit of type I restriction-modification complex EcoR124I.},
  year      = {2009},
  pages     = {94--5},
  volume    = {16},
  file      = {2009_Lapkouski_94.pdf:by-author/L/Lapkouski/2009_Lapkouski_94.pdf:PDF},
  keywords  = {Restriction Endonucleases (REases)},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Larsen2002,
  author    = {Larsen, P. V. and Blæsild, P. and Sørensen, M. K.},
  journal   = {Biometrika},
  title     = {Improved Likelihood Ratio Tests on the von Mises-Fisher Distribution},
  year      = {2002},
  issn      = {00063444},
  pages     = {947--951},
  volume    = {89},
  abstract  = {Explicit expressions for the directed likelihood statistic, r, and two modified directed likelihood statistics, r* and rø, are given for several standard hypotheses on concentrations in von Mises-Fisher distributions, and for several standard hypotheses on mean directions in von Mises distributions.},
  file      = {:by-author/L/Larsen/2002_Larsen_947.pdf:PDF},
  language  = {English},
  owner     = {andrius},
  timestamp = {2013.05.28},
  creationdate = {2013-05-28T00:00:00},
  url       = {http://www.jstor.org/stable/4140550},
}

@Article{Larson2007,
  author    = {Larson, Steven B. and Day, John S. and Cudney, Robert and McPherson, Alexander},
  journal   = {Acta crystallographica. Section D, Biological crystallography},
  title     = {A novel strategy for the crystallization of proteins: X-ray diffraction validation.},
  year      = {2007},
  pages     = {310--8},
  volume    = {63},
  abstract  = {Recently, the hypothesis was advanced that protein crystallization could be driven by the inclusion of small molecules rich in hydrogen-bonding, hydrophobic and electrostatic bonding possibilities. Conventional organic and biologically active molecules would promote lattice formation by their mediation of intermolecular interactions in crystals. The results of an extensive series of crystallization experiments strongly supported the idea. Here, difference Fourier X-ray diffraction analyses of nine crystals grown in the experiments are presented, which convincingly demonstrate the validity of the hypothesis and illustrate some of the ways in which small molecules can participate in lattice interactions.},
  doi       = {10.1107/S0907444906053303},
  file      = {:by-author/L/Larson/2007_Larson_310.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Presentation{Larsson2007,
  author    = {Larsson},
  title     = {Generalized Born},
  year      = {2007},
  file      = {:by-author/L/Larsson/2007_Larsson_slides.pdf:PDF},
  owner     = {saulius},
  pages     = {slides},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Manuscript{Lasenby1996,
  author    = {Lasenby, Joan and Lasenby, Anthony and Chris Doran},
  title     = {A unified mathematical language for physics and engineering in the 21st century {\textbar} {Geometric} {Algebra}},
  year      = {1996},
  keywords  = {Algebra; Geometric Algebra; Mathematics},
  url       = {http://geometry.mrao.cam.ac.uk/2000/01/a-unified-mathematical-language-for-physics-and-engineering-in-the-21st-century/},
  file      = {Lasenby et al. - A unified mathematical language for physics and en.pdf:by-author/L/Lasenby/1996_Lasenby.pdf:PDF;Snapshot:by-author/L/Lasenby/1996_Lasenby.html:URL},
  owner     = {saulius},
  timestamp = {2016.03.31},
  creationdate = {2016-03-31T00:00:00},
  urldate   = {2016-03-30},
}

@Article{Laskowski1998,
  author    = {Laskowski, R. A. and MacArthur, M. W. and Thornton, J. M.},
  journal   = {Current opinion in structural biology},
  title     = {Validation of protein models derived from experiment.},
  year      = {1998},
  number    = {5},
  pages     = {631--639},
  volume    = {8},
  abstract  = {The growing number of protein structures solved at atomic resolution holds the promise of further improvements in geometry-based validation parameters. Additionally, the estimated standard uncertainties of the atomic coordinates have been computed for a number of X-ray structures, providing a measure of the coordinate precision. In NMR spectroscopy, a measure analogous to the crystallographic R-factor has been developed.},
  doi       = {10.1016/S0959-440X(98)80156-5},
  file      = {:by-author/L/Laskowski/1998_Laskowski_631.pdf:pdf},
  keywords  = {Structure Refinement; Validation; X-ray Crystallography},
  owner     = {saulius},
  pii       = {S0959-440X(98)80156-5},
  pubmed    = {9818269},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Article{Laskowski1993,
  author    = {Laskowski, R A and Moss, D S and Thornton, J M},
  journal   = {J Mol Biol},
  title     = {Main-chain bond lengths and bond angles in protein structures},
  year      = {1993},
  month     = {Jun},
  number    = {4},
  pages     = {1049--67},
  volume    = {231},
  abstract  = {The main-chain bond lengths and bond angles of protein structures are analysed as a function of resolution. Neither the means nor standard deviations of these parameters show any correlation with resolution over the resolution range investigated. This is as might be expected as bond lengths and bond angles are likely to be heavily influenced by the geometrical restraints applied during structure refinement. The size of this influence is then investigated by performing an analysis of variance on the mean values across the five most commonly used refinement methods. The differences in means are found to be highly statistically significant, suggesting that the different target values used by the different methods leave their imprint on the structures they refine. This has implications concerning the actual target values used during refinement and stresses the importance of the values being not only accurate but also consistent from one refinement method to another},
  address   = {Crystallography Department, Birkbeck College, London, England},
  file      = {1993_Laskowski_1049.pdf:by-author/L/Laskowski/1993_Laskowski_1049.pdf:PDF},
  owner     = {em},
  timestamp = {2016.06.16},
  creationdate = {2016-06-16T00:00:00},
  url       = {http://www.ncbi.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&dopt=abstract&list_uids=8515464},
}

@Article{Laskowski1993a,
  author    = {Roman A. Laskowski and David S. Moss and Janet M. Thornton},
  journal   = {J. Mol. Biol.},
  title     = {Main-chain Bond Lengths and Bond Angles in Protein Structures},
  year      = {1993},
  pages     = {1049--1067},
  volume    = {231},
  file      = {:by-author/L/Laskowski/1993_Laskowski_1049.pdf:PDF},
  owner     = {andrius},
  timestamp = {2013.04.21},
  creationdate = {2013-04-21T00:00:00},
}

@Article{Laughlin2008,
  author    = {Laughlin, John D. and Ha, Tal Soo and Jones, David N. M. and Smith, Dean P.},
  journal   = {Cell},
  title     = {Activation of pheromone-sensitive neurons is mediated by conformational activation of pheromone-binding protein.},
  year      = {2008},
  number    = {7},
  pages     = {1255--1265},
  volume    = {133},
  abstract  = {Detection of volatile odorants by olfactory neurons is thought to result from direct activation of seven-transmembrane odorant receptors by odor molecules. Here, we show that detection of the Drosophila pheromone, 11-cis vaccenyl acetate (cVA), is instead mediated by pheromone-induced conformational shifts in the extracellular pheromone-binding protein, LUSH. We show that LUSH undergoes a pheromone-specific conformational change that triggers the firing of pheromone-sensitive neurons. Amino acid substitutions in LUSH that are predicted to reduce or enhance the conformational shift alter sensitivity to cVA as predicted in vivo. One substitution, LUSH(D118A), produces a dominant-active LUSH protein that stimulates T1 neurons through the neuronal receptor components Or67d and SNMP in the complete absence of pheromone. Structural analysis of LUSH(D118A) reveals that it closely resembles cVA-bound LUSH. Therefore, the pheromone-binding protein is an inactive, extracellular ligand converted by pheromone molecules into an activator of pheromone-sensitive neurons and reveals a distinct paradigm for detection of odorants.},
  doi       = {10.1016/j.cell.2008.04.046},
  file      = {:by-author/L/Laughlin/2008_Laughlin_1255.pdf:pdf},
  keywords  = {Structure Refinement; Validation; X-ray Crystallography},
  mid       = {NIHMS678064},
  owner     = {saulius},
  pii       = {S0092-8674(08)00637-5},
  pmc       = {PMC4397981},
  pubmed    = {18585358},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@MastersThesis{Laure2005,
  author    = {Gunther Laure},
  school    = {Institute for Information Processing and Computer Supported New Media, Technischen Universität Graz},
  title     = {A Component Based Simulation Framework for Digital Signal Processors},
  year      = {2005},
  month     = {April},
  file      = {:by-author/L/Laure/2005_Laure_mscthesis.pdf:PDF},
  keywords  = {Computer Science (CS); Virtual Machines},
  owner     = {saulius},
  pages     = {mscthesis},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Patent{Laurent1983,
  nationality = {US},
  number      = {4390596},
  year        = {1983},
  yearfiled   = {1980},
  address     = {Paris, France},
  assignee    = {Rhone-Poulenc Industries},
  author      = {Serge Laurent},
  language    = {English},
  title       = {Encapsulation of electronic components in bis-imido polymer},
  url         = {https://www.google.com/patents/US4390596},
  file        = {1983_Laurent.pdf:by-author/L/Laurent/1983_Laurent.pdf:PDF},
  keywords    = {Tetraaminonaphthalene},
  owner       = {saulius},
  timestamp = {2017.02.11},
  creationdate = {2017-02-11T00:00:00},
}

@Presentation{Lauze2009,
  author    = {François Lauze},
  title     = {Introduction to Differential and Riemannian Geometry},
  year      = {2009},
  file      = {2009_Lauze.pdf:by-author/L/Lauze/2009_Lauze.pdf:PDF},
  keywords  = {Differential Geometry; Riemann},
  owner     = {saulius},
  timestamp = {2016.02.27},
  creationdate = {2016-02-27T00:00:00},
  url       = {http://www2.imm.dtu.dk/projects/manifold/Pres/lauze.pdf},
}

@TechReport{Lavaque-Manty2014,
  author      = {Danielle D. Lavaque-Manty},
  institution = {University of Michigan},
  title       = {Using peer review to improve student writing},
  year        = {2014},
  file        = {Using Peer Review to Improve Student Writing - UsingPeerReviewtoImproveStudentWriting.pdf:by-author/L/Lavaque-Manty/2014_Lavaque-Manty.pdf:application/pdf},
  owner       = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url         = {http://www.lsa.umich.edu/UMICH/sweetland/Home/Downloads/UsingPeerReviewtoImproveStudentWriting.pdf},
  urldate     = {2015-06-06},
}

@Article{Lavery1989,
  author      = {R. Lavery and H. Sklenar},
  journal     = {J. Biomol. Struct. Dyn.},
  title       = {Defining the structure of irregular nucleic acids: conventions and principles.},
  year        = {1989},
  month       = {Feb},
  number      = {4},
  pages       = {655--667},
  volume      = {6},
  abstract    = {The algorithm "Curves", that we have recently presented in this journal (J. Biolmol. Str. Dynam. 6, 63-91 (1988], is updated to take into account the conventions developed at the Cambridge meeting on DNA curvature (September 1988) and extended to the calculation of local parameters. In addition, the principles which govern the choices made in establishing the Curves algorithm are compared with the approaches adopted by other authors.},
  doi         = {10.1080/07391102.1989.10507728},
  file        = {1989_Lavery_655.pdf:by-author/L/Lavery/1989_Lavery_655.pdf:PDF},
  institution = {Institut de Biologie Physico-Chimique, Paris, France.},
  keywords    = {Algorithms; DNA; Nucleic Acid Conformation},
  language    = {eng},
  medline-pst = {ppublish},
  owner       = {em},
  pmid        = {2619933},
  timestamp = {2011.07.13},
  creationdate = {2011-07-13T00:00:00},
}

@Article{Lavery1988,
  author       = {R. Lavery and H. Sklenar},
  journal      = {J Biomol Struct Dyn},
  title        = {The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids.},
  year         = {1988},
  month        = {Aug},
  number       = {1},
  pages        = {63--91},
  volume       = {6},
  abstract     = {An algorithm is presented which solves the problem of obtaining a rigorous helicoidal description of an irregular nucleic acid segment. Central to this approach is the definition of a function describing simultaneously the curvature of the nucleic acid segment in question and the corresponding stepwise variation of helicoidal parameters along the segment. Minimisation of this function leads to an optimal distribution of the conformational irregularity of the segment between these two components. Further, it is shown that this approach can be applied equally easily to single or double stranded nucleic acids. The results of this analysis yield both the absolute helicoidal parameters of individual bases/base pairs and the relative helicoidal parameters between successive bases/base pairs as well as the overall locus of the helical axis. The possibilities of this mathematical approach are demonstrated with the help of a computer program termed "Curves" which is applied to the study of a number of different nucleic acid structures.},
  creationdate = {2011-07-13T00:00:00},
  doi          = {10.1080/07391102.1988.10506483},
  file         = {1988_Lavery_63.pdf:by-author/L/Lavery/1988_Lavery_63.pdf:PDF},
  institution  = {Institut de Biologie Physico-Chimique, Paris, France.},
  keywords     = {Algorithms; Analysis; Anticodon; Base Composition; Base Sequence; Chemistry; Crystallography; DNA; Genetic; Models; Molecular; Nucleic Acid Conformation; Physical; Physicochemical Phenomena; RNA},
  language     = {eng},
  medline-pst  = {ppublish},
  owner        = {em},
  pmid         = {2482765},
  timestamp    = {2011.07.13},
}

@Article{Lavina2014,
  author    = {Lavina, Barbara and Dera, Przemyslaw and Downs, Robert T.},
  journal   = {Reviews in Mineralogy and Geochemistry},
  title     = {Modern {X}-ray diffraction methods in mineralogy and geosciences},
  year      = {2014},
  pages     = {1--31},
  volume    = {78},
  file      = {[PDF] from arizona.edu:by-author/L/Lavina/2014_Lavina_1.pdf:application/pdf;Snapshot:by-author/L/Lavina/2014_Lavina_1.html:text/html},
  groups    = {sg/NAR2012},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://rimg.geoscienceworld.org/content/78/1/1.short},
  urldate   = {2015-08-31},
}

@Misc{Lavor2007,
  author    = {Carlile Lavor and Leo Liberti and Nelson Maculan},
  title     = {An overview of distinct approaches for the molecular distance geometry problem},
  year      = {2007},
  abstract  = {We present a general overview of some of the most recent approaches for solving the molecular distance geometry problem, namely, the ABBIE algorithm, the DGSOL algorithm, d.c. optimization algorithms, the geometric build-up algorithm, and the BP algorithm.},
  file      = {:by-author/L/Lavor/2007_Lavor.pdf:PDF},
  owner     = {saulius},
  timestamp = {2011.12.14},
  creationdate = {2011-12-14T00:00:00},
}

@Conference{Lavor2005,
  author    = {Carlile Lavor and Leo Liberti and Nelson Maculan},
  booktitle = {CBRN 2005 conference},
  title     = {Grover's Algorithm applied to the molecular distance geometry problem},
  year      = {2005},
  month     = {August},
  file      = {2005_Lavor.ps.gz:by-author/L/Lavor/2005_Lavor.ps.gz:PDF},
  owner     = {saulius},
  timestamp = {2011.12.21},
  creationdate = {2011-12-21T00:00:00},
}

@InProceedings{Lavor2010,
  author    = {Lavor, C. and Liberti, L. and Mucherino, A.},
  booktitle = {Bioinformatics and Biomedicine Workshops (BIBMW), 2010 IEEE International Conference on},
  title     = {On the solution of molecular distance geometry problems with interval data},
  year      = {2010},
  month     = {dec.},
  pages     = {77 -82},
  abstract  = {The Molecular Distance Geometry Problem consists in finding the three-dimensional conformation of a protein using some of the distances between its atoms provided by experiments of Nuclear Magnetic Resonance. This is a continuous search problem that can be discretized under some assumptions on the known distances. We discuss the case where some of the distances are subject to uncertainty within a given nonnegative interval. We show that a discretization is still possible and propose an algorithm to solve the problem. Computational experiments on a set of artificially generated instances are presented.},
  doi       = {10.1109/BIBMW.2010.5703777},
  file      = {:by-author/L/Lavor/2010_Lavor_77.pdf:PDF},
  keywords  = {Bioinformatics; Biological NMR; Data Acquisition; Discretization; Macromolecules; Molecular Biophysics; Molecular Configurations; Molecular Distance Geometry Problem; Nuclear Magnetic Resonance; Protein Data Bank; Proteins; Search Problem; Search Problems; Three-dimensional Protein Conformation},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Lavrijsen2013,
  author    = {Reinoud Lavrijsen and Ji-Hyun Lee and Amalio Fernandez-Pacheco and Dorothee C. M. C. Petit and Rhodri Mansell and Russell P. Cowburn},
  journal   = {Nature},
  title     = {Magnetic ratchet for three-dimensional spintronic memory and logic},
  year      = {2013},
  pages     = {647--650},
  volume    = {493},
  abstract  = {One of the key challenges for future electronic memory and logic devices is finding viable ways of moving from today’s two- dimensional structures, which hold data in an x–y mesh of cells, to three-dimensional structures in which data are stored in an x–y–z lattice of cells. This could allow a many-fold increase in perform- ance. A suggested solution is the shift register1,2—a digital building block that passes data from cell to cell along a chain. In conven- tional digital microelectronics, two-dimensional shift registers are routinely constructed from a number of connected transistors. However, for three-dimensional devices the added process com- plexity and space needed for such transistors would largely cancel out the benefits of moving into the third dimension. ‘Physical’ shift registers, in which an intrinsic physical phenomenon is used to move data near-atomic distances, without requiring conventional transistors, are therefore much preferred. Here we demonstrate a way of implementing a spintronic unidirectional vertical shift regis- ter between perpendicularly magnetized ferromagnets of subnano- metre thickness, similar to the layers used in non-volatile magnetic random-access memory3. By carefully controlling the thickness of each magnetic layer and the exchange coupling between the layers, we form a ratchet that allows information in the form of a sharp magnetic kink soliton to be unidirectionally pumped (or ‘shifted’) from one magnetic layer to another. This simple and efficient shift-register concept suggests a route to the creation of three- dimensional microchips for memory and logic applications.},
  doi       = {10.1038/nature11733},
  file      = {:by-author/L/Lavrijsen/2013_Lavrijsen_647.pdf:PDF},
  owner     = {andrius},
  timestamp = {2013.02.04},
  creationdate = {2013-02-04T00:00:00},
}

@Article{Law2014,
  author    = {Law, Vivian and Knox, Craig and Djoumbou, Yannick and Jewison, Tim and Guo, An Chi and Liu, Yifeng and Maciejewski, Adam and Arndt, David and Wilson, Michael and Neveu, Vanessa and Tang, Alexandra and Gabriel, Geraldine and Ly, Carol and Adamjee, Sakina and Dame, Zerihun T. and Han, Beomsoo and Zhou, You and Wishart, David S.},
  journal   = {Nucleic Acids Research},
  title     = {DrugBank 4.0: shedding new light on drug metabolism},
  year      = {2014},
  pages     = {D1091--D1097},
  volume    = {42},
  abstract  = {DrugBank (http://www.drugbank.ca) is a comprehensive online database containing extensive biochemical and pharmacological information about drugs, their mechanisms and their targets. Since it was first described in 2006, DrugBank has rapidly evolved, both in response to user requests and in response to changing trends in drug research and development. Previous versions of DrugBank have been widely used to facilitate drug and in silico drug target discovery. The latest update, DrugBank 4.0, has been further expanded to contain data on drug metabolism, absorption, distribution, metabolism, excretion and toxicity (ADMET) and other kinds of quantitative structure activity relationships (QSAR) information. These enhancements are intended to facilitate research in xenobiotic metabolism (both prediction and characterization), pharmacokinetics, pharmacodynamics and drug design/discovery. For this release, >1200 drug metabolites (including their structures, names, activity, abundance and other detailed data) have been added along with >1300 drug metabolism reactions (including metabolizing enzymes and reaction types) and dozens of drug metabolism pathways. Another 30 predicted or measured ADMET parameters have been added to each DrugCard, bringing the average number of quantitative ADMET values for Food and Drug Administration-approved drugs close to 40. Referential nuclear magnetic resonance and MS spectra have been added for almost 400 drugs as well as spectral and mass matching tools to facilitate compound identification. This expanded collection of drug information is complemented by a number of new or improved search tools, including one that provides a simple analyses of drug–target, –enzyme and –transporter associations to provide insight on drug–drug interactions.},
  doi       = {10.1093/nar/gkt1068},
  eprint    = {http://nar.oxfordjournals.org/content/42/D1/D1091.full.pdf+html},
  file      = {:by-author/L/Law/2014_Law_D1091.pdf:PDF},
  keywords  = {DrugBank},
  owner     = {antanas},
  timestamp = {2014.07.02},
  creationdate = {2014-07-02T00:00:00},
  url       = {http://nar.oxfordjournals.org/content/42/D1/D1091.abstract},
}

@Article{Lawrence2008,
  author    = {Peter A. Lawrence},
  journal   = {Ethics In Science and Environmental Politics},
  title     = {Lost in publication: how measurement harms science},
  year      = {2008},
  pages     = {9--11},
  volume    = {8},
  abstract  = {Measurement of scientific productivity is difficult. The measures used (impact factor of the journal, citations to the paper being measured) are crude. But these measures are now so univer- sally adopted that they determine most things that matter: tenure or unemployment, a postdoctoral grant or none, success or failure. As a result, scientists have been forced to downgrade their primary aim from making discoveries to publishing as many papers as possible — and trying to work them into high impact factor journals. Consequently, scientific behaviour has become distorted and the utility, quality and objectivity of articles has deteriorated. Changes to the way scientists are assessed are urgently needed, and I suggest some here.},
  doi       = {10.3354/esep00079},
  file      = {e08\:9 - e008p009.pdf:by-author/L/Lawrence/2008_Lawrence_9.pdf:application/pdf},
  groups    = {sg/Bibliometrics},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://www.int-res.com/articles/esep2008/8/e008p009.pdf},
  urldate   = {2015-07-06},
}

@Article{LeBail2010,
  author    = {Le Bail, Armel},
  journal   = {Physical Chemistry Chemical Physics},
  title     = {Databases of virtual inorganic crystal structures and their applications},
  year      = {2010},
  pages     = {8521--8530},
  volume    = {12},
  doi       = {10.1039/C003907C},
  file      = {[PDF] from researchgate.net:by-author/L/LeBail/2010_LeBail_8521.pdf:application/pdf;Snapshot:by-author/L/LeBail/2010_LeBail_8521.html:text/html},
  groups    = {sg/JAC2009},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://pubs.rsc.org/en/content/articlehtml/2010/cp/c003907c},
  urldate   = {2015-08-31},
}

@Article{LeBail2010a,
  author    = {Le Bail, Armel},
  journal   = {Powder Diffraction},
  title     = {Ab initio structure determination of bethanechol chloride},
  year      = {2010},
  pages     = {229--234},
  volume    = {25},
  abstract  = {Many pharmaceutical compounds in daily use have a well defined molecular formula but were never completely characterized crystallographically (or results stay unpublished), so the question of a possible polymorphism has no answer, opening some place for industrial competition. A typical example is bethanechol chloride, also called carbamyl-β-methylcholine chloride (Major and Bonnett, 1943), a quaternary amine which is a cholinergic agent. This compound is a synthetic ester structurally and pharmacologi- cally related to acetylcholine. It acts principally as stimulant of the parasympathetic nervous system. It has been used for a long time in urology and gastroenterology, and more recently it has found new applications in the treatment of Alzheimer’s disease (Cummings and Kaufer, 1996) and cerebral palsy (Carter, 2008). The PDF contains two entries (00-043-1748 and 00-046-1964), both are unindexed and show some discrepancies. The aim of the present work is to provide more in depth results, in spite of the absence of single crystal, by solving the structure from the powder data by using methodologies which continuously have demon- strated their efficiency during repeated blind tests ͑Le Bail et al., 2009.},
  doi       = {10.1154/1.3478380},
  file      = {2010_LeBail_229.pdf:by-author/L/LeBail/2010_LeBail_229.pdf:PDF},
  keywords  = {Ab Initio; Acetylcholine; Bethanechol Chloride; Carbamyl β Methylcholine Chloride; Crystal Structure; Polymorphism; Powder Diffraction},
  owner     = {saulius},
  timestamp = {2012.10.30},
  creationdate = {2012-10-30T00:00:00},
}

@Article{LeBail2008a,
  author    = {Le Bail, Armel},
  journal   = {Powder Diffraction Suppl.},
  title     = {Frontiers Between Crystal-structure Prediction and Determination by Powder Diffractometry},
  year      = {2008},
  pages     = {S5--S12},
  abstract  = {The fuzzy frontiers between structure determination by powder diffractometry and crystal structure prediction are discussed. The application of a search-match program combined with a database of more than 60,000 predicted powder diffraction patterns is demonstrated. Immediate structure solution (before indexing) is shown to be possible by this method if the discrepancies between the predicted crystal structure cell parameters and the actual ones are < 1%. Incomplete chemistry of the hypothetical models (missing interstitial cations, water molecules, etc) is not necessarily a barrier to a successful identification (in spite of inducing large intensity errors), provided the search-match is made with chemical restrictions on the elements present in both the virtual and experimental compounds.},
  doi       = {10.1154/1.2903488},
  file      = {:by-author/B/Bail/2008_LeBail_S5.pdf:PDF},
  keywords  = {Crystal Structure Prediction (CSP); Powder Diffraction; Prediction; Search-match; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2016.01.22},
  creationdate = {2016-01-22T00:00:00},
}

@Article{LeBail2005,
  author           = {Le Bail, Armel},
  journal          = {Journal of Applied Crystallography},
  title            = {Inorganic structure prediction with {\it GRINSP}},
  year             = {2005},
  pages            = {389--395},
  volume           = {38},
  abstract         = {A new computer program is described, GRINSP (geometrically restrained inorganic structure prediction), which allows the exploration of the possibilities of occurrence of 3-, 4-, 5- and 6-connected three-dimensional networks. Hypothetical (as well as known structure) models for binary compounds are produced with exclusive connection of polyhedra by corners, such as [MX3] triangles in M2X3 formulation, [MX4] tetrahedra in MX2 (zeolites or dense SiO2 polymorphs), [MX5] polyhedra in M2X5, and finally [MX6] octahedra in MX3 polymorphs. Moreover, hypothetical ternary compounds are built up by combinations of either two different polyhedra or two different radii for two different cations adopting the same coordination. The cost function is based on the agreement of the model interatomic distances with ideal distances provided by the user. The Monte Carlo algorithm first finds structure candidates selected after the verification of the expected geometry, and then optimizes the cell parameters and the atomic coordinates. A satellite software (GRINS) uses the predicted models and produces the characteristics of isostructural compounds which would be obtained by cationic substitutions. A huge list of CIF files of hypothetical boron oxide polymorphs (including nanotubes), zeolites, aluminium and 3d-element fluorides, fluoroaluminates, borosilicates, titanosilicates, gallophosphates etc., is freely available at the PCOD (Predicted Crystallography Open Database).},
  creationdate     = {2008-07-28T00:00:00},
  doi              = {10.1107/S0021889805002384},
  file             = {2005_LeBail_389.pdf:by-author/L/LeBail/2005_LeBail_389.pdf:PDF},
  keywords         = {CIF; GRINSP; Monte-Carlo Simulations; PCOD; Prediction; X-ray Crystallography; Zeolites},
  modificationdate = {2023-08-07T10:23:05},
  owner            = {saulius},
  timestamp        = {2008.07.28},
  url              = {http://dx.doi.org/10.1107/S0021889805002384},
}

@Article{LeBail2011,
  author    = {Le Bail, Armel and L. Smrčok},
  journal   = {Powder Diffraction},
  title     = {Ab initio structure determination of 3,4-diaminopyridin-1-ium dihydrogen phosphate},
  year      = {2011},
  pages     = {321--325},
  volume    = {26},
  abstract  = {The structure of 3,4-diaminopyridin-1-ium dihydrogen phosphate, [C5H3(NH)(NH2)2]+ (H2PO4)-, is solved from conventional X-ray powder diffraction data in direct space (monoclinic unit cell with a = 16.0725(9) Å, b = 7.7301(3) Å, c = 14.6189(9) Å, β = 96.869(1)°, V = 1803.2(2) Å3, Z = 8, and space group I2/c), and optimized by energy minimization in the solid state. In the crystal structure of the title compound, dihydrogenphosphate tetrahedra are linked by strong hydrogen O-H…O bonds forming chains running parallel to the b-axis. Antiparallelly π–π stacked DAP cations form molecular columns in the spaces between the chains. Although the dominant interaction of the molecules with their surroundings is electrostatic, their bonding are further enhanced by N-H…O and C-H…O hydrogen bonds.},
  doi       = {10.1154/1.3660160},
  file      = {2011_LeBail_321.pdf:by-author/L/LeBail/2011_LeBail_321.pdf:PDF},
  keywords  = {Ab Initio; Crystal Structure; Density Functional Theory (DFT); Diaminopyridine; Dihydrogen Phosphate; Lambert Eaton Myasthenic Syndrome; Powder Diffraction; VASP},
  owner     = {saulius},
  timestamp = {2012.10.30},
  creationdate = {2012-10-30T00:00:00},
}

@Article{LePage1982,
  author    = {Le Page, Y.},
  journal   = {Journal of Applied Crystallography},
  title     = {The derivation of the axes of the conventional unit cell from the dimensions of the Buerger-reduced cell},
  year      = {1982},
  pages     = {255--259},
  volume    = {15},
  doi       = {10.1107/S0021889882011959},
  file      = {:by-author/L/LePage/1982_LePage_255.pdf:PDF},
  groups    = {sg/Cell sg/Reduction, sg/Cell reduction},
  keywords  = {Algorithms; Niggli Cell; Reduced Cell; Unit Cell; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2014.11.06},
  creationdate = {2014-11-06T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0021889882011959},
}

@Article{LePage2005,
  author           = {Le Page, Yvon and Rodgers, John R.},
  journal          = {Journal of Applied Crystallography},
  title            = {Quantum software interfaced with crystal-structure databases: tools, results and perspectives},
  year             = {2005},
  pages            = {697--705},
  volume           = {38},
  abstract         = {Version 2.0 of Toth's {\it Materials Toolkit} runs under Windows and prepares ASCII input files for popular {\it ab initio} packages such as {\it ABINIT}, {\it VASP} {\it etc}. Those packages, obtainable from their respective developers, may run in desktop or supercomputer setups with Linux or Windows operating systems. The {\it Toolkit} input is taken at will from a direct plug into CRYSTMET, with 93000 crystal-structure entries for metals and inorganic compounds, from CIF files of public-domain crystal-structure databases, or cut-and-paste from electronic journals followed by minimal free-format editing. The collection of fully general and highly graphical tools grouped on two command screens operates on the structure description stored in an editable ASCII screen. After the model has been searched, modified and evaluated in a few keystrokes with the above tools, its ASCII input files for a selection of {\it ab initio} packages are produced by selecting the meaningful flags and run options on a dialog. The tedious structure manipulation or decomposition into multiple simulations is performed in the background. Execution is followed by production of a plain-English job report. Four examples among the numerous possible applications of the {\it Toolkit} illustrate the fact that daunting topics, like the symmetry of chlorapatite, the voids and channels in the hydrogen-storage material EuNi${\sb 5}$, the energy per unit area of the contact plane for spinel twin in diamond, and the hardness of lonsdaleite {\it versus} diamond, are amenable to processing by materials scientists more versed in experiment than theory. The manual with tutorials and availability information can be found at http://www.tothcanada.com/toolkit/.},
  creationdate     = {2015-08-03T00:00:00},
  doi              = {10.1107/S0021889805017358},
  file             = {:./by-author/P/Page/2005_Page_697.pdf:PDF},
  groups           = {am/CRYSTMET},
  keywords         = {Adsorption; CIF; Catalysis; Channels; Clusters; Computer Programs; Diamond; Elasticity; Epitaxy; Hardness; Surfaces; Twinning},
  modificationdate = {2023-08-07T10:23:05},
  owner            = {antanas},
  timestamp        = {2015.08.03},
  url              = {http://dx.doi.org/10.1107/S0021889805017358},
}

@Article{Leach1990,
  author    = {Leach, A R and Dolata, D P and Prout, K},
  journal   = {Journal of chemical information and computer sciences},
  title     = {Automated conformational analysis and structure generation: algorithms for molecular perception.},
  year      = {1990},
  pages     = {316--24},
  volume    = {30},
  abstract  = {Many methodologies for performing automated conformational analysis require some means of "perceiving" a molecule to determine features of interest. Algorithms for finding rings, bond orders, and stereocenters and detecting the presence of substructural fragments have been developed. These algorithms are described, emphasizing their importance in conformational analysis.},
  file      = {1990_Leach_316.pdf:by-author/L/Leach/1990_Leach_316.pdf:PDF},
  keywords  = {Ring Perception},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Lebedev2003,
  author    = {Lebedev, Andrey A. and Tickle, Ian J. and Laskowski, Roman A. and Moss, David S.},
  journal   = {Acta Crystallographica Section D},
  title     = {Estimation of weights and validation: a marginal likelihood approach},
  year      = {2003},
  pages     = {1557--1566},
  volume    = {59},
  doi       = {10.1107/S0907444903014367},
  file      = {he0315.pdf:by-author/L/Lebedev/2003_Lebedev_1557.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444903014367},
}

@Article{LeBowitz1986,
  author    = {LeBowitz, J. H. and McMacken, R.},
  journal   = {The Journal of biological chemistry},
  title     = {The Escherichia coli dnaB replication protein is a DNA helicase.},
  year      = {1986},
  pages     = {4738--48},
  volume    = {261},
  abstract  = {Genetic and biochemical analyses indicate that the Escherichia coli dnaB replication protein functions in the propagation of replication forks in the bacterial chromosome. We have found that the dnaB protein is a DNA helicase that is capable of unwinding extensive stretches of double-stranded DNA. We constructed a partially duplex DNA substrate, containing two preformed forks of single-stranded DNA, which was used to characterize this helicase activity. The dnaB helicase depends on the presence of a hydrolyzable ribonucleoside triphosphate, is maximally stimulated by a combination of E. coli single-stranded DNA-binding protein and E. coli primase, is inhibited by antibody directed against dnaB protein, and is inhibited by prior coating of the single-stranded regions of the helicase substrate with the E. coli single-stranded DNA-binding protein. It was determined that the dnaB protein moves 5' to 3' along single-stranded DNA, apparently in a processive fashion. To invade the duplex portion of the helicase substrate, the dnaB protein requires a 3'-terminal extension of single-stranded DNA in the strand to which it is not bound. Under optimal conditions at 30 degrees C, greater than 1 kilobase pair of duplex DNA can be unwound within 30 s. Based on these findings and other available data, we propose that the dnaB protein is the primary replicative helicase of E. coli and that it actively and processively migrates along the lagging strand template, serving both to unwind the DNA duplex in advance of the leading strand and to potentiate synthesis by the bacterial primase of RNA primers for the nascent (Okazaki) fragments of the lagging strand.},
  file      = {:by-author/L/LeBowitz/1986_LeBowitz_4738.pdf:PDF},
  keywords  = {Ecoli; {gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@InProceedings{Ledoux2007,
  author    = {Ledoux, H.},
  booktitle = {Voronoi Diagrams in Science and Engineering, 2007. ISVD '07. 4th International Symposium on},
  title     = {Computing the 3D Voronoi Diagram Robustly: An Easy Explanation},
  year      = {2007},
  month     = {July},
  pages     = {117--129},
  doi       = {10.1109/ISVD.2007.10},
  file      = {:./by-author/L/Ledoux/2007_Ledoux.pdf:PDF},
  keywords  = {3D Geometric Computing; 3D Voronoi Diagram; Algorithm Design and Analysis; Application Software; Computational Geometry; Data Mining; Data Structures; Delaunay Tetrahedralization; Distributed Computing; Geographic Information Systems; Programming Profession; Robustness; Sorting},
  owner     = {antanas},
  timestamp = {2016.05.10},
  creationdate = {2016-05-10T00:00:00},
}

@Article{Lee200X,
  author    = {Lee},
  title     = {Models, Parameters and Priors in Bayesian Inference},
  year      = {200X},
  abstract  = {Batchelder and Smith (2004) critiqued the use of Bayesian statistical inference for model selection and evaluation, arguing that it can lead to invalid and contradictory conclusions. Their argument centered around a series of concrete examples purporting to show the problems inherent in adopting the Bayesian approach. This paper addresses Batchelder and Smith’s critique by re-analyzing their examples us- ing correct Bayesian methods, and demonstrates that their negative conclusions are not warranted. Throughout the re-analysis, the central role of infor- mation in the Bayesian approach is emphasized. In particular, it is argued a careful consideration of avail- able information is required to understand the rela- tionship between parameters, models, and data, and the setting of prior probability distributions.},
  file      = {:by-author/L/Lee/200X_Lee.pdf:PDF},
  groups    = {sg/Bayesian},
  keywords  = {Bayesian Statistics; Mathematics},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Lee2011,
  author    = {Lee, Chang Yeon and Farha, Omar K. and Hong, Bong Jin and Sarjeant, Amy A. and Nguyen, SonBinh T. and Hupp, Joseph T.},
  journal   = {Journal of the American Chemical Society},
  title     = {Light-harvesting metal-organic frameworks (MOFs): efficient strut-to-strut energy transfer in bodipy and porphyrin-based MOFs.},
  year      = {2011},
  pages     = {15858--61},
  volume    = {133},
  abstract  = {A pillared-paddlewheel type metal-organic framework material featuring bodipy- and porphyrin-based struts, and capable of harvesting light across the entire visible spectrum, has been synthesized. Efficient-essentially quantitative-strut-to-strut energy transfer (antenna behavior) was observed for the well-organized donor-acceptor assembly consituting the ordered MOF structure.},
  doi       = {10.1021/ja206029a},
  file      = {:by-author/L/Lee/2011_Lee_15858.pdf:PDF},
  groups    = {sg/MOF, sg/MOFs, am/MOFs},
  keywords  = {Light Harvesting Antena; Metal-Organic Frameworks (MOF)},
  owner     = {saulius},
  timestamp = {2013.01.05},
  creationdate = {2013-01-05T00:00:00},
}

@Article{Lee2005a,
  author    = {David A. Lee and Eve J. Higginbotham},
  journal   = {Am J Health-Syst Pharm},
  title     = {Glaucoma and its treatment: A review},
  year      = {2005},
  pages     = {691--699},
  volume    = {62},
  file      = {2005_Lee_691.pdf:by-author/L/Lee/2005_Lee_691.pdf:PDF},
  groups    = {sg/reviews, sg/medicine},
  keywords  = {Carbonic Anhydrases},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Lee1996,
  author    = {Lee, D H and Granja, J R and Martinez, J A and Severin, K and Ghadri, M R},
  journal   = {Nature},
  title     = {A self-replicating peptide.},
  year      = {1996},
  pages     = {525--8},
  volume    = {382},
  abstract  = {The production of amino acids and their condensation to polypeptides under plausibly prebiotic conditions have long been known. But despite the central importance of molecular self-replication in the origin of life, the feasibility of peptide self-replication has not been established experimentally. Here we report an example of a self-replicating peptide. We show that a 32-residue alpha-helical peptide based on the leucine-zipper domain of the yeast transcription factor GCN4 can act autocatalytically in templating its own synthesis by accelerating the thioester-promoted amide-bond condensation of 15- and 17-residue fragments in neutral, dilute aqueous solutions. The self-replication process displays parabolic growth pattern with the initial rates of product formation correlating with the square-foot of initial template concentration.},
  file      = {1996_Lee_525.pdf:by-author/L/Lee/1996_Lee_525.pdf:PDF},
  keywords  = {Chemical Prebiotic; Evolution},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Misc{Lee2006a,
  author    = {Edward A Lee},
  title     = {The Problem with Threads},
  year      = {2006},
  abstract  = {Threads are a seemingly straightforward adaptation of the dominant sequential model of computation to concurrent systems. Languages require little or no syntactic changes to sup- port threads, and operating systems and architectures have evolved to efficiently support them. Many technologists are pushing for increased use of multithreading in software in order to take advantage of the predicted increases in parallelism in computer architectures. In this paper, I argue that this is not a good idea. Although threads seem to be a small step from sequential computation, in fact, they represent a huge step. They discard the most essential and appeal- ing properties of sequential computation: understandability, predictability, and determinism. Threads, as a model of computation, are wildly nondeterministic, and the job of the program- mer becomes one of pruning that nondeterminism. Although many research techniques improve the model by offering more effective pruning, I argue that this is approaching the problem backwards. Rather than pruning nondeterminism, we should build from essentially determinis- tic, composable components. Nondeterminism should be explicitly and judiciously introduced where needed, rather than removed where not needed. The consequences of this principle are profound. I argue for the development of concurrent coordination languages based on sound, composable formalisms. I believe that such languages will yield much more reliable, and more concurrent programs.},
  file      = {:by-author/L/Lee/2006_Lee.pdf:PDF},
  owner     = {saulius},
  timestamp = {2011.12.13},
  creationdate = {2011-12-13T00:00:00},
}

@Article{Lee2006,
  author    = {Lee, Joohyun and Cooper, Bret},
  journal   = {Molecular bioSystems},
  title     = {Alternative workflows for plant proteomic analysis.},
  year      = {2006},
  pages     = {621--6},
  volume    = {2},
  abstract  = {High-throughput separations are intrinsic to the detection and analysis of peptides and proteins by mass spectrometry (MS). Together, efficient separation and MS can lead to the identification of thousands of proteins in a sample, cell or tissue and help build proteome maps that can be used to define a cell type or cellular state. Although 2D gels have been successfully used to separate proteins for subsequent MS analysis, alternative separation efficiencies and, consequently deeper results could be obtained with HPLC or other separation techniques that improve throughput. This highlight is aimed toward plant scientists who have special separation needs due to the nature of plant cells and who could benefit from knowing options and requirements for adopting alternative separation protocols. Through the various sample processing and protein separation strategies, plant biologists should be able to improve the quality of their proteomic reference maps and gain new information about the proteins that define plant cells.},
  file      = {:by-author/L/Lee/2006_Lee_621.pdf:PDF},
  keywords  = {{gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Lee2012,
  author    = {Lee, J. Jack and Chu, Caleb T.},
  journal   = {Statistics in medicine},
  title     = {Bayesian Clinical Trials in Action},
  year      = {2012},
  issn      = {0277-6715},
  pages     = {2955--2972},
  volume    = {31},
  abstract  = {Although the frequentist paradigm has been the predominant approach to clinical trial design since the 1940s, it has several notable limitations. The alternative Bayesian paradigm has been greatly enhanced by advancements in computational algorithms and computer hardware. Compared to its frequentist counterpart, the Bayesian framework has several unique advantages, and its incorporation into clinical trial design is occurring more frequently. Using an extensive literature review to assess how Bayesian methods are used in clinical trials, we find them most commonly used for dose finding, efficacy monitoring, toxicity monitoring, diagnosis/decision making, and for studying pharmacokinetics/pharmacodynamics. The additional infrastructure required for implementing Bayesian methods in clinical trials may include specialized software programs to run the study design, simulation, and analysis, and Web-based applications, which are particularly useful for timely data entry and analysis. Trial success requires not only the development of proper tools but also timely and accurate execution of data entry, quality control, adaptive randomization, and Bayesian computation. The relative merit of the Bayesian and frequentist approaches continues to be the subject of debate in statistics. However, more evidence can be found showing the convergence of the two camps, at least at the practical level. Ultimately, better clinical trial methods lead to more efficient designs, lower sample sizes, more accurate conclusions, and better outcomes for patients enrolled in the trials. Bayesian methods offer attractive alternatives for better trials. More such trials should be designed and conducted to refine the approach and demonstrate its real benefit in action.},
  doi       = {10.1002/sim.5404},
  file      = {Lee and Chu - 2012 - Bayesian Clinical Trials in Action.pdf:by-author/L/Lee/2012_Lee_2955.pdf:application/pdf},
  groups    = {sg/Clinical Trials},
  owner     = {saulius},
  pmcid     = {PMC3495977},
  pmid      = {22711340},
  timestamp = {2015.12.14},
  creationdate = {2015-12-14T00:00:00},
  url       = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3495977/},
  urldate   = {2015-12-12},
}

@Article{Lee2007,
  author    = {Lee, Jong-Bum and Lee, Kyung-Bai and Shin, Joon-Kook and Yi, Seung-Hun},
  journal   = {Journal of the Korean Mathematical Society},
  title     = {{UNIMODULAR} {GROUPS} {OF} {TYPE} ℝ $^{\textrm{3}}$ ⋊ ℝ},
  year      = {2007},
  issn      = {0304-9914},
  pages     = {1121--1137},
  volume    = {44},
  doi       = {10.4134/JKMS.2007.44.5.1121},
  file      = {Lee et al. - 2007 - UNIMODULAR GROUPS OF TYPE ℝ sup3sup ⋊ ℝ.pdf:by-author/L/Lee/2007_Lee_1121.pdf:application/pdf},
  language  = {en},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://koreascience.or.kr/journal/view.jsp?kj=DBSHBB&py=2007&vnc=v44n5&sp=1121},
  urldate   = {2015-10-10},
}

@Manuscript{Lee,
  author    = {Kent Lee and Hantao Zhang},
  title     = {Formal Development of a Minimal Register Allocation Algorithm},
  keywords  = {Automated Reasoning; Computer Science (CS); Cover Set Induction; Program Verification},
  file      = {:by-author/L/Lee/XXXX_Lee.dvi:DVI},
  owner     = {saulius},
  timestamp = {2015.03.03},
  creationdate = {2015-03-03T00:00:00},
}

@Manuscript{Lee1999,
  author    = {Oukseh Lee and Kwangkeun Yi},
  title     = {Reconstructing the Types of Stack-Machine Codes},
  year      = {1999},
  keywords  = {Computer Science (CS); Stack Machines},
  abstract  = {It is frequently needed to compile stack-machine codes into register-machine codes. One important optimization in such compilers is reducing the stack access overhead. But an effective mapping of stack values into registers is not straightforward. In this article, we present a formal yet effective technique of inferring the two types of each stack value. We infer the type of a stack value when it is pushed (push-type) and the type when it is used (pop-type). These two type information is safely estimated across the basic blocks by a global data-flow analysis. Using this type information, we can safely use as many typed registers as possible in storing stack values. We implemented our analysis for a real compiler and its experiments show that the speed-up is 5% to 24%.},
  file      = {:by-author/L/Lee/1999_Lee.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Lee1991,
  author    = {Peter Lee and Heinz Graafsma and Yan Gao and Hwo-Shuenn Sheu and Philip Coppens and Stephen J. Golden and and Fred F. Lange},
  journal   = {Acta Cryst. A},
  title     = {Modulated structure of an 800 A epitactic film of the superconductor Bi2Sr2CaCu2Os as studied by synchrotron radiation},
  year      = {1991},
  pages     = {57--59},
  volume    = {47},
  file      = {:by-author/L/Lee/1991_Lee_57.pdf:PDF},
  keywords  = {Modulated Structures},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Lee2002,
  author    = {Lee, Sandra J. and Zelen, Marvin},
  journal   = {Cancer treatment and research},
  title     = {Statistical models for screening: planning public health programs.},
  year      = {2002},
  pages     = {19--36},
  volume    = {113},
  file      = {:by-author/L/Lee/2002_Lee_19.pdf:PDF},
  keywords  = {{gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Lee2005b,
  author    = {Lee, Ting-Yu and Wooten, Alfred J. and Luci, Jeffrey J. and Swenson, Dale C. and Messerle, Louis},
  journal   = {Chemical Communications},
  title     = {Four-electron reduction of dinitrogen during solution disproportionation of the organodimetallic ([small eta]-C5Me4R)2Ta2([small mu ]-Cl)4 (R = Me{,} Et) to a new [small mu ]-[small eta]1{,}[small eta]1-N2 complex and odd-electron organotrimetallic cluster},
  year      = {2005},
  pages     = {5444--5446},
  volume    = {0},
  abstract  = {(CMeR)TaCl (d-d) disproportionates under dinitrogen to [(CMeR)TaCl]([small mu ]-N) and the cluster cation (CMeR)Ta([small mu ]-Cl) with anionic (CMeR)TaCl.},
  doi       = {10.1039/B508148C},
  file      = {:by-author/L/Lee/2005_Lee_5444.pdf:PDF},
  issue     = {43},
  owner     = {antanas},
  publisher = {The Royal Society of Chemistry},
  timestamp = {2013.03.07},
  creationdate = {2013-03-07T00:00:00},
  url       = {http://dx.doi.org/10.1039/B508148C},
}

@InProceedings{Lee2005,
  author    = {Lee, Wang-Chien and Zheng, Baihua},
  booktitle = {Distributed Computing Systems, 2005. ICDCS 2005. Proceedings. 25th IEEE International Conference on},
  title     = {DSI: A Fully Distributed Spatial Index for Location-Based Wireless Broadcast Services},
  year      = {2005},
  pages     = {349--358},
  publisher = {IEEE},
  abstract  = {Recent announcement of the MSN Direct Service has demonstrated the feasibility and industrial interest in utilizing wireless broadcast for pervasive information services. To support location-based services in wireless data broadcast systems, a distributed spatial index (called DSI) is proposed in this paper. DSI is highly efficient because it has a linear yet fully distributed structure that facilitates multiple search paths to be naturally mixed together by sharing links. Moreover, DSI is very resilient in error-prone wireless communication environments. Search algorithms for two classical location-based queries, window queries and kNN queries, based on DSI are presented. Performance evaluation of DSI shows that DSI significantly outperforms R-tree and Hilbert Curve Index, two state-of-the-art spatial indexing techniques for wireless data broadcast.},
  doi       = {10.1109/ICDCS.2005.26},
  file      = {:by-author/L/Lee/2005_Lee_349.pdf:PDF},
  issn      = {1063-6927},
  keywords  = {Database Indexing; Distributed Spatial Index; Distributed Structure; Error-prone Wireless Communication; Hilbert Curve Index; Information Services; KNN Queries; Location-based Queries; Location-based Services; Location-based Wireless Broadcast Services; MSN Direct Service; Mobile Computing; Multiple Search Paths; Performance Evaluation; Query Formulation; R Tree Index; Search Algorithms; Spatial Indexing; Visual Databases; Window Queries; Wireless Data Broadcast Systems},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Lee2005c,
  author    = {Zee-Won Lee and Kyung-Bok Lee and Jang-Hee Hong and Jae-Hong Kim and Inpyo Choi and Insung S. Choi},
  journal   = {Chemistry Letters},
  title     = {Single Cell Array of Biotinylated Cells Using Surface Functionalization and Microcontact Printing},
  year      = {2005},
  pages     = {S1--S5},
  file      = {:by-author/L/Lee/2005_Lee_X.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.11.20},
  creationdate = {2012-11-20T00:00:00},
}

@Article{Lefebvre1999,
  author    = {Lefebvre, S. D. and Wong, M. L. and Morrical, S. W.},
  journal   = {The Journal of biological chemistry},
  title     = {Simultaneous interactions of bacteriophage T4 DNA replication proteins gp59 and gp32 with single-stranded (ss) DNA. Co-modulation of ssDNA binding activities in a DNA helicase assembly intermediate.},
  year      = {1999},
  pages     = {22830--8},
  volume    = {274},
  abstract  = {The T4 gp59 protein is the major accessory protein of the phage's replicative DNA helicase, gp41. gp59 helps load gp41 at DNA replication forks by promoting its assembly onto single-stranded (ss) DNA covered with cooperatively bound molecules of gp32, the T4 single-strand DNA binding protein (ssb). A gp59-gp32-ssDNA ternary complex is an obligatory intermediate in this helicase loading mechanism. Here, we characterize the properties of gp59-gp32-ssDNA complexes and reveal some of the biochemical interactions that occur within them. Our results indicate the following: (i) gp59 is able to co-occupy ssDNA pre-saturated with either gp32 or gp32-A (a truncated gp32 species lacking interactions with gp59); (ii) gp59 destabilizes both gp32-ssDNA and (gp32-A)-ssDNA interactions; (iii) interactions of gp59 with the A-domain of gp32 alter the ssDNA-binding properties of gp59; and (iv) gp59 organizes gp32-ssDNA versus (gp32-A)-ssDNA into morphologically distinct complexes. Our results support a model in which gp59-gp32 interactions are non-essential for the co-occupancy of both proteins on ssDNA but are essential for the formation of structures competent for helicase assembly. The data argue that specific "cross-talk" between gp59 and gp32, involving conformational changes in both, is a key feature of the gp41 helicase assembly pathway.},
  file      = {:by-author/L/Lefebvre/1999_Lefebvre_22830.pdf:PDF},
  keywords  = {Solid-state Batteries (SSB); {gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Manuscript{Legato2003,
  author    = {Wilfred J. Legato},
  title     = {A Weakest Precondition Model for Assembly Language Programs},
  year      = {2003},
  keywords  = {Computer Science (CS); Correctnes Proofs; Program Verification; Weakest Preconditions},
  abstract  = {This paper describes a formal model, based upon Dijkstra’s weakest preconditions [4], for reasoning about assembly language programs. The model applies more generally to any finite state machine. It extends earlier work of Floyd [5], Hoare [10] and Dijkstra [4], by automatically generating closed form expressions for the weakest precondition of arbitrary loops.},
  file      = {:by-author/L/Legato/2003_Legato.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Misc{Leha2011,
  author    = {Leha, Andreas},
  title     = {The emacs org-mode - reproducible research and beyond},
  year      = {2011},
  file      = {Leha - 2011 - The Emacs Org-mode - Reproducible Research.pdf:by-author/L/Leha/2011_Leha.pdf:application/pdf},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://web.warwick.ac.uk/statsdept/user2011/TalkSlides/Contributed/16Aug_1115_FocusI_4-ReportingWorkflows_3-Leha.pdf},
  urldate   = {2015-06-06},
}

@Article{Lehman1960,
  author    = {Lehman, I. R. and Pratt, E. A.},
  journal   = {The Journal of biological chemistry},
  title     = {On the structure of the glucosylated hydroxymethylcytosine nucleotides of coliphages T2, T4, and T6.},
  year      = {1960},
  pages     = {3254--9},
  volume    = {235},
  file      = {:by-author/L/LEHMAN/1960_LEHMAN_3254.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Presentation{Leinweber1997,
  author    = {James E. Leinweber},
  title     = {Cryptography},
  year      = {1997},
  file      = {:by-author/L/Leinweber/1997_Leinweber.ppt:PPT},
  keywords  = {Computer Science (CS); Cryptography},
  owner     = {saulius},
  timestamp = {2015.03.03},
  creationdate = {2015-03-03T00:00:00},
}

@Manual{Leisch2008,
  title     = {Sweave User Manual},
  author    = {Friedrich Leisch},
  year      = {2008},
  file      = {:by-author/L/Leisch/2008_Leisch.pdf:PDF},
  keywords  = {Latex; R},
  owner     = {andrius},
  timestamp = {2012.10.24},
  creationdate = {2012-10-24T00:00:00},
  url       = {http://www.stat.uni-muenchen.de/~leisch/Sweave/Sweave-manual.pdf},
}

@Article{Leitans2015,
  author      = {Janis Leitans and Andris Kazaks and Agnese Balode and Jekaterina Ivanova and Raivis Zalubovskis and Claudiu T Supuran and Kaspars Tars},
  journal     = {J Med Chem},
  title       = {An Efficient Expression and Crystallization System of the Cancer Asociated Carbonic Anhydrase Isoform IX.},
  year        = {2015},
  month       = {Oct},
  abstract    = {Human carbonic anhydrase IX (CA IX) is overexpressed in a number of solid tumors and is considered as a marker for cellular hypoxia, while it is not produced in most of the normal tis-sue. CA IX contributes to acidification of extracellular matrix, which in turn favors growth and metastasis of tumor. Therefore, CA IX is considered a promising anti-cancer drug target. How-ever, specific targeting of CA IX is challenging due to the fact that human genome encodes 15 different isoforms of carbonic anhydrases with a high degree of homology. Furthermore, struc-ture-based drug design of CA IX inhibitors so far has been largely unsuccessful due to technical difficulties in expression and crystallization of enzyme. Currently, only one baculovirus pro-duced CA IX structure in complex with unspecific CA inhibitor acetazolamide is available in Protein Data Bank. We have developed an efficient production system of the catalytic domain of CA IX in methylotrophic yeast Pichia pastoris. The produced protein can be easily crystal-lized in the presence of inhibitors as we have demonstrated for several 2-thiophene-sulfonamide compounds. We have also observed significant differences in binding modes of chemically identical compounds to CA IX and CA II, which can be further exploited in design of CA IX specific inhibitors.},
  doi         = {10.1021/acs.jmedchem.5b01343},
  file        = {2015_Leitans_000.pdf:by-author/L/Leitans/2015_Leitans_000.pdf:PDF},
  groups      = {sg/hCA9},
  language    = {eng},
  medline-pst = {aheadofprint},
  owner       = {alexey},
  pmid        = {26522624},
  timestamp = {2015.11.09},
  creationdate = {2015-11-09T00:00:00},
  url         = {http://dx.doi.org/10.1021/acs.jmedchem.5b01343},
}

@Manual{Leitch2000,
  title     = {Programming Algol 68 Made Easy},
  author    = {Sian Leitch},
  year      = {2000},
  file      = {:by-author/L/Leitch/2000_Leitch.pdf:PDF},
  keywords  = {Algol; Algol 68; Computer Science (CS); Programming Languages},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Lejaeghere2014,
  author           = {Lejaeghere, K. and Van Speybroeck, V. and Van Oost, G. and Cottenier, S.},
  journal          = {Critical Reviews in Solid State and Materials Sciences},
  title            = {Error Estimates for Solid-State Density-Functional Theory Predictions: An Overview by Means of the Ground-State Elemental Crystals},
  year             = {2014},
  pages            = {1--24},
  volume           = {39},
  abstract         = {Predictions of observable properties by density-functional theory calculations (DFT) are used increasingly often by experimental condensed-matter physicists and materials engineers as data. These predictions are used to analyze recent measurements, or to plan future experiments in a rational way. Increasingly more experimental scientists in these fields therefore face the natural question: what is the expected error for such a first-principles prediction? Information and experience about this question is implicitly available in the computational community, scattered over two decades of literature. The present review aims to summarize and quantify this implicit knowledge. This eventually leads to a practical protocol that allows any scientist—experimental or theoretical—to determine justifiable error estimates for many basic property predictions, without having to perform additional DFT calculations. A central role is played by a large and diverse test set of crystalline solids, containing all ground-state elemental crystals (except most lanthanides). For several properties of each crystal, the difference between DFT results and experimental values is assessed. We discuss trends in these deviations and review explanations suggested in the literature. A prerequisite for such an error analysis is that different implementations of the same first-principles formalism provide the same predictions. Therefore, the reproducibility of predictions across several mainstream methods and codes is discussed too. A quality factor Δ expresses the spread in predictions from two distinct DFT implementations by a single number. To compare the PAW method to the highly accurate APW+lo approach, a code assessment of VASP and GPAW (PAW) with respect to WIEN2k (APW+lo) yields Δ-values of 1.9 and 3.3 meV/atom, respectively. In both cases the PAW potentials recommended by the respective codes have been used. These differences are an order of magnitude smaller than the typical difference with experiment, and therefore predictions by APW+lo and PAW are for practical purposes identical.},
  creationdate     = {2014-07-31T00:00:00},
  doi              = {10.1080/10408436.2013.772503},
  eprint           = {http://dx.doi.org/10.1080/10408436.2013.772503},
  file             = {2014_Lejaeghere_1.pdf:by-author/L/Lejaeghere/2014_Lejaeghere_1.pdf:PDF},
  keywords         = {Citing COD; Comparison With Experiment; Density Functional Theory (DFT); Errors},
  modificationdate = {2023-01-27T14:55:25},
  owner            = {saulius},
  timestamp        = {2014.07.31},
  url              = {http://dx.doi.org/10.1080/10408436.2013.772503},
}

@Article{Lemmen2000,
  author    = {Christian Lemmen and Thomas Lengauer},
  journal   = {Journal of Computer-Aided Molecular Design},
  title     = {Computational methods for the structural alignment of molecules},
  year      = {2000},
  pages     = {215--232},
  volume    = {14},
  file      = {:by-author/L/Lemmen/2000_Lemmen_215.pdf:PDF},
  keywords  = {Algorithms; Computational Methods; Review; Structural Alignment; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2012.05.15},
  creationdate = {2012-05-15T00:00:00},
}

@Presentation{Lends2011,
  author     = {Alons Lends and Edvards Liepinsh},
  title      = {NMR and molecular modeling of inhibitor binding to carbonic anhydrases},
  year       = {2011},
  conference = {EAST NMR},
  file       = {:by-author/L/Lends/2011_Lends.ppt:PPT},
  groups     = {sg/physical sg/methods},
  owner      = {saulius},
  timestamp = {2015.03.03},
  creationdate = {2015-03-03T00:00:00},
}

@Article{Lengauer2000,
  author    = {Lengauer, Thomas and Zimmer, Ralf},
  journal   = {Briefings in Bioinformatics},
  title     = {Protein structure prediction methods for drug design},
  year      = {2000},
  pages     = {275--288},
  volume    = {1},
  abstract  = {Along the long path from genomic data to a new drug, the knowledge of three-dimensional protein structure can be of significant help in several places. This paper points out such places, discusses the virtues of protein structure knowledge and reviews bioinformatics methods for gaining such knowledge on the protein structure.},
  doi       = {10.1093/bib/1.3.275},
  eprint    = {http://bib.oxfordjournals.org/content/1/3/275.full.pdf+html},
  file      = {:by-author/L/Lengauer/2000_Lengauer_275.pdf:PDF},
  keywords  = {Drug Design},
  owner     = {antanas},
  timestamp = {2013.04.26},
  creationdate = {2013-04-26T00:00:00},
  url       = {http://bib.oxfordjournals.org/content/1/3/275.abstract},
}

@TechReport{Lensink2016,
  author      = {Marc F. Lensink and Sameer Velankar and Shoshana J. Wodak},
  institution = {University of Lille, CNRS, France; European Bioinformatics Institute (EMBL-EBI), Hinxton, UK; Structural Biology Group, VUB-VIB, Brussels, Belgium},
  title       = {Modeling protein-protein assemblies: the CASP12-CAPRI Round 37 challenge of the summer of 2016},
  year        = {2016},
  file        = {2016_Lensink.pdf:by-author/L/Lensink/2016_Lensink.pdf:PDF},
  keywords    = {CAPRI; CASP; Interface Prediction; Protein Complex Prediction; Protein Structure Prediction; Venclovas},
  owner       = {saulius},
  timestamp = {2016.12.27},
  creationdate = {2016-12-27T00:00:00},
  url         = {http://predictioncenter.org/casp12/doc/presentations/CASP12_CAPRI_Lensink.pdf},
}

@Article{Lenski2003,
  author    = {Lenski, Richard E. and Ofria, Charles and Pennock, Robert T. and Adami, Christoph},
  journal   = {Nature},
  title     = {The evolutionary origin of complex features},
  year      = {2003},
  issn      = {0028-0836},
  month     = {May},
  number    = {6936},
  pages     = {139--144},
  volume    = {423},
  abstract  = {A long-standing challenge to evolutionary theory has been whether it can explain the origin of complex organismal features. We examined this issue using digital organisms—computer programs that self-replicate, mutate, compete and evolve. Populations of digital organisms often evolved the ability to perform complex logic functions requiring the coordinated execution of many genomic instructions. Complex functions evolved by building on simpler functions that had evolved earlier, provided that these were also selectively favoured. However, no particular intermediate stage was essential for evolving complex functions. The first genotypes able to perform complex functions differed from their non-performing parents by only one or two mutations, but differed from the ancestor by many mutations that were also crucial to the new functions. In some cases, mutations that were deleterious when they appeared served as stepping-stones in the evolution of complex features. These findings show how complex functions can originate by random mutation and natural selection.},
  doi       = {10.1038/nature01568},
  file      = {2003_Lenski_139.pdf:by-author/L/Lenski/2003_Lenski_139.pdf:PDF;2003_Lenski_139suppl.pdf:by-author/L/Lenski/2003_Lenski_139suppl.pdf:PDF},
  keywords  = {Artifiacial Life; Program Evolution; Software Evolution},
  owner     = {saulius},
  publisher = {Nature Publishing Group},
  timestamp = {2016.04.26},
  creationdate = {2016-04-26T00:00:00},
  url       = {http://dx.doi.org/10.1038/nature01568},
}

@Webpage{Lenstra2006,
  author    = {Arjen Lenstra and Xiaoyun Wang and Benne de Weger},
  retrieved = {2015-03-11},
  title     = {Colliding X.509 Certificates for Different Identities},
  url       = {http://www.win.tue.nl/~bdeweger/CollidingCertificates/index.html},
  year      = {2006},
  abstract  = {We announce a pair of valid X.509 certificates, based on the MD5 hash-function, that have identical signatures.},
  file      = {:by-author/L/Lenstra/2006_Lenstra.odt:OpenDocument text;:by-author/L/Lenstra/2006_Lenstra/MD5CollisionCA.cer:Text;:by-author/L/Lenstra/2006_Lenstra/MD5Collision.certificate2.cer:Text;:by-author/L/Lenstra/2006_Lenstra/MD5Collision.certificate1.cer:Text},
  keywords  = {Computer Science (CS); Computer Security; Cryptography; Hash Collisions; MD5},
  owner     = {saulius},
  timestamp = {2015.03.11},
  creationdate = {2015-03-11T00:00:00},
}

@Manual{Lentvorski2014,
  title     = {Tutorial: Allocating Foreign Data on the Lisp Heap},
  author    = {Lentvorski, Jr., Andrew P.},
  year      = {2014},
  file      = {:by-author/L/Lentvorski/2014_Lentvorski.odt:PDF},
  owner     = {saulius},
  timestamp = {2014.03.23},
  creationdate = {2014-03-23T00:00:00},
}

@PhdThesis{Leon2009,
  author     = {Léon, François},
  school     = {Université de Caen},
  title      = {Développement de l'analyse quantitative de texture utilisant des détecteurs bidimensionnels: application à la texture magnétique.},
  year       = {2009},
  file       = {[PDF] from archives-ouvertes.fr:by-author/L/Léon/2009_Léon.pdf:application/pdf;Snapshot:by-author/L/Léon/2009_Léon.html:text/html},
  groups     = {sg/JAC2009},
  owner      = {saulius},
  shorttitle = {Développement de l'analyse quantitative de texture utilisant des détecteurs bidimensionnels},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url        = {https://tel.archives-ouvertes.fr/tel-00401873/},
  urldate    = {2015-08-31},
}

@InProceedings{Leone1996,
  author    = {Mark Leone and Peter Lee},
  booktitle = {Workshop Record of WCSSS'96: The Inaugural Workshop on Compiler Support for System Software},
  title     = {A Declarative Approach to Run-Time Code Generation},
  year      = {1996},
  month     = {February},
  pages     = {8--17},
  abstract  = {Run-time code generation promises to improve the performance and reliability of current and future systems. Optimizations performed at run time make use of values and invariants that cannot be exploited at compile time, yielding code that is superior to statically optimal code. Most previous approaches to run-time code generation have been _imperative_. The programmer is responsible for specifying the code to be optimized at run time (often as a "template" of machine code), performing certain optimizations, insuring that dynamically constructed code is well formed, invoking a compiler and dynamically linking to the resulting code, and insuring correctness by invalidating or updating code when the values used to optimize it change. Each of these duties is laborious and error prone. Various ad-hoc techniques have been suggested to ameliorate the situation, but we believe that this imperative approach is inherently clumsy and unsafe. We advocate a _declarative_ approach to run-time code generation: the programmer should express algorithms in a high-level language that permits the _compiler_ to discover and safely exploit opportunities for dynamic optimization. The key benefits of a declarative approach to run-time code generation are: o Safety: the programmer does not write explicit code for generating code, but instead submits an ordinary program to the compiler o Portability: the compiler encapsulates all of the details of run-time code generation o Speed: the compiler can use semantics-based transformation techniques to specialize run-time code generators, reducing code generation time by an order of magnitude over previous imperative approaches. Our goals may appear to be impossibly lofty; on the contrary, we have early evidence from experiments with a prototype compiler that automatic run-time code generation can be practical. Our compiler, called Fabius, compiles ordinary programs written in a subset of Standard ML into code that generates and executes native code at run time.},
  file      = {:by-author/L/Leone/1996_Leone_8.ps:PostScript;:by-author/L/Leone/1996_Leone_8.pdf:PDF},
  owner     = {saulius},
  timestamp = {2013.08.10},
  creationdate = {2013-08-10T00:00:00},
  url       = {http://www.cs.cmu.edu/afs/cs.cmu.edu/user/mleone/papers/declarative-rtcg.ps},
}

@InProceedings{Leone1994,
  author    = {Mark Leone and Peter Lee},
  booktitle = {Proceedings of the ACM SIGPLAN Workshop on Partial Evaluation and Semantics-Based Program Manipulation},
  title     = {Lightweight Run-Time Code Generation},
  year      = {1994},
  month     = {June},
  pages     = {97--106},
  abstract  = {Run-time code generation is an alternative and complement to compile-time program analysis and optimization. Static analyses are inherently imprecise because most interesting aspects of run-time behavior are uncomputable. By deferring aspects of compilation to run time, more precise information about program behavior can be exploited, leading to greater opportunities for code improvement. The cost of performing optimization at run time is of paramount importance, since it must be repaid by improved performance in order to obtain an overall speedup. This paper describes a lightweight approach to run-time code generation, called _deferred compilation_, in which compile-time specialization is employed to reduce the cost of optimizing and generating code at run time. Implementation strategies developed for a prototype compiler are discussed, and the results of preliminary experiments demonstrating significant overall speedup are presented.},
  file      = {:by-author/L/Leone/1994_Leone_97.pdf:PDF;:by-author/L/Leone/1994_Leone_97.ps:PostScript},
  owner     = {saulius},
  timestamp = {2013.08.10},
  creationdate = {2013-08-10T00:00:00},
  url       = {http://www.cs.cmu.edu/afs/cs.cmu.edu/user/mleone/papers/lw-rtcg.ps},
}

@Webpage{Leong1998a,
  author    = {Philip Leong},
  retrieved = {2015-03-07},
  title     = {MSL16 Processor},
  url       = {http://www.cse.cuhk.edu.hk/~phwl/mt/public/archives/old/msl16/msl16.html},
  year      = {1998},
  abstract  = {The MSL16 machine is a CPU optimised to run the Forth programming language. It is similar to the minimal instruction set computers described in Jeff Fox's Forth microprocessor page , but implemented on a Xilinx FPGA. When the system is stable, the VHDL source code for the CPU and all the code will be released to make a complete public domain CPU.},
  file      = {:by-author/L/Leong/1998_Leong.war:;:by-author/L/Leong/1998_Leong.ps:PostScript;:by-author/L/Leong/1998_Leong.pdf:PDF},
  keywords  = {Computer Science (CS); Stack-machines},
  owner     = {saulius},
  timestamp = {2015.03.02},
  creationdate = {2015-03-02T00:00:00},
}

@Manuscript{Leong1998,
  author    = {P. H. W. Leong and P. K. Tsang and T. K. Lee},
  title     = {A FPGA based Forth microprocessor},
  year      = {1998},
  file      = {:by-author/L/Leong/1998_Leong.ps:PostScript;:by-author/L/Leong/1998_Leong.pdf:PDF},
  owner     = {saulius},
  timestamp = {2015.02.27},
  creationdate = {2015-02-27T00:00:00},
}

@Article{Lepikhov2001,
  author    = {Lepikhov, K. and Tchernov, A. and Zheleznaja, L. and Matvienko, N. and Walter, J. and Trautner, T. A.},
  journal   = {Nucleic acids research},
  title     = {Characterization of the type IV restriction modification system BspLU11III from Bacillus sp. LU11.},
  year      = {2001},
  pages     = {4691--8},
  volume    = {29},
  abstract  = {We report the characterization and cloning of the genes for an unusual type IV restriction-modification system, BspLU11III, from Bacillus sp. LU11. The system consists of two methyltransferases and one endonuclease, which also possesses methyltransferase activity. The three genes of the restriction-modification system, bsplu11IIIMa, bsplu11IIIMb and bsplu11IIIR, are closely linked and tandemly arranged. The corresponding enzymes recognize the dsDNA sequence 5'-GGGAC-3'/5'-GTCCC-3', with M.BspLU11IIIa modifying the A (underlined) of one strand and M.BspLU11IIIb the inner C (underlined) of the other strand. R.BspLU11III has both endonuclease and adenine-specific methyltransferase activities and is able to protect the DNA against cleavage by itself. In contrast to all type IV restriction-modification systems described so far, which have only one adenine-specific methyltransferase, BspLU11III is the first type IV restriction-modification system that includes two methyltransferases, one of them being cytosine specific.},
  file      = {:by-author/L/Lepikhov/2001_Lepikhov_4691.pdf:PDF},
  keywords  = {McrBC},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Leppilampi2003,
  author    = {Leppilampi, Mari and Saarnio, Juha and Karttunen, Tuomo J and Kivelä, Jyrki and Pastoreková, Silvia and Pastorek, Jaromir and Waheed, Abdul and Sly, William S and Parkkila, Seppo},
  journal   = {World journal of gastroenterology : WJG},
  title     = {Carbonic anhydrase isozymes IX and XII in gastric tumors.},
  year      = {2003},
  pages     = {1398--403},
  volume    = {9},
  file      = {2003_Leppilampi_1398.pdf:by-author/L/Leppilampi/2003_Leppilampi_1398.pdf:PDF},
  groups    = {sg/cancer, sg/hCA9, sg/hCA12},
  keywords  = {Carbonic Anhydrases},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Lesk1985,
  author    = {Arthur M. Lesk},
  journal   = {Journal of Molecular Graphics},
  title     = {Programming the Evans \&amp; Sutherland \{PS\} 300: I. A preprocessor with macro facilities},
  year      = {1985},
  issn      = {0263-7855},
  pages     = {25 - 31},
  volume    = {3},
  abstract  = {The Evans and Sutherland \{PS\} 300 is a powerful computer graphics device, programmable in a specialized line-drawing graphics language processed by internal firmware. We describe here a preprocessor to facilitate the generation of programs for the \{PS\} 300. It converts programs from a concise and easy-to-write style into a form acceptable to the \{PS\} 300 command interpreter. In addition to the expansion of abbreviations, the preprocessor supports macro definitions with substitutable parameters, and symbol definitions and replacements. All special features are embedded transparently in the \{PS\} 300 language itself. These features create a programming environment appropriate and convenient for generating function networks for the \{PS\} 300. It has been useful in producing robust and supple (i.e., easy to modify) programs for molecular graphics, but is not limited to this area of applications.},
  doi       = {10.1016/0263-7855(85)80010-2},
  file      = {1985_Lesk_25.pdf:by-author/L/Lesk/1985_Lesk_25.pdf:PDF},
  keywords  = {Data Management; Evans and Sutherland PS 300 Workstations; M68000 CPU; Macro; Molecular Graphics; Preprocessor; Programing Language},
  owner     = {saulius},
  timestamp = {2014.01.26},
  creationdate = {2014-01-26T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/0263785585800102},
}

@Manuscript{Lesk1998,
  author    = {M. E. Lesk},
  title     = {Some Applications of Inverted Indexes on the UNIX System},
  year      = {1998},
  keywords  = {Computer Science (CS); Refer; Text Processing; Typesetting; Unix},
  file      = {:by-author/L/Lesk/1998_Lesk.ps:PostScript;:by-author/L/Lesk/1998_Lesk.pdf:PDF},
  owner     = {saulius},
  timestamp = {2015.02.27},
  creationdate = {2015-02-27T00:00:00},
}

@Manuscript{Lesk1978,
  author    = {M. E. Lesk},
  title     = {Typing Documents on the UNIX System: Using the −ms Macros with Troff and Nroff},
  year      = {1978},
  keywords  = {Computer Science (CS); Macros; Nroff; Phototypesetting; Roff; Text Formatting; Troff; Typesetting; Unix},
  month     = {November},
  file      = {:by-author/L/Lesk/1978_Lesk.ps:PostScript;:by-author/L/Lesk/1978_Lesk.pdf:PDF},
  owner     = {saulius},
  timestamp = {2015.02.27},
  creationdate = {2015-02-27T00:00:00},
}

@TechReport{Lesk1976,
  author      = {M. E. Lesk},
  institution = {Bell Laboratories, Murray Hill, New Jersey 07974},
  title       = {Tbl — A Program to Format Tables},
  year        = {1976},
  month       = {June},
  abstract    = {Tbl is a document formatting preprocessor for troff or nroff which makes even fairly complex tables easy to specify and enter. It is available on the PDP-11 UNIX* system and on Honeywell 6000 GCOS. Tables are made up of columns which may be indepen- dently centered, right-adjusted, left-adjusted, or aligned by decimal points. Headings may be placed over single columns or groups of columns. A table entry may contain equations, or may consist of several rows of text. Horizontal or vertical lines may be drawn as desired in the table, and any table or element may be enclosed in a box.},
  file        = {:by-author/L/Lesk/1976_Lesk.ps:PostScript;:by-author/L/Lesk/1976_Lesk.pdf:PDF},
  keywords    = {Computer Science (CS); Groff; Roff; Tbl; Troff; Typesetting; Unix},
  owner       = {saulius},
  timestamp = {2015.02.27},
  creationdate = {2015-02-27T00:00:00},
}

@Article{Leslie2006,
  author    = {Leslie, Andrew G W},
  journal   = {Acta Crystallogr D Biol Crystallogr},
  title     = {The integration of macromolecular diffraction data},
  year      = {2006},
  month     = {Jan},
  number    = {Pt 1},
  pages     = {48--57},
  volume    = {62},
  abstract  = {The objective of any modern data-processing program is to produce from a set of diffraction images a set of indices (hkls) with their associated intensities (and estimates of their uncertainties), together with an accurate estimate of the crystal unit-cell parameters. This procedure should not only be reliable, but should involve an absolute minimum of user intervention. The process can be conveniently divided into three stages. The first (autoindexing) determines the unit-cell parameters and the orientation of the crystal. The unit-cell parameters may indicate the likely Laue group of the crystal. The second step is to refine the initial estimate of the unit-cell parameters and also the crystal mosaicity using a procedure known as post-refinement. The third step is to integrate the images, which consists of predicting the positions of the Bragg reflections on each image and obtaining an estimate of the intensity of each reflection and its uncertainty. This is carried out while simultaneously refining various detector and crystal parameters. Basic features of the algorithms employed for each of these three separate steps are described, principally with reference to the program MOSFLM},
  address   = {MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, England},
  doi       = {10.1107/S0907444905039107},
  file      = {2006_Leslie_48.pdf:by-author/L/Leslie/2006_Leslie_48.pdf:PDF},
  keywords  = {Image Integration; Image Processing; X-ray Crystallography},
  owner     = {em},
  timestamp = {2016.06.16},
  creationdate = {2016-06-16T00:00:00},
  url       = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&dopt=abstract&list_uids=16369093},
}

@Article{Lesser1990,
  author    = {Lesser, D. R. and Kurpiewski, M. R. and Jen-Jacobson, L.},
  journal   = {Science (New York, N.Y.)},
  title     = {The energetic basis of specificity in the Eco RI endonuclease--DNA interaction.},
  year      = {1990},
  pages     = {776--86},
  volume    = {250},
  abstract  = {High sequence selectivity in DNA-protein interactions was analyzed by measuring discrimination by Eco RI endonuclease between the recognition site GAATTC and systematically altered DNA sites. Base analogue substitutions that preserve the sequence-dependent conformational motif of the GAATTC site permit deletion of single sites of protein-base contact at a cost of +1 to +2 kcal/mol. However, the introduction of any one incorrect natural base pair costs +6 to +13 kcal/mol in transition state interaction energy, the resultant of the following interdependent factors: deletion of one or two hydrogen bonds between the protein and a purine base; unfavourable steric apposition between a group on the protein and an incorrectly placed functional group on a base; disruption of a pyrimidine contact with the protein; loss of some crucial interactions between protein and DNA phosphates; and an increased energetic cost of attaining the required DNA conformation in the transition state complex. Eco RI endonuclease thus achieves stringent discrimination by both &quot;direct readout&quot; (protein-base contracts) and &quot;indirect readout&quot; (protein-phosphate contacts and DNA conformation) of the DNA sequence.},
  file      = {:by-author/L/Lesser/1990_Lesser_776.pdf:PDF},
  keywords  = {Readout},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Levene1923,
  author    = {Levene, P. A. and Simms, Henry S.},
  journal   = {Journal of Biological Chemistry},
  title     = {Calculation of isoelectric points},
  year      = {1923},
  pages     = {801--813},
  volume    = {55},
  eprint    = {http://www.jbc.org/content/55/4/801.full.pdf+html},
  file      = {1923_Levene_801.pdf:by-author/L/Levene/1923_Levene_801.pdf:PDF},
  keywords  = {Isoelectric Point; Protein Physics},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://www.jbc.org/content/55/4/801.short},
}

@Manuscript{Leventhal2006,
  author    = {Adam Leventhal},
  title     = {Double-Parity RAID-Z},
  year      = {2006},
  url       = {https://blogs.oracle.com/ahl/entry/double_parity_raid_z},
  abstract  = {The basic notion behind double-parity RAID or RAID-6 is that a stripe can survive two failures without losing data where RAID-5 can survive only a single failure. There are a number of different ways of implementing double-parity RAID; the way Jeff and Bill had chosen (due to its computational simplicity and lack of legal encumbrance) was one described by H. Peter Anvin in this paper (http://kernel.org/pub/linux/kernel/people/hpa/raid6.pdf). It's a nice read, but I'll attempt to summarize some of the math.},
  file      = {:by-author/L/Leventhal/2006_Leventhal.odt:OpenDocument text},
  owner     = {saulius},
  timestamp = {2012.11.27},
  creationdate = {2012-11-27T00:00:00},
}

@Article{Levin2003,
  author    = {Mikhail K. Levin and Smita S. Patel},
  journal   = {Molecular Motors},
  title     = {Helicases as Molecular Motors},
  year      = {2003},
  pages     = {manuscript},
  file      = {:by-author/L/Levin/2003_Levin_manuscript.pdf:PDF},
  keywords  = {{gp41} Helicase},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Levine1985,
  author    = {Dov Levine and T. C. Lubensky and Stelland Ostlund and Sriram Ramaswamy and Paul Joseph Steinhardt and John Toner},
  title     = {Elasticity and Dislocations in Pentagonal and Icosahedral Quasicrystals},
  year      = {1985},
  pages     = {1520--1523},
  volume    = {54},
  file      = {Dov Levine et al. - 1985 - Elasticity and Dislocations in Pentagonal and Icos.pdf:by-author/L/Levine/1985_Levine_1520.pdf:application/pdf},
  language  = {English},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://physics.princeton.edu/~steinh/ElasticQC.pdf},
  urldate   = {2015-09-08},
}

@Article{Levine1986,
  author    = {Levine, Dow and Steinhardt, Paul J.},
  journal   = {Physical review. B, Condensed matter},
  title     = {Quasicrystals. I. Definition and structure.},
  year      = {1986},
  pages     = {596--616},
  volume    = {34},
  file      = {:by-author/L/Levine/1986_Levine_596.pdf:PDF},
  keywords  = {Quasicrystals},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Levinthal1966,
  author    = {Levinthal, C.},
  journal   = {Sci Am.},
  title     = {Molecular model-building by computer},
  year      = {1966},
  pages     = {42--52},
  volume    = {214},
  abstract  = {In which biochemists observe models of giant molecules as they are displayed on a screen by a computer and try to fold them into shapes that they assume in nature.},
  file      = {1966_Levinthal_42.pdf:by-author/L/Levinthal/1966_Levinthal_42.pdf:PDF},
  owner     = {saulius},
  timestamp = {2013.04.01},
  creationdate = {2013-04-01T00:00:00},
}

@InCollection{Levy2012,
  author    = {Roger Levy},
  booktitle = {Probabilistic Models in the Study of Language},
  publisher = {rlevy@ucsd.edu},
  title     = {Confidence Intervals and Hypothesis Testing},
  year      = {2012},
  chapter   = {5},
  pages     = {78--106},
  file      = {:by-author/L/Levy/2012_Levy_78.pdf:PDF},
  groups    = {sg/Bayesian},
  journal   = {Canadian journal of psychiatry. Revue canadienne de psychiatrie},
  keywords  = {Bayesian Statistics},
  owner     = {saulius},
  timestamp = {2012.09.30},
  creationdate = {2012-09-30T00:00:00},
}

@Article{Lewis1916,
  author    = {Lewis, Gilbert N.},
  journal   = {Journal of the American Chemical Society},
  title     = {The atom and the molecule},
  year      = {1916},
  pages     = {762--785},
  volume    = {38},
  doi       = {10.1021/ja02261a002},
  file      = {1916_Lewis_762.pdf:by-author/L/Lewis/1916_Lewis_762.pdf:PDF},
  keywords  = {Chemical Bond; Electronic Structure},
  owner     = {saulius},
  timestamp = {2014.04.16},
  creationdate = {2014-04-16T00:00:00},
}

@Presentation{Lewis2013,
  author    = {Roger J. Lewis},
  title     = {An Overview of Bayesian Adaptive Clinical Trial Design},
  year      = {2013},
  file      = {2013_Lewis.pdf:by-author/L/Lewis/2013_Lewis.pdf:PDF},
  groups    = {sg/Clinical Trials},
  owner     = {saulius},
  timestamp = {2015.12.14},
  creationdate = {2015-12-14T00:00:00},
  url       = {http://www.berryconsultants.com/wp-content/uploads/2012/09/An-Overview-of-Bayesian-Adaptive-Clinical-Trial-Design.pdf},
  urldate   = {2015-12-12},
}

@Article{Li2016,
  author    = {Gao-Peng Li and Hong-Yun Yang and Yong-Zhi Li and Lei Hou and Bin Liu and Yao-Yu Wang},
  journal   = {{ChemPlusChem}},
  title     = {Structural Diversity of Three Pyrazoyl-Carboxyl Bifunctional Ligand-Based Metal-Organic Frameworks: Luminescence and Magnetic Properties},
  year      = {2016},
  month     = {nov},
  doi       = {10.1002/cplu.201600521},
  file      = {:by-author/L/Li/2016_Li_a.pdf:PDF;Li2016.pdf:by-author/L/Li/2016_Li.pdf:PDF},
  groups    = {sg/MOF, sg/MOFs, am/MOFs},
  keywords  = {Synhesis},
  owner     = {saulius},
  publisher = {Wiley-Blackwell},
  timestamp = {2017.01.31},
  creationdate = {2017-01-31T00:00:00},
  url       = {https://doi.org/10.1002%2Fcplu.201600521},
}

@InProceedings{Li2005,
  author    = {Li, Hongga and Lu, Hua and Huang, Bo and Huang, Zhiyong},
  booktitle = {Proceedings of the 13th annual ACM international workshop on Geographic information systems},
  title     = {Two Ellipse-based Pruning Methods for Group Nearest Neighbor Queries},
  year      = {2005},
  pages     = {192--199},
  publisher = {ACM},
  abstract  = {Group nearest neighbor (GNN) queries are a relatively new type of operations in spatial database applications. Differ- ent from a traditional kNN query which specifies a single query point only, a GNN query has multiple query points. Because of the number of query points and their arbitrary distribution in the data space, a GNN query is much more complex than a kNN query. In this paper, we propose two pruning strategies for GNN queries which take into account the distribution of query points. Our methods employ an ellipse to approximate the extent of multiple query points, and then derive a distance or minimum bounding rectan- gle (MBR) using that ellipse to prune intermediate nodes in a depth-first search via an R∗ -tree. These methods are also applicable to the best-first traversal paradigm. We con- duct extensive performance studies. The results show that the proposed pruning strategies are more efficient than the existing methods.},
  doi       = {10.1145/1097064.1097092},
  file      = {:by-author/L/Li/2005_Li_192.pdf:PDF},
  isbn      = {1-59593-146-5},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://doi.acm.org/10.1145/1097064.1097092},
}

@Article{Li2013,
  author    = {Li Li},
  journal   = {Journal of Biological Chemistry},
  title     = {Casting Doubt on the RNA World Hypothesis: Aminoacylating Urzymes Challenge the RNA World Hypothesis},
  year      = {2013},
  pages     = {26864},
  volume    = {288},
  doi       = {10.1074/jbc.P113.496125},
  eprint    = {http://www.jbc.org/content/288/37/26864.full.pdf+html},
  file      = {2013_Li_26864.pdf:by-author/L/Li/2013_Li_26864.pdf:PDF},
  keywords  = {Criticism; RNA World},
  owner     = {saulius},
  timestamp = {2013.09.27},
  creationdate = {2013-09-27T00:00:00},
  url       = {http://www.jbc.org/content/288/37/26864.short},
}

@Article{Li2013a,
  author    = {Li, Li and Francklyn, Christopher and Carter, Charles W.},
  journal   = {Journal of Biological Chemistry},
  title     = {Aminoacylating Urzymes Challenge the RNA World Hypothesis},
  year      = {2013},
  pages     = {26856--26863},
  volume    = {288},
  abstract  = {We describe experimental evidence that ancestral peptide catalysts substantially accelerated development of genetic coding. Structurally invariant 120–130-residue Urzymes (Ur = primitive plus enzyme) derived from Class I and Class II aminoacyl-tRNA synthetases (aaRSs) acylate tRNA far faster than the uncatalyzed rate of nonribosomal peptide bond formation from activated amino acids. These new data allow us to demonstrate statistically indistinguishable catalytic profiles for Class I and II aaRSs in both amino acid activation and tRNA acylation, over a time period extending to well before the assembly of full-length enzymes and even further before the Last Universal Common Ancestor. Both Urzymes also exhibit ∼60% of the contemporary catalytic proficiencies. Moreover, they are linked by ancestral sense/antisense genetic coding, and their evident modularities suggest descent from even simpler ancestral pairs also coded by opposite strands of the same gene. Thus, aaRS Urzymes substantially pre-date modern aaRS but are, nevertheless, highly evolved. Their unexpectedly advanced catalytic repertoires, sense/antisense coding, and ancestral modularities imply considerable prior protein-tRNA co-evolution. Further, unlike ribozymes that motivated the RNA World hypothesis, Class I and II Urzyme·tRNA pairs represent consensus ancestral forms sufficient for codon-directed synthesis of nonrandom peptides. By tracing aaRS catalytic activities back to simpler ancestral peptides, we demonstrate key steps for a simpler and hence more probable peptide·RNA development of rapid coding systems matching amino acids with anticodon trinucleotides.},
  doi       = {10.1074/jbc.M113.496125},
  eprint    = {http://www.jbc.org/content/288/37/26856.full.pdf+html},
  file      = {2013_Li_26856.pdf:by-author/L/Li/2013_Li_26856.pdf:PDF},
  owner     = {saulius},
  timestamp = {2013.09.25},
  creationdate = {2013-09-25T00:00:00},
  url       = {http://www.jbc.org/content/288/37/26856.abstract},
}

@Article{Li2006,
  author    = {Li, L.-C. and Okino, S. T. and Zhao, H. and Pookot, D. and Place, R. F. and Urakami, S. and Enokida, H. and Dahiya, R.},
  journal   = {Proceedings of the National Academy of Sciences},
  title     = {Small {dsRNAs} induce transcriptional activation in human cells},
  year      = {2006},
  issn      = {1091-6490},
  month     = {Nov},
  number    = {46},
  pages     = {17337–17342},
  volume    = {103},
  doi       = {10.1073/pnas.0607015103},
  file      = {:by-author/L/Li/2006_Li_17337.pdf:PDF},
  groups    = {am/RNA activation},
  owner     = {andrius},
  publisher = {Proceedings of the National Academy of Sciences},
  timestamp = {2016.08.23},
  creationdate = {2016-08-23T00:00:00},
  url       = {http://dx.doi.org/10.1073/pnas.0607015103},
}

@Article{Li2002,
  author    = {Li, Weizhong and Jaroszewski, Lukasz and Godzik, Adam},
  journal   = {Bioinformatics},
  title     = {Tolerating some redundancy significantly speeds up clustering of large protein databases},
  year      = {2002},
  pages     = {77--82},
  volume    = {18},
  abstract  = {Motivation: Sequence clustering replaces groups of similar sequences in a database with single representatives. Clustering large protein databases like the NCBI Non-Redundant database (NR) using even the best currently available clustering algorithms is very time-consuming and only practical at relatively high sequence identity thresholds. Our previous program, CD-HI, clustered NR at 90% identity in ∼1 h and at 75% identity in ∼1 day on a 1 GHz Linux PC (Li et al. , Bioinformatics, 17, 282, 2001); however even faster clustering speed is needed because the size of protein databases are rapidly growing and many applications desire a lower attainable thresholds.Results: For our previous algorithm (CD-HI), we have employed short-word filters to speed up the clustering. In this paper, we show that tolerating some redundancy makes for more efficient use of these short-word filters and increases the program’s speed 100 times. Our new program implements this technique and clusters NR at 70% identity within 2 h, and at 50% identity in ∼5 days. Although some redundancy is present after clustering, our new program’s results only differ from our previous program’s by less than 0.4%.Availability: The program and its previous version are available at http://bioinformatics.burnham-inst.org/cd-hiContact: liwz@burnham-inst.org; adam@burnham-inst.org},
  doi       = {10.1093/bioinformatics/18.1.77},
  eprint    = {http://bioinformatics.oxfordjournals.org/content/18/1/77.full.pdf+html},
  file      = {2002_Li_77.pdf:by-author/L/Li/2002_Li_77.pdf:PDF},
  keywords  = {Algorithms; Bioinformatics; Cd-hit; Clustering; Index; Non Redundant Database; Sequence Alignment},
  owner     = {saulius},
  timestamp = {2013.04.10},
  creationdate = {2013-04-10T00:00:00},
  url       = {http://bioinformatics.oxfordjournals.org/content/18/1/77.abstract},
}

@Article{Li2001a,
  author    = {Li, Weizhong and Jaroszewski, Lukasz and Godzik, Adam},
  journal   = {Bioinformatics},
  title     = {Clustering of highly homologous sequences to reduce the size of large protein databases},
  year      = {2001},
  pages     = {282--283},
  volume    = {17},
  abstract  = {Summary: We present a fast and flexible program for clustering large protein databases at different sequence identity levels. It takes less than 2 h for the all-against-all sequence comparison and clustering of the non-redundant protein database of over 560000 sequences on a high-end PC. The output database, including only the representative sequences, can be used for more efficient and sensitive database searches.Availability: The program is available from http://bioinformatics.burnham-inst.org/cd-hi Contact: liwz@sdsc.edu or adam@burnham-inst.org},
  doi       = {10.1093/bioinformatics/17.3.282},
  eprint    = {http://bioinformatics.oxfordjournals.org/content/17/3/282.full.pdf+html},
  file      = {2001_Li_282.pdf:by-author/L/Li/2001_Li_282.pdf:PDF},
  keywords  = {Algorithms; Bioinformatics; Cd-hit; Clustering; Index; Non Redundant Database; Sequence Alignment},
  owner     = {saulius},
  timestamp = {2013.04.10},
  creationdate = {2013-04-10T00:00:00},
  url       = {http://bioinformatics.oxfordjournals.org/content/17/3/282.abstract},
}

@Article{Li2001,
  author    = {Xuehe Li and Corinne L. D. Gibb and Marie E. Kuebel and Bruce C. Gibb},
  journal   = {Tetrahedron},
  title     = {Two new ligands for carbonic anhydrase mimicry},
  year      = {2001},
  pages     = {1175--1182},
  volume    = {57},
  abstract  = {The syntheses of tris(2-nicotinic acid)methanol methyl ether 5 and tris(2-picolinic acid)methanol methyl ether 6, two tridentate ligands designed to also act as scaffolds for constructing chiral environments around their metal binding sites, is described. Improved yields for the essential lithiation±alkylation reactions that generate the trispyridyl core of these types of ligands are reported.},
  file      = {2001_Li_1175.pdf:by-author/L/Li/2001_Li_1175.pdf:PDF},
  groups    = {sg/inhibitors},
  keywords  = {Carbonic Anhydrases},
  owner     = {saulius},
  timestamp = {2012.11.20},
  creationdate = {2012-11-20T00:00:00},
}

@Article{Li2009,
  author    = {Yunqi Li and Ambrish Roy and Yang Zhang},
  journal   = {PLoS ONE},
  title     = {{HAAD}: a quick algorithm for accurate prediction of hydrogen atoms in protein structures},
  year      = {2009},
  pages     = {e6701},
  volume    = {4},
  abstract  = {Hydrogen constitutes nearly half of all atoms in proteins and their positions are essential for analyzing hydrogen-bonding interactions and refining atomic-level structures. However, most protein structures determined by experiments or computer prediction lack hydrogen coordinates. We present a new algorithm, HAAD, to predict the positions of hydrogen atoms based on the positions of heavy atoms. The algorithm is built on the basic rules of orbital hybridization followed by the optimization of steric repulsion and electrostatic interactions. We tested the algorithm using three independent data sets: ultra-high-resolution X-ray structures, structures determined by neutron diffraction, and NOE proton-proton distances. Compared with the widely used programs CHARMM and REDUCE, HAAD has a significantly higher accuracy, with the average RMSD of the predicted hydrogen atoms to the X-ray and neutron diffraction structures decreased by 26% and 11%, respectively. Furthermore, hydrogen atoms placed by HAAD have more matches with the NOE restraints and fewer clashes with heavy atoms. The average CPU cost by HAAD is 18 and 8 times lower than that of CHARMM and REDUCE, respectively. The significant advantage of HAAD in both the accuracy and the speed of the hydrogen additions should make HAAD a useful tool for the detailed study of protein structure and function. Both an executable and the source code of HAAD are freely available at http://zhang.bioinformatics.ku.edu/HAAD.},
  doi       = {10.1371/journal.pone.0006701},
  file      = {2009_Li_e6701.pdf:by-author/L/Li/2009_Li_e6701.pdf:PDF},
  keywords  = {Algorithms; Bioinformatics; Geometry},
  owner     = {alexey},
  pmcid     = {PMC2724740},
  pmid      = {19693270},
  timestamp = {2012.07.18},
  creationdate = {2012-07-18T00:00:00},
}

@Article{Liebeschuetz2012,
  author    = {Liebeschuetz, John and Hennemann, Jana and Olsson, Tjelvar and Groom, Colin R.},
  journal   = {Journal of Computer-Aided Molecular Design},
  title     = {The good, the bad and the twisted: a survey of ligand geometry in protein crystal structures},
  year      = {2012},
  issn      = {1573-4951},
  month     = {Jan},
  number    = {2},
  pages     = {169–183},
  volume    = {26},
  abstract  = {The protein databank now contains the structures of over 11,000 ligands bound to proteins. These structures are invaluable in applied areas such as structure-based drug design, but are also the substrate for understanding the energetics of intermolecular interactions with proteins. Despite their obvious importance, the careful analysis of ligands bound to protein structures lags behind the analysis of the protein structures themselves. We present an analysis of the geometry of ligands bound to proteins and highlight the role of small molecule crystal structures in enabling molecular modellers to critically evaluate a ligand model’s quality and investigate protein-induced strain.},
  doi       = {10.1007/s10822-011-9538-6},
  file      = {2012_Liebeschuetz_169.pdf:by-author/L/Liebeschuetz/2012_Liebeschuetz_169.pdf:PDF},
  groups    = {sg/Crystallography, am/Crystallography, am/Data quality},
  owner     = {andrius},
  publisher = {Springer Nature},
  timestamp = {2016.12.28},
  creationdate = {2016-12-28T00:00:00},
  url       = {http://dx.doi.org/10.1007/s10822-011-9538-6},
}

@Article{Liedl2005,
  author    = {Liedl, Tim and Simmel, Friedrich C.},
  journal   = {Nano Letters},
  title     = {Switching the conformation of a {DNA} molecule with a chemical oscillator},
  year      = {2005},
  issn      = {1530-6984},
  pages     = {1894--1898},
  volume    = {5},
  abstract  = {pH oscillations generated by a nonequilibrium chemical reaction are used to switch a pH-sensitive DNA structure between two distinct conformations. The utilization of a chemical oscillator represents a novel method for achieving autonomous motion in molecular devices. The oscillatory reaction is a variant of the Landolt reaction and produces pH variations in the range between pH 5 and 7. In this range, a cytosine-rich DNA strand can be switched between a random coil conformation and the folded i-motif structure. The conformational changes are monitored simultaneously with the pH value in fluorescence-resonance energy-transfer experiments.},
  doi       = {10.1021/nl051180j},
  file      = {Liedl and Simmel - 2005 - Switching the Conformation of a DNA Molecule with .pdf:by-author/L/Liedl/2005_Liedl_1894.pdf:application/pdf;ACS Full Text Snapshot:by-author/L/Liedl/2005_Liedl_1894.html:text/html},
  groups    = {sg/biomolecular},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://dx.doi.org/10.1021/nl051180j},
  urldate   = {2015-08-05},
}

@Article{Lifshitz2000,
  author    = {Lifshitz},
  title     = {The Definition of Quasicrystals},
  year      = {2000},
  abstract  = {It is argued that the definition of quasicrystals should not include the requirement that they possess an axis of symmetry that is forbidden in periodic crystals. The term “quasicrystal” should simply be regarded as an abbreviation for “quasiperiodic crystal,” possibly with two provisos, as discussed below. The argument is supported by theoretical as well as experimental examples of quasicrystals without any forbidden symmetry.},
  file      = {:by-author/L/Lifshitz/2000_Lifshitz.pdf:PDF},
  keywords  = {Quasicrystals},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Lifshitz2003,
  author    = {Ron Lifshitz},
  journal   = {Foundations of Physics},
  title     = {Quasicrystals: A Matter of Definition},
  year      = {2003},
  pages     = {1703--1711},
  volume    = {33},
  abstract  = {It is argued that the prevailing definition of quasicrystals, requiring them to contain an axis of symmetry that is forbidden in periodic crystals, is inadequate. This definition is too restrictive in that it excludes an important and interesting collection of structures that exhibit all the well-known properties of quasicrystals without possessing any forbidden symmetries.},
  file      = {:by-author/L/Lifshitz/2003_Lifshitz_1703.pdf:PDF},
  keywords  = {Incommensurate Crystals; Quasicrystals; Quasiperiodic Crystals; Symmetry},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Liger-Belair2008,
  author    = {Liger-Belair, Gérard and Polidori, Guillaume and Jeandet, Philippe},
  journal   = {Chemical Society reviews},
  title     = {Recent advances in the science of champagne bubbles.},
  year      = {2008},
  pages     = {2490--511},
  volume    = {37},
  abstract  = {The so-called effervescence process, which enlivens champagne and sparkling wines tasting, is the result of the fine interplay between CO(2)-dissolved gas molecules, tiny air pockets trapped within microscopic particles during the pouring process, and some liquid properties. This critical review summarizes recent advances obtained during the past decade concerning the physicochemical processes behind the nucleation, rise, and burst of bubbles found in glasses poured with champagne and sparkling wines. Those phenomena observed in close-up through high-speed photography are often visually appealing. Let's hope that your enjoyment of champagne will be enhanced after reading this fully illustrated review dedicated to the deep beauties of nature often hidden behind many everyday phenomena (51 references).},
  file      = {:by-author/L/Liger-Belair/2008_Liger-Belair_2490.pdf:PDF},
  keywords  = {Chemistry},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@Article{Liljeroth2007,
  author    = {Liljeroth, Peter and Repp, Jascha and Meyer, Gerhard},
  journal   = {Science},
  title     = {Current-induced hydrogen tautomerization and conductance switching of naphthalocyanine molecules},
  year      = {2007},
  issn      = {0036-8075, 1095-9203},
  pages     = {1203--1206},
  volume    = {317},
  abstract  = {The bistability in the position of the two hydrogen atoms in the inner cavity of single free-base naphthalocyanine molecules constitutes a two-level system that was manipulated and probed by low-temperature scanning tunneling microscopy. When adsorbed on an ultrathin insulating film, the molecules can be switched in a controlled fashion between the two states by excitation induced by the inelastic tunneling current. The tautomerization reaction can be probed by resonant tunneling through the molecule and is expressed as considerable changes in the conductivity of the molecule. We also demonstrated a coupling of the switching process so that the charge injection in one molecule induced tautomerization in an adjacent molecule.},
  doi       = {10.1126/science.1144366},
  file      = {Full Text PDF:by-author/L/Liljeroth/2007_Liljeroth_1203.pdf:application/pdf;Snapshot:by-author/L/Liljeroth/2007_Liljeroth_1203.html:text/html},
  groups    = {sg/chemical},
  language  = {en},
  owner     = {saulius},
  pmid      = {17761878},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://www.sciencemag.org/content/317/5842/1203},
  urldate   = {2015-08-06},
}

@Article{Lim2017,
  author    = {Kwang Soo Lim and So Yeon Jeong and Dong Won Kang and Jeong Hwa Song and Hyuna Jo and Woo Ram Lee and Won Ju Phang and Dohyun Moon and Chang Seop Hong},
  journal   = {Chemistry - A European Journal},
  title     = {Luminescent Metal-Organic Framework Sensor: Exceptional Cd2$\mathplus$ Turn-On Detection and First In Situ Visualization of Cd2$\mathplus$ Ion Diffusion into a Crystal},
  year      = {2017},
  month     = {jan},
  doi       = {10.1002/chem.201604252},
  file      = {:by-author/L/Lim/2017_Lim.pdf:PDF},
  groups    = {sg/MOF, sg/MOFs, am/MOFs},
  keywords  = {Ligand Sythesis},
  owner     = {saulius},
  publisher = {Wiley-Blackwell},
  timestamp = {2017.01.31},
  creationdate = {2017-01-31T00:00:00},
  url       = {https://doi.org/10.1002%2Fchem.201604252},
}

@Article{Limbach1994,
  author    = {Patrick A. Limbach and Pamela F. Crain and James A. McCloskey},
  journal   = {Nucleic Acids Research},
  title     = {Summary: the modified nucleosides of RNA},
  year      = {1994},
  pages     = {2183--2196},
  volume    = {22},
  abstract  = {A comprehensive listing is made of posttranscriptionally modified nucleosides from RNA reported in the literature through mid-1994. Included are chemical structures, common names, symbols, Chemical Abstracts registry numbers (for ribonucleoside and corresponding base), Chemical Abstracts Index Name, phylogenetic sources, and initial literature citations for structural characterization or occurrence, and for chemical synthesis. The listing is categorized by type of RNA: tRNA, rRNA, mRNA, snRNA, and other RNAs. A total of 93 different modified nucleosides have been reported in RNA, with the largest number and greatest structural diversity in tRNA, 79; and 28 in rRNA, 12 in mRNA, 11 in snRNA and 3 in other small RNAs.},
  doi       = {10.1093/nar/22.12.2183},
  file      = {1994_Limbach_2183.pdf:by-author/L/Limbach/1994_Limbach_2183.pdf:PDF},
  owner     = {saulius},
  timestamp = {2013.09.26},
  creationdate = {2013-09-26T00:00:00},
}

@Article{Lin2002,
  author    = {Chun-Yuan Lin and Jen-Shiuh Liu and Yeh-Ching Chung},
  journal   = {IEEE Transactions On Computers},
  title     = {Efficient Representation Scheme for Multidimensional Array Operations},
  year      = {2002},
  pages     = {327--345},
  volume    = {51},
  abstract  = {Array operations are used in a large number of important scientific codes, such as molecular dynamics, finite element methods, climate modeling, etc. To implement these array operations efficiently, many methods have been proposed in the literature. However, the majority of these methods are focused on the two-dimensional arrays. When extended to higher dimensional arrays, these methods usually do not perform well. Hence, designing efficient algorithms for multidimensional array operations becomes an important issue. In this paper, we propose a new scheme, extended Karnaugh map representation (EKMR), for the multidimensional array representation. The main idea of the EKMR scheme is to represent a multidimensional array by a set of two-dimensional arrays. Hence, efficient algorithm design for multidimensional array operations becomes less complicated. To evaluate the proposed scheme, we design efficient algorithms for multidimensional array operations, matrix-matrix addition/subtraction and matrix-matrix multiplications, based on the EKMR and the traditional matrix representation (TMR) schemes. Both theoretical analysis and experimental test for these array operations were conducted. Since Fortran 90 provides a rich set of intrinsic functions for multidimensional array operations, in the experimental test, we also compare the performance of intrinsic functions provided by the Fortran 90 compiler and those based on the EKMR scheme. The experimental results show that the algorithms based on the EKMR scheme outperform those based on the TMR scheme and those provided by the Fortran 90 compiler.},
  file      = {:by-author/L/Lin/2002_Lin_327.pdf:PDF},
  owner     = {andrius},
  timestamp = {2013.02.08},
  creationdate = {2013-02-08T00:00:00},
}

@InBook{Lin2016,
  author    = {Lin, Jimmy and Crane, Matt and Trotman, Andrew and Callan, Jamie and Chattopadhyaya, Ishan and Foley, John and Ingersoll, Grant and Macdonald, Craig and Vigna, Sebastiano},
  editor    = {Ferro, Nicola and Crestani, Fabio and Moens, Marie-Francine and Mothe, Josiane and Silvestri, Fabrizio and Di Nunzio, Giorgio Maria and Hauff, Claudia and Silvello, Gianmaria},
  pages     = {408--420},
  publisher = {Springer International Publishing},
  title     = {Toward Reproducible Baselines: The Open-Source IR Reproducibility Challenge},
  year      = {2016},
  address   = {Cham},
  isbn      = {978-3-319-30671-1},
  abstract  = {The Open-Source IR Reproducibility Challenge brought together developers of open-source search engines to provide reproducible baselines of their systems in a common environment on Amazon EC2. The product is a repository that contains all code necessary to generate competitive ad hoc retrieval baselines, such that with a single script, anyone with a copy of the collection can reproduce the submitted runs. Our vision is that these results would serve as widely accessible points of comparison in future IR research. This project represents an ongoing effort, but we describe the first phase of the challenge that was organized as part of a workshop at SIGIR 2015. We have succeeded modestly so far, achieving our main goals on the Gov2 collection with seven open-source search engines. In this paper, we describe our methodology, share experimental results, and discuss lessons learned as well as next steps.},
  booktitle = {Advances in Information Retrieval: 38th European Conference on IR Research, ECIR 2016, Padua, Italy, March 20--23, 2016. Proceedings},
  doi       = {10.1007/978-3-319-30671-1_30},
  file      = {2016_Lin_408.pdf:by-author/L/Lin/2016_Lin_408.pdf:PDF},
  keywords  = {Computer Science (CS); Data Management; Reproducible Research},
  owner     = {saulius},
  timestamp = {2016.11.21},
  creationdate = {2016-11-21T00:00:00},
  url       = {http://dx.doi.org/10.1007/978-3-319-30671-1_30},
}

@Manuscript{Lin2016a,
  author    = {Lin, Jimmy and Crane, Matt and Trotman, Andrew and Callan, Jamie and Chattopadhyaya, Ishan and Foley, John and Ingersoll, Grant and Macdonald, Craig and Vigna, Sebastiano},
  title     = {Toward Reproducible Baselines: The Open-Source IR Reproducibility Challenge},
  year      = {2016},
  keywords  = {Computer Science (CS); Data Management; Reproducible Research},
  url       = {http://www.cs.cmu.edu/~callan/Papers/ecir16-jimmylin.pdf},
  abstract  = {The Open-Source IR Reproducibility Challenge brought together developers of open-source search engines to provide reproducible baselines of their systems in a common environment on Amazon EC2. The product is a repository that contains all code necessary to generate competitive ad hoc retrieval baselines, such that with a single script, anyone with a copy of the collection can reproduce the submitted runs. Our vision is that these results would serve as widely accessible points of comparison in future IR research. This project represents an ongoing effort, but we describe the first phase of the challenge that was organized as part of a workshop at SIGIR 2015. We have succeeded modestly so far, achieving our main goals on the Gov2 collection with seven open-source search engines. In this paper, we describe our methodology, share experimental results, and discuss lessons learned as well as next steps.},
  file      = {2016_Lin.pdf:by-author/L/Lin/2016_Lin.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.11.21},
  creationdate = {2016-11-21T00:00:00},
}

@TechReport{Lin2013,
  author    = {Meng-Yun Lin},
  title     = {Bayesian Statistics},
  year      = {2013},
  file      = {Meng-Yun Lin - 2013 - Bayesian Statistics.pdf:by-author/L/Lin/2013_Lin.pdf:application/pdf},
  groups    = {sg/Clinical Trials},
  owner     = {saulius},
  timestamp = {2015.12.14},
  creationdate = {2015-12-14T00:00:00},
  url       = {http://www.bu.edu/sph/files/2014/05/Bayesian-Statistics_final_20140416.pdf},
  urldate   = {2015-12-12},
}

@Article{Lin2006,
  author    = {Lin, Po-Chiao and Ueng, Shau-Hua and Tseng, Mei-Chun and Ko, Jia-Ling and Huang, Kuo-Ting and Yu, Sheng-Chieh and Adak, Avijit Kumar and Chen, Yu-Ju and Lin, Chun-Cheng},
  journal   = {Angewandte Chemie (International ed. in English)},
  title     = {Site-specific protein modification through Cu(I)-catalyzed 1,2,3-triazole formation and its implementation in protein microarray fabrication.},
  year      = {2006},
  pages     = {4286--90},
  volume    = {45},
  file      = {:by-author/L/Lin/2006_Lin_4286.pdf:PDF},
  keywords  = {Bioconjugation},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@Article{Lin2011,
  author    = {Sheng Lin and Yong-Bin Kim and Fabrizio Lombardi},
  journal   = {IEEE transactions on nanotechnology},
  title     = {{CNTFET}-based design of ternary logic gates and arithmetic circuits},
  year      = {2011},
  month     = {March},
  number    = {2},
  volume    = {10},
  abstract  = {This paper presents a novel design of ternary logic gates using carbon nanotube (CNT) FETs (CNTFETs). Ternary logic is a promising alternative to the conventional binary logic design technique, since it is possible to accomplish simplicity and energy efficiency in modern digital design due to the reduced cir- cuit overhead such as interconnects and chip area. A resistive-load CNTFET-based ternary logic design has been proposed to imple- ment ternary logic based on CNTFET. In this paper, a novel design technique for ternary logic gates based on CNTFETs is proposed and compared with the existing resistive-load CNTFET logic gate designs. Especially, the proposed ternary logic gate design tech- nique combined with the conventional binary logic gate design technique provides an excellent speed and power consumption characteristics in datapath circuit such as full adder and multiplier. Extensive simulation results using SPICE are reported to show that the proposed ternary logic gates consume significantly lower power and delay than the previous resistive-load CNTFET gates imple- mentations. In realistic circuit application, the utilization of the proposed ternary gates combined with binary gates results in over 90% reductions in terms of the power delay product.},
  file      = {:by-author/L/Lin/2011_Lin.pdf:PDF},
  keywords  = {Carbon Nanotube (CNT) FET (CNTFET); Computer Science (CS); Logic Circuits; Multiple-valued Logic (MVL) Design; Ternary Logic},
  owner     = {saulius},
  timestamp = {2015.03.03},
  creationdate = {2015-03-03T00:00:00},
}

@Manuscript{Lin2009,
  author    = {Sheng Lin and Yong-Bin Kim and Fabrizio Lombardi},
  title     = {CNTFET-Based Design of Ternary Logic Gates and Arithmetic Circuits},
  year      = {2009},
  keywords  = {Carbon Nanotube Field Effect Transistor; Computer Science (CS); Logic Circuits; Multiple-valued Logic Design; Ternary Logic},
  abstract  = {This paper presents a novel design of ternary logic gates using carbon nanotube FETs (CNTFETs). Ternary logic is a promising alternative to the conventional binary logic design technique since it is possible to accomplish simplicity and energy efficiency in modern digital design due to the reduced circuit overhead such as interconnects and chip area. A resistive-load CNTFET-based ternary logic design has been proposed to implement ternary logic based on CNTFET. In this paper, a novel design technique for ternary logic gates based on CNTFETs is proposed and compared with the existing resistive load CNTFET logic gate designs. Especially, the proposed ternary logic gate design technique combined with the conventional binary logic gate design technique provides an excellent speed and power consumption characteristics in datapath circuit such as full adder and multiplier. Extensive simulation results using SPICE are reported to show that the proposed ternary logic gates consume significantly lower power and delay than the previous resistive load CNTFET gates implementations. In realistic circuit application, the utilization of the proposed ternary gates combined with binary gates results in over 90% reductions in terms of the power delay product.},
  file      = {:by-author/L/Lin/2009_Lin_manuscript.pdf:PDF},
  owner     = {saulius},
  pages     = {manuscript},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Manuscript{Lin2009a,
  author    = {Sheng Lin and Yong-Bin Kim and Fabrizio Lombardi},
  title     = {A novel {CNTFET}-based ternary logic gate design},
  year      = {2009},
  keywords  = {Computer Science (CS); Logic-circuits; Ternary},
  abstract  = {This paper presents a novel design of ternary logic inverters using carbon nanotube FETs (CNTFETs). Multiple-valued logic (MVL) circuits have attracted substantial interest due to the capability of increasing information content per unit area. In the past extensive design techniques for MVL circuits (especially ternary logic inverters) have been proposed for implementation in CMOS technology. In CNTFET device, the threshold voltage of the transistor can be controlled by controlling the chirality vector (i.e. the diameter); in this paper this feature is exploited to design ternary logic inverters. New designs are proposed and compared with existing CNTFET-based designs. Extensive simulation results using SPICE demonstrate that power delay product is improved by 300% comparing to the conventional ternary gate design.},
  file      = {:by-author/L/Lin/2009_Lin.pdf:},
  owner     = {saulius},
  timestamp = {2015.03.03},
  creationdate = {2015-03-03T00:00:00},
}

@Article{Lin2016b,
  author    = {Shaoyang Lin and Yuliana Pineda-Galvan and William A. Maza and Charity C. Epley and Jie Zhu and Matthew C. Kessinger and Yulia Pushkar and Amanda J. Morris},
  journal   = {{ChemSusChem}},
  title     = {Electrochemical Water Oxidation by a Catalyst-Modified Metal-Organic Framework Thin Film},
  year      = {2016},
  month     = {dec},
  doi       = {10.1002/cssc.201601181},
  file      = {Lin2016.pdf:by-author/L/Lin/2016_Lin_a.pdf:PDF},
  groups    = {sg/MOF, sg/MOFs, am/MOFs},
  owner     = {saulius},
  publisher = {Wiley-Blackwell},
  timestamp = {2017.01.31},
  creationdate = {2017-01-31T00:00:00},
  url       = {https://doi.org/10.1002%2Fcssc.201601181},
}

@Article{Lin1996,
  author    = {Shu-Kun Lin},
  journal   = {Electronic Journal of Theoretical Chemistry},
  title     = {Gibbs paradox of entropy of mixing: experimental facts and its and rejection and the theoretical consequences},
  year      = {1996},
  pages     = {135--150},
  volume    = {1},
  abstract  = {Gibbs paradox statement of entropy of mixing has been regarded as the theoretical foundation of statistical mechanics, quantum theory and biophysics. A large number of relevant chemical and physical observations show that the Gibbs paradox statement is false.We also disprove the Gibbs paradox statement through consideration of symmetry, similarity, entropy additivity and the defined property of ideal gas. A theory with its basic principles opposingGibbs paradox statementemerges: entropy ofmixing increases continuouslywith the increase in similarity of the relevant properties. Many outstanding problems, such as the validity of Pauling’s resonance theory and the biophysical problem of protein folding and the related hydrophobic effect, etc. can be considered on a new theoretical basis. A new energy transduction mechanism, the deformation, is also briefly discussed.},
  file      = {:by-author/L/Lin/1996_Lin_135.pdf:PDF},
  keywords  = {Distinguishability; Entropy; Entropy of Mixing; Gibbs Paradox; Mixing of Quantum States; Similarity; Symmetry},
  owner     = {saulius},
  timestamp = {2012.10.02},
  creationdate = {2012-10-02T00:00:00},
}

@Article{Lin2001,
  author    = {Lin, T. C. and Wang, C. X. and Joyce, C. M. and Konigsberg, W. H.},
  journal   = {Biochemistry},
  title     = {3'-5' Exonucleolytic activity of DNA polymerases: structural features that allow kinetic discrimination between ribo- and deoxyribonucleotide residues.},
  year      = {2001},
  pages     = {8749--55},
  volume    = {40},
  abstract  = {We have determined rates for the excision of nucleotides from the 3' termini of chimeric DNA-RNA oligonucleotides using the Klenow fragment (KF) and two other DNA polymerases, from phages T4 and T7. For these studies, we synthesized DNA-RNA chimeric oligonucleotides with RNA residues in defined positions. When a ribonucleotide residue was placed at the 3' terminus, all three DNA polymerases removed it at the same rate as they did for substrates composed solely of deoxynucleotide residues. There was a decrease in the excision rate, however, when a ribonucleotide residue was located at the second or third position from the 3' terminus. When both the second and third positions were occupied by ribonucleotide residues, the excision rate for the 3' terminal nucleotide was reduced even further and was almost identical to the rate observed when the DNA polymerases encountered single-stranded RNA. The magnitude of the effect of ribonucleotide residues on the excision rate was lower when Mn(2+) replaced Mg(2+) as the essential divalent cation. Two KF mutations, Y423A and N420A, selectively affected the excision rates for the chimeric substrates. Specifically, Y423A totally abolished the rate reduction when there was a single ribonucleotide residue immediately preceding the 3' terminus, whereas N420A diminished, but did not eliminate, the rate reduction relative to that of wild-type KF when the single ribonucleotide residue occupied either the second or third position from the 3' terminus. These results are consistent with the structure of a KF-ss DNA complex from which it can be deduced, by modeling, that a 2' OH group on the second sugar from the 3' terminus would sterically clash with the Tyr 423 side chain, and a 2' OH group on the third sugar would clash with the side chain of Asn 420. The corresponding mutations in T4 DNA polymerase did not affect the rate of hydrolysis of the chimeric oligonucleotides. Thus, there appears to be a major difference in the kinetic behavior of KF and T4 DNA polymerase with respect to the exonuclease reaction. These results are discussed with respect to their possible biological relevance to DNA replication.},
  file      = {:by-author/L/Lin/2001_Lin_8749.pdf:PDF},
  keywords  = {{gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@InBook{Lin2004,
  author    = {Xiaodong Lin and Yu Zhu},
  editor    = {David Banks and Frederick R. McMorris and Phipps Arabie and Wolfgang Gaul},
  pages     = {259--268},
  publisher = {Springer},
  title     = {Degenerate {E}xpectation-{M}aximization Algorithm for Local Dimension Reduction},
  year      = {2004},
  booktitle = {Classification, Clustering, and Data Mining Applications},
  doi       = {10.1007/978-3-642-17103-1_25},
  file      = {:by-author/L/Lin/2004_Lin.pdf:PDF},
  keywords  = {Expectation Maximisation},
  owner     = {andrius},
  timestamp = {2013.02.13},
  creationdate = {2013-02-13T00:00:00},
}

@Article{Lincoln2009,
  author    = {Lincoln, Tracey A and Joyce, Gerald F},
  journal   = {Science (New York, N.Y.)},
  title     = {Self-sustained replication of an RNA enzyme.},
  year      = {2009},
  pages     = {1229--32},
  volume    = {323},
  file      = {2009_Lincoln_1229.pdf:by-author/L/Lincoln/2009_Lincoln_1229.pdf:PDF},
  keywords  = {Ribozymes},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@InProceedings{Lindahl2003,
  author    = {Lindahl, Tobias and Sagonas, Konstantinos},
  booktitle = {Proceedings of the 14th international conference on Implementation of functional languages},
  title     = {Unboxed compilation of floating point arithmetic in a dynamically typed language environment},
  year      = {2003},
  address   = {Berlin, Heidelberg},
  pages     = {134--149},
  publisher = {Springer-Verlag},
  series    = {IFL'02},
  file      = {:by-author/L/Lindahl/2003_Lindahl.pdf:PDF},
  isbn      = {3-540-40190-3},
  location  = {Madrid, Spain},
  numpages  = {16},
  owner     = {andrius},
  timestamp = {2013.02.14},
  creationdate = {2013-02-14T00:00:00},
}

@Presentation{Lindeman2010,
  author    = {Jeffrey A. Lindeman},
  title     = {Patenting crystalline forms of pharmaceuticals},
  year      = {2010},
  file      = {:by-author/L/Lindeman/2010_Lindeman.pdf:PDF},
  keywords  = {Drug Design; Patents; Polymorphs},
  owner     = {saulius},
  timestamp = {2014.11.06},
  creationdate = {2014-11-06T00:00:00},
  url       = {http://www.icdd.com/ppxrd/09/presentations/2010-ppxrd-Lindeman.pdf},
}

@Article{Linding2003,
  author    = {Linding, Rune and Russell, Robert B. and Neduva, Victor and Gibson, Toby J.},
  journal   = {Nucleic acids research},
  title     = {{GlobPlot}: Exploring protein sequences for globularity and disorder},
  year      = {2003},
  pages     = {3701--3708},
  volume    = {31},
  abstract  = {A major challenge in the proteomics and structural genomics era is to predict protein structure and function, including identification of those proteins that are partially or wholly unstructured. Non-globular sequence segments often contain short linear peptide motifs (e.g. SH3-binding sites) which are important for protein function. We present here a new tool for discovery of such unstructured, or disordered regions within proteins. GlobPlot (http://globplot.embl.de) is a web service that allows the user to plot the tendency within the query protein for order/globularity and disorder. We show examples with known proteins where it successfully identifies inter-domain segments containing linear motifs, and also apparently ordered regions that do not contain any recognised domain. GlobPlot may be useful in domain hunting efforts. The plots indicate that instances of known domains may often contain additional N- or C-terminal segments that appear ordered. Thus GlobPlot may be of use in the design of constructs corresponding to globular proteins, as needed for many biochemical studies, particularly structural biology. GlobPlot has a pipeline interface--GlobPipe--for the advanced user to do whole proteome analysis. GlobPlot can also be used as a generic infrastructure package for graphical displaying of any possible propensity.},
  doi       = {10.1093/nar/gkg519},
  file      = {:by-author/L/Linding/2003_Linding_3701.pdf:PDF},
  keywords  = {Intrinsically Unfolded Prot; Predicting},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Lindley1990,
  author    = {Dennis V. Lindley},
  journal   = {Statistical Science},
  title     = {The 1988 Wald Memory Lectures: The Present Position in Bayesian Statistics},
  year      = {1990},
  pages     = {44--89},
  volume    = {5},
  file      = {Lindley1990.pdf:by-author/L/Lindley/1990_Lindley_44.pdf:PDF},
  groups    = {sg/Bayesian},
  keywords  = {Bayesian Statistics},
  owner     = {saulius},
  timestamp = {2011.10.13},
  creationdate = {2011-10-13T00:00:00},
}

@Article{Lindley1987,
  author    = {Dennis V. Lindley},
  journal   = {Statistical Science},
  title     = {The Probability Approach to the Treatment of Uncertainty in Artificial Intelligence and Expert Systems},
  year      = {1987},
  pages     = {17--24},
  volume    = {2},
  file      = {Lindley1987.pdf:by-author/L/Lindley/1987_Lindley_17.pdf:PDF},
  groups    = {sg/Bayesian},
  keywords  = {Bayesian Statistics},
  owner     = {saulius},
  timestamp = {2011.10.13},
  creationdate = {2011-10-13T00:00:00},
}

@Article{Lindskog1997,
  author    = {Lindskog, S},
  journal   = {Pharmacology \&amp; therapeutics},
  title     = {Structure and mechanism of carbonic anhydrase.},
  year      = {1997},
  pages     = {1--20},
  volume    = {74},
  file      = {1997_Lindskog_1.pdf:by-author/L/Lindskog/1997_Lindskog_1.pdf:PDF},
  groups    = {sg/reviews},
  keywords  = {Carbonic Anhydrases},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Link2003,
  author    = {Link, A. James and Tirrell, David A.},
  journal   = {Journal of the American Chemical Society},
  title     = {Cell Surface Labeling of Escherichia coli via Copper(I)-Catalyzed [3+2] Cycloaddition},
  year      = {2003},
  pages     = {11164--11165},
  volume    = {125},
  abstract  = {Labeling of the cell surface of Escherichia coli was accomplished by expression of a recombinant outer membrane protein, OmpC, in the presence of the unnatural amino acid azidohomoalanine, which acts as a methionine surrogate. The surface-exposed azide moieties of whole cells were biotinylated via Cu(1)-catalyzed [3+2] azide-alkyne cycloaddition. The specificity of labeling of both wild-type OmpC and a mutant containing additional methionine sites for azidohomoalanine incorporation was confirmed by Western blotting. Flow cytometry was performed to examine the specificity of the labeling. Cells that express the mutant form of OmpC in the presence of azidohomoalanine, which were biotinylated and stained with fluorescent avidin, exhibit a mean fluorescence 10-fold higher than the background. Incorporation of an unnatural amino acid can thus be determined on a single-cell basis.},
  doi       = {10.1021/ja036765z},
  file      = {:by-author/L/Link/2003_Link_11164.pdf:PDF},
  keywords  = {Bioconjugation},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
  url       = {http://pubs.acs.org/doi/abs/10.1021/ja036765z},
}

@Article{Link2004,
  author    = {Link, A. James and Vink, Mandy K. S. and Tirrell, David A.},
  journal   = {Journal of the American Chemical Society},
  title     = {Presentation and detection of azide functionality in bacterial cell surface proteins.},
  year      = {2004},
  pages     = {10598--602},
  volume    = {126},
  abstract  = {An improved protocol for copper-catalyzed triazole formation on the bacterial cell surface is described. Addition of highly pure CuBr to cells treated with azidohomoalanine (2) leads to ca. 10-fold more extensive cell surface labeling than previously observed. This highly active catalyst allows detection of the methionine analogues azidoalanine (1), azidonorvaline (3), and azidonorleucine (4) in cell surface proteins. Azidoalanine was previously believed to be silent with regard to the cellular protein synthesis machinery.},
  file      = {:by-author/L/Link/2004_Link_10598.pdf:PDF},
  keywords  = {Bioconjugation},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@Article{Lintner2010,
  author    = {Nathanael G. Lintner and Kenneth A. Frankel and Susan E. Tsutakawa and Donald L. Alsbury and Valérie Copié and Mark J. Young and John A. Tainer and C. Martin Lawrence},
  journal   = {Journal of Molecular Biology},
  title     = {The Structure of the {CRISPR}-Associated Protein {Csa3} Provides Insight into the Regulation of the {CRISPR/Cas} System},
  year      = {2010},
  pages     = {939--955},
  volume    = {405},
  doi       = {10.1016/j.jmb.2010.11.019},
  file      = {:by-author/L/Lintner/2010_Lintner_339.pdf:PDF},
  groups    = {sg/CRISPR-Cas},
  keywords  = {CRISPR},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Lintner2011,
  author    = {Lintner, Nathanael G. and Kerou, Melina and Brumfield, Susan K. and Graham, Shirley and Liu, Huanting and Naismith, James H. and Sdano, Matthew and Peng, Nan and She, Qunxin and Copie, Valerie and Young, Mark J. and White, Malcolm F. and Lawrence, C. Martin},
  journal   = {Journal of Biological Chemistry},
  title     = {Structural and Functional Characterization of an Archaeal Clustered Regularly Interspaced Short Palindromic Repeat ({CRISPR})-associated Complex for Antiviral Defense ({CASCADE})},
  year      = {2011},
  pages     = {21643–21656},
  volume    = {286},
  doi       = {10.1074/jbc.M111.238485},
  file      = {2011_Lintner_21643.pdf:by-author/L/Lintner/2011_Lintner_21643.pdf:PDF},
  groups    = {sg/CRISPR-Cas},
  keywords  = {CRISPR; Cascade},
  owner     = {em},
  timestamp = {2013.01.07},
  creationdate = {2013-01-07T00:00:00},
}

@Manuscript{Linton1990,
  author    = {Linton, S. A.},
  title     = {Constructing Matrix Representations of Finitely Presented Groups},
  year      = {1990},
  abstract  = {The Todd-Coxeter coset enumeration algorithm is one of the most powerful tools of computational group theory. It may be viewed as a means of constructing permutation representations of nitely presented groups. In this paper we present an analogous algorithm for directly constructing matrix representations over many elds. In fact the algorithm is more general than this, and can be used to construct matrix representations of nitely generated algebras. The algorithm (with some restrictions) has been implemented as a C program and some results obtained with this implementation are described.},
  file      = {:by-author/L/Linton/1990_Linton.pdf:PDF},
  owner     = {saulius},
  timestamp = {2013.03.22},
  creationdate = {2013-03-22T00:00:00},
}

@Article{Lionnet2007,
  author    = {Lionnet, Timothée and Spiering, Michelle M. and Benkovic, Stephen J. and Bensimon, David and Croquette, Vincent},
  journal   = {Proceedings of the National Academy of Sciences of the United States of America},
  title     = {Real-time observation of bacteriophage T4 gp41 helicase reveals an unwinding mechanism.},
  year      = {2007},
  pages     = {19790--5},
  volume    = {104},
  abstract  = {Helicases are enzymes that couple ATP hydrolysis to the unwinding of double-stranded (ds) nucleic acids. The bacteriophage T4 helicase (gp41) is a hexameric helicase that promotes DNA replication within a highly coordinated protein complex termed the replisome. Despite recent progress, the gp41 unwinding mechanism and regulatory interactions within the replisome remain unclear. Here we use a single tethered DNA hairpin as a real-time reporter of gp41-mediated dsDNA unwinding and single-stranded (ss) DNA translocation with 3-base pair (bp) resolution. Although gp41 translocates on ssDNA as fast as the in vivo replication fork ( approximately 400 bp/s), its unwinding rate extrapolated to zero force is much slower ( approximately 30 bp/s). Together, our results have two implications: first, gp41 unwinds DNA through a passive mechanism; second, this weak helicase cannot efficiently unwind the T4 genome alone. Our results suggest that important regulations occur within the replisome to achieve rapid and processive replication.},
  file      = {:by-author/L/Lionnet/2007_Lionnet_19790.pdf:PDF},
  keywords  = {{gp41}; {gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Lipkin2004,
  author    = {Lipkin, H. J.},
  journal   = {eprint arXiv:cond-mat/0405023},
  title     = {Physics of Debye-Waller Factors},
  year      = {2004},
  month     = may,
  pages     = {0405023v1},
  abstract  = {This note has no new results and is therefore not intended to be submitted to a "research" journal in the foreseeable future, but to be available to the numerous individuals who are interested in this issue. The Debye-Waller factor is the ratio of the coherent scattering or absorption cross section of a photon or electron by particles bound in a complex system to the value for the same process on an analgous free particle. It is often interpreted also as the probability of the coherent process, normalized to unity, with the difference between unity and the Debye Waller factor interpreted as the probability of incoherent processes. The Debye-Waller factor is then interpreted as a measure of decoherence. The breakdown of this description for a test particle which cannot give or lose energy is not generally appreciated. Prime examples are: Bragg scattering, the M\"ossbauer effect and related phenomena at zero temperature. The physics of the change in the interpretation of the Debye-Waller factor is summarized here in a hopefully pedagogical manner.},
  adsnote   = {Provided by the SAO/NASA Astrophysics Data System},
  adsurl    = {http://adsabs.harvard.edu/abs/2004cond.mat..5023L},
  eprint    = {arXiv:cond-mat/0405023},
  file      = {:by-author/L/Lipkin/2004_Lipkin_0405023v1.pdf:PDF},
  keywords  = {Atomic Displacement Parameters; Crystallography; Debye-Waller Factor; Mesoscopic Systems; Quantum Hall Effect; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2013.05.03},
  creationdate = {2013-05-03T00:00:00},
  url       = {http://arxiv.org/abs/cond-mat/0405023v1},
}

@Article{Lipkus2008,
  author    = {Lipkus, Alan H. and Yuan, Qiong and Lucas, Karen A. and Funk, Susan A. and Bartelt, 3rd, William F. and Schenck, Roger J. and Trippe, Anthony J. and <CollectiveName>CAS Registry</CollectiveName> ,},
  journal   = {The Journal of organic chemistry},
  title     = {Structural diversity of organic chemistry. A scaffold analysis of the CAS Registry.},
  year      = {2008},
  pages     = {4443--51},
  volume    = {73},
  abstract  = {By analyzing the scaffold content of the CAS Registry, we attempt to characterize in a comprehensive way the structural diversity of organic chemistry. The scaffold of a molecule is taken to be its framework, defined as all its ring systems and all the linkers that connect them. Framework data from more than 24 million organic compounds is analyzed. The distribution of frameworks among compounds is found to be top-heavy, i.e., a small percentage of frameworks occur in a large percentage of compounds. When frameworks are analyzed at the graph level, an even more top-heavy distribution is found: half of the compounds can be described by only 143 framework shapes. The most significant finding is that the framework distribution conforms almost exactly to a power law. This suggests that the more often a framework has been used as the basis for a compound, the more likely it is to be used in another compound. This may be explained by the cost of synthesis: making a new derivative of a framework is probably less costly if many other derivatives are known. We believe this power law is evidence that the minimization of synthetic cost has been a key factor in shaping the known universe of organic chemistry.},
  file      = {:by-author/L/Lipkus/2008_Lipkus_4443.pdf:PDF},
  owner     = {saulius},
  timestamp = {2014.01.26},
  creationdate = {2014-01-26T00:00:00},
}

@Manual{LispWorks2014,
  title     = {LispWorks Foreign Language Interface User Guide and Reference},
  author    = {LispWorks},
  year      = {2014},
  file      = {:by-author/L/LispWorks/2014_LispWorks.odt:PDF},
  owner     = {saulius},
  timestamp = {2014.03.23},
  creationdate = {2014-03-23T00:00:00},
}

@Article{Li-Thiao-Te2012,
  author    = {Li-Thiao-Té, Sébastien},
  journal   = {Procedia Computer Science},
  title     = {Literate Program Execution for Reproducible Research and Executable Papers},
  year      = {2012},
  issn      = {1877-0509},
  pages     = {439--448},
  volume    = {9},
  abstract  = {Lepton is an automaton for literate executable papers. It enables researchers to publish their work in the form of a script or program that can generate the research paper along with the corresponding source code, input data and output results. Lepton files do not contain pre-computed results, but the full set of instructions for reproducing the results presented in the manuscript. Taking inspiration from literate programming for code review and code re-use, we have written Lepton to facilitate the review and re-use of computational methods. Lepton is designed to provide strong guarantees for the reproducibil-ity of the results, many features for easily applying the methods to new data while remaining unobtrusive and easy to deploy in any environment. Lepton is designed for writing reproducible technical reports during method development, and journal manuscripts when the research is polished. Developped independently from the Elsevier Executable Paper Grand Challenge, it addresses similar issues and objectives. This manuscript was written with Lepton.},
  doi       = {10.1016/j.procs.2012.04.047},
  file      = {2012_Li-Thiao-Té_439.pdf:by-author/L/Li-Thiao-Té/2012_Li-Thiao-Té_439.pdf:PDF},
  groups    = {sg/Methods and tools},
  keywords  = {Executable Papers; Lepton System; Reproducible Research},
  owner     = {saulius},
  publisher = {Elsevier BV},
  timestamp = {2016.11.17},
  creationdate = {2016-11-17T00:00:00},
  url       = {http://dx.doi.org/10.1016/j.procs.2012.04.047},
}

@Article{Li-Thiao-Te2012a,
  author    = {Li-Thiao-Té, Sébastien},
  journal   = {Procedia Computer Science},
  title     = {Literate Program Execution for Teaching Computational Science},
  year      = {2012},
  issn      = {1877-0509},
  pages     = {1723--1732},
  volume    = {9},
  abstract  = {Class material for computer science courses often contains algorithms and code snippets, as well as the results of their execution. Usually, these are written and tested outside the source document then included via copy-and-paste. Making sure that the code compiles and that the results really correspond to the included code is the teacher's responsibility. Using techniques and ideas from literate programming, we propose to include source code and executable instruc-tions inside the source document. To support this, we have implemented Lepton which is a tool for extracting source code, compiling, executing, and including the results of the documented programs. Consequently, copy-and-paste is eliminated and code output is guaranteed to be up-to-date with source code. This manuscript was written with Lepton.},
  doi       = {10.1016/j.procs.2012.04.190},
  file      = {2012_Li-Thiao-Té_1723.pdf:by-author/L/Li-Thiao-Té/2012_Li-Thiao-Té_1723.pdf:PDF},
  groups    = {sg/Methods and tools},
  keywords  = {Executable Papers; Lepton System; Reproducible Research},
  owner     = {saulius},
  publisher = {Elsevier BV},
  timestamp = {2016.11.17},
  creationdate = {2016-11-17T00:00:00},
  url       = {http://dx.doi.org/10.1016/j.procs.2012.04.190},
}

@Manuscript{Little2008a,
  author    = {Little},
  title     = {Domain Swapping in Allosteric Modulation of DNA Specificity},
  year      = {2008},
  keywords  = {For Review; Manuscripts},
  file      = {:by-author/L/Little/2008_Little_manuscript.pdf:PDF},
  owner     = {saulius},
  pages     = {manuscript},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Little2008,
  author       = {Elizabeth J Little and Andrea C Babic and Nancy C Horton},
  journal      = {Structure},
  title        = {Early interrogation and recognition of DNA sequence by indirect readout.},
  year         = {2008},
  month        = {Dec},
  number       = {12},
  pages        = {1828--1837},
  volume       = {16},
  abstract     = {Control of replication, transcription, recombination and repair requires proteins capable of finding particular DNA sequences in a background of a large excess of nonspecific sequences. Such recognition can involve direct readout, with direct contacts to the bases of DNA, or in some cases through the less well-characterized indirect readout mechanisms. In order to measure the relative contributions of direct and indirect readout by a sequence specific endonuclease, HincII, a mutant enzyme deficient in a direct contact, was characterized, and surprisingly showed no loss of sequence specificity. The three dimensional crystal structure shows the loss of most of the direct readout contacts to the DNA, possibly capturing an early stage in target site recognition using predominately indirect readout to prescreen sites before full sequence interrogation.},
  creationdate = {2011-06-10T00:00:00},
  doi          = {10.1016/j.str.2008.09.009},
  file         = {2008_Little_manuscript.pdf:by-author/L/Little/2008_Little_manuscript.pdf:PDF},
  institution  = {Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, AZ 85721, USA.},
  keywords     = {Alanine; Amino Acid Sequence; Amino Acid Substitution; Bacterial; Base Pairing; Base Sequence; Crystallization; Crystallography; DNA; DNA Restriction Enzymes; Haemophilus Influenzae; Hydrogen Bonding; Models; Molecular; Molecular Sequence Data; Nucleic Acid Conformation; Protein Structure; Secondary; Tertiary; X-Ray; X-Ray Diffraction},
  owner        = {em},
  pii          = {S0969-2126(08)00380-8},
  pmid         = {19081059},
  timestamp    = {2011.06.10},
  url          = {http://dx.doi.org/10.1016/j.str.2008.09.009},
}

@Article{Little2005,
  author    = {Little, Elizabeth J and Horton, Nancy C},
  journal   = {Journal of molecular biology},
  title     = {DNA-induced conformational changes in type II restriction endonucleases: the structure of unliganded HincII.},
  year      = {2005},
  pages     = {76--88},
  volume    = {351},
  abstract  = {The 2.1A crystal structure of the unliganded type II restriction endonuclease, HincII, is described. Although the asymmetric unit contains only a single monomer, crystal lattice contacts bring two monomers together to form a dimer very similar to that found in the DNA bound form. Comparison with the published DNA bound structure reveals that the DNA binding pocket is expanded in the unliganded structure. Comparison of the unliganded and DNA liganded structures reveals a simple rotation of subunits by 11 degrees each, or 22 degrees total, to a more closed structure around the bound DNA. Comparison of this conformational change to that observed in the other type II restriction endonucleases where DNA bound and unliganded forms have both been characterized, shows considerable variation in the types of conformational changes that can occur. The conformational changes in three can be described by a simple rotation of subunits, while in two others both rotation and translation of subunits relative to one another occurs. In addition, the endonucleases having subunits that undergo the greatest amount of rotation upon DNA binding are found to be those that distort the bound DNA the least, suggesting that DNA bending may be less facile in dimers possessing greater flexibility.},
  file      = {Little_2005_76-HincII-apo-structure.pdf:by-author/L/Little/2005_Little_76.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Little2005a,
  author      = {Elizabeth J Little and Nancy C Horton},
  journal     = {J Mol Biol},
  title       = {DNA-induced conformational changes in type II restriction endonucleases: the structure of unliganded HincII.},
  year        = {2005},
  month       = {Aug},
  number      = {1},
  pages       = {76--88},
  volume      = {351},
  abstract    = {The 2.1A crystal structure of the unliganded type II restriction endonuclease, HincII, is described. Although the asymmetric unit contains only a single monomer, crystal lattice contacts bring two monomers together to form a dimer very similar to that found in the DNA bound form. Comparison with the published DNA bound structure reveals that the DNA binding pocket is expanded in the unliganded structure. Comparison of the unliganded and DNA liganded structures reveals a simple rotation of subunits by 11 degrees each, or 22 degrees total, to a more closed structure around the bound DNA. Comparison of this conformational change to that observed in the other type II restriction endonucleases where DNA bound and unliganded forms have both been characterized, shows considerable variation in the types of conformational changes that can occur. The conformational changes in three can be described by a simple rotation of subunits, while in two others both rotation and translation of subunits relative to one another occurs. In addition, the endonucleases having subunits that undergo the greatest amount of rotation upon DNA binding are found to be those that distort the bound DNA the least, suggesting that DNA bending may be less facile in dimers possessing greater flexibility.},
  doi         = {10.1016/j.jmb.2005.05.063},
  file        = {2005_Little_76.pdf:by-author/L/Little/2005_Little_76.pdf:PDF},
  institution = {Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, AZ 85721, USA.},
  keywords    = {Binding Sites; Crystallization; Crystallography; DNA; Deoxyribonucleases; Dimerization; Protein Binding; Protein Conformation; Protein Subunits; Type II Site-Specific; X-Ray},
  owner       = {em},
  pii         = {S0022-2836(05)00631-5},
  pmid        = {15993893},
  timestamp = {2011.06.10},
  creationdate = {2011-06-10T00:00:00},
  url         = {http://dx.doi.org/10.1016/j.jmb.2005.05.063},
}

@Article{Liu1995,
  author    = {Chuanhai Liu and Donald B. Rubin},
  journal   = {Statistica Sinica},
  title     = {{ML} estimation of the {t} distribution using {EM} and its extensions, {ECM} and {ECME}},
  year      = {1995},
  pages     = {19--39},
  volume    = {5},
  abstract  = {The multivariate t distribution has many potential applications in applied statistics. Current computational advances will make it routinely available in practice in the near future. Here we focus on maximum likelihood estimation of the parameters of the multivariate t, with known and unknown degrees of freedom, with and without missing data, and with and without covariates. We describe EM, ECM and ECME algorithms and indicate their relative computational efficiencies. All three algorithms are analytically quite simple, and all have stable monotone convergence to a local maximum likelihood estimate. ECME, however, can have a dramatically faster rate of convergence.},
  file      = {:by-author/L/Liu/1995_Liu_19.pdf:PDF},
  groups    = {am/Student's t, am/Expectation maximisation},
  keywords  = {Expectation Maximisation},
  owner     = {andrius},
  timestamp = {2016.03.14},
  creationdate = {2016-03-14T00:00:00},
  url       = {http://www3.stat.sinica.edu.tw/statistica/oldpdf/A5n12.pdf},
}

@Article{Liu1981,
  author    = {Liu, C. C. and Alberts, B. M.},
  journal   = {The Journal of biological chemistry},
  title     = {Characterization of the DNA-dependent GTPase activity of T4 gene 41 protein, an essential component of the T4 bacteriophage DNA replication apparatus.},
  year      = {1981},
  pages     = {2813--20},
  volume    = {256},
  abstract  = {The product specified by T4 bacteriophage gene 41 is known from genetic analyses to be essential for phage DNA replication in vivo. Correspondingly, the purified gene 41 protein is an essential component of an efficient in vitro DNA replication system reconstructed from seven purified T4 replication proteins; it is required both for the synthesis of short RNA primers (in conjunction with the T4 gene 61 protein) and for the rapid unwinding of the double-helical DNA template at a replication fork. The purified gene 41 protein exhibits a DNA-dependent GTPase (and ATPase) activity. In this report, we have used this associated GTPase activity as a biochemical probe for the analysis of the interactions between DNA and the 41 protein. Our results suggest that, upon binding GTP, the 41 protein monomer is induced to form a dimer, which can them form a tight complex with single-stranded DNA. Driven by the repeated hydrolysis of GTP molecules, the 41 protein dimer appears to run rapidly along the bound DNA chain. Studies with the synthetic GTP analogue, GTP gamma S, suggest that GTP hydrolysis is required for this 41 protein movement, but that it is not essential for the function of the 41 protein in RNA primer synthesis. In sum, our observations suggest that a 41 protein dimer runs along the lagging strand template at a DNA replication fork; from this position, it functions as a DNA helicase and simultaneously interacts with the T4 gene 61 protein to make the pentaribonucleotide primers which initiate Okazaki pieces at specific primer initiation sites.},
  file      = {:by-author/L/Liu/1981_Liu_2813.pdf:PDF},
  keywords  = {Oligomer; {gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Liu1981a,
  author    = {Liu, C. C. and Alberts, B. M.},
  journal   = {The Journal of biological chemistry},
  title     = {Characterization of RNA primer synthesis in the T4 bacteriophage in vitro DNA replication system.},
  year      = {1981},
  pages     = {2821--9},
  volume    = {256},
  abstract  = {In the presence of any natural single-stranded DNA, the bacteriophage T4 gene 41 and gene 61 proteins catalyze the synthesis of a group of pentaribonucleotides. These RNA molecules are homogeneous in chain length, but heterogeneous in sequence. In the presence of the other five T4 replication proteins, these pentaribonucleotides are utilized with high efficiency as primers for de novo DNA chain initiations on the lagging strand in the T4 DNA replication process. By using a two-dimensional fractionation system plus a variety of enzymatic analyses, the pentaribonucleotides are found to have either a unique pppApC dinucleotide or a pppG as their starting residue, followed in both cases by many different sequences. However, when natural T4 DNA containing glucosylated 5-hydroxylmethyl cytosine is used as template, only the pppApC-initiated class of RNA primers is made. Alone, the gene 41 protein exhibits a DNA-dependent GTPase (and ATPase) activity, with nucleoside diphosphate and inorganic phosphate as products. By blocking this GTPase activity with the synthetic GTP analogue, GTP gamma S, we show that limited RNa primer synthesis can occur without this nucleotide hydrolysis by the 41 protein, but that prolonged RNA primer synthesis requires such hydrolysis. This result, viewed in the light of the observations presented in the accompanying paper, suggests that the gene 41 protein acts as a "mobile promoter," perhaps leaving the gene 61 protein to perform the actual polymerization and chain termination functions in the synthetic process.},
  file      = {:by-author/L/Liu/1981_Liu_2821.pdf:PDF},
  keywords  = {{gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Liu2010b,
  author    = {Liu, Chang C. and Schultz, Peter G.},
  journal   = {Annual Review of Biochemistry},
  title     = {Adding New Chemistries to the Genetic Code},
  year      = {2010},
  issn      = {1545-4509},
  month     = {Jun},
  number    = {1},
  pages     = {413–444},
  volume    = {79},
  doi       = {10.1146/annurev.biochem.052308.105824},
  file      = {:by-author/L/Liu/2010_Liu_413.pdf:PDF},
  groups    = {am/Expanded genetic code},
  owner     = {andrius},
  publisher = {Annual Reviews},
  timestamp = {2016.04.29},
  creationdate = {2016-04-29T00:00:00},
  url       = {http://dx.doi.org/10.1146/annurev.biochem.052308.105824},
}

@Article{Liu2005,
  author    = {Gaohua Liu and Zhaohui Li and Yiwen Chiang and Thomas Acton and Gaetano T. Montelione and Diana Murray and Thomas Szyperski},
  journal   = {Protein Science},
  title     = {High-quality homology models derived from NMR and X-ray structures of E. coli proteins YgdK and Suf E suggest that all members of the YgdK/Suf E protein family are enhancers of cysteine desulfurases},
  year      = {2005},
  pages     = {1597--1608},
  volume    = {14},
  abstract  = {The structural biology of proteins mediating iron-sulfur (Fe-S) cluster assembly is central for understanding several important biological processes. Here we present the NMR structure of the 16-kDa protein YgdK from Escherichia coli , which shares 35% sequence identity with the E. coli protein SufE. The SufE X-ray crystal structure was solved in parallel with the YdgK NMR structure in the Northeast Structural Genomics (NESG) consortium. Both proteins are (1) key components for Fe-S metabolism, (2) exhibit the same distinct fold, and (3) belong to a family of at least 70 prokaryotic and eukaryotic sequence homologs. Accurate homology models were calculated for the YgdK/SufE family based on YgdK NMR and SufE crystal structure. Both structural templates contributed equally, exemplifying synergy of NMR and X-ray crystallography. SufE acts as an enhancer of the cysteine desulfurase activity of SufS by SufE–SufS complex formation. A homology model of CsdA, a desulfurase encoded in the same operon as YgdK, was modeled using the X-ray structure of SufS as a template. Protein surface and electrostatic complementarities strongly suggest that YgdK and CsdA likewise form a functional two-component desulfurase complex. Moreover, structural features of YgdK and SufS, which can be linked to their interaction with desulfurases, are conserved in all homology models. It thus appears very likely that all members of the YgdK/SufE family act as enhancers of Suf-S-like desulfurases. The present study exemplifies that "refined" selection of two (or more) targets enables high-quality homology modeling of large protein families.},
  doi       = {10.1110/ps.041322705},
  file      = {:by-author/L/Liu/2005_Liu_1597.war:WAR},
  keywords  = {Fe-S Cluster; Homology Modeling; IscU; NMR; Protein-modeling; SufE; YgdK},
  owner     = {saulius},
  timestamp = {2015.03.02},
  creationdate = {2015-03-02T00:00:00},
}

@Article{Liu2005a,
  author    = {Liu, Gaohua and Li, Zhaohui and Chiang, Yiwen and Acton, Thomas and Montelione, Gaetano T. and Murray, Diana and Szyperski, Thomas},
  journal   = {Protein science : a publication of the Protein Society},
  title     = {High-quality homology models derived from NMR and X-ray structures of E. coli proteins YgdK and Suf E suggest that all members of the YgdK/Suf E protein family are enhancers of cysteine desulfurases.},
  year      = {2005},
  pages     = {1597--608},
  volume    = {14},
  abstract  = {The structural biology of proteins mediating iron-sulfur (Fe-S) cluster assembly is central for understanding several important biological processes. Here we present the NMR structure of the 16-kDa protein YgdK from Escherichia coli, which shares 35% sequence identity with the E. coli protein SufE. The SufE X-ray crystal structure was solved in parallel with the YdgK NMR structure in the Northeast Structural Genomics (NESG) consortium. Both proteins are (1) key components for Fe-S metabolism, (2) exhibit the same distinct fold, and (3) belong to a family of at least 70 prokaryotic and eukaryotic sequence homologs. Accurate homology models were calculated for the YgdK/SufE family based on YgdK NMR and SufE crystal structure. Both structural templates contributed equally, exemplifying synergy of NMR and X-ray crystallography. SufE acts as an enhancer of the cysteine desulfurase activity of SufS by SufE-SufS complex formation. A homology model of CsdA, a desulfurase encoded in the same operon as YgdK, was modeled using the X-ray structure of SufS as a template. Protein surface and electrostatic complementarities strongly suggest that YgdK and CsdA likewise form a functional two-component desulfurase complex. Moreover, structural features of YgdK and SufS, which can be linked to their interaction with desulfurases, are conserved in all homology models. It thus appears very likely that all members of the YgdK/SufE family act as enhancers of Suf-S-like desulfurases. The present study exemplifies that &quot;refined&quot; selection of two (or more) targets enables high-quality homology modeling of large protein families.},
  file      = {:by-author/L/Liu/2005_Liu_1597.pdf:PDF},
  keywords  = {Protein Modeling},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Liu2012,
  author    = {Liu, Jinxuan and Lukose, Binit and Shekhah, Osama and Arslan, Hasan Kemal and Weidler, Peter and Gliemann, Hartmut and Brase, Stefan and Grosjean, Sylvain and Godt, Adelheid and Feng, Xinliang and Mullen, Klaus and Magdau, Ioan-Bogdan and Heine, Thomas and Woll, Christof},
  journal   = {Sci. Rep.},
  title     = {A novel series of isoreticular metal organic frameworks: realizing metastable structures by liquid phase epitaxy},
  year      = {2012},
  pages     = {srep00921},
  volume    = {2},
  doi       = {10.1038/srep00921},
  file      = {2012_Liu_srep00921.pdf:by-author/L/Liu/2012_Liu_srep00921.pdf:PDF},
  keywords  = {Materials Chemistry; Metal-Organic Frameworks (MOF); Nanoparticles; Quantum Chemistry; Surface Patterning},
  owner     = {saulius},
  publisher = {Macmillan Publishers Limited. All rights reserved},
  timestamp = {2013.01.05},
  creationdate = {2013-01-05T00:00:00},
  url       = {http://dx.doi.org/10.1038/srep00921},
}

@Article{Liu2010,
  author    = {Jie Liu and Scott W. Morrical},
  journal   = {Virology Journal},
  title     = {Assembly and dynamics of the bacteriophage T4 homologous recombination machinery},
  year      = {2010},
  pages     = {357},
  volume    = {7},
  file      = {:by-author/L/Liu/2010_Liu_357.pdf:PDF},
  keywords  = {{gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://www.virologyj.com/content/7/1/357},
}

@Article{Liu2010a,
  author           = {Pu Liu and Dimitris K. Agrafiotis and Douglas L. Theobald},
  journal          = {J. Comp. Chem.},
  title            = {Fast determination of the optimal rotational matrix for macromolecular superpositions},
  year             = {2010},
  pages            = {1561--1563},
  volume           = {31},
  abstract         = {Finding the rotational matrix that minimizes the sum of squared deviations between two vectors is an important problem in bioinformatics and crystallography. Traditional algorithms involve the inversion or decomposition of a 3 × 3 or 4 × 4 matrix, which can be computationally expensive and numerically unstable in certain cases. Here, we present a simple and robust algorithm to rapidly determine the optimal rotation using a Newton‐Raphson quaternion‐based method and an adjoint matrix. Our method is at least an order of magnitude more efficient than conventional inversion/decomposition methods, and it should be particularly useful for high‐throughput analyses of molecular conformations.},
  creationdate     = {2012-05-15T00:00:00},
  doi              = {10.1002/jcc.21439},
  file             = {:by-author/L/Liu/2010_Liu_1561.pdf:PDF},
  groups           = {sg/Molecule superposion, sg/Superposition, sg/Bioinf. Algorithms},
  keywords         = {Structure Superposition},
  modificationdate = {2024-05-12T16:46:33},
  owner            = {saulius},
  timestamp        = {2012.05.15},
}

@Article{Liu2012a,
  author    = {Liu, Qun and Dahmane, Tassadite and Zhang, Zhen and Assur, Zahra and Brasch, Julia and Shapiro, Lawrence and Mancia, Filippo and Hendrickson, Wayne A.},
  journal   = {Science},
  title     = {Structures from Anomalous Diffraction of Native Biological Macromolecules},
  year      = {2012},
  pages     = {1033--1037},
  volume    = {336},
  abstract  = {Crystal structure analyses for biological macromolecules without known structural relatives entail solving the crystallographic phase problem. Typical de novo phase evaluations depend on incorporating heavier atoms than those found natively; most commonly, multi- or single-wavelength anomalous diffraction (MAD or SAD) experiments exploit selenomethionyl proteins. Here, we realize routine structure determination using intrinsic anomalous scattering from native macromolecules. We devised robust procedures for enhancing the signal-to-noise ratio in the slight anomalous scattering from generic native structures by combining data measured from multiple crystals at lower-than-usual x-ray energy. Using this multicrystal SAD method (5 to 13 equivalent crystals), we determined structures at modest resolution (2.8 to 2.3 angstroms) for native proteins varying in size (127 to 1148 unique residues) and number of sulfur sites (3 to 28). With no requirement for heavy-atom incorporation, such experiments provide an attractive alternative to selenomethionyl SAD experiments.},
  doi       = {10.1126/science.1218753},
  eprint    = {http://www.sciencemag.org/content/336/6084/1033.full.pdf},
  file      = {2012_Liu_1033.pdf:by-author/L/Liu/2012_Liu_1033.pdf:PDF},
  keywords  = {X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2014.03.24},
  creationdate = {2014-03-24T00:00:00},
  url       = {http://www.sciencemag.org/content/336/6084/1033.abstract},
}

@Article{Liu2003,
  author    = {Liu, Qun and Weaver, Arthur J and Xiang, Tao and Thiel, Daniel J and Hao, Quan},
  journal   = {Acta crystallographica. Section D, Biological crystallography},
  title     = {Low-resolution molecular replacement using a six-dimensional search.},
  year      = {2003},
  pages     = {1016--9},
  volume    = {59},
  file      = {2003_Liu_1016.pdf:by-author/L/Liu/2003_Liu_1016.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Liu2004,
  author    = {Suxing Liu and W. Robert Bishop and Bimal Dasmahapatra and Yaolin Wang},
  journal   = {Drug Development Research},
  title     = {Pharmacogenomics of the P53 Tumor Suppressor and Its Role in Cancer Chemoresistance},
  year      = {2004},
  pages     = {254--272},
  volume    = {62},
  abstract  = {Drug resistance remains a key obstacle to successful cancer treatment. The implementa- tion of pharmacogenomics is widely proclaimed as a route to revolutionize the face of cancer therapy. Here we discuss the pharmacogenomics of the p53 tumor suppressor and its role in cancer chemosensitivity. It has been proposed that p53 has a profound impact on the response to chemotherapy and participates in development of drug resistance in tumor cells. This is based on the dual role of p53 as a guardian of genome integrity and as a key mediator of apoptosis. Alterations of the p53 gene occur in approximately 50% of human cancer, and human tumor cells retaining wild-type p53 often have epigenetic defects in the p53 pathway. Extensive mechanistic studies of drug action suggest that virtually all cancer cells have a dysfunctional p53 system (including p53 and its associated proteins, both upstream regulators and downstream targets). Various experimental approaches to correct the p53 pathway defects in tumor cells are discussed. Many studies have correlated p53 status with prognosis and therapy response in tumors. However, the impact of p53 status on drug resistance of tumors is still controversial. The impact of p53 on chemosensitivity is complex and multifactorial, depending on the genotypic/phenotypic context of the cell. Recent technological achievements have fostered a renewed interest in pharmacogenomics of p53 and its association with drug response. These include high-throughput tissue microarray analysis of p53 protein expression, single nucleotide polymorphism genotyping of the p53 gene, and gene expression profiling to identify the gene signature of p53-associated chemoresistance. Knowledge from pharmaco- genomic studies will provide an opportunity for improvements in drug efficacy through effective stratification of patients, and early identification of those individuals most likely to respond effectively to a c specific therapy.},
  file      = {:by-author/L/Liu/2004_Liu_254.pdf:PDF},
  keywords  = {Drug Design},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Liu2012b,
  author    = {Liu, Tong and Zhang, Ping and Dai, Wu-Sheng and Xie, Mi},
  journal   = {Physica A: Statistical Mechanics and its Applications},
  title     = {An intermediate distribution between Gaussian and Cauchy distributions},
  year      = {2012},
  issn      = {0378-4371},
  month     = {Nov},
  number    = {22},
  pages     = {5411–5421},
  volume    = {391},
  doi       = {10.1016/j.physa.2012.06.035},
  file      = {2012_Liu_5411.pdf:by-author/L/Liu/2012_Liu_5411.pdf:PDF},
  groups    = {am/Distributions},
  owner     = {andrius},
  publisher = {Elsevier BV},
  timestamp = {2017.02.15},
  creationdate = {2017-02-15T00:00:00},
  url       = {https://arxiv.org/abs/1208.5109},
}

@Article{Liu1997,
  author    = {Xuesong Liu and Hua Zou and Clive Slaughter and Xiaodong Wang},
  journal   = {Cell},
  title     = {DFF, a Heterodimeric Protein That Functions Downstream of Caspase-3 to Trigger DNA Fragmentation during Apoptosis},
  year      = {1997},
  pages     = {175--184},
  volume    = {89},
  abstract  = {We have identified and purified from HeLa cytosol a protein that induces DNA fragmentation in coincubated nuclei after it is activated by caspase-3. This protein, designated DNA Fragmentation Factor (DFF), is a heterodimer of 40 kDa and 45 kDa subunits. The amino acid sequence of the 45 kDa subunit, determined from its cDNA sequence, reveals it to be a novel protein. Caspase-3 cleaves the 45 kDa subunit at two sites to generate an active factor that produces DNA fragmentation without further requirement for caspase-3 or other cytosolic proteins. In cells undergoing apoptosis, the 45 kDa subunit is cleaved in the same pattern as it is cleaved by caspase-3 in vitro. These data delineate a direct signal transduction pathway during apoptosis: caspase-3 to DFF to DNA fragmentation.},
  file      = {Liu_1997_175_DFF.pdf:by-author/L/Liu/1997_Liu_175.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Liu2009,
  author    = {Yu-Shen Liu and Yi Fang and Karthik Ramani},
  journal   = {BMC Bioinformatics},
  title     = {Using least median of squares for structural superposition of flexible proteins},
  year      = {2010},
  pages     = {10:29},
  volume    = {31},
  doi       = {10.1186/1471-2105-10-29},
  file      = {:by-author/L/Liu/2009_Liu_10-29.pdf:PDF},
  groups    = {sg/Molecule superposion, sg/Superposition, sg/Bioinf. Algorithms},
  keywords  = {Structure Superposition},
  owner     = {saulius},
  timestamp = {2012.05.15},
  creationdate = {2012-05-15T00:00:00},
}

@Article{Liu2004a,
  author    = {Liu, Zhenfeng and Yan, Hanchi and Wang, Kebin and Kuang, Tingyun and Zhang, Jiping and Gui, Lulu and An, Xiaomin and Chang, Wenrui},
  journal   = {Nature},
  title     = {Crystal structure of spinach major light-harvesting complex at 2.72[thinsp]A resolution},
  year      = {2004},
  issn      = {0028-0836},
  pages     = {287--292},
  volume    = {428},
  abstract  = {The major light-harvesting complex of photosystem II (LHC-II) serves as the principal solar energy collector in the photosynthesis of green plants and presumably also functions in photoprotection under high-light conditions. Here we report the first X-ray structure of LHC-II in icosahedral proteoliposome assembly at atomic detail. One asymmetric unit of a large R32 unit cell contains ten LHC-II monomers. The 14 chlorophylls (Chl) in each monomer can be unambiguously distinguished as eight Chla and six Chlb molecules. Assignment of the orientation of the transition dipole moment of each chlorophyll has been achieved. All Chlb are located around the interface between adjacent monomers, and together with Chla they are the basis for efficient light harvesting. Four carotenoid-binding sites per monomer have been observed. The xanthophyll-cycle carotenoid at the monomer–monomer interface may be involved in the non-radiative dissipation of excessive energy, one of the photoprotective strategies that have evolved in plants.},
  comment   = {10.1038/nature02373},
  file      = {2004_Liu_287.pdf:by-author/L/Liu/2004_Liu_287.pdf:PDF},
  keywords  = {Carotenoids; Crystall Structure; Light-harvesting Antenna; Photosythesis; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2013.10.20},
  creationdate = {2013-10-20T00:00:00},
  url       = {http://dx.doi.org/10.1038/nature02373},
}

@Article{Lloyd2012,
  author    = {Lloyd, Seth},
  journal   = {Science},
  title     = {Quantum Procrastination},
  year      = {2012},
  pages     = {621--622},
  volume    = {338},
  doi       = {10.1126/science.1229825},
  eprint    = {http://www.sciencemag.org/content/338/6107/621.full.pdf},
  file      = {2012_Lloyd_621.pdf:by-author/L/Lloyd/2012_Lloyd_621.pdf:PDF},
  keywords  = {Delayed Choice Experiments; Quantum Mechanics (QM); Wave Particle Duality},
  owner     = {saulius},
  timestamp = {2012.11.02},
  creationdate = {2012-11-02T00:00:00},
  url       = {http://www.sciencemag.org/content/338/6107/621.short},
}

@Article{LoConte2000,
  author    = {Lo Conte, Loredana and Ailey, Bart and Hubbard, Tim J. P. and Brenner, Steven E. and Murzin, Alexey G. and Chothia, Cyrus},
  journal   = {Nucleic Acids Research},
  title     = {SCOP: a Structural Classification of Proteins database},
  year      = {2000},
  pages     = {257--259},
  volume    = {28},
  abstract  = {The Structural Classification of Proteins (SCOP) database provides a detailed and comprehensive description of the relationships of known protein structures. The classification is on hierarchical levels: the first two levels, family and superfamily, describe near and distant evolutionary relationships; the third, fold, describes geometrical relationships. The distinction between evolutionary relationships and those that arise from the physics and chemistry of proteins is a feature that is unique to this database so far. The sequences of proteins in SCOP provide the basis of the ASTRAL sequence libraries that can be used as a source of data to calibrate sequence search algorithms and for the generation of statistics on, or selections of, protein structures. Links can be made from SCOP to PDB-ISL: a library containing sequences homologous to proteins of known structure. Sequences of proteins of unknown structure can be matched to distantly related proteins of known structure by using pairwise sequence comparison methods to find homologues in PDB-ISL. The database and its associated files are freely accessible from a number of WWW sites mirrored from URL http://scop.mrc-lmb. cam.ac.uk/scop/},
  doi       = {10.1093/nar/28.1.257},
  eprint    = {http://nar.oxfordjournals.org/content/28/1/257.full.pdf+html},
  file      = {LoConte_2000_257-SCOP.pdf:by-author/L/LoConte/2000_LoConte_257.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://nar.oxfordjournals.org/content/28/1/257.abstract},
}

@Article{Loeb1924,
  author    = {Loeb, J.},
  journal   = {The Journal of general physiology},
  title     = {Hydrophilic and hydrophobic colloids and the influence of electrolytes on membrane potentials and cataphoretic potentials},
  year      = {1924},
  pages     = {307--28},
  volume    = {6},
  abstract  = {1. In order to be able to compare the effects of electrolytes on membrane potentials and cataphoretic potentials it seems necessary to distinguish between the charging and depressing effect of electrolytes on these potentials. Only low concentrations of acids and alkalies have a charging effect on the membrane potentials of proteins, while low concentrations of neutral salts have only a depressing effect; in the case of the cataphoretic potentials, low concentrations of salts have a charging effect as have also low concentrations of alkalies and in some cases low concentrations of acids. This difference finds its explanation in the difference of the origin of the two potentials and there can therefore be no common theory for the charging effect of electrolytes in the two cases. 2. There exists, however, an analogy in the depressing action of electrolytes on the two types of potentials inasmuch when the maximal P.D. is reached, all three kinds of electrolytes, acids, alkalies, and neutral salts, have a depressing effect on both types of potentials (taking into due consideration the effect of changes in the hydrogen ion concentration). 3. This depressing effect is adequately explained for the membrane potentials of protein solutions and protein gels on the basis of the Donnan equilibrium, and the question arises whether the same explanation may also hold for the cataphoretic potentials. 4. The active ion in the depressing action of electrolytes on membrane potentials as well as on cataphoretic potentials has the opposite sign of charge from that of the colloidal particle. It had been shown before that only the valency but not the chemical nature of the active ion determines the depressing effect in the case of membrane potentials and it is shown in this paper that the same is true for the cataphoretic potentials of particles of collodion, mastic, Acheson's graphite, and denatured egg albumin. 5. It is shown that the same valency rule holds also for the effect of acids on the cataphoretic potentials of collodion particles coated with gelatin, and that the ratio of the effect of dibasic to that of mono-basic acids is approximately 0.66, as Donnan's theory of membrane potentials would demand. 6. If we have a right to conclude from the validity of the valency rule for cataphoretic potentials that the depressing effect of electrolytes on the cataphoretic P.D. is determined by the Donnan equilibrium, we can understand the analogy between the depressing action of electrolytes on membrane potentials of hydrophilic colloids and on the cataphoretic potentials of hydrophobic colloids. We can also understand the analogy between the influence of electrolytes on the precipitation of hydrophobic colloids and on the depression of the values of all those properties of hydrophilic colloids which depend on the Donnan equilibrium, since the precipitation of hydrophobic colloids occurs when the cataphoretic P.D. is depressed below a critical value.},
  file      = {1924_Loeb_307.pdf:by-author/L/Loeb/1924_Loeb_307.pdf:PDF},
  keywords  = {Poisson-Boltzmann eq; Protein Physics; Solvatation},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Loenen2003,
  author    = {Loenen, Wil A. M.},
  journal   = {Nucleic acids research},
  title     = {Tracking EcoKI and DNA fifty years on: a golden story full of surprises.},
  year      = {2003},
  pages     = {7059--69},
  volume    = {31},
  abstract  = {1953 was a historical year for biology, as it marked the birth of the DNA helix, but also a report by Bertani and Weigle on 'a barrier to infection' of bacteriophage lambda in its natural host, Escherichia coli K-12, that could be lifted by 'host-controlled variation' of the virus. This paper lay dormant till Nobel laureate Arber and PhD student Dussoix showed that the lambda DNA was rejected and degraded upon infection of different bacterial hosts, unless it carried host-specific modification of that DNA, thus laying the foundations for the phenomenon of restriction and modification (R-M). The restriction enzyme of E.coli K-12, EcoKI, was purified in 1968 and required S-adenosylmethionine (AdoMet) and ATP as cofactors. By the end of the decade there was substantial evidence for a chromosomal locus hsdK with three genes encoding restriction (R), modification (M) and specificity (S) subunits that assembled into a large complex of &gt;400 kDa. The 1970s brought the message that EcoKI cut away from its DNA recognition target, to which site the enzyme remained bound while translocating the DNA past itself, with concomitant ATP hydrolysis and subsequent double-strand nicks. This translocation event created clearly visible DNA loops in the electron microscope. EcoKI became the archetypal Type I R-M enzyme with curious DNA translocating properties reminiscent of helicases, recognizing the bipartite asymmetric site AAC(N6)GTGC. Cloning of the hsdK locus in 1976 facilitated molecular understanding of this sophisticated R-M complex and in an elegant 'pas de deux' Murray and Dryden constructed the present model based on a large body of experimental data plus bioinformatics. This review celebrates the golden anniversary of EcoKI and ends with the exciting progress on the vital issue of restriction alleviation after DNA damage, also first reported in 1953, which involves intricate control of R subunit activity by the bacterial proteasome ClpXP, important results that will keep scientists on the EcoKI track for another 50 years to come.},
  file      = {:by-author/L/Loenen/2003_Loenen_7059.pdf:PDF},
  keywords  = {TypeI},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@PhdThesis{Loginov2006,
  author    = {Alexey A. Loginov},
  school    = {University of Wisconsin–madison},
  title     = {Refinement-based program verification via three-valued-logic analysis},
  year      = {2006},
  file      = {:by-author/L/Loginov/2006_Loginov_dissertation.pdf:PDF},
  groups    = {sg/Correctness proofs},
  keywords  = {Computer Science (CS); Correctness Proofs},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Lognone2014,
  author    = {Lognoné, Quentin and Gascoin, Franck and Lebedev, Oleg I. and Lutterotti, Luca and Gascoin, Stéphanie and Chateigner, Daniel},
  journal   = {Journal of the American Ceramic Society},
  title     = {Quantitative texture analysis of spark plasma textured n-{Bi}2Te3},
  year      = {2014},
  pages     = {2038--2045},
  volume    = {97},
  file      = {[PDF] from ensicaen.fr:by-author/L/Lognoné/2014_Lognoné_2038.pdf:application/pdf;Snapshot:by-author/L/Lognoné/2014_Lognoné_2038.html:text/html},
  groups    = {sg/JAC2009},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://onlinelibrary.wiley.com/doi/10.1111/jace.12970/full},
  urldate   = {2015-08-31},
}

@Presentation{Lohkamp2009,
  author    = {Lohkamp, Bernhard},
  title     = {Ligand fitting and Validation with {Coot}},
  year      = {2009},
  file      = {:by-author/L/Lohkamp/2009_Lohkamp_slides.pdf:PDF},
  keywords  = {Grow Krystal},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{London2008,
  author    = {Nir London and Ora Schueler-Furman},
  title     = {Supplemental Data for Funnel Hunting in a Rough Terrain: Learning and Discriminating Native Energy Funnels},
  year      = {2008},
  pages     = {suppl},
  file      = {:by-author/L/London/2008_London_suppl.pdf:PDF},
  keywords  = {Protein Folding},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{London2008a,
  author    = {London, Nir and Schueler-Furman, Ora},
  journal   = {Structure (London, England : 1993)},
  title     = {Funnel hunting in a rough terrain: learning and discriminating native energy funnels.},
  year      = {2008},
  pages     = {269--79},
  volume    = {16},
  abstract  = {Protein folding and binding is commonly depicted as a search for the minimum energy conformation. Modeling of protein complex structures by RosettaDock often results in a set of low-energy conformations near the native structure. Ensembles of low-energy conformations can appear, however, in other regions, especially when backbone movements occur upon binding. What then characterizes the energy landscape near the correct orientation? We applied a machine learning algorithm to distinguish ensembles of low-energy conformations around the native conformation from other low-energy ensembles. The resulting classifier, FunHunt, identifies the native orientation in 50/52 protein complexes in a test set. The features used by FunHunt teach us about the nature of native interfaces. Remarkably, the energy decrease of trajectories toward near-native orientations is significantly larger than for other orientations. This provides a possible explanation for the stability of association in the native orientation.},
  file      = {:by-author/L/London/2008_London_269.pdf:PDF},
  keywords  = {Protein Folding},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Long2014,
  author    = {F. Long and S. Grazulis and A. Merkys and G. Murshudov},
  journal   = {Acta Cryst. A},
  title     = {A new generation of CCP4 monomer library based on Crystallography Open Database},
  year      = {2014},
  pages     = {C338},
  volume    = {70},
  file      = {2014_Long_C338.pdf:by-author/L/Long/2014_Long_C338.pdf:PDF},
  owner     = {saulius},
  timestamp = {2015.05.13},
  creationdate = {2015-05-13T00:00:00},
  url       = {http://journals.iucr.org/a/issues/2014/a1/00/a51638/a51638.pdf},
}

@Article{Long2017,
  author           = {Fei Long and Robert A. Nicholls and Paul Emsley and Saulius Gražulis and Andrius Merkys and Antanas Vaitkus and Garib N. Murshudov},
  journal          = {Acta Crystallographica Section D},
  title            = {{ACEDRG}: A stereo-chemical description generator for ligands},
  year             = {2017},
  month            = {Feb},
  number           = {2},
  pages            = {112--122},
  volume           = {73},
  abstract         = {The program AceDRG is designed for the derivation of stereochemical information about small molecules. It uses local chemical and topological environment-based atom typing to derive and organize bond lengths and angles from a small-molecule database: the Crystallography Open Database (COD). Information about the hybridization states of atoms, whether they belong to small rings (up to seven-membered rings), ring aromaticity and nearest- neighbour information is encoded in the atom types. All atoms from COD have been classified according to the generated atom types. All bonds and angles have also been classified according to the atom types and, in a certain sense, bond types. Derived data are tabulated in a machine-readable form that is freely available from CCP4. AceDRG can also generate stereochemical information, provided that the basic bonding pattern of a ligand is known. The basic bonding pattern is perceived from one of the computational chemistry file formats, including SMILES, mmCIF, SDF MOL and SYBYL MOL2 files. Using the bonding chemistry, atom types, and bond and angle tables generated from COD, AceDRG derives the ‘ideal’ bond lengths, angles, plane groups, aromatic rings and chirality information, and writes them to an mmCIF file that can be used by the refinement program REFMAC5 and the model-building program Coot. Other refinement and model-building programs such as PHENIX and BUSTER can also use these files. AceDRG also generates one or more coordinate sets corresponding to the most favourable conformation(s) of a given ligand. AceDRG employs RDKit for chemistry perception and for initial conformation generation, as well as for the interpretation of SMILES strings, SDF MOL and SYBYL MOL2 files.},
  creationdate     = {2016-11-18T00:00:00},
  doi              = {10.1107/S2059798317000067},
  file             = {2017_Long_112.pdf:by-author/L/Long/2017_Long_112.pdf:PDF},
  groups           = {am/My papers},
  keywords         = {CIF},
  modificationdate = {2023-08-07T10:23:04},
  owner            = {andrius},
  timestamp        = {2016.11.18},
}

@Article{Long2017a,
  author    = {Fei Long and Robert A. Nicholls and Paul Emsley and Saulius Gražulis and Andrius Merkys and Antanas Vaitkus and Garib N. Murshudov},
  journal   = {Acta Crystallographica Section D},
  title     = {Validation and extraction of stereochemical information from small molecular databases},
  year      = {2017},
  month     = {Feb},
  number    = {2},
  pages     = {103--111},
  volume    = {73},
  abstract  = {A freely available small-molecule structure database, the Crystallography Open Database (COD), is used for the extraction of molecular-geometry information on small-molecule compounds. The results are used for the generation of new ligand descriptions, which are subsequently used by macromolecular model- building and structure-refinement software. To increase the reliability of the derived data, and therefore the new ligand descriptions, the entries from this database were subjected to very strict validation. The selection criteria made sure that the crystal structures used to derive atom types, bond and angle classes are of sufficiently high quality. Any suspicious entries at a crystal or molecular level were removed from further consideration. The selection criteria included (i) the resolution of the data used for refinement (entries solved at 0.84 A resolution or higher) and (ii) the structure-solution method (structures must be from a single-crystal experiment and all atoms of generated molecules must have full occupancies), as well as basic sanity checks such as (iii) consistency between the valences and the number of connections between atoms, (iv) acceptable bond-length deviations from the expected values and (v) detection of atomic collisions. The derived atom types and bond classes were then validated using high-order moment-based statistical techniques. The results of the statistical analyses were fed back to fine-tune the atom typing. The developed procedure was repeated four times, resulting in fine-grained atom typing, bond and angle classes. The procedure will be repeated in the future as and when new entries are deposited in the COD. The whole procedure can also be applied to any source of small-molecule structures, including the Cambridge Structural Database and the ZINC database.},
  doi       = {10.1107/S2059798317000079},
  file      = {2017_Long_103.pdf:by-author/L/Long/2017_Long_103.pdf:PDF},
  groups    = {am/My papers},
  owner     = {andrius},
  timestamp = {2016.11.18},
  creationdate = {2016-11-18T00:00:00},
}

@Manuscript{Long2006,
  author    = {Quan Long and Qiu Zongyan and Wang Shuling},
  title     = {A Weakest Precondition Semantics for OO Languages: An OO-Separation Logic Approach},
  year      = {2006},
  keywords  = {Computer Science (CS); Program Verification; Weakest Preconditions},
  abstract  = {In recent years, many researchers in the programming language and formal methods communities have been investigating weakest precondition (WP) semantics for object-oriented (OO) programs. Based on a modified version of Separation Logic, OO Separation Logic, we develop in this article a WP seman- tics for an OO language with most important object-oriented features including subtypes, visibility, inheritance, dynamic binding and reference types. Giving a clear comparison to existing work, we conclude that the WP semantics defined here captures the essentials of object-orientation. Further, in the WP semantic model, we define program transformation in terms of refinement. With some case studies, we show that, supported by the semantics defined, it is easier to model many practical program transformations in a reasonable way.},
  file      = {:by-author/L/Long/2006_Long.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Lonie2012,
  author    = {David C. Lonie and Eva Zurek},
  journal   = {Computer Physics Communications},
  title     = {Identifying duplicate crystal structures: XtalComp, an open-source solution},
  year      = {2012},
  pages     = {690--697},
  volume    = {183},
  doi       = {10.1016/j.cpc.2011.11.007},
  file      = {2012_Lonie_690manuscript.pdf:by-author/L/Lonie/2012_Lonie_690.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Presentation{Lopresti2008,
  author    = {Dan Lopresti},
  title     = {Introduction to Bioinformatics},
  year      = {2008},
  file      = {:by-author/L/Lopresti/2008_Lopresti.pdf:PDF},
  owner     = {saulius},
  timestamp = {2014.03.23},
  creationdate = {2014-03-23T00:00:00},
}

@Webpage{Loredo2006,
  author    = {Tom Loredo},
  retrieved = {2008-07-28},
  title     = {BIPS: Bayesian Inference for the Physical Sciences},
  url       = {http://www.astro.cornell.edu/staff/loredo/bayes/},
  year      = {2006},
  file      = {:by-author/L/Loredo/2006_Loredo.war:},
  groups    = {sg/Bayesian},
  keywords  = {Bayesian Statistics; Mathematics},
  owner     = {saulius},
  timestamp = {2015.03.02},
  creationdate = {2015-03-02T00:00:00},
}

@Article{Lorenz1991,
  author    = {Lorenz, S. and Betzel, C. and Raderschall, E. and Dauter, Z. and Wilson, K. S. and Erdmann, V. A.},
  journal   = {Journal of molecular biology},
  title     = {Crystallization and preliminary diffraction studies of 5 S rRNA from the thermophilic bacterium Thermus flavus.},
  year      = {1991},
  pages     = {399--402},
  volume    = {219},
  abstract  = {Crystals of purified 5 S rRNA from Thermus flavus have been obtained. The crystals diffract up to 8 A resolution, using synchrotron radiation, and have the monoclinic space-group C2. The unit cell has the dimensions a = 190 A, b = 110 A, c = 138 A and beta = 117 degrees. The cell volume suggests the presence of four 5 S rRNA molecules per asymmetric unit.},
  file      = {:by-author/L/Lorenz/1991_Lorenz_399.pdf:PDF},
  keywords  = {Ribosome Structure},
  owner     = {saulius},
  timestamp = {2012.06.25},
  creationdate = {2012-06-25T00:00:00},
}

@Webpage{Lott1999,
  author    = {Christopher Lott},
  retrieved = {2009-02-06},
  title     = {General reading for software engineers},
  url       = {http://www.faqs.org/faqs/software-eng/part3/section-4.html},
  month     = {October},
  year      = {1999},
  file      = {:by-author/L/Lott/1999_Lott.war:},
  keywords  = {Computer Science (CS)},
  owner     = {saulius},
  timestamp = {2015.03.02},
  creationdate = {2015-03-02T00:00:00},
}

@Manuscript{Louis2003,
  author    = {Godfrey Louis and A. Santhosh Kumar},
  title     = {New biology of red rain extremophiles prove cometary panspermia},
  year      = {2003},
  school    = {School of Pure and Applied Physics, Mahatma Gandhi University},
  abstract  = {This paper reports the extraordinary biology of the microorganisms from the mysterious red rain of Kerala, India. These chemosynthetic organisms grow optimally at an extreme high temperature of 300 degrees C in hydrothermal conditions and can metabolize inorganic and organic compounds including hydrocarbons. Stages found in their life cycle show reproduction by a special multiple fission process and the red cells found in the red rain are identified as the resting spores of these microbes. While these extreme hyperthermophiles contain proteins, our study shows the absence of DNA in these organisms, indicating a new primitive domain of life with alternate thermostable genetics. This new biology proves our earlier hypothesis that these microbes are of extraterrestrial origin and also supports our earlier argument that the mysterious red rain of Kerala is due to the cometary delivery of the red spores into the stratosphere above Kerala.},
  comment   = {I am not sure how real it is -- it sounds suspicius},
  file      = {:by-author/L/Louis/2003_Louis.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.11.27},
  creationdate = {2012-11-27T00:00:00},
}

@Manuscript{Louis2003a,
  author    = {Godfrey Louis and A. Santhosh Kumar},
  title     = {Cometary panspermia explains the red rain of Kerala},
  year      = {2003},
  school    = {School of Pure and Applied Physics, Mahatma Gandhi University},
  comment   = {Sounds very suspicius...},
  file      = {:by-author/L/Louis/2003_Louis_a.pdf:PDF},
  owner     = {saulius},
  pages     = {a},
  timestamp = {2012.11.27},
  creationdate = {2012-11-27T00:00:00},
}

@Presentation{Louis2010,
  author    = {Thomas A. Louis},
  title     = {Bayesian Clinical Trials: Why Bother?},
  year      = {2010},
  file      = {2010_Louis.pdf:by-author/L/Louis/2010_Louis.pdf:PDF},
  groups    = {sg/Clinical Trials},
  owner     = {saulius},
  timestamp = {2015.12.14},
  creationdate = {2015-12-14T00:00:00},
  url       = {http://www.biostat.jhsph.edu/~tlouis/presentations/Bayes-trials_why-bother_TALouis.pdf},
  urldate   = {2015-12-12},
}

@Article{Lovelace2000,
  author    = {Lovelace, Jeff and Snell, Edward H. and Pokross, Matthew and Arvai, Andrew S. and Nielsen, Chris and Xuong, Nguyen-Huu and Bellamy, Henry D. and Borgstahl, Gloria E. O.},
  journal   = {Journal of Applied Crystallography},
  title     = {{\it BEAM-ish}: a graphical user interface for the physical characterization of macromolecular crystals},
  year      = {2000},
  pages     = {1187--1188},
  volume    = {33},
  abstract  = {BEAM-ish is a graphical user interface that manages the processing of multiple super-fine [varphi]-sliced diffraction images and seamlessly integrates several programs for mosaicity calculations.},
  doi       = {10.1107/S0021889800005732},
  file      = {:by-author/L/Lovelace/2000_Lovelace_1187.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0021889800005732},
}

@Article{Lovell2003,
  author    = {Lovell, Simon C. and Davis, Ian W. and Arendall, 3rd., W. Bryan and de Bakker, Paul I. W. and Word, J. Michael and Prisant, Michael G. and Richardson, Jane S. and Richardson, David C.},
  journal   = {Proteins},
  title     = {Structure validation by Calpha geometry: phi,psi and Cbeta deviation.},
  year      = {2003},
  pages     = {437--50},
  volume    = {50},
  abstract  = {Geometrical validation around the Calpha is described, with a new Cbeta measure and updated Ramachandran plot. Deviation of the observed Cbeta atom from ideal position provides a single measure encapsulating the major structure-validation information contained in bond angle distortions. Cbeta deviation is sensitive to incompatibilities between sidechain and backbone caused by misfit conformations or inappropriate refinement restraints. A new phi,psi plot using density-dependent smoothing for 81,234 non-Gly, non-Pro, and non-prePro residues with B &lt; 30 from 500 high-resolution proteins shows sharp boundaries at critical edges and clear delineation between large empty areas and regions that are allowed but disfavored. One such region is the gamma-turn conformation near +75 degrees,-60 degrees, counted as forbidden by common structure-validation programs; however, it occurs in well-ordered parts of good structures, it is overrepresented near functional sites, and strain is partly compensated by the gamma-turn H-bond. Favored and allowed phi,psi regions are also defined for Pro, pre-Pro, and Gly (important because Gly phi,psi angles are more permissive but less accurately determined). Details of these accurate empirical distributions are poorly predicted by previous theoretical calculations, including a region left of alpha-helix, which rates as favorable in energy yet rarely occurs. A proposed factor explaining this discrepancy is that crowding of the two-peptide NHs permits donating only a single H-bond. New calculations by Hu et al. [Proteins 2002 (this issue)] for Ala and Gly dipeptides, using mixed quantum mechanics and molecular mechanics, fit our nonrepetitive data in excellent detail. To run our geometrical evaluations on a user-uploaded file, see MOLPROBITY (http://kinemage.biochem.duke.edu) or RAMPAGE (http://www-cryst.bioc.cam.ac.uk/rampage).},
  file      = {:by-author/L/Lovell/2003_Lovell_437.pdf:PDF},
  keywords  = {Grow Krystal; Protein Bioinformatics; Quality Estimation},
  owner     = {em},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Lovell2000,
  author           = {Lovell, S. C. and Word, J. M. and Richardson, J. S. and Richardson, D. C.},
  journal          = {Proteins},
  title            = {The penultimate rotamer library.},
  year             = {2000},
  pages            = {389--408},
  volume           = {40},
  abstract         = {All published rotamer libraries contain some rotamers that exhibit impossible internal atomic overlaps if built in ideal geometry with all hydrogen atoms. Removal of uncertain residues (mainly those with B-factors &gt;/=40 or van der Waals overlaps &gt;/=0.4 A) greatly improves the clustering of rotamer populations. Asn, Gln, or His side chains additionally benefit from flipping of their planar terminal groups when required by atomic overlaps or H-bonding. Sensitivity to skew and to the boundaries of chi angle bins is avoided by using modes rather than traditional mean values. Rotamer definitions are listed both as the modal values and in a preferred version that maximizes common atoms between related rotamers. The resulting library shows significant differences from previous ones, differences validated by considering the likelihood of systematic misfitting of models to electron density maps and by plotting changes in rotamer frequency with B-factor. Few rotamers now show atomic overlaps in ideal geometry; those overlaps are relatively small and can be understood in terms of bond angle distortions compensated by favorable interactions. The new library covers 94.5% of examples in the highest quality protein data with 153 rotamers and can make a significant contribution to improving the accuracy of new structures. Proteins 2000;40:389-408.},
  creationdate     = {2008-07-28T00:00:00},
  file             = {:by-author/L/Lovell/2000_Lovell_389.pdf:PDF},
  keywords         = {B-factor; Grow Krystal},
  modificationdate = {2024-03-14T11:08:26},
  owner            = {em},
  timestamp        = {2008.07.28},
}

@Article{Lowe2011,
  author    = {Daniel M. Lowe and Peter T. Corbett and Peter Murray-Rust and Robert C. Glen},
  journal   = {Journal of chemical information and modeling},
  title     = {Chemical name to structure: OPSIN, an open source solution.},
  year      = {2011},
  pages     = {739},
  volume    = {51},
  abstract  = {We have produced an open source, freely available, algorithm (Open Parser for Systematic IUPAC Nomenclature, OPSIN) that interprets the majority of organic chemical nomenclature in a fast and precise manner. This has been achieved using an approach based on a regular grammar. This grammar is used to guide tokenization, a potentially difficult problem in chemical names. From the parsed chemical name, an XML parse tree is constructed that is operated on in a stepwise manner until the structure has been reconstructed from the name. Results from OPSIN on various computer generated name/structure pair sets are presented. These show exceptionally high precision (99.8%+) and, when using general organic chemical nomenclature, high recall (98.7-99.2%). This software can serve as the basis for future open source developments of chemical name interpretation.},
  doi       = {10.1021/ci100384d},
  file      = {:by-author/L/Lowe/2011_Lowe_739.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Lozano2012,
  author    = {Lozano, George A. and Larivière, Vincent and Gingras, Yves},
  journal   = {Journal of the American Society for Information Science and Technology},
  title     = {The weakening relationship between the impact factor and papers’ citations in the digital age},
  year      = {2012},
  issn      = {1532-2882},
  month     = {Oct},
  number    = {11},
  pages     = {2140--2145},
  volume    = {63},
  abstract  = {Historically, papers have been physically bound to the journal in which they were published; but in the digital age papers are available individually, no longer tied to their respective journals. Hence, papers now can be read and cited based on their own merits, indepen- dently of the journal’s physical availability, reputation, or impact factor (IF). We compare the strength of the relationship between journals’ IFs and the actual cita- tions received by their respective papers from 1902 to 2009. Throughout most of the 20th century, papers’ citation rates were increasingly linked to their respec- tive journals’ IFs. However, since 1990, the advent of the digital age, the relation between IFs and paper cita- tions has been weakening. This began first in physics, a field that was quick to make the transition into the electronic domain. Furthermore, since 1990 the overall proportion of highly cited papers coming from highly cited journals has been decreasing and, of these highly cited papers, the proportion not coming from highly cited journals has been increasing. Should this pattern continue, it might bring an end to the use of the IF as a way to evaluate the quality of journals, papers, and researchers.},
  doi       = {10.1002/asi.22731},
  file      = {2012_Lozano_2140.pdf:by-author/L/Lozano/2012_Lozano_2140.pdf:PDF},
  groups    = {sg/Bibliometrics},
  keywords  = {Bibliometry; Citations; Impact Factor (IF); Impact Factors},
  owner     = {saulius},
  publisher = {Wiley-Blackwell},
  timestamp = {2017.01.07},
  creationdate = {2017-01-07T00:00:00},
  url       = {http://dx.doi.org/10.1002/asi.22731},
}

@Article{Lozovskaya1990,
  author    = {Lozovskaya, E. R. and Scheinker, V. S. and Evgen'ev, M. B.},
  journal   = {Genetics},
  title     = {A hybrid dysgenesis syndrome in Drosophila virilis.},
  year      = {1990},
  pages     = {619--23},
  volume    = {126},
  abstract  = {A new example of &quot;hybrid dysgenesis&quot; has been demonstrated in the F1 progeny of crosses between two different strains of Drosophila virilis. The dysgenic traits were observed only in hybrids obtained when wild-type females (of the Batumi strain 9 from Georgia, USSR) were crossed to males from a marker strain (the long-established laboratory strain, strain 160, carrying recessive markers on all its autosomes). The phenomena observed include high frequencies of male and female sterility, male recombination, chromosomal nondisjunction, transmission ratio distortion and the appearance of numerous visible mutations at different loci in the progeny of dysgenic crosses. The sterility demonstrated in the present study is similar to that of P-M dysgenesis in Drosophila melanogaster and apparently results from underdevelopment of the gonads in both sexes, this phenomenon being sensitive to developmental temperature. However, in contrast to the P-M and I-R dysgenic systems in D. melanogaster, in D. virilis the highest level of sterility (95-98%) occurs at 23-25 degrees. Several of the mutations isolated from the progeny of dysgenic crosses (e.g., singed) proved to be unstable and reverted to wild type. We hypothesize that a mobile element (&quot;Ulysses&quot;) which we have recently isolated from a dysgenically induced white eye mutation may be responsible for the phenomena observed.},
  file      = {:by-author/L/Lozovskaya/1990_Lozovskaya_619.pdf:PDF},
  keywords  = {Mobile Genetic Elements},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Lu2017,
  author    = {Chao Lu and Dongxing Wang and Jingjing Zhao and Song Han and Wei Chen},
  journal   = {Advanced Functional Materials},
  title     = {A Continuous Carbon Nitride Polyhedron Assembly for High-Performance Flexible Supercapacitors},
  year      = {2017},
  month     = {jan},
  pages     = {1606219},
  comment   = {Synthesis of CNTs Wired Zeolite Imidazolate Framework -- can we use it? (S.G.)},
  doi       = {10.1002/adfm.201606219},
  file      = {Lu2017.pdf:by-author/L/Lu/2017_Lu_1606219.pdf:PDF},
  groups    = {sg/MOF, sg/MOFs, am/MOFs},
  keywords  = {Sythesis},
  owner     = {saulius},
  publisher = {Wiley-Blackwell},
  timestamp = {2017.01.31},
  creationdate = {2017-01-31T00:00:00},
  url       = {https://doi.org/10.1002%2Fadfm.201606219},
}

@Article{Lu2013,
  author    = {Xiaoyu Lu and Sunil Dhar},
  title     = {The Application of {Bayesian} Adaptive Design in Clinical Trials},
  year      = {2013},
  pages     = {67--72},
  volume    = {3},
  doi       = {10.5923.j.ajms.20130302.01},
  file      = {Bayesian, Adaptive, Clinical Trials, Dose Finding - 10.5923.j.ajms.20130302.01.pdf:by-author/L/Lu/2013_Lu_67.pdf:application/pdf},
  groups    = {sg/Clinical Trials},
  language  = {English},
  owner     = {saulius},
  timestamp = {2015.12.14},
  creationdate = {2015-12-14T00:00:00},
  url       = {http://article.sapub.org/pdf/10.5923.j.ajms.20130302.01.pdf},
  urldate   = {2015-12-12},
}

@Article{Lu2003,
  author       = {Lu, Xiang-Jun and Olson, Wilma K.},
  journal      = {Nucleic acids research},
  title        = {3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures.},
  year         = {2003},
  pages        = {5108--21},
  volume       = {31},
  abstract     = {We present a comprehensive software package, 3DNA, for the analysis, reconstruction and visualization of three-dimensional nucleic acid structures. Starting from a coordinate file in Protein Data Bank (PDB) format, 3DNA can handle antiparallel and parallel double helices, single-stranded structures, triplexes, quadruplexes and other complex tertiary folding motifs found in both DNA and RNA structures. The analysis routines identify and categorize all base interactions and classify the double helical character of appropriate base pair steps. The program makes use of a recently recommended reference frame for the description of nucleic acid base pair geometry and a rigorous matrix-based scheme to calculate local conformational parameters and rebuild the structure from these parameters. The rebuilding routines produce rectangular block representations of nucleic acids as well as full atomic models with the sugar-phosphate backbone and publication quality 'standardized' base stacking diagrams. Utilities are provided to locate the base pairs and helical regions in a structure and to reorient structures for effective visualization. Regular helical models based on X-ray diffraction measurements of various repeating sequences can also be generated within the program.},
  comment      = {Citation 19 has incorrect volume, should be vol. 205 instead of 208 (see entry Diekmann1989).},
  creationdate = {2008-07-28T00:00:00},
  doi          = {10.1093/nar/gkg680},
  file         = {:by-author/L/Lu/2003_Lu_5108.pdf:PDF},
  keywords     = {Base Pairing; Biochemistry; Chemistry; DNA; DNA Geometry; Definitions; Hydrogen Bonding; Models; Molecular; Nucleic Acid Conformation; Nucleic Acids; RNA Geometry; Roll; Software; Structural Biology; Twist},
  owner        = {saulius},
  timestamp    = {2008.07.28},
}

@Article{Lubys1999,
  author    = {Lubys, A. and Jurenaite, S. and Janulaitis, A.},
  journal   = {Nucleic acids research},
  title     = {Structural organization and regulation of the plasmid-borne type II restriction-modification system Kpn2I from Klebsiella pneumoniae RFL2.},
  year      = {1999},
  pages     = {4228--34},
  volume    = {27},
  abstract  = {Kpn 2I enzymes of a type II restriction-modification (R-M) system from the bacterium Klebsiella pneumoniae strain RFL2 recognize the sequence 5'-TCCGGA-3'. The Kpn 2I R-M genes have been cloned and expressed in Escherichia coli. DNA sequence analysis revealed the presence of two convergently transcribed open reading frames (ORFs) coding for a restriction endonuclease (Enase) of 301 amino acids (34. 8 kDa) and methyltransferase (Mtase) of 375 amino acids (42.1 kDa). The 3'-terminal ends of these genes ( kpn2IR and kpn2IM, respectively) overlap by 11 bp. In addition, a small ORF (gene kpn2IC ) capable of coding for a protein of 96 amino acids in length (10.6 kDa) was found upstream of kpn2IM. The direction of kpn2IC transcription is opposite to that of kpn2IM. The predicted amino acid sequence of this ORF includes a probable helix-turn-helix motif. We show that the product of kpn2IC represses expression of the Kpn 2I Mtase but has no influence on expression of the Enase gene. Such a mode of regulation is unique among R-M systems analyzed so far. The Kpn 2I R-M is located on the K.pneumoniae RFL2 plasmid pKp4.3, which is able to replicate in E.coli cells.},
  file      = {:by-author/L/Lubys/1999_Lubys_4228.pdf:PDF},
  keywords  = {Kpn2I; TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Webpage{Lucas2008,
  author    = {John Lucas},
  retrieved = {2008-07-28},
  title     = {References for Criticisms of the Gödelian Argument},
  url       = {http://users.ox.ac.uk/~jrlucas/Godel/referenc.html},
  year      = {2008},
  file      = {:by-author/L/Lucas/2008_Lucas.war:},
  keywords  = {Goedel's Theorem},
  owner     = {saulius},
  timestamp = {2015.03.02},
  creationdate = {2015-03-02T00:00:00},
}

@Webpage{Lucas2010,
  author    = {J. R. Lucas},
  retrieved = {2010-11-12},
  title     = {The Goedelian argument},
  url       = {http://www.leaderu.com/truth/2truth08.html},
  year      = {2010},
  file      = {:by-author/L/Lucas/2010_Lucas.odt:},
  keywords  = {Goedel's Theorem},
  owner     = {saulius},
  timestamp = {2015.03.03},
  creationdate = {2015-03-03T00:00:00},
}

@Article{Lukacs2001,
  author    = {Lukacs, C M and Aggarwal, A K},
  journal   = {Current opinion in structural biology},
  title     = {BglII and MunI: what a difference a base makes.},
  year      = {2001},
  pages     = {14--8},
  volume    = {11},
  abstract  = {Restriction endonucleases are resilient to alterations in their DNA-binding specificities. Structures of the BglII and MunI endonucleases bound to their palindromic DNA sites, which differ by only their outer base pairs from the recognition sequences of BamHI and EcoRI, respectively, have recently been determined. A comparison of these complexes reveals surprising differences and similarities in structure, and provides a basis for understanding the immutability of restriction endonucleases.},
  file      = {Lukacs_2001_14.pdf:by-author/L/Lukacs/2001_Lukacs_14.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Presentation{Lukinavicius2015,
  author    = {Gražvydas Lukinavičius},
  title     = {Įvadas į super-skiriamosios gebos fluorescencijos mikroskopijos metodus},
  year      = {2015},
  file      = {2015_Lukinavičius_a.pdf:by-author/L/Lukinavičius/2015_Lukinavičius_a.pdf:PDF},
  keywords  = {Fluorescence; Microscopy; Super-resolution},
  owner     = {saulius},
  timestamp = {2015.04.10},
  creationdate = {2015-04-10T00:00:00},
}

@Presentation{Lukinavicius2015a,
  author    = {Gražvydas Lukinavičius},
  title     = {Ląstelės struktūrų žymėjimo būdai ir jų pasirinkimas},
  year      = {2015},
  file      = {2015_Lukinavičius_b.pdf:by-author/L/Lukinavičius/2015_Lukinavičius_b.pdf:PDF},
  keywords  = {Fluorescence; Microscopy; Super-resolution},
  owner     = {saulius},
  timestamp = {2015.04.10},
  creationdate = {2015-04-10T00:00:00},
}

@Presentation{Lukinavicius2015b,
  author    = {Gražvydas Lukinavičius},
  title     = {Super-skiriamosios gebos mikroskopijos taikymo pavyzdžiai},
  year      = {2015},
  file      = {2015_Lukinavičius_c.pdf:by-author/L/Lukinavičius/2015_Lukinavičius_c.pdf:PDF},
  keywords  = {Fluorescence; Microscopy; Super-resolution},
  owner     = {saulius},
  timestamp = {2015.04.10},
  creationdate = {2015-04-10T00:00:00},
}

@Presentation{Lukinavicius2015c,
  author    = {Gražvydas Lukinavičius},
  title     = {Biologinių struktūrų analizė naudojant įvairių mikroskopijos tipų derinį},
  year      = {2015},
  file      = {2015_Lukinavičius_d.pdf:by-author/L/Lukinavičius/2015_Lukinavičius_d.pdf:PDF},
  keywords  = {Fluorescence; Microscopy; Super-resolution},
  owner     = {saulius},
  timestamp = {2015.04.10},
  creationdate = {2015-04-10T00:00:00},
}

@Article{Lunin1991,
  author    = {Lunin, V. Yu. and Skovoroda, T. P.},
  journal   = {Acta Crystallographica Section A},
  title     = {Frequency-restrained structure-factor refinement. I. Histogram simulation},
  year      = {1991},
  pages     = {45--52},
  volume    = {47},
  abstract  = {An analysis of the frequencies of different values encountered in protein electron-density syntheses reveals characteristic shapes for their distributions (histograms). This property can be used to refine ill-defined phases (and, perhaps, some of the moduli) of structure factors, and thus to obtain more-interpret- able electron-density maps. A simple empirical model is designed which can predict the histogram for a protein with an undetermined structure provided its unit-cell volume and charge are known. The param- eters of the histogram model are derived from a set of proteins with known spatial structures. The appli- cation of the simulated histogram is illustrated by an improved electron-density map for the 'dry' form of the protein y-crystallin IIIb.},
  doi       = {10.1107/S0108767390010042},
  file      = {:by-author/L/Lunin/1991_Lunin_45.pdf:PDF},
  keywords  = {Refinement; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0108767390010042},
}

@Article{Lunina2003,
  author    = {Lunina, Natalia and Lunin, Vladimir Y. and Urzhumtsev, Alexandre},
  journal   = {Acta Crystallographica Section D},
  title     = {Connectivity-based {\it ab initio} phasing: from low resolution to a secondary structure},
  year      = {2003},
  pages     = {1702--1715},
  volume    = {59},
  doi       = {10.1107/S0907444903015154},
  file      = {fw5000.pdf:by-author/L/Lunina/2003_Lunina_1702.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444903015154},
}

@Article{Luo2005,
  author    = {Luo, Jia and Bruice, Thomas C.},
  journal   = {Proceedings of the National Academy of Sciences of the United States of America},
  title     = {Low-frequency normal mode in DNA HhaI methyltransferase and motions of residues involved in the base flipping.},
  year      = {2005},
  pages     = {16194--8},
  volume    = {102},
  abstract  = {The results of normal-mode analyses are in accord with the proposal that a low-frequency motion of the HhaI methyltransferase enzyme is responsible for base flipping in bound DNA. The vectors of the low-frequency normal mode of residues Ser-85 and Ile-86 point directly to the phosphate and ribose moieties of the DNA backbone near the target base in position to rotate the dihedral angles and flip the base out of the DNA duplex. The vector of residue Gln-237 on the major groove is in the proper orientation to assist base separation. Our results favor the major groove pathway and the protein active process in base flipping.},
  file      = {:by-author/L/Luo/2005_Luo_16194.pdf:PDF},
  keywords  = {HhaI},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Luo1996,
  author    = {Luo, Z. and Wang, R. and Lai, L.},
  journal   = {Journal of Chemical Information and Computer Sciences},
  title     = {RASSE: a new method for structure-based drug design.},
  year      = {1996},
  pages     = {1187--1194},
  volume    = {36},
  abstract  = {A novel method, RASSE, has been developed to suggest reasonable structures which can fit well to the binding sites of receptors. Molecules are generated by an iterative growing procedure in which atoms are added to existing fragments. Potential ligands are then picked out by special scoring rules. This atomgrowing based method is characterized by combinatorial searching of atom types and conformations. To some extent, it is the computer simulation of combinatorial chemistry. This method has been applied to the design of inhibitors for E. coli dihydrofolate reductase and human phospholipase A2. The results demonstrate that this program is capable of generating reasonable structures, thus proving its power in drug design.},
  doi       = {10.1021/ci950277w},
  file      = {:by-author/L/Luo/1996_Luo_1187.pdf:PDF},
  keywords  = {Drug Design},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
  url       = {http://pubs.acs.org/doi/abs/10.1021/ci950277w},
}

@Article{Luscombe2001,
  author      = {Luscombe, N. M. and Laskowski, R. A. and Thornton, J. M.},
  journal     = {Nucleic Acids Res},
  title       = {Amino acid-base interactions: a three-dimensional analysis of protein-DNA interactions at an atomic level.},
  year        = {2001},
  pages       = {2860--2874},
  volume      = {29},
  abstract    = {To assess whether there are universal rules that govern amino acid-base recognition, we investigate hydrogen bonds, van der Waals contacts and water-mediated bonds in 129 protein-DNA complex structures. DNA-backbone interactions are the most numerous, providing stability rather than specificity. For base interactions, there are significant base-amino acid type correlations, which can be rationalised by considering the stereochemistry of protein side chains and the base edges exposed in the DNA structure. Nearly two-thirds of the direct read-out of DNA sequences involves complex networks of hydrogen bonds, which enhance specificity. Two-thirds of all protein-DNA interactions comprise van der Waals contacts, compared to about one-sixth each of hydrogen and water-mediated bonds. This highlights the central importance of these contacts for complex formation, which have previously been relegated to a secondary role. Although common, water-mediated bonds are usually non-specific, acting as space-fillers at the protein-DNA interface. In conclusion, the majority of amino acid-base interactions observed follow general principles that apply across all protein-DNA complexes, although there are individual exceptions. Therefore, we distinguish between interactions whose specificities are 'universal' and 'context-dependent'. An interactive Web-based atlas of side chain-base contacts provides access to the collected data, including analyses and visualisation of the three-dimensional geometry of the interactions.},
  doi         = {10.1093/nar/29.13.2860},
  file        = {2001_Luscombe_2860.pdf:by-author/L/Luscombe/2001_Luscombe_2860.pdf:PDF},
  institution = {Biomolecular Structures and Modelling Unit, Department of Biochemistry and Molecular Biology, University College, Gower Street, London WC1E 6BT, UK.},
  keywords    = {Amino Acid; Base Pairing; Chemistry/genetics/metabolism; Chemistry/metabolism; DNA; DNA Binding Proteins; Databases as Topic; Hydrogen Bonding; Internet; Metabolism; Nucleic Acid Conformation; Protein Binding; Protein Conformation; Sequence Homology; Software; Static Electricity; Substrate Specificity; Water},
  language    = {eng},
  medline-pst = {ppublish},
  owner       = {saulius},
  pmid        = {11433033},
  timestamp = {2012.09.16},
  creationdate = {2012-09-16T00:00:00},
  url         = {http://nar.oxfordjournals.org/content/29/13/2860},
}

@Article{Luscombe1997,
  author      = {Luscombe, N. M. and Laskowski, R. A. and Thornton, J. M.},
  journal     = {Nucleic Acids Res},
  title       = {NUCPLOT: a program to generate schematic diagrams of protein-nucleic acid interactions.},
  year        = {1997},
  pages       = {4940--4945},
  volume      = {25},
  abstract    = {Proteins that bind to DNA are found in all areas of genetic activity within the cell. To help understand how these proteins perform their various functions, it is useful to analyse which residues are involved in binding to the DNA and how they interact with the bases and sugar-phosphate backbone of nucleic acids. Here we describe a program called NUCPLOT which can automatically identify these interactions from the 3D atomic coordinates of the complex from a PDB file and generate a plot that shows all the interactions in a schematic manner. The program produces a PostScript output file representing hydrogen, van der Waals and covalent bonds between the protein and the DNA. The resulting diagram is both clear and simple and allows immediate identification of important interactions within the structure. It also facilitates comparison of binding found in different structures. NUCPLOT is a completely automatic program, which can be used for any protein-DNA complex and will also work for certain protein-RNA structures.},
  doi         = {10.1093/nar/25.24.4940},
  file        = {1997_Luscombe_4940.pdf:by-author/L/Luscombe/1997_Luscombe_4940.pdf:PDF},
  institution = {Biomolecular Structure and Modelling Unit, Department of Biochemistry and Molecular Biology, University College, Gower Street, London WC1E 6BT, UK.},
  keywords    = {Chemistry/metabolism; Computer Graphics; Computer Simulation; DNA; DNA-Binding Proteins; Hydrogen Bonding; Macromolecular Substances; Models; Molecular; Nucleic Acid Conformation; Protein Binding; Protein Conformation; RNA; RNA-Binding Proteins; Repressor Proteins; Transcription Factors; Viral Proteins; Viral Regulatory and Accessory Proteins},
  language    = {eng},
  medline-pst = {ppublish},
  owner       = {saulius},
  pii         = {gka795},
  pmid        = {9396800},
  timestamp = {2012.09.16},
  creationdate = {2012-09-16T00:00:00},
  url         = {http://nar.oxfordjournals.org/content/25/24/4940},
}

@Article{Lushnikov2006,
  author    = {Lushnikov, Alexander Y. and Potaman, Vladimir N. and Oussatcheva, Elena A. and Sinden, Richard R. and Lyubchenko, Yuri L.},
  journal   = {Biochemistry},
  title     = {DNA strand arrangement within the SfiI-DNA complex: atomic force microscopy analysis.},
  year      = {2006},
  pages     = {152--8},
  volume    = {45},
  abstract  = {The SfiI restriction enzyme binds to DNA as a tetramer holding two usually distant DNA recognition sites together before cleavage of the four DNA strands. To elucidate structural properties of the SfiI-DNA complex, atomic force microscopy (AFM) imaging of the complexes under noncleaving conditions (Ca2+ instead of Mg2+ in the reaction buffer) was performed. Intramolecular complexes formed by protein interaction between two binding sites in one DNA molecule (cis interaction) as well as complexes formed by the interaction of two sites in different molecules (trans interaction) were analyzed. Complexes were identified unambiguously by the presence of a tall spherical blob at the DNA intersections. To characterize the path of DNA within the complex, the angles between the DNA helices in the proximity of the complex were systematically analyzed. All the data show clear-cut bimodal distributions centered around peak values corresponding to 60 degrees and 120 degrees. To unambiguously distinguish between the crossed and bent models for the DNA orientation within the complex, DNA molecules with different arm lengths flanking the SfiI binding site were designed. The analysis of the AFM images for complexes of this type led to the conclusion that the DNA recognition sites within the complex are crossed. The angles of 60 degrees or 120 degrees between the DNA helices correspond to a complex in which one of the helices is flipped with respect to the orientation of the other. Complexes formed by five different recognition sequences (5'-GGCCNNNNNGGCC-3'), with different central base pairs, were also analyzed. Our results showed that complexes containing the two possible orientations of the helices were formed almost equally. This suggests no preferential orientation of the DNA cognate site within the complex, suggesting that the central part of the DNA binding site does not form strong sequence specific contacts with the protein.},
  file      = {:by-author/L/Lushnikov/2006_Lushnikov_152.pdf:PDF},
  keywords  = {Tetra; TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Manuscript{Lutterotti2015,
  author     = {Lutterotti, Luca and Chateigner, Daniel and Pillière, Henry and Fontugne, Christophe},
  title      = {Full-pattern search-match using the {C}rystallography {O}pen {D}atabase: an internet tool},
  year       = {2015},
  url        = {http://www.ecole.ensicaen.fr/~chateign/danielc/abstracts/Lutterotti_abstract_RXMatiere2013_FPSM.pdf},
  file       = {2015_Lutterotti.pdf:by-author/L/Lutterotti/2015_Lutterotti.pdf:PDF},
  groups     = {sg/JAC2009, sg/NAR2012},
  owner      = {saulius},
  shorttitle = {Full-pattern search-match using the crystallography open database},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  urldate    = {2015-08-31},
}

@Manuscript{Luxemburg2005,
  author    = {Robert Luxemburg},
  title     = {Die Gesellschaft des Geistigen Eigentums},
  year      = {2005},
  keywords  = {SocialSci},
  language  = {German},
  file      = {:by-author/L/Luxemburg/2005_Luxemburg.txt:},
  owner     = {saulius},
  timestamp = {2015.03.10},
  creationdate = {2015-03-10T00:00:00},
}

@Article{Luzzati1952,
  author    = {Luzzati, V.},
  journal   = {Acta Crystallographica},
  title     = {Traitement statistique des erreurs dans la determination des structures cristallines},
  year      = {1952},
  month     = {Nov},
  number    = {6},
  pages     = {802--810},
  volume    = {5},
  doi       = {10.1107/S0365110X52002161},
  file      = {1952_Luzzati_802.pdf:by-author/L/Luzzati/1952_Luzzati_802.pdf:PDF},
  keywords  = {Error Treatment; X-ray Crystallography},
  language  = {French},
  owner     = {saulius},
  timestamp = {2016.03.05},
  creationdate = {2016-03-05T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0365110X52002161},
}

@Presentation{Lynch2005,
  author    = {Benjamin Lynch and Patton Fast},
  title     = {Introduction to Computational Chemistry},
  year      = {2005},
  file      = {2005_Lynch_slides.pdf:by-author/L/Lynch/2005_Lynch_slides.pdf:PDF},
  keywords  = {QM/MM; Quantum Mechanics (QM); Simulations},
  month     = {jun},
  owner     = {saulius},
  timestamp = {2013.10.20},
  creationdate = {2013-10-20T00:00:00},
  url       = {http://static.msi.umn.edu/tutorial/chemistryphysics/IntroCompChem.pdf},
}

@Article{Lynch2012,
  author    = {John G. Lynch},
  journal   = {Science},
  title     = {Business Journals Combat Coercive Citation},
  year      = {2012},
  pages     = {1169},
  volume    = {335},
  file      = {2012_Lynch_1169.pdf:by-author/L/Lynch/2012_Lynch_1169.pdf:PDF},
  groups    = {sg/Bibliometrics},
  keywords  = {Bibliometrics; Impact Factor (IF); Publication; Publishing; Self Citation},
  owner     = {saulius},
  timestamp = {2013.04.03},
  creationdate = {2013-04-03T00:00:00},
  url       = {http://www.sciencemag.org/content/335/6073/1169.1.full.pdf},
}

@Article{Lynds2008,
  author    = {Lynds, Peter},
  title     = {On a Finite Universe with no Beginning or End},
  year      = {2008},
  file      = {:by-author/L/Lynds/2008_Lynds.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.05.02},
  creationdate = {2012-05-02T00:00:00},
}

@Article{Muller2003,
  author    = {M{\"{u}}ller, Peter and K{\"{o}}pke, Sinje and Sheldrick, George M.},
  journal   = {Acta Crystallographica Section D},
  title     = {Is the bond-valence method able to identify metal atoms in protein structures?},
  year      = {2003},
  pages     = {32--37},
  volume    = {59},
  doi       = {10.1107/S0907444902018000},
  file      = {gr2278.pdf:by-author/M/Muller/2003_Muller_32.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444902018000},
}

@Article{Ma1997,
  author     = {Ma, Jianpeng and Karplus, Martin},
  journal    = {Proceedings of the National Academy of Sciences},
  title      = {Molecular switch in signal transduction: reaction paths of the conformational changes in ras p21},
  year       = {1997},
  issn       = {0027-8424, 1091-6490},
  pages      = {11905--11910},
  volume     = {94},
  abstract   = {Conformational changes in ras p21 triggered by the hydrolysis of GTP play an essential role in the signal transduction pathway. The path for the conformational change is determined by molecular dynamics simulation with a holonomic constraint directing the system from the known GTP-bound structure (with the γ-phosphate removed) to the GDP-bound structure. The simulation is done with a shell of water molecules surrounding the protein. In the switch I region, the side chain of Tyr-32, which undergoes a large displacement, moves through the space between loop 2 and the rest of the protein, rather than on the outside of the protein. As a result, the charged residues Glu-31 and Asp-33, which interact with Raf in the homologous RafRBD–Raps complex, remain exposed during the transition. In the switch II region, the conformational changes of α2 and loop 4 are strongly coupled. A transient hydrogen bonding complex between Arg-68 and Tyr-71 in the switch II region and Glu-37 in switch I region stabilizes the intermediate conformation of α2 and facilitates the unwinding of a helical turn of α2 (residues 66–69), which in turn permits the larger scale motion of loop 4. Hydrogen bond exchange between the protein and solvent molecules is found to be important in the transition. Possible functional implications of the results are discussed.},
  file       = {Full Text PDF:by-author/M/Ma/1997_Ma_11905.pdf:application/pdf;Snapshot:by-author/M/Ma/1997_Ma_11905.html:text/html},
  groups     = {sg/biomolecular},
  keywords   = {Constrained Molecular Dynamics; GTP; Molecular Signals; Phosphate Hydrolysis},
  language   = {en},
  owner      = {saulius},
  pmid       = {9342335},
  shorttitle = {Molecular switch in signal transduction},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url        = {http://www.pnas.org/content/94/22/11905},
  urldate    = {2015-08-05},
}

@Article{Ma2005,
  author    = {Ma, Jin-Biao and Yuan, Yu-Ren and Meister, Gunter and Pei, Yi and Tuschl, Thomas and Patel, Dinshaw J.},
  journal   = {Nature},
  title     = {Structural basis for 5[prime]-end-specific recognition of guide RNA by the A. fulgidus Piwi protein},
  year      = {2005},
  issn      = {0028-0836},
  pages     = {666--670},
  volume    = {434},
  abstract  = {RNA interference (RNAi) is a conserved sequence-specific gene regulatory mechanism1, 2, 3 mediated by the RNA-induced silencing complex (RISC), which is composed of a single-stranded guide RNA and an Argonaute protein. The PIWI domain, a highly conserved motif within Argonaute, has been shown to adopt an RNase H fold4, 5 critical for the endonuclease cleavage activity of RISC4, 5, 6. Here we report the crystal structure of Archaeoglobus fulgidus Piwi protein bound to double-stranded RNA, thereby identifying the binding pocket for guide-strand 5′-end recognition and providing insight into guide-strand-mediated messenger RNA target recognition. The phosphorylated 5′ end of the guide RNA is anchored within a highly conserved basic pocket, supplemented by the carboxy-terminal carboxylate and a bound divalent cation. The first nucleotide from the 5′ end of the guide RNA is unpaired and stacks over a conserved tyrosine residue, whereas successive nucleotides form a four-base-pair RNA duplex. Mutation of the corresponding amino acids that contact the 5′ phosphate in human Ago2 resulted in attenuated mRNA cleavage activity. Our structure of the Piwi–RNA complex, and that determined elsewhere7, provide direct support for the 5′ region of the guide RNA serving as a nucleation site for pairing with target mRNA and for a fixed distance separating the RISC-mediated mRNA cleavage site from the anchored 5′ end of the guide RNA.},
  comment   = {10.1038/nature03514},
  file      = {2005_Ma_666.pdf:by-author/M/Ma/2005_Ma_666.pdf:PDF},
  keywords  = {Crystal Structure; Mrr; Piwi; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2014.04.15},
  creationdate = {2014-04-15T00:00:00},
  url       = {http://dx.doi.org/10.1038/nature03514},
}

@Article{Ma2004,
  author    = {Ma, Yujie and Wang, Tongsheng and Villemain, Jana L. and Giedroc, David P. and Morrical, Scott W.},
  journal   = {The Journal of biological chemistry},
  title     = {Dual functions of single-stranded DNA-binding protein in helicase loading at the bacteriophage T4 DNA replication fork.},
  year      = {2004},
  pages     = {19035--45},
  volume    = {279},
  abstract  = {Semi-conservative DNA synthesis reactions catalyzed by the bacteriophage T4 DNA polymerase holoenzyme are initiated by a strand displacement mechanism requiring gp32, the T4 single-stranded DNA (ssDNA)-binding protein, to sequester the displaced strand. After initiation, DNA helicase acquisition by the nascent replication fork leads to a dramatic increase in the rate and processivity of leading strand DNA synthesis. In vitro studies have established that either of two T4-encoded DNA helicases, gp41 or dda, is capable of stimulating strand displacement synthesis. The acquisition of either helicase by the nascent replication fork is modulated by other protein components of the fork including gp32 and, in the case of the gp41 helicase, its mediator/loading protein gp59. Here, we examine the relationships between gp32 and the gp41/gp59 and dda helicase systems, respectively, during T4 replication using altered forms of gp32 defective in either protein-protein or protein-ssDNA interactions. We show that optimal stimulation of DNA synthesis by gp41/gp59 helicase requires gp32-gp59 interactions and is strongly dependent on the stability of ssDNA binding by gp32. Fluorescence assays demonstrate that gp59 binds stoichiometrically to forked DNA molecules; however, gp59-forked DNA complexes are destabilized via protein-protein interactions with the C-terminal "A-domain" fragment of gp32. These and previously published results suggest a model in which a mobile gp59-gp32 cluster bound to lagging strand ssDNA is the target for gp41 helicase assembly. In contrast, stimulation of DNA synthesis by dda helicase requires direct gp32-dda protein-protein interactions and is relatively unaffected by mutations in gp32 that destabilize its ssDNA binding activity. The latter data support a model in which protein-protein interactions with gp32 maintain dda in a proper active state for translocation at the replication fork. The relationship between dda and gp32 proteins in T4 replication appears similar to the relationship observed between the UL9 helicase and ICP8 ssDNA-binding protein in herpesvirus replication.},
  file      = {:by-author/M/Ma/2004_Ma_19035.pdf:PDF},
  keywords  = {Primosoma; {gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Maarseveen2006,
  author    = {van Maarseveen, Jan H. and Reek, Joost N. H. and Back, Jaap Willem},
  journal   = {Angewandte Chemie (International ed. in English)},
  title     = {Transition-metal catalysis as a tool for the covalent labeling of proteins.},
  year      = {2006},
  pages     = {1841--3},
  volume    = {45},
  file      = {:by-author/v/vanMaarseveen/2006_vanMaarseveen_1841.pdf:PDF},
  keywords  = {Bioconjugation},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@Article{Macivcek1994,
  author    = {Mac{\'\i}{\v{c}}ek, J. and Gradinarov, S. and Bontchev, R. and Balarew, C.},
  journal   = {Acta Crystallographica Section C},
  title     = {A short dynamically symmetrical hydrogen bond in the structure of K[Mg(H${\sb 0.5}$SO${\sb 4}$)${\sb 2}$(H${\sb 2}$O)${\sb 2}$]},
  year      = {1994},
  pages     = {1185--1188},
  volume    = {50},
  doi       = {10.1107/S0108270194002027},
  file      = {:by-author/M/Macíček/1994_Macíček_1185.pdf:PDF},
  owner     = {antanas},
  timestamp = {2013.04.11},
  creationdate = {2013-04-11T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0108270194002027},
}

@Article{MacElrevey2007,
  author    = {MacElrevey, Celeste and Spitale, Robert C. and Krucinska, Jolanta and Wedekind, Joseph E.},
  journal   = {Acta crystallographica. Section D, Biological crystallography},
  title     = {A posteriori design of crystal contacts to improve the X-ray diffraction properties of a small RNA enzyme.},
  year      = {2007},
  pages     = {812--25},
  volume    = {63},
  abstract  = {The hairpin ribozyme is a small catalytic RNA comprising two helix-loop-helix domains linked by a four-way helical junction (4WJ). In its most basic form, each domain can be formed independently and reconstituted without a 4WJ to yield an active enzyme. The production of such minimal junctionless hairpin ribozymes is achievable by chemical synthesis, which has allowed structures to be determined for numerous nucleotide variants. However, abasic and other destabilizing core modifications hinder crystallization. This investigation describes the use of a dangling 5'-U to form an intermolecular U.U mismatch, as well as the use of synthetic linkers to tether the loop A and B domains, including (i) a three-carbon propyl linker (C3L) and (ii) a nine-atom triethylene glycol linker (S9L). Both linker constructs demonstrated similar enzymatic activity, but S9L constructs yielded crystals that diffracted to 2.65 A resolution or better. In contrast, C3L variants diffracted to 3.35 A and exhibited a 15 A expansion of the c axis. Crystal packing of the C3L construct showed a paucity of 6(1) contacts, which comprise numerous backbone to 2'-OH hydrogen bonds in junctionless and S9L complexes. Significantly, the crystal packing in minimal structures mimics stabilizing features observed in the 4WJ hairpin ribozyme structure. The results demonstrate how knowledge-based design can be used to improve diffraction and overcome otherwise destabilizing defects.},
  doi       = {10.1107/S090744490702464X},
  file      = {:by-author/M/MacElrevey/2007_MacElrevey_812.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@PhdThesis{Macernis2011,
  author    = {Mindaugas Mačernis},
  school    = {Vilnius University},
  title     = {Aplinkos poveikis fotoindukuotiems reiškiniams organinėse molekulėse},
  year      = {2011},
  abstract  = {Biologijoje vienas pagrindinių ląstelės makroenergetinių junginių yra adenozintrifosfatas (ATP), kurio sintezei reikalingi protonai (H+). Biologinės molekulės yra nuolatos sintetinamos ląstelėje, pasitelkiant ATP mainų reakciją, kuri, kaip biochemijoje žinoma, yra stimuliuojama fotosinteze [1,2] arba ląsteliniu kvėpavimu [2]. Ląstelinio kvėpavimo mechanizme yra panaudojamas elektrocheminis protonų potencialas, kurį užtikrinti padeda protonų siurbliai. Vienas iš tipinių tokių modelinių siurblių yra bakteriorodopsinas, kurio akty- viajame centre yra atskiriamas protonas. Bakteriorodopsiną sudaro per proto- nuotą Šifo bazę su baltymu sujungtas retinalis [3]. Visgi veikimo principas nė- ra iki galo aiškus [4]. Gyvuose organizmuose retinalis (vitaminas A yra jo at- maina) yra susintetinamas iš β-karotino. Pastarasis priskiriamas karotinoidų klasei, kurie tarpusavyje yra panašios struktūros (bei panašūs į retinalį) [2]. Įdomu tai, kad karotinoidai dalyvaudami fotosintezėje [1], iš esmės atlieka visai kitokias funkcijas. Jie sugeria skirtingo bangos ilgio spinduliuotę negu chlorofilo molekulės, o taip pat atlieka ir apsauginį vaidmenį, t.y. veikia kaip antioksidantai [5]. Pastarasis mechanizmas taip pat nėra iki galo aiškus [1,6]. Skirtingose aplinkose panašių vidinių struktūrų molekulių savybės kinta. Šiame darbe gilinsimės į molekulių elektronines struktūros ir elektroninių spektrų pokyčius, kuriuos nulemia aplinka. Biologinių sistemų modeliavimas yra sudėtingas ir dažnai apsiribojama tik atskirų molekulių būsenų energijų skaičiavimais. Dažnai tik labai tikslūs ab initio kvantinės chemijos metodai leidžia pasiekti reikiamą tikslumą. Pavyz- džiui, modeliuojant karotinoido molekules, kurios, didelės apšvitos sąlygomis, siejamos su nefotocheminiu fotosintezės gesinimu fotosistemoje 2 [7], būtina atsižvelgti į elektronų koreliaciją [1,5,8]. Tačiau, modeliuoti tik atskirų mole- kulių elektroninę struktūrą ir spektrus nepakanka. Tiriamoms savybėms labai svarbi tiriamų molekulių sąveika su aplinkoje esančiomis molekulėmis ar molekuliniais dariniais. Aplinka gali įtakoti įvairias molekulių savybes. Atsižvelgiant į tai, kad tiriamos sistemos yra santykinai labai didelės, tenka modeliuoti sistemas supaprastintais skaičiavimo metodais. Šių metodų galimybių supratimas tampa taip pat labai svarbus. Atskirų molekulių skaičiavimas ir reiškinių jose modeliavimas dažnai galimi tik pasitelkus tikslius ab initio metodus, kas pareikalauja didelių kompiuterinių resursų: superkompiuterių bei lygiagrečių skaičiavimų klasterių.},
  file      = {2011_Mačernis_phdthesis.pdf:by-author/M/Mačernis/2011_Mačernis_phdthesis.pdf:PDF},
  keywords  = {Molecular Simulations; Quantum Mechanics (QM)},
  owner     = {saulius},
  timestamp = {2013.10.20},
  creationdate = {2013-10-20T00:00:00},
  url       = {http://vddb.laba.lt/fedora/get/LT-eLABa-0001:E.02~2011~D_20110307_144822-12362/DS.005.0.01.ETD},
}

@Manual{Macias2000,
  title     = {Documentation for mem_8.bin and alu_test.bin Binary Cell Matrix Files},
  author    = {Macias},
  year      = {2000},
  file      = {:by-author/M/Macias/2000_Macias.pdf:PDF},
  groups    = {sg/Cell Matrix},
  keywords  = {Cell Matrix; Computer Science (CS)},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Presentation{Maciulevicius2008,
  author       = {S. Maciulevičius},
  title        = {Lygiagrečiosios sistemos. Architektūra},
  year         = {2008},
  organization = {Kompiuterių katedra, 209 k.},
  file         = {:by-author/M/Maciulevičius/2008_Maciulevičius.ppt:PPT},
  keywords     = {Computer Science (CS); Databases; Spatial Databases Indexing},
  owner        = {saulius},
  timestamp = {2015.03.03},
  creationdate = {2015-03-03T00:00:00},
}

@Article{MacKerell2003,
  author    = {MacKerell},
  title     = {When DNA Flips Out},
  year      = {2003},
  pages     = {26},
  file      = {:by-author/M/MacKerell/2003_MacKerell_26.pdf:PDF},
  keywords  = {MTases},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Mackerell2004,
  author    = {Mackerell, Alexander D. Jr},
  journal   = {Journal of Computational Chemistry},
  title     = {Empirical Force Fields for Biological Macromolecules: Overview and Issues},
  year      = {2004},
  pages     = {1584--1604},
  abstract  = {Empirical force field-based studies of biological macromolecules are becoming a common tool for investigating their structure–activity relationships at an atomic level of detail. Such studies facilitate interpretation of experimental data and allow for information not readily accessible to experimental methods to be obtained. A large part of the success of empirical force field-based methods is the quality of the force fields combined with the algorithmic advances that allow for more accurate reproduction of experimental observables. Presented is an overview of the issues associated with the development and application of empirical force fields to biomolecular systems. This is followed by a summary of the force fields commonly applied to the different classes of biomolecules; proteins, nucleic acids, lipids, and carbohydrates. In addition, issues associated with computational studies on “heterogeneous” biomolecular systems and the transferability of force fields to a wide range of organic molecules of pharmacological interest are discussed.},
  file      = {:by-author/M/Mackerell/2004_Mackerell_1584.pdf:PDF},
  keywords  = {Forcefields},
  owner     = {andrius},
  timestamp = {2012.05.07},
  creationdate = {2012-05-07T00:00:00},
}

@Article{Madden2006,
  author    = {Madden, Timothy J and McGuigan, William and Molitsky, Michael J and Naday, Istvan and McArthur, Alan and Westbrook, Edwin M},
  journal   = {IEEE transactions on nuclear science},
  title     = {Lens-Coupled CCD Detector for X-ray Crystallography.},
  year      = {2006},
  pages     = {729--734},
  volume    = {2},
  abstract  = {An x-ray crystallography detector (Blue-1) has been built based upon a Fairchild 486 back-illuminated CCD and a custom lens system designed by Optics One Inc. The advantages of our Blue-1 lens system over more conventional fiber-optic tapers are: lower noise and higher efficiency; improved point spread function; negligible spatial distortion; and lack of "chicken-wire" patterns. Also, the engineering is simpler because the CCD is not bonded to the fiber-optic taper. A unique mechanical design has been employed to accurately focus the image on the CCD. The detector software is based on MATLAB and takes advantage of its powerful imaging and signal processing libraries. The CCD timing can be updated on the fly by using a "CCD controller language" to specify timing.},
  file      = {2006_Madden_729.pdf:by-author/M/Madden/2006_Madden_729.pdf:PDF},
  keywords  = {Detectors; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Madsen2013,
  author    = {Madsen, Anders {\O}stergaard and Civalleri, Bartolomeo and Ferrabone, Matteo and Pascale, Fabien and Erba, Alessandro},
  journal   = {Acta Crystallographica Section A},
  title     = {Anisotropic displacement parameters for molecular crystals from periodic Hartree{--}Fock and density functional theory calculations},
  year      = {2013},
  pages     = {309--321},
  volume    = {69},
  abstract  = {Fully periodic Hartree-Fock and density functional theory calculations have been used to compute the anisotropic displacement parameters (ADPs) of molecular crystals at different temperatures by using the CRYSTAL code. Crystalline urea was adopted as a benchmark system to investigate the dependence on basis set and Hamiltonian. The results were compared with ADPs derived from neutron diffraction experiments. The approach can estimate the internal ADPs, corresponding to the contributions of high-frequency intramolecular vibrations, and for these internal contributions the results are almost independent of the basis set and Hamiltonian. Much larger variations and discrepancies from neutron diffraction experiments are seen for the external, low-frequency modes, which become dominant at higher temperatures. The approach was then tested on benzene and urotropine. Finally, ADPs of L-alanine were predicted at the B3LYP/6-31G(d,p) level of theory. The total ADPs, including low-frequency external modes, are underestimated, but can be brought into good agreement with the experimental ADPs by introducing a Grüneisen parameter, which partly accounts for anharmonicity of the potential energy surface, but likely also contains contributions from other deficiencies of the calculations.},
  doi       = {10.1107/S0108767313005011},
  file      = {2013_Madsen_309.pdf:by-author/M/Madsen/2013_Madsen_309.pdf:PDF},
  keywords  = {Anisotropic Temperature Factors; Crystallography; Density Functional Theory (DFT); Hartree-Fock},
  owner     = {saulius},
  timestamp = {2013.04.18},
  creationdate = {2013-04-18T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0108767313005011},
}

@Article{Mahajan2006,
  author    = {Mahajan},
  title     = {Large Scale Molecular Dynamics Simulations for the Derivation of Solvation Free Energies of Strongly Hydrophobic Molecules},
  year      = {2006},
  pages     = {173},
  file      = {:by-author/M/Mahajan/2006_Mahajan_173.pdf:PDF},
  keywords  = {Molecular Dynamics (MD)},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@MastersThesis{Mahlke1992,
  author    = {Scott Alan Mahlke},
  school    = {Graduate College of the University of Illinois at Urbana-Champaign},
  title     = {Design and implementation of a portable global code optimizer},
  year      = {1992},
  file      = {:by-author/M/Mahlke/1992_Mahlke.ps.Z:PostScript;:by-author/M/Mahlke/1992_Mahlke.pdf:PDF},
  keywords  = {Computer Science (CS)},
  owner     = {saulius},
  timestamp = {2015.02.28},
  creationdate = {2015-02-28T00:00:00},
}

@Article{Mai2017,
  author    = {Hien Duy Mai and Khezina Rafiq and Hyojong Yoo},
  journal   = {Chemistry - A European Journal},
  title     = {Nano Metal-Organic Framework-Derived Inorganic Hybrid Nanomaterials: Synthetic Strategies and Applications},
  year      = {2017},
  month     = {jan},
  doi       = {10.1002/chem.201604703},
  file      = {:by-author/M/Mai/2017_Mai.pdf:PDF},
  groups    = {sg/MOF, sg/MOFs, am/MOFs},
  owner     = {saulius},
  publisher = {Wiley-Blackwell},
  timestamp = {2017.01.31},
  creationdate = {2017-01-31T00:00:00},
  url       = {https://doi.org/10.1002%2Fchem.201604703},
}

@Manuscript{Maisonobe2007,
  author    = {Maisonobe},
  title     = {Finding The Circle That Best Fits a Set of Points},
  year      = {2007},
  keywords  = {Algorithms; Circle Fitting; Computer Science (CS)},
  file      = {:by-author/M/Maisonobe/2007_Maisonobe.pdf:PDF},
  groups    = {sg/Arc fitting, sg/Bioinf. Algorithms},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Maiti2004,
  author           = {Maiti, Rajarshi and Van Domselaar, Gary H. and Zhang, Haiyan and Wishart, David S.},
  journal          = {Nucleic acids research},
  title            = {{SuperPose}: a simple server for sophisticated structural superposition},
  year             = {2004},
  issn             = {1362-4962},
  month            = jul,
  number           = {Web Server},
  pages            = {W590-4},
  volume           = {32},
  abstract         = {The SuperPose web server rapidly and robustly calculates both pairwise and multiple protein structure superpositions using a modified quaternion eigenvalue approach. SuperPose generates sequence alignments, structure alignments, PDB (Protein Data Bank) coordinates and RMSD statistics, as well as difference distance plots and images (both static and interactive) of the superimposed molecules. SuperPose employs a simple interface that requires only PDB files or accession numbers as input. All other superposition decisions are made by the program. SuperPose is uniquely able to superimpose structures that differ substantially in sequence, size or shape. It is also capable of handling a much larger range of superposition queries and situations than many standalone programs and yields results that are intuitively more in agreement with known biological or structural data. The SuperPose web server is freely accessible at http://wishart.biology.ualberta.ca/SuperPose/.},
  creationdate     = {2012-10-21T00:00:00},
  doi              = {10.1093/nar/gkh477},
  file             = {:by-author/M/Maiti/2004_Maiti_W590.pdf:PDF},
  keywords         = {Protein Bioinformatics; Rotational Superposition; Structure Superposition; Superposition},
  modificationdate = {2024-05-12T11:36:53},
  owner            = {saulius},
  publisher        = {Oxford University Press (OUP)},
  timestamp        = {2012.10.21},
}

@Article{Makarova2011b,
  author    = {Kira S Makarova and L. Aravind and Yuri I. Wolf and Eugene V Koonin},
  journal   = {Biology Direct},
  title     = {Unification of {Cas} protein families and a simple scenario for the origin and evolution of {CRISPR-Cas} systems},
  year      = {2011},
  pages     = {6:38},
  file      = {:by-author/M/Makarova/2011_Makarova_6\:38.pdf:PDF},
  groups    = {sg/CRISPR-Cas},
  keywords  = {CRISPR},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Makarova2011a,
  author    = {Kira S. Makarova and Daniel H. Haft and Rodolphe Barrangou and Stan J. J. Brouns and Emmanuelle Charpentier and Philippe Horvath and Sylvain Moineau and Francisco J. M. Mojica and Yuri I. Wolf and Alexander F. Yakunin and John van der Oost and Eugene V. Koonin},
  journal   = {Nature Reviews Microbiology},
  title     = {Evolution and classification of the {CRISPR-Cas} systems},
  year      = {2011},
  pages     = {1},
  abstract  = {Abstract | The CRISPR–Cas (clustered regularly interspaced short palindromic repeats–CRISPR-associated proteins) modules are adaptive immunity systems that are present in many archaea and bacteria. These defence systems are encoded by operons that have an extraordinarily diverse architecture and a high rate of evolution for both the cas genes and the unique spacer content. Here, we provide an updated analysis of the evolutionary relationships between CRISPR–Cas systems and Cas proteins. Three major types of CRISPR–Cas system are delineated, with a further division into several subtypes and a few chimeric variants. Given the complexity of the genomic architectures and the extremely dynamic evolution of the CRISPR–Cas systems, a unified classification of these systems should be based on multiple criteria. Accordingly, we propose a ‘polythetic’ classification that integrates the phylogenies of the most common cas genes, the sequence and organization of the CRISPR repeats and the architecture of the CRISPR–cas loci.},
  doi       = {10.1038/nrmicro2577},
  file      = {:by-author/M/Makarova/2011_Makarova_1.pdf:PDF},
  groups    = {sg/CRISPR-Cas},
  keywords  = {CRISPR; Review},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Makarova2013,
  author    = {Makarova, Kira S. and Wolf, Yuri I. and Koonin, Eugene V.},
  journal   = {Nucleic Acids Research},
  title     = {Comparative genomics of defense systems in archaea and bacteria},
  year      = {2013},
  pages     = {4360--4377},
  volume    = {41},
  abstract  = {Our knowledge of prokaryotic defense systems has vastly expanded as the result of comparative genomic analysis, followed by experimental validation. This expansion is both quantitative, including the discovery of diverse new examples of known types of defense systems, such as restriction-modification or toxin-antitoxin systems, and qualitative, including the discovery of fundamentally new defense mechanisms, such as the CRISPR-Cas immunity system. Large-scale statistical analysis reveals that the distribution of different defense systems in bacterial and archaeal taxa is non-uniform, with four groups of organisms distinguishable with respect to the overall abundance and the balance between specific types of defense systems. The genes encoding defense system components in bacterial and archaea typically cluster in defense islands. In addition to genes encoding known defense systems, these islands contain numerous uncharacterized genes, which are candidates for new types of defense systems. The tight association of the genes encoding immunity systems and dormancy- or cell death-inducing defense systems in prokaryotic genomes suggests that these two major types of defense are functionally coupled, providing for effective protection at the population level.},
  doi       = {10.1093/nar/gkt157},
  eprint    = {http://nar.oxfordjournals.org/content/41/8/4360.full.pdf+html},
  file      = {2013_Makarova_4360.pdf:by-author/M/Makarova/2013_Makarova_4360.pdf:PDF},
  groups    = {sg/CRISPR-Cas},
  owner     = {saulius},
  timestamp = {2015.01.30},
  creationdate = {2015-01-30T00:00:00},
  url       = {http://nar.oxfordjournals.org/content/41/8/4360.abstract},
}

@Article{Makarova2009,
  author    = {Makarova, Kira S. and Wolf, Yuri I. and van der Oost, John and Koonin, Eugene V.},
  journal   = {Biology Direct},
  title     = {Prokaryotic homologs of Argonaute proteins are predicted to function as key components of a novel system of defense against mobile genetic elements},
  year      = {2009},
  pages     = {1--15},
  volume    = {4},
  abstract  = {Background In eukaryotes, RNA interference (RNAi) is a major mechanism of defense against viruses and transposable elements as well of regulating translation of endogenous mRNAs. The RNAi systems recognize the target RNA molecules via small guide RNAs that are completely or partially complementary to a region of the target. Key components of the RNAi systems are proteins of the Argonaute-PIWI family some of which function as slicers, the nucleases that cleave the target RNA that is base-paired to a guide RNA. Numerous prokaryotes possess the CRISPR-associated system (CASS) of defense against phages and plasmids that is, in part, mechanistically analogous but not homologous to eukaryotic RNAi systems. Many prokaryotes also encode homologs of Argonaute-PIWI proteins but their functions remain unknown. Results We present a detailed analysis of Argonaute-PIWI protein sequences and the genomic neighborhoods of the respective genes in prokaryotes. Whereas eukaryotic Ago/PIWI proteins always contain PAZ (oligonucleotide binding) and PIWI (active or inactivated nuclease) domains, the prokaryotic Argonaute homologs (pAgos) fall into two major groups in which the PAZ domain is either present or absent. The monophyly of each group is supported by a phylogenetic analysis of the conserved PIWI-domains. Almost all pAgos that lack a PAZ domain appear to be inactivated, and the respective genes are associated with a variety of predicted nucleases in putative operons. An additional, uncharacterized domain that is fused to various nucleases appears to be a unique signature of operons encoding the short (lacking PAZ) pAgo form. By contrast, almost all PAZ-domain containing pAgos are predicted to be active nucleases. Some proteins of this group (e.g., that from Aquifex aeolicus) have been experimentally shown to possess nuclease activity, and are not typically associated with genes for other (putative) nucleases. Given these observations, the apparent extensive horizontal transfer of pAgo genes, and their common, statistically significant over-representation in genomic neighborhoods enriched in genes encoding proteins involved in the defense against phages and/or plasmids, we hypothesize that pAgos are key components of a novel class of defense systems. The PAZ-domain containing pAgos are predicted to directly destroy virus or plasmid nucleic acids via their nuclease activity, whereas the apparently inactivated, PAZ-lacking pAgos could be structural subunits of protein complexes that contain, as active moieties, the putative nucleases that we predict to be co-expressed with these pAgos. All these nucleases are predicted to be DNA endonucleases, so it seems most probable that the putative novel phage/plasmid-defense system targets phage DNA rather than mRNAs. Given that in eukaryotic RNAi systems, the PAZ domain binds a guide RNA and positions it on the complementary region of the target, we further speculate that pAgos function on a similar principle (the guide being either DNA or RNA), and that the uncharacterized domain found in putative operons with the short forms of pAgos is a functional substitute for the PAZ domain. Conclusion The hypothesis that pAgos are key components of a novel prokaryotic immune system that employs guide RNA or DNA molecules to degrade nucleic acids of invading mobile elements implies a functional analogy with the prokaryotic CASS and a direct evolutionary connection with eukaryotic RNAi. The predictions of the hypothesis including both the activities of pAgos and those of the associated endonucleases are readily amenable to experimental tests.},
  doi       = {10.1186/1745-6150-4-29},
  file      = {:by-author/M/Makarova/2009_Makarova_1.pdf:PDF},
  groups    = {sg/CRISPR-Cas},
  keywords  = {Argonaute; Bacterial Defense; Evolution; PAgo; PIWI; RNA Interference},
  owner     = {em},
  timestamp = {2013.10.29},
  creationdate = {2013-10-29T00:00:00},
}

@Article{Makarova2011,
  author    = {Makarova, Kira S. and Wolf, Yuri I. and Snir, Sagi and Koonin, Eugene V.},
  journal   = {Journal of bacteriology},
  title     = {Defense islands in bacterial and archaeal genomes and prediction of novel defense systems.},
  year      = {2011},
  pages     = {6039--56},
  volume    = {193},
  abstract  = {The arms race between cellular life forms and viruses is a major driving force of evolution. A substantial fraction of bacterial and archaeal genomes is dedicated to antivirus defense. We analyzed the distribution of defense genes and typical mobilome components (such as viral and transposon genes) in bacterial and archaeal genomes and demonstrated statistically significant clustering of antivirus defense systems and mobile genes and elements in genomic islands. The defense islands are enriched in putative operons and contain numerous overrepresented gene families. A detailed sequence analysis of the proteins encoded by genes in these families shows that many of them are diverged variants of known defense system components, whereas others show features, such as characteristic operonic organization, that are suggestive of novel defense systems. Thus, genomic islands provide abundant material for the experimental study of bacterial and archaeal antivirus defense. Except for the CRISPR-Cas systems, different classes of defense systems, in particular toxin-antitoxin and restriction-modification systems, show nonrandom clustering in defense islands. It remains unclear to what extent these associations reflect functional cooperation between different defense systems and to what extent the islands are genomic &quot;sinks&quot; that accumulate diverse nonessential genes, particularly those acquired via horizontal gene transfer. The characteristics of defense islands resemble those of mobilome islands. Defense and mobilome genes are nonrandomly associated in islands, suggesting nonadaptive evolution of the islands via a preferential attachment-like mechanism underpinned by the addictive properties of defense systems such as toxins-antitoxins and an important role of horizontal mobility in the evolution of these islands.},
  file      = {:by-author/M/Makarova/2011_Makarova_6039.pdf:PDF},
  groups    = {sg/CRISPR-Cas},
  keywords  = {CRISPR},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@MastersThesis{Makarova2012,
  author    = {Natalya Makarova},
  school    = {Department of Statistics, College of Arts and Sciences, Kansas State University},
  title     = {A Simulation Study Of The Robustness Of Prediction Intervals For An Independent Observation Obtained From A Random Sample From An Assumed Location-scale Family Of Distributions},
  year      = {2012},
  abstract  = {Suppose that based on data consisting of independent repetitions of an experiment a researcher wants to predict the outcome of the next independent outcome of the experiment. The researcher models the data as being realizations of independent, identically distributed random variables { Xi, i=1,2,..n} having density f() and the next outcome as the value of an independent random variable Y , also having density f() . We assume that the density f() lies in one of three location-scale families: standard normal (symmetric); Cauchy (symmetric, heavy-tailed); extreme value (asymmetric.). The researcher does not know the values of the location and scale parameters. For f() = f0() lying in one of these families, an exact prediction interval for Y can be constructed using equivariant estimators of the location and scale parameters to form a pivotal quantity based on { Xi, i=1,2,..n} and Y. This report investigates via a simulation study the performance of these prediction intervals in terms of coverage rate and length when the assumption that f() = f0() is correct and when it is not. The simulation results indicate that prediction intervals based on the assumption of normality perform quite well with normal and extreme value data and reasonably well with Cauchy data when the sample sizes are large. The heavy tailed Cauchy assumption only leads to prediction intervals that perform well with Cauchy data and is not robust when the data are normal and extreme value. Similarly, the asymmetric extreme value model leads to prediction intervals that only perform well with extreme value data. Overall, this study indicates robustness with respect to a mismatch between the assumed and actual distributions in some cases and a lack of robustness in others.},
  file      = {:by-author/M/Makarova/2012_Makarova_mscthesis.pdf:PDF},
  keywords  = {R; Simulation},
  owner     = {andrius},
  timestamp = {2014.04.22},
  creationdate = {2014-04-22T00:00:00},
  url       = {http://hdl.handle.net/2097/14749},
}

@Article{Makholm2005,
  author     = {Makholm, Henning and Wells, J. B.},
  journal    = {SIGPLAN Not.},
  title      = {Type inference, principal typings, and let-polymorphism for first-class mixin modules},
  year       = {2005},
  issn       = {0362-1340},
  pages      = {156--167},
  volume     = {40},
  acmid      = {1086386},
  address    = {New York, NY, USA},
  doi        = {10.1145/1090189.1086386},
  file       = {2005_Makholm_ICFP_ACM_conf_proceedings_156--type_inference_principal_typings_let-polymorphism.pdf:by-author/M/Makholm/2005_Makholm.pdf:PDF},
  issue_date = {September 2005},
  keywords   = {Computer Science (CS); Polymorphism; Record Concatenation; Row Unification; Type Systems; type systems.mixin modules},
  numpages   = {12},
  owner      = {saulius},
  publisher  = {ACM},
  timestamp = {2012.11.27},
  creationdate = {2012-11-27T00:00:00},
  url        = {http://doi.acm.org/10.1145/1090189.1086386},
}

@PhdThesis{Makin2005,
  author    = {Sumner Makin},
  school    = {Clare College, University of Cambridge},
  title     = {Studies of Amyloid Nanostructure},
  year      = {2005},
  abstract  = {Amyloid fibril self-assembly, from a disparate group of soluble precursor peptides, is central to the pathology of many diseases. Knowledge of the structure and formation of these fibrils is critical to the understanding required for the rational design of drugs capable of inhibiting fibrillogenesis and promoting disaggregation. Amyloidogenic potential is thought to be an almost universal property of protein. It is therefore desirable that the three-dimensional structure and architecture of amyloid be understood. The insolubility and texture of the amyloid fibrils frustrate the usual techniques of X-ray crystallography and solution nuclear magnetic resonance. We have investigated the structure of amyloid fibrils formed from various peptides, including islet amyloid polypeptide (type II diabetes) and designed peptides. Computer programs have been written which enable structural analysis using data from X-ray fibre diffraction, electron microscopy and electron diffraction. Our twelve-residue, sequence-designed peptide forms fibrous nano-crystallites, which diffract to high resolution (> 0.1 nm). Our analyses favour a hydrogen-bonded $\beta$-sheet as the fundamental crystalline entity within these fibrils and show how the fibril is held together. Fine structural details have been revealed, including salt-bridges and $\pi$-$\pi$ bonding between adjacent phenylalanine residues. Consequently, the data from many different fibrils contributes to the understanding of the formation and structure of the generic amyloid fibril.},
  file      = {:by-author/M/Makin/2005_Makin_phdthesis.pdf:PDF},
  owner     = {saulius},
  pages     = {phdthesis},
  timestamp = {2012.09.18},
  creationdate = {2012-09-18T00:00:00},
}

@Manuscript{Makin2004,
  author    = {Thomas R. Makin},
  title     = {Hotel checking: you can check out any time you want, but can you ever leave? The patenting of business methods},
  year      = {2004},
  keywords  = {Patentai; Teise},
  file      = {:by-author/M/Makin/2004_Makin.doc:DOC},
  owner     = {saulius},
  timestamp = {2015.02.28},
  creationdate = {2015-02-28T00:00:00},
}

@Article{Makovets1999,
  author    = {Makovets, S. and Doronina, V. A. and Murray, N. E.},
  journal   = {Proceedings of the National Academy of Sciences of the United States of America},
  title     = {Regulation of endonuclease activity by proteolysis prevents breakage of unmodified bacterial chromosomes by type I restriction enzymes.},
  year      = {1999},
  pages     = {9757--62},
  volume    = {96},
  abstract  = {ClpXP-dependent proteolysis has been implicated in the delayed detection of restriction activity after the acquisition of the genes (hsdR, hsdM, and hsdS) that specify EcoKI and EcoAI, representatives of two families of type I restriction and modification (R-M) systems. Modification, once established, has been assumed to provide adequate protection against a resident restriction system. However, unmodified targets may be generated in the DNA of an hsd(+) bacterium as the result of replication errors or recombination-dependent repair. We show that ClpXP-dependent regulation of the endonuclease activity enables bacteria that acquire unmodified chromosomal target sequences to survive. In such bacteria, HsdR, the polypeptide of the R-M complex essential for restriction but not modification, is degraded in the presence of ClpXP. A mutation that blocks only the modification activity of EcoKI, leaving the cell with approximately 600 unmodified targets, is not lethal provided that ClpXP is present. Our data support a model in which the HsdR component of a type I restriction endonuclease becomes a substrate for proteolysis after the endonuclease has bound to unmodified target sequences, but before completion of the pathway that would result in DNA breakage.},
  file      = {:by-author/M/Makovets/1999_Makovets_9757.pdf:PDF},
  keywords  = {TypeI},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Makovets2004,
  author    = {Makovets, Svetlana and Powell, Lynn M. and Titheradge, Annette J. B. and Blakely, Garry W. and Murray, Noreen E.},
  journal   = {Molecular microbiology},
  title     = {Is modification sufficient to protect a bacterial chromosome from a resident restriction endonuclease?},
  year      = {2004},
  pages     = {135--47},
  volume    = {51},
  abstract  = {It has been generally accepted that DNA modification protects the chromosome of a bacterium encoding a restriction and modification system. But, when target sequences within the chromosome of one such bacterium (Escherichia coli K-12) are unmodified, the cell does not destroy its own DNA; instead, ClpXP inactivates the nuclease, and restriction is said to be alleviated. Thus, the resident chromosome is recognized as 'self' rather than 'foreign' even in the absence of modification. We now provide evidence that restriction alleviation may be a characteristic of Type I restriction-modification systems, and that it can be achieved by different mechanisms. Our experiments support disassembly of active endonuclease complexes as a potential mechanism. We identify amino acid substitutions in a restriction endonuclease, which impair restriction alleviation in response to treatment with a mutagen, and demonstrate that restriction alleviation serves to protect the chromosome even in the absence of mutagenic treatment. In the absence of efficient restriction alleviation, a Type I restriction enzyme cleaves host DNA and, under these conditions, homologous recombination maintains the integrity of the bacterial chromosome.},
  file      = {:by-author/M/Makovets/2004_Makovets_135.pdf:PDF},
  keywords  = {TypeI},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Presentation{Makowski2010,
  author    = {Lee Makowski},
  title     = {{WAXS} – going beyond {SAXS}},
  year      = {2010},
  file      = {:by-author/M/Makowski/2010_Makowski_slides.pdf:PDF},
  keywords  = {SAXS},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Unpublished{Malcolm19XX,
  author    = {Grant Malcolm and Joseph A. Goguen},
  note      = {Programming Research Group, Oxford University},
  title     = {An Executable Course in the Algebraic Semantics of Imperative Programs},
  year      = {19XX},
  file      = {19xx_Malcolm_manuscript.ps:by-author/M/Malcolm/19xx_Malcolm_manuscript.ps:PostScript},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@Article{Malinowski2007,
  author     = {Malinowski, Elzbieta and Zim\'{a}nyi, Esteban},
  journal    = {Geoinformatica},
  title      = {Logical Representation of a Conceptual Model for Spatial Data Warehouses},
  year       = {2007},
  issn       = {1384-6175},
  pages      = {431--457},
  volume     = {11},
  abstract   = {The MultiDimER model is a conceptual model used for representing a multidimensional view of data for Data Warehouse (DW) and On-Line Analytical Processing (OLAP) applications. This model includes a spatial extension allowing spatiality in levels, hierarchies, fact relationships, and measures. In this way decision-making users can represent in an abstract manner their analysis needs without considering complex implementation issues and spatial OLAP tools developers can have a common vision for representing spatial data in a multidimensional model. In this paper we propose the transformation of a conceptual schema based on the MultiDimER constructs to an object-relational schema. We based our mapping on the SQL:2003 and SQL/MM standards giving examples of commercial implementation using Oracle 10g with its spatial extension. Further we use spatial integrity constraints to ensure the semantic equivalence of the conceptual and logical schemas. We also show some examples of Oracle spatial functions, including aggregation functions required for the manipulation of spatial data. The described mappings to the object-relational model along with the examples using a commercial system show the feasibility of implementing spatial DWs in current commercial DBMSs. Further, using integrated architectures, where spatial and thematic data is defined within the same DBMS, facilitates the system management simplifying data definition and manipulation.},
  acmid      = {1295836},
  address    = {Hingham, MA, USA},
  doi        = {10.1007/s10707-007-0022-3},
  file       = {:by-author/M/Malinowski/2007_Malinowski_431.pdf:PDF},
  issue_date = {December 2007},
  keywords   = {Logical Modeling; Spatial Data Warehouses; Spatial Databases; Spatial Hierarchies; Spatial Measures},
  numpages   = {27},
  owner      = {saulius},
  publisher  = {Kluwer Academic Publishers},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url        = {http://dx.doi.org/10.1007/s10707-007-0022-3},
}

@Article{Mallam2011,
  author    = {Mallam, Anna L. and Jarmoskaite, Inga and Tijerina, Pilar and Del Campo, Mark and Seifert, Soenke and Guo, Liang and Russell, Rick and Lambowitz, Alan M.},
  journal   = {Proc. Natl. Acad. Sci. U.S.A.},
  title     = {Solution structures of DEAD-box RNA chaperones reveal conformational changes and nucleic acid tethering by a basic tail.},
  year      = {2011},
  pages     = {12254--9},
  volume    = {108},
  abstract  = {The mitochondrial DEAD-box proteins Mss116p of Saccharomyces cerevisiae and CYT-19 of Neurospora crassa are ATP-dependent helicases that function as general RNA chaperones. The helicase core of each protein precedes a C-terminal extension and a basic tail, whose structural role is unclear. Here we used small-angle X-ray scattering to obtain solution structures of the full-length proteins and a series of deletion mutants. We find that the two core domains have a preferred relative orientation in the open state without substrates, and we visualize the transition to a compact closed state upon binding RNA and adenosine nucleotide. An analysis of complexes with large chimeric oligonucleotides shows that the basic tails of both proteins are attached flexibly, enabling them to bind rigid duplex DNA segments extending from the core in different directions. Our results indicate that the basic tails of DEAD-box proteins contribute to RNA-chaperone activity by binding nonspecifically to large RNA substrates and flexibly tethering the core for the unwinding of neighboring duplexes.},
  file      = {:by-author/M/Mallam/2011_Mallam_12254.pdf:PDF;2011_Mallam_12254-suppl.pdf:by-author/M/Mallam/2011_Mallam_12254-suppl.pdf:PDF},
  keywords  = {Examples; SAXS},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Manuscript{Maloy2001,
  author    = {S. Maloy},
  title     = {Guidelines for Writing a Scientific Paper},
  year      = {2001},
  keywords  = {Scientific Writing},
  url       = {http://www.sci.sdsu.edu/~smaloy/MicrobialGenetics/topics/scientific-writing.pdf},
  file      = {:by-author/M/Maloy/2001_Maloy.pdf:PDF},
  owner     = {andrius},
  timestamp = {2013.02.06},
  creationdate = {2013-02-06T00:00:00},
}

@Article{Malyshev2014,
  author    = {Malyshev, Denis A. and Dhami, Kirandeep and Lavergne, Thomas and Chen, Tingjian and Dai, Nan and Foster, Jeremy M. and Corrêa, Ivan R. and Romesberg, Floyd E.},
  journal   = {Nature},
  title     = {A semi-synthetic organism with an expanded genetic alphabet},
  year      = {2014},
  issn      = {1476-4687},
  month     = {May},
  number    = {7500},
  pages     = {385–388},
  volume    = {509},
  doi       = {10.1038/nature13314},
  file      = {:by-author/M/Malyshev/2014_Malyshev_385.pdf:PDF},
  groups    = {am/Expanded genetic code},
  owner     = {andrius},
  publisher = {Nature Publishing Group},
  timestamp = {2016.05.02},
  creationdate = {2016-05-02T00:00:00},
  url       = {http://dx.doi.org/10.1038/nature13314},
}

@Article{Malyshev2012,
  author    = {Malyshev, D. A. and Dhami, K. and Quach, H. T. and Lavergne, T. and Ordoukhanian, P. and Torkamani, A. and Romesberg, F. E.},
  journal   = {Proceedings of the National Academy of Sciences},
  title     = {Efficient and sequence-independent replication of DNA containing a third base pair establishes a functional six-letter genetic alphabet},
  year      = {2012},
  issn      = {1091-6490},
  month     = {Jul},
  number    = {30},
  pages     = {12005–12010},
  volume    = {109},
  doi       = {10.1073/pnas.1205176109},
  file      = {:by-author/M/Malyshev/2012_Malyshev_12005.pdf:PDF},
  groups    = {am/Expanded genetic code},
  owner     = {andrius},
  publisher = {Proceedings of the National Academy of Sciences},
  timestamp = {2016.05.02},
  creationdate = {2016-05-02T00:00:00},
  url       = {http://dx.doi.org/10.1073/pnas.1205176109},
}

@Article{Malyshev2015,
  author    = {Malyshev, Denis A. and Romesberg, Floyd E.},
  journal   = {Angew. Chem. Int. Ed.},
  title     = {The Expanded Genetic Alphabet},
  year      = {2015},
  issn      = {1433-7851},
  month     = {Aug},
  number    = {41},
  pages     = {11930–11944},
  volume    = {54},
  doi       = {10.1002/anie.201502890},
  file      = {:by-author/M/Malyshev/2015_Malyshev_11930.pdf:PDF},
  groups    = {am/Expanded genetic code},
  owner     = {andrius},
  publisher = {Wiley-Blackwell},
  timestamp = {2016.05.03},
  creationdate = {2016-05-03T00:00:00},
  url       = {http://dx.doi.org/10.1002/anie.201502890},
}

@Article{Mamin2013,
  author    = {H. J. Mamin and M. Kim and M. H. Sherwood and C. T. Rettner and K. Ohno and D. D. Awschalom and D. Rugar},
  journal   = {Science},
  title     = {Nanoscale Nuclear Magnetic Resonance with a Nitrogen-Vacancy Spin Sensor},
  year      = {2013},
  pages     = {557--560},
  volume    = {339},
  abstract  = {Extension of nuclear magnetic resonance (NMR) to nanoscale samples has been a longstanding challenge because of the insensitivity of conventional detection methods. We demonstrated the use of an individual, near-surface nitrogen-vacancy (NV) center in diamond as a sensor to detect proton NMR in an organic sample located external to the diamond. Using a combination of electron spin echoes and proton spin manipulation, we showed that the NV center senses the nanotesla field fluctuations from the protons, enabling both time-domain and spectroscopic NMR measurements on the nanometer scale.},
  doi       = {10.1126/science.1231540},
  file      = {:by-author/M/Mamin/2013_Mamin_557.pdf:PDF},
  owner     = {andrius},
  timestamp = {2013.02.04},
  creationdate = {2013-02-04T00:00:00},
}

@Article{Mamoulis2003,
  author    = {Nikos Mamoulis and Dimitris Papadias},
  journal   = {IEEE Transactions on Knowledge and Data Engineering},
  title     = {Slot Index Spatial Join},
  year      = {2003},
  pages     = {211--231},
  volume    = {15},
  abstract  = {Efficient processing of spatial joins is very important due to their high cost and frequent application in spatial databases and other areas involving multidimensional data. This paper proposes slot index spatial join (SISJ), an algorithm that joins a nonindexed data set with one indexed by an R-tree. We explore two optimization techniques that reduce the space requirements and the computational cost of SISJ and we compare it, analytically and experimentally, with other spatial join methods for two cases: 1) when the nonindexed input is read from disk and 2) when it is an intermediate result of a preceding database operator in a complex query plan. The importance of buffer splitting between consecutive join operators is also demonstrated through a two-join case study and a method that estimates the optimal splitting is proposed. Our evaluation shows that SISJ outperforms alternative methods in most cases and is suitable for limited memory conditions.},
  file      = {:by-author/M/Mamoulis/2003_Mamoulis_211.pdf:PDF},
  owner     = {saulius},
  publisher = {IEEE},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.125.1014},
}

@Article{Mamoulis2001,
  author    = {Mamoulis, Nikos and Papadias, Dimitris},
  journal   = {ACM Transactions on Database Systems},
  title     = {Multiway Spatial Joins},
  year      = {2001},
  issn      = {0362-5915},
  pages     = {424--475},
  volume    = {26},
  abstract  = {Due to the evolution of Geographical Information Systems, large collections of spatial data having various thematic contents are currently available. As a result, the interest of users is not limited to simple spatial selections and joins, but complex query types that implicate numerous spatial inputs become more common. Although several algorithms have been proposed for computing the result of pairwise spatial joins, limited work exists on processing and optimization of multiway spatial joins. In this article, we review pairwise spatial join algorithms and show how they can be combined for multiple inputs. In addition, we explore the application of synchronous traversal (ST), a methodology that processes synchronously all inputs without producing intermediate results. Then, we integrate the two approaches in an engine that includes ST and pairwise algorithms, using dynamic programming to determine the optimal execution plan. The results show that, in most cases, multiway spatial joins are best processed by combining ST with pairwise methods. Finally, we study the optimization of very large queries by employing randomized search algorithms.},
  doi       = {10.1145/503099.503101},
  file      = {:by-author/M/Mamoulis/2001_Mamoulis_424.pdf:PDF},
  owner     = {saulius},
  publisher = {ACM},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://doi.acm.org/10.1145/503099.503101},
}

@PhdThesis{Manakova2001,
  author    = {Elena Manakova},
  school    = {Fakultät für Chemie der Technischen Universität München},
  title     = {Study of structure and function of GroESL chaperonin system using small angle scattering},
  year      = {2001},
  file      = {:by-author/M/Manakova/2001_Manakova_phdthesis.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@Article{Manakova2012a,
  author      = {Elena Manakova and Saulius Grazulis and Mindaugas Zaremba and Giedre Tamulaitiene and Dmitrij Golovenko and Virginijus Siksnys},
  journal     = {Nucleic Acids Res},
  title       = {Structural mechanisms of the degenerate sequence recognition by Bse634I restriction endonuclease.},
  year        = {2012},
  month       = {Aug},
  number      = {14},
  pages       = {6741--6751},
  volume      = {40},
  abstract    = {Restriction endonuclease Bse634I recognizes and cleaves the degenerate DNA sequence 5'-R/CCGGY-3' (R stands for A or G; Y for T or C, '/' indicates a cleavage position). Here, we report the crystal structures of the Bse634I R226A mutant complexed with cognate oligoduplexes containing ACCGGT and GCCGGC sites, respectively. In the crystal, all potential H-bond donor and acceptor atoms on the base edges of the conserved CCGG core are engaged in the interactions with Bse634I amino acid residues located on the α6 helix. In contrast, direct contacts between the protein and outer base pairs are limited to van der Waals contact between the purine nucleobase and Pro203 residue in the major groove and a single H-bond between the O2 atom of the outer pyrimidine and the side chain of the Asn73 residue in the minor groove. Structural data coupled with biochemical experiments suggest that both van der Waals interactions and indirect readout contribute to the discrimination of the degenerate base pair by Bse634I. Structure comparison between related enzymes Bse634I (R/CCGGY), NgoMIV (G/CCGGC) and SgrAI (CR/CCGGYG) reveals how different specificities are achieved within a conserved structural core.},
  doi         = {10.1093/nar/gks300},
  file        = {2012_Manakova_6741.pdf:by-author/M/Manakova/2012_Manakova_6741.pdf:PDF},
  groups      = {sg/NgoMIV, sg/Bse634I structures, sg/Bse634I},
  institution = {Department of Protein-DNA Interactions, Institute of Biotechnology Vilnius University, Graiciuno 8, LT-02241 Vilnius, Lithuania.},
  keywords    = {Base Pairing; Catalytic Domain; Chemistry/genetics/metabolism; Chemistry/metabolism; Crystallization; DNA; DNA Cleavage; Deoxyribonucleases; Models; Molecular; Mutation; Protein Binding; Protein Conformation; Type II Site-Specific},
  language    = {eng},
  medline-pst = {ppublish},
  owner       = {em},
  pii         = {gks300},
  pmid        = {22495930},
  timestamp = {2016.06.09},
  creationdate = {2016-06-09T00:00:00},
  url         = {http://dx.doi.org/10.1093/nar/gks300},
}

@Article{Manakova2011,
  author    = {Manakova, Elena and Grazulis, Saulius and Zaremba, Mindaugas and Tamulaitiene, Giedre and Golovenko, Dmitrij and Siksnys, Virginijus},
  journal   = {Nucleic acids research},
  title     = {Structural mechanisms of the degenerate sequence recognition by {Bse634I} restriction endonuclease},
  year      = {2011},
  pages     = {suppl},
  file      = {:by-author/M/Manakova/2011_Manakova_suppl.pdf:PDF},
  groups    = {sg/Bse634I structures, sg/Bse634I},
  keywords  = {Bse634I; TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Mandal2004,
  author    = {Mandal, Maumita and Breaker, Ronald R.},
  journal   = {Nature structural \&amp; molecular biology},
  title     = {Adenine riboswitches and gene activation by disruption of a transcription terminator.},
  year      = {2004},
  pages     = {29--35},
  volume    = {11},
  abstract  = {A class of riboswitches that recognizes guanine and discriminates against other purine analogs was recently identified. RNAs that carry the consensus sequence and structural features of guanine riboswitches are located in the 5' untranslated region (UTR) of numerous prokaryotic genes, where they control the expression of proteins involved in purine salvage and biosynthesis. We report that three representatives of this riboswitch class bind adenine with values for apparent dissociation constant (apparent K(d)) that are several orders of magnitude lower than those for binding guanine. Because preference for adenine is attributable to a single nucleotide substitution, the RNA most likely recognizes its ligand by forming a Watson-Crick base pair. In addition, the adenine riboswitch associated with the ydhL gene of Bacillus subtilis functions as a genetic 'on' switch, wherein adenine binding causes a structural rearrangement that precludes formation of an intrinsic transcription terminator stem.},
  file      = {:by-author/M/Mandal/2004_Mandal_29.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Maniatis2005,
  author     = {Maniatis, Petros and Roussopoulos, Mema and Giuli, T. J. and Rosenthal, David S. H. and Baker, Mary},
  journal    = {ACM Trans. Comput. Syst.},
  title      = {The LOCKSS peer-to-peer digital preservation system},
  year       = {2005},
  issn       = {0734-2071},
  pages      = {2--50},
  volume     = {23},
  abstract   = {The LOCKSS project has developed and deployed in a world-wide test a peer-to-peer system for preserving access to journals and other archival information published on the Web. It consists of a large number of independent, low-cost, persistent Web caches that cooperate to detect and repair damage to their content by voting in “opinion polls.” Based on this experience, we present a design for and simulations of a novel protocol for voting in systems of this kind. It incorporates rate limi- tation and intrusion detection to ensure that even some very powerful adversaries attacking over many years have only a small probability of causing irrecoverable damage before being detected.},
  acmid      = {1047917},
  address    = {New York, NY, USA},
  doi        = {10.1145/1047915.1047917},
  file       = {2005_Maniatis_2.pdf:by-author/M/Maniatis/2005_Maniatis_2.pdf:PDF},
  issue_date = {February 2005},
  keywords   = {Databases; Digital Preservation; Rate Limiting; Replicated Storage},
  numpages   = {49},
  owner      = {saulius},
  publisher  = {ACM},
  timestamp = {2012.10.25},
  creationdate = {2012-10-25T00:00:00},
  url        = {http://doi.acm.org/10.1145/1047915.1047917},
}

@Article{Manjasetty2008,
  author    = {Manjasetty, Babu A and Turnbull, Andrew P and Panjikar, Santosh and Büssow, Konrad and Chance, Mark R},
  journal   = {Proteomics},
  title     = {Automated technologies and novel techniques to accelerate protein crystallography for structural genomics.},
  year      = {2008},
  pages     = {612--25},
  volume    = {8},
  abstract  = {The sequence infrastructure that has arisen through large-scale genomic projects dedicated to protein analysis, has provided a wealth of information and brought together scientists and institutions from all over the world. As a consequence, the development of novel technologies and methodologies in proteomics research is helping to unravel the biochemical and physiological mechanisms of complex multivariate diseases at both a functional and molecular level. In the late sixties, when X-ray crystallography had just been established, the idea of determining protein structure on an almost universal basis was akin to an impossible dream or a miracle. Yet only forty years after, automated protein structure determination platforms have been established. The widespread use of robotics in protein crystallography has had a huge impact at every stage of the pipeline from protein cloning, over-expression, purification, crystallization, data collection, structure solution, refinement, validation and data management- all of which have become more or less automated with minimal human intervention necessary. Here, recent advances in protein crystal structure analysis in the context of structural genomics will be discussed. In addition, this review aims to give an overview of recent developments in high throughput instrumentation, and technologies and strategies to accelerate protein structure/function analysis.},
  file      = {2008_Manjasetty_612.pdf:by-author/M/Manjasetty/2008_Manjasetty_612.pdf:PDF},
  keywords  = {Structure Determination; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Presentation{Mankin2009,
  author    = {Alexander Mankin},
  title     = {Nucleotide sequence databases, Database search, Sequence alignment and comparison},
  year      = {2009},
  file      = {2009_Mankin.pdf:by-author/M/Mankin/2009_Mankin.pdf:PDF},
  keywords  = {Algorithms; BLAST; Bioinformatics; FASTA; Sequence Alignment; Sequence Search},
  owner     = {saulius},
  timestamp = {2015.04.16},
  creationdate = {2015-04-16T00:00:00},
  url       = {http://mankinlab.cpb.uic.edu/lectures/PMMP412.Genomics/9.Working_with_sequence_databases.pdf},
}

@Article{Mann2006,
  author     = {Mann, Paul B},
  journal    = {SIGPLAN Not.},
  title      = {A Translational BNF Grammar Notation (TBNF)},
  year       = {2006},
  issn       = {0362-1340},
  pages      = {16--23},
  volume     = {41},
  acmid      = {1147218},
  address    = {New York, NY, USA},
  doi        = {10.1145/1147214.1147218},
  file       = {2006_Mann_16.pdf:by-author/M/Mann/2006_Mann_16.pdf:PDF},
  issue_date = {April 2006},
  keywords   = {AST; BNF; Compiler Compiler; EBNF; Grammar; Grammarware; Intermediate Code; LALR; LL; LR; Language Recognition; Parser; Parser Generator; Syntax},
  numpages   = {8},
  owner      = {saulius},
  publisher  = {ACM},
  timestamp = {2015.06.12},
  creationdate = {2015-06-12T00:00:00},
  url        = {http://doi.acm.org/10.1145/1147214.1147218},
}

@Article{Manolaridis2009,
  author    = {Manolaridis, Ioannis and Mumtsidu, Eleni and Konarev, Peter and Makhov, Alexander M. and Fullerton, Stephen W. and Sinz, Andrea and Kalkhof, Stefan and McGeehan, John E. and Cary, Peter D. and Griffith, Jack D. and Svergun, Dmitri and Kneale, Geoff G. and Tucker, Paul A.},
  journal   = {The Journal of biological chemistry},
  title     = {Structural and biophysical characterization of the proteins interacting with the herpes simplex virus 1 origin of replication.},
  year      = {2009},
  pages     = {16343--53},
  volume    = {284},
  abstract  = {The C terminus of the herpes simplex virus type 1 origin-binding protein, UL9ct, interacts directly with the viral single-stranded DNA-binding protein ICP8. We show that a 60-amino acid C-terminal deletion mutant of ICP8 (ICP8DeltaC) also binds very strongly to UL9ct. Using small angle x-ray scattering, the low resolution solution structures of UL9ct alone, in complex with ICP8DeltaC, and in complex with a 15-mer double-stranded DNA containing Box I of the origin of replication are described. Size exclusion chromatography, analytical ultracentrifugation, and electrophoretic mobility shift assays, backed up by isothermal titration calorimetry measurements, are used to show that the stoichiometry of the UL9ct-dsDNA15-mer complex is 2:1 at micromolar protein concentrations. The reaction occurs in two steps with initial binding of UL9ct to DNA (Kd approximately 6 nM) followed by a second binding event (Kd approximately 0.8 nM). It is also shown that the stoichiometry of the ternary UL9ct-ICP8DeltaC-dsDNA15-mer complex is 2:1:1, at the concentrations used in the different assays. Electron microscopy indicates that the complex assembled on the extended origin, oriS, rather than Box I alone, is much larger. The results are consistent with a simple model whereby a conformational switch of the UL9 DNA-binding domain upon binding to Box I allows the recruitment of a UL9-ICP8 complex by interaction between the UL9 DNA-binding domains.},
  file      = {:by-author/M/Manolaridis/2009_Manolaridis_16343.pdf:PDF},
  keywords  = {MONSA; SAXS},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Manosas2009,
  author    = {Manosas, Maria and Spiering, Michelle M. and Zhuang, Zhihao and Benkovic, Stephen J. and Croquette, Vincent},
  journal   = {Nature chemical biology},
  title     = {Coupling DNA unwinding activity with primer synthesis in the bacteriophage T4 primosome.},
  year      = {2009},
  pages     = {904--12},
  volume    = {5},
  abstract  = {The unwinding and priming activities of the bacteriophage T4 primosome, which consists of a hexameric helicase (gp41) translocating 5' to 3' and an oligomeric primase (gp61) synthesizing primers 5' to 3', have been investigated on DNA hairpins manipulated by a magnetic trap. We find that the T4 primosome continuously unwinds the DNA duplex while allowing for primer synthesis through a primosome disassembly mechanism or a new DNA looping mechanism. A fused gp61-gp41 primosome unwinds and primes DNA exclusively via the DNA looping mechanism. Other proteins within the replisome control the partitioning of these two mechanisms by disfavoring primosome disassembly, thereby increasing primase processivity. In contrast to T4, priming in bacteriophage T7 and Escherichia coli involves discrete pausing of the primosome and dissociation of the primase from the helicase, respectively. Thus nature appears to use several strategies to couple the disparate helicase and primase activities within primosomes.},
  file      = {:by-author/M/Manosas/2009_Manosas_904.pdf:PDF},
  keywords  = {Primosoma; {gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Manosas2009a,
  author    = {Maria Manosas and Michelle M. Spiering and Zhihao Zhuang and Stephen J. Benkovic and Vincent Croquette},
  journal   = {Nature chemical biology},
  title     = {Coupling {DNA} unwinding activity with primer synthesis in the bacteriophage {T4} primosome},
  year      = {2009},
  pages     = {suppl},
  file      = {:by-author/M/Manosas/2009_Manosas_suppl.pdf:PDF},
  keywords  = {{gp41} Helicase},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Manosas2010,
  author    = {Manosas, Maria and Xi, Xu Guang and Bensimon, David and Croquette, Vincent},
  journal   = {Nucleic acids research},
  title     = {Active and passive mechanisms of helicases.},
  year      = {2010},
  pages     = {5518--26},
  volume    = {38},
  abstract  = {In this work, we discuss the active or passive character of helicases. In the past years, several studies have used the theoretical framework proposed by Betterton and Julicher [Betterton, M.D. and Julicher, F. (2005) Opening of nucleic-acid double strands by helicases: active versus passive opening. Phys. Rev. E, 71, 11904-11911.] to analyse the unwinding data and assess the mechanism of the helicase under study (active versus passive). However, this procedure has given rise to apparently contradictory interpretations: helicases exhibiting similar behaviour have been classified as both active and passive enzymes [Johnson, D.S., Bai, L. Smith, B.Y., Patel, S.S. and Wang, M.D. (2007) Single-molecule studies reveal dynamics of DNA unwinding by the ring-shaped T7 helicase. Cell, 129, 1299-1309; Lionnet, T., Spiering, M.M., Benkovic, S.J., Bensimon, D. and Croquette, V. (2007) Real-time observation of bacteriophage T4 gp41 helicase reveals an unwinding mechanism Proc. Natl Acid. Sci., 104, 19790-19795]. In this work, we show that when the helicase under study has not been previously well characterized (namely, if its step size and rate of slippage are unknown) a multi-parameter fit to the afore-mentioned model can indeed lead to contradictory interpretations. We thus propose to differentiate between active and passive helicases on the basis of the comparison between their observed translocation velocity on single-stranded nucleic acid and their unwinding rate of double-stranded nucleic acid (with various GC content and under different tensions). A threshold separating active from passive behaviour is proposed following an analysis of the reported activities of different helicases. We study and contrast the mechanism of two helicases that exemplify these two behaviours: active for the RecQ helicase and passive for the gp41 helicase.},
  file      = {:by-author/M/Manosas/2010_Manosas_5518.pdf:PDF},
  keywords  = {{gp41} Helicase},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Mansy2008,
  author    = {Mansy, Sheref S. and Schrum, Jason P. and Krishnamurthy, Mathangi and Tobe, Sylvia and Treco, Douglas A. and Szostak, Jack W.},
  journal   = {Nature},
  title     = {Template-directed synthesis of a genetic polymer in a model protocell},
  year      = {2008},
  issn      = {0028-0836},
  pages     = {122--125},
  volume    = {454},
  abstract  = {Contemporary phospholipid-based cell membranes are formidable barriers to the uptake of polar and charged molecules ranging from metal ions to complex nutrients. Modern cells therefore require sophisticated protein channels and pumps to mediate the exchange of molecules with their environment. The strong barrier function of membranes has made it difficult to understand the origin of cellular life and has been thought to preclude a heterotrophic lifestyle for primitive cells. Although nucleotides can cross dimyristoyl phosphatidylcholine membranes through defects formed at the gel-to-liquid transition temperature1, 2, phospholipid membranes lack the dynamic properties required for membrane growth. Fatty acids and their corresponding alcohols and glycerol monoesters are attractive candidates for the components of protocell membranes because they are simple amphiphiles that form bilayer membrane vesicles3, 4, 5 that retain encapsulated oligonucleotides3, 6 and are capable of growth and division7, 8, 9. Here we show that such membranes allow the passage of charged molecules such as nucleotides, so that activated nucleotides added to the outside of a model protocell spontaneously cross the membrane and take part in efficient template copying in the protocell interior. The permeability properties of prebiotically plausible membranes suggest that primitive protocells could have acquired complex nutrients from their environment in the absence of any macromolecular transport machinery; that is, they could have been obligate heterotrophs.},
  comment   = {10.1038/nature07018},
  doi       = {10.1038/nature07018},
  file      = {2008_Mansy_122.pdf:by-author/M/Mansy/2008_Mansy_122.pdf:PDF},
  keywords  = {Bilayer Membranes; Origin of Life; RNA World; Self-replicating Molecules; Self-replicating RNA; Synthetic Biology; Vesicles},
  owner     = {saulius},
  publisher = {Macmillan Publishers Limited. All rights reserved},
  timestamp = {2015.03.16},
  creationdate = {2015-03-16T00:00:00},
  url       = {http://dx.doi.org/10.1038/nature07018},
}

@Webpage{Maone,
  author    = {Giorgio Maone},
  retrieved = {2009-02-07},
  title     = {Pure Java(TM), Pure Evil(TM) Popups},
  url       = {http://hackademix.net/2007/08/07/java-evil-popups},
  file      = {:by-author/M/Maone/XXXX_Maone.net_»_Pure_Java™,_Pure_Evil™_Popups.war:WAR},
  keywords  = {Computer Science (CS); Computer Security; Java; Programming Languages; Web Design; Web Security},
  owner     = {saulius},
  timestamp = {2015.03.02},
  creationdate = {2015-03-02T00:00:00},
}

@TechReport{Marco2010,
  author      = {Salathe Marco},
  institution = {Paul Scherrer Institut, Ecole Polytechnique F{\'{e}}d{\'{e}}rale de Lausanne},
  title       = {Evaluation of the sphere of confusion of goniometer devices and analysis of the SmarAct linear positioners},
  year        = {2010},
  month       = {mar},
  file        = {:by-author/M/Marco/2010_Marco.pdf:PDF},
  keywords    = {Goniometer; Sphere of Confusion; X-ray Crystallography; X-ray Diffractometer},
  owner       = {saulius},
  timestamp = {2014.06.29},
  creationdate = {2014-06-29T00:00:00},
  url         = {http://www.psi.ch/sls/pxii/ResearchEN/Internship_Report_Marco_Salathe_2010.pdf},
}

@TechReport{Marcus2015,
  author      = {Adam Marcus and Ivan Oransky},
  institution = {Retraction Watch},
  title       = {If a Retracted Study Falls in the Forest...},
  year        = {2015},
  file        = {c533cbcb-f6f0-43ff-a64a-967071e1783b.pdf:by-author/M/Marcus/2015_Marcus.pdf:application/pdf},
  groups      = {sg/Bibliometrics},
  owner       = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url         = {http://files.ctctcdn.com/47dd037a001/c533cbcb-f6f0-43ff-a64a-967071e1783b.pdf},
  urldate     = {2015-07-06},
}

@Article{Margelevicius2010,
  author    = {Margelevičius, M. and Laganeckas, M. and Venclovas, Č.},
  journal   = {Bioinformatics},
  title     = {{COMA} server for protein distant homology search},
  year      = {2010},
  pages     = {1905--1906},
  volume    = {26},
  abstract  = {Detection of distant homology is a widely used computational approach for studying protein evolution, structure and function. Here, we report a homology search web server based on sequence profile–profile comparison. The user may perform searches in one of several regularly updated profile databases using either a single sequence or a multiple sequence alignment as an input. The same profile databases can also be downloaded for local use. The capabilities of the server are illustrated with the identification of new members of the highly diverse PD-(D/E)XK nuclease superfamily.},
  doi       = {10.1093/bioinformatics/btq306},
  file      = {:by-author/M/Margelevičius/2010_Margelevičius_1905.pdf:PDF},
  keywords  = {Proteins; Structure Prediction},
  owner     = {andrius},
  timestamp = {2013.12.02},
  creationdate = {2013-12-02T00:00:00},
}

@Article{Margelevicius2010a,
  author    = {Margelevičius, Mindaugas and Venclovas, Česlovas},
  journal   = {BMC Bioinformatics},
  title     = {Detection of distant evolutionary relationships between protein families using theory of sequence profile-profile comparison},
  year      = {2010},
  pages     = {89},
  volume    = {11},
  abstract  = {Background: Detection of common evolutionary origin (homology) is a primary means of inferring protein structure and function. At present, comparison of protein families represented as sequence profiles is arguably the most effective homology detection strategy. However, finding the best way to represent evolutionary information of a protein sequence family in the profile, to compare profiles and to estimate the biological significance of such comparisons, remains an active area of research. Results: Here, we present a new homology detection method based on sequence profile-profile comparison. The method has a number of new features including position-dependent gap penalties and a global score system. Position-dependent gap penalties provide a more biologically relevant way to represent and align protein families as sequence profiles. The global score system enables an analytical solution of the statistical parameters needed to estimate the statistical significance of profile-profile similarities. The new method, together with other state-of-the- art profile-based methods (HHsearch, COMPASS and PSI-BLAST), is benchmarked in all-against-all comparison of a challenging set of SCOP domains that share at most 20% sequence identity. For benchmarking, we use a reference ("gold standard”) free model-based evaluation framework. Evaluation results show that at the level of protein domains our method compares favorably to all other tested methods. We also provide examples of the new method outperforming structure-based similarity detection and alignment. The implementation of the new method both as a standalone software package and as a web server is available at http://www.ibt.lt/bioinformatics/ coma. Conclusion: Due to a number of developments, the new profile-profile comparison method shows an improved ability to match distantly related protein domains. Therefore, the method should be useful for annotation and homology modeling of uncharacterized proteins.},
  doi       = {10.1186/1471-2105-11-89},
  file      = {:by-author/M/Margelevičius/2010_Margelevičius_89.pdf:PDF},
  keywords  = {Proteins; Structure Prediction},
  owner     = {andrius},
  timestamp = {2013.12.02},
  creationdate = {2013-12-02T00:00:00},
  url       = {http://www.biomedcentral.com/1471-2105/11/89},
}

@Article{Margelevicius2005,
  author    = {Margelevičius, Mindaugas and Venclovas, Česlovas},
  journal   = {BMC Bioinformatics},
  title     = {{PSI-BLAST-ISS}: an intermediate sequence search tool for estimation of the position-specific alignment reliability},
  year      = {2005},
  issn      = {1471-2105},
  pages     = {185},
  volume    = {6},
  abstract  = {BACKGROUND:Protein sequence alignments have become indispensable for virtually any evolutionary, structural or functional study involving proteins. Modern sequence search and comparison methods combined with rapidly increasing sequence data often can reliably match even distantly related proteins that share little sequence similarity. However, even highly significant matches generally may have incorrectly aligned regions. Therefore when exact residue correspondence is used to transfer biological information from one aligned sequence to another, it is critical to know which alignment regions are reliable and which may contain alignment errors.RESULTS:PSI-BLAST-ISS is a standalone Unix-based tool designed to delineate reliable regions of sequence alignments as well as to suggest potential variants in unreliable regions. The region-specific reliability is assessed by producing multiple sequence alignments in different sequence contexts followed by the analysis of the consistency of alignment variants. The PSI-BLAST-ISS output enables the user to simultaneously analyze alignment reliability between query and multiple homologous sequences. In addition, PSI-BLAST-ISS can be used to detect distantly related homologous proteins. The software is freely available at: http://www.ibt.lt/bioinformatics/iss webcite.CONCLUSION:PSI-BLAST-ISS is an effective reliability assessment tool that can be useful in applications such as comparative modelling or analysis of individual sequence regions. It favorably compares with the existing similar software both in the performance and functional features.},
  doi       = {10.1186/1471-2105-6-185},
  file      = {:by-author/M/Margelevičius/2005_Margelevičius_185.pdf:PDF},
  keywords  = {Proteins; Structure Prediction},
  owner     = {andrius},
  pubmedid  = {16033659},
  timestamp = {2013.11.25},
  creationdate = {2013-11-25T00:00:00},
  url       = {http://www.biomedcentral.com/1471-2105/6/185},
}

@Article{Margolus1987,
  author    = {Norman Margolus and Tommaso Toffoli},
  journal   = {Complex Systems},
  title     = {Cellular Automata Machines},
  year      = {1987},
  pages     = {967--993},
  volume    = {1},
  abstract  = {The advantages of an architecture optimized for cellular automata (CA) simulations are so great that, for large-scale CA experiments, it becomes absurd to use any other kind of computer .},
  file      = {1987_Margolus_967.pdf:by-author/M/Margolus/1987_Margolus_967.pdf:PDF},
  groups    = {sg/Cellular automata},
  keywords  = {Cellular Automata; Computations; Computer Architecture; Computer Science (CS)},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://www.complex-systems.com/pdf/01-5-5.pdf},
}

@Manuscript{Mariani2000,
  author    = {R. Mariani and F. Pessolano and R. Saletti},
  title     = {A New CMOS Ternary Logic Design for Low-power Low-voltage Circuits},
  year      = {2000},
  keywords  = {Computer Science (CS); Logic Circuits; Ternary Logic},
  abstract  = {This paper shows a new approach to low-power low-voltage CMOS Multiple- Valued (MVL) Ternary Logic, the “complete model”. This logic uses standard technology processes and requires only an extra power supply more than binary CMOS circuits. Using an original characterisation of CMOS multivalued dynamic gates, it is shown as the advantages obtained are better noise margins and a lower power consumption as compared to other CMOS ternary solutions. As application of this approach, it is then discussed how general purpose asynchronous circuits can be designed with complete model ternary logic elements.},
  file      = {:by-author/M/Mariani/2000_Mariani.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Marians2000,
  author    = {Kenneth J. Marians},
  journal   = {Structure},
  title     = {Crawling and Wiggling on DNA: Structural Insights to the Mechanism of DNA Unwinding by Helicases},
  year      = {2000},
  pages     = {R227–R235},
  volume    = {8},
  abstract  = {Crystal structures have recently been solved of the monomeric DNA helicase PcrA bound to forked DNA, and of the hexameric helicase domain of the bacteriophage T7 gene 4 protein, a replication fork DNA helicase/primase. These structures have led to the elaboration of the first molecular models to describe DNA helicase action.},
  file      = {:by-author/M/Marians/2000_Marians_227.pdf:PDF},
  keywords  = {{gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Marino2005,
  author    = {Marino, Tiziana and Russo, Nino and Toscano, Marirosa},
  journal   = {Journal of the American Chemical Society},
  title     = {A comparative study of the catalytic mechanisms of the zinc and cadmium containing carbonic anhydrase.},
  year      = {2005},
  pages     = {4242--53},
  volume    = {127},
  abstract  = {The catalytic mechanism for the conversion of carbon dioxide to hydrogen carbonate by a cadmium containing carbonic anhydrase was explored at density functional level employing two different models to simulate the active center of the enzyme. In the first model, the histidine residues around the metal ion were replaced with imidazole groups. Instead, in the second one, the simplest model was extended introducing two amino acidic residues generally present in the neighbor of enzyme and a deep water molecule. The results showed that cadmium carbonic anhydrase follows a reaction mechanism that is favored thermodynamically but not kinetically with respect to that of the most usual zinc-containing enzyme, both in a vacuum and in a protein environment.},
  file      = {2005_Marino_4242.pdf:by-author/M/Marino/2005_Marino_4242.pdf:PDF},
  groups    = {sg/reviews},
  keywords  = {Carbonic Anhydrases},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Mark1981,
  author    = {Mark, K. K. and Studier, F. W.},
  journal   = {The Journal of biological chemistry},
  title     = {Purification of the gene 0.3 protein of bacteriophage T7, an inhibitor of the DNA restriction system of Escherichia coli.},
  year      = {1981},
  pages     = {2573--8},
  volume    = {256},
  abstract  = {The gene 0.3 protein of bacteriophage T7 prevents the DNA restriction system of EScherichia coli from interfering with T7 infection. A mutant strain of T7 that greatly overproduces the 0.3 protein has been constructed and used for purification of this protein. The 0.3 protein ws found to be extremely acidic and can be separated from virtually all other proteins of the infected cell by chromatography on DEAE-cellulose. Residual contaminating proteins and nucleic acids can be removed by gel filtration, but an even simpler final purification is possible, because under appropriate conditions the 0.3 protein is soluble in high concentrations of ethanol. Thus, a simple, essentially two-step purification can produce about 50 mg of pure 0.3 protein from 30 liters of culture. The purified protein appears to be a dimer of identical subunits. AS expected from its known function during infection, the purified 0.3 protein inhibits the nuclease and ATPase activities of partially purified Eco B, the DNA restriction enzyme of E. coli B, but it does not interfere with several different type II endonucleases tested. The inhibition of Eco B appears to require stoichiometric rather than catalytic amounts of 0.3 protein.},
  file      = {:by-author/M/Mark/1981_Mark_2573.pdf:PDF},
  keywords  = {Antirestriction},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Markind1998,
  author    = {Markind, J E},
  journal   = {American journal of health-system pharmacy : AJHP : official journal of the American Society of Health-System Pharmacists},
  title     = {Topiramate: a new antiepileptic drug.},
  year      = {1998},
  pages     = {554--62},
  volume    = {55},
  abstract  = {The pharmacology, pharmacokinetics, clinical efficacy, adverse effects, drug interactions, and dosage of topiramate are reviewed. Topiramate is indicated for use in the adjunctive treatment of adult partial-onset epilepsy. A sulfamate-substituted monosaccharide, it is structurally distinct from other antiepileptic agents. Topiramate acts by blocking the spread of seizures. Oral topiramate has high bioavailability and low protein binding, and as monotherapy its half-life permits once- or twice-daily administration. The drug is excreted largely unchanged in the urine. Clinical trials have shown that topiramate is effective as adjunctive therapy in treating adult partial-onset epilepsy with or without secondarily generalized seizures. In adults with refractory partial epilepsy, topiramate has shown efficacy when carbamazepine or phenytoin has failed. Topiramate may also be effective against partial-onset epilepsy and Lennox-Gastaut syndrome in children, but more pediatric studies are needed. CNS adverse effects are the most common; weight loss and nephrolithiasis have also been reported. The drug does not appear to interact significantly with other antiepileptic agents, but enzyme inducers like phenytoin and carbamazepine can decrease serum topiramate levels by 50%. The initial dosage is 50 mg nightly for seven nights, followed by an increase weekly to 400 mg/day in two divided doses. Topiramate is more costly than other anticonvulsants; however, drug therapy accounts for less than 10% of the total direct cost of epilepsy treatment. Topiramate offers an effective, well-tolerated option in patients with adult partial-onset seizures.},
  file      = {1998_Markind_554.pdf:by-author/M/Markind/1998_Markind_554.pdf:PDF},
  groups    = {sg/medicine},
  keywords  = {Carbonic Anhydrases},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Markley1988,
  author           = {F. Landis Markley},
  journal          = {The Journal of Astronautical Sciences},
  title            = {Attitude determination using vector observations and the singular value decomposition},
  year             = {1988},
  pages            = {245--258},
  volume           = {38},
  abstract         = {A new method for finding the attitude matrix minimizing Wahba's loss function, based on the singular value decompisition of a 3x3 matrix, is presented. Equations are given for the covariance matrix of the attitude estimate, as wel as fo rthe eigenvalues and eigenvectors of this matrix, in terms of the singular value decomposition matrces. The singular value decomposition method is comared with Shuster's implementation of Davenport's q-method, which is more efficient than the new algorithm but does not give the eigenvalues and eigenvectors of the covariance matrix. These are often useful for analysis, since the maximum eigenvalue and its eigenvector fine the magnitude and direction of the largest component of the attitude uncertainty.},
  creationdate     = {2012-05-15T00:00:00},
  eprint           = {https://ntrs.nasa.gov/api/citations/19930015542/downloads/19930015542.pdf?attachment=true},
  file             = {:by-author/M/Markley/1988_Markley_245.pdf:PDF},
  groups           = {sg/Molecule superposion, sg/Superposition, sg/Bioinf. Algorithms},
  keywords         = {Structure Superposition},
  modificationdate = {2024-05-12T16:46:24},
  owner            = {saulius},
  timestamp        = {2012.05.15},
}

@Article{Marques2008,
  author      = {Sérgio M Marques and Elisa Nuti and Armando Rossello and Claudiu T Supuran and Tiziano Tuccinardi and Adriano Martinelli and M. Amélia Santos},
  journal     = {J Med Chem},
  title       = {Dual inhibitors of matrix metalloproteinases and carbonic anhydrases: iminodiacetyl-based hydroxamate-benzenesulfonamide conjugates.},
  year        = {2008},
  pages       = {7968--7979},
  volume      = {51},
  abstract    = {Matrix metalloproteinases (MMPs) and carbonic anhydrases (CAs) are two classes of zinc enzymes with different roles and catalytic targets, such as the degradation of most of the extracellular matrix (ECM) proteins and the regulation of the CO(2)/HCO(3)(-) equilibrium in the cells, respectively. Both families have isoforms which were proved to be involved in several stages of carcinogenic processes, and so the selective inhibition of these enzymes might be of interest in cancer therapy. We report herein the design, synthesis, and in vitro evaluation of a series of compounds possessing the iminodiacetic acid as the main backbone and two functional groups attached, namely, the hydroxamic acid and the arylsulfonamide (ArSO(2)NH(2)) moieties, to enable the inhibition of MMPs and CAs, respectively. These compounds were demonstrated to strongly inhibit both MMPs and CAs, some of them from the nanomolar to subnanomolar range. Furthermore, a docking study for MMPs was reported for the most promising compound in order to investigate its binding interactions with the different MMPs.},
  doi         = {10.1021/jm800964f},
  file        = {2008_Marques_7968.pdf:by-author/M/Marques/2008_Marques_7968.pdf:PDF},
  groups      = {sg/inhibitors},
  institution = {Centro de Química Estrutural, Instituto Superior Técnico, Av. Rovisco Pais 1, 1049-001 Lisboa, Portugal.},
  keywords    = {Anoxia; Carbonic Anhydrases; Chemical; Chemical Synthesis/chemistry; Chemistry; Drug Design; Enzyme Inhibitors; Humans; Hydroxamic Acids; Inhibitory Concentration 50; Matrix Metalloproteinases; Metabolism; Methods; Models; Molecular Conformation; Pharmaceutical; Protein Binding; Protein Isoforms; Sulfonamides; Zinc},
  language    = {eng},
  medline-pst = {ppublish},
  owner       = {alexey},
  pii         = {10.1021/jm800964f},
  pmid        = {19053764},
  timestamp = {2012.11.27},
  creationdate = {2012-11-27T00:00:00},
  url         = {http://dx.doi.org/10.1021/jm800964f},
}

@Article{Marraffini2010,
  author    = {Marraffini, Luciano A. and Sontheimer, Erik J.},
  journal   = {Nature reviews. Genetics},
  title     = {CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea.},
  year      = {2010},
  pages     = {181--90},
  volume    = {11},
  abstract  = {Sequence-directed genetic interference pathways control gene expression and preserve genome integrity in all kingdoms of life. The importance of such pathways is highlighted by the extensive study of RNA interference (RNAi) and related processes in eukaryotes. In many bacteria and most archaea, clustered, regularly interspaced short palindromic repeats (CRISPRs) are involved in a more recently discovered interference pathway that protects cells from bacteriophages and conjugative plasmids. CRISPR sequences provide an adaptive, heritable record of past infections and express CRISPR RNAs - small RNAs that target invasive nucleic acids. Here, we review the mechanisms of CRISPR interference and its roles in microbial physiology and evolution. We also discuss potential applications of this novel interference pathway.},
  file      = {:by-author/M/Marraffini/2010_Marraffini_181.pdf:PDF},
  groups    = {sg/CRISPR-Cas},
  keywords  = {CRISPR},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Marshall2007a,
  author    = {Marshall, Andrew},
  journal   = {Nature biotechnology},
  title     = {GM soybeans and health safety--a controversy reexamined.},
  year      = {2007},
  pages     = {981--7},
  volume    = {25},
  file      = {:by-author/M/Marshall/2007_Marshall_981.pdf:PDF},
  keywords  = {GMO Influence},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Marshall2007,
  author    = {Marshall, Jacqueline J. T. and Gowers, Darren M. and Halford, Stephen E.},
  journal   = {Journal of molecular biology},
  title     = {Restriction endonucleases that bridge and excise two recognition sites from DNA.},
  year      = {2007},
  pages     = {419--31},
  volume    = {367},
  abstract  = {Most restriction endonucleases bridge two target sites before cleaving DNA: examples include all of the translocating Type I and Type III systems, and many Type II nucleases acting at their sites. A subset of Type II enzymes, the IIB systems, recognise bipartite sequences, like Type I sites, but cut specified phosphodiester bonds near their sites, like Type IIS enzymes. However, they make two double-strand breaks, one either side of the site, to release the recognition sequence on a short DNA fragment; 34 bp long in the case of the archetype, BcgI. It has been suggested that BcgI needs to interact with two recognition sites to cleave DNA but whether this is a general requirement for Type IIB enzymes had yet to be established. Ten Type IIB nucleases were tested against DNA substrates with one or two copies of the requisite sequences. With one exception, they all bridged two sites before cutting the DNA, usually in concerted reactions at both sites. The sites were ideally positioned in cis rather than in trans and were bridged through 3-D space, like Type II enzymes, rather than along the 1-D contour of the DNA, as seen with Type I enzymes. The standard mode of action for the restriction enzymes that excise their recognition sites from DNA thus involves concurrent action at two DNA sites.},
  file      = {:by-author/M/Marshall/2007_Marshall_419.pdf:PDF},
  keywords  = {IIB; TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Manuscript{Marti2000,
  author    = {Sergio Marti and T.J. Giuli and Kevin Lai and Mary Baker},
  title     = {Mitigating Routing Misbehavior in Mobile Ad Hoc Networks},
  year      = {2000},
  keywords  = {Computer Science (CS); Networks},
  file      = {:by-author/M/Marti/2000_Marti.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Manuscript{Martin2008,
  author    = {David E. Martin and Peter A. Beling},
  title     = {Patent Litigation Risk Characterization: Prospective identification of financial risk in patent holdings},
  year      = {2008},
  keywords  = {Copyrights-trademarks-patents},
  abstract  = {Since 1982, United States, European and Asian businesses, institutions of higher learning, and individuals have grown increasingly reliant on securing proprietary rights in the form of patents to protect business interests and create economic opportunity. In the United States, a patent – the only Constitutionally enumerated property right accessible to every citizen – grants its holder the right to exclude others from practicing the invention disclosed therein. Contrary to public opinion, a patent conveys no affirmative business right to conduct any activity. Insofar as a patent discloses an invention that relies on other patented enablements for its performance, the grant of one patent does not obviate the rights already existing in other patents. As the “knowledge economy” has taken center stage as the moniker to describe the present business climate, the importance of patents as a substantial, if not exclusive, business property has risen. In the late 1990’s, accounting and consulting firms heralded an era in which the majority of business value came from intangible assets. The Intellectual Property (IP) management industry is in the early stages of its development and is projected to be a worldwide, multi-billion dollar industry. Although historical data is limited, British Technology Group, a multi-disciplinary consulting firm engaged in technology transfer, believes the industry represents a $3.0 trillion per year market, of which only $180 billion has been realized1 in the form of tangible commercial value.},
  file      = {:by-author/M/Martin/2008_Martin.doc:DOC},
  owner     = {saulius},
  timestamp = {2015.02.28},
  creationdate = {2015-02-28T00:00:00},
}

@Article{Martin2010,
  author    = {Martin, Ryan and Zhang, Jianchun and Liu, Chuanhai},
  journal   = {Statistical Science},
  title     = {Dempster–{Shafer} {Theory} and {Statistical} {Inference} with {Weak} {Beliefs}},
  year      = {2010},
  issn      = {0883-4237, 2168-8745},
  pages     = {72--87},
  volume    = {25},
  abstract  = {The Dempster–Shafer (DS) theory is a powerful tool for probabilistic reasoning based on a formal calculus for combining evidence. DS theory has been widely used in computer science and engineering applications, but has yet to reach the statistical mainstream, perhaps because the DS belief functions do not satisfy long-run frequency properties. Recently, two of the authors proposed an extension of DS, called the weak belief (WB) approach, that can incorporate desirable frequency properties into the DS framework by systematically enlarging the focal elements. The present paper reviews and extends this WB approach. We present a general description of WB in the context of inferential models, its interplay with the DS calculus, and the maximal belief solution. New applications of the WB method in two high-dimensional hypothesis testing problems are given. Simulations show that the WB procedures, suitably calibrated, perform well compared to popular classical methods. Most importantly, the WB approach combines the probabilistic reasoning of DS with the desirable frequency properties of classical statistics.},
  doi       = {10.1214/10-STS322},
  file      = {Martin et al. - 2010 - Dempster–Shafer Theory and Statistical Inference w.pdf:by-author/M/Martin/2010_Martin_72.pdf:PDF;Snapshot:by-author/M/Martin/2010_Martin_72.html:URL},
  groups    = {sg/Probability theory, sg/Bayesian},
  keywords  = {Bayesian; Belief Functions; Fiducial Argument; Frequentist; Hypothesis Testing; Inferential Model; Nonparametrics},
  language  = {EN},
  mrnumber  = {MR2741815},
  owner     = {saulius},
  timestamp = {2015.12.07},
  creationdate = {2015-12-07T00:00:00},
  url       = {http://projecteuclid.org/euclid.ss/1280841734},
  urldate   = {2015-12-07},
  zmnumber  = {05945286},
}

@Manuscript{Martin2000,
  author    = {Robert C. Martin},
  title     = {Design Principles and Design Patterns},
  year      = {2000},
  url       = {http://www.objectmentor.com/resources/publishedArticles.html},
  file      = {:by-author/M/Martin/2000_Martin.pdf:PDF},
  owner     = {saulius},
  timestamp = {2013.10.21},
  creationdate = {2013-10-21T00:00:00},
}

@Manuscript{Martin1997,
  author    = {Robert C. Martin},
  title     = {The Dependency Inversion Principle},
  year      = {1997},
  url       = {http://www.objectmentor.com/resources/publishedArticles.html},
  file      = {:by-author/M/Martin/1997_Martin_c.pdf:PDF},
  owner     = {saulius},
  timestamp = {2013.10.21},
  creationdate = {2013-10-21T00:00:00},
}

@Manuscript{Martin1997a,
  author    = {Robert C. Martin},
  title     = {Granularity},
  year      = {1997},
  url       = {http://www.objectmentor.com/resources/publishedArticles.html},
  file      = {:by-author/M/Martin/1997_Martin_d.pdf:PDF},
  owner     = {saulius},
  timestamp = {2013.10.21},
  creationdate = {2013-10-21T00:00:00},
}

@Manuscript{Martin1997b,
  author    = {Robert C. Martin},
  title     = {Design Patterns for Dealing with Dual Inheritance Hierarchies in C++},
  year      = {1997},
  url       = {http://www.objectmentor.com/resources/publishedArticles.html},
  file      = {:by-author/M/Martin/1997_Martin_b.pdf:PDF},
  owner     = {saulius},
  timestamp = {2013.10.21},
  creationdate = {2013-10-21T00:00:00},
}

@Manuscript{Martin1997c,
  author    = {Robert C. Martin},
  title     = {The Interface Segregation Principle},
  year      = {1997},
  url       = {http://www.objectmentor.com/resources/publishedArticles.html},
  file      = {:by-author/M/Martin/1997_Martin_e.pdf:PDF},
  owner     = {saulius},
  timestamp = {2013.10.21},
  creationdate = {2013-10-21T00:00:00},
}

@Manuscript{Martin1997d,
  author    = {Robert C. Martin},
  title     = {The Open-Closed Principle},
  year      = {1997},
  url       = {http://www.objectmentor.com/resources/publishedArticles.html},
  file      = {:by-author/M/Martin/1997_Martin_f.pdf:PDF},
  owner     = {saulius},
  timestamp = {2013.10.21},
  creationdate = {2013-10-21T00:00:00},
}

@Manuscript{Martin1997e,
  author    = {Robert C. Martin},
  title     = {Acyclic Visitor},
  year      = {1997},
  url       = {http://www.objectmentor.com/resources/publishedArticles.html},
  file      = {:by-author/M/Martin/1997_Martin_a.pdf:PDF},
  owner     = {saulius},
  timestamp = {2013.10.21},
  creationdate = {2013-10-21T00:00:00},
}

@Manuscript{Martin1997f,
  author    = {Robert C. Martin},
  title     = {Stability},
  year      = {1997},
  url       = {http://www.objectmentor.com/resources/publishedArticles.html},
  file      = {:by-author/M/Martin/1997_Martin_g.pdf:PDF},
  owner     = {saulius},
  timestamp = {2013.10.21},
  creationdate = {2013-10-21T00:00:00},
}

@Manuscript{Martinez199X,
  author    = {Martinez, M. Patiño-Martinéz and R. Jiménez-CPeris and S. Arévalo},
  title     = {Implementing transactions using Ada exceptions: which features are missing?},
  year      = {199X},
  keywords  = {Computer Science (CS); Exception Handling},
  file      = {:by-author/M/Martinez/199X_Martinez.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Martins1988,
  author    = {Martins, Jos\'e Lu\'\is and Cohen, Marvin L.},
  journal   = {Phys. Rev. B},
  title     = {Diagonalization of large matrices in pseudopotential band-structure calculations: Dual-space formalism},
  year      = {1988},
  pages     = {6134--6138},
  volume    = {37},
  abstract  = {Combining iterative methods of calculating the eigenvectors of a Hermitian matrix with a matrix-multiplication technique using the fast-Fourier-transform algorithm, we present an efficient method of performing total-energy and band-structure calculations in crystals with the plane-wave local-pseudopotential formalism. The method can be viewed as a dual-space formalism where part of the calculations is performed in momentum space and another part in coordinate space. Significant savings in both computer time and memory are obtained. Results of calculations for molecular hydrogen with matrix sizes as large as 7200 are presented as an example.},
  doi       = {10.1103/PhysRevB.37.6134},
  file      = {1988_Martins_6134.pdf:by-author/M/Martins/1988_Martins_6134.pdf:PDF},
  issue     = {11},
  keywords  = {Algorithms; Quantum Mechanics (QM); Schroedinger Equation},
  numpages  = {0},
  owner     = {saulius},
  publisher = {American Physical Society},
  timestamp = {2014.09.26},
  creationdate = {2014-09-26T00:00:00},
  url       = {http://link.aps.org/doi/10.1103/PhysRevB.37.6134},
}

@Article{Marzari1999,
  author    = {Marzari, Nicola and Vanderbilt, David and De Vita, Alessandro and Payne, M. C.},
  journal   = {Phys. Rev. Lett.},
  title     = {Thermal Contraction and Disordering of the {Al(110)} Surface},
  year      = {1999},
  pages     = {3296--3299},
  volume    = {82},
  doi       = {10.1103/PhysRevLett.82.3296},
  file      = {:by-author/M/Marzari/1999_Marzari_3296.pdf:PDF},
  issue     = {16},
  numpages  = {0},
  owner     = {andrius},
  publisher = {American Physical Society},
  timestamp = {2015.07.15},
  creationdate = {2015-07-15T00:00:00},
  url       = {http://link.aps.org/doi/10.1103/PhysRevLett.82.3296},
}

@Article{Masereel2002,
  author    = {Masereel, Bernard and Rolin, Stéphanie and Abbate, Francesco and Scozzafava, Andrea and Supuran, Claudiu T},
  journal   = {Journal of medicinal chemistry},
  title     = {Carbonic anhydrase inhibitors: anticonvulsant sulfonamides incorporating valproyl and other lipophilic moieties.},
  year      = {2002},
  pages     = {312--20},
  volume    = {45},
  abstract  = {A series of aromatic/heterocyclic sulfonamides incorporating valproyl moieties were prepared to design antiepileptic compounds possessing in their structure two moieties known to induce such a pharmacological activity: valproic acid, one of the most widely used antiepileptic drugs, and the sulfonamide residue included in acetazolamide and topiramate, two carbonic anhydrase inhibitors with antiepileptic properties. Some of these derivatives showed very high inhibitory potency against three carbonic anhydrase (CA) isozymes, such as CA I, CA II, and CA IV, involved in important physiological processes. Topiramate, a recently developed antiepileptic drug possessing a sulfamate moiety, also shares this property, although earlier literature data reported this compound to be a weak-moderate CA I, II, and IV inhibitor. The valproyl derivative of acetazolamide (5-valproylamido-1,3,4-thiadiazole-2-sulfonamide, 6M) was one of the best hCA I and hCA II inhibitor in the series and exhibited very strong anticonvulsant properties in an MES test in mice. In consequence, other 1,3,4-thiadiazolesulfonamide derivatives possessing potent CA inhibitory properties and substituted with different alkyl/arylcarboxamido/sulfonamido/ureido moieties in the 5 position have been investigated for their anticonvulsant effects in the same animal model. It was observed that some lipophilic derivatives, such as 5-benzoylamido-, 5-toluenesulfonylamido-, 5-adamantylcarboxamido-, and 5-pivaloylamido-1,3,4-thiadiazole-2-sulfonamide, show promising in vivo anticonvulsant properties and that these compounds may be considered as interesting leads for developing anticonvulsant or selective cerebrovasodilator drugs.},
  file      = {2002_Masereel_312.pdf:by-author/M/Masereel/2002_Masereel_312.pdf:PDF},
  groups    = {sg/medicine},
  keywords  = {Carbonic Anhydrases},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Manuscript{Maskus2004,
  author    = {Keith E. Maskus and Kamal Saggi and Thitima Puttitanun},
  title     = {Patent rights and international technology transfer through direct investment and licensing},
  year      = {2004},
  keywords  = {Economy},
  file      = {:by-author/M/Maskus/2004_Maskus.doc:DOC},
  owner     = {saulius},
  timestamp = {2015.02.28},
  creationdate = {2015-02-28T00:00:00},
}

@Article{Mason1943,
  author    = {Brian Mason},
  journal   = {Geologiska Föreningens i Stockholm Förhandlingar},
  title     = {Mineralogical aspects of the system Fe0-Fe203-Mn0-Mn203},
  year      = {1943},
  pages     = {97--180},
  file      = {1943_Mason_97phdthesis.pdf:by-author/M/Mason/1943_Mason_97phdthesis.pdf:PDF},
  keywords  = {Crystal Structures; Hematite; Mineralogy; Or COD Deposition},
  owner     = {saulius},
  timestamp = {2013.08.30},
  creationdate = {2013-08-30T00:00:00},
  url       = {http://su.diva-portal.org/smash/get/diva2:505303/FULLTEXT01.pdf},
}

@Presentation{Mason2001,
  author       = {T. E. Mason},
  title        = {Neutron Detectors for Materials Research},
  year         = {2001},
  organization = {Experimental Facilities Division, Spallation Neutron Source},
  file         = {2001_Mason_slides.ppt:by-author/M/Mason/2001_Mason_slides.ppt:PowerPoint},
  owner        = {saulius},
  timestamp = {2014.01.26},
  creationdate = {2014-01-26T00:00:00},
}

@InBook{Massa2004,
  author    = {Massa, Werner},
  chapter   = {2. Crystal Lattices},
  pages     = {4--11},
  publisher = {Springer},
  title     = {Crystal Structure Determination},
  year      = {2004},
  file      = {2004_Massa_3.pdf:by-author/M/Massa/2004_Massa_3.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.06.04},
  creationdate = {2012-06-04T00:00:00},
}

@Manuscript{Masson2010,
  author    = {Michael E. J. Masson},
  title     = {A Tutorial on a Practical Bayesian Alternative to Null - Hypothesis Significance Testing},
  year      = {2010},
  keywords  = {Bayessian Statistics; Hypothesis Testing},
  url       = {http://ruccs.rutgers.edu/~jacob/teaching/Stats/Papers/masson_bayesian.pdf},
  file      = {2010_Masson.pdf:by-author/M/Masson/2010_Masson.pdf:PDF},
  owner     = {saulius},
  timestamp = {2015.12.18},
  creationdate = {2015-12-18T00:00:00},
}

@Manual{Mathews2016,
  title        = {A Quick XDS Tutorial for SSRL},
  author       = {Irimpan Mathews},
  month        = {May},
  organization = {SSRL},
  year         = {2016},
  file         = {2016_Mathews_manual.pdf:by-author/M/Mathews/2016_Mathews_manual.pdf:PDF;2016_Mathews_manual.odt:by-author/M/Mathews/2016_Mathews_manual.odt:OpenDocument text},
  keywords     = {Data Reduction; Reflection Integration; Software; X-ray Crystallography; XDS},
  owner        = {saulius},
  timestamp = {2016.12.21},
  creationdate = {2016-12-21T00:00:00},
  url          = {http://smb.slac.stanford.edu/facilities/software/xds/},
}

@Article{Mativetsky2008,
  author    = {Mativetsky, Jeffrey M. and Pace, Giuseppina and Elbing, Mark and Rampi, Maria A. and Mayor, Marcel and Samorì, Paolo},
  journal   = {Journal of the American Chemical Society},
  title     = {Azobenzenes as light-controlled molecular electronic switches in nanoscale metal−molecule−metal junctions},
  year      = {2008},
  issn      = {0002-7863},
  pages     = {9192--9193},
  volume    = {130},
  abstract  = {Conductance switching associated with the photoisomerization of azobenzene-based (Azo) molecules was observed in nanoscopic metal?molecule?metal junctions. The junctions were formed by using a conducting atomic force microscope (C-AFM) approach, where a metallic AFM tip was used to electrically contact a gold-supported Azo self-assembled monolayer. The measured 30-fold increase in conductance is consistent with the expected decrease in tunneling barrier length resulting from the conformational change of the Azo molecule.},
  doi       = {10.1021/ja8018093},
  file      = {Mativetsky et al. - 2008 - Azobenzenes as Light-Controlled Molecular Electron.pdf:by-author/M/Mativetsky/2008_Mativetsky_9192.pdf:application/pdf;ACS Full Text Snapshot:by-author/M/Mativetsky/2008_Mativetsky_9192.html:text/html},
  groups    = {sg/chemical},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://dx.doi.org/10.1021/ja8018093},
  urldate   = {2015-08-05},
}

@Article{Matje2013,
  author    = {Matje, Douglas M. and Krivacic, Cody T. and Dahlquist, Frederick W. and Reich, Norbert O.},
  journal   = {Biochemistry},
  title     = {Distal Structural Elements Coordinate a Conserved Base Flipping Network},
  year      = {2013},
  pages     = {1669--1676},
  volume    = {52},
  abstract  = {One of the most dramatic illustrations of enzymatic promotion of a high-energy intermediate is observed in DNA modification and repair enzymes where an individual base is rotated (flipped) 180° around the deoxyribose–phosphate backbone and into the active site. While the end states have been extensively characterized, experimental techniques have yet to yield a full description of the base flipping process and the role played by the enzyme. The C5 cytosine methyltransferase M.HhaI coordinates an ensemble of reciprocal DNA and enzyme rearrangements to efficiently flip the target cytosine from the DNA helix. We sought to understand the role of individual amino acids during base flipping. Our results demonstrate that M.HhaI initiates base flipping before closure of the catalytic loop and utilizes the conserved serine 85 in the catalytic loop to accelerate flipping and maintain distortion of the DNA backbone. Serine 87, which forms specific contacts within the DNA helix after base flipping, is not involved in the flipping process or in maintaining the catalytically competent complex. At the base of the catalytic loop, glycine 98 acts as a hinge to allow conformational dynamism of the loop and mutation to alanine inhibits stabilization of the closed loop. Our results illustrate how an enzyme utilizes numerous, distal residues in concert to transform substrate recognition into catalysis.},
  doi       = {10.1021/bi301284f},
  eprint    = {http://pubs.acs.org/doi/pdf/10.1021/bi301284f},
  file      = {:by-author/M/Matje/2013_Matje_1669.pdf:PDF},
  keywords  = {Base Flipping; DNA; HhaI; Protein Structure; Proteins},
  owner     = {saulius},
  timestamp = {2013.03.27},
  creationdate = {2013-03-27T00:00:00},
  url       = {http://pubs.acs.org/doi/abs/10.1021/bi301284f},
}

@Article{Matje2013a,
  author    = {Matje, Douglas M. and Zhou, Hongjun and Smith, Darren A. and Neely, Robert K. and Dryden, David T. F. and Jones, Anita C. and Dahlquist, Frederick W. and Reich, Norbert O.},
  journal   = {Biochemistry},
  title     = {Enzyme-Promoted Base Flipping Controls DNA Methylation Fidelity},
  year      = {2013},
  pages     = {1677--1685},
  volume    = {52},
  abstract  = {A quantitative understanding of how conformational transitions contribute to enzyme catalysis and specificity remains a fundamental challenge. A suite of biophysical approaches was used to reveal several transient states of the enzyme–substrate complexes of the model DNA cytosine methyltransferase M.HhaI. Multidimensional, transverse relaxation-optimized nuclear magnetic resonance (NMR) experiments show that M.HhaI has the same conformation with noncognate and cognate DNA sequences. The high-affinity cognatelike mode requires the formation of a subset of protein–DNA interactions that drive the flipping of the target base from the helix to the active site. Noncognate substrates lacking these interactions undergo slow base flipping, and fluorescence tracking of the catalytic loop corroborates the NMR evidence of a loose, nonspecific binding mode prior to base flipping and subsequent closure of the catalytic loop. This slow flipping transition defines the rate-limiting step for the methylation of noncognate sequences. Additionally, we present spectroscopic evidence of an intermediate along the base flipping pathway that has been predicted but never previously observed. These findings provide important details of how conformational rearrangements are used to balance specificity with catalytic efficiency.},
  doi       = {10.1021/bi3012912},
  eprint    = {http://pubs.acs.org/doi/pdf/10.1021/bi3012912},
  file      = {:by-author/M/Matje/2013_Matje_1677.pdf:PDF},
  keywords  = {Base Flipping; DNA; HhaI; NMR; Protein Structure; Proteins},
  owner     = {saulius},
  timestamp = {2013.03.27},
  creationdate = {2013-03-27T00:00:00},
  url       = {http://pubs.acs.org/doi/abs/10.1021/bi3012912},
}

@Article{Matson1990,
  author    = {Matson, S. W. and Kaiser-Rogers, K. A.},
  journal   = {Annual review of biochemistry},
  title     = {DNA helicases.},
  year      = {1990},
  pages     = {289--329},
  volume    = {59},
  file      = {:by-author/M/Matson/1990_Matson_289.pdf:PDF},
  keywords  = {Ecoli; {gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Matson1983,
  author    = {Matson, S. W. and Richardson, C. C.},
  journal   = {The Journal of biological chemistry},
  title     = {DNA-dependent nucleoside 5'-triphosphatase activity of the gene 4 protein of bacteriophage T7.},
  year      = {1983},
  pages     = {14009--16},
  volume    = {258},
  abstract  = {The gene 4 protein of bacteriophage T7 is both a primase and a helicase. In this paper, we present a detailed description of a third activity, single-stranded DNA-dependent nucleoside 5'-triphosphate hydrolysis, and show that this activity is coupled to the unidirectional translocation of the gene 4 protein on single-stranded DNA (Tabor, S., and Richardson, C.C. (1981) Proc. Natl. Acad. Sci. U. S. A. 78, 205-209). The competitive inhibitor of NTP hydrolysis, beta, gamma-methylene dTTP, is also a potent inhibitor of gene 4 protein-dependent, RNA-primed DNA synthesis; inhibition is not due to a direct inhibition of T7 DNA polymerase or RNA primer synthesis. We conclude that the energy derived from the hydrolysis of NTPs by the gene 4 protein is required for translocation of the protein to primase recognition sites. Measurement of the rates of hydrolysis of NTPs using a variety of DNAs of known structure and length support the unidirectional translocation of the gene 4 protein on single-stranded DNA. Duplex DNA, RNA, and single-stranded DNA coated with single-stranded DNA-binding protein do not serve as effectors for the nucleoside triphosphatase of the gene 4 protein. Kinetic data suggest that the gene 4 protein does not remain bound to newly synthesized oligoribonucleotide primers but continues to search for other primase recognition sites. Although all the predominant naturally occurring NTPs except rCTP are hydrolyzed by the gene 4 protein, the enzyme shows specificity for dTTP with a Km of 0.4 mM. In the accompanying paper (Matson, S.W., Tabor, S., and Richardson, C.C. (1983) J. Biol. Chem. 258, 14017-14024), we show that the hydrolysis of NTPs is also required for the protein to function as a helicase in duplex regions of DNA.},
  file      = {:by-author/M/Matson/1983_Matson_14009.pdf:PDF},
  keywords  = {{gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Matson1983a,
  author    = {Matson, S. W. and Tabor, S. and Richardson, C. C.},
  journal   = {The Journal of biological chemistry},
  title     = {The gene 4 protein of bacteriophage T7. Characterization of helicase activity.},
  year      = {1983},
  pages     = {14017--24},
  volume    = {258},
  abstract  = {Gene 4 protein of bacteriophage T7 is a multifunctional enzyme that both stimulates T7 DNA polymerase during leading strand synthesis, and synthesizes RNA primers that initiate lagging strand synthesis. Both activities are dependent on the ability of the gene 4 protein to translocate unidirectionally (5' to 3') along single-stranded DNA (Tabor, S., and Richardson, C.C. (1981) Proc. Natl. Acad. Sci. U. S. A. 78, 205-209), a reaction that is coupled to the hydrolysis of nucleoside 5'-triphosphates. In this paper, we show that gene 4 protein, in the absence of other proteins, is a helicase, an activity previously inferred from its ability to stimulate T7 DNA polymerase on duplex DNA. We have designed a DNA substrate for use in characterizing the helicase activity which consists of a short DNA fragment bearing a single-stranded 3'-tail when annealed to circular, single-stranded M13 DNA. With such a DNA substrate, the gene 4 protein can disrupt the helical structure of a 96-nucleotide-long fragment, resulting in its displacement from the circle. Helicase activity requires a long stretch of at least 17 nucleotides of single-stranded DNA on the 5'-side of the duplex to be unwound. In addition, helicase activity is not observed unless a short (greater than 6 nucleotides) single-stranded 3'-tail is present. The helicase activity has an absolute requirement for hydrolysis of a nucleoside 5'-triphosphate. The inhibitor of nucleoside triphosphate hydrolysis, beta, gamma-methylene dTTP, is an effective inhibitor of helicase activity. Based on these results, we propose a model for the action of the gene 4 protein at a replication fork.},
  file      = {:by-author/M/Matson/1983_Matson_14017.pdf:PDF},
  keywords  = {T7; {gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Matsuura2003,
  author    = {Matsuura, Yoshiki and Chernov, Alexander A.},
  journal   = {Acta Crystallographica Section D},
  title     = {Morphology and the strength of intermolecular contacts in protein crystals},
  year      = {2003},
  pages     = {1347--1356},
  volume    = {59},
  doi       = {10.1107/S0907444903011107},
  file      = {gr2334.pdf:by-author/M/Matsuura/2003_Matsuura_1347.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444903011107},
}

@Article{Matsuzaki2008,
  author    = {Takao Matsuzaki and Yasuhiko Koezuka},
  journal   = {Acta Cryst. A},
  title     = {CPADD(Closest Packing Approach for denovo Drug Design) to inhibit VEGF/R and Notch/RBP/MAM systems},
  year      = {2008},
  pages     = {C38},
  booktitle = {IUCr Congress and General Assembly},
  file      = {:by-author/M/Matsuzaki/2008_Matsuzaki_C38.pdf:PDF},
  keywords  = {Drug Design},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Presentation{Mattson2001,
  author       = {Tim Mattson and Rudolf Eigenmann},
  title        = {OpenMP: An API for Writing Portable SMP Application Software},
  year         = {2001},
  organization = {Intel Corporation, Computational Sciences Laboratory; Purdue University, School of Electrical and Computer Engineering},
  file         = {:by-author/M/Mattson/2001_Mattson_slides.pdf:PDF},
  owner        = {saulius},
  pages        = {slides},
  timestamp = {2013.07.02},
  creationdate = {2013-07-02T00:00:00},
  url          = {http://software.intel.com/file/7462},
}

@Article{Matulis2003,
  author    = {Matulis},
  title     = {Makromolekulių Erdvinės Struktūros Tyrimo Metodai},
  year      = {2003},
  pages     = {chapter3-manuscript},
  file      = {:by-author/M/Matulis/2003_Matulis_chapter3.pdf:PDF},
  keywords  = {Manuscripts},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Matulis2001a,
  author    = {Matulis, D.},
  journal   = {Biophysical chemistry},
  title     = {Thermodynamics of the hydrophobic effect. III. Condensation and aggregation of alkanes, alcohols, and alkylamines.},
  year      = {2001},
  pages     = {67--82},
  volume    = {93},
  abstract  = {Knowledge of the energetics of the low solubility of non-polar compounds in water is critical for the understanding of such phenomena as protein folding and biomembrane formation. Solubility in water can be considered as one leg of the three-part thermodynamic cycle - vaporization from the pure liquid, hydration of the vapor in aqueous solution, and aggregation of the substance back into initial pure form as an immiscible phase. Previous studies on the model compounds n-alkanes, 1-alcohols, and 1-aminoalkanes have noted that the thermodynamic parameters (Gibbs free energy, DeltaG; enthalpy, DeltaH; entropy, DeltaS; and heat capacity, DeltaC(p)) associated with these three processes are generally linear functions of the number of carbons in the alkyl chains. Here we assess the accuracy and limitations of the assumption of additivity of CH(2) group contributions to the thermodynamic parameters for vaporization, hydration, and aggregation. Processes of condensation from pure gas to liquid and aqueous solution to aggregate are compared. Hydroxy, amino, and methyl headgroup contributions are estimated, liquid and solid aggregates are distinguished. Most data in the literature were obtained for compounds with short aliphatic hydrocarbon tails. Here we emphasize long aliphatic chain behavior and include our recent experimental data on long chain alkylamine aggregation in aqueous solution obtained by titration calorimetry and van't Hoff analysis. Contrary to what is observed for short compounds, long aliphatic compound aggregation has a large exothermic enthalpy and negative entropy.},
  file      = {:by-author/M/Matulis/2001_Matulis_67.pdf:PDF},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Matulis2001,
  author    = {Matulis, D. and Bloomfield, V. A.},
  journal   = {Biophysical chemistry},
  title     = {Thermodynamics of the hydrophobic effect. II. Calorimetric measurement of enthalpy, entropy, and heat capacity of aggregation of alkylamines and long aliphatic chains.},
  year      = {2001},
  pages     = {53--65},
  volume    = {93},
  abstract  = {The thermodynamics of long aliphatic chain alkylamine aggregation in aqueous solution was studied by isothermal titration calorimetry (ITC). Protonated alkylammonium cations with linear aliphatic chains of 10-14 carbon atoms were fully soluble in aqueous solution at the beginning of titration, but practically insoluble after deprotonation by titrating with sodium hydroxide. The alkylamines aggregated and precipitated during the reaction, enabling direct measurement of the enthalpy of aggregation. The enthalpy of aggregation became increasingly exothermic upon increasing the chain length. Hydrophobic aggregation was enthalpy-driven and entropy-opposed for alkylamines with 12-14 carbon atoms at room temperature. Direct observation of hydrophobic aggregation by ITC at constant temperature and pressure provided more accurate thermodynamic parameters than obtainable from van't Hoff analysis. Aggregation into liquid or solid phases could be distinguished by ITC, but not by van't Hoff analysis of alkylamine solubility data.},
  file      = {:by-author/M/Matulis/2001_Matulis_53.pdf:PDF},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Matulis2000,
  author    = {Matulis, D. and Rouzina, I. and Bloomfield, V. A.},
  journal   = {Journal of molecular biology},
  title     = {Thermodynamics of DNA binding and condensation: isothermal titration calorimetry and electrostatic mechanism.},
  year      = {2000},
  pages     = {1053--63},
  volume    = {296},
  abstract  = {The thermodynamics of binding of the trivalent cations cobalt hexammine and spermidine to plasmid DNA was studied by isothermal titration calorimetry. Two stages were observed in the course of titration, the first attributed to cation binding and the second to DNA condensation. A standard calorimetric data analysis was extended by applying an electrostatic binding model, which accounted for most of the observed data. Both the binding and condensation reactions were entropically driven (TDeltaS approximately +10 kcal/mol cation) and enthalpically opposed (DeltaH approximately +1 kcal/mol cation). As predicted from their relative sizes, the binding constants of the cations were indistinguishable, but cobalt hexammine had a much greater DNA condensing capacity because it is more compact than spermidine. The dependence of both the free energy of cobalt hexammine binding and the critical cobalt hexammine concentration for DNA condensation on temperature and monovalent cation concentration followed the electrostatic model quite precisely. The heat capacity changes of both stages were positive, perhaps reflecting both the temperature dependence of the dielectric constant of water and the burial of polar surfaces. DNA condensation occurred when about 67 % of the DNA phosphate charge was neutralized by cobalt hexammine and 87 % by spermidine. During condensation, the remaining DNA charge was neutralized.},
  file      = {:by-author/M/Matulis/2000_Matulis_1053.pdf:PDF},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Mavaddat1988,
  author    = {Mavaddat, Farhad and Behrooz Parhami},
  journal   = {Intl. J. Elect. Enging. Educ.},
  title     = {{URISC}: The Ultimate Reduced Instruction Set Computer},
  year      = {1988},
  pages     = {327--334},
  volume    = {25},
  file      = {:by-author/M/Mavaddat/1988_Mavaddat_327.pdf:PDF},
  keywords  = {CPU Design; Computer Architecture; Computer Science (CS); Hardware; Teaching; Teaching Electronics},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
  url       = {https://web.ece.ucsb.edu/~parhami/pubs_folder/parh88-ijeee-ultimate-risc.pdf},
}

@Article{Maxwell1962,
  author    = {Grover Maxwell},
  title     = {The Ontological Status of Theoretical Entities},
  year      = {1962},
  pages     = {1052},
  file      = {:by-author/M/Maxwell/1962_Maxwell_1052.pdf:PDF},
  keywords  = {Epistemology; Philosophy},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Mayewski2005,
  author    = {Mayewski, Stefan},
  journal   = {Proteins: Structure, Function, and Bioinformatics},
  title     = {A multibody, whole-residue potential for protein structures, with testing by Monte Carlo simulated annealing},
  year      = {2005},
  issn      = {1097-0134},
  number    = {2},
  pages     = {152--169},
  volume    = {59},
  abstract  = {A new multibody, whole-residue potential for protein tertiary structure is described. The potential is based on the local environment surrounding each main-chain α carbon (CA), defined as the set of all residues whose CA coordinates lie within a spherical volume of set radius in 3-dimensional (3D) space surrounding that position. It is shown that the relative positions of the CAs in these local environments belong to a set of preferred templates. The templates are derived by cluster analysis of the presently available database of over 3000 protein chains (750,000 residues) having not more than 30% sequence similarity. For each template is derived also a set of residue propensities for each topological position in the template. Using lookup tables of these derived templates, it is then possible to calculate an energy for any conformation of a given protein sequence. The application of the potential to ab initio protein tertiary structure prediction is evaluated by performing Monte Carlo simulated annealing on test protein sequences. Proteins 2005. © 2005 Wiley-Liss, Inc.},
  doi       = {10.1002/prot.20397},
  file      = {2005_Mayewski_152.pdf:by-author/M/Mayewski/2005_Mayewski_152.pdf:PDF},
  groups    = {sg/methods},
  keywords  = {Multibody Potentials; Packing Motifs; Simulated Annealing; Statistical Potentials; Structural Motifs; Structure Prediction},
  owner     = {saulius},
  publisher = {Wiley Subscription Services, Inc., A Wiley Company},
  timestamp = {2016.07.17},
  creationdate = {2016-07-17T00:00:00},
  url       = {http://dx.doi.org/10.1002/prot.20397},
}

@Article{Mayo1990,
  author    = {Mayo, Stephen L. and Barry D. Olafson and William A. Goddard III},
  journal   = {J . Phys. Chem.},
  title     = {{DREIDING}: A Generic Force Field for Molecular Simulations},
  year      = {1990},
  pages     = {8897--8909},
  volume    = {94},
  file      = {:by-author/M/Mayo/1990_Mayo_8897.pdf:PDF},
  owner     = {andrius},
  timestamp = {2012.07.05},
  creationdate = {2012-07-05T00:00:00},
}

@Article{Mayor2010,
  author     = {Mayor, Julien},
  journal    = {Quantitative Psychology and Measurement},
  title      = {Are scientists nearsighted gamblers? the misleading nature of impact factors},
  year       = {2010},
  pages      = {215},
  doi        = {10.3389/fpsyg.2010.00215},
  file       = {Full Text PDF:by-author/M/Mayor/2010_Mayor_215.pdf:application/pdf},
  groups     = {sg/Bibliometrics},
  owner      = {saulius},
  shorttitle = {Are scientists nearsighted gamblers?},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url        = {http://journal.frontiersin.org/article/10.3389/fpsyg.2010.00215/full},
  urldate    = {2015-07-06},
}

@Article{Mazoyer1987,
  author    = {Jacques Mazoyer},
  journal   = {Theoretical Computer Science},
  title     = {A six-state minimal time solution to the firing squad synchronization problem},
  year      = {1987},
  issn      = {0304-3975},
  number    = {2},
  pages     = {183--238},
  volume    = {50},
  abstract  = {From Balzer's work (1967), we know that the firing squad synchronization problem has a minimal-time solution with eight states. We show that such a solution exists with only six states. Our method is somewhat different from all previous ones: the initial line is iteratively divided in two inequal parts so that each new right part can be treated as the homothetical image of a shorter initial line.},
  doi       = {10.1016/0304-3975(87)90124-1},
  file      = {1987_Mazoyer_183.pdf:by-author/M/Mazoyer/1987_Mazoyer_183.pdf:PDF},
  keywords  = {Cellular Automata; Computer Science (CS)},
  owner     = {saulius},
  timestamp = {2016.07.17},
  creationdate = {2016-07-17T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/0304397587901241},
}

@Article{McCabe2014,
  author    = {McCabe, Patrick and Korb, Oliver and Cole, Jason},
  journal   = {Journal of Chemical Information and Modeling},
  title     = {Kernel Density Estimation Applied to Bond Length, Bond Angle, and Torsion Angle Distributions},
  year      = {2014},
  issn      = {1549-960X},
  month     = {May},
  number    = {5},
  pages     = {1284–1288},
  volume    = {54},
  abstract  = {We describe the method of kernel density estimation (KDE) and apply it to molecular structure data. KDE is a quite general nonparametric statistical method suitable even for multimodal data. The method generates smooth probability density function (PDF) representations and finds application in diverse fields such as signal processing and econometrics. KDE appears to have been under-utilized as a method in molecular geometry analysis, chemo-informatics, and molecular structure optimization. The resulting probability densities have advantages over histograms and, importantly, are also suitable for gradient-based optimization. To illustrate KDE, we describe its application to chemical bond length, bond valence angle, and torsion angle distributions and show the ability of the method to model arbitrary torsion angle distributions.},
  doi       = {10.1021/ci500156d},
  file      = {2014_McCabe_1284.pdf:by-author/M/McCabe/2014_McCabe_1284.pdf:PDF},
  groups    = {am/Statistics, sg/Crystallography, am/Crystallography},
  owner     = {andrius},
  publisher = {American Chemical Society (ACS)},
  timestamp = {2016.12.29},
  creationdate = {2016-12-29T00:00:00},
  url       = {http://dx.doi.org/10.1021/ci500156d},
}

@InProceedings{McCalpin2000,
  author    = {John D. McCalpin},
  booktitle = {Third Annual IEEE Workshop on Workload Characterization},
  title     = {An Industry Perspective on Performance Characterization: Applications vs. Benchmarks},
  year      = {2000},
  month     = {September},
  file      = {:by-author/M/McCalpin/2000_McCalpin.war:},
  keywords  = {Computer Science (CS)},
  owner     = {saulius},
  retrieved = {2008-07-28},
  timestamp = {2015.03.02},
  creationdate = {2015-03-02T00:00:00},
  url       = {http://www.cs.virginia.edu/~mccalpin/wwc-keynote.html},
}

@Article{McCammon1977,
  author    = {McCammon, J. A. and Gelin, B. R. and Karplus, M.},
  journal   = {Nature},
  title     = {Dynamics of folded proteins},
  year      = {1977},
  pages     = {585--590},
  volume    = {267},
  abstract  = {The dynamics of a folded globular protein (bovine pancreatic trypsin inhibitor) have been studied by solving the equations of motion for the atoms with an empirical potential energy function. The results provide the magnitude, correlations and decay of fluctuations about the average structure. These suggest that the protein interior is fluid-like in that the local atom motions have a diffusional character.},
  file      = {1977_McCammon_585.pdf:by-author/M/McCammon/1977_McCammon_585.pdf:PDF},
  owner     = {saulius},
  timestamp = {2013.04.01},
  creationdate = {2013-04-01T00:00:00},
}

@Article{McClelland1994,
  author    = {McClelland, M. and Nelson, M. and Raschke, E.},
  journal   = {Nucleic acids research},
  title     = {Effect of site-specific modification on restriction endonucleases and DNA modification methyltransferases.},
  year      = {1994},
  pages     = {3640--59},
  volume    = {22},
  abstract  = {Restriction endonucleases have site-specific interactions with DNA that can often be inhibited by site-specific DNA methylation and other site-specific DNA modifications. However, such inhibition cannot generally be predicted. The empirically acquired data on these effects are tabulated for over 320 restriction endonucleases. In addition, a table of known site-specific DNA modification methyltransferases and their specificities is presented along with EMBL database accession numbers for cloned genes.},
  file      = {:by-author/M/McClelland/1994_McClelland_3640.pdf:PDF},
  keywords  = {TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Manuscript{McClune2004,
  author    = {W. Frank McClune},
  title     = {PDF Editorial Staff Subcommittee: mineral, cement, metal and alloy definitions},
  year      = {2004},
  keywords  = {Definitions; Minerals; Terminology; X-ray Crystallography},
  month     = {March},
  file      = {:by-author/M/McClune/2004_McClune_mineral.pdf:PDF},
  owner     = {saulius},
  pages     = {mineral},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@Article{McCoy2007a,
  author    = {McCoy, Airlie J.},
  journal   = {Acta crystallographica. Section D, Biological crystallography},
  title     = {Solving structures of protein complexes by molecular replacement with Phaser.},
  year      = {2007},
  pages     = {32--41},
  volume    = {63},
  abstract  = {Molecular replacement (MR) generally becomes more difficult as the number of components in the asymmetric unit requiring separate MR models (i.e. the dimensionality of the search) increases. When the proportion of the total scattering contributed by each search component is small, the signal in the search for each component in isolation is weak or non-existent. Maximum-likelihood MR functions enable complex asymmetric units to be built up from individual components with a ;tree search with pruning' approach. This method, as implemented in the automated search procedure of the program Phaser, has been very successful in solving many previously intractable MR problems. However, there are a number of cases in which the automated search procedure of Phaser is suboptimal or encounters difficulties. These include cases where there are a large number of copies of the same component in the asymmetric unit or where the components of the asymmetric unit have greatly varying B factors. Two case studies are presented to illustrate how Phaser can be used to best advantage in the standard ;automated MR' mode and two case studies are used to show how to modify the automated search strategy for problematic cases.},
  doi       = {10.1107/S0907444906045975},
  file      = {:by-author/M/McCoy/2007_McCoy_32.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{McCoy2004,
  author    = {McCoy, Airlie J.},
  journal   = {Acta Crystallographica Section D},
  title     = {Liking likelihood},
  year      = {2004},
  pages     = {2169--2183},
  volume    = {60},
  doi       = {10.1107/S0907444904016038},
  file      = {ba5064.pdf:by-author/M/McCoy/2004_McCoy_2169.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444904016038},
}

@Article{McCoy2007,
  author    = {McCoy, Airlie J and Grosse-Kunstleve, Ralf W and Adams, Paul D and Winn, Martyn D and Storoni, Laurent C and Read, Randy J},
  journal   = {Journal of applied crystallography},
  title     = {Phaser crystallographic software.},
  year      = {2007},
  pages     = {658--674},
  volume    = {40},
  abstract  = {Phaser is a program for phasing macromolecular crystal structures by both molecular replacement and experimental phasing methods. The novel phasing algorithms implemented in Phaser have been developed using maximum likelihood and multivariate statistics. For molecular replacement, the new algorithms have proved to be significantly better than traditional methods in discriminating correct solutions from noise, and for single-wavelength anomalous dispersion experimental phasing, the new algorithms, which account for correlations between F(+) and F(-), give better phases (lower mean phase error with respect to the phases given by the refined structure) than those that use mean F and anomalous differences DeltaF. One of the design concepts of Phaser was that it be capable of a high degree of automation. To this end, Phaser (written in C++) can be called directly from Python, although it can also be called using traditional CCP4 keyword-style input. Phaser is a platform for future development of improved phasing methods and their release, including source code, to the crystallographic community.},
  file      = {2007_McCoy_658.pdf:by-author/M/McCoy/2007_McCoy_658.pdf:PDF},
  keywords  = {Phaser; Software; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{McDonald1988,
  author           = {Robert S. McDonald and Paul A. Wilks},
  journal          = {Appl. Spectrosc.},
  title            = {{JCAMP-DX}: A Standard Form for Exchange of Infrared Spectra in Computer Readable Form},
  year             = {1988},
  month            = {Jan},
  number           = {1},
  pages            = {151--162},
  volume           = {42},
  abstract         = {JCAMP-DX is a standard file form for exchange of infrared spectra and related chemical and physical information between spectrometer data systems of different manufacture, main-frame time-sharing systems, general purpose lab computers, and personal computers. It is compatible with all media: telephone, magnetic and optical disk, magnetic tape, and even the printed page (via optical reader).  All data are stored as labeled fields of variable length using printable ASCII characters. A JCAMP-DX spectrum is a text file which can be viewed, corrected, and annotated with a text editor. The present focus is on infrared spectra, but JCAMP-DX can easily accommodate Raman, UV, NMR, mass, and other types of spectra, x-ray powder patterns, chromatograms, thermograms, and other plots which require the capability of representing contours as well as peak position and intensity. JCAMP-DX also provides for combining adequate information about the sample and method of observation with its spectrum.},
  creationdate     = {2018-11-14T00:00:00},
  doi              = {10.1366/0003702884428734},
  file             = {:by-author/M/McDonald/1988_McDonald_151.pdf:PDF},
  keywords         = {Infrared Radiation},
  modificationdate = {2022-12-10T17:35:33},
  owner            = {andrius},
  publisher        = {OSA},
  timestamp        = {2018.11.14},
  url              = {http://www.jcamp-dx.org/protocols/dxir01.pdf},
}

@InBook{McDonald2000,
  author    = {Andrew D. McDonald and Markus G. Kuhn},
  chapter   = {StegFS: A Steganographic File System for Linux},
  editor    = {A. Pfitzmann},
  pages     = {463--477},
  publisher = {Springer Berlin Heidelberg},
  title     = {Information Hiding: Third International Workshop, IH'99, Dresden, Germany, September 29 - October 1, 1999 Proceedings},
  year      = {2000},
  address   = {Berlin, Heidelberg},
  note      = {The systems is described in: http://www.mcdonald.org.uk/StegFS/},
  abstract  = {Cryptographic file systems provide little protection against legal or illegal instruments that force the owner of data to release decryption keys for stored data once the presence of encrypted data on an inspected computer has been established. We are interested in how cryptographic file systems can be extended to provide additional protection for such a scenario and we have extended the standard Linux file system (Ext2fs) with a plausible-deniability encryption function. Even though it is obvious that our computer has harddisk encryption software installed and might contain some encrypted data, an inspector will not be able to determine whether we have revealed the access keys to all security levels or only those to a few selected ones. We describe the design of our freely available implementation of this steganographic file system and discuss its security and performance characteristics.},
  booktitle = {Information Hiding},
  doi       = {10.1007/10719724_32},
  file      = {2000_McDonald_463.pdf:by-author/M/McDonald/2000_McDonald_463.pdf:PDF},
  keywords  = {Computer Science (CS); Data Security; Encrypted File Systems; Encryption; Linux; Plausible Denyability; StegFS},
  owner     = {saulius},
  timestamp = {2016.03.21},
  creationdate = {2016-03-21T00:00:00},
  url       = {http://www.cl.cam.ac.uk/~mgk25/ih99-stegfs.pdf},
}

@Article{McGeehan2005,
  author    = {McGeehan, J. E. and Streeter, S. D. and Papapanagiotou, I. and Fox, G. C. and Kneale, G. G.},
  journal   = {Journal of molecular biology},
  title     = {High-resolution crystal structure of the restriction-modification controller protein C.AhdI from Aeromonas hydrophila.},
  year      = {2005},
  pages     = {689--701},
  volume    = {346},
  abstract  = {Restriction-modification (R-M) systems serve to protect the host bacterium from invading bacteriophage. The multi-component system includes a methyltransferase, which recognizes and methylates a specific DNA sequence, and an endonuclease which recognises the same sequence and cleaves within or close to this site. The endonuclease will only cleave DNA that is unmethylated at the specific site, thus host DNA is protected while non-host DNA is cleaved. However, following DNA replication, expression of the endonuclease must be delayed until the host DNA is appropriately methylated. In many R-M systems, this regulation is achieved at the transcriptional level via the controller protein, or C-protein. We have solved the first X-ray structure of an R-M controller protein, C.AhdI, to 1.69 A resolution using selenomethionine MAD. C.AhdI is part of a Type IIH R-M system from the pathogen Aeromonas hydrophila. The structure reveals an all-alpha protein that contains a classical helix-turn-helix (HTH) domain and can be assigned to the Xre family of transcriptional regulators. Unlike its monomeric structural homologues, an extended helix generates an interface that results in dimerisation of the free protein. The dimer is electrostatically polarised and a positively charged surface corresponds to the position of the DNA recognition helices of the HTH domain. Comparison with the structure of the lambda cI ternary complex suggests that C.AhdI activates transcription through direct contact with the sigma70 subunit of RNA polymerase.},
  file      = {:by-author/M/McGeehan/2005_McGeehan_689.pdf:PDF},
  keywords  = {TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{McGill2013,
  author    = {Keith J. McGill and Mojgan Asadi and Maria Toneva Karakasheva and Lawrence C. Andrews and Herbert J. Bernstein},
  journal   = {arXiv},
  title     = {The Geometry of Niggli Reduction III: SAUC -- Search of Alternate Unit Cells},
  year      = {2013},
  month     = {jul},
  pages     = {1307.1811v2},
  abstract  = {A crystallographic cell is a representation of a lattice, bu t each lattice can be represented just as well by any of an infinite number of such unit cells. Searching for matches to an experimentally determined crystallographic unit cell in a large collection of previously determined unit cells is a useful verification step in synchrotron data collection and can be a screen for “similar” structures, but it is more useful to search for a match to the lattice represented by the experimentally determined cell. For identification of substances with small cells, a unit cell match may be sufficient for unique identification. Due to experimental error and multiple choices of cells and differing choices of lattice centering representing the same lattice, simple searches based on raw cell edges and angles can miss similarities among lattices. A database of lattices using the G6 representation of the Niggli-reduced cell as the search key provides a more robust and complete search. Searching is implemented by finding the distance from the probe cell to related cells using a topological embedding of the Niggli reduction in G6, so that all cells representing similar lattices will be found. Comparison of results with those from older cell-based search algorithms suggests significant value in the new approach.},
  file      = {2013_McGill_1307.1811v2.pdf:by-author/M/McGill/2013_McGill_1307.1811v2.pdf:PDF},
  groups    = {sg/Cell reduction},
  keywords  = {Algorithms; Reduced Cell},
  owner     = {saulius},
  timestamp = {2016.11.30},
  creationdate = {2016-11-30T00:00:00},
  url       = {https://arxiv.org/abs/1307.1811},
}

@Manuscript{McIver2002,
  author    = {McIver, Linda and Damian Conway},
  title     = {Seven Deadly Sins of Introductory Programming Language Design},
  year      = {2002},
  keywords  = {Computer Science (CS); Programming Language Design},
  abstract  = {We discuss seven undesirable features common to many programming languages used to teach first-time program- mers, and illustrate typical pedagogical difficulties which stem from them with examples drawn from the program- ming languages ABC, Ada, C, C++, Eiffel, Haskell, LISP, Modula 3, Pascal, Prolog, Scheme, and Turing. We propose seven language design (or selection) principles which may reduce the incidence of such undesirable features.},
  file      = {:by-author/M/McIver/2002_McIver.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Manuscript{McKinnon1996,
  author       = {K.I.M. McKinnon},
  title        = {Convergence of the Nelder-Mead simplex method to a non-stationary point},
  year         = {1996},
  keywords     = {Computer Science (CS); Convergence; Nelder-Mead Method; Optimisation; Simplex Method},
  organization = {Department of Mathematics and Statistics, University of Edinburgh, The King's Buildings, Edinburgh EH9 3JZ},
  abstract     = {This paper analyses the behaviour of the Nelder-Mead simplex method for a family of examples which cause the method to converge to a non-stationary point. All the examples use continuous functions of two variables. The family of functions contains strictly convex functions with up to three continuous derivatives. In all the examples the method repeatedly applies the inside contraction step with the best vertex remaining xed. The simplices tend to a straight line which is orthogonal to the steepest descent direction. It is shown that this behaviour cannot occur f},
  file         = {:by-author/M/McKinnon/1996_McKinnon.ps:PostScript;:by-author/M/McKinnon/1996_McKinnon.pdf:PDF},
  journal      = {Submitted to SIAM Journal on Optimization},
  owner        = {saulius},
  timestamp = {2015.02.27},
  creationdate = {2015-02-27T00:00:00},
}

@Article{McLachlan1984,
  author    = {McLachlan, A. D.},
  journal   = {Biopolymers},
  title     = {How alike are the shapes of two random chains?},
  year      = {1984},
  pages     = {1325--31},
  volume    = {23},
  file      = {:by-author/M/McLachlan/1984_McLachlan_1325.pdf:PDF},
  keywords  = {Structure Comparison; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{McLachlan1982,
  author    = {McLachlan, A. D.},
  journal   = {Acta Crystallographica Section A},
  title     = {Rapid comparison of protein structures},
  year      = {1982},
  issn      = {1600-5724},
  pages     = {871--873},
  volume    = {38},
  abstract  = {An unusually fast method of superposing two sets of atomic coordinates for related molecular structures by least squares is described. It exploits the special nature of the problem and uses the method of conjugate gradients. The calculation takes about 0.003 s and is fast enough to be used in on-line graphics systems.},
  doi       = {10.1107/S0567739482001806},
  file      = {:by-author/M/McLachlan/1982_McLachlan_871.pdf:PDF},
  keywords  = {Algorithms; X-ray Crystallography},
  owner     = {saulius},
  publisher = {International Union of Crystallography},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0567739482001806},
}

@Article{McLachlan1972,
  author    = {McLachlan, A. D.},
  journal   = {Acta Crystallographica Section A},
  title     = {A mathematical procedure for superimposing atomic coordinates of proteins},
  year      = {1972},
  pages     = {656--657},
  volume    = {28},
  abstract  = {A procedure is given which determines the best rigid-body rotation and translation that matches a given set of measured atomic coordinates to a fixed set of guide coordinates and minimizes the weighted sum of squared deviations.},
  doi       = {10.1107/S0567739472001627},
  file      = {:by-author/M/McLachlan/1972_McLachlan_656.pdf:PDF},
  keywords  = {Algorithms; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Manuscript{McMahon200X,
  author    = {Brian McMahon},
  title     = {An integrated web resource for crystallography},
  year      = {200X},
  keywords  = {Crystallography; Data Access Policy; Data Exchange Standards; Data Management; Databases; Online Journals; World Wide Web},
  abstract  = {A recurring theme during the CODATA 2000 conference (Lake Maggiore, Italy, 15 - 19 October 2000) was the increasing convergence in data-rich branches of science between the storage and retrieval of data and the publication of conclusions drawn from the data. Web publishing technologies facilitate access to publications and data through the same interfaces and tools. For crystallography, the ability to deliver the experimental data alongside the research commentary offers tremendous advantages. A structured file format has been developed that allows not only submission of a research article accompanied by a complete supporting data set, but also automated validation of the description of the crystal structure reported in the article against the accompanying data. Such validation is an important component of the review process, and encourages better-quality publications. The adopted format is different from XML, but shares some of the properties of that markup language; and suggests the improvements in quality that might result in other subject areas from the adoption of similar methodology. The International Union of Crystallography fully exploits the convergence of publishing and data-handling technologies in its online journals and associated Web site.},
  file      = {:by-author/M/McMahon/200X_McMahon_54.pdf:PDF},
  owner     = {saulius},
  pages     = {54},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{McMahon2012,
  author    = {McMahon, Brian},
  journal   = {Journal of Cheminformatics},
  title     = {Applied and implied semantics in crystallographic publishing},
  year      = {2012},
  issn      = {1758-2946},
  pages     = {19},
  volume    = {4},
  abstract  = {BACKGROUND:Crystallography is a data-rich, software-intensive scientific discipline with a community that has undertaken direct responsibility for publishing its own scientific journals. That community has worked actively to develop information exchange standards allowing readers of structure reports to access directly, and interact with, the scientific content of the articles.RESULTS:Structure reports submitted to some journals of the International Union of Crystallography (IUCr) can be automatically validated and published through an efficient and cost-effective workflow. Readers can view and interact with the structures in three-dimensional visualization applications, and can access the experimental data should they wish to perform their own independent structure solution and refinement. The journals also layer on top of this facility a number of automated annotations and interpretations to add further scientific value.CONCLUSIONS:The benefits of semantically rich information exchange standards have revolutionised the scholarly publishing process for crystallography, and establish a model relevant to many other physical science disciplines.},
  doi       = {10.1186/1758-2946-4-19},
  file      = {2012_McMahon_19.pdf:by-author/M/McMahon/2012_McMahon_19.pdf:PDF},
  owner     = {saulius},
  pubmedid  = {22932420},
  timestamp = {2013.09.18},
  creationdate = {2013-09-18T00:00:00},
  url       = {http://www.jcheminf.com/content/4/1/19},
}

@Presentation{McMahon2008,
  author       = {Brian McMahon},
  title        = {Interactive visualization of data as a feature of online crystallography journal articles},
  year         = {2008},
  organization = {International Union of Crystallography},
  file         = {:by-author/M/McMahon/2008_McMahon_slides.pdf:PDF},
  keywords     = {Data Presentation; X-ray Crystallography},
  owner        = {saulius},
  pages        = {slides},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@InBook{McMahon2006,
  author           = {Brian McMahon},
  chapter          = {5.3},
  pages            = {499--525},
  title            = {Syntactic utilities for {CIF}},
  year             = {2006},
  volume           = {G},
  booktitle        = {International Tables for Crystallography},
  creationdate     = {2015-06-25T00:00:00},
  file             = {:by-author/M/McMahon/2006_McMahon_499.pdf:PDF},
  keywords         = {CIF},
  modificationdate = {2023-08-07T10:23:05},
  owner            = {andrius},
  timestamp        = {2015.06.25},
}

@Manuscript{McMahon2005,
  author    = {Brian McMahon},
  title     = {Semantically rich metadata in crystallographic publishing},
  year      = {2005},
  keywords  = {Crystallography; Data Management; Databases; Metadata; Workflow},
  abstract  = {Semantically-rich metadata assists publisher workflow and greatly increases the added value to the reader of a scientific publication. Where once bibliographic metadata provided the sole opportunity to locate and retrieve scientific publications, the experimental data on which scientific results are based itself is rich in metadata characterizing the data and the results derived from it. In crystallography, a community data exchange standard exists that has been used by specialist journals for over a decade and is increasingly enabling scientists to populate open-archive repositories of experimental results. By extracting and harvesting the relevant metadata, the possibility arises of linking data repository, journal and structure database together in a networked, distributed information resource. The metadata also have an essential role to play in assuring the quality of scientific data and publications.},
  file      = {:by-author/M/McMahon/2005_McMahon.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{McMahon1993,
  author           = {McMahon, B.},
  journal          = {Acta Crystallographica Section C},
  title            = {`How does my CIF become a printed paper?'},
  year             = {1993},
  pages            = {418--423},
  volume           = {49},
  creationdate     = {2008-07-28T00:00:00},
  doi              = {10.1107/S0108270193000800},
  file             = {es0183.pdf:by-author/M/McMahon/1993_McMahon_418.pdf:PDF},
  keywords         = {CIF},
  modificationdate = {2023-08-07T10:23:05},
  owner            = {saulius},
  timestamp        = {2008.07.28},
  url              = {http://dx.doi.org/10.1107/S0108270193000800},
}

@TechReport{McMahon2000,
  author           = {Brian McMahon and John Westbrook and Herbert Bernstein},
  institution      = {IUCr COMCIFS},
  title            = {COMCIFS Working Group on Dictionary Maintenance: Final report},
  year             = {2000},
  abstract         = {As the number of formal and informal uses of STAR and CIF grows, it becomes increasingly important to have a clear understanding of what defines a valid CIF data set. Particularly as cross-disciplinary investigations become more common, it becomes essential to understand how to merge CIFs from multiple disciplines, and to ensure efficient and reliable transitions among versions of dictionaries.},
  creationdate     = {2013-09-19T00:00:00},
  file             = {:by-author/M/McMahon/2000_McMahon.html:URL},
  keywords         = {CIF},
  modificationdate = {2023-08-07T10:23:05},
  owner            = {saulius},
  timestamp        = {2013.09.19},
  url              = {http://www.iucr.org/__data/assets/file/0003/18687/maintenance.html},
}

@Lecture{McMillan2003,
  author       = {McMillan},
  title        = {Computer Organization: Problem Set No. 2},
  year         = {2003},
  organization = {The University of North Carolina at Chapel Hill},
  file         = {:by-author/M/McMillan/2003_McMillan.pdf:PDF},
  keywords     = {Computer Architecture; Computer Science (CS); Hardware},
  owner        = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{McMillen2015,
  author    = {McMillen, Patrick and Holley, Scott A.},
  journal   = {Current opinion in cell biology},
  title     = {Integration of cell-cell and cell-ECM adhesion in vertebrate morphogenesis.},
  year      = {2015},
  pages     = {48--53},
  volume    = {36},
  abstract  = {In this review, we highlight recent re-evaluations of the classical cell sorting models and their application to understanding embryonic morphogenesis. Modern genetic and biophysical techniques reveal that tissue self-assembly is not solely a result of differential adhesion, but rather incorporates dynamic cytoskeletal tension and extracellular matrix assembly. There is growing evidence that these biomechanical modules cooperate to organize developing tissues. We describe the contributions of Cadherins and Integrins to tissue assembly and propose a model in which these very different adhesive regimes affect the same outcome through separate but convergent mechanisms.},
  doi       = {10.1016/j.ceb.2015.07.002},
  file      = {:by-author/M/McMillen/2015_McMillen_48.pdf:pdf},
  keywords  = {Structure Refinement; Validation; X-ray Crystallography},
  mid       = {NIHMS706398},
  owner     = {saulius},
  pii       = {S0955-0674(15)00077-0},
  pmc       = {PMC4639458},
  pubmed    = {26189063},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Article{McPeak2005,
  author    = {McPeak, Scotta and George C. Necula},
  journal   = {Computer Aided Verification},
  title     = {Data Structure Specifications via Local Equality Axioms},
  year      = {2005},
  pages     = {476--490},
  abstract  = {We describe a program verification methodology for spec- ifying global shape properties of data structures by means of axioms involving predicates on scalar fields, pointer equalities, and pointer dise- qualities, in the neighborhood of a memory cell. We show that such local invariants are both natural and sufficient for describing a large class of data structures. We describe a complete decision procedure for axioms without disequalities, and practical heuristics for the full language. The procedure has the key advantage that it can be extended easily with reasoning for any decidable theory of scalar fields.},
  file      = {:by-author/M/McPeak/2005_McPeak_476.pdf:PDF},
  groups    = {sg/Correctness proofs},
  keywords  = {Computer Science (CS); Correctness Proofs},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{McPherson2001,
  author    = {McPherson, A. and Malkin, A. J. and Kuznetsov, Yu. G. and Plomp, M.},
  journal   = {Acta Crystallographica Section D},
  title     = {Atomic force microscopy applications in macromolecular crystallography},
  year      = {2001},
  pages     = {1053--1060},
  volume    = {57},
  doi       = {10.1107/S0907444901008824},
  file      = {sx0045.pdf:by-author/M/McPherson/2001_McPherson_1053.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444901008824},
}

@Article{McRee2004,
  author    = {McRee, Duncan E.},
  journal   = {Acta Crystallographica Section D},
  title     = {Differential evolution for protein crystallographic optimizations},
  year      = {2004},
  pages     = {2276--2279},
  volume    = {60},
  doi       = {10.1107/S0907444904025491},
  file      = {ba5063.pdf:by-author/M/McRee/2004_McRee_2276.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444904025491},
}

@Article{Mechelke2010,
  author    = {Martin Mechelke and Michael Habeck},
  journal   = {BMC Bioinformatics},
  title     = {Robust probabilistic superposition and comparison of protein structures},
  year      = {2010},
  pages     = {363},
  volume    = {11},
  abstract  = {Background Protein structure comparison is a central issue in structural bioinformatics. The standard dissimilarity measure for protein structures is the root mean square deviation (RMSD) of representative atom positions such as α-carbons. To evaluate the RMSD the structures under comparison must be superimposed optimally so as to minimize the RMSD. How to evaluate optimal fits becomes a matter of debate, if the structures contain regions which differ largely - a situation encountered in NMR ensembles and proteins undergoing large-scale conformational transitions. Results We present a probabilistic method for robust superposition and comparison of protein structures. Our method aims to identify the largest structurally invariant core. To do so, we model non-rigid displacements in protein structures with outlier-tolerant probability distributions. These distributions exhibit heavier tails than the Gaussian distribution underlying standard RMSD minimization and thus accommodate highly divergent structural regions. The drawback is that under a heavy-tailed model analytical expressions for the optimal superposition no longer exist. To circumvent this problem we work with a scale mixture representation, which implies a weighted RMSD. We develop two iterative procedures, an Expectation Maximization algorithm and a Gibbs sampler, to estimate the local weights, the optimal superposition, and the parameters of the heavy-tailed distribution. Applications demonstrate that heavy-tailed models capture differences between structures undergoing substantial conformational changes and can be used to assess the precision of NMR structures. By comparing Bayes factors we can automatically choose the most adequate model. Therefore our method is parameter-free. Conclusions Heavy-tailed distributions are well-suited to describe large-scale conformational differences in protein structures. A scale mixture representation facilitates the fitting of these distributions and enables outlier-tolerant superposition.},
  doi       = {10.1186/1471-2105-11-363},
  file      = {:by-author/M/Mechelke/2010_Mechelke_363.pdf:PDF},
  groups    = {sg/Bayesian},
  owner     = {saulius},
  timestamp = {2011.12.21},
  creationdate = {2011-12-21T00:00:00},
  url       = {http://www.biomedcentral.com/1471-2105/11/363},
}

@Article{Meek1990,
  author    = {Meek, Brian},
  journal   = {Sigplan Notices},
  title     = {Two-Valued Datatypes},
  year      = {1990},
  month     = {August},
  volume    = {25},
  file      = {:by-author/M/Meek/1990_Meek_Sigplan.pdf:PDF},
  keywords  = {Computer Science (CS); Type Systems},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Mehl,
  author    = {Christian Mehl},
  title     = {On asymptotic convergence of nonsymmetric jacobi algorithms},
  year      = {2007},
  abstract  = {The asymptotic convergence behavior of cyclic versions of the nonsymmetric Jacobi algorithm for the computation of the Schur form of a general complex matrix is investigated. Similar to the symmetric case, the nonsymmetric Jacobi algorithm proceeds by applying a sequence of rotations that annihilate a pivot element in the strict lower triangular part of the matrix until convergence to the Schur form of the matrix is achieved. In this paper, it is shown that the cyclic nonsymmetric Jacobi method converges locally and asymptotically quadratically under mild hypotheses if special ordering schemes are chosen, namely ordering schemes that lead to so-called northeast directed sweeps. The theory is illustrated by the help of numerical experiments. In particular, it is shown that there are ordering schemes that lead to asymptotic quadratic convergence for the cyclic symmetric Jacobi method, but only to asymptotic linear convergence for the cyclic nonsymmetric Jacobi method. Finally, a generalization of the nonsymmetric Jacobi method to the computation of the Hamiltonian Schur form for Hamiltonian matrices is introduced and investigated.},
  file      = {:by-author/M/Mehl/2007_Mehl.pdf:PDF},
  owner     = {saulius},
  timestamp = {2011.12.13},
  creationdate = {2011-12-13T00:00:00},
}

@Article{Mehlhorn2010,
  author    = {Mehlhorn},
  title     = {Implementation of the Simplex Algorithm},
  year      = {2010},
  file      = {:by-author/M/Mehlhorn/2010_Mehlhorn.pdf:PDF},
  keywords  = {Computer Science (CS); Minimisation; Simplex Method},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@InProceedings{Meijer2007,
  author    = {Meijer, Erik},
  booktitle = {OOPSLA’07},
  title     = {Confessions of a Used Programming Language Salesman: Getting the Masses Hooked on Haskell},
  year      = {2007},
  pages     = {OOPSLA},
  abstract  = {When considering the past or the future, dear appren- tice, be mindful of the present. If, while considering the past, you become caught in the past, lost in the past, or enslaved by the past, then you have forgot- ten yourself in the present. If, while considering the future, you become caught in the future, lost in the fu- ture, or enslaved by the future, then you have forgot- ten yourself in the present. Conversely, when consid- ering the past, if you do not become caught, lost, or enslaved by the past, then you have remained mind- ful of the present. And if, when considering the future, you do not become caught, lost, or enslaved in the fu- ture, then you have remained mindful of the present.},
  file      = {:by-author/M/Meijer/2007_Meijer_OOPSLA.pdf:PDF},
  keywords  = {Compiler Design; Computer Science (CS); Programming Languages; Type Systems},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Manuscript{Meijer2004,
  author    = {Erik Meijer and Peter Drayton},
  title     = {Static Typing Where Possible, Dynamic Typing When Needed: The End of the Cold War Between Programming Languages},
  year      = {2004},
  keywords  = {Computer Science (CS); Type Systems},
  abstract  = {This paper argues that we should seek the golden middle way between dynamically and statically typed languages.},
  file      = {:by-author/M/Meijer/2004_Meijer_manuscript.pdf:PDF},
  owner     = {saulius},
  pages     = {manuscript},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Presentation{Meijers2010,
  author    = {Rob Meijers},
  title     = {Sample preparation and characterisation around {SAXS}},
  year      = {2010},
  file      = {:by-author/M/Meijers/2010_Meijers_slides.pdf:PDF},
  keywords  = {SAXS},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Meiss2000,
  author    = {Meiss, G. and Gimadutdinow, O. and Haberland, B. and Pingoud, A.},
  journal   = {Journal of molecular biology},
  title     = {Mechanism of DNA cleavage by the DNA/RNA-non-specific Anabaena sp. PCC 7120 endonuclease NucA and its inhibition by NuiA.},
  year      = {2000},
  pages     = {521--34},
  volume    = {297},
  abstract  = {A structural model of the DNA/RNA non-specific endonuclease NucA from Anabaena sp. PCC7120 that has been obtained on the basis of the three-dimensional structure of the related Serratia nuclease, suggests that the overall architecture of the active site including amino acid residues H124, N155 and E163 (corresponding to H89, N119 and E127 in Serratia nuclease) is similar in both nucleases. Substitution of these residues by alanine leads to a large reduction in activity (&lt;0.1 %), similarly as observed for Serratia nuclease demonstrating that both enzymes share a similar mechanism of catalysis with differences only in detail. NucA is inhibited by its specific polypeptide inhibitor with a K(i) value in the subpicomolar range, while the related Serratia nuclease at nanomolar concentrations is only inhibited at an approximately 1000-fold molar excess of NuiA. The artificial chromophoric substrate deoxythymidine 3',5'-bis-(p-nitrophenyl phosphate) is cleaved by NucA as well as by Serratia nuclease. Cleavage of this analogue by NucA, however, is not inhibited by NuiA, suggesting that small molecules gain access to the active site of NucA in the enzyme-inhibitor complex under conditions where cleavage of DNA substrates is completely inhibited. The active site residue E163 seems to be the main target amino acid for inhibition of NucA by NuiA, but R93, R122 and R167 (corresponding to K55, R87, R131 in Serratia nuclease) are also involved in the NucA/NuiA interaction. NuiA deletion mutants show that the structural integrity of the N and C-terminal region of the inhibitor is important for complex formation with NucA and inhibition of nuclease activity. Based on these results a mechanism of DNA cleavage by NucA and its inhibition by NuiA is proposed.},
  file      = {:by-author/M/Meiss/2000_Meiss_521.pdf:PDF},
  owner     = {em},
  timestamp = {2013.09.19},
  creationdate = {2013-09-19T00:00:00},
}

@Article{Meng2016,
  author    = {Meng, Xing and Jiang, Qian and Chang, Nannan and Wang, Xiaoxia and Liu, Chujun and Xiong, Jingwei and Cao, Huiqing and Liang, Zicai},
  journal   = {Nucleic Acids Research},
  title     = {Small activating {RNA} binds to the genomic target site in a seed-region-dependent manner},
  year      = {2016},
  issn      = {1362-4962},
  month     = {Feb},
  number    = {5},
  pages     = {2274–2282},
  volume    = {44},
  doi       = {10.1093/nar/gkw076},
  file      = {:by-author/M/Meng/2016_Meng_2274.pdf:PDF},
  groups    = {am/RNA activation},
  owner     = {andrius},
  publisher = {Oxford University Press (OUP)},
  timestamp = {2016.08.23},
  creationdate = {2016-08-23T00:00:00},
  url       = {http://dx.doi.org/10.1093/nar/gkw076},
}

@Article{Merali2010,
  author    = {Merali, Zeeya},
  title     = {Error: why scientific programming does not compute},
  year      = {2010},
  pages     = {775--777},
  volume    = {467},
  doi       = {10.1038/467775a},
  file      = {Merali - 2010 - Error Why scientific programming does not compute.pdf:by-author/M/Merali/2010_Merali_775.pdf:application/pdf},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://www.nature.com/news/2010/101013/pdf/467775a.pdf},
  urldate   = {2015-06-06},
}

@Article{Mercier2005,
  author    = {Mercier, Patrick H. J. and Le Page, Yvon and Whitfield, Pamela S. and Mitchell, Lyndon D. and Davidson, Isobel J. and White, T. J.},
  journal   = {Acta Crystallographica Section B},
  title     = {Geometrical parameterization of the crystal chemistry of {\it P}6${\sb 3}$/{\it m} apatites: comparison with experimental data and {\it ab initio} results},
  year      = {2005},
  pages     = {635--655},
  volume    = {61},
  doi       = {10.1107/S0108768105031125},
  file      = {:by-author/M/Mercier/2005_Mercier_635.pdf:PDF},
  keywords  = {For COD Deposition; For TCOD Deposition},
  owner     = {andrius},
  timestamp = {2015.09.28},
  creationdate = {2015-09-28T00:00:00},
}

@Article{Merckel2002,
  author    = {Merckel, Michael C. and Kajander, Tommi and Deacon, Ashley M. and Thompson, Andrew and Grossmann, J. G{\"{u}}nter and Kalkkinen, Nisse and Goldman, Adrian},
  journal   = {Acta Crystallographica Section D},
  title     = {3-Carboxy-{\it cis},{\it cis}-muconate lactonizing enzyme from {\it Neurospora crassa}: MAD phasing with 80 selenomethionines},
  year      = {2002},
  pages     = {727--734},
  volume    = {58},
  doi       = {10.1107/S0907444902002652},
  file      = {jn0101.pdf:by-author/M/Merckel/2002_Merckel_727.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444902002652},
}

@Manuscript{Meredith2005,
  author    = {Meredith},
  title     = {Nelder-Mead Algorithm},
  year      = {2005},
  keywords  = {Computer Science (CS); Minimisation; Simplex Method},
  file      = {:by-author/M/Meredith/2005_Meredith.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Merkiene2005,
  author    = {Merkiene, Egle and Klimasauskas, Saulius},
  journal   = {Nucleic acids research},
  title     = {Probing a rate-limiting step by mutational perturbation of AdoMet binding in the HhaI methyltransferase.},
  year      = {2005},
  pages     = {307--15},
  volume    = {33},
  abstract  = {DNA methylation plays important roles via regulation of numerous cellular mechanisms in diverse organisms, including humans. The paradigm bacterial methyltransferase (MTase) HhaI (M.HhaI) catalyzes the transfer of a methyl group from the cofactor S-adenosyl-L-methionine (AdoMet) onto the target cytosine in DNA, yielding 5-methylcytosine and S-adenosyl-L-homocysteine (AdoHcy). The turnover rate (k cat) of M.HhaI, and the other two cytosine-5 MTases examined, is limited by a step subsequent to methyl transfer; however, no such step has so far been identified. To elucidate the role of cofactor interactions during catalysis, eight mutants of Trp41, which is located in the cofactor binding pocket, were constructed and characterized. The mutants show full proficiency in DNA binding and base-flipping, and little variation is observed in the apparent methyl transfer rate k chem as determined by rapid-quench experiments using immobilized fluorescent-labeled DNA. However, the Trp41 replacements with short side chains substantially perturb cofactor binding (100-fold higher K(AdoMet)D and K(AdoMet)M) leading to a faster turnover of the enzyme (10-fold higher k cat). Our analysis indicates that the rate-limiting breakdown of a long-lived ternary product complex is initiated by the dissociation of AdoHcy or the opening of the catalytic loop in the enzyme.},
  file      = {:by-author/M/Merkiene/2005_Merkiene_307.pdf:PDF},
  keywords  = {HhaI},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Presentation{Merkys2016a,
  author       = {Andrius Merkys},
  title        = {Mažos aktyvuojančios RNR: mechanizmas ir taikymai},
  year         = {2016},
  course       = {Genetic engineering},
  organization = {Vilnius University Institute of Biotechnology},
  file         = {:by-author/M/Merkys/2016_Merkys_slides.pdf:PDF},
  owner        = {andrius},
  timestamp = {2016.10.13},
  creationdate = {2016-10-13T00:00:00},
}

@Presentation{Merkys2015,
  author    = {Andrius Merkys},
  title     = {Diary of a research},
  year      = {2015},
  file      = {2015_Merkys.pdf:by-author/M/Merkys/2015_Merkys.pdf:PDF},
  groups    = {am/My papers},
  owner     = {saulius},
  timestamp = {2015.06.15},
  creationdate = {2015-06-15T00:00:00},
}

@MastersThesis{Merkys2013,
  author    = {Andrius Merkys},
  school    = {Vilniaus Universitetas, Matematikos ir Informatikos Fakultetas, Informatikos Katedra},
  title     = {Kristalografinių žinių apie mažas molekules panaudojimas makromolekulių struktūrų patikslinimui: atviros mažų molekulių kristalografinės duomenų bazės pritaikymas Use of Prior Small Molecule Crystallographic Knowledge for Refinement of Macromolecular Structures: Application of the Crystallography Open Database},
  year      = {2013},
  type      = {Master thesis},
  abstract  = {Mažų molekulių stereocheminės informacijos rinkiniai, skirti mo- lekulių patikslinimui ir tikrinimui, susiduria su dviem apribojimais: licencijomis bei galimu atsilikimu nuo sparčiai besivystančių tyrimų rezultatų. Naujas mažų moleku- lių stereocheminės informacijos rinkinys išvedamas iš atviros prieigos mažų molekulių duomenų bazės COD naudojantis nauja mažų molekulių cheminės įvairovės aprašy- mo metodika bei Bajeso (Bayesian) karkasu, sukuriamos priemonės automatiniam rinkinio atnaujinimui realiame laike. Automatiniais metodais išvestas stereochemi- nės informacijos rinkinys yra palyginamas su ankstesniais darbais šioje srityje bei panaudojamas neįprastiems mažų molekulių geometriniams bruožams aptikti, bet galėtų būti pagerintas ištaisius COD duomenų klaidas bei pagerinus naudojamo ti- kėtinumo maksimizavimo algoritmo inicializaciją bei konvergavimo greitį. Libraries of small molecule stereochemical information, used for refinement and validation of small molecules and macromolecule-ligand complexes, are subjected to two limitations: licensing and possibility to become outdated. A novel library of small molecule stereochemical information is constructed from the Crystallography Open Database (COD), harnessing a new method for description of the variety of small molecule chemical environments and Bayesian framework. Means for automatic renewal of the library in the real time are devised. The result of the research is comparable to the previous works and proves to be useful in the detection of unusual geometric features in small molecules. The library can be improved by devising better means of initialisation of the expectation maximisation algorithm and speeding up the convergence.},
  file      = {:by-author/M/Merkys/2013_Merkys.pdf:PDF},
  groups    = {sg/Bayesian, am/My papers},
  keywords  = {Bayesian Statistics; Data Management; Databases; Statistics; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2014.03.25},
  creationdate = {2014-03-25T00:00:00},
}

@MastersThesis{Merkys2011,
  author    = {Andrius Merkys},
  school    = {Vilniaus Universitetas, Matematikos ir Informatikos Fakultetas, Matematinės Informatikos Katedra},
  title     = {Duomenų įkėlimo įrangos kūrimas atvirai mažų molekulių kristalografinei duomenų bazei COD},
  year      = {2011},
  type      = {BSc thesis},
  abstract  = {Šiame dokumente aprašomas atviros mažų molekulių kristalografinės duomenų bazės COD automatinės duomenų įkėlimo programinės įrangos, leidžiančios užtikrinti spartų duomenų bazės augimą, poreikis, kūrimas, kūrimo metu priimti sprendimai bei spręsti uždaviniai. This document presents the desciption of demand, solutions and development of the deposition software for small molecule open crystallographic database COD.},
  file      = {:by-author/M/Merkys/2011_Merkys.pdf:PDF},
  groups    = {am/My papers},
  keywords  = {COD; Data Management; Databases; Software Development; X-ray Crystallography},
  language  = {Lithuanian},
  owner     = {saulius},
  timestamp = {2014.03.25},
  creationdate = {2014-03-25T00:00:00},
}

@Article{Merkys2013a,
  author    = {Merkys, Andrius and Long, Fei and Murshudov, Garib N. and Gra{\v{z}}ulis, Saulius},
  journal   = {Acta Crystallographica Section A},
  title     = {Stereochemical statistics in {Crystallography Open Database}},
  year      = {2013},
  pages     = {s388--s389},
  volume    = {69},
  doi       = {10.1107/S0108767313096621},
  file      = {:by-author/M/Merkys/2013_Merkys_s388.pdf:PDF},
  groups    = {am/My papers},
  owner     = {andrius},
  timestamp = {2014.06.20},
  creationdate = {2014-06-20T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0108767313096621},
}

@Article{Merkys2016,
  author           = {Merkys, Andrius and Vaitkus, Antanas and Butkus, Justas and Okuli{\v{c}}-Kazarinas, Mykolas and Kairys, Visvaldas and Gra{\v{z}}ulis, Saulius},
  journal          = {Journal of Applied Crystallography},
  title            = {{\it COD::CIF::Parser}: an error-correcting {CIF} parser for the {P}erl language},
  year             = {2016},
  month            = {Feb},
  number           = {1},
  pages            = {292--301},
  volume           = {49},
  abstract         = {A syntax-correcting CIF parser, {\it COD::CIF::Parser}, is presented that can parse CIF 1.1 files and accurately report the position and the nature of the discovered syntactic problems. In addition, the parser is able to automatically fix the most common and the most obvious syntactic deficiencies of the input files. Bindings for Perl, C and Python programming environments are available. Based on {\it COD::CIF::Parser}, the {\it cod-tools} package for manipulating the CIFs in the Crystallography Open Database (COD) has been developed. The {\it cod-tools} package has been successfully used for continuous updates of the data in the automated COD data deposition pipeline, and to check the validity of COD data against the IUCr data validation guidelines. The performance, capabilities and applications of different parsers are compared.},
  creationdate     = {2016-01-06T00:00:00},
  doi              = {10.1107/S1600576715022396},
  file             = {:by-author/M/Merkys/2016_Merkys.pdf:PDF},
  groups           = {sg/COD, am/COD, am/My papers, sg/CIF, am/CIF},
  keywords         = {CIF},
  modificationdate = {2023-08-07T10:23:04},
  owner            = {andrius},
  timestamp        = {2016.01.06},
  url              = {http://dx.doi.org/10.1107/S1600576715022396},
}

@Article{Merlin2003,
  author    = {Merlin, Christophe and Masters, Millicent and McAteer, Sean and Coulson, Andrew},
  journal   = {Journal of bacteriology},
  title     = {Why is carbonic anhydrase essential to Escherichia coli?},
  year      = {2003},
  pages     = {6415--24},
  volume    = {185},
  abstract  = {The can (previously yadF) gene of Escherichia coli encodes a beta-class carbonic anhydrase (CA), an enzyme which interconverts CO(2) and bicarbonate. Various essential metabolic processes require either CO(2) or bicarbonate and, although carbon dioxide and bicarbonate spontaneously equilibrate in solution, the low concentration of CO(2) in air and its rapid diffusion from the cell mean that insufficient bicarbonate is spontaneously made in vivo to meet metabolic and biosynthetic needs. We calculate that demand for bicarbonate is 10(3)- to 10(4)-fold greater than would be provided by uncatalyzed intracellular hydration and that enzymatic conversion of CO(2) to bicarbonate is therefore necessary for growth. We find that can expression is ordinarily required for growth in air. It is dispensable if the atmospheric partial pressure of CO(2) is high or during anaerobic growth in a closed vessel at low pH, where copious CO(2) is generated endogenously. CynT, the single E. coli Can paralog, can, when induced with azide, replace Can; also, the gamma-CA from Methanosarcina thermophila can at least partially replace it. Expression studies showed that can transcription does not appear to respond to carbon dioxide concentration or to be autoregulated. However, can expression is influenced by growth rate and the growth cycle; it is expressed best in slow-growing cultures and at higher culture densities. Expression can vary over a 10-fold range during the growth cycle and is also elevated during starvation or heat stress.},
  file      = {2003_Merlin_6415.pdf:by-author/M/Merlin/2003_Merlin_6415.pdf:PDF},
  groups    = {sg/physiology},
  keywords  = {Carbonic Anhydrases},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Mernagh1998,
  author    = {Mernagh, D. R. and Janscak, P. and Firman, K. and Kneale, G. G.},
  journal   = {Biological chemistry},
  title     = {Protein-protein and protein-DNA interactions in the type I restriction endonuclease R.EcoR124I.},
  year      = {1998},
  pages     = {497--503},
  volume    = {379},
  abstract  = {The type I restriction-modification system EcoR124I recognizes and binds to the split DNA recognition sequence 5'-GAAN(6)RTCG-3'. The methyltransferase, consisting of HsdM and HsdS subunits with the composition M2S, can interact with one or more subunits of the HsdR subunit to form the endonuclease. The interaction of the methyltransferase with HsdR has been investigated by surface plasmon resonance, showing that there are two non-equivalent binding sites for HsdR which differ in binding affinity by at least two orders of magnitude. DNA footprinting experiments using Exonuclease III suggest that the addition of HsdR to the methyltransferase (at a stoichiometry of either 1:1 or 2:1) increases the stability of the resulting DNA-protein complex but does not increase the size of the footprint. More extensive in situ footprinting experiments using copper-phenanthroline on the DNA-protein complexes formed by M2S, R1M2S and R2M2S also show no difference in the detailed cleavage pattern, with approximately 18 nucleotides protected on both strands in each complex. Thus the HsdR subunit(s) of the endonuclease stabilise the interaction of the M2S complex with DNA, but do not directly contribute to DNA binding. In addition, the thymidine nucleotide in the tetranucleotide recognition sequence GTCG is hyper-reactive to cleavage in each case, suggesting that the DNA structure in this region is altered in these complexes.},
  file      = {:by-author/M/Mernagh/1998_Mernagh_497.pdf:PDF},
  keywords  = {TypeI},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Mernagh1996,
  author    = {Mernagh, D. R. and Kneale, G. G.},
  journal   = {Nucleic acids research},
  title     = {High resolution footprinting of a type I methyltransferase reveals a large structural distortion within the DNA recognition site.},
  year      = {1996},
  pages     = {4853--8},
  volume    = {24},
  abstract  = {The type I DNA methyltransferase M.EcoR124I is a multi-subunit enzyme that binds to the sequence GAAN6RTCG, transferring a methyl group from S-adenosyl methionine to a specific adenine on each DNA strand. We have investigated the protein-DNA interactions in the complex by DNase I and hydroxyl radical footprinting. The DNase I footprint is unusually large: the protein protects the DNA on both strands for at least two complete turns of the helix, indicating that the enzyme completely encloses the DNA in the complex. The higher resolution hydroxyl radical probe shows a smaller, but still extensive, 18 bp footprint encompassing the recognition site. Within this region, however, there is a remarkably hyper-reactive site on each strand. The two sites of enhanced cleavage are co-incident with the two adenines that are the target bases for methylation, showing that the DNA is both accessible and highly distorted at these sites. The hydroxyl radical footprint is unaffected by the presence of the cofactor S-adenosyl methionine, showing that the distorted DNA structure induced by M.EcoR124I is formed during the initial DNA binding reaction and not as a transient intermediate in the reaction pathway.},
  file      = {:by-author/M/Mernagh/1996_Mernagh_4853.pdf:PDF},
  keywords  = {TypeI},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Mernagh1998a,
  author    = {Mernagh, D. R. and Taylor, I. A. and Kneale, G. G.},
  journal   = {The Biochemical journal},
  title     = {Interaction of the type I methyltransferase M.EcoR124I with modified DNA substrates: sequence discrimination and base flipping.},
  year      = {1998},
  pages     = {719--25},
  volume    = {336 ( Pt 3)},
  abstract  = {We have analysed the DNA-protein contacts made between the type I DNA methyltransferase M.EcoR124I and its recognition sequence. The effects of base modifications have been probed by measuring the affinity of M.EcoR124I for the modified sequences relative to that for the wild-type sequence by using gel-retardation competition assays. These results, along with those from methylation interference footprinting and photo-affinity cross-linking have identified the location of potential DNA contacts within the DNA recognition site. Substitution of 6-thioguanosine for each of the three specific guanines in the recognition sequence leads to a large (10-20-fold) decrease in the strength of DNA binding, indicating the importance of hydrogen-bonding interactions in the major groove of DNA. In contrast, replacement of either (or both) of the adenines at the target site for methylation by the enzyme, to produce either a base pair mismatch or loss of the base, leads to a marked increase in DNA-binding affinity. The results strongly support the proposal that type I methyltransferases employ a base-flipping mechanism to methylate their target base.},
  file      = {:by-author/M/Mernagh/1998_Mernagh_719.pdf:PDF},
  keywords  = {MTases},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Merolla2014,
  author    = {Merolla, Paul A. and Arthur, John V. and Alvarez-Icaza, Rodrigo and Cassidy, Andrew S. and Sawada, Jun and Akopyan, Filipp and Jackson, Bryan L. and Imam, Nabil and Guo, Chen and Nakamura, Yutaka and Brezzo, Bernard and Vo, Ivan and Esser, Steven K. and Appuswamy, Rathinakumar and Taba, Brian and Amir, Arnon and Flickner, Myron D. and Risk, William P. and Manohar, Rajit and Modha, Dharmendra S.},
  journal   = {Science},
  title     = {A million spiking-neuron integrated circuit with a scalable communication network and interface},
  year      = {2014},
  pages     = {668--673},
  volume    = {345},
  abstract  = {Inspired by the brain’s structure, we have developed an efficient, scalable, and flexible non–von Neumann architecture that leverages contemporary silicon technology. To demonstrate, we built a 5.4-billion-transistor chip with 4096 neurosynaptic cores interconnected via an intrachip network that integrates 1 million programmable spiking neurons and 256 million configurable synapses. Chips can be tiled in two dimensions via an interchip communication interface, seamlessly scaling the architecture to a cortexlike sheet of arbitrary size. The architecture is well suited to many applications that use complex neural networks in real time, for example, multiobject detection and classification. With 400-pixel-by-240-pixel video input at 30 frames per second, the chip consumes 63 milliwatts.},
  doi       = {10.1126/science.1254642},
  eprint    = {http://www.sciencemag.org/content/345/6197/668.full.pdf},
  file      = {:by-author/M/Merolla/2014_Merolla_668.pdf:PDF},
  owner     = {andrius},
  timestamp = {2014.09.12},
  creationdate = {2014-09-12T00:00:00},
  url       = {http://www.sciencemag.org/content/345/6197/668.abstract},
}

@Article{Merritt1994,
  author    = {Merritt, E A and Murphy, M E},
  journal   = {Acta Crystallogr D Biol Crystallogr},
  title     = {Raster3D Version 2.0. A program for photorealistic molecular graphics},
  year      = {1994},
  month     = {Nov},
  number    = {Pt 6},
  pages     = {869--73},
  volume    = {50},
  abstract  = {Raster3D Version 2.0 is a program suite for the production of photorealistic molecular graphics images. The code is hardware independent, and is particularly suited for use in producing large raster images of macromolecules for output to a film recorder or high-quality color printer. The Raster3D suite contains programs for composing illustrations of space-filling models, ball-and-stick models and ribbon-and-cylinder representations. It may also be used to render figures composed using other graphics tools, notably the widely used program Molscript [Kraulis (1991). J. Appl. Cryst. 24, 946-950]},
  address   = {Department of Biological Structure SM-20, University of Washington, Seattle 98195, USA},
  doi       = {10.1107/S0907444994006396},
  file      = {1994_Merritt_869.pdf:by-author/M/Merritt/1994_Merritt_869.pdf:PDF},
  keywords  = {Molecular Graphics; Photorealistic Graphics; Raster3d; Ray-tracing},
  owner     = {em},
  pmid      = {15299354},
  timestamp = {2016.06.16},
  creationdate = {2016-06-16T00:00:00},
  url       = {http://www.ncbi.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&dopt=abstract&list_uids=15299354},
}

@Article{Mertens2010,
  author    = {Mertens, Haydyn D.T. and Svergun, Dmitri I.},
  journal   = {Journal of Structural Biology},
  title     = {Structural characterization of proteins and complexes using small-angle X-ray solution scattering},
  year      = {2010},
  pages     = {128–141},
  volume    = {172},
  abstract  = {Small-angle scattering of X-rays (SAXS) is an established method for the low-resolution structural characterization of biological macromolecules in solution. The technique provides three-dimensional low-resolution structures, using ab initio and rigid body modeling, and allow one to assess the oligomeric state of proteins and protein complexes. In addition, SAXS is a powerful tool for structure validation and the quantitative analysis of flexible systems, and is highly complementary to the high resolution methods of X-ray crystallography and NMR. At present, SAXS analysis methods have reached an advanced state, allowing for automated and rapid characterization of protein solutions in terms of low-resolution models, quaternary structure and oligomeric composition. In this communication, main approaches to the characterization of proteins and protein complexes using SAXS are reviewed. The tools for the analysis of proteins in solution are presented, and the impact that these tools have made in modern structural biology is discussed.},
  doi       = {10.1016/j.jsb.2010.06.012},
  file      = {:by-author/M/Mertens/2010_Mertens_128.pdf:PDF},
  keywords  = {EOM; Quality; SAXS},
  owner     = {em},
  timestamp = {2013.06.28},
  creationdate = {2013-06-28T00:00:00},
}

@Manuscript{Meseguer2006,
  author    = {Meseguer, Pedro},
  title     = {Interleaved Depth-First Search},
  year      = {2006},
  keywords  = {Algorithms; Alphametics; Computer Science (CS)},
  abstract  = {In tree search, depth-first search (DFS) often uses ordering successor heuristics. If the heuris- tic makes a mistake ordering a bad successor (without goals in its subtree) before good ones ( w i t h goals in their subtrees), DFS has to unsuc- cessfully traverse the whole bad subtree before finding a goal. To prevent this useless work, we present a new strategy called interleaved depth- first search (IDFS) , which searches depth-first several subtrees —called active— in parallel. IDFS assumes a single processor on which it in- terleaves DFS on active subtrees. When IDFS finds a mistake, it traverses partially the bad subtree. IDFS does not reexpand nodes and uses a memory amount linear in search depth ( with a bounded number of active subtrees). IDFS outperforms DFS if the heuristic improves from the first to the second tree level. Experimental results on hard solvable problems confirm the practical validity of IDFS .},
  file      = {:by-author/M/Meseguer/2006_Meseguer_1382.pdf:PDF},
  owner     = {saulius},
  pages     = {1382},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Mesirov2010,
  author    = {Mesirov, Jill P},
  journal   = {Science (New York, N.Y.)},
  title     = {Computer science. Accessible reproducible research.},
  year      = {2010},
  pages     = {415--416},
  volume    = {327},
  doi       = {10.1126/science.1179653},
  file      = {2010_Mesirov_415.pdf:by-author/M/Mesirov/2010_Mesirov_415.pdf:PDF},
  keywords  = {Data Management; Data Processing},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://science.sciencemag.org/content/327/5964/415},
}

@Presentation{Mete2009,
  author       = {Ersen Mete},
  title        = {DFT in practice : Part I. Plane wave expansion \& the Brillouin zone integration},
  year         = {2009},
  organization = {Balıkesir University, Balıkesir - Turkey},
  school       = {Department of Physics, Balıkesir University, Balıkesir - Turkey},
  file         = {:by-author/M/Mete/2009_Mete.pdf:PDF},
  keywords     = {Density Functional Theory (DFT)},
  owner        = {saulius},
  timestamp = {2014.11.06},
  creationdate = {2014-11-06T00:00:00},
  url          = {http://nanodft09.iyte.edu.tr/pdf/EM-L1.pdf},
}

@Article{Methfessel1989,
  author    = {Methfessel, M. and Paxton, A. T.},
  journal   = {Phys. Rev. B},
  title     = {High-precision sampling for {Brillouin-zone} integration in metals},
  year      = {1989},
  pages     = {3616--3621},
  volume    = {40},
  doi       = {10.1103/PhysRevB.40.3616},
  file      = {:by-author/M/Methfessel/1989_Methfessel_3616.pdf:PDF},
  issue     = {6},
  keywords  = {Density Functional Theory (DFT)},
  owner     = {andrius},
  publisher = {American Physical Society},
  timestamp = {2015.05.07},
  creationdate = {2015-05-07T00:00:00},
  url       = {http://link.aps.org/doi/10.1103/PhysRevB.40.3616},
}

@Article{Metropolis1987,
  author    = {Nicolas Metropolis},
  journal   = {Los Alamos Science},
  title     = {The Beginning of the Monte Carlo Method},
  year      = {1987},
  pages     = {125--130},
  volume    = {15},
  file      = {1987_Metropolis_125.pdf:by-author/M/Metropolis/1987_Metropolis_125.pdf:PDF},
  groups    = {sg/Molecular dynamics},
  keywords  = {Molecular Dynamics (MD); Monte Carlo},
  owner     = {saulius},
  timestamp = {2011.10.21},
  creationdate = {2011-10-21T00:00:00},
}

@Article{Metropolis1953,
  author    = {Nicholas Metropolis and Arianna W. Rosenbluth and Marshall N. Rosenbluth and Augusta H. Teller and and Edward Teller},
  journal   = {Journal of Chemical Physics},
  title     = {Equation of State Calculations by Fast Computing Machines},
  year      = {1953},
  pages     = {1087--1092},
  volume    = {21},
  doi       = {10.1063/1.1699114},
  file      = {1953_Metropolis_1087.pdf:by-author/M/Metropolis/1953_Metropolis_1087.pdf:PDF},
  groups    = {sg/Molecular dynamics},
  keywords  = {Molecular Dynamics (MD); Monte Carlo},
  owner     = {saulius},
  timestamp = {2011.10.21},
  creationdate = {2011-10-21T00:00:00},
  url       = {http://jcp.aip.org/resource/1/jcpsa6/v21/i6/p1087_s1},
}

@Article{Meyer1992,
  author    = {Meyer, Bertrand},
  title     = {Applying “Design by Contract”},
  year      = {1992},
  month     = {October},
  pages     = {40--51},
  file      = {:by-author/M/Meyer/1992_Meyer_40.pdf:PDF},
  keywords  = {Compiler Design; Computer Science (CS); Design by Contract; Eiffel; Programming Languages},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Manuscript{Meyer1993,
  author    = {Holger Meyer},
  title     = {prag - -compile diagrams for pic},
  year      = {1993},
  month     = {August},
  file      = {:by-author/M/Meyer/1993_Meyer.pdf:PDF;:by-author/M/Meyer/1993_Meyer/prag-1.0pl2.shar:Text},
  owner     = {saulius},
  timestamp = {2015.03.10},
  creationdate = {2015-03-10T00:00:00},
}

@Article{Meza2010,
  author    = {Meza, Juan C.},
  journal   = {Wiley Interdisciplinary Reviews: Computational Statistics},
  title     = {Steepest descent},
  year      = {2010},
  issn      = {1939-0068},
  pages     = {719--722},
  volume    = {2},
  abstract  = {The steepest descent method has a rich history and is one of the simplest and best known methods for minimizing a function. While the method is not commonly used in practice due to its slow convergence rate, understanding the convergence properties of this method can lead to a better understanding of many of the more sophisticated optimization methods. Here, we give a short introduction and discuss some of the advantages and disadvantages of this method. Some recent results on modified versions of the steepest descent method are also discussed.},
  doi       = {10.1002/wics.117},
  file      = {:by-author/M/Meza/2010_Meza_719.pdf:PDF},
  owner     = {andrius},
  publisher = {John Wiley \& Sons, Inc.},
  timestamp = {2012.11.29},
  creationdate = {2012-11-29T00:00:00},
  url       = {http://dx.doi.org/10.1002/wics.117},
}

@Manuscript{Mezini2003,
  author    = {Mira Mezini and Jens U. Pipka and Thorsten Dittmar and Wim Boot},
  title     = {Approaching the Fragile Base Class Problem by Binary Analysis},
  year      = {2003},
  keywords  = {Computer Science (CS); Fragile Base Class Problem; Object-oriented Programming},
  month     = {December},
  abstract  = {Adapting and/or extending component functionality to account for application specific needs generally involves both black-box and white-box composition techniques. However, decoupling of component and application specific code via a well defined interface is impossible in the presence of white-box composition, because current technology allows us to describe usage interfaces, but not the self-recursive patterns caused by inheritance. Due to this coupling application code is fragile with respect to changes in the implementation of the component. This is known as the fragile base class problem. In this paper, we present a framework for binary detection of conflicting situations at component (re)integration time. Detecting conflicts at integration time avoids unexpected erro- neous runtime behavior of the integrated components. Furthermore, the results of binary conflict detection can be used by other tools such as, e.g., debuggers or binary component adaptation tools to (automatically) make components and their extensions/adaptations compatible.},
  file      = {:by-author/M/Mezini/2003_Mezini.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@PhdThesis{Miao2010,
  author    = {Haixing Miao},
  school    = {School of Physics, The University of Western Australia},
  title     = {Exploring Macroscopic Quantum Mechanics in Optomechanical Devices},
  year      = {2010},
  abstract  = {Recent significant achievements in fabricating low-loss optical and mechanical elements have aroused intensive interest in optomechanical devices which couple optical fields to mechanical oscillators, e.g., in laser interferometer gravitational- wave (GW) detectors. Not only can such devices be used as sensitive probes for weak forces and tiny displacements, but they also lead to the possibilities of investigating quantum behaviors of macroscopic mechanical oscillators, both of which are the main topics of this thesis. They can shed light on improving the sensitivity of quantum-limited measurement, and on understanding the quantum- to-classical transition. This thesis is a collection of publications that I worked on together with the UWA group and the LIGO Macroscopic Quantum Mechanics (MQM) discussion group. In the first part of this thesis, we will discuss different approaches for surpassing the standard quantum limit for the displacement sensitivity of optomechanical devices, mostly in the context of GW detectors. They include: (i) Modifying the input optics. We consider filtering two frequency-independent squeezed light beams through a tuned resonant cavity to obtain an appropriate frequency depen- dence, which can be used to reduce the measurement noise of the GW detector over the entire detection band; (ii) Modifying the output optics. We study a time-domain variational readout scheme which measures the conserved dynamical quantity of a mechanical oscillator: the mechanical quadrature. This evades the measurement-induced back action and achieves a sensitivity limited only by the shot noise. This scheme is useful for improving the sensitivity of signal-recycled GW detectors, provided the signal-recycling cavity is detuned, and the optical spring effect is strong enough to shift the test-mass pendulum frequency from 1 Hz up to the detection band around 100 Hz; (iii) Modifying the dynamics. We explore frequency dependence in double optical springs in order to cancel the positive inertia of the test mass, which can significantly enhance the mechanical response and allow us to surpass the SQL over a broad frequency band. In the second part of this thesis, two essential procedures for an MQM experiment with optomechanical devices are considered: (i) state preparation, in which we prepare a mechanical oscillator in specific quantum states. We study the preparations of both Gaussian and non-Gaussian quantum states, and also the creation of quantum entanglements between the mechanical oscillator and the optical field. Specifically, for the Gaussian quantum states, e.g., the quantum ground state, we consider the use of passive cooling and optimal feedback control in cavity-assisted schemes. For non-Gaussian quantum states, we introduce the idea of coherently transferring quantum states from the optical field to the mechanical oscillator. For the quantum entanglement, we consider the entanglement between the mechanical oscillator and the finite degrees-of-freedom cavity modes, and also the infinite degrees-of-freedom continuum optical mode. (ii) state verification, in which we probe and verify the prepared quantum states. A similar time-dependent homodyne detection method as discussed in the first part is implemented to evade the back action, which allows us to achieve a verification accuracy that is below the Heisenberg limit. The experimental requirements and feasibilities of these two procedures are considered in both small-scale cavity-assisted optomechanical devices, and in large-scale advanced GW detectors.},
  file      = {2010_Miao_thesis.pdf:by-author/M/Miao/2010_Miao_thesis.pdf:PDF},
  keywords  = {Gravity Wave Detection; Mechanical Quantum Systems; Quantum Mechanics (QM)},
  owner     = {saulius},
  timestamp = {2013.10.22},
  creationdate = {2013-10-22T00:00:00},
  url       = {https://gwic.ligo.org/thesisprize/2010/miao_thesis.pdf},
}

@Misc{Sun1996,
  author    = {Sun Microsystems},
  title     = {A set of classes to parse, represent and display 3D wireframe models represented in Wavefront .obj format},
  year      = {1996},
  comment   = {Newer version can be found in http://www.johnloomis.org/cpe101/demos/WireFrame/ThreeD.java},
  file      = {:by-author/S/Sun/1996_Sun/ThreeD.java:Text},
  keywords  = {3D; Computer Science (CS); File Formats; Java; Programming Languages; Wavefrom File Format},
  owner     = {saulius},
  timestamp = {2015.03.11},
  creationdate = {2015-03-11T00:00:00},
  url       = {http://www.cs.colostate.edu/~anderson/cs510/java/ThreeD.java},
}

@Article{Middelburg1982,
  author     = {Middelburg, C. A.},
  journal    = {SIGPLAN Not.},
  title      = {The Effect of the PDP-11 Architecture on Code Generation for Chill},
  year       = {1982},
  issn       = {0362-1340},
  month      = mar,
  number     = {4},
  pages      = {149--157},
  volume     = {17},
  abstract   = {This paper outlines the implementation of the CCITT*) high level programming language CHILL on PDP-11 computers in the CHILL compiler constructed at the Dr. Neher Laboratories. The characteristics and structure of the compiler are briefly described. The relationship between the PDP-11 architecture and the implementation of CHILL is outlined in more detail.},
  acmid      = {801838},
  address    = {New York, NY, USA},
  doi        = {10.1145/960120.801838},
  file       = {1982_Middelburg_149.pdf:by-author/M/Middelburg/1982_Middelburg_149.pdf:PDF},
  issue_date = {April 1982},
  keywords   = {Code Generation; Compiler Construction; PDP-11},
  numpages   = {9},
  owner      = {saulius},
  publisher  = {ACM},
  timestamp = {2016.10.03},
  creationdate = {2016-10-03T00:00:00},
  url        = {http://doi.acm.org/10.1145/960120.801838},
}

@Article{Mierzejewska2016,
  author       = {Karolina Mierzejewska and Matthias Bochtler and Honorata Czapinska},
  journal      = {Nucleic Acids Res},
  title        = {On the role of steric clashes in methylation control of restriction endonuclease activity.},
  year         = {2016},
  month        = {Jan},
  number       = {1},
  pages        = {485--495},
  volume       = {44},
  abstract     = {Restriction-modification systems digest non-methylated invading DNA, while protecting host DNA against the endonuclease activity by methylation. It is widely believed that the methylated DNA would not 'fit' into the binding site of the endonuclease in the productive orientation, and thus steric clashes should account for most of the protection. We test this concept statistically by grafting methyl groups in silico onto non-methylated DNA in co-crystal structures with restriction endonucleases. Clash scores are significantly higher for protective than non-protective methylation (P < 0.05\% according to the Wilcoxon rank sum test). Structural data alone are sufficient to distinguish between protective and non-protective DNA methylation with 90\% confidence and decision thresholds of 1.1 Å and 48 Å(3) for the most severe distance-based and cumulative volume-based clash with the protein, respectively (0.1 Å was deducted from each interatomic distance to allow for coordinate errors). The most severe clashes are more pronounced for protective methyl groups attached to the nitrogen atoms (N6-methyladenines and N4-methylcytosines) than for C5-methyl groups on cytosines. Cumulative clashes are comparable for all three types of protective methylation.},
  creationdate = {2016-06-16T00:00:00},
  doi          = {10.1093/nar/gkv1341},
  file         = {:by-author/M/Mierzejewska/2016_Mierzejewska_485.pdf:PDF},
  institution  = {International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warsaw, Poland honorata@iimcb.gov.pl.},
  keywords     = {Chemistry/metabolism; DNA; DNA Methylation; DNA Restriction Enzymes; Datasets as Topic; Enzyme Activation; Molecular Conformation; Substrate Specificity},
  language     = {eng},
  medline-pst  = {ppublish},
  owner        = {em},
  pii          = {gkv1341},
  pmid         = {26635397},
  timestamp    = {2016.06.16},
  url          = {http://dx.doi.org/10.1093/nar/gkv1341},
}

@Article{Mierzejewska2014,
  author       = {Karolina Mierzejewska and Wojciech Siwek and Honorata Czapinska and Magdalena Kaus-Drobek and Monika Radlinska and Krzysztof Skowronek and Janusz M Bujnicki and Michal Dadlez and Matthias Bochtler},
  journal      = {Nucleic Acids Res},
  title        = {Structural basis of the methylation specificity of R.DpnI.},
  year         = {2014},
  month        = {Jul},
  number       = {13},
  pages        = {8745--8754},
  volume       = {42},
  abstract     = {R.DpnI consists of N-terminal catalytic and C-terminal winged helix domains that are separately specific for the Gm6ATC sequences in Dam-methylated DNA. Here we present a crystal structure of R.DpnI with oligoduplexes bound to the catalytic and winged helix domains and identify the catalytic domain residues that are involved in interactions with the substrate methyl groups. We show that these methyl groups in the Gm6ATC target sequence are positioned very close to each other. We further show that the presence of the two methyl groups requires a deviation from B-DNA conformation to avoid steric conflict. The methylation compatible DNA conformation is complementary with binding sites of both R.DpnI domains. This indirect readout of methylation adds to the specificity mediated by direct favorable interactions with the methyl groups and solvation/desolvation effects. We also present hydrogen/deuterium exchange data that support 'crosstalk' between the two domains in the identification of methylated DNA, which should further enhance R.DpnI methylation specificity.},
  creationdate = {2016-06-16T00:00:00},
  doi          = {10.1093/nar/gku546},
  file         = {:by-author/M/Mierzejewska/2014_Mierzejewska_8745.pdf:PDF},
  institution  = {International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warsaw, Poland mbochtler@iimcb.gov.pl.},
  keywords     = {Adenine; Analogs /&/ Derivatives/chemistry; Base Pairing; Catalytic Domain; Chemistry/metabolism; DNA; DNA Methylation; Deoxyribonucleases; Methyl-directed; Models; Molecular; Mutagenesis; Protein Structure; Restriction Endonuclease (RE); Site-Directed; Tertiary; Type II Site-Specific},
  language     = {eng},
  medline-pst  = {ppublish},
  owner        = {em},
  pii          = {gku546},
  pmid         = {24966351},
  timestamp    = {2016.06.16},
  url          = {http://dx.doi.org/10.1093/nar/gku546},
}

@Article{Mighell2001,
  author    = {Mighell},
  title     = {Determination of Reduced Cells in Crystallography},
  year      = {2001},
  pages     = {188},
  file      = {:by-author/M/Mighell/2001_Mighell_188.pdf:PDF},
  keywords  = {Crystal Cell; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Mighell2003,
  author    = {Alan D. Mighell},
  journal   = {Journal of Research of the National Institute of Standards and Technology},
  title     = {The Normalized Reduced Form and Cell Mathematical Tools for Lattice Analysis --- Symmetry and Similarity},
  year      = {2003},
  pages     = {447--452},
  volume    = {108},
  file      = {2003_Mighell_447.pdf:by-author/M/Mighell/2003_Mighell_447.pdf:PDF},
  keywords  = {Algorithms; Crystallographic Databases; Reduced Cell; Unit Cell; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2015.06.15},
  creationdate = {2015-06-15T00:00:00},
  url       = {http://nvlpubs.nist.gov/nistpubs/jres/108/6/j86mig.pdf},
}

@Article{Mighell1976,
  author    = {Mighell, A. D.},
  journal   = {Journal of Applied Crystallography},
  title     = {The reduced cell: its use in the identification of crystalline materials},
  year      = {1976},
  pages     = {491--498},
  volume    = {9},
  doi       = {10.1107/S0021889876011989},
  file      = {:by-author/M/Mighell/1976_Mighell_491.pdf:PDF},
  keywords  = {Algorithms; Niggli Cell; Reduced Cell; Unit Cell; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2014.11.06},
  creationdate = {2014-11-06T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0021889876011989},
}

@Article{Mighell1986,
  author    = {Mighell, A. D. and Himes, V. L.},
  journal   = {Acta Crystallographica Section A},
  title     = {Compound identification and characterization using lattice-formula matching techniques},
  year      = {1986},
  pages     = {101--105},
  volume    = {42},
  abstract  = {A lattice-formula matching technique has been developed to be used in conjunction with the NBS Crystal Data File [(1982), National Bureau of Standards, Gaithersburg, MD] for the identification and characterization of crystalline materials. This technique is reliable, efficient and highly selective. In the first step of the identification/characterization procedure, a unit cell defining the lattice is determined. The cell is reduced and derivative supercells and subcells are calculated. These cells are then checked against the NBS Crystal Data File in which all lattices have been represented by standard reduced cells. By routinely calculating derivative supercells and subcells and matching against the file of known compounds, it is possible to find related materials and/or to make an identification in spite of certain types of errors made by the experimentalists (e.g. missing rows of spots on diffraction photographs or the diffractometer etc.). Finally, the identification obtained by lattice matching is verified using known chemical data. Practical experience and an analysis of the data in the NBS Crystal Data File have proved that the lattice-formula combination is highly characteristic of a crystalline material. Since the method is subject to precise mathematical techniques, the entire procedure can be highly automated. Both the unit-cell determination and the identification/characterization procedure can be carried out in the same instrument. A Fortran program and the NBS Crystal Data File are available.},
  doi       = {10.1107/S0108767386099804},
  file      = {1986_Mighell_101.pdf:by-author/M/Mighell/1986_Mighell_101.pdf:PDF},
  keywords  = {Algorithms; Databases; Reduced Cell},
  owner     = {saulius},
  timestamp = {2014.11.10},
  creationdate = {2014-11-10T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0108767386099804},
}

@Article{Mighel1977,
  author    = {Alan D. Mighell and Helen M. Ondik and Bettijoyce Breen Molino},
  journal   = {J. Phys. Chem. Ref. Data},
  title     = {Crystal Data Space-Group Tables},
  year      = {1977},
  pages     = {675},
  volume    = {6},
  file      = {:by-author/M/Mighell/1977_Mighel_675.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.09.18},
  creationdate = {2012-09-18T00:00:00},
}

@Article{Mighell1980,
  author    = {Mighell, A. D. and Rodgers, J. R.},
  journal   = {Acta Crystallographica Section A},
  title     = {Lattice symmetry determination},
  year      = {1980},
  pages     = {321--326},
  volume    = {36},
  abstract  = {Transformation matrices required to obtain a conventional cell (Crystal Data cell) from the reduced cell have been applied to 47 000 crystalline compounds in the Crystal Data file. For 97% of the compounds, the calculations from the reduced cells yield conventional cells (lattice parameters, lattice type, and crystal system) that are entirely consistent with those reported in the original literature. In a few instances in which the reduced-cell matrix indicated a higher symmetry, the author has often noted that the crystal was unusual in some way or there was an error in the reported symmetry. Some implications of the results of this survey are: (1) metric symmetry as determined from the reduced cell is usually identical to the crystal-lattice symmetry; (2) determination of precise cell parameters defining any primitive cell of the lattice is valuable because from them one can conveniently determine the crystal system with a high degree of confidence (the results, however, should still be verified by checking equivalent intensities and systematic extinctions); (3) if the metric symmetry obtained from the reduced cell and the symmetry determined by other techniques do not agree, the reason should be sought as there are often important structural implications; (4) the sequence of steps in an automatic procedure for the determination of space groups could be: primitive cell, reduced cell, lattice metric symmetry, crystal-lattice symmetry, extinction conditions.},
  doi       = {10.1107/S0567739480000617},
  file      = {1980_Mighell_321.pdf:by-author/M/Mighell/1980_Mighell_321.pdf:PDF},
  keywords  = {Lattice Determination; Reduced Lattice},
  owner     = {saulius},
  timestamp = {2014.11.10},
  creationdate = {2014-11-10T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0567739480000617},
}

@Manuscript{Mikhajlov1998,
  author    = {Mikhajlov, Leonid and Emil Sekerinski},
  title     = {A Study of The Fragile Base Class Problem},
  year      = {1998},
  keywords  = {Computer Science (CS); Fragile Base Class Problem; Object-oriented Programming},
  abstract  = {In this paper we study the fragile base class problem. This problem occurs in open object-oriented systems employing code inher- itance as an implementation reuse mechanism. System developers un- aware of extensions to the system developed by its users may produce a seemingly acceptable revision of a base class which may damage its exten- sions. The fragile base class problem becomes apparent during mainte- nance of open object-oriented systems, but requires consideration during design. We express the fragile base class problem in terms of a exibility property. By means of ve orthogonal examples, violating the exibility property, we demonstrate di erent aspects of the problem. We formulate requirements for disciplining inheritance, and extend the re nement cal- culus to accommodate for classes, objects, class-based inheritance, and class re nement. We formulate and formally prove a exibility theorem demonstrating that the restrictions we impose on inheritance are suf- cient to permit safe substitution of a base class with its revision in presence of extension classes.},
  file      = {:by-author/M/Mikhajlov/1998_Mikhajlov.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@TechReport{Mikhajlov1997,
  author      = {Mikhajlov, Leonid and Emil Sekerinski},
  institution = {Turku Center for Computer Science},
  title       = {The Fragile Base Class Problem and Its Solution},
  year        = {1997},
  month       = {June},
  file        = {:by-author/M/Mikhajlov/1997_Mikhajlov.pdf:PDF},
  keywords    = {Computer Science (CS); Fragile Base Class Problem; Object-oriented Programming},
  owner       = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Mikheev2002,
  author    = {Mikheev, Andrei},
  journal   = {Computational Linguistics},
  title     = {Periods, Capitalized Words, etc.},
  year      = {2002},
  issn      = {0891-2017},
  pages     = {289--318},
  volume    = {28},
  abstract  = {In this article we present an approach for tackling three important aspects of text normalization: sentence boundary disambiguation, disambiguation of capitalized words in positions where capitalization is expected, and identification of abbreviations. As opposed to the two dominant techniques of computing statistics or writing specialized grammars, our document-centered approach works by considering suggestive local contexts and repetitions of individual words within a document. This approach proved to be robust to domain shifts and new lexica and produced performance on the level with the highest reported results. When incorporated into a part-of-speech tagger, it helped reduce the error rate significantly on capitalized words and sentence boundaries. We also investigated the portability to other languages and obtained encouraging results.},
  booktitle = {Computational Linguistics},
  doi       = {10.1162/089120102760275992},
  file      = {:by-author/M/Mikheev/2002_Mikheev_289.pdf:PDF},
  owner     = {saulius},
  publisher = {MIT Press},
  timestamp = {2011.12.13},
  creationdate = {2011-12-13T00:00:00},
  url       = {http://dx.doi.org/10.1162/089120102760275992},
}

@Article{Mikheev1994,
  author    = {Andrei Mikheev},
  journal   = {Computational Linguistics},
  title     = {Periods, Capitalized Words, etc.},
  year      = {1994},
  number    = {1},
  volume    = {16},
  file      = {:by-author/M/Mikheev/1994_Mikheev.pdf:PDF},
  owner     = {saulius},
  timestamp = {2011.12.13},
  creationdate = {2011-12-13T00:00:00},
}

@Article{Milburn1990,
  author     = {Milburn, M. V. and Tong, L. and deVos, A. M. and Brunger, A. and Yamaizumi, Z. and Nishimura, S. and Kim, S. H.},
  journal    = {Science},
  title      = {Molecular switch for signal transduction: structural differences between active and inactive forms of protooncogenic ras proteins},
  year       = {1990},
  issn       = {0036-8075, 1095-9203},
  pages      = {939--945},
  volume     = {247},
  abstract   = {Ras proteins participate as a molecular switch in the early steps of the signal transduction pathway that is associated with cell growth and differentiation. When the protein is in its GTP complexed form it is active in signal transduction, whereas it is inactive in its GDP complexed form. A comparison of eight three-dimensional structures of ras proteins in four different crystal lattices, five with a nonhydrolyzable GTP analog and three with GDP, reveals that the "on" and "off" states of the switch are distinguished by conformational differences that span a length of more than 40 A, and are induced by the gamma-phosphate. The most significant differences are localized in two regions: residues 30 to 38 (the switch I region) in the second loop and residues 60 to 76 (the switch II region) consisting of the fourth loop and the short alpha-helix that follows the loop. Both regions are highly exposed and form a continuous strip on the molecular surface most likely to be the recognition sites for the effector and receptor molecule(or molecules). The conformational differences also provide a structural basis for understanding the biological and biochemical changes of the proteins due to oncogenic mutations, autophosphorylation, and GTP hydrolysis, and for understanding the interactions with other proteins.},
  doi        = {10.1126/science.2406906},
  file       = {Full Text PDF:by-author/M/Milburn/1990_Milburn_939.pdf:application/pdf;Snapshot:by-author/M/Milburn/1990_Milburn_939.html:text/html},
  groups     = {sg/biomolecular},
  language   = {en},
  owner      = {saulius},
  pmid       = {2406906},
  shorttitle = {Molecular switch for signal transduction},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url        = {http://www.sciencemag.org/content/247/4945/939},
  urldate    = {2015-08-05},
}

@Article{Milichko2017,
  author    = {Valentin A. Milichko and Sergey V. Makarov and Alexey V. Yulin and Alexandr V. Vinogradov and Andrei A. Krasilin and Elena Ushakova and Vladimir P. Dzyuba and Evamarie Hey-Hawkins and Evgeny A. Pidko and Pavel A. Belov},
  journal   = {Advanced Materials},
  title     = {van der Waals Metal-Organic Framework as an Excitonic Material for Advanced Photonics},
  year      = {2017},
  month     = {jan},
  pages     = {1606034},
  doi       = {10.1002/adma.201606034},
  file      = {:by-author/M/Milichko/2017_Milichko_1606034.pdf:PDF},
  groups    = {sg/MOF, sg/MOFs, am/MOFs},
  owner     = {saulius},
  publisher = {Wiley-Blackwell},
  timestamp = {2017.01.31},
  creationdate = {2017-01-31T00:00:00},
  url       = {https://doi.org/10.1002%2Fadma.201606034},
}

@Article{Miller2003,
  author    = {Miller, Eric S. and Kutter, Elizabeth and Mosig, Gisela and Arisaka, Fumio and Kunisawa, Takashi and Rüger, Wolfgang},
  journal   = {Microbiology and molecular biology reviews : MMBR},
  title     = {Bacteriophage T4 genome.},
  year      = {2003},
  pages     = {86-156, table of contents},
  volume    = {67},
  abstract  = {Phage T4 has provided countless contributions to the paradigms of genetics and biochemistry. Its complete genome sequence of 168,903 bp encodes about 300 gene products. T4 biology and its genomic sequence provide the best-understood model for modern functional genomics and proteomics. Variations on gene expression, including overlapping genes, internal translation initiation, spliced genes, translational bypassing, and RNA processing, alert us to the caveats of purely computational methods. The T4 transcriptional pattern reflects its dependence on the host RNA polymerase and the use of phage-encoded proteins that sequentially modify RNA polymerase; transcriptional activator proteins, a phage sigma factor, anti-sigma, and sigma decoy proteins also act to specify early, middle, and late promoter recognition. Posttranscriptional controls by T4 provide excellent systems for the study of RNA-dependent processes, particularly at the structural level. The redundancy of DNA replication and recombination systems of T4 reveals how phage and other genomes are stably replicated and repaired in different environments, providing insight into genome evolution and adaptations to new hosts and growth environments. Moreover, genomic sequence analysis has provided new insights into tail fiber variation, lysis, gene duplications, and membrane localization of proteins, while high-resolution structural determination of the "cell-puncturing device," combined with the three-dimensional image reconstruction of the baseplate, has revealed the mechanism of penetration during infection. Despite these advances, nearly 130 potential T4 genes remain uncharacterized. Current phage-sequencing initiatives are now revealing the similarities and differences among members of the T4 family, including those that infect bacteria other than Escherichia coli. T4 functional genomics will aid in the interpretation of these newly sequenced T4-related genomes and in broadening our understanding of the complex evolution and ecology of phages-the most abundant and among the most ancient biological entities on Earth.},
  file      = {:by-author/M/Miller/2003_Miller_86.pdf:PDF},
  keywords  = {{gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@InBook{Miller1998a,
  author    = {Miller, Michael D.},
  chapter   = {Molecular Superposition},
  title     = {CMA29M},
  year      = {1998},
  file      = {:by-author/M/Miller/1998_Miller.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.05.16},
  creationdate = {2012-05-16T00:00:00},
}

@Article{Miller2005a,
  author    = {Miller, Mark D. and Hart, Jennifer A.},
  journal   = {Instructional course lectures},
  title     = {All-inside meniscal repair.},
  year      = {2005},
  pages     = {337--40},
  volume    = {54},
  abstract  = {All-inside meniscal repair has become a popular technique. The number of meniscal repairs done in the United States has increased dramatically since the introduction of the Meniscal Arrow (Linvatec Corp, Largo, FL). Although these devices are easy to use, there have been several compliations reported with their use. Newer devices (Mitek RapidLoc and Smith and Nephew Fas-T-Fix) allow tensioning of the construct after insertion. There are also problems and pitfalls with their use, but improvements continue to be made in all-inside meniscal repair devices.},
  file      = {:by-author/M/Miller/2005_Miller_337.pdf:PDF},
  keywords  = {TypeI},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@InBook{Miller2005,
  author    = {Mark S. Miller and Bill Tulloh and Jonathan S. Shapiro},
  editor    = {P. Van Roy},
  pages     = {2--20},
  publisher = {Springer-Verlag, Berlin, Heidelberg},
  title     = {The Structure of Authority: Why Security Is not a Separable Concern},
  year      = {2005},
  abstract  = {Common programming practice grants excess authority for the sake of functionality; programming principles require least authority for the sake of security. If we practice our principles, we could have both security and functionality. Treating security as a separate concern has not succeeded in bridging the gap between principle and practice, because it operates without knowledge of what constitutes least authority. Only when requests are made – whether by humans acting through a user interface, or by one object invoking another – can we determine how much authority is adequate. Without this knowledge, we must provide programs with enough authority to do anything they might be requested to do. We examine the practice of least authority at four major layers of abstraction – from humans in an organization down to individual objects within a programming language. We explain the special role of object- capability languages – such as E or the proposed Oz-E – in supporting practical least authority.},
  file      = {:by-author/M/Miller/2005_Miller_2.pdf:PDF},
  keywords  = {Computer Science (CS); Security; Unix},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
  url       = {http://www.erights.org/talks/no-sep/secnotsep.pdf},
}

@Article{Miller1998,
  author    = {Peter Miller},
  journal   = {AUUGN Journal of AUUG Inc.,},
  title     = {Recursive Make Considered Harmful},
  year      = {1998},
  pages     = {14--25},
  file      = {:by-author/M/Miller/1998_Miller_14.pdf:PDF},
  keywords  = {Computer Languages; Computer Science (CS); Make},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
  url       = {http://aegis.sourceforge.net/auug97.pdf},
}

@Presentation{Miller2009,
  author    = {Scott Miller},
  title     = {A New Bioinformatics-Inspired and Binary Analysis: Coding Style/Motif Identification},
  year      = {2009},
  file      = {:by-author/M/Miller/2009_Miller_slides.pdf:PDF},
  keywords  = {Presentations},
  owner     = {saulius},
  pages     = {slides},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Min1998,
  author    = {Jinrong Min and Jordi Benet-Buchholz and Roland Boese},
  journal   = {Chemical Communications},
  title     = {Ab initio structure determination of norbornene from powder diffraction data using molecular packing analysis method},
  year      = {1998},
  number    = {24},
  pages     = {2751--2752},
  abstract  = {The previously unknown crystal structre of the low temperature ordered phase of norbornene was solved from a set of powder diffraction data with severe preferred orientation collected on a laboratory X-ray diffractometer by first predicting the starting model by means of molecular packing analysis method{,} which was then refined against the experimental data by means of Rietveld method.},
  doi       = {10.1039/A807829G},
  file      = {1998_Min_2751.pdf:by-author/M/Min/1998_Min_2751.pdf:PDF},
  keywords  = {Powder Diffraction},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@InProceedings{Minamide1998,
  author    = {Minamide, Yasuhiko},
  booktitle = {POPL98},
  title     = {A functional representation of data structures with a hole},
  year      = {1998},
  pages     = {75--84},
  abstract  = {Data structures with a hole, in other words data structures with an uninitialized field, are useful to write efficient programs: they en- able us to construct functional data structures flexibly and write functions such as append and map as tail recursive functions. In this paper we present an approach to introducing data structures with a hole into call-by-value functional programming languages like ML. Data structures with a hole are formalized as a new form of X-abstraction called hole abstraction. The novel features of hole abstraction are that expressions inside hole abstraction are evalu- ated and application is implemented by destructive update of a hole. We present a simply typed call-by-value X-calculus extended with hole abstractions. Then we show a compilation method of hole ab- straction and prove correctness of the compilation.},
  file      = {:by-author/M/Minamide/1998_Minamide_POPL98.pdf:PDF},
  keywords  = {Computer Science (CS); Type Systems},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Mincione2005,
  author    = {Mincione, Francesco and Starnotti, Michele and Masini, Emanuela and Bacciottini, Lucia and Scrivanti, Chiara and Casini, Angela and Vullo, Daniela and Scozzafava, Andrea and Supuran, Claudiu T},
  journal   = {Bioorganic \&amp; medicinal chemistry letters},
  title     = {Carbonic anhydrase inhibitors: design of thioureido sulfonamides with potent isozyme II and XII inhibitory properties and intraocular pressure lowering activity in a rabbit model of glaucoma.},
  year      = {2005},
  pages     = {3821--7},
  volume    = {15},
  file      = {2005_Mincione_3821.pdf:by-author/M/Mincione/2005_Mincione_3821.pdf:PDF},
  groups    = {sg/inhibitors, sg/hCA2, sg/hCA12},
  keywords  = {Carbonic Anhydrases},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Minh2005,
  author    = {Minh, David D. L. and Bui, Jennifer M. and Chang, Chia-En and Jain, Tushar and Swanson, Jessica M. J. and McCammon, J. Andrew},
  journal   = {Biophysical journal},
  title     = {The entropic cost of protein-protein association: a case study on acetylcholinesterase binding to fasciculin-2.},
  year      = {2005},
  pages     = {L25-7},
  volume    = {89},
  file      = {:by-author/M/Minh/2005_Minh_L25.pdf:PDF},
  keywords  = {Poisson-Boltzmann eq; Protein Physics; Solvatation},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@Article{Minichino2003,
  author    = {Minichino, A. and Habash, J. and Raftery, J. and Helliwell, J. R.},
  journal   = {Acta Crystallographica Section D},
  title     = {The properties of (2{\it F${\sb o}$} {$-$} {\it F${\sb c}$}) and ({\it F${\sb o}$} {$-$}~{\it F${\sb c}$}) electron-density maps at medium-to-high resolutions},
  year      = {2003},
  pages     = {843--849},
  volume    = {59},
  doi       = {10.1107/S0907444903004219},
  file      = {en0077.pdf:by-author/M/Minichino/2003_Minichino_843.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444903004219},
}

@Article{Minjauw,
  author     = {Minjauw, Matthias},
  title      = {Atomaire laag depositie van ruthenium met de {ToRuS}-precursor: procesontwikkeling en in situ stress-metingen},
  file       = {[PDF] from ugent.be:by-author/M/Minjauw/XXXX_Minjauw.pdf:application/pdf},
  groups     = {sg/JAC2009},
  owner      = {saulius},
  shorttitle = {Atomaire laag depositie van ruthenium met de {ToRuS}-precursor},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url        = {http://lib.ugent.be/fulltxt/RUG01/002/061/250/RUG01-002061250_2013_0001_AC.pdf},
  urldate    = {2015-08-31},
}

@Article{Mirams2013,
  author     = {Mirams, Gary R. and Arthurs, Christopher J. and Bernabeu, Miguel O. and Bordas, Rafel and Cooper, Jonathan and Corrias, Alberto and Davit, Yohan and Dunn, Sara-Jane and Fletcher, Alexander G. and Harvey, Daniel G. and Marsh, Megan E. and Osborne, James M. and Pathmanathan, Pras and Pitt-Francis, Joe and Southern, James and Zemzemi, Nejib and Gavaghan, David J.},
  journal    = {PLoS Computational Biology},
  title      = {Chaste: {An} open source {C}++ library for computational physiology and biology},
  year       = {2013},
  issn       = {1553-734X},
  number     = {3},
  volume     = {9},
  abstract   = {Chaste — Cancer, Heart And Soft Tissue Environment — is an open source C++ library for the computational simulation of mathematical models developed for physiology and biology. Code development has been driven by two initial applications: cardiac electrophysiology and cancer development. A large number of cardiac electrophysiology studies have been enabled and performed, including high-performance computational investigations of defibrillation on realistic human cardiac geometries. New models for the initiation and growth of tumours have been developed. In particular, cell-based simulations have provided novel insight into the role of stem cells in the colorectal crypt. Chaste is constantly evolving and is now being applied to a far wider range of problems. The code provides modules for handling common scientific computing components, such as meshes and solvers for ordinary and partial differential equations (ODEs/PDEs). Re-use of these components avoids the need for researchers to ‘re-invent the wheel’ with each new project, accelerating the rate of progress in new applications. Chaste is developed using industrially-derived techniques, in particular test-driven development, to ensure code quality, re-use and reliability. In this article we provide examples that illustrate the types of problems Chaste can be used to solve, which can be run on a desktop computer. We highlight some scientific studies that have used or are using Chaste, and the insights they have provided. The source code, both for specific releases and the development version, is available to download under an open source Berkeley Software Distribution (BSD) licence at http://www.cs.ox.ac.uk/chaste, together with details of a mailing list and links to documentation and tutorials.},
  doi        = {10.1371/journal.pcbi.1002970},
  file       = {Mirams et al. - 2013 - Chaste An Open Source C++ Library for Computation.pdf:by-author/M/Mirams/2013_Mirams.pdf:application/pdf},
  owner      = {saulius},
  pmcid      = {PMC3597547},
  pmid       = {23516352},
  shorttitle = chaste,
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url        = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3597547/},
  urldate    = {2015-06-06},
}

@Manuscript{Miranda1991,
  author    = {Eliot Miranda},
  title     = {Portable Fast Direct Threaded Code},
  year      = {1991},
  keywords  = {Computer Science (CS); Threaded Code},
  file      = {:by-author/M/Miranda/1991_Miranda.html:},
  groups    = {sg/Threaded code},
  owner     = {saulius},
  timestamp = {2015.03.03},
  creationdate = {2015-03-03T00:00:00},
}

@Manuscript{Miranda1991a,
  author    = {Eliot Miranda},
  title     = {Threaded Code},
  year      = {1991},
  keywords  = {Computer Science (CS)},
  file      = {:by-author/M/Miranda/1991_Miranda_a.html:},
  groups    = {sg/Threaded code},
  owner     = {saulius},
  timestamp = {2015.03.03},
  creationdate = {2015-03-03T00:00:00},
}

@Article{Mirkin2003,
  author    = {Mirkin, N. and Frontana-Uribe, B. A. and Rodr{\'\i}guez-Romero, A. and Hern{\'{a}}ndez-Santoyo, A. and Moreno, A.},
  journal   = {Acta Crystallographica Section D},
  title     = {The influence of an internal electric field upon protein crystallization using the gel-acupuncture method},
  year      = {2003},
  pages     = {1533--1538},
  volume    = {59},
  doi       = {10.1107/S0907444903013027},
  file      = {gr2317.pdf:by-author/M/Mirkin/2003_Mirkin_1533.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444903013027},
}

@Article{Mirsky1936a,
  author    = {Mirsky, A. E.},
  journal   = {Proceedings of the National Academy of Sciences of the United States of America},
  title     = {The Visual Cycle and Protein Denaturation.},
  year      = {1936},
  pages     = {147--9},
  volume    = {22},
  file      = {:by-author/M/Mirsky/1936_Mirsky_147.pdf:PDF},
  keywords  = {Protein Denaturation},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Mirsky1936b,
  author    = {Mirsky, A. E. and Anson, M. L.},
  journal   = {The Journal of general physiology},
  title     = {Sulfhydryl and Disulfide Groups of Proteins: II. The Relation Between Number of SH and S-S Groups and Quantity of Insoluble Protein in Denaturation and in Reversal of Denaturation},
  year      = {1936},
  pages     = {427--38},
  volume    = {19},
  abstract  = {1. In native egg albumin no SH groups are detectable, whereas in completely coagulated albumin as many groups are detectable as are found in the hydrolyzed protein. In egg albumin partially coagulated by heat the soluble fraction contains no detectable groups, and the insoluble fraction contains the number found after hydrolysis. 2. In the reversal of denaturation of serum albumin, when insoluble protein regains its solubility, S-S groups which have been detectable in the denatured protein, disappear. 3. When egg albumin coagulates at an air-water interface, all the SH groups in the molecule become detectable. 4. In egg albumin coagulated by irradiation with ultraviolet light, the same number of SH groups are detectable as in albumin coagulated by a typical denaturing agent. 5. When serum albumin is denatured by urea, there is no evidence that S-S groups appear before the protein loses its solubility. 6. Protein denaturation is a definite chemical reaction: different quantitative methods agree in estimates of the extent of denaturation, and the same changes are observed in the protein when it is denatured by different agents. A protein molecule is either native or denatured. The denaturation of some proteins can be reversed.},
  file      = {:by-author/M/Mirsky/1936_Mirsky_427.pdf:PDF},
  keywords  = {Protein Denaturation},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Mirsky1936d,
  author    = {A. E. Mirsky and M. L. Anson},
  journal   = {The Journal of General Physiology},
  title     = {Sulfhydryl and disulfide groups of proteins: III. Sulfhydryl groups of native proteins -- hemoglobin and the proteins of the crystalline lens},
  year      = {1936},
  pages     = {439--450},
  volume    = {19},
  abstract  = {Hemoglobin and the proteins of the crystalline lens contain active SH groups while in the native state, the number of active groups increasing as the pH rises. All the SH groups of denatured globin and of the denatured lens proteins are active at a pH so low that practically none of the SH groups of native hemoglobin and of native lens protein are active. The effect of denaturation on the SH groups of a protein is to extend towards the acid side the pH range of their activity. It is possible to oxidize the iron-porphyrin and the SH groups of hemoglobin independently of each other.},
  file      = {:by-author/M/Mirsky/1936_Mirsky_439.pdf:PDF},
  keywords  = {Protein Denaturation},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
  url       = {http://www.jgp.org/cgi/content/abstract/19/3/439},
}

@Article{Mirsky1935,
  author    = {Mirsky, A. E. and Anson, M. L.},
  journal   = {The Journal of general physiology},
  title     = {Sulfhydryl and Disulfide Groups of Proteins: I. Methods of Estimation},
  year      = {1935},
  pages     = {307--23},
  volume    = {18},
  abstract  = {1. Methods have been described for reducing protein S-S groups, for oxidizing protein SH groups, and for estimating protein S-S and SH groups. 2. It has been found necessary in estimating the cystine content of proteins by the Folin-Marenzi method to take into account any cysteine that may be present. 3. A method for estimating the cysteine content of proteins has been described. 4. With these methods, estimations have been made of the S-S and SH groups and of the cystine and cysteine contents of a number of proteins. 5. In a denatured, but unhydrolyzed protein, the number of S-S and SH groups is equivalent to the quantity of cystine and cysteine found in the protein after hydrolysis.},
  file      = {:by-author/M/Mirsky/1935_Mirsky_307.pdf:PDF},
  keywords  = {Protein Denaturation},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Mirsky1935a,
  author    = {A. E. Mirsky and M. L. Anson},
  journal   = {The Journal of General Physiology},
  title     = {The Reducing Groups of Proteins},
  year      = {1935},
  pages     = {451--459},
  volume    = {19},
  abstract  = {1. Intact, unhydrolyzed proteins possess in addition to SH groups other reducing groups which can be oxidized by ferricyanide. 2. The activity of these reducing groups, like that of SH groups, is enhanced by denaturation of the protein and by increase of pH and temperature. 3. These groups differ from SH groups in the manner in which their activity is dependent on concentration of ferricyanide and time of contact with ferricyanide. 4. The activity of these groups is increased if protein SH groups are present. 5. The number and activity of these groups varies from protein to protein. 6. These groups are probably contained in the tyrosine and tryptophane components of proteins. 7. The significance of these reducing groups for an understanding of protein denaturation and the reducing properties of tissues is indicated.},
  file      = {:by-author/M/Mirsky/1935_Mirsky_451.pdf:PDF},
  keywords  = {Protein Denaturation},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Mirsky1930,
  author    = {A. E. Mirsky and M. L. Anson},
  journal   = {The Journal of General Physiology},
  title     = {Protein Coagulation and Its Reversal: Improved Methods for the Reversal Coagulation of Hemoglobin},
  year      = {1930},
  pages     = {477--481},
  volume    = {13},
  abstract  = {The coagulation of hemoglobin is probably reversible. Several methods are described for preparing soluble crystalline hemoglobin from hemoglobin denaturated by HC1 or trichloracetic acid. The yield is about 75 per cent.},
  file      = {:by-author/M/Mirsky/1930_Mirsky_477.pdf:PDF},
  keywords  = {Protein Denaturation},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Mirsky1936,
  author    = {A. E. Mirsky and Linus Pauling},
  journal   = {PNAS},
  title     = {On the structure of native, denatured, and coagulated proteins},
  year      = {1936},
  pages     = {439--447},
  volume    = {22},
  abstract  = {In this paper a structural theory of protein denaturation and coagulation is presented. Since denaturation is a fundamental property of a large group of proteins, a theory of denaturation is essentially a general theory of the structure of native and denatured proteins. In its present form our theory is definite and detailed in some respects and vague in others; refinement in regard to the latter could be achieved on the basis of the results of experi- ments which the theory suggests. The theory (some features of which have been proposed by other investigators) provides a simple structural interpretation not only of the phenomena connected with denaturation and coagulation which are usually discussed (specificity, solubility, etc.) but also of others, such as the availability of groups, the entropy of denatura- tion, the effect of ultra-violet light, the heat of activation and its depen- dence on pH, coagulation through dehydration, etc.},
  file      = {:by-author/M/Mirsky/1936_Mirsky_439PNAS.pdf:PDF},
  keywords  = {Protein Denaturation},
  owner     = {saulius},
  timestamp = {2013.03.22},
  creationdate = {2013-03-22T00:00:00},
}

@Article{Mirsky1936c,
  author    = {A. E. Mirsky and Linus Pauling},
  journal   = {Proceedings of the National Academy of Sciences},
  title     = {On the Structure of Native, Denatured, and Coagulated Proteins},
  year      = {1936},
  pages     = {439--447},
  volume    = {22},
  file      = {:by-author/M/Mirsky/1936_Mirsky_439.pdf:PDF},
  keywords  = {Protein Denaturation},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
  url       = {http://www.pnas.org/content/22/7/439.short},
}

@Book{Mitasiunas2003,
  author    = {Antanas Mitašiūnas},
  publisher = {Vilniaus universitetas, Matematikos ir informatikos fakultetas, Informatikos katedra},
  title     = {Kompiuterių architektūra},
  year      = {2003},
  file      = {:by-author/M/Mitašiūnas/2003_Mitašiūnas.pdf:PDF},
  keywords  = {Computer Science (CS)},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Presentation{Mitchell2006,
  author    = {John Mitchell},
  title     = {The Algol Family and ML},
  year      = {2006},
  file      = {2006_Mitchell.pdf:by-author/M/Mitchell/2006_Mitchell.pdf:PDF},
  keywords  = {Algol; Algol 60; Computer Languages; Computer Science (CS); Machine Learning (ML); Memory Management},
  owner     = {saulius},
  timestamp = {2015.04.09},
  creationdate = {2015-04-09T00:00:00},
  url       = {http://web.stanford.edu/class/cs242/slides/2006/ml.pdf},
}

@Article{Miteva2008,
  author    = {M. Miteva},
  journal   = {Biotechnology \& Biotechnological Equipment},
  title     = {Hierarchical structure-based virtual screening for drug design},
  year      = {2008},
  pages     = {634--638},
  volume    = {22},
  abstract  = {Virtual ligand screening (VLS) has become an established approach for identification of new hit compounds for drug discovery programs. Recently hierarchical structure-based VLS (SB-VLS) protocols consisting of different levels of filtering have been developed. It was demonstrated that such hierarchical procedures based on docking-scoring methodology significantly improve the speed and the quality of SB-VLS. Here we overview current SB-VLS methods and hierarchical VLS protocols. Finally we present recent success stories obtained with hierarchical VLS methods.},
  file      = {2008_Miteva_634.pdf:by-author/M/Miteva/2008_Miteva_634.pdf:PDF},
  keywords  = {Docking; Scoring; Structural Bioinformatics; Structure Based Drug Design; Virtual Screening},
  owner     = {saulius},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
  url       = {http://www.diagnosisp.com/dp/journals/view_article.php?journal_id=1&archive=0&issue_id=17&article_id=476},
}

@Article{Mitsuhashi2000,
  author    = {Mitsuhashi, S and Mizushima, T and Yamashita, E and Yamamoto, M and Kumasaka, T and Moriyama, H and Ueki, T and Miyachi, S and Tsukihara, T},
  journal   = {The Journal of biological chemistry},
  title     = {X-ray structure of beta-carbonic anhydrase from the red alga, Porphyridium purpureum, reveals a novel catalytic site for CO(2) hydration.},
  year      = {2000},
  pages     = {5521--6},
  volume    = {275},
  abstract  = {The carbonic anhydrases (CAs) fall into three evolutionarily distinct families designated alpha-, beta-, and gamma-CAs based on their primary structure. beta-CAs are present in higher plants, algae, and prokaryotes, and are involved in inorganic carbon utilization. Here, we describe the novel x-ray structure of beta-CA from the red alga, Porphyridium purpureum, at 2.2-A resolution using intrinsic zinc multiwavelength anomalous diffraction phasing. The CA monomer is composed of two internally repeating structures, being folded as a pair of fundamentally equivalent motifs of an alpha/beta domain and three projecting alpha-helices. The motif is obviously distinct from that of either alpha- or gamma-CAs. This homodimeric CA appears like a tetramer with a pseudo 222 symmetry. The active site zinc is coordinated by a Cys-Asp-His-Cys tetrad that is strictly conserved among the beta-CAs. No water molecule is found in a zinc-liganding radius, indicating that the zinc-hydroxide mechanism in alpha-CAs, and possibly in gamma-CAs, is not directly applicable to the case in beta-CAs. Zinc coordination environments of the CAs provide an interesting example of the convergent evolution of distinct catalytic sites required for the same CO(2) hydration reaction.},
  file      = {2000_Mitsuhashi_5521.pdf:by-author/M/Mitsuhashi/2000_Mitsuhashi_5521.pdf:PDF},
  groups    = {sg/beta},
  keywords  = {Carbonic Anhydrases},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Mizuno2007,
  author    = {Mizuno, Daisuke and Tardin, Catherine and Schmidt, C. F. and Mackintosh, F. C.},
  journal   = {Science (New York, N.Y.)},
  title     = {Nonequilibrium mechanics of active cytoskeletal networks.},
  year      = {2007},
  pages     = {370--3},
  volume    = {315},
  abstract  = {Cells both actively generate and sensitively react to forces through their mechanical framework, the cytoskeleton, which is a nonequilibrium composite material including polymers and motor proteins. We measured the dynamics and mechanical properties of a simple three-component model system consisting of myosin II, actin filaments, and cross-linkers. In this system, stresses arising from motor activity controlled the cytoskeletal network mechanics, increasing stiffness by a factor of nearly 100 and qualitatively changing the viscoelastic response of the network in an adenosine triphosphate-dependent manner. We present a quantitative theoretical model connecting the large-scale properties of this active gel to molecular force generation.},
  file      = {:by-author/M/Mizuno/2007_Mizuno_370.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Modig2003,
  author    = {Kristofer Modig and Bernd G. Pfrommer and Bertil Halle},
  journal   = {Physical Review Letters},
  title     = {Temperature-Dependent Hydrogen-Bond Geometry in Liquid Water},
  year      = {2003},
  pages     = {075502},
  volume    = {90},
  abstract  = {We have determined the hydrogen-bond geometry in liquid water from 0 to 80 degrees C by combining measurements of the proton magnetic shielding tensor with ab initio density functional calculations. The resulting moments of the distributions of hydrogen-bond length and angle are direct measures of thermal disorder in the hydrogen-bond network. These moments, and the distribution functions that can be reconstructed from them, impose quantitative constraints on structural models of liquid water.},
  doi       = {10.1103/PhysRevLett.90.075502},
  file      = {2003_Modig_075502:by-author/M/Modig/2003_Modig_075502.pdf:PDF},
  keywords  = {H Bonds; Water},
  owner     = {saulius},
  timestamp = {2011.10.13},
  creationdate = {2011-10-13T00:00:00},
}

@Misc{Modig2003a,
  author    = {Kristofer Modig and Bernd G. Pfrommer and Bertil Halle},
  title     = {Temperature-Dependent Hydrogen-Bond Geometry in Liquid Water},
  year      = {2003},
  file      = {2003_Modig_075502.pdf:by-author/M/Modig/2003_Modig.pdf:PDF},
  journal   = {manuscript},
  keywords  = {H Bonds; Thermodynamics; Water Structure},
  owner     = {saulius},
  timestamp = {2011.10.13},
  creationdate = {2011-10-13T00:00:00},
}

@Manuscript{Modig2003b,
  author    = {Kristofer Modig and Bernd G. Pfrommer and Bertil Halle},
  title     = {Temperature-Dependent Hydrogen-Bond Geometry in Liquid Water},
  year      = {2003},
  keywords  = {H Bonds; Water},
  file      = {:by-author/M/Modig/2003_Modig_manuscript.pdf:PDF},
  owner     = {saulius},
  pages     = {manuscript},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@Manuscript{Moeck2005,
  author    = {Peter Moeck and Ondřej Čertík and Bjoern Seipel and Rebecca Groebner and Lori Noice and Girish Upreti and Philip Fraundorf and Rolf Erni and Nigel~D. Browning and Andreas Kiesow and Jean-Pierre Jolivet},
  title     = {Fringe fingerprinting in two dimensions to identify unknown nanocrystals \& Crystallographic databases},
  year      = {2005},
  keywords  = {Computer Science (CS)},
  file      = {:by-author/M/Moeck/2005_Moeck.doc:DOC},
  owner     = {saulius},
  timestamp = {2015.02.28},
  creationdate = {2015-02-28T00:00:00},
}

@Manuscript{Moeck2005a,
  author    = {P. Moeck and O. Čertík and G. Upreti and W. Garrick and P. Fraundorf},
  title     = {Crystal structure visualizations in three dimensions with database support},
  year      = {2005},
  keywords  = {Computer Science (CS)},
  file      = {:by-author/M/Moeck/2005_Moeck_a.doc:DOC},
  owner     = {saulius},
  timestamp = {2015.02.28},
  creationdate = {2015-02-28T00:00:00},
}

@InProceedings{Moeck2009,
  author    = {Moeck, Peter and Rouvimov, Sergei},
  booktitle = {Semiconductor device research symposium, 2009. {ISDRS}'09. international},
  title     = {Structural fingerprinting of nanocrystals in the transmission electron microscope},
  year      = {2009},
  pages     = {1--2},
  publisher = {IEEE},
  file      = {[PDF] from researchgate.net:by-author/M/Moeck/2009_Moeck_1.pdf:application/pdf;Snapshot:by-author/M/Moeck/2009_Moeck_1.html:text/html},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=5378047},
  urldate   = {2015-08-31},
}

@InProceedings{Moeck2011,
  author    = {Moeck, Peter and Rouvimov, Sergei and Häusler, Ines and Neumann, Wolfgang and Nicolopoulos, Stavros},
  booktitle = {Nanotechnology ({IEEE}-{NANO}), 2011 11th {IEEE} conference on},
  title     = {Precession electron diffraction \& automated crystallite orientation/phase mapping in a transmission electron microscope},
  year      = {2011},
  pages     = {754--759},
  publisher = {IEEE},
  file      = {[PDF] from pdx.edu:by-author/M/Moeck/2011_Moeck_754.pdf:application/pdf;Snapshot:by-author/M/Moeck/2011_Moeck_754.html:text/html},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=6144300},
  urldate   = {2015-08-31},
}

@Article{Moeck2011a,
  author    = {Moeck, P. and Rouvimov, S. and Rauch, E. F. and Veron, M. and Kirmse, H. and Häusler, I. and Neumann, W. and Bultreys, D. and Maniette, Y. and Nicolopoulos, S.},
  journal   = {Crystal research and technology},
  title     = {High spatial resolution semi-automatic crystallite orientation and phase mapping of nanocrystals in transmission electron microscopes},
  year      = {2011},
  pages     = {589--606},
  volume    = {46},
  file      = {[PDF] from researchgate.net:by-author/M/Moeck/2011_Moeck_589.pdf:application/pdf;Snapshot:by-author/M/Moeck/2011_Moeck_589.html:text/html},
  groups    = {sg/JAC2009},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://onlinelibrary.wiley.com/doi/10.1002/crat.201000676/abstract},
  urldate   = {2015-08-31},
}

@Article{Moiseeva2007,
  author    = {Moiseeva, Natalia and Allaire, Marc},
  journal   = {Acta crystallographica. Section D, Biological crystallography},
  title     = {Using barium ions for heavy-atom derivatization and phasing of xylanase II from Trichoderma longibrachiatum.},
  year      = {2007},
  pages     = {1025--8},
  volume    = {63},
  abstract  = {This paper describes the use of barium chloride to produce a heavy-atom derivative of xylanase II crystals from Trichoderma longibrachiatum, which was obtained either by cocrystallization or soaking. SAD phasing led to interpretable electron-density maps that allowed unambiguous chain tracing. In the best case, with a data set collected at 9.5 keV, 88% of the residues were built, with 83% of the side chains assigned. The barium ions are found to mainly interact with main-chain carbonyl groups and water molecules. It is suggested that barium ions could also be used as a potential anomalous scatterer in the quick cryosoaking procedure for phasing.},
  doi       = {10.1107/S090744490703418X},
  file      = {:by-author/M/Moiseeva/2007_Moiseeva_1025.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@TechReport{Moler1995,
  author      = {Cleve Moler},
  institution = {MathWorks},
  title       = {A Tale of Two Numbers},
  year        = {1995},
  note        = {Actually today (in 2016) we should say "there was a very small chance" :) S.G.},
  abstract    = {With the Pentium, there is a very small chance of making a very large error.},
  file        = {1995_Moler.pdf:by-author/M/Moler/1995_Moler.pdf:PDF},
  keywords    = {CPU; Computations; Floating Point; Pentium Bug},
  owner       = {saulius},
  timestamp = {2016.10.05},
  creationdate = {2016-10-05T00:00:00},
  url         = {http://www.mathworks.com/tagteam/72895_92024v00Cleve_Tale_Two_Numbers_Win_1995.pdf},
}

@Article{Molnar1988,
  author    = {E. Molnár},
  journal   = {Computers \& Mathematics with Applications},
  title     = {Minimal presentation of crystallographic groups by fundamental polyhedra},
  year      = {1988},
  issn      = {0898-1221},
  pages     = {507 - 520},
  volume    = {16},
  abstract  = {There is a Poincaré's method to present a discrete isometry group G by means of a fundamental polyhedron F equipped with a face identification [1]. The identifying isometries generate the group G. The cycle relations, belonging to the edge segment equivalence classes of F, together with the occasional reflection relations, give us the presentation of G mentioned. The author's intention, to give a so-called minimal geometric presentation for each space group, has been realized in most cases, sometimes only by concave topological polyhedra [2–4]. In this paper we shall determine such a polyhedra with minimal number of (curved) faces, presenting minimally those 38 space groups which have a semi-direct decomposition G = G1 ∘ C2 is an invariant Coxeter subgroup generated by plane reflections and G1 is a so-called rod group leaving the fundamental domain of C2 and a straight line invariant [5]. This geometric presentation illustrated by figures can give us all the essential information on the structure of each space group.},
  doi       = {10.1016/0898-1221(88)90241-6},
  file      = {1988_Molnár_507.pdf:by-author/M/Molnár/1988_Molnár_507.pdf:PDF},
  keywords  = {Crystallography; Spacegroups; Symmetry},
  owner     = {saulius},
  timestamp = {2015.10.10},
  creationdate = {2015-10-10T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/0898122188902416},
}

@Article{Molnar2003,
  author    = {E. Molnár and I. Prok and J. Szirmai},
  journal   = {Mathematical and Computer Modelling},
  title     = {D-V cells and fundamental domains for crystallographic groups, algorithms, and graphic realizations},
  year      = {2003},
  issn      = {0895-7177},
  pages     = {929 - 943},
  volume    = {38},
  abstract  = {This work is related to graphic software in progress by our department to the computer package Carat, developed by colleagues in Aachen headed by Plesken. Carat is available via http://wwwb.math. rwth-aachende/carat/. Our software intends to help the applicants, e.g., crystallographers, and others in modelling real crystals. Furthermore, it will hopefully be developed for visualization of higher-dimensional (d = 4) and non-Euclidean (d = 2, 3) investigations. The well-known algorithms for Dirichlet-Voronoi (D-V) cell partition of n points in general position (Voronoi diagram) in Ed have the worst case complexity [1] O(dn⌈d2⌉+1)+O(d3n⌈d2⌉logn). It becomes more simple for a fixed dimension d, if we assume a transitive group action on the point set. In particular, we consider a point orbit under a (crystallographic) space group Γ in E3, and determine its D-V cell D and—depending on the stabilizer of the starting point—a fundamental domain F for Γ with an appropriate face pairing for a set of generators and algebraic presentation of Γ This latter algorithm with its graphic implementation is our new initiative in the topic. In general, the worst case time complexity exponentially increases only by the dimension d, but it is completely satisfactory for d = 2,3,4.},
  doi       = {10.1016/S0895-7177(03)90078-1},
  file      = {2003_Molnár_929.pdf:by-author/M/Molnár/2003_Molnár_929.pdf:PDF},
  keywords  = {Crystallographic Groups in D-space},
  owner     = {saulius},
  timestamp = {2015.10.10},
  creationdate = {2015-10-10T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/S0895717703900781},
}

@Article{Monastersky2013,
  author    = {Richard Monastersky},
  journal   = {Nature},
  title     = {Publishing frontiers: The library reboot},
  year      = {2013},
  pages     = {430--432},
  volume    = {495},
  abstract  = {As scientific publishing moves to embrace open data, libraries and researchers are trying to keep up.},
  doi       = {10.1038/495430a},
  file      = {2013_Monastersky_430.pdf:by-author/M/Monastersky/2013_Monastersky_430.pdf:PDF},
  keywords  = {Communication Policy; Open Access; Persistent Identifiers; Publishing; Research Management; Scientific Publication},
  owner     = {saulius},
  timestamp = {2013.04.03},
  creationdate = {2013-04-03T00:00:00},
}

@Article{Moncke-Buchner2009,
  author    = {Möncke-Buchner, Elisabeth and Rothenberg, Maja and Reich, Stefanie and Wagenführ, Katja and Matsumura, Hideo and Terauchi, Ryohei and Krüger, Detlev H. and Reuter, Monika},
  journal   = {Journal of molecular biology},
  title     = {Functional characterization and modulation of the DNA cleavage efficiency of type III restriction endonuclease EcoP15I in its interaction with two sites in the DNA target.},
  year      = {2009},
  pages     = {1309--19},
  volume    = {387},
  abstract  = {EcoP15I is a Type III restriction endonuclease requiring the interaction with two inversely oriented 5'-CAGCAG recognition sites for efficient DNA cleavage. Diverse models have been developed to explain how enzyme complexes bound to both sites move toward each other, DNA translocation, DNA looping and simple diffusion along the DNA. Conflicting data also exist about the impact of cofactor S-adenosyl-L-methionine (AdoMet), the AdoMet analogue sinefungin and the bases flanking the DNA recognition sequence on EcoP15I enzyme activity. To clarify the functional role of these questionable parameters on EcoP15I activity and to optimize the enzymatic reaction, we investigated the influence of cofactors, ionic conditions, bases flanking the recognition sequence and enzyme concentration. We found that AdoMet is not necessary for DNA cleavage. Moreover, the presence of AdoMet dramatically impaired DNA cleavage due to competing DNA methylation. Sinefungin neither had an appreciable effect on DNA cleavage by EcoP15I nor compensated for the second recognition site. Moreover, we discovered that adenine stretches on the 5' or 3' side of CAGCAG led to preferred cleavage of this site. The length of the adenine stretch was pivotal and had to be different on the two sides for most efficient cleavage. In the absence of AdoMet and with enzyme in molar excess over recognition sites, we observed minor cleavage at two communicating DNA sites simultaneously. These results could also be exploited in the high-throughput, quantitative transcriptome analysis method SuperSAGE to optimize the crucial EcoP15I digestion step.},
  file      = {:by-author/M/Möncke-Buchner/2009_Moncke-Buchner_1309.pdf:PDF},
  keywords  = {TypeIII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@InProceedings{Mondal2001,
  author    = {Mondal, Anirban and Kitsuregawa, Masaru and Ooi, Beng Chin and Tan, Kian Lee},
  booktitle = {Proceedings of the 9th ACM international symposium on Advances in geographic information systems},
  title     = {R-tree-based data migration and self-tuning strategies in shared-nothing spatial databases},
  year      = {2001},
  address   = {New York, NY, USA},
  pages     = {28--33},
  publisher = {ACM},
  series    = {GIS '01},
  abstract  = {In order to provide fast and timely answers to queries in the context of spatial databases and GIS, we present our solution for effective data migration and tuning strategies in shared-nothing parallel spatial databases. Our purpose is to improve the performance of the indexes. Our approach has the following features. First, our scheme is self-tuning, dynamic as well as query-centric and it can adapt to dynamically changing user access patterns. Second, a global distributed R-tree-based indexing method is employed to facilitate effective data migration. Third, unlike traditional partitioning strategies where each processing element (PE) contains data from a single region of space, we allow each PE to store data from multiple and disjoint regions. This minimizes overlap in regions as well as coverage.We implemented the proposed scheme and conducted an extensive performance study on Fujitsu's AP3000 machine with 32 workstations using real datasets. Our experimental results show that our load-balancing strategy can distribute the load effectively across the PEs in the system, thereby reducing response times of incoming queries.},
  doi       = {10.1145/512161.512169},
  file      = {:by-author/M/Mondal/2001_Mondal_28.pdf:PDF},
  isbn      = {1-58113-443-6},
  location  = {Atlanta, Georgia, USA},
  owner     = {saulius},
  timestamp = {2012.10.03},
  creationdate = {2012-10-03T00:00:00},
  url       = {http://doi.acm.org/10.1145/512161.512169},
}

@InProceedings{Mondal2004,
  author    = {Anirban Mondal and Yilifu Masaru Kitsuregawa},
  booktitle = {In Proceedings of the International Workshop on Peer-to-Peer Computing and Databases (held in conjunction with EDBT)},
  title     = {{P2PR}-tree: An {R}-tree-based spatial index for peer-to-peer environments},
  year      = {2004},
  pages     = {516--525},
  publisher = {Springer-Verlag},
  abstract  = {Abstract. The unprecedented growth and increased importance of geographically distributed spatial data has created a strong need for efficient sharing of such data. Interestingly, the ever-increasing popularity of peer-to-peer (P2P) systems has opened exciting possibilities for such sharing. This motivates our investigation into spatial indexing in P2P systems. While much work has been done towards expediting search in file-sharing P2P systems, issues concerning spatial indexing in P2P systems are significantly more complicated due to overlaps between spatial objects and the complexity of spatial queries. Incidentally, existing Rtree-based structures for distributed environments (e.g., the MC-Rtree) are not adequate for addressing the sheer scale, dynamism and heterogeneity of P2P environments. Hence, we propose the P2PR-tree (Peerto-Peer R-tree), which is a new spatial indexspecifically designed for P2P systems. The main features of P2PR-tree are two-fold. First, it is hierarchical and performs efficient pruning of the search space by maintaining minimal amount of information concerning peers that are far away and storing more information concerning nearby peers, thereby optimizing disk space usage. Second, it is completely decentralized, scalable and robust to peers joining/leaving the system. The results of our performance evaluation demonstrate that it is indeed practically feasible to share spatial data in a P2P system and that P2PR-tree is able to outperform MC-Rtree significantly.},
  file      = {:by-author/M/Mondal/2004_Mondal_516.pdf:PDF},
  keywords  = {Dynamism; P2P Systems; R Tree; Scale; Spatial Indexing},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Monkhorst1976,
  author    = {Monkhorst, Hendrik J. and Pack, James D.},
  journal   = {Phys. Rev. B},
  title     = {Special points for {Brillouin-zone} integrations},
  year      = {1976},
  pages     = {5188--5192},
  volume    = {13},
  doi       = {10.1103/PhysRevB.13.5188},
  file      = {:by-author/M/Monkhorst/1976_Monkhorst_5188.pdf:PDF},
  issue     = {12},
  keywords  = {Density Functional Theory (DFT)},
  owner     = {andrius},
  publisher = {American Physical Society},
  timestamp = {2015.05.07},
  creationdate = {2015-05-07T00:00:00},
  url       = {http://link.aps.org/doi/10.1103/PhysRevB.13.5188},
}

@PhdThesis{Monteiro2010,
  author    = {Monteiro, Julian Geraldes},
  school    = {Université de Nice},
  title     = {Modeling and Analysis of Reliable Peer-to-Peer Storage Systems},
  year      = {2010},
  file      = {2010_Monteiro_phdthesis.pdf:by-author/M/Monteiro/2010_Monteiro_phdthesis.pdf:PDF},
  keywords  = {Data Management; Distributed Storage; Reliability; Tahoe LAFS},
  owner     = {saulius},
  timestamp = {2014.09.23},
  creationdate = {2014-09-23T00:00:00},
  url       = {http://hal-unice.archives-ouvertes.fr/docs/00/54/57/24/PDF/these-jmonteiro.pdf},
}

@Article{Moon2010,
  author    = {Moon, Andrea F and Mueller, Geoffrey A and Zhong, Xuejun and Pedersen, Lars C},
  journal   = {Protein science : a publication of the Protein Society},
  title     = {A synergistic approach to protein crystallization: combination of a fixed-arm carrier with surface entropy reduction.},
  year      = {2010},
  pages     = {901--13},
  volume    = {19},
  abstract  = {Protein crystallographers are often confronted with recalcitrant proteins not readily crystallizable, or which crystallize in problematic forms. A variety of techniques have been used to surmount such obstacles: crystallization using carrier proteins or antibody complexes, chemical modification, surface entropy reduction, proteolytic digestion, and additive screening. Here we present a synergistic approach for successful crystallization of proteins that do not form diffraction quality crystals using conventional methods. This approach combines favorable aspects of carrier-driven crystallization with surface entropy reduction. We have generated a series of maltose binding protein (MBP) fusion constructs containing different surface mutations designed to reduce surface entropy and encourage crystal lattice formation. The MBP advantageously increases protein expression and solubility, and provides a streamlined purification protocol. Using this technique, we have successfully solved the structures of three unrelated proteins that were previously unattainable. This crystallization technique represents a valuable rescue strategy for protein structure solution when conventional methods fail.},
  file      = {2010_Moon_901.pdf:by-author/M/Moon/2010_Moon_901.pdf:PDF},
  keywords  = {Crystallisation; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@PhdThesis{Moonen1994,
  author      = {Leon Moonen},
  school      = {Hogeschool Eindhoven, Studierichting Hogere Informatica},
  title       = {A Virtual Assembler for an Abstract Machine: Design and implementation of an incremental and retargetable},
  year        = {1994},
  file        = {:by-author/M/Moonen/1994_Moonen.ps.gz:PostScript;:by-author/M/Moonen/1994_Moonen.pdf:PDF},
  institution = {Hogeschool Eindhoven, Studierichting Hogere Informatica},
  owner       = {saulius},
  timestamp = {2015.02.27},
  creationdate = {2015-02-27T00:00:00},
}

@Webpage{Moore2008,
  author    = {Charles H. Moore},
  retrieved = {2008-10-28},
  title     = {1% the code C programs},
  url       = {http://www.colorforth.com/1percent.html},
  year      = {2008},
  file      = {:by-author/M/Moore/2008_Moore.war:},
  keywords  = {Computer Science (CS); Computing Essays},
  owner     = {saulius},
  timestamp = {2015.03.02},
  creationdate = {2015-03-02T00:00:00},
}

@Article{Moore1965,
  author    = {Moore, Gordon E.},
  journal   = {Electronics},
  title     = {Cramming More Components onto Integrated Circuits},
  year      = {1965},
  issn      = {0018-9219},
  pages     = {114--117},
  volume    = {38},
  abstract  = {The future of integrated electronics is the future of electron- ics itself. The advantages of integration will bring about a proliferation of electronics, pushing this science into many new areas. Integrated circuits will lead to such wonders as home computers -- or at least terminals connected to a central com- puter--automatic controls for automobiles, and personal portable communications equipment. The electronic wrist- watch needs only a display to be feasible today. But the biggest potential lies in the production of large systems. In telephone communications, integrated circuits in digital filters will separate channels on multiplex equip- ment. Integrated circuits will also switch telephone circuits and perform data processing. Computers will be more powerful, and will be organized in completely different ways. For example, memories built of integrated electronics may be distributed throughout the machine instead of being concentrated in a central unit. In addition, the improved reliability made possible by integrated circuits will allow the construction of larger processing units. Machines similar to those in existence today will be built at lower costs and with faster turn-around.},
  doi       = {10.1109/JPROC.1998.658762},
  file      = {:by-author/M/Moore/1965_Moore_114.pdf:PDF},
  owner     = {saulius},
  publisher = {IEEE},
  timestamp = {2012.10.03},
  creationdate = {2012-10-03T00:00:00},
  url       = {http://dx.doi.org/10.1109/JPROC.1998.658762},
}

@Manuscript{Morandi2002,
  author    = {Patrick Morandi},
  title     = {Generators and Relations},
  year      = {2002},
  url       = {http://sierra.nmsu.edu/morandi/oldwebpages/math683fall2002/GeneratorsAndRelations.pdf},
  abstract  = {In this note we discuss several examples of describing groups with generators and relations. To begin, we recall some notation. First, if G is a group and S is a subset of G, then recall that the subgroup S generated by S is the smallest subgroup of G con taining S. One description is that h S i is equal to the intersection of all subgroups of G con taining S. Another is that S is the set of all elemen ts that can be expressed as pro ducts of elemen ts of S or inverses of elements of S. We can also consider the normal subgroup of G generated by S. This is the in tersection of all normal subgroups of G containing S. It is a simple exercise to show that this intersection is a normal subgroup of G. Another short exercise sho ws that this group is the subgroup of G generated by f xsx ° 1 : x 2 G; s 2 S g},
  file      = {2002_Morandi.pdf:by-author/M/Morandi/2002_Morandi.pdf:PDF},
  owner     = {saulius},
  timestamp = {2013.10.20},
  creationdate = {2013-10-20T00:00:00},
}

@Article{Moravcik2012,
  author    = {Moravčík, Roman and Štefániková, Mária and Čička, Roman and Čaplovič, L'ubomír and Kocúrová, Karin and Šturm, Roman},
  journal   = {Strojniški vestnik-Journal of Mechanical Engineering},
  title     = {Phase transformations in high alloy cold work tool steel},
  year      = {2012},
  pages     = {709--715},
  volume    = {58},
  file      = {[PDF] from sv-jme.eu:by-author/M/Moravčík/2012_Moravčík_709.pdf:application/pdf;Snapshot:by-author/M/Moravčík/2012_Moravčík_709.html:text/html},
  groups    = {sg/JAC2009},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://ojs.sv-jme.eu/index.php/sv-jme/article/view/sv-jme.2012.531},
  urldate   = {2015-08-31},
}

@Presentation{Moravec2009,
  author     = {Primož Moravec},
  title      = {Computational Group Theory: Coset Enumeration},
  year       = {2009},
  conference = {Computational Algebra Seminar, March 5, 2009},
  school     = {Univerza v Ljubljani},
  file       = {:by-author/M/Moravec/2009_Moravec_slides.pdf:PDF},
  owner      = {saulius},
  pages      = {slides},
  timestamp = {2013.03.22},
  creationdate = {2013-03-22T00:00:00},
}

@Article{More1996,
  author    = {Moré},
  title     = {Distance geometry optimization for protein structures},
  year      = {1996},
  pages     = {preprint},
  file      = {:by-author/M/Moré/1996_Moré_preprint.pdf:PDF},
  keywords  = {Distance Geometry; Protein Bioinformatics},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@InCollection{Moreau2008,
  author    = {Moreau, Luc and Freire, Juliana and Futrelle, Joe and McGrath, Robert E. and Myers, Jim and Paulson, Patrick},
  booktitle = {Provenance and Annotation of Data and Processes},
  publisher = {Springer Berlin Heidelberg},
  title     = {The {Open Provenance Model}: An Overview},
  year      = {2008},
  editor    = {Freire, Juliana and Koop, David and Moreau, Luc},
  isbn      = {978-3-540-89964-8},
  pages     = {323--326},
  series    = {Lecture Notes in Computer Science},
  volume    = {5272},
  abstract  = {Provenance is well understood in the context of art or digital libaries, where it respectively refers to the documented history of an art object, or the documentation of processes in a digital object's life cycle. Interest for provenance in the ``e-science community'' is also growing, since provenance is perceived as a crucial component of workflow systems that can help scientists ensure reproducibility of their scientific analyses and processes.},
  doi       = {10.1007/978-3-540-89965-5_31},
  file      = {:by-author/M/Moreau/2008_Moreau_323.pdf:PDF},
  owner     = {andrius},
  timestamp = {2015.08.07},
  creationdate = {2015-08-07T00:00:00},
  url       = {http://dx.doi.org/10.1007/978-3-540-89965-5_31},
}

@TechReport{Moreau2007,
  author      = {Moreau, Luc and Freire, Juliana and Futrelle, Joe and McGrath, Robert E. and Myers, Jim and Paulson, Patrick},
  institution = {University of Southampton},
  title       = {The {Open Provenance Model}},
  year        = {2007},
  file        = {:by-author/M/Moreau/2007_Moreau.pdf:PDF},
  owner       = {andrius},
  timestamp = {2015.08.19},
  creationdate = {2015-08-19T00:00:00},
  url         = {http://eprints.soton.ac.uk/264979/},
}

@InProceedings{Moreira2007,
  author    = {Adriano Moreira and Maribel Yasmina Santos},
  booktitle = {GRAPP 2007 - International Conference on Computer Graphics Theory and Applications},
  title     = {Concave hull: a k-nearest neighbours approach for the computation of the region occupied by a set of points},
  year      = {2007},
  abstract  = {This paper describes an algorit hm to compute the envelope of a set of points in a plane, which generates convex or non-convex hulls that represent the area occ upied by the given points. The proposed algorithm is based on a k -nearest neighbours approach, where the value of k , the only algorithm parameter, is used to control the “smoothness” of the final solution. The obtaine d results show that this algorithm is able to deal with arbitrary sets of points, and that the time to compute the polygons increases approxi mately linearly with the number of points.},
  file      = {2007_Moreira_61.pdf:by-author/M/Moreira/2007_Moreira_61.pdf:PDF},
  groups    = {sg/Concave Hull, sg/Bioinf. Algorithms},
  keywords  = {Algorithms; Computer Science (CS); Concave Hull; Contour; Convex Hull; K-nearest Neighbours (KNN); Polygon},
  owner     = {saulius},
  timestamp = {2015.12.16},
  creationdate = {2015-12-16T00:00:00},
  url       = {https://repositorium.sdum.uminho.pt/bitstream/1822/6429/1/ConcaveHull_ACM_MYS.pdf},
}

@Article{Moresco2001,
  author     = {Moresco, Francesca and Meyer, Gerhard and Rieder, Karl-Heinz and Tang, Hao and Gourdon, André and Joachim, Christian},
  journal    = {Physical Review Letters},
  title      = {Conformational changes of single molecules induced by scanning tunneling microscopy manipulation: {A} route to molecular switching},
  year       = {2001},
  pages      = {672--675},
  volume     = {86},
  abstract   = {A detailed experimental and theoretical investigation of the processes involved in the manipulation of individual specially designed porphyrin-based molecules by scanning tunneling microscopy at low temperature is presented. On a stepped Cu(211) surface, the interaction between tip and molecule was used to locally modify in a reversible way the internal configuration of a single molecule, thus drastically changing the tunneling current passing through it. Model calculations confirm that this manipulation realizes the principle of a conformational molecular switch.},
  doi        = {10.1103/PhysRevLett.86.672},
  file       = {Moresco et al. - 2001 - Conformational Changes of Single Molecules Induced.pdf:by-author/M/Moresco/2001_Moresco_672.pdf:application/pdf;APS Snapshot:by-author/M/Moresco/2001_Moresco_672.html:text/html},
  groups     = {sg/chemical},
  owner      = {saulius},
  shorttitle = {Conformational changes of single molecules induced by scanning tunneling microscopy manipulation},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url        = {http://link.aps.org/doi/10.1103/PhysRevLett.86.672},
  urldate    = {2015-08-05},
}

@Article{Morgan1965,
  author    = {H. L. Morgan},
  journal   = {J. Chem. Doc.},
  title     = {The Generation of a Unique Machine Description for Chemical Structures-A Technique Developed at Chemical Abstracts Service},
  year      = {1965},
  pages     = {107--113},
  volume    = {5},
  doi       = {10.1021/c160017a018},
  file      = {:by-author/M/Morgan/1965_Morgan_107.pdf:PDF},
  keywords  = {Chemical Database Search; Chemical Fingerprint; Chemoinformatics; Databases; Morgan Algorithm},
  owner     = {andrius},
  timestamp = {2014.01.24},
  creationdate = {2014-01-24T00:00:00},
}

@Article{Mori1999,
  author    = {Mori, K and Ogawa, Y and Ebihara, K and Tamura, N and Tashiro, K and Kuwahara, T and Mukoyama, M and Sugawara, A and Ozaki, S and Tanaka, I and Nakao, K},
  journal   = {The Journal of biological chemistry},
  title     = {Isolation and characterization of CA XIV, a novel membrane-bound carbonic anhydrase from mouse kidney.},
  year      = {1999},
  pages     = {15701--5},
  volume    = {274},
  abstract  = {Carbonic anhydrase (CA) is involved in various physiological processes such as acid-base balance and transport of carbon dioxide and ions. In this study, we have succeeded in the isolation of a novel CA from the mouse kidney by use of the signal sequence trap method. It is a 337-amino acid polypeptide with a calculated molecular mass of 37.5 kDa, consisting of a putative amino-terminal signal sequence, a CA domain, a transmembrane domain, and a short hydrophilic carboxyl terminus, which we designated CA XIV. The CA domain of CA XIV is highly homologous with those of known CAs, especially extracellular CAs including CA XII, IX, VI, and IV. The expression study of an epitope-tagged protein has suggested that CA XIV is located on the plasma membrane. When expressed in COS-7 cells, CA XIV exhibits CA activity that is predominantly associated with the membrane fraction. By Northern blot analysis, the gene expression of CA XIV is most abundant in the kidney and heart, followed by the skeletal muscle, brain, lung, and liver. In situ hybridization has revealed that, in the kidney, the gene is expressed intensely in the proximal convoluted tubule, which is the major segment for bicarbonate reabsorption and also in the outer border of the inner stripe of the outer medulla. In conclusion, we have cloned a functional cDNA encoding a novel membrane-bound CA. This study will bring new insights into our understanding of carbon dioxide metabolism and acid-base balance.},
  file      = {1999_Mori_15701.pdf:by-author/M/Mori/1999_Mori_15701.pdf:PDF},
  groups    = {sg/mCA14},
  keywords  = {CA14; Carbonic Anhydrases},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Moriarty2009,
  author    = {Moriarty, Nigel W. and Grosse-Kunstleve, Ralf W. and Adams, Paul D.},
  journal   = {Acta Crystallogr D},
  title     = {electronic Ligand Builder and Optimization Workbench (eLBOW): a tool for ligand coordinate and restraint generation},
  year      = {2009},
  issn      = {0907-4449},
  month     = {Sep},
  number    = {10},
  pages     = {1074--1080},
  volume    = {65},
  abstract  = {The electronic Ligand Builder and Optimization Workbench (eLBOW) is a program module of the PHENIX suite of computational crystallographic software. It is designed to be a flexible procedure that uses simple and fast quantum-chemical techniques to provide chemically accurate information for novel and known ligands alike. A variety of input formats and options allow the attainment of a number of diverse goals including geometry optimization and generation of restraints.},
  doi       = {10.1107/s0907444909029436},
  file      = {2009_Moriarty_1074.pdf:by-author/M/Moriarty/2009_Moriarty_1074.pdf:PDF},
  keywords  = {Macromolecular Refinement; Refinement Restrains; The Phenix Project},
  owner     = {saulius},
  publisher = {International Union of Crystallography (IUCr)},
  timestamp = {2016.09.28},
  creationdate = {2016-09-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444909029436},
}

@Article{Moroney2001,
  author    = {J. V. Moroney and S. G. Bartlett and G. Samuelsson},
  journal   = {Plant, Cell and Environment},
  title     = {Carbonic anhydrases in plants and algae},
  year      = {2001},
  pages     = {141--153},
  volume    = {24},
  abstract  = {Carbonic anhydrases catalyse the reversible hydration of CO2, increasing the interconversion between CO2 and HCO3- + H+ in living organisms. The three evolutionarily unrelated families of carbonic anhydrases are designated a-, b-and g-CA. Animals have only the a-carbonic anhy- drase type of carbonic anhydrase, but they contain multi- ple isoforms of this carbonic anhydrase. In contrast, higher plants, algae and cyanobacteria may contain members of all three CA families. Analysis of the Arabidopsis database reveals at least 14 genes potentially encoding carbonic anhydrases. The database also contains expressed sequence tags (ESTs) with homology to most of these genes. Clearly the number of carbonic anhydrases in plants is much greater than previously thought. Chlamydomonas, a uni- cellular green alga, is not far behind with five carbonic anhydrases already identified and another in the EST data- base. In algae, carbonic anhydrases have been found in the mitochondria, the chloroplast thylakoid, the cytoplasm and the periplasmic space. In C3 dicots, only two carbonic anhy- drases have been localized, one to the chloroplast stroma and one to the cytoplasm. A challenge for plant scientists is to identify the number, location and physiological roles of the carbonic anhydrases.},
  file      = {2001_Moroney_141.pdf:by-author/M/Moroney/2001_Moroney_141.pdf:PDF},
  groups    = {sg/reviews},
  keywords  = {Carbonic Anhydrases},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Morozov2004,
  author    = {Morozov, Alexandre V. and Kortemme, Tanja and Tsemekhman, Kiril and Baker, David},
  journal   = {Proceedings of the National Academy of Sciences of the United States of America},
  title     = {Close agreement between the orientation dependence of hydrogen bonds observed in protein structures and quantum mechanical calculations.},
  year      = {2004},
  pages     = {6946--51},
  volume    = {101},
  abstract  = {Hydrogen bonding is a key contributor to the exquisite specificity of the interactions within and between biological macromolecules, and hence accurate modeling of such interactions requires an accurate description of hydrogen bonding energetics. Here we investigate the orientation and distance dependence of hydrogen bonding energetics by combining two quite disparate but complementary approaches: quantum mechanical electronic structure calculations and protein structural analysis. We find a remarkable agreement between the energy landscapes obtained from the electronic structure calculations and the distributions of hydrogen bond geometries observed in protein structures. In contrast, molecular mechanics force fields commonly used for biomolecular simulations do not consistently exhibit close correspondence to either quantum mechanical calculations or experimentally observed hydrogen bonding geometries. These results suggest a route to improved energy functions for biological macromolecules that combines the generality of quantum mechanical electronic structure calculations with the accurate context dependence implicit in protein structural analysis.},
  file      = {:by-author/M/Morozov/2004_Morozov_6946.pdf:PDF},
  keywords  = {H Bonds; Protein Physics},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Morrical1996,
  author    = {Morrical, S. W. and Beernink, H. T. and Dash, A. and Hempstead, K.},
  journal   = {The Journal of biological chemistry},
  title     = {The gene 59 protein of bacteriophage T4. Characterization of protein-protein interactions with gene 32 protein, the T4 single-stranded DNA binding protein.},
  year      = {1996},
  pages     = {20198--207},
  volume    = {271},
  abstract  = {The gene 59 protein (gp59) of bacteriophage T4 stimulates the activities of gene 41 protein (gp41), the T4 replicative DNA helicase, by promoting the assembly of gp41 onto single-stranded (ss)-DNA molecules that are covered with cooperatively bound gene 32 protein (gp32). This helicase-ssDNA assembly process, which is important for the reconstitution of the primosome component of the T4 DNA replication fork, appears to require both gp59-gp41 and gp59-gp32 protein-protein interactions. In this study we characterize the physical and functional interactions of gp59 with gp32, the T4 ssDNA-binding protein. Experimental results presented herein indicate: 1) that gp59 binds specifically to both free and ssDNA-bound gp32 molecules; and 2) that in both cases binding involves contacts between gp59 and the acidic C-terminal domain of gp32 (the so-called "A-domain"). We further show that single-stranded DNA molecules coated with (gp32-A), a truncated form of gp32 lacking the A-domain, are refractory to gp59-dependent helicase assembly. The data indicate that specific contacts between gp59 molecules and the A-domains of gp32 molecules are essential for gp59-dependent assembly of gp41 onto gp32-ssDNA complexes. Our results are consistent with a model in which gp59 binds to gp32 molecules within the gp32-ssDNA complex and therein forms a target site for helicase-ssDNA assembly.},
  file      = {:by-author/M/Morrical/1996_Morrical_20198.pdf:PDF},
  keywords  = {{gp41} Helicase; {gp59}},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Morrical1994,
  author    = {Morrical, S. W. and Hempstead, K. and Morrical, M. D.},
  journal   = {The Journal of biological chemistry},
  title     = {The gene 59 protein of bacteriophage T4 modulates the intrinsic and single-stranded DNA-stimulated ATPase activities of gene 41 protein, the T4 replicative DNA helicase.},
  year      = {1994},
  pages     = {33069--81},
  volume    = {269},
  abstract  = {The T4 gene 59 protein (gp59) serves as an accessory protein to the essential T4-encoded DNA helicase, the gene 41 protein (gp41). gp59 stimulates gp41-dependent DNA synthesis reactions by promoting the assembly of gp41 onto single-stranded DNA (ssDNA), where the enzyme is activated to perform its DNA helicase functions. To better understand the mechanism of helicase-ssDNA assembly, we have studied the effects of gp59 on the intrinsic and ssDNA-stimulated ATPase activities of gp41. Our results indicate that gp59 exerts a direct effect upon the conformation and ATPase activity of gp41, by increasing the affinity of gp41 for ATP. In addition, we find that gp59 is nearly essential for promoting the assembly of gp41 onto ssDNA molecules that are covered with saturating amounts of the T4-encoded helix-destabilizing protein, gene 32 protein (gp32). Results of protein affinity chromatography experiments suggest that gp59 contains distinct binding sites for gp41 and gp32 and may therefore act as a molecular adapter between the helicase and helix-destabilizing proteins. Together, the data indicate that specific gp59-gp41 and gp59-gp32 protein-protein interactions both play important roles in the assembly of the helicase onto single-stranded DNA.},
  file      = {:by-author/M/Morrical/1994_Morrical_33069.pdf:PDF},
  keywords  = {{gp41} Helicase; {gp59}},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Morris1979,
  author    = {Morris, C. F. and Moran, L. A. and Alberts, B. M.},
  journal   = {The Journal of biological chemistry},
  title     = {Purification of gene 41 protein of bacteriophage T4.},
  year      = {1979},
  pages     = {6797--802},
  volume    = {254},
  abstract  = {The T4 bacteriophage gene 41 protein is known from genetic analysis to be essential for phage DNA replication in vivo. It became possible to monitor the activity of this protein during purification after development of an "in vitro complementation assay," which measures its stimulation of DNA synthesis in a concentrated crude lysate prepared from Escherichia coli cells infected with a T4 bacteriophage mutant in gene 41 (L. Moran and B. Alberts, manuscript in preparation). In this report, a purification procedure involving three chromatographic steps is described which reproducibly yields a 90% homogeneous preparation of this rather unstable protein. The major polypeptide chain present (58,000 daltons) is shown to cosediment with a DNA-dependent GTPase (and ATPase) activity, and to induce extensive in vitro DNA synthesis on both single- and double-stranded DNA templates when incubated with our preparations of five other purified T4 DNA replication proteins (plus deoxyribonucleoside and ribonucleoside triphosphates).},
  file      = {:by-author/M/Morris/1979_Morris_6797.pdf:PDF},
  keywords  = {{gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Morris2008,
  author    = {Morris, Kevin V. AND Santoso, Sharon AND Turner, Anne-Marie AND Pastori, Chiara AND Hawkins, Peter G.},
  journal   = {PLoS Genet},
  title     = {Bidirectional Transcription Directs Both Transcriptional Gene Activation and Suppression in Human Cells},
  year      = {2008},
  month     = {11},
  number    = {11},
  pages     = {1--9},
  volume    = {4},
  abstract  = {Non-coding RNAs have been shown to modulate transcriptional expression of genes in human cells. This form of gene regulation has been shown to be the result of RNA directing silent state epigenetic changes to the targeted gene promoter. Shortly after this seminal observation, small RNAs targeted to AT-rich regions of gene promoters were shown to modulate gene activation, termed RNA activation. While much is known regarding non-coding RNA-mediated transcriptional gene silencing, the mechanism of RNA activation has remained elusive. Here, we present evidence that RNA activation is the result of deregulation of endogenous bidirectional transcription. The antisense transcript in the bidirectionally transcribed gene is shown here to be operative in directing silent state epigenetic marks to the sense gene promoter. Suppression of the antisense transcript results in gene activation. Overall, these data support the notion that bidirectional transcription is an endogenous mechanism whereby RNA-directed gene regulation is operative and that RNA activation is the result of a disruption of this endogenous pathway. An understanding of this mode of RNA-based regulation will prove exceptionally useful in understanding gene expression as well as potential therapeutic approaches to controlling gene expression in human cells.},
  doi       = {10.1371/journal.pgen.1000258},
  file      = {2008_Morris_e1000258.pdf:by-author/M/Morris/2008_Morris_e1000258.pdf:PDF},
  groups    = {am/RNA activation},
  owner     = {andrius},
  publisher = {Public Library of Science},
  timestamp = {2016.09.13},
  creationdate = {2016-09-13T00:00:00},
  url       = {http://dx.doi.org/10.1371%2Fjournal.pgen.1000258},
}

@Article{Morris1999,
  author    = {Morris, P. D. and Raney, K. D.},
  journal   = {Biochemistry},
  title     = {DNA helicases displace streptavidin from biotin-labeled oligonucleotides.},
  year      = {1999},
  pages     = {5164--71},
  volume    = {38},
  abstract  = {Helicases are enzymes that use energy derived from nucleoside triphosphate hydrolysis to unwind double-stranded (ds) DNA, a process vital to virtually every phase of DNA metabolism. The helicases used in this study, gp41 and Dda, are from the bacteriophage T4, an excellent system for studying enzymes that process DNA. gp41 is the replicative helicase and has been shown to form a hexamer in the presence of ATP. In this study, protein cross-linking was performed in the presence of either linear or circular single-stranded (ss) DNA substrates to determine the topology of gp41 binding to ssDNA. Results indicate that the hexamer binds ssDNA by encircling it, in a manner similar to that of other hexameric helicases. A new assay was developed for studying enzymatic activity of gp41 and Dda on single-stranded DNA. The rate of dissociation of streptavidin from various biotinylated oligonucleotides was determined in the presence of helicase by an electrophoretic mobility shift assay. gp41 and Dda were found to significantly enhance the dissociation rate of streptavidin from biotin-labeled oligonucleotides in an ATP-dependent reaction. Helicase-catalyzed dissociation of streptavidin from the 3'-end of a biotin-labeled 62-mer oligonucleotide occurred with a first-order rate of 0.17 min-1, which is over 500-fold faster than the spontaneous dissociation rate of biotin from streptavidin. Dda activity leads to even faster displacement of streptavidin from the 3' end of the 62-mer, with a first-order rate of 7.9 s-1. This is more than a million-fold greater than the spontaneous dissociation rate. There was no enhancement of streptavidin dissociation from the 5'-biotin-labeled oligonucleotide by either helicase. The fact that each helicase was capable of dislodging streptavidin from the 3'-biotin label suggests that these enzymes are capable of imparting a force on a molecule blocking their path. The difference in displacement between the 5' and 3' ends of the oligonucleotide is also consistent with the possibility of a 5'-to-3' directional bias in translocation on ssDNA for each helicase.},
  file      = {:by-author/M/Morris/1999_Morris_5164.pdf:PDF},
  keywords  = {{gp41}; {gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Morris2004a,
  author    = {Morris, Richard J. and Blanc, Eric and Bricogne, G{\'{e}}rard},
  journal   = {Acta Crystallographica Section D},
  title     = {On the interpretation and use of {$\langle$}|{\it E}|${\sp 2}${$\rangle$}({\it d}*) profiles},
  year      = {2004},
  pages     = {227--240},
  volume    = {60},
  doi       = {10.1107/S0907444903025538},
  file      = {dz0021.pdf:by-author/M/Morris/2004_Morris_227.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444903025538},
}

@PhdThesis{Morrison1979,
  author    = {Ronald Morrison},
  school    = {Department of Computational Science, University of St Andrews, St Andrews},
  title     = {On the Development of Algol},
  year      = {1979},
  month     = {December},
  abstract  = {The thesis outlines the major problems in the design of high level programming languages. The complexity of these languages has caused the user problems in intellectual manageability. Part of this complexity is caused by lack of generality which also causes loss of power. The maxim of power through simplicity, simplicity through generality is established. To achieve this simplicity a number of ground rules, the principle of abstraction, the principle of correspondence and the principle of data type completeness are discussed and used to form a methodology for programming language design. The methodology is then put into practice and the language S-algol is designed as the first member of a family of languages. The second part of the thesis describes the implementation of the S-algol language. In particular a simple and effective method of compiler construction based on the technique of recursive descent is developed. The method uses a hierarchy of abstractions which are implemented as layers to define the compiler. The simplicity and success of the technique depends on the structuring of the layers and the choice of abstractions. The compiler is itself written in S-algol. An abstract machine to support the S-algol language is then proposed and implemented. This machine, the S-code machine, has two stacks and a heap with a garbage collector and a unique method of procedure entry and exit. A detailed description of the S-code machine for the PDP11 computer is given in the Appendices. The thesis then describes the measurement tools used to aid the implementor and the user. The results of improvements in efficiency when these tools are used on the compiler itself are discussed. Finally, the research is evaluated and a discussion of how it may be extended is given.},
  file      = {:by-author/M/Morrison/1979_Morrison.ps.gz:PostScript;:by-author/M/Morrison/1979_Morrison.pdf:PDF},
  groups    = {sg/Garbage collectors},
  owner     = {saulius},
  timestamp = {2015.02.27},
  creationdate = {2015-02-27T00:00:00},
}

@Manuscript{Mortera2006,
  author    = {J. Mortera and A. P. Dawid},
  title     = {Probability and Evidence},
  year      = {2006},
  keywords  = {Bayesian Statistics},
  abstract  = {Legal applications of probabilistic and statistical reasoning have a long his- tory, having exercised such pioneers as Nicolas Bernoulli, Condorcet, Laplace, Poisson and Cournot (Zabell 1988). After a period of neglect interest has resurfaced in recent years, and the topic has given rise to many challenging problems. Evidence presented in a case at law can be regarded as data, and the issue to be decided by the court as a hypothesis under test. The relationship between these may be immediate, or indirect, involving a long chain or tan- gled web of intermediate propositions. In any case there will be uncertainty about both the ultimate issue and the way in which the evidence relates to it, and such uncertainty can, in principle at least, be described probabilistically. But, even when appropriate probabilities can be agreed on, their correct handling is by no means obvious or intuitive, and fallacious arguments and inferences abound},
  file      = {:by-author/M/Mortera/2006_Mortera.pdf:PDF},
  groups    = {sg/Bayesian},
  owner     = {saulius},
  timestamp = {2012.09.30},
  creationdate = {2012-09-30T00:00:00},
}

@Manuscript{Moseley2006,
  author    = {Moseley, Ben and Peter Marks},
  title     = {Out of the Tar Pit},
  year      = {2006},
  keywords  = {Computer Science (CS); Software Design},
  month     = {February},
  abstract  = {Complexity is the single major difficulty in the successful develop- ment of large-scale software systems. Following Brooks we distinguish accidental from essential difficulty, but disagree with his premise that most complexity remaining in contemporary systems is essential. We identify common causes of complexity and discuss general approaches which can be taken to eliminate them where they are accidental in nature. To make things more concrete we then give an outline for a potential complexity-minimizing approach based on functional pro- gramming and Codd’s relational model of data.},
  file      = {:by-author/M/Moseley/2006_Moseley.pdf:PDF},
  groups    = {sg/Software project management},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@PhdThesis{Mosonyi2005,
  author    = {Mosonyi, Milán},
  school    = {Katholieke Universiteit Leuven, Faculteit Wetenschappen, Instituut voor Theoretische Fysica},
  title     = {Enropy, Information and Structure of Composite Quantum States},
  year      = {2005},
  file      = {:by-author/M/Mosonyi/2005_Mosonyi.ps.bz2:bz2},
  keywords  = {Quantum-mechanics},
  owner     = {saulius},
  timestamp = {2015.03.03},
  creationdate = {2015-03-03T00:00:00},
}

@Manuscript{Moss2006,
  author    = {Moss, Lawrence S.},
  title     = {Recursion Theorems and Self-Replication Via Text Register Machine Programs},
  year      = {2006},
  keywords  = {Computability; Computer Science (CS)},
  url       = {https://iulg.sitehost.iu.edu/trm/trm.pdf},
  abstract  = {Register machine programs provide explicit proofs of the $s^m_n$ -Theorem, Kleene’s Second Recursion Theorem, and Smullyan’s Double Recursion Theorem. Thus these programs provide a pedagogically useful approach. We develop this topic from scratch, hence without appeal to the existence of universal programs, pairing, quotation, or any form of coding device. None of the results are new from the point of view of computability theory apart from the particular formulations themselves. We introduce the notion of a text register machine; this is a register machine whose registers contain words from some alphabet and whose instructions are again words from the same alphabet. We work with a particular instruction set whose language of programs we call 1\#. Tools for writing and evaluating 1\# programs have been made freely available: see www.indiana.edu/iulg/trm.},
  file      = {:by-author/M/Moss/2006_Moss.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@TechReport{Moessenboeck1995,
  author    = {H. Mössenböck and N. Wirth},
  title     = {The Programming Language Oberon},
  year      = {1995},
  file      = {:by-author/M/Mössenböck/1995_Mössenböck.Report.ps.gz:PostScript;:by-author/M/Mössenböck/1995_Mössenböck.Report.pdf:PDF},
  owner     = {saulius},
  timestamp = {2015.02.27},
  creationdate = {2015-02-27T00:00:00},
}

@Article{Moulin2017,
  author    = {Robinson Moulin and Emilie Delahaye and Am{\'{e}}lie Bordage and Emiliano Fonda and Jean-Pierre Baltaze and Patricia Beaunier and Eric Rivi{\`{e}}re and Giulia Fornasieri and Anne Bleuzen},
  journal   = {European Journal of Inorganic Chemistry},
  title     = {Ordered Mesoporous Silica Monoliths as a Versatile Platform for the Study of Magnetic and Photomagnetic Prussian Blue Analogue Nanoparticles},
  year      = {2017},
  month     = {jan},
  comment   = {Probably not what we need.... (S.G.).},
  doi       = {10.1002/ejic.201601196},
  file      = {Moulin2017.pdf:by-author/M/Moulin/2017_Moulin.pdf:PDF},
  groups    = {sg/MOF, sg/MOFs, am/MOFs},
  keywords  = {Synthesis},
  owner     = {saulius},
  publisher = {Wiley-Blackwell},
  timestamp = {2017.01.31},
  creationdate = {2017-01-31T00:00:00},
  url       = {https://doi.org/10.1002%2Fejic.201601196},
}

@Manuscript{Mounet2016,
  author    = {Nicolas Mounet and Marco Gibertini and Philippe Schwaller and Davide Campi and Andrius Merkys and Antimo Marrazzo and Thibault Sohier and Ivano E. Castelli and Andrea Cepellotti and Giovanni Pizzi and Nicola Marzari},
  title     = {Novel two-dimensional materials from high-throughput computational exfoliation of experimentally known compounds},
  year      = {2017},
  month     = {Nov},
  url       = {https://arxiv.org/abs/1611.05234v1},
  abstract  = {We search for novel two-dimensional materials that can be easily exfoliated from their parent compounds. Starting from 108423 unique, experimentally known three-dimensional compounds we identify a subset of 5619 that appear layered according to robust geometric and bonding criteria. High-throughput calculations using van-der-Waals density-functional theory, validated against experimental structural data and calculated random-phase-approximation binding energies, allow to identify 1844 compounds that are either easily or potentially exfoliable, including all that are commonly exfoliated experimentally. In particular, the subset of 1053 easily exfoliable cases −layered materials held together mostly by dispersion interactions and with binding energies in the range of few tens of meV⋅\AA−2− contains several hundreds of entries with few atoms per primitive cell (273 with less than 6 atoms, 606 with less than 12), revealing a wealth of new structural prototypes, simple ternary compounds, and a large portfolio to search for optimal electronic, optical, magnetic, topological, or chemical properties.},
  file      = {:by-author/M/Mounet/2016_Mounet.pdf:PDF},
  groups    = {am/My papers},
  owner     = {andrius},
  timestamp = {2016.12.27},
  creationdate = {2016-12-27T00:00:00},
}

@Presentation{Mounet2015,
  author      = {Nicolas Mounet and Philippe Schwaller and Giovanni Pizzi and Andrea Cepellotti and Marco Gibertini and Castelli, Ivano Eligio and Andrius Merkys and Nicola Marzari},
  title       = {High-throughput prediction of two-dimensional materials},
  year        = {2015},
  file        = {:by-author/M/Mounet/2015_Mounet_poster.pdf:PDF},
  institution = {EPFL},
  owner       = {andrius},
  pages       = {poster},
  timestamp = {2015.09.18},
  creationdate = {2015-09-18T00:00:00},
}

@Article{Mount2001,
  author    = {David M. Mount and Nathan S. Netanyahu},
  journal   = {Computational Geometry},
  title     = {Efficient randomized algorithms for robust estimation of circular arcs and aligned ellipses},
  year      = {2001},
  pages     = {1--33},
  volume    = {19},
  file      = {2001_Mount_1.pdf:by-author/M/Mount/2001_Mount_1.pdf:PDF},
  groups    = {sg/Arc fitting, sg/Bioinf. Algorithms},
  keywords  = {Algorithms; Aligned Ellipse Fitting; Arc Fitting; Arrangements; Circular Arc Fitting; Computational Geometry; Mathematics; RM Estimator; Randomized Algorithms; Range Searching; Robust Estimation; Theil-Sen Estimator},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Presentation{Mrivi2011,
  author       = {Mrivi(?)},
  title        = {Message Passing (MPI) and GPU Programming},
  year         = {2011},
  conference   = {CINECA},
  organization = {ETH Zürich},
  school       = {Advanced School of Parallel Computing},
  file         = {:by-author/M/Mrivi/2011_Mrivi_slides.pdf:PDF},
  month        = {oct},
  owner        = {saulius},
  pages        = {slides},
  timestamp = {2013.07.02},
  creationdate = {2013-07-02T00:00:00},
}

@Article{Mroz2007,
  author     = {Mroz, Pawel and Pawlak, Anna and Satti, Minahil and Lee, Haeryeon and Wharton, Tim and Gali, Hariprasad and Sarna, Tadeusz and Hamblin, Michael R.},
  journal    = {Free Radical Biology and Medicine},
  title      = {Functionalized fullerenes mediate photodynamic killing of cancer cells: type {I} versus type {II} photochemical mechanism},
  year       = {2007},
  issn       = {0891-5849},
  pages      = {711--719},
  volume     = {43},
  abstract   = {Photodynamic therapy (PDT) employs the combination of nontoxic photosensitizers (PS) and harmless visible light to generate reactive oxygen species (ROS) and kill cells. Most clinically studied PS are based on the tetrapyrrole structure of porphyrins, chlorines, and related molecules, but new nontetrapyrrole PS are being sought. Fullerenes are soccer-ball shaped molecules composed of 60 or 70 carbon atoms and have attracted interest in connection with the search for biomedical applications of nanotechnology. Fullerenes are biologically inert unless derivatized with functional groups, whereupon they become soluble and can act as PS. We have compared the photodynamic activity of six functionalized fullerenes with 1, 2, or 3 hydrophilic or 1, 2, or 3 cationic groups. The octanol–water partition coefficients were determined and the relative contributions of Type I photochemistry (photogeneration of superoxide in the presence of NADH) and Type II photochemistry (photogeneration of singlet oxygen) were studied by measurement of oxygen consumption, 1270-nm luminescence and EPR spin trapping of the superoxide product. We studied three mouse cancer cell lines: (J774, LLC, and CT26) incubated for 24 h with fullerenes and illuminated with white light. The order of effectiveness as PS was inversely proportional to the degree of substitution of the fullerene nucleus for both the neutral and the cationic series. The monopyrrolidinium fullerene was the most active PS against all cell lines and induced apoptosis 4–6 h after illumination. It produced diffuse intracellular fluorescence when dichlorodihydrofluorescein was added as an ROS probe, suggesting a Type I mechanism for phototoxicity. We conclude that certain functionalized fullerenes have potential as novel PDT agents and phototoxicity may be mediated both by superoxide and by singlet oxygen.},
  doi        = {10.1016/j.freeradbiomed.2007.05.005},
  file       = {ScienceDirect Full Text PDF:by-author/M/Mroz/2007_Mroz_711.pdf:application/pdf;ScienceDirect Snapshot:by-author/M/Mroz/2007_Mroz_711.html:text/html},
  keywords   = {Apoptosis; Nanotechnology; Octanol-water Partition Coefficient; Photochemical Mechanism; Phototoxicity; Singlet Oxygen; Structure-function Relationship; Superoxide},
  owner      = {saulius},
  shorttitle = {Functionalized fullerenes mediate photodynamic killing of cancer cells},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url        = {http://www.sciencedirect.com/science/article/pii/S0891584907003218},
  urldate    = {2015-07-06},
}

@Article{Mruk2009,
  author    = {Mruk, Iwona and Blumenthal, Robert M.},
  journal   = {Nucleic acids research},
  title     = {Tuning the relative affinities for activating and repressing operators of a temporally regulated restriction-modification system.},
  year      = {2009},
  pages     = {983--98},
  volume    = {37},
  abstract  = {Most type II restriction-modification (R-M) systems produce separate endonuclease (REase) and methyltransferase (MTase) proteins. After R-M genes enter a new cell, MTase activity must appear before REase or the host chromosome will be cleaved. Temporal control of these genes thus has life-or-death consequences. PvuII and some other R-M systems delay endonuclease expression by cotranscribing the REase gene with the upstream gene for an autogenous activator/repressor (C protein). C.PvuII was previously shown to have low levels early, but positive feedback later boosts transcription of the C and REase genes. The MTase is expressed without delay, and protects the host DNA. C.PvuII binds to two sites upstream of its gene: O(L), associated with activation, and O(R), associated with repression. Even when symmetry elements of each operator are made identical, C.PvuII binds preferentially to O(L). In this study, the intra-operator spacers are shown to modulate relative C.PvuII affinity. In light of a recently reported C.Esp1396I-DNA co-crystal structure, in vitro and in vivo effects of altering O(L) and O(R) spacers were determined. The results suggest that the GACTnnnAGTC consensus is the primary determinant of C.PvuII binding affinity, with intra-operator spacers playing a fine-tuning role that affects mobility of this R-M system.},
  doi       = {10.1093/nar/gkn1010},
  file      = {:by-author/M/Mruk/2009_Mruk_983.pdf:PDF},
  keywords  = {TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Muchmore1999,
  author    = {Muchmore, S W},
  journal   = {Acta crystallographica. Section D, Biological crystallography},
  title     = {Experiences with CCD detectors on a home X-ray source.},
  year      = {1999},
  pages     = {1669--771},
  volume    = {55},
  file      = {1999_Muchmore_1669.pdf:by-author/M/Muchmore/1999_Muchmore_1669.pdf:PDF},
  keywords  = {Detectors; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Mucke2003,
  author    = {Mucke, Merlind and Kruger, Detlev H. and Reuter, Monika},
  journal   = {Nucleic acids research},
  title     = {Diversity of type II restriction endonucleases that require two DNA recognition sites.},
  year      = {2003},
  pages     = {6079--84},
  volume    = {31},
  abstract  = {Orthodox Type IIP restriction endonucleases, which are commonly used in molecular biological work, recognize a single palindromic DNA recognition sequence and cleave within or near this sequence. Several new studies have reported on structural and biochemical peculiarities of restriction endonucleases that differ from the orthodox in that they require two copies of a particular DNA recognition sequence to cleave the DNA. These two sites requiring restriction endonucleases belong to different subtypes of Type II restriction endonucleases, namely Types IIE, IIF and IIS. We compare enzymes of these three types with regard to their DNA recognition and cleavage properties. The simultaneous recognition of two identical DNA sites by these restriction endonucleases ensures that single unmethylated recognition sites do not lead to chromosomal DNA cleavage, and might reflect evolutionary connections to other DNA processing proteins that specifically function with two sites.},
  file      = {:by-author/M/Mucke/2003_Mucke_6079.pdf:PDF},
  keywords  = {TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Mucke2001,
  author    = {Mücke, M. and Reich, S. and Möncke-Buchner, E. and Reuter, M. and Krüger, D. H.},
  journal   = {Journal of molecular biology},
  title     = {DNA cleavage by type III restriction-modification enzyme EcoP15I is independent of spacer distance between two head to head oriented recognition sites.},
  year      = {2001},
  pages     = {687--98},
  volume    = {312},
  abstract  = {The type III restriction-modification enzyme EcoP15I requires the interaction of two unmethylated, inversely oriented recognition sites 5'-CAGCAG in head to head configuration to allow an efficient DNA cleavage. It has been hypothesized that two convergent DNA-translocating enzyme-substrate complexes interact to form the active cleavage complex and that translocation is driven by ATP hydrolysis. Using a half-automated, fluorescence-based detection method, we investigated how the distance between two inversely oriented recognition sites affects DNA cleavage efficiency. We determined that EcoP15I cleaves DNA efficiently even for two adjacent head to head or tail to tail oriented target sites. Hence, DNA translocation appears not to be required for initiating DNA cleavage in these cases. Furthermore, we report here that EcoP15I is able to cleave single-site substrates. When we analyzed the interaction of EcoP15I with DNA substrates containing adjacent target sites in the presence of non-hydrolyzable ATP analogues, we found that cleavage depended on the hydrolysis of ATP. Moreover, we show that cleavage occurs at only one of the two possible cleavage positions of an interacting pair of target sequences. When EcoP15I bound to a DNA substrate containing one recognition site in the absence of ATP, we observed a 36 nucleotide DNaseI-footprint that is asymmetric on both strands. All of our footprinting experiments showed that the enzyme did not cover the region around the cleavage site. Analyzing a DNA fragment with two head to head oriented recognition sites, EcoP15I protected 27-33 nucleotides around the recognition sequence, including an additional region of 26 bp between both cleavage sites. For all DNA substrates examined, the presence of ATP caused altered footprinting patterns. We assume that the altered patterns are most likely due to a conformational change of the enzyme. Overall, our data further refine the tracking-collision model for type III restriction enzymes.},
  file      = {:by-author/M/Mücke/2001_Mucke_687.pdf:PDF},
  keywords  = {TypeIII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Muckenheim1986,
  author    = {Muckenheim, W. and G. Ludwig and C. Dewdney and P. R. Holland and A. Kyprianidis and J. P. Vigier and N. Cufaro Petroni and M. S. Bartlett and E. T. Jaynes},
  journal   = {Physiscs Reports},
  title     = {A Review of Extended Probability},
  year      = {1986},
  pages     = {337--401},
  volume    = {133},
  abstract  = {Some results emerging from the formalism of quantum theory seem to idicate probabilities outside the conventional range between 0 and 1. This article draws attention to arguments in favour of extended probabilities, reviews some approaches to a formal account and interpretation, and presents a collection of statements of distinguished scientists about this strange topic.},
  file      = {1986_Muckenheim_337.pdf:by-author/M/Muckenheim/1986_Muckenheim_337.pdf:PDF},
  groups    = {sg/Bayesian},
  owner     = {saulius},
  timestamp = {2012.10.05},
  creationdate = {2012-10-05T00:00:00},
  url       = {http://bayes.wustl.edu/etj/articles/review.extended.prob.pdf},
}

@Manual{Mueller.odt2013,
  title     = {Automatic Memory Management in newLISP},
  author    = {Lutz Mueller},
  month     = {Nov},
  year      = {2013},
  abstract  = {ORO (One Reference Only) automatic memory management developed for newLISP is a fast and resources saving alternative to classic garbage collection algorithms in dynamic, interactive programming languages. This article explains how ORO memory management works},
  file      = {:by-author/M/Mueller/2013_Mueller.odt:PDF},
  groups    = {sg/Garbage collectors},
  keywords  = {LISP; Memory Management; NewLISP; ORO; One Reference Only; Programming Languages},
  owner     = {saulius},
  timestamp = {2014.03.23},
  creationdate = {2014-03-23T00:00:00},
}

@Webpage{Mueller2011,
  author    = {Lutz Mueller},
  retrieved = {2013-03-02},
  title     = {Automatic Memory Management in newLISPAutomatic Memory Management in newLISP},
  url       = {http://www.newlisp.org/MemoryManagement.html},
  year      = {2011},
  abstract  = {newLISP and any other interactive language system will constantly generate new memory objects during expression evaluation. The new memory objects are intermediate evaluation results, reassigned memory objects, or memory objects whose content was changed. If newLISP did not delete some of the objects created, it would eventually run out of available memory.},
  file      = {2011_Mueller.odt:by-author/M/Mueller/2011_Mueller.odt:OpenDocument text},
  owner     = {saulius},
  timestamp = {2013.06.03},
  creationdate = {2013-06-03T00:00:00},
}

@Article{Mueller-Dieckmann2004,
  author    = {Mueller-Dieckmann, Christoph and Polentarutti, Maurizio and Djinovic Carugo, Kristina and Panjikar, Santosh and Tucker, Paul A. and Weiss, Manfred S.},
  journal   = {Acta Crystallographica Section D},
  title     = {On the routine use of soft X-rays in macromolecular crystallography. Part II. Data-collection wavelength and scaling models},
  year      = {2004},
  pages     = {28--38},
  volume    = {60},
  doi       = {10.1107/S0907444903020833},
  file      = {dz0018.pdf:by-author/M/Mueller-Dieckmann/2004_Mueller-Dieckmann_28.pdf:PDF;Supplementary material:by-author/M/Mueller-Dieckmann/2004_Mueller-Dieckmann_28.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444903020833},
}

@Article{Mueser2010,
  author    = {Mueser, Timothy C. and Hinerman, Jennifer M. and Devos, Juliette M. and Boyer, Ryan A. and Williams, Kandace J.},
  journal   = {Virology journal},
  title     = {Structural analysis of bacteriophage T4 DNA replication: a review in the Virology Journal series on bacteriophage T4 and its relatives.},
  year      = {2010},
  pages     = {359},
  volume    = {7},
  abstract  = {The bacteriophage T4 encodes 10 proteins, known collectively as the replisome, that are responsible for the replication of the phage genome. The replisomal proteins can be subdivided into three activities; the replicase, responsible for duplicating DNA, the primosomal proteins, responsible for unwinding and Okazaki fragment initiation, and the Okazaki repair proteins. The replicase includes the gp43 DNA polymerase, the gp45 processivity clamp, the gp44/62 clamp loader complex, and the gp32 single-stranded DNA binding protein. The primosomal proteins include the gp41 hexameric helicase, the gp61 primase, and the gp59 helicase loading protein. The RNaseH, a 5' to 3' exonuclease and T4 DNA ligase comprise the activities necessary for Okazaki repair. The T4 provides a model system for DNA replication. As a consequence, significant effort has been put forth to solve the crystallographic structures of these replisomal proteins. In this review, we discuss the structures that are available and provide comparison to related proteins when the T4 structures are unavailable. Three of the ten full-length T4 replisomal proteins have been determined; the gp59 helicase loading protein, the RNase H, and the gp45 processivity clamp. The core of T4 gp32 and two proteins from the T4 related phage RB69, the gp43 polymerase and the gp45 clamp are also solved. The T4 gp44/62 clamp loader has not been crystallized but a comparison to the E. coli gamma complex is provided. The structures of T4 gp41 helicase, gp61 primase, and T4 DNA ligase are unknown, structures from bacteriophage T7 proteins are discussed instead. To better understand the functionality of T4 DNA replication, in depth structural analysis will require complexes between proteins and DNA substrates. A DNA primer template bound by gp43 polymerase, a fork DNA substrate bound by RNase H, gp43 polymerase bound to gp32 protein, and RNase H bound to gp32 have been crystallographically determined. The preparation and crystallization of complexes is a significant challenge. We discuss alternate approaches, such as small angle X-ray and neutron scattering to generate molecular envelopes for modeling macromolecular assemblies.},
  file      = {:by-author/M/Mueser/2010_Mueser_359.pdf:PDF},
  keywords  = {{gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Mueser2000,
  author    = {Mueser, T. C. and Jones, C. E. and Nossal, N. G. and Hyde, C. C.},
  journal   = {Journal of molecular biology},
  title     = {Bacteriophage T4 gene 59 helicase assembly protein binds replication fork DNA. The 1.45 A resolution crystal structure reveals a novel alpha-helical two-domain fold.},
  year      = {2000},
  pages     = {597--612},
  volume    = {296},
  abstract  = {The bacteriophage T4 gene 59 helicase assembly protein is required for recombination-dependent DNA replication, which is the predominant mode of DNA replication in the late stage of T4 infection. T4 gene 59 helicase assembly protein accelerates the loading of the T4 gene 41 helicase during DNA synthesis by the T4 replication system in vitro. T4 gene 59 helicase assembly protein binds to both T4 gene 41 helicase and T4 gene 32 single-stranded DNA binding protein, and to single and double-stranded DNA. We show here that T4 gene 59 helicase assembly protein binds most tightly to fork DNA substrates, with either single or almost entirely double-stranded arms. Our studies suggest that the helicase assembly protein is responsible for loading T4 gene 41 helicase specifically at replication forks, and that its binding sites for each arm must hold more than six, but not more than 12 nucleotides. The 1.45 A resolution crystal structure of the full-length 217-residue monomeric T4 gene 59 helicase assembly protein reveals a novel alpha-helical bundle fold with two domains of similar size. Surface residues are predominantly basic (pI 9.37) with clusters of acidic residues but exposed hydrophobic residues suggest sites for potential contact with DNA and with other protein molecules. The N-terminal domain has structural similarity to the double-stranded DNA binding domain of rat HMG1A. We propose a speculative model of how the T4 gene 59 helicase assembly protein might bind to fork DNA based on the similarity to HMG1, the location of the basic and hydrophobic regions, and the site size of the fork arms needed for tight fork DNA binding. The fork-binding model suggests putative binding sites for the T4 gene 32 single-stranded DNA binding protein and for the hexameric T4 gene 41 helicase assembly.},
  file      = {:by-author/M/Mueser/2000_Mueser_597.pdf:PDF},
  keywords  = {{gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Mugundhan2011,
  author    = {Mugundhan},
  journal   = {International Journal of Communication Engineering Applications},
  title     = {Ternary Logic Based Quantum/Reversible Shift Registers And Serial Adder Design},
  year      = {2011},
  pages     = {131--136},
  volume    = {2},
  abstract  = {The need for the hour for VLSI based circuits are power saving and a higher integration density. This can be achieved by using the reversible logic gates combined with Ternary or three valued logic gates. This paper provides an account of quantum ternary reversible flip flops and a serial adder implemented using the shift register thus synthesized.},
  file      = {:by-author/M/Mugundhan/2011_Mugundhan_131.pdf:PDF},
  keywords  = {Computer Science (CS); Logic Circuits; Ternary},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Mulepati2012,
  author    = {Mulepati, Sabin and Orr, Amberly and Bailey, Scott},
  journal   = {Journal of Biological Chemistry},
  title     = {Crystal Structure of the Largest Subunit of a Bacterial {RNA}-guided Immune Complex and Its Role in {DNA} Target Binding},
  year      = {2012},
  pages     = {22445--22449},
  volume    = {287},
  abstract  = {Prokaryotes make use of small RNAs encoded by CRISPR (clustered regularly interspaced short palindromic repeat) loci to provide immunity against bacteriophage or plasmid invasion. In Escherichia coli, the CRISPR-associated complex for antiviral defense (Cascade) utilizes these RNAs to target foreign DNA for destruction. CasA, the largest subunit of Cascade, is essential for its function. Here we report the crystal structure of Thermus thermophilus CasA. The structure is composed of two domains that are arranged in a chair-like conformation with a novel fold forming the larger N-terminal domain. Docking of the crystal structure into cryo-electron microscopy maps reveals two loops in CasA that likely have important functions in DNA target binding. Finally, DNA binding experiments show that CasA is essential for binding of Cascade to DNA target.},
  doi       = {10.1074/jbc.C112.379503},
  file      = {2012_Mulepati_22445.pdf:by-author/M/Mulepati/2012_Mulepati_22445.pdf:PDF},
  groups    = {sg/CRISPR-Cas},
  keywords  = {CRISPR; CasA; Cascade; Crystal Structure},
  owner     = {em},
  timestamp = {2013.01.07},
  creationdate = {2013-01-07T00:00:00},
}

@Manual{Mueller2013,
  title        = {Refinement of Disorder with SHELXL},
  author       = {Peter Müller},
  month        = {January},
  organization = {X-Ray Diffraction Facility, MIT Department of Chemistry},
  year         = {2013},
  file         = {2013_Müller_tutorial.pdf:by-author/M/Müller/2013_Müller_tutorial.pdf:PDF},
  keywords     = {Disorder; Refinement; SHELX; X-ray Crystallography},
  owner        = {saulius},
  timestamp = {2016.12.22},
  creationdate = {2016-12-22T00:00:00},
  url          = {http://shelx.uni-ac.gwdg.de/SHELX/pm_disorder.pdf},
}

@Manuscript{Muller-Langer2013,
  author    = {Frank Müller-Langer and Marc Scheufen},
  title     = {Academic Publishing and Open Access},
  year      = {2013},
  keywords  = {Open Access Publishing},
  url       = {http://ssrn.com/abstract=2198400},
  file      = {:by-author/M/Müller-Langer/2013_Müller-Langer.pdf:PDF},
  owner     = {saulius},
  timestamp = {2013.10.18},
  creationdate = {2013-10-18T00:00:00},
}

@Article{Muller-Langer2011,
  author    = {Frank Müller-Langer and Marc Scheufen},
  journal   = {Review of Economic Research on Copyright Issues},
  title     = {The Google Book Search Settlement: A Law And Economics Analysis},
  year      = {2011},
  pages     = {7--50},
  volume    = {8},
  abstract  = {Beginning in December 2004 Google has pursued a new project to create a book search engine (Google Book Search). The project has released a storm of controversy around the globe. While the supporters of Google Book Search conceive the project as a first reasonable step towards unlimited access to knowledge in the information age, its op- ponents fear profound negative effects due to an erosion of copyright law. Our law and economics analysis of the Book Search Project sug- gests that — from a copyright perspective — the proposed settlement may be beneficial to right holders, consumers, and Google. For instance, it may provide a solution to the still unsolved dilemma of orphan works. From a competition policy perspective, we stress the important aspect that Google’s pricing algorithm for orphan and unclaimed works effec- tively replicates a competitive Nash-Bertrand market outcome under post-settlement, third-party oversight.},
  file      = {:by-author/M/Müller-Langer/2011_Müller-Langer_7.pdf:PDF},
  keywords  = {Open Access Publishing},
  owner     = {saulius},
  timestamp = {2013.10.18},
  creationdate = {2013-10-18T00:00:00},
  url       = {http://papers.ssrn.com/sol3/papers.cfm?abstract_id=1775678},
}

@Article{Mulligan2008,
  author    = {Mulligan, Elizabeth A. and Dunn, John J.},
  journal   = {Protein Expr Purif.},
  title     = {Cloning, purification and initial characterization of {E}. coli {McrA}, a putative 5-methylcytosine-specific nuclease},
  year      = {2008},
  pages     = {98–103},
  volume    = {62},
  abstract  = {Expression strains of Escherichia coli BL21(DE3) overproducing the E. coli m5C McrA restriction protein were produced by cloning the mcrA coding sequence behind a T7 promoter. The recombinant mcrA minus BL21 (DE3) host produces active McrA as evidenced by its acquired ability to selectively restrict the growth of T7 phage containing DNA methylated in vitro by HpaII methylase. The mcrA coding region contains several non-optimal E. coli triplets. Addition of the pACYC-RIL tRNA encoding plasmid to the BL21(DE3) host increased the yield of recombinant McrA (rMcrA) upon induction about 5- to 10-fold. McrA protein expressed at 37 °C is insoluble but a significant fraction is recovered as soluble protein after autoinduction at 20 °C. rMcrA protein, which is predicted to contain a Cys4-Zn2+ finger and a catalytically important histidine triad in its putative nuclease domain, binds to several metal chelate resins without addition of a poly-histidine affinity tag. This feature was used to develop an efficient protocol for the rapid purification of nearly homogeneous rMcrA. The native protein is a dimer with a high α-helical content as measured by circular dichroism analysis. Under all conditions tested purified rMcrA does not have measurable nuclease activity on HpaII methylated (Cm5CGG) DNA, although the purified protein does specifically bind HpaII methylated DNA. These results have implications for understanding the in vivo activity of McrA in “restricting” m5C-containing DNA and suggest that rMcrA may have utility as a reagent for affinity purification of DNA fragments containing m5C residues.},
  doi       = {10.1016/j.pep.2008.06.016},
  file      = {:by-author/M/Mulligan/2008_Mulligan_98.pdf:PDF},
  keywords  = {McrA; Restriction Endonucleases (REases); TypeIV},
  owner     = {em},
  timestamp = {2013.01.17},
  creationdate = {2013-01-17T00:00:00},
}

@Article{Mulligan2010,
  author    = {Mulligan, Elizabeth A. and Hatchwell, Eli and McCorkle, Sean R. and Dumnn, John R.},
  journal   = {Nucleic Acids Research},
  title     = {Differential binding of {E}scherichia coli {McrA} protein to {DNA} sequences that contain the dinucleotide {m5CpG}},
  year      = {2010},
  pages     = {1997–2005},
  volume    = {38},
  abstract  = {The Escherichia coli McrA protein, a putative C5-methylcytosine/C5-hydroxyl methylcytosine-specific nuclease, binds DNA with symmetrically methylated HpaII sequences (Cm5CGG), but its precise recognition sequence remains undefined. To determine McrA’s binding specificity, we cloned and expressed recombinant McrA with a C-terminal StrepII tag (rMcrA-S) to facilitate protein purification and affinity capture of human DNA fragments with m5C residues. Sequence analysis of a subset of these fragments and electrophoretic mobility shift assays with model methylated and unmethylated oligonucleotides suggest that N(Y ` R) m5CGR is the canonical binding site for rMcrA-S. In addition to binding HpaII-methylated double-stranded DNA, rMcrA-S binds DNA containing a single, hemi-methylated HpaII site; however, it does not bind if A, C, T or U is placed across from the m5C residue, but does if I is opposite the m5C. These results provide the first systematic analysis of McrA’s in vitro binding specificity.},
  doi       = {10.1093/nar/gkp1120},
  file      = {:by-author/M/Mulligan/2010_Mulligan_1997.pdf:PDF},
  owner     = {em},
  timestamp = {2013.01.17},
  creationdate = {2013-01-17T00:00:00},
}

@Article{Mumenthaler1995,
  author    = {Mumenthaler, C. and Braun, W.},
  journal   = {Protein science : a publication of the Protein Society},
  title     = {Predicting the helix packing of globular proteins by self-correcting distance geometry.},
  year      = {1995},
  pages     = {863--71},
  volume    = {4},
  abstract  = {A new self-correcting distance geometry method for predicting the three-dimensional structure of small globular proteins was assessed with a test set of 8 helical proteins. With the knowledge of the amino acid sequence and the helical segments, our completely automated method calculated the correct backbone topology of six proteins. The accuracy of the predicted structures ranged from 2.3 A to 3.1 A for the helical segments compared to the experimentally determined structures. For two proteins, the predicted constraints were not restrictive enough to yield a conclusive prediction. The method can be applied to all small globular proteins, provided the secondary structure is known from NMR analysis or can be predicted with high reliability.},
  file      = {:by-author/M/Mumenthaler/1995_Mumenthaler_863.pdf:PDF},
  keywords  = {Distance Geometry; Protein Bioinformatics},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Munkres1957,
  author    = {James Munkres},
  journal   = {Journal of the Society for Industrial and Applied Mathematics},
  title     = {Algorithms for the assigment and transportation problems},
  year      = {1957},
  pages     = {32--38},
  volume    = {4},
  file      = {:by-author/M/Munkres/1957_Munkres_32.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@Article{Murata1994,
  author    = {Noboru Murata and Shuji Yoshizawa and Shun-ichi Amari},
  journal   = {IEEE Transactions On Neural Networks},
  title     = {Network Information Criterion - Determining the Number of Hidden Units for an Artificial Neural Network Model},
  year      = {1994},
  pages     = {865--872},
  volume    = {5},
  abstract  = {The problem of model selection, or determination of the number of hidden units, can be approached statistically, by generalizing Akaike's information criterion (AIC) to be applicable to unfaithful (i.e., unrealizable) models with general loss criteria including regularization terms. The relation between the training error and the generalization error is studied in terms of the number of the training examples and the complexity of a network which reduces to the number of parameters in the ordinary statistical theory of AIC. This relation leads to a new network information criterion which is useful for selecting the optimal network model based on a given training set},
  file      = {:by-author/M/Murata/1994_Murata_865.pdf:PDF},
  owner     = {andrius},
  timestamp = {2012.11.25},
  creationdate = {2012-11-25T00:00:00},
}

@Article{Murayama2007,
  author    = {Murayama},
  title     = {Notes on Clifford Algebra and Spin(N) Representations},
  year      = {2007},
  file      = {:by-author/M/Murayama/2007_Murayama.pdf:PDF},
  keywords  = {Clifford Algebra; Mathematics},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Murch2013,
  author    = {Murch, K. W. and Weber, S. J. and Macklin, C. and Siddiqi, I.},
  journal   = {Nature},
  title     = {Observing single quantum trajectories of a superconducting quantum bit},
  year      = {2013},
  issn      = {0028-0836},
  pages     = {211--214},
  volume    = {502},
  abstract  = {The length of time that a quantum system can exist in a superposition state is determined by how strongly it interacts with its environment. This interaction entangles the quantum state with the inherent fluctuations of the environment. If these fluctuations are not measured, the environment can be viewed as a source of noise, causing random evolution of the quantum system from an initially pure state into a statistical mixture—a process known as decoherence. However, by accurately measuring the environment in real time, the quantum system can be maintained in a pure state and its time evolution described by a ‘quantum trajectory’1, 2 determined by the measurement outcome. Here we use weak measurements to monitor a microwave cavity containing a superconducting quantum bit (qubit), and track the individual quantum trajectories3 of the system. In this set-up, the environment is dominated by the fluctuations of a single electromagnetic mode of the cavity. Using a near-quantum-limited parametric amplifier4, 5, we selectively measure either the phase or the amplitude of the cavity field, and thereby confine trajectories to either the equator or a meridian of the Bloch sphere. We perform quantum state tomography at discrete times along the trajectory to verify that we have faithfully tracked the state of the quantum system as it diffuses on the surface of the Bloch sphere. Our results demonstrate that decoherence can be mitigated by environmental monitoring, and validate the foundation of quantum feedback approaches based on Bayesian statistics6, 7, 8. Moreover, our experiments suggest a new means of implementing ‘quantum steering’9—the harnessing of action at a distance to manipulate quantum states through measurement.},
  doi       = {10.1038/nature12539},
  file      = {2013_Murch_211.pdf:by-author/M/Murch/2013_Murch_211.pdf:PDF},
  groups    = {sg/Bayesian},
  keywords  = {Quantum Mechanics (QM); Wavefunction Collapse},
  owner     = {saulius},
  publisher = {Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},
  timestamp = {2013.10.18},
  creationdate = {2013-10-18T00:00:00},
  url       = {http://dx.doi.org/10.1038/nature12539},
}

@Article{Murray2000,
  author    = {Murray, N. E.},
  journal   = {Microbiology and molecular biology reviews : MMBR},
  title     = {Type I restriction systems: sophisticated molecular machines (a legacy of Bertani and Weigle).},
  year      = {2000},
  pages     = {412--34},
  volume    = {64},
  abstract  = {Restriction enzymes are well known as reagents widely used by molecular biologists for genetic manipulation and analysis, but these reagents represent only one class (type II) of a wider range of enzymes that recognize specific nucleotide sequences in DNA molecules and detect the provenance of the DNA on the basis of specific modifications to their target sequence. Type I restriction and modification (R-M) systems are complex; a single multifunctional enzyme can respond to the modification state of its target sequence with the alternative activities of modification or restriction. In the absence of DNA modification, a type I R-M enzyme behaves like a molecular motor, translocating vast stretches of DNA towards itself before eventually breaking the DNA molecule. These sophisticated enzymes are the focus of this review, which will emphasize those aspects that give insights into more general problems of molecular and microbial biology. Current molecular experiments explore target recognition, intramolecular communication, and enzyme activities, including DNA translocation. Type I R-M systems are notable for their ability to evolve new specificities, even in laboratory cultures. This observation raises the important question of how bacteria protect their chromosomes from destruction by newly acquired restriction specifities. Recent experiments demonstrate proteolytic mechanisms by which cells avoid DNA breakage by a type I R-M system whenever their chromosomal DNA acquires unmodified target sequences. Finally, the review will reflect the present impact of genomic sequences on a field that has previously derived information almost exclusively from the analysis of bacteria commonly studied in the laboratory.},
  file      = {:by-author/M/Murray/2000_Murray_412.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Murray2002,
  author    = {Murray, Richard},
  journal   = {Veterinary journal (London, England : 1997)},
  title     = {A new initiative in lameness research - the Cochrane approach.},
  year      = {2002},
  pages     = {3--4},
  volume    = {164},
  file      = {:by-author/M/Murray/2002_Murray_3.pdf:PDF},
  keywords  = {Antirestriction},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@MastersThesis{Murray2003,
  author    = {Scott H. Murray},
  school    = {Department of mathematics, Australian National University},
  title     = {The {S}chreier-{S}ims algorithm},
  year      = {2003},
  type      = {BSc thesis},
  abstract  = {A base and strong generating set provides an effective computer representation for a permutation group. This representation helps us to calculate the group order, list the group elements, generate random elements, test for group membership and store group elements efficiently. Knowledge of a base and strong generating set essentially reduces these tasks to the calculation of certain orbits. Given an arbitrary generating set for a permutation group, the Schreier-Sims algorithm calculates a base and strong generating set. We describe several variations of this method, including the Todd-Coxeter, random and extending Schreier-Sims algorithms. Matrix groups over finite fields can also be represented by a base and strong generating set, by considering their action on the underlying vector space. A practical implementation of the random Schreier-Sims algorithm for matrix groups is described. We investigate the effectiveness of this implementation for computing with soluble groups, almost simple groups, simple groups and related constructions. We consider in detail several aspects of the implementation of the random Schreier-Sims algorithm. In particular, we examine the generation of random group elements and choice of “stopping condition”. The main difficulty in applying this algorithm to matrix groups is that the orbits which must be calculated are often very large. Shorter orbits can be found by extending the point set to include certain subspaces of the underlying vector space. We demonstrate that even greater improvements in the performance of the random Schreier-Sims algorithm can be achieved by using the orbits of eigenvectors and eigenspaces of the generators of the group.},
  file      = {:by-author/M/Murray/2003_Murray_bscthesis.pdf:PDF},
  owner     = {andrius},
  timestamp = {2013.04.15},
  creationdate = {2013-04-15T00:00:00},
}

@Article{Murray-Rust1998,
  author    = {Murray-Rust, Peter},
  journal   = {Acta Crystallographica Section D},
  title     = {The Globalization of Crystallographic Knowledge},
  year      = {1998},
  pages     = {1065--1070},
  volume    = {54},
  doi       = {10.1107/S0907444998009366},
  file      = {1998_Murray-Rust_1065.pdf:by-author/M/Murray-Rust/1998_Murray-Rust_1065.pdf:PDF},
  keywords  = {Data Access Policy; Data Management; Databases; Scientific Publication},
  owner     = {saulius},
  timestamp = {2014.06.24},
  creationdate = {2014-06-24T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444998009366},
}

@Article{Murray-Rust2011b,
  author    = {Murray-Rust, Peter and Adams, Sam and Downing, Jim and Townsend, Joe and Zhang, Yong},
  journal   = {Journal of Cheminformatics},
  title     = {The semantic architecture of the {W}orld-{W}ide {M}olecular {M}atrix ({WWMM})},
  year      = {2011},
  issn      = {1758-2946},
  pages     = {42},
  volume    = {3},
  abstract  = {The World-Wide Molecular Matrix (WWMM) is a ten year project to create a peer-to-peer (P2P) system for the publication and collection of chemical objects, including over 250, 000 molecules. It has now been instantiated in a number of repositories which include data encoded in Chemical Markup Language (CML) and linked by URIs and RDF. The technical specification and implementation is now complete. We discuss the types of architecture required to implement nodes in the WWMM and consider the social issues involved in adoption.},
  doi       = {10.1186/1758-2946-3-42},
  file      = {2011_Murray-Rust_42.pdf:by-author/M/Murray-Rust/2011_Murray-Rust_42.pdf:PDF},
  keywords  = {CML; Chemoinformatics; Computational Chemistry; Wwmm},
  owner     = {saulius},
  pubmedid  = {21999475},
  timestamp = {2014.07.17},
  creationdate = {2014-07-17T00:00:00},
  url       = {http://www.jcheminf.com/content/3/1/42},
}

@Article{Murray-Rust2005,
  author    = {Peter Murray-Rust and John B. O. Mitchell and Henry S. Rzepa},
  journal   = {BMC Bioinformatics},
  title     = {Communication and re-use of chemical information in bioscience},
  year      = {2005},
  issn      = {1471-2105},
  pages     = {180},
  volume    = {6},
  abstract  = {The current methods of publishing chemical information in bioscience articles are analysed. Using 3 papers as use-cases, it is shown that conventional methods using human procedures, including cut-and-paste are time-consuming and introduce errors. The meaning of chemical terms and the identity of compounds is often ambiguous. valuable experimental data such as spectra and computational results are almost always omitted. We describe an Open XML architecture at proof-of-concept which addresses these concerns. Compounds are identified through explicit connection tables or links to persistent Open resources such as PubChem. It is argued that if publishers adopt these tools and protocols, then the quality and quantity of chemical information available to bioscientists will increase and the authors, publishers and readers will find the process cost-effective.},
  doi       = {10.1186/1471-2105-6-180},
  file      = {2005_Murray-Rust_6:by-author/M/Murray-Rust/2005_Murray-Rust_6\:180.pdf:PDF},
  keywords  = {Chemoinformatics; Data Access Policy; Data Management},
  owner     = {saulius},
  pubmedid  = {16026614},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://www.biomedcentral.com/1471-2105/6/180},
}

@Article{Murray-Rust2005a,
  author    = {Peter Murray-Rust and John B. O. Mitchell and Henry S. Rzepa},
  journal   = {BMC Bioinformatics},
  title     = {Chemistry in Bioinformatics},
  year      = {2005},
  issn      = {1471-2105},
  pages     = {141},
  volume    = {6},
  abstract  = {Chemical information is now seen as critical for most areas of life sciences. But unlike Bioinformatics, where data is openly available and freely re-usable, most chemical information is closed and cannot be re-distributed without permission. This has led to a failure to adopt modern informatics and software techniques and therefore paucity of chemistry in bioinformatics. New technology, however, offers the hope of making chemical data (compounds and properties) free during the authoring process. We argue that the technology is already available; we require a collective agreement to enhance publication protocols.},
  doi       = {10.1186/1471-2105-6-141},
  file      = {2005_Murray-Rust_6:by-author/M/Murray-Rust/2005_Murray-Rust_6\:141.pdf:PDF},
  keywords  = {Chemoinformatics},
  owner     = {saulius},
  pubmedid  = {15941476},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Murray-Rust1985,
  author    = {P. Murray-Rust and J. Raftery},
  journal   = {Journal of Molecular Graphics},
  title     = {Computer analysis of molecular geometry: Part VI: Classification of differences in conformation},
  year      = {1985},
  issn      = {0263-7855},
  pages     = {50 - 59},
  volume    = {3},
  abstract  = {Techniques are outlined for the representation, classification and quantification of the differences of geometry in a set of molecules. For each molecule the atomic positions are defined by internal Cartesian coordinates determined either by least-squares fits to a common reference molecule or from the axes of inertia of each molecule. These Cartesian coordinates can be analysed by multivariate cluster and factor analytical techniques to classify the molecules into groups and to analyse the variation of geometry within the groups. The methods are applied to a set of 48 tripeptide fragments forming β-loops. It is shown that the type \{II\} turns form a class on their own, but that types I and \{III\} turns have very similar geometry and that their populations are not distinct. Within each group there is considerable variation in geometry.},
  doi       = {10.1016/0263-7855(85)80003-5},
  file      = {1985_Murray-Rust_50.pdf:by-author/M/Murray-Rust/1985_Murray-Rust_50.pdf:PDF},
  keywords  = {Multivariate Cluster Techniques},
  owner     = {saulius},
  timestamp = {2014.01.26},
  creationdate = {2014-01-26T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/0263785585800035},
}

@Article{Murray-Rust1985a,
  author    = {P Murray-Rust and J Raftery},
  journal   = {Journal of Molecular Graphics},
  title     = {Computer analysis of molecular geometry, part VII: the identification of chemical fragments in the cambridge structural data file},
  year      = {1985},
  issn      = {0263-7855},
  pages     = {60 - 68},
  volume    = {3},
  abstract  = {The geometrical information in the Cambridge Structural Data File can be interpreted automatically to provide information about chemical bond types and atom types. Methods for using the Data File as a criterion for selecting or rejecting molecular fragments and also to identify substituents are outlined. Facilities in the program Geostat are described. Problems that can arise because of the different nature of the information in the data files and the different operation of the Connser and Geom substructure searches are outlined, and some procedures to overcome them are reported.},
  doi       = {10.1016/0263-7855(85)80004-7},
  file      = {1985_Murray-Rust_60.pdf:by-author/M/Murray-Rust/1985_Murray-Rust_60.pdf:PDF},
  keywords  = {Data Analysis},
  owner     = {saulius},
  timestamp = {2014.01.26},
  creationdate = {2014-01-26T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/0263785585800047},
}

@Article{Murray-Rust2012,
  author    = {Murray-Rust, Peter and Rzepa, Henry},
  journal   = {Journal of Cheminformatics},
  title     = {Semantic physical science},
  year      = {2012},
  issn      = {1758-2946},
  pages     = {14},
  volume    = {4},
  abstract  = {The articles in this special issue arise from a workshop and symposium held in January 2012 (Semantic Physical Science'). We invited people who shared our vision for the potential of the web to support chemical and related subjects. Other than the initial invitations, we have not exercised any control over the content of the contributed articles.},
  doi       = {10.1186/1758-2946-4-14},
  file      = {2012_Murray-Rust_14.pdf:by-author/M/Murray-Rust/2012_Murray-Rust_14.pdf:PDF},
  keywords  = {Data Management},
  owner     = {saulius},
  pubmedid  = {22856527},
  timestamp = {2013.09.15},
  creationdate = {2013-09-15T00:00:00},
  url       = {http://www.jcheminf.com/content/4/1/14},
}

@Article{Murray-Rust2011a,
  author    = {Murray-Rust, Peter and Rzepa, Henry},
  journal   = {Journal of Cheminformatics},
  title     = {{CML}: Evolution and design},
  year      = {2011},
  issn      = {1758-2946},
  pages     = {44},
  volume    = {3},
  abstract  = {A retrospective view of the design and evolution of Chemical Markup Language (CML) is presented by its original authors.},
  doi       = {10.1186/1758-2946-3-44},
  file      = {2011_Murray-Rust_44.pdf:by-author/M/Murray-Rust/2011_Murray-Rust_44.pdf:PDF},
  keywords  = {CML; Chemoinformatics; Crystallography; Data Formats; Data Management; X-ray Crystallography; XML},
  owner     = {saulius},
  pubmedid  = {21999549},
  timestamp = {2014.06.24},
  creationdate = {2014-06-24T00:00:00},
  url       = {http://www.jcheminf.com/content/3/1/44},
}

@Article{Murray-Rust2006,
  author    = {Peter Murray-Rust and Henry Rzepa},
  journal   = {Journal of Digital Information},
  title     = {The Next Big Thing: From Hypermedia to Datuments},
  year      = {2004},
  issn      = {1368-7506},
  pages     = {130},
  volume    = {5},
  abstract  = {The concept of a datument as a hyperdocument for transmitting and preserving the complete content of a piece of scientific work is introduced. Currently the scientific publishing process loses almost all of the information environment that the author creates or possesses. It is shown that datuments can record and reproduce experiments and act as a lossless way of publishing science. This is illustrated with specific examples drawn from scientific documents and molecular science, showing how a datument containing molecular coordinates can be viewed in various styles and how typical documents deriving from organic and physical chemistry and expressed in XML can be transformed using XSLT.},
  file      = {2004_Murray-Rust_130.pdf:by-author/M/Murray-Rust/2004_Murray-Rust_130.pdf:PDF},
  owner     = {saulius},
  timestamp = {2013.11.09},
  creationdate = {2013-11-09T00:00:00},
  url       = {http://journals.tdl.org/jodi/index.php/jodi/article/view/130},
}

@Article{Murray-Rust2003,
  author    = {Peter Murray-Rust and Henry S. Rzepa},
  journal   = {OCLC Systems \& Services},
  title     = {XML for scientific publishing},
  year      = {2003},
  pages     = {162--169},
  volume    = {19},
  abstract  = {This article addresses the opportunities that XML can offer to the publishing scientist and explores why there has been such a relatively slow take-up. XML can revolutionize the way that scientists publish their work, but few publishers have shown enthusiasm for it. This article also describes the development of XML-based tools and technologies as alternative methods for scholarly communication in several science fields. These methods include combined data and text (datuments), robotic validation and the combination of markup languages. The authors believe that these methods will certainly challenge the current publishing practices and transform the librarian’s role in providing e-journal services.},
  doi       = {10.1108/10650750310698784},
  file      = {2003_Murray-Rust_162.pdf:by-author/M/Murray-Rust/2003_Murray-Rust_162.pdf:PDF},
  keywords  = {CML; Crystallography; Data Formats; Data Management; X-ray Crystallography; XML},
  owner     = {saulius},
  timestamp = {2014.06.24},
  creationdate = {2014-06-24T00:00:00},
}

@Article{Murray-Rust2003a,
  author    = {Murray-Rust, Peter and Rzepa, Henry S.},
  journal   = {Journal of Chemical Information and Computer Sciences},
  title     = {Chemical Markup, XML, and the World Wide Web. 4. CML Schema},
  year      = {2003},
  pages     = {757--772},
  volume    = {43},
  abstract  = {A revision to Chemical Markup Language (CML) is presented as a XML Schema compliant form, modularized into nonchemical and chemical components. STMML contains generic concepts for numeric data and scientific units, while CMLCore retains most of the chemical functionality of the original CML 1.0 and extends it by adding handlers for chemical substances, extended bonding models and names. We propose extension via new namespaced components for chemical queries, reactions, spectra, and computational chemistry. The conformance with XML schemas allows much greater control over datatyping, document validation, and structure.},
  doi       = {10.1021/ci0256541},
  eprint    = {http://pubs.acs.org/doi/pdf/10.1021/ci0256541},
  file      = {2003_Murray-Rust_757.pdf:by-author/M/Murray-Rust/2003_Murray-Rust_757.pdf:PDF},
  keywords  = {CML; Chemoinformatics; Crystallography; Data Formats; Data Management; X-ray Crystallography; XML},
  owner     = {saulius},
  timestamp = {2014.06.24},
  creationdate = {2014-06-24T00:00:00},
  url       = {http://pubs.acs.org/doi/abs/10.1021/ci0256541},
}

@Article{Murray-Rust2002,
  author    = {Peter Murray-Rust and Henry S. Rzepa},
  journal   = {Data Science Journal},
  title     = {STMML. A markup language for scientific, technical and medical publishing},
  year      = {2002},
  pages     = {128--192},
  volume    = {1},
  doi       = {10.2481/dsj.1.128},
  file      = {2002_Murray-Rust_128.pdf:by-author/M/Murray-Rust/2002_Murray-Rust_128.pdf:PDF},
  keywords  = {CML; Chemical-markup-language (CML); Chemoinformatics; Data Formats; Data Management; Data Structures; Data Types; Dictionaries; Extensible-markup-language (XML); Extensible-stylesheet-language-transformations (XSLT); Metadata; Scientific Units; Scientific-Technical-Medical (STM); Semantic-Web; Terminology; XML; XMLSchema},
  owner     = {saulius},
  timestamp = {2014.06.24},
  creationdate = {2014-06-24T00:00:00},
}

@Article{Murray-Rust2002a,
  author    = {Peter Murray-Rust and Henry S. Rzepa},
  journal   = {Data Science Journal},
  title     = {Scientific publications in XML - towards a global knowledge base},
  year      = {2002},
  pages     = {84--98},
  volume    = {1},
  doi       = {10.2481/dsj.1.84},
  file      = {2002_Murray-Rust_84.pdf:by-author/M/Murray-Rust/2002_Murray-Rust_84.pdf:PDF},
  keywords  = {CML; Chemoinformatics; Data Formats; Data Management; Scientific Publication; XML},
  owner     = {saulius},
  timestamp = {2014.06.24},
  creationdate = {2014-06-24T00:00:00},
}

@Article{Murray-Rust2001,
  author    = {Murray-Rust, Peter and Rzepa, Henry S.},
  journal   = {Journal of Chemical Information and Computer Sciences},
  title     = {Chemical Markup, XML and the World-Wide Web. 2. Information Objects and the CMLDOM},
  year      = {2001},
  pages     = {1113--1123},
  volume    = {41},
  abstract  = {We describe the development of a structured method of representing chemistry on the World-Wide Web using an object-oriented approach to information objects. We show how a document object model (DOM) for chemistry can be constructed using as its basis Chemical Markup Language (CML). Application of the CMLDOM to the development of chemical tools is described.},
  doi       = {10.1021/ci000404a},
  eprint    = {http://pubs.acs.org/doi/pdf/10.1021/ci000404a},
  file      = {2001_Murray-Rust_1113.pdf:by-author/M/Murray-Rust/2001_Murray-Rust_1113.pdf:PDF},
  keywords  = {CML; Chemoinformatics; Crystallography; Data Formats; Data Management; X-ray Crystallography; XML},
  owner     = {saulius},
  timestamp = {2014.06.24},
  creationdate = {2014-06-24T00:00:00},
  url       = {http://pubs.acs.org/doi/abs/10.1021/ci000404a},
}

@Article{Murray-Rust1999,
  author    = {Peter Murray-Rust and Henry S. Rzepa},
  journal   = {J. Chem. Inf. Comput. Sci.},
  title     = {Chemical Markup, XML, and the Worldwide Web. 1. Basic Principles},
  year      = {1999},
  pages     = {928--942},
  volume    = {39},
  abstract  = {Chemical markup language (CML) is an application of XML, the extensible markup language, developed for containing chemical information components within documents. Its design supports interoperability with the XML family of tools and protocols. It provides a base functionality for atomic, molecular, and crystallographic information and allows extensibility for other chemical applications. Legacy files can be imported into CML without information loss and can carry any desired chemical ontology. Some applications of CML (Markush structures, chemical searching) will be discussed in later articles. An XML document type declaration (DTD) for CML is included as a Chart.},
  doi       = {10.1021/ci990052b},
  file      = {:by-author/M/Murray-Rust/1999_Murray-Rust_928.pdf:PDF},
  keywords  = {CML; Chemoinformatics; Crystallography; Data Formats; Data Management; X-ray Crystallography; XML},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Murray-Rust2004,
  author    = {Murray-Rust, Peter and Rzepa, Henry S. and Williamson, Mark J. and Willighagen, Egon L.},
  journal   = {Journal of Chemical Information and Computer Sciences},
  title     = {Chemical Markup, XML, and the World Wide Web. 5. Applications of Chemical Metadata in RSS Aggregators},
  year      = {2004},
  pages     = {462--469},
  volume    = {44},
  abstract  = {Examples of the use of the RSS 1.0 (RDF Site Summary) specification together with CML (Chemical Markup Language) to create a metadata based alerting service termed CMLRSS for molecular content are presented. CMLRSS can be viewed either using generic software or with modular opensource chemical viewers and editors enhanced with CMLRSS modules. We discuss the more automated use of CMLRSS as a component of a World Wide Molecular Matrix of semantically rich chemical information.},
  doi       = {10.1021/ci034244p},
  eprint    = {http://pubs.acs.org/doi/pdf/10.1021/ci034244p},
  file      = {2004_Murray-Rust_462.pdf:by-author/M/Murray-Rust/2004_Murray-Rust_462.pdf:PDF},
  keywords  = {CML; Chemoinformatics; Crystallography; Data Formats; Data Management; X-ray Crystallography; XML},
  owner     = {saulius},
  timestamp = {2014.06.24},
  creationdate = {2014-06-24T00:00:00},
  url       = {http://pubs.acs.org/doi/abs/10.1021/ci034244p},
}

@Article{Murray-Rust2000,
  author    = {Murray-Rust, Peter and Rzepa, Henry S. and Wright, Michael and Zara, Stephen},
  journal   = {Chem. Commun.},
  title     = {A universal approach to web-based chemistry using XML and CML},
  year      = {2000},
  pages     = {1471--1472},
  abstract  = {We report the first fully operational system for managing complex chemical content entirely in interoperating XML-based markup languages.},
  doi       = {10.1039/B002483J},
  file      = {2000_Murray-Rust_1471.pdf:by-author/M/Murray-Rust/2000_Murray-Rust_1471.pdf:PDF},
  issue     = {16},
  keywords  = {CML; Chemoinformatics; Crystallography; Data Formats; Data Management; X-ray Crystallography; XML},
  owner     = {saulius},
  publisher = {The Royal Society of Chemistry},
  timestamp = {2014.06.24},
  creationdate = {2014-06-24T00:00:00},
  url       = {http://dx.doi.org/10.1039/B002483J},
}

@Article{Murray-Rust2011,
  author    = {Murray-Rust, Peter and Townsend, Joe and Adams, Sam and Phadungsukanan, Weerapong and Thomas, Jens},
  journal   = {Journal of Cheminformatics},
  title     = {The semantics of Chemical Markup Language (CML): dictionaries and conventions},
  year      = {2011},
  issn      = {1758-2946},
  pages     = {43},
  volume    = {3},
  abstract  = {The semantic architecture of CML consists of conventions, dictionaries and units. The conventions conform to a top-level specification and each convention can constrain compliant documents through machine-processing (validation). Dictionaries conform to a dictionary specification which also imposes machine validation on the dictionaries. Each dictionary can also be used to validate data in a CML document, and provide human-readable descriptions. An additional set of conventions and dictionaries are used to support scientific units. All conventions, dictionaries and dictionary elements are identifiable and addressable through unique URIs.},
  doi       = {10.1186/1758-2946-3-43},
  file      = {2011_Murray-Rust_43.pdf:by-author/M/Murray-Rust/2011_Murray-Rust_43.pdf:PDF},
  keywords  = {CML; Crystallography; Data Formats; Data Management; X-ray Crystallography; XML},
  owner     = {saulius},
  pubmedid  = {21999509},
  timestamp = {2014.06.23},
  creationdate = {2014-06-23T00:00:00},
  url       = {http://www.jcheminf.com/content/3/1/43},
}

@Manual{Murshudov2011,
  title     = {Simple {REFMAC} tutorials},
  author    = {Murshudov, Garib N.},
  year      = {2011},
  file      = {:by-author/M/Murshudov/2011_Murshudov_tutorial.pdf:PDF},
  owner     = {andrius},
  timestamp = {2013.04.15},
  creationdate = {2013-04-15T00:00:00},
}

@Article{Murshudov2011a,
  author    = {Murshudov, Garib N. and Skub{\'{a}}k, Pavol and Lebedev, Andrey A. and Pannu, Navraj S. and Steiner, Roberto A. and Nicholls, Robert A. and Winn, Martyn D. and Long, Fei and Vagin, Alexei A.},
  journal   = {Acta Crystallographica Section D},
  title     = {{\it REFMAC}5 for the refinement of macromolecular crystal structures},
  year      = {2011},
  pages     = {355--367},
  volume    = {67},
  abstract  = {This paper describes various components of the macromolecular crystallographic refinement program REFMAC5, which is distributed as part of the CCP4 suite. REFMAC5 utilizes different likelihood functions depending on the diffraction data employed (amplitudes or intensities), the presence of twinning and the availability of SAD/SIRAS experimental diffraction data. To ensure chemical and structural integrity of the refined model, REFMAC5 offers several classes of restraints and choices of model parameterization. Reliable models at resolutions at least as low as 4 Å can be achieved thanks to low-resolution refinement tools such as secondary-structure restraints, restraints to known homologous structures, automatic global and local NCS restraints, `jelly-body' restraints and the use of novel long-range restraints on atomic displacement parameters (ADPs) based on the Kullback-Leibler divergence. REFMAC5 additionally offers TLS parameterization and, when high-resolution data are available, fast refinement of anisotropic ADPs. Refinement in the presence of twinning is performed in a fully automated fashion. REFMAC5 is a flexible and highly optimized refinement package that is ideally suited for refinement across the entire resolution spectrum encountered in macromolecular crystallography.},
  doi       = {10.1107/S0907444911001314},
  file      = {2011_Murshudov_355.pdf:by-author/M/Murshudov/2011_Murshudov_355.pdf:PDF},
  keywords  = {Algorithms; Crystallography; Protein Crystallography; Structure Refinement; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2013.05.05},
  creationdate = {2013-05-05T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444911001314},
}

@Article{Murshudov1997a,
  author    = {Garib N. Murshudov and Alexei A. Vagin and Eleanor J. Dodson},
  journal   = {Acta Cryst. D},
  title     = {Refinement of Macromolecular Structures by the Maximum-Likelihood Method},
  year      = {1997},
  pages     = {240--255},
  volume    = {53},
  abstract  = {This paper reviews the mathematical basis of maximum likelihood. The likelihood function for macromolecular structures is extended to include prior phase information and experimental standard uncertainties. The assumption that different parts of a structure might have different errors is considered. A method for estimating erA using 'free' reflections is described and its effects analysed. The derived equations have been implemented in the program REFMAC. This has been tested on several proteins at different stages of refinement (bacterial a-amylase, cytochrome c', cross-linked insulin and oligopeptide binding protein). The results derived using the maximum-likelihood residual are consistently better than those obtained from least-squares refinement.},
  file      = {:by-author/M/Murshudov/1997_Murshudov_240.pdf:PDF},
  owner     = {andrius},
  timestamp = {2013.04.21},
  creationdate = {2013-04-21T00:00:00},
}

@Article{Murshudov1997,
  author    = {Murshudov, G N and Vagin, A A and Dodson, E J},
  journal   = {Acta Crystallogr D Biol Crystallogr},
  title     = {Refinement of macromolecular structures by the maximum-likelihood method},
  year      = {1997},
  month     = {May},
  number    = {Pt 3},
  pages     = {240--55},
  volume    = {53},
  abstract  = {This paper reviews the mathematical basis of maximum likelihood. The likelihood function for macromolecular structures is extended to include prior phase information and experimental standard uncertainties. The assumption that different parts of a structure might have different errors is considered. A method for estimating sigma(A) using 'free' reflections is described and its effects analysed. The derived equations have been implemented in the program REFMAC. This has been tested on several proteins at different stages of refinement (bacterial alpha-amylase, cytochrome c', cross-linked insulin and oligopeptide binding protein). The results derived using the maximum-likelihood residual are consistently better than those obtained from least-squares refinement},
  address   = {Chemistry Department, University of York, Heslington, England},
  file      = {1997_Murshudov_240.pdf:by-author/M/Murshudov/1997_Murshudov_240.pdf:PDF},
  owner     = {em},
  timestamp = {2016.06.16},
  creationdate = {2016-06-16T00:00:00},
  url       = {http://www.ncbi.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&dopt=abstract&list_uids=15299926},
}

@Article{Murthy1984,
  author           = {M. R. N. Murthy},
  journal          = {FEBS Letters},
  title            = {A fast method of comparing protein structures},
  year             = {1984},
  issn             = {0014-5793},
  pages            = {97--102},
  volume           = {168},
  abstract         = {Comparative studies on protein structures form an integral part of protein crystallography. Here, a fast method of comparing protein structures is presented. Protein structures are represented as a set of secondary structural elements. The method also provides information regarding preferred packing arrangements and evolutionary dynamics of secondary structural elements. This information is not easily obtained from previous methods. In contrast to those methods, the present one can be used only for proteins with some secondary structure. The method is illustrated with globin folds, cytochromes and dehydrogenases as examples.},
  creationdate     = {2012-05-15T00:00:00},
  doi              = {10.1016/0014-5793(84)80214-8},
  file             = {1984_Murthy_97.pdf:by-author/M/Murthy/1984_Murthy_97.pdf:PDF},
  groups           = {sg/Molecule superposion, sg/Superposition, sg/Bioinf. Algorithms},
  keywords         = {Comparison; Evolution; Homology; Packing; Protein Structure; Secondary Structure; Structure Superposition},
  modificationdate = {2024-05-12T16:47:18},
  owner            = {saulius},
  timestamp        = {2012.05.15},
  url              = {http://www.sciencedirect.com/science/article/pii/0014579384802148},
}

@Article{Murzin1994,
  author    = {Murzin, A G and Lesk, A M and Chothia, C},
  journal   = {Journal of molecular biology},
  title     = {Principles determining the structure of beta-sheet barrels in proteins. I. A theoretical analysis.},
  year      = {1994},
  pages     = {1369--81},
  volume    = {236},
  abstract  = {The major feature of many proteins is a large beta-sheet that twists and coils to form a closed structure in which the first strand is hydrogen bonded to the last: the beta-sheet barrel. McLachlan classified barrels in terms of two integral parameters: the number of strands in the beta-sheet, n, and the "shear number", S, a measure of the stagger of the strands in the beta-sheet. He showed that the mean radius of a barrel and the extent to which strands are tilted relative to its axis are determined by the values of n and S. Here we show that the (n, S) values determine all the other general structural features of regular beta-sheet barrels, in particular, optimal values of the twist and coiling angles that produce the closed beta-sheet, the hyperboloidal shape and the arrangement of residues in the barrel interior. Consideration of the residue arrangements in the interiors of different potential barrel structures, and of side-chain volumes, suggest that barrels, in which the interiors are close packed by the residues in beta-sheets with good geometries, have structures that correspond to one of only ten different combinations of n and S. In the accompanying paper, we demonstrate, by an analysis of all observed protein structures that contain beta-sheet barrels and for which atomic co-ordinates are available, the validity of these theoretical results.},
  file      = {1994_Murzin_1369.pdf:by-author/M/Murzin/1994_Murzin_1369.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Murzin1994a,
  author    = {Murzin, A G and Lesk, A M and Chothia, C},
  journal   = {Journal of molecular biology},
  title     = {Principles determining the structure of beta-sheet barrels in proteins. II. The observed structures.},
  year      = {1994},
  pages     = {1382--400},
  volume    = {236},
  abstract  = {In the accompanying paper we derived a set of principles that, we argue, govern the structure of beta-sheet barrels. Barrel structures are classified in terms of two integral parameters: the number of strands in the beta-sheet, n, and a measure of the stagger in the beta-sheet, S. We derived a set of equations that show how the (n, S) values of a barrel structure determine the arrangement of its strands; its general shape; the twist and coiling of the beta-sheet, and the arrangement of residues in the barrel interior. This work suggested that there are ten different combinations of n and S that form barrels with good beta-sheet geometries and interiors close packed by beta-sheet residues. In this paper we demonstrate the validity of these principles. We analyse in detail the observed structures of 39 different beta-sheet barrels. These structures include representatives of all the different barrel structures currently known and for which atomic co-ordinates are available. We show that the observed arrangement of the strands, and the extent of the twist and coiling of the beta-sheets, are very close to those calculated from the (n, S) values for the barrel. Of the 39 structures, 34 have one of the ten (n, S) values that we expect to form barrels with good beta-sheet geometries and interiors close packed by beta-sheet residues. The other five have one of two (n, S) values that give good beta-sheet geometries but radii so large the beta-sheet residues leave cavities at the centre of the barrels. In at least four of these cavities have a functional role.},
  file      = {1994_Murzin_1382.pdf:by-author/M/Murzin/1994_Murzin_1382.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@InProceedings{Myers1998,
  author    = {Myers,C. R. and Arwade,S.R. and Iesulauro,E. and Wawrzynek,P.A. and Grigoriu,M. and Ingraffea,A.R. and Dawson,P.R. and Miller,M.P. and Sethna,J.P.},
  booktitle = {Symposium J – Multiscale Modelling of Materials},
  title     = {Digital Material: A Framework for Multiscale Modeling of Defects in Solids},
  year      = {1998},
  month     = {1},
  pages     = {509},
  series    = {MRS Proceedings},
  volume    = {538},
  abstract  = {We are designing and developing a novel software environment - the Digital Material -to support materials modeling across many length and time scales, in order to develop improved descriptions of material structure and evolution. Software support is required for high-performance numerical kernels, lightweight infrastructures for prototyping, steering and analysis, information transfer across scales, coupling of disparate simulation modules, and collaboration between a multidisciplinary collection of researchers.},
  doi       = {10.1557/PROC-538-509},
  file      = {1998_Myers_509.pdf:by-author/M/Myers/1998_Myers_509.pdf:PDF;1998_Myers_509.ps:by-author/M/Myers/1998_Myers_509.ps:PostScript},
  keywords  = {Computational Chemistry},
  owner     = {saulius},
  timestamp = {2014.07.16},
  creationdate = {2014-07-16T00:00:00},
  url       = {http://www.lassp.cornell.edu/sethna/DM/Papers/MyersMRS98.ps},
}

@Article{Myers1995,
  author    = {Myers, Jeffrey K. and Nick Pace, C. and Martin Scholtz, J.},
  journal   = {Protein Science},
  title     = {Denaturant m values and heat capacity changes: Relation to changes in accessible surface areas of protein unfolding},
  year      = {1995},
  issn      = {1469-896X},
  pages     = {2138--2148},
  volume    = {4},
  abstract  = {Denaturant m values, the dependence of the free energy of unfolding on denaturant concentration, have been collected for a large set of proteins. The m value correlates very strongly with the amount of protein surface exposed to solvent upon unfolding, with linear correlation coefficients of R = 0.84 for urea and R = 0.87 for guanidine hydrochloride. These correlations improve to R = 0.90 when the effect of disulfide bonds on the accessible area of the unfolded protein is included. A similar dependence on accessible surface area has been found previously for the heat capacity change (ΔCp), which is confirmed here for our set of proteins. Denaturant m values and heat capacity changes also correlate well with each other. For proteins that undergo a simple two-state unfolding mechanism, the amount of surface exposed to solvent upon unfolding is a main structural determinant for both m values and ΔCp.},
  doi       = {10.1002/pro.5560041020},
  file      = {1995_Myers_2138.pdf:by-author/M/Myers/1995_Myers_2138.pdf:PDF},
  keywords  = {Denaturation; Guanidine Hydrochloride; Heat Capacity Changes; M Values; Protein Folding; Protein Stability; Solvent-accessible Surface Area; Urea},
  owner     = {saulius},
  publisher = {Cold Spring Harbor Laboratory Press},
  timestamp = {2015.03.13},
  creationdate = {2015-03-13T00:00:00},
  url       = {http://dx.doi.org/10.1002/pro.5560041020},
}

@Article{Myers1981,
  author    = {R. Thomas Myers},
  journal   = {Journal of Chemical Education},
  title     = {Rules for coordination number of metal ions},
  year      = {1981},
  pages     = {681},
  volume    = {58},
  abstract  = {A few simple rules will help students remember coordination numbers and geometry of the vast majority of complexes of metal cation encountered.},
  doi       = {10.1021/ed058p681.1},
  file      = {:./by-author/M/Myers/1981_Myers_681.pdf:PDF},
  keywords  = {Coordination Complex},
  owner     = {antanas},
  timestamp = {2014.01.15},
  creationdate = {2014-01-15T00:00:00},
  url       = {http://pubs.acs.org/doi/abs/10.1021/ed058p681.1},
}

@Article{Mylonas2007,
  author    = {Mylonas, Efstratios and Svergun, Dmitri I.},
  journal   = {Journal of Applied Crystallography},
  title     = {Accuracy of molecular mass determination of proteins in solution by small-angle X-ray scattering},
  year      = {2007},
  pages     = {s245–s249},
  volume    = {40},
  abstract  = {One of the most important overall parameters, which can be derived from small-angle X-ray scattering (SAXS) experiments on macromolecular solutions is the molecular mass (MM) of the solute. In particular, for a monodisperse protein solution, MM of the solute is calculated from the extrapolated scattering intensity at zero angle I(0). Assessing MM by SAXS provides valuable information about the oligomeric state and absence of unspecific aggregation in solution. The value of MM can either be estimated by comparison witha protein standard with a known MM or by determining the absolute scattering intensity using, e.g., water scattering. In both cases, knowledge about thesolute concentration and about the partial specific volume of the protein is required. By measuring 13 well characterized globular proteins with MMs ranging from 13.7 to 669 kDa we analyze the sources of possible systematic deviations and assess the accuracy of MM determination using SAXS. The data indicatethat all these proteins have approximately the same ‘effective’ value of the partial specific volume of about 0.7425 cm3 gÀ1. It is shown that both inter-protein and water calibration can be used for molecular mass determination by SAXS and in most cases the errors do not exceed 10%.},
  file      = {:by-author/M/Mylonas/2007-Mylonas_s245.pdf:PDF},
  keywords  = {Molecular Weight (MW); SAXS},
  owner     = {em},
  timestamp = {2013.06.28},
  creationdate = {2013-06-28T00:00:00},
}

@Presentation{MysonXXXX,
  author    = {Myson},
  title     = {Introduction to MPI and OpenMP},
  year      = {XXXX},
  file      = {:by-author/M/Myson/XXXX_Myson.pdf:PDF},
  owner     = {saulius},
  timestamp = {2013.07.02},
  creationdate = {2013-07-02T00:00:00},
}

@Presentation{Moller2003,
  author    = {Møller},
  title     = {Program Verification with Hoare Logic},
  year      = {2003},
  file      = {:by-author/M/Møller/2003_Møller_slides.pdf:PDF},
  groups    = {sg/Correctness proofs},
  keywords  = {Computer Science (CS); Correctness Proofs},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@InProceedings{Moller2001,
  author    = {Møller, Anders and Michael I. Schwartzbach},
  booktitle = {Proceedings of the ACM SIGPLAN 2001 Conference on Programming Language Design and Implementation},
  title     = {The Pointer Assertion Logic Engine},
  year      = {2001},
  abstract  = {We present a new framework for verifying partial specifica- tions of programs in order to catch type and memory errors and check data structure invariants. Our technique can ver- ify a large class of data structures, namely all those that can be expressed as graph types. Earlier versions were restricted to simple special cases such as lists or trees. Even so, our current implementation is as fast as the previous specialized tools. Programs are annotated with partial specifications ex- pressed in Pointer Assertion Logic, a new notation for ex- pressing properties of the program store. We work in the logical tradition by encoding the programs and partial speci- fications as formulas in monadic second-order logic. Validity of these formulas is checked by the MONA tool, which also can provide explicit counterexamples to invalid formulas. To make verification decidable, the technique requires ex- plicit loop and function call invariants. In return, the tech- nique is highly modular: every statement of a given program is analyzed only once. The main target applications are safety-critical data-type algorithms, where the cost of annotating a program with in- variants is justified by the value of being able to automati- cally verify complex properties of the program.},
  file      = {:by-author/M/Møller/2001_Møller.pdf:PDF},
  groups    = {sg/Correctness proofs},
  keywords  = {Computer Science (CS); Correctness Proofs},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Moeller2013,
  author      = {Magda Møller and Søren S Nielsen and Sekar Ramachandran and Yuxing Li and Giancarlo Tria and Werner Streicher and Maxim V Petoukhov and Richard A Cerione and Richard E Gillilan and Bente Vestergaard},
  journal     = {PLoS One},
  title       = {Small angle X-ray scattering studies of mitochondrial glutaminase C reveal extended flexible regions, and link oligomeric state with enzyme activity.},
  year        = {2013},
  pages       = {e74783},
  volume      = {8},
  abstract    = {Glutaminase C is a key metabolic enzyme, which is unregulated in many cancer systems and believed to play a central role in the Warburg effect, whereby cancer cells undergo changes to an altered metabolic profile. A long-standing hypothesis links enzymatic activity to the protein oligomeric state, hence the study of the solution behavior in general and the oligomer state in particular of glutaminase C is important for the understanding of the mechanism of protein activation and inhibition. In this report, this is extensively investigated in correlation to enzyme concentration or phosphate level, using a high-throughput microfluidic-mixing chip for the SAXS data collection, and we confirm that the oligomeric state correlates with activity. The in-depth solution behavior analysis further reveals the structural behavior of flexible regions of the protein in the dimeric, tetrameric and octameric state and investigates the C-terminal influence on the enzyme solution behavior. Our data enable SAXS-based rigid body modeling of the full-length tetramer states, thereby presenting the first ever experimentally derived structural model of mitochondrial glutaminase C including the N- and C-termini of the enzyme.},
  doi         = {10.1371/journal.pone.0074783},
  file        = {:by-author/M/Møller/2013_Moller_e74783.pdf:PDF},
  institution = {Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark.},
  keywords    = {SAXS},
  language    = {eng},
  medline-pst = {epublish},
  owner       = {em},
  pii         = {PONE-D-13-10091},
  pmid        = {24098668},
  timestamp = {2014.01.14},
  creationdate = {2014-01-14T00:00:00},
  url         = {http://dx.doi.org/10.1371/journal.pone.0074783},
}

@Article{Nabok2008,
  author    = {Nabok, Alexei and Tsargorodskaya, Anna},
  journal   = {Thin Solid Films},
  title     = {The method of total internal reflection ellipsometry for thin film characterisation and sensing},
  year      = {2008},
  issn      = {0040-6090},
  pages     = {8993--9001},
  volume    = {516},
  doi       = {10.1016/j.tsf.2007.11.077},
  file      = {:by-author/N/Nabok/2008_Nabok_8993.pdf:PDF},
  owner     = {saulius},
  publisher = {Elsevier BV},
  timestamp = {2015.02.25},
  creationdate = {2015-02-25T00:00:00},
  url       = {http://dx.doi.org/10.1016/j.tsf.2007.11.077},
}

@Manuscript{Nadel2004,
  author    = {Mark S. Nadel},
  title     = {How current copyright law discourages' creative output: the overlooked impact of marketing},
  year      = {2004},
  keywords  = {Patentai; Teise},
  file      = {:by-author/N/Nadel/2004_Nadel.doc:DOC},
  owner     = {saulius},
  timestamp = {2015.02.28},
  creationdate = {2015-02-28T00:00:00},
}

@Article{Nagano2002,
  author    = {Nagano, Nozomi and Orengo, Christine A and Thornton, Janet M},
  journal   = {Journal of molecular biology},
  title     = {One fold with many functions: the evolutionary relationships between TIM barrel families based on their sequences, structures and functions.},
  year      = {2002},
  pages     = {741--65},
  volume    = {321},
  abstract  = {The eightfold (betaalpha) barrel structure, first observed in triose-phosphate isomerase, occurs ubiquitously in nature. It is nearly always an enzyme and most often involved in molecular or energy metabolism within the cell. In this review we bring together data on the sequence, structure and function of the proteins known to adopt this fold. We highlight the sequence and functional diversity in the 21 homologous superfamilies, which include 76 different sequence families. In many structures, the barrels are "mixed and matched" with other domains generating additional variety. Global and local structure-based alignments are used to explore the distribution of the associated functional residues on this common structural scaffold. Many of the substrates/co-factors include a phosphate moiety, which is usually but not always bound towards the C-terminal end of the sequence. Some, but not all, of these structures, exhibit a structurally conserved "phosphate binding motif". In contrast metal-ligating residues and catalytic residues are distributed along the sequence. However, we also found striking structural superposition of some of these residues. Lastly we consider the possible evolutionary relationships between these proteins, whose sequences are so diverse that even the most powerful approaches find few relationships, yet whose active sites all cluster at one end of the barrel. This extreme example of the "one fold-many functions" paradigm illustrates the difficulty of assigning function through a structural genomics approach for some folds.},
  file      = {Nagano_2002_741-TIM_barrels.pdf:by-author/N/Nagano/2002_Nagano_741.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Nagelhus2005,
  author    = {Nagelhus, Erlend A and Mathiisen, Thomas M and Bateman, Allen C and Haug, Finn-M and Ottersen, Ole P and Grubb, Jeffrey H and Waheed, Abdul and Sly, William S},
  journal   = {Proceedings of the National Academy of Sciences of the United States of America},
  title     = {Carbonic anhydrase XIV is enriched in specific membrane domains of retinal pigment epithelium, Muller cells, and astrocytes.},
  year      = {2005},
  pages     = {8030--5},
  volume    = {102},
  abstract  = {Carbonic anhydrases (CAs) are ubiquitous enzymes important to many cell types throughout the body. They help determine levels of H(+) and HCO(-)(3) and thereby regulate intracellular and extracellular pH and volume. CA XIV, an extracellular membrane-bound CA, was recently shown to be present in brain and retina. Here, we analyze the subcellular distribution of CA XIV in retina by high-resolution immunogold cytochemistry and show that the distribution in retina (on glial cells but not neurons) is different from that reported for brain (on neurons but not glia). In addition, CA XIV is strongly expressed on retinal pigment epithelium (RPE). The specific membrane domains that express CA XIV were endfoot and nonendfoot membranes on Muller cells and astrocytes and apical and basolateral membranes of RPE. Gold particle density was highest on microvilli plasma membranes of RPE, where it was twice that of glial endfoot and Muller microvilli membranes and four times that of other glial membrane domains. Neither neurons nor capillary endothelial cells showed detectable labeling for CA XIV. This enrichment of CA XIV on specific membrane domains of glial cells and RPE suggests specialization for buffering pH and volume in retinal neurons and their surrounding extracellular spaces. We suggest that CA XIV is the target of CA inhibitors that enhance subretinal fluid absorption in macular edema. In addition, CA XIV may facilitate CO(2) removal from neural retina and modulate photoreceptor function.},
  file      = {2005_Nagelhus_8030.pdf:by-author/N/Nagelhus/2005_Nagelhus_8030.pdf:PDF},
  groups    = {sg/hCA14},
  keywords  = {CA14; Carbonic Anhydrases},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Nagem2001,
  author    = {Nagem, R. A. and Dauter, Z. and Polikarpov, I.},
  journal   = {Acta crystallographica. Section D, Biological crystallography},
  title     = {Protein crystal structure solution by fast incorporation of negatively and positively charged anomalous scatterers.},
  year      = {2001},
  pages     = {996--1002},
  volume    = {57},
  abstract  = {The preparation of derivatives by the traditional methods of soaking is one of the most time-consuming steps in protein crystal structure solution by X-ray diffraction techniques. The 'quick cryosoaking' procedure for derivatization with halides (monovalent anions) offers the possibility of significantly speeding up this process [Dauter et al. (2000), Acta Cryst. D56, 232-237]. In the present work, an extension of this technique is proposed and the use of two different classes of compounds (monovalent and polyvalent cations) that can be successfully utilized in the quick cryosoaking procedure for the derivatization and phasing of protein crystals is described. This approach has been tested on hen egg-white lysozyme and has been successfully used to solve the structure of a novel trypsin inhibitor. The possibility of using cations in the fast cryosoaking procedure gives additional flexibility in the process of derivatization and increases the chances of success in phase determination. This method can be applied to high-throughput crystallographic projects.},
  file      = {:by-author/N/Nagem/2001_Nagem_996.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Nagura2013,
  author    = {Nagura, Kazuhiko and Saito, Shohei and Yusa, Hitoshi and Yamawaki, Hiroshi and Fujihisa, Hiroshi and Sato, Hiroyasu and Shimoikeda, Yuichi and Yamaguchi, Shigehiro},
  journal   = {Journal of the American Chemical Society},
  title     = {Distinct responses to mechanical grinding and hydrostatic pressure in luminescent chromism of tetrathiazolylthiophene.},
  year      = {2013},
  pages     = {10322--5},
  volume    = {135},
  abstract  = {Luminescent mechanochromism has been intensively studied in the past few years. However, the difference in the anisotropic grinding and the isotropic compression is not clearly distinguished in many cases, in spite of the importance of this discrimination for the application of such mechanochromic materials. We now report the distinct luminescent responses of a new organic fluorophore, tetrathiazolylthiophene, to these stresses. The multichromism is achieved over the entire visible region using the single fluorophore. The different mechanisms of a blue shift by grinding crystals and of a red shift under hydrostatic pressure are fully investigated, which includes a high-pressure single-crystal X-ray diffraction analysis. The anisotropic and isotropic modes of mechanical loading suppress and enhance the excimer formation, respectively, in the 3D hydrogen-bond network.},
  file      = {Supporting info:by-author/N/Nagura/2013_Nagura_10322supp.pdf:PDF;:by-author/N/Nagura/2013_Nagura_10322.pdf:PDF},
  owner     = {saulius},
  timestamp = {2014.03.23},
  creationdate = {2014-03-23T00:00:00},
}

@Article{Nagy2006,
  author    = {Ferenc Nagy},
  journal   = {Journal of Universal Computer Science},
  title     = {Parameter Estimation of the {C}auchy Distribution in Information Theory Approach},
  year      = {2006},
  pages     = {1332--1344},
  volume    = {12},
  abstract  = {As we know the Cauchy distribution plays an important role in Probability Theory and Statistics. In this paper, we investigate the estimation of the location and the scale parameter. Both the one-dimensional problem and the multidimensional problem are studied for large sample. In the one-dimensional case, we give two algorithms for the estimation. The first one is an iterative method for which we prove the convergence and we show that the rate of convergence is geometric. The second algorithm provides an exact solution to the problem. In the multidimensional case, we give an algorithm analogous to the one-dimensional case. Computer experiments show that the rate of convergence is similar to the one-dimensional iterative algorithm.},
  doi       = {10.3217/jucs-012-09-1332},
  file      = {:by-author/N/Nagy/2006_Nagy_1332.pdf:PDF},
  owner     = {andrius},
  timestamp = {2013.03.05},
  creationdate = {2013-03-05T00:00:00},
  url       = {http://www.jucs.org/jucs_12_9/parameter_estimation_of_the/jucs_12_09_1332_1344_nagy.pdf},
}

@Manuscript{Nair2009,
  author    = {Ravi Sankar Parameswaran Nair and Scott C. Smith and Jia Di},
  title     = {Delay-Insensitive Ternary Logic},
  year      = {2009},
  keywords  = {Computer Science (CS); Logic-circuits; Ternary},
  abstract  = {This paper develops a delay-insensitive (DI) digital design paradigm that utilizes ternary logic as an alternative to dual-rail logic for encoding the DATA and NULL states. This new Delay-Insensitive Ternary Logic (DITL) paradigm is compared with other DI paradigms, such as Pre-Charge Half- Buffers (PCHB) and NULL Convention Logic (NCL), showing that DITL significantly outperforms PCHB and NCL in terms of energy consumption, and is also more area efficient than NCL. Utilizing the DITL paradigm for designing secure hardware applications is then discussed.},
  file      = {:by-author/N/Nair/2009_Nair.pdf:},
  owner     = {saulius},
  timestamp = {2015.03.03},
  creationdate = {2015-03-03T00:00:00},
}

@Article{Nair1995,
  author    = {Nair, S K and Krebs, J F and Christianson, D W and Fierke, C A},
  journal   = {Biochemistry},
  title     = {Structural basis of inhibitor affinity to variants of human carbonic anhydrase II.},
  year      = {1995},
  pages     = {3981--9},
  volume    = {34},
  abstract  = {The activities and structures of certain L198 variants of human carbonic anhydrase II (CAII) have been reported recently [Krebs, J. F., Rana, F., Dluhy, R. A., &amp; Fierke, C. A. (1993) Biochemistry 32, 4496-4505; Nair, S. K., &amp; Christianson, D. W. (1993) Biochemistry 32, 4506-4514]. In order to understand the structural basis of enzyme-inhibitor affinity, we now report the dissociation rate and equilibrium constants for acetazolamide and dansylamide binding to 13 variants of CAII containing substituted amino acids at position 198. These data indicate that inhibitor affinity is modulated by the hydrophobicity and charge of the 198 side chain. Furthermore, we have determined crystal structures of L198R, L198E, and L198F CAIIs complexed with the transition state analog acetazolamide. The substituted benzyl side chain of L198F CAII does not occlude the substrate association pocket, and it is therefore not surprising that this substitution has minimal effects on catalytic properties and inhibitor binding. Nevertheless, the F198 side chain undergoes a significant conformation change in order to accommodate the binding of acetazolamide; the same behavior is observed for the engineered side chain of L198R CAII. In contrast, the engineered side chain of L198E CAII does not alter its conformation upon inhibitor binding. We conclude that the mobility and hydrophobicity or residue 198 side chains affect enzyme-inhibitor (and enzyme-substrate) affinity, and these structure-function relationships are important for understanding the behavior of carbonic anhydrase isozyme III, which bears a wild-type F198 side chain.(ABSTRACT TRUNCATED AT 250 WORDS)},
  file      = {1995_Nair_3981.pdf:by-author/N/Nair/1995_Nair_3981.pdf:PDF},
  groups    = {sg/inhibitors, sg/hCA2},
  keywords  = {Carbonic Anhydrases},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Najmabad2007,
  author    = {Peyman Najmabadi and James J. La Clair and Michael D. Burkart},
  journal   = {Org. Biomol. Chem.},
  title     = {A systems perspective to digital structures in molecular analysis},
  year      = {2007},
  pages     = {214},
  volume    = {5},
  abstract  = {Within the last decade, the advance of miniaturization has opened the window to new systems that permit digital and molecular science to intersect, suggesting a new role for organic chemistry. Currently, fusion of molecules and electronic digits, as well as molecular-based digital structures, have expanded the conventional interpretation of the digit. This emergence has already generated new technological platforms with unique applications for molecular analysis and computation. We provide a brief overview of the conventional understanding of digital devices, examine the concept of molecular-based digits, and suggest new architectures by examining studies conducted on the compact discs. This analysis presents a perspective for the unique interaction of molecules and digits and the development of digital-based platforms for molecular analysis.},
  doi       = {10.1039/b614507h},
  file      = {2007_Najmabadi_214.pdf:by-author/N/Najmabadi/2007_Najmabadi_214.pdf:PDF},
  keywords  = {Data Processing},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Nakai1988,
  author    = {Nakai, H. and Richardson, C. C.},
  journal   = {The Journal of biological chemistry},
  title     = {Leading and lagging strand synthesis at the replication fork of bacteriophage T7. Distinct properties of T7 gene 4 protein as a helicase and primase.},
  year      = {1988},
  pages     = {9818--30},
  volume    = {263},
  abstract  = {Reactions at the replication fork of bacteriophage T7 have been reconstituted in vitro on a preformed replication fork. A minimum of three proteins is required to catalyze leading and lagging strand synthesis. The T7 gene 4 protein, which exists in two forms of molecular weight 56,000 and 63,000, provides helicase and primase activities. A tight complex of the T7 gene 5 protein and Escherichia coli thioredoxin provides DNA polymerase activity. Gene 4 protein and DNA polymerase catalyze processive leading strand synthesis. Gene 4 protein molecules serving as helicase remain bound to the template as leading strand synthesis proceeds greater than 40 kilobases. Primer synthesis for lagging strand synthesis is catalyzed by additional gene 4 protein molecules that undergo multiple association/dissociation steps to catalyze multiple rounds of primer synthesis. The smaller molecular weight form of gene 4 protein has been purified from an equimolar mixture of both forms. Removal of the large form results in the loss of primase activity but not of helicase activity. Submolar amounts of the large form present in a mixture of both forms are sufficient to restore high specific activity of primase characteristic of an equimolar mixture of both forms. These results suggest that the gene 4 primase is an oligomer which is composed of both molecular weight forms. The large form may be the distributive component of the primase which dissociates from the template after each round of primer synthesis.},
  file      = {:by-author/N/Nakai/1988_Nakai_9818.pdf:PDF},
  keywords  = {T7; {gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Manuscript{Nakamoto2009,
  author    = {Satoshi Nakamoto},
  title     = {Bitcoin: A Peer-to-Peer Electronic Cash System},
  year      = {2009},
  url       = {http://www.bitcoin.org},
  abstract  = {A purely peer-to-peer version of electronic cash would allow online payments to be sent directly from one party to another without going through a financial institution. Digital signatures provide part of the solution, but the main benefits are lost if a trusted third party is still required to prevent double-spending. We propose a solution to the double-spending problem using a peer-to-peer network. The network timestamps transactions by hashing them into an ongoing chain of hash-based proof-of-work, forming a record that cannot be changed without redoing the proof-of-work. The longest chain not only serves as proof of the sequence of events witnessed, but proof that it came from the largest pool of CPU power. As long as a majority of CPU power is controlled by nodes that are not cooperating to attack the network, they'll generate the longest chain and outpace attackers. The network itself requires minimal structure. Messages are broadcast on a best effort basis, and nodes can leave and rejoin the network at will, accepting the longest proof-of-work chain as proof of what happened while they were gone.},
  email     = {satoshin@gmx.com},
  file      = {2009_Nakamoto.pdf:by-author/N/Nakamoto/2009_Nakamoto.pdf:PDF},
  owner     = {saulius},
  timestamp = {2013.06.03},
  creationdate = {2013-06-03T00:00:00},
}

@Article{Nakamura2013,
  author    = {Nakamura, Akihiko and Ishida, Takuya and Fushinobu, Shinya and Kusaka, Katsuhiro and Tanaka, Ichiro and Inaka, Koji and Higuchi, Yoshiki and Masaki, Mika and Ohta, Kazunori and Kaneko, Satoshi and Niimura, Nobuo and Igarashi, Kiyohiko and Samajima, Masahiro},
  journal   = {Journal of Synchrotron Radiation},
  title     = {Phase-diagram-guided method for growth of a large crystal of glycoside hydrolase family 45 inverting cellulase suitable for neutron structural analysis},
  year      = {2013},
  pages     = {859–863},
  volume    = {20},
  abstract  = {Neutron protein crystallography (NPC) is a powerful tool for determining the hydrogen position and water orientation in proteins, but a much larger protein crystal is needed for NPC than for X-ray crystallography, and thus crystal preparation is a bottleneck. To obtain large protein crystals, it is necessary to know the properties of the target protein in the crystallization solution. Here, a crystal preparation method of fungal cellulase PcCel45A is reported, guided by the phase diagram. Nucleation and precipitation conditions were determined by sitting-drop vapor diffusion. Saturation and unsaturation conditions were evaluated by monitoring crystal dissolution, and a crystallization phase diagram was obtained. To obtain a large crystal, crystallization solution was prepared on a sitting bridge (diameter = 5 mm). Initial crystallization conditions were 40 ml of crystallization solution (40 mg mlÀ1 protein with 30.5% 3-methyl-1,5-pentane- diol in 50 mM tris-HCl pH 8.0) with a 1000 ml reservoir (61% 3-methyl-1,5,- pentanediol in 50 mM tris-HCl pH 8.0) at 293 K. After the first crystal appeared, the concentration of precipitant in the reservoir solution was reduced to 60% to prevent formation of further crystals. Finally, we obtained a crystal of 6 mm3 volume (3 mm  2 mm  1 mm), which was suitable for neutron diffraction.},
  doi       = {10.1107/S0909049513020943},
  file      = {:by-author/N/Nakamura/2013_Nakamura_859.pdf:PDF},
  keywords  = {Cellulase; Crystallization Phase Diagram; Neutron Diffraction; Neutron Protein Crystallography; Protein Crystallization},
  owner     = {em},
  timestamp = {2014.02.13},
  creationdate = {2014-02-13T00:00:00},
}

@Article{Nakamura2011,
  author    = {K. Nakamura and et al.},
  journal   = {Journal of Physics G: Nuclear and Particle Physics, Volume 37, Number 7A},
  title     = {n mean life},
  year      = {2011},
  number    = {7A},
  pages     = {075021},
  volume    = {37},
  file      = {2011_Nakamura_075021.pdf:by-author/N/Nakamura/2011_Nakamura_075021.pdf:PDF},
  keywords  = {Half-life; Neutron; Nuclear Physics; Nucleon; Physics},
  owner     = {saulius},
  timestamp = {2016.01.18},
  creationdate = {2016-01-18T00:00:00},
  url       = {http://pdg.lbl.gov/2011/listings/rpp2011-list-n.pdf},
}

@Presentation{Nakano2012,
  author    = {Aiichiro Nakano},
  title     = {Calculating π in Parallel Using MPI},
  year      = {2012},
  file      = {:by-author/N/Nakano/2012_Nakano_slides.pdf:PDF},
  owner     = {saulius},
  pages     = {slides},
  timestamp = {2013.07.02},
  creationdate = {2013-07-02T00:00:00},
}

@Article{Nakano2000,
  author    = {Nakano, S and Chadalavada, D M and Bevilacqua, P C},
  journal   = {Science (New York, N.Y.)},
  title     = {General acid-base catalysis in the mechanism of a hepatitis delta virus ribozyme.},
  year      = {2000},
  pages     = {1493--7},
  volume    = {287},
  file      = {2000_Nakano_1493.pdf:by-author/N/Nakano/2000_Nakano_1493.pdf:PDF},
  keywords  = {Ribozymes},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Nakayama1984,
  author    = {Nakayama, N. and Arai, N. and Bond, M. W. and Kaziro, Y. and Arai, K.},
  journal   = {The Journal of biological chemistry},
  title     = {Nucleotide sequence of dnaB and the primary structure of the dnaB protein from Escherichia coli.},
  year      = {1984},
  pages     = {97--101},
  volume    = {259},
  abstract  = {We have determined the nucleotide sequence of the dnaB gene and the primary structure of the dnaB protein of Escherichia coli (Arai, K., Yasuda, S., and Kornberg, A. (1981) J. Biol. Chem. 256, 5247-5252). The coding region for the dnaB protein is 1413 base pairs followed by double stop codons and preceded by a possible promoter sequence. The dnaB gene lacks a typical Shine-Dalgarno sequence. The primary structure deduced from the DNA sequence is consistent with the protein chemical data. The dnaB protein contains 470 amino acid residues and has a calculated molecular weight of 52,265. In the mature protein, the initiator methionine residue is removed in vivo leaving alanine as the NH2-terminal residue. Based on the amino acid sequence, we predict that the dnaB protein may be composed of two domains. A hydrophilic NH2-terminal region (residues 1-20) is followed by a compact domain and a possible hinge region (residues 21-172) consisting primarily of alpha-helix. The sites of facile tryptic cleavage are at the arginine residues at 14 and 171. The DNA-dependent ATPase domain (residues 172-470) is located at the COOH-terminal end of the protein.},
  file      = {:by-author/N/Nakayama/1984_Nakayama_97.pdf:PDF},
  keywords  = {Ecoli; {gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Nam2012,
  author    = {Nam, Ki Hyun and Huang, Qingqiu and Ke, Ailong},
  journal   = {FEBS Letters},
  title     = {Nucleic acid binding surface and dimer interface revealed by {CRISPR}-associated {CasB} protein structures},
  year      = {2012},
  pages     = {3956–3961},
  volume    = {586},
  abstract  = {The CRISPR system is an adaptive RNA-based microbial immune system against invasive genetic elements. CasB is an essential protein component in Type I-E Cascade. Here, we characterize CasB proteins from three different organisms as non-specific nucleic acid binding proteins. The Thermobifida fusca CasB crystal structure reveals conserved positive surface charges, which we show are important for its nucleic acid binding function. EM docking reveals that CasB dimerization aligns individual nucleic acid binding surfaces into a curved, elongated binding surface inside Type I-E Cascade, consistent with the putative functions of CasB in ds-DNA recruitment and crRNA–DNA duplex formation steps.},
  file      = {2012_Nam_3956.pdf:by-author/N/Nam/2012_Nam_3956.pdf:PDF},
  groups    = {sg/CRISPR-Cas},
  keywords  = {CRISPR; CasB; Cascade; Crystal Structure},
  owner     = {em},
  timestamp = {2013.01.07},
  creationdate = {2013-01-07T00:00:00},
}

@Article{Nam2011,
  author    = {Nam, Ki Hyun and Kurinov, Igor and Ke, Ailong},
  journal   = {The Journal of biological chemistry},
  title     = {Crystal structure of clustered regularly interspaced short palindromic repeats (CRISPR)-associated Csn2 protein revealed Ca2+-dependent double-stranded DNA binding activity.},
  year      = {2011},
  pages     = {30759--68},
  volume    = {286},
  abstract  = {Clustered regularly interspaced short palindromic repeats (CRISPR) and their associated protein genes (cas genes) are widespread in bacteria and archaea. They form a line of RNA-based immunity to eradicate invading bacteriophages and malicious plasmids. A key molecular event during this process is the acquisition of new spacers into the CRISPR loci to guide the selective degradation of the matching foreign genetic elements. Csn2 is a Nmeni subtype-specific cas gene required for new spacer acquisition. Here we characterize the Enterococcus faecalis Csn2 protein as a double-stranded (ds-) DNA-binding protein and report its 2.7 Å tetrameric ring structure. The inner circle of the Csn2 tetrameric ring is ∼26 Å wide and populated with conserved lysine residues poised for nonspecific interactions with ds-DNA. Each Csn2 protomer contains an α/β domain and an α-helical domain; significant hinge motion was observed between these two domains. Ca(2+) was located at strategic positions in the oligomerization interface. We further showed that removal of Ca(2+) ions altered the oligomerization state of Csn2, which in turn severely decreased its affinity for ds-DNA. In summary, our results provided the first insight into the function of the Csn2 protein in CRISPR adaptation by revealing that it is a ds-DNA-binding protein functioning at the quaternary structure level and regulated by Ca(2+) ions.},
  file      = {:by-author/N/Nam/2011_Nam_30759.pdf:PDF},
  groups    = {sg/CRISPR-Cas},
  keywords  = {CRISPR; Crystal Structure; Csn2},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Napolitano2014,
  author     = {Napolitano, Emilio and Dolci, Francesco and Campesi, Renato and Pistidda, Claudio and Hoelzel, Markus and Moretto, Pietro and Enzo, Stefano},
  journal    = {international journal of hydrogen energy},
  title      = {Crystal structure solution of {KMg} ({ND})({ND} 2): {An} ordered mixed amide/imide compound},
  year       = {2014},
  pages      = {868--876},
  volume     = {39},
  file       = {[PDF] from researchgate.net:by-author/N/Napolitano/2014_Napolitano_868.pdf:application/pdf;Snapshot:by-author/N/Napolitano/2014_Napolitano_868.html:text/html},
  groups     = {sg/JAC2009},
  owner      = {saulius},
  shorttitle = {Crystal structure solution of {KMg} ({ND})({ND} 2)},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url        = {http://www.sciencedirect.com/science/article/pii/S0360319913026463},
  urldate    = {2015-08-31},
}

@Presentation{Narasimhan2014,
  author      = {Narasimhan, Shobhana},
  title       = {"k-points" or {Brillouin} Zone Sums In Electronic Structure Calculations},
  year        = {2014},
  file        = {:by-author/N/Narasimhan/2014_Narasimhan_slides.pdf:PDF},
  institution = {JNCASR, Bangalore, India},
  owner       = {andrius},
  timestamp = {2015.07.21},
  creationdate = {2015-07-21T00:00:00},
}

@Presentation{Narasimhan2006,
  author       = {Narasimhan, Shobhana},
  title        = {Introduction to Density Functional Theory},
  year         = {2006},
  organization = {Theoretical Sciences Unit JNCASR, Bangalore},
  file         = {:by-author/N/Narasimhan/2006_Narasimhan_slides.pdf:PDF},
  owner        = {saulius},
  timestamp = {2013.09.19},
  creationdate = {2013-09-19T00:00:00},
}

@Manuscript{Narduzzo2003,
  author    = {Narduzzo, Alessandro and Alessandro Rossi},
  title     = {Modular Design and the Development of Complex Artifacts: Lessons from Free/Open Source Software},
  year      = {2003},
  keywords  = {Computer Science (CS); Modular Design},
  month     = {September},
  abstract  = {Organizational and managerial theories of modularity applied to the design and produc- tion of complex artifacts are used to interpret the rise and success of Free/Open Source software methodologies and practices in software engineering. Strengths and risks of the adoption of a modular approach in software project management are introduced and are re- lated to the achievements of various Free/Open Source Software projects (among them: the GNU operating system, the Linux kernel, the HURD kernel). It is suggested that mindful implementation of the principles of modularity may improve the rate of success of many Free/Open Source software projects. Specific case studies here depicted, as well as indirect observation of common programming practices employed by Free/Open Source developers and users, suggest a possible revision towards an improved theory of modularity that may be extended also to settings different from software production. Keywords: modularity, software project management, Free/Open Source Software, division of labor, coordination, information hiding.},
  file      = {:by-author/N/Narduzzo/2003_Narduzzo.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Nasim2004,
  author    = {Nasim, M. T. and Eperon, I. C. and Wilkins, B. M. and Brammar, W. J.},
  journal   = {Molecular microbiology},
  title     = {The activity of a single-stranded promoter of plasmid ColIb-P9 depends on its secondary structure.},
  year      = {2004},
  pages     = {405--17},
  volume    = {53},
  abstract  = {The leading region of the conjugal bacterial plasmid ColIb-P9 contains three dispersed repeats of a 328 bp sequence homologous to Frpo, a sequence from plasmid F that acts as a promoter in single-stranded DNA. One of these sequences, ssi3, inactive in the double-stranded form, promoted in vitro transcription exclusively from the single strand that is transferred during conjugation. Promoter activity was dependent on the presence of RNA polymerase holoenzyme containing sigma 70. Transcription initiated from the position predicted from folding the single-stranded DNA to form a pseudo double-stranded hairpin structure containing recognizable -35 and -10 promoter elements. Footprinting of RNA polymerase holoenzyme on single-stranded ssi3 DNA was consistent with this suggestion. Mutagenesis of the putative -35 region inactivated the promoter, but random mutations in the -10 region had little effect. The putative -10 region is a poor match to the consensus sequence and contains mismatched bases. Elimination of these mismatches invariably destroyed single-strand promoter activity. These observations reveal the crucial contribution of the unpaired bases in the -10 region in potentiating the formation of the productive open complex with RNA polymerase.},
  file      = {:by-author/N/Nasim/2004_Nasim_405.pdf:PDF},
  keywords  = {Antirestriction},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Nature2013,
  author    = {Nature},
  journal   = {Nature},
  title     = {The future of publishing: A new page},
  year      = {2013},
  pages     = {425},
  volume    = {425},
  abstract  = {After 350 years in the slow-moving world of print, scientific publishing has been thrust into a fast-paced online realm of cloud computing and ubiquitous sharing. The result has been an era of ferment, as established practices are challenged by new ones — most notably, the open-access model in which the author pays publication fees upfront.},
  doi       = {10.1038/495425a},
  file      = {2013_Nature_425.pdf:by-author/N/NATURE/2013_Nature_425.pdf:PDF},
  keywords  = {Communication Policy; Open Access; Publishing; Research Management; Scientific Publication},
  owner     = {saulius},
  timestamp = {2013.04.03},
  creationdate = {2013-04-03T00:00:00},
  url       = {http://www.nature.com/news/the-future-of-publishing-a-new-page-1.12665},
}

@Article{Nau2001,
  author    = {Robert F. Nau},
  journal   = {Theory and Decision},
  title     = {De Finetti Was Right: Probability Does Not Exist},
  year      = {2001},
  pages     = {89--124},
  volume    = {51},
  abstract  = {De Finetti’s treatise on the theory of probability begins with the provocative statement PROBABILITY DOES NOT EXIST, meaning that prob- ability does not exist in an objective sense. Rather, probability exists only subject- ively within the minds of individuals. De Finetti defined subjective probabilities in terms of the rates at which individuals are willing to bet money on events, even though, in principle, such betting rates could depend on state-dependent marginal utility for money as well as on beliefs. Most later authors, from Sav- age onward, have attempted to disentangle beliefs from values by introducing hypothetical bets whose payoffs are abstract consequences that are assumed to have state-independent utility. In this paper, I argue that de Finetti was right all along: PROBABILITY, considered as a numerical measure of pure belief uncon- taminated by attitudes toward money, does not exist. Rather, what exist are de Finetti’s ‘previsions’, or betting rates for money, otherwise known in the literature as ‘risk neutral probabilities’. But the fact that previsions are not measures of pure belief turns out not to be problematic for statistical inference, decision analysis, or economic modeling.},
  file      = {2001_Nau_89.pdf:by-author/N/Nau/2001_Nau_89.pdf:PDF},
  groups    = {sg/Bayesian},
  keywords  = {Bayesian Statistics; Beliefs; Decision Theory; Probability; Statistical Inference; Values},
  owner     = {saulius},
  timestamp = {2012.11.23},
  creationdate = {2012-11-23T00:00:00},
  url       = {http://faculty.fuqua.duke.edu/~rnau/definettiwasright.pdf},
}

@TechReport{Navarro2010,
  author      = {Dan Navarro and Amy Perfors},
  institution = {University of Adelaide},
  title       = {The Metropolis-Hastings Algorithm},
  year        = {2010},
  abstract    = {This note provides a discussion of the Metropolis-Hastings algorithm. If anything the notes doesn’t make sense please contact me (these notes were written by Dan: daniel.navarro@adelaide.edu.au) and I’ll try to fix them!},
  email       = {daniel.navarro@adelaide.edu.au},
  file        = {:by-author/N/Navarro/2010_Navarro_technote.pdf:PDF},
  keywords    = {Metropolis Hastings; Monte Carlo},
  owner       = {saulius},
  pages       = {technote},
  timestamp = {2012.10.04},
  creationdate = {2012-10-04T00:00:00},
}

@InBook{Naylor2008,
  author    = {Matthew Naylor and Colin Runciman},
  chapter   = {The Reduceron: Widening the von Neumann Bottleneck for Graph Reduction Using an FPGA},
  editor    = {Chitil, Olaf and Horv{\'a}th, Zolt{\'a}n and Zs{\'o}k, Vikt{\'o}ria},
  pages     = {219--236},
  publisher = {Springer Berlin Heidelberg},
  title     = {Implementation and Application of Functional Languages: 19th International Workshop, IFL 2007, Freiburg, Germany, September 27-29, 2007. Revised Selected Papers},
  year      = {2008},
  address   = {Berlin, Heidelberg},
  isbn      = {978-3-540-85373-2},
  doi       = {10.1007/978-3-540-85373-2_13},
  file      = {2008_Naylor_129.pdf:by-author/N/Naylor/2008_Naylor_129.pdf:PDF},
  keywords  = {Compiler Construction; Computer Science (CS); FPGA; Functional Programming; Haskel},
  owner     = {saulius},
  timestamp = {2016.03.28},
  creationdate = {2016-03-28T00:00:00},
  url       = {https://www.doc.ic.ac.uk/~wl/icprojects/papers/reduceron08.pdf},
}

@Article{Nebe1998,
  author    = {Gabriele Nebe},
  journal   = {Representation Theory},
  title     = {Finite quaternionic matrix groups},
  year      = {1998},
  pages     = {106--223},
  volume    = {2},
  doi       = {10.1090/S1088-4165-98-00011-9},
  file      = {:by-author/N/Nebe/1998_Nebe_106.pdf:PDF},
  keywords  = {Algebra; Group Theory; Mathematics; Quaternions; Symmetry},
  owner     = {saulius},
  timestamp = {2015.10.09},
  creationdate = {2015-10-09T00:00:00},
  url       = {http://www.ams.org/journals/ert/1998-002-05/S1088-4165-98-00011-9/home.html},
}

@Article{Neely2005,
  author    = {Neely, Robert K. and Daujotyte, Dalia and Grazulis, Saulius and Magennis, Steven W. and Dryden, David T. F. and Klimasauskas, Saulius and Jones, Anita C.},
  journal   = {Nucleic acids research},
  title     = {Time-resolved fluorescence of 2-aminopurine as a probe of base flipping in M.HhaI-DNA complexes.},
  year      = {2005},
  pages     = {6953--60},
  volume    = {33},
  abstract  = {DNA base flipping is an important mechanism in molecular enzymology, but its study is limited by the lack of an accessible and reliable diagnostic technique. A series of crystalline complexes of a DNA methyltransferase, M.HhaI, and its cognate DNA, in which a fluorescent nucleobase analogue, 2-aminopurine (AP), occupies defined positions with respect the target flipped base, have been prepared and their structures determined at higher than 2 A resolution. From time-resolved fluorescence measurements of these single crystals, we have established that the fluorescence decay function of AP shows a pronounced, characteristic response to base flipping: the loss of the very short (approximately 100 ps) decay component and the large increase in the amplitude of the long (approximately 10 ns) component. When AP is positioned at sites other than the target site, this response is not seen. Most significantly, we have shown that the same clear response is apparent when M.HhaI complexes with DNA in solution, giving an unambiguous signal of base flipping. Analysis of the AP fluorescence decay function reveals conformational heterogeneity in the DNA-enzyme complexes that cannot be discerned from the present X-ray structures.},
  file      = {:by-author/N/Neely/2005_Neely_6953.pdf:PDF},
  keywords  = {Ecl18kI EcoRII; TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Nekludova1994,
  author    = {Nekludova, L and Pabo, C O},
  journal   = {Proceedings of the National Academy of Sciences of the United States of America},
  title     = {Distinctive DNA conformation with enlarged major groove is found in Zn-finger-DNA and other protein-DNA complexes.},
  year      = {1994},
  pages     = {6948--52},
  volume    = {91},
  abstract  = {We have analyzed DNA conformations in a series of protein-DNA complexes, and we find that a distinctive conformation--with an enlarged major groove--occurs in a number of different complexes. During this analysis, we also developed a simplified model of DNA structure that illustrates the relative position of (i) the base pairs, (ii) the phosphate backbone, and (iii) the double-helical axis. This model highlights the key structural features of each duplex, facilitating the analysis and comparison of structures that are distinct from canonical A-DNA or B-DNA. Comparing DNA conformations in this way revealed that an otherwise unrelated set of protein-DNA complexes have interesting structural similarities, including an enlarged major groove. We refer to this class of structures as Beg-DNA (where eg means enlarged groove). Since related features occur in such a diverse set of protein-DNA complexes, we suggest that this conformation may have a significant role in protein-DNA recognition.},
  file      = {1994_Nekludova_6948.pdf:by-author/N/Nekludova/1994_Nekludova_6948.pdf:PDF},
  keywords  = {Stacking},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Nelder1965,
  author    = {J. A. Nelder and R. Mead},
  journal   = {The Computer Journal},
  title     = {A Simplex Method For Function Minimization},
  year      = {1965},
  pages     = {308--313},
  abstract  = {A method is described for the minimization of a function of n variables, which depends on the comparison of function values at the (n + 1) vertices of a general simplex, followed by the replacement of the vertex with the highest value by another point. The simplex adapts itself to the local landscape, and contracts on to the final minimum. The method is shown to be effective and computationally compact. A procedure is given for the estimation of the Hessian matrix in the neighbourhood of the minimum, needed in statistical estimation problems.},
  doi       = {10.1093/comjnl/7.4.308},
  file      = {:by-author/N/Nelder/1965_Nelder_308.pdf:PDF},
  owner     = {andrius},
  timestamp = {2012.11.23},
  creationdate = {2012-11-23T00:00:00},
}

@Article{Nelsen2004,
  author    = {Nelsen, Lita L},
  journal   = {Nature reviews. Molecular cell biology},
  title     = {A US perspective on technology transfer: the changing role of the university.},
  year      = {2004},
  pages     = {243--7},
  volume    = {5},
  file      = {Nelsen_2004_243-patents.pdf:by-author/N/Nelsen/2004_Nelsen_243.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Nelson1993,
  author    = {Nelson, M. and Raschke, E. and McClelland, M.},
  journal   = {Nucleic acids research},
  title     = {Effect of site-specific methylation on restriction endonucleases and DNA modification methyltransferases.},
  year      = {1993},
  pages     = {3139--54},
  volume    = {21},
  file      = {:by-author/N/Nelson/1993_Nelson_3139.pdf:PDF},
  keywords  = {TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Presentation{Nelson2004,
  author    = {Robert Nelson},
  title     = {Connectionism: Parallel Distributed Processing Applied to Problems in Language Learning},
  year      = {2004},
  file      = {:by-author/N/Nelson/2004_Nelson.ppt:PPT},
  keywords  = {Computer Science (CS)},
  owner     = {saulius},
  timestamp = {2015.03.03},
  creationdate = {2015-03-03T00:00:00},
}

@Presentation{Nelson2004a,
  author    = {Robert Nelson},
  title     = {Connectionism},
  year      = {2004},
  file      = {:by-author/N/Nelson/2004_Nelson.odp:},
  keywords  = {Computer Science (CS)},
  owner     = {saulius},
  timestamp = {2015.03.03},
  creationdate = {2015-03-03T00:00:00},
}

@Article{Nelson2008,
  author    = {Nelson, Scott W. and Kumar, Ravindra and Benkovic, Stephen J.},
  journal   = {The Journal of biological chemistry},
  title     = {RNA primer handoff in bacteriophage T4 DNA replication: the role of single-stranded DNA-binding protein and polymerase accessory proteins.},
  year      = {2008},
  pages     = {22838--46},
  volume    = {283},
  abstract  = {In T4 phage, coordinated leading and lagging strand DNA synthesis is carried out by an eight-protein complex termed the replisome. The control of lagging strand DNA synthesis depends on a highly dynamic replisome with several proteins entering and leaving during DNA replication. Here we examine the role of single-stranded binding protein (gp32) in the repetitive cycles of lagging strand synthesis. Removal of the protein-interacting domain of gp32 results in a reduction in the number of primers synthesized and in the efficiency of primer transfer to the polymerase. We find that the primase protein is moderately processive, and this processivity depends on the presence of full-length gp32 at the replication fork. Surprisingly, we find that an increase in the efficiency of primer transfer to the clamp protein correlates with a decrease in the dissociation rate of the primase from the replisome. These findings result in a revised model of lagging strand DNA synthesis where the primase remains as part of the replisome after each successful cycle of Okazaki fragment synthesis. A delay in primer transfer results in an increased probability of the primase dissociating from the replication fork. The interplay between gp32, primase, clamp, and clamp loader dictates the rate and efficiency of primer synthesis, polymerase recycling, and primer transfer to the polymerase.},
  file      = {:by-author/N/Nelson/2008_Nelson_22838.pdf:PDF},
  keywords  = {{gp41} Helicase},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Nelson2006,
  author    = {Nelson, Scott W. and Yang, Jingsong and Benkovic, Stephen J.},
  journal   = {The Journal of biological chemistry},
  title     = {Site-directed mutations of T4 helicase loading protein (gp59) reveal multiple modes of DNA polymerase inhibition and the mechanism of unlocking by gp41 helicase.},
  year      = {2006},
  pages     = {8697--706},
  volume    = {281},
  abstract  = {The T4 helicase loading protein (gp59) interacts with a multitude of DNA replication proteins. In an effort to determine the functional consequences of these protein-protein interactions, point mutations were introduced into the gp59 protein. Mutations were chosen based on the available crystal structure and focused on hydrophobic residues with a high degree of solvent accessibility. Characterization of the mutant proteins revealed a single mutation, Y122A, which is defective in polymerase binding and has weakened affinity for the helicase. The interaction between single-stranded DNA-binding protein and Y122A is unaffected, as is the affinity of Y122A for DNA substrates. When standard concentrations of helicase are employed, Y122A is unable to productively load the helicase onto forked DNA substrates. As a result of the loss of polymerase binding, Y122A cannot inhibit the polymerase during nucleotide idling or prevent it from removing the primer strand of a D-loop. However, Y122A is capable of inhibiting strand displacement synthesis by polymerase. The retention of strand displacement inhibition by Y122A, even in the absence of a gp59-polymerase interaction, indicates that there are two modes of polymerase inhibition by gp59. Inhibition of the polymerase activity only requires gp59 to bind to the replication fork, whereas inhibition of the exonuclease activity requires an interaction between the polymerase and gp59. The inability of Y122A to interact with both the polymerase and the helicase suggests a mechanism for polymerase unlocking by the helicase based on a direct competition between the helicase and polymerase for an overlapping binding site on gp59.},
  file      = {:by-author/N/Nelson/2006_Nelson_8697.pdf:PDF},
  keywords  = {{gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Neubuser1980,
  author    = {Neub{\"{u}}ser, J. and Wondratschek, H. and B{\"{u}}low, R.},
  journal   = {Acta Crystallographica Section A},
  title     = {On crystallography in higher dimensions. I. General definitions. Corrigendum},
  year      = {1980},
  pages     = {493},
  volume    = {36},
  abstract  = {It is pointed out that the definition of crystal system as given in Neubüser, Wondratschek & Billow [Acta Cryst. (1971), A27, 517-520] is not dimension-independent. Nevertheless it leads to no ambiguity for dimensions 1, 2, 3, and 4, which are the only ones in which it has been used in subsequent papers. An emendation will be given in Neubüser, Plesken & Wondratschek [match (Informal Commun. Math. Chem.) (1980), to be published].},
  doi       = {10.1107/S0567739480001027},
  file      = {:by-author/N/Neubuser/1980_Neubuser_493.pdf:PDF},
  keywords  = {Higher Dimesions; Spacegroups; Symmetry},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0567739480001027},
}

@Article{Neugebauerova2001,
  author    = {Svatava Neugebauerová and Jaroslav Kypr},
  journal   = {Journal of Biomolecular Structure \& Dynamics},
  title     = {Invariant and Variable Base Stacking Geometries in {B-DNA} and {A-DNA}},
  year      = {2001},
  pages     = {73},
  file      = {:by-author/N/Neugebauerova/2001_Neugebauerova_73.pdf:PDF},
  keywords  = {Conformation; Readout},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Neumann2010,
  author    = {Neumann, Heinz and Wang, Kaihang and Davis, Lloyd and Garcia-Alai, Maria and Chin, Jason W.},
  journal   = {Nature},
  title     = {Encoding multiple unnatural amino acids via evolution of a quadruplet-decoding ribosome},
  year      = {2010},
  issn      = {1476-4687},
  month     = {Feb},
  number    = {7287},
  pages     = {441–444},
  volume    = {464},
  doi       = {10.1038/nature08817},
  file      = {:by-author/N/Neumann/2010_Neumann_441.pdf:PDF},
  groups    = {am/Expanded genetic code},
  owner     = {andrius},
  publisher = {Nature Publishing Group},
  timestamp = {2016.05.02},
  creationdate = {2016-05-02T00:00:00},
  url       = {http://dx.doi.org/10.1038/nature08817},
}

@Article{Neumann2009,
  author    = {Neumann, Marcus Aurelius and Perrin, Marc-Antoine},
  journal   = {CrystEngComm},
  title     = {Can crystal structure prediction guide experimentalists to a new polymorph of paracetamol?},
  year      = {2009},
  pages     = {2475--2479},
  volume    = {11},
  abstract  = {The results of an extensive in silico polymorph screen with the program GRACE of paracetamol in all 230 space groups with one and two molecules in the asymmetric unit are presented. The three experimentally known forms I{,} II and III are found in the list of predicted crystal structures in the correct stability order with rank 1{,} 3 and 6{,} respectively. Structures with ranks 3 to 8 exhibit the same motif of 2-D hydrogen-bonded sheets. The hydrogen-bonding scheme of the rank 2 structure is markedly different from the known forms{,} consisting of two interpenetrating 3-D hydrogen-bonded networks. The excellent agreement with experiment and the prediction of one and only one new packing motif within the lattice energy window delimited by the known forms confirms the fitness for crystal structure prediction of the employed methodology. Analysis of the structure at rank 2 is used to propose experimental strategies that may lead to a new form IV of paracetamol.},
  doi       = {10.1039/B909819D},
  file      = {:by-author/N/Neumann/2009_Neumann_2475.pdf:PDF},
  issue     = {11},
  keywords  = {For TCOD Deposition},
  owner     = {andrius},
  publisher = {The Royal Society of Chemistry},
  timestamp = {2015.10.02},
  creationdate = {2015-10-02T00:00:00},
  url       = {http://pubs.rsc.org/en/Content/ArticleLanding/2009/CE/b909819d},
}

@Article{Neuwald2006,
  author    = {Neuwald, Andrew F.},
  journal   = {Nucleic acids research},
  title     = {Hypothesis: bacterial clamp loader ATPase activation through DNA-dependent repositioning of the catalytic base and of a trans-acting catalytic threonine.},
  year      = {2006},
  pages     = {5280--90},
  volume    = {34},
  abstract  = {The prokaryotic DNA polymerase III clamp loader complex loads the beta clamp onto DNA to link the replication complex to DNA during processive synthesis and unloads it again once synthesis is complete. This minimal complex consists of one delta, one delta' and three gamma subunits, all of which possess an AAA+ module--though only the gamma subunit exhibits ATPase activity. Here clues to underlying clamp loader mechanisms are obtained through Bayesian inference of various categories of selective constraints imposed on the gamma and delta' subunits. It is proposed that a conserved histidine is ionized via electron transfer involving structurally adjacent residues within the sensor 1 region of gamma's AAA+ module. The resultant positive charge on this histidine inhibits ATPase activity by drawing the negatively charged catalytic base away from the active site. It is also proposed that this arrangement is disrupted upon interaction of DNA with basic residues in gamma implicated previously in DNA binding, regarding which a lysine that is near the sensor 1 region and that is highly conserved both in bacterial and in eukaryotic clamp loader ATPases appears to play a critical role. gamma ATPases also appear to utilize a trans-acting threonine that is donated by helix 6 of an adjacent gamma or delta' subunit and that assists in the activation of a water molecule for nucleophilic attack on the gamma phosphorous atom of ATP. As eukaryotic and archaeal clamp loaders lack most of these key residues, it appears that eubacteria utilize a fundamentally different mechanism for clamp loader activation than do these other organisms.},
  file      = {:by-author/N/Neuwald/2006_Neuwald_5280.pdf:PDF},
  groups    = {sg/Bayesian},
  keywords  = {{gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Neuwald2005,
  author    = {Neuwald, Andrew F.},
  journal   = {Nucleic acids research},
  title     = {Evolutionary clues to eukaryotic DNA clamp-loading mechanisms: analysis of the functional constraints imposed on replication factor C AAA+ ATPases.},
  year      = {2005},
  pages     = {3614--28},
  volume    = {33},
  abstract  = {Ring-shaped sliding clamps encircle DNA and bind to DNA polymerase, thereby preventing it from falling off during DNA replication. In eukaryotes, sliding clamps are loaded onto DNA by the replication factor C (RFC) complex, which consists of five distinct subunits (A-E), each of which contains an AAA+ module composed of a RecA-like alpha/beta ATPase domain followed by a helical domain. AAA+ ATPases mediate chaperone-like protein remodeling. Despite remarkable progress in our understanding of clamp loaders, it is still unclear how recognition of primed DNA by RFC triggers ATP hydrolysis and how hydrolysis leads to conformational changes that can load the clamp onto DNA. While these questions can, of course, only be resolved experimentally, the design of such experiments is itself non-trivial and requires that one first formulate the right hypotheses based on preliminary observations. The functional constraints imposed on protein sequences during evolution are potential sources of information in this regard, inasmuch as these presumably are due to and thus reflect underlying mechanisms. Here, rigorous statistical procedures are used to measure and compare the constraints imposed on various RFC clamp-loader subunits, each of which performs a related but somewhat different, specialized function. Visualization of these constraints, within the context of the RFC structure, provides clues regarding clamp-loader mechanisms--suggesting, for example, that RFC-A possesses a triggering component for DNA-dependent ATP hydrolysis. It also suggests that, starting with RFC-A, four RFC subunits (A-D) are sequentially activated through a propagated switching mechanism in which a conserved arginine swings away from a position that disrupts the catalytic Walker B region and into contact with DNA thread through the center of the RFC/clamp complex. Strong constraints near regions of interaction between subunits and with the clamp likewise provide clues regarding possible coupling of hydrolysis-driven conformational changes to the clamp's release and loading onto DNA.},
  file      = {:by-author/N/Neuwald/2005_Neuwald_3614.pdf:PDF},
  keywords  = {{gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Neuwald1999,
  author    = {Neuwald, A. F. and Aravind, L. and Spouge, J. L. and Koonin, E. V.},
  journal   = {Genome research},
  title     = {AAA+: A class of chaperone-like ATPases associated with the assembly, operation, and disassembly of protein complexes.},
  year      = {1999},
  pages     = {27--43},
  volume    = {9},
  abstract  = {Using a combination of computer methods for iterative database searches and multiple sequence alignment, we show that protein sequences related to the AAA family of ATPases are far more prevalent than reported previously. Among these are regulatory components of Lon and Clp proteases, proteins involved in DNA replication, recombination, and restriction (including subunits of the origin recognition complex, replication factor C proteins, MCM DNA-licensing factors and the bacterial DnaA, RuvB, and McrB proteins), prokaryotic NtrC-related transcription regulators, the Bacillus sporulation protein SpoVJ, Mg2+, and Co2+ chelatases, the Halobacterium GvpN gas vesicle synthesis protein, dynein motor proteins, TorsinA, and Rubisco activase. Alignment of these sequences, in light of the structures of the clamp loader delta' subunit of Escherichia coli DNA polymerase III and the hexamerization component of N-ethylmaleimide-sensitive fusion protein, provides structural and mechanistic insights into these proteins, collectively designated the AAA+ class. Whole-genome analysis indicates that this class is ancient and has undergone considerable functional divergence prior to the emergence of the major divisions of life. These proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes. The hexameric architecture often associated with this class can provide a hole through which DNA or RNA can be thread; this may be important for assembly or remodeling of DNA-protein complexes.},
  file      = {:by-author/N/Neuwald/1999_Neuwald_27.pdf:PDF},
  owner     = {em},
  timestamp = {2013.09.19},
  creationdate = {2013-09-19T00:00:00},
}

@Article{Newman2007,
  author    = {Newman, Janet and Xu, Jian and Willis, Michael C.},
  journal   = {Acta crystallographica. Section D, Biological crystallography},
  title     = {Initial evaluations of the reproducibility of vapor-diffusion crystallization.},
  year      = {2007},
  pages     = {826--32},
  volume    = {63},
  abstract  = {Experiments were set up to test how the crystallization drop size affects the crystallization process; in the test cases studied, increasing the drop size led to increasing numbers of crystals. Other data produced from a high-throughput automation-system run were analyzed in order to gauge the effect of replication on the success of crystallization screening. With over 40-fold multiplicity, lysozyme was found to crystallize in over half of the conditions in a standard 96-condition screen. However, despite the fact that industry-standard lysozyme was used in our tests, it was rare that we obtained crystals reproducibly; this suggests that replication whilst screening might improve the success rate of macromolecular crystallization.},
  doi       = {10.1107/S0907444907025784},
  file      = {:by-author/N/Newman/2007_Newman_826.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Newman1994,
  author    = {Newman, Kenneth E.},
  journal   = {Chem. Soc. Rev.},
  title     = {Kirkwood-Buff solution theory: derivation and applications},
  year      = {1994},
  pages     = {31--40},
  volume    = {23},
  abstract  = {The development of rigorous theories of the liquid state and of multi-component liquid mixtures has always been hampered by both the complexity of the statistical mechanics and the complex nature of intermolecular interactions. There are two central themes within chemical thermodynamics. The first deals with internal energy or enthalpy. As an example let us consider the internal energy E of a monatomic solid subject only to pairwise interactions.},
  doi       = {10.1039/CS9942300031},
  file      = {1994_Newman_31.pdf:by-author/N/Newman/1994_Newman_31.pdf:PDF},
  groups    = {sg/Molecular dynamics},
  issue     = {1},
  keywords  = {Statistical Physics; Theory of Solutions},
  owner     = {saulius},
  publisher = {The Royal Society of Chemistry},
  timestamp = {2015.03.13},
  creationdate = {2015-03-13T00:00:00},
  url       = {http://dx.doi.org/10.1039/CS9942300031},
}

@TechReport{Newton1986,
  author      = {Thomas D. Newton},
  institution = {Carnegie Mellon University},
  title       = {An implementation of Ada generics},
  year        = {1986},
  file        = {:by-author/N/Newton/1986_Newton.pdf:PDF},
  owner       = {saulius},
  timestamp = {2015.01.21},
  creationdate = {2015-01-21T00:00:00},
  url         = {http://repository.cmu.edu/cgi/viewcontent.cgi?article=2585&context=compsci},
}

@Article{Ng2012,
  author    = {Ng, E.-P. and Chateigner, D. and Bein, T. and Valtchev, V. and Mintova, S.},
  journal   = {Science},
  title     = {Capturing Ultrasmall EMT Zeolite from Template-Free Systems},
  year      = {2012},
  issn      = {1095-9203},
  month     = {Dec},
  number    = {6064},
  pages     = {70--73},
  volume    = {335},
  abstract  = {Small differences between the lattice energies of different zeolites suggest that kinetic factors are of major importance in controlling zeolite nucleation. Thus, it is critical to control the nucleation kinetics in order to obtain a desired microporous material. Here, we demonstrate how careful investigation of the very early stages of zeolite crystallization in colloidal systems can provide access to important nanoscale zeolite phases while avoiding the use of expensive organic templates. We report the effective synthesis of ultrasmall (6- to 15-nanometer) crystals of the large-pore zeolite EMT from template-free colloidal precursors at low temperature (30°C) and very high yield.},
  doi       = {10.1126/science.1214798},
  file      = {2012_Ng_70.pdf:by-author/N/Ng/2012_Ng_70.pdf:PDF},
  keywords  = {Powder Diffraction; Zeolites},
  owner     = {saulius},
  publisher = {American Association for the Advancement of Science (AAAS)},
  timestamp = {2016.01.22},
  creationdate = {2016-01-22T00:00:00},
  url       = {http://dx.doi.org/10.1126/science.1214798},
}

@InProceedings{Nguyen1998,
  author    = {Nguyen, Dung},
  booktitle = {SIGCSE},
  title     = {Design Patterns for Data Structures},
  year      = {1998},
  pages     = {336--340},
  abstract  = {Design patterns provide ways to structure software componentsinto systemsthat are flexible, extensible, and have a high degreeof reusability. The statepattern, the null , object pattern, and the singleton pattern are used to implement common data structuressuch as lists and trees. These‘patterns help narrow the gap between me abstract views of the data structures and their concrete implementations. The smaller the gap, the higher the level of abstraction.’ The more abstract, the’less complex the coding structure. As‘ a result, algorithms are easier-~ to understand and more manageable. This paper advocates teaching the above design patterns in data structures courses.},
  file      = {:by-author/N/Nguyen/1998_Nguyen_SIGCSE.pdf:PDF},
  keywords  = {Computer Science (CS); Type Systems},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Nguyen2002,
  author    = {Nguyen, L. D. and Cajthamlová, K. and Nguyen, H. T. and Weiser, J. and Holubová, I. and Weiserová, M.},
  journal   = {Folia microbiologica},
  title     = {Identification of the EcoKI and EcoR124I Type I restriction--modification enzyme subunits by non-equilibrium pH gradient two-dimensional gel electrophoresis.},
  year      = {2002},
  pages     = {641--8},
  volume    = {47},
  abstract  = {Effectively optimized and reproducible procedure for monitoring the composition of type I restriction-modification endonucleases EcoKI and EcoR124I by non-equilibrium pH gradient two-dimensional (2-D) gel electrophoresis is described. Three subunits of the enzyme complex, which widely differ from one another in their isoelectric points and molar mass, were identified in crude cell extracts of E. coli. For the first time all three subunits of both EcoKI and EcoR124I were detected as distinct spots on a single 2-D gel. A sensitive immunoblotting procedure was suggested suitable for routine use in determining the identity of individual subunits. Potential application of this method for detailed studies of regulation of the function and stoichiometry of the enzyme complexes is discussed.},
  file      = {:by-author/N/Nguyen/2002_Nguyen_641.pdf:PDF},
  keywords  = {TypeI},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Nguyen2008,
  author    = {P. Q. Nguyen and T. Vidick},
  journal   = {Journal of Mathematical Cryptology},
  title     = {Sieve Algorithms for the Shortest Vector Problem are Practical},
  year      = {2008},
  pages     = {181--207},
  volume    = {2},
  abstract  = {The most famous lattice problem is the Shortest Vector Problem (SVP), which has many applications in cryptology. The best approximation algorithms known for SVP in high dimension rely on a subroutine for exact SVP in low dimension. In this paper, we assess the practicality of the best (theoretical) algorithm known for exact SVP in low dimension: the sieve algorithm proposed by Ajtai, Kumar and Sivakumar (AKS) in 2001. AKS is a randomized algorithm of time and space complexity $2^{O(n)}$, which is theoretically much lower than the super-exponential complexity of all alternative SVP algorithms. Surprisingly, no implementation and no practical analysis of AKS has ever been reported. It was in fact widely believed that AKS was impractical: for instance, Schnorr claimed in 2003 that the constant hidden in the $2^{O(n)}$ complexity was at least 30. In this paper, we show that AKS can actually be made practical: we present a heuristic variant of AKS whose running time is $(4/3+ \eps)^{n}$ polynomial-time operations, and whose space requirement is $(4/3+\eps)^{n/2}$ polynomially many bits. Our implementation can experimentally find shortest lattice vectors up to dimension 50, but is slower than classical alternative SVP algorithms in these dimensions.},
  doi       = {10.1515/JMC.2008.009},
  file      = {:by-author/N/Nguyen/2008_Nguyen_181.pdf:PDF},
  keywords  = {Closest Vector Problem; Simulations},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Nianyi1999,
  author    = {Chen Nianyi and Lu Wencong and Chen Ruiliang and Qin Pei and P Villars},
  journal   = {Journal of Alloys and Compounds},
  title     = {Regularities of formation of ternary intermetallic compounds: Part 1. Ternary intermetallic compounds between nontransition elements},
  year      = {1999},
  issn      = {0925-8388},
  pages     = {120--125},
  volume    = {289},
  abstract  = {The regularities of ternary intermetallic compound formation between nontransition metallic elements have been studied by the atomic parameter-pattern recognition method using Villars’s system of atomic parameters (Rsp, VE, and XMB). It has been found that the representative points of ternary compound forming alloy systems and that of ternary alloy systems without a ternary compound are distributed in different regions in the multi-dimensional space spanned by the atomic parameters or their functions. A hyperpolyhedron model obtained by pattern-recognition methods can be used to describe the boundaries of the zone of ternary compound formation in multi-dimensional space, with good computerized prediction for ternary intermetallic compound formation.},
  doi       = {10.1016/S0925-8388(99)00134-6},
  file      = {1999_Nianyi_120.pdf:by-author/N/Nianyi/1999_Nianyi_120.pdf:PDF},
  keywords  = {Ternary Intermetallic Compounds},
  owner     = {saulius},
  timestamp = {2014.09.07},
  creationdate = {2014-09-07T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/S0925838899001346},
}

@Article{Nicart2008,
  author    = {Florent Nicart},
  journal   = {Software --- Practice and Experience},
  title     = {Towards scalable virtuality in C++},
  year      = {2008},
  month     = {November},
  pages     = {1451--1473},
  abstract  = {This article describes a programming technique that allows a size reduction of C++ objects by designing classes in a particular way. In order to reduce the size of the objects to the extreme, a technique to simulate runtime polymorphism and avoid the addition of the implicit virtual pointer is presented.},
  doi       = {10.1002/spe.871},
  file      = {:by-author/N/Nicart/2008_Nicart_871.pdf:PDF},
  groups    = {sg/C++},
  keywords  = {Bitwise Fields; C++; C++ Classes; Computer Science (CS); Memory Usage; Polymorphism Simulation; Programming Languages; Space Saving; Virtual Function; Virtual Pointer},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Presentation{Nicholls2014,
  author      = {Robert Nicholls},
  title       = {Systematic and Statistical Analysis to Aid Improvement and Validation of {ACEDRG}},
  year        = {2014},
  file        = {:by-author/N/Nicholls/2014_Nicholls_slides.pdf:PDF},
  institution = {MRC Laboratory of Molecular Biology},
  owner       = {andrius},
  timestamp = {2015.07.22},
  creationdate = {2015-07-22T00:00:00},
}

@Manuscript{Nicholls2012a,
  author    = {Robert Nicholls},
  title     = {Select the Optimal Clustering Distance},
  year      = {2012},
  file      = {:by-author/N/Nicholls/2012_Nicholls.pdf:PDF},
  owner     = {saulius},
  timestamp = {2013.07.02},
  creationdate = {2013-07-02T00:00:00},
}

@Article{Nicholls2012,
  author    = {Nicholls, Robert A. and Long, Fei and Murshudov, Garib N.},
  journal   = {Acta Crystallographica Section D},
  title     = {Low-resolution refinement tools in {\it REFMAC}5},
  year      = {2012},
  pages     = {404--417},
  volume    = {68},
  abstract  = {Two aspects of low-resolution macromolecular crystal structure analysis are considered: (i) the use of reference structures and structural units for provision of structural prior information and (ii) map sharpening in the presence of noise and the effects of Fourier series termination. The generation of interatomic distance restraints by ProSMART and their subsequent application in REFMAC5 is described. It is shown that the use of such external structural information can enhance the reliability of derived atomic models and stabilize refinement. The problem of map sharpening is considered as an inverse deblurring problem and is solved using Tikhonov regularizers. It is demonstrated that this type of map sharpening can automatically produce a map with more structural features whilst maintaining connectivity. Tests show that both of these directions are promising, although more work needs to be performed in order to further exploit structural information and to address the problem of reliable electron-density calculation.},
  doi       = {10.1107/S090744491105606X},
  file      = {2012_Nicholls_404.pdf:by-author/N/Nicholls/2012_Nicholls_404.pdf:PDF},
  keywords  = {Algorithms; Crystallography; Protein Crystallography; Structure Refinement; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2013.05.05},
  creationdate = {2013-05-05T00:00:00},
  url       = {http://dx.doi.org/10.1107/S090744491105606X},
}

@Manuscript{Nicolaou1996,
  author    = {Alex Nicolaou},
  title     = {A survey of distributed languages},
  year      = {1996},
  keywords  = {Computer Science (CS); Distributed Languages; Java; Phantom; Programming Languages; Python},
  abstract  = {The huge popularity of the World-Wide Web has provided a new demand for languages that support an elegant model for distributed programming so that the Internet can be fully utilized by programmers. Several new languages have appeared that attempt to provide solutions for the Web. In this paper these languages are looked at as languages in their own right, rather than as special purpose Internet languages. By considering them as serious entries into the language market more interesting observations are possible, perhaps including an intuition as to which of the new languages will be best accepted and used in the future. The languages considered are Java, Phantom, and Python.},
  file      = {:by-author/N/Nicolaou/1996_Nicolaou.ps:PostScript;:by-author/N/Nicolaou/1996_Nicolaou.pdf:PDF},
  owner     = {saulius},
  timestamp = {2015.02.27},
  creationdate = {2015-02-27T00:00:00},
}

@Webpage{Nicolaou1996a,
  author    = {Alex Nicolaou},
  title     = {A survey of distributed languages},
  year      = {1996},
  file      = {:by-author/N/Nicolaou/1996_Nicolaou.html:},
  keywords  = {Computer Science (CS); Languages},
  owner     = {saulius},
  timestamp = {2015.03.03},
  creationdate = {2015-03-03T00:00:00},
}

@Manuscript{Nielsen2012,
  author    = {Frank Nielsen},
  title     = {{k-MLE}: A fast algorithm for learning statistical mixture models},
  year      = {2012},
  keywords  = {Expectation Maximisation; Gaussian Mixture Models},
  abstract  = {We describe k-MLE, a fast and efficient local search algorithm for learning finite statisti- cal mixtures of exponential families such as Gaussian mixture models. Mixture models are traditionally learned using the expectation-maximization (EM) soft clustering technique that monotonically increases the incomplete (expected complete) likelihood. Given prescribed mix- ture weights, the hard clustering k-MLE algorithm iteratively assigns data to the most likely weighted component and update the component models using Maximum Likelihood Estimators (MLEs). Using the duality between exponential families and Bregman divergences, we prove that the local convergence of the complete likelihood of k-MLE follows directly from the con- vergence of a dual additively weighted Bregman hard clustering. The inner loop of k-MLE can be implemented using any k-means heuristic like the celebrated Lloyd’s batched or Hartigan’s greedy swap updates. We then show how to update the mixture weights by minimizing a cross- entropy criterion that implies to update weights by taking the relative proportion of cluster points, and reiterate the mixture parameter update and mixture weight update processes until convergence. Hard EM is interpreted as a special case of k-MLE when both the component up- date and the weight update are performed successively in the inner loop. To initialize k-MLE, we propose k-MLE++, a careful initialization of k-MLE guaranteeing probabilistically a global bound on the best possible complete likelihood.},
  file      = {:by-author/N/Nielsen/2012_Nielsen_manuscript.pdf:PDF},
  groups    = {am/Expectation maximisation},
  owner     = {andrius},
  timestamp = {2013.11.07},
  creationdate = {2013-11-07T00:00:00},
}

@TechReport{Nieto-Santisteban2004,
  author      = {María A. Nieto-Santisteban and Jim Gray and Alexander S. Szalay and James Annis and Aniruddha R. Thakar and William J. O’Mullane},
  institution = {Microsoft Corporation},
  title       = {When Database Systems Meet The Grid},
  year        = {2004},
  abstract    = {We illustrate the benefits of combining database systems and Grid technologies for data-intensive applications. Using a cluster of SQL servers, we reimplemented an existing Grid application that finds galaxy clusters in a large astronomical database. The SQL implementation runs an order of magnitude faster than the earlier Tcl-C-file- based implementation. We discuss why and how Grid applications can take advantage of database systems.},
  booktitle   = {Proceedings of the 2005 CIDR Conference},
  file        = {:by-author/N/Nieto-Santisteban/2004_Nieto-Santisteban.pdf:PDF},
  owner       = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Niggli1929,
  author    = {Niggli, P.},
  journal   = {Geologiska Föreningen i Stockholm Förhandlingar},
  title     = {Krystallographische und strukturtheoretische Grundbegriffe (Handbuch der Experimentalphysik, Bd VII, 1)},
  year      = {1929},
  pages     = {121--122},
  volume    = {51},
  doi       = {10.1080/11035892909447060},
  file      = {1929_Niggli_121.pdf:by-author/N/Niggli/1929_Niggli_121.pdf:PDF},
  keywords  = {Reduced Cell},
  owner     = {saulius},
  timestamp = {2014.11.19},
  creationdate = {2014-11-19T00:00:00},
}

@Article{Nikolaienko2021,
  author  = {Tymofii Yu. Nikolaienko and Leonid A. Bulavin},
  journal = {Computational and Theoretical Chemistry},
  title   = {The machine-learned radii of atoms},
  year    = {2021},
  issn    = {2210-271X},
  pages   = {113389},
  volume  = {1204},
  doi     = {10.1016/j.comptc.2021.113389},
  file    = {2021_Nikolaienko_113389.pdf:by-author/N/Nikolaienko/2021_Nikolaienko_113389.pdf},
  url     = {https://www.sciencedirect.com/science/article/pii/S2210271X21002474},
  creationdate = {2021-10-08T14:56:19},
  owner     = {andrius},
  modificationdate = {2022-12-24T18:34+02:00},
}

@Article{Nikolajewa2005,
  author       = {Svetlana Nikolajewa and Andreas Beyer and Maik Friedel and Jens Hollunder and Thomas Wilhelm},
  journal      = {Nucleic Acids Res},
  title        = {Common patterns in type II restriction enzyme binding sites.},
  year         = {2005},
  number       = {8},
  pages        = {2726--2733},
  volume       = {33},
  abstract     = {Restriction enzymes are among the best studied examples of DNA binding proteins. In order to find general patterns in DNA recognition sites, which may reflect important properties of protein-DNA interaction, we analyse the binding sites of all known type II restriction endonucleases. We find a significantly enhanced GC content and discuss three explanations for this phenomenon. Moreover, we study patterns of nucleotide order in recognition sites. Our analysis reveals a striking accumulation of adjacent purines (R) or pyrimidines (Y). We discuss three possible reasons: RR/YY dinucleotides are characterized by (i) stronger H-bond donor and acceptor clusters, (ii) specific geometrical properties and (iii) a low stacking energy. These features make RR/YY steps particularly accessible for specific protein-DNA interactions. Finally, we show that the recognition sites of type II restriction enzymes are underrepresented in host genomes and in phage genomes.},
  creationdate = {2016-06-16T00:00:00},
  doi          = {10.1093/nar/gki575},
  file         = {:by-author/N/Nikolajewa/2005_Nikolajewa_2726.pdf:PDF;:by-author/N/Nikolajewa/2005_Nikolajewa-suppl.ods:OpenDocument spreadsheet},
  institution  = {Institute of Molecular Biotechnology Beutenbergstrasse 11, D-07745 Jena, Germany.},
  keywords     = {Bacteriophages; Base Sequence; Binding Sites; Chemistry/metabolism; DNA; DNA-Binding Proteins; Deoxyribonucleases; Escherichia Coli K12; GC Rich Sequence; Genetics; Hydrogen Bonding; Type II Site-Specific},
  language     = {eng},
  medline-pst  = {epublish},
  owner        = {em},
  pii          = {33/8/2726},
  pmid         = {15888729},
  timestamp    = {2016.06.16},
  url          = {http://dx.doi.org/10.1093/nar/gki575},
}

@Article{Nikolajewa2005a,
  author    = {Nikolajewa, Svetlana and Beyer, Andreas and Friedel, Maik and Hollunder, Jens and Wilhelm, Thomas},
  journal   = {Nucleic acids research},
  title     = {Common patterns in type II restriction enzyme binding sites.},
  year      = {2005},
  pages     = {2726--33},
  volume    = {33},
  abstract  = {Restriction enzymes are among the best studied examples of DNA binding proteins. In order to find general patterns in DNA recognition sites, which may reflect important properties of protein-DNA interaction, we analyse the binding sites of all known type II restriction endonucleases. We find a significantly enhanced GC content and discuss three explanations for this phenomenon. Moreover, we study patterns of nucleotide order in recognition sites. Our analysis reveals a striking accumulation of adjacent purines (R) or pyrimidines (Y). We discuss three possible reasons: RR/YY dinucleotides are characterized by (i) stronger H-bond donor and acceptor clusters, (ii) specific geometrical properties and (iii) a low stacking energy. These features make RR/YY steps particularly accessible for specific protein-DNA interactions. Finally, we show that the recognition sites of type II restriction enzymes are underrepresented in host genomes and in phage genomes.},
  file      = {:by-author/N/Nikolajewa/2005_Nikolajewa-suppl.ods:OpenDocument spreadsheet;:by-author/N/Nikolajewa/2005_Nikolajewa_2726.pdf:PDF},
  keywords  = {CCGG; DNA Conformation; Indirect Readout; Recognition; Restriction Endonuclease (RE); Review; Specificity},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Nilsson2002,
  author    = {Nilsson, Kristina and Lecerof, David and Sigfridssona, Emma and Rydea, Ulf},
  journal   = {Acta Crystallographica Section D},
  title     = {An Automatic Method to Generate Force-field Parameters for Hetero-compounds},
  year      = {2002},
  pages     = {274--289},
  volume    = {59},
  file      = {:by-author/N/Nilsson/2002_Nilsson_274.pdf:PDF},
  keywords  = {X-ray Crystallography},
  owner     = {andrius},
  timestamp = {2012.05.07},
  creationdate = {2012-05-07T00:00:00},
}

@Article{Nishimasu2014,
  author    = {Nishimasu, Hiroshi and Ran, Ann and Hsu, Patrick D. and Konermann, Silvana and Shehata, Soraya I. and Dohmae, Naoshi and Ishitani, Ryuichiro and Zhang, Feng and Nureki, Osamu},
  journal   = {Cell},
  title     = {Crystal Structure of Cas9 in Complex with Guide RNA and Target DNA},
  year      = {2014},
  pages     = {1--15},
  volume    = {156},
  abstract  = {The CRISPR-associated endonuclease Cas9 can be targeted to specific genomic loci by single guide RNAs (sgRNAs). Here, we report the crystal structure of Streptococcus pyogenes Cas9 in complex with sgRNA and its target DNA at 2.5 A resolution. The structure revealed a bilobed architecture composed of target recognition and nuclease lobes, accommo- dating the sgRNA:DNA heteroduplex in a positively charged groove at their interface. Whereas the recognition lobe is essential for binding sgRNA and DNA, the nuclease lobe contains the HNH and RuvC nuclease domains, which are properly posi- tioned for cleavage of the complementary and noncomplementary strands of the target DNA, respectively. The nuclease lobe also contains a carboxyl-terminal domain responsible for the inter- action with the protospacer adjacent motif (PAM). This high-resolution structure and accompanying functional analyses have revealed the molecular mechanism of RNA-guided DNA targeting by Cas9, thus paving the way for the rational design of new, versatile genome-editing technologies.},
  doi       = {10.1016/j.cell.2014.02.001},
  file      = {:by-author/N/Nishimori/2005_Nishimori_3828.pdf:PDF},
  groups    = {sg/CRISPR-Cas},
  keywords  = {CRISPR; Cas9; Crystal Structure},
  owner     = {em},
  timestamp = {2014.02.14},
  creationdate = {2014-02-14T00:00:00},
}

@Article{Nishimori2005,
  author    = {Nishimori, Isao and Vullo, Daniela and Innocenti, Alessio and Scozzafava, Andrea and Mastrolorenzo, Antonio and Supuran, Claudiu T},
  journal   = {Bioorganic \&amp; medicinal chemistry letters},
  title     = {Carbonic anhydrase inhibitors: inhibition of the transmembrane isozyme XIV with sulfonamides.},
  year      = {2005},
  pages     = {3828--33},
  volume    = {15},
  file      = {2005_Nishimori_3828.pdf:by-author/N/Nishimori/2005_Nishimori_3828.pdf:PDF},
  groups    = {sg/inhibitors, sg/hCA14},
  keywords  = {CA14; Carbonic Anhydrases},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Nishio2004,
  author    = {Nishio, Motohiro},
  journal   = {Cryst. Eng. Comm.},
  title     = {CH/{\pi} hydrogen bonds in crystals},
  year      = {2004},
  pages     = {130--158},
  volume    = {6},
  doi       = {10.1039/b313104a},
  file      = {Nishio_2004_130-weak_CHpi-Hbonds.pdf:by-author/N/Nishio/2004_Nishio_130.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://pubs.rsc.org/en/Content/ArticleLanding/2004/CE/b313104a},
}

@TechReport{NISO2004,
  author      = {NISO},
  institution = {NISO},
  title       = {Understanding Metadata},
  year        = {2004},
  file        = {:by-author/N/NISO/2004_NISO.pdf:PDF},
  isbn        = {1-880124-62-9},
  owner       = {saulius},
  timestamp = {2014.09.08},
  creationdate = {2014-09-08T00:00:00},
  url         = {http://www.niso.org/publications/press/UnderstandingMetadata.pdf},
}

@Article{Nityananda1982,
  author    = {Rajaram Nityananda and Ramesh Narayan},
  journal   = {J. Astrophys. Astr.},
  title     = {Maximum Entropy Image Reconstruction – A Practical Non- Information-Theoretic Approach},
  year      = {1982},
  pages     = {419--450},
  volume    = {3},
  abstract  = {The maximum entropy method (MEM) of image reconstruct- tion is discussed in the context of incomplete Fourier information (as in aperture synthesis). Several current viewpoints on the conceptual foundation of the method are analysed and found to be unsatisfactory. It is concluded that the MEM is a form of model-fitting, the model being a non-linear transform of a band-limited function. A whole family of ‘entropies’ can be constructed to give reconstructions which (a) are individually unique, (b) have sharpened peaks and (c) have flattened baselines. The widely discussed 1nB and – B1nB forms of the entropy are particular cases and lead to Lorentzian and Gaussian shaped peaks respectively. However, they hardly exhaust the possibilities–for example, B1/2 is equally good. The two essential features of peak sharpening and baseline flattening are shown to depend on a parameter which can be controlled by adding a suitable constant to the zero spacing correlation ρ00. This process, called FLOATing, effectively tames much of the unphysical behaviour noted in earlier studies of the MEM. A numerical scheme for obtaining the MEM reconstruction is described. This incorporates the FLOAT feature and uses the fast Fourier transform (FFT), requiring about a hundred FFTs for convergence. Using a model brightness distribution, the MEM reconstructions obtained for different entropies and different values of the resolution parameter are compared. The results sub- stantiate the theoretically deduced properties of the MEM. To allow for noise in the data, the least-squares approach has been widely used. It is shown that this method is biased since it leads to deter- ministic residuals which do not have a Gaussian distribution. It is suggest- ed that fitting the noisy data exactly has the advantage of being unbiased even though the noise appears in the final map. A comparison of the strengths and weaknesses of the MEM and CLEAN suggests that the MEM already has a useful role to play in image reconstruction.},
  file      = {:by-author/N/Nityananda/1982_Nityananda_419.pdf:PDF},
  keywords  = {Image Reconstruction; MaxEnt; Maximum Entropy},
  owner     = {saulius},
  timestamp = {2012.10.05},
  creationdate = {2012-10-05T00:00:00},
  url       = {http://repository.ias.ac.in/26460/1/307.pdf},
}

@Article{Niv2007,
  author    = {Niv, Masha Y. and Ripoll, Daniel R. and Vila, Jorge A. and Liwo, Adam and Vanamee, Eva S. and Aggarwal, Aneel K. and Weinstein, Harel and Scheraga, Harold A.},
  journal   = {Nucleic acids research},
  title     = {Topology of Type II REases revisited; structural classes and the common conserved core.},
  year      = {2007},
  pages     = {2227--37},
  volume    = {35},
  abstract  = {Type II restriction endonucleases (REases) are deoxyribonucleases that cleave DNA sequences with remarkable specificity. Type II REases are highly divergent in sequence as well as in topology, i.e. the connectivity of secondary structure elements. A widely held assumption is that a structural core of five beta-strands flanked by two alpha-helices is common to these enzymes. We introduce a systematic procedure to enumerate secondary structure elements in an unambiguous and reproducible way, and use it to analyze the currently available X-ray structures of Type II REases. Based on this analysis, we propose an alternative definition of the core, which we term the alphabetaalpha-core. The alphabetaalpha-core includes the most frequently observed secondary structure elements and is not a sandwich, as it consists of a five-strand beta-sheet and two alpha-helices on the same face of the beta-sheet. We use the alphabetaalpha-core connectivity as a basis for grouping the Type II REases into distinct structural classes. In these new structural classes, the connectivity correlates with the angles between the secondary structure elements and with the cleavage patterns of the REases. We show that there exists a substructure of the alphabetaalpha-core, namely a common conserved core, ccc, defined here as one alpha-helix and four beta-strands common to all Type II REase of known structure.},
  file      = {:by-author/N/Niv/2007_Niv_2227.pdf:PDF},
  keywords  = {Evolution; TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@InBook{Nobile2014,
  author    = {Nobile, Nicola and Suen, Ching Y.},
  chapter   = {Text Segmentation for Document Recognition},
  editor    = {Doermann, David and Tombre, Karl},
  pages     = {257--290},
  publisher = {Springer London},
  title     = {Handbook of Document Image Processing and Recognition},
  year      = {2014},
  address   = {London},
  isbn      = {978-0-85729-859-1},
  abstract  = {Document segmentation is the process of dividing a document (handwritten or printed) into its base components (lines, words, characters). Once the zones (text and non-text) have been identified, the segmentation of the text elements can begin. Several challenges exist which need to be worked out in order to segment the elements correctly. For line segmentation, touching, broken, or overlapping text lines frequently occur. Handwritten documents have the additional challenge of curvilinear lines. Once a line has been segmented, it is processed to further segment it into characters. Similar problems of touching and broken elements exist for characters. An added level of complexity exists since documents have a degree of noise which can come from scanning, photocopying, or from physical damage. Historical documents have some amount of degradation to them. In addition, variation of typefaces, for printed text, and styles for handwritten text bring new difficulties for segmentation and recognition algorithms. This chapter contains descriptions of some methodologies, presented from recent research, that propose solutions that overcome these obstacles. Line segmentation solutions include horizontal projection, region growth techniques, probability density, and the level set method as possible, albeit partial, solutions. A method of angle stepping to detect angles for slanted lines is presented. Locating the boundaries of characters in historical, degraded ancient documents employs multi-level classifiers, and a level set active contour scheme as a possible solution. Mathematical expressions are generally more complex since the layout does not follow standard and typical text blocks. Lines can be composed of split sections (numerator and denominator), can have symbols spanning and overlapping other elements, and contain a higher concentration of superscript and subscript characters than regular text lines. Template matching is described as a partial solution to segment these characters. The methods described here apply to both printed and handwritten. They have been tested on Latin-based scripts as well as Arabic, Dari, Farsi, Pashto, and Urdu.},
  doi       = {10.1007/978-0-85729-859-1_8},
  file      = {2014_Nobile_257.pdf:by-author/N/Nobile/2014_Nobile_257.pdf:PDF},
  groups    = {sg/Text segmentation},
  keywords  = {OCR; Text Segmentation},
  owner     = {saulius},
  timestamp = {2016.02.05},
  creationdate = {2016-02-05T00:00:00},
  url       = {http://dx.doi.org/10.1007/978-0-85729-859-1_8},
}

@Article{Nodelman1999,
  author    = {Nodelman, I. M. and Bowman, G. D. and Lindberg, U. and Schutt, C. E.},
  journal   = {Journal of molecular biology},
  title     = {X-ray structure determination of human profilin II: A comparative structural analysis of human profilins.},
  year      = {1999},
  pages     = {1271--85},
  volume    = {294},
  abstract  = {Human profilins are multifunctional, single-domain proteins which directly link the actin microfilament system to a variety of signalling pathways via two spatially distinct binding sites. Profilin binds to monomeric actin in a 1:1 complex, catalyzes the exchange of the actin-bound nucleotide and regulates actin filament barbed end assembly. Like SH3 domains, profilin has a surface-exposed aromatic patch which binds to proline-rich peptides. Various multidomain proteins including members of the Ena/VASP and formin families localize profilin:actin complexes through profilin:poly-L-proline interactions to particular cytoskeletal locations (e.g. focal adhesions, cleavage furrows). Humans express a basic (I) and an acidic (II) isoform of profilin which exhibit different affinities for peptides and proteins rich in proline residues. Here, we report the crystallization and X-ray structure determination of human profilin II to 2.2 A. This structure reveals an aromatic extension of the previously defined poly-L-proline binding site for profilin I. In contrast to serine 29 of profilin I, tyrosine 29 in profilin II is capable of forming an additional stacking interaction and a hydrogen bond with poly-L-proline which may account for the increased affinity of the second isoform for proline-rich peptides. Differential isoform specificity for proline-rich proteins may be attributed to the differences in charged and hydrophobic residues in and proximal to the poly-L-proline binding site. The actin-binding face remains nearly identical with the exception of five amino acid differences. These observations are important for the understanding of the functional and structural differences between these two classes of profilin isoforms.},
  file      = {:by-author/N/Nodelman/1999_Nodelman_1271.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Nolan2006,
  author    = {James M. Nolan and Vasiliy Petrov and Claire Bertrand and Henry M. Krisch and Jim D. Karam},
  journal   = {Virology Journal},
  title     = {Genetic diversity among five T4-like bacteriophages},
  year      = {2006},
  pages     = {30},
  volume    = {3},
  abstract  = {Background: Bacteriophages are an important repository of genetic diversity. As one of the major constituents of terrestrial biomass, they exert profound effects on the earth's ecology and microbial evolution by mediating horizontal gene transfer between bacteria and controlling their growth. Only limited genomic sequence data are currently available for phages but even this reveals an overwhelming diversity in their gene sequences and genomes. The contribution of the T4-like phages to this overall phage diversity is difficult to assess, since only a few examples of complete genome sequence exist for these phages. Our analysis of five T4-like genomes represents half of the known T4-like genomes in GenBank. Results: Here, we have examined in detail the genetic diversity of the genomes of five relatives of bacteriophage T4: the Escherichia coli phages RB43, RB49 and RB69, the Aeromonas salmonicida phage 44RR2.8t (or 44RR) and the Aeromonas hydrophila phage Aeh1. Our data define a core set of conserved genes common to these genomes as well as hundreds of additional open reading frames (ORFs) that are nonconserved. Although some of these ORFs resemble known genes from bacterial hosts or other phages, most show no significant similarity to any known sequence in the databases. The five genomes analyzed here all have similarities in gene regulation to T4. Sequence motifs resembling T4 early and late consensus promoters were observed in all five genomes. In contrast, only two of these genomes, RB69 and 44RR, showed similarities to T4 middle-mode promoter sequences and to the T4 motA gene product required for their recognition. In addition, we observed that each phage differed in the number and assortment of putative genes encoding host-like metabolic enzymes, tRNA species, and homing endonucleases. Conclusion: Our observations suggest that evolution of the T4-like phages has drawn on a highly diverged pool of genes in the microbial world. The T4-like phages harbour a wealth of genetic material that has not been identified previously. The mechanisms by which these genes may have arisen may differ from those previously proposed for the evolution of other bacteriophage genomes.},
  doi       = {10.1186/1743-422X-3-30},
  file      = {2006_Nolan_30.pdf:by-author/N/Nolan/2006_Nolan_30.pdf:PDF},
  keywords  = {Genome; Phages; T4; {gp41} Helicase},
  owner     = {em},
  timestamp = {2011.06.25},
  creationdate = {2011-06-25T00:00:00},
}

@Article{Noller1992,
  author    = {Noller, H F and Hoffarth, V and Zimniak, L},
  journal   = {Science (New York, N.Y.)},
  title     = {Unusual resistance of peptidyl transferase to protein extraction procedures.},
  year      = {1992},
  pages     = {1416--9},
  volume    = {256},
  file      = {1992_Noller_1416.pdf:by-author/N/Noller/1992_Noller_1416.pdf:PDF},
  keywords  = {Ribozymes},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Noorden2013,
  author    = {Richard van Noorden},
  journal   = {Nature},
  title     = {Open access: The true cost of science publishing},
  year      = {2013},
  pages     = {426--429},
  volume    = {495},
  abstract  = {Cheap open-access journals raise questions about the value publishers add for their money.},
  doi       = {10.1038/495426a},
  file      = {2013_Noorden_426.pdf:by-author/N/Noorden/2013_Noorden_426.pdf:PDF},
  keywords  = {Communication Policy; Open Access; Publishing; Research Management; Scientific Publication},
  owner     = {saulius},
  timestamp = {2013.04.03},
  creationdate = {2013-04-03T00:00:00},
}

@Article{Noort2004,
  author    = {van Noort, John and van der Heijden, Thijn and Dutta, Christina F. and Firman, Keith and Dekker, Cees},
  journal   = {Nucleic acids research},
  title     = {Initiation of translocation by Type I restriction-modification enzymes is associated with a short DNA extrusion.},
  year      = {2004},
  pages     = {6540--7},
  volume    = {32},
  abstract  = {Recognition of 'foreign' DNA by Type I restriction-modification (R-M) enzymes elicits an ATP-dependent switch from methylase to endonuclease activity, which involves DNA translocation by the restriction subunit HsdR. Type I R-M enzymes are composed of three (Hsd) subunits with a stoichiometry of HsdR2:HsdM2:HsdS1 (R2-complex). However, the EcoR124I R-M enzyme can also exist as a cleavage deficient, sub-assembly of HsdR1:HsdM2:HsdS1 (R1-complex). ATPS was used to trap initial translocation complexes, which were visualized by Atomic Force Microscopy (AFM). In the R1-complex, a small bulge, associated with a shortening in the contour-length of the DNA of 8 nm, was observed. This bulge was found to be sensitive to single-strand DNA nucleases, indicative of non-duplexed DNA. R2-complexes appeared larger in the AFM images and the DNA contour length showed a shortening of approximately 11 nm, suggesting that two bulges were formed. Disclosure of the structure of the first stage after the recognition-translocation switch of Type I restriction enzymes forms an important first step in resolving a detailed mechanistic picture of DNA translocation by SF-II DNA translocation motors.},
  file      = {:by-author/v/vanNoort/2004_Noort_6540.pdf:PDF},
  keywords  = {TypeI},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Norcum2005,
  author    = {Norcum, Mona T. and Warrington, J. Anthony and Spiering, Michelle M. and Ishmael, Faoud T. and Trakselis, Michael A. and Benkovic, Stephen J.},
  journal   = {Proceedings of the National Academy of Sciences of the United States of America},
  title     = {Architecture of the bacteriophage T4 primosome: electron microscopy studies of helicase (gp41) and primase (gp61).},
  year      = {2005},
  pages     = {3623--6},
  volume    = {102},
  abstract  = {Replication of DNA requires helicase and primase activities as part of a primosome assembly. In bacteriophage T4, helicase and primase are separate polypeptides for which little structural information is available and whose mechanism of association within the primosome is not yet understood. Three-dimensional structural information is provided here by means of reconstructions from electron microscopic images. Structures have been calculated for complexes of each of these proteins with ssDNA in the presence of MgATPgammaS. Both the helicase (gp41) and primase (gp61) complexes are asymmetric hexagonal rings. The gp41 structure suggests two distinct forms that have been termed "open" and "closed." The gp61 structure is clearly a six-membered ring, which may be a trimer of dimers or a traditional hexamer of monomers. This structure provides conclusive evidence for an oligomeric primase-to-ssDNA stoichiometry of 6:1.},
  file      = {:by-author/N/Norcum/2005_Norcum_3623.pdf:PDF},
  keywords  = {{gp41}; {gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@InProceedings{Nordstrom1978,
  author    = {Nordström, Bengt},
  booktitle = {ACM '78 Proceedings of the 1978 annual conference},
  title     = {Assignments and high level data types},
  year      = {1978},
  pages     = {630--638},
  volume    = {2},
  abstract  = {If x and y are integer variables or any other variables of a "simple" type, then the meaning of the assignment x:=y is quite similar in different prograu~aing languages. The value of y is copied (into a register) and then stored into x so that a fresh copy of the value of y becomes the current value of x. On the other hand if x and y are compound objects the the situation is quite different: some languages don't allow assign- ments at all, and other languages call for a conditional copying depending on the form of the right hand side. This paper argues for a unified view on assignment with semantics, that can be described in terms independent of the complexity of the type of the variables involved. We also present some alternatives to assignments and discuss their consequences for programming with complex data types.},
  doi       = {10.1145/800178.810101},
  file      = {:by-author/N/Nordstrom/1978_Nordstrom_ACM78.pdf:PDF},
  keywords  = {Adress; Assignment; Computer Science (CS); Data Types; Mathematical Semantics; Pointers; Programming Languages; Type Systems},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Nordstrom2000,
  author    = {Nordstrom, Darrell Kirk and Alpers, Charles N. aand Ptacek, Carol J. and Blowes, David W.},
  journal   = {Environmental Science \& Technology},
  title     = {Negative pH and Extremely Acidic Mine Waters from Iron Mountain, California},
  year      = {2000},
  pages     = {254--258},
  volume    = {34},
  abstract  = {Extremely acidic mine waters with pH values as low as −3.6, total dissolved metal concentrations as high as 200 g/L, and sulfate concentrations as high as 760 g/L, have been encountered underground in the Richmond Mine at Iron Mountain, CA. These are the most acidic waters known. The pH measurements were obtained by using the Pitzer method to define pH for calibration of glass membrane electrodes. The calibration of pH below 0.5 with glass membrane electrodes becomes strongly nonlinear but is reproducible to a pH as low as −4. Numerous efflorescent minerals were found forming from these acid waters. These extreme acid waters were formed primarily by pyrite oxidation and concentration by evaporation with minor effects from aqueous ferrous iron oxidation and efflorescent mineral formation.},
  doi       = {10.1021/es990646v},
  file      = {2000_Nordstrom_254.pdf:by-author/N/Nordstrom/2000_Nordstrom_254.pdf:PDF},
  issne     = {1520-5851},
  issnp     = {0013-936X},
  issue     = {2},
  keywords  = {Acidic Mine Waste; Extreme pH; Negative pH; Pyrite; Waste Water; {pH}},
  owner     = {saulius},
  publisher = {American Chemical Society},
  timestamp = {2013.10.18},
  creationdate = {2013-10-18T00:00:00},
  url       = {http://libgen.org/scimag/index.php?doi=10.1021/es990646v},
}

@Manuscript{Norvaisa2006,
  author    = {Norvaiša, Rimas},
  title     = {Kurtas Gödelis. 100-osios gimimo metinės},
  year      = {2006},
  keywords  = {Goedel's Theorem},
  month     = {July},
  file      = {:by-author/N/Norvaiša/2006_Norvaiša.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Nose1984,
  author    = {Nosé, Shuichi},
  journal   = {The Journal of Chemical Physics},
  title     = {A unified formulation of the constant temperature molecular dynamics methods},
  year      = {1984},
  number    = {1},
  pages     = {511--519},
  volume    = {81},
  doi       = {10.1063/1.447334},
  file      = {1984_Nosé_511.pdf:by-author/N/Nosé/1984_Nosé_511.pdf:PDF},
  groups    = {sg/Molecular dynamics},
  keywords  = {Molecular Dynamics (MD); Thermostate},
  owner     = {saulius},
  timestamp = {2016.02.24},
  creationdate = {2016-02-24T00:00:00},
  url       = {http://scitation.aip.org/content/aip/journal/jcp/81/1/10.1063/1.447334},
}

@Article{Nossal1992,
  author    = {Nossal, N. G.},
  journal   = {The FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
  title     = {Protein-protein interactions at a DNA replication fork: bacteriophage T4 as a model.},
  year      = {1992},
  pages     = {871--8},
  volume    = {6},
  abstract  = {The DNA replication system of bacteriophage T4 serves as a relatively simple model for the types of reactions and protein-protein interactions needed to carry out and coordinate the synthesis of the leading and lagging strands of a DNA replication fork. At least 10 phage-encoded proteins are required for this synthesis: T4 DNA polymerase, the genes 44/62 and 45 polymerase accessory proteins, gene 32 single-stranded DNA binding protein, the genes 61, 41, and 59 primase-helicase, RNase H, and DNA ligase. Assembly of the polymerase and the accessory proteins on the primed template is a stepwise process that requires ATP hydrolysis and is strongly stimulated by 32 protein. The 41 protein helicase is essential to unwind the duplex ahead of polymerase on the leading strand, and to interact with the 61 protein to synthesize the RNA primers that initiate each discontinuous fragment on the lagging strand. An interaction between the 44/62 and 45 polymerase accessory proteins and the primase-helicase is required for primer synthesis on 32 protein-covered DNA. Thus it is possible that the signal for the initiation of a new fragment by the primase-helicase is the release of the polymerase accessory proteins from the completed adjacent fragment.},
  file      = {:by-author/N/Nossal/1992_Nossal_871.pdf:PDF},
  keywords  = {{gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Nossal1979,
  author    = {Nossal, N. G.},
  journal   = {The Journal of biological chemistry},
  title     = {DNA replication with bacteriophage T4 proteins. Purification of the proteins encoded by T4 genes 41, 45, 44, and 62 using a complementation assay.},
  year      = {1979},
  pages     = {6026--31},
  volume    = {254},
  abstract  = {The proteins encoded by bacteriophage T4 genes 41, 45, 44, and 62 are known from the genetic studies of Epstein et al. ((1963) Cold Spring Harbor Symp. Quant. Biol. 28, 375--394) to be required for viral DNA synthesis. A convenient assay for each of these proteins is described which is based on the specific stimulation by each protein of DNA synthesis in extracts of Escherichia coli infected with mutants of bacteriophage T4 unable to make that protein. The T4 41 protein, 45 protein, and the complex of the 44 and 62 proteins have been highly purified. For each protein there is co-chromatography during the final purification step of (i) activity in the complementation assay, (ii) activity required for DNA synthesis with other purified T4 proteins, and (iii) a subunit of the size previously identified as that of the corresponding gene product.},
  file      = {:by-author/N/Nossal/1979_Nossal_6026.pdf:PDF},
  keywords  = {{gp41}; {gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Nowotny2005,
  author    = {Nowotny, Marcin and Gaidamakov, Sergei A and Crouch, Robert J and Yang, Wei},
  journal   = {Cell},
  title     = {Crystal structures of RNase H bound to an RNA/DNA hybrid: substrate specificity and metal-dependent catalysis.},
  year      = {2005},
  pages     = {1005--16},
  volume    = {121},
  abstract  = {RNase H belongs to a nucleotidyl-transferase superfamily, which includes transposase, retroviral integrase, Holliday junction resolvase, and RISC nuclease Argonaute. We report the crystal structures of RNase H complexed with an RNA/DNA hybrid and a mechanism for substrate recognition and two-metal-ion-dependent catalysis. RNase H specifically recognizes the A form RNA strand and the B form DNA strand. Structure comparisons lead us to predict the catalytic residues of Argonaute and conclude that two-metal-ion catalysis is a general feature of the superfamily. In nucleases, the two metal ions are asymmetrically coordinated and have distinct roles in activating the nucleophile and stabilizing the transition state. In transposases, they are symmetrically coordinated and exchange roles to alternately activate a water and a 3'-OH for successive strand cleavage and transfer by a ping-pong mechanism.},
  file      = {Nowotny_2005_1005-RNase_H_complex_struct.pdf:by-author/N/Nowotny/2005_Nowotny_1005.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Manuscript{Noy2002,
  author      = {Natalya F. Noy and Deborah L. McGuinness},
  title       = {Ontology development 101: a guide to creating your first ontology},
  year        = {2002},
  institution = {Stanford University, Stanford, CA, 94305},
  url         = {https://protege.stanford.edu/publications/ontology_development/ontology101.pdf},
  eprint      = {CS; ontologies; Protege},
  file        = {:by-author/N/Noy/2002_Noy_1.pdf:PDF},
  note        = {Publication date taken as the PDF file creation date (S.G.)},
  owner       = {andrius},
  pages       = {1--25},
  timestamp = {2015.10.22},
  creationdate = {2015-10-22T00:00:00},
}

@Article{Noyan1999,
  author    = {Noyan, I. C. and Kaldor, S. K. and Wang, P.-C. and Jordan-Sweet, J.},
  journal   = {Review of Scientific Instruments},
  title     = {A cost-effective method for minimizing the sphere-of-confusion error of x-ray microdiffractometers},
  year      = {1999},
  pages     = {1300--1304},
  volume    = {70},
  abstract  = {Microdiffractometers are used to obtain x-ray diffraction data from regions that are tens of microns or less in size. If a microdiffractometer’s rotation circles do not share the same center, or if the feature of interest on a sample does not lie at the center of all rotations, the sample feature will, upon rotation of the diffractometer circles, precess through a finite volume known as the sphere of confusion (SoC). If the size of the beam used for diffraction analysis is smaller than the SoC diameter, the beam may actually move off the region of interest. In this article, we describe a new technique, based on x-ray fluorescenceimaging and coordinate transforms, which can maintain the sample position to within ±6 μm over all rotations even when a commercial diffractometer is used as the base for the microdiffractometer system. In this scheme, a grid held in place on the specimen surface is mapped using fluorescent radiation at various sample tilts. The transformation matrices, which relate the grid coordinates to the sample stage coordinates at different sample tilts, can then be used to bring the sample stage into coincidence with its original position.},
  doi       = {10.1063/1.1149588},
  file      = {1999_Noyan_1300.pdf:by-author/N/Noyan/1999_Noyan_1300.pdf:PDF},
  keywords  = {Goniometer; Sphere of Confusion; X-ray Crystallography; X-ray Diffractometer},
  owner     = {saulius},
  timestamp = {2014.06.29},
  creationdate = {2014-06-29T00:00:00},
  url       = {http://scitation.aip.org/content/aip/journal/rsi/70/2/10.1063/1.1149588},
}

@Article{Nozaki1971,
  author    = {Nozaki, Y and Tanford, C},
  journal   = {The Journal of biological chemistry},
  title     = {The solubility of amino acids and two glycine peptides in aqueous ethanol and dioxane solutions. Establishment of a hydrophobicity scale.},
  year      = {1971},
  pages     = {2211--7},
  volume    = {246},
  file      = {1971_Nozaki_2211.pdf:by-author/N/Nozaki/1971_Nozaki_2211.pdf:PDF},
  keywords  = {Hydrophobicity; Protein Physics},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Nuland1994,
  author    = {Nico A.J. van Nuland and Ilona W. Hangyi and René C. van Schaik and Herman J.C. Berendsen and Wilfred F. van Gunsteren and Ruud M. Scheek and George T. Robillard},
  journal   = {Journal of Molecular Biology},
  title     = {The High-resolution Structure of the Histidine-containing Phosphocarrier Protein HPr from Escherichia coli Determined by Restrained Molecular Dynamics from Nuclear Magnetic Resonance Nuclear Overhauser Effect Data},
  year      = {1994},
  pages     = {544--559},
  volume    = {237},
  abstract  = {The solution structure of the histidine-containing phosphocarrier protein HPr from Escherichia coli has been determined by NMR in combination with distance geometry and restrained molecular dynamics. The structure is based on 1520 experimental restraints identified from both three-dimensional 1 H-1H-13C and 1 H-1H-15N nuclear Overhauser effect multiple quantum coherence spectroscopy and two dimensional 1H-1H nuclear Overhauser effect spectra. Thirty-two four-dimensional coordinate frames were produced by metric matrix distance geometry, subjected to distance bounds driven dynamics, projected into three-dimensional space and again subjected to distance-bounds driven dynamics. These 32 distance geometry structures were refined further by restrained molecular dynamics (40 ps) in the GROMOS in vacuo force field. All 32 structures reached acceptable energy minima while satisfying the imposed restraints. Two of these structures were subjected to a further 200 ps of molecular dynamics simulation in water, using time-dependent distance restraining, followed by a 200 ps free simulation without any distance restraining. The resulting structure is very similar to the X-ray structure of Bacillus subtilis HPr, but differs mainly in the position of the two loops containing the active site histidine residue 15 and residues 53 to 57 relative to the rest of the structure. The unfavorable φ torsion angle that was found for residue 16 in the active center of unphosphorylated Streptococcus faecalis HPr was proposed to play a role in the activity of the protein. Although present at the early stages of the structure calculations, this torsion-angle strain disappeared in the final model obtained from molecular dynamics simulations in water using time-averaged distance restraining and upon releasing the distance restraints. This suggests that the strain may be an artifact of crystallization conditions instead of an essential element in the phosphorylation/dephosphorylation process.},
  doi       = {10.1006/jmbi.1994.1254},
  file      = {:by-author/N/Nuland/1994_Nuland_544.pdf:PDF},
  keywords  = {Distance Geometry; HPr; Molecular Dynamics (MD); Nuclear Magnetic Resonance; PTS; Protein Bioinformatics; Structure Refinement},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/S002228368471254X},
}

@Manual{Nuutila1989,
  title     = {XE cross-compiler},
  author    = {Nuutila},
  year      = {1989},
  file      = {:by-author/N/Nuutila/1989_Nuutila.pdf:PDF},
  keywords  = {Computer Science (CS); Languages; XE},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Nuzzo2014,
  author    = {Nuzzo, Regina},
  journal   = {Nature},
  title     = {Scientific method: statistical errors.},
  year      = {2014},
  pages     = {150--2},
  volume    = {506},
  file      = {:by-author/N/Nuzzo/2014_Nuzzo_150.pdf:PDF},
  owner     = {saulius},
  timestamp = {2014.03.23},
  creationdate = {2014-03-23T00:00:00},
  url       = {http://www.nature.com/news/scientific-method-statistical-errors-1.14700},
}

@Article{Nwachukwu2013,
  author    = {Jerome C. Nwachukwu and Mark R. Southern and James R. Kiefer and Pavel V. Afonine and Paul D. Adams and Thomas C. Terwilliger and Kendall W. Nettles},
  journal   = {Structure},
  title     = {Improved Crystallographic Structures Using Extensive Combinatorial Refinement},
  year      = {2013},
  issn      = {0969-2126},
  pages     = {1923 - 1930},
  volume    = {21},
  abstract  = {Summary Identifying errors and alternate conformers and modeling multiple main-chain conformers in poorly ordered regions are overarching problems in crystallographic structure determination that have limited automation efforts and structure quality. Here, we show that implementation of a full factorial designed set of standard refinement approaches, termed ExCoR (Extensive Combinatorial Refinement), significantly improves structural models compared to the traditional linear tree approach, in which individual algorithms are tested linearly and are only incorporated if the model improves. ExCoR markedly improved maps and models and reveals building errors and alternate conformations that were masked by traditional refinement approaches. Surprisingly, an individual algorithm that renders a model worse in isolation could still be necessary to produce the best overall model, suggesting that model distortion allows escape from local minima of optimization target function, here shown to be a hallmark limitation of the traditional approach. ExCoR thus provides a simple approach to improving structure determination.},
  doi       = {10.1016/j.str.2013.07.025},
  file      = {2013_Nwachukwu_1923.pdf:by-author/N/Nwachukwu/2013_Nwachukwu_1923.pdf:PDF},
  mid       = {NIHMS523061},
  owner     = {saulius},
  pii       = {S0969-2126(13)00339-0},
  pmc       = {PMC4070946},
  pubmed    = {24076406},
  timestamp = {2013.11.06},
  creationdate = {2013-11-06T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/S0969212613003390},
}

@Article{OBoyle2011a,
  author    = {O'Boyle, Noel and Guha, Rajarshi and Willighagen, Egon and Adams, Samuel and Alvarsson, Jonathan and Bradley, Jean-Claude and Filippov, Igor and Hanson, Robert and Hanwell, Marcus and Hutchison, Geoffrey and James, Craig and Jeliazkova, Nina and Lang, Andrew and Langner, Karol and Lonie, David and Lowe, Daniel and Pansanel, Jerome and Pavlov, Dmitry and Spjuth, Ola and Steinbeck, Christoph and Tenderholt, Adam and Theisen, Kevin and Murray-Rust, Peter},
  journal   = {Journal of Cheminformatics},
  title     = {Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on},
  year      = {2011},
  issn      = {1758-2946},
  pages     = {37},
  volume    = {3},
  abstract  = {BACKGROUND:The Blue Obelisk movement was established in 2005 as a response to the lack of Open Data, Open Standards and Open Source (ODOSOS) in chemistry. It aims to make it easier to carry out chemistry research by promoting interoperability between chemistry software, encouraging cooperation between Open Source developers, and developing community resources and Open Standards.RESULTS:This contribution looks back on the work carried out by the Blue Obelisk in the past 5 years and surveys progress and remaining challenges in the areas of Open Data, Open Standards, and Open Source in chemistry.CONCLUSIONS:We show that the Blue Obelisk has been very successful in bringing together researchers and developers with common interests in ODOSOS, leading to development of many useful resources freely available to the chemistry community.},
  doi       = {10.1186/1758-2946-3-37},
  file      = {:by-author/O/OBoyle/2011_OBoyle_37.pdf:PDF},
  keywords  = {Bioinformatics; Data Access Policy; Data Management},
  owner     = {saulius},
  pubmedid  = {21999342},
  timestamp = {2014.05.14},
  creationdate = {2014-05-14T00:00:00},
  url       = {http://www.jcheminf.com/content/3/1/37},
}

@Presentation{OBoyle2014,
  author    = {Noel M. O'Boyle},
  title     = {Making the most of a QM calculation},
  year      = {2014},
  file      = {2014_OBoyle_slides.ppt:by-author/O/OBoyle/2014_OBoyle_slides.ppt:PowerPoint},
  keywords  = {Data Management; Density Functional Theory (DFT); Quantum Chemistry; Quantum Mechanics (QM)},
  note      = {Year is the download year; the publicatione year was not specified.},
  owner     = {saulius},
  timestamp = {2014.10.21},
  creationdate = {2014-10-21T00:00:00},
  url       = {http://www.redbrick.dcu.ie/~noel/talks/Runcorn_MakingthemostofQM.ppt},
}

@Article{ODonnell1978,
  author    = {O'Donnell, M. and Edwin T. Jaynes and J. G. Miller},
  journal   = {Journal of the Acoustical Society of America},
  title     = {General Relationships between Ultrasonic Attenuation and Dispersion},
  year      = {1978},
  pages     = {1935--1937},
  volume    = {63},
  abstract  = {General relationships between the ultrasonic attenuation and dispersion are presented. The validity of these nonlocal relationships hinges only on the properties of causality and linearity, and does not depend upon details of the mechanism responsible for the attenuation and dispersion. Approximate, nearly local relationships are presented and are demonstrated to predict accurately the ultrasonic dispersion in solutions of hemoglobin from the resuts of attenuation measurements.},
  doi       = {10.1121/1.381902},
  file      = {1978_O'Donnell_1935.pdf:by-author/O/ODonnell/1978_O'Donnell_1935.pdf:PDF},
  groups    = {sg/Bayesian},
  owner     = {saulius},
  timestamp = {2012.10.05},
  creationdate = {2012-10-05T00:00:00},
  url       = {http://bayes.wustl.edu/etj/articles/general.relationship.pdf},
}

@Article{OHagan1979,
  author    = {O'Hagan, A.},
  journal   = {Journal of the Royal Statistical Society. Series B},
  title     = {On Outlier Rejection Phenomena in Bayes Inference},
  year      = {1979},
  number    = {3},
  pages     = {358--367},
  volume    = {41},
  comment   = {Inference is considered for a location parameter given a random sample. Outliers are not explicitly modelled, but rejection of extreme observations occurs naturally in any Bayesian analysis of data from distributions with suitably thick tails. For other distributions outlier rejection behaviour can never occur. These phenomena motivate new definitions of outlier-proneness and outlier-resistance. The definitions and methodology are Bayesian but the conclusions also have meaning for non- Bayesians because they are proved for arbitrary prior distributions. Thus, for example, the t distribution is said to be outlier-prone because it is shown that any admissible inference procedure applied to a t sample will effectively ignore extreme outlying observations regardless of prior information. On the other hand, the normal distribution, for example, is said to be outlier-resistant because it never allows outlier rejection, regardless of prior information},
  file      = {:by-author/O/OHagan/1997_OHagan_358.pdf:PDF},
  groups    = {am/Outliers},
  owner     = {andrius},
  timestamp = {2016.12.12},
  creationdate = {2016-12-12T00:00:00},
  url       = {http://www.jstor.org/stable/2985064},
}

@Article{Sullivan2000,
  author    = {David O'Sullivan and Denis P. Twomey and Aidan Coffey and Colin Hill and Gerald F. Fitzgerald and R. Paul Ross},
  journal   = {Molecular Microbiology},
  title     = {Novel type {I} restriction specificities through domain shuffling of {HsdS} subunits in {L}actococcus lactis},
  year      = {2000},
  pages     = {866--875},
  abstract  = {This study identifies a natural system in Lactococcus lactis, in which a restriction modification specificity subunit resident on a 6159 bp plasmid (pAH33) alters the specificity of a functional R/M mechanism encoded by a 20.3 kb plasmid, pAH82. The new specificity was identified after phenotypic and mole- cular analysis of a 26.5 kb co-integrate plasmid (pAH90), which was detected after bacteriophage challenge of the parent strain. Analysis of the regions involved in the co-integration revealed that two novel hybrid hsdS genes had been formed during the co- integration event. The HsdS chimeras had inter- changed the C- and N-terminal variable domains of the parent subunits, generating two new restriction specificities. Comparison of the parent hsdS genes with other type I specificity determinants revealed that the region of the hsdS genes responsible for the co-integration event is highly conserved among lactococcal type I hsdS determinants. Thus, as hsdS determinants are widespread in the genus Lactococ- cus, new restriction specificities may evolve rapidly after homologous recombination between these genes. This study demonstrates that, similar to previous observations in Gram-negative bacteria, a Gram-positive bacterium can acquire novel restric- tion specificities naturally through domain shuffling of resident HsdS subunits.},
  file      = {:by-author/S/Sullivan/2000_Sullivan_866.pdf:PDF},
  keywords  = {TypeI},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Oakley2005,
  author    = {Oakley, Aaron J. and Loscha, Karin V. and Schaeffer, Patrick M. and Liepinsh, Edvards and Pintacuda, Guido and Wilce, Matthew C. J. and Otting, Gottfried and Dixon, Nicholas E.},
  journal   = {The Journal of biological chemistry},
  title     = {Crystal and solution structures of the helicase-binding domain of Escherichia coli primase.},
  year      = {2005},
  pages     = {11495--504},
  volume    = {280},
  abstract  = {During bacterial DNA replication, the DnaG primase interacts with the hexameric DnaB helicase to synthesize RNA primers for extension by DNA polymerase. In Escherichia coli, this occurs by transient interaction of primase with the helicase. Here we demonstrate directly by surface plasmon resonance that the C-terminal domain of primase is responsible for interaction with DnaB6. Determination of the 2.8-angstroms crystal structure of the C-terminal domain of primase revealed an asymmetric dimer. The monomers have an N-terminal helix bundle similar to the N-terminal domain of DnaB, followed by a long helix that connects to a C-terminal helix hairpin. The connecting helix is interrupted differently in the two monomers. Solution studies using NMR showed that an equilibrium exists between a monomeric species with an intact, extended but naked, connecting helix and a dimer in which this helix is interrupted in the same way as in one of the crystal conformers. The other conformer is not significantly populated in solution, and its presence in the crystal is due largely to crystal packing forces. It is proposed that the connecting helix contributes necessary structural flexibility in the primase-helicase complex at replication forks.},
  file      = {:by-author/O/Oakley/2005_Oakley_11495.pdf:PDF},
  keywords  = {{gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@InProceedings{Oberheide2011,
  author    = {Jon Oberheide and Zach Lanier},
  title     = {DON'T ROOT ROBOTS! - BSides Detroit 2011 Slide},
  year      = {2011},
  comment   = {DON'T ROOT ROBOTS! - BSides Detroit 2011 Slide # 1},
  file      = {:by-author/O/Oberheide/2011_Oberheide.pdf:PDF},
  owner     = {saulius},
  timestamp = {2013.08.10},
  creationdate = {2013-08-10T00:00:00},
}

@Article{Obmolova2000,
  author    = {Obmolova, G. and Ban, C. and Hsieh, P. and Yang, W.},
  journal   = {Nature},
  title     = {Crystal structures of mismatch repair protein MutS and its complex with a substrate DNA.},
  year      = {2000},
  pages     = {703--10},
  volume    = {407},
  abstract  = {DNA mismatch repair is critical for increasing replication fidelity in organisms ranging from bacteria to humans. MutS protein, a member of the ABC ATPase superfamily, recognizes mispaired and unpaired bases in duplex DNA and initiates mismatch repair. Mutations in human MutS genes cause a predisposition to hereditary nonpolyposis colorectal cancer as well as sporadic tumours. Here we report the crystal structures of a MutS protein and a complex of MutS with a heteroduplex DNA containing an unpaired base. The structures reveal the general architecture of members of the MutS family, an induced-fit mechanism of recognition between four domains of a MutS dimer and a heteroduplex kinked at the mismatch, a composite ATPase active site composed of residues from both MutS subunits, and a transmitter region connecting the mismatch-binding and ATPase domains. The crystal structures also provide a molecular framework for understanding hereditary nonpolyposis colorectal cancer mutations and for postulating testable roles of MutS.},
  file      = {:by-author/O/Obmolova/2000_Obmolova_703.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Ochman2000,
  author    = {Ochman, H. and Jones, I. B.},
  journal   = {The EMBO journal},
  title     = {Evolutionary dynamics of full genome content in Escherichia coli.},
  year      = {2000},
  pages     = {6637--43},
  volume    = {19},
  abstract  = {The evolutionary history of the entire Escherichia coli chromosome was traced by examining the distribution of the approximately 4300 open reading frames (ORFs) from E.coli MG1655 among strains of known genealogical relationships. Using this framework to deduce the incidence of gene transfer and gene loss, a total of 67 events-37 additions and 30 deletions-were required to account for the distribution of all genes now present in the MG1655 chromosome. Nearly 90% of the ORFs were common to all strains examined, but, given the variation in gene content and chromosome size, strains can contain well over a megabase of unique DNA, conferring traits that distinguish them from other members of the species. Moreover, strains vary widely in their frequencies of deletions, which probably accounts for the variation in genome size within the species.},
  file      = {:by-author/O/Ochman/2000_Ochman_6637.pdf:PDF},
  keywords  = {Evolution},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@TechReport{Odersky2003,
  author      = {Martin Odersky and Vincent Cremet and Christine Röckl and Matthias Zenger},
  institution = {Ecole Polytechnique Fédérale de Lausanne, INR Ecublens, 1015 Lausanne, Switzerland, martin.odersky@epfl.ch},
  title       = {A Nominal Theory of Objects with Dependent Types},
  year        = {2003},
  file        = {:by-author/O/Odersky/2003_Odersky.pdf:PDF},
  keywords    = {Computer Science (CS); Type Systems},
  owner       = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Odlyzko2001,
  author    = {Odlyzko},
  title     = {Internet pricing and the history of communications},
  year      = {2001},
  abstract  = {There are repeating patterns in the histories of communication technologies, including ordinary mail, the telegraph, the telephone, and the Internet. In particular, the typical story for each service is that quality rises, prices decrease, and usage increases to produce increased total revenues. At the same time, prices become simpler. The historical analogies of this paper suggest that the Internet will evolve in a similar way, towards simplicity. The schemes that aim to provide differentiated service levels and sophisticated pricing schemes are unlikely to be widely adopted. Price and quality differentiation are valuable tools that can provide higher revenues and increase utilization efficiency of a network, and thus in general increase social welfare. Such measures, most noticeable in airline pricing, are spreading to many services and products, especially high-tech ones. However, it appears that as communication services become less expensive and are used more fre- quently, those arguments lose out to customers’ desire for simplicity. In practice, user preferences express themselves through willingness to pay more for simple pricing plans. In addition, there is a strong “threshhold” effect to usage-sensitive billing. Even tiny charges based on utilization decrease usage substantially. In a rapidly growing market, it is in the service providers’ interest to encourage usage, and that argues for simple, preferably flat rate, pricing. Histori- cal evidence suggests that when service costs decrease, such arguments prevail over the need to operate a network at high utilization levels and to extract the highest possible revenues.},
  file      = {:by-author/O/Odlyzko/2001_Odlyzko.pdf:PDF},
  keywords  = {Economy},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Presentation{Ohlssen2009,
  author    = {David Ohlssen and Hayley Jones and Beat Neuenschwander and Amy Racine and Michael Branson},
  title     = {A case-study examining the use of {Bayesian} methods for subgroup analysis in Clinical Trials},
  year      = {2009},
  file      = {David Ohlssen et al. - 2009 - A case-study examining the use of Bayesian methods.pdf:by-author/O/Ohlssen/2009_Ohlssen.pdf:PDF},
  groups    = {sg/Clinical Trials},
  owner     = {saulius},
  timestamp = {2015.12.14},
  creationdate = {2015-12-14T00:00:00},
  url       = {http://www.mdanderson.org/education-and-research/departments-programs-and-labs/departments-and-divisions/division-of-quantitative-sciences/pdf/davidohlssen.pdf.pdf},
  urldate   = {2015-12-12},
}

@InProceedings{Ohori1993,
  author    = {Ohori, Atsushi and Kato, Kazuhiko},
  booktitle = {ACM-20th PoPL},
  title     = {Semantics for Communication Primitives in a Polymorphic Language},
  year      = {1993},
  pages     = {POPL},
  file      = {:by-author/O/Ohori/1993_Ohori_POPL.pdf:PDF},
  keywords  = {Computer Science (CS); Type Systems},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Ohta2004,
  author    = {Ohta, Satoko and Alam, Mohammad Taufiq and Arakawa, Hideo and Ikai, Atsushi},
  journal   = {Biophysical journal},
  title     = {Origin of mechanical strength of bovine carbonic anhydrase studied by molecular dynamics simulation.},
  year      = {2004},
  pages     = {4007--20},
  volume    = {87},
  abstract  = {The forced unfolding process of bovine carbonic anhydrase II (BCA II) was examined at the atomic level by the molecular dynamics (MD) simulation. By force spectroscopy, experimentally obtained force-extension curves (F-E curves) showed a prominent force peak after 50 nm extension. F-E curves obtained from our simulation had three force peaks appearing after extensions of 10-17 nm, 40 nm, and 53 nm, each signifying a brittle fracture of a specific local structure. Upon undergoing the final fracture at 53 nm of extension, the entire molecule became a single flexible chain and was further extended to its full theoretical length, almost as a random coil. This feature of the 53-nm peak strongly suggested its close correspondence to the experimentally observed force peak at approximately 60-nm extension. The 53-nm peak in the molecular dynamics simulation corresponded to the unfolding process of the beta-sheeted core that includes zinc-coordinating histidine residues. These results suggest that the structural change occurring at 50-60 nm in atomic force microscopy experiments corresponded to the destruction of the zinc coordination site.},
  file      = {2004_Ohta_4007.pdf:by-author/O/Ohta/2004_Ohta_4007.pdf:PDF},
  groups    = {sg/modelling, sg/bovine},
  keywords  = {Carbonic Anhydrases},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Oijen2003,
  author    = {van Oijen, Antoine M and Blainey, Paul C and Crampton, Donald J and Richardson, Charles C and Ellenberger, Tom and Xie, X Sunney},
  journal   = {Science (New York, N.Y.)},
  title     = {Single-molecule kinetics of lambda exonuclease reveal base dependence and dynamic disorder.},
  year      = {2003},
  pages     = {1235--8},
  volume    = {301},
  file      = {2003_Oijen_1235.pdf:by-author/v/vanOijen/2003_vanOijen_1235.pdf:PDF},
  keywords  = {Stacking},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Oijen2010,
  author    = {van Oijen, Antoine M. and Loparo, Joseph J.},
  journal   = {Annual review of biophysics},
  title     = {Single-molecule studies of the replisome.},
  year      = {2010},
  pages     = {429--48},
  volume    = {39},
  abstract  = {Replication of DNA is carried out by the replisome, a multiprotein complex responsible for the unwinding of parental DNA and the synthesis of DNA on each of the two DNA strands. The impressive speed and processivity with which the replisome duplicates DNA are a result of a set of tightly regulated interactions between the replication proteins. The transient nature of these protein interactions makes it challenging to study the dynamics of the replisome by ensemble-averaging techniques. This review describes single-molecule methods that allow the study of individual replication proteins and their functioning within the replisome. The ability to mechanically manipulate individual DNA molecules and record the dynamic behavior of the replisome while it duplicates DNA has led to an improved understanding of the molecular mechanisms underlying DNA replication.},
  file      = {:by-author/v/vanOijen/2010_vanOijen_429.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Okonogi2002,
  author    = {Okonogi, T. M. and Alley, S. C. and Reese, A. W. and Hopkins, P. B. and Robinson, B. H.},
  journal   = {Biophysical journal},
  title     = {Sequence-dependent dynamics of duplex DNA: the applicability of a dinucleotide model.},
  year      = {2002},
  pages     = {3446--59},
  volume    = {83},
  abstract  = {The short-time (submicrosecond) bending dynamics of duplex DNA were measured to determine the effect of sequence on dynamics. All measurements were obtained from a single site on duplex DNA, using a single, site-specific modified base containing a rigidly tethered, electron paramagnetic resonance active spin probe. The observed dynamics are interpreted in terms of single-step sequence-dependent bending force constants, determined from the mean squared amplitude of bending relative to the end-to-end vector using the modified weakly bending rod model. The bending dynamics at a single site are a function of the sequence of the nucleotides constituting the duplex DNA. We developed and examined several dinucleotide-based models for flexibility. The models indicate that the dominant feature of the dynamics is best explained in terms of purine- and pyrimidine-type steps, although distinction is made among all 10 unique steps: It was found that purine-purine steps (which are the same as pyrimidine-pyrimidine steps) were near average in flexibility, but the pyrimidine-purine steps (5' to 3') were nearly twice as flexible, whereas purine-pyrimidine steps were more than half as flexible as average DNA. Therefore, the range of stepwise flexibility is approximately fourfold and is characterized by both the type of base pair step (pyrimidine/purine combination) and the identity of the bases within the pair (G, A, T, or C). All of the four models considered here underscore the complexity of the dependence of dynamics on DNA sequence with certain sequences not satisfactorily explainable in terms of any dinucleotide model. These findings provide a quantitative basis for interpreting the dynamics and kinetics of DNA-sequence-dependent biological processes, including protein recognition and chromatin packaging.},
  file      = {:by-author/O/Okonogi/2002_Okonogi_3446.pdf:PDF},
  keywords  = {Deform; Readout},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Okhotnikov2016,
  author    = {Okhotnikov, Kirill and Charpentier, Thibault and Cadars, Sylvian},
  title     = {Supercell program: a combinatorial structure-generation approach for the local-level modeling of atomic substitutions and partial occupancies in crystals},
  journal   = {Journal of Cheminformatics},
  year      = {2016},
  volume    = {8},
  number    = {1},
  pages     = {17},
  month     = {Mar},
  issn      = {1758-2946},
  doi       = {10.1186/s13321-016-0129-3},
  file      = {:by-author/O/Okhotnikov/2016_Okhotnikov_17.pdf:PDF},
  publisher = {Springer Science and Business Media LLC},
  url       = {https://doi.org/10.1186/s13321-016-0129-3},
  owner     = {antanas},
  creationdate = {2021-12-16T18:46:33},
  modificationdate = {2022-12-24T18:39+02:00},
}

@Article{Oldham2008,
  author    = {Michael L. Oldham and Amy L. Davidson and Jue Chen},
  journal   = {Current Opinion in Structural Biology},
  title     = {Structural insights into {ABC} transporter mechanism},
  year      = {2008},
  issn      = {0959-440X},
  pages     = {726--733},
  volume    = {18},
  abstract  = {ATP-binding cassette (ABC) transporters utilize the energy from ATP hydrolysis to transport substances across the membrane. In recent years, crystal structures of several ABC transporters have become available. These structures show that both importers and exporters oscillate between two conformations: an inward-facing conformation with the substrate translocation pathway open to the cytoplasm and an outward-facing conformation with the translocation pathway facing the opposite side of the membrane. In this review, conformational differences found in the structures of homologous ABC transporters are analyzed to understand how alternating-access is achieved. It appears that rigid-body rotations of the transmembrane subunits, coinciding with the opening and closing of the nucleotide-binding subunits, couples ATP hydrolysis to substrate translocation.},
  doi       = {10.1016/j.sbi.2008.09.007},
  file      = {:by-author/O/Oldham/2008_Oldham_726.pdf:PDF},
  owner     = {andrius},
  timestamp = {2014.04.03},
  creationdate = {2014-04-03T00:00:00},
}

@Article{Olechnovic2013,
  author    = {Olechnovič, K. and Kulberkytė, E. and Venclovas, Č.},
  journal   = {Proteins},
  title     = {{CAD}-score: A new contact area difference-based function for evaluation of protein structural models},
  year      = {2013},
  pages     = {149--162},
  volume    = {81},
  abstract  = {Evaluation of protein models against the native structure is essential for the development and benchmarking of protein structure prediction methods. Although a number of evaluation scores have been proposed to date, many aspects of model assessment still lack desired robustness. In this study we present CAD-score, a new evaluation function quantifying differen- ces between physical contacts in a model and the reference structure. The new score uses the concept of residue-residue contact area difference (CAD) introduced by Abagyan and Totrov (J Mol Biol 1997; 268:678–685). Contact areas, the underlying basis of the score, are derived using the Voronoi tessellation of protein structure. The newly introduced CAD-score is a con- tinuous function, confined within fixed limits, free of any arbitrary thresholds or parameters. The built-in logic for treat- ment of missing residues allows consistent ranking of models of any degree of completeness. We tested CAD-score on a large set of diverse models and compared it to GDT-TS, a widely accepted measure of model accuracy. Similarly to GDT-TS, CAD- score showed a robust performance on single-domain proteins, but displayed a stronger preference for physically more real- istic models. Unlike GDT-TS, the new score revealed a balanced assessment of domain rearrangement, removing the neces- sity for different treatment of single-domain, multi-domain, and multi-subunit structures. Moreover, CAD-score makes it possible to assess the accuracy of inter-domain or inter-subunit interfaces directly. In addition, the approach offers an alternative to the superposition-based model clustering. The CAD-score implementation is available both as a web server and a standalone software package at http://www.ibt.lt/bioinformatics/cad-score/.},
  doi       = {10.1002/prot.24172},
  file      = {:by-author/O/Olechnovič/2013_Olechnovič_149.pdf:PDF},
  keywords  = {Structure Prediction},
  owner     = {andrius},
  timestamp = {2013.11.22},
  creationdate = {2013-11-22T00:00:00},
}

@Article{Olechnovic2011,
  author    = {Olechnovič, K. and Margelevičius, M. and Venclovas Č.},
  journal   = {Bioinformatics},
  title     = {Voroprot: an interactive tool for the analysis and visualization of complex geometric features of protein structure},
  year      = {2011},
  pages     = {723--724},
  volume    = {27},
  abstract  = {We present Voroprot, an interactive cross-platform software tool that provides a unique set of capabilities for exploring geometric features of protein structure. Voroprot allows the construction and visualization of the Apollonius diagram (also known as the additively weighted Voronoi diagram), the Apollonius graph, protein alpha shapes, interatomic contact surfaces, solvent accessible surfaces, pockets and cavities inside protein structure.},
  doi       = {10.1093/bioinformatics/btq720},
  file      = {:by-author/O/Olechnovič/2011_Olechnovič_723.pdf:PDF},
  keywords  = {Proteins; Structure Prediction},
  owner     = {andrius},
  timestamp = {2013.11.22},
  creationdate = {2013-11-22T00:00:00},
}

@Article{Olechnovic2014a,
  author     = {Olechnovič, Kliment and Venclovas, Ceslovas},
  journal    = {Nucleic Acids Res.},
  title      = {The {CAD}-score web server: contact area-based comparison of structures and interfaces of proteins, nucleic acids and their complexes},
  year       = {2014},
  issn       = {1362-4962},
  month      = jul,
  number     = {Web Server issue},
  pages      = {W259--263},
  volume     = {42},
  abstract   = {The Contact Area Difference score (CAD-score) web server provides a universal framework to compute and analyze discrepancies between different 3D structures of the same biological macromolecule or complex. The server accepts both single-subunit and multi-subunit structures and can handle all the major types of macromolecules (proteins, RNA, DNA and their complexes). It can perform numerical comparison of both structures and interfaces. In addition to entire structures and interfaces, the server can assess user-defined subsets. The CAD-score server performs both global and local numerical evaluations of structural differences between structures or interfaces. The results can be explored interactively using sortable tables of global scores, profiles of local errors, superimposed contact maps and 3D structure visualization. The web server could be used for tasks such as comparison of models with the native (reference) structure, comparison of X-ray structures of the same macromolecule obtained in different states (e.g. with and without a bound ligand), analysis of nuclear magnetic resonance (NMR) structural ensemble or structures obtained in the course of molecular dynamics simulation. The web server is freely accessible at: http://www.ibt.lt/bioinformatics/cad-score.},
  doi        = {10.1093/nar/gku294},
  file       = {2014_Olechnovič_W259.pdf:by-author/O/Olechnovič/2014_Olechnovič_W259.pdf:PDF},
  keywords   = {DNA; DNA-Binding Proteins; Internet; Models; Molecular; Nucleic Acid Conformation; Protein Conformation; Proteins; RNA; RNA-Binding Proteins; Software},
  language   = {eng},
  owner      = {saulius},
  pmcid      = {PMC4086110},
  pmid       = {24838571},
  shorttitle = {The {CAD}-score web server},
  timestamp = {2016.10.12},
  creationdate = {2016-10-12T00:00:00},
}

@Article{Olechnovic2014b,
  author    = {Olechnovič, Kliment and Venclovas, Ceslovas},
  journal   = {Nucleic Acids Res.},
  title     = {The use of interatomic contact areas to quantify discrepancies between {RNA} 3D models and reference structures},
  year      = {2014},
  issn      = {1362-4962},
  month     = may,
  number    = {9},
  pages     = {5407--5415},
  volume    = {42},
  abstract  = {Growing interest in computational prediction of ribonucleic acid (RNA) three-dimensional structure has highlighted the need for reliable and meaningful methods to compare models and experimental structures. We present a structure superposition-free method to quantify both the local and global accuracy of RNA structural models with respect to the reference structure. The method, initially developed for proteins and here extended to RNA, closely reflects physical interactions, has a simple definition, a fixed range of values and no arbitrary parameters. It is based on the correspondence of respective contact areas between nucleotides or their components (base or backbone). The better is the agreement between respective contact areas in a model and the reference structure, the more accurate the model is considered to be. Since RNA bases account for the largest contact areas, we further distinguish stacking and non-stacking contacts. We have extensively tested the contact area-based evaluation method and found it effective in both revealing local discrepancies and ranking models by their overall quality. Compared to other reference-based RNA model evaluation methods, the new method shows a stronger emphasis on stereochemical quality of models. In addition, it takes into account model completeness, enabling a meaningful evaluation of full models and those missing some residues.},
  doi       = {10.1093/nar/gku191},
  file      = {2014_Olechnovič_5407.pdf:by-author/O/Olechnovič/2014_Olechnovič_5407.pdf:PDF},
  keywords  = {Base Pairing; Binding Sites; Computer Simulation; Hydrogen Bonding; Models; Molecular; Molecular Sequence Annotation; Nucleic Acid Conformation; RNA},
  language  = {eng},
  owner     = {saulius},
  pmcid     = {PMC4027170},
  pmid      = {24623815},
  timestamp = {2016.10.12},
  creationdate = {2016-10-12T00:00:00},
}

@Article{Olechnovic2014,
  author    = {Kliment Olechnovič and Česlovas Venclovas},
  journal   = {Journal of Computational Chemistry},
  title     = {Voronota: A Fast and Reliable Tool for Computing the Vertices of the {V}oronoi Diagram of Atomic Balls},
  year      = {2014},
  pages     = {672--681},
  volume    = {35},
  doi       = {10.1002/jcc.23538},
  file      = {:by-author/O/Olechnovič/2014_Olechnovič_672.pdf:PDF},
  owner     = {andrius},
  timestamp = {2014.03.10},
  creationdate = {2014-03-10T00:00:00},
}

@Article{Olechnovic2021,
  author  = {Olechnovič, Kliment and Venclovas, Česlovas},
  title   = {{VoroContacts}: a tool for the analysis of interatomic contacts in macromolecular structures},
  journal = {Bioinformatics},
  volume  = {37},
  number  = {24},
  pages   = {4873--4875},
  year    = {2021},
  month   = {06},
  issn    = {1367-4803},
  doi     = {10.1093/bioinformatics/btab448},
  file    = {:by-author/O/Olechnovič/2021_Olechnovič_4873.pdf:PDF},
  url     = {https://doi.org/10.1093/bioinformatics/btab448},
  eprint  = {https://academic.oup.com/bioinformatics/article-pdf/37/24/4873/41726954/btab448.pdf},
  owner     = {andrius},
  creationdate = {2022-02-10T17:10:33},
  modificationdate = {2022-12-24T18:42+02:00},
}

@Manual{Olex2Team2011,
  title     = {Olex2 Manual (Commands)},
  author    = {{Olex2 Team}},
  month     = {September},
  year      = {2011},
  file      = {2011_Olex2Team_manual.pdf:by-author/O/Olex2Team/2011_Olex2Team_manual.pdf:PDF},
  keywords  = {Chemical Crystallography; Olex2; Small Molecule; Software; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2016.12.21},
  creationdate = {2016-12-21T00:00:00},
  url       = {http://www.olex2.org/olex2-distro/1.1/update/etc/documentation/Commands.pdf},
}

@Article{Olieric2009,
  author    = {Olieric, Vincent and Rieder, Ulrike and Lang, Kathrin and Serganov, Alexander and Schulze-Briese, Clemens and Micura, Ronald and Dumas, Philippe and Ennifar, Eric},
  journal   = {RNA (New York, N.Y.)},
  title     = {A fast selenium derivatization strategy for crystallization and phasing of RNA structures.},
  year      = {2009},
  pages     = {707--15},
  volume    = {15},
  abstract  = {Site-specific 2'-methylseleno RNA labeling is a promising tool for tackling the phase problem in RNA crystallography. We have developed an efficient strategy for crystallization and structure determination of RNA and RNA/protein complexes based on preliminary crystallization screening of 2'-OCH(3)-modified RNA sequences, prior to the replacement of 2'-OCH(3) groups with their 2'-SeCH(3) counterparts. The method exploits the similar crystallization properties of 2'-OCH(3)- and 2'-SeCH(3)-modified RNAs and has been successfully validated for two test cases. In addition, our data show that 2'-SeCH(3)-modified RNA have an increased resistance to X-ray radiolysis in comparison with commonly used 5-halogen-modified RNA, which permits collection of experimental electron density maps of remarkable quality.},
  file      = {:by-author/O/Olieric/2009_Olieric_707.pdf:PDF},
  keywords  = {Ribosome Structure},
  owner     = {saulius},
  timestamp = {2012.06.25},
  creationdate = {2012-06-25T00:00:00},
}

@Article{Olsen2004,
  author    = {Olsen, Johan Gotthardt and Flensburg, Claus and Olsen, Ole and Bricogne, Gerard and Henriksen, Anette},
  journal   = {Acta Crystallographica Section D},
  title     = {Solving the structure of the bubble protein using the anomalous sulfur signal from single-crystal in-house Cu{\it K}{$\alpha$} diffraction data only},
  year      = {2004},
  pages     = {250--255},
  volume    = {60},
  doi       = {10.1107/S0907444903025927},
  file      = {dz5012.pdf:by-author/O/Olsen/2004_Olsen_250.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444903025927},
}

@InProceedings{Olshen1993,
  author    = {Richard A. Olshen},
  booktitle = {1993 IT Symposium Plenary Lecture},
  title     = {Binary Trees for Classification, Regression, and Clustering, with Applications to Lossy Data Compression},
  year      = {1993},
  publisher = {IEEE},
  abstract  = {This note is a survey of my plenary talk at the IEEE International Symposium in San Antonio in January, 1993. The subject matter then and here is binary tree-structured methods for classi cation, regression, survival analysis, and clustering, including a survey of unifying themes and applications, and an introduction to mathematical issues that arise in studying their asymptotic properties. I emphasize the CARTTM algorithms of Breiman et al. and applications of the clustering algorithms to predictive, pruned, tree-structured vector quantization (predictive PTSVQ). The talk was a partial summary of collaborations with many authors over an eighteen year period. The talk could hardly do justice to the various collaborations or to the contributions by others, and this note su ers all the more for its brevity. However, I hope that the list of references included will enable interested readers to pursue the subject matter I raise, on their own.},
  file      = {:by-author/O/Olshen/1993_Olshen.pdf:PDF;:by-author/O/Olshen/1993_Olshen.ps:PostScript},
  owner     = {saulius},
  timestamp = {2013.08.10},
  creationdate = {2013-08-10T00:00:00},
}

@Presentation{Olson2009,
  author    = {Wilma K. Olson},
  title     = {Protein-nucleic acid interactions},
  year      = {2009},
  file      = {:by-author/O/Olson/2009_Olson_slides.pdf:PDF},
  keywords  = {Presentations},
  owner     = {saulius},
  pages     = {slides},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Olson2001,
  author    = {Olson, W. K. and Bansal, M. and Burley, S. K. and Dickerson, R. E. and Gerstein, M. and Harvey, S. C. and Heinemann, U. and Lu, X. J. and Neidle, S. and Shakked, Z. and Sklenar, H. and Suzuki, M. and Tung, C. S. and Westhof, E. and Wolberger, C. and Berman, H. M.},
  journal   = {Journal of molecular biology},
  title     = {A standard reference frame for the description of nucleic acid base-pair geometry.},
  year      = {2001},
  pages     = {229--237},
  volume    = {313},
  doi       = {10.1006/jmbi.2001.4987},
  file      = {:by-author/O/Olson/2001_Olson_229.pdf:PDF},
  keywords  = {Biochemistry; DNA Geometry; Nucleic Acids; RNA Geometry; Readout; Review; Structural Biology},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Olson1998,
  author       = {Olson, W. K. and Gorin, A. A. and Lu, X. J. and Hock, L. M. and Zhurkin, V. B.},
  journal      = {Proceedings of the National Academy of Sciences of the United States of America},
  title        = {{DNA} sequence-dependent deformability deduced from protein-{DNA} crystal complexes.},
  year         = {1998},
  pages        = {11163--11168},
  volume       = {95},
  abstract     = {The deformability of double helical DNA is critical for its packaging in the cell, recognition by other molecules, and transient opening during biochemically important processes. Here, a complete set of sequence-dependent empirical energy functions suitable for describing such behavior is extracted from the fluctuations and correlations of structural parameters in DNA-protein crystal complexes. These elastic functions provide useful stereochemical measures of the local base step movements operative in sequence-specific recognition and protein-induced deformations. In particular, the pyrimidine-purine dimers stand out as the most variable steps in the DNA-protein complexes, apparently acting as flexible "hinges" fitting the duplex to the protein surface. In addition to the angular parameters widely used to describe DNA deformations (i.e., the bend and twist angles), the translational parameters describing the displacements of base pairs along and across the helical axis are analyzed. The observed correlations of base pair bending and shearing motions are important for nonplanar folding of DNA in nucleosomes and other nucleoprotein complexes. The knowledge-based energies also offer realistic three-dimensional models for the study of long DNA polymers at the global level, incorporating structural features beyond the scope of conventional elastic rod treatments and adding a new dimension to literal analyses of genomic sequences.},
  creationdate = {2008-07-28T00:00:00},
  doi          = {10.1073/pnas.95.19.11163},
  file         = {1998_Olson_11163.pdf:by-author/O/Olson/1998_Olson_11163.pdf:PDF},
  keywords     = {Chemistry; DNA; Dimerization; Models; Molecular; Nucleic Acid Conformation; Protein Binding; Proteins; Purines; Pyrimidines; Readout; Stacking},
  owner        = {em},
  timestamp    = {2008.07.28},
}

@Article{Omiecinski1990,
  author     = {Omiecinski, Edward and Scheuermann, Peter},
  journal    = {ACM Transactions on Database Systems},
  title      = {A parallel algorithm for record clustering},
  year       = {1990},
  issn       = {0362-5915},
  pages      = {599--624},
  volume     = {15},
  abstract   = {We present an efficient heuristic algorithm for record clustering that can run on a SIMD machine. We introduce the P-tree, and its associated numbering scheme, which in the split phase allows each processor independently to compute the unique cluster number of a record satisfying an arbitrary query. We show that by restricting ourselves in the merge phase to combining only sibling clusters, we obtain a parallel algorithm whose speedup ratio is optimal in the number of processors used. Finally, we report on experiments showing that our method produces substantial savings in an enviornment with relatively little overlap among the queries.},
  address    = {New York, NY, USA},
  doi        = {10.1145/99935.99947},
  file       = {:by-author/O/Omiecinski/1990_Omiecinski_599.pdf:PDF},
  issue_date = {Dec. 1990},
  owner      = {saulius},
  publisher  = {ACM},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url        = {http://doi.acm.org/10.1145/99935.99947},
}

@Article{Ong2015,
  author    = {Ong, Shyue Ping and Cholia, Shreyas and Jain, Anubhav and Brafman, Miriam and Gunter, Dan and Ceder, Gerbrand and Persson, Kristin A.},
  journal   = {Computational Materials Science},
  title     = {The Materials Application Programming Interface (API): A simple, flexible and efficient API for materials data based on REpresentational State Transfer (REST) principles},
  year      = {2015},
  issn      = {0927-0256},
  month     = {Feb},
  pages     = {209–215},
  volume    = {97},
  abstract  = {In this paper, we describe the Materials Application Programming Interface (API), a simple, flexible and efficient interface to programmatically query and interact with the Materials Project database based on the REpresentational State Transfer (REST) pattern for the web. Since its creation in Aug 2012, the Materials API has been the Materials Project’s de facto platform for data access, supporting not only the Materials Project’s many collaborative efforts but also enabling new applications and analyses. We will highlight some of these analyses enabled by the Materials API, particularly those requiring consolidation of data on a large number of materials, such as data mining of structural and property trends, and generation of phase diagrams. We will conclude with a discussion of the role of the API in building a community that is developing novel applications and analyses based on Materials Project data.},
  doi       = {10.1016/j.commatsci.2014.10.037},
  file      = {2015_Ong_209.pdf:by-author/O/Ong/2015_Ong_209.pdf:PDF},
  owner     = {andrius},
  publisher = {Elsevier BV},
  timestamp = {2017.03.12},
  creationdate = {2017-03-12T00:00:00},
  url       = {http://dx.doi.org/10.1016/j.commatsci.2014.10.037},
}

@Article{Ong2013,
  author           = {Shyue Ping Ong and William Davidson Richards and Anubhav Jain and Geoffroy Hautier and Michael Kocher and Shreyas Cholia and Dan Gunter and Vincent L. Chevrier and Kristin A. Persson and Gerbrand Ceder},
  journal          = {Computational Materials Science},
  title            = {{Python Materials Genomics} (pymatgen): A robust, open-source python library for materials analysis},
  year             = {2013},
  issn             = {0927-0256},
  pages            = {314--319},
  volume           = {68},
  creationdate     = {2015-07-27T00:00:00},
  doi              = {http://dx.doi.org/10.1016/j.commatsci.2012.10.028},
  file             = {:by-author/O/Ong/2013_Ong_314.pdf:PDF},
  keywords         = {Materails Science; Pymatgen; Python; Quantum Mechanics (QM)},
  modificationdate = {2023-04-13T08:18:32},
  owner            = {andrius},
  timestamp        = {2015.07.27},
  url              = {http://www.sciencedirect.com/science/article/pii/S0927025612006295},
}

@Article{Onoda2000,
  author     = {Onoda, Mitsuko and Chen, Xue-an and Sato, Akira and Wada, Hiroaki},
  journal    = {Journal of Solid State Chemistry},
  title      = {Crystal structure of {Cu}2Gd2/3S2: interlayer short-range order of {Gd} vacancies},
  year       = {2000},
  issn       = {0022-4596},
  pages      = {332--339},
  volume     = {152},
  abstract   = {The average structure of ternary sulfide Cu2Gd2/3S2 has been refined using single-crystal X-ray diffraction data: space group P3, a=b=3.899(1), c=6.421(2) Å, Z=1, RF=0.036, and wRF=0.041 for 418 reflections and 8 structural parameters. The average structure is based on hexagonal close packing of S with Cu in tetrahedral sites and Gd in octahedral sites, the latter sites being occupied to 2/3. Diffuse streaks observed by electron diffraction, however, indicate a trigonal strict periodicity of A=6.753 Å=√3a within (001) and a vague period of C=12.842 Å=2c, suggesting a layer structure with an intralayer order and interlayer short-range order of Gd vacancies. A model of the real structure has been proposed, and the diffuse scattering has been simulated by the matrix method for one-dimensional disorder. The calculated intensity distribution corresponds to the observed distribution of the diffuse streaks in the electron diffraction pattern and to the intensity distribution measured on an X-ray single-crystal diffractometer; the total X-ray powder diffraction pattern of Cu2Gd2/3S2 can be reproduced almost completely by calculation.},
  doi        = {10.1006/jssc.2000.8652},
  file       = {Onoda et al. - 2000 - Crystal Structure of Cu2Gd23S2 Interlayer Short-.pdf:by-author/O/Onoda/2000_Onoda_332.pdf:application/pdf;ScienceDirect Snapshot:by-author/O/Onoda/2000_Onoda_332.html:text/html},
  keywords   = {Crystal Structure; Cu2Gd2/3S2; Electron Diffraction; X-ray Diffraction; defects.},
  owner      = {saulius},
  shorttitle = {Crystal structure of {Cu}2Gd2/3S2},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url        = {http://www.sciencedirect.com/science/article/pii/S0022459600986523},
  urldate    = {2015-08-18},
}

@Article{Oost2009,
  author    = {van der Oost, John and Brouns, Stan J.J.},
  journal   = {Cell},
  title     = {RNAi: Prokaryotes Get in on the Act},
  year      = {2009},
  pages     = {863--865},
  volume    = {139},
  abstract  = {The small CRISPR-derived RNAs of bacteria and archaea provide adaptive immunity by targeting the DNA of invading viruses and plasmids. Hale et al. (2009) now report on a new variant CRISPR/ Cas complex in the archaeon Pyrococcus furiosus that uses guide RNAs to specifically target and cleave RNA not DNA.},
  doi       = {10.1016/j.cell.2009.11.018},
  file      = {:by-author/O/Oost/2009_Oost_863.pdf:PDF},
  groups    = {sg/CRISPR-Cas},
  keywords  = {CRISPR; Cas Complex; RNA Cleavage; Review},
  owner     = {em},
  timestamp = {2013.10.01},
  creationdate = {2013-10-01T00:00:00},
}

@Article{Opavsky1996,
  author    = {Opavský, R and Pastoreková, S and Zelník, V and Gibadulinová, A and Stanbridge, E J and Závada, J and Kettmann, R and Pastorek, J},
  journal   = {Genomics},
  title     = {Human MN/CA9 gene, a novel member of the carbonic anhydrase family: structure and exon to protein domain relationships.},
  year      = {1996},
  pages     = {480--7},
  volume    = {33},
  abstract  = {We have isolated, sequenced, and characterized a human MN/CA9 gene. This gene is a novel member of the carbonic anhydrase (CA) family, which codes for widely distributed catalysts of the reversible conversion of carbon dioxide to carbonic acid. So far, MN/CA IX is the only tumor-associated CA isoenzyme. The entire genomic sequence of MN/CA9, including the 5'-flanking region, encompasses 10.9 kb. The coding sequence is divided into 11 exons, whose organization and relationships to predicted protein domains suggest that the gene arose by exon shuffling. Exon 1 encodes a signal peptide and a proteoglycan-related region. Exons 2-8 code for a CA domain with a highly conserved active site. The exon/intron pattern of the CA coding region is similar but not identical to other described animal kingdom alpha-CA genes. Exons 10 and 11 encode a transmembrane anchor and an intracytoplasmic tail, respectively. We have also determined the transcription initiation and termination sites by RNase protection assay and analyzed the 3. 5-kb region upstream of the MN/CA9 gene. Sequence of the proximate 5' end of the flanking region shows extensive homology to the long terminal repeats of HERV-K endogenous retroviruses. The putative MN/CA9 promoter immediately preceding the transcription start site does not possess a TATA box, but contains consensus sequences for the AP1, AP2, p53, and Inr transcription factors. This study will allow further investigations of the molecular events regulating expression of MN/CA IX as well as elucidation of its biological function.},
  file      = {1996_Opavsky_480.pdf:by-author/O/Opavský/1996_Opavský_480.pdf:PDF},
  groups    = {sg/hCA9},
  keywords  = {CA9; Carbonic Anhydrases},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Manual{OpenEyeScientificSoftware2004,
  title     = {Smallest Set of Smallest Rings (SSSR) considered Harmful},
  author    = {OpenEye Scientific Software, Inc.},
  month     = {July},
  year      = {2004},
  booktitle = {OEChem - Python Theory Manual, Version 1.5.1},
  file      = {:by-author/O/OpenEyeScientificSoftware/2004_OpenEyeScientificSoftware.pdf:PDF;:by-author/O/OpenEyeScientificSoftware/2004_OpenEyeScientificSoftware.war:WAR},
  keywords  = {Ring-perception},
  owner     = {saulius},
  retrieved = {2015-03-06},
  timestamp = {2015.03.03},
  creationdate = {2015-03-03T00:00:00},
  url       = {http://www.ics.uci.edu/~dock/manuals/oechem/cplusprog/node127.html},
}

@Article{Opgenorth1998,
  author           = {Opgenorth, J. and Plesken, W. and Schulz, T.},
  journal          = {Acta Crystallographica Section A},
  title            = {Crystallographic algorithms and tables},
  year             = {1998},
  pages            = {517--531},
  volume           = {54},
  abstract         = {A survey of definitions, theorems and algorithms for crystallographic groups are given in a dimension-independent fashion. These and some tables (including the Bravais groups up to dimension 6) form the basis of the computer package {\it CARAT}, which can handle crystallographic space groups up to dimension 6.},
  creationdate     = {2015-10-11T00:00:00},
  doi              = {10.1107/S010876739701547X},
  file             = {1998_Opgenorth_517.pdf:by-author/O/Opgenorth/1998_Opgenorth_517.pdf:PDF},
  keywords         = {Algebra; Correspondence of Crystallographic and Mathematical Terms; Crystallographic Terms; Crystallography; Mathematical Terms; Spacegroups},
  modificationdate = {2024-02-27T11:35:37},
  owner            = {saulius},
  timestamp        = {2015.10.11},
  url              = {http://dx.doi.org/10.1107/S010876739701547X},
}

@Presentation{Orbanz2012,
  author    = {Peter Orbanz},
  title     = {Bayesian Nonparametrics: Part I},
  year      = {2012},
  file      = {:by-author/O/Orbanz/2012_Orbanz_slides.pdf:PDF},
  groups    = {sg/Bayesian},
  keywords  = {Bayesian Statistics},
  owner     = {saulius},
  pages     = {slides},
  timestamp = {2012.09.30},
  creationdate = {2012-09-30T00:00:00},
}

@Presentation{Orbanz2011,
  author     = {Peter Orbanz and Yee Whye Teh},
  title      = {Modern Bayesian Nonparametrics},
  year       = {2011},
  conference = {NIPS 2011},
  school     = {Cambridge University and Columbia University; Gatsby Computational Neuroscience Unit, UCL},
  file       = {:by-author/O/Orbanz/2011_Orbanz_slides.pdf:PDF},
  groups     = {sg/Bayesian},
  keywords   = {Bayesian Statistics},
  owner      = {saulius},
  pages      = {slides},
  timestamp = {2012.09.30},
  creationdate = {2012-09-30T00:00:00},
}

@Article{Ord2002,
  author    = {Ord, Toby},
  title     = {Hypercomputation: computing more than the {T}uring machine},
  year      = {2002},
  file      = {:by-author/O/Ord/2002_Ord.pdf:PDF},
  keywords  = {Computer Science (CS); Super Turing Computations},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Orengo1999,
  author    = {Orengo, C A and Pearl, F M and Bray, J E and Todd, A E and Martin, A C and Lo Conte, L and Thornton, J M},
  journal   = {Nucleic acids research},
  title     = {The CATH Database provides insights into protein structure/function relationships.},
  year      = {1999},
  pages     = {275--9},
  volume    = {27},
  abstract  = {We report the latest release (version 1.4) of the CATH protein domains database (http://www.biochem.ucl.ac.uk/bsm/cath). This is a hierarchical classification of 13 359 protein domain structures into evolutionary families and structural groupings. We currently identify 827 homologous families in which the proteins have both structual similarity and sequence and/or functional similarity. These can be further clustered into 593 fold groups and 32 distinct architectures. Using our structural classification and associated data on protein functions, stored in the database (EC identifiers, SWISS-PROT keywords and information from the Enzyme database and literature) we have been able to analyse the correlation between the 3D structure and function. More than 96% of folds in the PDB are associated with a single homologous family. However, within the superfolds, three or more different functions are observed. Considering enzyme functions, more than 95% of clearly homologous families exhibit either single or closely related functions, as demonstrated by the EC identifiers of their relatives. Our analysis supports the view that determining structures, for example as part of a 'structural genomics' initiative, will make a major contribution to interpreting genome data.},
  file      = {Orengo_1999_275.pdf:by-author/O/Orengo/1999_Orengo_275.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Orgel2004,
  author    = {Leslie E. Orgel},
  journal   = {Critical Reviews in Biochemistry and Molecular Biology},
  title     = {Prebiotic Chemistry and the Origin of the RNA World},
  year      = {2004},
  pages     = {99--123},
  volume    = {39},
  abstract  = {The demonstration that ribosomal peptide synthesis is a ribozyme-catalyzed reaction makes it almost certain that there was once an RNA World. The central problem for origin-of-life studies, therefore, is to understand how a protein-free RNA World became established on the primitive Earth. We first review the literature on the prebiotic synthesis of the nucleotides, the nonenzymatic synthesis and copying of polynucleotides, and the selection of ribozyme catalysts of a kind that might have facilitated polynucleotide replication. This leads to a brief outline of the Molecular Biologists' Dream, an optimistic scenario for the origin of the RNA World. In the second part of the review we point out the many unresolved problems presented by the Molecular Biologists' Dream. This in turn leads to a discussion of genetic systems simpler than RNA that might have “invented” RNA. Finally, we review studies of prebiotic membrane formation.},
  doi       = {10.1080/10409230490460765},
  eprint    = {http://informahealthcare.com/doi/pdf/10.1080/10409230490460765},
  file      = {2004_Orgel_99.pdf:by-author/O/Orgel/2004_Orgel_99.pdf:PDF},
  keywords  = {RNA World},
  owner     = {saulius},
  timestamp = {2013.09.27},
  creationdate = {2013-09-27T00:00:00},
  url       = {http://informahealthcare.com/doi/abs/10.1080/10409230490460765},
}

@Article{Orlov2008,
  author    = {Orlov, Ivan and Palatinus, Lukas and Chapuis, Gervais},
  journal   = {Journal of Applied Crystallography},
  title     = {From space to superspace and back: Superspace Group Finder},
  year      = {2008},
  pages     = {1182--1186},
  volume    = {41},
  abstract  = {The symmetry of a commensurately modulated crystal structure can be described in two different ways: in terms of a conventional three-dimensional space group or using the superspace concept in (3 + {\it d}) dimensions. The three-dimensional space group is obtained as a real-space section of the (3 + {\it d}) superspace group. A complete network was constructed linking (3 + 1) superspace groups and the corresponding three-dimensional space groups derived from rational sections. A database has been established and is available at http://superspace.epfl.ch/finder/. It is particularly useful for finding common superspace groups for various series of modular (`composition-flexible') structures and phase transitions. The use of the database is illustrated with examples from various fields of crystal chemistry.},
  doi       = {10.1107/S0021889808034390},
  file      = {2008_Orlov_1182.pdf:by-author/O/Orlov/2008_Orlov_1182.pdf:PDF},
  keywords  = {Algorithms; Commensurate Modulation; Databases; Spacegroups; Superspace Approach; Superspace Group Finder; Symmetry; Symmetry Groups; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2015.06.15},
  creationdate = {2015-06-15T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0021889808034390},
}

@Article{Orlowski2008,
  author    = {Orlowski, Jerzy and Bujnicki, Janusz M.},
  journal   = {Nucleic acids research},
  title     = {Structural and evolutionary classification of Type II restriction enzymes based on theoretical and experimental analyses.},
  year      = {2008},
  pages     = {3552--69},
  volume    = {36},
  abstract  = {For a very long time, Type II restriction enzymes (REases) have been a paradigm of ORFans: proteins with no detectable similarity to each other and to any other protein in the database, despite common cellular and biochemical function. Crystallographic analyses published until January 2008 provided high-resolution structures for only 28 of 1637 Type II REase sequences available in the Restriction Enzyme database (REBASE). Among these structures, all but two possess catalytic domains with the common PD-(D/E)XK nuclease fold. Two structures are unrelated to the others: R.BfiI exhibits the phospholipase D (PLD) fold, while R.PabI has a new fold termed 'half-pipe'. Thus far, bioinformatic studies supported by site-directed mutagenesis have extended the number of tentatively assigned REase folds to five (now including also GIY-YIG and HNH folds identified earlier in homing endonucleases) and provided structural predictions for dozens of REase sequences without experimentally solved structures. Here, we present a comprehensive study of all Type II REase sequences available in REBASE together with their homologs detectable in the nonredundant and environmental samples databases at the NCBI. We present the summary and critical evaluation of structural assignments and predictions reported earlier, new classification of all REase sequences into families, domain architecture analysis and new predictions of three-dimensional folds. Among 289 experimentally characterized (not putative) Type II REases, whose apparently full-length sequences are available in REBASE, we assign 199 (69%) to contain the PD-(D/E)XK domain. The HNH domain is the second most common, with 24 (8%) members. When putative REases are taken into account, the fraction of PD-(D/E)XK and HNH folds changes to 48% and 30%, respectively. Fifty-six characterized (and 521 predicted) REases remain unassigned to any of the five REase folds identified so far, and may exhibit new architectures. These enzymes are proposed as the most interesting targets for structure determination by high-resolution experimental methods. Our analysis provides the first comprehensive map of sequence-structure relationships among Type II REases and will help to focus the efforts of structural and functional genomics of this large and biotechnologically important class of enzymes.},
  file      = {:by-author/O/Orlowski/2008_Orlowski_3552.pdf:PDF},
  keywords  = {Evolution; TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Orthaber2000,
  author    = {Orthaber, Doris and Bergmann, Alexander and Glatter, Otto},
  journal   = {Journal of Applied Crystallography},
  title     = {SAXS experiments on absolute scale with Kratky systems using water as a secondary standard},
  year      = {2000},
  pages     = {218±225},
  volume    = {33},
  abstract  = {For small-angle scattering, of X-rays (SAXS) and neutrons (SANS), the importance of absolute calibration has been recognized since the inception of the technique. The work reported here focuses on SAXS measurements using Kratky slit systems. In former days, only molecular weights or scattering per particle were determined, but today absolute calibration implies the use of the unit of cmÀ1 for the scattering curve. It is necessary to measure the so-called absolute intensity, which is the ratio of the scattering intensity to the primary intensity P0. Basically there are two possible ways to determine the absolute intensity. The ®rst one is the direct method, which involves the mechanical attenuation of the primary beam by a rotating disc or a moving slit. The second is the indirect method, using secondary standards. Water is well suited as a calibration standard because of the angle-independent scattering. The essential advantage is that the scattering of water only depends on the physical property of isothermal compressibility. Before presenting an example of the practical performance of this method, the most important theoretical equations for an SAS experiment on the absolute scale are summarized. With the slit collimation system, the scattering curve of water can be measured with high enough statistical accuracy. As a ®rst example, the scattering curve of the protein lysozyme on the absolute scale is presented. The second example is the determination of the aggregation number of a triblock copolymer P94 (EO17± PO42±EO17). Taking into account that at least 10% of the polymer sample consists of diblocks, the accuracy of around 10% for the determined aggregation number is rather good. The data of P94 are also considered on the particle scale in order to obtain the radial scattering-length density distribution.},
  file      = {:by-author/O/Orthaber/2000_Orthaber_218.pdf:PDF},
  keywords  = {Kratky Plot; Molecular Weight (MW); SAXS},
  owner     = {em},
  timestamp = {2013.08.29},
  creationdate = {2013-08-29T00:00:00},
}

@Article{Ortiz2009,
  author    = {C. Ortiz and O. Eriksson and M. Klintenberg},
  journal   = {Computational Materials Science},
  title     = {Data mining and accelerated electronic structure theory as a tool in the search for new functional materials},
  year      = {2009},
  issn      = {0927-0256},
  pages     = {1042 - 1049},
  volume    = {44},
  abstract  = {A highly accelerated electronic structure implementation and data mining algorithms have been combined with structural data from the inorganic crystal structure database to generate materials properties for about 22,000 inorganic compounds. It is shown how data mining algorithms employed on the database can identify new functional materials with desired materials properties, resulting in a prediction of 136 novel materials with potential for use as detector materials for ionizing radiation. The methodology behind the automatized ab initio approach is presented, results are tabulated and a version of the complete database is made available at the internet web site &lt;http://gurka.fysik.uu.se/ESP/&gt; (Ref. [1]).},
  doi       = {10.1016/j.commatsci.2008.07.016},
  file      = {2009_Ortiz_1042.pdf:by-author/O/Ortiz/2009_Ortiz_1042.pdf:PDF},
  keywords  = {Electronic Structure Theory},
  owner     = {saulius},
  timestamp = {2014.07.31},
  creationdate = {2014-07-31T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/S0927025608003534},
}

@TechReport{Ossanna1992a,
  author      = {Joseph F. Ossanna and Brian W. Kernighan},
  institution = {AT\&T Bell Laboratories},
  title       = {Troff User's Manual},
  year        = {1992},
  month       = {Nov},
  file        = {:by-author/O/Ossanna/1992_Ossanna_tr54.pdf:PDF;:by-author/O/Ossanna/1992_Ossanna_tr54.ps.gz:PDF},
  keywords    = {Computer Science (CS); Groff; Manual; Nroff; Troff; Typesetting; Unix},
  owner       = {saulius},
  pages       = {tr54.ps.gz},
  timestamp = {2012.11.20},
  creationdate = {2012-11-20T00:00:00},
  url         = {http://cm.bell-labs.com/cm/cs/cstr/54.ps.gz},
}

@Article{Oster1935,
  author    = {Oster, R. H. and Arnold, W. A.},
  journal   = {The Journal of general physiology},
  title     = {RESULTS OF IRRADIATING SACCHAROMYCES WITH MONOCHROMATIC ULTRA-VIOLET LIGHT : IV. RELATION OF ENERGY TO OBSERVED INHIBITORY EFFECTS.},
  year      = {1935},
  pages     = {351--5},
  volume    = {18},
  abstract  = {Data obtained on yeast irradiated with monochromatic ultra-violet radiation has been analyzed for the number of quantum hits involved in the production of different degrees of inhibition of cell division, according to the method proposed by Mme. Curie (1929). Sufficient data are not available for a rigorous determination, but the calculated results tend to indicate that a multiple hit to kill relation is followed, that different numbers of hits are involved in the production of different degrees of inhibition, and that this number increases with increase in the degree of damage sustained.},
  file      = {:by-author/O/Oster/1935_Oster_351.pdf:PDF},
  keywords  = {Protein Denaturation},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Ota1997,
  author    = {Ota, M. and Nishikawa, K.},
  journal   = {Protein engineering},
  title     = {Assessment of pseudo-energy potentials by the best-five test: a new use of the three-dimensional profiles of proteins.},
  year      = {1997},
  pages     = {339--51},
  volume    = {10},
  abstract  = {We propose a new assessment, called the best-five test, for the pseudo-energy potential empirically derived from the protein structural database. The object of the test is the three-dimensional (3D) profiles of proteins, which are directly connected to the pseudo-energy potentials. In the 3D profile, the fitness of each amino acid type is ranked at each residue site of a protein. A site whose native residue type is ranked within the best-five out of 20 amino acids is regarded as satisfactory and the ratio of the satisfactory sites over all the sites of all the proteins examined is indicative of the efficiency of the pseudo-energy potential employed. We applied the test to our potential function consisting of four terms; side-chain packing, hydration, backbone hydrogen-bonding and local conformation, by setting various kinds of definitions for each term. Through this test, the validity of the minus average operation is confirmed, where the energy level of potential functions is adjusted by referring to the random-environmental state of the proteins. Especially in the side-chain packing function, the success ratio increases from about 30 to 50% with this operation. Failure without the operation is ascribed to bulky hydrophobic residues, which almost always occupy higher ranking positions in the 3D profile table. A maximum success ratio of 55.6% was attained with the final potential set consisting of the above four terms. The efficiency of the final set was further checked in the fold-recognition test for distantly related proteins. The best-five test is a new use of the 3D profile table for assessing the ability of the pseudo-energy potentials.},
  file      = {:by-author/O/Ota/1997_Ota_339.pdf:PDF},
  keywords  = {Protein Bioinformatics; Quality Estimation},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Ouhenia2008,
  author    = {Ouhenia, S and Chateigner, D and Belkhir, M A and Guilmeau, E},
  journal   = {Journal of structural biology},
  title     = {Microstructure and crystallographic texture of Charonia lampas lampas shell.},
  year      = {2008},
  pages     = {175--84},
  volume    = {163},
  abstract  = {Charonia lampas lampas shell is studied using scanning electron microscopy and X-ray diffraction combined analysis of the preferred orientations and cell parameters. The Charonia shell is composed of three crossed lamellar layers of biogenic aragonite. The outer layer exhibits a 001 fibre texture, the intermediate crossed lamellar layer is radial with a split of its c-axis and single twin pattern of its a-axis, and the inner layer is comarginal with split c-axis and double twinning. A lost of texture strength is quantified from the inner layer outward. Unit-cell refinements evidence the intercrystalline organic influence on the aragonite unit-cell parameters anisotropic distortion and volume changes in the three layers. The simulation of the macroscopic elastic tensors of the mineral part of the three layers, from texture data, reveals an optimisation of the elastic coefficient to compression and shear in all directions of the shell as an overall.},
  file      = {2008_Ouhenia_175.pdf:by-author/O/Ouhenia/2008_Ouhenia_175.pdf:PDF},
  keywords  = {Textures; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Owolabi1988,
  author    = {Owolabi, O.},
  journal   = {Journal of Chemical Information and Computer Sciences},
  title     = {An efficient graph approach to matching chemical structures},
  year      = {1988},
  pages     = {221--226},
  volume    = {28},
  abstract  = {A matrix minimization method for the generation of canonical orderings for the nodes of a graph is outlined, with particular emphasis on its application in matching chemical structures. By use of both the connectedness and the attributes of each node in the representative graph, the modified adjacency matrix is reduced to a canonical form. This canonical matrix is unique for each distinct compound represented. For storage and comparison, a canonical linear string is generated for each compound. All known structures are compiled only once in this efficient manner, and the string representation also permits best-match retrieval. Examples are given to illustrate the procedure.},
  doi       = {10.1021/ci00060a008},
  file      = {:by-author/O/Owolabi/1988_Owolabi_221.pdf:PDF},
  keywords  = {Chemical Graph Matching},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
  url       = {http://pubs.acs.org/doi/abs/10.1021/ci00060a008},
}

@Article{Oxman2005,
  author    = {Oxman, Andrew D and Sackett, David L and Chalmers, Iain and Prescott, Trine E},
  journal   = {Journal of the Royal Society of Medicine},
  title     = {A surrealistic mega-analysis of redisorganization theories},
  year      = {2005},
  issn      = {0141-0768},
  pages     = {563--568},
  volume    = {98},
  abstract  = {Background We are sick and tired of being redisorganized., Objective To systematically review the empirical evidence for organizational theories and repeated reorganizations., Methods We did not find anything worth reading, other than Dilbert, so we fantasized. Unfortunately, our fantasies may well resemble many people's realities. We are sorry about this, but it is not our fault., Results We discovered many reasons for repeated reorganizations, the most common being ‘no good reason’. We estimated that trillions of dollars are being spent on strategic and organizational planning activities each year, thus providing lots of good reasons for hundreds of thousands of people, including us, to get into the business. New leaders who are intoxicated with the prospect of change further fuel perpetual cycles of redisorganization. We identified eight indicators of successful redisorganizations, including large consultancy fees paid to friends and relatives., Conclusions We propose the establishment of ethics committees to review all future redisorganization proposals in order to put a stop to uncontrolled, unplanned experimentation inflicted on providers and users of the health services.},
  file      = {PubMed Central Full Text PDF:by-author/O/Oxman/2005_Oxman_563.pdf:application/pdf},
  owner     = {saulius},
  pmcid     = {PMC1299350},
  pmid      = {16319441},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1299350/},
  urldate   = {2015-07-06},
}

@Article{Ozensoy2005,
  author    = {Ozensoy, Ozen and Puccetti, Luca and Fasolis, Giuseppe and Arslan, Oktay and Scozzafava, Andrea and Supuran, Claudiu T},
  journal   = {Bioorganic \&amp; medicinal chemistry letters},
  title     = {Carbonic anhydrase inhibitors: inhibition of the tumor-associated isozymes IX and XII with a library of aromatic and heteroaromatic sulfonamides.},
  year      = {2005},
  pages     = {4862--6},
  volume    = {15},
  file      = {2005_Ozensoy_4862.pdf:by-author/O/Ozensoy/2005_Ozensoy_4862.pdf:PDF},
  groups    = {sg/inhibitors, sg/hCA9, sg/hCA12},
  keywords  = {Carbonic Anhydrases},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{OBoyle2011,
  author    = {Noel M. O’Boyle and Michael Banck and Craig A. James and Chris Morley and Tim Vandermeersch and Geoffrey R. Hutchison},
  journal   = {Journal of Cheminformatics},
  title     = {{O}pen {B}abel: An open chemical toolbox},
  year      = {2011},
  pages     = {33},
  volume    = {3},
  doi       = {10.1186/1758-2946-3-33},
  file      = {:by-author/O/OBoyle/2011_OBoyle_33.pdf:PDF},
  owner     = {andrius},
  timestamp = {2013.04.14},
  creationdate = {2013-04-14T00:00:00},
}

@Presentation{Brien2009,
  author    = {Frank O’Brien},
  title     = {The Apollo Guidance Computer: Architecture and Operation},
  year      = {2009},
  file      = {2009_Brien.pdf:by-author/B/Brien/2009_Brien.pdf:PDF},
  groups    = {sg/Apollo Guidance Computer (history), sg/Apollo Guidance Computer},
  keywords  = {Apollo; Computer; Control Computer; Embedded Systems; High; Lunar Missions; Systems},
  owner     = {saulius},
  timestamp = {2016.02.08},
  creationdate = {2016-02-08T00:00:00},
  url       = {http://tcf.pages.tcnj.edu/files/2013/12/Apollo-Guidance-Computer-2009.pdf},
}

@Presentation{Brien2004,
  author    = {Frank O’Brien},
  title     = {The Apollo Guidance Computer: Architecture and Operation},
  year      = {2004},
  file      = {2004_Brien.pdf:by-author/B/Brien/2004_Brien.pdf:PDF},
  groups    = {sg/Apollo Guidance Computer (history), sg/Apollo Guidance Computer},
  keywords  = {Apollo; Computer; Control Computer; Embedded Systems; High; Lunar Missions; Systems},
  owner     = {saulius},
  timestamp = {2016.02.08},
  creationdate = {2016-02-08T00:00:00},
  url       = {http://tcf.pages.tcnj.edu/files/2013/12/Apollo-Guidance-Computer.pdf},
}

@Article{Halloran2012,
  author    = {O’Halloran, Kevin P. and Zhao, Chongchao and Ando, Nicole S. and Schultz, Arthur J. and Koetzle, Thomas F. and Piccoli, Paula M. B. and Hedman, Britt and Hodgson, Keith O. and Bobyr, Elena and Kirk, Martin L. and Knottenbelt, Sushilla and Depperman, Ezra C. and Stein, Benjamin and Anderson, Travis M. and Cao, Rui and Geletii, Yurii V. and Hardcastle, Kenneth I. and Musaev, Djamaladdin G. and Neiwert, Wade A. and Fang, Xikui and Morokuma, Keiji and Wu, Shaoxiong and Kögerler, Paul and Hill, Craig L.},
  journal   = {Inorg. Chem.},
  title     = {Revisiting the Polyoxometalate-Based Late-Transition-Metal-Oxo Complexes: The “Oxo Wall” Stands},
  year      = {2012},
  issn      = {1520-510X},
  pages     = {7025–7031},
  volume    = {51},
  doi       = {10.1021/ic2008914},
  file      = {:by-author/O/OHalloran/2012_OHalloran_7025.pdf:PDF},
  owner     = {saulius},
  publisher = {American Chemical Society (ACS)},
  timestamp = {2015.02.27},
  creationdate = {2015-02-27T00:00:00},
  url       = {http://dx.doi.org/10.1021/ic2008914},
}

@Article{Neil2008,
  author    = {Lauren L. O’Neil and Olaf Wiest},
  journal   = {Org. Biomol. Chem.},
  title     = {Sequence dependence in base flipping: experimental and computational studies},
  year      = {2008},
  pages     = {485--492},
  volume    = {6},
  abstract  = {Base flipping is the movement of a DNA base from an intrahelical, base-stacked position to an extrahelical, solvent-exposed position. As there are favorable interactions for an intrahelical base, both hydrogen bonding and base stacking, base flipping is expected to be energetically prohibitive for an undamaged DNA duplex. For damaged DNA bases, however, the energetic cost of base flipping may be considerably lower. Using a selective, non-covalent assay for base flipping, the sequence dependence of base flipping in DNA sequences containing an abasic site has been studied. The dissociation constants of the zinc–cyclen complex to small molecules and single strands of DNA as well as the equilibrium constants for base flipping have been determined for these sequences. Molecular dynamics simulations of the zinc-cyclen complex bound to both single- and double-stranded DNA have been performed in an attempt to rationalize the differences in the dissociation constants obtained for the two systems. The results are compared to previous studies of base flipping in DNA containing an abasic site.},
  doi       = {10.1039/b713318a},
  file      = {2008_Neil_485.pdf:by-author/N/Neil/2008_Neil_485.pdf:PDF},
  groups    = {sg/applications},
  keywords  = {Base Pairs; Bases; DNA; Stacking},
  owner     = {em},
  timestamp = {2008.11.05},
  creationdate = {2008-11-05T00:00:00},
}

@Article{Neill1998,
  author    = {Mary O’Neill and David T. F. Dryden and Noreen E. Murray},
  journal   = {The EMBO Journal},
  title     = {Localization of a protein-{DNA} interface by random mutagenesis},
  year      = {1998},
  pages     = {7118--7127},
  file      = {:by-author/N/Neill/1998_Neill_7118.pdf:PDF},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Presentation{Sullivan2005,
  author    = {Bryan O’Sullivan},
  title     = {Cvs Is Dead ... And Centralised Revision Control Is So Second Millennium},
  year      = {2005},
  file      = {:by-author/O/OSullivan/2005_OSullivan_slides.pdf:PDF},
  keywords  = {Computer Science (CS); Version Control},
  owner     = {saulius},
  pages     = {slides},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Pabo2000,
  author    = {Pabo, C O and Nekludova, L},
  journal   = {J Mol Biol},
  title     = {Geometric analysis and comparison of protein-DNA interfaces: why is there no simple code for recognition?},
  year      = {2000},
  month     = {Aug},
  number    = {3},
  pages     = {597--624},
  volume    = {301},
  abstract  = {Structural studies of protein-DNA complexes have shown that there are many distinct families of DNA-binding proteins, and have shown that there is no simple code describing side-chain/base interactions. However, systematic analysis and comparison of protein-DNA complexes has been complicated by the diversity of observed contacts, the sheer number of complexes currently available and the absence of any consistent method of comparison that retains detailed structural information about the protein-DNA interface. To address these problems, we have developed geometric methods for characterizing the local structural environment in which particular side-chain/base interactions are observed. In particular, we develop methods for analyzing and comparing spatial relationships at the protein-DNA interface. Our method involves attaching local coordinate systems to the DNA bases and to the C(alpha) atoms of the peptide backbone (these are relatively rigid structural units). We use these tools to consider how the position and orientation of the polypeptide backbone (with respect to the DNA) helps to determine what contacts are possible at any given position in a protein-DNA complex. Here, we focus on base contacts that are made in the major groove, and we use spatial relationships in analyzing: (i) the observed patterns of side-chain/base interactions; (ii) observed helix docking orientations; (iii) family/subfamily relationships among DNA-binding proteins; and (iv) broader questions about evolution, altered specificity mutants and the limits for the design of new DNA-binding proteins. Our analysis, which highlights differences in spatial relationships in different complexes and at different positions in a complex, helps explain why there is no simple, general code for protein-DNA recognition},
  address   = {Howard Hughes Medical Institute, Department of Biology 68-580, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. pabo@,it.edu},
  file      = {2000_Pabo_567.pdf:by-author/P/Pabo/2000_Pabo_567.pdf:PDF},
  owner     = {em},
  timestamp = {2016.06.16},
  creationdate = {2016-06-16T00:00:00},
  url       = {http://www.ncbi.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&dopt=abstract&list_uids=10966773},
}

@Article{Pabo2000a,
  author    = {Carl O. Pabo and Lena Nekludova},
  journal   = {J. Mol. Biol.},
  title     = {Geometric Analysis and Comparison of Protein-{DNA} Interfaces: Why is there no Simple Code for Recognition?},
  year      = {2000},
  pages     = {567},
  doi       = {10.1006/jmbi.2000.3918},
  file      = {:by-author/P/Pabo/2000_Pabo_567.pdf:PDF},
  keywords  = {DNA Protein; Readout},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Pace1996,
  author    = {Pace, C. N. and Shirley, B. A. and McNutt, M. and Gajiwala, K.},
  journal   = {The FASEB Journal},
  title     = {Forces contributing to the conformational stability of proteins.},
  year      = {1996},
  pages     = {75--83},
  volume    = {10},
  abstract  = {For 35 years, the prevailing view has been that the hydrophobic effect is the dominant force in protein folding. The importance of hydrogen bonding was always clear, but whether it made a net favorable contribution to protein stability was not. Studies of mutant proteins have improved our understanding of the forces stabilizing proteins. They suggest that hydrogen bonding and the hydrophobic effect make large but comparable contributions to the stability of globular proteins.},
  eprint    = {http://www.fasebj.org/content/10/1/75.full.pdf+html},
  file      = {1996_Pace_75.pdf:by-author/P/Pace/1996_Pace_75.pdf:PDF},
  keywords  = {Hydrogen Bonds; Hydrophobic Effect; Protein Folding},
  owner     = {saulius},
  timestamp = {2015.03.13},
  creationdate = {2015-03-13T00:00:00},
  url       = {http://www.fasebj.org/content/10/1/75.abstract},
}

@InProceedings{applications2007,
  author    = {António Pacheco and Carlos Serrão},
  booktitle = {Innovative Algorithms and Techniques in Automation, Industrial Electronics and Telecommunications},
  title     = {Developing secure Web-applications – Security criteria for the development of e-Democracy Web-applications},
  year      = {2007},
  editor    = {T. Sobh et al.},
  pages     = {79--84},
  publisher = {Springer},
  abstract  = {One of the most important requirements in interact, the nature of Internet communications, and the},
  file      = {:by-author/P/Pacheco/2007_Pacheco_79.pdf:PDF},
  owner     = {saulius},
  timestamp = {2013.08.11},
  creationdate = {2013-08-11T00:00:00},
}

@Article{Padilla2003,
  author    = {Padilla, Jennifer E. and Yeates, Todd O.},
  journal   = {Acta Crystallographica Section D},
  title     = {A statistic for local intensity differences: robustness to anisotropy and pseudo-centering and utility for detecting twinning},
  year      = {2003},
  pages     = {1124--1130},
  volume    = {59},
  doi       = {10.1107/S0907444903007947},
  file      = {wd0007.pdf:by-author/P/Padilla/2003_Padilla_1124.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444903007947},
}

@Article{Padmaja1991,
  author    = {N. Padmaja and S. Ramakumar and M. A. Viswamitra},
  journal   = {Acta Cryst. C},
  title     = {Structure of 5-Methylcytidine},
  year      = {1991},
  pages     = {1445--1448},
  volume    = {47},
  abstract  = {4-Amino- 5-methyl- 1-fl-D-ribo furanosyl- 2(1H)-pyrimidinone, CIoHIsN3Os, Mr = 257-2, monoclinic, P21, a = 5.632(1), b = 14"636 (3), c = 13.914(3)A, /3=90.57(1) °, V = l 1 4 6 . 9 A 3~ Z = 4, Dx = 1.49 Mg m -3, A(Cu Ka) = 1.5418 A, p, = 0"98 mm-~, F(000) = 544, T = 295 K, R = 0.036 for 2025 unique observed reflections with F_> 3~r(F). The bond lengths, bond angles and conformation of the two independent molecules in the asymmetric unit are essentially similar. The cytosine bases are not protonated. Bases are in anti conformation, sugars show C(Y)-endo pucker (3E) and gg conformation about the C(4')--C(5') bond for both molecules. The structure is stabilized by a number of hydrogen bonds between molecules A and molecules B. No base-stacking interactions Were observed in the present structure. This is in agreement with the observation made in a comparison of methylated and unmethylated cytosine structures which showed that methylation at the 5 position of the cytosine base could result in reduced base-stacking interactions.},
  doi       = {10.1107/S0108270190012264},
  file      = {:by-author/P/Padmaja/1991_Padmaja_1445.pdf:PDF},
  keywords  = {For COD Deposition; Methylcytidine; Modified RNA Bases; Nucleic Acids Bases; RNA Bases; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2013.09.27},
  creationdate = {2013-09-27T00:00:00},
  url       = {http://scripts.iucr.org/cgi-bin/paper?AB0162},
}

@Article{Page2003,
  author    = {Page, Rebecca and Grzechnik, Slawomir K. and Canaves, Jaume M. and Spraggon, Glen and Kreusch, Andreas and Kuhn, Peter and Stevens, Raymond C. and Lesley, Scott A.},
  journal   = {Acta Crystallographica Section D},
  title     = {Shotgun crystallization strategy for structural genomics: an optimized two-tiered crystallization screen against the {\it Thermotoga maritima} proteome},
  year      = {2003},
  pages     = {1028--1037},
  volume    = {59},
  doi       = {10.1107/S0907444903007790},
  file      = {he0318.pdf:by-author/P/Page/2003_Page_1028.pdf:PDF;Supplementary data:by-author/P/Page/2003_Page_1028.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444903007790},
}

@Manuscript{LePage2008,
  author    = {Yvon le Page},
  title     = {19th century basics spearhead 21st century progress : some autobiographic details},
  year      = {2008},
  keywords  = {History; X-ray Crystallography},
  file      = {:by-author/P/Page/2008_Page.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Manuscript{Page2008,
  author    = {Yvon Le Page},
  title     = {19th century basics spearhead 21st century progress : some autobiographic details},
  year      = {2008},
  keywords  = {History; X-ray Crystallography},
  file      = {:by-author/P/Page/2008_Page.doc:DOC},
  owner     = {saulius},
  timestamp = {2015.02.28},
  creationdate = {2015-02-28T00:00:00},
}

@Presentation{Palatinus2006,
  author       = {Lukas Palatinus},
  title        = {Structure determination of incommensurate phases. An introduction to structure solution and refinement},
  year         = {2006},
  organization = {EPFL Lausanne, Switzerland},
  file         = {:by-author/P/Palatinus/2006_Palatinus.ppt:PPT},
  keywords     = {Incommensurate Structures},
  note         = {File corrupt?},
  owner        = {saulius},
  timestamp = {2015.03.03},
  creationdate = {2015-03-03T00:00:00},
  url          = {http://cristallo.epfl.ch/poster/2006/lukas-palatinus-tutorial_aperiodic06.ppt},
}

@Manuscript{Pan1998,
  author    = {Heping Pan and Daniel McMichael},
  title     = {Fuzzy causal probabilistic networks - a new ideal and practical inference engine},
  year      = {1998},
  keywords  = {Bayesian Statistics; Fuzzy Logics},
  url       = {http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.39.1482&rep=rep1&type=pdf},
  abstract  = {Fuzziness and randomness are two distinct components of uncertainty. While fuzzy sets are a rigorous softening of random sets, many of the operations defined in fuzzy logic lack a complete formalism, and are not strongly supported by experimental evidence. Causal Probabilistic Networks (CPN) or Bayesian networks provide an ultimately exible inferencemechanism based on Bayesian probability principles. However, CPNs suffer from the overwhelmingly large conditional probability tables with discrete variables. Fuzzification of continuous or crisp variables reduces the size of conditional probability tables to practically acceptable levels and these tables exhaustively encompass all the intuitive and fuzzy rules for inference problems. In this way, we reach a new inference engine, called fuzzy causal probabilistic networks, which provides a rigorous formalism for inference under fuzziness and randomness.},
  file      = {1998_Pan.pdf:by-author/P/Pan/1998_Pan.pdf:PDF},
  groups    = {sg/CRISPR-Cas, sg/Bayesian},
  owner     = {saulius},
  timestamp = {2012.10.09},
  creationdate = {2012-10-09T00:00:00},
}

@Manuscript{Panagiotidou2003,
  author    = {Effimia Panagiotidou},
  title     = {The patentability of computer programs, according to the commission's new proposal for a directive and to the epo boards of appeal decisions},
  year      = {2003},
  keywords  = {Patentai; Teise},
  file      = {:by-author/P/Panagiotidou/2003_Panagiotidou.doc:DOC},
  owner     = {saulius},
  timestamp = {2015.02.28},
  creationdate = {2015-02-28T00:00:00},
}

@Manuscript{Panagopoulos2003,
  author    = {Panagopoulos, Ioannis and George Papakonstantinou and Nikitas Alexandridis},
  title     = {A Comparative Evaluation of Models and Specification Languages for Embedded System Design},
  year      = {2003},
  keywords  = {Computer Language Design; Computer Science (CS)},
  abstract  = {The HW/SW Codesign approach in the design of embedded systems and their increasing complexity has turned the need of simplifying the specifi- cation of both the desired behaviour and the final implementation a very crucial task in the design process. Towards this effort programmers and designers have introduced a plethora of model-specification language pairs that can effectively reduce the complexity of the captured functionality, raise the level of abstrac- tion and support several design tasks (such as verification, performance estima- tion etc). Due to the lack of a set of well-defined features for the comparative evaluation of those pairs industry is still reluctant in taking advantage of their full potential. Additionally, design teams are introducing new models and speci- fication languages which sometimes add nothing new to already existing ones. Although VSIA’ s [13] model taxonomy has been proven very useful in classi- fying models for the specification of the system’s implementation our approach deals with the specification of the initial desired behaviour. By introducing two evaluation axes for models, introducing a 3 dimensional space for the taxonomy of specification languages and classifying the latter with respect to the model they are used to express, we present a complete feature-based approach that can be used not only for the selection of the most appropriate model-specification language pair for the design at hand but also for the classification and evalua- tion of new models and specification languages introduced for embedded sys- tem design.},
  file      = {:by-author/P/Panagopoulos/2003_Panagopoulos.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Pandey2009,
  author    = {Pandey, Manjula and Syed, Salman and Donmez, Ilker and Patel, Gayatri and Ha, Taekjip and Patel, Smita S.},
  journal   = {Nature},
  title     = {Coordinating DNA replication by means of priming loop and differential synthesis rate.},
  year      = {2009},
  pages     = {940--3},
  volume    = {462},
  abstract  = {Genomic DNA is replicated by two DNA polymerase molecules, one of which works in close association with the helicase to copy the leading-strand template in a continuous manner while the second copies the already unwound lagging-strand template in a discontinuous manner through the synthesis of Okazaki fragments. Considering that the lagging-strand polymerase has to recycle after the completion of every Okazaki fragment through the slow steps of primer synthesis and hand-off to the polymerase, it is not understood how the two strands are synthesized with the same net rate. Here we show, using the T7 replication proteins, that RNA primers are made 'on the fly' during ongoing DNA synthesis and that the leading-strand T7 replisome does not pause during primer synthesis, contrary to previous reports. Instead, the leading-strand polymerase remains limited by the speed of the helicase; it therefore synthesizes DNA more slowly than the lagging-strand polymerase. We show that the primase-helicase T7 gp4 maintains contact with the priming sequence during ongoing DNA synthesis; the nascent lagging-strand template therefore organizes into a priming loop that keeps the primer in physical proximity to the replication complex. Our findings provide three synergistic mechanisms of coordination: first, primers are made concomitantly with DNA synthesis; second, the priming loop ensures efficient primer use and hand-off to the polymerase; and third, the lagging-strand polymerase copies DNA faster, which allows it to keep up with leading-strand DNA synthesis overall.},
  file      = {:by-author/P/Pandey/2009_Pandey_940.pdf:PDF},
  keywords  = {T7; {gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Panis2001,
  author    = {Bart Panis and Nguyen Tien Thinh},
  title     = {Cryopreservation of Musa germplasm},
  year      = {2001},
  file      = {:by-author/P/Panis/2001_Panis.pdf:PDF},
  keywords  = {Cryo Preservation},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Presentation{Panjikar2009a,
  author       = {Panjikar},
  title        = {Solving structure with Auto-Rickshaw},
  year         = {2009},
  organization = {EMBL},
  file         = {:by-author/P/Panjikar/2009_Panjikar_slides.pdf:PDF},
  owner        = {saulius},
  pages        = {slides},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Panne2001,
  author    = {Panne, D. and Müller, S. A. and Wirtz, S. and Engel, A. and Bickle, T. A.},
  journal   = {The EMBO journal},
  title     = {The McrBC restriction endonuclease assembles into a ring structure in the presence of G nucleotides.},
  year      = {2001},
  pages     = {3210--7},
  volume    = {20},
  abstract  = {McrBC from Escherichia coli K-12 is a restriction enzyme that belongs to the family of AAA(+) proteins and cuts DNA containing modified cytosines. Two proteins are expressed from the mcrB gene: a full-length version, McrB(L), and a short version, McrB(S). McrB(L) binds specifically to the methylated recognition site and is, therefore, the DNA-binding moiety of the McrBC endonuclease. McrB(S) is devoid of DNA-binding activity. We observed that the quaternary structure of the endonuclease depends on binding of the cofactors. In gel filtration experiments, McrB(L) and McrB(S) form high molecular weight oligomers in the presence of Mg(2+) and GTP, GDP or GTP-gamma-S. Oligomerization did not require the presence of DNA and was independent of GTP hydrolysis. Electron micrographs of negatively stained McrB(L) and McrB(S) revealed ring-shaped particles with a central channel. Mass analysis by scanning transmission electron microscopy indicates that McrB(L) and McrB(S) form single heptameric rings as well as tetradecamers. In the presence of McrC, a subunit that is essential for DNA cleavage, the tetradecameric species was the major form of the endonuclease.},
  file      = {:by-author/P/Panne/2001_Panne_3210.pdf:PDF},
  keywords  = {McrBC},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Panne1999,
  author    = {Panne, D. and Raleigh, E. A. and Bickle, T. A.},
  journal   = {Journal of molecular biology},
  title     = {The McrBC endonuclease translocates DNA in a reaction dependent on GTP hydrolysis.},
  year      = {1999},
  pages     = {49--60},
  volume    = {290},
  abstract  = {McrBC specifically recognizes and cleaves methylated DNA in a reaction dependent on GTP hydrolysis. DNA cleavage requires at least two recognition sites that are optimally separated by 40-80 bp, but can be spaced as far as 3 kb apart. The nature of the communication between two recognition sites was analyzed on DNA substrates containing one or two recognition sites. DNA cleavage of circular DNA required only one methylated recognition site, whereas the linearized form of this substrate was not cleaved. However, the linearized substrate was cleaved if a Lac repressor was bound adjacent to the recognition site. These results suggest a model in which communication between two remote sites is accomplished by DNA translocation rather than looping. A mutant protein with defective GTPase activity cleaved substrates with closely spaced recognition sites, but not substrates where the sites were further apart. This indicates that McrBC translocates DNA in a reaction dependent on GTP hydrolysis. We suggest that DNA cleavage occurs by the encounter of two DNA-translocating McrBC complexes, or can be triggered by non-specific physical obstacles like the Lac repressor bound on the enzyme's path along DNA. Our results indicate that McrBC belongs to the general class of DNA &quot;motor proteins&quot;, which use the free energy associated with nucleoside 5'-triphosphate hydrolysis to translocate along DNA.},
  file      = {:by-author/P/Panne/1999_Panne_49.pdf:PDF},
  keywords  = {McrBC},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Panne1998,
  author    = {Panne, D. and Raleigh, E. A. and Bickle, T. A.},
  journal   = {The EMBO journal},
  title     = {McrBs, a modulator peptide for McrBC activity.},
  year      = {1998},
  pages     = {5477--83},
  volume    = {17},
  abstract  = {McrBC is a methylation-dependent endonuclease from Escherichia coli K-12. The enzyme recognizes DNA with modified cytosines preceded by a purine. McrBC restricts DNA that contains at least two methylated recognition sites separated by 40-80 bp. Two gene products, McrBL and McrBs, are produced from the mcrB gene and one, McrC, from the mcrC gene. DNA cleavage in vitro requires McrBL, McrC, GTP and Mg2+. We found that DNA cleavage was optimal at a ratio of 3-5 McrBL per molecule of McrC, suggesting that formation of a multisubunit complex with several molecules of McrBL is required for cleavage. To understand the role of McrBs, we have purified the protein and analyzed its role in vitro. At the optimal ratio of 3-5 McrBL per molecule of McrC, McrBs acted as an inhibitor of DNA cleavage. Inhibition was due to sequestration of McrC and required the presence of GTP, suggesting that the interaction is GTP dependent. If McrC was in excess, a condition resulting in suboptimal DNA cleavage, addition of McrBs enhanced DNA cleavage, presumably due to sequestration of excess McrC. We suggest that the role of McrBs is to modulate McrBC activity by binding to McrC.},
  file      = {:by-author/P/Panne/1998_Panne_5477.pdf:PDF},
  keywords  = {McrBC},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Pannu2003,
  author    = {Pannu, Navraj S. and McCoy, Airlie J. and Read, Randy J.},
  journal   = {Acta Crystallographica Section D},
  title     = {Application of the complex multivariate normal distribution to crystallographic methods with insights into multiple isomorphous replacement phasing},
  year      = {2003},
  pages     = {1801--1808},
  volume    = {59},
  doi       = {10.1107/S090744490301936X},
  file      = {wd5000.pdf:by-author/P/Pannu/2003_Pannu_1801.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S090744490301936X},
}

@Article{Pannu2004,
  author    = {Pannu, Navraj S. and Read, Randy J.},
  journal   = {Acta Crystallographica Section D},
  title     = {The application of multivariate statistical techniques improves single-wavelength anomalous diffraction phasing},
  year      = {2004},
  pages     = {22--27},
  volume    = {60},
  doi       = {10.1107/S0907444903020808},
  file      = {wd5005.pdf:by-author/P/Pannu/2004_Pannu_22.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444903020808},
}

@Article{Pantazatos2004,
  author    = {Pantazatos, Dennis and Kim, Jack S. and Klock, Heath E. and Stevens, Raymond C. and Wilson, Ian A. and Lesley, Scott A. and Woods, Jr, Virgil L.},
  journal   = {Proceedings of the National Academy of Sciences of the United States of America},
  title     = {Rapid refinement of crystallographic protein construct definition employing enhanced hydrogen/deuterium exchange MS.},
  year      = {2004},
  pages     = {751--6},
  volume    = {101},
  abstract  = {Crystallographic efforts often fail to produce suitably diffracting protein crystals. Unstructured regions of proteins play an important role in this problem and considerable advantage can be gained in removing them. We have developed a number of enhancements to amide hydrogen/high-throughput and high-resolution deuterium exchange MS (DXMS) technology that allow rapid identification of unstructured regions in proteins. To demonstrate the utility of this approach for improving crystallization success, DXMS analysis was attempted on 24 Thermotoga maritima proteins with varying crystallization and diffraction characteristics. Data acquisition and analysis for 21 of these proteins was completed in 2 weeks and resulted in the localization and prediction of several unstructured regions within the proteins. When compared with those targets of known structure, the DXMS method correctly localized even small regions of disorder. DXMS analysis was then correlated with the propensity of such targets to crystallize and was further used to define truncations that improved crystallization. Truncations that were defined solely on DXMS analysis demonstrated greatly improved crystallization and have been used for structure determination. This approach represents a rapid and generalized method that can be applied to structural genomics or other targets in a high-throughput manner.},
  file      = {:by-author/P/Pantazatos/2004_Pantazatos_751.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Pappu2000,
  author    = {Pappu, R. V. and Srinivasan, R. and Rose, G. D.},
  journal   = {Proceedings of the National Academy of Sciences of the United States of America},
  title     = {The Flory isolated-pair hypothesis is not valid for polypeptide chains: implications for protein folding.},
  year      = {2000},
  pages     = {12565--70},
  volume    = {97},
  abstract  = {Using an all-atom representation, we exhaustively enumerate all sterically allowed conformations for short polyalanyl chains. Only intrachain interactions are considered, including one adjustable parameter, a favorable backbone energy (e.g., a peptide hydrogen bond). The counting is used to reevaluate Flory's isolated-pair hypothesis, the simplifying assumption that each phi,psi pair is sterically independent. This hypothesis is a conceptual linchpin in helix-coil theories and protein folding. Contrary to the hypothesis, we find that systematic local steric effects can extend beyond nearest-chain neighbors and can restrict the size of accessible conformational space significantly. As a result, the entropy price that must be paid to adopt any specific conformation is far less than previously thought.},
  file      = {:by-author/P/Pappu/2000_Pappu_12565.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Park2010c,
  author    = {Park, Chad and Joshi, Hemant K. and Agrawal, Alka and Ghare, M. Imran and Little, Elizabeth J. and Dunten, Pete W. and Bitinaite, Jurate and Horton, Nancy C.},
  journal   = {PLoS Biology},
  title     = {Domain Swapping in Allosteric Modulation of DNA Specificity},
  year      = {2010},
  pages     = {e1000554},
  volume    = {8},
  abstract  = {SgrAI is a type IIF restriction endonuclease that cuts an unusually long recognition sequence and exhibits allosteric self- modulation of cleavage activity and sequence specificity. Previous studies have shown that DNA bound dimers of SgrAI oligomerize into an activated form with higher DNA cleavage rates, although previously determined crystal structures of SgrAI bound to DNA show only the DNA bound dimer. A new crystal structure of the type II restriction endonuclease SgrAI bound to DNA and Ca2+ is now presented, which shows the close association of two DNA bound SgrAI dimers. This tetrameric form is unlike those of the homologous enzymes Cfr10I and NgoMIV and is formed by the swapping of the amino-terminal 24 amino acid residues. Two mutations predicted to destabilize the swapped form of SgrAI, P27W and P27G, have been made and shown to eliminate both the oligomerization of the DNA bound SgrAI dimers as well as the allosteric stimulation of DNA cleavage by SgrAI. A mechanism involving domain swapping is proposed to explain the unusual allosteric properties of SgrAI via association of the domain swapped tetramer of SgrAI bound to DNA into higher order oligomers.},
  doi       = {10.1371/journal.pbio.1000554},
  file      = {2010_Park_e1000554.pdf:by-author/P/Park/2010_Park_e1000554.pdf:PDF},
  groups    = {sg/Cfr10I, sg/NgoMIV},
  keywords  = {SgrAI; TypeII},
  owner     = {em},
  timestamp = {2013.01.04},
  creationdate = {2013-01-04T00:00:00},
}

@Article{Park2010a,
  author      = {Chad K Park and Hemant K Joshi and Alka Agrawal and M. Imran Ghare and Elizabeth J Little and Pete W Dunten and Jurate Bitinaite and Nancy C Horton},
  journal     = {PLoS Biol},
  title       = {Domain swapping in allosteric modulation of DNA specificity.},
  year        = {2010},
  number      = {12},
  pages       = {e1000554},
  volume      = {8},
  abstract    = {SgrAI is a type IIF restriction endonuclease that cuts an unusually long recognition sequence and exhibits allosteric self-modulation of cleavage activity and sequence specificity. Previous studies have shown that DNA bound dimers of SgrAI oligomerize into an activated form with higher DNA cleavage rates, although previously determined crystal structures of SgrAI bound to DNA show only the DNA bound dimer. A new crystal structure of the type II restriction endonuclease SgrAI bound to DNA and Ca(2+) is now presented, which shows the close association of two DNA bound SgrAI dimers. This tetrameric form is unlike those of the homologous enzymes Cfr10I and NgoMIV and is formed by the swapping of the amino-terminal 24 amino acid residues. Two mutations predicted to destabilize the swapped form of SgrAI, P27W and P27G, have been made and shown to eliminate both the oligomerization of the DNA bound SgrAI dimers as well as the allosteric stimulation of DNA cleavage by SgrAI. A mechanism involving domain swapping is proposed to explain the unusual allosteric properties of SgrAI via association of the domain swapped tetramer of SgrAI bound to DNA into higher order oligomers.},
  doi         = {10.1371/journal.pbio.1000554},
  file        = {2010_Park_e1000554.pdf:by-author/P/Park/2010_Park_e1000554.pdf:PDF;2010_Park_8818.pdf:by-author/P/Park/2010_Park_8818.pdf:PDF},
  groups      = {sg/Cfr10I, sg/NgoMIV},
  institution = {Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona, United States of America.},
  keywords    = {Allosteric Regulation; Calcium; DNA; DNA Cleavage; Deoxyribonucleases; Dimerization; Electrophoresis; Models; Molecular; Polyacrylamide Gel; Protein Multimerization; Protein Structure; Quaternary; Streptomyces Griseus; Type II Site-Specific},
  owner       = {em},
  pmid        = {21151881},
  timestamp = {2011.06.08},
  creationdate = {2011-06-08T00:00:00},
  url         = {http://dx.doi.org/10.1371/journal.pbio.1000554},
}

@Article{Park2010,
  author      = {Chad K Park and Amanda P Stiteler and Santosh Shah and M. Imran Ghare and Jurate Bitinaite and Nancy C Horton},
  journal     = {Biochemistry},
  title       = {Activation of DNA cleavage by oligomerization of DNA-bound SgrAI.},
  year        = {2010},
  month       = {Oct},
  number      = {41},
  pages       = {8818--8830},
  volume      = {49},
  abstract    = {SgrAI is a type II restriction endonuclease that cuts an unusually long recognition sequence and exhibits allosteric self-modulation of DNA activity and sequence specificity. Precleaved primary site DNA has been shown to be an allosteric effector [Hingorani-Varma, K., and Bitinaite, J. (2003) J. Biol. Chem. 278, 40392-40399], stimulating cleavage of both primary (CR|CCGGYG, where the vertical bar indicates a cut site, R denotes A or G, and Y denotes C or T) and secondary [CR|CCGGY(A/C/T) and CR|CCGGGG] site DNA sequences. The fact that DNA is the allosteric effector of this endonuclease suggests at least two DNA binding sites on the functional SgrAI molecule, yet crystal structures of SgrAI [Dunten, P. W., et al. (2008) Nucleic Acids Res. 36, 5405-5416] show only one DNA duplex bound to one dimer of SgrAI. We show that SgrAI forms species larger than dimers or tetramers [high-molecular weight species (HMWS)] in the presence of sufficient concentrations of SgrAI and its primary site DNA sequence that are dependent on the concentration of the DNA-bound SgrAI dimer. Analytical ultracentrifugation indicates that the HMWS is heterogeneous, has sedimentation coefficients of 15-20 s, and is composed of possibly 4-12 DNA-bound SgrAI dimers. SgrAI bound to secondary site DNA will not form HMWS itself but can bind to HMWS formed with primary site DNA and SgrAI. Uncleaved, as well as precleaved, primary site DNA is capable of stimulating HMWS formation. Stimulation of DNA cleavage by SgrAI, at primary as well as secondary sites, is also dependent on the concentration of primary site DNA (cleaved or uncleaved) bound SgrAI dimers. SgrAI bound to secondary site DNA does not have significant stimulatory activity. We propose that the oligomers of DNA-bound SgrAI (i.e., HMWS) are the activated, or activatable, forms of the enzyme.},
  doi         = {10.1021/bi100557v},
  file        = {2010_Park_e1000554.pdf:by-author/P/Park/2010_Park_e1000554.pdf:PDF;2010_Park_8818.pdf:by-author/P/Park/2010_Park_8818.pdf:PDF},
  institution = {Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA.},
  keywords    = {Allosteric Regulation; DNA; Deoxyribonucleases; Kinetics; Protein Multimerization; Type II Site-Specific},
  owner       = {em},
  pmid        = {20836535},
  timestamp = {2011.06.08},
  creationdate = {2011-06-08T00:00:00},
  url         = {http://dx.doi.org/10.1021/bi100557v},
}

@Article{Park2010b,
  author    = {Park, Chad K. and Stiteler, Amanda P. and Shah, Santosh and Ghare, M. Imran and Bitinaite, Jurate and Horton, Nancy C.},
  journal   = {Biochemistry},
  title     = {Activation of DNA cleavage by oligomerization of DNA-bound SgrAI.},
  year      = {2010},
  pages     = {8818--30},
  volume    = {49},
  abstract  = {SgrAI is a type II restriction endonuclease that cuts an unusually long recognition sequence and exhibits allosteric self-modulation of DNA activity and sequence specificity. Precleaved primary site DNA has been shown to be an allosteric effector [Hingorani-Varma, K., and Bitinaite, J. (2003) J. Biol. Chem. 278, 40392-40399], stimulating cleavage of both primary (CR|CCGGYG, where the vertical bar indicates a cut site, R denotes A or G, and Y denotes C or T) and secondary [CR|CCGGY(A/C/T) and CR|CCGGGG] site DNA sequences. The fact that DNA is the allosteric effector of this endonuclease suggests at least two DNA binding sites on the functional SgrAI molecule, yet crystal structures of SgrAI [Dunten, P. W., et al. (2008) Nucleic Acids Res. 36, 5405-5416] show only one DNA duplex bound to one dimer of SgrAI. We show that SgrAI forms species larger than dimers or tetramers [high-molecular weight species (HMWS)] in the presence of sufficient concentrations of SgrAI and its primary site DNA sequence that are dependent on the concentration of the DNA-bound SgrAI dimer. Analytical ultracentrifugation indicates that the HMWS is heterogeneous, has sedimentation coefficients of 15-20 s, and is composed of possibly 4-12 DNA-bound SgrAI dimers. SgrAI bound to secondary site DNA will not form HMWS itself but can bind to HMWS formed with primary site DNA and SgrAI. Uncleaved, as well as precleaved, primary site DNA is capable of stimulating HMWS formation. Stimulation of DNA cleavage by SgrAI, at primary as well as secondary sites, is also dependent on the concentration of primary site DNA (cleaved or uncleaved) bound SgrAI dimers. SgrAI bound to secondary site DNA does not have significant stimulatory activity. We propose that the oligomers of DNA-bound SgrAI (i.e., HMWS) are the activated, or activatable, forms of the enzyme.},
  file      = {:by-author/P/Park/2010_Park_8818.pdf:PDF},
  keywords  = {SgrAI; TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Park2012,
  author    = {Suk-Youl Park and Hyun-Ju Lee and Jung-Mi Song and Jiali Sun and Hyo-Jeong Hwang and Kosuke Nishi and Jeong-Sun Kim},
  journal   = {Acta Crystallographica Section D},
  title     = {Structural characterization of a modification subunit of a putative type {I} restriction enzyme from {Vibrio vulnificus} {YJ016}},
  year      = {2012},
  pages     = {1570–1577},
  volume    = {68},
  doi       = {10.1107/S0907444912038826},
  file      = {:by-author/P/Park/2012_Park_1570.pdf:PDF},
  owner     = {andrius},
  timestamp = {2014.09.14},
  creationdate = {2014-09-14T00:00:00},
}

@Article{Parker2005,
  author    = {Parker, James S. and Roe, Mark and Barford, David},
  journal   = {Nature},
  title     = {Structural insights into mRNA recognition from a PIWI domain–siRNA guide complex},
  year      = {2005},
  pages     = {663--666},
  volume    = {434},
  abstract  = {RNA interference and related RNA silencing phenomena use short RNA. The structure contains a highly conserved metal-binding antisense guide RNA molecules to repress the expression of target site that anchors the 5 0 nucleotide of the guide RNA. The first genes1,2. Argonaute proteins3, containing amino-terminal PAZ base pair of the duplex is unwound, separating the 5 0 nucleotide (for PIWI/Argonaute/Zwille) domains and carboxy-terminal of the guide from the complementary nucleotide on the target PIWI domains, are core components of these mechanisms. strand, which exits with the 3 0 overhang through a short channel. Here we show the crystal structure of a Piwi protein from The remaining base-paired nucleotides assume an A-form helix, Archaeoglobus fulgidus (AfPiwi) in complex with a small inter- accommodated within a channel in the PIWI domain, which can fering RNA (siRNA)-like duplex, which mimics the 5 0 end of a be extended to place the scissile phosphate of the target strand guide RNA strand bound to an overhanging target messenger adjacent to the putative slicer catalytic site. This study provides insights into mechanisms of target mRNA recognition and cleavage by an Argonaute–siRNA guide complex},
  file      = {:by-author/P/Parker/2005_Parker_663.pdf:PDF},
  keywords  = {Argonaute; Crystal Structure; PAgo; PIWI; Silencing},
  owner     = {em},
  timestamp = {2014.05.22},
  creationdate = {2014-05-22T00:00:00},
}

@Article{Parker2004,
  author           = {Parker, James S and Roe, S Mark and Barford, David},
  journal          = {The EMBO Journal},
  title            = {Crystal structure of a PIWI protein suggests mechanisms for siRNA recognition and slicer activity},
  year             = {2004},
  pages            = {4727–4737},
  volume           = {23},
  creationdate     = {2014-05-22T00:00:00},
  doi              = {10.1038/sj.emboj.7600488},
  file             = {:by-author/P/Parker/2004_Parker_2747.pdf:PDF},
  keywords         = {Argonaute; Crystal Structure; PAgo; PIWI Domain; RISC; RNAi; {siRNA}},
  modificationdate = {2022-11-04T22:30:33},
  owner            = {em},
  timestamp        = {2014.05.22},
}

@Article{Parkinson1996,
  author    = {Parkinson, G. and Vojtechovsky, J. and Clowney, L. and Br{\"{u}}nger, A. T. and Berman, H. M.},
  journal   = {Acta Crystallographica Section D},
  title     = {New Parameters for the Refinement of Nucleic Acid-Containing Structures},
  year      = {1996},
  pages     = {57--64},
  volume    = {52},
  abstract  = {Structures at atomic resolution (up to 1.0 A) which contain bases, sugars or the phosphodiester linkage, were selected from the Nucleic Acid Database or the Cambridge Structural Database to build a nucleic acid dictionary from X-ray refined structures. The dictionary consists of the average values for bond distances, bond angles and dihedral angles. The variance of the sample is used to provide information about the expected r.m.s. deviations of the refined parameters. A dictionary was constructed for refinement trials in X-PLOR. The dictionary includes RNA and DNA in C2'-endo and C3'-endo sugar pucker conformations, as well as values for the backbone dihedrals. Tests were performed on the dictionary using three structures: a B-DNA, a Z-DNA and a protein-DNA complex. During the course of refinement, all three structures showed significant improvements as measured by r.m.s. deviations and R factors when compared to the previous DNA dictionary.},
  doi       = {10.1107/S0907444995011115},
  file      = {:by-author/P/Parkinson/1996_Parkinson_57.pdf:PDF},
  keywords  = {X-ray Crystallography},
  owner     = {andrius},
  timestamp = {2012.05.09},
  creationdate = {2012-05-09T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444995011115},
}

@Article{Parkkila2002,
  author    = {Parkkila, Seppo and Kivelä, Antti J and Kaunisto, Kari and Parkkila, Anna-Kaisa and Hakkola, Jukka and Rajaniemi, Hannu and Waheed, Abdul and Sly, William S},
  journal   = {BMC gastroenterology},
  title     = {The plasma membrane carbonic anhydrase in murine hepatocytes identified as isozyme XIV.},
  year      = {2002},
  pages     = {13},
  volume    = {2},
  file      = {2002_Parkkila_13.pdf:by-author/P/Parkkila/2002_Parkkila_13.pdf:PDF},
  groups    = {sg/mCA14},
  keywords  = {CA14; Carbonic Anhydrases},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Parkkila2001,
  author    = {Parkkila, S and Parkkila, A K and Rajaniemi, H and Shah, G N and Grubb, J H and Waheed, A and Sly, W S},
  journal   = {Proceedings of the National Academy of Sciences of the United States of America},
  title     = {Expression of membrane-associated carbonic anhydrase XIV on neurons and axons in mouse and human brain.},
  year      = {2001},
  pages     = {1918--23},
  volume    = {98},
  abstract  = {Although long suspected from histochemical evidence for carbonic anhydrase (CA) activity on neurons and observations that CA inhibitors enhance the extracellular alkaline shifts associated with synaptic transmission, an extracellular CA in brain had not been identified. A candidate for this CA was suggested by the recent discovery of membrane CA (CA XIV) whose mRNA is expressed in mouse and human brain and in several other tissues. For immunolocalization of CA XIV in mouse and human brain, we developed two antibodies, one against a secretory form of enzymatically active recombinant mouse CA XIV, and one against a synthetic peptide corresponding to the 24 C-terminal amino acids in the human enzyme. Immunostaining for CA XIV was found on neuronal membranes and axons in both mouse and human brain. The highest expression was seen on large neuronal bodies and axons in the anterolateral part of pons and medulla oblongata. Other CA XIV-positive sites included the hippocampus, corpus callosum, cerebellar white matter and peduncles, pyramidal tract, and choroid plexus. Mouse brain also showed a positive reaction in the molecular layer of the cerebral cortex and granular cellular layer of the cerebellum. These observations make CA XIV a likely candidate for the extracellular CA postulated to have an important role in modulating excitatory synaptic transmission in brain.},
  file      = {2001_Parkkila_1918.pdf:by-author/P/Parkkila/2001_Parkkila_1918.pdf:PDF},
  groups    = {sg/hCA14, sg/mCA14},
  keywords  = {CA14; Carbonic Anhydrases},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@InProceedings{Parr2004,
  author    = {Parr, Terence},
  booktitle = {ACM WWW2004},
  title     = {Enforcing Strict Model-View Separation in Template Engines},
  year      = {2004},
  month     = {May},
  pages     = {17--20},
  abstract  = {The mantra of every experienced web application developer is the same: thou shalt separate business logic from display. Ironically, almost all template engines allow violation of this separation prin- ciple, which is the very impetus for HTML template engine devel- opment. This situation is due mostly to a lack of formal definition of separation and fear that enforcing separation emasculates a tem- plate’s power. I show that not only is strict separation a worthy de- sign principle, but that we can enforce separation while providing a potent template engine. I demonstrate my StringTemplate en- gine, used to build jGuru.com and other commercial sites, at work solving some nontrivial generational tasks. My goal is to formalize the study of template engines, thus, pro- viding a common nomenclature, a means of classifying template generational power, and a way to leverage interesting results from formal language theory. I classify three types of restricted tem- plates analogous to Chomsky’s type 1..3 grammar classes and for- mally define separation including the rules that embody separation. Because this paper provides a clear definition of model-view sep- aration, template engine designers may no longer blindly claim en- forcement of separation. Moreover, given theoretical arguments and empirical evidence, programmers no longer have an excuse to entangle model and view.},
  file      = {:by-author/P/Parr/2004_Parr_ACM.pdf:PDF},
  keywords  = {Computer Science (CS); GUI},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Parsons2005,
  author    = {Jerod Parsons and J. Bradley Holmes and J. Maurice Rojas and Jerry Tsai and Charlie E. M. Strauss},
  journal   = {Journal of computational chemistry},
  title     = {Practical conversion from torsion space to {C}artesian space for in silico protein synthesis.},
  year      = {2005},
  pages     = {1063},
  volume    = {26},
  abstract  = {Many applications require a method for translating a large list of bond angles and bond lengths to precise atomic Cartesian coordinates. This simple but computationally consuming task occurs ubiquitously in modeling proteins, DNA, and other polymers as well as in many other fields such as robotics. To find an optimal method, algorithms can be compared by a number of operations, speed, intrinsic numerical stability, and parallelization. We discuss five established methods for growing a protein backbone by serial chain extension from bond angles and bond lengths. We introduce the Natural Extension Reference Frame (NeRF) method developed for Rosetta's chain extension subroutine, as well as an improved implementation. In comparison to traditional two-step rotations, vector algebra, or Quaternion product algorithms, the NeRF algorithm is superior for this application: it requires 47% fewer floating point operations, demonstrates the best intrinsic numerical stability, and offers prospects for parallel processor acceleration. The NeRF formalism factors the mathematical operations of chain extension into two independent terms with orthogonal subsets of the dependent variables; the apparent irreducibility of these factors hint that the minimal operation set may have been identified. Benchmarks are made on Intel Pentium and Motorola PowerPC CPUs.},
  doi       = {10.1002/jcc.20237},
  file      = {:by-author/P/Parsons/2005_Parsons_1063.pdf:PDF},
  keywords  = {Bioinformatics; Internal Coordinates; Z-matrix},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Parthe1973,
  author    = {Parth{\'{e}}, E. and Hornstra, J.},
  journal   = {Acta Crystallographica Section A},
  title     = {Corrections to the tables in chapter 5.1. {\it Reduced cells}, given in the 1969 edition of volume I of {\it International Tables}},
  year      = {1973},
  pages     = {309},
  volume    = {29},
  doi       = {10.1107/S056773947300077X},
  file      = {:by-author/P/Parthe/1973_Parthe_309.pdf:PDF},
  keywords  = {Algorithms; Niggli Cell; Reduced Cell; Unit Cell; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2014.11.06},
  creationdate = {2014-11-06T00:00:00},
  url       = {http://dx.doi.org/10.1107/S056773947300077X},
}

@Presentation{Pas2010,
  author    = {Ruud van der Pas},
  title     = {An Overview of OpenMP},
  year      = {2010},
  file      = {:by-author/P/Pas/2010_Pas_slides.pdf:PDF},
  owner     = {saulius},
  pages     = {slides},
  timestamp = {2013.07.02},
  creationdate = {2013-07-02T00:00:00},
}

@Presentation{vanderPas2005,
  author       = {Ruud van der Pas},
  title        = {An Introduction Into OpenMP},
  year         = {2005},
  conference   = {IWOMP 2005},
  organization = {Scalable Systems Group, Sun Microsystems},
  school       = {University of Oregon, Eugene, Oregon, USA},
  file         = {:by-author/P/Pas/2005_Pas_slides.pdf:PDF},
  owner        = {saulius},
  pages        = {slides},
  timestamp = {2013.07.02},
  creationdate = {2013-07-02T00:00:00},
}

@InBook{Păsăreanu2004,
  author    = {Păsăreanu, Corina S. and Visser, Willem},
  editor    = {Graf, Susanne and Mounier, Laurent},
  pages     = {164--181},
  publisher = {Springer Berlin Heidelberg},
  title     = {Verification of Java Programs Using Symbolic Execution and Invariant Generation},
  year      = {2004},
  address   = {Berlin, Heidelberg},
  isbn      = {978-3-540-24732-6},
  abstract  = {Software verification is recognized as an important and dif- ficult problem. We present a novel framework, based on symbolic exe- cution, for the automated verification of software. The framework uses annotations in the form of method specifications and loop invariants. We present a novel iterative technique that uses invariant strengthening and approximation for discovering these loop invariants automatically. The technique handles different types of data (e.g. boolean and numeric constraints, dynamically allocated structures and arrays) and it allows for checking universally quantified formulas. Our framework is built on top of the Java PathFinder model checking toolset and it was used for the verification of several non-trivial Java programs.},
  booktitle = {Model Checking Software: 11th International SPIN Workshop, Barcelona, Spain, April 1-3, 2004. Proceedings},
  doi       = {10.1007/978-3-540-24732-6_13},
  file      = {2004_Pasareanu_164.pdf:by-author/P/Pasareanu/2004_Pasareanu_164.pdf:PDF},
  groups    = {sg/Correctness proofs},
  keywords  = {Computer Science (CS); Correctness Proofs},
  owner     = {saulius},
  timestamp = {2016.11.25},
  creationdate = {2016-11-25T00:00:00},
  url       = {http://dx.doi.org/10.1007/978-3-540-24732-6_13},
}

@Manuscript{Pasareanu2005,
  author    = {Păsăreanu, Corina S and Willem Visser},
  title     = {Verification of Java Programs using Symbolic Execution and Invariant Generation},
  year      = {2005},
  doi       = {10.1007/978-3-540-24732-6_13},
  keywords  = {Computer Science (CS); Correctness Proofs},
  abstract  = {Software verification is recognized as an important and dif- ficult problem. We present a novel framework, based on symbolic exe- cution, for the automated verification of software. The framework uses annotations in the form of method specifications and loop invariants. We present a novel iterative technique that uses invariant strengthening and approximation for discovering these loop invariants automatically. The technique handles different types of data (e.g. boolean and numeric constraints, dynamically allocated structures and arrays) and it allows for checking universally quantified formulas. Our framework is built on top of the Java PathFinder model checking toolset and it was used for the verification of several non-trivial Java programs.},
  file      = {:by-author/P/Pasareanu/2005_Pasareanu.pdf:PDF},
  groups    = {sg/Correctness proofs},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Pascal2002,
  author    = {Fabian Pascal},
  journal   = {DM Review Magazine},
  title     = {The Dangerous Illusion: Denormalizaion, Performance and Integrity. Part 2},
  year      = {2002},
  month     = {June},
  file      = {:by-author/P/Pascal/2002_Pascal.html:},
  keywords  = {Computer Science (CS); Databases; Denormalization_for_performance},
  owner     = {saulius},
  timestamp = {2015.03.03},
  creationdate = {2015-03-03T00:00:00},
}

@Article{Pascal2002a,
  author    = {Fabian Pascal},
  journal   = {DM Review Magazine},
  title     = {The Dangerous Illusion: Denormalizaion, Performance and Integrity. Part 1},
  year      = {2002},
  month     = {June},
  file      = {:by-author/P/Pascal/2002_Pascal_a.html:},
  keywords  = {Computer Science (CS); Databases; Denormalization_for_performance},
  owner     = {saulius},
  timestamp = {2015.03.03},
  creationdate = {2015-03-03T00:00:00},
}

@Article{Pastorekova2004,
  author    = {Pastorekova, Silvia and Parkkila, Seppo and Pastorek, Jaromir and Supuran, Claudiu T},
  journal   = {Journal of enzyme inhibition and medicinal chemistry},
  title     = {Carbonic anhydrases: current state of the art, therapeutic applications and future prospects.},
  year      = {2004},
  pages     = {199--229},
  volume    = {19},
  abstract  = {Carbonic anhydrases (CAs, EC 4.2.1.1) are wide-spread enzymes, present in mammals in at least 14 different isoforms. Some of these isozymes are cytosolic (CA I, CA II, CA III, CA VII, CA XIII), others are membrane-bound (CA IV, CA IX, CA XII and CA XIV), CA V is mitochondrial and CA VI is secreted in the saliva and milk. Three cytosolic acatalytic forms are also known (CARP VIII, CARP X and CARP XI). The catalytically active isoforms, which play important physiological and patho-physiological functions, are strongly inhibited by aromatic and heterocyclic sulfonamides. The catalytic and inhibition mechanisms of these enzymes are understood in great detail, and this greatly helped the design of potent inhibitors, some of which possess important clinical applications. The use of such CA inhibitors (CAIs) as antiglaucoma drugs are discussed in detail, together with the recent developments that led to isozyme-specific and organ-selective inhibitors. A recent discovery is connected with the involvement of CAs and their sulfonamide inhibitors in cancer: many potent CAIs were shown to inhibit the growth of several tumor cell lines in vitro and in vivo, thus constituting interesting leads for developing novel antitumor therapies. Future prospects for drug design of inhibitors of these ubiquitous enzymes are dealt with. Although activation of CAs has been a controversial issue for some time, recent kinetic, spectroscopic and X-ray crystallographic experiments offered an explanation of this phenomenon, based on the catalytic mechanism. It has been demonstrated recently, that molecules that act as carbonic anhydrase activators (CAAs) bind at the entrance of the enzyme active site participating in facilitated proton transfer processes between the active site and the reaction medium. In addition to CA II-activator adducts, X-ray crystallographic studies have been also reported for ternary complexes of this isozyme with activators and anion (azide) inhibitors. Structure-activity correlations for diverse classes of activators is discussed for the isozymes for which the phenomenon has been studied, i.e., CA I, II, III and IV. The possible physiological relevance of CA activation/inhibition is also addressed, together with recent pharmacological/ biomedical applications of such compounds in different fields of life sciences.},
  file      = {2004_Pastorekova_199.pdf:by-author/P/Pastorekova/2004_Pastorekova_199.pdf:PDF},
  groups    = {sg/reviews},
  keywords  = {Carbonic Anhydrases},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Patashnik2003,
  author    = {Oren Patashnik},
  journal   = {TUGboat},
  title     = {BibTEX yesterday, today, and tomorrow},
  year      = {2003},
  pages     = {25},
  volume    = {24},
  abstract  = {This paper looks back at the last 20 years of BibTEX, and also looks ahead, if not to the next 20 years, then at least to BibTEX 1.0},
  file      = {:by-author/P/Patashnik/2003_Patashnik_25.pdf:PDF},
  keywords  = {Bibtex; Computer Science (CS)},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
  url       = {http://tug.org/TUGboat/tb24-1/patashnik.pdf},
}

@Article{Patel1982,
  author    = {Patel, D J and Pardi, A and Itakura, K},
  journal   = {Science (New York, N.Y.)},
  title     = {DNA conformation, dynamics, and interactions in solution.},
  year      = {1982},
  pages     = {581--90},
  volume    = {216},
  file      = {1982_Patel_581.pdf:by-author/P/Patel/1982_Patel_581.pdf:PDF},
  keywords  = {Stacking},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Patel2011,
  author    = {Patel, Gayatri and Johnson, Daniel S. and Sun, Bo and Pandey, Manjula and Yu, Xiong and Egelman, Edward H. and Wang, Michelle D. and Patel, Smita S.},
  journal   = {The Journal of biological chemistry},
  title     = {A257T linker region mutant of T7 helicase-primase protein is defective in DNA loading and rescued by T7 DNA polymerase.},
  year      = {2011},
  pages     = {20490--9},
  volume    = {286},
  abstract  = {The helicase and primase activities of the hexameric ring-shaped T7 gp4 protein reside in two separate domains connected by a linker region. This linker region is part of the subunit interface between monomers, and point mutations in this region have deleterious effects on the helicase functions. One such linker region mutant, A257T, is analogous to the A359T mutant of the homologous human mitochondrial DNA helicase Twinkle, which is linked to diseases such as progressive external opthalmoplegia. Electron microscopy studies show that A257T gp4 is normal in forming rings with dTTP, but the rings do not assemble efficiently on the DNA. Therefore, A257T, unlike the WT gp4, does not preassemble on the unwinding DNA substrate with dTTP without Mg(II), and its DNA unwinding activity in ensemble assays is slow and limited by the DNA loading rate. Single molecule assays measured a 45 times slower rate of A257T loading on DNA compared with WT gp4. Interestingly, once loaded, A257T has almost WT-like translocation and DNA unwinding activities. Strikingly, A257T preassembles stably on the DNA in the presence of T7 DNA polymerase, which restores the ensemble unwinding activity of A257T to ∼75% of WT, and the rescue does not require DNA synthesis. The DNA loading rate of A257T, however, remains slow even in the presence of the polymerase, which explains why A257T does not support T7 phage growth. Similar types of defects in the related human mitochondrial DNA helicase may be responsible for inefficient DNA replication leading to the disease states.},
  file      = {:by-author/P/Patel/2011_Patel_20490.pdf:PDF},
  keywords  = {{gp41} Helicase},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Patel1992,
  author    = {Patel, J. and Taylor, I. and Dutta, C. F. and Kneale, G. and Firman, K.},
  journal   = {Gene},
  title     = {High-level expression of the cloned genes encoding the subunits of and intact DNA methyltransferase, M.EcoR124.},
  year      = {1992},
  pages     = {21--7},
  volume    = {112},
  abstract  = {We have cloned the genes coding for the two subunits (HsdM and HsdS) of the type-I DNA methyltransferase (MTase), M.EcoR124, into the specially constructed expression vector, pJ119. These subunits have been synthesized together as an intact MTase. We have also cloned the individual subunit-encoding genes under the control of the T7 gene 10 promoter or the lacUV5 promoter. High levels of expression have been obtained in all cases. While HsdM was found to be soluble, HsdS was insoluble. However, in the presence of the co-produced HsdM subunit, HsdS was found in the soluble fraction as part of an active MTase. We have partially purified the cloned multi-subunit enzyme and shown that it is capable of DNA methylation both in vivo and in vitro.},
  file      = {:by-author/P/Patel/1992_Patel_21.pdf:PDF},
  keywords  = {TypeI},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@InProceedings{Patel1996,
  author    = {Patel, Jignesh M. and DeWitt, David J.},
  booktitle = {Proceedings of the 1996 ACM SIGMOD international conference on Management of data},
  title     = {Partition based spatial-merge join},
  year      = {1996},
  pages     = {259--270},
  publisher = {ACM},
  abstract  = {This paper describes PBSM (Partition Based Spatial-Merge), a new algorithm for performing spatial join operation. This algorithm is especially effective when neither of the inputs to the join have an index on the joining attribute. Such a situation could arise if both inputs to the join are intermediate results in a complex query, or in a parallel environment where the inputs must be dynamically redistributed. The PBSM algorithm partitions the inputs into manageable chunks, and joins them using a computational geometry based plane-sweeping technique. This paper also presents a performance study comparing the the traditional indexed nested loops join algorithm, a spatial join algorithm based on joining spatial indices, and the PBSM algorithm. These comparisons are based on complete implementations of these algorithms in Paradise, a database system for handling GIS applications. Using real data sets, the performance study examines the behavior of these spatial join algorithms in a variety of situations, including the cases when both, one, or none of the inputs to the join have an suitable index. The study also examines the effect of clustering the join inputs on the performance of these join algorithms. The performance comparisons demonstrates the feasibility, and applicability of the PBSM join algorithm.},
  doi       = {10.1145/233269.233338},
  file      = {:by-author/P/Patel/1996_Patel_259.pdf:PDF},
  isbn      = {0-89791-794-4},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://doi.acm.org/10.1145/233269.233338},
}

@Article{Patel2011a,
  author    = {Patel, Pitambar and Ramana, Chepuri V.},
  journal   = {Organic \& Biomolecular Chemistry},
  title     = {Divergent Pd(II) and Au(III) mediated nitroalkynol cycloisomerizations.},
  year      = {2011},
  pages     = {7327--34},
  volume    = {9},
  abstract  = {A new cycloisomerization reaction comprising the simultaneous addition of nitro and alcohol groups across C≡C leading to skeletally diverse small molecules is documented.},
  file      = {:by-author/P/Patel/2011_Patel_7327.pdf:PDF},
  keywords  = {For COD Deposition; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@Article{Patel2006,
  author    = {Patel, Smita S. and Donmez, Ilker},
  journal   = {The Journal of biological chemistry},
  title     = {Mechanisms of helicases.},
  year      = {2006},
  pages     = {18265--8},
  volume    = {281},
  file      = {:by-author/P/Patel/2006_Patel_18265.pdf:PDF},
  keywords  = {{gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Patel2000,
  author    = {Patel, S. S. and Picha, K. M.},
  journal   = {Annual review of biochemistry},
  title     = {Structure and function of hexameric helicases.},
  year      = {2000},
  pages     = {651--97},
  volume    = {69},
  abstract  = {Helicases are motor proteins that couple the hydrolysis of nucleoside triphosphate (NTPase) to nucleic acid unwinding. The hexameric helicases have a characteristic ring-shaped structure, and all, except the eukaryotic minichromosomal maintenance (MCM) helicase, are homohexamers. Most of the 12 known hexameric helicases play a role in DNA replication, recombination, and transcription. A human genetic disorder, Bloom's syndrome, is associated with a defect in one member of the class of hexameric helicases. Significant progress has been made in understanding the biochemical properties, structures, and interactions of these helicases with DNA and nucleotides. Cooperativity in nucleotide binding was observed in many, and sequential NTPase catalysis has been observed in two proteins, gp4 of bacteriophage T7 and rho of Escherichia coli. The crystal structures of the oligomeric T7 gp4 helicase and the hexamer of RepA helicase show structural features that substantiate the observed cooperativity, and both are consistent with nucleotide binding at the subunit interface. Models are presented that show how sequential NTP hydrolysis can lead to unidirectional and processive translocation. Possible unwinding mechanisms based on the DNA exclusion model are proposed here, termed the wedge, torsional, and helix-destabilizing models.},
  file      = {:by-author/P/Patel/2000_Patel_651.pdf:PDF},
  keywords  = {T7; {gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Webpage{Paterno1998,
  author    = {Marc Paterno},
  retrieved = {2008-07-28},
  title     = {Probability Theory as Extended Logic Local Reference List},
  url       = {http://d0server1.fnal.gov/users/paterno/public_html/probability/default.htm},
  month     = {October},
  year      = {1998},
  file      = {:by-author/P/Paterno/1998_Paterno.war:},
  groups    = {sg/Bayesian},
  keywords  = {Bayesian Statistics; Mathematics},
  owner     = {saulius},
  timestamp = {2015.03.02},
  creationdate = {2015-03-02T00:00:00},
}

@Article{Patterson1957,
  author    = {Patterson, A. L. and Love, W. E.},
  journal   = {Acta Crystallographica},
  title     = {Remarks on the Delaunay reduction},
  year      = {1957},
  pages     = {111--116},
  volume    = {10},
  abstract  = {Delaunay's reduction of a primitive cell to a standard form is summarized with emphasis on important points which have been omitted in the current accounts of his work. A new reduction is introduced which has the same object as that of Delaunay but which is more rapidly convergent though less general. The counterpart of the Delaunay reduction in reciprocal space is also investigated and comment is made on the relation of the Delaunay standard form to others which have been suggested.},
  doi       = {10.1107/S0365110X57000328},
  file      = {1957_Patterson_111.pdf:by-author/P/Patterson/1957_Patterson_111.pdf:PDF},
  groups    = {sg/Cell sg/Reduction, sg/Cell reduction},
  keywords  = {Algorithms; Data Management; Reduced Cell; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2014.11.18},
  creationdate = {2014-11-18T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0365110X57000328},
}

@Article{Patterson2009,
  author    = {Patterson, Mark},
  journal   = {EMBO Reports},
  title     = {Is the end in cite?},
  year      = {2009},
  issn      = {1469-221X},
  pages     = {1186},
  volume    = {10},
  doi       = {10.1038/embor.2009.235},
  file      = {PubMed Central Full Text PDF:by-author/P/Patterson/2009_Patterson_1186.pdf:application/pdf},
  groups    = {sg/Bibliometrics},
  owner     = {saulius},
  pmcid     = {PMC2775191},
  pmid      = {19881532},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2775191/},
  urldate   = {2015-07-06},
}

@Manuscript{Pattis2013,
  author    = {Richard E. Pattis},
  title     = {EBNF: A Notation to Describe Syntax},
  year      = {2013},
  keywords  = {EBNF},
  url       = {http://www.ics.uci.edu/~pattis/ICS-33/lectures/ebnf.pdf},
  comment   = {Similar document is also at http://www.ics.uci.edu/~pattis/misc/ebnf2.pdf},
  file      = {2013_Pattis_manuscript.pdf:by-author/P/Pattis/2013_Pattis_manuscript.pdf:PDF},
  owner     = {saulius},
  timestamp = {2014.08.20},
  creationdate = {2014-08-20T00:00:00},
}

@InBook{Pattis2005,
  author    = {Richard E. Pattis},
  chapter   = {2},
  pages     = {5--25},
  title     = {EBNF: A Notation to Describe Syntax},
  year      = {2005},
  file      = {2005_Pattis_5.pdf:by-author/P/Pattis/2005_Pattis_5.pdf:PDF},
  keywords  = {EBNF},
  owner     = {saulius},
  timestamp = {2014.08.20},
  creationdate = {2014-08-20T00:00:00},
  url       = {http://www.ics.uci.edu/~pattis/misc/ebnf.pdf},
}

@PhdThesis{Paukkeri2012,
  author    = {Mari-Sanna Paukkeri},
  school    = {Aalto University School of Science Department of Information and Computer Science},
  title     = {Language- And Domain-independent Text Mining},
  year      = {2012},
  abstract  = {The field of natural language processing (NLP) has developed enormously during the last decades. The availability of constantly increasing amount of textual data in electronic form has accelerated also the development of statistical methods for NLP, in which characteris- tics of natural languages are learned from large corpora. Statistical methods have shown their applicability in information retrieval, in which documents of various languages and domains are returned according to user queries, statistical machine translation which is easily applicable to new languages, document clustering to group semantically similar doc- uments, and many information extraction tasks, including keyphrase extraction, document summarization and discovering linguistic features. However, a majority of the NLP research, including also many statistical methods, is concentrated on the English language, using various language-specific tools and resources, such as part-of-speech taggers and ontologies, which are not directly applicable to other languages. Furthermore, methods developed for English alone may not be suitable for languages with different syntax or writing system. In this dissertation, language-independent methods for natural language processing are developed and discussed. Language-independent methods can be applied to a variety of languages without requiring additional language-specific resources. Also dialects, historical forms of languages, languages of few speakers and languages used in specific domains are accessible with language-independent methods. As the main contribution of this thesis, Likey, a language-independent method for key- phrase extraction and feature selection is developed. The method is applied to keyphrase extraction from encyclopedias and scientific articles in eleven languages, and further used as a feature selection method for automatic taxonomy learning and in a novel approach to user modelling in document difficulty assessment. Another major contribution is related to document representations: a set of dimensionality reduction and distance measures are compared in a document clustering task, a novel language-independent direct evaluation method for document representations is proposed, and linguistic features are used for doc- ument clustering in a lexical choice task.},
  file      = {:by-author/P/Paukkeri/2012_Paukkeri_phdthesis.pdf:PDF},
  keywords  = {Natural Language Processing},
  owner     = {andrius},
  timestamp = {2012.11.10},
  creationdate = {2012-11-10T00:00:00},
}

@Article{Paukkeri2012a,
  author    = {Mari-Sanna Paukkeri and Alberto Pérez García-Plaza and Víctor Fresno and Raquel Martínez Unanue and Timo Honkela},
  journal   = {Applied Soft Computing},
  title     = {Learning a Taxonomy From a Set of Text Documents},
  year      = {2012},
  pages     = {1138–1148},
  volume    = {12},
  abstract  = {We present a methodology for learning a taxonomy from a set of text documents that each describes one concept. The taxonomy is obtained by clustering the concept definition documents with a hierarchical approach to the Self-Organizing Map. In this study, we compare three different feature extraction approaches with varying degree of language independence. The feature extraction schemes include fuzzy logic-based feature weighting and selection, statistical keyphrase extraction, and the traditional tf-idf weighting scheme. The experiments are conducted for English, Finnish, and Spanish. The results show that while the rule-based fuzzy logic systems have an advantage in automatic taxonomy learning, taxonomies can also be constructed with tolerable results using statistical methods without domain- or style-specific knowledge.},
  doi       = {10.1016/j.asoc.2011.11.009},
  file      = {:by-author/P/Paukkeri/2012_Paukkeri_1138.pdf:PDF},
  keywords  = {Natural Language Processing},
  owner     = {andrius},
  timestamp = {2012.11.13},
  creationdate = {2012-11-13T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/S1568494611004340},
}

@Article{Paukkeri2010,
  author    = {Mari-Sanna Paukkeri and Timo Honkela},
  journal   = {Proceedings of the 5th International Workshop on Semantic Evaluation (SemEval)},
  title     = {Likey: Unsupervised Language-independent Keyphrase Extraction},
  year      = {2010},
  pages     = {162–165},
  abstract  = {Likey is an unsupervised statistical approach for keyphrase extraction. The method is language-independent and the only language-dependent component is the reference corpus with which the documents to be analyzed are compared. In this study, we have also used another language-dependent component: an English-specific Porter stemmer as a preprocessing step. In our experiments of keyphrase extraction from scientific articles, the Likey method outperforms both supervised and unsupervised baseline methods.},
  file      = {:by-author/P/Paukkeri/2010_Paukkeri_162.pdf:PDF},
  keywords  = {Natural Language Processing},
  owner     = {andrius},
  timestamp = {2012.11.13},
  creationdate = {2012-11-13T00:00:00},
}

@Article{Paukkeri2008,
  author    = {Mari-Sanna Paukkeri and Ilari T. Nieminen and Matti Pöllä and Timo Honkela},
  journal   = {Coling 2008: Companion volume: Posters},
  title     = {A Language-Independent Approach to Keyphrase Extraction and Evaluation},
  year      = {2008},
  pages     = {83–86},
  abstract  = {We present Likey, a language-independent keyphrase extraction method based on statistical analysis and the use of a reference corpus. Likey has a very light-weight preprocessing phase and no parameters to be tuned. Thus, it is not restricted to any single language or language family. We test Likey having exactly the same configuration with 11 European languages. Furthermore, we present an automatic evaluation method based on Wikipedia intra-linking.},
  file      = {:by-author/P/Paukkeri/2008_Paukkeri_83.pdf:PDF},
  keywords  = {Natural Language Processing},
  owner     = {andrius},
  timestamp = {2012.11.13},
  creationdate = {2012-11-13T00:00:00},
}

@Manuscript{Paul2006,
  author    = {Nicolas Paul and Luc Fety and Michel Terre},
  title     = {A non-iterative algorithm to estimate the modes of univariate mixtures with well-separated components},
  year      = {2006},
  keywords  = {Algorithms; Expectation Maximisation; Gaussian Mixture Models},
  url       = {http://arXiv.org/abs/physics/0612073v1},
  abstract  = {This paper deals with the estimation of the modes of an univariate mixture when the number of components is known and when the component density are well separated. We propose an algorithm based on the minimization of the ”kp” criterion we introduced in a previous work. In this paper we show that the global minimum of this criterion can be reached with a linear least square minimization followed by a roots finding algorithm. This is a major advantage compared to classical iterative algorithms such as K-means or EM which suffer from the potential convergence to some local extrema of the cost function they use. Our algorithm performances are finally illustrated through simulations of a five components mixture.},
  file      = {:by-author/P/Paul/2006_Paul.pdf:PDF},
  owner     = {andrius},
  timestamp = {2013.10.04},
  creationdate = {2013-10-04T00:00:00},
}

@Article{Pauling1932,
  author    = {Pauling, L.},
  journal   = {Contribution From The Gates Chemical Laboratory, California Institue Of Technology},
  title     = {The nature of the chemical bond. IV. The energy of single bonds and the relativeelectronegativity of atoms},
  year      = {1932},
  month     = {sep},
  number    = {326},
  pages     = {3570--3582},
  file      = {1932_Pauling_3570.pdf:by-author/P/Pauling/1932_Pauling_3570.pdf:PDF},
  keywords  = {Atomic Radii; Chemical Bond; Covalent Radii; Electronegativity},
  owner     = {saulius},
  timestamp = {2014.02.21},
  creationdate = {2014-02-21T00:00:00},
  url       = {http://ecourses.dbnet.ntua.gr/fsr/10586/Electronegativity.pdf},
}

@Article{Pauling1928,
  author    = {Pauling, L.},
  journal   = {Proceedings of the National Academy of Sciences of the United States of America},
  title     = {The Shared-Electron Chemical Bond.},
  year      = {1928},
  pages     = {359--62},
  volume    = {14},
  file      = {:by-author/P/Pauling/1928_Pauling_359.pdf:PDF},
  keywords  = {Pauling; Protein Structures},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Paulino2008,
  author    = {Hervé Paulino and Luís Lopes},
  journal   = {Software -- Practice and Experience},
  title     = {A programming language for service-oriented computing with mobile agents},
  year      = {2008},
  pages     = {705--734},
  volume    = {38},
  abstract  = {We present MOB, a service-oriented scripting language, for programming mobile agents. We argue that combining the service-oriented and mobile agent paradigms provides a very natural model for program- ming a large class of distributed applications. In MOB, mobile agents in a network simultaneously provide and use services. The service interfaces constitute contracts that bind agents among themselves. The language features static type-checking to guarantee that contracts are respected at run-time. Other language features, such as redundant service providers, allow a certain degree of fault-tolerance by allowing applications to switch servers dynamically in case a failure is detected (e.g. a server crash). For these reasons, the target applications we envision more interesting to develop using MOB are services for networks with highly dynamic, volatile resources or simply highly adaptive, reconfigurable applica- tions for more classical networks. The paper presents MOB and its implementation from an application programmer’s and a systems developer’s view.},
  doi       = {10.1002/spe.842},
  file      = {:by-author/P/Paulino/2008_Paulino_705.pdf:PDF},
  keywords  = {Computer Science (CS); Mob; Programming Languages},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Manual{Paulson2016,
  title        = {Old Introduction to Isabelle},
  author       = {Lawrence C. Paulson},
  organization = {Computer Laboratory University of Cambridge},
  year         = {2016},
  file         = {2016_Paulson.pdf:by-author/P/Paulson/2016_Paulson.pdf:PDF},
  keywords     = {Functional Programming; Higher Order Logic; Intuitionist Proofs; Proof Assistant},
  owner        = {saulius},
  timestamp = {2016.11.04},
  creationdate = {2016-11-04T00:00:00},
  url          = {http://isabelle.in.tum.de/dist/Isabelle2016/doc/intro.pdf},
}

@Article{Pavlovska2002,
  author    = {Pavlovska, A and Werner, S and Maximov, B and Mill, B},
  journal   = {Acta crystallographica. Section B, Structural science},
  title     = {Pressure-induced phase transitions of piezoelectric single crystals from the langasite family: La3Nb0.5Ga5.5O14 and La3Ta0.5Ga5.5O14.},
  year      = {2002},
  pages     = {939--47},
  volume    = {58},
  file      = {2002_Pavlovska_939.pdf:by-author/P/Pavlovska/2002_Pavlovska_939.pdf:PDF},
  keywords  = {For COD Deposition; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Pawlak2005,
  author    = {Pawlak, Sebastian D. and Radlinska, Monika and Chmiel, Agnieszka A. and Bujnicki, Janusz M. and Skowronek, Krzysztof J.},
  journal   = {Nucleic acids research},
  title     = {Inference of relationships in the 'twilight zone' of homology using a combination of bioinformatics and site-directed mutagenesis: a case study of restriction endonucleases Bsp6I and PvuII.},
  year      = {2005},
  pages     = {661--71},
  volume    = {33},
  abstract  = {Thus far, identification of functionally important residues in Type II restriction endonucleases (REases) has been difficult using conventional methods. Even though known REase structures share a fold and marginally recognizable active site, the overall sequence similarities are statistically insignificant, unless compared among proteins that recognize identical or very similar sequences. Bsp6I is a Type II REase, which recognizes the palindromic DNA sequence 5'GCNGC and cleaves between the cytosine and the unspecified nucleotide in both strands, generating a double-strand break with 5'-protruding single nucleotides. There are no solved structures of REases that recognize similar DNA targets or generate cleavage products with similar characteristics. In straightforward comparisons, the Bsp6I sequence shows no significant similarity to REases with known structures. However, using a fold-recognition approach, we have identified a remote relationship between Bsp6I and the structure of PvuII. Starting from the sequence-structure alignment between Bsp6I and PvuII, we constructed a homology model of Bsp6I and used it to predict functionally significant regions in Bsp6I. The homology model was supported by site-directed mutagenesis of residues predicted to be important for dimerization, DNA binding and catalysis. Completing the picture of sequence-structure-function relationships in protein superfamilies becomes an essential task in the age of structural genomics and our study may serve as a paradigm for future analyses of superfamilies comprising strongly diverged members with little or no sequence similarity.},
  file      = {:by-author/P/Pawlak/2005_Pawlak_661.pdf:PDF},
  keywords  = {TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Payne1992,
  author    = {Payne, M. C. and Teter, M. P. and Allan, D. C. and Arias, T. A. and Joannopoulos, J. D.},
  journal   = {Rev. Mod. Phys.},
  title     = {Iterative minimization techniques for ab initio total-energy calculations: molecular dynamics and conjugate gradients},
  year      = {1992},
  pages     = {1045--1097},
  volume    = {64},
  abstract  = {This article describes recent technical developments that have made the total-energy pseudopotential the most powerful ab initio quantum-mechanical modeling method presently available. In addition to presenting technical details of the pseudopotential method, the article aims to heighten awareness of the capabilities of the method in order to stimulate its application to as wide a range of problems in as many scientific disciplines as possible.},
  doi       = {10.1103/RevModPhys.64.1045},
  file      = {1992_Payne_1045.pdf:by-author/P/Payne/1992_Payne_1045.pdf:PDF},
  groups    = {sg/Molecular dynamics},
  issue     = {4},
  keywords  = {Chemoinformatics; Computational Chemistry; Density Functional Theory (DFT); Minimisation; Quantum Chemistry},
  numpages  = {0},
  owner     = {saulius},
  publisher = {American Physical Society},
  timestamp = {2014.07.21},
  creationdate = {2014-07-21T00:00:00},
  url       = {http://link.aps.org/doi/10.1103/RevModPhys.64.1045},
}

@Article{Peakman2009,
  author    = {Peakman, Luke J. and Szczelkun, Mark D.},
  journal   = {Nucleic acids research},
  title     = {S-adenosyl homocysteine and DNA ends stimulate promiscuous nuclease activities in the Type III restriction endonuclease EcoPI.},
  year      = {2009},
  pages     = {3934--45},
  volume    = {37},
  abstract  = {In the absence of the methyl donor S-adenosyl methionine and under certain permissive reaction conditions, EcoPI shows non-specific endonuclease activity. We show here that the cofactor analogue S-adenosyl homocysteine promotes this promiscuous DNA cleavage. Additionally, an extensive exonuclease-like processing of the DNA is also observed that can even result in digestion of non-specific DNA in trans. We suggest a model for how DNA communication events initiating from non-specific sites, and in particular free DNA ends, could produce the observed cleavage patterns.},
  file      = {:by-author/P/Peakman/2009_Peakman_3934.pdf:PDF},
  keywords  = {TypeIII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Peakman2004,
  author    = {Peakman, Luke J. and Szczelkun, Mark D.},
  journal   = {Nucleic acids research},
  title     = {DNA communications by Type III restriction endonucleases--confirmation of 1D translocation over 3D looping.},
  year      = {2004},
  pages     = {4166--74},
  volume    = {32},
  abstract  = {DNA cleavage by Type III restriction enzymes is governed strictly by the relative arrangement of recognition sites on a DNA substrate--endonuclease activity is usually only triggered by sequences in head-to-head orientation. Tens to thousands of base pairs can separate these sites. Long distance communication over such distances could occur by either one-dimensional (1D) DNA translocation or 3D DNA looping. To distinguish between these alternatives, we analysed the activity of EcoPI and EcoP15I on DNA catenanes in which the recognition sites were either on the same or separate rings. While substrates with a pair of sites located on the same ring were cleaved efficiently, catenanes with sites on separate rings were not cleaved. These results exclude a simple 3D DNA-looping activity. To characterize the interactions further, EcoPI was incubated with plasmids carrying two recognition sites interspersed with two 21res sites for site-specific recombination by Tn21 resolvase; inhibition of recombination would indicate the formation of stable DNA loops. No inhibition was observed, even under conditions where EcoPI translocation could also occur.},
  file      = {:by-author/P/Peakman/2004_Peakman_4166.pdf:PDF},
  keywords  = {TypeIII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Pearse2014,
  author    = {Pearse, Rupert M. and Harrison, David A. and MacDonald, Neil and Michael A. Gillies and Mark Blunt and Gareth Ackland and Michael P. W. Grocott and Aoife Ahern and Kathryn Griggs and Rachael Scott and Charles Hinds and Kathryn Rowan},
  journal   = {The Journal of the American Medical Association},
  title     = {Effect of a perioperative, cardiac output–guided hemodynamic therapy algorithm on outcomes following major gastrointestinal surgery: A randomized clinical trial and systematic review},
  year      = {2014},
  pages     = {2181--2190},
  volume    = {311},
  abstract  = {Importance Small trials suggest that postoperative outcomes may be improved by the use of cardiac output monitoring to guide administration of intravenous fluid and inotropic drugs as part of a hemodynamic therapy algorithm. Objective To evaluate the clinical effectiveness of a perioperative, cardiac output–guided hemodynamic therapy algorithm. Design, Setting, and Participants OPTIMISE was a pragmatic, multicenter, randomized, observer-blinded trial of 734 high-risk patients aged 50 years or older undergoing major gastrointestinal surgery at 17 acute care hospitals in the United Kingdom. An updated systematic review and meta-analysis were also conducted including randomized trials published from 1966 to February 2014. Interventions Patients were randomly assigned to a cardiac output–guided hemodynamic therapy algorithm for intravenous fluid and inotrope (dopexamine) infusion during and 6 hours following surgery (n=368) or to usual care (n=366). Main Outcomes and Measures The primary outcome was a composite of predefined 30-day moderate or major complications and mortality. Secondary outcomes were morbidity on day 7; infection, critical care–free days, and all-cause mortality at 30 days; all-cause mortality at 180 days; and length of hospital stay. Results Baseline patient characteristics, clinical care, and volumes of intravenous fluid were similar between groups. Care was nonadherent to the allocated treatment for less than 10% of patients in each group. The primary outcome occurred in 36.6% of intervention and 43.4% of usual care participants (relative risk [RR], 0.84 [95% CI, 0.71-1.01]; absolute risk reduction, 6.8% [95% CI, −0.3% to 13.9%]; P = .07). There was no significant difference between groups for any secondary outcomes. Five intervention patients (1.4%) experienced cardiovascular serious adverse events within 24 hours compared with none in the usual care group. Findings of the meta-analysis of 38 trials, including data from this study, suggest that the intervention is associated with fewer complications (intervention, 488/1548 [31.5%] vs control, 614/1476 [41.6%]; RR, 0.77 [95% CI, 0.71-0.83]) and a nonsignificant reduction in hospital, 28-day, or 30-day mortality (intervention, 159/3215 deaths [4.9%] vs control, 206/3160 deaths [6.5%]; RR, 0.82 [95% CI, 0.67-1.01]) and mortality at longest follow-up (intervention, 267/3215 deaths [8.3%] vs control, 327/3160 deaths [10.3%]; RR, 0.86 [95% CI, 0.74-1.00]). Conclusions and Relevance In a randomized trial of high-risk patients undergoing major gastrointestinal surgery, use of a cardiac output–guided hemodynamic therapy algorithm compared with usual care did not reduce a composite outcome of complications and 30-day mortality. However, inclusion of these data in an updated meta-analysis indicates that the intervention was associated with a reduction in complication rates. Trial Registration isrctn.org Identifier: ISRCTN04386758},
  doi       = {10.1001/jama.2014.5305},
  eprint    = {/data/Journals/JAMA/930297/joi140061.pdf},
  file      = {Effect of a Perioperative, Cardiac Output–Guided H.pdf:by-author/P/Pearse/2014_Pearse_2181.pdf:PDF;Effect of a Perioperative, Cardiac Output–Guided H.html:by-author/P/Pearse/2014_Pearse_2181.html:URL},
  groups    = {sg/Clinical Trials},
  owner     = {saulius},
  timestamp = {2015.12.14},
  creationdate = {2015-12-14T00:00:00},
  url       = {http://dx.doi.org/10.1001/jama.2014.5305},
  urldate   = {2015-12-12},
}

@Article{Pearson2010,
  author    = {Brett J. Pearson and David P. Jackson},
  journal   = {Am. J. Phys.},
  title     = {A hands-on introduction to single photons and quantum mechanics for undergraduates},
  year      = {2010},
  pages     = {471--484},
  volume    = {78},
  doi       = {10.1119/1.3354986},
  file      = {2010_Pearson_471.pdf:by-author/P/Pearson/2010_Pearson_471.pdf:PDF},
  keywords  = {Quantum Mechanics (QM); Quantum Optics; Teaching},
  owner     = {saulius},
  timestamp = {2013.10.22},
  creationdate = {2013-10-22T00:00:00},
  url       = {http://www.dickinson.edu/uploadedFiles/academics/programs/physics-and-astronomy/Physics_and_Astronomy/Pearson_QuantumOptics.pdf},
}

@Article{Pedersen2010,
  author    = {Jan Skov Pedersen},
  title     = {Form and Structure Factors: Modeling and Interactions},
  year      = {2010},
  pages     = {slides},
  file      = {:by-author/P/Pedersen/2010_Pedersen_slides.pdf:PDF},
  keywords  = {SAXS},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@InProceedings{Pedersen2006,
  author    = {Pedersen, Rasmus and Schoeberl, Martin},
  booktitle = {Proceedings of the 4th International Workshop on Java Technologies for Real-time and Embedded Systems},
  title     = {Exact Roots for a Real-time Garbage Collector},
  year      = {2006},
  address   = {New York, NY, USA},
  pages     = {77--84},
  publisher = {ACM},
  series    = {JTRES '06},
  abstract  = {Garbage collection is traditionally not used in real-time systems due to the unpredictable temporal behavior of current implementations of a garbage collector. However, without garbage collection the programming model is very different from standard Java. It is the opinion of the authors that garbage collection algorithms can be adapted to meet even the requirements for hard real-time systems.One important property of a real-time garbage collector is to identify only the real roots on the root scan. Misinterpreting primitive values as false root pointers can result in an unpredictable worst case memory consumption. In this paper we propose a method to add information on the stack layout to the runtime data structure in order to find the roots exactly. Furthermore, interpreting this information during the collection process is implemented to be worst-case execution time analyzable.},
  acmid     = {1168013},
  doi       = {10.1145/1167999.1168013},
  file      = {2006_Pedersen_77.pdf:by-author/P/Pedersen/2006_Pedersen_77.pdf:PDF},
  groups    = {sg/Garbage collectors, sg/Java},
  isbn      = {1-59593-544-4},
  keywords  = {Garbage Collection; Java; Real-time; Root Set},
  location  = {Paris, France},
  numpages  = {8},
  owner     = {saulius},
  timestamp = {2015.12.16},
  creationdate = {2015-12-16T00:00:00},
  url       = {http://doi.acm.org/10.1145/1167999.1168013},
}

@Article{Peel2000,
  author    = {Peel, D. and McLachlan, G. J.},
  journal   = {Statistics and Computing},
  title     = {Robust mixture modelling using the {t} distribution},
  year      = {2000},
  issn      = {0960-3174},
  number    = {4},
  pages     = {339–348},
  volume    = {10},
  comment   = {Normal mixture models are being increasingly used to model the distributions of a wide variety of random phenomena and to cluster sets of continuous multivariate data. However, for a set of data containing a group or groups of observations with longer than normal tails or atypical observations, the use of normal components may unduly affect the fit of the mixture model. In this paper, we consider a more robust approach by modelling the data by a mixture of t distributions. The use of the ECM algorithm to fit this t mixture model is described and examples of its use are given in the context of clustering multivariate data in the presence of atypical observations in the form of background noise.},
  doi       = {10.1023/a:1008981510081},
  file      = {2000_Peel_339.pdf:by-author/P/Peel/2000_Peel_339.pdf:PDF},
  groups    = {am/Student's t},
  owner     = {andrius},
  publisher = {Springer Nature},
  timestamp = {2016.12.07},
  creationdate = {2016-12-07T00:00:00},
  url       = {http://dx.doi.org/10.1023/A:1008981510081},
}

@Presentation{Pehlke2001,
  author       = {Eckhard Pehlke},
  title        = {The Plane-Wave Pseudopotential Method},
  year         = {2001},
  organization = {Universität Essen},
  school       = {Institut für Laser- und Plasmaphysik},
  file         = {:by-author/P/Pehlke/2001_Pehlke.pdf:PDF},
  keywords     = {Density Functional Theory (DFT); Plane Waves; Pseudopotentials},
  owner        = {saulius},
  timestamp = {2014.11.06},
  creationdate = {2014-11-06T00:00:00},
  url          = {http://th.fhi-berlin.mpg.de/th/Meetings/FHImd2001/pehlke1.pdf},
}

@Article{Pence2010,
  author    = {Harry E. Pence and Antony Williams},
  journal   = {Chemical Education Today},
  title     = {ChemSpider: An Online Chemical Information Resource},
  year      = {2010},
  pages     = {1123--1124},
  volume    = {87},
  abstract  = {ChemSpider is a free, online chemical database offering access to physical and chemical properties, molecular structure, spectral data, synthetic methods, safety information, and nomenclature for almost 25 million unique chemical compounds sourced and linked to almost 400 separate data sources on the Web. ChemSpider is quickly becoming the primary chemistry Internet portal and it can be very useful for both chemical teaching and research.},
  doi       = {10.1021/ed100697w},
  file      = {2010_Pence_1123.pdf:by-author/P/Pence/2010_Pence_1123.pdf:PDF},
  keywords  = {ChemSpider; Chemoinformatics; Databases},
  owner     = {saulius},
  timestamp = {2011.08.13},
  creationdate = {2011-08-13T00:00:00},
}

@Article{Pendas2002,
  author    = {Pendás, A. Martı́n and Luaña, V. and Pueyo, L. and Francisco, E. and Mori-Sánchez, P.},
  journal   = {The Journal of Chemical Physics},
  title     = {Hirshfeld surfaces as approximations to interatomic surfaces},
  year      = {2002},
  pages     = {1017--1023},
  volume    = {117},
  doi       = {10.1063/1.1483851},
  file      = {2002_Pendás_1017.pdf:by-author/P/Pendás/2002_Pendás_1017.pdf:PDF},
  keywords  = {Hirshfeld Surfaces},
  owner     = {saulius},
  timestamp = {2014.08.11},
  creationdate = {2014-08-11T00:00:00},
  url       = {http://scitation.aip.org/content/aip/journal/jcp/117/3/10.1063/1.1483851},
}

@Article{Peng2011,
  author    = {Peng, Roger D.},
  journal   = {Science},
  title     = {Reproducible Research in Computational Science},
  year      = {2011},
  pages     = {1226--1227},
  volume    = {334},
  abstract  = {Computational science has led to exciting new developments, but the nature of the work has exposed limitations in our ability to evaluate published findings. Reproducibility has the potential to serve as a minimum standard for judging scientific claims when full independent replication of a study is not possible.},
  doi       = {10.1126/science.1213847},
  eprint    = {http://www.sciencemag.org/content/334/6060/1226.full.pdf},
  file      = {:by-author/P/Peng/2011_Peng_1226.pdf:PDF},
  keywords  = {Data Management},
  owner     = {saulius},
  timestamp = {2012.04.09},
  creationdate = {2012-04-09T00:00:00},
  url       = {http://www.sciencemag.org/content/334/6060/1226.abstract},
}

@Article{Peng2009,
  author    = {Peng, Roger D.},
  journal   = {Biostatistics},
  title     = {Reproducible research and Biostatistics},
  year      = {2009},
  pages     = {405--408},
  volume    = {10},
  doi       = {10.1093/biostatistics/kxp014},
  eprint    = {http://biostatistics.oxfordjournals.org/content/10/3/405.full.pdf+html},
  file      = {:by-author/P/Peng/2009_Peng_405.pdf:PDF},
  keywords  = {Data Management},
  owner     = {saulius},
  timestamp = {2012.04.09},
  creationdate = {2012-04-09T00:00:00},
  url       = {http://biostatistics.oxfordjournals.org/content/10/3/405.short},
}

@Article{Peng2006,
  author    = {Peng, Roger D. and Dominici, Francesca and Zeger, Scott L.},
  journal   = {American Journal of Epidemiology},
  title     = {Reproducible Epidemiologic Research},
  year      = {2006},
  pages     = {783--789},
  volume    = {163},
  abstract  = {The replication of important findings by multiple independent investigators is fundamental to the accumulation of scientific evidence. Researchers in the biologic and physical sciences expect results to be replicated by independent data, analytical methods, laboratories, and instruments. Epidemiologic studies are commonly used to quantify small health effects of important, but subtle, risk factors, and replication is of critical importance where results can inform substantial policy decisions. However, because of the time, expense, and opportunism of many current epidemiologic studies, it is often impossible to fully replicate their findings. An attainable minimum standard is “reproducibility,” which calls for data sets and software to be made available for verifying published findings and conducting alternative analyses. The authors outline a standard for reproducibility and evaluate the reproducibility of current epidemiologic research. They also propose methods for reproducible research and implement them by use of a case study in air pollution and health.},
  doi       = {10.1093/aje/kwj093},
  eprint    = {http://aje.oxfordjournals.org/content/163/9/783.full.pdf+html},
  file      = {:by-author/P/Peng/2006_Peng_783.pdf:PDF},
  keywords  = {Data Management},
  owner     = {saulius},
  timestamp = {2012.04.09},
  creationdate = {2012-04-09T00:00:00},
  url       = {http://aje.oxfordjournals.org/content/163/9/783.abstract},
}

@Unpublished{Peng2008,
  author    = {Peng, Roger D. and Eckel, Sandrah P.},
  title     = {Distributed reproducible research using cached computations},
  year      = {2008},
  file      = {Peng and Eckel - 2008 - Distributed reproducible research using cached com.pdf:by-author/P/Peng/2008_Peng.pdf:application/pdf},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://www.biostat.jhsph.edu/~rpeng/papers/archive/distRR.pdf},
  urldate   = {2015-06-06},
}

@Manuscript{Pengley2014,
  author    = {Rob Pengley},
  title     = {TTL logic gates},
  year      = {2014},
  keywords  = {Electronics},
  url       = {http://www.allaboutcircuits.com/pdf/worksheets/ttl.pdf},
  file      = {:by-author/u/unknown/XXXX_unknown_problem.pdf:PDF},
  owner     = {saulius},
  pages     = {problem-sheet},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Pennadam2004,
  author    = {Pennadam, Sivanand S. and Lavigne, Matthieu D. and Dutta, Christina F. and Firman, Keith and Mernagh, Darren and Górecki, Dariusz C. and Alexander, Cameron},
  journal   = {Journal of the American Chemical Society},
  title     = {Control of a multisubunit DNA motor by a thermoresponsive polymer switch.},
  year      = {2004},
  pages     = {13208--9},
  volume    = {126},
  abstract  = {The conjugation of thermoresponsive polymers to multisubunit, multifunctional hybrid type 1 DNA restriction-modification (R-M) enzymes enables temperature-controlled &quot;switching&quot; of DNA methylation by the conjugate. Polymers attached to the enzyme at a subunit distal to the methylation subunit allow retention of DNA recognition and ATPase activity while controlling methylation of plasmid DNA. This regulation of enzyme activity arises from the coil-globule phase transitions of the polymer as shown in light scattering and gel retardation assays.},
  file      = {:by-author/P/Pennadam/2004_Pennadam_13208.pdf:PDF},
  keywords  = {TypeI},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Pennec2006,
  author    = {Pennec, Xavier},
  journal   = {J. Math. Imaging Vis.},
  title     = {Intrinsic Statistics on Riemannian Manifolds: Basic Tools for Geometric Measurements},
  year      = {2006},
  issn      = {1573-7683},
  month     = {Jul},
  number    = {1},
  pages     = {127--154},
  volume    = {25},
  doi       = {10.1007/s10851-006-6228-4},
  file      = {2006_Pennec_127.pdf:by-author/P/Pennec/2006_Pennec_127.pdf:PDF},
  keywords  = {Mathematics; Riemann Geometry},
  owner     = {saulius},
  publisher = {Springer Science + Business Media},
  timestamp = {2016.06.02},
  creationdate = {2016-06-02T00:00:00},
  url       = {http://dx.doi.org/10.1007/s10851-006-6228-4},
}

@Presentation{Pennings2012,
  author    = {Marinus Pennings},
  title     = {OpenMP by Example},
  year      = {2012},
  file      = {:by-author/P/Pennings/2012_Pennings_slides.pdf:PDF},
  owner     = {saulius},
  pages     = {slides},
  timestamp = {2013.07.02},
  creationdate = {2013-07-02T00:00:00},
}

@Article{Pennisi1998,
  author    = {Elizabeth Pennisi},
  journal   = {Science},
  title     = {Direct Descendants From an RNA World},
  year      = {1998},
  pages     = {673},
  volume    = {280},
  doi       = {10.1126/science.280.5364.673},
  file      = {:by-author/P/Pennisi/1998_Pennisi_673.war:WAR},
  keywords  = {Evolution; RNA-world; Ribozymes},
  owner     = {saulius},
  timestamp = {2015.03.02},
  creationdate = {2015-03-02T00:00:00},
}

@Article{Pepponi2012,
  author    = {Giancarlo Pepponi and Saulius Gražulis and Daniel Chateigner},
  journal   = {Nuclear Instruments and Methods in Physics Research Section B: Beam Interactions with Materials and Atoms},
  title     = {{MPOD}: A {M}aterial {P}roperty {O}pen {D}atabase linked to structural information},
  year      = {2012},
  issn      = {0168-583X},
  note      = {E-MRS 2011 Spring Meeting, Symposium M: X-ray techniques for materials research-from laboratory sources to free electron lasers},
  number    = {0},
  pages     = {10--14},
  volume    = {284},
  doi       = {10.1016/j.nimb.2011.08.070},
  file      = {2012_Pepponi_10.pdf:by-author/P/Pepponi/2012_Pepponi_10.pdf:PDF},
  groups    = {sg/JAC2009},
  keywords  = {Material Properties},
  owner     = {saulius},
  timestamp = {2014.02.11},
  creationdate = {2014-02-11T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/S0168583X11008639},
}

@Article{Perakakis2010,
  author    = {Pandelis Perakakis and Michael Taylor and Marco Mazza and Varvara Trachana},
  journal   = {Scientometrics},
  title     = {Natural selection of academic papers},
  year      = {2010},
  pages     = {553--559},
  volume    = {85},
  abstract  = {Academic papers, like genes, code for ideas or technological innovations that structure and transform the scientific organism and consequently the society at large. Genes are subject to the process of natural selection which ensures that only the fittest survive and contribute to the phenotype of the organism. The process of selection of academic papers, however, is far from natural. Commercial for-profit publishing houses have taken control over the evaluation and access to scientific information with serious consequences for the dissemination and advancement of knowledge. Academic authors and librarians are reacting by developing an alternative publishing system based on free-access journals and self-archiving in institutional repositories and global disciplinary libraries. Despite the emergence of such trends, the journal monopoly, rather than the scientific community, is still in control of selecting papers and setting academic standards. Here we propose a dynamical and transparent peer review process, which we believe will accelerate the transition to a fully open and free-for-all science that will allow the natural selection of the fittest ideas.},
  doi       = {10.1007/s11192-010-0253-1},
  file      = {2010_Perakakis_553.pdf:by-author/P/Perakakis/2010_Perakakis_553.pdf:PDF},
  owner     = {saulius},
  timestamp = {2013.09.26},
  creationdate = {2013-09-26T00:00:00},
}

@Article{Perakakis2011,
  author    = {Pandelis Perakakis and Michael Taylor and Marco G. Mazza and Varvara Trachana},
  journal   = {Scientometrics},
  title     = {Understanding the role of open peer review and dynamic academic articles},
  year      = {2011},
  pages     = {669--673},
  volume    = {88},
  abstract  = {We welcome the commentary by L. Egghe (Scientometrics, this issue) stimulating discussion on our recent article “Natural selection of academic papers” (NSAP) (Scientometrics, 85(2):553–559, 2010) that focuses on an important modern issue at the heart of the scientific enterprise—the open and continuous evaluation and evolution of research. We are also grateful to the editor of Scientometrics for giving us the opportunity to respond to some of the arguments by L. Egghe that we believe are inaccurate or require further comment.},
  doi       = {10.1007/s11192-011-0402-1},
  file      = {2011_Perakakis_669.pdf:by-author/P/Perakakis/2011_Perakakis_669.pdf:PDF},
  owner     = {saulius},
  timestamp = {2013.09.26},
  creationdate = {2013-09-26T00:00:00},
}

@Article{Perakyla1998,
  author    = {Mikael Peräkylä},
  journal   = {Journal of the American Chemical Society},
  title     = {A Model Study of the Enzyme-Catalyzed Cytosine Methylation Using ab Initio Quantum Mechanical and Density Functional Theory Calculations: pKa of the Cytosine N3 in the Intermediates and Transition States of the Reaction},
  year      = {1998},
  pages     = {12895},
  volume    = {120},
  abstract  = {The reaction mechanism of the DNA (cytosine-5)-methyltransferase-catalyzed cytosine methylation was investigated using ab initio quantum mechanical (at the MP2/6-31+G*//HF/6-31+G* and MP2/6-31+G*//HF/3-21+G* levels) and density functional theory calculations (Becke3LYP/6-31+G*) in the gas phase and in solution. The effects of aqueous solvation on the reaction energies were included by using an isodensity surface-polarized continuum model. The quantum mechanical model consisted of 1-methylcytosine (the model of the target cytosine), methylthiolate (the model of the side chain of the catalytic cysteine), and trimethylsulfonium (the model of the methyl-donating AdoMet). In addition, an approach is presented to estimate the pKa of the cytosine N3 in the reaction intermediates and transition states and on the calculated reaction profiles. The approach involves calculation of the gas-phase proton affinities and solvation energies of the neutral and protonated forms of the molecules using ab initio quantum mechanical and continuum solvation methods. The calculated aqueous-phase proton affinities were calibrated using a set of 13 nitrogen acids with pKa values from 0.5 to 17.5. The correlation coefficient (r2) between the calculated aqueous proton affinities and the experimental pKa's was 0.988. During the attack of methylthiolate on C6 of the cytosine, the pKa of the N3 atom of the cytosine was calculated to increase from 5 to 17. In the subsequent reaction step, where C5 of the cytosine is methylated, the pKa of N3 drops from 17 to 5. The protonation and deprotonation of the N3 atom was calculated to catalyze the two reaction steps. It seems likely that in the DNA (cytosine-5)-methyltransferase-catalyzed cytosine methylation proton transfers take place between Glu119 of the active site and N3 of the cytosine. The implications of the model calculations for the DNA (cytosine-5)-methyltransferase-catalyzed reactions are discussed.},
  doi       = {10.1021/ja981405a},
  file      = {:by-author/P/Peräkylä/1998_Peräkylä_12895.pdf:PDF},
  keywords  = {HhaI},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
  url       = {http://pubs.acs.org/doi/abs/10.1021/ja981405a},
}

@PhdThesis{PerezCovarrubias2015,
  author    = {Pérez Covarrubias, Luis Adrian},
  title     = {Desarrollo de materiales nanoestructurados basados en metales nobles, no nobles y sus mezclas empleando líquidos iónicos como medio de reacción},
  year      = {2015},
  file      = {[PDF] from uaq.mx:by-author/P/PérezCovarrubias/2015_PérezCovarrubias.pdf:application/pdf;Snapshot:by-author/P/PérezCovarrubias/2015_PérezCovarrubias.html:text/html},
  groups    = {sg/NAR2012},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://ri.uaq.mx/handle/123456789/2962},
  urldate   = {2015-08-31},
}

@Article{Perez2008,
  author    = {Pérez, Alberto and Lankas, Filip and Luque, F. Javier and Orozco, Modesto},
  journal   = {Nucleic acids research},
  title     = {Towards a molecular dynamics consensus view of B-DNA flexibility.},
  year      = {2008},
  pages     = {2379--94},
  volume    = {36},
  abstract  = {We present a systematic study of B-DNA flexibility in aqueous solution using long-scale molecular dynamics simulations with the two more recent versions of nucleic acids force fields (CHARMM27 and parmbsc0) using four long duplexes designed to contain several copies of each individual base pair step. Our study highlights some differences between pambsc0 and CHARMM27 families of simulations, but also extensive agreement in the representation of DNA flexibility. We also performed additional simulations with the older AMBER force fields parm94 and parm99, corrected for non-canonical backbone flips. Taken together, the results allow us to draw for the first time a consensus molecular dynamics picture of B-DNA flexibility.},
  file      = {:by-author/P/Pérez/2008_Perez_2379.pdf:PDF},
  keywords  = {Readout},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Manuscript{Perl2012,
  author    = {Thomas Perl},
  title     = {Python Garbage Collector Implementations CPython, PyPy and GaS},
  year      = {2012},
  abstract  = {Python is a dynamic language with multiple implementations that utilize different garbage collection mechanisms. This paper compares CPython with PyPy and highlights differences in behavior caused by different GCs. Section 1 discusses Python in general, sections 2 and 3 introduce the garbage collectors of CPython and PyPy. The dif- ferences in behavior are discussed in section 4 with examples. An alternative to implementing new GCs in high-level languages (PyPy’s approach) is using an external library (GaS, section 5).},
  file      = {:by-author/P/Perl/2012_Perl.pdf:PDF},
  groups    = {sg/Garbage collectors},
  owner     = {saulius},
  timestamp = {2012.09.18},
  creationdate = {2012-09-18T00:00:00},
}

@Article{Persson2001,
  author    = {Persson, M and Harbridge, J R and Hammarström, P and Mitri, R and Mårtensson, L G and Carlsson, U and Eaton, G R and Eaton, S S},
  journal   = {Biophysical journal},
  title     = {Comparison of electron paramagnetic resonance methods to determine distances between spin labels on human carbonic anhydrase II.},
  year      = {2001},
  pages     = {2886--97},
  volume    = {80},
  abstract  = {Four doubly spin-labeled variants of human carbonic anhydrase II and corresponding singly labeled variants were prepared by site-directed spin labeling. The distances between the spin labels were obtained from continuous-wave electron paramagnetic resonance spectra by analysis of the relative intensity of the half-field transition, Fourier deconvolution of line-shape broadening, and computer simulation of line-shape changes. Distances also were determined by four-pulse double electron-electron resonance. For each variant, at least two methods were applicable and reasonable agreement between methods was obtained. Distances ranged from 7 to 24 A. The doubly spin-labeled samples contained some singly labeled protein due to incomplete labeling. The sensitivity of each of the distance determination methods to the non-interacting component was compared.},
  file      = {2001_Persson_2886.pdf:by-author/P/Persson/2001_Persson_2886.pdf:PDF},
  groups    = {sg/physical sg/methods},
  keywords  = {Carbonic Anhydrases},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Pertsemlidis2001,
  author    = {Alexander Pertsemlidis and Fondon, III, John W.},
  journal   = {Genome Biology},
  title     = {Having a BLAST with bioinformatics (and avoiding BLASTphemy)},
  year      = {2001},
  pages     = {reviews2002.1–2002.10},
  doi       = {10.1186/gb-2001-2-10-reviews2002},
  file      = {:by-author/P/Pertsemlidis/2001_Pertsemlidis_reviews2002.1–2002.10.pdf:PDF},
  owner     = {saulius},
  timestamp = {2013.07.02},
  creationdate = {2013-07-02T00:00:00},
  url       = {http://genomebiology.com/2001/2/10/reviews/2002},
}

@Article{Peruzzo2012,
  author    = {Peruzzo, Alberto and Shadbolt, Peter and Brunner, Nicolas and Popescu, Sandu and O’Brien, Jeremy L.},
  journal   = {Science},
  title     = {A Quantum Delayed-Choice Experiment},
  year      = {2012},
  pages     = {634--637},
  volume    = {338},
  abstract  = {Quantum systems exhibit particle- or wavelike behavior depending on the experimental apparatus they are confronted by. This wave-particle duality is at the heart of quantum mechanics. Its paradoxical nature is best captured in the delayed-choice thought experiment, in which a photon is forced to choose a behavior before the observer decides what to measure. Here, we report on a quantum delayed-choice experiment in which both particle and wave behaviors are investigated simultaneously. The genuinely quantum nature of the photon’s behavior is certified via nonlocality, which here replaces the delayed choice of the observer in the original experiment. We observed strong nonlocal correlations, which show that the photon must simultaneously behave both as a particle and as a wave.},
  doi       = {10.1126/science.1226719},
  eprint    = {http://www.sciencemag.org/content/338/6107/634.full.pdf},
  file      = {2012_Peruzzo_634.pdf:by-author/P/Peruzzo/2012_Peruzzo_634.pdf:PDF},
  keywords  = {Delayed Choice Experiments; Quantum Mechanics (QM); Wave Particle Duality},
  owner     = {saulius},
  timestamp = {2012.11.02},
  creationdate = {2012-11-02T00:00:00},
  url       = {http://www.sciencemag.org/content/338/6107/634.abstract},
}

@Article{Peter2004,
  author    = {Peter, Christine and Oostenbrink, Chris and van Dorp, Arthur and van Gunsteren, Wilfred F.},
  journal   = {The Journal of chemical physics},
  title     = {Estimating entropies from molecular dynamics simulations.},
  year      = {2004},
  pages     = {2652--61},
  volume    = {120},
  abstract  = {While the determination of free-energy differences by MD simulation has become a standard procedure for which many techniques have been developed, total entropies and entropy differences are still hardly ever computed. An overview of techniques to determine entropy differences is given, and the accuracy and convergence behavior of five methods based on thermodynamic integration and perturbation techniques was evaluated using liquid water as a test system. Reasonably accurate entropy differences are obtained through thermodynamic integration in which many copies of a solute are desolvated. When only one solute molecule is involved, only two methods seem to yield useful results, the calculation of solute-solvent entropy through thermodynamic integration, and the calculation of solvation entropy through the temperature derivative of the corresponding free-energy difference. One-step perturbation methods seem unsuitable to obtain entropy estimates.},
  doi       = {10.1063/1.1636153},
  file      = {:by-author/P/Peter/2004_Peter_2652.pdf:PDF},
  groups    = {sg/Molecular dynamics, sg/entropy computation},
  keywords  = {Molecular Dynamics (MD)},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
  url       = {http://scitation.aip.org/content/aip/journal/jcp/120/6/10.1063/1.1636153},
}

@Manuscript{Peterson1995,
  author    = {Maximilian R. Peterson},
  title     = {Now you see it, now you don't: was it a patentable machine or an unpatentable "algorithm"? On principle and expediency in current patent law doctrines relating to computer-implemented inventions},
  year      = {1995},
  keywords  = {Patentai; Teise},
  file      = {:by-author/P/Peterson/1995_Peterson.doc:DOC},
  owner     = {saulius},
  timestamp = {2015.02.28},
  creationdate = {2015-02-28T00:00:00},
}

@Webpage{Petit-Bianco2012,
  author    = {Alexandre Petit-Bianco},
  retrieved = {2012-01-25},
  title     = {No Silver Bullet - Garbage Collection for Java in Embedded Systems},
  url       = {http://gcc.gnu.org/java/papers/nosb.html},
  file      = {:by-author/P/Petit-Bianco/XXXX_Petit-Bianco.odt:},
  groups    = {sg/Garbage collectors},
  keywords  = {Computer Science (CS); Garbage Collectors},
  owner     = {saulius},
  timestamp = {2015.03.03},
  creationdate = {2015-03-03T00:00:00},
}

@Presentation{Petoukhov2010,
  author    = {Petoukhov, M. V.},
  title     = {SASREF: Global Rigid Body Modelling},
  year      = {2010},
  file      = {:by-author/P/Petoukhov/2010_Petoukhov_slides.pdf:PDF},
  keywords  = {SAXS},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Presentation{Petoukhov2010a,
  author    = {Petoukhov, M. V.},
  title     = {DamClust: Assessment of multimodality},
  year      = {2010},
  course    = {EMBO Practical Course on Solution Scattering from Biological Macromolecules},
  file      = {:by-author/P/Petoukhov/2010_Petoukhov_slides2.pdf:PDF},
  keywords  = {SAXS},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Petoukhov2013a,
  author      = {Maxim V Petoukhov and Isabelle M L Billas and Maria Takacs and Melissa A Graewert and Dino Moras and Dmitri I Svergun},
  journal     = {Biochemistry},
  title       = {Reconstruction of quaternary structure from X-ray scattering by equilibrium mixtures of biological macromolecules.},
  year        = {2013},
  pages       = {6844--6855},
  volume      = {52},
  abstract    = {A recent renaissance in small-angle X-ray scattering (SAXS) made this technique a major tool for the low-resolution structural characterization of biological macromolecules in solution. The major limitation of existing methods for reconstructing 3D models from SAXS is imposed by the requirement of solute monodispersity. We present a novel approach that couples low-resolution 3D SAXS reconstruction with composition analysis of mixtures. The approach is applicable to polydisperse and difficult to purify systems, including weakly associated oligomers and transient complexes. Ab initio shape analysis is possible for symmetric homo-oligomers, whereas rigid body modeling is applied also to dissociating complexes when atomic structures of the individual subunits are available. In both approaches, the sample is considered as an equilibrium mixture of intact complexes/oligomers with their dissociation products or free subunits. The algorithms provide the 3D low-resolution model (for ab initio modeling, also the shape of the monomer) and the volume fractions of the bound and free state(s). The simultaneous fitting of multiple scattering data sets collected under different conditions allows one to restrain the modeling further. The possibilities of the approach are illustrated in simulated and experimental SAXS data from protein oligomers and multisubunit complexes including nucleoproteins. Using this approach, new structural insights are provided in the association behavior and conformations of estrogen-related receptors ERRα and ERRγ. The possibility of 3D modeling from the scattering by mixtures significantly widens the range of applicability of SAXS and opens novel avenues in the analysis of oligomeric mixtures and assembly/dissociation processes.},
  doi         = {10.1021/bi400731u},
  file        = {:by-author/P/Petoukhov/2013_Petoukhov_6844.pdf:PDF},
  institution = {European Molecular Biology Laboratory, Hamburg Outstation , Notkestrasse 85, Hamburg 22607, Germany.},
  keywords    = {Oligomer; SASREFMX; SAXS},
  language    = {eng},
  medline-pst = {ppublish},
  owner       = {em},
  pmid        = {24000896},
  timestamp = {2014.01.14},
  creationdate = {2014-01-14T00:00:00},
  url         = {http://dx.doi.org/10.1021/bi400731u},
}

@Article{Petoukhov2012,
  author    = {Petoukhov, Maxim V. and Franke, Daniel and Shkumatov, Alexander V. and Tria, Giancarlo and Kikhney, Alexey G.and Gajda, Michal and Gorba, Christian and Mertens, Haydyn D. T. and Konarev, Petr V. and Svergun, Dmitri I.},
  journal   = {J. Appl. Cryst.},
  title     = {New developments in the ATSAS program package for small-angle scattering data analysis},
  year      = {2012},
  pages     = {342--350},
  volume    = {45},
  abstract  = {New developments in the program package ATSAS (version 2.4) for the processing and analysis of isotropic small-angle X-ray and neutron scattering data are described. They include (i) multiplatform data manipulation and display tools, (ii) programs for automated data processing and calculation of overall parameters, (iii) improved usage of high- and low-resolution models from other structural methods, (iv) new algorithms to build three-dimensional models from weakly interacting oligomeric systems and complexes, and (v) enhanced tools to analyse data from mixtures and flexible systems. The new ATSAS release includes installers for current major platforms (Windows, Linux and Mac OSX) and provides improved indexed user documentation. The web-related developments, including a user discussion forum and a widened online access to run ATSAS programs, are also presented},
  doi       = {10.1107/S0021889812007662},
  file      = {:by-author/P/Petoukhov/2012_Petoukhov_342.pdf:PDF},
  keywords  = {DAMCLUST; GASBORMX; Molecular Weight (MW); Oligomer; SASREFMX; SAXS},
  owner     = {em},
  timestamp = {2013.10.25},
  creationdate = {2013-10-25T00:00:00},
}

@Article{Petoukhov2007,
  author    = {Maxim V. Petoukhov and Peter V. Konarev and Alexey G. Kikhneya and Dmitri I. Svergun},
  journal   = {J. Appl. Cryst.},
  title     = {ATSAS 2.1 – towards automated and web-supported small-angle scattering data analysis},
  year      = {2007},
  pages     = {s223--s228},
  volume    = {40},
  abstract  = {Small-angle scattering (SAS) is frequently employed for screening large numbers of samples and for studying these samples under different conditions, including space- and time-resolved analysis. These measurements produce immense amounts of data, especially on modern high-flux and high-brilliance sources (e.g. third-generation synchrotrons). In biological SAS, like high- throughput macromolecular crystallography, large-scale analysis of proteins and macromolecular complexes is also emerging. Automation of data analysis becomes an indispensable prerequisite for adequate evaluation of high- throughput SAS experiments. Here a prototype of an automated data-analysis system for isotropic solution scattering based on the further development of the programs belonging to the package ATSAS 2.1 is reported. This system allows the major analysis tasks starting from the raw data processing and, for monodisperse systems, finishing with a three-dimensional model, to be performed automatically. Convenient web interfaces for the online use of individual ATSAS programs are also provided.},
  file      = {2007_Petoukhov_s223.pdf:by-author/P/Petoukhov/2007_Petoukhov_s223.pdf:PDF},
  keywords  = {Automation; SAXS},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Petoukhov2013d,
  author      = {Maxim V Petoukhov and Dmitri I Svergun},
  journal     = {Int J Biochem Cell Biol},
  title       = {Applications of small-angle X-ray scattering to biomacromolecular solutions.},
  year        = {2013},
  pages       = {429--437},
  volume      = {45},
  abstract    = {Small-angle scattering of X-rays (SAXS) is an established method for low-resolution structural characterization of biological macromolecules in solution. Being complementary to the high resolution methods (X-ray crystallography and NMR), SAXS is often used in combination with them. The technique provides overall three-dimensional structures using ab initio reconstructions and hybrid modeling, and allows one to quantitatively characterize equilibrium mixtures as well as flexible systems. Recent progress in SAXS instrumentation, most notably, high brilliance synchrotron sources, has paved the way for high throughput automated SAXS studies allowing screening of external conditions (pH, temperature, ligand binding etc.). The modern approaches for SAXS data analysis are presented in this review including rapid characterization of macromolecular solutions in terms of low-resolution shapes, validation of high-resolution models in close-to-native conditions, quaternary structure analysis of complexes and quantitative description of the oligomeric composition in mixtures. Practical aspects of SAXS as a standalone tool and its combinations with other structural, biophysical or bioinformatics methods are reviewed. The capabilities of the technique are illustrated by a selection of recent applications for the studies of biological molecules. Future perspectives on SAXS and its potential impact to structural molecular biology are discussed.},
  doi         = {10.1016/j.biocel.2012.10.017},
  file        = {:by-author/P/Petoukhov/2013_Petoukhov_429.pdf:PDF},
  institution = {European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, 22607 Hamburg, Germany.},
  keywords    = {Actins; Animals; Biomolecular; Calmodulin; Chemistry; Dihydrolipoyllysine-Residue Acetyltransferase; Glutamate Decarboxylase; Humans; Models; Molecular; Nuclear Magnetic Resonance; Osmolar Concentration; Plant Proteins; Protein Structure; Quaternary; SAXS; Scattering; Small Angle; Solutions; X-Ray Diffraction},
  language    = {eng},
  medline-pst = {ppublish},
  owner       = {em},
  pii         = {S1357-2725(12)00363-9},
  pmid        = {23142499},
  timestamp = {2014.01.14},
  creationdate = {2014-01-14T00:00:00},
  url         = {http://dx.doi.org/10.1016/j.biocel.2012.10.017},
}

@Article{Petoukhov2005,
  author    = {Petoukhov, Maxim V. and Svergun, Dmitri I.},
  journal   = {Biophysical journal},
  title     = {Global rigid body modeling of macromolecular complexes against small-angle scattering data.},
  year      = {2005},
  pages     = {1237--50},
  volume    = {89},
  abstract  = {New methods to automatically build models of macromolecular complexes from high-resolution structures or homology models of their subunits or domains against x-ray or neutron small-angle scattering data are presented. Depending on the complexity of the object, different approaches are employed for the global search of the optimum configuration of subunits fitting the experimental data. An exhaustive grid search is used for hetero- and homodimeric particles and for symmetric oligomers formed by identical subunits. For the assemblies or multidomain proteins containing more then one subunit/domain per asymmetric unit, heuristic algorithms based on simulated annealing are used. Fast computational algorithms based on spherical harmonics representation of scattering amplitudes are employed. The methods allow one to construct interconnected models without steric clashes, to account for the particle symmetry and to incorporate information from other methods, on distances between specific residues or nucleotides. For multidomain proteins, addition of missing linkers between the domains is possible. Simultaneous fitting of multiple scattering patterns from subcomplexes or deletion mutants is incorporated. The efficiency of the methods is illustrated by their application to complexes of different types in several simulated and practical examples. Limitations and possible ambiguity of rigid body modeling are discussed and simplified docking criteria are provided to rank multiple models. The methods described are implemented in publicly available computer programs running on major hardware platforms.},
  file      = {:by-author/P/Petoukhov/2005_Petoukhov_1237.pdf:PDF},
  keywords  = {BUNCH; Experiment; SASREF; SAXS},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Presentation{Petricek2006,
  author       = {Václav Petříček and Michal Dušek and Lukáš Palatinus},
  title        = {Jana2006},
  year         = {2006},
  organization = {Institute of Physics, Prague, Czech Republic},
  file         = {:by-author/P/Palatinus/2006_Palatinus_a.ppt:PPT},
  keywords     = {Incommensurate-structures},
  owner        = {saulius},
  timestamp = {2015.03.03},
  creationdate = {2015-03-03T00:00:00},
  url          = {http://jana.fzu.cz/jana2006.ppt},
}

@InBook{Petrikaite2011,
  author    = {Vilma Petrikaitė and Daumantas Matulis},
  chapter   = {2},
  editor    = {Mizutani Tadashi},
  pages     = {77--92},
  publisher = {InTech},
  title     = {Thermodynamics of Natural and Synthetic Inhibitor Binding to Human Hsp90, Application of Thermodynamics to Biological and Materials Science},
  year      = {2011},
  isbn      = {978-953-307-980-6},
  month     = {January},
  comment   = {ISBN: 978-953-307-980-6},
  file      = {2011_Petrikaitė_77.pdf:by-author/P/Petrikaitė/2011_Petrikaitė_77.pdf:PDF},
  keywords  = {Hsp90; Protein TD; Thermodynamics},
  owner     = {saulius},
  timestamp = {2011.11.27},
  creationdate = {2011-11-27T00:00:00},
  url       = {http://www.intechopen.com/articles/show/title/thermodynamics-of-natural-and-synthetic-inhibitor-binding-to-human-hsp90},
}

@Manuscript{Petz2001,
  author    = {Dénes Petz},
  title     = {Entropy, von Neumann and the von Neumann entropy},
  year      = {2001},
  keywords  = {Entropy; Statistical Mechanics},
  abstract  = {The highway of the development of entropy is marked by many great names, for example, Clausius, Gibbs, Boltzmann, Szilérd, von Neumann, Shannon, Jaynes, and several others. In this article the emphasis is put on von Neumann and on quantum mechanics. The selection of the subjects reflects the taste (and the knowledge) of the author and it must be rather restrictive. In the past 50 years entropy has broken out of thermodynamics and statistical mechanics and invaded communication theory, ergodic theory and shown up in mathematical statistics, social and life sciences. It is practically impossible to present all of its features. The favourite subjects of entropy is about macroscopic phenomena, irreversibility and incomplete knowledge. In the strictly mathematical sense entropy is related to the asymptotics of probabilities or it is a kind of asymptotic behaviour of probabilities. This paper is organized as follows. After a short introduction to entropy, von Neumann’s gedanken experiment is repeated, which led him to the formula of thermodynamic entropy of a statistical operator. In the analysis of his ideas we stress the role of (the lack of) superselection sectors and summarize von Neumann’s knowledge about quantum mechanical entropy. The final part of this article is devoted to some important developments of the von Neumann entropy which were discovered long after von Neumann’s work. Subadditivity and interpretation of the von Neumann entropy as the capacity of a communication channel are among those.},
  file      = {:by-author/P/Petz/2001_Petz.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.09.26},
  creationdate = {2012-09-26T00:00:00},
}

@Article{Petzold2008,
  author    = {Petzold, Holm and Weisheit, Thomas and Gorls, Helmar and Breitzke, Hergen and Buntkowsky, Gerd and Escudero, Daniel and Gonzalez, Leticia and Weigand, Wolfgang},
  journal   = {Dalton Transactions},
  title     = {Selective carbon-carbon bond cleavage of 2{,}2[prime or minute]-dibromotolane via photolysis of its appropriate (diphosphine)Pt0 complex in the solid state},
  year      = {2008},
  pages     = {1979--1981},
  volume    = {0},
  abstract  = {By irradiating crystals of a (diphosphine)Pt0 complex containing 2{,}2[prime or minute]-dibromotolane as ligand with sunlight{,} a rare example of selective carbon-carbon bond cleavage in the solid state could be observed.},
  doi       = {10.1039/B801230J},
  file      = {:./by-author/P/Petzold/2008_Petzold_1979.pdf:PDF},
  issue     = {15},
  owner     = {antanas},
  publisher = {The Royal Society of Chemistry},
  timestamp = {2013.03.07},
  creationdate = {2013-03-07T00:00:00},
  url       = {http://dx.doi.org/10.1039/B801230J},
}

@Manuscript{Pfeil2012,
  author    = {Thomas Pfeil and Andreas Grübl and Sebastian Jeltsch and Eric Müller and Paul Müller and Mihai Petrovici and Michael Schmuker and Daniel Brüderle and Johannes Schemmel and Karlheinz Meier},
  title     = {Six Networks On A Universal Neuromorphic Computing Substrate},
  year      = {2012},
  url       = {http://arxiv.org/abs/1210.7083v1},
  abstract  = {In this study, we present a highly configurable neuromorphic computing substrate and use it for emulating several types of neural networks. At the heart of this system lies a mixed-signal chip, with analog implementations of neurons and synapses and digital transmission of action potentials. Major advantages of this emulation device, which has been explicitly designed as a universal neural network emulator, are its inherent parallelism, a high speed-up factor and low power consumption com- pared to conventional computers. Its configurability allows the realization of almost arbitrary network topologies and the use of widely varied neuronal and synaptic parameters. Fixed-pattern noise inherent to analog circuitry is reduced by calibration routines. An integrated development environment allows neuroscientists to operate the device without any prior knowledge of neuromorphic circuit design. As a showcase for the capabilities of the system, we describe the successful emulation of six different neural networks which cover a broad spectrum of both structure and functionality.},
  file      = {:by-author/P/Pfeil/2012_Pfeil_1.pdf:PDF},
  owner     = {andrius},
  timestamp = {2012.11.27},
  creationdate = {2012-11-27T00:00:00},
}

@Article{Phadungsukanan2012,
  author    = {Phadungsukanan, Weerapong and Kraft, Markus and Townsend, Joe and Murray-Rust, Peter},
  journal   = {Journal of Cheminformatics},
  title     = {The semantics of Chemical Markup Language (CML) for computational chemistry : CompChem},
  year      = {2012},
  issn      = {1758-2946},
  pages     = {15},
  volume    = {4},
  abstract  = {This paper introduces a subdomain chemistry format for storing computational chemistry data called CompChem. It has been developed based on the design, concepts and methodologies of Chemical Markup Language (CML) by adding computational chemistry semantics on top of the CML Schema. The format allows a wide range of ab initio quantum chemistry calculations of individual molecules to be stored. These calculations include, for example, single point energy calculation, molecular geometry optimization, and vibrational frequency analysis. The paper also describes the supporting infrastructure, such as processing software, dictionaries, validation tools and database repositories. In addition, some of the challenges and difficulties in developing common computational chemistry dictionaries are discussed. The uses of CompChem are illustrated by two practical applications.},
  doi       = {10.1186/1758-2946-4-15},
  file      = {2012_Phadungsukanan_15.pdf:by-author/P/Phadungsukanan/2012_Phadungsukanan_15.pdf:PDF},
  keywords  = {CML; Crystallography; Data Formats; Data Management; X-ray Crystallography; XML},
  owner     = {saulius},
  pubmedid  = {22870956},
  timestamp = {2013.09.19},
  creationdate = {2013-09-19T00:00:00},
  url       = {http://www.jcheminf.com/content/4/1/15},
}

@Article{Pham2011,
  author    = {Nam Pham and Bogdan M. Wilamowski},
  journal   = {Journal of Computing},
  title     = {Improved Nelder Mead’s Simplex Method and Applications},
  year      = {2011},
  pages     = {55--63},
  file      = {:by-author/P/Pham/2011_Pham_55.pdf:PDF},
  keywords  = {Computer Science (CS); Minimisation; Simplex Method},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Phillips1950,
  author    = {Phillips, D. C. and Rogers, D. and Wilson, A. J. C.},
  journal   = {Acta Crystallographica},
  title     = {Reliability index for centrosymmetric and non-centrosymmetric structures},
  year      = {1950},
  pages     = {398--399},
  volume    = {3},
  doi       = {10.1107/S0365110X50001130},
  file      = {1950_Phillips_398.pdf:by-author/P/Phillips/1950_Phillips_398.pdf:PDF},
  keywords  = {Data Quality; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2014.03.24},
  creationdate = {2014-03-24T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0365110X50001130},
}

@Article{Piccirilli1992,
  author    = {Piccirilli, J A and McConnell, T S and Zaug, A J and Noller, H F and Cech, T R},
  journal   = {Science (New York, N.Y.)},
  title     = {Aminoacyl esterase activity of the Tetrahymena ribozyme.},
  year      = {1992},
  pages     = {1420--4},
  volume    = {256},
  file      = {1992_Piccirilli_1420.pdf:by-author/P/Piccirilli/1992_Piccirilli_1420.pdf:PDF},
  keywords  = {Ribozymes},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Piccoli2007,
  author    = {Piccoli, Paula M. B. and Koetzle, Thomas F. and Schultz, Arthur J.},
  journal   = {Comments on Inorganic Chemistry},
  title     = {Single crystal neutron diffraction for the inorganic chemist – a practical guide},
  year      = {2007},
  pages     = {3--38},
  volume    = {28},
  abstract  = {Advances and upgrades in neutron sources and instrumentation are poised to make neutron diffraction more accessible to inorganic chemists than ever before. These improvements will pave the way for single crystal investigations that currently may be difficult, for example due to small crystal size or large unit cell volume. This article aims to highlight what can presently be achieved in neutron diffraction and looks forward toward future applications of neutron scattering in inorganic chemistry.},
  doi       = {10.1080/02603590701394741},
  eprint    = {http://www.tandfonline.com/doi/pdf/10.1080/02603590701394741},
  file      = {2007_Piccoli_3.pdf:by-author/P/Piccoli/2007_Piccoli_3.pdf:PDF},
  keywords  = {Neutron Crystallography; Neutron Diffraction},
  owner     = {saulius},
  timestamp = {2014.02.14},
  creationdate = {2014-02-14T00:00:00},
  url       = {http://www.tandfonline.com/doi/abs/10.1080/02603590701394741},
}

@Article{Picha2000,
  author    = {Picha, K. M. and Ahnert, P. and Patel, S. S.},
  journal   = {Biochemistry},
  title     = {DNA binding in the central channel of bacteriophage T7 helicase-primase is a multistep process. Nucleotide hydrolysis is not required.},
  year      = {2000},
  pages     = {6401--9},
  volume    = {39},
  abstract  = {Many helicases assemble into ring-shaped hexamers and bind DNA in their central channel. This raises the question as to how the DNA gets into the central channel to form a topologically linked complex. We have used the presteady-state stopped-flow kinetic method and protein fluorescence changes to investigate the mechanism of single-stranded DNA (ssDNA) binding to the bacteriophage T7 helicase-primase, gp4A'. We have found that the kinetics of 30-mer ssDNA binding to a preformed gp4A' hexamer in the presence of both Mg-dTMP-PCP and Mg-dTTP are similar, indicating that Mg-dTTP binding is sufficient and hydrolysis is not necessary for efficient DNA binding. Multiple transient changes in gp4A' fluorescence revealed a four-step mechanism for DNA binding with Mg-dTTP. These transient changes were analyzed by global fitting and kinetic simulation to determine the intrinsic rate constants of this four-step mechanism. The initial steps, including the bimolecular encounter of the DNA with the helicase and a subsequent conformational change, were fast. We propose that these initial steps of DNA binding occur at a readily accessible site, which is likely to be on the outside of the hexamer ring. The binding of the 30-mer ssDNA at this loading site is followed by slower conformational changes that allow the DNA to transit into the central channel of gp4A' via a ring-opening or threading pathway.},
  file      = {:by-author/P/Picha/2000_Picha_6401.pdf:PDF},
  keywords  = {T7; {gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Picha1998,
  author    = {Picha, K. M. and Patel, S. S.},
  journal   = {The Journal of biological chemistry},
  title     = {Bacteriophage T7 DNA helicase binds dTTP, forms hexamers, and binds DNA in the absence of Mg2+. The presence of dTTP is sufficient for hexamer formation and DNA binding.},
  year      = {1998},
  pages     = {27315--9},
  volume    = {273},
  abstract  = {The role of Mg2+ in dTTP hydrolysis, dTTP binding, hexamer formation, and DNA binding was studied in bacteriophage T7 DNA helicase (4A' protein). The steady state kcat for the dTTPase activity was 200-300-fold lower in the absence of MgCl2, but the Km was only slightly affected. Direct dTTP binding experiments showed that the Kd of dTTP was unaffected, but the stoichiometry of dTTP binding was different in the absence of Mg2+. Two dTTPs were found to bind tightly in the absence of Mg2+ in contrast to three to four in the presence of Mg2+. In the presence of DNA there was little difference in the stoichiometry of dTTP binding to 4A'. These results indicate that Mg2+ is not necessary for dTTP binding, but Mg2+ is required for optimal hydrolysis of dTTP. Gel filtration of 4A' in the presence of dTTP without Mg2+ showed that Mg2+ was not necessary, and dTTP was sufficient for hexamer formation. The hexamers formed in the presence of dTTP without Mg2+ were capable of binding single-stranded DNA. However, the 4A' hexamers formed in the presence of dTDP with or without Mg2+ did not bind DNA, indicating that hexamer formation itself is not sufficient for DNA binding. The hexamers need to be in the correct conformation, in this case in the dTTP-bound state, to interact with the DNA. Thus, the gamma-phosphate of dTTP plays an important role in causing a conformational change in the protein that leads to stable interactions of 4A' with the DNA.},
  file      = {:by-author/P/Picha/1998_Picha_27315.pdf:PDF},
  keywords  = {{gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Pickart2000,
  author    = {Pickart, C. M. and VanDemark, A. P.},
  journal   = {Nature structural biology},
  title     = {Opening doors into the proteasome.},
  year      = {2000},
  pages     = {999--1001},
  volume    = {7},
  file      = {:by-author/P/Pickart/2000_Pickart_999.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Pickwell2006,
  author    = {E. Pickwell and V. P. Wallace},
  journal   = {Journal of Applied Physics D: Applied Physics},
  title     = {Biomedical applications of terahertz technology},
  year      = {2006},
  pages     = {R301-R310},
  volume    = {39},
  abstract  = {We review the development of terahertz (THz) technology and describe a typical system used in biomedical applications. By considering where the THz regime lies in the electromagnetic spectrum, we see that THz radiation predominantly excites vibrational modes that are present in water. Thus, water absorption dominates spectroscopy and imaging of soft tissues. However, there are advantages of THz methods that make it attractive for pharmaceutical and clinical applications. In this review, we consider applications ranging from THz spectroscopy of crystalline drugs to THz imaging of skin cancer.},
  doi       = {10.1088/0022-3727/39/17/R01},
  file      = {:by-author/P/Pickwell/2006_Pickwell_R301.pdf:PDF},
  keywords  = {Physics; Terahertz EM Waves},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
  url       = {http://stacks.iop.org/0022-3727/39/i=17/a=R01},
}

@Article{Piekarowicz2001,
  author    = {Piekarowicz, A. and Kłyz, A. and Kwiatek, A. and Stein, D. C.},
  journal   = {Molecular microbiology},
  title     = {Analysis of type I restriction modification systems in the Neisseriaceae: genetic organization and properties of the gene products.},
  year      = {2001},
  pages     = {1199--210},
  volume    = {41},
  abstract  = {The hsd locus (host specificity of DNA) was identified in the Neisseria gonorrhoeae genome. The DNA fragment encoding this locus produced an active restriction and modification (R/M) system when cloned into Escherichia coli. This R/M system was designated NgoAV. The cloned genomic fragment (7800 bp) has the potential to encode seven open reading frames (ORFs). Several of these ORFs had significant homology with other proteins found in the databases: ORF1, the hsdM, a methylase subunit (HsdM); ORF2, a homologue of dinD; ORF3, a homologue of hsdS; ORF4, a homologue of hsdS; and ORF5, an endonuclease subunit hsdR. The endonuclease and methylase subunits possessed strongest protein sequence homology to the EcoR124II R/M system, indicating that NgoAV belongs to the type IC R/M family. Deletion analysis showed that only ORF3 imparted the sequence specificity of the RM.NgoAV system, which recognizes an interrupted palindrome sequence (GCAN(8-)TGC). The genetic structure of ORF3 (208 amino acids) is almost identical to the structure of the 5' truncated hsdS genes of EcoDXXI or EcoR124II R/M systems obtained by in vitro manipulation. Genomic sequence analysis allowed us to identify hsd loci with a very high homology to RM.NgoAV in two strains of Neisseria meningitidis. However, significant differences in the organization and structure of the hsdS genes in both these systems suggests that, if functional, they would possess recognition sites that differ from the gonococcus and from themselves.},
  file      = {:by-author/P/Piekarowicz/2001_Piekarowicz_1199.pdf:PDF},
  keywords  = {TypeI},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Pieper1997,
  author    = {Pieper, U. and Brinkmann, T. and Krüger, T. and Noyer-Weidner, M. and Pingoud, A.},
  journal   = {Journal of molecular biology},
  title     = {Characterization of the interaction between the restriction endonuclease McrBC from E. coli and its cofactor GTP.},
  year      = {1997},
  pages     = {190--9},
  volume    = {272},
  abstract  = {McrBC, a GTP-dependent restriction enzyme from E. coli K-12, cleaves DNA containing methylated cytosine residues 40 to 80 residues apart and 3'-adjacent to a purine residue (PumCN40-80PumC). The presence of the three consensus sequences characteristic for guanine nucleotide binding proteins in one of the two subunits of McrBC suggests that this subunit is responsible for GTP binding and hydrolysis. We show here that (i) McrB binds GTP with an affinity of 10(6) M-1 and that GTP binding stabilizes McrB against thermal denaturation. (ii) McrB binds GDP about 50-fold and ATP at least three orders of magnitude more weakly than GTP. (iii) McrB hydrolyzes GTP in the presence of Mg2+ with a steady-state rate of approximately 0.5 min-1. (iv) McrC stimulates GTP hydrolysis 30-fold, but substrate DNA has no detectable effect on the GTPase activity of McrB, neither by itself nor in the presence of McrC. (v) Substitution of N339 and N376 with alanine allowed us to identify NTAD (339 to 342) rather than NKKA (376 to 379) as the equivalent of the third consensus sequence motif characteristic for guanine nucleotide binding proteins, NKXD.},
  file      = {:by-author/P/Pieper/1997_Pieper_190.pdf:PDF},
  keywords  = {McrBC},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Pieper2002,
  author    = {Pieper, Uwe and Groll, Detlef H. and Wünsch, Sandra and Gast, Frank-Ulrich and Speck, Christian and Mücke, Norbert and Pingoud, Alfred},
  journal   = {Biochemistry},
  title     = {The GTP-dependent restriction enzyme McrBC from Escherichia coli forms high-molecular mass complexes with DNA and produces a cleavage pattern with a characteristic 10-base pair repeat.},
  year      = {2002},
  pages     = {5245--54},
  volume    = {41},
  abstract  = {The GTP-dependent restriction enzyme McrBC consists of two polypeptides: one (McrB) that is responsible for GTP binding and hydrolysis as well as DNA binding and another (McrC) that is responsible for DNA cleavage. It recognizes two methylated or hemimethylated RC sites (R(m)C) at a distance of approximately 30 to more than 2000 base pairs and cleaves the DNA close to one of the two R(m)C sites. This process is strictly coupled to GTP hydrolysis and involves the formation of high-molecular mass complexes. We show here using footprinting techniques, surface plasmon resonance, and scanning force microscopy experiments that in the absence of McrC, McrB binds to a single R(m)C site. If a second R(m)C site is present on the DNA, it is occupied independently by McrB. Whereas the DNA-binding domain of McrB forms 1:1 complexes with each R(m)C site and shows a clear footprint on both R(m)C sites, full-length McrB forms complexes with a stoichiometry of at least 4:1 at each R(m)C site, resulting in a slightly more extended footprint. In the presence of McrC, McrB forms high-molecular mass complexes of unknown stoichiometry, which are considerably larger than the complexes formed with McrB alone. In these complexes and when GTP is present, the DNA is cleaved next to one of the R(m)C sites at distances differing by one to five helical turns, suggesting that in the McrBC-DNA complex only a few topologically well-defined phosphodiester bonds of the DNA are accessible for the nucleolytic center of McrC.},
  file      = {:by-author/P/Pieper/2002_Pieper_5245.pdf:PDF},
  keywords  = {McrBC},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Pieper2002a,
  author    = {Pieper, Uwe and Pingoud, Alfred},
  journal   = {Biochemistry},
  title     = {A mutational analysis of the PD...D/EXK motif suggests that McrC harbors the catalytic center for DNA cleavage by the GTP-dependent restriction enzyme McrBC from Escherichia coli.},
  year      = {2002},
  pages     = {5236--44},
  volume    = {41},
  abstract  = {McrBC is a unique restriction enzyme which binds specifically to the bipartite recognition sequence R(m)CN( approximately )(30)(-)( approximately )(2000)R(m)C and in the presence of GTP translocates the DNA and cleaves both strands at multiple positions within the two R(m)C "half-sites". It is known that McrBC is composed of two subunits: McrB which binds and hydrolyzes GTP and specifically interacts with DNA and McrC whose function is not clear but which has been suspected to harbor the catalytic center for DNA cleavage. A multiple-sequence alignment of the amino acid sequence of Escherichia coli McrC and of six presumably homologous open reading frames from various bacterial species shows that a sequence motif found in many restriction enzymes, but also in other nucleases, the PD.D/EXK motif, is conserved among these sequences. A mutational analysis, in which the carboxylates (aspartic acid in McrC) of this motif were substituted with alanine or asparagine and lysine was substituted with alanine or arginine, strongly suggests that Asp244, Asp257, and Lys259 represent the catalytic center of E. coli McrC. Whereas the variants D244A (or -N), D257A (or -N), and K259A are inactive in DNA cleavage (K259R has residual DNA cleavage activity), they interact with McrB like wild-type McrC, as can be deduced from the finding that they stimulate the McrB-catalyzed GTP hydrolysis to the same extent as wild-type McrC. Thus, whereas McrC variants defective in DNA cleavage can stimulate the GTPase activity of McrB, the DNase activity of McrC is not supported by McrB variants defective in GTP hydrolysis.},
  file      = {:by-author/P/Pieper/2002_Pieper_5236.pdf:PDF},
  keywords  = {McrBC},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Pieper1999,
  author    = {Pieper, U. and Schweitzer, T. and Groll, D. H. and Gast, F. U. and Pingoud, A.},
  journal   = {Journal of molecular biology},
  title     = {The GTP-binding domain of McrB: more than just a variation on a common theme?},
  year      = {1999},
  pages     = {547--56},
  volume    = {292},
  abstract  = {The methylation-dependent restriction endonuclease McrBC from Escherichia coli K12 cleaves DNA containing two R(m)C dinucleotides separated by about 40 to 2000 base-pairs. McrBC is unique in that cleavage is totally dependent on GTP hydrolysis. McrB is the GTP binding and hydrolyzing subunit, whereas MrC stimulates its GTP hydrolysis. The C-terminal part of McrB contains the sequences characteristic for GTP-binding proteins, consisting of the GxxxxGK(S/T) motif (position 201-208), followed by the DxxG motif (position 300-303). The third motif (NKxD) is present only in a non-canonical form (NTAD 333-336). Here we report a mutational analysis of the putative GTP-binding domain of McrB. Amino acid substitutions were initially performed in the three proposed GTP-binding motifs. Whereas substitutions in motif 1 (P203V) and 2 (D300N) show the expected, albeit modest effects, mutation in the motif 3 is at variance with the expectations. Unlike the corresponding EF-Tu and ras -p21 variants, the D336N mutation in McrB does not change the nucleotide specificity from GTP to XTP, but results in a lack of GTPase stimulation by McrC. The finding that McrB is not a typical G protein motivated us to perform a search for similar sequences in DNA databases. Eight microbial sequences were found, mainly from unfinished sequencing projects, with highly conserved sequence blocks within a presumptive GTP-binding domain. From the five sequences showing the highest homology, 17 invariant charged or polar residues outside the classical three GTP-binding motifs were identified and subsequently exchanged to alanine. Several mutations specifically affect GTP affinity and/or GTPase activity. Our data allow us to conclude that McrB is not a typical member of the superfamily of GTP-binding proteins, but defines a new subfamily within the superfamily of GTP-binding proteins, together with similar prokaryotic proteins of as yet unidentified function.},
  file      = {:by-author/P/Pieper/1999_Pieper_547.pdf:PDF},
  keywords  = {McrBC},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Pierce2000,
  author    = {Benjamin C. Pierce and David N. Turner},
  journal   = {ACM Transactions on Programming Languages and Systems},
  title     = {Local Type Inference},
  year      = {2000},
  issn      = {0164-0925},
  pages     = {1--44},
  volume    = {22},
  abstract  = {We study two partial type inference methods for a language combining subtyping and impredica- tive polymorphism. Both methods are local in the sense that missing annotations are recovered using only information from adjacent nodes in the syntax tree, without long-distance constraints such as unification variables. One method infers type arguments in polymorphic applications using a local constraint solver. The other infers annotations on bound variables in function abstractions by propagating type constraints downward from enclosing application nodes. We motivate our design choices by a statistical analysis of the uses of type inference in a sizable body of existing ML code.},
  acmid     = {345100},
  address   = {New York, NY, USA},
  doi       = {10.1145/345099.345100},
  file      = {2000_Pierce_1.pdf:by-author/P/Pierce/2000_Pierce_1.pdf:PDF},
  keywords  = {Computer Science (CS); Polymorphism; Subtyping; Type Inference; Type Systems},
  owner     = {saulius},
  publisher = {ACM},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://doi.acm.org/10.1145/345099.345100},
}

@Article{Pierce2008,
  author    = {Pierce, Veronica and Kang, Myungshim and Aburi, Mahalaxmi and Weerasinghe, Samantha and Smith, PaulE.},
  journal   = {Cell Biochemistry and Biophysics},
  title     = {Recent Applications of Kirkwood–Buff Theory to Biological Systems},
  year      = {2008},
  issn      = {1085-9195},
  pages     = {1--22},
  volume    = {50},
  doi       = {10.1007/s12013-007-9005-0},
  file      = {2008_Pierce_1.pdf:by-author/P/Pierce/2008_Pierce_1.pdf:PDF},
  keywords  = {Computer Simulation; Cosolvents; Kirkwood-Buff Theory; Osmolytes; Preferential Binding; Preferential Interactions; Protein Denaturation; Statistical Physics; Theory of Solutions},
  language  = {English},
  owner     = {saulius},
  publisher = {Humana Press Inc},
  timestamp = {2015.03.13},
  creationdate = {2015-03-13T00:00:00},
  url       = {http://dx.doi.org/10.1007/s12013-007-9005-0},
}

@Article{Pieters2006,
  author    = {Pieters, Roland J.},
  journal   = {Chembiochem: a European Journal of Chemical Biology},
  title     = {Inhibition and Detection of Galectins},
  year      = {2006},
  pages     = {721--8},
  volume    = {7},
  abstract  = {More and more studies report on the roles that galectins play in numerous types of cancer. These roles can be varied, as has been shown particularly for galectin-3. These studies have created the need for inhibitors that can block unwanted effects, and the need to detect galectins in tissues, in order to better understand their role, and aid in diagnosis and prognosis. Since galectins bind beta-galactosides, monovalent galactose-derived inhibitors have been prepared but also peptidic ones have appeared. Since galectins often induce crosslinking and partake in aggregation phenomena, multivalency has been a successful design element in inhibitor development. Currently, there are no cheap and convenient solutions available for the detection of, ideally multiple, galectins in tissue samples, although antibody-based methods such as ELISA and Western blot analysis are being used. Besides these, a chemical probe-based method also shows potential as an alternative.},
  file      = {:by-author/P/Pieters/2006_Pieters_721.pdf:PDF},
  keywords  = {Bioconjugation},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@Article{Piga2015,
  author    = {Piga, Giampaolo and Brunetti, Antonio and Lasio, Barbara and Malfatti, Luca and Galobart, Àngel and Dalla Vecchia, FabioM. and Enzo, Stefano},
  journal   = {Applied Physics A},
  title     = {New insights about the presence of celestite into fossil bones from Molí del Baró 1 site (Isona i Conca Dellá, Lleida, Spain)},
  year      = {2015},
  issn      = {0947-8396},
  pages     = {487--496},
  volume    = {118},
  abstract  = {We have addressed an X-ray fluorescence (XRF) and X-ray diffraction (XRD) on a collection of thirteen fossil bone belonging to the Molí del Baró 1 paleontological site located near Sant Romà d'Abella (Isona i Conca Dellà Municipality, Lleida Province, Spain, dated to about 66.5 Ma, to investigate the fossilization occurred in this site in terms of physico-chemical properties. As a general behaviour, the XRD patterns showed the bioapatite mineral at a varying level of percentage, and accordingly, the correspondent XRF spectra turned out to be mainly dominated by the presence of Ca, obviously accompanied by phosphorus. Simultaneously, other elements such as Sr, Fe, Ba and Zn were found at non-negligible concentration levels and helped to assign the phase components in the XRD spectra. In three specimens, it was observed by XRD the rather unusual case where the original bioapatite bone mineral was completely substituted for by other mineralogical phases. In addition to this, celestite was also found as an important phase in ten specimens out of the thirteen examined. The occurrence of celestite in the bone structure appears a rather unusual observation within the literature of bones diagenesis. Its provenance is generally ascribed to marine vertebrate organisms, but the presence in the fossil bones of this site, where no evidence of marine environment exists, can be reconciled with occurrence of refluxing processes involving diagenetically altered fluids which were discharged into beds containing strontium sulphate-rich waters.},
  doi       = {10.1007/s00339-014-8814-4},
  file      = {2015_Piga_487.pdf:by-author/P/Piga/2015_Piga_487.pdf:PDF},
  language  = {English},
  owner     = {saulius},
  publisher = {Springer Berlin Heidelberg},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://dx.doi.org/10.1007/s00339-014-8814-4},
  urldate   = {2015-08-31},
}

@Article{Pilati2000,
  author    = {Pilati, Tullio and Forni, Alessandra},
  journal   = {Journal of Applied Crystallography},
  title     = {{\it SYMMOL} {--} a program to find the maximum symmetry in an atom cluster: an upgrade},
  year      = {2000},
  pages     = {417},
  volume    = {33},
  doi       = {10.1107/S0021889800001801},
  file      = {2000_Pilati_417.pdf:by-author/P/Pilati/2000_Pilati_417.pdf:PDF},
  keywords  = {Algorithms; Atom Clusters; Maximum Symmetry; Spacegroups; Symmetry; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2015.06.15},
  creationdate = {2015-06-15T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0021889800001801},
}

@Article{Pilati1998,
  author    = {Pilati, T. and Forni, A.},
  journal   = {Journal of Applied Crystallography},
  title     = {{\it SYMMOL}: a program to find the maximum symmetry group in an atom cluster, given a prefixed tolerance},
  year      = {1998},
  pages     = {503--504},
  volume    = {31},
  abstract  = {{\it SYMMOL} is a new stand-alone program to find the maximum symmetry compatible with a given tolerance. The input requirements are cell parameters, atomic coordinates and the tolerance. The output is a set of symmetrized coordinates, the point-group label and the point-group elements. Some parameters quantifying the deviation from the exact symmetry are also calculated.},
  doi       = {10.1107/S0021889898002180},
  file      = {1998_Pilati_503.pdf:by-author/P/Pilati/1998_Pilati_503.pdf:PDF},
  keywords  = {Algorithms; Crystallographic Software; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2015.06.15},
  creationdate = {2015-06-15T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0021889898002180},
}

@Webpage{Pilch2005,
  author    = {Hartmut Pilch},
  retrieved = {2010-03-05},
  title     = {Collective Shields against Software Patents?},
  url       = {http://swpat.ffii.de/analysis/shield/index.en.html},
  year      = {2005},
  abstract  = {Building a patent portfolio is hardly a realistic option for the self-defense of the free/opensource software community. However this community has a certain chance of leveraging prior art to its advantage, especially if it does this in a cost-efficient manner and realises the potential of legal insecurity inherent in the software patent system. So called Defensive Publishing, as has been proposed by initiatives like the Foresight Institute, however appears to be an incredibly silly approach. The most urgent task at this moment (spring 2001) is to time-stamp every CVS archive and every mailing list on which software ideas are developped.},
  file      = {:by-author/P/Pilch/2005_Pilch.war:},
  keywords  = {Copyrights-trademarks-patents},
  owner     = {saulius},
  timestamp = {2015.03.02},
  creationdate = {2015-03-02T00:00:00},
}

@Book{Pilgrim2002,
  author    = {Mark Pilgrim},
  publisher = {http://diveintopython.org/},
  title     = {Dive Into Python},
  year      = {2002},
  file      = {:by-author/P/Pilgrim/2002_Pilgrim.zip:ZIP;:by-author/P/Pilgrim/2002_Pilgrim.pdf:PDF},
  keywords  = {Computer Science (CS); Programming Languages; Python},
  owner     = {saulius},
  timestamp = {2015.03.10},
  creationdate = {2015-03-10T00:00:00},
  url       = {http://diveintopython.org/},
}

@Book{Pingoud2004,
  author    = {Pingoud},
  title     = {Restriction Endonucleases},
  year      = {2004},
  file      = {:by-author/P/Pingoud/2004_Pingoud.pdf:PDF},
  keywords  = {{gp41} Helicase},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Pingoud2005,
  author    = {Pingoud, A. and Fuxreiter, M. and Pingoud, V. and Wende, W.},
  journal   = {Cellular and molecular life sciences : CMLS},
  title     = {Type II restriction endonucleases: structure and mechanism.},
  year      = {2005},
  pages     = {685--707},
  volume    = {62},
  abstract  = {Type II restriction endonucleases are components of restriction modification systems that protect bacteria and archaea against invading foreign DNA. Most are homodimeric or tetrameric enzymes that cleave DNA at defined sites of 4-8 bp in length and require Mg2+ ions for catalysis. They differ in the details of the recognition process and the mode of cleavage, indicators that these enzymes are more diverse than originally thought. Still, most of them have a similar structural core and seem to share a common mechanism of DNA cleavage, suggesting that they evolved from a common ancestor. Only a few restriction endonucleases discovered thus far do not belong to the PD...D/ExK family of enzymes, but rather have active sites typical of other endonuclease families. The present review deals with new developments in the field of Type II restriction endonucleases. One of the more interesting aspects is the increasing awareness of the diversity of Type II restriction enzymes. Nevertheless, structural studies summarized herein deal with the more common subtypes. A major emphasis of this review will be on target site location and the mechanism of catalysis, two problems currently being addressed in the literature.},
  file      = {:by-author/P/Pingoud/2005_Pingoud_685.pdf:PDF},
  keywords  = {Obzor},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Pingoud2001,
  author      = {Pingoud, A. and Jeltsch, A.},
  journal     = {Nucleic acids research},
  title       = {Structure and function of type II restriction endonucleases.},
  year        = {2001},
  pages       = {3705--27},
  volume      = {29},
  abstract    = {More than 3000 type II restriction endonucleases have been discovered. They recognize short, usually palindromic, sequences of 4-8 bp and, in the presence of Mg(2+), cleave the DNA within or in close proximity to the recognition sequence. The orthodox type II enzymes are homodimers which recognize palindromic sites. Depending on particular features subtypes are classified. All structures of restriction enzymes show a common structural core comprising four beta-strands and one alpha-helix. Furthermore, two families of enzymes can be distinguished which are structurally very similar (EcoRI-like enzymes and EcoRV-like enzymes). Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone. In contrast, specific binding is characterized by an intimate interplay between direct (interaction with the bases) and indirect (interaction with the backbone) readout. Typically approximately 15-20 hydrogen bonds are formed between a dimeric restriction enzyme and the bases of the recognition sequence, in addition to numerous van der Waals contacts to the bases and hydrogen bonds to the backbone, which may also be water mediated. The recognition process triggers large conformational changes of the enzyme and the DNA, which lead to the activation of the catalytic centers. In many restriction enzymes the catalytic centers, one in each subunit, are represented by the PD. D/EXK motif, in which the two carboxylates are responsible for Mg(2+) binding, the essential cofactor for the great majority of enzymes. The precise mechanism of cleavage has not yet been established for any enzyme, the main uncertainty concerns the number of Mg(2+) ions directly involved in cleavage. Cleavage in the two strands usually occurs in a concerted fashion and leads to inversion of configuration at the phosphorus. The products of the reaction are DNA fragments with a 3'-OH and a 5'-phosphate.},
  doi         = {10.1093/nar/29.18.3705},
  file        = {:by-author/P/Pingoud/2001_Pingoud_3705.pdf:PDF},
  institution = {Institut für Biochemie (FB 08), Justus-Liebig-Universität, Heinrich-Buff-Ring 58, D-35392 Giessen, Germany. alfred.m.pingoud@chemie.bio.uni-giessen.de},
  keywords    = {Base Sequence; Binding Sites; Chemistry/metabolism; DNA; Deoxyribonucleases; Genetics; Genetics/metabolism; Obzor; Protein Conformation; Type II Site-Specific},
  language    = {English},
  owner       = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Pingoud1997,
  author       = {A. Pingoud and A. Jeltsch},
  journal      = {Eur J Biochem},
  title        = {Recognition and cleavage of DNA by type-II restriction endonucleases.},
  year         = {1997},
  month        = {May},
  number       = {1},
  pages        = {1--22},
  volume       = {246},
  abstract     = {Restriction endonucleases are enzymes which recognize short DNA sequences and cleave the DNA in both strands. Depending on the enzymological properties different types are distinguished. Type II restriction endonucleases are homodimers which recognize short palindromic sequences 4-8 bp in length and, in the presence of Mg2+, cleave the DNA within or next to the recognition site. They are capable of non-specific binding to DNA and make use of linear diffusion to locate their target site. Binding and recognition of the specific site involves contacts to the bases of the recognition sequence and the phosphodiester backbone over approximately 10-12 bp. In general, recognition is highly redundant which explains the extreme specificity of these enzymes. Specific binding is accompanied by conformational changes over both the protein and the DNA. This mutual induced fit leads to the activation of the catalytic centers. The precise mechanism of cleavage has not yet been established for any restriction endonuclease. Currently two models are discussed: the substrate-assisted catalysis mechanism and the two-metal-ion mechanism. Structural similarities identified between EcoRI, EcoRV, BamHI, PvuII and Cfr10I suggest that many type II restriction endonucleases are not only functionally but also evolutionarily related.},
  creationdate = {2016-06-16T00:00:00},
  file         = {:by-author/P/Pingoud/1997_Pingoud_1.pdf:PDF},
  institution  = {Institut für Biochemie, Fachbereich Biologie, Justus-Liebig-Universität, Giessen, Germany.},
  keywords     = {Binding Sites; Catalysis; Chemistry/metabolism; DNA; Deoxyribonuclease EcoRI; Deoxyribonucleases; Diffusion; Metabolism; Metals; Models; Molecular; Nucleic Acid Conformation; Protein Conformation; Type II Site-Specific},
  language     = {eng},
  medline-pst  = {ppublish},
  owner        = {em},
  pmid         = {9210460},
  timestamp    = {2016.06.16},
}

@Article{Pingoud2011,
  author      = {Alfred Pingoud and Wolfgang Wende},
  journal     = {Chembiochem},
  title       = {Generation of novel nucleases with extended specificity by rational and combinatorial strategies.},
  year        = {2011},
  month       = {Jul},
  number      = {10},
  pages       = {1495--1500},
  volume      = {12},
  doi         = {10.1002/cbic.201100055},
  file        = {:by-author/P/Pingoud/2011_Pingoud_1495.pdf:PDF},
  institution = {Justus-Liebig-Universitaet Giessen, Institut für Biochemie, Giessen, Germany.},
  keywords    = {Amino Acid Sequence; Animals; Chemistry/genetics/metabolism; DNA; DNA Cleavage; Endonucleases; Humans; Metabolism; Models; Molecular; Molecular Sequence Data; Protein Conformation; Protein Engineering; Substrate Specificity},
  language    = {eng},
  medline-pst = {ppublish},
  owner       = {em},
  pmid        = {21560218},
  timestamp = {2016.06.16},
  creationdate = {2016-06-16T00:00:00},
  url         = {http://dx.doi.org/10.1002/cbic.201100055},
}

@Article{Pingoud2007,
  author    = {Pingoud, Alfred and Wende, Wolfgang},
  journal   = {Structure (London, England : 1993)},
  title     = {A sliding restriction enzyme pauses.},
  year      = {2007},
  pages     = {391--3},
  volume    = {15},
  file      = {:by-author/P/Pingoud/2007_Pingoud_391.pdf:PDF},
  keywords  = {Struct; TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Pingoud2007a,
  author    = {Alfred Pingoud and Wolfgang Wende},
  journal   = {Structure},
  title     = {A sliding restriction enzyme pauses.},
  year      = {2007},
  month     = {Apr},
  number    = {4},
  pages     = {391--393},
  volume    = {15},
  doi       = {10.1016/j.str.2007.04.001},
  file      = {2007_Pingoud_391.pdf:by-author/P/Pingoud/2007_Pingoud_391.pdf:PDF},
  keywords  = {Binding Sites; DNA; Deoxyribonucleases; Type II Site-Specific},
  owner     = {em},
  pii       = {S0969-2126(07)00114-1},
  pmid      = {17437711},
  timestamp = {2011.06.10},
  creationdate = {2011-06-10T00:00:00},
  url       = {http://dx.doi.org/10.1016/j.str.2007.04.001},
}

@Article{Pingoud2014,
  author           = {Alfred Pingoud and Geoffrey G. Wilson and Wolfgang Wende},
  journal          = {Nucleic Acids Res.},
  title            = {Type {II} restriction endonucleases -- a historical perspective and more.},
  year             = {2014},
  month            = {Jul},
  number           = {12},
  pages            = {7489--7527},
  volume           = {42},
  abstract         = {This article continues the series of Surveys and Summaries on restriction endonucleases (REases) begun this year in Nucleic Acids Research. Here we discuss 'Type II' REases, the kind used for DNA analysis and cloning. We focus on their biochemistry: what they are, what they do, and how they do it. Type II REases are produced by prokaryotes to combat bacteriophages. With extreme accuracy, each recognizes a particular sequence in double-stranded DNA and cleaves at a fixed position within or nearby. The discoveries of these enzymes in the 1970s, and of the uses to which they could be put, have since impacted every corner of the life sciences. They became the enabling tools of molecular biology, genetics and biotechnology, and made analysis at the most fundamental levels routine. Hundreds of different REases have been discovered and are available commercially. Their genes have been cloned, sequenced and overexpressed. Most have been characterized to some extent, but few have been studied in depth. Here, we describe the original discoveries in this field, and the properties of the first Type II REases investigated. We discuss the mechanisms of sequence recognition and catalysis, and the varied oligomeric modes in which Type II REases act. We describe the surprising heterogeneity revealed by comparisons of their sequences and structures.},
  creationdate     = {2016-06-16T00:00:00},
  doi              = {10.1093/nar/gku447},
  file             = {:by-author/P/Pingoud/Pingoud_et_al_SUPPLEMENTARY_MATERIAL.pdf:PDF;:by-author/P/Pingoud/2014_Pingoud_7489.pdf:PDF},
  institution      = {Institute of Biochemistry, Justus-Liebig-University Giessen, Heinrich-Buff-Ring 58, D-35392 Giessen, Germany.},
  keywords         = {20th Century; 21st Century; Chemistry/genetics/history/metabolism; Chemistry/metabolism; DNA; Deoxyribonucleases; Evolution; History; Molecular; Protein Engineering; Restriction Endonuclease (RE); Restriction Mapping; Review; Type II Site-Specific},
  language         = {eng},
  medline-pst      = {ppublish},
  modificationdate = {2024-06-27T10:46:17},
  owner            = {em},
  pii              = {gku447},
  pmid             = {24878924},
  timestamp        = {2016.06.16},
  url              = {http://dx.doi.org/10.1093/nar/gku447},
}

@Article{Pingoud2003,
  author    = {Pingoud, Vera and Conzelmann, Charlotte and Kinzebach, Steffen and Sudina, Anna and Metelev, Valeri and Kubareva, Elena and Bujnicki, Janusz M. and Lurz, Rudi and Lüder, Gerhild and Xu, Shuang-Yong and Pingoud, Alfred},
  journal   = {Journal of molecular biology},
  title     = {PspGI, a type II restriction endonuclease from the extreme thermophile Pyrococcus sp.: structural and functional studies to investigate an evolutionary relationship with several mesophilic restriction enzymes.},
  year      = {2003},
  pages     = {913--29},
  volume    = {329},
  abstract  = {We present here the first detailed biochemical analysis of an archaeal restriction enzyme. PspGI shows sequence similarity to SsoII, EcoRII, NgoMIV and Cfr10I, which recognize related DNA sequences. We demonstrate here that PspGI, like SsoII and unlike EcoRII or NgoMIV and Cfr10I, interacts with and cleaves DNA as a homodimer and is not stimulated by simultaneous binding to two recognition sites. PspGI and SsoII differ in their basic biochemical properties, viz. stability against chemical denaturation and proteolytic digestion, DNA binding and the pH, MgCl(2) and salt-dependence of their DNA cleavage activity. In contrast, the results of mutational analyses and cross-link experiments show that PspGI and SsoII have a very similar DNA binding site and catalytic center as NgoMIV and Cfr10I (whose crystal structures are known), and presumably also as EcoRII, in spite of the fact that these enzymes, which all recognize variants of the sequence -/CC-GG- (/ denotes the site of cleavage), are representatives of different subgroups of type II restriction endonucleases. A sequence comparison of all known restriction endonuclease sequences, furthermore, suggests that several enzymes recognizing other DNA sequences also share amino acid sequence similarities with PspGI, SsoII and EcoRII in the region of the presumptive active site. These results are discussed in an evolutionary context.},
  doi       = {10.1016/S0022-2836(03)00523-0},
  file      = {:by-author/P/Pingoud/2003_Pingoud_913.pdf:PDF},
  groups    = {sg/Cfr10I, sg/NgoMIV},
  keywords  = {Restriction-modification Systems; TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/S0022283603005230},
}

@Article{Pingoud2003a,
  author       = {Vera Pingoud and Charlotte Conzelmann and Steffen Kinzebach and Anna Sudina and Valeri Metelev and Elena Kubareva and Janusz M Bujnicki and Rudi Lurz and Gerhild Lüder and Shuang-Yong Xu and Alfred Pingoud},
  journal      = {J Mol Biol},
  title        = {PspGI, a type II restriction endonuclease from the extreme thermophile Pyrococcus sp.: structural and functional studies to investigate an evolutionary relationship with several mesophilic restriction enzymes.},
  year         = {2003},
  month        = {Jun},
  number       = {5},
  pages        = {913--929},
  volume       = {329},
  abstract     = {We present here the first detailed biochemical analysis of an archaeal restriction enzyme. PspGI shows sequence similarity to SsoII, EcoRII, NgoMIV and Cfr10I, which recognize related DNA sequences. We demonstrate here that PspGI, like SsoII and unlike EcoRII or NgoMIV and Cfr10I, interacts with and cleaves DNA as a homodimer and is not stimulated by simultaneous binding to two recognition sites. PspGI and SsoII differ in their basic biochemical properties, viz. stability against chemical denaturation and proteolytic digestion, DNA binding and the pH, MgCl(2) and salt-dependence of their DNA cleavage activity. In contrast, the results of mutational analyses and cross-link experiments show that PspGI and SsoII have a very similar DNA binding site and catalytic center as NgoMIV and Cfr10I (whose crystal structures are known), and presumably also as EcoRII, in spite of the fact that these enzymes, which all recognize variants of the sequence -/CC-GG- (/ denotes the site of cleavage), are representatives of different subgroups of type II restriction endonucleases. A sequence comparison of all known restriction endonuclease sequences, furthermore, suggests that several enzymes recognizing other DNA sequences also share amino acid sequence similarities with PspGI, SsoII and EcoRII in the region of the presumptive active site. These results are discussed in an evolutionary context.},
  creationdate = {2011-11-23T00:00:00},
  file         = {2003_Pingoud_913.pdf:by-author/P/Pingoud/2003_Pingoud_913.pdf:PDF},
  groups       = {sg/Cfr10I, sg/NgoMIV},
  institution  = {Institut für Biochemie, Justus-Liebig-Universität, Heinrich-Buff-Ring 58, D-35392 Giessen, Germany. vera.pingoud@chemie.bio.uni-giessen.de},
  keywords     = {Amino Acid; Amino Acid Sequence; Archaeal Proteins; Azides; Binding Sites; Catalytic Domain; Chemistry; Chemistry/genetics; Chemistry/genetics/metabolism; Chemistry/metabolism; Chromatography; Cross-Linking Reagents; Cysteine; DNA; DNA Mutational Analysis; DNA Restriction Enzymes; Deoxyribonucleases; Disulfides; Electron; Enzyme Stability; Enzymology; Escherichia Coli; Evolution; Gel; Genetics; Hydrogen-Ion Concentration; Magnesium; Methods; Microscopy; Models; Molecular; Molecular Sequence Data; Oligodeoxyribonucleotides; Photochemistry; Protein Denaturation; Pyrococcus; Salts; Sequence Homology; Type II Site-Specific},
  language     = {eng},
  medline-pst  = {ppublish},
  owner        = {em},
  pii          = {S0022283603005230},
  pmid         = {12798682},
  timestamp    = {2011.11.23},
}

@Article{Pingoud2002,
  author    = {Pingoud, Vera and Kubareva, Elena and Stengel, Gudrun and Friedhoff, Peter and Bujnicki, Janusz M. and Urbanke, Claus and Sudina, Anna and Pingoud, Alfred},
  journal   = {The Journal of biological chemistry},
  title     = {Evolutionary relationship between different subgroups of restriction endonucleases.},
  year      = {2002},
  pages     = {14306--14},
  volume    = {277},
  abstract  = {The type II restriction endonuclease SsoII shows sequence similarity with 10 other restriction endonucleases, among them the type IIE restriction endonuclease EcoRII, which requires binding to an effector site for efficient DNA cleavage, and the type IIF restriction endonuclease NgoMIV, which is active as a homotetramer and cleaves DNA with two recognition sites in a concerted reaction. We show here that SsoII is an orthodox type II enzyme, which is active as a homodimer and does not require activation by binding to an effector site. Nevertheless, it shares with EcoRII and NgoMIV a very similar DNA-binding site and catalytic center as shown here by a mutational analysis, indicative of an evolutionary relationship between these three enzymes. We suggest that a similar relationship exists between other orthodox type II, type IIE, and type IIF restriction endonucleases. This may explain why similarities may be more pronounced between members of different subtypes of restriction enzymes than among the members of a given subtype.},
  file      = {:by-author/P/Pingoud/2002_Pingoud_14306.pdf:PDF},
  groups    = {sg/NgoMIV},
  keywords  = {Evolution; TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Pingoud2005a,
  author    = {Pingoud, Vera and Sudina, Anna and Geyer, Hildegard and Bujnicki, Janusz M. and Lurz, Rudi and Lüder, Gerhild and Morgan, Richard and Kubareva, Elena and Pingoud, Alfred},
  journal   = {The Journal of biological chemistry},
  title     = {Specificity changes in the evolution of type II restriction endonucleases: a biochemical and bioinformatic analysis of restriction enzymes that recognize unrelated sequences.},
  year      = {2005},
  pages     = {4289--98},
  volume    = {280},
  abstract  = {How restriction enzymes with their different specificities and mode of cleavage evolved has been a long standing question in evolutionary biology. We have recently shown that several Type II restriction endonucleases, namely SsoII (downward arrow CCNGG), PspGI (downward arrow CCWGG), Eco-RII (downward arrow CCWGG), NgoMIV (G downward arrow CCGGC), and Cfr10I (R downward arrow CCGGY), which recognize similar DNA sequences (as indicated, where the downward arrows denote cleavage position), share limited sequence similarity over an interrupted stretch of approximately 70 amino acid residues with MboI, a Type II restriction endonuclease from Moraxella bovis (Pingoud, V., Conzelmann, C., Kinzebach, S., Sudina, A., Metelev, V., Kubareva, E., Bujnicki, J. M., Lurz, R., Luder, G., Xu, S. Y., and Pingoud, A. (2003) J. Mol. Biol. 329, 913-929). Nevertheless, MboI has a dissimilar DNA specificity (downward arrow GATC) compared with these enzymes. In this study, we characterize MboI in detail to determine whether it utilizes a mechanism of DNA recognition similar to SsoII, PspGI, EcoRII, NgoMIV, and Cfr10I. Mutational analyses and photocross-linking experiments demonstrate that MboI exploits the stretch of approximately 70 amino acids for DNA recognition and cleavage. It is therefore likely that MboI shares a common evolutionary origin with SsoII, PspGI, EcoRII, NgoMIV, and Cfr10I. This is the first example of a relatively close evolutionary link between Type II restriction enzymes of widely different specificities.},
  file      = {:by-author/P/Pingoud/2005_Pingoud_4289.pdf:PDF},
  groups    = {sg/Cfr10I, sg/NgoMIV},
  keywords  = {TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Pingoud2009,
  author    = {Pingoud, Vera and Wende, Wolfgang and Friedhoff, Peter and Reuter, Monika and Alves, Jürgen and Jeltsch, Albert and Mones, Letif and Fuxreiter, Monika and Pingoud, Alfred},
  journal   = {Journal of molecular biology},
  title     = {On the divalent metal ion dependence of DNA cleavage by restriction endonucleases of the EcoRI family.},
  year      = {2009},
  pages     = {140--60},
  volume    = {393},
  abstract  = {Restriction endonucleases of the PD...D/EXK family need Mg(2+) for DNA cleavage. Whereas Mg(2+) (or Mn(2+)) promotes catalysis, Ca(2+) (without Mg(2+)) only supports DNA binding. The role of Mg(2+) in DNA cleavage by restriction endonucleases has elicited many hypotheses, differing mainly in the number of Mg(2+) involved in catalysis. To address this problem, we measured the Mg(2+) and Mn(2+) concentration dependence of DNA cleavage by BamHI, BglII, Cfr10I, EcoRI, EcoRII (catalytic domain), MboI, NgoMIV, PspGI, and SsoII, which were reported in co-crystal structure analyses to bind one (BglII and EcoRI) or two (BamHI and NgoMIV) Me(2+) per active site. DNA cleavage experiments were carried out at various Mg(2+) and Mn(2+) concentrations at constant ionic strength. All enzymes show a qualitatively similar Mg(2+) and Mn(2+) concentration dependence. In general, the Mg(2+) concentration optimum (between approximately 1 and 10 mM) is higher than the Mn(2+) concentration optimum (between approximately 0.1 and 1 mM). At still higher Mg(2+) or Mn(2+) concentrations, the activities of all enzymes tested are reduced but can be reactivated by Ca(2+). Based on these results, we propose that one Mg(2+) or Mn(2+) is critical for restriction enzyme activation, and binding of a second Me(2+) plays a role in modulating the activity. Steady-state kinetics carried out with EcoRI and BamHI suggest that binding of a second Mg(2+) or Mn(2+) mainly leads to an increase in K(m), such that the inhibitory effect of excess Mg(2+) or Mn(2+) can be overcome by increasing the substrate concentration. Our conclusions are supported by molecular dynamics simulations and are consistent with the structural observations of both one and two Me(2+) binding to these enzymes.},
  file      = {:by-author/P/Pingoud/2009_Pingoud_140.pdf:PDF},
  groups    = {sg/Cfr10I, sg/NgoMIV},
  owner     = {em},
  timestamp = {2013.09.19},
  creationdate = {2013-09-19T00:00:00},
}

@Article{Pinkett2007,
  author    = {Pinkett, H. W. and Lee, A. T. and Lum, P. and Locher, K. P. and Rees, D. C.},
  journal   = {Science (New York, N.Y.)},
  title     = {An inward-facing conformation of a putative metal-chelate-type ABC transporter.},
  year      = {2007},
  pages     = {373--7},
  volume    = {315},
  abstract  = {The crystal structure of a putative metal-chelate-type adenosine triphosphate (ATP)-binding cassette (ABC) transporter encoded by genes HI1470 and HI1471 of Haemophilus influenzae has been solved at 2.4 angstrom resolution. The permeation pathway exhibits an inward-facing conformation, in contrast to the outward-facing state previously observed for the homologous vitamin B12 importer BtuCD. Although the structures of both HI1470/1 and BtuCD have been solved in nucleotide-free states, the pairs of ABC subunits in these two structures differ by a translational shift in the plane of the membrane that coincides with a repositioning of the membrane-spanning subunits. The differences observed between these ABC transporters involve relatively modest rearrangements and may serve as structural models for inward- and outward-facing conformations relevant to the alternating access mechanism of substrate translocation.},
  file      = {:by-author/P/Pinkett/2007_Pinkett_373.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@InBook{Pirovano2010,
  author    = {Pirovano, Walter and Heringa, Jaap},
  chapter   = {Protein Secondary Structure Prediction},
  editor    = {O. Carugo and F. Eisenhaber},
  pages     = {327–348},
  publisher = {Springer Nature},
  title     = {Data Mining Techniques for the Life Sciences},
  year      = {2010},
  isbn      = {http://id.crossref.org/isbn/978-1-60327-241-4},
  month     = {Oct},
  doi       = {10.1007/978-1-60327-241-4_19},
  file      = {2010_Pirovano_327.pdf:by-author/P/Pirovano/2010_Pirovano_327.pdf:PDF},
  issn      = {1940-6029},
  owner     = {andrius},
  timestamp = {2017.03.30},
  creationdate = {2017-03-30T00:00:00},
  url       = {http://dx.doi.org/10.1007/978-1-60327-241-4_19},
}

@Article{Pitici2002,
  author    = {Pitici, Felicia and Beveridge, David L. and Baranger, Anne M.},
  journal   = {Biopolymers},
  title     = {Molecular dynamics simulation studies of induced fit and conformational capture in U1A-RNA binding: do molecular substates code for specificity?},
  year      = {2002},
  pages     = {424--35},
  volume    = {65},
  abstract  = {Molecular dynamics (MD) simulations on stem loop 2 of U1 small nuclear RNA and a construct of the U1A protein were carried out to obtain predictions of the structures for the unbound forms in solution and to elucidate dynamical aspects of induced fit upon binding. A crystal structure of the complex between the U1A protein and stem loop 2 RNA and an NMR structure for the uncomplexed form of the U1A protein are available from Oubridge et al. (Nature, 1994, Vol. 372, pp. 432-438) and Avis et al. (Journal of Molecular Biology, 1996, Vol. 257, pp. 398-411), respectively. As a consequence, U1A-RNA binding is a particularly attractive case for investigations of induced fit in protein-nucleic acid complexation. When combined with the available structural data, the results from simulations indicate that structural adaptation of U1A protein and RNA define distinct mechanisms for induced fit. For the protein, the calculations indicate that induced fit upon binding involves a non-native thermodynamic substate in which the structure is preorganized for binding. In contrast, induced fit of the RNA involves a distortion of the native structure in solution to an unstable form. However, the RNA solution structures predicted from simulation show evidence that structures in which groups of bases are favorably oriented for binding the U1A protein are thermally accessible. These results, which quantify with computational modeling recent proposals on induced fit and conformational capture by Leuillot and Varani (Biochemistry, 2001, Vol. 40, pp. 7947-7956) and by Williamson (Nature Structural Biology, 2000, Vol. 7, pp. 834-837) suggest an important role for intrinsic molecular architecture and substates other than the native form in the specificity of protein-RNA interactions.},
  file      = {:by-author/P/Pitici/2002_Pitici_424.pdf:PDF},
  groups    = {sg/applications},
  keywords  = {Protein Ligand Complexes},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@InProceedings{Piumarta1998,
  author    = {Ian Piumarta and Fabio Riccardi and Inria Rocquencourt},
  booktitle = {In SIGPLAN ’98 Conference on Programming Language Design and Implementation},
  title     = {Optimizing Direct Threaded Code By Selective Inlining},
  year      = {1998},
  pages     = {291--300},
  publisher = {ACM Press},
  file      = {PDF:by-author/P/Piumarta/1998_Piumarta_291.pdf:PDF},
  groups    = {sg/Compiler construction, sg/Threaded code},
  keywords  = {Compiler Construction; Computer Science (CS); Optimisation; Threaded Code},
  owner     = {saulius},
  timestamp = {2015.08.06},
  creationdate = {2015-08-06T00:00:00},
  url       = {http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.23.8829},
}

@Article{Piwowar2013,
  author    = {Piwowar, Heather A. and Vision, Todd J.},
  journal   = {PeerJ},
  title     = {Data reuse and the open data citation advantage},
  year      = {2013},
  issn      = {2167-8359},
  month     = oct,
  pages     = {e175},
  volume    = {1},
  abstract  = {\textbf{Background.} Attribution to the original contributor upon reuse of published data is important both as a reward for data creators and to document the provenance of research findings. Previous studies have found that papers with publicly available datasets receive a higher number of citations than similar studies without available data. However, few previous analyses have had the statistical power to control for the many variables known to predict citation rate, which has led to uncertain estimates of the “citation benefit”. Furthermore, little is known about patterns in data reuse over time and across datasets. \textbf{Method and Results.} Here, we look at citation rates while controlling for many known citation predictors and investigate the variability of data reuse. In a multivariate regression on 10,555 studies that created gene expression microarray data, we found that studies that made data available in a public repository received 9% (95% confidence interval: 5% to 13%) more citations than similar studies for which the data was not made available. Date of publication, journal impact factor, open access status, number of authors, first and last author publication history, corresponding author country, institution citation history, and study topic were included as covariates. The citation benefit varied with date of dataset deposition: a citation benefit was most clear for papers published in 2004 and 2005, at about 30%. Authors published most papers using their own datasets within two years of their first publication on the dataset, whereas data reuse papers published by third-party investigators continued to accumulate for at least six years. To study patterns of data reuse directly, we compiled 9,724 instances of third party data reuse via mention of GEO or ArrayExpress accession numbers in the full text of papers. The level of third-party data use was high: for 100 datasets deposited in year 0, we estimated that 40 papers in PubMed reused a dataset by year 2, 100 by year 4, and more than 150 data reuse papers had been published by year 5. Data reuse was distributed across a broad base of datasets: a very conservative estimate found that 20% of the datasets deposited between 2003 and 2007 had been reused at least once by third parties. \textbf{Conclusion.} After accounting for other factors affecting citation rate, we find a robust citation benefit from open data, although a smaller one than previously reported. We conclude there is a direct effect of third-party data reuse that persists for years beyond the time when researchers have published most of the papers reusing their own data. Other factors that may also contribute to the citation benefit are considered. We further conclude that, at least for gene expression microarray data, a substantial fraction of archived datasets are reused, and that the intensity of dataset reuse has been steadily increasing since 2003.},
  doi       = {10.7717/peerj.175},
  file      = {2013_Piwowar_e175.pdf:by-author/P/Piwowar/2013_Piwowar_e175.pdf:PDF},
  groups    = {sg/Bibliometrics},
  keywords  = {Bibliometrics; Data Archiving; Data Repositories; Data Reuse; Gene Expression Microarray; Incentives; Information Science; Open Data},
  owner     = {saulius},
  timestamp = {2016.10.16},
  creationdate = {2016-10-16T00:00:00},
  url       = {https://doi.org/10.7717/peerj.175},
}

@Article{Pizzi2016,
  author    = {Pizzi, Giovanni and Cepellotti, Andrea and Sabatini, Riccardo and Marzari, Nicola and Kozinsky, Boris},
  journal   = {Computational Materials Science},
  title     = {{AiiDA}: automated interactive infrastructure and database for computational science},
  year      = {2016},
  pages     = {218--230},
  volume    = {111},
  doi       = {10.1016/j.commatsci.2015.09.013},
  file      = {:by-author/P/Pizzi/2016_Pizzi_218.pdf:PDF},
  owner     = {andrius},
  timestamp = {2015.10.02},
  creationdate = {2015-10-02T00:00:00},
}

@Article{Pizzi2015,
  author     = {Pizzi, Giovanni and Cepellotti, Andrea and Sabatini, Riccardo and Marzari, Nicola and Kozinsky, Boris},
  journal    = {arXiv preprint arXiv:1504.01163},
  title      = {{AiiDA}: automated interactive infrastructure and database for computational science},
  year       = {2015},
  file       = {[PDF] from arxiv.org:by-author/P/Pizzi/2015_Pizzi.pdf:application/pdf;Snapshot:by-author/P/Pizzi/2015_Pizzi.html:text/html},
  groups     = {sg/NAR2012},
  owner      = {saulius},
  shorttitle = {AiiDA},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url        = {http://arxiv.org/abs/1504.01163},
  urldate    = {2015-08-31},
}

@Manuscript{Pizzi2015a,
  author    = {Pizzi, Giovanni and Cepellotti, Andrea and Sabatini, Riccardo and Marzari, Nicola and Kozinsky, Boris},
  title     = {{AiiDA}: Automated Interactive Infrastructure and Database for Computational Science},
  year      = {2015},
  url       = {http://arxiv.org/abs/1504.01163},
  file      = {:by-author/P/Pizzi/2015_Pizzi_1504.01163.pdf:PDF},
  groups    = {sg/NAR2012},
  owner     = {andrius},
  timestamp = {2015.04.22},
  creationdate = {2015-04-22T00:00:00},
}

@Article{Plankensteiner2006,
  author    = {Plankensteiner, Kristof and Reiner, Hannes and Rode, Bernd M},
  journal   = {Molecular diversity},
  title     = {Amino acids on the rampant primordial Earth: electric discharges and the hot salty ocean.},
  year      = {2006},
  pages     = {3--7},
  volume    = {10},
  abstract  = {For more than 50 years scientists who study prebiotic chemistry have been dealing with chemical evolution as it could have possibly taken place on the primordial Earth. Since we will never know what processes have really taken place around 3.8 to 4 billion years ago we can only come up with plausible reaction pathways that work well in an early Earth scenario as indicated by geochemists. In our work we have investigated the plausibility of one particularly important branch of prebiotic chemistry, the formation of amino acids, by electric discharge in a neutral atmosphere composed of carbon dioxide, nitrogen, and water vapour above liquid water. We have found yields of various amino acids under different temperature conditions, with and without sodium chloride in a simulated primordial lake or ocean within extremely short reaction times compared to the timespan available for prebiotic evolution.},
  doi       = {10.1007/s11030-006-7009-0},
  file      = {2006_Plankensteiner_3.pdf:by-author/P/Plankensteiner/2006_Plankensteiner_3.pdf:PDF},
  keywords  = {Chemical Prebiotic; Evolution},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Plankensteiner2005,
  author    = {Kristof Plankensteiner and Hannes Reiner and Bernd M. Rode},
  journal   = {Current Organic Chemistry},
  title     = {Prebiotic Chemistry: The Amino Acid and Peptide World},
  year      = {2005},
  pages     = {1107--1114},
  volume    = {9},
  abstract  = {In this review the idea of a “Peptide/Protein World” preceding the widely rooted idea of the “RNA world” is presented and elaborated. To support this idea, the formation of the building blocks of nucleic acids and peptides and their assembly to biopolymers in a primordial earth scenario is discussed. Furthermore, chemical stability problems of the building blocks and the assembled biomolecules are presented, and finally their ability to efficiently replicate and chemically evolve is argued. Taking into account various problems in all these areas for nucleic acids and nucleotides, the idea of the “Peptide/Protein World” is brought up, stating that peptides and proteins would have come first in chemical evolution with an “RNA world” appearing only later with the protective help of protein shells.},
  doi       = {10.2174/1385272054553640},
  file      = {2005_Plankensteiner_1107.pdf:by-author/P/Plankensteiner/2005_Plankensteiner_1107.pdf:PDF},
  keywords  = {Chemical Prebiotic; Evolution},
  owner     = {saulius},
  timestamp = {2012.11.20},
  creationdate = {2012-11-20T00:00:00},
}

@Article{Plankensteiner2005a,
  author    = {Plankensteiner, Kristof and Reiner, Hannes and Rode, Bernd M},
  journal   = {Origins of life and evolution of the biosphere : the journal of the International Society for the Study of the Origin of Life},
  title     = {Catalytically increased prebiotic peptide formation: ditryptophan, dilysine, and diserine.},
  year      = {2005},
  pages     = {411--9},
  volume    = {35},
  abstract  = {"Mutual" amino acid catalysis of glycine on the formation of ditryptophan, dilysine, and diserine in the prebiotically relevant Salt-Induced Peptide Formation (SIPF) Reaction was investigated varying the starting concentration and chirality of the educt amino acid, and analyzing the increase of yield resulting from this catalytic effect. Our results show the possibility of an amplified diverse pool of peptides being available for chemical evolution of larger peptides and proteins using also these more complicated amino acids for the evolution of more complex functions in future biochemical cycles and thus for the emergence of life. Catalytic effects are especially high in the case of serine, the most basic amino acid of the three, but are also significant for the other two examples investigated in the present work. Besides that, especially for serine, but also in the case of tryptophan, differences in catalytic yield increase according to the chiral form of the amino acid used could be observed.},
  doi       = {10.1007/s11084-005-1971-x},
  file      = {2005_Plankensteiner_411.pdf:by-author/P/Plankensteiner/2005_Plankensteiner_411.pdf:PDF},
  keywords  = {Chemical Prebiotic},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Plankensteiner2007,
  author    = {Kristof Plankensteiner and Hannes Reiner and Bernd M. Rode and Tomas Mikoviny and Armin Wisthaler and Armin Hansel and Tilmann D. Märk and Georg Fischer and Helmut Lammer and Helmut O. Rucker},
  journal   = {Icarus},
  title     = {Discharge experiments simulating chemical evolution on the surface of Titan},
  year      = {2007},
  issn      = {0019-1035},
  pages     = {616--619},
  volume    = {187},
  abstract  = {Saturn's moon Titan has been considered as one of the few places in our Solar System, where atmospheric and surface conditions could have produced organic compounds essential as precursors for an evolution of life. The Cassini–Huygens mission has provided new data on Titan's atmosphere and surface, which enabled us to simulate the chemical processes occurring under these conditions. Possible lightning events on Titan cannot only produce higher hydrocarbons, but also allow surface water ice to participate in the reaction scenario, resulting in CHO, CHN, and CHON compounds including several molecules relevant for the formation of amino acids and nucleic acids.},
  doi       = {10.1016/j.icarus.2006.12.018},
  file      = {2007_Plankensteiner_616.pdf:by-author/P/Plankensteiner/2007_Plankensteiner_616.pdf:PDF;tables.csv:by-author/P/Plankensteiner/2007_Plankensteiner_616/tables.csv:CSV},
  keywords  = {Prebiotic Chemistry},
  owner     = {saulius},
  timestamp = {2012.11.20},
  creationdate = {2012-11-20T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/S0019103507000218},
}

@Article{Plankensteiner2002,
  author    = {Plankensteiner, Kristof and Righi, Alessandro and Rode, Bernd M},
  journal   = {Origins of life and evolution of the biosphere : the journal of the International Society for the Study of the Origin of Life},
  title     = {Glycine and diglycine as possible catalytic factors in the prebiotic evolution of peptides.},
  year      = {2002},
  pages     = {225--36},
  volume    = {32},
  abstract  = {Mutual catalytic effects within the Salt-Induced Peptide Formation (SIPF) Reaction might be one little puzzle piece in the complicated process of the formation of complex peptidic systems and their chemical evolution on the prebiotic earth. The catalytic effects of glycine and diglycine on the formation of dipeptides from mixed amino acid systems in the SIPF Reaction was investigated for systems with leucine, proline, valine and aspartic acid and showed to result in a significant increase of the yield of the majority of the produced dipeptides. The results of the experiments strongly confirm previous theories on the catalytic mechanism and show the ability of the SIPF Reaction to produce a very diverse set of peptide products with relevance to the formation of a biosphere.},
  doi       = {10.1023/A:1016523207700},
  file      = {2002_Plankensteiner_225.pdf:by-author/P/Plankensteiner/2002_Plankensteiner_225.pdf:PDF},
  keywords  = {Chemical Prebiotic; Evolution},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{PlasmidFactory2006,
  author    = {PlasmidFactory},
  title     = {On-Stock Service for reporter gene vectors},
  year      = {2006},
  file      = {:by-author/P/PlasmidFactory/2006_PlasmidFactory.pdf:PDF},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Plesken1984,
  author    = {W. Plesken and W. Hanrath},
  journal   = {Mathematics of computation},
  title     = {The lattices of six-dimensional Euclidean space},
  year      = {1984},
  pages     = {573--587},
  volume    = {43},
  abstract  = {The lattices of full rank of the six-dimensional Euclidean space are classified according to their automorphism groups (Bravais classification). We find 826 types of such lattices.},
  doi       = {10.1090/S0025-5718-1984-0758205-5},
  file      = {:by-author/P/Plesken/1984_Plesken_573.pdf:PDF},
  keywords  = {Algebra; Bravais Lattices; Group Theory; Integral Matrix Groups; Spacegroups; Symmetry},
  owner     = {saulius},
  timestamp = {2015.10.09},
  creationdate = {2015-10-09T00:00:00},
  url       = {http://www.ams.org/journals/mcom/1984-43-168/S0025-5718-1984-0758205-5/S0025-5718-1984-0758205-5.pdf},
}

@Article{Plesken1998,
  author    = {Plesken, W. and Opgenorth, J. and Schulz, T.},
  journal   = {Journal of Applied Crystallography},
  title     = {{\it CARAT} {--} a package for mathematical crystallography},
  year      = {1998},
  pages     = {827--828},
  volume    = {31},
  doi       = {10.1107/S0021889897019468},
  file      = {1998_Plesken_827.pdf:by-author/P/Plesken/1998_Plesken_827.pdf:PDF},
  keywords  = {Dimension-independent Concepts; Higher-dimensional Space Groups; Point-group Classification; Space-group Classification},
  owner     = {saulius},
  timestamp = {2015.10.10},
  creationdate = {2015-10-10T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0021889897019468},
}

@Article{Plesken2000,
  author           = {Wilhelm Plesken and Tilman Schulz},
  journal          = {Experimental Mathematics},
  title            = {Counting crystallographic groups in low dimensions},
  year             = {2000},
  pages            = {407--411},
  volume           = {9},
  abstract         = {We present the results of our computations concerning the space groups of dimension 5 and 6. We find 222 018 and 28927922 isomorph ism types of these groups, respectively. Some overall statistics on the number of Q-classes and Z-classes in dimensions up to six are provided. The computations were done with the package CARAT, which can parametrize, construct and identify all crystallographic groups up to dimension 6.},
  creationdate     = {2015-10-09T00:00:00},
  doi              = {10.1080/10586458.2000.10504417},
  eprint           = {http://dx.doi.org/10.1080/10586458.2000.10504417},
  file             = {:by-author/P/Plesken/2000_Plesken_407.pdf:PDF},
  keywords         = {Algebra; Bravais Lattices; Group Theory; Integral Matrix Groups; Spacegroups; Symmetry},
  modificationdate = {2024-10-30T15:08:12},
  owner            = {saulius},
  timestamp        = {2015.10.09},
  url              = {http://dx.doi.org/10.1080/10586458.2000.10504417},
}

@Article{Plymen1974,
  author    = {R. J. Plymen and R. M. G. Young},
  title     = {One the Spin Algebra of a Real Hilbert Space},
  year      = {1974},
  pages     = {286},
  file      = {:by-author/P/Plymen/1974_Plymen_286.pdf:PDF},
  keywords  = {Mathematics; Spin; Spinors},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Pocker2000,
  author    = {Pocker, Y},
  journal   = {Cellular and molecular life sciences : CMLS},
  title     = {Water in enzyme reactions: biophysical aspects of hydration-dehydration processes.},
  year      = {2000},
  pages     = {1008--17},
  volume    = {57},
  abstract  = {Water has been recognized as one of the major structuring factors in biological macromolecules. Indeed, water clusters influence many aspects of biological function, and the water-protein interaction has long been recognized as a major determinant of chain folding, conformational stability, internal dynamics, binding specificity and catalysis. I discuss here several themes arising from recent progress in understanding structural aspects of 'direct' and 'indirect' ligands in terms of enzyme-substrate interactions, and the role of water bridges in enzyme catalysis. The review also attempts to illuminate issues relating to efficiency, through solvent interactions associated with enzymic specificity, and versatility. Over the years, carbonic anhydrase (CA; carbonate hydrolyase, EC 4.2.1.1) has played a significant role in the continuing delineation of principles underlying the role of water in enzyme reactions. As a result of its pronounced catalytic power and robust constitution CA was transformed into a veritable 'laboratory' in which active site mechanisms were rigorously tested and explored.},
  file      = {2000_Pocker_1008.pdf:by-author/P/Pocker/2000_Pocker_1008.pdf:PDF},
  groups    = {sg/reviews, sg/modelling},
  keywords  = {Carbonic Anhydrases},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Pocock1997,
  author    = {Stuart J. Pocock},
  journal   = {Biometrika},
  title     = {Group sequential methods in the design and analysis of clinical trials},
  year      = {1997},
  pages     = {191--199},
  volume    = {64},
  abstract  = {In clinical trials with sequential patient entry, fixed sample size designs are unjustified on ethical grounds and sequential designs are often impracticable. One solution is a group sequential design dividing patient entry into a number of equal-sized groups so that the decision to stop the trial or continue is based on repeated significance tests of the accumulated data after each group is evaluated. Exact results are obtained for a trial with two treatments and a normal response with known variance. The design problem of determining the required size and number of groups is also considered. Simulation shows that these normal results may be adapted to other types of response data. An example shows that group sequential designs can sometimes be statistically superior to standard sequential designs.},
  file      = {1997_Pocock_191.pdf:by-author/P/Pocock/1997_Pocock_191.pdf:PDF},
  keywords  = {Clinical Trials; Experiment Planning; Group Sequential Planning; Repeated Significance Test; Statistics},
  owner     = {saulius},
  timestamp = {2012.11.20},
  creationdate = {2012-11-20T00:00:00},
}

@Manuscript{Podgornik2008,
  author    = {Rudolf Podgornik},
  title     = {Anton Peterlin and DNA},
  year      = {2008},
  abstract  = {I will present an overview of Peterlin’s work on the determination of DNA persistence length by analysing the Bunce - Doty light scattering experiments in terms of the Kratky - Porod wormlike chain model. I will describe the theory he used, the general ramifications of the experimental method and the unavoidable limitations of his result, as well as their impact on the development of DNA science.},
  file      = {:by-author/P/Podgornik/2008_Podgornik.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.09.18},
  creationdate = {2012-09-18T00:00:00},
}

@Article{Ponder2003,
  author    = {Jay W. Ponder and David A. Case},
  journal   = {Advances in Protein Chemistry},
  title     = {Force Fields for Protein Simulations},
  year      = {2003},
  pages     = {27--85},
  file      = {:by-author/P/Ponder/2003_Ponder_27.pdf:PDF},
  keywords  = {Forcefields},
  owner     = {andrius},
  timestamp = {2012.05.07},
  creationdate = {2012-05-07T00:00:00},
}

@Article{Poon2007,
  author    = {Poon, Billy K and Chen, Xiaorui and Lu, Mingyang and Vyas, Nand K and Quiocho, Florante A and Wang, Qinghua and Ma, Jianpeng},
  journal   = {Proceedings of the National Academy of Sciences of the United States of America},
  title     = {Normal mode refinement of anisotropic thermal parameters for a supramolecular complex at 3.42-A crystallographic resolution.},
  year      = {2007},
  pages     = {7869--74},
  volume    = {104},
  abstract  = {Here we report a normal-mode-based protocol for modeling anisotropic thermal motions of proteins in x-ray crystallographic refinement. The foundation for this protocol is a recently developed elastic normal mode analysis that produces much more accurate eigenvectors without the tip effect. The effectiveness of the procedure is demonstrated on the refinement of a 3.42-A structure of formiminotransferase cyclodeaminase, a 0.5-MDa homooctameric enzyme. Using an order of magnitude fewer adjustable thermal parameters than the conventional isotropic refinement, this protocol resulted in a decrease of the values of R(cryst) and R(free) and improvements of the density map. Several poorly resolved regions in the original isotropically refined structure became clearer so that missing side chains were fitted easily and mistraced backbone was corrected. Moreover, the distribution of anisotropic thermal ellipsoids revealed functionally important structure flexibility. This normal-mode-based refinement is an effective way of describing anisotropic thermal motions in x-ray structures and is particularly attractive for the refinement of very large and flexible supramolecular complexes at moderate resolutions.},
  file      = {2007_Poon_7869.pdf:by-author/P/Poon/2007_Poon_7869.pdf:PDF},
  keywords  = {Normal Mode Refinement; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Poon2010,
  author    = {Poon, Billy K. and Grosse-Kunstleve, Ralf W. and Zwart, Peter H. and Sauter, Nicholas K.},
  journal   = {Acta Crystallographica Section D},
  title     = {Detection and correction of underassigned rotational symmetry prior to structure deposition},
  year      = {2010},
  pages     = {503--513},
  volume    = {66},
  doi       = {10.1107/S0907444910001502},
  file      = {:by-author/P/Poon/2010_Poon_503.pdf:PDF},
  keywords  = {Correction; LABELIT; Underassigned Rotational Symmetry; Validation},
  owner     = {antanas},
  timestamp = {2014.07.04},
  creationdate = {2014-07-04T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444910001502},
}

@Article{Pophale2013,
  author    = {Pophale, Ramdas and Daeyaert, Frits and Deem, Michael W.},
  journal   = {J. Mater. Chem. A},
  title     = {Computational Prediction of Chemically-Synthesizable Organic Structure Directing Agents for Zeolites},
  year      = {2013},
  abstract  = {We describe a computational procedure to predict chemically synthesizable organic structure directing agents for zeolites. To identify these structure-directing agents{,} we apply transformations from organic chemistry to a library of available reagents. The compounds are scored based upon stability under synthesis conditions{,} rigidity{,} volume{,} geometric compatibility{,} and energy of interaction with the target zeolite. We illustrate the method on the three zeolites AEI{,} ITE{,} and STF.},
  doi       = {10.1039/C3TA10626H},
  file      = {2013_Pophale.pdf:by-author/P/Pophale/2013_Pophale.pdf:PDF},
  keywords  = {Algorithms; Structure Predicion; Zeolites},
  owner     = {saulius},
  publisher = {The Royal Society of Chemistry},
  timestamp = {2013.04.27},
  creationdate = {2013-04-27T00:00:00},
  url       = {http://dx.doi.org/10.1039/C3TA10626H},
}

@Manual{Popov2007,
  title        = {BEST: Determination of optimal X-ray data collection strategy for protein crystals. User's manual for Version 3.1},
  address      = {c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany},
  author       = {Alexander N. Popov and Gleb P. Bourenkov},
  month        = {jan},
  organization = {EMBL Hamburg Outstation},
  year         = {2007},
  file         = {2007_Popov_manual.odt:by-author/P/Popov/2007_Popov_manual.odt:OpenDocument text;2007_Popov_manual.pdf:by-author/P/Popov/2007_Popov_manual.pdf:PDF},
  keywords     = {BEST; Data Collection; Software; Strategy; X-ray Crystallography},
  owner        = {saulius},
  timestamp = {2016.12.21},
  creationdate = {2016-12-21T00:00:00},
  url          = {http://www.embl-hamburg.de/BEST/best3.1_manual.html},
}

@Article{Popov2003,
  author    = {Popov, Alexander N. and Bourenkov, Gleb P.},
  journal   = {Acta Crystallographica Section D},
  title     = {Choice of data-collection parameters based on statistic modelling},
  year      = {2003},
  pages     = {1145--1153},
  volume    = {59},
  doi       = {10.1107/S0907444903008163},
  file      = {dz0006.pdf:by-author/P/Popov/2003_Popov_1145.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444903008163},
}

@Manuscript{Popov2003a,
  author    = {Nikolaj Popov},
  title     = {Verification Using Weakest Precondition Strategy},
  year      = {2003},
  keywords  = {Computer Science (CS); Correctness Proofs},
  url       = {http://www.sfb013.uni-linz.ac.at/reports/2003/pdf-files/sfb03-33.pdf},
  abstract  = {We describe the weakest precondition strategy for verifying programs. This is a method which takes a specification and an annotated program and generates so|called verification conditions: mathematical lemmata which have to be proved in order to obtain a formal correctness proof for the program with respect to its specification. There are rules for generating the intermediate pre| and post| conditions algorithmically. Based on these rules, we have developed a package for generating verification conditions.},
  comment   = {http://www.risc.jku.at/publications/download/risc_2052/popov_abstr.pdf
Review:
Verification Using Weakest Precondition Strategy Extended Abstract Nikolaj Popov* Research Institute for Symbolic Computation, 4232 Hagenberg, Austria popov@risc.uni−linz.ac.at Abstract. We describe the weakest precondition strategy for verifying programs. This is a method which takes a specification and an annotated program and generates so|called verification conditions: mathematical lemmata which have to be proved in order to obtain a formal correctness proof for the program with respect to its specification. There are rules for generating the intermediate pre| and post| conditions algorithmically. Based on these rules, we have developed a package for generating verification conditions. This work is supported by FWF (Austrian National Science Foundation) − SFB project F1302. 1 Weakest Preconditions and Predicate Transformation We have seen [Kovacs03] a verification method using inference rules of Hoare Logic. However, there exists another strategy for program verification using the so|called "weakest precondition predicate transformer" (wp) developed by E. W. Dijkstra [Dijkstra76]. This approach is also based on Hoare Logic. Let us assume we want to verify a program where we know the postcondition but not the precondition: {?}S{R} In general, there could be arbitrarily many preconditions Q which are valid for the program S and a postcondition R. However, there is precisely one precondition describ- ing the maximal set of possible initial states such that the execution of S leads to a state satisfying R. This Q is called the weakest precondition. (A condition Q is weaker than P iff P Þ Q .)},
  file      = {:by-author/P/Popov/2003_Popov.pdf:PDF},
  owner     = {saulius},
  timestamp = {2013.08.10},
  creationdate = {2013-08-10T00:00:00},
}

@Article{Portnoy2011,
  author    = {Victoria Portnoy and Vera Huang and Robert F. Place and Long-Cheng Li},
  journal   = {Wiley Interdisciplinary Reviews: RNA},
  title     = {Small RNA and transcriptional upregulation},
  year      = {2011},
  pages     = {748--760},
  volume    = {2},
  doi       = {10.1002/wrna.90},
  file      = {2011_Portnoy_748.pdf:by-author/P/Portnoy/2011_Portnoy_748.pdf:PDF},
  groups    = {am/RNA activation},
  issne     = {1757-7012},
  issnp     = {1757-7004},
  issue     = {5},
  owner     = {andrius},
  timestamp = {2016.09.16},
  creationdate = {2016-09-16T00:00:00},
}

@Article{Portnoy2016,
  author    = {Portnoy, Victoria and Lin, Szu Hua Sharon and Li, Kathy H and Burlingame, Alma and Hu, Zheng-Hui and Li, Hao and Li, Long-Cheng},
  journal   = {Cell Research},
  title     = {{saRNA}-guided {Ago2} targets the {RITA} complex to promoters to stimulate transcription},
  year      = {2016},
  issn      = {1748-7838},
  month     = {Feb},
  number    = {3},
  pages     = {320–335},
  volume    = {26},
  doi       = {10.1038/cr.2016.22},
  file      = {:by-author/P/Portnoy/2016_Portnoy_320.pdf:PDF},
  groups    = {am/RNA activation},
  owner     = {andrius},
  publisher = {Nature Publishing Group},
  timestamp = {2016.08.24},
  creationdate = {2016-08-24T00:00:00},
  url       = {http://dx.doi.org/10.1038/cr.2016.22},
}

@PhdThesis{Posada2015,
  author    = {Andrés Orlando Garzón Posada},
  school    = {Universidad Nacional de Colombia},
  title     = {Síntesis y caracterización de un material compuesto a base de polietileno de alta densidad y magnetita pulverizada},
  year      = {2015},
  file      = {[PDF] from unal.edu.co:by-author/P/Posada/2015_Posada.pdf:application/pdf;Snapshot:by-author/P/Posada/2015_Posada.html:text/html},
  groups    = {sg/JAC2009},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://www.bdigital.unal.edu.co/48467/},
  urldate   = {2015-08-31},
}

@Presentation{Poschl2003,
  author    = {Ulrich Pöschl},
  title     = {Interactive Journal Concept for future Scientific Quality Assurance},
  year      = {2003},
  school    = {Technical University of Munich, Institute of Hydrochemistry},
  file      = {:by-author/P/Pöschl/2003_Pöschl_slides.pdf:PDF},
  keywords  = {Publication Quality; Scientific Publications},
  owner     = {saulius},
  pages     = {slides},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Potterton2003,
  author    = {Potterton, Elizabeth and Briggs, Peter and Turkenburg, Maria and Dodson, Eleanor},
  journal   = {Acta Crystallographica Section D},
  title     = {A graphical user interface to the {\it CCP}4 program suite},
  year      = {2003},
  pages     = {1131--1137},
  volume    = {59},
  doi       = {10.1107/S0907444903008126},
  file      = {hv0002.pdf:by-author/P/Potterton/2003_Potterton_1131.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444903008126},
}

@Article{Potterton2004,
  author    = {Potterton, Liz and McNicholas, Stuart and Krissinel, Eugene and Gruber, Jan and Cowtan, Kevin and Emsley, Paul and Murshudov, Garib N. and Cohen, Serge and Perrakis, Anastassis and Noble, Martin},
  journal   = {Acta Crystallographica Section D},
  title     = {Developments in the {\it CCP}4 molecular-graphics project},
  year      = {2004},
  pages     = {2288--2294},
  volume    = {60},
  doi       = {10.1107/S0907444904023716},
  file      = {ba5074.pdf:by-author/P/Potterton/2004_Potterton_2288.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444904023716},
}

@Article{Powell1964,
  author    = {M. J. D. Powell},
  journal   = {The Computer Journal},
  title     = {An Efficient Method for Finding The Minimum of A Function of Several Variables Without Calculating Derivatives},
  year      = {1964},
  pages     = {155--162},
  volume    = {7},
  abstract  = {A simple variation of the well-known method of minimizing a function of several variables by changing one parameter at a time is described. This variation is such that when the procedure is applied to a quadratic form, it causes conjugate directions to be chosen, so the ultimate rate of convergence is fast when the method is used to minimize a general function. A further variation completes the method, and its ensures that the convergence rate from a bad approximation to a minimum is always efficient. Practical applications of the procedure have proved to be very satisfactory, and numerical examples are given in which functions of up to twenty variables are minimized.},
  file      = {:by-author/P/Powell/1964_Powell_155.pdf:PDF},
  owner     = {andrius},
  timestamp = {2012.11.28},
  creationdate = {2012-11-28T00:00:00},
}

@Article{Powers1999,
  author    = {Powers, L. and Griep, M. A.},
  journal   = {Biochemistry},
  title     = {Escherichia coli primase zinc is sensitive to substrate and cofactor binding.},
  year      = {1999},
  pages     = {7413--20},
  volume    = {38},
  abstract  = {The ligation state of the single zinc site in primase from Escherichia coli changes when various substrates and cofactors are added alone or in combination as determined by X-ray absorption spectroscopy. X-ray absorption spectroscopy (XAS) provides information about the local structure (approximately 5 A) of atoms surrounding the metal and has been widely used to characterize metalloproteins. The zinc site in native primase and in primase bound to low (30 mM) magnesium acetate was found to be tetrahedrally ligated by three sulfurs at an average distance of 2.36 +/- 0.02 A and one histidine nitrogen located at a distance of 2.15 +/- 0.03 A. When ATP, ATP and (dT)17, or ATP, low magnesium acetate and (dT)17 was added to primase, one (or two) additional nitrogen/oxygen ligands were coordinated to the zinc together with the histidine nitrogen at an average distance of 2.15 +/- 0.03 A. These additional ligands are likely from adjacent phosphates from ATP. Another structure was observed for the primase-(dT)17 complex in which an additional nitrogen/oxygen ligand likely from the phosphate backbone together with the histidine nitrogen was located at a significantly shorter average distance of 2.05 +/- 0.03 A. High magnesium acetate (300 mM) completely inactivates primase in a reversible manner such that the region near the zinc ligands becomes accessible to proteolytic digestion [Urlacher, T. M., and Griep, M. A. (1995) Biochemistry 34, 16708-16714]. In this inactive complex, additional oxygen/nitrogen ligands from acetate as well as the histidine nitrogen are located at a distance of 2.20 +/- 0.03 A from the zinc site. To test whether the catalytic magnesium was binding within approximately 5 A of the zinc, we incubated primase with high (300 mM) manganese acetate. The functional properties of magnesium and manganese are similar, but the larger atomic number of manganese enhances the X-ray backscattering, making it possible to identify. Since no significant difference was observed from the manganese-incubated sample, the catalytic metal-binding site is likely located &gt;5 A from the zinc. These studies clearly show that primase zinc ligation changes upon binding substrates.},
  file      = {:by-author/P/Powers/1999_Powers_7413.pdf:PDF},
  keywords  = {Ecoli; {gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Prabhu2005,
  author    = {Prabhu, Ninad V. and Sharp, Kim A.},
  journal   = {Annual review of physical chemistry},
  title     = {Heat capacity in proteins.},
  year      = {2005},
  pages     = {521--48},
  volume    = {56},
  abstract  = {Heat capacity (Cp) is one of several major thermodynamic quantities commonly measured in proteins. With more than half a dozen definitions, it is the hardest of these quantities to understand in physical terms, but the richest in insight. There are many ramifications of observed Cp changes: The sign distinguishes apolar from polar solvation. It imparts a temperature (T) dependence to entropy and enthalpy that may change their signs and which of them dominate. Protein unfolding usually has a positive deltaCp, producing a maximum in stability and sometimes cold denaturation. There are two heat capacity contributions, from hydration and protein-protein interactions; which dominates in folding and binding is an open question. Theoretical work to date has dealt mostly with the hydration term and can account, at least semiquantitatively, for the major Cp-related features: the positive and negative Cp of hydration for apolar and polar groups, respectively; the convergence of apolar group hydration entropy at T approximately 112 degrees C; the decrease in apolar hydration Cp with increasing T; and the T-maximum in protein stability and cold denaturation.},
  file      = {:by-author/P/Prabhu/2005_Prabhu_521.pdf:PDF},
  keywords  = {Heat Capacity; Protein Physics},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Pravarthana2013,
  author     = {Pravarthana, Dhanapal and Chateigner, D. and Lutterotti, L. and Lacotte, M. and Marinel, S. and Dubos, P. A. and Hervas, I. and Hug, E. and Salvador, Paul A. and Prellier, W.},
  journal    = {Journal of Applied Physics},
  title      = {Growth and texture of spark plasma sintered {Al}2O3 ceramics: {A} combined analysis of {X}-rays and electron back scatter diffraction},
  year       = {2013},
  pages      = {153510},
  volume     = {113},
  file       = {[PDF] from arxiv.org:by-author/P/Pravarthana/2013_Pravarthana_153510.pdf:application/pdf;Snapshot:by-author/P/Pravarthana/2013_Pravarthana_153510.html:text/html},
  groups     = {sg/JAC2009},
  owner      = {saulius},
  shorttitle = {Growth and texture of spark plasma sintered {Al}2O3 ceramics},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url        = {http://scitation.aip.org/content/aip/journal/jap/113/15/10.1063/1.4802439},
  urldate    = {2015-08-31},
}

@TechReport{Prechelt2000,
  author      = {Prechelt, Lutz},
  institution = {Fakultät für Informatik, Universität Karlsruhe, D-76128 Karlsruhe, Germany, +49/721/608-4068, Fax: +49/721/608-7343, http://wwwipd.ira.uka.de/EIR/},
  title       = {An empirical comparison of C, C++, Java, Perl, Python, Rexx, and Tcl for a search/string-processing program},
  year        = {2000},
  month       = {March},
  abstract    = {80 implementations of the same set of requirements, created by 74 different programmers in vari- ous languages, are compared for several properties, such as run time, memory consumption, source text length, comment density, program structure, reliability, and the amount of effort required for writing them. The results indicate that, for the given programming problem, “scripting languages” (Perl, Python, Rexx, Tcl) are more productive than conventional languages. In terms of run time and memory consumption, they often turn out better than Java and not much worse than C or C++. In general, the differences between languages tend to be smaller than the typical differences due to different programmers within the same language.},
  file        = {:by-author/P/Prechelt/2000_Prechelt.pdf:PDF},
  groups      = {sg/C++},
  keywords    = {Computer Language Comparison; Computer Science (CS)},
  owner       = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Premkumar2005,
  author    = {Premkumar, Lakshmanane and Greenblatt, Harry M and Bageshwar, Umesh K and Savchenko, Tatyana and Gokhman, Irena and Sussman, Joel L and Zamir, Ada},
  journal   = {Proceedings of the National Academy of Sciences of the United States of America},
  title     = {Three-dimensional structure of a halotolerant algal carbonic anhydrase predicts halotolerance of a mammalian homolog.},
  year      = {2005},
  pages     = {7493--8},
  volume    = {102},
  abstract  = {Protein molecular adaptation to drastically shifting salinities was studied in dCA II, an alpha-type carbonic anhydrase (EC 4.2.1.1) from the exceptionally salt-tolerant unicellular green alga Dunaliella salina. The salt-inducible, extracellular dCA II is highly salt-tolerant and thus differs from its mesophilic homologs. The crystal structure of dCA II, determined at 1.86-A resolution, is globally similar to other alpha-type carbonic anhydrases except for two extended alpha-helices and an added Na-binding loop. Its unusual electrostatic properties include a uniformly negative surface electrostatic potential of lower magnitude than that observed in the highly acidic halophilic proteins and an exceptionally low positive potential at a site adjoining the catalytic Zn(2+) compared with mesophilic homologs. The halotolerant dCA II also differs from typical halophilic proteins in retaining conformational stability and solubility in low to high salt concentrations. The crucial role of electrostatic features in dCA II halotolerance is strongly supported by the ability to predict the unanticipated halotolerance of the murine CA XIV isozyme, which was confirmed biochemically. A proposal for the functional significance of the halotolerance of CA XIV in the kidney is presented.},
  file      = {2005_Premkumar_7493.pdf:by-author/P/Premkumar/2005_Premkumar_7493.pdf:PDF},
  groups    = {sg/algal},
  keywords  = {CA14; Carbonic Anhydrases},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Prescher2005,
  author    = {Prescher, Jennifer A. and Bertozzi, Carolyn R.},
  journal   = {Nature chemical biology},
  title     = {Chemistry in living systems.},
  year      = {2005},
  pages     = {13--21},
  volume    = {1},
  abstract  = {Dissecting complex cellular processes requires the ability to track biomolecules as they function within their native habitat. Although genetically encoded tags such as GFP are widely used to monitor discrete proteins, they can cause significant perturbations to a protein's structure and have no direct extension to other classes of biomolecules such as glycans, lipids, nucleic acids and secondary metabolites. In recent years, an alternative tool for tagging biomolecules has emerged from the chemical biology community--the bioorthogonal chemical reporter. In a prototypical experiment, a unique chemical motif, often as small as a single functional group, is incorporated into the target biomolecule using the cell's own biosynthetic machinery. The chemical reporter is then covalently modified in a highly selective fashion with an exogenously delivered probe. This review highlights the development of bioorthogonal chemical reporters and reactions and their application in living systems.},
  file      = {:by-author/P/Prescher/2005_Prescher_13.pdf:PDF},
  keywords  = {Bioconjugation},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@Manuscript{Previtali2001,
  author    = {Luca Previtali and Brenno Lrati and Erik Wilde},
  title     = {BibTeXML: an XML representation of BibTeX},
  year      = {2001},
  keywords  = {BibTeX; Bibliography; Converters; Markup; XML},
  url       = {http://wwwconference.org/www10/cdrom/posters/1090.pdf},
  file      = {2001_Previtali_poster.pdf:by-author/P/Previtali/2001_Previtali_poster.pdf:PDF},
  owner     = {saulius},
  timestamp = {2014.01.26},
  creationdate = {2014-01-26T00:00:00},
}

@Article{Price1989,
  author    = {Price, C. and Lingner, J. and Bickle, T. A. and Firman, K. and Glover, S. W.},
  journal   = {Journal of molecular biology},
  title     = {Basis for changes in DNA recognition by the EcoR124 and EcoR124/3 type I DNA restriction and modification enzymes.},
  year      = {1989},
  pages     = {115--25},
  volume    = {205},
  abstract  = {EcoR124 and EcoR124/3 are type I DNA restriction and modification systems. The EcoR124/3 system arose from the EcoR124 system some 15 years ago and at the electron microscopic DNA heteroduplex level the genes for both systems are still apparently identical. We have shown that the DNA sequences recognized by the two systems are GAA(N6)RTCG for EcoR124 and GAA(N7)RTCG for EcoR124/3. The sequences thus differ only in the length of the non-specific spacer. This difference nevertheless places the two specific domains of the EcoR124/3 recognition sequence 0.34 nm further apart and rotates them 36 degrees with respect to those of EcoR124, which implies major structural differences in the proteins recognizing these sequences. We have now determined the nucleotide sequences of the hsdS and hsdM genes of both systems and of the hsdR gene of EcoR124/3. The hsdS gene products provide DNA sequence specificity in both restriction and modification, the hsdM gene products are necessary for modification and all three hsd gene products are required for restriction. The only difference that we have detected between the two systems is that a 12 base-pair sequence towards the middle of the hsdS gene is repeated twice in the EcoR124 gene and three times in the EcoR124/3 gene. We have deleted one of the repeats in the EcoR124/3 gene and shown that this changes the specificity to that of EcoR124. Thus, the extra four amino acids in the middle of the EcoR124/3 hsdS gene product, which in an alpha-helical configuration would extend 0.6 nm, are sufficient to explain the differences in sequence recognition. We suggest that the EcoR124/3 system was generated by an unequal crossing over and argue that this kind of specificity change should not be rare in Nature.},
  file      = {:by-author/P/Price/1989_Price_115.pdf:PDF},
  keywords  = {TypeI},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Prichard2013,
  author    = {Prichard, Craig},
  journal   = {Organization},
  title     = {All the lonely papers, where do they all belong?},
  year      = {2013},
  pages     = {143--150},
  volume    = {20},
  abstract  = {Organization has published 569 papers in its 20 years. Of these 44% have been cited less than four times, and just on 9%, or 48 papers, have never been cited at all—not even by their own authors. What might we make of these lonely and seemingly neglected papers? Are they the Eleanor Rigbys and the Father McKenzies of the academic world? As a contribution to the Journal’s 20th Anniversary issue this paper offers a discussion of Organization’s uncited 48.},
  doi       = {10.1177/1350508412461145},
  eprint    = {http://org.sagepub.com/content/20/1/143.full.pdf+html},
  file      = {2013_Prichard_143.pdf:by-author/P/Prichard/2013_Prichard_143.pdf:PDF},
  keywords  = {Academic Publishing; Citation Databases; Google Scholar; Referencing; Thomson Reuters Web of Science; Uncitation},
  owner     = {saulius},
  timestamp = {2013.04.03},
  creationdate = {2013-04-03T00:00:00},
  url       = {http://org.sagepub.com/content/20/1/143.abstract},
}

@Article{Priem2013,
  author    = {Priem, Jason},
  journal   = {Nature},
  title     = {Scholarship: Beyond the paper},
  year      = {2013},
  issn      = {0028-0836},
  pages     = {437--440},
  volume    = {495},
  abstract  = {The journal and article are being superseded by algorithms that filter, rate and disseminate scholarship as it happens},
  doi       = {10.1038/495437a},
  file      = {2013_Priem_437.pdf:by-author/P/Priem/2013_Priem_437.pdf:PDF},
  keywords  = {Data Access Policy; Data Management; Scientific Publication},
  owner     = {saulius},
  publisher = {Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},
  timestamp = {2013.04.03},
  creationdate = {2013-04-03T00:00:00},
  url       = {http://dx.doi.org/10.1038/495437a},
}

@Article{Pringle2010,
  author    = {Pringle, Heather},
  journal   = {Science (New York, N.Y.)},
  title     = {Space science. NASA dives into its past to retrieve vintage satellite data.},
  year      = {2010},
  pages     = {1322--3},
  volume    = {327},
  abstract  = {Last month, researchers working out of an abandoned McDonald's restaurant on the grounds of NASA Ames Research Center recovered data collected by NASA's Nimbus II satellite on 23 September 1966. The satellite soared over Earth in a polar orbit every 108 minutes, taking pictures of cloud cover and measuring heat radiated from the planet's surface, and creating a photo mosaic of the globe 43 years ago. The resulting image is the oldest and most detailed from NASA's Earth-observing satellites. It's also the latest success story in what researchers call techno-archaeology: pulling data from archaic storage systems. Once forgotten and largely unreadable with modern equipment, old data tapes are providing researchers with new information on changes in the surfaces of Earth and the moon.},
  doi       = {10.1126/science.327.5971.1322},
  eprint    = {http://www.sciencemag.org/content/327/5971/1322.full.pdf},
  file      = {2010_Pringle_1322.pdf:by-author/P/Pringle/2010_Pringle_1322.pdf:PDF},
  keywords  = {Data Processing},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://www.sciencemag.org/content/327/5971/1322.short},
}

@TechReport{Printezis2000,
  author      = {Printezis, Tony and David Detlefs},
  institution = {Sun Microsystems},
  title       = {A Generational Mostly-concurrent Garbage Collector},
  year        = {2000},
  abstract    = {This paper reports our experiences with a mostly-concurrent incremental garbage collector, implemented in the context of a high performance virtual machine for the JavaTM programming language. The garbage collector is based on the “mostly parallel” collection algorithm of Boehm et al., and can be used as the old generation of a generational memory system. It overloads effi- cient write-barrier code already generated to support generational garbage collection to also identify objects that were modified during concurrent marking. These objects must be rescanned to ensure that the concurrent marking phase marks all live objects. This algorithm minimises maximum garbage collection pause times, while having only a small impact on the average gar- bage collection pause time and overall execution time. We support our claims with experimental results, for both a synthetic benchmark and real programs.},
  file        = {:by-author/P/Printezis/2000_Printezis_techreport.pdf:PDF},
  groups      = {sg/Garbage collectors},
  keywords    = {Computer Science (CS); Garbage Collectors},
  owner       = {saulius},
  pages       = {techreport},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Manuscript{Printezis2000a,
  author    = {Printezis, Tony and David Detlefs},
  title     = {A Generational Mostly-concurrent Garbage Collector},
  year      = {2000},
  keywords  = {Computer Science (CS); Garbage Collectors},
  abstract  = {This paper reports our experiences with a mostly-concurrent incremental garbage collector, implemented in the context of a high performance virtual machine for the JavaTM programming language. The garbage collector is based on the “mostly parallel” collection algorithm of Boehm et al. and can be used as the old generation of a generational memory system. It overloads efficient write-barrier code already generated to support generational garbage collection to also identify objects that were modified during concurrent marking. These objects must be rescanned to ensure that the concurrent marking phase marks all live objects. This algorithm minimises maximum garbage collection pause times, while having only a small impact on the average garbage collection pause time and overall execution time. We support our claims with experimental results, for both a synthetic benchmark and real programs.},
  file      = {:by-author/P/Printezis/2000_Printezis.pdf:PDF},
  groups    = {sg/Garbage collectors},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@InProceedings{Pritchard1994,
  author    = {Paul Pritchard},
  booktitle = {Cornell University},
  title     = {Improved Incremental Prime Number Sieves},
  year      = {1994},
  pages     = {280--288},
  publisher = {Springer-Verlag},
  file      = {1994_Pritchard.pdf:by-author/P/Pritchard/1994_Pritchard.pdf:PDF},
  groups    = {sg/Prime Number Sieves, sg/Prime Numbers, sg/Bioinf. Algorithms},
  keywords  = {Algorithm; Prime Numbers; Sieve of Eratosthenes; Wheel Factorization},
  owner     = {saulius},
  timestamp = {2016.09.18},
  creationdate = {2016-09-18T00:00:00},
  url       = {http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.52.835},
}

@Article{Prive1987,
  author    = {Privé, G. G. and Heinemann, U. and Chandrasegaran, S. and Kan, L. S. and Kopka, M. L. and Dickerson, R. E.},
  journal   = {Science (New York, N.Y.)},
  title     = {Helix geometry, hydration, and G.A mismatch in a B-DNA decamer.},
  year      = {1987},
  pages     = {498--504},
  volume    = {238},
  abstract  = {The DNA double helix is not a regular, featureless barberpole molecule. Different base sequences have their own special signature, in the way that they influence groove width, helical twist, bending, and mechanical rigidity or resistance to bending. These special features probably help other molecules such as repressors to read and recognize one base sequence in preference to another. Single crystal x-ray structure analysis is beginning to show us the various structures possible in the B-DNA family. The DNA decamer C-C-A-A-G-A-T-T-G-G appears to be a better model for mixed-sequence B-DNA than was the earlier C-G-C-G-A-A-T-T-C-G-C-G, which is more akin to regions of poly(dA).poly(dT). The G.A mismatch base pairs at the center of the decamer are in the anti-anti conformation about their bonds from base to sugar, in agreement with nuclear magnetic resonance evidence on this and other sequences, and in contrast to the anti-syn geometry reported for G.A pairs in C-G-C-G-A-A-T-T-A-G-C-G. The ordered spine of hydration seen earlier in the narrow-grooved dodecamer has its counterpart, in this wide-grooved decamer, in two strings of water molecules lining the walls of the minor groove, bridging from purine N3 or pyrimidine O2, to the following sugar O4'. The same strings of hydration are present in the phosphorothioate analog of G-C-G-C-G-C. Unlike the spine, which is broken up by the intrusion of amine groups at guanines, these water strings are found in general, mixed-sequence DNA because they can pass by unimpeded to either side of a guanine N2 amine. The spine and strings are perceived as two extremes of a general pattern of hydration of the minor groove, which probably is the dominant factor in making B-DNA the preferred form at high hydration.},
  file      = {:by-author/P/Privé/1987_Prive_498.pdf:PDF},
  keywords  = {Conformation; Readout},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Webpage{Proffitt2008,
  author    = {Jacob Proffitt},
  retrieved = {2009-02-07},
  title     = {TDD Proven Effective! Or is it?},
  url       = {http://theruntime.com/blogs/jacob/archive/2008/01/22/tdd-proven-effective-or-is-it.aspx},
  month     = {January},
  year      = {2008},
  file      = {:by-author/P/Proffitt/2008_Proffitt.war:},
  keywords  = {Computer Science (CS); Test Driven Development},
  owner     = {saulius},
  timestamp = {2015.03.02},
  creationdate = {2015-03-02T00:00:00},
}

@Article{Prokofjev1962,
  author    = {Prokof'ev, Yu. A. and Spivak, P. E.},
  journal   = {The Soviet Journal of Atomic Energy},
  title     = {The half-life of the neutron},
  year      = {1962},
  issn      = {1573-8205},
  number    = {4},
  pages     = {294--294},
  volume    = {12},
  doi       = {10.1007/BF01683239},
  file      = {1962_Prokofjev_294.pdf:by-author/P/1962_Prokofjev_294.pdf:PDF},
  keywords  = {Half-life; Neutron; Nuclear Physics; Nucleon; Physics},
  owner     = {saulius},
  timestamp = {2016.01.18},
  creationdate = {2016-01-18T00:00:00},
  url       = {http://dx.doi.org/10.1007/BF01683239},
}

@Article{Prosseda2010,
  author    = {Prosseda, Gianni and Mazzola, Alessia and Di Martino, Maria Letizia and Tielker, Denis and Micheli, Gioacchino and Colonna, Bianca},
  journal   = {Biochemistry},
  title     = {A temperature-induced narrow DNA curvature range sustains the maximum activity of a bacterial promoter in vitro.},
  year      = {2010},
  pages     = {2778--85},
  volume    = {49},
  abstract  = {Among the molecular strategies bacteria have set up to quickly match their transcriptional program to new environments, changes in sequence-mediated DNA curvature play a crucial role. Bacterial promoters, especially those of mesophilic bacteria, are in general preceded by a curved region. The marked thermosensitivity of curved DNA stretches allows bacteria to rapidly sense outer temperature variations and affects transcription by favoring the binding of activators or repressors. Curved DNA is also able to influence the transcriptional activity of a bacterial promoter directly, without the involvement of trans-acting regulators. This study attempts to quantitatively analyze the role of DNA curvature in thermoregulated gene expression using a real-time in vitro transcription model system based on a specific fluorescence molecular beacon. By analyzing the temperature-dependent expression of a reporter gene in a construct carrying a progressively decreasing bent sequence upstream from the promoter, we show that with a decrease in temperature a narrow curvature range accounts for a significant enhancement of promoter activity. This strengthens the view that DNA curvature-mediated regulation of gene expression is likely a strategy offering fine-tuning control possibilities and that, considering the widespread presence of curved sequences upstream from bacterial promoters, it may represent one of the most primitive forms of gene regulation.},
  file      = {:by-author/P/Prosseda/2010_Prosseda_2778.pdf:PDF},
  keywords  = {Obzor},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Protozanova2002,
  author    = {Protozanova, Ekaterina and Demidov, Vadim V. and Soldatenkov, Viatcheslav and Chasovskikh, Sergey and Frank-Kamenetskii, Maxim D.},
  journal   = {EMBO reports},
  title     = {Tailoring the activity of restriction endonuclease PleI by PNA-induced DNA looping.},
  year      = {2002},
  pages     = {956--61},
  volume    = {3},
  abstract  = {DNA looping is one of the key factors allowing proteins bound to different DNA sites to signal one another via direct contacts. We demonstrate that DNA looping can be generated in an arbitrary chosen site by sequence-directed targeting of double-stranded DNA with pseudocomplementary peptide-nucleic acids (pcPNAs). We designed pcPNAs to mask the DNA from cleavage by type IIs restriction enzyme PleI while not preventing the enzyme from binding to its primary DNA recognition site. Direct interaction between two protein molecules (one bound to the original recognition site and the other to a sequence-degenerated site) results in a totally new activity of PleI: it produces a nick near the degenerate site. The PNA-induced nicking efficiency varies with the distance between the two protein-binding sites in a phase with the DNA helical periodicity. Our findings imply a general approach for the fine-tuning of proteins bound to DNA sites well separated along the DNA chain.},
  file      = {:by-author/P/Protozanova/2002_Protozanova_956.pdf:PDF},
  keywords  = {TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Proveti,
  author    = {Proveti, J. R. C. and Porto, P. S. S. and Muniz, E. P. and Pereira, R. D. and Araujo, D. R. and Silveira, M. B.},
  journal   = {Journal of Sol-Gel Science and Technology},
  title     = {Sol–gel proteic method using orange albedo pectin for obtaining cobalt ferrite particles},
  pages     = {31--37},
  volume    = {75},
  file      = {[PDF] from researchgate.net:by-author/P/Proveti/XXXX_Proveti_31.pdf:application/pdf;Snapshot:by-author/P/Proveti/XXXX_Proveti_31.html:text/html},
  groups    = {sg/JAC2009},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://link.springer.com/article/10.1007/s10971-015-3671-y},
  urldate   = {2015-08-31},
}

@Article{Puccetti2005,
  author    = {Puccetti, Luca and Fasolis, Giuseppe and Vullo, Daniela and Chohan, Zahid H and Scozzafava, Andrea and Supuran, Claudiu T},
  journal   = {Bioorganic \&amp; medicinal chemistry letters},
  title     = {Carbonic anhydrase inhibitors. Inhibition of cytosolic/tumor-associated carbonic anhydrase isozymes I, II, IX, and XII with Schiff's bases incorporating chromone and aromatic sulfonamide moieties, and their zinc complexes.},
  year      = {2005},
  pages     = {3096--101},
  volume    = {15},
  file      = {2005_Puccetti_3096.pdf:by-author/P/Puccetti/2005_Puccetti_3096.pdf:PDF},
  groups    = {sg/inhibitors, sg/hCA1, sg/hCA2, sg/hCA9, sg/hCA12},
  keywords  = {Carbonic Anhydrases},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@PhdThesis{Pulgarin2013,
  author    = {Villegas Pulgarín},
  title     = {Diseno de nuevos materiales duros por métodos ab initio},
  year      = {2013},
  file      = {[PDF] from eafit.edu.co:by-author/P/Pulgarín/2013_Pulgarín.pdf:PDF;Snapshot:by-author/P/Pulgarín/2013_Pulgarín.html:URL},
  groups    = {sg/NAR2012},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://repository.eafit.edu.co/handle/10784/1397},
  urldate   = {2015-08-31},
}

@Article{Punna2005,
  author    = {Punna, Sreenivas and Kuzelka, Jane and Wang, Qian and Finn, M. G.},
  journal   = {Angewandte Chemie (International ed. in English)},
  title     = {Head-to-tail peptide cyclodimerization by copper-catalyzed azide-alkyne cycloaddition.},
  year      = {2005},
  pages     = {2215--20},
  volume    = {44},
  file      = {:by-author/P/Punna/2005_Punna_2215.pdf:PDF},
  keywords  = {Bioconjugation},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@Article{Purdy2002,
  author    = {Purdy, Michael D. and Ge, Pinghua and Chen, Jiyan and Selvin, Paul R. and Wiener, Michael C.},
  journal   = {Acta Crystallographica Section D},
  title     = {Thiol-reactive lanthanide chelates for phasing protein X-ray diffraction data},
  year      = {2002},
  pages     = {1111--1117},
  volume    = {58},
  doi       = {10.1107/S0907444902006509},
  file      = {en0061.pdf:by-author/P/Purdy/2002_Purdy_1111.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444902006509},
}

@Article{Pusey2005,
  author    = {Pusey, Marc L and Liu, Zhi-Jie and Tempel, Wolfram and Praissman, Jeremy and Lin, Dawei and Wang, Bi-Cheng and Gavira, José A and Ng, Joseph D},
  journal   = {Progress in biophysics and molecular biology},
  title     = {Life in the fast lane for protein crystallization and X-ray crystallography.},
  year      = {2005},
  pages     = {359--86},
  volume    = {88},
  abstract  = {The common goal for structural genomic centers and consortiums is to decipher as quickly as possible the three-dimensional structures for a multitude of recombinant proteins derived from known genomic sequences. Since X-ray crystallography is the foremost method to acquire atomic resolution for macromolecules, the limiting step is obtaining protein crystals that can be useful of structure determination. High-throughput methods have been developed in recent years to clone, express, purify, crystallize and determine the three-dimensional structure of a protein gene product rapidly using automated devices, commercialized kits and consolidated protocols. However, the average number of protein structures obtained for most structural genomic groups has been very low compared to the total number of proteins purified. As more entire genomic sequences are obtained for different organisms from the three kingdoms of life, only the proteins that can be crystallized and whose structures can be obtained easily are studied. Consequently, an astonishing number of genomic proteins remain unexamined. In the era of high-throughput processes, traditional methods in molecular biology, protein chemistry and crystallization are eclipsed by automation and pipeline practices. The necessity for high-rate production of protein crystals and structures has prevented the usage of more intellectual strategies and creative approaches in experimental executions. Fundamental principles and personal experiences in protein chemistry and crystallization are minimally exploited only to obtain "low-hanging fruit" protein structures. We review the practical aspects of today's high-throughput manipulations and discuss the challenges in fast pace protein crystallization and tools for crystallography. Structural genomic pipelines can be improved with information gained from low-throughput tactics that may help us reach the higher-bearing fruits. Examples of recent developments in this area are reported from the efforts of the Southeast Collaboratory for Structural Genomics (SECSG).},
  file      = {2005_Pusey_359.pdf:by-author/P/Pusey/2005_Pusey_359.pdf:PDF},
  keywords  = {Crystallisation; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Putnam2007,
  author    = {Putnam, Christopher D. and Hammel, Michal and Hura, Greg L. and Tainer, John A.},
  journal   = {Quarterly Reviews of Biophysics},
  title     = {X-ray solution scattering (SAXS) combined with crystallography and computation: defining accurate macromolecular structures, conformations and assemblies in solution},
  year      = {2007},
  pages     = {191–285},
  volume    = {40},
  abstract  = {Crystallography supplies unparalleled detail on structural information critical for mechanistic analyses ; however, it is restricted to describing low energy conformations of macromolecules within crystal lattices. Small angle X-ray scattering (SAXS) offers complementary information about macromolecular folding, unfolding, aggregation, extended conformations, flexibly linked domains, shape, conformation, and assembly state in solution, albeit at the lower resolution range of about 50 A to 10 A resolution, but without the size limitations inherent in NMR and electron microscopy studies. Together these techniques can allow multi-scale modeling to create complete and accurate images of macromolecules for modeling allosteric mechanisms, supramolecular complexes, and dynamic molecular machines acting in diverse processes ranging from eukaryotic DNA replication, recombination and repair to microbial membrane secretion and assembly systems. This review addresses both theoretical and practical concepts, concerns and considerations for using these techniques in conjunction with computational methods to productively combine solution scattering data with high- resolution structures. Detailed aspects of SAXS experimental results are considered with a focus on data interpretation tools suitable to model protein and nucleic acid macromolecular structures, including membrane protein, RNA, DNA, and protein–nucleic acid complexes. The methods discussed provide the basis to examine molecular interactions in solution and to study macromolecular flexibility and conformational changes that have become increasingly relevant for accurate understanding, simulation, and prediction of mechanisms in structural cell biology and nanotechnology.},
  doi       = {10.1017/S0033583507004635},
  file      = {:by-author/P/Putnam/2007_Putnam_191.pdf:PDF},
  keywords  = {Protein Crystallography; Review; SAXS},
  owner     = {em},
  timestamp = {2014.05.22},
  creationdate = {2014-05-22T00:00:00},
}

@Article{Pyatkov2004,
  author    = {Pyatkov, Konstantin I. and Arkhipova, Irina R. and Malkova, Natalia V. and Finnegan, David J. and Evgen'ev, Michael B.},
  journal   = {Proceedings of the National Academy of Sciences of the United States of America},
  title     = {Reverse transcriptase and endonuclease activities encoded by Penelope-like retroelements.},
  year      = {2004},
  pages     = {14719--24},
  volume    = {101},
  abstract  = {Penelope-like elements are a class of retroelement that have now been identified in &gt;50 species belonging to at least 10 animal phyla. The Penelope element isolated from Drosophila virilis is the only transpositionally active representative of this class isolated so far. The single ORF of Penelope and its relatives contains regions homologous to a reverse transcriptase of atypical structure and to the GIY-YIG, or Uri, an endonuclease (EN) domain not previously found in retroelements. We have expressed the single ORF of Penelope in a baculovirus expression system and have shown that it encodes a polyprotein with reverse transcriptase activity that requires divalent cations (Mn2+ and Mg2+). We have also expressed and purified the EN domain in Escherichia coli and have demonstrated that it has EN activity in vitro. Mutations in the conserved residues of the EN catalytic module abolish its nicking activity, whereas the DNA-binding properties of the mutant proteins remain unaffected. Only one strand of the target sequence is cleaved, and there is a certain degree of cleavage specificity. We propose that the Penelope EN cleaves the target DNA during transposition, generating a primer for reverse transcription. Our results show that an active Uri EN has been adopted by a retrotransposon.},
  file      = {:by-author/P/Pyatkov/2004_Pyatkov_14719.pdf:PDF},
  keywords  = {Mobile Genetic Elements},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Pyatkov2002,
  author    = {Pyatkov, Konstantin I. and Shostak, Natalia G. and Zelentsova, Elena S. and Lyozin, George T. and Melekhin, Michael I. and Finnegan, David J. and Kidwell, Margaret G. and Evgen'ev, Michael B.},
  journal   = {Proceedings of the National Academy of Sciences of the United States of America},
  title     = {Penelope retroelements from Drosophila virilis are active after transformation of Drosophila melanogaster.},
  year      = {2002},
  pages     = {16150--5},
  volume    = {99},
  abstract  = {The Penelope family of retroelements was first described in species of the Drosophila virilis group. Intact elements encode a reverse transcriptase and an endonuclease of the UvrC type, which may play a role in Penelope integration. Penelope is a key element in the induction of D. virilis hybrid dysgenesis, which involves the mobilization of several unrelated families of transposable elements. We here report the successful introduction of Penelope into the germ line of Drosophila melanogaster by P element-mediated transformation with three different constructs. Penelope is actively transcribed in the D. melanogaster genome only in lines transformed with a construct containing a full-length Penelope clone. The transcript is identical to that detected in D. virilis dysgenic hybrids. Most newly transposed Penelope elements have a very complex organization. Significant proliferation of Penelope copy number occurred in some lines during the 24-month period after transformation. The absence of copy number increase with two other constructs suggests that the 5' andor 3' UTRs of Penelope are required for successful transposition in D. melanogaster. No insect retroelement has previously been reported to be actively transcribed and to increase in copy number after interspecific transformation.},
  file      = {:by-author/P/Pyatkov/2002_Pyatkov_16150.pdf:PDF},
  keywords  = {Mobile Genetic Elements},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Pyykkoe2012,
  author    = {Pekka Pyykkö},
  journal   = {Physical Review B},
  title     = {Refitted tetrahedral covalent radii for solids},
  year      = {2012},
  pages     = {024115},
  volume    = {85},
  doi       = {10.1103/PhysRevB.85.024115},
  file      = {:by-author/P/Pyykkö/2012_Pyykkö_024115.pdf:PDF},
  owner     = {antanas},
  timestamp = {2014.06.17},
  creationdate = {2014-06-17T00:00:00},
  url       = {http://journals.aps.org/prb/abstract/10.1103/PhysRevB.85.024115},
}

@Article{Pyykkoe2009,
  author    = {Pyykkö, Pekka and Atsumi, Michiko},
  journal   = {Chemistry – A European Journal},
  title     = {Molecular Single-Bond Covalent Radii for Elements 1–118},
  year      = {2009},
  issn      = {1521-3765},
  pages     = {186--197},
  volume    = {15},
  abstract  = {A self-consistent system of additive covalent radii, R(AB)=r(A) + r(B), is set up for the entire periodic table, Groups 1–18, Z=1–118. The primary bond lengths, R, are taken from experimental or theoretical data corresponding to chosen group valencies. All r(E) values are obtained from the same fit. Both E–E, E–H, and E–CH3 data are incorporated for most elements, E. Many E–E′ data inside the same group are included. For the late main groups, the system is close to that of Pauling. For other elements it is close to the methyl-based one of Suresh and Koga [J. Phys. Chem. A2001, 105, 5940] and its predecessors. For the diatomic alkalis MM′ and halides XX′, separate fits give a very high accuracy. These primary data are then absorbed with the rest. The most notable exclusion are the transition-metal halides and chalcogenides which are regarded as partial multiple bonds. Other anomalies include H2 and F2. The standard deviation for the 410 included data points is 2.8 pm.},
  doi       = {10.1002/chem.200800987},
  file      = {2009_Pyykkö_186.pdf:by-author/P/Pyykkö/2009_Pyykkö_186.pdf:PDF},
  keywords  = {Ab Initio Calculations; Alkali Metals; Covalent Radii; Heavy Metals; Single Bonds; Superheavy Elements},
  owner     = {saulius},
  publisher = {WILEY-VCH Verlag},
  timestamp = {2014.02.21},
  creationdate = {2014-02-21T00:00:00},
  url       = {http://dx.doi.org/10.1002/chem.200800987},
}

@Article{Pyykkoe2009a,
  author    = {Pyykkö, Pekka and Atsumi, Michiko},
  journal   = {Chemistry – A European Journal},
  title     = {Molecular Double-Bond Covalent Radii for Elements {L}i–{E}112},
  year      = {2009},
  issn      = {1521-3765},
  pages     = {12770--12779},
  volume    = {15},
  abstract  = {The previous systems of triple-bond and single-bond self-consistent, additive covalent radii, R(AB)=r(A)+ r(B), are completed with a fit for σ2π2 double-bonds.The primary bond lengths, R, are taken from experimental or theoretical data corresponding to chosen group valencies. All r(E) values are obtained from the same, self-consistent fit. Many of the calculated primary data came from ECH2 and HECH2 models. Homonuclear LEEL, formaldehyde-type Group 14–Group 16 and open-shell, X3 Σ Group-16 dimer data are included. The standard deviation for the 316 included data points is 3 pm.},
  doi       = {10.1002/chem.200901472},
  file      = {2009_Pyykkö_12770.pdf:by-author/P/Pyykkö/2009_Pyykkö_12770.pdf:PDF},
  keywords  = {Ab Initio Calculations; Covalent Radii; Double Bonds; Heavy Metals},
  owner     = {saulius},
  publisher = {WILEY-VCH Verlag},
  timestamp = {2014.02.21},
  creationdate = {2014-02-21T00:00:00},
  url       = {http://dx.doi.org/10.1002/chem.200901472},
}

@Article{Pyykkoe2005,
  author    = {Pyykkö, Pekka and Riedel, Sebastian and Patzschke, Michael},
  journal   = {Chemistry – A European Journal},
  title     = {Triple-Bond Covalent Radii},
  year      = {2005},
  issn      = {1521-3765},
  pages     = {3511--3520},
  volume    = {11},
  abstract  = {A system of additive covalent radii is proposed for σ2 π4 triple bonds involving elements from Be to E 112 (eka-mercury). Borderline cases with weak multiple bonding are included. Only the elements in Group 1, the elements Zn–Hg in Group 12 and Ne in Group 18 are then totally excluded. Gaps are left at late actinides and some lanthanides. The standard deviation for the 324 included data points is 3.2 pm.},
  doi       = {10.1002/chem.200401299},
  file      = {2005_Pyykkö_3511.pdf:by-author/P/Pyykkö/2005_Pyykkö_3511.pdf:PDF},
  keywords  = {Ab Initio Calculations; Covalent Radii; Density Functional Calculations; Heavy Metals; Superheavy Elements; Triple Bonds},
  owner     = {saulius},
  publisher = {WILEY-VCH Verlag},
  timestamp = {2014.02.21},
  creationdate = {2014-02-21T00:00:00},
  url       = {http://dx.doi.org/10.1002/chem.200401299},
}

@Article{Qi2007,
  author    = {Liqun Qi},
  journal   = {J. Math. Anal. Appl.},
  title     = {Eigenvalues and invariants of tensors},
  year      = {2007},
  pages     = {1363--1377},
  volume    = {325},
  doi       = {10.1016/j.jmaa.2006.02.071},
  file      = {2007_Qi_1363.pdf:by-author/Q/Qi/2007_Qi_1363.pdf:PDF},
  owner     = {saulius},
  timestamp = {2011.12.13},
  creationdate = {2011-12-13T00:00:00},
}

@Manuscript{Qian1998,
  author    = {Zhenyu Qian},
  title     = {A Formal Specification of Java Virtual Machine Instructions for Objects, Methods and Subroutines},
  year      = {1998},
  abstract  = {In this chapter we formally specify a subset of Java Virtual Machine (JVM) instructions for objects, methods and subroutines based on the o cial JVM Speci cation, the o cial Java Language Speci cation and Sun's JDK 1.1.4 imple- mentation of the JVM. Our formal speci cation describes the runtime behaviors of the instructions in relevant memory areas as state transitions and most structural and linking constraints on the instructions as a static typing system. The typing system includes a core of the Bytecode Veri er and resembles data- ow analysis. We state some properties based on our formal speci cation and sketch the proofs. One of these properties is that if a JVM program is statically well-typed with respect to the typing system, then the runtime data of the program will be type-correct. Our formal speci cation clari es some ambiguities and incompleteness and removes some (in our view) unnecessary restrictions in the description of the o cial JVM Speci cation.},
  file      = {:by-author/Q/Qian/1998_Qian.ps.gz:PostScript;:by-author/Q/Qian/1998_Qian.pdf:PDF},
  owner     = {saulius},
  timestamp = {2015.02.27},
  creationdate = {2015-02-27T00:00:00},
}

@Article{Qiu2004,
  author    = {Qiu, X. H. and Nazin, G. V. and Ho, W.},
  journal   = {Physical Review Letters},
  title     = {Mechanisms of reversible conformational transitions in a single molecule},
  year      = {2004},
  pages     = {196806},
  volume    = {93},
  abstract  = {The reversible interconversion between two nonplanar conformations of single Zn(II) Etioporphyrin I molecules adsorbed on a NiAl(110) surface at 13 K was induced by a scanning tunneling microscope (STM). The threshold voltage for the conformational change at negative sample bias depends linearly on the tip-sample distance, suggesting an electrostatic force mechanism. The reverse conversion involves inelastic electron tunneling via a molecular electronic resonance at 1.25 eV. In contrast with the photon-induced conformational changes, an electrically induced mechanism is realized with the STM.},
  doi       = {10.1103/PhysRevLett.93.196806},
  file      = {Qiu et al. - 2004 - Mechanisms of Reversible Conformational Transition.pdf:by-author/Q/Qiu/2004_Qiu_196806.pdf:application/pdf;APS Snapshot:by-author/Q/Qiu/2004_Qiu_196806.html:text/html},
  groups    = {sg/chemical},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://link.aps.org/doi/10.1103/PhysRevLett.93.196806},
  urldate   = {2015-08-05},
}

@Article{Quast2015,
  author    = {Quast, Robert B. and Mrusek, Devid and Hoffmeister, Christian and Sonnabend, Andrei and Kubick, Stefan},
  journal   = {FEBS Letters},
  title     = {Cotranslational incorporation of non-standard amino acids using cell-free protein synthesis},
  year      = {2015},
  issn      = {0014-5793},
  month     = {May},
  number    = {15},
  pages     = {1703--1712},
  volume    = {589},
  doi       = {10.1016/j.febslet.2015.04.041},
  file      = {:by-author/Q/Quast/2015_Quast_1703.pdf:PDF},
  groups    = {am/Expanded genetic code},
  owner     = {andrius},
  publisher = {Wiley-Blackwell},
  timestamp = {2016.05.24},
  creationdate = {2016-05-24T00:00:00},
  url       = {http://dx.doi.org/10.1016/j.febslet.2015.04.041},
}

@Article{Quillin2000,
  author           = {Quillin, M. L. and Matthews, B. W.},
  journal          = {Acta crystallographica. Section D, Biological crystallography},
  title            = {Accurate calculation of the density of proteins},
  year             = {2000},
  pages            = {791--4},
  volume           = {56},
  abstract         = {On the basis of theoretical calculations, Andersson &amp; Hovmöller have recently suggested that the long-established value of 1.35 g cm(-3) for the mean density of proteins should be revised to 1.22 g cm(-3) [Andersson &amp; Hovmöller (2000), Acta Cryst. D56, 789-790]. To substantiate their assertion, these authors used the Voronoi algorithm to calculate the mean atomic volume for 30 representative protein structures. The Voronoi procedure requires that atoms of interest be bounded on all sides by other atoms. Volume calculations for surface atoms that are not surrounded or are only sparsely surrounded by other atoms either are not possible or may be unreliable. In an attempt to circumvent this problem, Andersson &amp; Hovmöller rejected atoms with calculated volumes that were indeterminate or were greater than 50 A(3). In the present study, it is shown that this criterion is not sufficiently restrictive to ensure accurate volume determinations. When only strictly buried atoms are included in the volume calculations using the Voronoi algorithm, the mean density is found to be 1.47 +/- 0.05 g cm(-3). In addition, an alternate procedure based on the Connolly algorithm that permits all protein atoms to be included in volume calculations gives 1.43 +/- 0.03 g cm(-3) for the mean density of the same set of proteins. The latter two calculated values are mutually consistent and are in better agreement with the experimental value.},
  creationdate     = {2012-11-09T00:00:00},
  file             = {:by-author/Q/Quillin/2000_Quillin_791.pdf:PDF},
  keywords         = {Density; Grow Krystal},
  modificationdate = {2023-05-02T10:17:10},
  owner            = {em},
  timestamp        = {2012.11.09},
}

@Presentation{QuirosOlozabal2013,
  author       = {Quirós Olozábal, Miguel},
  title        = {Searching the Crystallography Open Database by Definition of Molecular Fragments},
  year         = {2013},
  organization = {Department of Inorganic Chemistry, University of Granada},
  school       = {University of Granada},
  file         = {:by-author/Q/Quirós-Olozábal/2013_Quirós-Olozábal_Vilnius-slides.pdf:PDF;:by-author/Q/Quirós-Olozábal/2013_Quirós-Olozábal_Vilnius-slides.odp:OpenDocument presentation},
  keywords     = {COD; Crystallography; Databases},
  owner        = {saulius},
  timestamp = {2013.05.03},
  creationdate = {2013-05-03T00:00:00},
}

@Article{Quispel2008,
  author    = {G R W Quispel and D I McLaren},
  journal   = {Journal of Physics A: Mathematical and Theoretical},
  title     = {A new class of energy-preserving numerical integration methods},
  year      = {2008},
  pages     = {045206},
  volume    = {41},
  abstract  = {The first ever energy-preserving B-series numerical integration method for (ordinary) differential equations is presented and applied to several Hamiltonian systems. Related novel Lie algebraic results are also discussed.},
  doi       = {10.1088/1751-8113/41/4/045206},
  file      = {2008_Quispel_045206.pdf:by-author/Q/Quispel/2008_Quispel_045206.pdf:PDF},
  owner     = {saulius},
  timestamp = {2015.03.20},
  creationdate = {2015-03-20T00:00:00},
  url       = {http://stacks.iop.org/1751-8121/41/i=4/a=045206},
}

@Presentation{Rabenseifner2002,
  author       = {Rolf Rabenseifner},
  title        = {Introduction to the Message Passing Interface (MPI)},
  year         = {2002},
  organization = {High-Performance Computing-Center Stuttgart (HLRS)},
  school       = {University of Stuttgart},
  file         = {:by-author/R/Rabenseifner/2002_Rabenseifner_slides.pdf:PDF},
  owner        = {saulius},
  pages        = {slides},
  timestamp = {2013.07.02},
  creationdate = {2013-07-02T00:00:00},
  url          = {https://fs.hlrs.de/projects/rabenseifner/publ/mpi_HPC-Europa_20Apr2005_noAnimation.pdf},
}

@Article{Rabesandratana2013,
  author    = {Rabesandratana, Tania},
  journal   = {Science},
  title     = {The Seer of Science Publishing},
  year      = {2013},
  pages     = {66--67},
  volume    = {342},
  doi       = {10.1126/science.342.6154.66},
  eprint    = {http://www.sciencemag.org/content/342/6154/66.full.pdf},
  file      = {2013_Rabesandratana_66.pdf:by-author/R/Rabesandratana/2013_Rabesandratana_66.pdf:PDF},
  keywords  = {F1000; F1000 Research; Open Access; Peer Review; Scientific Data Dissemination; Scientific Publishing},
  owner     = {saulius},
  timestamp = {2014.07.16},
  creationdate = {2014-07-16T00:00:00},
  url       = {http://www.sciencemag.org/content/342/6154/66.short},
}

@TechReport{Rabin2014,
  author    = {Rabin, Michael O. and Rivest, Ronald L.},
  title     = {Practical provably correct voter privacy end-to-end voting employing multiparty computations and split value representation of votes},
  year      = {2014},
  file      = {practical_provably_correct_voter_privacy_end_to_end.pdf:by-author/R/Rabin/2014_Rabin.pdf:application/pdf},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {https://www.omnicompete.com/files/practical_provably_correct_voter_privacy_end_to_end.pdf},
  urldate   = {2015-08-21},
}

@Article{Rackham2005,
  author    = {Rackham, Oliver and Chin, Jason W},
  journal   = {Nat Chem Biol},
  title     = {A network of orthogonal ribosome·mRNA pairs},
  year      = {2005},
  issn      = {1552-4450},
  month     = {Jul},
  number    = {3},
  pages     = {159--166},
  volume    = {1},
  doi       = {10.1038/nchembio719},
  file      = {:by-author/R/Rackham/2005_Rackham_159.pdf:PDF},
  groups    = {am/Expanded genetic code},
  owner     = {andrius},
  publisher = {Nature Publishing Group},
  timestamp = {2016.05.17},
  creationdate = {2016-05-17T00:00:00},
  url       = {http://dx.doi.org/10.1038/nchembio719},
}

@Presentation{Radnai2003,
  author    = {Zolán Radnai},
  title     = {Minimum image convention in non-cubic simulation cells},
  year      = {2003},
  file      = {:by-author/R/Radnai/2003_Radnai.ps.gz:PostScript;:by-author/R/Radnai/2003_Radnai.pdf:PDF},
  month     = {July},
  owner     = {saulius},
  timestamp = {2015.02.27},
  creationdate = {2015-02-27T00:00:00},
}

@Article{Rae1997,
  author    = {Rae, A. D. and Craig, D. C. and Dance, I. G. and Scudder, M. L. and Dean, P. A. W. and Kmetic, M. A. and Payne, N. C. and Vittal, J. J.},
  journal   = {Acta Crystallographica Section B},
  title     = {The Pseudo-Symmetric Structure of Pb(SPh)${\sb 2}$},
  year      = {1997},
  pages     = {457--465},
  volume    = {53},
  abstract  = {The crystal structure of Pb(SC6Hs)2 is pseudo-C-centred orthorhombic, a = 54.06(1), b = 11.468 (1), c = 7.4387(8)A,, ~ = [3 = "7 = 90 ° , Z = 16, and may be described as a partial ordering of a 1:1 disordered parent structure of symmetry Pmcn, Z = 4 (a t = a/2, b t = b/2, c ~ = c), in which the mirror imposes a 1:1 disorder on two-dimensionally polymeric layers perpendicular to a*. An ideally ordered structure has monoclinic space group C l l 2 t / d (P21/c using an alternative axis system b, c, [a + b]/2), but may also be described as two inversion-related substructures of Cmc2~ pseudo- symmetry, where the b-glide planes of one substructure coincide with the mirror planes of the other and vice versa. Moving one substructure by b/2 relative to the other creates a different orientation of the structure. The crystal studied showed a partial disorder of each substructure relative to origins b/2 apart [0.964 (4):0.036 for one substructure and 0.584 (3):0.416 for the other]. This lowers the symmetry of the average structure to C1121 with intensities realistically described as K2[(1 - 15)lF(hkl)l2 + blF(hkl)12], where K 2 for h odd, k odd reflections is 0.444 (7) of the value for h even, k even reflections, 6 is 0.325 (5) and F(hkl) is the structure factor for an ideally ordered structure. Final values for R of 0.046 and 0.090 were obtained for the 844 h even, k even and 687 h odd, k odd reflections with l(h) > 3cr(l(h)) used in refinement. A bond-valence interpretation of the bonding within the polymeric layer structure is given.},
  doi       = {10.1107/S0108768196015819},
  file      = {:by-author/R/Rae/1997_Rae_457.pdf:PDF},
  keywords  = {For COD Deposition; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0108768196015819},
}

@Article{Rafajova2003,
  author    = {Monika Rafajová and Miriam Zatovicová and Richard Kettmann and Jaromír Pastorek and Silvia Pastoreková},
  journal   = {International Journal Of Oncology},
  title     = {Induction by hypoxia combined with low glucose or low bicarbonate and high posttranslational stability upon reoxygenation contribute to carbonic anhydrase IX expression in cancer cells},
  year      = {2003},
  pages     = {995--1004},
  volume    = {24},
  abstract  = {Hypoxia is an important factor of tumor micro- environment that significantly influences behaviour of tumor cells via activation of genes whose products are involved in adaptation to hypoxic stress, such as vascular endothelial growth factor (VEGF) and glucose transporter (GLUT-1). Carbonic anhydrase IX (CA IX) is one of the most strongly hypoxia-inducible proteins with potential value as an intrinsic marker of hypoxia. However, intratumoral distribution of CA IX only partially overlaps with distribution of VEGF and GLUT-1 indicating that regulation of CA IX differs from the regulation of other hypoxic markers. Therefore, we analysed CA IX expression in response to hypoxia combined with other stresses, and determined the stability of CA IX protein upon reoxygenation using HeLa cells as a model. We found that both hypoxia-induced transcription and CA IX protein level are further increased by reduced glucose or bicarbonate concentrations. Post-translational stability of CA IX was assessed by monitoring the quantity of biotinylated protein extracted at different time points from the cells labelled immediately after shift to reoxygenation. CA IX protein half-life in reoxygenated cells was 38 h and was independent of the duration of the foregoing hypoxia. This finding has potential implications for interpretation of clinical data as it suggests that CA IX expression may detect not only actually hypoxic tumor regions, but also the regions affected by hypoxia and adverse microenvironmental stresses before biopsy or tumor removal.},
  file      = {2003_Rafajova_995.pdf:by-author/R/Rafajova/2003_Rafajova_995.pdf:PDF},
  groups    = {sg/hCA9},
  keywords  = {Carbonic Anhydrases},
  owner     = {saulius},
  timestamp = {2008.08.14},
  creationdate = {2008-08-14T00:00:00},
}

@Article{Rafkind2009,
  author    = {Rafkind, Jon and Adam Wick and John Regehr and Matthew Flatt},
  title     = {Precise Garbage Collection for C},
  year      = {2009},
  pages     = {manuscript},
  abstract  = {Magpie is a source-to-source transformation for C programs that enables precise garbage collection, where precise means that integers are not confused with pointers, and the liveness of a pointer is apparent at the source level. Precise GC is primarily useful for long-running programs and programs that interact with untrusted components. In particular, we have successfully deployed precise GC in the C implementation of a language run-time system that was originally designed to use conservative GC. We also report on our experience in transforming parts of the Linux kernel to use precise GC instead of manual memory management.},
  file      = {:by-author/R/Rafkind/2009_Rafkind_manuscript.pdf:PDF},
  groups    = {sg/Garbage collectors, sg/C++},
  keywords  = {Computer Science (CS); Conservative Garbage Collection; Garbage Collectors; Precise Garbage Collection; The C Programming Language},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Raghavendra2004,
  author    = {Raghavendra, Nidhanapati K. and Rao, Desirazu N.},
  journal   = {Nucleic acids research},
  title     = {Unidirectional translocation from recognition site and a necessary interaction with DNA end for cleavage by Type III restriction enzyme.},
  year      = {2004},
  pages     = {5703--11},
  volume    = {32},
  abstract  = {Type III restriction enzymes have been demonstrated to require two unmethylated asymmetric recognition sites oriented head-to-head to elicit double-strand break 25-27 bp downstream of one of the two sites. The proposed DNA cleavage mechanism involves ATP-dependent DNA translocation. The sequence context of the recognition site was suggested to influence the site of DNA cleavage by the enzyme. In this investigation, we demonstrate that the cleavage site of the R.EcoP15I restriction enzyme does not depend on the sequence context of the recognition site. Strikingly, this study demonstrates that the enzyme can cleave linear DNA having either recognition sites in the same orientation or a single recognition site. Cleavage occurs predominantly at a site proximal to the DNA end in the case of multiple site substrates. Such cleavage can be abolished by the binding of Lac repressor downstream (3' side) but not upstream (5' side) of the recognition site. Binding of HU protein has also been observed to interfere with R.EcoP15I cleavage activity. In accordance with a mechanism requiring two enzyme molecules cooperating to elicit double-strand break on DNA, our results convincingly demonstrate that the enzyme translocates on DNA in a 5' to 3' direction from its recognition site and indicate a switch in the direction of enzyme motion at the DNA ends. This study demonstrates a new facet in the mode of action of these restriction enzymes.},
  file      = {:by-author/R/Raghavendra/2004_Raghavendra_5703.pdf:PDF},
  keywords  = {TypeIII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Raghavendra2003,
  author    = {Raghavendra, Nidhanapathi K. and Rao, Desirazu N.},
  journal   = {Nucleic acids research},
  title     = {Functional cooperation between exonucleases and endonucleases--basis for the evolution of restriction enzymes.},
  year      = {2003},
  pages     = {1888--96},
  volume    = {31},
  abstract  = {Many types of restriction enzymes cleave DNA away from their recognition site. Using the type III restriction enzyme, EcoP15I, which cleaves DNA 25-27 bp away from its recognition site, we provide evidence to show that an intact recognition site on the cleaved DNA sequesters the restriction enzyme and decreases the effective concentration of the enzyme. EcoP15I restriction enzyme is shown here to perform only a single round of DNA cleavage. Significantly, we show that an exonuclease activity is essential for EcoP15I restriction enzyme to perform multiple rounds of DNA cleavage. This observation may hold true for all restriction enzymes cleaving DNA sufficiently far away from their recognition site. Our results highlight the importance of functional cooperation in the modulation of enzyme activity. Based on results presented here and other data on well-characterised restriction enzymes, a functional evolutionary hierarchy of restriction enzymes is discussed.},
  file      = {:by-author/R/Raghavendra/2003_Raghavendra_1888.pdf:PDF},
  keywords  = {Evolution; TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Raghunathan1997,
  author    = {Raghunathan, G. and Jernigan, R. L.},
  journal   = {Protein science : a publication of the Protein Society},
  title     = {Ideal architecture of residue packing and its observation in protein structures.},
  year      = {1997},
  pages     = {2072--83},
  volume    = {6},
  abstract  = {A simple model of sphere packing has been investigated as an ideal model for long-range interactions for the packing of non-bonded residues in protein structures. By superposing all residues, the geometry of packing around a central residue is investigated. It is found that all residues conform almost perfectly to this lattice model for sphere packing when a radius of 6.5 A is used to define non-bonded (virtual) interacting residues. Side-chain positions with respect to sequential backbone segments are relatively regular as well. This lattice can readily be used in conformation simulations to reduce the conformational space.},
  file      = {:by-author/R/Raghunathan/1997_Raghunathan_2072.pdf:PDF},
  keywords  = {Protein Structures; Residue Packing},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Presentation{Raginis2017,
  author    = {Erikas Raginis},
  title     = {Serveriai},
  year      = {2017},
  file      = {2017_Raginis_05.pdf:by-author/R/Raginis/2017_Raginis_05.pdf:PDF},
  owner     = {erikas},
  timestamp = {2017.05.15},
  creationdate = {2017-05-15T00:00:00},
}

@Presentation{Raha2004,
  author       = {Kaushik Raha},
  title        = {Calculation of Binding Affinity in Ligand-Protein Interaction},
  year         = {2004},
  organization = {Merz Research Group},
  file         = {:by-author/R/Raha/2004_Raha_slides.pdf:PDF},
  keywords     = {Protein Ligand Complexes},
  owner        = {saulius},
  pages        = {slides},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Rahman2009,
  author    = {Syed Asad Rahman and Matthew Bashton and Gemma L. Holliday and Rainer Schrader and Janet M. Thornton},
  journal   = {Journal of Cheminformatics},
  title     = {Small Molecule Subgraph Detector ({SMSD}) toolkit},
  year      = {2009},
  pages     = {1--12},
  volume    = {1},
  doi       = {10.1186/1758-2946-1-12},
  file      = {:by-author/R/Rahman/2009_Rahman_1.pdf:PDF},
  owner     = {andrius},
  timestamp = {2014.11.11},
  creationdate = {2014-11-11T00:00:00},
  url       = {http://www.jcheminf.com/content/1/1/12},
}

@Manuscript{Rainey2004,
  author    = {Rainey, Michael and David S. Wise},
  title     = {Embedding Quadtree Matrices in a Lazy Functional Language},
  year      = {2004},
  keywords  = {Computer Science (CS); Functional; Languages},
  abstract  = {A technique for supporting quadtree matrices in a lazy functional langauge is presented that ameliorates tensions between performance and purity. In large matrix computations the facility to update in-place is a requisite for high performance. Thus, techniques for applying safe side effects to quadtree matrices are presented. Performance enhancements come via intrinsic properties of quadtree matrices, e.g., locality of reference. The expres- siveness of quadtree matrix algorithms is enhanced by the tools of the higher-order, typed language, Haskell. Matrix-matrix multiply and Cholesky factorization are provided with time comparisons to C. In contrast to our earlier work, the protocol is convenient even for Fortran programmers and its performance scales nicely and compares well with Fortran enough to demonstrate that lazy languages can compete.},
  file      = {:by-author/R/Rainey/2004_Rainey.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Rajagopalan1996,
  author    = {Rajagopalan, P and Wudl, F and Schinazi, R F and Boudinot, F D},
  journal   = {Antimicrobial Agents and Chemotherapy},
  title     = {Pharmacokinetics of a water-soluble fullerene in rats.},
  year      = {1996},
  issn      = {0066-4804},
  pages     = {2262--2265},
  volume    = {40},
  abstract  = {Fullerenes are the recently discovered third allotropic form of carbon. The biological activities of these compounds are being studied for various purposes. The bis(monosuccinimide) derivative of p p'-bis(2-amino-ethyl)-diphenyl-C60 (MSAD-C60) is a water-soluble fullerene derivative. MSAD-C60 has been shown to have antiviral activity against human immunodeficiency virus types 1 and 2 in vitro and to have virucidal and anti-human immunodeficiency virus protease activities. Moreover, MSAD-C60 has been shown to be well tolerated in mice after intraperitoneal administration. The purpose of the present study was to develop a high-performance liquid chromatographic analytical methodology for MSAD-C60 and to characterize the preclinical pharmacokinetics of the compound in rats. Following intravenous administration of the fullerene derivative at a dose of 15 mg/kg of body weight, the concentrations of MSAD-C60 in plasma declined either bi- or triexponentially. The mean terminal-phase half-life of MSAD-C60 was 6.8 +/- 1.1 h (mean +/- standard deviation). Binding studies indicated that the compound is greater than 99\% bound to plasma proteins. The average total clearance of the compound was 0.19 +/- 0.06 liter/h/kg. Urine samples obtained 24 h after intravenous administration did not contain detectable levels of the compound, indicating the absence of a significant renal clearance mechanism. The steady-state volume of distribution of MSAD-C60 averaged 2.1 +/- 0.8 liters/kg, indicating that the compound distributes into tissues. At a dose of 15 mg/kg, MSAD-C60 appeared to be well tolerated. However, a dose of 25 mg/kg resulted in shortness of breath and violent movement of the rats, followed by death within 5 min of dosing. Further controlled toxicity studies are needed to fully evaluate the toxicity of the compound.},
  file      = {PubMed Central Full Text PDF:by-author/R/Rajagopalan/1996_Rajagopalan_2262.pdf:application/pdf},
  owner     = {saulius},
  pmcid     = {PMC163515},
  pmid      = {8891126},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC163515/},
  urldate   = {2015-07-06},
}

@InCollection{Rajan2006,
  author    = {Rajan, H. and Uchida, H. and Bryan, D.L. and Swaminathan, R. and Downs, R.T. and Hall-Wallace, M},
  booktitle = {Geoinformatics: Data to Knowledge},
  publisher = {Geological Society of America},
  title     = {Building the American Mineralogist Crystal Structure Database: A recipe for construction of a small Internet database},
  year      = {2006},
  address   = {Boulder, CO, United States},
  editor    = {Sinha, A.K.},
  pages     = {73--80},
  series    = {Geological Society of America Special Papers},
  volume    = {397},
  abstract  = {Crystal structure data represent one of the most important resources for developing scientific knowledge and should be archived in ways that make them easy to access and preserve. The American Mineralogist Crystal Structure Database currently contains every crystal structure published in American Mineralogist, The Canadian Mineralogist, European Journal of Mineralogy, and Physics and Chemistry of Minerals. It is maintained by the American and Canadian mineralogical societies and is freely accessible through the Internet. The database consists of the data, server-side search and retrieval software and user-side analysis software. It is managed through a partnership of PHP and MySQL programming that provide dynamic construction of Web pages and search procedures. The purpose of this paper is to describe the database and its implementation and to illustrate how to construct similar small, interactive Internet databases.},
  doi       = {10.1130/2006.2397(06)},
  file      = {2006_Rajan_73.pdf:by-author/R/Rajan/2006_Rajan_73.pdf:PDF},
  groups    = {am/AMCSD},
  journal   = {Geological Society of America Special Paper},
  keywords  = {AMCSD; Databases},
  owner     = {saulius},
  timestamp = {2011.10.20},
  creationdate = {2011-10-20T00:00:00},
}

@Presentation{Rajendra2011,
  author    = {Anoop Rajendra},
  title     = {Introduction to MPI Programming},
  year      = {2011},
  file      = {:by-author/R/Rajendra/2011_Rajendra_slides.pdf:PDF},
  owner     = {saulius},
  pages     = {slides},
  timestamp = {2013.07.02},
  creationdate = {2013-07-02T00:00:00},
}

@Article{Rajkumar2006,
  author    = {Ganeshalingam Rajkumar and Hind A. Al-Khayat and Felicity Eakins and Carlo Knupp and John M. Squire},
  journal   = {Fibre Diffraction Review},
  title     = {The CCP13 FibreFix Program Suite and Recent Updates},
  year      = {2006},
  pages     = {10--14},
  volume    = {14},
  doi       = {10.1382/fdr.2006.1403},
  file      = {:by-author/R/Rajkumar/2006_Rajkumar_10.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.09.18},
  creationdate = {2012-09-18T00:00:00},
}

@Article{RALEIGH1991,
  author    = {Raleigh, E. A. and Benner, J. and Bloom, F. and Braymer, H. D. and Decruz, E. and Dharmalingam, K. and Heitman, J. and Noyer-Weidner, M. and Piekarowicz, A. and Kretz, P. L. and Short, J. M. and Woodcock, D.},
  journal   = {Journal Of Bacteriology},
  title     = {Nomenclature Relating to Restriction of Modified {DNA} in {E}scherichia coli},
  year      = {1991},
  pages     = {2707--2709},
  volume    = {173},
  abstract  = {At least three restriction systems that attack DNA containing naturally modified bases have been found in common Escherichia coli K-12 strains. These systems are McrA, McrBC, and Mrr. A brief summary of the genetic and phenotypic properties so far observed in laboratory strains is set forth, together with a proposed nomenclature for describing these properties.},
  file      = {:by-author/R/Raleigh/1991_Raleigh_2707.pdf:PDF},
  keywords  = {McrA; McrBC; Mrr; Restriction Endonuclease (RE); TypeIV},
  owner     = {em},
  timestamp = {2013.02.21},
  creationdate = {2013-02-21T00:00:00},
}

@Article{RALEIGH1986,
  author    = {Raleigh, Elisabeth A. and Wilson, Geoffrey},
  journal   = {Proc. Natl. Acad. Sci.},
  title     = {Escherichia coli {K-12} restricts {DNA} containing 5-methylcytosine},
  year      = {1986},
  pages     = {9070--9074},
  volume    = {83},
  abstract  = {We have observed that plasmids containing certain cloned modification methylase genes of type H restriction-modification systems cannot be transformed into many laboratory strains of Escherichia coli K-12. The investigation of this phenomenon, reported here, has revealed (i) DNA containing 5-methylcytosine is biologically restricted by these strains, while DNA containing 6-methyladenine is not; (ii) restriction is due to two genetically distinct systems that differ in their sequence specificities, which we have named mcrA and mcrB (for moiffied cytosine restriction). Since 5-methylcyto- sine containing DNA is widespread in nature, the Mcr systems probably have a broad biological role. Mcr restriction may seriously interfere with molecular cloning of 5-methylcytosine- containing foreign DNAs. The Mcr phenotypes of some com- monly used strains of E. coli K-12 are reported.},
  file      = {:by-author/R/Raleigh/1986_Raleigh_9070.pdf:PDF},
  keywords  = {McrA; Restriction Endonucleases (REases); TypeIV},
  owner     = {em},
  timestamp = {2013.01.17},
  creationdate = {2013-01-17T00:00:00},
}

@Article{Raleigh1988,
  author    = {Raleigh, E.A. and Murray, N.E. and Revel, H. and Blumenthal, R.M. and Westaway, D. and Reith, A.D. and Rigby, P.W.J. and Elhai,J. and Hanahan, D.},
  journal   = {Nucleic Acids Research},
  title     = {{McrA} and {McrB} restriction phenotypes of some {E.coli} strains and implications for gene cloning},
  year      = {1988},
  pages     = {1563--1575},
  volume    = {16},
  abstract  = {The McrA and McrB (modified cytosine restriction) systems of E. coli interfere with incoming DNA containing methylcytosine. DNA from many organisms, including all mammalian and plant DNA, is expected to be sensitive, and this could interfere with cloning experiments. The McrA and B phenotypes of a few strains have been reported previously (1-4). The Mcr phenotypes of 94 strains, primarily derived from E. coli K12, are tabulated here. We briefly review some evidence suggesting that McrB restriction of mouse-modified DNA does occur in vivo and does in fact interfere with cloning of specific mouse sequences.},
  file      = {:by-author/R/Raleigh/1988_Raleigh_1563.pdf:PDF},
  keywords  = {McrA; McrBC; Restriction Endonucleases (REases); TypeIV},
  owner     = {em},
  timestamp = {2013.01.17},
  creationdate = {2013-01-17T00:00:00},
}

@Article{Raleigh1989,
  author    = {Raleigh, E.A. and Trimarchi, R. and Revel, H.},
  journal   = {Genetics},
  title     = {Genetic and Physical Mapping of the {mcrA} ({rglA}) and {mcrB} ({rglB}) Loci of {E}scherichia coli {K-12}},
  year      = {1989},
  pages     = {279--296},
  volume    = {122},
  abstract  = {We have genetically analyzed, cloned and physically mapped the modified cytosine-specific restriction determinants mcrA (rglA)and mcrB (rglB) of Escherichia coli K-12. The independently discovered Rgl and Mcr restriction systems are shown to be identical by three criteria: 1) mutants with the RglA-or RglB- phenotypes display the corresponding McrA- or McrB- phenotypes, and vice versa; 2) the gene(s)for RglA and McrA residetogether at one locus, while gene@)for RglB and McrB are coincident at a different locus; and 3) RglA+ and RglB'recombinant clones complement for the corresponding Mcr-deficient lesions. The mcrA (rglA) gene(s) is on the excisable element e14, just clockwise of purB at 25 min. The mcrB (rglB)gene(s),at 99 min, is in a cluster of restriction functions that includes hsd and mrr, determinants of host-specific restriction (EcoK) and methyladenine-specific restriction respectively. Gene order is mcrB-hsdS-hsdM-hsdR-mrr-serB. Possible models for the acqusition of these restriction determinantsby enteric bacteria are discussed.},
  file      = {:by-author/R/Raleigh/1989_Raleigh_279.pdf:PDF},
  keywords  = {McrA; McrBC; Restriction Endonuclease (RE); TypeIV},
  owner     = {em},
  timestamp = {2013.02.21},
  creationdate = {2013-02-21T00:00:00},
}

@Electronic{Ram2002,
  author       = {Vasudev Ram},
  language     = {English},
  month        = {Jun},
  note         = {retrieved 2012-11-18},
  organization = {IBM},
  title        = {Developing a Linux command-line utility: Best practices and thoughtful coding make for solid command-line tools},
  url          = {http://www.ibm.com/developerworks/linux/library/l-clutil/},
  year         = {2002},
  abstract     = {Learn how to write Linux command-line utilities that are foolproof enough even for end users. Starting with an overview of solid command-line best practices and finishing with a comprehensive tour of a working page-selection tool, this article gives you the background you need to begin writing your own utilities.},
  file         = {:by-author/R/Ram/2002_Ram.html:URL},
  keywords     = {Linux; Programming; Software Development; Unix; Utilities},
  owner        = {saulius},
  timestamp = {2012.11.19},
  creationdate = {2012-11-19T00:00:00},
}

@Article{Ramachary2011,
  author    = {Ramachary, Dhevalapally B and Jain, Sangeeta},
  journal   = {Organic \&amp; biomolecular chemistry},
  title     = {Sequential one-pot combination of multi-component and multi-catalysis cascade reactions: an emerging technology in organic synthesis.},
  year      = {2011},
  pages     = {1277--300},
  volume    = {9},
  file      = {2011_Ramachary_1277.pdf:by-author/R/Ramachary/2011_Ramachary_1277.pdf:PDF},
  keywords  = {Chemistry; One Pot Syntheses},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Ramagopal2003,
  author    = {Ramagopal, Udupi A. and Dauter, Miroslawa and Dauter, Zbigniew},
  journal   = {Acta Crystallographica Section D},
  title     = {Phasing on anomalous signal of sulfurs: what is the limit?},
  year      = {2003},
  pages     = {1020--1027},
  volume    = {59},
  doi       = {10.1107/S0907444903007467},
  file      = {wd0006.pdf:by-author/R/Ramagopal/2003_Ramagopal_1020.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444903007467},
}

@Article{Ramakrishnan1965,
  author    = {Ramakrishnan, C. and Ramachandran, G.N.},
  journal   = {Biophysical Journal},
  title     = {Stereochemical Criteria for Polypeptide and Protein Chain Conformations. Ii. Allowed Conformations for a Pair of Peptide Units},
  year      = {1965},
  issn      = {0006-3495},
  month     = {Nov},
  number    = {6},
  pages     = {909--933},
  volume    = {5},
  abstract  = {The conformation of a polypeptide or protein chain may be specified by stating the orientations of the two linked peptide residues at each alpha carbon atom in the chain, namely the two dihedral angles 4, 4' about the single bonds N-aC and aC-C' from a defined standard conformation. By us- ing certain criteria of minimum contact distances between the various atoms, the allowed anges of ($\phi$, $\phi$') have been worked out for three values of the angle N-aC-C' ($\tau$), namely 105, 110, and 1150 for non-glycyl, and 110 and 115° for glycyl residues. The theory is compared with all the available crystallographic data (up to early 1965) on simple (di- and tri-) peptides, cyclic peptides, poly- peptide and protein structures, and the observed data fully support the conclu- sions from theory. The effect of the gamma carbon atom, in its three possible positions, is also discussed, and is found to alter the outer limits of the allowed region of ($\phi$), $\phi$') only slightly. The paper contains exhaustive references to the published data on these structures, using x-ray diffraction.},
  doi       = {10.1016/s0006-3495(65)86759-5},
  file      = {1965_Ramakrishnan_909.pdf:by-author/R/Ramakrishnan/1965_Ramakrishnan_909.pdf:PDF},
  keywords  = {Protein Backbone Conformation; Ramachandran Plot; Seminal Paper},
  owner     = {saulius},
  pmcid     = {PMC1367910},
  pmcurl    = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1367910},
  pmid      = {5884016},
  publisher = {Elsevier BV},
  pubmedurl = {https://www.ncbi.nlm.nih.gov/pubmed/5884016},
  timestamp = {2016.12.08},
  creationdate = {2016-12-08T00:00:00},
  url       = {http://dx.doi.org/10.1016/S0006-3495(65)86759-5},
}

@Article{Ramakrishnan2014,
  author    = {Ramakrishnan, Raghunathan and Dral, Pavlo O. and Rupp, Matthias and von Lilienfeld, O. Anatole},
  journal   = {Scientific Data},
  title     = {Quantum chemistry structures and properties of 134 kilo molecules},
  year      = {2014},
  issn      = {2052-4463},
  volume    = {1},
  doi       = {10.1038/sdata.2014.22},
  file      = {Ramakrishnan et al. - 2014 - Quantum chemistry structures and properties of 134.pdf:by-author/R/Ramakrishnan/2014_Ramakrishnan.pdf:application/pdf;Quantum chemistry structures and properties of 134 kilo molecules \: Scientific Data:by-author/R/Ramakrishnan/2014_Ramakrishnan.html:text/html},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://www.nature.com/articles/sdata201422},
  urldate   = {2015-09-24},
}

@Article{Ramakrishnan2014a,
  author    = {Ramakrishnan, Raghunathan and Dral, Pavlo O. and Rupp, Matthias and von Lilienfeld, O. Anatole},
  journal   = {Scientific Data},
  title     = {Quantum chemistry structures and properties of 134 kilo molecules},
  year      = {2014},
  pages     = {140022},
  volume    = {1},
  abstract  = {Computational de novo design of new drugs and materials requires rigorous and unbiased exploration of chemical compound space. However, large uncharted territories persist due to its size scaling combinatorially with molecular size. We report computed geometric, energetic, electronic, and thermodynamic properties for 134k stable small organic molecules made up of CHONF. These molecules correspond to the subset of all 133,885 species with up to nine heavy atoms (CONF) out of the GDB-17 chemical universe of 166 billion organic molecules. We report geometries minimal in energy, corresponding harmonic frequencies, dipole moments, polarizabilities, along with energies, enthalpies, and free energies of atomization. All properties were calculated at the B3LYP/6-31G(2df,p) level of quantum chemistry. Furthermore, for the predominant stoichiometry, C7H10O2, there are 6,095 constitutional isomers among the 134k molecules. We report energies, enthalpies, and free energies of atomization at the more accurate G4MP2 level of theory for all of them. As such, this data set provides quantum chemical properties for a relevant, consistent, and comprehensive chemical space of small organic molecules. This database may serve the benchmarking of existing methods, development of new methods, such as hybrid quantum mechanics/machine learning, and systematic identification of structure-property relationships.},
  doi       = {10.1038/sdata.2014.22},
  file      = {2014_Ramakrishnan_140022.pdf:by-author/R/Ramakrishnan/2014_Ramakrishnan_140022.pdf:PDF},
  owner     = {saulius},
  publisher = {Macmillan Publishers Limited},
  timestamp = {2015.10.09},
  creationdate = {2015-10-09T00:00:00},
  url       = {http://dx.doi.org/10.1038/sdata.2014.22},
}

@Article{Ramamurthy1996,
  author    = {Ramamurthy, Shankara and York, Bryant W. and Giacovazzo, Carmelo},
  title     = {On the scalability of parallel triplet generation for protein crystallography},
  year      = {1996},
  pages     = {344--352},
  acmid     = {331204},
  address   = {New York, NY, USA},
  booktitle = {Proceedings of the 1996 ACM symposium on Applied Computing},
  doi       = {10.1145/331119.331204},
  file      = {1996_Ramamurthy_344.pdf:by-author/R/Ramamurthy/1996_Ramamurthy_344.pdf:PDF},
  isbn      = {0-89791-820-7},
  keywords  = {Algorithms; Crystallographic Phasing; Crystallography; Direct Phasing; Triplet Relations},
  location  = {Philadelphia, Pennsylvania, United States},
  numpages  = {9},
  owner     = {saulius},
  publisher = {ACM},
  series    = {SAC '96},
  timestamp = {2012.05.18},
  creationdate = {2012-05-18T00:00:00},
  url       = {http://doi.acm.org/10.1145/331119.331204},
}

@Article{Rambo2013a,
  author      = {Robert P Rambo and John A Tainer},
  journal     = {Nature},
  title       = {Accurate assessment of mass, models and resolution by small-angle scattering.},
  year        = {2013},
  pages       = {477--481},
  volume      = {496},
  abstract    = {Modern small-angle scattering (SAS) experiments with X-rays or neutrons provide a comprehensive, resolution-limited observation of the thermodynamic state. However, methods for evaluating mass and validating SAS-based models and resolution have been inadequate. Here we define the volume of correlation, Vc, a SAS invariant derived from the scattered intensities that is specific to the structural state of the particle, but independent of concentration and the requirements of a compact, folded particle. We show that Vc defines a ratio, QR, that determines the molecular mass of proteins or RNA ranging from 10 to 1,000 kilodaltons. Furthermore, we propose a statistically robust method for assessing model-data agreements (χ(2)free) akin to cross-validation. Our approach prevents over-fitting of the SAS data and can be used with a newly defined metric, RSAS, for quantitative evaluation of resolution. Together, these metrics (Vc, QR, χ(2)free and RSAS) provide analytical tools for unbiased and accurate macromolecular structural characterizations in solution.},
  doi         = {10.1038/nature12070},
  file        = {:by-author/R/Rambo/2013_Rambo_477.pdf:PDF},
  institution = {Life Sciences Division, Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA. rprambo@lbl.gov},
  keywords    = {Aldose-Ketose Isomerases; Chemical; Chemistry; DNA-Binding Proteins; Genetics; Models; Molecular; Molecular Conformation; Molecular Weight (MW); Pliability; RNA; Reproducibility of Results; Riboswitch; Scattering; Small Angle; Solutions; Viral},
  language    = {eng},
  medline-pst = {ppublish},
  owner       = {em},
  pii         = {nature12070},
  pmid        = {23619693},
  timestamp = {2014.01.14},
  creationdate = {2014-01-14T00:00:00},
  url         = {http://dx.doi.org/10.1038/nature12070},
}

@Article{Rambo2013c,
  author      = {Robert P Rambo and John A Tainer},
  journal     = {Annu Rev Biophys},
  title       = {Super-resolution in solution X-ray scattering and its applications to structural systems biology.},
  year        = {2013},
  pages       = {415--441},
  volume      = {42},
  abstract    = {Small-angle X-ray scattering (SAXS) is a robust technique for the comprehensive structural characterizations of biological macromolecular complexes in solution. Here, we present a coherent synthesis of SAXS theory and experiment with a focus on analytical tools for accurate, objective, and high-throughput investigations. Perceived SAXS limitations are considered in light of its origins, and we present current methods that extend SAXS data analysis to the super-resolution regime. In particular, we discuss hybrid structural methods, illustrating the role of SAXS in structure refinement with NMR and ensemble refinement with single-molecule FRET. High-throughput genomics and proteomics are far outpacing macromolecular structure determinations, creating information gaps between the plethora of newly identified genes, known structures, and the structure-function relationship in the underlying biological networks. SAXS can bridge these information gaps by providing a reliable, high-throughput structural characterization of macromolecular complexes under physiological conditions.},
  doi         = {10.1146/annurev-biophys-083012-130301},
  file        = {:by-author/R/Rambo/2013_Rambo_415.pdf:PDF},
  institution = {Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA. rprambo@lbl.gov},
  keywords    = {Animals; Biomolecular; Chemistry; DNA; Fluorescence Resonance Energy Transfer; Humans; Macromolecular Substances; Methods; Nuclear Magnetic Resonance; Proteins; Review; SAXS; Scattering; Small Angle; Systems Biology; X-Ray Diffraction},
  language    = {eng},
  medline-pst = {ppublish},
  owner       = {em},
  pmid        = {23495971},
  timestamp = {2014.01.14},
  creationdate = {2014-01-14T00:00:00},
  url         = {http://dx.doi.org/10.1146/annurev-biophys-083012-130301},
}

@Article{Rambo2011,
  author    = {Rambo, Robert P. and Tainer, John A.},
  journal   = {Biopolymers},
  title     = {Characterizing Flexible and Instrinsically Unstructured Biological Macromolecules by SAS using the Porod-Debye Law},
  year      = {2011},
  pages     = {559–571},
  volume    = {95},
  abstract  = {Unstructured proteins, RNA or DNA components provide functionally important flexibility that is key to many macromolecular assemblies throughout cell biology. As objective, quantitative experimental measures of flexibility and disorder in solution are limited, small angle scattering (SAS), and in particular small angle X-ray scattering (SAXS), provides a critical technology to assess macromolecular flexibility as well as shape and assembly. Here, we consider the Porod- Debye law as a powerful tool for detecting biopolymer flexibility in SAS experiments. We show that the Porod-Debye region fundamentally describes the nature of the scattering intensity decay, which captures information needed for distinguishing between folded and flexible particles. Particularly for comparative SAS experiments, application of the law, as described here, can distinguish between discrete conformational changes and localized flexibility relevant to molecular recognition and interaction networks. This approach aids insightful analyses of fully and partly flexible macromolecules that is more robust and conclusive than traditional Kratky analyses. Furthermore, we demonstrate for prototypic SAXS data that the ability to calculate particle density by the Porod-Debye criteria, as shown here, provides an objective quality assurance parameter that may prove of general use for SAXS modeling and validation.},
  doi       = {10.1002/bip.21638},
  file      = {:by-author/R/Rambo/2011_Rambo_559.pdf:PDF},
  keywords  = {Flexibility; Guinier Region; Kratky Plot; Molecular Weight (MW); Porod; Porod-Debye Law; Protein Structure; Review; SAXS},
  owner     = {em},
  timestamp = {2014.05.22},
  creationdate = {2014-05-22T00:00:00},
}

@Article{Raney1996,
  author    = {Raney, K. D. and Carver, T. E. and Benkovic, S. J.},
  journal   = {The Journal of biological chemistry},
  title     = {Stoichiometry and DNA unwinding by the bacteriophage T4 41:59 helicase.},
  year      = {1996},
  pages     = {14074--81},
  volume    = {271},
  abstract  = {The bacteriophage T4 41 protein is a replicative helicase that forms a hexamer in the presence of ATP and associates with the T4 59 protein. The stoichiometry of the 41:59 helicase complex and its mechanism for DNA unwinding have been investigated using steady-state and single-turnover kinetics. A partial duplex DNA fork containing two regions of single-stranded DNA (ssDNA) of 30 nucleotides each, and 30 base pairs served as the substrate. 59 was found to increase the steady-state unwinding rate of the substrate by 200-fold over the rate of 41 alone. Maximum unwinding occurred when 59 and 41 were equimolar, revealing a 1:1 stoichiometry for the complex. Varying 41 while holding 59 constant resulted in sigmoidal kinetics suggesting strong cooperativity for formation of the 41 hexamer and providing a lower limit for hexamer assembly of 65 nM. Substrates were prepared that contained a biotin-streptavidin block in either the leading or lagging strand of the duplex region of the substrate. The first order rate constant for unwinding was reduced only when the block was placed in the lagging strand of the DNA fork, indicating that the helicase interacts primarily with the lagging DNA strand.},
  file      = {:by-author/R/Raney/1996_Raney_14074.pdf:PDF},
  keywords  = {{gp41}; {gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Rao1996,
  author    = {Rao, S.T. and Sundaralingam, M.},
  journal   = {Acta Crystallographica Section D},
  title     = {Studies of monoclinic hen egg-white lysozyme. IV. X-ray refinement at 1.8 {\AA} resolution and a comparison of the variable regions in the polymorphic forms},
  year      = {1996},
  pages     = {170--175},
  volume    = {52},
  doi       = {10.1107/S0907444995009504},
  file      = {1996_Rao_170.pdf:by-author/R/Rao/1996_Rao_170.pdf:PDF},
  keywords  = {Crazy Spacegroups; Structures},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444995009504},
}

@Manuscript{Rasmussen2001,
  author    = {Carl Edward Rasmussen and Zoubin Ghahramani},
  title     = {Occam’s Razor},
  year      = {2001},
  keywords  = {Bayesian Statistics; Occam’s Razor},
  url       = {http://www.gatsby.ucl.ac.uk/~edward/pub/occam.pdf},
  abstract  = {The Bayesian paradigm apparently only sometimes gives rise to Occam’s Razor; at other times very large models perform well. We give simple examples of both kinds of behaviour. The two views are reconciled when measuring complexity of functions, rather than of the machinery used to implement them. We analyze the complexity of functions for some linear in the parameter models that are equivalent to Gaussian Processes, and always find Occam’s Razor at work.},
  file      = {:by-author/R/Rasmussen/2001_Rasmussen.pdf:PDF},
  groups    = {sg/Bayesian},
  owner     = {saulius},
  timestamp = {2012.11.24},
  creationdate = {2012-11-24T00:00:00},
}

@Article{Rasmussen_2015,
  author    = {Rasmussen, Filip A. and Thygesen, Kristian S.},
  journal   = {The Journal of Physical Chemistry C},
  title     = {Computational 2D Materials Database: Electronic Structure of Transition-Metal Dichalcogenides and Oxides},
  year      = {2015},
  issn      = {1932-7455},
  month     = {Jun},
  number    = {23},
  pages     = {13169–13183},
  volume    = {119},
  doi       = {10.1021/acs.jpcc.5b02950},
  file      = {:by-author/R/Rasmussen/2015_Rasmussen_13169.pdf:PDF},
  owner     = {andrius},
  publisher = {American Chemical Society (ACS)},
  timestamp = {2016.01.19},
  creationdate = {2016-01-19T00:00:00},
  url       = {http://dx.doi.org/10.1021/acs.jpcc.5b02950},
}

@Article{Rastorguev1998,
  author    = {Rastorguev, S. M. and Zavilgelsky, G. B. and Tchurikov, N. A.},
  journal   = {FEBS letters},
  title     = {IncI1 plasmid R64 encodes the ArsR protein that alleviates type I restriction.},
  year      = {1998},
  pages     = {21--3},
  volume    = {426},
  abstract  = {The host-controlled EcoK restriction of unmodified phage lambda was five-fold alleviated in the wild-type Escherichia coli strain K12 carrying the R64 plasmid of the incompatibility group I1. The relevant gene was mapped between the origin of vegetative replication (rep, oriV) and the tet(r) gene about 60 kbp downstream from the origin of transfer, oriT. We cloned this gene inside the 613 bp long EcoRI-PstI fragment and sequenced it. Only one 351 bp long open reading frame (ORF) starting at 124 bp from the beginning of the insert was found in the sequence. Computer search in the current databases revealed that the putative protein is identical to the ArsR protein specified by the IncFI plasmid R773. ArsR is a repressor of the arsenical resistance (ars) operon, arsRDABC. There are no arsABC genes in the R64 plasmid since plasmid R64- (or pSR8)-mediated resistance of E. coli K12 cells to the arsenicals arsenate and arsenite was not detected. The gene arsR and the antirestriction genes ard (ardA and ardB) are non-homologous. However, comparison of the deduced amino acid sequence of ArsR with the ArdA and ArdB sequences revealed only one small region of similarity, a 9 amino acid motif found in different antirestriction proteins that is hypothesized to be an interaction site for antirestriction proteins with restriction endonucleases.},
  file      = {:by-author/R/Rastorguev/1998_Rastorguev_21.pdf:PDF},
  keywords  = {Antirestriction},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Rath2003,
  author    = {Stephanie Rath and Martin Kunz and Ronald Miletich},
  journal   = {American Mineralogist},
  title     = {Pressure-induced phase transition in malayaite, CaSnOSiO4},
  year      = {2003},
  pages     = {293--300},
  volume    = {88},
  abstract  = {A single crystal high-pressure diffraction study in a diamond-anvil cell shows that monoclinic malayaite (CaSnOSiO4) transforms into a triclinic high-pressure polymorph at Pc = 4.95(1) GPa. No discontinuity was observed for the individual crystallographic axes or the volume compressibility. Instead, the A2/a – A-1 phase transition reveals itself by significant deviations of the a and g angles from 90∞. The bulk elastic properties of the triclinic phase cannot be distinguished from those of the monoclinic structure within experimental uncertainty (A2/a: V0 = 389.68(3) Å3, K0 = 121(1) GPa, and K' = 4.2(5); A-1: V0 = 390.3(1) Å3, K0 = 118.3(7) GPa, K' = 4). Fitting the compressibility to all data gives values of V0 = 389.64(3) Å3, K0 = 121.6(7) GPa and K' = 4.6(2). Structure refinements at four different pressures reveal the structural details of the monoclinic A2/a and triclinic A-1 phases. Below the transition temperature the SiO4 polyhedra show some non-rigid distortion, whereas the SnO6 polyhedra remain almost unchanged. At the phase transition, the SiO4 tetrahedra show further angular twisting while the SnO6 chains shift parallel to [-101], inducing a reduction in symmetry. Furthermore, at pressures above 5 GPa the Ca atoms are displaced almost parallel to [100], causing a change in coordination from CaO7 polyhedra to sheets of CaO8 parallel to (-111). At 7.394(4) GPa the cell parameters of the triclinic structure are a = 6.9958(4) Å, b = 8.8080(9) Å, c = 6.4968(4) Å, a = 89.078(7)∞, b = 112.745(5)∞, g = 91.230(7)∞ , V = 369.10(5) Å3; space-group A-1.},
  file      = {2003_Rath_293.pdf:by-author/R/Rath/2003_Rath_293.pdf:PDF},
  keywords  = {A1 Spacegroup; For COD Deposition; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Presentation{Rauber2016,
  author    = {Andreas Rauber},
  title     = {Enabling Precise Identification and Citability of Dynamic Data: Recommendations of the RDA Working Group WGDC},
  year      = {2016},
  file      = {2016_Rauber_slides.pdf:by-author/R/Rauber/2016_Rauber_slides.pdf:PDF},
  keywords  = {Data Citation; Reproducible Research; Scientific Databases},
  owner     = {saulius},
  timestamp = {2016.10.03},
  creationdate = {2016-10-03T00:00:00},
}

@Manuscript{Rauber2016a,
  author    = {Andreas Rauber and Ari Asmi and Dieter van Uytvanck and Stefan Pröll},
  title     = {Identification of Reproducible Subsets for Data Citation, Sharing and Re-Use},
  year      = {2016},
  keywords  = {Data Citation; Reproducible Research; Scientific Databases},
  url       = {https://www.rd-alliance.org/system/files/documents/TCDL-RDA-Guidelines_160411.pdf},
  abstract  = {Research data is changing over time as new records are added, errors are corrected and obsolete records are deleted from a data set. Scholars rarely use an entire data set or stream data as it is, but rather select specific subsets tailored to their research questions. In order to keep such experi- ments reproducible and to share and cite the particular data used in a study, researchers need means of identifying the exact version of a subset as it was used during a specific exe- cution of a workflow, even if the data source is continuously evolving. In this paper we present 14 recommendations on how to adapt a data source for providing identifiable subsets for the long term, elaborated by the RDA Working Group on Dynamic Data Citation (WGDC). The proposed solution is based upon versioned data, timestamping and a query based subsetting mechanism. We provide a detailed discussion of the recommendations, the rationale behind them, and give examples of how to implement them.},
  file      = {2016_Rauber_manuscript.pdf:by-author/R/Rauber/2016_Rauber_manuscript.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.10.03},
  creationdate = {2016-10-03T00:00:00},
}

@TechReport{Rauber2015,
  author      = {Andreas Rauber and Ari Asmi and Dieter van Uytvanck and Stefan Pröll},
  institution = {RDA},
  title       = {Data Citation of Evolving Data: Recommendations of the Working Group on Data Citation (WGDC)},
  year        = {2015},
  abstract    = {These WGDC recommendations enable researchers and data centers to identify and cite data used in experiments and studies. Instead of providing static data exports or textual descriptions of data subsets, we support a dynamic, query centric view of data sets. The proposed solution enables precise identification of the very subset and version of data used, supporting reproducibility of processes, sharing and reuse of data.},
  comment     = {Examples at: https://rd-alliance.org/group/data-citation-wg/wiki/collaboration-environments.html},
  file        = {2015_Rauber.pdf:by-author/R/Rauber/2015_Rauber.pdf:PDF},
  keywords    = {Data Citation; Reproducible Research; Scientific Databases},
  owner       = {saulius},
  timestamp = {2016.10.03},
  creationdate = {2016-10-03T00:00:00},
  url         = {https://www.rd-alliance.org/system/files/documents/RDA-DC-Recommendations_151020.pdf},
}

@Article{Ravelli2006,
  author    = {Raimond B. G. Ravelli and Elspeth F. Garman},
  journal   = {Current Opinion in Structural Biology},
  title     = {Radiation damage in macromolecular cryocrystallography},
  year      = {2006},
  issn      = {0959-440X},
  pages     = {624--629},
  volume    = {16},
  abstract  = {X-ray radiation damage to cryocooled (∼100 K) macromolecular crystals has emerged as a general problem, especially since the advent of third generation synchrotron undulator sources. Interest in understanding the physical and chemical phenomena behind the observed effects is growing rapidly. The specific structural damage seen in electron density maps has to be accounted for when studying intermediates, and can sometimes be related to biological function. Radiation damage induces non-isomorphism, thus hampering traditional phasing methods. However, specific damage can also be used to obtain phases. With an increased knowledge of expected crystal lifetime, beamline characteristics and types of damage, macromolecular crystallographers might soon be able to account for radiation damage in data collection, processing and phasing.},
  doi       = {10.1016/j.sbi.2006.08.001},
  file      = {2006_Ravelli_624.pdf:by-author/R/Ravelli/2006_Ravelli_624.pdf:PDF},
  keywords  = {Cryo-cooling; Protein Crystallography; Radation Damage; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2014.03.24},
  creationdate = {2014-03-24T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/S0959440X06001369},
}

@Article{Ray2005,
  author    = {Ray, Surajit and Lindsay, Bruce G.},
  journal   = {The Annals of Statistics},
  title     = {The topography of multivariate normal mixtures},
  year      = {2005},
  issn      = {0090-5364},
  month     = {Oct},
  number    = {5},
  pages     = {2042--2065},
  volume    = {33},
  doi       = {10.1214/009053605000000417},
  file      = {:by-author/R/Ray/2005_Ray_2042.pdf:PDF},
  keywords  = {Mathematics; Statistics},
  owner     = {andrius},
  publisher = {Institute of Mathematical Statistics},
  timestamp = {2020.10.01},
  creationdate = {2020-10-01T00:00:00},
  url       = {https://doi.org/10.1214/009053605000000417},
}

@Article{RayChaudhuri2000,
  author    = {RayChaudhuri, D. and Gordon, G. S. and Wright, A.},
  journal   = {Nature structural biology},
  title     = {How does a bacterium find its middle?},
  year      = {2000},
  pages     = {997--9},
  volume    = {7},
  file      = {:by-author/R/RayChaudhuri/2000_RayChaudhuri_997.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Manuscript{Raymond2011,
  author    = {Eric S. Raymond},
  title     = {Making Pictures With GNU PIC},
  year      = {2011},
  keywords  = {Computer Science (CS); Groff; Pic; Roff; Troff; Typesetting; Unix},
  url       = {http://www.kohala.com/start/troff/troff.html},
  abstract  = {The pic language is a troff extension that makes it easy to create and alter box-and- arrow diagrams of the kind frequently used in technical papers and textbooks. This paper is both an introduction to and reference for gpic(1), the implementation distributed by the Free Software Foundation for use with groff(1).},
  file      = {:by-author/R/Raymond/2011_Raymond.ps:PostScript;:by-author/R/Raymond/2011_Raymond.pdf:PDF},
  owner     = {saulius},
  timestamp = {2015.02.27},
  creationdate = {2015-02-27T00:00:00},
}

@Webpage{Raymond2003,
  author    = {Eric Steven Raymond},
  retrieved = {2008-07-28},
  title     = {The Art of Unix Programming},
  url       = {http://www.faqs.org/docs/artu/index.html},
  year      = {2003},
  file      = {:by-author/R/Raymond/2003_Raymond.war:},
  keywords  = {Computer Science (CS)},
  owner     = {saulius},
  timestamp = {2015.03.02},
  creationdate = {2015-03-02T00:00:00},
}

@Article{Razvi2007,
  author    = {Razvi, Abbas and Scholtz, J. Martin},
  journal   = {Protein Science},
  title     = {Lessons in stability from thermophilic proteins},
  year      = {2006},
  issn      = {1469-896X},
  pages     = {1569--1578},
  volume    = {15},
  abstract  = {Studies that compare proteins from thermophilic and mesophilic organisms can provide insights into ability of thermophiles to function at their high habitat temperatures and may provide clues that enable us to better define the forces that stabilize all proteins. Most of the comparative studies have focused on thermal stability and show, as expected, that thermophilic proteins have higher Tm values than their mesophilic counterparts. Although these comparisons are useful, more detailed thermodynamic analyses are required to reach a more complete understanding of the mechanisms thermophilic protein employ to remain folded over a wider range of temperatures. This complete thermodynamic description allows one to generate a stability curve for a protein that defines how the conformational stability (ΔG) varies with temperature. Here we compare stability curves for many pairs of homologous proteins from thermophilic and mesophilc organisms. Of the basic methods that can be employed to achieve enhanced thermostability, we find that most thermophilic proteins use the simple method that raises the ΔG at all temperatures as the principal way to increase their Tm. We discuss and compare this thermodynamic method with the possible alternatives. In addition we propose ways that structural alterations and changes to the amino acid sequences might give rise to varied methods used to obtain thermostability.},
  doi       = {10.1110/ps.062130306},
  file      = {2007_Razvi_1569.pdf:by-author/R/Razvi/2007_Razvi_1569.pdf:PDF},
  keywords  = {Protein Folding; Protein Stability Curves; Thermodynamics; Thermophiles; Thermostability},
  owner     = {saulius},
  publisher = {Cold Spring Harbor Laboratory Press},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1110/ps.062130306},
}

@Article{Read2003,
  author    = {Read, Randy J.},
  journal   = {Acta Crystallographica Section D},
  title     = {New ways of looking at experimental phasing},
  year      = {2003},
  pages     = {1891--1902},
  volume    = {59},
  doi       = {10.1107/S0907444903017918},
  file      = {ba5044.pdf:by-author/R/Read/2003_Read_1891.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444903017918},
}

@Article{Read2011,
  author    = {Read, Randy J. and Adams, Paul D. and Arendall, 3rd, W. Bryan and Brunger, Axel T. and Emsley, Paul and Joosten, Robbie P. and Kleywegt, Gerard J. and Krissinel, Eugene B. and Lütteke, Thomas and Otwinowski, Zbyszek and Perrakis, Anastassis and Richardson, Jane S. and Sheffler, William H. and Smith, Janet L. and Tickle, Ian J. and Vriend, Gert and Zwart, Peter H.},
  journal   = {Structure (London, England : 1993)},
  title     = {A new generation of crystallographic validation tools for the protein data bank.},
  year      = {2011},
  number    = {10},
  pages     = {1395--1412},
  volume    = {19},
  abstract  = {This report presents the conclusions of the X-ray Validation Task Force of the worldwide Protein Data Bank (PDB). The PDB has expanded massively since current criteria for validation of deposited structures were adopted, allowing a much more sophisticated understanding of all the components of macromolecular crystals. The size of the PDB creates new opportunities to validate structures by comparison with the existing database, and the now-mandatory deposition of structure factors creates new opportunities to validate the underlying diffraction data. These developments highlighted the need for a new assessment of validation criteria. The Task Force recommends that a small set of validation data be presented in an easily understood format, relative to both the full PDB and the applicable resolution class, with greater detail available to interested users. Most importantly, we recommend that referees and editors judging the quality of structural experiments have access to a concise summary of well-established quality indicators.},
  doi       = {10.1016/j.str.2011.08.006},
  file      = {:by-author/R/Read/2011_Read_1395.pdf:pdf},
  keywords  = {Structure Refinement; Validation; X-ray Crystallography},
  owner     = {saulius},
  pii       = {S0969-2126(11)00285-1},
  pmc       = {PMC3195755},
  pubmed    = {22000512},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Article{Reddy2014,
  author    = {Reddy, Vishnu and Sanchez, Juan A. and Bottke, William F. and Cloutis, Edward A. and Izawa, Matthew RM and O’Brien, David P. and Mann, Paul and Cuddy, Matthew and Le Corre, Lucille and Gaffey, Michael J. and {others}},
  journal   = {Icarus},
  title     = {Chelyabinsk meteorite explains unusual spectral properties of baptistina asteroid family},
  year      = {2014},
  pages     = {116--130},
  volume    = {237},
  file      = {[PDF] from arxiv.org:by-author/R/Reddy/2014_Reddy_116.pdf:application/pdf;Snapshot:by-author/R/Reddy/2014_Reddy_116.html:text/html},
  groups    = {sg/JAC2009},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/S001910351400219X},
  urldate   = {2015-08-31},
}

@Article{Reddy2000,
  author    = {Reddy, Y. V. and Rao, D. N.},
  journal   = {Journal of molecular biology},
  title     = {Binding of EcoP15I DNA methyltransferase to DNA reveals a large structural distortion within the recognition sequence.},
  year      = {2000},
  pages     = {597--610},
  volume    = {298},
  abstract  = {EcoP15I DNA methyltransferase, a member of the type III restriction-modification system, binds to the sequence 5'-CAGCAG-3' transferring a methyl group from S-adenosyl-l-methionine to the second adenine base. We have investigated protein-DNA interactions in the methylase-DNA complex by three methods. Determination of equilibrium dissociation constants indicated that the enzyme had higher affinity for DNA containing mismatches at the target base within the recognition sequence. Potassium permanganate footprinting studies revealed that there was a hyper-reactive permanganate cleavage site coincident with adenine that is the target base for methylation. More importantly, to detect DNA conformational alterations within the enzyme-DNA complexes, we have used a fluorescence-based assay. When EcoP15I DNA methyltransferase bound to DNA containing 2-aminopurine substitutions within the cognate sequence, an eight to tenfold fluorescent enhancement resulting from enzymatic flipping of the target adenine base was observed. Furthermore, fluorescence spectroscopy analysis showed that the changes attributable to structural distortion were specific for only the bases within the recognition sequence. More importantly, we observed that both the adenine bases in the recognition site appear to be structurally distorted to the same extent. While the target adenine base is probably flipped out of the DNA duplex, our results also suggest that fluorescent enhancements could be derived from protein-DNA interactions other than base flipping. Taken together, our results support the proposed base flipping mechanism for adenine methyltransferases.},
  file      = {:by-author/R/Reddy/2000_Reddy_597.pdf:PDF},
  keywords  = {TypeIII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@PhdThesis{Reich2003,
  author    = {Andreas Reich},
  school    = {Fakultät Chemie der Universität Stuttgart},
  title     = {Synthese und Strukturaufklärung neuer endohedraler Fullerene},
  year      = {2003},
  file      = {:by-author/R/Reich/2003_Reich_phdthesis.pdf:PDF;:by-author/R/Reich/2003_Reich_phdthesis_suppl/Ba_Co_OEP__2C6H6_DOS.pdf:PDF;:by-author/R/Reich/2003_Reich_phdthesis_suppl/Sr_Co_OEP_2C6H6_DOS.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.06.04},
  creationdate = {2012-06-04T00:00:00},
  url       = {http://elib.uni-stuttgart.de/opus/volltexte/2004/1618/},
}

@Article{Reich2004,
  author    = {Reich, Stefanie and Gössl, Illdiko and Reuter, Monika and Rabe, Jürgen P. and Krüger, Detlev H.},
  journal   = {Journal of molecular biology},
  title     = {Scanning force microscopy of DNA translocation by the Type III restriction enzyme EcoP15I.},
  year      = {2004},
  pages     = {337--43},
  volume    = {341},
  abstract  = {Type III restriction enzymes are multifunctional heterooligomeric enzymes that cleave DNA at a fixed position downstream of a non-symmetric recognition site. For effective DNA cleavage these restriction enzymes need the presence of two unmethylated, inversely oriented recognition sites in the DNA molecule. DNA cleavage was proposed to result from ATP-dependent DNA translocation, which is expected to induce DNA loop formation, and collision of two enzyme-DNA complexes. We used scanning force microscopy to visualise the protein interaction with linear DNA molecules containing two EcoP15I recognition sites in inverse orientation. In the presence of the cofactors ATP and Mg(2+), EcoP15I molecules were shown to bind specifically to the recognition sites and to form DNA loop structures. One of the origins of the protein-clipped DNA loops was shown to be located at an EcoP15I recognition site, the other origin had an unspecific position in between the two EcoP15I recognition sites. The data demonstrate for the first time DNA translocation by the Type III restriction enzyme EcoP15I using scanning force microscopy. Moreover, our study revealed differences in the DNA-translocation processes mediated by Type I and Type III restriction enzymes.},
  file      = {:by-author/R/Reich/2004_Reich_337.pdf:PDF},
  keywords  = {TypeIII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Reinhard2013,
  author      = {Linda Reinhard and Hubert Mayerhofer and Arie Geerlof and Jochen Mueller-Dieckmann and Manfred S Weiss},
  journal     = {Acta Crystallogr Sect F Struct Biol Cryst Commun},
  title       = {Optimization of protein buffer cocktails using Thermofluor.},
  year        = {2013},
  pages       = {209--214},
  volume      = {69},
  abstract    = {The stability and homogeneity of a protein sample is strongly influenced by the composition of the buffer that the protein is in. A quick and easy approach to identify a buffer composition which increases the stability and possibly the conformational homogeneity of a protein sample is the fluorescence-based thermal-shift assay (Thermofluor). Here, a novel 96-condition screen for Thermofluor experiments is presented which consists of buffer and additive parts. The buffer screen comprises 23 different buffers and the additive screen includes small-molecule additives such as salts and nucleotide analogues. The utilization of small-molecule components which increase the thermal stability of a protein sample frequently results in a protein preparation of higher quality and quantity and ultimately also increases the chances of the protein crystallizing.},
  doi         = {10.1107/S1744309112051858},
  file        = {:by-author/R/Reinhard/2013_Reinhard.pdf:PDF},
  groups      = {sg/MOFs, am/MOFs},
  institution = {EMBL Hamburg Outstation, c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany.},
  keywords    = {Bacterial Proteins; Biological Assay; Buffers; Chemistry/metabolism; Enzymology; Fluorescence; Metabolism; Methods; Mycobacterium Tuberculosis; Protein Unfolding; Proteins; Solutions; Temperature},
  language    = {eng},
  medline-pst = {ppublish},
  owner       = {alexey},
  pii         = {S1744309112051858},
  pmid        = {23385769},
  timestamp = {2013.11.12},
  creationdate = {2013-11-12T00:00:00},
  url         = {http://dx.doi.org/10.1107/S1744309112051858},
}

@Article{Reinhardt2017,
  author    = {Reinhardt, Maxwell and Dalgleish, Simon and Shuku, Yoshiaki and Reissig, Louisa and Matsushita, Michio M. and Crain, Jason and Awaga, Kunio and Robertson, Neil},
  journal   = {Phys. Chem. Chem. Phys.},
  title     = {Molecular and thin film properties of cobalt half-sandwich compounds for optoelectronic application},
  year      = {2017},
  issn      = {1463-9084},
  doi       = {10.1039/c6cp08685c},
  file      = {2017_Reinhardt.pdf:by-author/R/Reinhardt/2017_Reinhardt.pdf:PDF},
  keywords  = {Diaminonaphthalene; Organic Semiconductors},
  owner     = {saulius},
  publisher = {Royal Society of Chemistry (RSC)},
  timestamp = {2017.02.11},
  creationdate = {2017-02-11T00:00:00},
  url       = {http://dx.doi.org/10.1039/C6CP08685C},
}

@Article{Remiens2011,
  author    = {Rémiens, D. and Yang, L. and Ponchel, F. and Légier, J. F. and Chateigner, D. and Wang, G. and Dong, X.},
  journal   = {Journal of Applied Physics},
  title     = {X-ray combined analysis of fiber-textured and epitaxial {Ba} ({Sr}, {Ti}) {O}3 thin films deposited by radio frequency sputtering},
  year      = {2011},
  pages     = {114106},
  volume    = {109},
  file      = {[PDF] from ensicaen.fr:by-author/R/Rémiens/2011_Rémiens_114106.pdf:application/pdf;Snapshot:by-author/R/Rémiens/2011_Rémiens_114106.html:text/html},
  groups    = {sg/JAC2009},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://scitation.aip.org/content/aip/journal/jap/109/11/10.1063/1.3592282},
  urldate   = {2015-08-31},
}

@Article{Remington1978,
  author           = {Remington, S. J. and Matthews, B. W.},
  journal          = {Proceedings of the National Academy of Sciences},
  title            = {A general method to assess similarity of protein structures, with applications to {T4} bacteriophage lysozyme},
  year             = {1978},
  pages            = {2180--2184},
  volume           = {75},
  abstract         = {A method is proposed that permits the structural similarity between any pair of proteins to be analyzed in a completely general manner. In the proposed procedure, all possible structural segments of a given length from one protein are compared with all possible segments from the other protein. This set of comparisons reveals any structural similarities between the two proteins being compared, and also provides a basis for estimating the probability that a particular degree of structural homology could have occurred by chance. Application of the method to the comparison of T4 bacteriophage lysozyme and carp calcium-binding protein suggests that the previously reported structural similarity between parts of these two proteins [Tufty, R. M.& Kretsinger, R. H. (1975) Science 187, 167-169] is no better than would be expected by chance. On the other hand, the structural correspondence between phage lysozyme and hen egg-white lysozyme [Rossman, M.G. & Argos, P. (1976) J. Mol. Biol. 105, 75-96] does appear to be significant.},
  creationdate     = {2012-05-15T00:00:00},
  eprint           = {http://www.pnas.org/content/75/5/2180.full.pdf+html},
  file             = {1978_Remington_2180.pdf:by-author/R/Remington/1978_Remington_2180.pdf:PDF},
  keywords         = {Structure Comparison},
  modificationdate = {2023-05-02T10:19:30},
  owner            = {saulius},
  timestamp        = {2012.05.15},
  url              = {http://www.pnas.org/content/75/5/2180.abstract},
}

@Article{Remko2001,
  author    = {Remko, Milan and Rode, Bernd Michael},
  journal   = {Phys. Chem. Chem. Phys.},
  title     = {Catalyzed peptide bond formation in the gas phase},
  year      = {2001},
  pages     = {4667--4673},
  volume    = {3},
  abstract  = {The reactions between glycine and ammonia and the dimerization of glycine with and without Mg{,} Ni{,} Cu and Zn cations as catalysts have been studied as model reactions for peptide bond formation using the Becke3LYP functional with 6-311 + G(d{,}p) and 6-31 + G(d) basis sets. The B3LYP method was also used to characterize the 12 gas-phase complexes of neutral glycine{,} its amide and glycylglycine with Lewis acids Mg{,} Ni{,} Cu and Zn{,} respectively. Enthalpies and Gibbs energies for each reaction have been calculated to determine the thermodynamics of the reactions investigated. A substantial decrease in the reaction enthalpies and Gibbs energies was found for glycine-ammonia and glycine-glycine reactions catalyzed by Mg{,} Ni{,} Cu and Zn ions compared with those of the uncatalyzed amide bond formation. The formation of a dipeptide is a more exothermic process than the creation of simple amide from glycine. The catalytic effect of the transition metal ions Ni Cu and Zn is of similar strength and more pronounced than that of the Mg cation. The basicity order of the bases investigated is: NHCHCOH<NHCHCONH<NHCHCONHCHCOH. Interaction enthalpies and Gibbs energies of metal ion-base complexes increase as Mg<Zn<Cu<Ni.},
  doi       = {10.1039/B105623A},
  file      = {2001_Remko_4667.pdf:by-author/R/Remko/2001_Remko_4667.pdf:PDF},
  issue     = {21},
  keywords  = {Chemical Prebiotic; Evolution},
  owner     = {saulius},
  publisher = {The Royal Society of Chemistry},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1039/B105623A},
}

@Article{Renka1997,
  author     = {Renka, Robert J.},
  journal    = {ACM Trans. Math. Softw.},
  title      = {Algorithm 772: STRIPACK: Delaunay Triangulation and Voronoi Diagram on the Surface of a Sphere},
  year       = {1997},
  issn       = {0098-3500},
  pages      = {416--434},
  volume     = {23},
  abstract   = {STRIPACK is a Fortran 77 software package that employs an incremental algorithm to construct a Delaunay triangulation and, optionally, a Voronoi diagram of a set of points (nodes) on the surface of the unit sphere. The triangulation covers the convex hull of the nodes, which need not be the entire surface, while the Voronoi diagram covers the entire surface. The package provides a wide range of capabilities including an efficient means of updating the triangulation with nodal additions or deletions. For N nodes, the storage requirement for the triangulation is 13N integer storage locations in addition to 3N nodal corrdinates. Using an off-line algorithm and work space of size 3N, the triangulation can be constructed with time complexity O(NlogN).},
  acmid      = {275329},
  address    = {New York, NY, USA},
  doi        = {10.1145/275323.275329},
  file       = {1997_Renka_416.pdf:by-author/R/Renka/1997_Renka_416.pdf:PDF},
  issue_date = {Sept. 1997},
  keywords   = {Algorithms; Computer Science (CS); Delaunay Triangulation; Dirichlet Tessellation; Sphere; Thiessen Regions; Voronoi Diagram},
  numpages   = {19},
  owner      = {saulius},
  publisher  = {ACM},
  timestamp = {2014.09.16},
  creationdate = {2014-09-16T00:00:00},
  url        = {http://doi.acm.org/10.1145/275323.275329},
}

@Manuscript{Renna2004,
  author    = {Scott Renna},
  title     = {Bluetooth Specification v1.1: Vulnerabilities and Security Concerns},
  year      = {2004},
  keywords  = {Computer Science (CS); Security},
  abstract  = {This paper serves as a discussion of vulnerabilities and security concerns pertaining to the Bluetooth v1.1 Specification as implemented on the Sony Ericsson T610 Cellular Phone. Over the past 6 months there have been discoveries that allow for malicious users to read and download sensitive personal information directly from particular Bluetooth equipped devices. First, an overview of the Bluetooth specification and how exactly it works is presented. Second, a discussion on current security holes and a review of the tools available that can be used to exploit them, as well as recommendations. Finally, a quick look at a tool used for capturing Bluetooth traffic and how this all relates to today’s IDS environments and what the future may hold. The device used in this paper as a demonstration of these holes is a Sony Ericsson T610 cellular phone. It is important to note here that these vulnerabilities are a result of the design errors within the implementation of Bluetooth on the T610 and not the Bluetooth protocol itself.},
  file      = {:by-author/R/Renna/2004_Renna.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Resch2013,
  author    = {Jason K. Resch and Ilya Volvovski},
  journal   = {CoRR},
  title     = {Reliability Models for Highly Fault-tolerant Storage Systems},
  year      = {2013},
  pages     = {1310.4702v1},
  volume    = {abs/1310.4702},
  abstract  = {We found that a reliability model commonly used to estimate Mean-Time-To-Data-Loss (MTTDL), while suitable for modeling RAID 0 and RAID 5, fails to accurately model systems having a fault-tolerance greater than 1. Therefore, to model the reliability of RAID 6, Triple-Replication, or k-of-n systems requires an alternate technique. In this paper, we explore some alternatives, and evaluate their efficacy by comparing their predictions to simulations. Our main result is a new formula which more accurately models storage system reliability.},
  bibsource = {dblp computer science bibliography, http://dblp.org},
  biburl    = {http://dblp.uni-trier.de/rec/bib/journals/corr/ReschV13},
  file      = {2013_Resch_1310.4702v1.pdf:by-author/R/Resch/2013_Resch_1310.4702v1.pdf:PDF},
  keywords  = {Computer Storage; Data Management; RAID; Reliability; Tahoe LAFS},
  owner     = {saulius},
  timestamp = {2014.10.21},
  creationdate = {2014-10-21T00:00:00},
  url       = {http://arxiv.org/abs/1310.4702},
}

@Manuscript{HamptonResearch2009,
  author    = {Hampton Research},
  title     = {Tips from Recent Advances in Macromolecular Crystallization Meetings},
  year      = {2009},
  url       = {http://hamptonresearch.com/documents/growth_101/23.pdf},
  file      = {:by-author/H/Hampton/2009_HamptonRes_251.pdf:PDF},
  owner     = {saulius},
  pages     = {251--257},
  timestamp = {2013.11.06},
  creationdate = {2013-11-06T00:00:00},
}

@Article{Resnati2015,
  author       = {Resnati, G. and Boldyreva, E. and Bombicz, P. and Kawano, M.},
  journal      = {{IUCrJ}},
  title        = {Supramolecular interactions in the solid state},
  year         = {2015},
  issn         = {2052-2525},
  number       = {6},
  pages        = {675--690},
  volume       = {2},
  abstract     = {In the last few decades, supramolecular chemistry has been at the forefront of chemical research, with the aim of understanding chemistry beyond the covalent bond. Since the long-range periodicity in crystals is a product of the directionally specific short-range intermolecular interactions that are responsible for molecular assembly, analysis of crystalline solids provides a primary means to investigate intermolecular interactions and recognition phenomena. This article discusses some areas of contemporary research involving supramolecular interactions in the solid state. The topics covered are: (1) an overview and historical review of halogen bonding; (2) exploring non-ambient conditions to investigate intermolecular interactions in crystals; (3) the role of intermolecular interactions in morphotropy, being the link between isostructurality and polymorphism; (4) strategic realisation of kinetic coordination polymers by exploiting multi-interactive linker molecules. The discussion touches upon many of the prerequisites for controlled preparation and characterization of crystalline materials.},
  date         = {2015-11-01},
  doi          = {10.1107/S2052252515014608},
  file         = {Full Text PDF:by-author/R/Resnati/2015_Resnati_675.pdf:PDF;Snapshot:by-author/R/Resnati/2015_Resnati_675.html:URL},
  groups       = {sg/MOF, sg/MOFs, am/MOFs},
  journaltitle = {{IUCrJ}},
  keywords     = {Coordination Polymers; Crystal Engineering; Halogen Bonding; Intermolecular Interactions; Kinetic Assembly; Metal-Organic Frameworks (MOF); Non-ambient Conditions; Phase Transitions; Polymorphism; Self-assembly},
  langid       = {english},
  owner        = {saulius},
  rights       = {http://creativecommons.org/licenses/by/2.0/uk},
  shortjournal = {{IUCrJ}},
  timestamp = {2017.01.29},
  creationdate = {2017-01-29T00:00:00},
  url          = {http://scripts.iucr.org/cgi-bin/paper?bi5049},
  urldate      = {2017-01-29},
}

@Webpage{Retter2016,
  author    = {Adam Retter and David Underdown and Rob Walpole},
  retrieved = {2016-11-21},
  title     = {{CSV} schema 1.1: a language for defining and validating {CSV} data},
  url       = {http://digital-preservation.github.io/csv-schema/csv-schema-1.1.html},
  siteurl   = {https://digital-preservation.github.io/csv-schema/},
  year      = {2016},
  file      = {2016_Retter.pdf:by-author/R/Retter/2016_Retter.pdf:PDF},
  keywords  = {CSV; Computer Science (CS); Data Management; Reproducible Research; Schema; Verification},
  owner     = {saulius},
  timestamp = {2016.11.21},
  creationdate = {2016-11-21T00:00:00},
}

@Webpage{Retter2014,
  author    = {Adam Retter and David Underdown and Rob Walpole},
  retrieved = {2016-11-21},
  title     = {{CSV} schema 1.0: a language for defining and validating {CSV} data},
  url       = {http://digital-preservation.github.io/csv-schema/csv-schema-1.0.html},
  siteurl   = {https://digital-preservation.github.io/csv-schema/},
  year      = {2014},
  file      = {2014_Retter.pdf:by-author/R/Retter/2014_Retter.pdf:PDF},
  keywords  = {CSV; Computer Science (CS); Data Management; Reproducible Research; Schema; Verification},
  owner     = {saulius},
  timestamp = {2016.11.21},
  creationdate = {2016-11-21T00:00:00},
}

@Article{Reuter1993,
  author       = {M. Reuter and D. Kupper and C. D. Pein and M. Petrusyte and V. Siksnys and B. Frey and D. H. Krüger},
  journal      = {Anal Biochem},
  title        = {Use of specific oligonucleotide duplexes to stimulate cleavage of refractory DNA sites by restriction endonucleases.},
  year         = {1993},
  month        = {Mar},
  number       = {2},
  pages        = {232--237},
  volume       = {209},
  abstract     = {There are numerous restriction endonucleases (ENases) which are known never to achieve total cleavage of certain unmethylated target DNAs. In addition to EcoRII we found seven ENases (AtuBI, Cfr9I, Eco57I, Ksp632I, NaeI, NarI, and SauBMKI) that were stimulated by oligodeoxyribonucleotide (oligo) duplexes containing enzyme-specific recognition sequences to cut the target DNAs much more efficiently and in most cases even to completion. These enzymes are class-II and class-IIS Enases isolated from different bacterial species and possess a varying number of specific sites in the refractory DNA substrates. For DNA analysis and large-scale preparation of certain restriction fragments where complete digestions are essential we recommend taking into account the fact that various ENases can be activated by specific oligo duplexes to drive restriction digestions to completion.},
  creationdate = {2016-06-09T00:00:00},
  doi          = {10.1006/abio.1993.1113},
  file         = {1993_Reuter_232.pdf:by-author/R/Reuter/1993_Reuter_232.pdf:PDF},
  institution  = {Institute of Virology, Humboldt University, Berlin, Germany.},
  keywords     = {Analysis/chemistry; Base Sequence; Binding Sites; Chemistry; DNA; DNA Restriction Enzymes; Enzyme Activation; Molecular Sequence Data; Nucleic Acid Conformation; Oligodeoxyribonucleotides; Restriction Mapping; Substrate Specificity},
  language     = {eng},
  medline-pst  = {ppublish},
  owner        = {em},
  pii          = {S0003-2697(83)71113-9},
  pmid         = {8385888},
  timestamp    = {2016.06.09},
  url          = {http://dx.doi.org/10.1006/abio.1993.1113},
}

@Article{Reuter1993a,
  author    = {Reuter, M. and Kupper, D. and Pein, C. D. and Petrusyte, M. and Siksnys, V. and Frey, B. and Krüger, D. H.},
  journal   = {Analytical biochemistry},
  title     = {Use of specific oligonucleotide duplexes to stimulate cleavage of refractory DNA sites by restriction endonucleases.},
  year      = {1993},
  pages     = {232--7},
  volume    = {209},
  abstract  = {There are numerous restriction endonucleases (ENases) which are known never to achieve total cleavage of certain unmethylated target DNAs. In addition to EcoRII we found seven ENases (AtuBI, Cfr9I, Eco57I, Ksp632I, NaeI, NarI, and SauBMKI) that were stimulated by oligodeoxyribonucleotide (oligo) duplexes containing enzyme-specific recognition sequences to cut the target DNAs much more efficiently and in most cases even to completion. These enzymes are class-II and class-IIS Enases isolated from different bacterial species and possess a varying number of specific sites in the refractory DNA substrates. For DNA analysis and large-scale preparation of certain restriction fragments where complete digestions are essential we recommend taking into account the fact that various ENases can be activated by specific oligo duplexes to drive restriction digestions to completion.},
  file      = {:by-author/R/Reuter/1993_Reuter_232.pdf:PDF},
  keywords  = {Ecl18kI EcoRII; TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Revusky1966,
  author    = {Revusky, S. H.},
  journal   = {Journal of the experimental analysis of behavior},
  title     = {An electro-mechanical flip-flop with applications to counting, timing and randomization.},
  year      = {1966},
  pages     = {431--4},
  volume    = {9},
  file      = {:by-author/R/Revusky/1966_Revusky_431.pdf:PDF},
  keywords  = {Electronics},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Rew1990,
  author    = {Rew, R. and Davis, G.},
  journal   = {Computer Graphics and Applications, IEEE},
  title     = {NetCDF: an interface for scientific data access},
  year      = {1990},
  issn      = {0272-1716},
  pages     = {76--82},
  volume    = {10},
  abstract  = {The network common data form (NetCDF), a data abstraction for storing and retrieving multidimensional data, is described. NetCDF is distributed as a software library that provides a concrete implementation of that abstraction. The implementation provides a machine-independent format for representing scientific data. Together, the abstraction, library, and data format support the creation, access, and sharing of scientific information. NetCDF is useful for supporting objects that contain dissimilar kinds of data in a heterogeneous network environment and for writing application software that does not depend on application-specific formats. Independence from particular machine representations is achieved by using a nonproprietary standard for external data representation. The discussion covers NetCDF data abstraction and interface; dimensions, variables, and attributes; direct access and hyperslab access, the NetCDF library; the data format; ncdump and ncgen utilities; experience, usability, and performance; limitations of NetCDF; and future plans.<>},
  doi       = {10.1109/38.56302},
  file      = {1990_Rew_76.pdf:by-author/R/Rew/1990_Rew_76.pdf:PDF},
  keywords  = {Computer Languages; Data Description Languages; Data Management; File Formats; NetCDF; Ontologies},
  owner     = {saulius},
  timestamp = {2013.08.20},
  creationdate = {2013-08-20T00:00:00},
}

@Manual{Rew2011,
  title        = {The {NetCDF} Users Guide},
  author       = {Russ Rew and Glenn Davis and Steve Emmerson and Harvey Davies and Ed Hartnett and Dennis Heimbigner},
  organization = {Unidata Program Center},
  year         = {2011},
  file         = {:by-author/R/Rew/2011_Rew.pdf:PDF},
  owner        = {andrius},
  timestamp = {2016.01.13},
  creationdate = {2016-01-13T00:00:00},
  url          = {http://www.unidata.ucar.edu/software/netcdf/docs/netcdf.pdf},
}

@Article{Rey2007,
  author    = {Rey, Felix A.},
  journal   = {Nature},
  title     = {Virology: holed up in a natural crystal.},
  year      = {2007},
  pages     = {35--7},
  volume    = {446},
  file      = {:by-author/R/Rey/2007_Rey_35.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Reymond2010,
  author    = {Reymond, Jean-Louis and van Deursen, Ruud and Blum, Lorenz C. and Ruddigkeit, Lars},
  journal   = {Med. Chem. Commun.},
  title     = {Chemical space as a source for new drugs},
  year      = {2010},
  pages     = {30--38},
  volume    = {1},
  abstract  = {The chemical space is the ensemble of all possible molecules{,} which is believed to contain at least 1060 organic molecules below 500 Da of possible interest for drug discovery. This review summarizes the development of the chemical space concept from enumerating acyclic hydrocarbons in the 1800{'}s to the recent assembly of the chemical universe database GDB. Chemical space travel algorithms can be used to explore defined regions of chemical space by generating focused virtual libraries. Maps of the chemical space are produced from property spaces visualized by principal component analysis or by self-organizing maps{,} and from structural analyses such as the scaffold-tree or the MQN-system. Virtual screening of virtual chemical space followed by synthesis and testing of the best hits leads to the discovery of new drug molecules.},
  doi       = {10.1039/C0MD00020E},
  file      = {2010_Reymond_30.pdf:by-author/R/Reymond/2010_Reymond_30.pdf:PDF},
  issue     = {1},
  owner     = {saulius},
  publisher = {The Royal Society of Chemistry},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1039/C0MD00020E},
}

@Article{Reynolds2014,
  author    = {Reynolds, Charles H.},
  journal   = {ACS Medicinal Chemistry Letters},
  title     = {Protein–Ligand Cocrystal Structures: We Can Do Better},
  year      = {2014},
  pages     = {727--729},
  volume    = {5},
  abstract  = {There is a large body of evidence that many protein–ligand cocrystal structures contain poorly refined ligand geometries. These errors result in bound structures that have nonideal bond lengths and angles, are strained, contain improbable conformations, and have bad protein–ligand contacts. Many of these problems can be greatly reduced with better refinement models.},
  doi       = {10.1021/ml500220a},
  eprint    = {http://dx.doi.org/10.1021/ml500220a},
  file      = {2014_Reynolds_727.pdf:by-author/R/Reynolds/2014_Reynolds_727.pdf:PDF},
  owner     = {saulius},
  timestamp = {2014.09.25},
  creationdate = {2014-09-25T00:00:00},
  url       = {http://dx.doi.org/10.1021/ml500220a},
}

@Article{Ricco2018,
  author    = {Riccò, Raffaele and Liang, Weibin and Li, Shaobo and Gassensmith, Jeremiah J. and Caruso, Frank and Doonan, Christian and Falcaro, Paolo},
  journal   = {ACS Nano},
  title     = {Metal–Organic Frameworks for Cell and Virus Biology: A Perspective},
  year      = {2018},
  issn      = {1936-086X},
  month     = {Jan},
  number    = {1},
  pages     = {13--23},
  volume    = {12},
  doi       = {10.1021/acsnano.7b08056},
  file      = {:by-author/R/Ricco/2018_Ricco_13.pdf:PDF},
  keywords  = {Metal-Organic Frameworks (MOF); Viruses},
  owner     = {andrius},
  publisher = {American Chemical Society (ACS)},
  timestamp = {2020.07.28},
  creationdate = {2020-07-28T00:00:00},
  url       = {https://doi.org/10.1021/acsnano.7b08056},
}

@Presentation{Rice2007,
  author    = {Ken Rice and Thomas Lumley},
  title     = {Writing Loops},
  year      = {2007},
  file      = {:by-author/R/Rice/2007_Rice_slides.pdf:PDF},
  keywords  = {R},
  owner     = {andrius},
  timestamp = {2013.10.07},
  creationdate = {2013-10-07T00:00:00},
}

@Article{Rice1996,
  author    = {Rice, P. A. and Yang, S. and Mizuuchi, K. and Nash, H. A.},
  journal   = {Cell},
  title     = {Crystal structure of an IHF-DNA complex: a protein-induced DNA U-turn.},
  year      = {1996},
  pages     = {1295--306},
  volume    = {87},
  abstract  = {Integration host factor (IHF) is a small heterodimeric protein that specifically binds to DNA and functions as an architectural factor in many cellular processes in prokaryotes. Here, we report the crystal structure of IHF complexed with 35 bp of DNA. The DNA is wrapped around the protein and bent by &gt;160 degrees, thus reversing the direction of the helix axis within a very short distance. Much of the bending occurs at two large kinks where the base stacking is interrupted by intercalation of a proline residue. IHF contacts the DNA exclusively via the phosphodiester backbone and the minor groove and relies heavily on indirect readout to recognize its binding sequence. One such readout involves a six-base A tract, providing evidence for the importance of a narrow minor groove.},
  file      = {:by-author/R/Rice/1996_Rice_1295.pdf:PDF},
  keywords  = {DNA Protein; Readout},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Manuscript{Richards2006,
  author    = {Richards, Martin},
  title     = {The BCPL Cintcode and Cintpos User Guide},
  year      = {2006},
  keywords  = {BCPL; Computer Science (CS); Programming Languages},
  url       = {http://www.cl.cam.ac.uk/~mr10/bcplman.pdf},
  abstract  = {BCPL is a simple systems programming language with a small fast compiler which is easily ported to new machines. The language was first implemented in 1967 and has been in continuous use since then. It is a typeless and provides machine independent pointer arithmetic allowing a simple way to represent vectors and structures. BCPL functions are recursive and variadic but, like C, do not allow dynamic free variables, and so can be represented by just their entry addresses. There is no built-in garbage collector and all input-output is done using library calls. This document describes the new revised version of the BCPL Cintcode Sys- tem giving a definition of the language, its library and running environment. It also describes a native code version of the system and the Cintpos portable operating system. Installation instructions are included.},
  file      = {:by-author/R/Richards/2006_Richards.pdf:PDF},
  groups    = {sg/Garbage collectors, sg/BCPL},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@InProceedings{Richards2001,
  author    = {Martin Richards},
  title     = {Data Structures and Algorithms},
  year      = {2001},
  comment   = {Data Structures and Algorithms CST IB, CST II(General) and Diploma Martin Richards mr@cl.cam.ac.uk October 2001 Computer Laboratory University of Cambridge (Version October 11, 2001)},
  file      = {:by-author/R/Richards/2001_Richards.ps:PostScript;:by-author/R/Richards/2001_Richards.pdf:PDF},
  owner     = {saulius},
  timestamp = {2013.08.10},
  creationdate = {2013-08-10T00:00:00},
}

@Article{Richardson1989,
  author    = {Richardson, R. W. and Nossal, N. G.},
  journal   = {The Journal of biological chemistry},
  title     = {Trypsin cleavage in the COOH terminus of the bacteriophage T4 gene 41 DNA helicase alters the primase-helicase activities of the T4 replication complex in vitro.},
  year      = {1989},
  pages     = {4732--9},
  volume    = {264},
  abstract  = {The bacteriophage T4 gene 41 protein is a 5' to 3' DNA helicase which unwinds DNA ahead of the growing replication fork and, together with the T4 gene 61 protein, also functions as a primase to initiate DNA synthesis on the lagging strand. Proteolytic cleavage by trypsin approximately 20 amino acids from the COOH terminus of the 41 protein produces 41T, a 51,500-dalton fragment (possibly still associated with small COOH-terminal fragments) which still retains the ssDNA-stimulated GTPase (ATPase) activity, the 61 protein-stimulated DNA helicase activity, and the ability to act with 61 protein to synthesize pentaribonucleotide primers. In the absence of the T4 gene 32 ssDNA binding protein, the primase-helicase composed of the tryptic fragment (41T) and 61 proteins efficiently primes DNA synthesis on circular ssDNA templates by the T4 DNA polymerase and the three T4 polymerase accessory proteins. In contrast, the 41T protein is defective as a helicase or a primase component on 32 protein-covered DNA. Thus, unlike the intact protein, 41T does not support RNA-dependent DNA synthesis on 32 protein-covered ssDNA and does not stimulate strand displacement DNA synthesis on a nicked duplex DNA template. High concentrations of 32 protein strongly inhibit RNA primer synthesis with either 41 T or intact 41 protein. The 44/62 and 45 polymerase accessory proteins (and even the 44/62 proteins to some extent) substantially reverse the 32 protein inhibition of RNA primer synthesis with intact 41 protein but not with 41T protein. We propose that the COOH-terminal region of the 41 protein is required for its interaction with the T4 polymerase accessory proteins, permitting the synthesis and utilization of RNA primers and helicase function within the T4 replication complex. When this region is altered, as in 41T protein, the protein is unable to assemble a functional primase-helicase in the replication complex. An easy and rapid purification of T4 41 protein produced by a plasmid encoding this gene (Hinton, D. M., Silver, L. L., and Nossal, N. G. (1985) J. Biol. Chem. 260, 12851-12857) is also described.},
  file      = {:by-author/R/Richardson/1989_Richardson_4732.pdf:PDF},
  keywords  = {Purification; {gp41}; {gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Richardson1989a,
  author    = {Richardson, R. W. and Nossal, N. G.},
  journal   = {The Journal of biological chemistry},
  title     = {Characterization of the bacteriophage T4 gene 41 DNA helicase.},
  year      = {1989},
  pages     = {4725--31},
  volume    = {264},
  abstract  = {The T4 gene 41 protein and the gene 61 protein function together as a primase-helicase within the seven protein bacteriophage T4 multienzyme complex that replicates duplex DNA in vitro. We have previously shown that the 41 protein is a 5' to 3' helicase that requires a single-stranded region on the 5' side of the duplex to be unwound and is stimulated by the 61 protein (Venkatesan, M., Silver L. L., and Nossal, N. G. (1982) J. biol. Chem. 257, 12426-12434). The 41 protein, in turn, is required for pentamer primer synthesis by the 61 protein. We now show that the 41 protein helicase unwinds a partially duplex DNA molecule containing a performed fork more efficiently than a DNA molecule without a fork. Optimal helicase activity requires greater than 29 nucleotides of single-stranded DNA on the 3' side of the duplex (analogous to the leading strand template). This result suggests the 41 protein helicase interacts with the leading strand template as well as the lagging strand template as it unwinds the duplex region at the replication fork. As the single-stranded DNA on the 3' side of a short duplex (51 base pairs) is lengthened, the stimulation of the 41 protein helicase by the 61 protein is diminished. However, both the 61 protein and a preformed fork are essential for efficient unwinding of longer duplex regions (650 base pairs). These findings suggest that the 61 protein promotes both the initial unwinding of the duplex to form a fork and subsequent unwinding of longer duplexes by the 41 protein. A stable protein-DNA complex, detected by a gel mobility shift of phi X174 single-stranded DNA, requires both the 41 and 61 proteins and a rNTP (preferably rATP or rGTP, the nucleotides with the greatest effect on the helicase activity). In the accompanying paper, we report the altered properties of a proteolytic fragment of the 41 protein helicase and its effect on in vitro DNA synthesis in the T4 multienzyme replication system.},
  file      = {:by-author/R/Richardson/1989_Richardson_4725.pdf:PDF},
  keywords  = {{gp41}; {gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Richter2013,
  author    = {Richter, Hagen and Randau, Lennart and Plagens, André},
  journal   = {International Journal of Molecular Sciences},
  title     = {Exploiting CRISPR/Cas: Interference Mechanisms and Applications},
  year      = {2013},
  pages     = {14518--14531},
  volume    = {14},
  abstract  = {The discovery of biological concepts can often provide a framework for the development of novel molecular tools, which can help us to further understand and manipulate life. One recent example is the elucidation of the prokaryotic adaptive immune system, clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR- associated (Cas) that protects bacteria and archaea against viruses or conjugative plasmids. The immunity is based on small RNA molecules that are incorporated into versatile multi-domain proteins or protein complexes and specifically target viral nucleic acids via base complementarity. CRISPR/Cas interference machines are utilized to develop novel genome editing tools for different organisms. Here, we will review the latest progress in the elucidation and application of prokaryotic CRISPR/Cas systems and discuss possible future approaches to exploit the potential of these interference machineries.},
  doi       = {10.3390/ijms140714518},
  file      = {:by-author/R/Richter/2013_Richter_14518.pdf:PDF},
  groups    = {sg/CRISPR-Cas},
  keywords  = {CRISPR; CRISPR/Cas; Cas9; Cascade; CrRNA; Genome Editing; Interference; RGEN; TALEN; ZNF},
  owner     = {em},
  timestamp = {2014.05.22},
  creationdate = {2014-05-22T00:00:00},
}

@Article{Rietveld1969,
  author    = {H. M. Rietveld},
  journal   = {J. Appl. Cryst.},
  title     = {A Profile Refinement Method for Nuclear and Magnetic Structures},
  year      = {1969},
  pages     = {65--71},
  volume    = {2},
  file      = {:by-author/R/Rietveld/1969_Rietveld_65.war:},
  keywords  = {Rietveld Refinement},
  owner     = {saulius},
  timestamp = {2015.03.02},
  creationdate = {2015-03-02T00:00:00},
  url       = {http://www.ccp14.ac.uk/ccp/web-mirrors/hugorietveld/xtal/paper2/paper2.html},
}

@Article{Rietveld1967,
  author    = {Hugo M. Rietveld},
  journal   = {Acta Cryst.},
  title     = {Line profiles of neutron powder-diffraction peaks for structure refinement},
  year      = {1967},
  pages     = {151--152},
  volume    = {22},
  abstract  = {A structure refinement procedure is described, which obtains a least-squares fit between the calculated and observed intensities measured at equal angular intervals on a neutron powder-diffractometer. It is shown that the structure parameters are significantly more reliable than those determined by a method using the integrated intensities of overlapping peaks.},
  doi       = {10.1107/S0365110X67000234},
  file      = {:by-author/R/Rietveld/1967_Rietveld_151.war:WAR},
  keywords  = {Powder Diffraction; Rietveld Refinement},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://scripts.iucr.org/cgi-bin/paper?a05418},
}

@Article{Rietveld1967a,
  author    = {H. M. Rietveld},
  journal   = {Acta Cryst.},
  title     = {Line profiles of neutron powder-diffraction peaks for structure refinement},
  year      = {1967},
  pages     = {151--152},
  volume    = {22},
  abstract  = {A structure refinement procedure is described, which obtains a least-squares fit between the calculated and observed intensities measured at equal angular intervals on a neutron powder-diffractometer. It is shown that the structure parameters are significantly more reliable than those determined by a method using the integrated intensities of overlapping peaks.},
  file      = {:by-author/R/Rietveld/1967_Rietveld_151a.war:WAR},
  keywords  = {Rietveld Refinement},
  owner     = {saulius},
  timestamp = {2015.03.02},
  creationdate = {2015-03-02T00:00:00},
  url       = {http://www.ccp14.ac.uk/ccp/web-mirrors/hugorietveld/xtal/paper1/paper1.html},
}

@Article{Rijpstra2013,
  author    = {Rijpstra, Kim and Cottenier, Stefaan and Waroquier, Michel and Van Speybroeck, Veronique},
  journal   = {CrystEngComm},
  title     = {Crystal structure prediction for supersaturated AZO: the case of Zn3Al2O6},
  year      = {2013},
  pages     = {10440--10444},
  volume    = {15},
  abstract  = {Increasing the Al concentration in Al-doped ZnO (AZO) is one way of improving the conductivity of this transparent conductive oxide (TCO). Beyond a certain concentration{,} an unwanted secondary phase develops with a low conductivity. Its stoichiometry is Zn3Al2O6{,} and its crystal structure has not yet been convincingly determined. By applying unbiased ab initio structure prediction tools{,} we predict the crystal structure of Zn3Al2O6 to be monoclinic with space group Pm. It can be described as a nanofabric{,} with one-dimensional Al2O3 wires penetrating a ZnO matrix. This crystal has a formation energy that is lower than any structure proposed before{,} and is consistent with all available experimental information. Knowledge of the nature of this phase can help to avoid its formation and therefore to engineer AZO crystals with an increased level of Al-doping and associated increased conductivity.},
  doi       = {10.1039/C3CE41009A},
  file      = {2013_Rijpstra_10440.pdf:by-author/R/Rijpstra/2013_Rijpstra_10440.pdf:PDF},
  groups    = {sg/Crystal structure prediction},
  issue     = {48},
  keywords  = {Citing COD; Crystal Structure Prediction (CSP); Density Functional Theory (DFT)},
  owner     = {saulius},
  publisher = {The Royal Society of Chemistry},
  timestamp = {2014.07.31},
  creationdate = {2014-07-31T00:00:00},
  url       = {http://dx.doi.org/10.1039/C3CE41009A},
}

@PhdThesis{Rimseliene2004,
  author    = {Renata Rimšelienė},
  school    = {Biotechnologijos Institutas},
  title     = {Restrikcijos endonukleazės Eco57I pakeisto specifiškumo mutantų konstravimas},
  year      = {2004},
  file      = {:by-author/R/Rimšelienė/2004_Rimseliene_phdthesis.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@Article{Rimseliene2001,
  author    = {Rimseliene, R. and Janulaitis, A.},
  journal   = {The Journal of biological chemistry},
  title     = {Mutational analysis of two putative catalytic motifs of the type IV restriction endonuclease Eco57I.},
  year      = {2001},
  pages     = {10492--7},
  volume    = {276},
  abstract  = {The role of two sequence motifs (SM) as putative cleavage catalytic centers (77)PDX(13)EAK (SM I) and (811)PDX(20)DQK (SM II) of type IV restriction endonuclease Eco57I was studied by site-directed mutational analysis. Substitutions within SM I; D78N, D78A, D78K, and E92Q reduced cleavage activity of Eco57I to a level undetectable both in vivo and in vitro. Residual endonucleolytic activity of the E92Q mutant was detected only when the Mg(2+) in the standard reaction mixture was replaced with Mn(2+). The mutants D78N and E92Q retained the ability to interact with DNA specifically. The mutants also retained DNA methylation activity of Eco57I. The properties of the SM I mutants indicate that Asp(78) and Glu(92) residues are essential for cleavage activity of the Eco57I, suggesting that the sequence motif (77)PDX(13)EAK represents the cleavage active site of this endonuclease. Eco57I mutants containing single amino acid substitutions within SM II (D812A, D833N, D833A) revealed only a small or moderate decrease of cleavage activity as compared with wild-type Eco57I, indicating that the SM II motif does not represent the catalytic center of Eco57I. The results, taken together, allow us to conclude that the Eco57I restriction endonuclease has one catalytic center for cleavage of DNA.},
  file      = {:by-author/R/Rimseliene/2001_Rimseliene_10492.pdf:PDF},
  keywords  = {TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Lecture{Rinke2014,
  author    = {Patrick Rinke},
  title     = {Electronic Structure Theory},
  year      = {2014},
  file      = {:by-author/R/Rinke/2014_Rinke.pdf:PDF},
  owner     = {saulius},
  timestamp = {2014.04.03},
  creationdate = {2014-04-03T00:00:00},
  url       = {http://www.fhi-berlin.mpg.de/~rinke/lecture.pdf},
}

@Manuscript{Ritchie2000,
  author    = {Dennis M. Ritchie},
  title     = {The Limbo Programming Language},
  year      = {2000},
  keywords  = {Computer Science (CS); Limbo; Programming Languages},
  url       = {http://www.vitanuova.com/inferno/papers/limbo.html},
  file      = {:by-author/R/Ritchie/2000_Ritchie.war:WAR},
  owner     = {saulius},
  timestamp = {2015.03.02},
  creationdate = {2015-03-02T00:00:00},
}

@Article{Rius1991,
  author    = {Rius, J. and Miravitlles, C.},
  journal   = {Acta Crystallographica Section A},
  title     = {Improvement of the tangent formula by constraints based on additional information},
  year      = {1991},
  pages     = {52--55},
  volume    = {47},
  abstract  = {The first part of this communication describes a simple procedure by which the non-centrosymmetric form of the tangent formula is adapted to incorporate the `centrosymmetry constraint' for centrosymmetric structures, thus allowing refinement of phases uniformly distributed from 0 to 2[pi] to the expected values 0 or 2[pi]. The convergence of the resulting formula is illustrated with two structures. In the second part, a modified tangent formula including the constraint based on the zero points of the Patterson function is derived. To do this, both the Cochran integral [integral]v [rho]3 dV and the sum over all zero points of the Patterson function of [rho]2 are expressed in terms of the phases of the strong E's. The modified tangent formula is then obtained assuming that the difference between the two corresponds to a large positive maximum for the correct phases. Finally, it is shown how the information supplied by the weak E's and by the zero points can be treated in an unified way, so that a combined tangent formula can be derived.},
  doi       = {10.1107/S0108767390009692},
  file      = {:by-author/R/Rius/1991_Rius_52.pdf:PDF},
  keywords  = {Direct Methods; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0108767390009692},
}

@TechReport{Rivest2014,
  author    = {Rivest, Ronald L. and Rabin, Michael O.},
  title     = {Practical end-to-end verifiable voting via split-value representations and randomized partial checking},
  year      = {2014},
  file      = {practical_end_to_end_verifiable_voting_via_split_value_2014.pdf:by-author/R/Rivest/2014_Rivest.pdf:application/pdf},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {https://www.omnicompete.com/files/practical_end_to_end_verifiable_voting_via_split_value_2014.pdf},
  urldate   = {2015-08-21},
}

@Manuscript{Rizzo2000,
  author    = {Ann Marie Rizzo},
  title     = {Note and Comment: the aftermath of State Street Bank \& Trust v. Signature Financial Group: effects of united states electronic commerce business method patentability on international legal and economic systems},
  year      = {2000},
  keywords  = {Patentai; Teise},
  file      = {:by-author/R/Rizzo/2000_Rizzo.RTF:DOC},
  owner     = {saulius},
  timestamp = {2015.02.28},
  creationdate = {2015-02-28T00:00:00},
}

@Webpage{Rizzo2008,
  author    = {Robert C. Rizzo},
  retrieved = {2008-07-28},
  title     = {Quantifying Molecular Recognition},
  url       = {http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/index.html},
  year      = {2008},
  file      = {:by-author/R/Rizzo/2008_Rizzo.war:},
  keywords  = {Poisson-Boltzmann eq; Protein-physics; Solvatation},
  owner     = {saulius},
  timestamp = {2015.03.02},
  creationdate = {2015-03-02T00:00:00},
}

@Article{Robbins2010,
  author    = {Arthur H. Robbins and John F. Domsic and Mavis Agbandje-Mckenna and Robert Mckenna},
  journal   = {Acta Crystallographica Section D},
  title     = {Structure of a monoclinic polymorph of human carbonic anhydrase II with a doubled a axis},
  year      = {2010},
  pages     = {628--634},
  volume    = {66},
  abstract  = {The crystal structure of human carbonic anhydrase II with a doubled a axis from that of the usually observed monoclinic cell has been determined and refined to 1.4 Å resolution. The two molecules comprising the asymmetric unit are related by a noncrystallographic translation of ½ along a, but one of the molecules has two alternate orientations related by a rotation of approximately 2°.},
  doi       = {10.1107/S0907444910006797},
  file      = {:by-author/R/Robbins/2010_Robbins_628.pdf:PDF},
  groups    = {sg/hCA2},
  owner     = {saulius},
  timestamp = {2011.12.13},
  creationdate = {2011-12-13T00:00:00},
}

@InProceedings{Robert2010,
  author    = {C.P. Robert and G. Casella},
  booktitle = {Introducing Monte Carlo Methods with R, Use R},
  title     = {Metropolis–Hastings Algorithms},
  year      = {2010},
  pages     = {167},
  publisher = {Springer Science+Business Media, LLC},
  doi       = {10.1007/978-1-4419-1576-4_6},
  file      = {:by-author/R/Robert/2010_Robert_167.pdf:PDF},
  keywords  = {Metropolis Hastings; Monte Carlo},
  owner     = {saulius},
  timestamp = {2012.10.04},
  creationdate = {2012-10-04T00:00:00},
}

@Article{Roberts2006,
  author    = {Roberts, Hugh and Williams, Jason and Tate, Bruce},
  journal   = {Contact dermatitis},
  title     = {Allergic contact dermatitis to panthenol and cocamidopropyl PG dimonium chloride phosphate in a facial hydrating lotion.},
  year      = {2006},
  pages     = {369--70},
  volume    = {55},
  abstract  = {Dexpanthenol is the alcohol corresponding to pantothenic acid (the water-soluble vitamin B(5)). Although it is a common ingredient in many pharmaceuticals and cosmetics, contact allergy is relatively uncommon. Cocamidopropyl PG dimonium chloride phosphate is a phospholipid complex derived from pure coconut oil, and contact allergy is rare. We report a case of allergic contact dermatitis to panthenol and cocamidopropyl PG dimonium chloride phosphate in a facial hydrating lotion.},
  file      = {:by-author/R/Roberts/2006_Roberts.pdf:PDF},
  keywords  = {Obzor},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Roberts2005a,
  author    = {Roberts, R. J.},
  journal   = {Proceedings of the National Academy of Sciences},
  title     = {How restriction enzymes became the workhorses of molecular biology},
  year      = {2005},
  issn      = {1091-6490},
  month     = {Apr},
  number    = {17},
  pages     = {5905--5908},
  volume    = {102},
  abstract  = {Restriction enzymes have proved to be invaluable for the physical mapping of DNA. They offer unparalleled opportunities for diagnosing DNA sequence content and are used in fields as disparate as criminal forensics and basic research. In fact, without restriction enzymes, the biotechnology industry would certainly not have flourished as it has. The first experiments demonstrating the utility of restriction enzymes were carried out by Danna and Nathans and reported in 1971. This pioneering study set the stage for the modern practice of molecular biology in which restriction enzymes are ubiquitous tools, although they are often taken for granted.
Today, it is difficult to imagine a time when our laboratory freezers were not well stocked with restriction enzymes, when DNA sequencing was not possible, or when genes were only accessible to the geneticists and could not be simply cloned out by recombinant DNA technology. Yet, in December 1971, a key paper appeared in PNAS that set the stage for much of what is now routine ( 1). In that paper, Kathleen Danna and Daniel Nathans of Johns Hopkins University (Baltimore) showed for the first time that the restriction enzyme called “endonuclease R,” discovered by Hamilton Smith and Kent Wilcox ( 2), could be used to produce specific fragments of simian virus 40 (SV40) DNA. Moreover, the authors showed that these fragments could be nicely separated from one another by electrophoresis on a polyacrylamide gel. The resulting picture ( Fig. 1) provided an immediate visual example of just how powerful the combination of restriction endonucleases and gel electrophoresis would be. Earlier that year, I had been fortunate to listen to a seminar given by Nathans at Harvard Medical School (Boston) and immediately began to think of the possibilities. It was a defining moment in my life when I realized that my half-formed plans for future research would be dropped and a new avenue pursued. It was because of this presentation that I developed my own lifelong passion for restriction endonucleases.},
  doi       = {10.1073/pnas.0500923102},
  file      = {2005_Roberts_5905.pdf:by-author/R/Roberts/2005_Roberts_5905.pdf:PDF},
  keywords  = {History; Restriction Endonucleases (REases)},
  owner     = {saulius},
  publisher = {Proceedings of the National Academy of Sciences},
  timestamp = {2016.12.04},
  creationdate = {2016-12-04T00:00:00},
  url       = {http://dx.doi.org/10.1073/pnas.0500923102},
}

@Article{Roberts2003b,
  author       = {Richard J Roberts and Marlene Belfort and Timothy Bestor and Ashok S Bhagwat and Thomas A Bickle and Jurate Bitinaite and Robert M Blumenthal and Sergey Kh Degtyarev and David T F Dryden and Kevin Dybvig and Keith Firman and Elizaveta S Gromova and Richard I Gumport and Stephen E Halford and Stanley Hattman and Joseph Heitman and David P Hornby and Arvydas Janulaitis and Albert Jeltsch and Jytte Josephsen and Antal Kiss and Todd R Klaenhammer and Ichizo Kobayashi and Huimin Kong and Detlev H Krüger and Sanford Lacks and Martin G Marinus and Michiko Miyahara and Richard D Morgan and Noreen E Murray and Valakunja Nagaraja and Andrzej Piekarowicz and Alfred Pingoud and Elisabeth Raleigh and Desirazu N Rao and Norbert Reich and Vladimir E Repin and Eric U Selker and Pang-Chui Shaw and Daniel C Stein and Barry L Stoddard and Waclaw Szybalski and Thomas A Trautner and James L Van Etten and Jorge M B Vitor and Geoffrey G Wilson and Shuang-yong Xu},
  journal      = {Nucleic Acids Res},
  title        = {A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes.},
  year         = {2003},
  month        = {Apr},
  number       = {7},
  pages        = {1805--1812},
  volume       = {31},
  abstract     = {A nomenclature is described for restriction endonucleases, DNA methyltransferases, homing endonucleases and related genes and gene products. It provides explicit categories for the many different Type II enzymes now identified and provides a system for naming the putative genes found by sequence analysis of microbial genomes.},
  creationdate = {2016-06-09T00:00:00},
  file         = {:by-author/R/Roberts/2003_Roberts_1805.pdf:PDF},
  institution  = {New England Biolabs, Beverly, MA 01915, USA. roberts@neb.com},
  keywords     = {Base Sequence; Binding Sites; Classification/genetics/metabolism; DNA; DNA Restriction Enzymes; Genetics/metabolism; Methyltransferases; Terminology as Topic},
  language     = {eng},
  medline-pst  = {ppublish},
  owner        = {em},
  pmid         = {12654995},
  timestamp    = {2016.06.09},
}

@Article{Roberts2003,
  author    = {Roberts, Richard J and Belfort, Marlene and Bestor, Timothy and Bhagwat, Ashok S and Bickle, Thomas A and Bitinaite, Jurate and Blumenthal, Robert M and Degtyarev, Sergey Kh and Dryden, David T F and Dybvig, Kevin and Firman, Keith and Gromova, Elizaveta S and Gumport, Richard I and Halford, Stephen E and Hattman, Stanley and Heitman, Joseph and Hornby, David P and Janulaitis, Arvydas and Jeltsch, Albert and Josephsen, Jytte and Kiss, Antal and Klaenhammer, Todd R and Kobayashi, Ichizo and Kong, Huimin and Krüger, Detlev H and Lacks, Sanford and Marinus, Martin G and Miyahara, Michiko and Morgan, Richard D and Murray, Noreen E and Nagaraja, Valakunja and Piekarowicz, Andrzej and Pingoud, Alfred and Raleigh, Elisabeth and Rao, Desirazu N and Reich, Norbert and Repin, Vladimir E and Selker, Eric U and Shaw, Pang-Chui and Stein, Daniel C and Stoddard, Barry L and Szybalski, Waclaw and Trautner, Thomas A and Van Etten, James L and Vitor, Jorge M B and Wilson, Geoffrey G and Xu, Shuang-yong},
  journal   = {Nucleic acids research},
  title     = {A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes.},
  year      = {2003},
  pages     = {1805--12},
  volume    = {31},
  abstract  = {A nomenclature is described for restriction endonucleases, DNA methyltransferases, homing endonucleases and related genes and gene products. It provides explicit categories for the many different Type II enzymes now identified and provides a system for naming the putative genes found by sequence analysis of microbial genomes.},
  file      = {Roberts_2003_1805-RE-nomenclature.pdf:by-author/R/Roberts/2003_Roberts_1805.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Roberts2015a,
  author       = {Richard J Roberts and Tamas Vincze and Janos Posfai and Dana Macelis},
  journal      = {Nucleic Acids Res},
  title        = {REBASE--a database for DNA restriction and modification: enzymes, genes and genomes.},
  year         = {2015},
  month        = {Jan},
  number       = {Database issue},
  pages        = {D298--D299},
  volume       = {43},
  abstract     = {REBASE is a comprehensive and fully curated database of information about the components of restriction-modification (RM) systems. It contains fully referenced information about recognition and cleavage sites for both restriction enzymes and methyltransferases as well as commercial availability, methylation sensitivity, crystal and sequence data. All genomes that are completely sequenced are analyzed for RM system components, and with the advent of PacBio sequencing, the recognition sequences of DNA methyltransferases (MTases) are appearing rapidly. Thus, Type I and Type III systems can now be characterized in terms of recognition specificity merely by DNA sequencing. The contents of REBASE may be browsed from the web http://rebase.neb.com and selected compilations can be downloaded by FTP (ftp.neb.com). Monthly updates are also available via email.},
  creationdate = {2016-06-09T00:00:00},
  doi          = {10.1093/nar/gku1046},
  file         = {:by-author/R/Roberts/2015_Roberts_D298.pdf:PDF},
  institution  = {New England Biolabs, Ipswich, MA 01938, USA.},
  keywords     = {Chemistry/genetics/metabolism; DNA; DNA Modification Methylases; DNA Restriction Enzymes; Databases; Genes; Genetic; Genomics; Internet; Sequence Analysis; Software},
  language     = {eng},
  medline-pst  = {ppublish},
  owner        = {em},
  pii          = {gku1046},
  pmid         = {25378308},
  timestamp    = {2016.06.09},
  url          = {http://dx.doi.org/10.1093/nar/gku1046},
}

@Article{Roberts2010,
  author      = {Roberts, Richard J. and Vincze, Tamas and Posfai, Janos and Macelis, Dana},
  journal     = {Nucleic Acids Res},
  title       = {REBASE--a database for DNA restriction and modification: enzymes, genes and genomes.},
  year        = {2010},
  pages       = {D234--D236},
  volume      = {38},
  abstract    = {REBASE is a comprehensive database of information about restriction enzymes, DNA methyltransferases and related proteins involved in the biological process of restriction-modification (R-M). It contains fully referenced information about recognition and cleavage sites, isoschizomers, neoschizomers, commercial availability, methylation sensitivity, crystal and sequence data. Experimentally characterized homing endonucleases are also included. The fastest growing segment of REBASE contains the putative R-M systems found in the sequence databases. Comprehensive descriptions of the R-M content of all fully sequenced genomes are available including summary schematics. The contents of REBASE may be browsed from the web (http://rebase.neb.com) and selected compilations can be downloaded by ftp (ftp.neb.com). Additionally, monthly updates can be requested via email.},
  doi         = {10.1093/nar/gkp874},
  file        = {2010_Roberts_D234.pdf:by-author/R/Roberts/2010_Roberts_D234.pdf:PDF},
  institution = {New England Biolabs, Inc, 240 County Road, Ipswich, MA 01938, USA.},
  keywords    = {Archaeal; Bacterial; Binding Sites; Computational Biology; DNA Modification Methylases; DNA Restriction Enzymes; Databases; Genetic; Genetics; Genome; Genomics; Information Storage and Retrieval; Internet; Methods; Methods/trends; Protein; Protein Structure; Software; Substrate Specificity; Tertiary},
  language    = {eng},
  medline-pst = {ppublish},
  owner       = {saulius},
  pii         = {gkp874},
  pmid        = {19846593},
  timestamp = {2012.01.30},
  creationdate = {2012-01-30T00:00:00},
  url         = {http://dx.doi.org/10.1093/nar/gkp874},
}

@Article{Roberts2010c,
  author       = {Richard J Roberts and Tamas Vincze and Janos Posfai and Dana Macelis},
  journal      = {Nucleic Acids Res},
  title        = {REBASE--a database for DNA restriction and modification: enzymes, genes and genomes.},
  year         = {2010},
  month        = {Jan},
  number       = {Database issue},
  pages        = {D234--D236},
  volume       = {38},
  abstract     = {REBASE is a comprehensive database of information about restriction enzymes, DNA methyltransferases and related proteins involved in the biological process of restriction-modification (R-M). It contains fully referenced information about recognition and cleavage sites, isoschizomers, neoschizomers, commercial availability, methylation sensitivity, crystal and sequence data. Experimentally characterized homing endonucleases are also included. The fastest growing segment of REBASE contains the putative R-M systems found in the sequence databases. Comprehensive descriptions of the R-M content of all fully sequenced genomes are available including summary schematics. The contents of REBASE may be browsed from the web (http://rebase.neb.com) and selected compilations can be downloaded by ftp (ftp.neb.com). Additionally, monthly updates can be requested via email.},
  creationdate = {2011-06-10T00:00:00},
  doi          = {10.1093/nar/gkp874},
  file         = {2010_Roberts_D234.pdf:by-author/R/Roberts/2010_Roberts_D234.pdf:PDF},
  institution  = {New England Biolabs, Inc, 240 County Road, Ipswich, MA 01938, USA.},
  keywords     = {Archaeal; Bacterial; Binding Sites; Computational Biology; DNA Modification Methylases; DNA Restriction Enzymes; Databases; Genetic; Genome; Genomics; Information Storage and Retrieval; Internet; Protein; Protein Structure; Software; Substrate Specificity; Tertiary},
  owner        = {em},
  pii          = {gkp874},
  pmid         = {19846593},
  timestamp    = {2011.06.10},
  url          = {http://dx.doi.org/10.1093/nar/gkp874},
}

@Article{Roberts2005,
  author    = {Roberts, Richard J. and Vincze, Tamas and Posfai, Janos and Macelis, Dana},
  journal   = {Nucleic acids research},
  title     = {REBASE--restriction enzymes and DNA methyltransferases.},
  year      = {2005},
  pages     = {D230-2},
  volume    = {33},
  abstract  = {REBASE is a comprehensive database of information about restriction enzymes, DNA methyltransferases and related proteins involved in restriction-modification. It contains both published and unpublished work with information about recognition and cleavage sites, isoschizomers, commercial availability, crystal and sequence data. Experimentally characterized homing endonucleases are also included. Additionally, REBASE contains complete and up-to-date information about the methylation sensitivity of restriction endonucleases. An extensive analysis is included of the restriction-modification systems that are predicted to be present in the sequenced bacterial and archaeal genomes from GenBank. The contents of REBASE are available by browsing from the web (http://rebase.neb.com/rebase/rebase.html) and through selected compilations by ftp (ftp.neb.com) and as monthly updates that can be requested via email.},
  file      = {:by-author/R/Roberts/2005_Roberts_D230.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Roberts2003a,
  author    = {Roberts, Richard J and Vincze, Tamas and Posfai, Janos and Macelis, Dana},
  journal   = {Nucleic acids research},
  title     = {REBASE: restriction enzymes and methyltransferases.},
  year      = {2003},
  pages     = {418--20},
  volume    = {31},
  abstract  = {REBASE contains comprehensive information about restriction enzymes, DNA methyltransferases and related proteins such as nicking enzymes, specificity subunits and control proteins. It contains published and unpublished references, recognition and cleavage sites, isoschizomers, commercial availability, crystal and sequence data. Homing endonucleases are also included. REBASE contains the most complete and up-to-date information about the methylation sensitivity of restriction endonucleases. In addition, there is extensive information about the known and putative restriction-modification (R-M) systems in more than 100 sequenced bacterial and archaeal genomes. The data is available on the web (http://rebase.neb.com/rebase/rebase.html), through ftp (ftp.neb.com) and as monthly updates via email.},
  file      = {Roberts_2003_418-REBASE.pdf:by-author/R/Roberts/2003_Roberts_418.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Robertson2007,
  author    = {Robertson, Michael P and Scott, William G},
  journal   = {Science (New York, N.Y.)},
  title     = {The structural basis of ribozyme-catalyzed RNA assembly.},
  year      = {2007},
  pages     = {1549--53},
  volume    = {315},
  file      = {2007_Robertson_1549.pdf:by-author/R/Robertson/2007_Robertson_1549.pdf:PDF},
  keywords  = {Ribozymes},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Manuscript{Robertz2002,
  author    = {Sven Gestegard Robertz},
  title     = {Anagram Generation Using Sentence Probabilities},
  year      = {2002},
  keywords  = {Algorithms; Anagrams; Computer Science (CS)},
  abstract  = {An anagram is a word or phrase made by transposing the letters of another word or phrase, and is a popular kind of puzzle. Finding anagrams for a word or a phrase is a difficult task due to the huge number of possible permutations of the letters, and using computers for anagram generation has been increasingly popular. This paper presents an attempt on constructing an automatic anagram generator based on sentence probabilities. Using a relatively small corpus of one million words, a simple implementation using bigram probabilities proved to yield quite satisfactory results but is too inclusive due to the limited context recorded in bigrams. A trigram based version produces much less incorrect results but would need a larger corpus since it is much more exclusive.},
  file      = {:by-author/R/Robertz/2002_Robertz.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Robinson2015,
  author    = {Robinson, Donald A. and Yoo, Jason J. and Castañeda, Alma D. and Gu, Brett and Dasari, Radhika and Crooks, Richard M. and Stevenson, Keith J.},
  journal   = {ACS nano},
  title     = {Increasing the collision rate of particle impact electroanalysis with magnetically guided {Pt}-decorated iron oxide nanoparticles},
  year      = {2015},
  file      = {[PDF] from utexas.edu:by-author/R/Robinson/2015_Robinson.pdf:application/pdf;Snapshot:by-author/R/Robinson/2015_Robinson.html:text/html},
  groups    = {sg/JAC2009},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://pubs.acs.org/doi/abs/10.1021/acsnano.5b02892},
  urldate   = {2015-08-31},
}

@Electronic{Robinson,
  author    = {Tim Robinson},
  title     = {Memory Management 2},
  file      = {:by-author/R/Robinson/XXXX_Robinson.pdf:PDF},
  owner     = {saulius},
  timestamp = {2011.12.13},
  creationdate = {2011-12-13T00:00:00},
}

@Article{Rocha2001,
  author    = {Rocha, E. P. and Danchin, A. and Viari, A.},
  journal   = {Genome research},
  title     = {Evolutionary role of restriction/modification systems as revealed by comparative genome analysis.},
  year      = {2001},
  pages     = {946--58},
  volume    = {11},
  abstract  = {Type II restriction modification systems (RMSs) have been regarded either as defense tools or as molecular parasites of bacteria. We extensively analyzed their evolutionary role from the study of their impact in the complete genomes of 26 bacteria and 35 phages in terms of palindrome avoidance. This analysis reveals that palindrome avoidance is not universally spread among bacterial species and that it does not correlate with taxonomic proximity. Palindrome avoidance is also not universal among bacteriophage, even when their hosts code for RMSs, and depends strongly on the genetic material of the phage. Interestingly, palindrome avoidance is intimately correlated with the infective behavior of the phage. We observe that the degree of palindrome and restriction site avoidance is significantly and consistently less important in phages than in their bacterial hosts. This result brings to the fore a larger selective load for palindrome and restriction site avoidance on the bacterial hosts than on their infecting phages. It is then consistent with a view where type II RMSs are considered as parasites possibly at the verge of mutualism. As a consequence, RMSs constitute a nontrivial third player in the host-parasite relationship between bacteria and phages.},
  file      = {:by-author/R/Rocha/2001_Rocha_946.pdf:PDF},
  keywords  = {Evolution},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Rocha2005,
  author    = {Rocha, Eduardo P. C. and Cornet, Emmanuel and Michel, Bénédicte},
  journal   = {PLoS genetics},
  title     = {Comparative and evolutionary analysis of the bacterial homologous recombination systems.},
  year      = {2005},
  pages     = {e15},
  volume    = {1},
  abstract  = {Homologous recombination is a housekeeping process involved in the maintenance of chromosome integrity and generation of genetic variability. Although detailed biochemical studies have described the mechanism of action of its components in model organisms, there is no recent extensive assessment of this knowledge, using comparative genomics and taking advantage of available experimental data on recombination. Using comparative genomics, we assessed the diversity of recombination processes among bacteria, and simulations suggest that we missed very few homologs. The work included the identification of orthologs and the analysis of their evolutionary history and genomic context. Some genes, for proteins such as RecA, the resolvases, and RecR, were found to be nearly ubiquitous, suggesting that the large majority of bacterial genomes are capable of homologous recombination. Yet many genomes show incomplete sets of presynaptic systems, with RecFOR being more frequent than RecBCD/AddAB. There is a significant pattern of co-occurrence between these systems and antirecombinant proteins such as the ones of mismatch repair and SbcB, but no significant association with nonhomologous end joining, which seems rare in bacteria. Surprisingly, a large number of genomes in which homologous recombination has been reported lack many of the enzymes involved in the presynaptic systems. The lack of obvious correlation between the presence of characterized presynaptic genes and experimental data on the frequency of recombination suggests the existence of still-unknown presynaptic mechanisms in bacteria. It also indicates that, at the moment, the assessment of the intrinsic stability or recombination isolation of bacteria in most cases cannot be inferred from the identification of known recombination proteins in the genomes.},
  file      = {:by-author/R/Rocha/2005_Rocha_e15.pdf:PDF},
  keywords  = {Evolution},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Rochkind1975,
  author    = {Rochkind, Marc J.},
  journal   = {IEEE Transactions on Software Engineering},
  title     = {The Source Code Control System},
  year      = {1975},
  pages     = {364--370},
  volume    = {1},
  file      = {:by-author/R/Rochkind/1975_Rochkind_364.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@Manuscript{Roddick1999,
  author    = {John F. Roddick},
  title     = {A Survey of Schema Versioning Issues for Database Systems},
  year      = {1999},
  keywords  = {Computer Science (CS); Database Schema; Database Versioning; Reproducible Research},
  url       = {https://pdfs.semanticscholar.org/310c/0b3199fb14dc300b78db5f138a7aeab3d4d5.pdf},
  abstract  = {Schema versioning is one of a number of related areas dealing with the same general problem - that of using multiple heterogeneous schemata for various database related tasks. In particular, schema versioning, and its weaker companion, schema evolution, deal with the need to retain current data and software system functionality in the face of changing database structure. Schema versioning and schema evolution offer a solution to the problem by enabling intelligent handling of any temporal mismatch between data and data structure. This survey discusses the modelling, architectural and query language issues relating to the support of evolving schemata in database systems. An indication of the future directions of schema versioning research are also given},
  comment   = {Cited by Rauber2016a in this revision.},
  file      = {1999_Roddick.pdf:by-author/R/Roddick/1999_Roddick.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.11.21},
  creationdate = {2016-11-21T00:00:00},
}

@Article{Rode1999a,
  author    = {Rode, B M},
  journal   = {Peptides},
  title     = {Peptides and the origin of life.},
  year      = {1999},
  pages     = {773--86},
  volume    = {20},
  abstract  = {Considering the state-of-the-art views of the geochemical conditions of the primitive earth, it seems most likely that peptides were produced ahead of all other oligomer precursors of biomolecules. Among all the reactions proposed so far for the formation of peptides under primordial earth conditions, the salt-induced peptide formation reaction in connection with adsorption processes on clay minerals would appear to be the simplest and most universal mechanism known to date. The properties of this reaction greatly favor the formation of biologically relevant peptides within a wide variation of environmental conditions such as temperature, pH, and the presence of inorganic compounds. The reaction-inherent preferences of certain peptide linkages make the argument of 'statistical impossibility' of the evolutionary formation of the 'right' peptides and proteins rather insignificant. Indeed, the fact that these sequences are reflected in the preferential sequences of membrane proteins of archaebacteria and prokaryonta distinctly indicates the relevance of this reaction for chemical peptide evolution. On the basis of these results and the recent findings of self-replicating peptides, some ideas have been developed as to the first steps leading to life on earth.},
  doi       = {10.1016/S0196-9781(99)00062-5},
  file      = {1999_Rode_773.pdf:by-author/R/Rode/1999_Rode_773.pdf:PDF},
  keywords  = {Chemical Prebiotic},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Rode2007,
  author    = {Rode, Bernd M and Fitz, Daniel and Jakschitz, Thomas},
  journal   = {Chemistry \&amp; biodiversity},
  title     = {The first steps of chemical evolution towards the origin of life.},
  year      = {2007},
  pages     = {2674--702},
  volume    = {4},
  doi       = {10.1002/cbdv.200790220},
  file      = {2007_Rode_2674.pdf:by-author/R/Rode/2007_Rode_2674.pdf:PDF},
  keywords  = {Chemical Prebiotic; Evolution},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Rode1999b,
  author    = {Rode, B M and Flader, W and Sotriffer, C and Righi, A},
  journal   = {Peptides},
  title     = {Are prions a relic of an early stage of peptide evolution?},
  year      = {1999},
  pages     = {1513--1516},
  volume    = {20},
  abstract  = {The rather unique properties of prions and their presence in very different kinds of living species suggest that this type of molecule was created at a very early stage of evolution and may even represent a relic from a time where peptide evolution was ongoing and RNA/DNA did not yet exist. A comparison of the most frequently occurring amino acid sequences in known prions with the sequences preferentially formed in the salt-induced peptide formation reaction, the most simple mechanism enabling the formation of peptides under primitive earth conditions, shows a remarkable coincidence that strongly supports this hypothesis.},
  doi       = {10.1016/S0196-9781(99)00163-1},
  file      = {1999_Rode_1513.pdf:by-author/R/Rode/1999_Rode_1513.pdf:PDF},
  keywords  = {Chemical Prebiotic},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Rode2006,
  author    = {Bernd M. Rode and Thomas S. Hofer},
  journal   = {Pure Appl. Chem.},
  title     = {How to access structure and dynamics of solutions: The capabilities of computational methods (Special Topic Article)},
  year      = {2006},
  pages     = {525--539},
  volume    = {78},
  abstract  = {The progress of computational chemistry in the treatment of liquid systems is outlined, and the combination of the statistical methods (Monte Carlo, MC, and molecular dynamics, MD) with quantum mechanics as the main foundation of this progress is emphasized. The difficulties of experimental studies of liquid systems without having obtained sophisticated theoretical models describing the structural entities and the dynamical behavior of these liquids demonstrate that chemistry research is in a transition phase, where theory and high-performance computing have not only become a valuable supplement, but an essential and almost indispensable component to secure a correct interpretation of measured data.},
  doi       = {10.1351/pac200678030525},
  file      = {2006_Rode_525.pdf:by-author/R/Rode/2006_Rode_525.pdf:PDF},
  groups    = {sg/Molecular dynamics},
  keywords  = {Ab Initio Simulation Methods; Picosecond Dynamics; QM/MM Simulations; QMCF/MD Simulations; Quantum Chemistry; Statistical Simulations; Structure of Liquids},
  owner     = {saulius},
  timestamp = {2011.05.18},
  creationdate = {2011-05-18T00:00:00},
}

@Article{Rode2006a,
  author    = {Rode, Bernd M. and Hofer, Thomas S. and Randolf, Bernhard R. and Schwenk, Christian F. and Xenides, Demetrios and Vchirawongkwin, Viwat},
  journal   = {Theoretical Chemistry Accounts},
  title     = {Ab initio quantum mechanical charge field (QMCF) molecular dynamics: a QM/MM – MD procedure for accurate simulations of ions and complexes},
  year      = {2006},
  issn      = {1432-881X},
  pages     = {77--85},
  volume    = {115},
  abstract  = {A new formalism for quantum mechanical / molec- ular mechanical (QM/MM) dynamics of chemical species in solution has been developed, which does not require the con- struction of any other potential functions except those for solvent–solvent interactions, maintains all the advantages of large simulation boxes and ensures the accuracy of ab initio quantum mechanics for all forces acting in the chemically most relevant region. Interactions between solute and more distant solvent molecules are incorporated by a dynamically adjusted force field corresponding to the actual molecular configuration of the simulated system and charges derived from the electron distribution in the solvate. The new for- malism has been tested with some examples of hydrated ions, for which accurate conventional ab initio QM/MM simula- tions have been previously performed, and the comparison shows equivalence and in some aspects superiority of the new method. As this simulation procedure does not require any tedious construction of two-and three-body interaction poten- tials inherent to conventional QM/MM approaches, it opens the straightforward access to ab initio molecular dynamics simulations of any kind of solutes, such as metal complexes and other composite species in solution.},
  doi       = {10.1007/s00214-005-0049-1},
  file      = {2006_Rode_77.pdf:by-author/R/Rode/2006_Rode_77.pdf:PDF},
  groups    = {sg/Molecular dynamics},
  issue     = {2-3},
  keywords  = {Quantum Chemistry},
  language  = {English},
  owner     = {saulius},
  publisher = {Springer-Verlag},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1007/s00214-005-0049-1},
}

@Article{Rode1999c,
  author    = {Rode, B M and Son, H L and Suwannachot, Y},
  journal   = {Origins of life and evolution of the biosphere : the journal of the International Society for the Study of the Origin of Life},
  title     = {The combination of salt induced peptide formation reaction and clay catalysis: a way to higher peptides under primitive earth conditions.},
  year      = {1999},
  pages     = {273--86},
  volume    = {29},
  abstract  = {Two reactions with suggested prebiotic relevance for peptide evolution, the salt induced peptide formation reaction and the peptide chain elongation/stabilization on clay minerals have been combined in experimental series starting from dipeptides and dipeptide/amino acid mixtures. The results show that both reactions can take place simultaneously in the same reaction environment and that the presence of mineral catalysts favours the formation of higher oligopeptides. These findings lend further support to the relevance of these reactions for peptide evolution on the primitive earth. The detailed effects of the specific clay mineral depend both on the nature of the mineral and the reactants in solution.},
  doi       = {10.1023/A:1006540101290},
  file      = {1999_Rode_273.pdf:by-author/R/Rode/1999_Rode_273.pdf:PDF},
  keywords  = {Chemical Prebiotic},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Rode1999,
  author    = {Bernd Michael Rode and Yuttana Suwannachot},
  journal   = {Coordination Chemistry Reviews},
  title     = {The possible role of Cu(II) for the origin of life},
  year      = {1999},
  pages     = {1085--1099},
  volume    = {190–192},
  abstract  = {The most crucial prerequisite for the origin of life — most probably long before RNA/ DNA-based reproduction could develop— was the formation of peptides and proteins under the conditions of the primitive earth. All reactions formerly proposed to have enabled this step of chemical evolution are highly questionable concerning their realizability under prebiotic conditions. However, the salt-induced peptide formation (SIPF) reaction, found some years ago, provides much more encouraging aspects for the creation of various peptides under such conditions. The necessary reagents — besides amino acids — are only sodium chloride and copper ions, and for both there is sufficient evidence of their presence on the primitive earth. The SIPF reaction occurs readily within a wide spectrum of environmental conditions (atmosphere, temperature etc.) and combines preferentially a-amino acids to peptides. Since it is applicable to all amino acids investigated so far, it has been possible to compare its preferentially formed peptide linkages with those found in the membrane proteins of the oldest still living organisms, namely archebacteria. The coincidence of these preferences is so high that it could have occurred by chance only with a probability of 10 − 18. This leads to the conclusions that the SIPF reaction has been the basis for the formation of first peptide and protein matrices on earth (later reproduced by other, more efficient mechanisms and thus conserved, with some evolutionary variations, in these old organisms until now) and that, hence, Cu(II) has played a most significant role in the origin of life on earth.},
  doi       = {10.1016/S0010-8545(99)00159-9},
  file      = {1999_Rode_1085.pdf:by-author/R/Rode/1999_Rode_1085.pdf:PDF},
  keywords  = {Chemical Evolution; Chemical Prebiotic; Evolution; Origin of Life; Role of Cu(II); Salt Induced Peptide Formation (SIPF)},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Rodgers2000,
  author    = {Rodgers, A. J. and Wilce, M. C.},
  journal   = {Nature structural biology},
  title     = {Structure of the gamma-epsilon complex of ATP synthase.},
  year      = {2000},
  pages     = {1051--4},
  volume    = {7},
  abstract  = {ATP synthases (F(1)F(o)-ATPases) use energy released by the movement of protons down a transmembrane electrochemical gradient to drive the synthesis of ATP, the universal biological energy currency. Proton flow through F(o) drives rotation of a ring of c-subunits and a complex of the gamma and epsilon-subunits, causing cyclical conformational changes in F(1) that are required for catalysis. The crystal structure of a large portion of F(1) has been resolved. However, the structure of the central portion of the enzyme, through which conformational changes in F(o) are communicated to F(1), has until now remained elusive. Here we report the crystal structure of a complex of the epsilon-subunit and the central domain of the gamma-subunit refined at 2.1 A resolution. The structure reveals how rotation of these subunits causes large conformational changes in F(1), and thereby provides new insights into energy coupling between F(o) and F(1).},
  file      = {:by-author/R/Rodgers/2000_Rodgers_1051.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Webpage{Rodriguez1993,
  author    = {Brad Rodriguez},
  retrieved = {2015-08-06},
  title     = {Moving FORTH. Part 1: Design Decisions in the Forth Kernel},
  url       = {http://www.bradrodriguez.com/papers/moving1.htm},
  year      = {1993},
  file      = {ODT:by-author/R/Rodriguez/1993_Rodriguez.odt:LibreOfficeDocument},
  owner     = {saulius},
  timestamp = {2015.08.06},
  creationdate = {2015-08-06T00:00:00},
}

@Article{Rodriguez-Gonzalez2013,
  author     = {Rodríguez-González, Benito and Vereda, Fernando and de Vicente, Juan and Hidalgo-Álvarez, Roque},
  journal    = {The Journal of Physical Chemistry C},
  title      = {Rough and hollow spherical magnetite microparticles: revealing the morphology, internal structure, and growth mechanism},
  year       = {2013},
  pages      = {5397--5406},
  volume     = {117},
  file       = {[PDF] from researchgate.net:by-author/R/Rodríguez-González/2013_Rodríguez-González_5397.pdf:application/pdf;Snapshot:by-author/R/Rodríguez-González/2013_Rodríguez-González_5397.html:text/html},
  groups     = {sg/JAC2009},
  owner      = {saulius},
  shorttitle = {Rough and hollow spherical magnetite microparticles},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url        = {http://pubs.acs.org/doi/abs/10.1021/jp3100206},
  urldate    = {2015-08-31},
}

@Manuscript{Roessle19XX,
  author    = {Roessle},
  title     = {The conformational switching of the GroES upon formation of the activated GroEL/GroES complex},
  year      = {19XX},
  abstract  = {Chaperonins are a special group of oligomeric proteins that supports the protein folding in the cytoplasm of a cell if spontaneous folding fails. The chaperonin system GroE form E. coli consists of two proteins GroEL and GroES, both oligomeric proteins with 7-fold symmetry. The co-chaperonin GroES has a dome shaped overall architecture built of seven identical subunits. This heptamer binds in the presence of nucleotides to the cylindrical shaped double ring GroEL main chaperonin. The crystal structure of the asymmetric GroEL/GroES complex shows large conformational changes of GroEL upon GroES binding, whereas GroES differs only slightly from the non-bound structure. Small angle neutron scattering (SANS) experiments using deuterated D-labelled GroES, GroEL and a single ring GroEL mutant under contrast matching conditions identified a conformational switching of the GroES upon binding to GroEL. This conformational GroES intermediate shows a by an angle of 10O flattened dome-shaped GroES and appears at the single ring mutant as well as at the symmetric GroEL-(GroES)2 complex. This movement of the GroES is not found in the high-resolution crystal structure of the asymmetric complex. Beside this small movement of the GroES an inward tilt of the GroES bound GroEL cis-ring of 4O is visible in the crystal structure. The SANS results of the single ring GroEL mutant indicates that the single ring mutant does not undergo these conformational change upon the GroES binding. The results indicate a switching of the GroEL/GroES system between two different conformational states whereas the crystal structure shows the “activated cis-ring” structure.},
  file      = {:by-author/R/Roessle/19XX_Roessle_manuscript.pdf:PDF},
  owner     = {saulius},
  pages     = {manuscript},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Presentation{Roessle2010,
  author    = {Roessle},
  title     = {Data recording, reduction and processing},
  year      = {2010},
  file      = {:by-author/R/Roessle/2010_Roessle_slides.pdf:PDF},
  keywords  = {SAXS},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@TechReport{Roetzheim2004,
  author      = {William Roetzheim},
  institution = {Cost Xpert Group, Inc.},
  title       = {Estimating Software Costs},
  year        = {2004},
  note        = {4 article series},
  abstract    = {In extensive research of over 20,000 software development projects spanning 18 years, it is found that more projects are doomed fr om poor cost and schedule estimates than they ever are from technical, political, or development team problems. Yet, so few companies and indi v i duals really underst and that software estimating can be a science , not just an art . It really is possible to accurately and consistently estimate development co sts and schedules for a wide range of projects. This series of 4 articles will provide you the tools you need to understand step-by-step approac hes to esti mating the cost and schedule for your projects. A l though there is a wide range of software cost estimating tools on the market to help with this process, we will focus in this series of articles on understanding the fundamental concepts. You will be able to implement the concepts in these articles using nothi ng more complicated than a spreadsheet.},
  file        = {2004_Roetzheim_1.pdf:by-author/R/Roetzheim/2004_Roetzheim_1.pdf:PDF},
  keywords    = {Computer Science (CS); Software Cost Estimation; Software Development; Software Engineering},
  owner       = {saulius},
  timestamp = {2015.11.19},
  creationdate = {2015-11-19T00:00:00},
  url         = {http://cs.iupui.edu/~mroberts/n361/SDArticle1.pdf},
}

@TechReport{Roetzheim2004a,
  author      = {William Roetzheim},
  institution = {Cost Xpert Group, Inc.},
  title       = {Project Cost Adjustments},
  year        = {2004},
  note        = {4 article series},
  abstract    = {Research by Capers Jones has indicated that formal software cost estimating techniques can roughly double the probability of your software project being completed successfully, but few companies and individuals really understand that software estimating can be a science, not just an art. It really is possible to accurately and consistently estimate development costs and schedules for a wide range of projects. This series of 4 articles provides you the tools you need to understand step-by-step approaches to estimating the cost and schedule for your projects. Although there is a wide range of software cost estimating tools on the market to help with this process, we focus in this series of articles on understanding the fundamental concepts. You will be able to implement the concepts in these articles using nothing more complicated than a spreadsheet.},
  file        = {2004_Roetzheim_1.pdf:by-author/R/Roetzheim/2004_Roetzheim_2.pdf:PDF},
  keywords    = {Computer Science (CS); Software Cost Estimation; Software Development; Software Engineering},
  owner       = {saulius},
  timestamp = {2015.11.19},
  creationdate = {2015-11-19T00:00:00},
  url         = {http://cs.iupui.edu/~mroberts/n361/SDArticle2.pdf},
}

@TechReport{Roetzheim2004b,
  author      = {William Roetzheim},
  institution = {Cost Xpert Group, Inc.},
  title       = {Dealing with Reuse},
  year        = {2004},
  note        = {4 article series},
  abstract    = {This article explains how to quantify the impact of software reuse and commercial components/libraries on your estimate.},
  file        = {2004_Roetzheim_1.pdf:by-author/R/Roetzheim/2004_Roetzheim_3.pdf:PDF},
  keywords    = {Computer Science (CS); Software Cost Estimation; Software Development; Software Engineering},
  owner       = {saulius},
  timestamp = {2015.11.19},
  creationdate = {2015-11-19T00:00:00},
  url         = {http://cs.iupui.edu/~mroberts/n361/SDArticle3.pdf},
}

@TechReport{Roetzheim2004c,
  author      = {William Roetzheim},
  institution = {Cost Xpert Group, Inc.},
  title       = {Creating the Project Plan},
  year        = {2004},
  note        = {4 article series},
  abstract    = {One of the most difficult tasks for a project manager is the creation of the project baseline plan that will be used to manage the development effort. Even with a correct estimate of effort and time, it is easy to forget tasks, incorrectly allocate effort among tasks, or fail to allow enough resources for maintenance. Even in this area, we find that software estimating can be a science, not just an art. It really is possible to accurately and consistently estimate development costs and schedules for a wide range of projects, then quickly create a project plan. This series of 4 articles provides you the tools you need to understand step-by-step approaches to estimating the cost and schedule for your projects. Although there is a wide range of software cost estimating tools on the market to help with this process, we focus in this series of articles on understanding the fundamental concepts. You will be able to implement the concepts in these articles using nothing more complicated than a spreadsheet.},
  file        = {2004_Roetzheim_4.pdf:by-author/R/Roetzheim/2004_Roetzheim_4.pdf:PDF},
  keywords    = {Computer Science (CS); Software Cost Estimation; Software Development; Software Engineering},
  owner       = {saulius},
  timestamp = {2015.11.19},
  creationdate = {2015-11-19T00:00:00},
  url         = {http://cs.iupui.edu/~mroberts/n361/SDArticle4.pdf},
}

@Article{Rogers2010,
  author    = {Rogers, David and Hahn, Mathew},
  journal   = {Journal of Chemical Information and Modeling},
  title     = {Extended-Connectivity Fingerprints},
  year      = {2010},
  pages     = {742--754},
  volume    = {50},
  abstract  = {Extended-connectivity fingerprints (ECFPs) are a novel class of topological fingerprints for molecular characterization. Historically, topological fingerprints were developed for substructure and similarity searching. ECFPs were developed specifically for structure−activity modeling. ECFPs are circular fingerprints with a number of useful qualities: they can be very rapidly calculated; they are not predefined and can represent an essentially infinite number of different molecular features (including stereochemical information); their features represent the presence of particular substructures, allowing easier interpretation of analysis results; and the ECFP algorithm can be tailored to generate different types of circular fingerprints, optimized for different uses. While the use of ECFPs has been widely adopted and validated, a description of their implementation has not previously been presented in the literature.},
  doi       = {10.1021/ci100050t},
  eprint    = {http://pubs.acs.org/doi/pdf/10.1021/ci100050t},
  file      = {2010_Rogers_742.pdf:by-author/R/Rogers/2010_Rogers_742.pdf:PDF},
  keywords  = {Algorithms; Chemical Fingerprints; Chemoinformatics; Databases; Morgan Fingerprints},
  owner     = {saulius},
  timestamp = {2014.04.30},
  creationdate = {2014-04-30T00:00:00},
  url       = {http://pubs.acs.org/doi/abs/10.1021/ci100050t},
}

@Article{Rogers1960,
  author    = {Rogers, David J. and Tanimoto, Taffee T.},
  journal   = {Science},
  title     = {A Computer Program for Classifying Plants},
  year      = {1960},
  pages     = {1115--1118},
  file      = {:by-author/R/Rogers/1960_Rogers_1115.pdf:PDF},
  owner     = {andrius},
  timestamp = {2012.06.16},
  creationdate = {2012-06-16T00:00:00},
}

@Article{Rohde2015,
  author    = {Rohde, Peter P. and Dowling, Jonathan P.},
  journal   = {Science},
  title     = {The on-ramp to the all-optical quantum information processing highway},
  year      = {2015},
  issn      = {0036-8075, 1095-9203},
  pages     = {696--696},
  volume    = {349},
  abstract  = {Since the first formulations of quantum mechanics in the early 20th century, it became clear that the enormous complexity of quantum-mechanical systems presented intractable computational problems. Richard Feynman was the first to turn this problem on its head. He asked whether we could exploit this quantum complexity to construct a computer based on these same quantum mechanical principles, offering exponential algorithmic improvements, and whether such a computer could efficiently simulate quantum systems that our classical computers are unable to simulate. This challenge initiated the field of quantum computing and is today a major field of research in the physics and computer science communities. One hurdle has been to construct devices that match the flexible programmability of classical computers. On page 711 of this issue, Carolan et al. (1) present a step in that direction, a fully reconfigurable optical waveguide circuit that can be programmed to implement arbitrary linear optics transformations on up to six optical modes.},
  doi       = {10.1126/science.aac7250},
  file      = {Rohde and Dowling - 2015 - The on-ramp to the all-optical quantum information.pdf:by-author/R/Rohde/2015_Rohde_696.pdf:application/pdf;Snapshot:by-author/R/Rohde/2015_Rohde_696.html:text/html},
  language  = {en},
  owner     = {saulius},
  pmid      = {26273045},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://www.sciencemag.org/content/349/6249/696},
  urldate   = {2015-09-10},
}

@Article{Rohs2010,
  author    = {Rohs, Remo and Jin, Xiangshu Jin and west, Sean M. and Joshi, Rohit and Honig, Barry and Mann, Richard S.},
  journal   = {Annu. Rev. Biochem.},
  title     = {Origins of Specificity in Protein-DNA Recognition},
  year      = {2010},
  pages     = {233–269},
  volume    = {79},
  abstract  = {Specific interactions between proteins and DNA are fundamental to many biological processes. In this review, we provide a revised view of protein-DNA interactions that emphasizes the importance of the three- dimensional structures of both macromolecules. We divide protein- DNA interactions into two categories: those when the protein recog- nizes the unique chemical signatures of the DNA bases (base readout) and those when the protein recognizes a sequence-dependent DNA shape (shape readout). We further divide base readout into those inter- actions that occur in the major groove from those that occur in the minor groove. Analogously, the readout of the DNA shape is subdivided into global shape recognition (for example, when the DNA helix exhibits an overall bend) and local shape recognition (for example, when a base pair step is kinked or a region of the minor groove is narrow). Based on the >1500 structures of protein-DNA complexes now available in the Protein Data Bank, we argue that individual DNA-binding pro- teins combine multiple readout mechanisms to achieve DNA-binding specificity. Specificity that distinguishes between families frequently in- volves base readout in the major groove, whereas shape readout is often exploited for higher resolution specificity, to distinguish between mem- bers within the same DNA-binding protein family.},
  doi       = {10.1146/annurev-biochem-060408-091030},
  file      = {:by-author/R/Rohs/2010_Rohs_233.pdf:PDF},
  keywords  = {DNA Base Recognition; DNA Conformation; DNA Recognition; DNA Shape Recognition; Direct Readout; Indirect Readout; Narrow Minor Groove; Protein-DNA Binding},
  owner     = {em},
  timestamp = {2013.09.30},
  creationdate = {2013-09-30T00:00:00},
}

@Article{Romero-Isart2010,
  author    = {Oriol Romero-Isart and Mathieu L. Juan and Romain Quidant and J. Ignacio Cirac},
  journal   = {New Journal of Physics},
  title     = {Toward quantum superposition of living organisms},
  year      = {2010},
  pages     = {033015},
  volume    = {12},
  abstract  = {The most striking feature of quantum mechanics is the existence of superposition states, where an object appears to be in different situations at the same time. The existence of such states has been previously tested with small objects, such as atoms, ions, electrons and photons (Zoller et al 2005 Eur. Phys. J. D 36 203–28), and even with molecules (Arndt et al 1999 Nature 401 680–2). More recently, it has been shown that it is possible to create superpositions of collections of photons (Deléglise et al 2008 Nature 455 510–14), atoms (Hammerer et al 2008 arXiv:0807.3358) or Cooper pairs (Friedman et al 2000 Nature 406 43–6). Very recent progress in optomechanical systems may soon allow us to create superpositions of even larger objects, such as micro-sized mirrors or cantilevers (Marshall et al 2003 Phys. Rev. Lett. 91 130401; Kippenberg and Vahala 2008 Science 321 1172–6; Marquardt and Girvin 2009 Physics 2 40; Favero and Karrai 2009 Nature Photon. 3 201–5), and thus to test quantum mechanical phenomena at larger scales. Here we propose a method to cool down and create quantum superpositions of the motion of sub-wavelength, arbitrarily shaped dielectric objects trapped inside a high-finesse cavity at a very low pressure. Our method is ideally suited for the smallest living organisms, such as viruses, which survive under low-vacuum pressures (Rothschild and Mancinelli 2001 Nature 406 1092–101) and optically behave as dielectric objects (Ashkin and Dziedzic 1987 Science 235 1517–20). This opens up the possibility of testing the quantum nature of living organisms by creating quantum superposition states in very much the same spirit as the original Schrödinger's cat 'gedanken' paradigm (Schrödinger 1935 Naturwissenschaften 23 807–12, 823–8, 844–9). We anticipate that our paper will be a starting point for experimentally addressing fundamental questions, such as the role of life and consciousness in quantum mechanics.},
  file      = {2010_Romero-Isart_033015.pdf:by-author/R/Romero-Isart/2010_Romero-Isart_033015.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.05.16},
  creationdate = {2012-05-16T00:00:00},
  url       = {http://stacks.iop.org/1367-2630/12/i=3/a=033015},
}

@Article{Roentgen1896,
  author    = {Röntgen, Wilhelm Conrad},
  journal   = {Nature},
  title     = {On a New Kind of Rays},
  year      = {1896},
  pages     = {274--276},
  volume    = {53},
  abstract  = {A DISCHARGE from a large induction coil is passed through a Hittorf’s vacuum tube, or through a well-exhausted Crookes' or Lenard’s tube. The tube is surrounded by a fairly close-fitting shield of black paper; it is then possible to see, in a completely darkened room, that paper covered on one side with barium platino-cyanide lights up with brilliant fluorescence when brought into the neighbourhood of the tube, whether the painted side or the other be turned towards the tube. The fluorescence is still visible at two metres distance. It is easy to show that the origin of the fluorescence lies within the vacuum tube},
  doi       = {10.1038/053274b0},
  file      = {1896_Roentgen_274.pdf:by-author/R/Roentgen/1896_Roentgen_274.pdf:PDF},
  keywords  = {X-ray Discovery},
  owner     = {saulius},
  timestamp = {2014.03.23},
  creationdate = {2014-03-23T00:00:00},
}

@InProceedings{Rosen1988,
  author    = {Rosen, B. K. and Wegman, M. N. and Zadeck, F. K.},
  booktitle = {Proceedings of the 15th ACM SIGPLAN-SIGACT Symposium on Principles of Programming Languages},
  title     = {Global Value Numbers and Redundant Computations},
  year      = {1988},
  address   = {New York, NY, USA},
  pages     = {12--27},
  publisher = {ACM},
  series    = {POPL '88},
  abstract  = {We propose a redundancy elimination algorithm that is {\it global} (in that it deals with the entire program), yet able to recognize redundancy among expressions that are lexically different. The algorithm also takes advantage of second order offects: transformations based on the discovery that two computations compute the same value may create opportunities to discover that {\it other} computations are equivalent.},
  acmid     = {73562},
  comment   = {http://www.cs.wustl.edu/~cytron/cs531/Resources/Papers/valnum.pdf},
  doi       = {10.1145/73560.73562},
  file      = {1988_Rosen_12.pdf:by-author/R/Rosen/1988_Rosen_12.pdf:PDF},
  isbn      = {0-89791-252-7},
  keywords  = {Compilers; Computer Science (CS); Optimisation},
  location  = {San Diego, California, USA},
  numpages  = {16},
  owner     = {saulius},
  timestamp = {2014.11.21},
  creationdate = {2014-11-21T00:00:00},
  url       = {http://doi.acm.org/10.1145/73560.73562},
}

@Article{Rosen2009,
  author    = {Rosén, Josefin and Gottfries, Johan and Muresan, Sorel and Backlund, Anders and Oprea, Tudor I.},
  journal   = {Journal of Medicinal Chemistry},
  title     = {Novel Chemical Space Exploration via Natural Products},
  year      = {2009},
  pages     = {1953--1962},
  volume    = {52},
  abstract  = {Natural products (NPs) are a rich source of novel compound classes and new drugs. In the present study we have used the chemical space navigation tool ChemGPS-NP to evaluate the chemical space occupancy by NPs and bioactive medicinal chemistry compounds from the database WOMBAT. The two sets differ notably in coverage of chemical space, and tangible leadlike NPs were found to cover regions of chemical space that lack representation in WOMBAT. Property based similarity calculations were performed to identify NP neighbors of approved drugs. Several of the NPs revealed by this method were confirmed to exhibit the same activity as their drug neighbors. The identification of leads from a NP starting point may prove a useful strategy for drug discovery in the search for novel leads with unique properties.},
  doi       = {10.1021/jm801514w},
  eprint    = {http://pubs.acs.org/doi/pdf/10.1021/jm801514w},
  file      = {2009_Rosén_1953.pdf:by-author/R/Rosén/2009_Rosén_1953.pdf:PDF},
  owner     = {saulius},
  timestamp = {2013.04.01},
  creationdate = {2013-04-01T00:00:00},
  url       = {http://pubs.acs.org/doi/abs/10.1021/jm801514w},
}

@Article{Rosen2009a,
  author    = {Rosén, Josefin and Lövgren, Anders and Kogej, Thierry and Muresan, Sorel and Gottfries, Johan and Backlund, Anders},
  journal   = {Journal of Computer-Aided Molecular Design},
  title     = {ChemGPS-NPWeb: chemical space navigation online},
  year      = {2009},
  issn      = {0920-654X},
  pages     = {253--259},
  volume    = {23},
  abstract  = {Internet has become a central source for information, tools, and services facilitating the work for medicinal chemists and drug discoverers worldwide. In this paper we introduce a web-based public tool, ChemGPS-NPWeb (http://chemgps.bmc.uu.se), for comprehensive chemical space navigation and exploration in terms of global mapping onto a consistent, eight dimensional map over structure derived physico-chemical characteristics. ChemGPS-NPWeb can assist in compound selection and prioritization; property description and interpretation; cluster analysis and neighbourhood mapping; as well as comparison and characterization of large compound datasets. By using ChemGPS-NPWeb, researchers can analyze and compare chemical libraries in a consistent manner. In this study it is demonstrated how ChemGPS-NPWeb can assist in interpreting results from two large datasets tested for activity in biological assays for pyruvate kinase and Bcl-2 family related protein interactions, respectively. Furthermore, a more than 30-year-old suggestion of “chemical similarity” between the natural pigments betalains and muscaflavins is tested.},
  doi       = {10.1007/s10822-008-9255-y},
  file      = {2009_Rosén_253.pdf:by-author/R/Rosén/2009_Rosén_253.pdf:PDF},
  keywords  = {Biologically Active Compounds; ChemGPS NP; Chemical Space; Drug Discovery; Internet Tool; Natural Products},
  language  = {English},
  owner     = {saulius},
  publisher = {Springer Netherlands},
  timestamp = {2013.04.01},
  creationdate = {2013-04-01T00:00:00},
  url       = {http://dx.doi.org/10.1007/s10822-008-9255-y},
}

@Article{Rosenberg2005,
  author    = {Rosenberg, Oren S and Deindl, Sebastian and Sung, Rou-Jia and Nairn, Angus C. and Kuriyan, John},
  journal   = {Cell},
  title     = {Structure of the Autoinhibited Kinase Domain of CaMKII and SAXS Analysis of the Holoenzyme},
  year      = {2005},
  pages     = {849–860},
  volume    = {123},
  abstract  = {Ca2+/calmodulin-dependent protein kinase- II (CaMKII) is unique among protein kinases for its dodecameric assembly and its com- plex response to Ca2+. The crystal struc- ture of the autoinhibited kinase domain of ̊ CaMKII, determined at 1.8 A resolution, re- veals an unexpected dimeric organization in which the calmodulin-responsive regula- tory segments form a coiled-coil strut that blocks peptide and ATP binding to the oth- erwise intrinsically active kinase domains. A threonine residue in the regulatory seg- ment, which when phosphorylated renders CaMKII calmodulin independent, is held apart from the catalytic sites by the organi- zation of the dimer. This ensures a strict Ca2+ dependence for initial activation. The structure of the kinase dimer, when com- bined with small-angle X-ray scattering data for the holoenzyme, suggests that inactive CaMKII forms tightly packed autoinhibited assemblies that convert upon activation into clusters of loosely tethered and inde- pendent kinase domains.},
  doi       = {10.1016/j.cell.2005.10.029},
  file      = {:by-author/R/Rosenberg/2005_Rosenberg_849.pdf:PDF},
  keywords  = {Crystal Structure; Kinase; SAXS},
  owner     = {em},
  timestamp = {2013.10.01},
  creationdate = {2013-10-01T00:00:00},
}

@Article{Rosenstein2012,
  author    = {Jacob K Rosenstein and Meni Wanunu and Christopher A Merchant and Marija Drndic and Kenneth L Shepard},
  journal   = {Nature Methods},
  title     = {Integrated nanopore sensing platform with sub-microsecond temporal resolution},
  year      = {2012},
  pages     = {487--492},
  volume    = {9},
  abstract  = {Nanopore sensors have attracted considerable interest for high-throughput sensing of individual nucleic acids and proteins without the need for chemical labels or complex optics. A prevailing problem in nanopore applications is that the transport kinetics of single biomolecules are often faster than the measurement time resolution. Methods to slow down biomolecular transport can be troublesome and are at odds with the natural goal of high-throughput sensing. Here we introduce a low-noise measurement platform that integrates a complementary metal-oxide semiconductor (CMOS) preamplifier with solid-state nanopores in thin silicon nitride membranes. With this platform we achieved a signal-to-noise ratio exceeding five at a bandwidth of 1 MHz, which to our knowledge is the highest bandwidth nanopore recording to date. We demonstrate transient signals as brief as 1 μs from short DNA molecules as well as current signatures during molecular passage events that shed light on submolecular DNA configurations in small nanopores.},
  doi       = {10.1038/nmeth.1932},
  file      = {2012_Rosenstein_487.pdf:by-author/R/Rosenstein/2012_Rosenstein_487.pdf:PDF;Supplementary information:by-author/R/Rosenstein/2012_Rosenstein_487suppl.pdf:PDF;:http\://www.nature.com/nmeth/journal/v9/n5/abs/nmeth.1932.html#supplementary-information:URL},
  owner     = {saulius},
  timestamp = {2012.06.13},
  creationdate = {2012-06-13T00:00:00},
}

@Article{Rosi2005,
  author    = {Nathaniel L. Rosi and Jaheon Kim and Mohamed Eddaoudi and Banglin Chen and Michael O{\textquotesingle}Keeffe and Omar M. Yaghi},
  journal   = {Journal of the American Chemical Society},
  title     = {Rod Packings and Metal-Organic Frameworks Constructed from Rod-Shaped Secondary Building Units},
  year      = {2005},
  month     = {feb},
  number    = {5},
  pages     = {1504--1518},
  volume    = {127},
  comment   = {Describes synthesis cited in: "Large-Pore Apertures in a Series of Metal-Organic Frameworks", Hexiang Deng et al. Science 336, 1018 (2012); DOI: 10.1126/science.1220131. A very simple synthesis! Vis.: A solid mixture of Zn(NO3)2‚6H2O (24.6 mg, 0.083 mmol) and 4,4′-biphenyldicarboxylic acid (H2BPDC) (10 mg, 0.041 mmol) was dissolved in a 20 mL vial containing DEF (12 mL), 30% H2O2 (0.40 mL), and CH3NH2 (0.20 mL, 70.3 mM in DMF). The mixture was allowed to stand in a capped vial for 7 d at room temperature. Colorless crystals of MOF-69A were collected and air-dried (21 mg, 86.1% yield based on H2BPDC). Structures available in COD :).},
  doi       = {10.1021/ja045123o},
  file      = {Rosi2005.pdf:by-author/R/Rosi/2005_Rosi_1504.pdf:PDF},
  groups    = {sg/MOF, sg/MOFs, am/MOFs},
  keywords  = {Concept; Synthesis},
  owner     = {saulius},
  publisher = {American Chemical Society ({ACS})},
  timestamp = {2017.01.31},
  creationdate = {2017-01-31T00:00:00},
  url       = {http://yaghi.berkeley.edu/pdfPublications/Rod-PkgsMtlOrgFrJAmChemSoc2005.pdf},
}

@MastersThesis{Rosiere2003,
  author    = {Emmanuel Donin de Rosiere},
  school    = {ENST Bretagne},
  title     = {From stack removing in stack-based languages to BibTEX++},
  year      = {2003},
  file      = {:by-author/R/Rosiere/2003_Rosiere_mscthesis.pdf:PDF},
  keywords  = {Bibtex; Computer Science (CS)},
  owner     = {saulius},
  pages     = {mscthesis},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@InCollection{Rosner2009,
  author    = {Gary L. Rosner and B. Nebiyou Bekele},
  title     = {Bayesian Designs in Clinical Trials},
  year      = {2009},
  pages     = {109--118},
  file      = {2009_Rosner_109.pdf:by-author/R/Rosner/2009_Rosner_109.pdf:PDF},
  groups    = {sg/Clinical Trials},
  language  = {English},
  owner     = {saulius},
  timestamp = {2015.12.14},
  creationdate = {2015-12-14T00:00:00},
  url       = {http://people.csail.mit.edu/mrosenblum/Teaching/adaptive_designs_2010/Kelly.pdf},
  urldate   = {2015-12-12},
}

@Article{Ross2014,
  author    = {Ross, Jason P and Kassir, Zena},
  journal   = {Mol Ther Nucleic Acids},
  title     = {The Varied Roles of Nuclear Argonaute-Small {RNA} Complexes and Avenues for Therapy},
  year      = {2014},
  issn      = {2162-2531},
  month     = {Oct},
  number    = {10},
  pages     = {e203},
  volume    = {3},
  doi       = {10.1038/mtna.2014.54},
  file      = {:by-author/R/Ross/2014_Ross_e203.pdf:PDF},
  groups    = {am/RNA activation},
  owner     = {andrius},
  publisher = {Nature Publishing Group},
  timestamp = {2016.08.24},
  creationdate = {2016-08-24T00:00:00},
  url       = {http://dx.doi.org/10.1038/mtna.2014.54},
}

@Manuscript{Ross2007,
  author    = {Ross, Seamus},
  title     = {Digital Preservation, Archival Science and Methodological Foundations for Digital Libraries},
  year      = {2007},
  keywords  = {Data Access Policy; Data Management; Digital Preservation},
  file      = {2007_Ross_keynote-lecture.pdf:by-author/R/Ross/2007_Ross_keynote-lecture.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.10.25},
  creationdate = {2012-10-25T00:00:00},
}

@Article{Rossmann2007,
  author    = {Rossmann, Michael G. and Arisaka, Fumio and Battisti, Anthony J. and Bowman, Valorie D. and Chipman, Paul R. and Fokine, Andrei and Hafenstein, Susan and Kanamaru, Shuji and Kostyuchenko, Victor A. and Mesyanzhinov, Vadim V. and Shneider, Mikhail M. and Morais, Marc C. and Leiman, Petr G. and Palermo, Laura M. and Parrish, Colin R. and Xiao, Chuan},
  journal   = {Acta crystallographica. Section D, Biological crystallography},
  title     = {From structure of the complex to understanding of the biology.},
  year      = {2007},
  pages     = {9--16},
  volume    = {63},
  abstract  = {The most extensive structural information on viruses relates to apparently icosahedral virions and is based on X-ray crystallography and on cryo-electron microscopy (cryo-EM) single-particle reconstructions. Both techniques lean heavily on imposing icosahedral symmetry, thereby obscuring any deviation from the assumed symmetry. However, tailed bacteriophages have icosahedral or prolate icosahedral heads that have one obvious unique vertex where the genome can enter for DNA packaging and exit when infecting a host cell. The presence of the tail allows cryo-EM reconstructions in which the special vertex is used to orient the head in a unique manner. Some very large dsDNA icosahedral viruses also develop special vertices thought to be required for infecting host cells. Similarly, preliminary cryo-EM data for the small ssDNA canine parvovirus complexed with receptor suggests that these viruses, previously considered to be accurately icosahedral, might have some asymmetric properties that generate one preferred receptor-binding site on the viral surface. Comparisons are made between rhinoviruses that bind receptor molecules uniformly to all 60 equivalent binding sites, canine parvovirus, which appears to have a preferred receptor-binding site, and bacteriophage T4, which gains major biological advantages on account of its unique vertex and tail organelle.},
  doi       = {10.1107/S0907444906047330},
  file      = {:by-author/R/Rossmann/2007_Rossmann_9.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Rossner2007,
  author    = {Rossner, Mike and Van Epps, Heather and Hill, Emma},
  journal   = {The Journal of cell biology},
  title     = {Show me the data.},
  year      = {2007},
  pages     = {1091--2},
  volume    = {179},
  file      = {:by-author/R/Rossner/2007_Rossner_1091.pdf:PDF},
  groups    = {sg/Bibliometrics},
  keywords  = {Impact Factors},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Rost1999,
  author    = {Rost, Burkhard},
  journal   = {Protein Engineering},
  title     = {Twilight zone of protein sequence alignments},
  year      = {1999},
  pages     = {85--94},
  volume    = {12},
  abstract  = {Sequence alignments unambiguously distinguish between protein pairs of similar and non-similar structure when the pairwise sequence identity is high (>40% for long alignments). The signal gets blurred in the twilight zone of 20–35% sequence identity. Here, more than a million sequence alignments were analysed between protein pairs of known structures to re-define a line distinguishing between true and false positives for low levels of similarity. Four results stood out. (i) The transition from the safe zone of sequence alignment into the twilight zone is described by an explosion of false negatives. More than 95% of all pairs detected in the twilight zone had different structures. More precisely, above a cut-off roughly corresponding to 30% sequence identity, 90% of the pairs were homologous; below 25% less than 10% were. (ii) Whether or not sequence homology implied structural identity depended crucially on the alignment length. For example, if 10 residues were similar in an alignment of length 16 (>60%), structural similarity could not be inferred. (iii) The `more similar than identical' rule (discarding all pairs for which percentage similarity was lower than percentage identity) reduced false positives significantly. (iv) Using intermediate sequences for finding links between more distant families was almost as successful: pairs were predicted to be homologous when the respective sequence families had proteins in common. All findings are applicable to automatic database searches.},
  doi       = {10.1093/protein/12.2.85},
  eprint    = {http://peds.oxfordjournals.org/content/12/2/85.full.pdf+html},
  file      = {1999_Rost_85.pdf:by-author/R/Rost/1999_Rost_85.pdf:PDF},
  keywords  = {Algorithms; Bioinformatics; Distant Homologies; Sequence Alingment; Short Fragment Frequences},
  owner     = {saulius},
  timestamp = {2013.04.10},
  creationdate = {2013-04-10T00:00:00},
  url       = {http://peds.oxfordjournals.org/content/12/2/85.abstract},
}

@Article{Rothenberg1999,
  author    = {Rothenberg},
  title     = {Avoiding technological quicksand; Finding a viable technical foundation for digital preservation},
  year      = {1999},
  file      = {:by-author/R/Rothenberg/1999_Rothenberg.pdf:PDF},
  keywords  = {Computer Science (CS); Computing History; Data Management},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Manuscript{Rothenberg1999a,
  author    = {Jeff Rothenberg},
  title     = {Ensuring the Longevity of Digital Information},
  year      = {1999},
  keywords  = {Computer Science (CS); Computing History; Data Management},
  file      = {1999_Rothenberg_a.pdf:by-author/R/Rothenberg/1999_Rothenberg_a.pdf:PDF},
  owner     = {saulius},
  timestamp = {2013.08.10},
  creationdate = {2013-08-10T00:00:00},
}

@Article{Rouillon2013,
  author    = {Rouillon, Christophe and Zhou, Min and Zhang, Jing and Politis, Argyris and Beilsten-Edmands, Victoria and Cannone, Giuseppe and Graham, Shirley and Robinson, Carol V. and Spagnolo, Laura and White, Malcolm F.},
  journal   = {Molecular Cell},
  title     = {Structure of the CRISPR Interference Complex CSM Reveals Key Similarities with Cascade},
  year      = {2013},
  pages     = {124–134},
  volume    = {52},
  abstract  = {The Clustered Regularly Interspaced Palindromic Repeats (CRISPR) system is an adaptive immune system in prokaryotes. Interference complexes en- coded by CRISPR-associated (cas) genes utilize small RNAs for homology-directed detection and subsequent degradation of invading genetic ele- ments, and they have been classified into three main types (I–III). Type III complexes share the Cas10 subunit but are subclassifed as type IIIA (CSM) and type IIIB (CMR), depending on their spec- ificity for DNA or RNA targets, respectively. The role of CSM in limiting the spread of conjugative plasmids in Staphylococcus epidermidis was first described in 2008. Here, we report a detailed investigation of the composition and structure of the CSM complex from the archaeon Sulfolobus solfataricus, using a combination of electron microscopy, mass spec- trometry, and deep sequencing. This reveals a three-dimensional model for the CSM complex that includes a helical component strikingly reminiscent of the backbone structure of the type I (Cascade) family.},
  doi       = {10.1016/j.molcel.2013.08.020},
  file      = {:by-author/R/Rouillon/2013_Rouillon_124.pdf:PDF},
  groups    = {sg/CRISPR-Cas},
  keywords  = {CRISPR; Cascade; Csm Complex; EM Structure; Effector Complex},
  owner     = {em},
  timestamp = {2014.05.26},
  creationdate = {2014-05-26T00:00:00},
}

@Article{Rowicka2004,
  author    = {Rowicka, Malgorzata and Kudlicki, Andrzej and Zelinka, Jan and Otwinowski, Zbyszek},
  journal   = {Acta Crystallographica Section A},
  title     = {Coordinate transformations in modern crystallographic computing},
  year      = {2004},
  month     = {Nov},
  number    = {6},
  pages     = {542--549},
  volume    = {60},
  abstract  = {A review of 4{$\times$}4-matrix notation and of tensor formalism focused on crystallographic applications is presented. A discussion of examples shows how this notation simplifies tasks encountered in crystallographic computing.},
  doi       = {10.1107/S0108767304017398},
  file      = {2004_Rowicka_542.pdf:by-author/R/Rowicka/2004_Rowicka_542.pdf:PDF},
  keywords  = {Coordinate Transformations; Matrix Notation; Tensor Formalism},
  owner     = {saulius},
  timestamp = {2016.10.03},
  creationdate = {2016-10-03T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0108767304017398},
}

@Article{Rozenberg1998,
  author    = {Rozenberg, H. and Rabinovich, D. and Frolow, F. and Hegde, R. S. and Shakked, Z.},
  journal   = {Proceedings of the National Academy of Sciences of the United States of America},
  title     = {Structural code for DNA recognition revealed in crystal structures of papillomavirus E2-DNA targets.},
  year      = {1998},
  pages     = {15194--9},
  volume    = {95},
  abstract  = {Transcriptional regulation in papillomaviruses depends on sequence-specific binding of the regulatory protein E2 to several sites in the viral genome. Crystal structures of bovine papillomavirus E2 DNA targets reveal a conformational variant of B-DNA characterized by a roll-induced writhe and helical repeat of 10.5 bp per turn. A comparison between the free and the protein-bound DNA demonstrates that the intrinsic structure of the DNA regions contacted directly by the protein and the deformability of the DNA region that is not contacted by the protein are critical for sequence-specific protein/DNA recognition and hence for gene-regulatory signals in the viral system. We show that the selection of dinucleotide or longer segments with appropriate conformational characteristics, when positioned at correct intervals along the DNA helix, can constitute a structural code for DNA recognition by regulatory proteins. This structural code facilitates the formation of a complementary protein-DNA interface that can be further specified by hydrogen bonds and nonpolar interactions between the protein amino acids and the DNA bases.},
  file      = {:by-author/R/Rozenberg/1998_Rozenberg_15194.pdf:PDF},
  keywords  = {DNA Protein; Deform; Readout},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Ruark1928,
  author    = {Ruark, A. E.},
  journal   = {Proceedings of the National Academy of Sciences of the United States of America},
  title     = {The Limits of Accuracy in Physical Measurements.},
  year      = {1928},
  pages     = {322--8},
  volume    = {14},
  file      = {:by-author/R/Ruark/1928_Ruark_322.pdf:PDF},
  keywords  = {Quantum Mechanics (QM)},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Ruark1928a,
  author    = {Ruark, A. E.},
  journal   = {Proceedings of the National Academy of Sciences of the United States of America},
  title     = {A Critical Experiment on the Statistical Interpretation of Quantum Mechanics.},
  year      = {1928},
  pages     = {328--30},
  volume    = {14},
  file      = {:by-author/R/Ruark/1928_Ruark_328.pdf:PDF},
  keywords  = {Quantum Mechanics (QM)},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Presentation{Ruber2011,
  author       = {Roger Ruber},
  title        = {The European Spallation Source},
  year         = {2011},
  organization = {Uppsala University},
  file         = {2011_Ruber_slides.pdf:by-author/R/Ruber/2011_Ruber_slides.pdf:PDF},
  keywords     = {European Spallation Source; Neutron Diffraction; Neutron Source; Research Infrastructure},
  owner        = {saulius},
  timestamp = {2014.01.21},
  creationdate = {2014-01-21T00:00:00},
  url          = {http://www.bigscience4business.nl/presentatie/Ontwikkelingen%20en%20voortgang%20bouw%20European%20Spallation%20Source.pdf},
}

@Presentation{Rudberg2011,
  author    = {Elias Rudberg},
  title     = {Distributed memory parallelization using MPI},
  year      = {2011},
  file      = {:by-author/R/Rudberg/2011_Rudberg_slides.pdf:PDF},
  owner     = {saulius},
  pages     = {slides},
  timestamp = {2013.07.02},
  creationdate = {2013-07-02T00:00:00},
}

@Manuscript{Rudner2001,
  author    = {Rudner},
  title     = {Measurement Decision Theory},
  year      = {2001},
  keywords  = {Philosophy},
  file      = {:by-author/R/Rudner/2001_Rudner.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Presentation{Rupp2013,
  author    = {Bernhard Rupp},
  title     = {The road to scientific serfdom},
  year      = {2013},
  file      = {:by-author/R/Rupp/2013_Rupp.pdf:PDF},
  owner     = {saulius},
  timestamp = {2014.03.23},
  creationdate = {2014-03-23T00:00:00},
}

@Article{Rupp2004,
  author    = {Rupp, Bernhard and Wang, Junwen},
  journal   = {Methods},
  title     = {Predictive models for protein crystallization},
  year      = {2004},
  pages     = {390--407},
  volume    = {34},
  abstract  = {Crystallization of proteins is a nontrivial task, and despite the substantial eVorts in robotic automation, crystallization screening is still largely based on trial-and-error sampling of a limited subset of suitable reagents and experimental parameters. Funding of high throughput crystallography pilot projects through the NIH Protein Structure Initiative provides the opportunity to collect crys- tallization data in a comprehensive and statistically valid form. Data mining and machine learning algorithms thus have the potential to deliver predictive models for protein crystallization. However, the underlying complex physical reality of crystallization, combined with a generally ill-deWned and sparsely populated sampling space, and inconsistent scoring and annotation make the development of predictive models non-trivial. We discuss the conceptual problems, and review strengths and limitations of current approaches towards crystallization prediction, emphasizing the importance of comprehensive and valid sampling protocols. In view of limited overlap in techniques and sampling parameters between the publicly funded high throughput crystallography initiatives, exchange of information and standardization should be encouraged, aiming to eVectively integrate data mining and machine learning eVorts into a comprehensive predictive framework for protein crystallization. Similar experimental design and knowledge discovery strategies should be applied to valid analysis and prediction of protein expression, solubilization, and puriWcation, as well as crystal handling and cryo-protection.},
  doi       = {10.1016/j.ymeth.2004.03.031},
  file      = {:by-author/R/Rupp/2004_Rupp_390.pdf:PDF},
  keywords  = {Crystal Structure; High Throughput Crystallization; Machine Learning (ML); Predictive Models; Protein Crystallization; Review; Statistical Analysis; Structural Genomics},
  owner     = {em},
  timestamp = {2014.05.22},
  creationdate = {2014-05-22T00:00:00},
}

@Article{Ruse1931,
  author    = {H. S. Ruse},
  journal   = {Proc. London Math. Soc.},
  title     = {Taylor's theorem in the tensor calculus},
  year      = {1931},
  pages     = {87--92},
  volume    = {s2-32},
  file      = {1931_Ruse_87.pdf:by-author/R/Ruse/1931_Ruse_87.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@InProceedings{Russell1978,
  author    = {Russell, Robert D.},
  booktitle = {Proceedings of the 5th Annual Symposium on Computer Architecture},
  title     = {The PDP-11: A Case Study of How Not to Design Condition Codes},
  year      = {1978},
  address   = {New York, NY, USA},
  pages     = {190--194},
  publisher = {ACM},
  series    = {ISCA '78},
  abstract  = {This paper investigates a design weakness in the PDP-11 architecture, namely the condition code bits. Experience with the machine has demonstrated a number of “traps” for the unwary programmer stemming directly from an inconsistent and sometimes confusing scheme of condition code settings. This is particularly annoying in view of the otherwise clean architectural characteristics of the machine. A number of “principles” are proposed that would correct the deficiencies and could therefore be used as a guide for designing future machines. The paper also presents some measurements based on actual programmatic usage of the PDP-11 that question the validity of a condition code scheme as an efficient architectural technique.},
  acmid     = {803047},
  doi       = {10.1145/800094.803047},
  file      = {1978_Russell_190.pdf:by-author/R/Russell/1978_Russell_190.pdf:PDF},
  keywords  = {Compiler Construction; Computer Architecture; PDP-11},
  numpages  = {5},
  owner     = {saulius},
  timestamp = {2016.10.03},
  creationdate = {2016-10-03T00:00:00},
  url       = {http://doi.acm.org/10.1145/800094.803047},
}

@Article{Ruth2013,
  author    = {David Ruth and Mike Williams},
  journal   = {Rice University News \& Media},
  title     = {Rice technique points toward {2-D} devices},
  year      = {2013},
  file      = {:by-author/R/Ruth/2013_Ruth.odt:OpenDocument text},
  keywords  = {Electronics},
  owner     = {andrius},
  timestamp = {2013.01.31},
  creationdate = {2013-01-31T00:00:00},
  url       = {http://news.rice.edu/2013/01/27/rice-technique-points-toward-2-d-devices/},
}

@Article{Rutkauskas2014a,
  author      = {Danielis Rutkauskas and Milda Petkelyte and Paulius Naujalis and Giedrius Sasnauskas and Gintautas Tamulaitis and Mindaugas Zaremba and Virginijus Siksnys},
  journal     = {J Phys Chem B},
  title       = {Restriction enzyme Ecl18kI-induced DNA looping dynamics by single-molecule FRET.},
  year        = {2014},
  month       = {Jul},
  number      = {29},
  pages       = {8575--8582},
  volume      = {118},
  abstract    = {Many type II restriction endonucleases require binding of two copies of a recognition site for efficient DNA cleavage. Simultaneous interaction of the enzyme with two DNA sites results in DNA loop formation. It was demonstrated with the tethered particle motion technique that such looping is a dynamic process where a DNA loop is repeatedly formed and disrupted. Here we use a better and in the context of protein-induced DNA looping virtually unexploited strategy of single-molecule Förster resonance energy transfer of surface immobilized biomolecules to quantitatively study the dynamics of Ecl18kI endonuclease-induced DNA looping and determine the rate constants of loop formation and disruption. We show that two DNA-bound Ecl18kI dimers efficiently form a bridging tetramer looping out intervening DNA with a rate that is only a few orders of magnitude lower than the diffusion limited rate. On the other hand, the existence of Ecl18kI tetramer is only transient, and the loop is rapidly disrupted within about 1 s.},
  doi         = {10.1021/jp504546v},
  file        = {2014_Rutkauskas_17356.pdf:by-author/R/Rutkauskas/2014_Rutkauskas_17356.pdf:PDF},
  groups      = {sg/inhibitors},
  institution = {Institute of Physics, Center for Physical Sciences and Technology , Savanoriu 231, LT-02300, Vilnius, Lithuania.},
  keywords    = {Base Sequence; Chemistry/genetics/metabolism; DNA; Deoxyribonucleases; Fluorescence Resonance Energy Transfer; Kinetics; Metabolism; Models; Molecular; Nucleic Acid Conformation; Type II Site-Specific},
  language    = {eng},
  medline-pst = {ppublish},
  owner       = {em},
  pmid        = {24971497},
  timestamp = {2016.06.09},
  creationdate = {2016-06-09T00:00:00},
  url         = {http://dx.doi.org/10.1021/jp504546v},
}

@Article{Rutkauskas2014,
  author      = {Kęstutis Rutkauskas and Asta Zubrienė and Ingrida Tumosienė and Kristina Kantminienė and Marytė Kažemėkaitė and Alexey Smirnov and Justina Kazokaitė and Vaida Morkūnaitė and Edita Capkauskaitė and Elena Manakova and Saulius Gražulis and Zigmuntas J Beresnevičius and Daumantas Matulis},
  journal     = {Molecules},
  title       = {4-Amino-substituted Benzenesulfonamides as Inhibitors of Human Carbonic Anhydrases.},
  year        = {2014},
  pages       = {17356--17380},
  volume      = {19},
  abstract    = {A series of N-aryl-β-alanine derivatives and diazobenzenesulfonamides containing aliphatic rings were designed, synthesized, and their binding to carbonic anhydrases (CA) I, II, VI, VII, XII, and XIII was studied by the fluorescent thermal shift assay and isothermal titration calorimetry. The results showed that 4-substituted diazobenzenesulfonamides were more potent CA binders than N-aryl-β-alanine derivatives. Most of the N-aryl-β-alanine derivatives showed better affinity for CA II while diazobenzenesulfonamides possessed nanomolar affinities towards CA I isozyme. X-ray crystallographic structures showed the modes of binding of both compound groups.},
  comment     = {Acknowledgments !!! This research was funded by the European Social Fund under the Global Grant measure (No. VP1-3.1.-SMM-07-K-02-009). Authors thank FP7-REGPOT-2009-1 grant “MoBiLi” agreement No.: 245721, and the COST projects TD0905 and CM0804.},
  doi         = {10.3390/molecules191117356},
  file        = {2014_Rutkauskas_17356.pdf:by-author/R/Rutkauskas/2014_Rutkauskas_17356.pdf:PDF},
  groups      = {sg/inhibitors},
  institution = {Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Graičiūno 8, Vilnius LT-02241, Lithuania. daumantas.matulis@bti.vu.lt.},
  language    = {eng},
  medline-pst = {epublish},
  owner       = {alexey},
  pii         = {molecules191117356},
  pmid        = {25353386},
  timestamp = {2014.11.10},
  creationdate = {2014-11-10T00:00:00},
  url         = {http://dx.doi.org/10.3390/molecules191117356},
}

@Manuscript{Ryan1998,
  author    = {Conor Ryan and J. J. Collins and Michael O. Neill},
  title     = {Grammatical Evolution: Evolving Programs for an Arbitary Language},
  year      = {1998},
  keywords  = {Computer Science (CS); Program Evolution},
  file      = {:by-author/R/Ryan/1998_Ryan.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Rychkov2014,
  author    = {Rychkov, Denis A. and Arkhipov, Sergey G. and Boldyreva, Elena V.},
  journal   = {Journal of Applied Crystallography},
  title     = {Simple and efficient modifications of well known techniques for reliable growth of high-quality crystals of small bioorganic molecules},
  year      = {2014},
  month     = {Aug},
  number    = {4},
  volume    = {47},
  doi       = {10.1107/S1600576714011273},
  file      = {2014_Rychkov_1435.pdf:by-author/R/Rychkov/2014_Rychkov_1435.pdf:PDF},
  keywords  = {Crystal Growth; Crystallisation},
  owner     = {saulius},
  timestamp = {2014.08.01},
  creationdate = {2014-08-01T00:00:00},
  url       = {http://dx.doi.org/10.1107/S1600576714011273},
}

@Article{Rzepa2013,
  author    = {Rzepa, Henry},
  journal   = {Journal of Cheminformatics},
  title     = {Chemical datuments as scientific enablers},
  year      = {2013},
  issn      = {1758-2946},
  pages     = {6},
  volume    = {5},
  abstract  = {This article is an attempt to construct a chemical datument as a means of presenting insights into chemical phenomena in a scientific journal. An exploration of the interactions present in a small fragment of duplex Z-DNA and the nature of the catalytic centre of a carbon-dioxide/alkene epoxide alternating co-polymerisation is presented in this datument, with examples of the use of three software tools, one based on Java, the other two using Javascript and HTML5 technologies. The implications for the evolution of scientific journals are discussed.},
  doi       = {10.1186/1758-2946-5-6},
  file      = {2013_Rzepa_6.pdf:by-author/R/Rzepa/2013_Rzepa_6.pdf:PDF},
  owner     = {saulius},
  pubmedid  = {23343381},
  timestamp = {2013.09.18},
  creationdate = {2013-09-18T00:00:00},
  url       = {http://www.jcheminf.com/content/5/1/6},
}

@Article{Rzepa2009,
  author    = {Rzepa, Henry S.},
  journal   = {Nature Chemistry},
  title     = {The importance of being bonded},
  year      = {2009},
  pages     = {510--512},
  volume    = {1},
  abstract  = {The concept of the chemical bond has been around for quite some time and there are many models that try to explain what is going on in that hazy world of electron density that glues atoms together. But molecules that challenge our notion of just what a chemical bond is continue to be reported, often presenting us with more questions than answers. In an era where the diffusion of chemistry into other subjects is ever increasing, the nature of the chemical bond is one theoretical concept that arguably represents the very core of the subject. All chemists when asked would probably say that they 'know a bond when they see one', but they might be harder pressed to provide definitions for the current menagerie in the bonding zoo.},
  doi       = {10.1038/nchem.373},
  file      = {2009_Rzepa_510.pdf:by-author/R/Rzepa/2009_Rzepa_510.pdf:PDF},
  issne     = {1755-4349},
  issnp     = {1755-4330},
  issue     = {7},
  owner     = {saulius},
  publisher = {Nature Publishing Group},
  timestamp = {2013.11.09},
  creationdate = {2013-11-09T00:00:00},
  url       = {http://libgen.org/scimag/index.php?doi=10.1038/nchem.373},
}

@Presentation{Saad2007,
  author    = {Yousef Saad},
  title     = {Solving large eigenvalue problems in electronic structure calculations},
  year      = {2007},
  lecture   = {Brisbane, Sept. 21, 2007},
  school    = {University of Queensland},
  file      = {2007_Saad_slides.pdf:by-author/S/Saad/2007_Saad_slides.pdf:PDF},
  keywords  = {Algorithms; Density Functional Theory (DFT); Eigenvalues; Quantum Chemistry; Quantum Mechanics (QM)},
  owner     = {saulius},
  timestamp = {2014.04.16},
  creationdate = {2014-04-16T00:00:00},
  url       = {http://www-users.cs.umn.edu/~saad/PDF/UQ_talk.pdf},
}

@Article{Saal2013,
  author    = {Saal, James E. and Kirklin, Scott and Aykol, Muratahan and Meredig, Bryce and Wolverton, C.},
  journal   = {The Journal of The Minerals, Metals \& Materials Society},
  title     = {Materials Design and Discovery with High-Throughput Density Functional Theory: The {O}pen {Q}uantum {M}aterials {D}atabase ({OQMD})},
  year      = {2013},
  issn      = {1047-4838},
  pages     = {1501--1509},
  volume    = {65},
  abstract  = {High-throughput density functional theory (HT DFT) is fast becoming a powerful tool for accelerating materials design and discovery by the amassing tens and even hundreds of thousands of DFT calculations in large databases. Complex materials problems can be approached much more efficiently and broadly through the sheer quantity of structures and chemistries available in such databases. Our HT DFT database, the Open Quantum Materials Database (OQMD), contains over 200,000 DFT calculated crystal structures and will be freely available for public use at http://oqmd.org. In this review, we describe the OQMD and its use in five materials problems, spanning a wide range of applications and materials types: (I) Li-air battery combination catalyst/electrodes, (II) Li-ion battery anodes, (III) Li-ion battery cathode coatings reactive with HF, (IV) Mg-alloy long-period stacking ordered (LPSO) strengthening precipitates, and (V) training a machine learning model to predict new stable ternary compounds.},
  doi       = {10.1007/s11837-013-0755-4},
  file      = {2013_Saal_1501.pdf:by-author/S/Saal/2013_Saal_1501.pdf:PDF},
  groups    = {am/OQMD},
  language  = {English},
  owner     = {saulius},
  publisher = {Springer US},
  timestamp = {2014.09.27},
  creationdate = {2014-09-27T00:00:00},
  url       = {http://dx.doi.org/10.1007/s11837-013-0755-4},
}

@Article{Sadamoto2004,
  author    = {Sadamoto, Reiko and Niikura, Kenichi and Ueda, Taichi and Monde, Kenji and Fukuhara, Norio and Nishimura, Shin-Ichiro},
  journal   = {Journal of the American Chemical Society},
  title     = {Control of bacteria adhesion by cell-wall engineering.},
  year      = {2004},
  pages     = {3755--61},
  volume    = {126},
  abstract  = {UDP-MurNAc-pentapeptide derivative bacterial cell-wall precursors were synthesized as effective tools for surface display on living bacteria. Lactobacilli were incubated in the ketone-modified precursor-containing medium, and the ketone moiety was displayed on the bacterial surface through cell-wall biosynthesis. Oligomannose was coupled with the ketone moiety on the bacterial surface via a aminooxyl linker, thereby displaying this oligosaccharide on the surface of the bacteria. The increase in the adhesion of the sugar-displaying bacteria onto a concanavalin A-attached film compared to that of native bacteria was confirmed by microscopic observation and surface plasmon resonance measurement. The incorporation of the artificial cell-wall precursors was enhanced when incubated with fosfomycin, an inhibitor of cell-wall precursor biosynthesis.},
  file      = {:by-author/S/Sadamoto/2004_Sadamoto_3755.pdf:PDF},
  keywords  = {Bioconjugation},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@Article{Sadhasivam2017,
  author    = {Velu Sadhasivam and Rajendiran Balasaravanan and Chinnadurai Chithiraikumar and Ayyanar Siva},
  journal   = {{ChemistrySelect}},
  title     = {Incorporating Pd({OAc})2 on Imine Functionalized Microporous Covalent Organic Frameworks: A Stable and Efficient Heterogeneous Catalyst for Suzuki-Miyaura Coupling in Aqueous Medium},
  year      = {2017},
  month     = {jan},
  number    = {3},
  pages     = {1063--1070},
  volume    = {2},
  doi       = {10.1002/slct.201601440},
  file      = {:by-author/S/Sadhasivam/2017_Sadhasivam_1063.pdf:PDF},
  groups    = {sg/MOF, sg/MOFs, am/MOFs},
  keywords  = {Synthesis},
  owner     = {saulius},
  publisher = {Wiley-Blackwell},
  timestamp = {2017.01.31},
  creationdate = {2017-01-31T00:00:00},
  url       = {https://doi.org/10.1002%2Fslct.201601440},
}

@Article{Sadowski2013,
  author    = {Sadowski, Peter and Baldi, Pierre},
  journal   = {Journal of Chemical Information and Modeling},
  title     = {Small-Molecule 3D Structure Prediction Using Open Crystallography Data},
  year      = {2013},
  pages     = {3127--3130},
  volume    = {53},
  abstract  = {Predicting the 3D structures of small molecules is a common problem in chemoinformatics. Even the best methods are inaccurate for complex molecules, and there is a large gap in accuracy between proprietary and free algorithms. Previous work presented COSMOS, a novel data-driven algorithm that uses knowledge of known structures from the Cambridge Structural Database and demonstrates performance that was competitive with proprietary algorithms. However, dependence on the Cambridge Structural Database prevented its widespread use. Here, we present an updated version of the COSMOS structure predictor, complete with a free structure library derived from open data sources. We demonstrate that COSMOS performs better than other freely available methods, with a mean RMSD of 1.16 and 1.68 Å for organic and metal–organic structures, respectively, and a mean prediction time of 60 ms per molecule. This is a 17\% and 20\% reduction, respectively, in RMSD compared to the free predictor provided by Open Babel, and it is 10 times faster. The ChemDB Web portal provides a COSMOS prediction Web server, as well as downloadable copies of the COSMOS executable and library of molecular substructures.},
  doi       = {10.1021/ci4005282},
  eprint    = {http://dx.doi.org/10.1021/ci4005282},
  file      = {2013_Sadowski_3127.pdf:by-author/S/Sadowski/2013_Sadowski_3127.pdf:PDF},
  owner     = {saulius},
  timestamp = {2015.06.12},
  creationdate = {2015-06-12T00:00:00},
  url       = {http://dx.doi.org/10.1021/ci4005282},
}

@Article{Saecker2002,
  author    = {Saecker, Ruth M. and Record, Jr, M. Thomas},
  journal   = {Current opinion in structural biology},
  title     = {Protein surface salt bridges and paths for DNA wrapping.},
  year      = {2002},
  pages     = {311--9},
  volume    = {12},
  abstract  = {The organization of large regions of DNA on the surface of proteins is critical to many DNA 'transactions', including replication, transcription, recombination and repair, as well as the packaging of chromosomal DNA. Recent thermodynamic and structural studies of DNA binding by integration host factor indicate that the disruption of protein surface salt bridges (dehydrated ion pairs) dominates the observed thermodynamics of integration host factor binding and, more generally, allows the wrapping of DNA on protein surfaces. The proposed thermodynamic signature of wrapping with coupled salt bridge disruption includes large negative salt-concentration-dependent enthalpy, entropy and heat capacity changes and smaller than expected magnitudes of the observed binding constant and its power dependence on salt concentration. Examination of the free structures of proteins recently shown to wrap DNA leads us to hypothesize that a pattern of surface salt bridges interspersed with cationic sidechains provides a structural signature for wrapping and that the number and organization of salt bridges and cationic groups dictate the thermodynamics and topology of DNA wrapping, which in turn are critical to function.},
  file      = {:by-author/S/Saecker/2002_Saecker_311.pdf:PDF},
  keywords  = {Jen Jacobson},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@TechReport{Safford2002,
  author      = {David Safford},
  institution = {IBM Research},
  title       = {Clarifying Misinformation on TCPA},
  year        = {2002},
  month       = {October},
  abstract    = {In a recent papers, Ross Anderson [8], Bill Arbaugh [10], and Lucky Green [12] criticize TCPA [1] and Palladium [3] claiming that they are a disaster for the consumer, serving only to enforce Digital Rights Management (DRM). These papers have incited widespread consumer concern, even leading to an anti-TCPA website [9] calling for letter writing campaigns to TCPA member companies. Unfortunately these papers misrepresent TCPA in that they: improperly lump together TCPA, Palladium, and DRM present speculation about TCPA as fact are full of technical misunderstandings of the TCPA Specification This report analyzes these anti-TCPA papers, pointing out these errors in detail, and showing that their conclusions about TCPA are simply wrong. This paper defends only TCPA. Palladium and DRM have to defend themselves. Note: I have a system with a TCPA chip running both Windows and Linux, and have verified all of the following comments on actual hardware. All views are my own, not necessarily those of IBM.},
  file        = {:by-author/S/Safford/2002_Safford.pdf:PDF},
  keywords    = {Computer Science (CS); Security; Trusted Computing},
  owner       = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Webpage{Safuan1997,
  author    = {Tracey Safuan},
  retrieved = {2008-07-28},
  title     = {LIMBO - features},
  url       = {http://www.doc.ic.ac.uk/~nd/surprise_97/journal/vol4/msa1/limbo.html},
  month     = {June},
  year      = {1997},
  file      = {:by-author/S/Safuan/1997_Safuan.war:WAR},
  keywords  = {Computer Science (CS); Limbo; Programming Languages},
  owner     = {saulius},
  timestamp = {2015.03.02},
  creationdate = {2015-03-02T00:00:00},
}

@Article{Sagan1997,
  author    = {Sagan, C and Chyba, C},
  journal   = {Science (New York, N.Y.)},
  title     = {The early faint sun paradox: organic shielding of ultraviolet-labile greenhouse gases},
  year      = {1997},
  pages     = {1217--21},
  volume    = {276},
  file      = {1997_Sagan_1217.pdf:by-author/S/Sagan/1997_Sagan_1217.pdf:PDF},
  keywords  = {Chemical Prebiotic; Evolution},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Saghatelian2004,
  author    = {Saghatelian, Alan and Jessani, Nadim and Joseph, Arul and Humphrey, Mark and Cravatt, Benjamin F.},
  journal   = {Proceedings of the National Academy of Sciences of the United States of America},
  title     = {Activity-based probes for the proteomic profiling of metalloproteases.},
  year      = {2004},
  pages     = {10000--5},
  volume    = {101},
  abstract  = {Metalloproteases (MPs) are a large and diverse class of enzymes implicated in numerous physiological and pathological processes, including tissue remodeling, peptide hormone processing, and cancer. MPs are tightly regulated by multiple posttranslational mechanisms in vivo, hindering their functional analysis by conventional genomic and proteomic methods. Here we describe a general strategy for creating activity-based proteomic probes for MPs by coupling a zinc-chelating hydroxamate to a benzophenone photocrosslinker, which promote selective binding and modification of MP active sites, respectively. These probes labeled active MPs but not their zymogen or inhibitor-bound counterparts and were used to identify members of this enzyme class up-regulated in invasive cancer cells and to evaluate the selectivity of MP inhibitors in whole proteomes. Interestingly, the matrix metalloproteinase inhibitor GM6001 (ilomastat), which is currently in clinical development, was found to also target the neprilysin, aminopeptidase, and dipeptidylpeptidase clans of MPs. These results demonstrate that MPs can display overlapping inhibitor sensitivities despite lacking sequence homology and stress the need to evaluate MP inhibitors broadly across this enzyme class to develop agents with suitable target selectivities in vivo. Activity-based profiling offers a powerful means for conducting such screens, as this approach can be carried out directly in whole proteomes, thereby facilitating the discovery of disease-associated MPs concurrently with inhibitors that selectively target these proteins.},
  file      = {:by-author/S/Saghatelian/2004_Saghatelian_10000.pdf:PDF},
  keywords  = {Bioconjugation},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@Presentation{Sagiv2003,
  author       = {Mooly Sagiv and Eran Yahav},
  title        = {Modern Compiler Design. Symbol Tables and Semantic Checks. Part I},
  year         = {2003},
  organization = {Tel-Aviv University},
  school       = {School of Computer Science},
  file         = {:by-author/S/Sagiv/2003_Sagiv.ppt:PPT},
  keywords     = {Compiler-symbol-tables; Computer Science (CS)},
  owner        = {saulius},
  timestamp = {2015.03.03},
  creationdate = {2015-03-03T00:00:00},
}

@Article{Saha1995,
  author    = {Saha, S. and Rao, D. N.},
  journal   = {Journal of molecular biology},
  title     = {ATP hydrolysis is required for DNA cleavage by EcoPI restriction enzyme.},
  year      = {1995},
  pages     = {559--67},
  volume    = {247},
  abstract  = {The type III restriction endonuclease EcoPI, coded by bacteriophage P1, cleaves unmodified DNA in the presence of ATP and magnesium ions. We show that purified EcoPI restriction enzyme fails to cleave DNA in the presence of non-hydrolyzable ATP analogs. More importantly, this study demonstrates that EcoPI restriction enzyme has an inherent ATPase activity, and ATP hydrolysis is necessary for DNA cleavage. Furthermore, we show that the progress curve of the reaction with EcoPI restriction enzyme exhibits a lag which is dependent on the enzyme concentration. Kinetic analysis of the progress curves of the reaction suggest slow transitions that can occur during the reaction, characteristic of hysteretic enzymes. The role of ATP in the cleavage mechanism of type III restriction enzymes is discussed.},
  file      = {:by-author/S/Saha/1995_Saha_559.pdf:PDF},
  keywords  = {TypeIII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Hassane2006,
  author    = {Said Hassane, Fatouma and Frisch, Benoît and Schuber, Francis},
  journal   = {Bioconjugate Chemistry},
  title     = {Targeted Liposomes: Convenient Coupling of Ligands to Preformed Vesicles Using “Click Chemistry”},
  year      = {2006},
  pages     = {849--854},
  volume    = {17},
  abstract  = {An efficient and convenient chemoselective conjugation method based on “click chemistry” was developed for coupling ligands to the surface of preformed liposomes. It can be performed under mild conditions in aqueous buffers; the use of a water soluble Cu(I) chelator, such as bathophenanthrolinedisulfonate, was essential to obtain good yields in reasonable reaction times. A model reaction was achieved in which, in a single step, an unprotected α-d-mannosyl derivative carrying a spacer arm functionalized with an azide group was conjugated to the surface of vesicles presenting a synthetic lipid carrying a terminal alkyne function. When liposomes composed of saturated phospholipids were used, the reaction conditions developed in the present work did not damage the membranes as measured by the absence of leakage of entrapped 5,6-carboxyfluorescein. Moreover, as assessed by agglutination experiments using concanavalin A, the mannose residues were perfectly accessible on the surface of the targeted vesicles.},
  doi       = {10.1021/bc050308l},
  file      = {:by-author/S/SaidHassane/2006_SaidHassane_849.pdf:PDF},
  keywords  = {Bioconjugation},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
  url       = {http://pubs.acs.org/doi/abs/10.1021/bc050308l},
}

@Article{Sain1999,
  author    = {Stephan R. Sain and H. L. Gray and Wayne A. Woodward and Mark D. Fisk},
  journal   = {Bulletin of the Seismological Society of America},
  title     = {Outlier Detection from a Mixture Distribution When Training Data Are Unlabeled},
  year      = {1999},
  month     = {February},
  number    = {1},
  pages     = {294--304},
  volume    = {89},
  abstract  = {We consider the difficult task of using seismic signals (or any other discriminants) for detecting nuclear explosions from the large number of background signals such as earthquakes and mining blasts. Given a ground-truth database (i.e., labeled data), Fisk et aL (1996) consider the problem of detecting outliers (nuclear explosions) from a single background-signal population, and their approach has been applied successfully in several regions around the world. Wang et al. (1997) attack the problem in terms of modeling the background as a mixture distribution and looking for outliers (nuclear events) from that mixture. However, those authors only considered the case in which at least some fraction of the training sample was labeled, that is, at least some ground-truth information was available, and the number of distinct classes of events was known. In the current article, we extend these results to the case in which no events in the training sample are labeled and also to the case in which the number of event types represented in the training sample is unknown. One can view the mixture approach as a robust method for fitting a density to training data that may not be normally distributed whether or not the data consist of identi- fiable components that have a physical interpretation. The technique is demonstrated using simulated data as well as two sets of seismic data.},
  file      = {1999_Sain_294.pdf:by-author/S/Sain/1999_Sain_294.pdf:PDF},
  groups    = {am/Outliers},
  owner     = {andrius},
  timestamp = {2017.01.05},
  creationdate = {2017-01-05T00:00:00},
  url       = {https://pdfs.semanticscholar.org/eef1/bb217a8235643318e38122605a8ca5d1d07a.pdf},
}

@InProceedings{Sakurai2000,
  author    = {Sakurai, Yasushi and Yoshikawa, Masatoshi and Uemura, Shunsuke and Kojima, Haruhiko},
  booktitle = {Proceedings of the ninth international conference on Information and knowledge management},
  title     = {The Subspace Coding Method: A New Indexing Scheme for High-Dimensional Data},
  year      = {2000},
  address   = {New York, NY, USA},
  pages     = {210--218},
  publisher = {ACM},
  series    = {CIKM '00},
  abstract  = {This paper presents a new indexing scheme, the Subspace Coding Method (SCM), that offers high performance simi- larity retrieval. It is based on an analysis of the two superior access methods proposed so far: the SR-tree and the VA- File. Our experimental test by real data provides that the SR-tree offers better performance. However, as dimension- ality increases, the large volume of entries in non-leaf nodes degrades the search performance. Based on the analysis, we introduce the SCM, a new indexing scheme applicable to any tree index employing MBR (Minimum Bounding Rectangle) and/or MBS (Minimum Bounding Sphere). The basic idea of the SCM is the introduction of Virtual Bounding Rectan- gle (VBR) and Virtual Bounding quasiSphere (VBS), which contain and approximate MBR and MBS, respectively. Un- like the approximation of absolute vector positions used in the VA-File, VBRs and VBSs are relative to the parent’s VBR. The experimental results demonstrate the effective- ness of the SCM.},
  doi       = {10.1145/354756.354821},
  file      = {:by-author/S/Sakurai/2000_Sakurai_210.pdf:PDF},
  isbn      = {1-58113-320-0},
  location  = {McLean, Virginia, United States},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://doi.acm.org/10.1145/354756.354821},
}

@Manual{Sali2013,
  title     = {{MODELLER}: A Program for Protein Structure Modeling},
  author    = {Andrej Šali},
  year      = {2013},
  comment   = {release 9.12, r9480},
  file      = {:by-author/Š/Šali/2013_Šali_manual.pdf:PDF},
  keywords  = {Structure Prediction},
  owner     = {andrius},
  timestamp = {2013.12.06},
  creationdate = {2013-12-06T00:00:00},
}

@Manuscript{Salib2004,
  author    = {Salib, Michael},
  title     = {Faster than C: Static Type Inference with Starkiller},
  year      = {2004},
  keywords  = {Computer Science (CS); Python; Type Inference},
  month     = {March},
  abstract  = {Pure Python code is slow, primarily due to the dynamic nature of the language. I have begun building a compiler to produce fast native code from Python source programs. While compilation can improve performance, any such gains will be modest unless the compiler can statically resolve most of the dynamism present in source programs. Static type inference for Python programs would enable the safe removal of most type checks and most instances of dynamic dispatch and dynamic binding from the generated code. Removing dynamic dispatch and binding leads to large performance benefits since their existence precludes many traditional optimization techniques, such as inlining. I have built a static type inferencer for Python called Starkiller. Given a Python source file, it can deduce the types of all expressions in the program without actually running it. Starkiller’s primary goal is to take a Python source program as input and deduce the information needed to make native code compilation of that program easy. This paper is describes Starkiller’s design and operation. It is partially adapted from a draft of my Master’s thesis.},
  file      = {:by-author/S/Salib/2004_Salib.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Salinas2000,
  author    = {Salinas, F. and Benkovic, S. J.},
  journal   = {Proceedings of the National Academy of Sciences of the United States of America},
  title     = {Characterization of bacteriophage T4-coordinated leading- and lagging-strand synthesis on a minicircle substrate.},
  year      = {2000},
  pages     = {7196--201},
  volume    = {97},
  abstract  = {The DNA replication complex of bacteriophage T4 has been assembled as a single unit on a minicircle substrate with a replication fork that permits an independent measurement of the amount of DNA synthesis on both the leading and lagging strands. The assembled replisome consists of the T4 polymerase [gene product 43 (gp43)], clamp protein (gp45), clamp loader (gp44/62), helicase (gp41), helicase accessory factor (gp59), primase (gp61), and single-stranded DNA binding protein (gp32). We demonstrate that on the minicircle the synthesis of the leading and lagging strands are coordinated and that the C-terminal domain of the gp32 protein regulates this coordination. We show that the reconstituted replisome encompasses two coupled holoenzyme complexes and present evidence that this coupling might include a gp43 homodimer interaction.},
  file      = {:by-author/S/Salinas/2000_Salinas_7196.pdf:PDF},
  keywords  = {Replisoma; {gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Salje2013,
  author     = {Salje, Ekhard KH and Lampronti, Giulio I. and Soto-Parra, D. I. and Baró, Jordi and Planes, Antoni and Vives, Eduard},
  journal    = {American Mineralogist},
  title      = {Noise of collapsing minerals: predictability of the compressional failure in goethite mines},
  year       = {2013},
  pages      = {609--615},
  volume     = {98},
  file       = {[PDF] from minsocam.org:by-author/S/Salje/2013_Salje_609.pdf:application/pdf},
  groups     = {sg/JAC2009},
  owner      = {saulius},
  shorttitle = {Noise of collapsing minerals},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url        = {http://www.minsocam.org/msa/ammin/TOC/Abstracts/2013_Abstracts/Apr13_Abstracts/Salje_p609_13.pdf},
  urldate    = {2015-08-31},
}

@Article{Salmena2011,
  author    = {Leonardo Salmena and Laura Poliseno and Yvonne Tay and Lev Kats and Pier Paolo Pandolfi},
  journal   = {Cell},
  title     = {A {ceRNA} Hypothesis: The Rosetta Stone of a Hidden RNA Language?},
  year      = {2011},
  issn      = {0092-8674},
  number    = {3},
  pages     = {353--358},
  volume    = {146},
  doi       = {http://dx.doi.org/10.1016/j.cell.2011.07.014},
  file      = {:by-author/S/Salmena/2011_Salmena_353.pdf:PDF},
  groups    = {am/RNA activation},
  owner     = {andrius},
  timestamp = {2016.08.22},
  creationdate = {2016-08-22T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/S0092867411008129},
}

@TechReport{Salomaa2002,
  author      = {Arto Salomaa and Peter Sósik},
  institution = {Turku Center for Computer Science},
  title       = {Watson-Crik D0L Systems: the Power of One Transition},
  year        = {2002},
  file        = {:by-author/S/Salomaa/2002_Salomaa.ps.gz:PostScript;:by-author/S/Salomaa/2002_Salomaa.pdf:PDF},
  owner       = {saulius},
  timestamp = {2015.02.27},
  creationdate = {2015-02-27T00:00:00},
}

@Article{Saltikov2002,
  author    = {Saltikov, Chad W. and Olson, Betty H.},
  journal   = {Applied and environmental microbiology},
  title     = {Homology of Escherichia coli R773 arsA, arsB, and arsC genes in arsenic-resistant bacteria isolated from raw sewage and arsenic-enriched creek waters.},
  year      = {2002},
  pages     = {280--8},
  volume    = {68},
  abstract  = {The occurrence and diversity of the Escherichia coli R773 ars operon were investigated among arsenic-resistant enteric and nonenteric bacteria isolated from raw sewage and arsenic-enriched creek waters. Selected isolates from each creek location were screened for ars genes by colony hybridization and PCR. The occurrence of arsA, arsB, and arsC determined by low-stringency colony hybridization (31 to 53% estimated mismatch) was 81, 87, and 86%, respectively, for 84 bacteria isolated on arsenate- and arsenite-amended media from three locations. At moderate stringency (21 to 36% estimated mismatch), the occurrence decreased to 42, 56, and 63% for arsA, arsB, and arsC, respectively. PCR results showed that the ars operon is conserved in some enteric bacteria isolated from creek waters and raw sewage. The occurrence of the arsBC genotype was about 50% in raw sewage enteric bacteria, while arsA was detected in only 9.4% of the isolates (n = 32). The arsABC and arsBC genotypes occurred more frequently in enteric bacteria isolated from creek samples: 71.4 and 85.7% (n = 7), respectively. Average sequence divergence within arsB for six creek enteric bacteria was 20% compared to that of the E. coli R773 ars operon. Only 1 of 11 pseudomonads screened by PCR was positive for arsB. The results from this study suggest that significant divergence has occurred in the ars operon among As-resistant E. coli strains and in Pseudomonas spp.},
  file      = {:by-author/S/Saltikov/2002_Saltikov_280.pdf:PDF},
  keywords  = {Antirestriction},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Samai2010,
  author    = {Samai, Poulami and Smith, Paul and Shuman, Stewart},
  journal   = {Acta crystallographica. Section F, Structural biology and crystallization communications},
  title     = {Structure of a CRISPR-associated protein Cas2 from Desulfovibrio vulgaris.},
  year      = {2010},
  pages     = {1552--6},
  volume    = {66},
  file      = {2010_Samai_1552.pdf:by-author/S/Samai/2010_Samai_1552.pdf:PDF},
  groups    = {sg/CRISPR-Cas},
  keywords  = {CRISPR; Protein Structures},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{SanBiagio1998,
  author    = {San Biagio, P. L. and D. Bulone and V. Martorana and M. B. Palma-Vittorelli and M. U. Palma},
  journal   = {Eur. Biophys. J.},
  title     = {Physics and biophysics of solvent induced forces: hydrophobic interactions and context-dependent hydration},
  year      = {1998},
  pages     = {183--196},
  volume    = {27},
  abstract  = {Solvent induced forces (SIFs) among solutes derive from solvent structural modification due to solutes, and consequent thermodynamic drive towards minimiza- tion of related free energy costs. The role of SIFs in bio- molecular conformation and function is appreciated by ob- serving that typical SIF values fall within the 20 – 200 pN interval, and that proteins are stable by only a few kcal mol–1 (1 kcal mol–1 corresponds to 70 pN Å). Here we study SIFs, in systems of increasing complexity, using Mo- lecular Dynamics (MD) simulations which give time- and space-resolved details on the biologically significant scale of single protein residues and sidechains. Of particular biological relevance among our results are a strong mod- ulability of hydrophobic SIFs by electric charges and the dependence of this modulability upon charge sign. More generally, the present results extend our understanding of the recently reported strong context-dependence of SIFs and the related potential of mean force (PMF). This con- text-dependence can be strong enough to propagate (by re- lay action) along a composite solute, and to reverse SIFs acting on a given element, relative to expectations based on its specific character (hydrophobic/ philic, charged). High specificity such as that of SIFs highlighted by the present results is of course central to biological function. Biological implications of the present results cover issues such as biomolecular functional interactions and folding (including chaperoning and pathological conformational changes), coagulation, molecular recognition, effects of phosphorylation and more.},
  file      = {SanBiagio_1998_183-hydrophobic_interactions.pdf:by-author/S/SanBiagio/1998_SanBiagio_183.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Martin1995,
  author    = {San Martin, M. Carmen and N. Patrick J. Stamford and Nada Dammerova and Nicholas E. Dixon},
  journal   = {Journal of Structural Biology},
  title     = {A structural Model for the {\em Escherichia coli\/} {DnaB} helicase based on electron microscopy data},
  year      = {1995},
  pages     = {167--176},
  volume    = {114},
  abstract  = {The DnaB protein is the major replicative DNA helicase in {\em Escherichia coli\/}. It hydrolyzes ATP to promote its translocation in the 5' to 3' direction on single-stranded DNA teplates, facilitating the separation of strands of duplex DNA in its path. This places it on the lagging strands at replication forks during chromosomal DNA replication. Electron microscopic images of negatively stained DnaB protein have been studied and processed to produce a three-dimensional reconstruction of the protein oligomer at 2.7~nm resolution. While it is known that the native protein is a complex of six identical 52-kDa subunits, the specimen shows threefold rather than sixfold symmetry, with three outer stain-excluding regions surrounding another six, more massive, lobules. There is a channel through the particle that appears fully open on both sides. Based on these results, a structural model for the oligomer is presented, and functional implications are considered.},
  file      = {:by-author/M/Martin/1995_Martin_167.pdf:PDF},
  keywords  = {Ecoli; {gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Sandenaw1988,
  author    = {Thomas A. Sandenaw},
  title     = {Incommensurate/Commensurate Charge-Density-Wave States as a Source for Plutonium Metal Behavior},
  year      = {1988},
  file      = {:by-author/S/Sandenaw/1988_Sandenaw.pdf:PDF},
  keywords  = {Incommensurate Structures},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Sandin2005,
  author    = {Sandin, Peter and Wilhelmsson, L Marcus and Lincoln, Per and Powers, Vicki E C and Brown, Tom and Albinsson, Bo},
  journal   = {Nucleic acids research},
  title     = {Fluorescent properties of DNA base analogue tC upon incorporation into DNA--negligible influence of neighbouring bases on fluorescence quantum yield.},
  year      = {2005},
  pages     = {5019--25},
  volume    = {33},
  abstract  = {The quantum yield of the fluorescent tricyclic cytosine analogue, 1,3-diaza-2-oxophenothiazine, tC, is high and virtually unaffected by incorporation into both single- and double-stranded DNA irrespective of neighbouring bases (0.17-0.24 and 0.16-0.21, respectively) and the corresponding fluorescence decay curves are all mono-exponential, properties that are unmatched by any base analogue so far. The fluorescence lifetimes increase when going from tC free in solution (3.2 ns) to single- and double-stranded DNA (on average 5.7 and 6.3 ns, respectively). The mono-exponential decays further support previous NMR results where it was found that tC has a well-defined position and geometry within the DNA helix. Furthermore, we find that the oxidation potential of tC is 0.4 V lower than for deoxyguanosine, the natural base with the lowest oxidation potential. This suggests that tC may be of interest in charge transfer studies in DNA as an electron hole acceptor. We also present a novel synthetic route to the phosphoramidite form of tC. The results presented here together with previous work show that tC is a very good C-analogue that induces minimal perturbation to the native structure of DNA. This makes tC unique as a fluorescent base analogue and is thus highly interesting in a range of applications for studying e.g. structure, dynamics and kinetics in nucleic acid systems.},
  file      = {2005_Sandin_5019.pdf:by-author/S/Sandin/2005_Sandin_5019.pdf:PDF},
  keywords  = {{pH} Sensitive DNA Base Analogues},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{SantaLucia1998,
  author    = {SantaLucia, J.},
  journal   = {Proceedings of the National Academy of Sciences},
  title     = {A unified view of polymer, dumbbell, and oligonucleotide {DNA} nearest-neighbor thermodynamics},
  year      = {1998},
  issn      = {1091-6490},
  month     = {Feb},
  number    = {4},
  pages     = {1460–1465},
  volume    = {95},
  doi       = {10.1073/pnas.95.4.1460},
  file      = {1998_SantaLucia_1460.pdf:by-author/S/SantaLucia/1998_SantaLucia_1460.pdf:PDF},
  owner     = {andrius},
  publisher = {Proceedings of the National Academy of Sciences},
  timestamp = {2017.02.28},
  creationdate = {2017-02-28T00:00:00},
  url       = {http://www.pnas.org/content/95/4/1460},
}

@Article{Santamaria2010,
  author    = {Santamaria, Fidel and Gonzalez, Jossina and Augustine, George J. and Raghavachari, Sridhar},
  journal   = {PLoS computational biology},
  title     = {Quantifying the effects of elastic collisions and non-covalent binding on glutamate receptor trafficking in the post-synaptic density.},
  year      = {2010},
  pages     = {e1000780},
  volume    = {6},
  abstract  = {One mechanism of information storage in neurons is believed to be determined by the strength of synaptic contacts. The strength of an excitatory synapse is partially due to the concentration of a particular type of ionotropic glutamate receptor (AMPAR) in the post-synaptic density (PSD). AMPAR concentration in the PSD has to be plastic, to allow the storage of new memories; but it also has to be stable to preserve important information. Although much is known about the molecular identity of synapses, the biophysical mechanisms by which AMPAR can enter, leave and remain in the synapse are unclear. We used Monte Carlo simulations to determine the influence of PSD structure and activity in maintaining homeostatic concentrations of AMPARs in the synapse. We found that, the high concentration and excluded volume caused by PSD molecules result in molecular crowding. Diffusion of AMPAR in the PSD under such conditions is anomalous. Anomalous diffusion of AMPAR results in retention of these receptors inside the PSD for periods ranging from minutes to several hours in the absence of strong binding of receptors to PSD molecules. Trapping of receptors in the PSD by crowding effects was very sensitive to the concentration of PSD molecules, showing a switch-like behavior for retention of receptors. Non-covalent binding of AMPAR to anchored PSD molecules allowed the synapse to become well-mixed, resulting in normal diffusion of AMPAR. Binding also allowed the exchange of receptors in and out of the PSD. We propose that molecular crowding is an important biophysical mechanism to maintain homeostatic synaptic concentrations of AMPARs in the PSD without the need of energetically expensive biochemical reactions. In this context, binding of AMPAR with PSD molecules could collaborate with crowding to maintain synaptic homeostasis but could also allow synaptic plasticity by increasing the exchange of these receptors with the surrounding extra-synaptic membrane.},
  file      = {:by-author/S/Santamaria/2010_Santamaria_e1000780.pdf:PDF},
  keywords  = {Noncovalent Interactions; Protein Physics},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@Article{Santoro1974,
  author    = {Santoro, A.},
  journal   = {Acta Crystallographica Section A},
  title     = {Characterization of twinning},
  year      = {1974},
  pages     = {224--231},
  volume    = {30},
  abstract  = {A new twinning condition is derived. It is more general than Friedel's ratios [Friedel, G. (1964). Leçons de Cristallographie, p. 249, Paris: Blanchard], and it allows one to predict not only the twin laws of a crystalline species, but also the regular associations of crystals mutually oriented according to non-crystallographic rotations. The deviation suffered by the twin lattice at the composition surface is better described in terms of the new twinning condition than in terms of the twin obliquity.},
  doi       = {10.1107/S0567739474000465},
  file      = {:by-author/S/Santoro/1974_Santoro_224.pdf:PDF},
  keywords  = {Twins; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0567739474000465},
}

@Article{Santoro1973,
  author    = {Santoro, A. and Mighell, A. D.},
  journal   = {Acta Crystallographica Section A},
  title     = {Coincidence-site lattices},
  year      = {1973},
  pages     = {169--175},
  volume    = {29},
  abstract  = {Coincidence-site lattices are characterized mathematically, in the general case, by a method that can be applied to a pair of original lattices of any symmetry, either metrically identical or metrically different, does not involve inspection and is readily adaptable to computer calculations. The procedure is illustrated by several numerical examples. The proposed characterization of coincidence-site lattices is based on the theory of derivative lattices and makes extensive use of the concepts of superlattice and sublattice. Appended is a simple procedure for determining the transformation matrices needed to generate superlattices and sublattices of any multiplicity.},
  doi       = {10.1107/S0567739473000434},
  file      = {1973_Santoro_169.pdf:by-author/S/Santoro/1973_Santoro_169.pdf:PDF},
  groups    = {sg/Crystal structure prediction},
  keywords  = {Algorithms; Enumeration; Lattices; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2015.06.12},
  creationdate = {2015-06-12T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0567739473000434},
}

@Article{Santoro1972,
  author    = {Santoro, A. and Mighell, A. D.},
  journal   = {Acta Crystallographica Section A},
  title     = {Properties of crystal lattices: the derivative lattices and their determination},
  year      = {1972},
  pages     = {284--287},
  volume    = {28},
  abstract  = {Derivative lattices are classified as super, sub and composite, on the basis of the properties of the transformation matrices relating them to the lattice from which they are derived. A method for obtaining the transformation matrices generating these lattices is given. The method has been applied to the derivation of the unique super and sublattices in a few important cases.},
  doi       = {10.1107/S0567739472000737},
  file      = {1972_Santoro_284.pdf:by-author/S/Santoro/1972_Santoro_284.pdf:PDF},
  groups    = {sg/Crystal structure prediction},
  keywords  = {Algorithms; Enumeration; Lattices; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2015.06.12},
  creationdate = {2015-06-12T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0567739472000737},
}

@Article{Santoro1970,
  author    = {Santoro, A. and Mighell, A. D.},
  journal   = {Acta Crystallographica Section A},
  title     = {Determination of reduced cells},
  year      = {1970},
  pages     = {124--127},
  volume    = {26},
  abstract  = {An analysis is given of the relation between the reduced cells defined by Niggli and the cells obtained by applying Buerger's algorithm. It is shown that in many instances a cell based on the shortest three non-coplanar translations must be transformed to obtain the reduced cell. The required transformations for all cases have been derived and are presented in this paper.},
  doi       = {10.1107/S0567739470000177},
  file      = {:by-author/S/Santoro/1970_Santoro_124.pdf:PDF},
  groups    = {sg/Cell sg/Reduction, sg/Cell reduction},
  keywords  = {Crystal Cell; Reduced Cell; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0567739470000177},
}

@Article{Sapranauskas2011,
  author    = {Sapranauskas, Rimantas and Gasiunas, Giedrius and Fremaux, Christophe and Barrangou, Rodolphe and Horvath, Philippe and Siksnys, Virginijus},
  journal   = {Nucleic acids research},
  title     = {The Streptococcus thermophilus CRISPR/Cas system provides immunity in Escherichia coli.},
  year      = {2011},
  pages     = {9275--82},
  volume    = {39},
  abstract  = {The CRISPR/Cas adaptive immune system provides resistance against phages and plasmids in Archaea and Bacteria. CRISPR loci integrate short DNA sequences from invading genetic elements that provide small RNA-mediated interference in subsequent exposure to matching nucleic acids. In Streptococcus thermophilus, it was previously shown that the CRISPR1/Cas system can provide adaptive immunity against phages and plasmids by integrating novel spacers following exposure to these foreign genetic elements that subsequently direct the specific cleavage of invasive homologous DNA sequences. Here, we show that the S. thermophilus CRISPR3/Cas system can be transferred into Escherichia coli and provide heterologous protection against plasmid transformation and phage infection. We show that interference is sequence-specific, and that mutations in the vicinity or within the proto-spacer adjacent motif (PAM) allow plasmids to escape CRISPR-encoded immunity. We also establish that cas9 is the sole cas gene necessary for CRISPR-encoded interference. Furthermore, mutation analysis revealed that interference relies on the Cas9 McrA/HNH- and RuvC/RNaseH-motifs. Altogether, our results show that active CRISPR/Cas systems can be transferred across distant genera and provide heterologous interference against invasive nucleic acids. This can be leveraged to develop strains more robust against phage attack, and safer organisms less likely to uptake and disseminate plasmid-encoded undesirable genetic elements.},
  file      = {:by-author/S/Sapranauskas/2011_Sapranauskas_9275.pdf:PDF},
  groups    = {sg/CRISPR-Cas},
  keywords  = {CRISPR},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Sapranauskas2000,
  author    = {Sapranauskas, R. and Sasnauskas, G. and Lagunavicius, A. and Vilkaitis, G. and Lubys, A. and Siksnys, V.},
  journal   = {The Journal of biological chemistry},
  title     = {Novel subtype of type IIs restriction enzymes. BfiI endonuclease exhibits similarities to the EDTA-resistant nuclease Nuc of Salmonella typhimurium.},
  year      = {2000},
  pages     = {30878--85},
  volume    = {275},
  abstract  = {The type IIs restriction enzyme BfiI recognizes the non-palindromic nucleotide sequence 5'-ACTGGG-3' and cleaves complementary DNA strands 5/4 nucleotides downstream of the recognition sequence. The genes coding for the BfiI restriction-modification (R-M) system were cloned/sequenced and biochemical characterization of BfiI restriction enzyme was performed. The BfiI R-M system contained three proteins: two N4-methylcytosine methyltransferases and a restriction enzyme. Sequencing of bisulfite-treated methylated DNA indicated that each methyltransferase modifies cytosines on opposite strands of the recognition sequence. The N-terminal part of the BfiI restriction enzyme amino acid sequence revealed intriguing similarities to an EDTA-resistant nuclease of Salmonella typhimurium. Biochemical analyses demonstrated that BfiI, like the nuclease of S. typhimurium, cleaves DNA in the absence of Mg(2+) ions and hydrolyzes an artificial substrate bis(p-nitrophenyl) phosphate. However, unlike the nonspecific S. typhimurium nuclease, BfiI restriction enzyme cleaves DNA specifically. We propose that the DNA-binding specificity of BfiI stems from the C-terminal part of the protein. The catalytic N-terminal subdomain of BfiI radically differs from that of type II restriction enzymes and is presumably similar to the EDTA-resistant nonspecific nuclease of S. typhimurium; therefore, BfiI did not require metal ions for catalysis. We suggest that BfiI represents a novel subclass of type IIs restriction enzymes that differs from the archetypal FokI endonuclease by the fold of its cleavage domain, the domain location, and reaction mechanism.},
  file      = {:by-author/S/Sapranauskas/2000_Sapranauskas_30878.pdf:PDF},
  keywords  = {BfiI; TypeII},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Sapranauskas2000a,
  author    = {Rimantas Sapranauskas and Giedrius Sasnauskas and Arunas Lagunavicius and Giedrius Vilkaitis and Arvydas Lubys and Virginijus Siksnys},
  journal   = {The Journal of Biological Chemistry},
  title     = {Novel Subtype of Type IIs Restriction Enzymes},
  year      = {2000},
  pages     = {proofs},
  file      = {:by-author/S/Sapranauskas/2000_Sapranauskas_proofs.pdf:PDF},
  keywords  = {Manuscripts},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@InProceedings{Sardana2007,
  author    = {Anjali Sardana and Bhavana Gandhi and Ramesh Joshi},
  booktitle = {Innovative Algorithms and Techniques in Automation, Industrial Electronics and Telecommunications},
  title     = {A Novel Online Technique to Characterize and Mitigate DoS Attacks using EPSD and Honeypots},
  year      = {2007},
  editor    = {T. Sobh et al.},
  pages     = {49--54},
  publisher = {Springer},
  abstract  = {Denial of Service Denial of Service (DoS) attacks pose a severe security threat to the steady functioning of any network. These attacks aim at depleting the resources of a server or an administrative network by overwhelming it with enormous and useless traffic. The outcome of this is the fact that legitimate users are denied service. Though an array of schemes has been proposed for the detection of the presence of these attacks, characterizing of the flows as a normal flow or a malicious one, identifying the sources of the attacks and mitigating the effects of the attacks once they have been detected, there is still a dearth of complete frameworks that encompass multiple stages of the process of defense against DoS attacks. In this paper, we propose a novel framework which deals with the characterization of the TCP and UDP flows, identification of the source of the flow once it has been characterized as an attack flow and mitigating the influence of the attack. The characterization of the flows has been achieved by an innovative Exactly Periodic Subspace Decomposition (EPSD) based approach, whereas a proactive roaming honeypot scheme has been deployed for the identification of the source of the attack flow and mitigation of the effects of the same. We validate the effectiveness of the approach with simulation in ns-2 on a Linux platform.},
  file      = {:by-author/S/Sardana/2007_Sardana_49.pdf:PDF},
  owner     = {saulius},
  timestamp = {2013.07.02},
  creationdate = {2013-07-02T00:00:00},
}

@Manual{Sarjeant2013,
  title        = {Structure Solution and Refinement with Olex2: A guide for Chem 435 Students},
  author       = {Amy A. Sarjeant},
  month        = {January},
  organization = {Department of Chemistry, Northwestern University, Evanston IL},
  year         = {2013},
  file         = {2013_Sarjeant_manual.pdf:by-author/S/Sarjeant/2013_Sarjeant_manual.pdf:PDF},
  keywords     = {Chemical Crystallography; Olex2; Small Molecule; Software; X-ray Crystallography},
  owner        = {saulius},
  timestamp = {2016.12.21},
  creationdate = {2016-12-21T00:00:00},
  url          = {http://imserc.facilities.northwestern.edu/files/2013/11/Olex2atNUv1.1.pdf},
}

@Presentation{Sarkar2005,
  author    = {Sudeshna Sarkar},
  title     = {Expectation Maximization. Hierarchical Clustering},
  year      = {2005},
  course    = {COMP-652},
  lecture   = {Lecture 19},
  file      = {:by-author/S/Sarkar/2005_Sarkar_slides.pdf:PDF},
  owner     = {saulius},
  pages     = {slides},
  timestamp = {2013.07.02},
  creationdate = {2013-07-02T00:00:00},
  url       = {http://www.facweb.iitkgp.ernet.in/~sudeshna/courses/ML06/ml-lecture19.pdf},
}

@InProceedings{Sarmenta1998,
  author    = {Luis F. G. Sarmenta},
  booktitle = {2nd International Conference on World-Wide Computing and its Applications (WWCA'98)},
  title     = {Bayanihan: Web-Based Volunteer Computing Using Java},
  year      = {1998},
  abstract  = {This paper presents and discusses the idea of Web-based volunteer computing, which allows people to cooperate in solving a large parallel problem by using standard Web browsers to volunteer their computers' processing power. Because volunteering requires no prior human contact and very little technical knowledge, it becomes very easy to build very large volunteer computing networks. At its full potential, volunteer computing can make it possible to build world-wide massively parallel computing networks more powerful than any supercomputer. Even on a smaller, more practical scale, volunteer computing can be used within companies or institutions to provide supercomputer-like facilities by harnessing the computing power of existing workstations. Many interesting variations are possible, including networks of information appliances (NOIAs), paid volunteer systems, and barter trade of compute cycles. In this paper, we discuss these possibilities, and identify several issues that will need to be addressed in order to successfully implement them. We also present an overview of the current work being done in the Bayanihan volunteer computing project.},
  file      = {:by-author/S/Sarmenta/1998_Sarmenta.pdf:PDF;:by-author/S/Sarmenta/1998_Sarmenta.ps:PostScript},
  owner     = {saulius},
  timestamp = {2012.06.04},
  creationdate = {2012-06-04T00:00:00},
}

@Article{Sashital2011,
  author    = {Sashital, Dipali G. and Jinek, Martin and Doudna, Jennifer A.},
  journal   = {Nature structural \&amp; molecular biology},
  title     = {An RNA-induced conformational change required for CRISPR RNA cleavage by the endoribonuclease Cse3.},
  year      = {2011},
  pages     = {680--7},
  volume    = {18},
  abstract  = {Clustered regularly interspaced short palindromic repeat (CRISPR) chromosomal loci found in prokaryotes provide an adaptive immune system against bacteriophages and plasmids. CRISPR-specific endoRNases produce short RNA molecules (crRNAs) from CRISPR transcripts, which harbor sequences complementary to invasive nucleic acid elements and ensure their selective targeting by CRISPR-associated (Cas) proteins. The extreme sequence divergence of CRISPR-specific endoRNases and their RNA substrates has obscured homology-based comparison of RNA recognition and cleavage mechanisms. Here, we show that Cse3 type CRISPR-specific endoRNases bind a hairpin structure and residues downstream of the cleavage site within the repetitive segment of cognate CRISPR RNA. Cocrystal structures of Cse3-RNA complexes reveal an RNA-induced conformational change in the enzyme active site that aligns the RNA strand for site-specific cleavage. These studies provide insight into a catalytically essential RNA recognition mechanism by a large class of CRISPR-related endoRNases.},
  file      = {:by-author/S/Sashital/2011_Sashital_680.pdf:PDF},
  groups    = {sg/CRISPR-Cas},
  keywords  = {CRISPR},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Sashital2012,
  author    = {Dipali G. Sashital and Blake Wiedenheft and Jennifer A. Doudna},
  journal   = {Molecular Cell},
  title     = {Mechanism of Foreign {DNA} Selection in a Bacterial Adaptive Immune System},
  year      = {2012},
  pages     = {606a},
  doi       = {10.1016/j.molcel.2012.03.020},
  file      = {:by-author/S/Sashital/2012_Sashital_606a.pdf:PDF},
  groups    = {sg/CRISPR-Cas},
  keywords  = {CRISPR},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@PhdThesis{Sasnauskas2004,
  author    = {Sasnauskas, Giedrius},
  school    = {Vilniaus universitetas, Biotechnologijos institutas},
  title     = {Naujas {IIs} Tipo Restrikcijos Endonukleazių Pogrupis},
  year      = {2004},
  file      = {:by-author/S/Sasnauskas/2004_Sasnauskas_phdthesis.pdf:PDF},
  keywords  = {BfiI; TypeII},
  owner     = {em},
  pages     = {phdthesis},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Sasnauskas2007,
  author    = {Sasnauskas, Giedrius and Connolly, Bernard A. and Halford, Stephen E. and Siksnys, Virginijus},
  journal   = {Proceedings of the National Academy of Sciences},
  title     = {Site-specific DNA transesterification catalyzed by a restriction enzyme},
  year      = {2007},
  number    = {7},
  pages     = {2115--2120},
  volume    = {104},
  abstract  = {Most restriction endonucleases use Mg2+ to hydrolyze phosphodiester bonds at specific DNA sites. We show here that BfiI, a metal-independent restriction enzyme from the phospholipase D superfamily, catalyzes both DNA hydrolysis and transesterification reactions at its recognition site. In the presence of alcohols such as ethanol or glycerol, it attaches the alcohol covalently to the 5′ terminus of the cleaved DNA. Under certain conditions, the terminal 3′-OH of one DNA strand can attack the target phosphodiester bond in the other strand to create a DNA hairpin. Transesterification reactions on DNA with phosphorothioate linkages at the target bond proceed with retention of stereoconfiguration at the phosphorus, indicating, uniquely for a restriction enzyme, a two-step mechanism. We propose that BfiI first makes a covalent enzyme–DNA intermediate, and then it resolves it by a nucleophilic attack of water or an alcohol, to yield hydrolysis or transesterification products, respectively.},
  doi       = {10.1073/pnas.0608689104},
  eprint    = {http://www.pnas.org/content/104/7/2115.full.pdf},
  file      = {2007_Sasnauskas_2115.pdf:by-author/S/Sasnauskas/2007_Sasnauskas_2115.pdf:PDF},
  keywords  = {BfiI; Restriction Endonucleases (REases); Transesterification},
  owner     = {saulius},
  timestamp = {2016.09.30},
  creationdate = {2016-09-30T00:00:00},
  url       = {http://www.pnas.org/content/104/7/2115.abstract},
}

@Article{Sasnauskas2003,
  author    = {Sasnauskas, Giedrius and Halford, Stephen E and Siksnys, Virginijus},
  journal   = {Proceedings of the National Academy of Sciences of the United States of America},
  title     = {How the BfiI restriction enzyme uses one active site to cut two DNA strands.},
  year      = {2003},
  pages     = {6410--5},
  volume    = {100},
  abstract  = {Unlike other restriction enzymes, BfiI functions without metal ions. It recognizes an asymmetric DNA sequence, 5'-ACTGGG-3', and cuts top and bottom strands at fixed positions downstream of this sequence. Many restriction enzymes are dimers of identical subunits, with one active site for each DNA strand. Others, like FokI, dimerize transiently during catalysis. BfiI is also a dimer but it has only one active site, at the dimer interface. We show here that BfiI remains a dimer as it makes double-strand breaks in DNA and that its single active site acts sequentially, first on the bottom and then the top strand. Hence, after cutting the bottom strand, a rearrangement of either the protein and/or the DNA in the BfiI-DNA complex must switch the active site to the top strand. Low pH values selectively block top-strand cleavage, converting BfiI into a nicking enzyme that cleaves only the bottom strand. The switch to the top strand may depend on the ionization of the cleaved 5' phosphate in the bottom strand. BfiI thus uses a mechanism for making double-strand breaks that is novel among restriction enzymes.},
  file      = {Sasnauskas_2003_6410-bfiI_mechanism.pdf:by-author/S/Sasnauskas/2003_Sasnauskas_6410.pdf:PDF},
  keywords  = {BfiI; TypeII},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Sasnauskas1999,
  author    = {Sasnauskas, G. and Jeltsch, A. and Pingoud, A. and Siksnys, V.},
  journal   = {Biochemistry},
  title     = {Plasmid DNA cleavage by MunI restriction enzyme: single-turnover and steady-state kinetic analysis.},
  year      = {1999},
  pages     = {4028--36},
  volume    = {38},
  abstract  = {Mutational analysis has previously indicated that D83 and E98 residues are essential for DNA cleavage activity and presumably chelate a Mg2+ ion at the active site of MunI restriction enzyme. In the absence of metal ions, protonation of an ionizable residue with a pKa &gt; 7.0, most likely one of the active site carboxylates, controls the DNA binding specificity of MunI [Lagunavicius, A., Grazulis, S., Balciunaite, E., Vainius, D., and Siksnys, V. (1997) Biochemistry 36, 11093-11099.]. Thus, competition between H+ and Mg2+ binding at the active site of MunI presumably plays an important role in catalysis/binding. In the present study we have identified elementary steps and intermediates in the reaction pathway of plasmid DNA cleavage by MunI and elucidated the effect of pH and Mg2+ ions on the individual steps of the DNA cleavage reaction. The kinetic analysis indicated that the multiple-turnover rate of plasmid cleavage by MunI is limited by product release throughout the pH range 6.0-9.3. Quenched-flow experiments revealed that open circle DNA is an obligatory intermediate in the reaction pathway. Under optimal reaction conditions, open circle DNA remains bound to the MunI; however it is released into the solution at low [MgCl2]. Rate constants for the phoshodiester bond hydrolysis of the first (k1) and second (k2) strand of plasmid DNA at pH 7.0 and 10 mM MgCl2 more than 100-fold exceed the kcat value which is limited by product dissociation. The analysis of the pH and [Mg2+] dependences of k1 and k2 revealed that both H+ and Mg2+ ions compete for the binding to the same residue at the active site of MunI. Thus, the decreased rate of phosphodiester hydrolysis by MunI at pH &lt; 7.0 may be due to the reduction of affinity for the Mg2+ binding at the active site. Kinetic analysis of DNA cleavage by MunI yielded estimates for the association-dissociation rate constants of enzyme-substrate complex and demonstrated the decreased stability of the MunI-DNA complex at pH values above 8.0.},
  doi       = {10.1021/bi982456n},
  file      = {:by-author/S/Sasnauskas/1999_Sasnauskas_4028.pdf:PDF},
  keywords  = {BfiI; TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Sasnauskas2010,
  author    = {Sasnauskas, Giedrius and Zakrys, Linas and Zaremba, Mindaugas and Cosstick, Richard and Gaynor, James W. and Halford, Stephen E. and Siksnys, Virginijus},
  journal   = {Nucleic acids research},
  title     = {A novel mechanism for the scission of double-stranded DNA: BfiI cuts both 3'-5' and 5'-3' strands by rotating a single active site.},
  year      = {2010},
  pages     = {2399--410},
  volume    = {38},
  abstract  = {Metal-dependent nucleases that generate double-strand breaks in DNA often possess two symmetrically-equivalent subunits, arranged so that the active sites from each subunit act on opposite DNA strands. Restriction endonuclease BfiI belongs to the phospholipase D (PLD) superfamily and does not require metal ions for DNA cleavage. It exists as a dimer but has at its subunit interface a single active site that acts sequentially on both DNA strands. The active site contains two identical histidines related by 2-fold symmetry, one from each subunit. This symmetrical arrangement raises two questions: first, what is the role and the contribution to catalysis of each His residue; secondly, how does a nuclease with a single active site cut two DNA strands of opposite polarities to generate a double-strand break. In this study, the roles of active-site histidines in catalysis were dissected by analysing heterodimeric variants of BfiI lacking the histidine in one subunit. These variants revealed a novel mechanism for the scission of double-stranded DNA, one that requires a single active site to not only switch between strands but also to switch its orientation on the DNA.},
  file      = {:by-author/S/Sasnauskas/2010_Sasnauskas_2399.pdf:PDF},
  owner     = {em},
  timestamp = {2013.09.19},
  creationdate = {2013-09-19T00:00:00},
}

@Manuscript{Satapathy2011,
  author    = {Ajit K. Satapathy and Charles C. Richardson},
  title     = {The Glutamate Switch of Bacteriophage {T7} {DNA} Helicase: Role in Coupling {NTP} and {DNA} Binding to {NTP} Hydrolysis},
  year      = {2011},
  keywords  = {{gp41} Helicase},
  file      = {:by-author/S/Satapathy/2011_Satapathy_preprint.pdf:PDF},
  owner     = {em},
  pages     = {preprint},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Sauter2004,
  author    = {Sauter, Nicholas K and Grosse-Kunstleve, Ralf W and Adams, Paul D},
  journal   = {Journal of applied crystallography},
  title     = {Robust indexing for automatic data collection.},
  year      = {2004},
  pages     = {399--409},
  volume    = {37},
  abstract  = {Improved methods for indexing diffraction patterns from macromolecular crystals are presented. The novel procedures include a more robust way to verify the position of the incident X-ray beam on the detector, an algorithm to verify that the deduced lattice basis is consistent with the observations, and an alternative approach to identify the metric symmetry of the lattice. These methods help to correct failures commonly experienced during indexing, and increase the overall success rate of the process. Rapid indexing, without the need for visual inspection, will play an important role as beamlines at synchrotron sources prepare for high-throughput automation.},
  file      = {2004_Sauter_399.pdf:by-author/S/Sauter/2004_Sauter_399.pdf:PDF},
  keywords  = {Indexing; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Savage2009,
  author    = {Savage, Caroline J. and Vickers, Andrew J.},
  journal   = {PloS one},
  title     = {Empirical study of data sharing by authors publishing in PLoS journals.},
  year      = {2009},
  pages     = {e7078},
  volume    = {4},
  doi       = {10.1371/journal.pone.0007078},
  file      = {:by-author/S/Savage/2009_Savage_e7078.pdf:PDF},
  keywords  = {Data Sharing; Scientific Publications},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@Article{Sawada2009,
  author    = {Sawada, Tomohisa and Yoshizawa, Michito and Sato, Sota and Fujita, Makoto},
  journal   = {Nature Chemistry},
  title     = {Minimal nucleotide duplex formation in water through enclathration in self-assembled hosts},
  year      = {2009},
  issn      = {1755-4349},
  month     = {Feb},
  number    = {1},
  pages     = {53--56},
  volume    = {1},
  doi       = {10.1038/nchem.100},
  file      = {2009_Sawada_53.pdf:by-author/S/Sawada/2009_Sawada_53.pdf:PDF},
  owner     = {saulius},
  publisher = {Springer Nature},
  timestamp = {2017.02.02},
  creationdate = {2017-02-02T00:00:00},
  url       = {http://dx.doi.org/10.1038/nchem.100},
}

@Article{Sawaya1999,
  author    = {Sawaya, M. R. and Guo, S. and Tabor, S. and Richardson, C. C. and Ellenberger, T.},
  journal   = {Cell},
  title     = {Crystal structure of the helicase domain from the replicative helicase-primase of bacteriophage T7.},
  year      = {1999},
  pages     = {167--77},
  volume    = {99},
  abstract  = {Helicases that unwind DNA at the replication fork are ring-shaped oligomeric enzymes that move along one strand of a DNA duplex and catalyze the displacement of the complementary strand in a reaction that is coupled to nucleotide hydrolysis. The helicase domain of the replicative helicase-primase protein from bacteriophage T7 crystallized as a helical filament that resembles the Escherichia coli RecA protein, an ATP-dependent DNA strand exchange factor. When viewed in projection along the helical axis of the crystals, six protomers of the T7 helicase domain resemble the hexameric rings seen in electron microscopic images of the intact T7 helicase-primase. Nucleotides bind at the interface between pairs of adjacent subunits where an arginine is near the gamma-phosphate of the nucleotide in trans. The bound nucleotide stabilizes the folded conformation of a DNA-binding motif located near the center of the ring. These and other observations suggest how conformational changes are coupled to DNA unwinding activity.},
  file      = {:by-author/S/Sawaya/1999_Sawaya_167.pdf:PDF},
  keywords  = {{gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@TechReport{Sawitzki1998,
  author      = {G. Sawitzki},
  institution = {StatLab Heidelberg, Im Neuenheimer Feld 294, D-69120 Heidelberg},
  title       = {The excess mass approach and the analysis of multi-modality},
  year        = {1998},
  month       = {dec},
  abstract    = {The excess mass approach is a general approach to statistical analysis. It can be used to formulate a probabilistic model for clustering and can be applied to the analysis of multi-modality. Intuitively, a mode is present where an excess of probability mass is concentrated. This intuitive idea can be formalized directly by means of the excess mass functional. There is no need for intervening steps like initial density estimation. The excess mass measures the local difference of a given distribution to a reference model, usually the uniform distribution. The excess mass defines a functional which can be estimated efficiently from the data and can be used to test for multi-modality.},
  file        = {:by-author/S/Sawitzki/1998_Sawitzki.pdf:PDF},
  owner       = {saulius},
  timestamp = {2012.09.18},
  creationdate = {2012-09-18T00:00:00},
}

@Article{Sayle2008,
  author    = {Sayle, Roger},
  journal   = {J. Chem. Inf. Model.},
  title     = {Foreign Language Translation of Chemical Nomenclature by Computer},
  year      = {2008},
  pages     = {519},
  file      = {:by-author/S/Sayle/2008_Sayle_519.pdf:PDF},
  keywords  = {Chemical Language Processing},
  owner     = {andrius},
  timestamp = {2012.05.07},
  creationdate = {2012-05-07T00:00:00},
}

@InProceedings{Scaffidi2008,
  author    = {Scaffidi, Christopher and Brad Myers and Mary Shaw},
  booktitle = {ICSE’08},
  title     = {Topes: Reusable Abstractions for Validating Data},
  year      = {2008},
  abstract  = {Programmers often omit input validation when inputs can appear in many different formats or when validation criteria cannot be precisely specified. To enable validation in these situations, we present a new technique that puts valid inputs into a consistent format and that identifies “questionable” inputs which might be valid or invalid, so that these values can be double-checked by a person or a program. Our technique relies on the concept of a “tope”, which is an application-independent abstraction describ- ing how to recognize and transform values in a category of data. We present our definition of topes and describe a development environment that supports the implementation and use of topes. Experiments with web application and spreadsheet data indicate that using our technique improves the accuracy and reusability of validation code and also improves the effectiveness of subsequent data cleaning such as duplicate identification.},
  file      = {:by-author/S/Scaffidi/2008_Scaffidi_ICSE08.pdf:PDF},
  keywords  = {Computer Science (CS); Type Systems},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Scalfani2016,
  author           = {Scalfani, Vincent F. and Williams, Antony J. and Tkachenko, Valery and Karapetyan, Karen and Pshenichnov, Alexey and Hanson, Robert M. and Liddie, Jahred M. and Bara, Jason E.},
  journal          = {Journal of Cheminformatics},
  title            = {Programmatic conversion of crystal structures into {3D} printable files using {J}mol},
  year             = {2016},
  issn             = {1758-2946},
  month            = {Nov},
  number           = {1},
  volume           = {8},
  abstract         = {Background: Three-dimensional (3D) printed crystal structures are useful for chemistry teaching and research. Current manual methods of converting crystal structures into 3D printable files are time-consuming and tedious. To overcome this limitation, we developed a programmatic method that allows for facile conversion of thousands of crystal structures directly into 3D printable files.
Results: A collection of over 30,000 crystal structures in crystallographic information file (CIF) format from the Crystal- lography Open Database (COD) were programmatically converted into 3D printable files (VRML format) using Jmol scripting. The resulting data file conversion of the 30,000 CIFs proceeded as expected, however some inconsistencies and unintended results were observed with co-crystallized structures, racemic mixtures, and structures with large counterions that led to 3D printable files not containing the desired chemical structure. Potential solutions to these challenges are considered and discussed. Further, a searchable Jmol 3D Print website was created that allows users to both discover the 3D file dataset created in this work and create custom 3D printable files for any structure in the COD.
Conclusions: Over 30,000 crystal structures were programmatically converted into 3D printable files, allowing users to have quick access to a sizable collection of 3D printable crystal structures. Further, any crystal structure (>350,000) in the COD can now be conveniently converted into 3D printable file formats using the Jmol 3D Print website cre- ated in this work. The 3D Print website also allows users to convert their own CIFs into 3D printable files. 3D file data, scripts, and the Jmol 3D Print website are provided openly to the community in an effort to promote discovery and use of 3D printable crystal structures. The 3D file dataset and Jmol 3D Print website will find wide use with researchers and educators seeking to 3D print chemical structures, while the scripts will be useful for programmatically converting large database collections of crystal structures into 3D printable files.},
  creationdate     = {2016-12-01T00:00:00},
  doi              = {10.1186/s13321-016-0181-z},
  file             = {2016_Scalfani_s13321-016-0181-z.pdf:by-author/S/Scalfani/2016_Scalfani_s13321-016-0181-z.pdf:PDF},
  keywords         = {3D Printing; CIF; Crystallography; Crystals; Dataset; JSmol; Jmol; Open Data; Visualization},
  modificationdate = {2024-03-07T10:58:03},
  owner            = {saulius},
  publisher        = {Springer Nature},
  timestamp        = {2016.12.01},
  url              = {http://dx.doi.org/10.1186/s13321-016-0181-z},
}

@Manuscript{Scarman1985,
  author    = {Lord Scarman and Lord~Edmund-Davies~Lord~Bridge~of Harwich and Lord Templeman and Lord Griffiths},
  title     = {British Leyland Motor Corporation Ltd. and Another Respondents v. Armstrong Patents Co. Ltd. and Another Appellants},
  year      = {1985},
  keywords  = {Patentai; Teise},
  abstract  = {Copyright--Infringement--Indirect copying--Motor car exhaust pipes-- Manufacture of replacements by copying original exhaust pipe--Whether reproduction of engineering drawing--Whether car owners' right to repair overriding rights of copyright owner},
  file      = {:by-author/S/Scarman/1985_Scarman. v Armstrong Patents Co..doc:DOC},
  owner     = {saulius},
  timestamp = {2015.02.28},
  creationdate = {2015-02-28T00:00:00},
}

@Article{Schaeben2007,
  author    = {Helmut Schaeben and Ralf Hielscher and Jean-Jacques Fundenberger and Daniel Potts and Jurgen Prestin},
  journal   = {J. Appl. Cryst.},
  title     = {Orientation density function-controlled pole probability density function measurements: automated adaptive control of texture goniometers},
  year      = {2007},
  pages     = {570--579},
  volume    = {40},
  file      = {2007_Schaeben_570.pdf:by-author/S/Schaeben/2007_Schaeben_570.pdf:PDF},
  keywords  = {Textures; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Schaerli2010,
  author    = {Schaerli, Yolanda and Stein, Viktor and Spiering, Michelle M. and Benkovic, Stephen J. and Abell, Chris and Hollfelder, Florian},
  journal   = {Nucleic acids research},
  title     = {Isothermal DNA amplification using the T4 replisome: circular nicking endonuclease-dependent amplification and primase-based whole-genome amplification.},
  year      = {2010},
  pages     = {e201},
  volume    = {38},
  abstract  = {In vitro reconstitution of the bacteriophage T4 replication machinery provides a novel system for fast and processive isothermal DNA amplification. We have characterized this system in two formats: (i) in circular nicking endonuclease-dependent amplification (cNDA), the T4 replisome is supplemented with a nicking endonuclease (Nb.BbvCI) and a reverse primer to generate a well-defined uniform double-stranded linear product and to achieve up to 1100-fold linear amplification of a plasmid in 1 h. (ii) The T4 replisome with its primase (gp61) can also support priming and exponential amplification of genomic DNA in primase-based whole-genome amplification (T4 pWGA). Low amplification biases between 4.8 and 9.8 among eight loci for 0.3-10 ng template DNA suggest that this method is indeed suitable for uniform whole-genome amplification. Finally, the utility of the T4 replisome for isothermal DNA amplification is demonstrated in various applications, including incorporation of functional tags for DNA labeling and immobilization; template generation for in vitro transcription/translation and sequencing; and colony screening and DNA quantification.},
  file      = {:by-author/S/Schaerli/2010_Schaerli_e201.pdf:PDF},
  keywords  = {{gp41} Helicase},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Schafer1994,
  author    = {Schafer, Andreas and Schwarzer, Astrid and Kalinowski, Jorn and Puhler, Alfred},
  journal   = {J. Bacteriol.},
  title     = {Cloning and Characterization of a DNA Region Encoding a Stress-Sensitive Restriction System from Corynebacterium glutamicum ATCC 13032 and Analysis of Its Role in Intergeneric Conjugation with Escherichia coli},
  year      = {1994},
  pages     = {7309--7319},
  volume    = {176},
  abstract  = {RP4-mediated transfer of mobilizable plasmids in intergeneric conjugation of Escherichia coli donors with Corynebacterium glutamicum ATCC 13032 is severely affected by a restriction system in the recipient that can be inactivated by a variety of exogenous stress factors. In this study a rapid test procedure based on intergeneric conjugal plasmid transfer that permitted the distinction between restriction-negative and restriction-positive C. gludamicum clones was developed. By using this procedure, clones of the restriction- deficient mutant strain C. glutamicum RM3 harboring a plasmid library of the wild-type chromosome were checked for their restriction properties. A complemented clone with a restriction-positive phenotype was isolated and found to contain a plasmid with a 7-kb insertion originating from the wild-type chromosome. This plasmid, termed pRES806, is able to complement the restriction-deficient phenotype of different C. glutamicum mutants. Sequence analysis revealed the presence of two open reading frames (orfl and orfj) on the complementing DNA fragment. The region comprising orfi and orf2 displayed a strikingly low G+C content and was present exclusively in C. glutamicum strains. Gene disruption experiments with the wild type proved that orfi is essential for complementation, but inactivation of o42 also resulted in a small but significant increase in fertility. These results were confirmed by infection assays with the bacteriophage CL31 from Corynebacterum lilum ATCC 15990.},
  file      = {:by-author/S/Schafer/1994_Schäfer_7309.pdf:PDF},
  keywords  = {CglI; Restriction Endonuclease (RE)},
  owner     = {em},
  timestamp = {2014.05.22},
  creationdate = {2014-05-22T00:00:00},
}

@Manuscript{Schaffer2001,
  author    = {Evan Schaffer and Mike Wolf},
  title     = {The UNIX Shell As a Fourth Generation Languag},
  year      = {2001},
  keywords  = {Computer Science (CS); Programming Languages; Shell},
  abstract  = {There are many database systems available for UNIX. But almost all are software prisons that you must get into and leave the power of UNIX behind. Most were developed on operating systems other than UNIX. Consequently their developers had very few software features to build upon, and wrote the functionality they needed directly, without regard for the features provided by the operating system. The resulting database systems are large, complex programs which degrade total system performance, especially when they are run in a multi-user environment. UNIX provides hundreds of programs that can be piped together to easily perform almost any function imaginable. Nothing comes close to providing the functions that come standard with UNIX. Programs and philosophies carried over from other systems put walls between the user and UNIX, and the power of UNIX is thrown away. The shell, extended with a few relational operators, is the fourth generation language most appropriate to the UNIX environment.},
  file      = {:by-author/S/Schaffer/2001_Schaffer.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Schamberger2002,
  author    = {Schamberger, Jens and Clarke, Ronald J},
  journal   = {Biophysical journal},
  title     = {Hydrophobic ion hydration and the magnitude of the dipole potential.},
  year      = {2002},
  pages     = {3081--8},
  volume    = {82},
  abstract  = {The magnitude of the dipole potential of lipid membranes is often estimated from the difference in conductance between the hydrophobic ions, tetraphenylborate, and tetraphenylarsonium or tetraphenylphosphonium. The calculation is based on the tetraphenylarsonium-tetraphenylborate hypothesis that the magnitude of the hydration energies of the anions and cations are equal (i.e., charge independent), so that their different rates of transport across the membrane are solely due to differential interactions with the membrane phase. Here we investigate the validity of this assumption by quantum mechanical calculations of the hydration energies. Tetraphenylborate (Delta G(hydr) = -168 kJ mol(-1)) was found to have a significantly stronger interaction with water than either tetraphenylarsonium (Delta G(hydr) = -145 kJ mol(-1)) or tetraphenylphosphonium (Delta G(hydr) = -157 kJ mol(-1)). Taking these differences into account, literature conductance data were recalculated to yield values of the dipole potential 57 to 119 mV more positive in the membrane interior than previous estimates. This may partly account for the discrepancy of at least 100 mV generally observed between dipole potential values calculated from lipid monolayers and those determined on bilayers.},
  file      = {2002_Schamberger_3081.pdf:by-author/S/Schamberger/2002_Schamberger_3081.pdf:PDF},
  keywords  = {Ion Hydration; Protein Physics},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Schenk2016,
  author       = {Schenk, Claudia and Kutzscher, Christel and Drache, Franziska and Helten, Stella and Senkovska, Irena and Kaskel, Stefan},
  title        = {Metal--Organic Frameworks for Thin-Layer Chromatographic Applications},
  year         = {2016},
  issn         = {1944-8244},
  abstract     = {Preparation of thin-layer chromatographic ({TLC}) plates based on metal--organic frameworks ({MOFs}) as porous stationary phases is described. {DUT}-67 ({DUT} = Dresden University of Technology), a zirconium based {MOF}, was used in combination with a fluorescent indicator as stationary phase for analyzing a small selection of a wide spectrum of relevant analytes. The successful separation of benzaldehyde from trans-cinnamaldehyde and 4-aminophenol from 2-aminotoluene is reported as a model system using optimized eluent mixtures containing acetic acid.},
  date         = {2016-12-08},
  doi          = {10.1021/acsami.6b13092},
  file         = {2016_Schenk.pdf:by-author/S/Schenk/2016_Schenk.pdf:PDF},
  groups       = {sg/MOFs, am/MOFs},
  journaltitle = {{ACS} Applied Materials \& Interfaces},
  owner        = {saulius},
  shortjournal = {{ACS} Appl. Mater. Interfaces},
  timestamp = {2017.01.24},
  creationdate = {2017-01-24T00:00:00},
  url          = {http://dx.doi.org/10.1021/acsami.6b13092},
  urldate      = {2017-01-24},
}

@Article{Scherer2002,
  author    = {Scherer, Frederic M},
  journal   = {Academic medicine : journal of the Association of American Medical Colleges},
  title     = {The economics of human gene patents.},
  year      = {2002},
  pages     = {1348--67},
  volume    = {77},
  abstract  = {The author examines patents on DNA sequences, including data on gene sequence grants issued by the PTO during a 33-month period from 1998 to 2001. Policy supporting patents on DNA sequences and other elemental information that are far "upstream" in the product development pathway is contrasted with the economic bases and rationale for patents to pharmaceuticals, which require a protracted and expensive process of development and testing but that can be relatively cheaply and competitively imitated once they are approved and disclosed. How to allocate appropriately the economic returns among the upstream and downstream inventors is a challenging problem for economic theory, as well as for contemporary biomedical research, and is perhaps most familiarly embodied in licensing and cross-licensing disputes involving "reach-through" and "reach-back" rights. Such disputes can generate enormous transaction costs. They may become increasingly frequent and vexing with respect to the scope and overlap of patent claims on human gene sequences. On the basis of his analyses, the author argues that genome patent claims should be interpreted narrowly. He is particularly concerned with ensuring that the development of new (therapeutic) products is not blocked or retarded by a multiplicity of prior patent claims, but he is pessimistic that the diversity of participants in biotechnology will provide a "sufficient community of interest to organize comprehensive low-royalty cross-licensing" regimes. Accordingly, he suggests mandatory arbitration as one mechanism for resolving such problems.},
  file      = {Scherer_2002_1348-Econ-Gene-Patents.pdf:by-author/S/Scherer/2002_Scherer_1348.pdf:PDF},
  keywords  = {Economy},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Scheres2004,
  author    = {Scheres, Sjors H. W. and Gros, Piet},
  journal   = {Acta Crystallographica Section D},
  title     = {The potentials of conditional optimization in phasing and model building of protein crystal structures},
  year      = {2004},
  pages     = {2202--2209},
  volume    = {60},
  doi       = {10.1107/S0907444904008996},
  file      = {ba5060.pdf:by-author/S/Scheres/2004_Scheres_2202.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444904008996},
}

@Article{Scheres2001,
  author    = {Scheres, Sjors H. W. and Gros, Piet},
  journal   = {Acta Crystallographica Section D},
  title     = {Conditional optimization: a new formalism for protein structure refinement},
  year      = {2001},
  pages     = {1820--1828},
  volume    = {57},
  doi       = {10.1107/S0907444901015414},
  file      = {2001_Scheres_1820.pdf:by-author/S/Scheres/2001_Scheres_1820.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444901015414},
}

@Article{Schierling2011,
  author    = {Schierling, Benno and Dannemann, Nadine and Gabsalilow, Lilia and Wende, Wolfgang and Cathomen, Toni and Pingoud, Alfred},
  journal   = {Nucleic acids research},
  title     = {A novel zinc-finger nuclease platform with a sequence-specific cleavage module.},
  year      = {2012},
  pages     = {2623--38},
  volume    = {40},
  abstract  = {Zinc-finger nucleases (ZFNs) typically consist of three to four zinc fingers (ZFs) and the non-specific DNA-cleavage domain of the restriction endonuclease FokI. In this configuration, the ZFs constitute the binding module and the FokI domain the cleavage module. Whereas new binding modules, e.g. TALE sequences, have been considered as alternatives to ZFs, no efforts have been undertaken so far to replace the catalytic domain of FokI as the cleavage module in ZFNs. Here, we have fused a three ZF array to the restriction endonuclease PvuII to generate an alternative ZFN. While PvuII adds an extra element of specificity when combined with ZFs, ZF-PvuII constructs must be designed such that only PvuII sites with adjacent ZF-binding sites are cleaved. To achieve this, we introduced amino acid substitutions into PvuII that alter K(m) and k(cat) and increase fidelity. The optimized ZF-PvuII fusion constructs cleave DNA at addressed sites with a &gt;1000-fold preference over unaddressed PvuII sites in vitro as well as in cellula. In contrast to the 'analogous' ZF-FokI nucleases, neither excess of enzyme over substrate nor prolonged incubation times induced unaddressed cleavage in vitro. These results present the ZF-PvuII platform as a valid alternative to conventional ZFNs.},
  file      = {:by-author/S/Schierling/2011_Schierling_2623.pdf:PDF},
  owner     = {em},
  timestamp = {2013.09.19},
  creationdate = {2013-09-19T00:00:00},
}

@Article{Schierling2012a,
  author       = {Benno Schierling and Nadine Dannemann and Lilia Gabsalilow and Wolfgang Wende and Toni Cathomen and Alfred Pingoud},
  journal      = {Nucleic Acids Res},
  title        = {A novel zinc-finger nuclease platform with a sequence-specific cleavage module.},
  year         = {2012},
  month        = {Mar},
  number       = {6},
  pages        = {2623--2638},
  volume       = {40},
  abstract     = {Zinc-finger nucleases (ZFNs) typically consist of three to four zinc fingers (ZFs) and the non-specific DNA-cleavage domain of the restriction endonuclease FokI. In this configuration, the ZFs constitute the binding module and the FokI domain the cleavage module. Whereas new binding modules, e.g. TALE sequences, have been considered as alternatives to ZFs, no efforts have been undertaken so far to replace the catalytic domain of FokI as the cleavage module in ZFNs. Here, we have fused a three ZF array to the restriction endonuclease PvuII to generate an alternative ZFN. While PvuII adds an extra element of specificity when combined with ZFs, ZF-PvuII constructs must be designed such that only PvuII sites with adjacent ZF-binding sites are cleaved. To achieve this, we introduced amino acid substitutions into PvuII that alter K(m) and k(cat) and increase fidelity. The optimized ZF-PvuII fusion constructs cleave DNA at addressed sites with a >1000-fold preference over unaddressed PvuII sites in vitro as well as in cellula. In contrast to the 'analogous' ZF-FokI nucleases, neither excess of enzyme over substrate nor prolonged incubation times induced unaddressed cleavage in vitro. These results present the ZF-PvuII platform as a valid alternative to conventional ZFNs.},
  creationdate = {2016-06-16T00:00:00},
  doi          = {10.1093/nar/gkr1112},
  file         = {:by-author/S/Schierling/2011_Schierling_2623.pdf:PDF},
  institution  = {Institute of Biochemistry, Justus-Liebig University, Heinrich-Buff-Ring 58, D-35392 Giessen, Germany. hiroshi.arakawa@ifom-ieo-campus.it},
  keywords     = {Base Sequence; Chemistry/genetics/metabolism; Chemistry/metabolism; DNA; DNA Cleavage; DNA-Binding Proteins; Deoxyribonucleases; HEK293 Cells; Humans; Osmolar Concentration; Protein Structure; Recombinant Fusion Proteins; Substrate Specificity; Tertiary; Type II Site-Specific; Zinc Fingers},
  language     = {eng},
  medline-pst  = {ppublish},
  owner        = {em},
  pii          = {gkr1112},
  pmid         = {22135304},
  timestamp    = {2016.06.16},
  url          = {http://dx.doi.org/10.1093/nar/gkr1112},
}

@Article{Schierling2010,
  author       = {Benno Schierling and Ann-Josée Noël and Wolfgang Wende and Le Thi Hien and Eugeny Volkov and Elena Kubareva and Tatiana Oretskaya and Michael Kokkinidis and Andreas Römpp and Bernhard Spengler and Alfred Pingoud},
  journal      = {Proc Natl Acad Sci U S A},
  title        = {Controlling the enzymatic activity of a restriction enzyme by light.},
  year         = {2010},
  month        = {Jan},
  number       = {4},
  pages        = {1361--1366},
  volume       = {107},
  abstract     = {For many applications it would be desirable to be able to control the activity of proteins by using an external signal. In the present study, we have explored the possibility of modulating the activity of a restriction enzyme with light. By cross-linking two suitably located cysteine residues with a bifunctional azobenzene derivative, which can adopt a cis- or trans-configuration when illuminated by UV or blue light, respectively, enzymatic activity can be controlled in a reversible manner. To determine which residues when cross-linked show the largest "photoswitch effect," i.e., difference in activity when illuminated with UV vs. blue light, > 30 variants of a single-chain version of the restriction endonuclease PvuII were produced, modified with azobenzene, and tested for DNA cleavage activity. In general, introducing single cross-links in the enzyme leads to only small effects, whereas with multiple cross-links and additional mutations larger effects are observed. Some of the modified variants, which carry the cross-links close to the catalytic center, can be modulated in their DNA cleavage activity by a factor of up to 16 by illumination with UV (azobenzene in cis) and blue light (azobenzene in trans), respectively. The change in activity is achieved in seconds, is fully reversible, and, in the case analyzed, is due to a change in V(max) rather than K(m).},
  creationdate = {2016-06-16T00:00:00},
  doi          = {10.1073/pnas.0909444107},
  file         = {:by-author/S/Schierling/2010_Schierling_1361.pdf:PDF},
  institution  = {Institute of Biochemistry, Justus-Liebig University, Giessen, Germany.},
  keywords     = {Alternative Splicing; Azo Compounds; Binding Sites; Biocatalysis; Chemistry; Chemistry/genetics/metabolism; Cross-Linking Reagents; Crystallography; DNA Restriction Enzymes; Design; Enzyme Activation; Isomerism; Light; Models; Molecular; Photo; Protein Binding; Protein Interaction Domains and Motifs; Protein Structure; Radiation Effects; Restriction Endonuclease (RE); Tertiary; Ultraviolet Rays; X-Ray},
  language     = {eng},
  medline-pst  = {ppublish},
  owner        = {em},
  pii          = {0909444107},
  pmid         = {20080559},
  timestamp    = {2016.06.16},
  url          = {http://dx.doi.org/10.1073/pnas.0909444107},
}

@Article{Schiff2012,
  author    = {Schiff, Jeremy and Poirier, Bill},
  journal   = {The Journal of Chemical Physics},
  title     = {Communication: Quantum mechanics without wavefunctions},
  year      = {2012},
  pages     = {031102},
  volume    = {136},
  abstract  = {We present a self-contained formulation of spin-free non-relativistic quantum mechanics that makes no use of wavefunctions or complex amplitudes of any kind. Quantum states are represented as ensembles of real-valued quantum trajectories, obtained by extremizing an action and satisfying energy conservation. The theory applies for arbitrary configuration spaces and system dimensionalities. Various beneficial ramifications—theoretical, computational, and interpretational—are discussed.},
  doi       = {10.1063/1.3680558},
  file      = {:by-author/S/Schiff/2012_Schiff_031102.pdf:PDF},
  keywords  = {Computational Chemistry; Density Functional Theory (DFT); Quantum Chemistry},
  owner     = {saulius},
  timestamp = {2014.07.21},
  creationdate = {2014-07-21T00:00:00},
  url       = {http://scitation.aip.org/content/aip/journal/jcp/136/3/10.1063/1.3680558},
}

@Article{Schinazi1993,
  author    = {Schinazi, R F and Sijbesma, R and Srdanov, G and Hill, C L and Wudl, F},
  journal   = {Antimicrobial Agents and Chemotherapy},
  title     = {Synthesis and virucidal activity of a water-soluble, configurationally stable, derivatized {C}60 fullerene.},
  year      = {1993},
  issn      = {0066-4804},
  pages     = {1707--1710},
  volume    = {37},
  abstract  = {The bis(monosuccinimide) derivative of p,p'-bis(2-aminoethyl)diphenyl-C60 (compound 1), prepared by the fulleroid route, is active against human immunodeficiency virus type 1 (HIV-1) and HIV-2 (50\% effective concentration [EC50] averaging approximately 6 microM) in acutely or chronically infected human lymphocytes and is active in vitro against 3'-azido-3'-deoxythymidine-resistant HIV-1 (EC50, approximately 3 microM). The virucidal properties of compound 1 were confirmed by virus inactivation assays. Compound 1 was noncytotoxic up to 100 microM in peripheral blood mononuclear cells and H9, Vero, and CEM cells. In cell-free assays, whereas the fullerene showed comparable activity against HIV-1 reverse transcriptase and DNA polymerase alpha (50\% inhibitory concentration of approximately 5 microM), it demonstrated selective activity against HIV-1 protease.},
  file      = {PubMed Central Full Text PDF:by-author/S/Schinazi/1993_Schinazi_1707.pdf:application/pdf},
  owner     = {saulius},
  pmcid     = {PMC188048},
  pmid      = {8215289},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC188048/},
  urldate   = {2015-07-06},
}

@Article{Schindler2000,
  author    = {Schindler, Thomas and Bornmann, William and Pellicena, Patricia and Miller, W. Todd and Clarkson, Bayard and Kuriyan, John},
  journal   = {Science},
  title     = {Structural Mechanism for STI-571 Inhibition of Abelson Tyrosine Kinase},
  year      = {2000},
  pages     = {1938--1942},
  volume    = {289},
  abstract  = {The inadvertent activation of the Abelson tyrosine kinase (Abl) causes chronic myelogenous leukemia (CML). A small-molecule inhibitor of Abl (STI-571) is effective in the treatment of CML. We report the crystal structure of the catalytic domain of Abl, complexed to a variant of STI-571. Critical to the binding of STI-571 is the adoption by the kinase of an inactive conformation, in which a centrally located “activation loop” is not phosphorylated. The conformation of this loop is distinct from that in active protein kinases, as well as in the inactive form of the closely related Src kinases. These results suggest that compounds that exploit the distinctive inactivation mechanisms of individual protein kinases can achieve both high affinity and high specificity.},
  doi       = {10.1126/science.289.5486.1938},
  eprint    = {http://www.sciencemag.org/content/289/5486/1938.full.pdf},
  file      = {2000_Schindler_1938.pdf:by-author/S/Schindler/2000_Schindler_1938.pdf:PDF},
  owner     = {saulius},
  timestamp = {2013.04.01},
  creationdate = {2013-04-01T00:00:00},
  url       = {http://www.sciencemag.org/content/289/5486/1938.abstract},
}

@Article{Schirle2012,
  author    = {Schirle, Nicole T. and MacRae, Ian J.},
  journal   = {The Enzymes},
  title     = {Structure and Mechanism of Argonaute Proteins},
  year      = {2012},
  pages     = {83--100},
  volume    = {32},
  abstract  = {RNA silencing refers to a group of widespread gene-regulatory pathways rooted in many facets of eukaryotic biology, including brain development, stem-cell and germ-line maintenance, and cancer progression. At the molecular level, RNA-silencing pathways, such as the RNA interference (RNAi) and microRNA (miRNA) regulatory path- ways, are mediated by a specialized family of RNA-binding proteins named Argonaute. Argonaute proteins are uniquely capable of binding small regulatory RNAs and using the encoded sequence information to locate and silence complementary target RNAs. The versatility and power of RNA silencing arises from the fact that Argonaute can be loaded with a small RNA of any sequence and thus can be programmed to target es- sentially any RNA for silencing. Here, we review current understanding of Argonaute proteins in terms of molecular structure, function, and mechanism.},
  file      = {:by-author/S/Schirle/2012_Schirle_83.pdf:PDF},
  keywords  = {Argonaute; MiRNA; RNA Silencing; RNAi; Review},
  owner     = {em},
  timestamp = {2013.10.01},
  creationdate = {2013-10-01T00:00:00},
  url       = {http://dx.doi.org/10.1016/B978-0-12-404741-9.00004-0},
}

@Article{Schmidt2006,
  author    = {Schmidt, Martin U and Hofmann, Detlef W M and Buchsbaum, Christian and Metz, Hans Joachim},
  journal   = {Angewandte Chemie (International ed. in English)},
  title     = {Crystal structures of Pigment Red 170 and derivatives, as determined by X-ray powder diffraction.},
  year      = {2006},
  pages     = {1313--7},
  volume    = {45},
  file      = {Schmidt_2006_1313.pdf:by-author/S/Schmidt/2006_Schmidt_1313.pdf:PDF},
  keywords  = {Powder Diffraction; Rietveld Refinement},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Schmidt-Ehrenberg2002,
  author           = {Johannes Schmidt-Ehrenberg and Daniel Baum and Hans-Christian Hege},
  journal          = {IEEE Visualisation},
  title            = {Visualizing dynamic molecular conformations},
  year             = {2002},
  pages            = {235--242},
  abstract         = {The bioactivity of a molecule strongly depends on its metastable conformational shapes and the transitions between these. Therefore, conformation analysis and visualization is a basic prerequisite for the understanding of biochemical processes. We present techniques for visual analysis of metastable molecular conformations. Core of these are flexibly applicable methods for alignment of molecular geometries, as well as methods for depicting shape and ’fuzziness’ of metastable conformations. All analysis tools are provided in an integrated working environment. The described techniques are demonstrated with pharmaceutically active biomolecules.},
  booktitle        = {IEEE Visualization, 2002. VIS 2002.},
  collection       = {VISUAL-02},
  creationdate     = {2012-05-15T00:00:00},
  doi              = {10.1109/VISUAL.2002.1183780},
  file             = {:by-author/S/Schmidt-Ehrenberg/2002_Schmidt-Ehrenberg_235.pdf:PDF},
  groups           = {sg/Molecule superposion, sg/Superposition, sg/Bioinf. Algorithms},
  keywords         = {Structure Superposition},
  modificationdate = {2024-05-12T16:52:01},
  owner            = {saulius},
  publisher        = {IEEE},
  series           = {VISUAL-02},
  timestamp        = {2012.05.15},
}

@Unpublished{SchmittXXXX,
  author    = {Schmitt, Michael},
  note      = {Abteilung Neuroinformatik, Universitaet Ulm, D-89069, Germany},
  title     = {On the Complexity of Consistency Problems for Neurons with Binary Weights},
  year      = {XXXX},
  file      = {:by-author/S/Schmitt/XXXX_Schmitt.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Schmitz2008,
  author    = {Sylvain Schmitz},
  journal   = {Electronic Notes in Theoretical Computer Science},
  title     = {An Experimental Ambiguity Detection Tool},
  year      = {2008},
  issn      = {1571-0661},
  note      = {Proceedings of the Seventh Workshop on Language Descriptions, Tools, and Applications (LDTA 2007)},
  number    = {2},
  pages     = {69 - 84},
  volume    = {203},
  abstract  = {Although programs convey an unambiguous meaning, the grammars used in practice to describe their syntax are often ambiguous, and completed with disambiguation rules. Whether these rules achieve to remove all the ambiguities while preserving the original intended language can be difficult to ensure. We present an experimental ambiguity detection tool for GNU/bison, and illustrate how it can assist a grammatical development for a subset of Standard ML.},
  doi       = {http://dx.doi.org/10.1016/j.entcs.2008.03.045},
  file      = {2008_Schmitz_69.pdf:by-author/S/Schmitz/2008_Schmitz_69.pdf:PDF},
  keywords  = {Bison; Compiler Construction; Computer Languages; Formal Grammar; Grammar Verification; Programming Languages; Yacc},
  owner     = {saulius},
  timestamp = {2015.06.15},
  creationdate = {2015-06-15T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/S1571066108001503},
}

@Article{Schneider1990,
  author    = {Schneider, Thomas D. and Stephens, R.Michael},
  journal   = {Nucleic Acids Research},
  title     = {Sequence logos: a new way to display consensus sequences},
  year      = {1990},
  number    = {20},
  pages     = {6097--6100},
  volume    = {18},
  abstract  = {A graphical method is presented for displaying the patterns in a set of aligned sequences. The characters representing the sequence are stacked on top of each other for each position in the aligned sequences. The height of each letter is made proportional to Its frequency, and the letters are sorted so the most common one is on top. The height of the entire stack is then adjusted to signify the information content of the sequences at that position. From these ‘sequence logos’, one can determine not only the consensus sequence but also the relative frequency of bases and the information content (measured In bits) at every position in a site or sequence. The logo displays both significant residues and subtle sequence patterns.},
  doi       = {10.1093/nar/18.20.6097},
  eprint    = {http://nar.oxfordjournals.org/content/18/20/6097.full.pdf+html},
  file      = {1990_Schneider_6097.pdf:by-author/S/Schneider/1990_Schneider_6097.pdf:PDF},
  groups    = {sg/Data representation},
  keywords  = {Sequence Information Content; Sequence Logo},
  owner     = {saulius},
  timestamp = {2016.05.14},
  creationdate = {2016-05-14T00:00:00},
  url       = {http://nar.oxfordjournals.org/content/18/20/6097.abstract},
}

@Article{Schneider1986,
  author    = {Thomas D. Schneider and Gary D. Stormo and Larry Gold and Andrzej Ehrenfeucht},
  journal   = {Journal of Molecular Biology},
  title     = {Information content of binding sites on nucleotide sequences},
  year      = {1986},
  issn      = {0022-2836},
  number    = {3},
  pages     = {415 - 431},
  volume    = {188},
  abstract  = {Repressors, polymerases, ribosomes and other macromolecules bind to specific nucleic acid sequences. They can find a binding site only if the sequence has a recognizable pattern. We define a measure of the information (Rsequence) in the sequence patterns at binding sites. It allows one to investigate how information is distributed across the sites and to compare one site to another. One can also calculate the amount of information (Rfrequency) that would be required to locate the sites, given that they occur with some frequency in the genome. Several Escherichia coli binding sites were analyzed using these two independent empirical measurements. The two amounts of information are similar for most of the sites we analyzed. In contrast, bacteriophage T7 RNA polymerase binding sites contain about twice as much information as is necessary for recognition by the T7 polymerase, suggesting that a second protein may bind at T7 promoters. The extra information can be accounted for by a strong symmetry element found at the T7 promoters. This element may be an operator. If this model is correct, these promoters and operators do not share much information. The comparisons between Rsequence and Rfrequency suggest that the information at binding sites is just sufficient for the sites to be distinguished from the rest of the genome.},
  doi       = {http://dx.doi.org/10.1016/0022-2836(86)90165-8},
  file      = {1986_Schneider_415.pdf:by-author/S/Schneider/1986_Schneider_415.pdf:PDF},
  groups    = {sg/Sequence analysis},
  keywords  = {Bioinformatics; Inofrmation Theory},
  owner     = {saulius},
  timestamp = {2016.05.14},
  creationdate = {2016-05-14T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/0022283686901658},
}

@InProceedings{Schneider1996,
  author           = {Schneider, Thomas R.},
  booktitle        = {Proceedings of the CCP4 Study Weekend},
  title            = {What can we Learn from Anisotropic Temperature Factors},
  year             = {1996},
  editor           = {E. Dodson and M. Moore and A. Ralph and S. Bailey},
  organization     = {European Molecular Biology Laboratory (EMBL) c/o DESY, Notkestr. 85, 22603 Hamburg},
  pages            = {133--144},
  abstract         = {Brighter X-ray sources, sensitive area detectors and the use of cryogenic techniques enable the collection of atomic resolution (i.e. dmin < 1.2 A[1]) data on an increasing number of protein crystals [2]. Such data provide a sound basis for the refinement of models with more parameters than previously acceptable. One possible approach is to replace the individual isotropic B-factor model by an anisotropic approximation. Besides resulting in much clearer electron density maps and frequently giving crystallographic R-values below 10 %, refined anisotropic temperature factors provide an interesting new piece of information: the direction dependence of the atomic mean square displacements. Some basic concepts to access this information and their application to models of protein molecules in the crystalline state will be described in this article. More comprehensive introductions can be found in the articles by Dunitz et al. [3, 4] and Trueblood [5] and in the book by Willis & Pryor [6]},
  creationdate     = {2008-07-28T00:00:00},
  file             = {:by-author/S/Schneider/1996_Schneider_133.pdf:PDF},
  journal          = {Proceedings of the CCP4 Study Weekend},
  keywords         = {Anisotropic B Factors; B-factor; Crystallography; Definition; Protein Crystallography; Structural Biology; Thermal Displacement Parameters; X-ray Crystallography},
  modificationdate = {2024-03-14T11:26:21},
  owner            = {saulius},
  timestamp        = {2008.07.28},
}

@Article{Schneider2004,
  author    = {Schneider, Thomas R.},
  journal   = {Acta Crystallographica Section D},
  title     = {Domain identification by iterative analysis of error-scaled difference distance matrices},
  year      = {2004},
  pages     = {2269--2275},
  volume    = {60},
  doi       = {10.1107/S0907444904023492},
  file      = {ba5071.pdf:by-author/S/Schneider/2004_Schneider_2269.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444904023492},
}

@Article{Schneider2002a,
  author    = {Schneider, Thomas R.},
  journal   = {Acta Crystallographica Section D},
  title     = {A genetic algorithm for the identification of conformationally invariant regions in protein molecules},
  year      = {2002},
  pages     = {195--208},
  volume    = {58},
  doi       = {10.1107/S0907444901019291},
  file      = {jn0097.pdf:by-author/S/Schneider/2002_Schneider_195.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444901019291},
}

@Manual{Schneider2002b,
  title        = {Tutorial on how to solve a Se-substructure using SHELXD},
  author       = {Thomas R. Schneider},
  month        = {July, 4},
  organization = {Dept. of Structural Chemistry University of Goettingen trs@shelx.uni-ac.gwdg.de},
  year         = {2002},
  abstract     = {The Solution of the substructure during the course of a MAD-phasing experiment consists of four steps: 1. Evaluation of the data quality. In particular, it is important to determine the maximum resolution for which signficant anomalous signal is present. 2. Derivation of substructure factors. These can be: delta F's or deltaFA's. better choice depends on the circumstances and still is a matter of debate. 3. Solving the substructure. Different methods (Patterson and/or Direct Methods) can be used to find the anomalous scatterers. 4. Validation of the substructure sites. As some phasing algorithm require substantial computing resources it is advisable to check which of the sites found in the previous step are likely to be correct.},
  file         = {:by-author/S/Schneider/2002_Schneider_1.pdf:PDF},
  keywords     = {MAD Phasing; Phasing; SHELXD; Se},
  owner        = {em},
  timestamp = {2016.07.15},
  creationdate = {2016-07-15T00:00:00},
  url          = {http://smb.slac.stanford.edu/news/summer_school/presentations2002/mad_stanford_jun02.pdf},
}

@Article{Schneider2000,
  author    = {Schneider, T. R.},
  journal   = {Acta crystallographica. Section D, Biological crystallography},
  title     = {Objective comparison of protein structures: error-scaled difference distance matrices.},
  year      = {2000},
  pages     = {714--21},
  volume    = {56},
  abstract  = {Understanding of macromolecular function in many cases relies on the comparison of related structural models. Commonly used least-squares superposition methods suffer from bias introduced into the comparison process by the subjective choice of atoms employed for the superposition. Difference distance matrices are a more objective means of comparing structures as they do not depend on a particular superposition scheme. However, they suffer from very high noise originating from coordinate errors. Modern refinement programs allow the rigorous estimation of standard uncertainties for individual atomic positions. These errors can be propagated through the calculation of a difference distance matrix allowing one to assess the significance level of structural differences. An algorithm is presented which produces an intuitive graphical representation of difference distance matrices after normalization to their error levels. Two examples where its application was revealing are described. Alternatives are suggested for cases where rigorous estimation of individual errors by the inversion of the full least-squares matrix is not feasible. The method offers an unbiased way to detect significant similarities and differences between related structures, as encountered in studies of complexes and mutants or when multiple models are obtained from experiments such as crystal structures involving non-crystallographic symmetry or different crystal modifications, or ensembles derived from NMR spectroscopy.},
  file      = {:by-author/S/Schneider/2000_Schneider_714.pdf:PDF},
  keywords  = {Protein Bioinformatics; Structure Comparison},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Schneidman2012,
  author    = {Dina Schneidman-Duhovny and Seung Joong Kim and Andrej Sali},
  journal   = {BMC Structural Biology},
  title     = {Integrative structural modeling with small angle Xray scattering profiles},
  year      = {2012},
  doi       = {10.1186/1472-6807-12-17},
  file      = {:by-author/S/Schneidman/2012_Schneidman.pdf:PDF},
  keywords  = {SAXS},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@TechReport{Schneier1997,
  author      = {Bruce Schneier},
  institution = {Counterpane Systems},
  title       = {Why Cryptography Is Harder Than It Looks},
  year        = {1997},
  file        = {:by-author/S/Schneier/1997_Schneier.pdf:PDF},
  keywords    = {Computer Science (CS); Cryptography},
  owner       = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Webpage{Schneier1997a,
  author    = {Bruce Schneier},
  retrieved = {2015-03-11},
  title     = {Why Cryptography Is Harder Than It Looks},
  url       = {https://www.schneier.com/essays/archives/1997/01/why_cryptography_is.html},
  year      = {1997},
  file      = {1997_Schneier.odt:by-author/S/Schneier/1997_Schneier.odt:OpenDocument text},
  journal   = {Information Security Bulletin},
  keywords  = {Computer Science (CS); Cryptography},
  owner     = {saulius},
  timestamp = {2015.03.11},
  creationdate = {2015-03-11T00:00:00},
}

@PhdThesis{Schoeberl2005,
  author    = {Martin Schoeberl},
  school    = {Vienna University of Technology},
  title     = {JOP: A Java Optimized Processor for Embedded Real-Time Systems},
  year      = {2005},
  comment   = {More info at http://www.jopdesign.com/thesis/index.jsp},
  file      = {2005_Schoeberl_thesis.pdf:by-author/S/Schoeberl/2005_Schoeberl_thesis.pdf:PDF;2005_Schoeberl_jop_20050117_thesis.zip:by-author/S/Schoeberl/2005_Schoeberl_jop_20050117_thesis.zip:ZIP},
  groups    = {sg/Compiler construction, sg/Garbage collectors, sg/Java},
  keywords  = {Computer Science (CS); Garbage Collection; Java},
  owner     = {saulius},
  timestamp = {2015.12.16},
  creationdate = {2015-12-16T00:00:00},
  url       = {http://www.jopdesign.com/thesis/thesis.pdf},
}

@PhdThesis{Schoffel2012,
  author     = {Schoffel, Markus},
  school     = {Citeseer},
  title      = {Multifunctional rare earth vanadate nanoparticles: luminescent labels, oxidant sensors and magnetic resonance imaging contrast agents},
  year       = {2012},
  file       = {[PDF] from psu.edu:by-author/S/Schoffel/2012_Schoffel.pdf:application/pdf},
  owner      = {saulius},
  shorttitle = {Multifunctional rare earth vanadate nanoparticles},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url        = {http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.397.9082&rep=rep1&type=pdf},
  urldate    = {2015-08-31},
}

@Manuscript{SchoffelenXXXX,
  author    = {S. Schoffelen and K. E. Beatty and D. A. Tirrell and J. C. M. van Hest},
  title     = {Selective protein labeling in E. coli cells through the click reaction between a fluorogenic coumarin and alkyl amino acids - improving the viability of E. coli cells and reducing the length of the procedure},
  year      = {XXXX},
  file      = {:by-author/S/Schoffelen/XXXX_Schoffelen.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Manuscript{Scholliers2011,
  author    = {Scholliers, Christophe and Éric Tanter and Wolfgang De Meuter},
  title     = {Computational Contracts},
  year      = {2011},
  keywords  = {Computer Languages; Computer Science (CS); Oregon Workshop; Scheme},
  abstract  = {Pre/post contracts for higher-order functions, as proposed by Find- ler and Felleisen and provided in Racket, allow run-time verification and blame assignment of higher-order functions. However these contracts treat contracted functions as black boxes, allowing verification of only input and output. It turns out that many interesting concerns about the behaviour of a function require going beyond that black-box approach, in order to control the actual computation that follows from a function. Examples are prohibiting or verifying that certain functions are called, checking access permissions, time or memory constraints, interaction protocols, etc. To address this need for grey-box verification, while preserving support for higher-order programming and blame assignment, we introduce the notion of computational contracts. A computational contract is a contract over the execution of a contracted entity. We show various applications of computational contracts, and explain how to assign blame in case of a violation. Computational contracts have been integrated with the existing contract system of Racket. Computational contracts is the first contract model with blame assignment in a higher-order setting that provides a systematic way to perform grey box verification.},
  file      = {:by-author/S/Scholliers/2011_Scholliers.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Scholtz1995,
  author    = {J. Martin Scholtz and Doug Barrick and Eunice J. York and John M. Stewart and Robert L. Baldwin},
  journal   = {Proc. Natl. Acad. Sci.},
  title     = {Urea unfolding of peptide helices as a model for interpreting protein unfolding},
  year      = {1995},
  pages     = {185--189},
  volume    = {92},
  abstract  = {To provide a model system for understand- ing how the unfolding of protein a-helices by urea contributes to protein denaturation, urea unfolding was measured for a homologous series of helical peptides with the repeating sequence Ala-Glu-Ala-Ala-Lys-Ala and chain lengths varying from 14 to 50 residues. The dependence of the helix propa- gation parameter of the Zimm-Bragg model for helix-coil transition theory (s) on urea molarity ([urea]) was deter- mined at 0°C with data for the entire set of peptides, and a linear dependence of In s on [urea] was found. The results were fitted by the binding-site model and by the solvent-exchange model for the interaction of urea with the peptides. Each of these thermodynamic models is able to describe the data quite well and we are not able to discern any difference between the ability of each model to fit the data. Thus a linear relation, In s = In so - (m/R7).[urea], fits the data for av-helix unfolding, just as others have found for protein unfolding. When the m value determined here for a-helix unfolding is multiplied by the number of helical residues in partly helical protein molecules, the resulting values agree within a factor of 2 with observed m values for these proteins. This result indicates that the interaction between urea and peptide groups accounts for a major part of the denaturing action of urea on proteins, as predicted earlier by some model studies with small molecules},
  file      = {1995_Scholtz_185.pdf:by-author/S/Scholtz/1995_Scholtz_185.pdf:PDF},
  keywords  = {Hermodicamics; Hydrogen Bonds; Protein Folding; Protein Stability; Urea Unfolding},
  owner     = {saulius},
  pmcid     = {PMC42842},
  pmid      = {7816813},
  timestamp = {2015.03.13},
  creationdate = {2015-03-13T00:00:00},
  url       = {http://www.pnas.org/content/92/1/185.abstract},
}

@Article{Schonemann1966,
  author           = {Peter H. Schönemann},
  journal          = {Psychometrika},
  title            = {A generalized solution of the orthogonal {P}rocrustes problem},
  year             = {1966},
  pages            = {1--10},
  volume           = {31},
  abstract         = {A solutionT of the least-squares problemAT=B +E, givenA andB so that trace (EprimeE)= minimum andTprimeT=I is presented. It is compared with a less general solution of the same problem which was given by Green [5]. The present solution, in contrast to Green's, is applicable to matricesA andB which are of less than full column rank. Some technical suggestions for the numerical computation ofT and an illustrative example are given. This paper is based on parts of a thesis submitted to the Graduate College of the University of Illinois in partial fulfillment of the requirements for a Ph.D. degree in Psychology. The work reported here was carried out while the author was employed by the Statistical Service Unit Research, U. of Illinois. It is a pleasure to express my appreciation to Prof. K. W. Dickman, director of this unit, for his continuous support and encouragement in this and other work. I also gratefully acknowledge my debt to Prof. L. Humphreys for suggesting the problem and to Prof. L. R. Tucker, who derived (1.7) and (1.8) in summation notation, suggested an iterative solution (not reported here) and who provided generous help and direction at all stages of the project.},
  creationdate     = {2012-05-15T00:00:00},
  doi              = {10.1007/BF02289451},
  file             = {:by-author/S/Schönemann/1996_Schönemann_1.pdf:PDF},
  groups           = {sg/Molecule superposion, sg/Superposition, sg/Bioinf. Algorithms},
  keywords         = {Procrustes; Structure Superposition},
  modificationdate = {2024-05-12T10:59:21},
  owner            = {saulius},
  timestamp        = {2012.05.15},
  url              = {http://www.springerlink.com/content/l8023011278587w7/},
}

@Article{Schoenleber2006,
  author     = {Schönleber, Andreas and Zúñiga, F. Javier and Perez-Mato, J. Manuel and Darriet, Jacques and zur Loye, Hans-Conrad},
  journal    = {Acta Crystallographica Section B Structural Science},
  title      = {Description of {Ba} $_{\textrm{ 1 + \textit{x} }}$ {Ni} $_{\textrm{ \textit{x} }}$ {Rh} $_{\textrm{ 1 − \textit{x} }}$ {O} $_{\textrm{3}}$ with \textit{x} = 0.1170 (5) in superspace: modulated composite \textit{versus} modulated-layer structure},
  year       = {2006},
  issn       = {0108-7681},
  pages      = {197--204},
  volume     = {62},
  doi        = {10.1107/S0108768105039212},
  file       = {Schönleber et al. - 2006 - Description of Ba1 + xNixRh1 − xO3 with x = 0.1170.pdf:by-author/S/Schönleber/2006_Schönleber_197.pdf:application/pdf;Snapshot:by-author/S/Schönleber/2006_Schönleber_197.html:text/html},
  owner      = {saulius},
  shorttitle = {Description of {Ba} $_{\textrm{ 1 + \textit{x} }}$ {Ni} $_{\textrm{ \textit{x} }}$ {Rh} $_{\textrm{ 1 − \textit{x} }}$ {O} $_{\textrm{3}}$ with \textit{x} = 0.1170 (5) in superspace},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url        = {http://scripts.iucr.org/cgi-bin/paper?S0108768105039212},
  urldate    = {2015-10-09},
}

@Article{Schopf1993,
  author    = {Schopf, J W},
  journal   = {Science (New York, N.Y.)},
  title     = {Microfossils of the Early Archean Apex chert: new evidence of the antiquity of life.},
  year      = {1993},
  pages     = {640--6},
  volume    = {260},
  file      = {1993_Schopf_640.pdf:by-author/S/Schopf/1993_Schopf_640.pdf:PDF},
  keywords  = {Chemical Prebiotic; Evolution},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Schostak2008,
  author    = {Schostak, Nataliya and Pyatkov, Konstantin and Zelentsova, Elena and Arkhipova, Irina and Shagin, Dmitrii and Shagina, Irina and Mudrik, Elena and Blintsov, Anatolii and Clark, Ivan and Finnegan, David J. and Evgen'ev, Michael},
  journal   = {Nucleic acids research},
  title     = {Molecular dissection of Penelope transposable element regulatory machinery.},
  year      = {2008},
  pages     = {2522--9},
  volume    = {36},
  abstract  = {Penelope-like elements (PLEs) represent a new class of retroelements identified in more than 80 species belonging to at least 10 animal phyla. Penelope isolated from Drosophila virilis is the only known transpositionally active representative of this class. Although the size and structure of the Penelope major transcript has been previously described in both D. virilis and D. melanogaster transgenic strains, the architecture of the Penelope regulatory region remains unknown. In order to determine the localization of presumptive Penelope promoter and enhancer-like elements, segments of the putative Penelope regulatory region were linked to a CAT reporter gene and introduced into D. melanogaster by P-element-mediated transformation. The results obtained using ELISA to measure CAT expression levels and RNA studies, including RT-PCR, suggest that the active Penelope transposon contains an internal promoter similar to the TATA-less promoters of LINEs. The results also suggest that some of the Penelope regulatory sequences control the preferential expression in the ovaries of the adult flies by enhancing expression in the ovary and reducing expression in the carcass. The possible significance of the intron within Penelope for the function and evolution of PLEs, and the effect of Penelope insertions on adjacent genes, are discussed.},
  file      = {:by-author/S/Schostak/2008_Schostak_2522.pdf:PDF},
  keywords  = {Mobile Genetic Elements},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@InProceedings{Schrijvers2006,
  author    = {Schrijvers, Tom and Maurice Bruynooghe},
  booktitle = {PPDP},
  title     = {Polymorphic Algebraic Data Type Reconstruction},
  year      = {2006},
  abstract  = {One of the disadvantages of statically typed languages is the programming overhead caused by writing all the necessary type information: Both type declarations and type definitions are typically required. Traditional type inference aims at relieving the programmer from the former. We present a rule-based constraint rewriting algorithm that reconstructs both type declarations and type definitions, allowing the programmer to effectively program type-less in a strictly typed language. This effectively combines strong points of dynamically typed languages (rapid prototyping) and statically typed ones (documentation, optimized compilation). Moreover it allows to quickly port code from a statically untyped to a statically typed setting. Our constraint-based algorithm reconstructs uniform polymorphic definitions of algebraic data types and simultaneously infers the types of all expressions and functions (supporting polymorphic recursion) in the program. The declarative nature of the algorithm allows us to easily show that it has a number of highly desirable properties such as soundness, completeness and various optimality properties. Moreover, we show how to easily extend and adapt it to suit a number of different language constructs and type system features.},
  file      = {:by-author/S/Schrijvers/2006_Schrijvers_PPDP.pdf:PDF},
  keywords  = {Computer Science (CS); Type Systems},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Schrock1996,
  author    = {Schrock, R. D. and Alberts, B.},
  journal   = {The Journal of biological chemistry},
  title     = {Processivity of the gene 41 DNA helicase at the bacteriophage T4 DNA replication fork.},
  year      = {1996},
  pages     = {16678--82},
  volume    = {271},
  abstract  = {The gene 41 protein is the DNA helicase associated with the bacteriophage T4 DNA replication fork. This protein is a major component of the primosome, being essential for coordinated leading and lagging strand DNA synthesis. Models suggest that such DNA helicases are loaded only onto DNA at origins of replication, and that they remain with the ensuing replication fork until replication is terminated. To test this idea, we have measured the extent of processivity of the 41 protein in the context of an in vitro DNA replication system composed of eight purified proteins (the gene 43, 44/62, 45, 32, 41, 59, and 61 proteins). After starting DNA replication in the presence of these proteins, we diluted the 41 helicase enough to prevent any association of new helicase molecules and analyzed the replication products. We measured an association half-life of 11 min, revealing that the 41 protein is processive enough to finish replicating the entire 169-kilobase T4 genome at the observed replication rate of approximately 400 nucleotides/s. This processivity of the 41 protein does not require the 59 protein, the protein that catalyzes 41 protein assembly onto 32 protein-covered single-stranded DNA. The stability we measure for the 41 protein as part of the replication fork is greater than estimated for it alone on single-stranded DNA. We suggest that the 41 protein interacts with the polymerase holoenzyme at the fork, both stabilizing the other protein components and being stabilized thereby.},
  file      = {:by-author/S/Schrock/1996_Schrock_16678.pdf:PDF},
  keywords  = {{gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Schroder2010,
  author    = {Schröder, Gunnar F. and Levitt, Michael and Brunger, Axel T.},
  journal   = {Nature},
  title     = {Super-resolution biomolecular crystallography with low-resolution data.},
  year      = {2010},
  pages     = {1218--22},
  volume    = {464},
  abstract  = {X-ray diffraction plays a pivotal role in the understanding of biological systems by revealing atomic structures of proteins, nucleic acids and their complexes, with much recent interest in very large assemblies like the ribosome. As crystals of such large assemblies often diffract weakly (resolution worse than 4 A), we need methods that work at such low resolution. In macromolecular assemblies, some of the components may be known at high resolution, whereas others are unknown: current refinement methods fail as they require a high-resolution starting structure for the entire complex. Determining the structure of such complexes, which are often of key biological importance, should be possible in principle as the number of independent diffraction intensities at a resolution better than 5 A generally exceeds the number of degrees of freedom. Here we introduce a method that adds specific information from known homologous structures but allows global and local deformations of these homology models. Our approach uses the observation that local protein structure tends to be conserved as sequence and function evolve. Cross-validation with R(free) (the free R-factor) determines the optimum deformation and influence of the homology model. For test cases at 3.5-5 A resolution with known structures at high resolution, our method gives significant improvements over conventional refinement in the model as monitored by coordinate accuracy, the definition of secondary structure and the quality of electron density maps. For re-refinements of a representative set of 19 low-resolution crystal structures from the Protein Data Bank, we find similar improvements. Thus, a structure derived from low-resolution diffraction data can have quality similar to a high-resolution structure. Our method is applicable to the study of weakly diffracting crystals using X-ray micro-diffraction as well as data from new X-ray light sources. Use of homology information is not restricted to X-ray crystallography and cryo-electron microscopy: as optical imaging advances to subnanometre resolution, it can use similar tools.},
  file      = {:by-author/S/Schröder/2010_Schroder_1218.pdf:PDF},
  owner     = {saulius},
  timestamp = {2014.03.23},
  creationdate = {2014-03-23T00:00:00},
}

@Article{Schroeder2004,
  author    = {Schröder, Ludger and Watkin, David John and Cousson, Alain and Cooper, Richard Ian and Paulus, Werner},
  journal   = {Journal of Applied Crystallography},
  title     = {{\it CRYSTALS} enhancements: refinement of atoms continuously disordered along a line, on a ring or on the surface of a sphere},
  year      = {2004},
  pages     = {545--550},
  volume    = {37},
  abstract  = {The program CRYSTALS [Betteridge, Carruthers, Cooper, Prout & Watkin (2003). J. Appl. Cryst. 36, 1487] has been extended to include an option for the refinement of a continuous electron density distribution lying along a line, a ring or on the surface of a sphere. These additional non-atomic electron distributions can be refined in any combination with traditional anisotropically distributed spherical atoms, including the refinement of `partial' atoms overlapping with the special electron distributions.},
  doi       = {10.1107/S0021889804009847},
  file      = {2004_Schröder_545.pdf:by-author/S/Schröder/2004_Schröder_545.pdf:PDF},
  keywords  = {Crystallography; Structure Refinement; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2013.07.18},
  creationdate = {2013-07-18T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0021889804009847},
}

@Article{Schuermann2003,
  author    = {Schuermann, Jonathan P. and Tanner, John J.},
  journal   = {Acta Crystallographica Section D},
  title     = {MRSAD: using anomalous dispersion from S atoms collected at Cu{\it K}{$\alpha$} wavelength in molecular-replacement structure determination},
  year      = {2003},
  pages     = {1731--1736},
  volume    = {59},
  doi       = {10.1107/S0907444903015725},
  file      = {dz5000.pdf:by-author/S/Schuermann/2003_Schuermann_1731.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444903015725},
}

@Article{Schultes2000,
  author    = {Schultes, E A and Bartel, D P},
  journal   = {Science (New York, N.Y.)},
  title     = {One sequence, two ribozymes: implications for the emergence of new ribozyme folds.},
  year      = {2000},
  pages     = {448--52},
  volume    = {289},
  file      = {2000_Schultes_448.pdf:by-author/S/Schultes/2000_Schultes_448.pdf:PDF},
  keywords  = {Ribozymes},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Schultz1991,
  author    = {Schultz, S. C. and Shields, G. C. and Steitz, T. A.},
  journal   = {Science (New York, N.Y.)},
  title     = {Crystal structure of a CAP-DNA complex: the DNA is bent by 90 degrees.},
  year      = {1991},
  pages     = {1001--7},
  volume    = {253},
  abstract  = {The 3 angstrom resolution crystal structure of the Escherichia coli catabolite gene activator protein (CAP) complexed with a 30-base pair DNA sequence shows that the DNA is bent by 90 degrees. This bend results almost entirely from two 40 degrees kinks that occur between TG/CA base pairs at positions 5 and 6 on each side of the dyad axis of the complex. DNA sequence discrimination by CAP derives both from sequence-dependent distortion of the DNA helix and from direct hydrogen-bonding interactions between three protein side chains and the exposed edges of three base pairs in the major groove of the DNA. The structure of this transcription factor--DNA complex provides insights into possible mechanisms of transcription activation.},
  file      = {:by-author/S/Schultz/1991_Schultz_1001.pdf:PDF},
  keywords  = {Readout},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Schulze1997,
  author    = {Peter Schulze and Juli Feigon},
  journal   = {Nature},
  title     = {Chirality errors in nucleic acid structures},
  year      = {1997},
  pages     = {668},
  volume    = {387},
  file      = {1997_Schulze_668.pdf:by-author/S/Schulze/1997_Schulze_668.pdf:PDF;1997_Schulze_668.djvu:by-author/S/Schulze/1997_Schulze_668.djvu:Djvu},
  keywords  = {Data Quality; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Schuttelkopf2004,
  author    = {Schüttelkopf, Alexander W. and van Aalten, Daan M. F.},
  journal   = {Acta crystallographica. Section D, Biological crystallography},
  title     = {PRODRG: a tool for high-throughput crystallography of protein-ligand complexes.},
  year      = {2004},
  pages     = {1355--63},
  volume    = {60},
  abstract  = {The small-molecule topology generator PRODRG is described, which takes input from existing coordinates or various two-dimensional formats and automatically generates coordinates and molecular topologies suitable for X-ray refinement of protein-ligand complexes. Test results are described for automatic generation of topologies followed by energy minimization for a subset of compounds from the Cambridge Structural Database, which shows that, within the limits of the empirical GROMOS87 force field used, structures with good geometries are generated. X-ray refinement in X-PLOR/CNS, REFMAC and SHELX using PRODRG-generated topologies produces results comparable to refinement with topologies from the standard libraries. However, tests with distorted starting coordinates show that PRODRG topologies perform better, both in terms of ligand geometry and of crystallographic R factors.},
  file      = {:by-author/S/Schüttelkopf/2004_Schüttelkopf_1355.pdf:PDF},
  keywords  = {Topology Parameters},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@Article{Schwab2000,
  author           = {Schwab, M. and Karrenbach, N. and Claerbout, J.},
  journal          = {Computing in Science Engineering},
  title            = {Making scientific computations reproducible},
  year             = {2000},
  issn             = {1521-9615},
  pages            = {61--67},
  volume           = {2},
  creationdate     = {2012-04-09T00:00:00},
  doi              = {10.1109/5992.881708},
  file             = {:by-author/S/Schwab/2000_Schwab_61.pdf:PDF},
  keywords         = {Authors; Computational Results; Data Management; Document Handling; File Organisation; Natural Sciences Computing; ReDoc; Reproducible Research; Reproducible Scientific Computations; Research Paper; Research and Development Management; Software Filing System; Standardized Rules},
  modificationdate = {2023-01-03T09:25:17},
  owner            = {saulius},
  timestamp        = {2012.04.09},
}

@Article{Schwabedissen2014,
  author    = {Schwabedissen, Jan and Lane, Paul D. and Masters, Sarah L. and Hassler, Karl and Wann, Derek A.},
  journal   = {Dalton Transactions},
  title     = {Gas-phase structures of sterically crowded disilanes studied by electron diffraction and quantum chemical methods: 1,1,2,2-tetrakis(trimethylsilyl)disilane and 1,1,2,2-tetrakis(trimethylsilyl)dimethyldisilane},
  year      = {2014},
  issn      = {1477-9234},
  pages     = {10175--10182},
  volume    = {43},
  doi       = {10.1039/c4dt00628c},
  file      = {:by-author/S/Schwabedissen/2014_Schwabedissen_10175.pdf:PDF},
  owner     = {saulius},
  publisher = {Royal Society of Chemistry (RSC)},
  timestamp = {2015.02.25},
  creationdate = {2015-02-25T00:00:00},
  url       = {http://dx.doi.org/10.1039/c4dt00628c},
}

@MastersThesis{Schwaller2015,
  author    = {Philippe Schwaller},
  school    = {École Polytechnique Fédérale de Lausanne},
  title     = {Discovering layered structures in the {ICSD} database. {IcsdDbImporter} and {LowDimFinder} - two plugins for the high-throughput platform {AiiDA}},
  year      = {2015},
  month     = {Jan},
  type      = {semester project},
  file      = {:by-author/S/Schwaller/2015_Schwaller.pdf:PDF},
  owner     = {andrius},
  timestamp = {2016.01.27},
  creationdate = {2016-01-27T00:00:00},
}

@MastersThesis{Schwaller2015a,
  author    = {Philippe Schwaller},
  school    = {École Polytechnique Fédérale de Lausanne},
  title     = {Discovering layered structures in the {ICSD} database. Creation of a database of {ab initio} calculation \& development of {AiiDA} workflows},
  year      = {2015},
  month     = {Jun},
  type      = {semester project},
  file      = {:by-author/S/Schwaller/2015_Schwaller_June.pdf:PDF},
  groups    = {am/ICSD},
  owner     = {andrius},
  timestamp = {2016.10.06},
  creationdate = {2016-10-06T00:00:00},
}

@Presentation{Schwartz2008,
  author    = {Baron Schwartz},
  title     = {The MySQL Query Cache},
  year      = {2008},
  file      = {:by-author/S/Schwartz/2008_Schwartz_slides.pdf:PDF},
  keywords  = {Computer Science (CS); Databases; Query},
  owner     = {saulius},
  pages     = {slides},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Schwartz2004,
  author    = {Barry Schwartz},
  journal   = {The Chronicle of Higher Eductation},
  title     = {The Tyranny of Choice},
  year      = {2004},
  month     = {January},
  abstract  = {The modern university has become a kind of intellectual shopping mall. Universities offer a wide array of different "goods" and allow, even encourage, students -- the "customers" -- to shop around until they find what they like. Individual customers are free to "purchase" whatever bundles of knowledge they want, and the university provides whatever its customers demand. In some rather prestigious institutions, this shopping-mall view has been carried to an extreme. In the first few weeks of classes, students sample the merchandise. They go to a class, stay 10 minutes to see what the professor is like, then walk out, often in the middle of the professor's sentence, to try another class. Students come and go in and out of classes just as browsers go in and out of stores in a mall. Does increased affluence and increased choice mean we have more happy people? Not at all. Three recently published books -- by the psychologist David Myers, the political scientist Robert E. Lane, and the journalist Gregg Easterbrook -- point out how the growth of material affluence has not brought with it an increase in subjective well-being. Indeed, they argue that we are actually experiencing a decrease in well-being.},
  file      = {:by-author/S/Schwartz/2004_Schwartz.war:WAR},
  keywords  = {Choice Fatigue; SocialSci},
  owner     = {saulius},
  timestamp = {2015.03.02},
  creationdate = {2015-03-02T00:00:00},
  url       = {http://chronicle.com/weekly/v50/i20/20b00601.htm},
}

@Article{Schwarz2011,
  author    = {Schwarz, Friedrich W. and van Aelst, Kara and Toth, Julia and Seidel , Rafl and Szczelkun, Mark D.},
  journal   = {Nucleic Acids Research},
  title     = {DNA cleavage site selection by Type III restriction enzymes provides evidence for head-on protein collisions following 1D bidirectional motion},
  year      = {2011},
  pages     = {8042–8051},
  volume    = {39},
  abstract  = {DNA cleavage by the Type III Restriction–Modification enzymes requires communication in 1D between two distant indirectly-repeated recognitions sites, yet results in non-specific dsDNA cleavage close to only one of the two sites. To test a recently proposed ATP-triggered DNA sliding model, we addressed why one site is selected over another during cleavage. We examined the relative cleavage of a pair of identical sites on DNA substrates with different distances to a free or protein blocked end, and on a DNA substrate using different relative concentrations of protein. Under these conditions a bias can be induced in the cleavage of one site over the other. Monte-Carlo simulations based on the sliding model reproduce the experimentally observed behaviour. This suggests that cleavage site selection simply reflects the dynamics of the preceding stochastic enzyme events that are consistent with bidirectional motion in 1D and DNA cleavage following head-on protein collision.},
  doi       = {10.1093/nar/gkr502},
  file      = {:by-author/S/Schwarz/2011_Schwarz_8042.pdf:PDF},
  keywords  = {Restriction Endonucleases (REases); Type III},
  owner     = {em},
  timestamp = {2013.01.30},
  creationdate = {2013-01-30T00:00:00},
}

@Article{Schwarz1978,
  author    = {Gideon Schwarz},
  journal   = {The Annals of Statistics},
  title     = {Estimating the Dimension of a Model},
  year      = {1978},
  note      = {The PDF is also available at: http://www.andrew.cmu.edu/user/kk3n/simplicity/schwarzbic.pdf},
  pages     = {461--464},
  abstract  = {The problem of selecting one of a number of models of different dimensions is treated by finding its Bayes solution, and evaluating the leading terms of its asymptotic expansion. These terms are a valid large-sample criterion beyond the Bayesian context, since they do not depend on the a priori distribution.},
  doi       = {10.1214/aos/1176344136},
  file      = {:by-author/S/Schwarz/1978_Schwarz_461.pdf:PDF},
  groups    = {sg/Bayesian, am/Model selection},
  keywords  = {Bayesian Statistics; Computer Science (CS); Statistics},
  owner     = {andrius},
  timestamp = {2012.11.13},
  creationdate = {2012-11-13T00:00:00},
  url       = {http://projecteuclid.org/euclid.aos/1176344136},
}

@Article{SCIENCE2007,
  author    = {SCIENCE},
  title     = {From Ecology to Evolution},
  year      = {2007},
  pages     = {1463},
  file      = {:by-author/S/SCIENCE/2007_SCIENCE_1463.pdf:PDF},
  keywords  = {Ribozymes},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Scipioni2002,
  author    = {Scipioni, Anita and Anselmi, Claudio and Zuccheri, Giampaolo and Samori, Bruno and De Santis, Pasquale},
  journal   = {Biophysical journal},
  title     = {Sequence-dependent DNA curvature and flexibility from scanning force microscopy images.},
  year      = {2002},
  pages     = {2408--18},
  volume    = {83},
  abstract  = {This paper reports a study of the sequence-dependent DNA curvature and flexibility based on scanning force microscopy (SFM) images. We used a palindromic dimer of a 1878-bp pBR322 fragment and collected a large pool of SFM images. The curvature of each imaged chain was measured in modulus and direction. It was found that the ensemble curvature modulus does not allow the separation of static and dynamic contributions to the curvature, whereas the curvature, when its direction in the two dimensions is taken into account, permits the direct separation of the intrinsic curvature contributions static and dynamic contributions. The palindromic symmetry also acted as an internal gauge of the validity of the SFM images statistical analysis. DNA static curvature resulted in good agreement with the predicted sequence-dependent intrinsic curvature. Furthermore, DNA sequence-dependent flexibility was found to correlate with the occurrence of A.T-rich dinucleotide steps along the chain and, in general, with the normalized basepair stacking energy distribution.},
  file      = {:by-author/S/Scipioni/2002_Scipioni_2408.pdf:PDF},
  keywords  = {Conformation; Readout},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Scolnick1997,
  author    = {Laura R. Scolnick and Adrienne M. Clements and John Liao and Lori Crenshaw and Mark Hellberg and Jesse May and Tom R. Dean and David W. Christianson},
  journal   = {J. Am. Chem. Soc.},
  title     = {Novel Binding Mode of Hydroxamate Inhibitors to Human Carbonic Anhydrase II},
  year      = {1997},
  pages     = {850--851},
  volume    = {119},
  abstract  = {Peptidylhydroxamic acids are potent inhibitors of zinc enzymes, such as thermolysin and the pharmaceutically-im- portant matrix metalloproteinases.1 The X-ray crystallographic structure determinations of enzyme-inhibitor complexes re- veal that the coordination of the active site zinc ion by the hydroxamate group is the primary determinant of enzyme- inhibitor affinity: the CdO and OH groups simultaneously coordinate to zinc to form an energetically-favorable 5-mem- bered chelate complex.2 Since this interaction contributes to nanomolar affinity between appropriately designed peptidylhy- droxamic acids and target proteinases,1-3 we wondered whether hydroxamic acids could be exploited as inhibitors of other pharmaceutically-important zinc enzymes. In particular, will hydroxamic acids effectively inhibit human carbonic anhydrase II (CAII)?},
  file      = {1997_Scolnick_850.pdf:by-author/S/Scolnick/1997_Scolnick_850.pdf:PDF},
  groups    = {sg/inhibitors, sg/hCA2},
  keywords  = {Carbonic Anhydrases; Inhibitors},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Scott2008,
  author    = {Scott, D J and Manos, S and Coveney, P V and Rossiny, J C H and Fearn, S and Kilner, J A and Pullar, R C and Alford, N Mc N and Axelsson, A-K and Zhang, Y and Chen, L and Yang, S and Evans, J R G and Sebastian, M T},
  journal   = {Journal of chemical information and modeling},
  title     = {Functional ceramic materials database: an online resource for materials research.},
  year      = {2008},
  pages     = {449--55},
  volume    = {48},
  abstract  = {We present work on the creation of a ceramic materials database which contains data gleaned from literature data sets as well as new data obtained from combinatorial experiments on the London University Search Instrument. At the time of this writing, the database contains data related to two main groups of materials, mainly in the perovskite family. Permittivity measurements of electroceramic materials are the first area of interest, while ion diffusion measurements of oxygen ion conductors are the second. The nature of the database design does not restrict the type of measurements which can be stored; as the available data increase, the database may become a generic, publicly available ceramic materials resource.},
  file      = {2008_Scott_449.pdf:by-author/S/Scott/2008_Scott_449.pdf:PDF},
  keywords  = {Structural Databases},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Sears2005b,
  author    = {Alice Sears and Luke J. Peakman and Geoffrey G. Wilson and Mark D. Szczelkun},
  journal   = {Nucleic Acids Research},
  title     = {Characterization of the Type {III} restriction endonuclease {PstII} from {P}rovidencia stuartii},
  year      = {2005},
  pages     = {4775--4787},
  volume    = {33},
  abstract  = {A new Type III restriction endonuclease designated PstII has been purified from Providencia stuartii. PstII recognizes the hexanucleotide sequence 5'-CTGATG(N)(25-26/27-28)-3'. Endonuclease activity requires a substrate with two copies of the recognition site in head-to-head repeat and is dependent on a low level of ATP hydrolysis ( approximately 40 ATP/site/min). Cleavage occurs at just one of the two sites and results in a staggered cut 25-26 nt downstream of the top strand sequence to generate a two base 5'-protruding end. Methylation of the site occurs on one strand only at the first adenine of 5'-CATCAG-3'. Therefore, PstII has characteristic Type III restriction enzyme activity as exemplified by EcoPI or EcoP15I. Moreover, sequence asymmetry of the PstII recognition site in the T7 genome acts as an historical imprint of Type III restriction activity in vivo. In contrast to other Type I and III enzymes, PstII has a more relaxed nucleotide specificity and can cut DNA with GTP and CTP (but not UTP). We also demonstrate that PstII and EcoP15I cannot interact and cleave a DNA substrate suggesting that Type III enzymes must make specific protein-protein contacts to activate endonuclease activity.},
  doi       = {10.1093/nar/gki787},
  file      = {:by-author/S/Sears/2005_Sears_4775.pdf:PDF},
  keywords  = {TypeIII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
  url       = {http://nar.oxfordjournals.org/content/33/15/4775},
}

@Article{Sears2005a,
  author    = {Sears, Alice and Szczelkun, Mark D.},
  journal   = {Nucleic acids research},
  title     = {Subunit assembly modulates the activities of the Type III restriction-modification enzyme PstII in vitro.},
  year      = {2005},
  pages     = {4788--96},
  volume    = {33},
  abstract  = {We demonstrate that, like other Type III restriction endonuclease, PstII does not turnover such that a DNA substrate is only fully cleaved at a Res2Mod2-to-site ratio of approximately 1:1. However, unlike other Type III enzymes, the cleavage rate profiles varied with protein concentration: using 5 nM DNA and 25 nM PstII, approximately half of the DNA was cut at a fast rate while the remainder was cut 24 times more slowly; in comparison, with 100 nM PstII cleavage occurs at a single fast rate. The inclusion of the methyl donor S-adenosyl methionine does not alter the rates with 100 nM PstII but with 25 nM PstII the reaction stopped after completion of the initial fast cleavage phase owing to methylation. Concentration-dependent rates were also observed in methylation assays: at 100 nM PstII, a single slow rate was measured while at lower PstII concentrations both fast and slow rates were measured. We propose a model in which the intact Res2Mod2 complex favoured at high PstII concentrations is a fast endonuclease/slow methyltransferase while the various subassemblies which coexist at lower concentrations are fast methyltransferases. A potential role for disassembly in control of restriction activity in vivo is discussed.},
  file      = {:by-author/S/Sears/2005_Sears_4788.pdf:PDF},
  keywords  = {TypeIII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Sebaihia2006,
  author    = {Sebaihia, Mohammed and Wren, Brendan W and Mullany, Peter and Fairweather, Neil F and Minton, Nigel and Stabler, Richard and Thomson, Nicholas R and Roberts, Adam P and Cerdeño-Tárraga, Ana M and Wang, Hongmei and et al.},
  journal   = {Nat Genet},
  title     = {The multidrug-resistant human pathogen Clostridium difficile has a highly mobile, mosaic genome},
  year      = {2006},
  issn      = {1061-4036},
  month     = {Jun},
  number    = {7},
  pages     = {779--786},
  volume    = {38},
  abstract  = {We determined the complete genome sequence of Clostridium difficile strain 630, a virulent and multidrug-resistant strain. Our analysis indicates that a large proportion (11%) of the genome consists of mobile genetic elements, mainly in the form of conjugative transposons. These mobile elements are putatively responsible for the acquisition by C. difficile of an extensive array of genes involved in antimicrobial resistance, virulence, host interaction and the production of surface structures. The metabolic capabilities encoded in the genome show multiple adaptations for survival and growth within the gut environment. The extreme genome variability was confirmed by whole-genome microarray analysis; it may reflect the organism's niche in the gut and should provide information on the evolution of virulence in this organism.},
  doi       = {10.1038/ng1830},
  file      = {2006_Sebaihia_779.pdf:by-author/S/Sebaihia/2006_Sebaihia_779.pdf:PDF},
  groups    = {sg/CRISPR-Cas, sg/Virus sg/CRISPR-Cas systems},
  keywords  = {CRISPR; CRISPR-Cas},
  owner     = {saulius},
  publisher = {Nature Publishing Group},
  timestamp = {2016.05.14},
  creationdate = {2016-05-14T00:00:00},
  url       = {http://dx.doi.org/10.1038/ng1830},
}

@PhdThesis{Sedlmaier2011,
  author    = {Stefan Josef Sedlmaier},
  school    = {Ludwig-Maximilians-Universität München, Fakultät für Chemie und Pharmazie},
  title     = {Synthesis, Identification, and Characterization of Novel, Condensed Oxonitridophosphates and Phosphorus Oxonitrides},
  year      = {2011},
  file      = {2011_Sedlmaier_thesis.pdf:by-author/S/Sedlmaier/2011_Sedlmaier_thesis.pdf:PDF},
  keywords  = {Inorganic Chemistry; NPO; Synthesis},
  owner     = {saulius},
  timestamp = {2016.01.22},
  creationdate = {2016-01-22T00:00:00},
  url       = {http://www.cristal.org/PON-thesis.pdf},
}

@Article{Seeber1840,
  author    = {Ludwig August Seeber},
  journal   = {Journal für die reine und angewandte Mathematik},
  title     = {Recension der "Untersuchungen über die Eigenschaften der positiven ternären quadratischen Formen von Ludwig August Seeber"},
  year      = {1840},
  pages     = {312--320},
  volume    = {20},
  file      = {1840_Seeber_312.pdf:by-author/S/Seeber/1840_Seeber_312.pdf:PDF},
  groups    = {sg/Cell reduction, sg/Quadratic forms},
  keywords  = {Quadratic Forms; Reduction},
  owner     = {saulius},
  timestamp = {2016.04.13},
  creationdate = {2016-04-13T00:00:00},
  url       = {http://www.digizeitschriften.de/dms/img/?PID=GDZPPN002142279},
}

@Article{Seeman1978,
  author    = {Nadrian C. Seeman and John M. Rosenberg and Alexander Rich},
  journal   = {PNAS},
  title     = {Sequence-specific recognition of double helical nucleic acids by proteins},
  year      = {1978},
  pages     = {804--808},
  file      = {:by-author/S/Seeman/1976_Seeman_804.pdf:PDF},
  keywords  = {DNA Protein; H Bonds; Hydrogen Bonds; Readout},
  owner     = {em},
  timestamp = {2012.09.16},
  creationdate = {2012-09-16T00:00:00},
}

@Article{Seglen1992,
  author    = {Seglen, Per O.},
  journal   = {Journal of the American Society for Information Science},
  title     = {The skewness of science},
  year      = {1992},
  issn      = {1097-4571},
  pages     = {628--638},
  volume    = {43},
  abstract  = {Scientific publications are cited to a variable extent. Distributions of article citedness are therefore found to be very skewed even for articles written by the same author, approaching linearity in a semilog plot. It is suggested that this pattern reflects a basic probability distribution with some similarity to the upper part of a normal (Gaussian) distribution. Such a distribution would be expected for various kinds of highly specialized human activity, parallels being found in the distribution of performance by top athletes and in the publication activity of university scientists. A similar skewness in the distribution of mean citedness of different authors may combine with the variability in citedness of each author's articles to form a two-leveled citational hierarchy. Such a model would be capable of accounting for the extremely skewed distribution of citedness observed for all articles within a scientific field, which approaches linearity in a double-log rather than in a semilog plot. The skewness implies that there will always be a large fraction of uncited publications, the size of the fraction depending on the citation practices (such as the number of references per publication) within the field in question. However, as part of a continuous probability distribution even uncited articles have a definite probability of contributing to scientific progress. Since it is furthermore impossible to eliminate uncited articles for statistical reasons, they should be the cause of neither worry nor remedy. The citational variability between articles in a journal is less (semilog linearity) than in the corresponding field as a whole, suggesting that each journal represents a select, stratified sample of the field. However, the variability is still too large to make the journal impact factor (the average citedness of the journal's articles) suitable as a parameter for evaluation of science. Fifteen percent of a journal's articles collect 50\% of the citations, and the most cited half of the articles account for nearly 90\% of the citations. Awarding the same value to all articles would therefore tend to conceal rather than to bring out differences between the contributing authors. The skewness in the citedness distribution of each author's articles, the large overlap between different authors and the existence of field-dependent systematic differences in citedness would seem to make even article citations unsuitable for evaluation of individual scientists or research groups. At the national level, citations may be more useful, provided due corrections are made for the field effects. © 1992 John Wiley \& Sons, Inc.},
  copyright = {Copyright © 1992 John Wiley \& Sons, Inc.},
  doi       = {10.1002/(SICI)1097-4571(199210)43:9<628::AID-ASI5>3.0.CO;2-0},
  file      = {Full Text PDF:by-author/S/Seglen/1992_Seglen_628.pdf:application/pdf;Snapshot:by-author/S/Seglen/1992_Seglen_628.html:text/html},
  groups    = {sg/Bibliometrics},
  language  = {en},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://onlinelibrary.wiley.com/doi/10.1002/(SICI)1097-4571(199210)43:9<628::AID-ASI5>3.0.CO;2-0/abstract},
  urldate   = {2015-07-06},
}

@Article{Seidel2005,
  author    = {Ralf Seidel and Joost G. P. Bloom and John van Noort and Christina F. Dutta and Nynke H. Dekker and Keith Firman and Mark D. Szczelkun and Cees Dekker},
  journal   = {The EMBO Journal},
  title     = {Dynamics of initiation, termination and reinitiation of {DNA} translocation by the motor protein {EcoR124I}},
  year      = {2005},
  pages     = {1--10},
  doi       = {10.1038/sj.emboj.7600881},
  file      = {:by-author/S/Seidel/2005_Seidel_1.pdf:PDF},
  keywords  = {TypeI},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Seidel2004,
  author    = {Seidel, Ralf and van Noort, John and van der Scheer, Carsten and Bloom, Joost G. P. and Dekker, Nynke H. and Dutta, Christina F. and Blundell, Alex and Robinson, Terence and Firman, Keith and Dekker, Cees},
  journal   = {Nature structural \&amp; molecular biology},
  title     = {Real-time observation of DNA translocation by the type I restriction modification enzyme EcoR124I.},
  year      = {2004},
  pages     = {838--43},
  volume    = {11},
  abstract  = {Type I restriction enzymes bind sequence-specifically to unmodified DNA and subsequently pull the adjacent DNA toward themselves. Cleavage then occurs remotely from the recognition site. The mechanism by which these members of the superfamily 2 (SF2) of helicases translocate DNA is largely unknown. We report the first single-molecule study of DNA translocation by the type I restriction enzyme EcoR124I. Mechanochemical parameters such as the translocation rate and processivity, and their dependence on force and ATP concentration, are presented. We show that the two motor subunits of EcoR124I work independently. By using torsionally constrained DNA molecules, we found that the enzyme tracks along the helical pitch of the DNA molecule. This assay may be directly applicable to investigating the tracking of other DNA-translocating motors along their DNA templates.},
  file      = {:by-author/S/Seidel/2004_Seidel_838.pdf:PDF},
  keywords  = {TypeI},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Presentation{Seitsonen2006,
  author    = {Ari-Paavo Seitsonen},
  title     = {Plane Wave Basis Sets},
  year      = {2006},
  file      = {:by-author/S/Seitsonen/2006_Seitsonen.pdf:PDF},
  keywords  = {Basis Sets; Density Functional Theory (DFT); Plane Waves},
  owner     = {saulius},
  timestamp = {2014.11.06},
  creationdate = {2014-11-06T00:00:00},
  url       = {https://extras.csc.fi/chem/courses/cpmd/tue/lecture-pw_pp.pdf},
}

@Article{Selimi2014,
  author    = {Selimi, Mennan and Freitag, Felix},
  journal   = {2014 IEEE Fourth International Conference on Big Data and Cloud Computing},
  title     = {Tahoe-LAFS Distributed Storage Service in Community Network Clouds},
  year      = {2014},
  month     = {Dec},
  abstract  = {Community networks are successful large scale, decentralized IP networks, built and operated by citizens for citizens. Cloud computing infrastructures present in today's Internet hardly exist in community networks. But the demand for cloud storage, and in particular secure cloud storage, increases also from within the communities. We deploy in community networks Tahoe-LAFS, a decentralized storage system with provider-independent security that guarantees privacy to the users. The correct functionality of Tahoe-LAFS in the community network is our first performance evaluation goal. Secondly, acceptable user experience is needed in order to make users willing to join the cloud, to create an eco-system around this cloud storage service. Our approach for the performance evaluation is to reproduce in our experimental scenario the real use case. We evaluate how the Tahoe-LAFS storage system performs when it is deployed over a WAN setting on cloud nodes in a community network. In experiments we characterize with different file sizes the upload and download times of Tahoe-LAFS, in relation to the bandwidth and latency between the client and the storage nodes. While we observe higher upload and faster download times, Tahoe-LAFS performed correctly in the challenging environment of the community network. Our results suggest Tahoe-LAFS as a promising application for privacy-preserving, secure and fault-tolerant cloud-based storage services in community networks.},
  doi       = {10.1109/bdcloud.2014.24},
  file      = {2014_Selimi.pdf:by-author/S/Selimi/2014_Selimi.pdf:PDF},
  isbn      = {http://id.crossref.org/isbn/978-1-4799-6719-3},
  keywords  = {Computer Science (CS); Tahoe-LAFS},
  owner     = {saulius},
  publisher = {Institute of Electrical \& Electronics Engineers (IEEE)},
  timestamp = {2016.07.20},
  creationdate = {2016-07-20T00:00:00},
  url       = {http://dx.doi.org/10.1109/BDCloud.2014.24},
}

@Article{Selling1874,
  author    = {Eduar Selling},
  journal   = {Journal für die reine und angewandte Mathematik},
  title     = {Ueber die binären und ternären quadratischen Formen},
  year      = {1874},
  pages     = {143--229},
  volume    = {77},
  file      = {1874_Selling_143.pdf:by-author/S/Selling/1874_Selling_143.pdf:PDF},
  groups    = {sg/Cell reduction, sg/Quadratic forms},
  keywords  = {Cell Reduction; Quadratic Forms},
  owner     = {saulius},
  timestamp = {2016.04.12},
  creationdate = {2016-04-12T00:00:00},
  url       = {http://www.digizeitschriften.de/dms/img/?PID=GDZPPN002155559},
}

@Presentation{Semchenko2008,
  author       = {Igor Semchenko and Sergei Khakhomov and Alexei Balmakov},
  title        = {Modern artificial electromagnetic materials and design of DNA-like metamaterials},
  year         = {2008},
  organization = {Physics of Wave Processes Laboratory Department of Optics},
  school       = {Francisk Skorina Gomel State University},
  file         = {:by-author/S/Semchenko/2008_Semchenko_slides.pdf:PDF},
  keywords     = {X-ray Crystallography},
  owner        = {saulius},
  pages        = {slides},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Semisotnov1996,
  author    = {Semisotnov, Gennady V. and Kihara, Hiroshi and Kotova, Nina V. and Kimura, Kazumoto and Amemiya, Yoshiyuki and Wakabayashi, Katsuzo and Serdyuk, Igor N. and Timchenko, Alexander A. and Chiba, Kaori and Nikaido, Kiyokazu and Ikura, Teikichi and Kuwajima, Kunihiro},
  journal   = {J. Mol. Biol.},
  title     = {Protein Globularization During Folding. A Study by Synchrotron Small-angle X-ray Scattering},
  year      = {1996},
  pages     = {559--574},
  volume    = {262},
  abstract  = {Various conformational states of polypeptide chains were investigated by synchrotron small-angle X-ray scattering (SAXS). SAXS patterns of proteins and model polypeptides in globular states (native and ‘‘molten globule’’) and in non-globular states (unfolded protein as well as randomly coiled, partially a-helical and partially b-structural synthetic polypeptides) were analyzed in terms of Guinier and Kratky plots. Large differences in the SAXS pattern have been found between globular and non-globular conformations of the polypeptide chains, and they have been interpreted in terms of differences in the shape and size of the globular and non-globular scatterers with the same molecular mass. The equilibrium and time-resolved unfolding curves of bovine carbonic anhydrase and yeast phosphoglycerate kinase were monitored by integrated SAXS intensity, and were found to be coincident with the curves measured by other physicochemical techniques, such as tryptophan fluorescence and peptide circular dichroism spectra. The intermolecular association of the protein ‘‘molten globule’’-like intermediates accumulated during the guanidine hydrochloride-induced unfolding of bovine carbonic anhydrase has been investigated by various SAXS parameters. It has been shown that the integrated SAXS intensity is much less sensitive to the protein intermolecular association than the zero angle intensity and the radius of gyration. We propose the integrated SAXS intensity as a global parameter which is particularly appropriate for fast kinetic studies of protein coil to globule transitions. Time-resolved refolding curves of the above proteins were monitored by the integrated SAXS intensity to investigate the globularization process in protein folding. Two fast kinetic processes for bovine carbonic anhydrase and two fast (each within two seconds) as well as two slow (within 500 seconds) kinetic processes for yeast phosphoglycerate kinase have been recorded. The kinetic processes reflect both protein intramolecular globularization and its intermolecular association.},
  file      = {:by-author/S/Semisotnov/1996_Semisotnov_559.pdf:PDF},
  groups    = {sg/physical sg/methods},
  timestamp = {2013.08.29},
  creationdate = {2013-08-29T00:00:00},
}

@Article{SEMISOTNOV2003,
  author    = {SEMISOTNOV, Gennady V. and TIMCHENKO, Alexander A. and MELNIK, Bogdan S. and KIMURA , Kazumoto and KIHARA, Hiroshi},
  journal   = {Photon Factory Activity Report 2002},
  title     = {Kratky plot as a tool to evaluate the molecular mass of globular proteins},
  year      = {2003},
  pages     = {256},
  volume    = {20},
  abstract  = {The molecular mass is one of the main characteristics of proteins. The X-ray or neuron scattering allows to determine the molecular mass of proteins by an extrapolation of the scattered intensity to zero scattering angle by Guinier plot [1]. However, this approach requires the knowledge of exact protein concentration, correction on the experimental conditions and absolute scale for the scattered intensity. Besides, it is ineffective in the presence of nonspecific intermolecular association. Here we have proposed the other approach based on Kratky plot maximum position to be dependent on Rg in the case of globular proteins [2]. The small-angle X-ray scattering (SAXS) patterns have been measured for several globular proteins with known molecular weight from 10 kDa up to 800 kDa and the dependence of the Kratky plot maximum position on molecular mass of protein has been determined. This approach permits to evaluate the molecular mass of proteins without the correction on experimental conditions and even in the presence of their moderate nonspecific association.},
  file      = {:by-author/S/Semisotnov/2002_Semisotnov_1.pdf:PDF},
  keywords  = {Molecular Weight (MW); SAXS},
  owner     = {em},
  timestamp = {2013.08.29},
  creationdate = {2013-08-29T00:00:00},
}

@Article{Sena2015,
  author    = {Sena, H. J. and Urquieta-González, E. A.},
  journal   = {Blucher Chemical Engineering Proceedings},
  title     = {Catalisadores de {Fe}2O3 e {Mn}2O3 suportados sobre {H}-mor e {CeH}-mor–{Avaliação} na {Oxidação} de {CO}},
  year      = {2015},
  pages     = {9844--9851},
  volume    = {1},
  file      = {[PDF] from blucher.com.br:by-author/S/Sena/2015_Sena_9844.pdf:application/pdf},
  groups    = {sg/NAR2012},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://www.proceedings.blucher.com.br/download-pdf/245/17869},
  urldate   = {2015-08-31},
}

@Article{Senthil2007,
  author    = {Senthil, Kumar M},
  journal   = {The PracTEX Journal},
  title     = {LATEX Tools for Life Scientists (BioTEXniques?)},
  year      = {2007},
  pages     = {1},
  volume    = {4},
  file      = {:by-author/S/Senthil/2007_Senthil_1.pdf:PDF},
  keywords  = {Bioinformatics; Latex},
  owner     = {saulius},
  timestamp = {2011.10.13},
  creationdate = {2011-10-13T00:00:00},
}

@Presentation{Seo2009,
  author    = {Seo},
  title     = {Multidimensional Data Visualization},
  year      = {2009},
  file      = {:by-author/S/Seo/2009_Seo.pdf:PDF},
  keywords  = {Computer Science (CS); Data Presentation},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Seo2003,
  author    = {Seo, Tae Seok and Li, Zengmin and Ruparel, Hameer and Ju, Jingyue},
  journal   = {The Journal of organic chemistry},
  title     = {Click chemistry to construct fluorescent oligonucleotides for DNA sequencing.},
  year      = {2003},
  pages     = {609--12},
  volume    = {68},
  abstract  = {&quot;Click chemistry&quot; 1,3-dipolar cycloaddition between alkynyl 6-carboxyfluorescein (FAM) and azido-labeled single-stranded (ss) DNA was carried out under aqueous conditions to produce FAM-labeled ssDNA in quantitative yield. The FAM-labeled ssDNA was successfully used as a primer to produce DNA sequencing products with single-base resolution in a capillary electrophoresis DNA sequencer with laser-induced fluorescence detection.},
  file      = {:by-author/S/Seo/2003_Seo_609.pdf:PDF},
  keywords  = {Bioconjugation},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@Manuscript{Seol2003,
  author    = {Eunyoung Seol},
  title     = {Running C/C++ Program in parallel using MPI},
  year      = {2003},
  url       = {http://sole.googlecode.com/svn-history/r6/trunk/References/mpi.pdf},
  abstract  = {MPI (Message Passing Interface) is one of the most popular library for mes- sage passing within a parallel program. MPI can be used with Fortran and C/C++, and this paper discusses how to create parallel C/C++ program using MPI.},
  file      = {:by-author/S/Seol/2003_Seol.pdf:PDF},
  owner     = {saulius},
  timestamp = {2013.07.02},
  creationdate = {2013-07-02T00:00:00},
}

@Article{Serebryanaya2008,
  author      = {Serebryanaya, N. and Dubitskii, G. and Blank, V. and Mavrin, B. and Chernozatonskii, L. and Skryleva, E. and Skokan, E. and Aksenenkov, V.},
  journal     = {Polymer Science Series A},
  title       = {Effect of high-pressure high-temperature treatment on the structure of a hexagonal modification of fullerite C\&lt;sub\&gt;60\&lt;/sub\&gt;},
  year        = {2009},
  issn        = {0965-545X},
  pages       = {1049--1059},
  volume      = {51},
  abstract    = {Powder X-ray diffraction, X-ray photoelectron spectroscopy, Raman spectroscopy, and molecular dynamics have been employed to investigate structural transformations in hexagonal and cubic modifications of fullerite C60 after the action of high pressure (4 GPa) within the temperature range 20–1450°C. It has been found that fullerene molecules polymerize to afford polymer structures only in the case of face-centered cubic samples. Under the effect of high pressure and temperature, fullerite C60 with a hexagonal close-packed structure is initially transformed into the cubic modification and, then, forms polymerized structures, which, during an increase in the treatment temperature, become less stable and ordered than the same polymerized structures obtained directly from cubic fullerite C60. X-ray photoelectron spectroscopy measurements suggest deformation of the cages of fullerene molecules in the polymerized structures.},
  affiliation = {Ministry of Education and Science of the Russian Federation Technological Institute of Superhard and New Carbon Materials ul. Tsentral’naya 7a Troitsk, Moscow oblast 142190 Russia},
  file        = {:by-author/S/Serebryanaya/2008_Serebryanaya_abstract.pdf:PDF},
  issue       = {10},
  keywords    = {COD; Chemistry; Coauthors; Materials Science},
  owner       = {saulius},
  publisher   = {MAIK Nauka/Interperiodica distributed exclusively by Springer Science+Business Media LLC.},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
  url         = {http://dx.doi.org/10.1134/S0965545X09100010},
}

@Article{Seress1997,
  author    = {Ákos Seress},
  journal   = {Notices of The AMS},
  title     = {An Introduction to Computational Group Theory},
  year      = {1997},
  month     = {jun jul},
  pages     = {671--679},
  abstract  = {Can one rotate only one corner piece in Rubik’s cube? What are the energy levels of the buckyball molecule? Are the graphs on Figure 1 isomorphic? What is the Galois group of the polynomial x 8 +2 x 7 +28 x 6 + 1728 x + 3456? What are the possible symmetry groups of crystals? These are all questions which, directly or in a not so obvious way, lead to problems in computational group theory.},
  file      = {1997_Seress_671.pdf:by-author/S/Seress/1997_Seress_671.pdf:PDF},
  keywords  = {CGT; Computational Group Theory; Coset Enumeration; Coxeter Algorithm; GAP; Magma},
  owner     = {saulius},
  timestamp = {2013.10.20},
  creationdate = {2013-10-20T00:00:00},
  url       = {http://www.ams.org/notices/199706/seress.pdf},
}

@Article{Serrano2011,
  author    = {Serrano, Manuel},
  title     = {HopTeX - Compiling HTML to LaTeX with CSS},
  year      = {2011},
  abstract  = {This article1 presents HopTeX, a new application for authoring HTML and LATEX documents. The content of the document is either be expressed in H TML or in a blending of H TML and a dedicated wiki syntax, for the sake of conciseness and readability. The rendering of the document is expressed by a set of C SS rules. The main originality of HOPTEX is to consider LATEX as a new media type for HTML and to express the compilation from H TML to LTEX by the means of dedicated style sheet rules. HOPTEX can then be used to generate high quality documents for both paper printed version and electronic version. The online version of this paper is available at the HOPTEX web page. It can be read using a regular Web browser or using Smartphone browsers.},
  file      = {:by-author/S/Serrano/2011_Serrano.pdf:PDF},
  keywords  = {Computer Languages; Computer Science (CS); Oregon Workshop; Scheme},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Manuscript{Serrano2000,
  author    = {Serrano, Manuel and Hans-J. Boehm},
  title     = {Understanding Memory Allocation of Scheme Programs},
  year      = {2000},
  keywords  = {Computer Science (CS); Garbage Collectors},
  file      = {:by-author/S/Serrano/2000_Serrano_techreport.pdf:PDF},
  groups    = {sg/Garbage collectors},
  owner     = {saulius},
  pages     = {techreport},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Serrier-Garcia2013,
  author    = {Serrier-Garcia, L. and Cuevas, J. C. and Cren, T. and Brun, C. and Cherkez, V. and Debontridder, F. and Fokin, D. and Bergeret, F. S. and Roditchev, D.},
  journal   = {Phys. Rev. Lett.},
  title     = {Scanning Tunneling Spectroscopy Study of the Proximity Effect in a Disordered Two-Dimensional Metal},
  year      = {2013},
  pages     = {157003},
  volume    = {110},
  doi       = {10.1103/PhysRevLett.110.157003},
  file      = {2013_Serrier-Garcia_157003.pdf:by-author/S/Serrier-Garcia/2013_Serrier-Garcia_157003.pdf:PDF},
  issue     = {15},
  keywords  = {Density Functional Theory (DFT); Scanning Tunnel Microscopy; Single Molecule Switches},
  numpages  = {5},
  owner     = {saulius},
  publisher = {American Physical Society},
  timestamp = {2014.10.21},
  creationdate = {2014-10-21T00:00:00},
  url       = {http://link.aps.org/doi/10.1103/PhysRevLett.110.157003},
}

@Article{Serva1998,
  author    = {Serva, S. and Weinhold, E. and Roberts, R. J. and Klimasauskas, S.},
  journal   = {Nucleic acids research},
  title     = {Chemical display of thymine residues flipped out by DNA methyltransferases.},
  year      = {1998},
  pages     = {3473--9},
  volume    = {26},
  abstract  = {The DNA cytosine-C5 methyltransferase M. Hha I flips its target base out of the DNA helix during interaction with the substrate sequence GCGC. Binary and ternary complexes between M. Hha I and hemimethylated DNA duplexes were used to examine the suitability of four chemical methods to detect flipped-out bases in protein-DNA complexes. These methods probe the structural peculiarities of pyrimidine bases in DNA. We find that in cases when the target cytosine is replaced with thymine (GTGC), KMnO4proved an efficient probe for positive display of flipped-out thymines. The generality of this procedure was further verified by examining a DNA adenine-N6 methyltransferase, M. Taq I, in which case an enhanced reactivity of thymine replacing the target adenine (TCGT) in the recognition sequence TCGA was also observed. Our results support the proposed base-flipping mechanism for adenine methyltransferases, and offer a convenient laboratory tool for detection of flipped-out thymines in protein-DNA complexes.},
  file      = {:by-author/S/Serva/1998_Serva_3473.pdf:PDF},
  keywords  = {HhaI},
  owner     = {saulius},
  timestamp = {2012.11.05},
  creationdate = {2012-11-05T00:00:00},
}

@Article{Setyawan2010,
  author    = {Wahyu Setyawan and Stefano Curtarolo},
  journal   = {Computational Materials Science},
  title     = {High-throughput electronic band structure calculations: Challenges and tools},
  year      = {2010},
  issn      = {0927-0256},
  number    = {2},
  pages     = {299 - 312},
  volume    = {49},
  abstract  = {The article is devoted to the discussion of the high-throughput approach to band structures calculations. We present scientific and computational challenges as well as solutions relying on the developed framework (Automatic Flow, AFLOW/ACONVASP). The key factors of the method are the standardization and the robustness of the procedures. Two scenarios are relevant: (1) independent users generating databases in their own computational systems (off-line approach) and (2) teamed users sharing computational information based on a common ground (on-line approach). Both cases are integrated in the framework: for off-line approaches, the standardization is automatic and fully integrated for the 14 Bravais lattices, the primitive and conventional unit cells, and the coordinates of the high symmetry k-path in the Brillouin zones. For on-line tasks, the framework offers an expandable web interface, where the user can prepare and set up calculations following the proposed standard. Few examples of band structures are included. LSDA+U parameters (U, J) are also presented for Nd, Sm, and Eu.},
  comment   = {Cited in Pymatgen Web page, https://pymatgen.org/pymatgen.symmetry.analyzer.html.},
  doi       = {http://dx.doi.org/10.1016/j.commatsci.2010.05.010},
  file      = {2010_Setyawan_199.pdf:by-author/S/Setyawan/2010_Setyawan_199.pdf:PDF},
  keywords  = {High-throughput; Material Science},
  owner     = {saulius},
  timestamp = {2016.10.25},
  creationdate = {2016-10-25T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/S0927025610002697},
}

@Article{Shafer2003,
  author    = {Shafer},
  title     = {Comments on “Constructing a Logic of Plausible Inference: A Guide to Cox’s Theorem”, by Kevin S. Van Horn},
  year      = {2003},
  file      = {:by-author/S/Shafer/2003_Shafer.pdf:PDF},
  groups    = {sg/Bayesian},
  keywords  = {Bayesian Statistics; Mathematics},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Shafer2002,
  author    = {Shafer},
  title     = {Dempster-Shafer Theory},
  year      = {2002},
  pages     = {c},
  file      = {:by-author/S/Shafer/2002_Shafer_c.pdf:PDF},
  groups    = {sg/Bayesian},
  keywords  = {Mathematics; Non Bayesian Updating},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Shafer2002a,
  author    = {Shafer},
  title     = {Perspectives on the Theory and Practice of Belief Functions},
  year      = {2002},
  file      = {:by-author/S/Shafer/2002_Shafer.pdf:PDF},
  groups    = {sg/Bayesian},
  keywords  = {Mathematics; Non Bayesian Updating},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Shafer2002b,
  author    = {Shafer},
  title     = {Belief Function},
  year      = {2002},
  pages     = {b},
  file      = {:by-author/S/Shafer/2002_Shafer_b.pdf:PDF},
  groups    = {sg/Bayesian},
  keywords  = {Mathematics; Non Bayesian Updating},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Shafer1982,
  author    = {Glenn Shafer},
  journal   = {Journal of the Royal Statistical Society. Series B (Methodological)},
  title     = {Belief Functions and Parametric Models},
  year      = {1982},
  pages     = {322--352},
  volume    = {44},
  abstract  = {The theory of belief functions assesses evidence by fitting it to a scale of canonical examples in which the meaning of a message depends on chance. In order to analyse parametric statistical problems within the framework of this theory, we must specify the evidence on which the parametric model is based. This article gives several examples to show how the nature of this evidence affects the analysis. These examples also illustrate how the theory of belief functions can deal with problems where the evidence is too weak to support a parametric model.},
  file      = {:by-author/S/Shafer/1982_Shafer_322.pdf:PDF},
  groups    = {sg/Bayesian},
  keywords  = {Mathematics; Non Bayesian Updating},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Shafer2011,
  author    = {Shafer, Glenn and Shen, Alexander and Vereshchagin, Nikolai and Vovk, Vladimir},
  journal   = {Statistical Science},
  title     = {Test Martingales, {Bayes} Factors and p-Values},
  year      = {2011},
  issn      = {0883-4237, 2168-8745},
  pages     = {84--101},
  volume    = {26},
  abstract  = {A nonnegative martingale with initial value equal to one measures evidence against a probabilistic hypothesis. The inverse of its value at some stopping time can be interpreted as a Bayes factor. If we exaggerate the evidence by considering the largest value attained so far by such a martingale, the exaggeration will be limited, and there are systematic ways to eliminate it. The inverse of the exaggerated value at some stopping time can be interpreted as a p-value. We give a simple characterization of all increasing functions that eliminate the exaggeration.},
  doi       = {10.1214/10-STS347},
  file      = {Shafer et al. - 2011 - Test Martingales, Bayes Factors and p-Values.pdf:by-author/S/Shafer/2011_Shafer_84.pdf:PDF;Snapshot:by-author/S/Shafer/2011_Shafer_84.html:URL},
  groups    = {sg/Bayesian},
  keywords  = {Bayes Factors; Evidence; Hypothesis Testing; Martingales; P-values},
  language  = {EN},
  mrnumber  = {MR2849911},
  owner     = {saulius},
  timestamp = {2015.12.07},
  creationdate = {2015-12-07T00:00:00},
  url       = {http://projecteuclid.org/euclid.ss/1307626567},
  urldate   = {2015-12-07},
  zmnumber  = {1219.62050},
}

@Article{Shalizi2009,
  author    = {Cosma Rohilla Shalizi},
  journal   = {Electronic Journal of Statistics},
  title     = {Dynamics of Bayesian updating with dependent data and misspecified models},
  year      = {2009},
  pages     = {1039--1074},
  volume    = {3},
  doi       = {10.1214/09-EJS485},
  file      = {2009_Shalizi_1039.pdf:by-author/S/Shalizi/2009_Shalizi_1039.pdf:PDF},
  groups    = {sg/Bayesian},
  keywords  = {Bayesian Statistics},
  owner     = {saulius},
  timestamp = {2012.10.04},
  creationdate = {2012-10-04T00:00:00},
  url       = {http://arxiv.org/abs/0901.1342},
}

@Article{Shamoo1986,
  author    = {Shamoo, Y. and Adari, H. and Konigsberg, W. H. and Williams, K. R. and Chase, J. W.},
  journal   = {Proceedings of the National Academy of Sciences of the United States of America},
  title     = {Cloning of T4 gene 32 and expression of the wild-type protein under lambda promoter PL regulation in Escherichia coli.},
  year      = {1986},
  pages     = {8844--8},
  volume    = {83},
  abstract  = {Bacteriophage T4 gene 32 encodes a single-stranded DNA binding protein required for T4 DNA replication, recombination, and repair. Previous attempts at cloning gene 32 have failed due to a presumably deleterious effect on host cell viability. In addition, overexpression of gene 32 would be expected to be limited by the autoregulatory ability of the gene 32 product g32P. A repetitive A + T-rich sequence flanking the ribosome binding site of gene 32 has been implicated in this translational regulation. To circumvent these problems, the wild-type gene for g32P has been reconstructed in M13 using restriction fragments from T4 g32am453 and synthetic oligodeoxynucleotides so that it no longer includes its native promoter and putative autoregulatory region. The g32am453 codon TAG was changed back to TGG as in wild-type gene 32 using site-directed oligodeoxynucleotide mutagenesis. In vectors containing the lambda leftward promoter PL, gene 32 is overexpressed with the resulting transcripts being depressed at g32P concentrations that repress the wild-type gene 32 transcripts.},
  file      = {:by-author/S/Shamoo/1986_Shamoo_8844.pdf:PDF},
  keywords  = {Purification; {gp32}; {gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Shamoo1995,
  author    = {Shamoo, Y. and Friedman, A. M. and Parsons, M. R. and Konigsberg, W. H. and Steitz, T. A.},
  journal   = {Nature},
  title     = {Crystal structure of a replication fork single-stranded DNA binding protein (T4 gp32) complexed to DNA.},
  year      = {1995},
  pages     = {362--6},
  volume    = {376},
  abstract  = {The single-stranded DNA (ssDNA) binding protein gp32 from bacteriophage T4 is essential for T4 DNA replication, recombination and repair. In vivo gp32 binds ssDNA as the replication fork advances and stimulates replisome processivity and accuracy by a factor of several hundred. Gp32 binding affects nearly every major aspect of DNA metabolism. Among its important functions are: (1) configuring ssDNA templates for efficient use by the replisome including DNA polymerase; (2) melting out adventitious secondary structures; (3) protecting exposed ssDNA from nucleases; and (4) facilitating homologous recombination by binding ssDNA during strand displacement. We have determined the crystal structure of the gp32 DNA binding domain complexed to ssDNA at 2.2 A resolution. The ssDNA binding cleft comprises regions from three structural subdomains and includes a positively charged surface that runs parallel to a series of hydrophobic pockets formed by clusters of aromatic side chains. Although only weak electron density is seen for the ssDNA, it indicates that the phosphate backbone contacts an electropositive cleft of the protein, placing the bases in contact with the hydrophobic pockets. The DNA mobility implied by the weak electron density may reflect the role of gp32 as a sequence-independent ssDNA chaperone allowing the largely unstructured ssDNA to slide freely through the cleft.},
  file      = {:by-author/S/Shamoo/1995_Shamoo_362.pdf:PDF},
  keywords  = {{gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Shang2017,
  author    = {Lu Shang and Yunhui Liang and Mengzhu Li and Geoffrey I. N. Waterhouse and Pei Tang and Ding Ma and Li-Zhu Wu and Chen-Ho Tung and Tierui Zhang},
  journal   = {Advanced Functional Materials},
  title     = {{\textquotedblleft}Naked{\textquotedblright} Magnetically Recyclable Mesoporous Au-$\upgamma$-Fe2 O3 Nanocrystal Clusters: A Highly Integrated Catalyst System},
  year      = {2017},
  month     = {jan},
  pages     = {1606215},
  doi       = {10.1002/adfm.201606215},
  file      = {Shang2017.pdf:by-author/S/Shang/2017_Shang_1606215.pdf:PDF},
  groups    = {sg/MOF, sg/MOFs, am/MOFs},
  owner     = {saulius},
  publisher = {Wiley-Blackwell},
  timestamp = {2017.01.31},
  creationdate = {2017-01-31T00:00:00},
  url       = {https://doi.org/10.1002%2Fadfm.201606215},
}

@Article{Shannon1948,
  author    = {C. E. Shannon},
  journal   = {The Bell System Technical Journal},
  title     = {A Mathematical Theory of Communication},
  year      = {1948},
  pages     = {379--423},
  volume    = {27},
  file      = {:by-author/S/Shannon/1948_Shannon_379.pdf:PDF;:by-author/S/Shannon/1948_Shannon_379.ps:PostScript},
  owner     = {saulius},
  timestamp = {2013.08.10},
  creationdate = {2013-08-10T00:00:00},
}

@Article{Shapiro1965,
  author    = {Shapiro, S. S. and Wilk, M. B.},
  journal   = {Biometrika},
  title     = {An analysis of variance test for normality (complete samples)},
  year      = {1965},
  pages     = {591--611},
  volume    = {52},
  file      = {:by-author/S/Shapiro/1965_Shapiro_591.pdf:PDF},
  keywords  = {Statistical Tests},
  owner     = {andrius},
  timestamp = {2012.09.13},
  creationdate = {2012-09-13T00:00:00},
}

@Presentation{Sharkey2005,
  author    = {Amanda Sharkey},
  title     = {Adaptive Robotics},
  year      = {2005},
  file      = {:by-author/S/Sharkey/2005_Sharkey.ppt:PPT},
  keywords  = {AdaptiveRobotics},
  owner     = {saulius},
  timestamp = {2015.03.03},
  creationdate = {2015-03-03T00:00:00},
}

@Article{Sharma2003,
  author    = {Prince Sharma and David R. D’Souza and Deepali Bhandari and Vijay Parashar and Neena Capalash},
  journal   = {Biochemistry and Molecular Biology Education},
  title     = {Demonstration of the Principles of Restriction Endonuclease Cleavage Reactions Using Thermostable {Bfl} {I} from {A}noxybacillus flavithermus},
  year      = {2003},
  pages     = {392--396},
  volume    = {31},
  file      = {:by-author/S/Sharma/2003_Sharma_392.pdf:PDF},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{She2012,
  author    = {She, Zhun and Gao, Zeng-Qiang and Liu, Ying and Wang, Wen-Jia and Liu, Guang-Feng and Shtykova, Eleonora V. and Xu, Jian-Hua and Dong, Yu-Hui},
  journal   = {FEBS Lett.},
  title     = {Structural and SAXS analysis of the budding yeast SHU-complex proteins},
  year      = {2012},
  pages     = {2306–2312},
  volume    = {586},
  abstract  = {In Saccharomyces cerevisiae, four proteins, Shu1, Shu2, Psy3 and Csm2, form a stable SHU-complex both in vivo and in vitro. These proteins are involved in the early stages of the homologous recom- bination DNA damage repair process. In this paper, the crystal structure of the Psy3–Csm2 sub-com- plex is presented at 1.8 Å resolution and successfully fitted into our small angle X-ray scattering (SAXS) data of the SHU-complex. Taken together with our electrophoretic mobility shift assay (EMSA) results, a model is proposed for the SHU–protein complex coupled with DNA.},
  doi       = {10.1016/j.febslet.2012.06.024},
  file      = {:by-author/S/She/2012_She_2306.pdf:PDF},
  owner     = {em},
  timestamp = {2013.10.01},
  creationdate = {2013-10-01T00:00:00},
  url       = {http://dx.doi.org/10.1016/j.febslet.2012.06.024},
}

@Article{Shechner2009,
  author    = {Shechner, David M and Grant, Robert A and Bagby, Sarah C and Koldobskaya, Yelena and Piccirilli, Joseph A and Bartel, David P},
  journal   = {Science (New York, N.Y.)},
  title     = {Crystal structure of the catalytic core of an RNA-polymerase ribozyme.},
  year      = {2009},
  pages     = {1271--5},
  volume    = {326},
  file      = {2009_Shechner_1271.pdf:by-author/S/Shechner/2009_Shechner_1271.pdf:PDF;:by-author/S/Shechner/2009_Shechner_1271-supp.pdf:PDF},
  keywords  = {Ribozymes},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Shechtman1984,
  author    = {Shechtman, D. and Blech, I. and Gratias, D. and Cahn, J. W.},
  journal   = {Phys. Rev. Lett.},
  title     = {Metallic Phase with Long-Range Orientational Order and No Translational Symmetry},
  year      = {1984},
  pages     = {1951--1953},
  volume    = {53},
  abstract  = {We have observed a metallic solid (Al-14-at.%-Mn) with long-range orientational order, but with icosahedral point group symmetry, which is inconsistent with lattice translations. Its diffraction spots are as sharp as those of crystals but cannot be indexed to any Bravais lattice. The solid is metastable and forms from the melt by a first-order transition.},
  doi       = {10.1103/PhysRevLett.53.1951},
  file      = {1984_Shechtman_1951.pdf:by-author/S/Shechtman/1984_Shechtman_1951.pdf:PDF},
  issue     = {20},
  numpages  = {0},
  owner     = {saulius},
  publisher = {American Physical Society},
  timestamp = {2014.09.25},
  creationdate = {2014-09-25T00:00:00},
  url       = {http://link.aps.org/doi/10.1103/PhysRevLett.53.1951},
}

@Article{Shen2003,
  author    = {Shen, Qun and Wang, Jun},
  journal   = {Acta Crystallographica Section D},
  title     = {Recursive direct phasing with reference-beam diffraction},
  year      = {2003},
  pages     = {809--814},
  volume    = {59},
  doi       = {10.1107/S0907444903003664},
  file      = {gr2325.pdf:by-author/S/Shen/2003_Shen_809.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444903003664},
}

@PhdThesis{Sherburne2000,
  author    = {Sherburne, Craig K.},
  school    = {University of Alberta},
  title     = {Conjugal and Genetic Analysis of the {IncHI1} Plasmid, {R27}},
  year      = {2000},
  file      = {:by-author/S/Sherburne/2000_Sherburne_phdthesis.pdf:PDF},
  owner     = {em},
  pages     = {phdthesis},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Shereda2009,
  author    = {Shereda, Robert D. and Kozlov, Alexander G. and Lohman, Timothy M. and Cox, Michael M. and Keck, James L.},
  journal   = {Critical Reviews in Biochemistry and Molecular Biology},
  title     = {SSB as an Organizer/Mobilizer of Genome Maintenance Complexes},
  year      = {2008},
  pages     = {289--318},
  volume    = {43},
  abstract  = {When duplex DNA is altered in almost any way (replicated, recombined, or repaired), single strands of DNA are usually intermediates, and single-stranded DNA binding (SSB) proteins are present. These proteins have often been described as inert, protective DNA coatings. Continuing research is demonstrating a far more complex role of SSB that includes the organization and/or mobilization of all aspects of DNA metabolism. Escherichia coli SSB is now known to interact with at least 14 other proteins that include key components of the elaborate systems involved in every aspect of DNA metabolism. Most, if not all, of these interactions are mediated by the amphipathic C-terminus of SSB. In this review, we summarize the extent of the eubacterial SSB interaction network, describe the energetics of interactions with SSB, and highlight the roles of SSB in the process of recombination. Similar themes to those highlighted in this review are evident in all biological systems.},
  doi       = {10.1080/10409230802341296},
  eprint    = {http://informahealthcare.com/doi/pdf/10.1080/10409230802341296},
  file      = {:by-author/S/Shereda/2009_Shereda_289.pdf:PDF},
  keywords  = {{gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://informahealthcare.com/doi/abs/10.1080/10409230802341296},
}

@Article{Sheu2003,
  author    = {Sheu, Sheh-Yi and Yang, Dah-Yen and Selzle, H. L. and Schlag, E. W.},
  journal   = {Proceedings of the National Academy of Sciences of the United States of America},
  title     = {Energetics of hydrogen bonds in peptides.},
  year      = {2003},
  pages     = {12683--7},
  volume    = {100},
  abstract  = {Hydrogen bonds and their relative strengths in proteins are of importance for understanding protein structure and protein motions. The correct strength of such hydrogen bonds is experimentally known to vary greatly from approximately 5-6 kcal/mol for the isolated bond to approximately 0.5-1.5 kcal/mol for proteins in solution. To estimate these bond strengths, here we suggest a direct novel kinetic procedure. This analyzes the timing of the trajectories of a properly averaged dynamic ensemble. Here we study the observed rupture of these hydrogen bonds in a molecular dynamics calculation as an alternative to using thermodynamics. This calculation is performed for the isolated system and contrasted with results for water. We find that the activation energy for the rupture of the hydrogen bond in a beta-sheet under isolated conditions is 4.76 kcal/mol, and the activation energy is 1.58 kcal/mol for the same beta-sheet in water. These results are in excellent agreement with observations and suggest that such a direct calculation can be useful for the prediction of hydrogen bond strengths in various environments of interest.},
  file      = {:by-author/S/Sheu/2003_Sheu_12683.pdf:PDF},
  groups    = {sg/applications},
  keywords  = {H Bonds; Protein Physics},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Shewchuk1994,
  author    = {Jonathan Richard Shewchuk},
  title     = {An Introduction to the Conjugate Gradient Method Without the Agonizing Pain Edition 1 1/4},
  year      = {1994},
  abstract  = {The Conjugate Gradient Method is the most prominent iterative method for solving sparse systems of linear equations. Unfortunately, many textbook treatments of the topic are written with neither illustrations nor intuition, and their victims can be found to this day babbling senselessly in the corners of dusty libraries. For this reason, a deep, geometric understanding of the method has been reserved for the elite brilliant few who have painstakingly decoded the mumblings of their forebears. Nevertheless, the Conjugate Gradient Method is a composite of simple, elegant ideas that almost anyone can understand. Of course, a reader as intelligent as yourself will learn them almost effortlessly. The idea of quadratic forms is introduced and used to derive the methods of Steepest Descent, Conjugate Directions, and Conjugate Gradients. Eigenvectors are explained and used to examine the convergence of the Jacobi Method, Steepest Descent, and Conjugate Gradients. Other topics include preconditioning and the nonlinear Conjugate Gradient Method. I have taken pains to make this article easy to read. Sixty-six illustrations are provided. Dense prose is avoided. Concepts are explained in several different ways. Most equations are coupled with an intuitive interpretation.},
  file      = {:by-author/S/Shewchuk/1994_Shewchuk.pdf:PDF},
  keywords  = {Conjugate Gradient; Mathematics},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Presentation{Shi2008,
  author    = {Yunhe Shi and Kevin Casey and Anton Ertl and David Gregg},
  title     = {Virtual Machine Showdown: stack versus registers},
  year      = {2008},
  file      = {2008_Shi_slides.pdf:by-author/S/Shi/2008_Shi_slides.pdf:PDF},
  keywords  = {Computer Architecture; Register Machines; Stack Machines; Virtual Machines},
  owner     = {saulius},
  timestamp = {2014.10.21},
  creationdate = {2014-10-21T00:00:00},
  url       = {http://www.complang.tuwien.ac.at/anton/euroforth/ef08/papers/gregg.pdf},
}

@InProceedings{Shi2005,
  author    = {Yunhe Shi and David Gregg and Andrew Beatty and M. Anton Ertl},
  booktitle = {VEE’05},
  title     = {Virtual Machine Showdown: Stack Versus Registers},
  year      = {2005},
  pages     = {153--163},
  file      = {2005_Shi_153.pdf:by-author/S/Shi/2005_Shi_153.pdf:PDF},
  owner     = {saulius},
  timestamp = {2014.10.21},
  creationdate = {2014-10-21T00:00:00},
  url       = {http://static.usenix.org/events/vee05/full_papers/p153-yunhe.pdf},
}

@InProceedings{Shibberu2010,
  author           = {Shibberu, Yosi and Holder, Allen and Lutz, Kyla},
  booktitle        = {Proceedings of the 6th international conference on Bioinformatics Research and Applications},
  title            = {Fast protein structure alignment},
  year             = {2010},
  address          = {Berlin, Heidelberg},
  pages            = {152--165},
  publisher        = {Springer-Verlag},
  series           = {ISBRA'10},
  creationdate     = {2012-05-15T00:00:00},
  doi              = {10.1007/978-3-642-13078-6_18},
  file             = {:by-author/S/Shibberu/2010_Shibberu.pdf:PDF},
  groups           = {sg/Molecule superposion, sg/Superposition, sg/Bioinf. Algorithms},
  isbn             = {3-642-13077-1, 978-3-642-13077-9},
  keywords         = {Structure Superposition},
  location         = {Storrs, CT},
  modificationdate = {2024-05-12T16:47:44},
  owner            = {saulius},
  timestamp        = {2012.05.15},
  url              = {http://dx.doi.org/10.1007/978-3-642-13078-6_18},
}

@Manuscript{Shieh2005,
  author    = {Shieh},
  title     = {Structural snapshot of a base flipping intermediate},
  year      = {2005},
  file      = {:by-author/S/Shieh/2005_Shieh_manuscript.pdf:PDF},
  owner     = {saulius},
  pages     = {manuscript},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@InProceedings{Shields1998,
  author    = {Shields, Mark and Tim Sheard and Simon Peyton Jones},
  booktitle = {POPL},
  title     = {Dynamic Typing as Staged Type Inference},
  year      = {1998},
  pages     = {289--302},
  file      = {:by-author/S/Shields/1998_Shields_POPL.pdf:PDF},
  keywords  = {Computer Science (CS); Type Systems},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Shimada1955,
  author    = {Shimada, A. and Okaya, Y. and Nakaura, M.},
  journal   = {Acta Crystallographica},
  title     = {The crystal structure of {\it cyclo}hexylamine hydrochloride},
  year      = {1955},
  pages     = {819--822},
  volume    = {8},
  abstract  = {The crystal structure of cyclohexylamine hydrochloride has been determined, making use of the isomorphism of the hydrochloride with the corresponding hydrobromide and the Okaya~-:Nitta inequality method. Both compounds crystallize with the symmetry of C~v-Pca21.The dimensions of t;he unit cell, containing four chemical units, are a = 9.36, b ---- 11-47, c ---- 7.41 ~ for the hydro- chloride and a ---- 9.56, b ---- 11.29, c ---- 7.83 /k for the hydrobromide. The cyclohexyl ring has the puckered form, while the crystal structure may be described as having a layer structure made by nitrogen and chlorine atoms, to which the cyclohexyl rings are anchored by the equatorial C-N bonds. A discussion on the relation between the present structure, alkylamine hydrohalides and aniline hydrochloride is given.},
  doi       = {10.1107/S0365110X55002466},
  file      = {:by-author/S/Shimada/1955_Shimada_819.pdf:PDF},
  keywords  = {For COD Deposition; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0365110X55002466},
}

@Article{Shinde2012,
  author    = {Archana A. Shinde and D. G. Chougule},
  journal   = {IJCSET},
  title     = {Text Pre-processing and Text Segmentation for OCR},
  year      = {2012},
  number    = {1},
  pages     = {810--812},
  volume    = {2},
  file      = {2012_Shinde_810.pdf:by-author/S/Shinde/2012_Shinde_810.pdf:PDF},
  groups    = {sg/Text segmentation},
  keywords  = {OCR; Text Segmentation},
  owner     = {saulius},
  timestamp = {2016.02.05},
  creationdate = {2016-02-05T00:00:00},
  url       = {http://ijcset.net/docs/Volumes/volume2issue1/ijcset2012020111.pdf},
}

@Article{Shiozawa2009,
  author    = {Shiozawa, Kumiko and Konarev, Petr V. and Neufeld, Christian and Wilmanns, Matthias and Svergun, Dmitri I.},
  journal   = {The Journal of biological chemistry},
  title     = {Solution structure of human Pex5.Pex14.PTS1 protein complexes obtained by small angle X-ray scattering.},
  year      = {2009},
  pages     = {25334--42},
  volume    = {284},
  abstract  = {The Pex5p receptor recognizes newly synthesized peroxisomal matrix proteins which have a C-terminal peroxisomal targeting signal to the peroxisome. After docking to protein complexes on the membrane, these proteins are translocated across the membrane. The docking mechanism remains unclear, as no structural data on the multicomponent docking complex are available. As the interaction of the cargo-loaded Pex5p receptor and the peroxisomal membrane protein Pex14p is the essential primary docking step, we have investigated the solution structure of these complexes by small angle x-ray scattering and static light scattering. Titration studies yielded a 1:6 stoichiometry for the Pex5p.Pex14p complex, and low resolution structural models were reconstructed from the x-ray scattering data. The free full-length human Pex5p is monomeric in solution, with an elongated, partially unfolded N-terminal domain. The model of the complex reveals that the N terminus of Pex5p remains extended in the presence of cargo and Pex14p, the latter proteins being significantly intermingled with the Pex5p moiety. These results suggest that the extended structure of Pex5p may play a role in interactions with other substrates such as lipids and membrane proteins during the formation of functional multiprotein complexes.},
  file      = {:by-author/S/Shiozawa/2009_Shiozawa_25334.pdf:PDF},
  keywords  = {DAMMIN; Experiment; MONSA; SASREF; SAXS},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Shlyakhtenko2007,
  author    = {Shlyakhtenko, Luda S and Gilmore, Jamie and Portillo, Alex and Tamulaitis, Gintautas and Siksnys, Virginijus and Lyubchenko, Yuri L},
  journal   = {Biochemistry},
  title     = {Direct visualization of the EcoRII-DNA triple synaptic complex by atomic force microscopy.},
  year      = {2007},
  pages     = {11128--36},
  volume    = {46},
  abstract  = {Interactions between distantly separated DNA regions mediated by specialized proteins lead to the formation of synaptic protein-DNA complexes. This is a ubiquitous phenomenon which is critical in various genetic processes. Although such interactions typically occur between two sites, interactions among three specific DNA regions have been identified, and a corresponding model has been proposed. Atomic force microscopy was used to test this model for the EcoRII restriction enzyme and provide direct visualization and characterization of synaptic protein-DNA complexes involving three DNA binding sites. The complex appeared in the images as a two-loop structure, and the length measurements proved the site specificity of the protein in the complex. The protein volume measurements showed that an EcoRII dimer is the core of the three-site synaptosome. Other complexes were identified and analyzed. The protein volume data showed that the dimeric form of the protein is responsible for the formation of other types of synaptic complexes as well. The applications of these results to the mechanisms of the protein-DNA interactions are discussed.},
  file      = {2007_Shlyakhtenko_11128.pdf:by-author/S/Shlyakhtenko/2007_Shlyakhtenko_11128.pdf:PDF},
  keywords  = {Restriction Endonucleases (REases)},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Shlyakhtenko2007a,
  author       = {Luda S Shlyakhtenko and Jamie Gilmore and Alex Portillo and Gintautas Tamulaitis and Virginijus Siksnys and Yuri L Lyubchenko},
  journal      = {Biochemistry},
  title        = {Direct visualization of the EcoRII-DNA triple synaptic complex by atomic force microscopy.},
  year         = {2007},
  month        = {Oct},
  number       = {39},
  pages        = {11128--11136},
  volume       = {46},
  abstract     = {Interactions between distantly separated DNA regions mediated by specialized proteins lead to the formation of synaptic protein-DNA complexes. This is a ubiquitous phenomenon which is critical in various genetic processes. Although such interactions typically occur between two sites, interactions among three specific DNA regions have been identified, and a corresponding model has been proposed. Atomic force microscopy was used to test this model for the EcoRII restriction enzyme and provide direct visualization and characterization of synaptic protein-DNA complexes involving three DNA binding sites. The complex appeared in the images as a two-loop structure, and the length measurements proved the site specificity of the protein in the complex. The protein volume measurements showed that an EcoRII dimer is the core of the three-site synaptosome. Other complexes were identified and analyzed. The protein volume data showed that the dimeric form of the protein is responsible for the formation of other types of synaptic complexes as well. The applications of these results to the mechanisms of the protein-DNA interactions are discussed.},
  creationdate = {2011-06-10T00:00:00},
  doi          = {10.1021/bi701123u},
  file         = {2007_Shlyakhtenko_11128.pdf:by-author/S/Shlyakhtenko/2007_Shlyakhtenko_11128.pdf:PDF},
  institution  = {Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, Nebraska 68198-6025, USA.},
  keywords     = {Atomic Force; Chemistry/metabolism; DNA; Deoxyribonucleases; Methods; Microscopy; Models; Molecular; Protein Binding; Type II Site-Specific},
  language     = {eng},
  medline-pst  = {ppublish},
  owner        = {em},
  pmid         = {17845057},
  timestamp    = {2011.06.10},
  url          = {http://dx.doi.org/10.1021/bi701123u},
}

@Article{Shmueli2008,
  author    = {Shmueli, U. and Schiltz, M. and Flack, H. D.},
  journal   = {Acta Crystallographica Section A},
  title     = {Intensity statistics of Friedel opposites},
  year      = {2008},
  pages     = {476--483},
  volume    = {64},
  abstract  = {A previous analysis of the average intensity and mean-square intensity difference of Friedel opposites, confined to the space group P1 [Flack & Shmueli (2007). Acta Cryst. A63, 257-265], is here extended to all the non-centrosymmetric space groups. The present analysis presumes purely non-centrosymmetric content of the unit cell. An important result of this study is that the average intensity and mean-square intensity difference of Friedel opposites have the same values for all the non-centrosymmetric space groups as those previously obtained for the triclinic space group P1. The ratios of average intensity and root-mean-square intensity difference to their triclinic equivalents were derived and exemplified for general as well as for special reflections. For the latter, enhancements were obtained which are shown to be due to those of average intensity and not to a mechanism related to Friedel opposites being explicitly considered.},
  doi       = {10.1107/S0108767308013421},
  file      = {2008_Shmueli_476.pdf:by-author/S/Shmueli/2008_Shmueli_476.pdf:PDF},
  keywords  = {X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2012.12.14},
  creationdate = {2012-12-14T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0108767308013421},
}

@Manuscript{Shu2007,
  author    = {Lan Shu and Xiangzhi He},
  title     = {Hierarchical Visualization of Multidimensional Data},
  year      = {2007},
  keywords  = {Computer Science (CS); Data Presentation},
  file      = {:by-author/S/Shu/2007_Shu.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Shuck2014,
  author     = {Shuck, Justin},
  journal    = {PSU McNair Scholars Online Journal},
  title      = {Open-access crystallography database administration: preparation and upload of 400 structures},
  year       = {2014},
  pages      = {3},
  volume     = {8},
  file       = {[PDF] from pdx.edu:by-author/S/Shuck/2014_Shuck_3.pdf:PDF;Snapshot:by-author/S/Shuck/2014_Shuck_3.html:URL},
  owner      = {saulius},
  shorttitle = {Open-access crystallography database administration},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url        = {http://pdxscholar.library.pdx.edu/mcnair/vol8/iss1/3/?utm_source=pdxscholar.library.pdx.edu%2Fmcnair%2Fvol8%2Fiss1%2F3&utm_medium=PDF&utm_campaign=PDFCoverPages},
  urldate    = {2015-08-31},
}

@Manuscript{Sicard2005,
  author    = {Sicard},
  title     = {A very simple microprocessor},
  year      = {2005},
  abstract  = {This application note gives and introduction to microprocessor architecture. The goal of the project is to build a 4-bit processor at logic level and then to simulate the processor at layout level.},
  file      = {:by-author/S/Sicard/2005_Sicard.pdf:PDF},
  owner     = {saulius},
  timestamp = {2013.03.22},
  creationdate = {2013-03-22T00:00:00},
}

@Article{Siddiqui2001,
  author    = {Siddiqui, A. S. and Dengler, U. and Barton, G. J.},
  journal   = {Bioinformatics (Oxford, England)},
  title     = {3Dee: a database of protein structural domains.},
  year      = {2001},
  pages     = {200--1},
  volume    = {17},
  abstract  = {The 3Dee database is a repository of protein structural domains. It stores alternative domain definitions for the same protein, organises domains into sequence and structural hierarchies, contains non-redundant set(s) of sequences and structures, multiple structure alignments for families of domains, and allows previous versions of the database to be regenerated. AVAILABILITY: 3Dee is accessible on the World Wide Web at the URL http://barton.ebi.ac.uk/servers/3Dee.html.},
  file      = {:by-author/S/Siddiqui/2001_Siddiqui_200.pdf:PDF},
  keywords  = {Protein Domains},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Manuscript{Sidorov2011,
  author    = {Sidorov, S. A. and Shumakov, M. N.},
  title     = {DSSP and Forth. Compare Analysis},
  year      = {2011},
  keywords  = {Computer Science (CS); DSSP; Forth; Programming Languages; Ternary Computers; Ternary Logics},
  url       = {http://brokestream.com/daf.txt},
  file      = {2011_Sidorov.txt:by-author/S/Sidorov/2011_Sidorov.txt:Text},
  owner     = {saulius},
  timestamp = {2015.03.09},
  creationdate = {2015-03-09T00:00:00},
}

@Article{Siegel2004,
  author    = {Siegel, P.H.},
  title     = {Terahertz Technology in Biology and Medicine},
  year      = {2004},
  pages     = {2438},
  file      = {:by-author/S/Siegel/2004_Siegel_2438.pdf:PDF},
  keywords  = {Biology; Biology Applications; IEEE IMS 2004; MTT Transactions; Medical Sciences; Medicine; Microwave Measurement; Microwave Technology; Molecular Line Spectroscopy; Physics; Plasma Diagnostics; Space Science; Terahertz EM Waves; Terahertz Irradiation; Terahertz Measurements; Terahertz Sensing; Terahertz Technology},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@Manual{Sigma2003,
  title        = {Thermolysin from Bacillus thermoproteolyticus rokko},
  author       = {Sigma},
  organization = {Sigma},
  year         = {2003},
  file         = {:by-author/S/Sigma/2003_Sigma_product-sheet.pdf:PDF},
  keywords     = {Microbiology},
  owner        = {em},
  pages        = {product-sheet},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Siksnys2004,
  author    = {Siksnys},
  title     = {Structure and Function of the Tetrameric Restriction Enzymes},
  year      = {2004},
  pages     = {237},
  file      = {:by-author/S/Siksnys/2004_Siksnys_237.pdf:PDF},
  keywords  = {Restriction Endonucleases (REases); Reviews},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Siksnys1999,
  author       = {V. Siksnys and R. Skirgaila and G. Sasnauskas and C. Urbanke and D. Cherny and S. Grazulis and R. Huber},
  journal      = {Journal of molecular biology},
  title        = {The Cfr10I restriction enzyme is functional as a tetramer.},
  year         = {1999},
  month        = {Sep},
  number       = {5},
  pages        = {1105--1118},
  volume       = {291},
  abstract     = {It is thought that most of the type II restriction endonucleases interact with DNA as homodimers. Cfr10I is a typical type II restriction enzyme that recognises the 5'-Pu decreases CCGGPy sequence and cleaves it as indicated by the arrow. Gel-filtration and analytical ultracentrifugation data presented here indicate that Cfr10I is a homotetramer in isolation. The only SfiI restriction enzyme that recognises the long interrupted recognition sequence 5'-GGCCNNNNNGGCC has been previously reported to operate as a tetramer however, its structure is unknown. Analysis of Cfr10I crystals revealed that a single molecule in the asymmetric unit is repeated by D2 symmetry to form a tetramer. To determine whether the packing of the Cfr10I in the crystal reflects the quaternary structure of the protein in solution, the tryptophan W220 residue located at the putative dimer-dimer interface was mutated to alanine, and the structural and functional consequences of the substitution were analysed. Equilibrium sedimentation experiments revealed that, in contrast to the wild-type Cfr10I, the W220A mutant exists in solution predominantly as a dimer. In addition, the tetramer seems to be a catalytically important form of Cfr10I, since the DNA cleavage activity of the W220A mutant is < 0.1\% of that of the wild-type enzyme. Further, analysis of plasmid DNA cleavage suggests that the Cfr10I tetramer is able to interact with two copies of the recognition sequence, located on the same DNA molecule. Indeed, electron microscopy studies demonstrated that two distant recognition sites are brought together through the DNA looping induced by the simultaneous binding of the Cfr10I tetramer to both sites. These data are consistent with the tetramer being a functionally important form of Cfr10I.},
  creationdate = {2016-06-09T00:00:00},
  doi          = {10.1006/jmbi.1999.2977},
  file         = {1999_Siksnys_1105.pdf:by-author/S/Siksnys/1999_Siksnys_1105.pdf:PDF},
  groups       = {sg/Cfr10I},
  institution  = {Institute of Biotechnology, Lithuania. Siksnys@ibt.lt},
  keywords     = {Amino Acid Sequence; Amino Acid Substitution; Binding Sites; Catalysis; Chemistry/genetics/metabolism; Chemistry/genetics/metabolism/ultrastructure; Chromatography; Crystallization; DNA; Deoxyribonucleases; Dimerization; Electron; Escherichia Coli; Gel; Genetics; Microscopy; Models; Molecular; Molecular Sequence Data; Molecular Weight (MW); Mutagenesis; Nucleic Acid; Nucleic Acid Conformation; Plasmids; Protein Conformation; Recombinant Proteins; Repetitive Sequences; Site-Directed; Superhelical; Tetra; Tetramers; Type II Site-Specific; TypeII; Ultracentrifugation},
  language     = {eng},
  medline-pst  = {ppublish},
  owner        = {em},
  pii          = {S0022-2836(99)92977-7},
  pmid         = {10518946},
  timestamp    = {2016.06.09},
  url          = {http://dx.doi.org/10.1006/jmbi.1999.2977},
}

@Article{Siksnys1994,
  author    = {Siksnys, V. and Zareckaja, N. and Vaisvila, R. and Timinskas, A. and Stakenas, P. and Butkus, V. and Janulaitis, A.},
  journal   = {Gene},
  title     = {CAATTG-specific restriction-modification munI genes from Mycoplasma: sequence similarities between R.MunI and R.EcoRI.},
  year      = {1994},
  pages     = {1--8},
  volume    = {142},
  abstract  = {The genes coding for the MunI restriction-modification (R-M) system, which recognize the sequence 5'-CAATTG, have been cloned and expressed in Escherichia coli, and their nucleotide sequences have been determined. The restriction endonuclease (ENase; R.MunI) is encoded by an open reading frame (ORF) of 606 bp, and a 699-bp ORF codes for the methyltransferase (MTase). The two genes are transcribed divergently from a 355-bp region. The gene encoding the ENase is preceded by a short co-linear ORF of 222 bp. The deduced amino acid (aa) sequence of this short ORF (SORF) closely resembles the sequences of a family of regulatory proteins that are associated with other type-II R-M systems. Comparative analysis of the deduced aa sequence of R.MunI revealed several regions of similarity to the EcoRI and RsrI ENases that recognize the GAATTC sequence. The similar mode of interaction of MunI, EcoRI and RsrI with the tetranucleotide AATT, common to the recognition sequences of these ENases, was suggested.},
  file      = {:by-author/S/Siksnys/1994_Siksnys_1.pdf:PDF},
  keywords  = {MunI; TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Silva2011,
  author       = {George Silva and Laurent Poirot and Roman Galetto and Julianne Smith and Guillermo Montoya and Philippe Duchateau and Frédéric Pâques},
  journal      = {Curr Gene Ther},
  title        = {Meganucleases and other tools for targeted genome engineering: perspectives and challenges for gene therapy.},
  year         = {2011},
  month        = {Feb},
  number       = {1},
  pages        = {11--27},
  volume       = {11},
  abstract     = {The importance of safer approaches for gene therapy has been underscored by a series of severe adverse events (SAEs) observed in patients involved in clinical trials for Severe Combined Immune Deficiency Disease (SCID) and Chromic Granulomatous Disease (CGD). While a new generation of viral vectors is in the process of replacing the classical gamma-retrovirus-based approach, a number of strategies have emerged based on non-viral vectorization and/or targeted insertion aimed at achieving safer gene transfer. Currently, these methods display lower efficacies than viral transduction although many of them can yield more than 1\% of engineered cells in vitro. Nuclease-based approaches, wherein an endonuclease is used to trigger site-specific genome editing, can significantly increase the percentage of targeted cells. These methods therefore provide a real alternative to classical gene transfer as well as gene editing. However, the first endonuclease to be in clinic today is not used for gene transfer, but to inactivate a gene (CCR5) required for HIV infection. Here, we review these alternative approaches, with a special emphasis on meganucleases, a family of naturally occurring rare-cutting endonucleases, and speculate on their current and future potential.},
  creationdate = {2011-11-24T00:00:00},
  doi          = {10.2174/156652311794520111},
  file         = {2011_Silva_11.pdf:by-author/S/Silva/2011_Silva_11.pdf:PDF},
  institution  = {Cellectis Genome Surgery, 102 Avenue Gaston Roussel, Romainville Cedex, France.},
  keywords     = {Adverse Effects/trends; Animals; CCR5; Endodeoxyribonucleases; Endonucleases; Etiology; Gene Therapy; Genetic Vectors; Genetics; Genome; HIV Infections; Humans; Insertional; Mice; Mutagenesis; Physiology; Receptors; SCID},
  language     = {eng},
  medline-pst  = {ppublish},
  owner        = {em},
  pii          = {ABS- 58},
  pmid         = {21182466},
  publisher    = {Bentham Science Publishers Ltd.},
  timestamp    = {2011.11.24},
}

@Article{Silvello2015,
  author    = {Silvello, Gianmaria},
  journal   = {D-Lib Magazine},
  title     = {A Methodology for Citing Linked Open Data Subsets},
  year      = {2015},
  issn      = {1082-9873},
  month     = {Jan},
  number    = {1/2},
  volume    = {21},
  abstract  = {In this paper we discuss the problem of data citation with a specific focus on Linked Open Data. We outline the main requirements a data citation methodology must fulfill: (i) uniquely identify the cited objects; (ii) provide descriptive metadata; (iii) enable variable granularity citations; and (iv) produce both human- and machine-readable references. We propose a methodology based on named graphs and RDF quad semantics that allows us to create citation meta-graphs respecting the outlined requirements. We also present a compelling use case based on search engines experimental evaluation data and possible applications of the citation methodology.},
  doi       = {10.1045/january2015-silvello},
  file      = {2015_Silvello.pdf:by-author/S/Silvello/2015_Silvello.pdf:PDF},
  groups    = {sg/Linked Open sg/Data, sg/Methods and tools},
  keywords  = {Data Citation; Linked Open Data; RDF},
  owner     = {saulius},
  publisher = {CNRI Acct},
  timestamp = {2016.11.17},
  creationdate = {2016-11-17T00:00:00},
  url       = {http://dx.doi.org/10.1045/january2015-silvello},
}

@Article{Sims2003,
  author    = {Sims, Gregory E and Kim, Sung-Hou},
  journal   = {Nucleic acids research},
  title     = {Global mapping of nucleic acid conformational space: dinucleoside monophosphate conformations and transition pathways among conformational classes.},
  year      = {2003},
  pages     = {5607--16},
  volume    = {31},
  abstract  = {A global conformational space of 6253 dinucleoside monophosphate (DMP) units consisting of RNA and DNA (free and protein/drug-bound) was 'mapped' using high resolution crystal structures cataloged in the Nucleic Acid Database (NDB). The torsion angles of each DMP were clustered in a reduced three-dimensional space using a classical multi-dimensional scaling method. The mapping of the conformational space reveals nine primary clusters which distinguish among the common A-, B- and Z-forms and their various substates, plus five secondary clusters for kinked or bent structures. Conformational relationships and possible transitional pathways among the substates are also examined using the conformational states of DNA and RNA bound with proteins or drugs as potential pathway intermediates.},
  file      = {2003_Sims_5607.pdf:by-author/S/Sims/2003_Sims_5607.pdf:PDF},
  keywords  = {Readout; Stacking},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Simsek2014,
  author    = {Şimşek, Telem and Akansel, Serkan and Özcan, Şadan and Ceylan, Abdullah},
  journal   = {Ceramics International},
  title     = {Synthesis of {MnFe} 2 {O} 4 nanocrystals by wet-milling under atmospheric conditions},
  year      = {2014},
  pages     = {7953--7956},
  volume    = {40},
  file      = {[PDF] from researchgate.net:by-author/Ş/Şimşek/2014_Şimşek_7953a.pdf:application/pdf;[PDF] from researchgate.net:by-author/Ş/Şimşek/2014_Şimşek_7953.pdf:application/pdf;Snapshot:by-author/Ş/Şimşek/2014_Şimşek_7953a.html:text/html;Snapshot:by-author/Ş/Şimşek/2014_Şimşek_7953.html:text/html},
  groups    = {sg/JAC2009, sg/NAR2012},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/S0272884213017604},
  urldate   = {2015-08-31},
}

@MastersThesis{Simukovic,
  author    = {Simukovic, Elena},
  title     = {Enhanced publications–integration von forschungsdaten beim wissenschaftlichen publizieren},
  file      = {[PDF] from researchgate.net:by-author/S/Simukovic/XXXX_Simukovic.pdf:application/pdf},
  groups    = {sg/NAR2012},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://www.researchgate.net/profile/Elena_Simukovic/publication/257651610_Enhanced_publications__Integration_von_Forschungsdaten_beim_wissenschaftlichen_Publizieren/links/00b7d52595ff5c712e000000.pdf},
  urldate   = {2015-08-31},
}

@MastersThesis{Simukovic2012,
  author    = {Simukovic, Elena},
  title     = {Enhanced publications},
  year      = {2012},
  file      = {[PDF] from hu-berlin.de:by-author/S/Simukovic/2012_Simukovic.pdf:PDF;Snapshot:by-author/S/Simukovic/2012_Simukovic.html:URL},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://edoc.hu-berlin.de/docviews/abstract.php?id=39816},
  urldate   = {2015-08-31},
}

@MastersThesis{Simukovic2012a,
  author           = {Elena Simukovic},
  school           = {Humboldt-Universität zu Berlin, Philosophische Fakultät I, Institut für Bibliotheks- und Informationswissenschaft},
  title            = {{E}nhanced publications – {I}ntegration von {F}orschungsdaten beim wissenschaftlichen {P}ublizieren},
  year             = {2012},
  creationdate     = {2013-01-08T00:00:00},
  file             = {:by-author/S/Simukovic/2012_Simukovic_mscthesis.pdf:PDF},
  keywords         = {Citing COD; Crystallography; Data Access Policy; Data Management; Databases},
  modificationdate = {2024-05-16T08:42:27},
  owner            = {saulius},
  pages            = {mscthesis},
  timestamp        = {2013.01.08},
  url              = {http://edoc.hu-berlin.de/master/simukovic-elena-2012-11-23/PDF/simukovic.pdf},
}

@InProceedings{Singh2008,
  author    = {Singh, Sarvjeet and Chris Mayfield and Sagar Mittal and Sunil Prabhakar and Susanne Hambrusch and Rahul Shah},
  booktitle = {SIGMOD’08},
  title     = {Orion 2.0: Native Support for Uncertain Data},
  year      = {2008},
  month     = {June},
  pages     = {1239--1241},
  abstract  = {Orion is a state-of-the-art uncertain database management system with built-in support for probabilistic data as first class data types. In contrast to other uncertain databases, Orion supports both attribute and tuple uncertainty with arbitrary correlations. This enables the database engine to handle both discrete and continuous pdfs in a natural and accurate manner. The underlying model is closed under the basic relational operators and is consistent with Possible Worlds Semantics. We demonstrate how Orion simplifies the design and enhances the capabilities of two example ap- plications: managing sensor data (continuous uncertainty) and inferring missing values (discrete uncertainty).},
  file      = {:by-author/S/Singh/2008_Singh_1239.pdf:PDF},
  keywords  = {Computer Science (CS); Continuous; Databases},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Singleton2000,
  author    = {Singleton, M. R. and Sawaya, M. R. and Ellenberger, T. and Wigley, D. B.},
  journal   = {Cell},
  title     = {Crystal structure of T7 gene 4 ring helicase indicates a mechanism for sequential hydrolysis of nucleotides.},
  year      = {2000},
  pages     = {589--600},
  volume    = {101},
  abstract  = {We have determined the crystal structure of an active, hexameric fragment of the gene 4 helicase from bacteriophage T7. The structure reveals how subunit contacts stabilize the hexamer. Deviation from expected six-fold symmetry of the hexamer indicates that the structure is of an intermediate on the catalytic pathway. The structural consequences of the asymmetry suggest a "binding change" mechanism to explain how cooperative binding and hydrolysis of nucleotides are coupled to conformational changes in the ring that most likely accompany duplex unwinding. The structure of a complex with a nonhydrolyzable ATP analog provides additional evidence for this hypothesis, with only four of the six possible nucleotide binding sites being occupied in this conformation of the hexamer. This model suggests a mechanism for DNA translocation.},
  file      = {:by-author/S/Singleton/2000_Singleton_589.pdf:PDF},
  keywords  = {{gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Sinha1980,
  author    = {Sinha, N. K. and Morris, C. F. and Alberts, B. M.},
  journal   = {The Journal of biological chemistry},
  title     = {Efficient in vitro replication of double-stranded DNA templates by a purified T4 bacteriophage replication system.},
  year      = {1980},
  pages     = {4290--3},
  volume    = {255},
  abstract  = {A wide variety of double-stranded DNA templates are replicated extensively in an in vitro DNA replication system containing the purified proteins specified by seven T4 bacteriophage DNA replication genes (32, 41, 43, 44, 62, 45, and 61). In favorable conditions, this multiprotein system catalyzes the synthesis of several copies of the input DNA template in a 30- to 60-min incubation. The replication forks produced in vitro move in a highly processive fashion, at approximately the in vivo rate of 500 nucleotides per s. The DNA synthesized on the lagging side of the in vitro replication fork is made discontinuously, as it is in vivo, giving rise to "Okazaki pieces" averaging some 10,000 nucleotides in length; in contrast, DNA is polymerized in a continuous manner on the leading side of the in vitro fork. Although the mechanism by which the seven-protein in vitro DNA replication system propagates replication forks closely resembles the in vivo mechanism, it lacks the capacity to remove RNA primers, to reseal Okazaki pieces, and to initiate replication forks at defined DNA origins; supplementation of the system with additional T4-specific replication proteins will be required to facilitate these latter three functions.},
  file      = {:by-author/S/Sinha/1980_Sinha_4290.pdf:PDF},
  keywords  = {{gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Sinitsina2000,
  author    = {Sinitsina, O. I. and Stoletov, K. V. and Bugreev, D. V. and Maksakova, G. A. and Bugreeva, I. F. and Vasyunina, E. A. and Nevinsky, G. A.},
  journal   = {Medical science monitor : international medical journal of experimental and clinical research},
  title     = {Formation of the D-loop structure complexes between DNA and oligonucleotides and affinity modification of DNA by chemically reactive derivatives of oligonucleotides lead to the recombination.},
  year      = {2000},
  pages     = {653--7},
  volume    = {6},
  file      = {:by-author/S/Sinitsina/2000_Sinitsina_653.pdf:PDF},
  keywords  = {MSM},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Sinkunas2011,
  author    = {Tomas Sinkunas and Giedrius Gasiunas and Christophe Fremaux and Rodolphe Barrangou and Philippe Horvath and Virginijus Siksnys},
  journal   = {The EMBO Journal},
  title     = {{Cas3} is a single-stranded {DNA} nuclease and {ATP}-dependent helicase in the {CRISPR/Cas} immune system},
  year      = {2011},
  pages     = {1--8},
  abstract  = {Clustered regularly interspaced short palindromic repeat (CRISPR) is a recently discovered adaptive prokaryotic immune system that provides acquired immunity against foreign nucleic acids by utilizing small guide crRNAs (CRISPR RNAs) to interfere with invading viruses and plasmids. In Escherichia coli, Cas3 is essential for crRNA-guided interference with virus proliferation. Cas3 contains N-terminal HD phosphohydrolase and C-terminal Superfamily 2 (SF2) helicase domains. Here, we provide the first report of the cloning, expression, purification and in vitro functional analysis of the Cas3 protein of the Streptococcus thermophilus CRISPR4 (Ecoli subtype) system. Cas3 possesses a single-stranded DNA (ssDNA)- stimulated ATPase activity, which is coupled to unwinding of DNA/DNA and RNA/DNA duplexes. Cas3 also shows ATP-independent nuclease activity located in the HD domain with a preference for ssDNA substrates. To dissect the contribution of individual domains, Cas3 separation- of-function mutants (ATPase þ /nucleaseÀ and ATPaseÀ/ nuclease þ ) were obtained by site-directed mutagenesis. We propose that the Cas3 ATPase/helicase domain acts as a motor protein, which assists delivery of the nuclease activity to Cascade–crRNA complex targeting foreign DNA.},
  doi       = {10.1038/emboj.2011.41},
  file      = {:by-author/S/Sinkunas/2011_Sinkunas_1.pdf:PDF},
  groups    = {sg/CRISPR-Cas},
  keywords  = {CRISPR; CRISPR4; Cas3},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Sippl1995,
  author    = {Manfred J Sippl},
  journal   = {Current Opinion in Structural Biology},
  title     = {Knowledge-based potentials for proteins},
  year      = {1995},
  pages     = {229--235},
  volume    = {5},
  abstract  = {Knowledge based potentials and energy functions extracted from a number are of databases of known protein structures. Recent developments have shown that this type of potential i s successful in manyareas of protein structure research. Among these are quality assessment and error recognition of folds and the prediction.of unknown structures by fold-recognition techniques.},
  file      = {1995_Sippl_229.pdf:by-author/S/Sippl/1995_Sippl_229.pdf:PDF},
  keywords  = {Restrains},
  owner     = {saulius},
  timestamp = {2012.05.23},
  creationdate = {2012-05-23T00:00:00},
}

@Article{Sippl1993,
  author    = {Sippl, Manfred J.},
  journal   = {Proteins},
  title     = {Recognition of errors in three-dimensional protein structures},
  year      = {1993},
  pages     = {355--362},
  volume    = {17},
  doi       = {10.1002/prot.340170404},
  file      = {1993_Sippl_355.pdf:by-author/S/Sippl/1993_Sippl_355.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Sistla2004,
  author    = {Sistla, Srivani and Rao, Desirazu N.},
  journal   = {Critical reviews in biochemistry and molecular biology},
  title     = {S-Adenosyl-L-methionine-dependent restriction enzymes.},
  year      = {2004},
  pages     = {1--19},
  volume    = {39},
  abstract  = {Restriction-modification (R-M) enzymes are classified into type I, II, III, and IV, based on their recognition sequence, subunit composition, cleavage position, and cofactor requirements. While the role of S-Adenosyl-L-methionine (AdoMet) as the methyl group donor in the methylation reaction is undisputed, its requirement in DNA cleavage reaction has been subject to intense study. AdoMet is a prerequisite for the DNA cleavage by most type I enzymes known so far, with the exception of R.EcoR124I. A number of new type II restriction enzymes belonging to the type IIB and IIG family were found to show AdoMet dependence for their cleavage reaction. The type III enzymes have been found to require AdoMet for their restriction function. AdoMet functions as an allosteric effector of the DNA cleavage reaction and has been shown to bring about conformational changes in the protein upon binding.},
  file      = {:by-author/S/Sistla/2004_Sistla_1.pdf:PDF},
  keywords  = {Obzor},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Skarzynski2006,
  author    = {Skarzynski, Tadeusz and Thorpe, James},
  journal   = {Acta crystallographica. Section D, Biological crystallography},
  title     = {Industrial perspective on X-ray data collection and analysis.},
  year      = {2006},
  pages     = {102--7},
  volume    = {62},
  file      = {2006_Skarzynski_102.pdf:by-author/S/Skarzynski/2006_Skarzynski_102.pdf:PDF},
  keywords  = {Industrial Crystallography; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Skilling1984,
  author    = {Skilling, J. and Bryan, R.~K.},
  journal   = {Mon. Not. R. astr. Soc},
  title     = {Maximum Entropy Image Reconstruction - General Algorithm},
  year      = {1984},
  pages     = {111},
  volume    = {211},
  adsnote   = {Provided by the SAO/NASA Astrophysics Data System},
  adsurl    = {http://adsabs.harvard.edu/abs/1984MNRAS.211..111S},
  file      = {1984_Skilling_111.pdf:by-author/S/Skilling/1984_Skilling_111.pdf:PDF},
  keywords  = {MaxEnt; Maximum Entropy},
  owner     = {saulius},
  timestamp = {2012.10.05},
  creationdate = {2012-10-05T00:00:00},
  url       = {http://adsabs.harvard.edu/abs/1984MNRAS.211..111S},
}

@Article{Skinner2006,
  author    = {Skinner, John M. and Cowan, Matt and Buono, Rick and Nolan, William and Bosshard, Heinz and Robinson, Howard H. and H{\'{e}}roux, Annie and Soares, Alexei S. and Schneider, Dieter K. and Sweet, Robert M.},
  journal   = {Acta Crystallographica Section D},
  title     = {Integrated software for macromolecular crystallography synchrotron beamlines II: revision, robots and a database},
  year      = {2006},
  pages     = {1340--1347},
  volume    = {62},
  abstract  = {This manuscript chronicles the evolution of software used originally to control a diffractometer at a macromolecular crystallography beamline. The system has been augmented and rewritten. A modular and carefully organized suite of programs now handles the whole experimental environment from a single vantage point. It provides automatic logging of the experiment and communication with the user, all the way from an initial proposal to perform the work to the end of data collection. This has included construction of a relational database to organize all details of the experiment and incorporation of a robotic specimen changer to provide automation for high-throughput applications.},
  doi       = {10.1107/S0907444906030162},
  file      = {2006_Skinner_1340.pdf:by-author/S/Skinner/2006_Skinner_1340.pdf:PDF},
  keywords  = {Crystallography; X-ray Crystallography; Xray Software},
  owner     = {saulius},
  timestamp = {2012.12.20},
  creationdate = {2012-12-20T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444906030162},
}

@Article{Skirgaila1998a,
  author      = {R. Skirgaila and S. Grazulis and D. Bozic and R. Huber and V. Siksnys},
  journal     = {J Mol Biol},
  title       = {Structure-based redesign of the catalytic/metal binding site of Cfr10I restriction endonuclease reveals importance of spatial rather than sequence conservation of active centre residues.},
  year        = {1998},
  month       = {Jun},
  number      = {2},
  pages       = {473--481},
  volume      = {279},
  abstract    = {According to the crystal structure of Cfr10I restriction endonuclease the acidic residues D134, E71 and E204 are clustered together and presumably chelate metal ion(s) at the active site. Indeed, investigation of the DNA cleavage properties of substitutional mutants of Cfr10I D134A, E71Q, E71A and E204Q reveals that D134, E71 and E204 residues are essential for cleavage activity, supporting their active site function. Structural comparison indicates that the D134 residue of Cfr10I spatially overlaps with aspartate residues D91 and D74, from the invariant active site motifs 90PDX19EAK and 73PDX15DIK of EcoRI and EcoRV, respectively. However, structural studies in conjunction with mutational analyses suggest that the sequence motif 133PDX55KX13E corresponds to the active site of Cfr10I, but differs from canonical active site motifs of EcoRI and EcoRV. According to the crystal structure of Cfr10I the serine S188 residue from the 188SVK sequence motif is a spatial equivalent of the acidic residue from the (E/D)XK-part of the active site motif, which is conserved between EcoRI and EcoRV. Site-directed mutagenesis experiments of Cfr10I, however, revealed that the S188 was not so important for catalysis while the E204 residue located 2.8 A away indeed was essential for cleavage, suggesting that the glutamate E204 rather than the S188 residue contributes to the metal binding site in Cfr10I. In addition, model-building studies suggest that mutual interchange of the E204 and S188 residues should lead only to minor positional differences of the carboxylate residues of glutamate side-chains. The double mutant S188E/E204S was therefore prepared by site-directed mutagenesis where the active site motif 133PDX55KX13E of Cfr10I was changed to a canonical motif 133PDX53EVK, which is similar to that of EcoRI and EcoRV. Interestingly, the double mutant S188E/E204S of Cfr10I with redesigned active site structure, exhibited 10\% of Wt cleavage activity in a gamma DNA cleavage assay. Thus, structure guided redesign of the catalytic/metal binding site of Cfr10I, provides novel experimental evidence to suggest that spatial rather than sequence conservation plays the dominant role in the formation of restriction enzyme active sites.},
  doi         = {10.1006/jmbi.1998.1803},
  file        = {1998_Skirgaila_595.pdf:by-author/S/Skirgaila/1998_Skirgaila_595.pdf:PDF;1998_Skirgaila_473.pdf:by-author/S/Skirgaila/1998_Skirgaila_473.pdf:PDF},
  groups      = {sg/Cfr10I},
  institution = {Institute of Biotechnology, Vilnius, Lithuania.},
  keywords    = {Amino Acid Sequence; Base Sequence; Binding Sites; Conserved Sequence; DNA Primers; Deoxyribonuclease EcoRI; Deoxyribonucleases; Escherichia Coli; Metals; Models; Molecular; Mutagenesis; Protein Conformation; Site-Directed; Type II Site-Specific},
  owner       = {em},
  pii         = {S0022-2836(98)91803-4},
  pmid        = {9642051},
  timestamp = {2011.06.08},
  creationdate = {2011-06-08T00:00:00},
  url         = {http://dx.doi.org/10.1006/jmbi.1998.1803},
}

@Article{Skirgaila1998,
  author    = {Skirgaila, R. and Siksnys, V.},
  journal   = {Biological chemistry},
  title     = {Ca2+-ions stimulate DNA binding specificity of Cfr10I restriction enzyme.},
  year      = {1998},
  pages     = {595--8},
  volume    = {379},
  abstract  = {The Cfr10I restriction enzyme recognizes the degenerate hexanucleotide sequence 5'-Pu/CCGGPy-3' and cleaves it as indicated. DNA binding studies of Cfr10I endonuclease were performed using gel mobility shift assay. Analysis of Cfr10I binding to DNA revealed that in the absence of metal ions Cfr10I binds to DNA containing or lacking the recognition sequence with similar low affinity. Addition of Ca2+ to the binding buffer stimulated manifestation of DNA binding specificity of Cfr10I.},
  file      = {:by-author/S/Skirgaila/1998_Skirgaila_595.pdf:PDF},
  groups    = {sg/Cfr10I},
  keywords  = {Tetra; TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Skolnick2006,
  author    = {Jeffrey Skolnick},
  journal   = {Current Opinion in Structural Biology},
  title     = {In quest of an empirical potential for protein structure prediction},
  year      = {2006},
  issn      = {0959-440X},
  note      = {<ce:title>Theory and simulation/Macromolecular assemblages</ce:title> <ce:subtitle>Joel Janin and Michael Levitt/Edward H Egelman and Andrew GW Leslie</ce:subtitle>},
  number    = {2},
  pages     = {166--171},
  volume    = {16},
  abstract  = {Key to successful protein structure prediction is a potential that recognizes the native state from misfolded structures. Recent advances in empirical potentials based on known protein structures include improved reference states for assessing random interactions, sidechain-orientation-dependent pair potentials, potentials for describing secondary or supersecondary structural preferences and, most importantly, optimization protocols that sculpt the energy landscape to enhance the correlation between native-like features and the energy. Improved clustering algorithms that select native-like structures on the basis of cluster density also resulted in greater prediction accuracy. For template-based modeling, these advances allowed improvement in predicted structures relative to their initial template alignments over a wide range of target–template homology. This represents significant progress and suggests applications to proteome-scale structure prediction.},
  doi       = {10.1016/j.sbi.2006.02.004},
  file      = {2006_Skolnick_166.pdf:by-author/S/Skolnick/2006_Skolnick_166.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.05.15},
  creationdate = {2012-05-15T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/S0959440X06000376},
}

@Article{Skowron2003,
  author    = {Skowron, Piotr M. and Majewski, Jarosław and Zylicz-Stachula, Agnieszka and Rutkowska, Sylwia M. and Jaworowska, Izabela and Harasimowicz-Słowińska, Renata I.},
  journal   = {Nucleic acids research},
  title     = {A new Thermus sp. class-IIS enzyme sub-family: isolation of a 'twin' endonuclease TspDTI with a novel specificity 5'-ATGAA(N(11/9))-3', related to TspGWI, TaqII and Tth111II.},
  year      = {2003},
  pages     = {e74},
  volume    = {31},
  abstract  = {The TspDTI restriction endonuclease, which shows a novel recognition specificity 5'-ATGAA(N(11/9))-3', was isolated from Thermus sp. DT. TspDTI appears to be a 'twin' of restriction endonuclease TspGWI from Thermus sp. GW, as we have previously reported. TspGWI was isolated from the same location as TspDTI, it recognizes a related sequence 5'-ACGGA(N(11/9))-3' and has conserved cleavage positions. Both enzymes resemble two other class-IIS endonucleases from Thermus sp.: TaqII and Tth111II. N-terminal amino acid sequences of TspGWI tryptic peptides exhibit 88.9-100% similarity to the TaqII sequence. All four enzymes were purified to homogeneity; their polypeptide sizes (114.5-122 kDa) make them the largest class-IIS restriction endonucleases known to date. The existence of a Thermus sp. sub-family of class-IIS restriction endonucleases of a common origin is herein proposed.},
  file      = {:by-author/S/Skowron/2003_Skowron_e74.pdf:PDF},
  keywords  = {Restriction Endonucleases (REases); TspDTI; TspGWI},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Skowronek2012,
  author    = {Skowronek, Krzysztof and Boniecki, Michal J. and Kluge, Boguslaw and Bujnicki, Janusz M.},
  journal   = {Nucleic Acids Research},
  title     = {Rational engineering of sequence specificity in {R.MwoI} restriction endonuclease},
  year      = {2012},
  pages     = {8579–8592},
  volume    = {40},
  abstract  = {R.MwoI is a Type II restriction endonucleases enzyme (REase), which specifically recognizes a palindromic interrupted DNA sequence 50 -GCNNNNNNNGC-30 (where N indicates any nucleotide), and hydrolyzes the phosphodiester bond in the DNA between the 7th and 8th base in both strands. R.MwoI exhibits remote sequence similarity to R.BglI, a REase with known structure, which recognizes an interrupted palindromic target 50 -GCCNNNNNGGC-30 . A homology model of R.MwoI in complex with DNA was constructed and used to predict functionally important amino acid residues that were subsequently targeted by mutagenesis. The model, together with the supporting experimental data, revealed regions important for recognition of the common bases in DNA sequences recognized by R.BglI and R.MwoI. Based on the bioinformatics analysis, we designed substitutions of the S310 residue in R.MwoI to arginine or glutamic acid, which led to enzyme variants with altered sequence selectivity compared with the wild-type enzyme. The S310R variant of R.MwoI preferred the 50 -GCCNNNNNGGC-30 sequence as a target, similarly to R.BglI, whereas the S310E variant preferentially cleaved a subset of the MwoI sites, depending on the identity of the 3rd and 9th nucleotide residues. Our results represent a case study of a REase sequence specificity alteration by a single amino acid substitution, based on a theoretical model in the absence of a crystal structure.},
  doi       = {10.1093/nar/gks570},
  file      = {:by-author/S/Skowronek/2012_Skowronek_8579.pdf:PDF},
  keywords  = {MwoI; Restriction Endonucleases (REases); TypeII},
  owner     = {em},
  timestamp = {2013.01.17},
  creationdate = {2013-01-17T00:00:00},
}

@Article{Skubak2004,
  author    = {Skub{\'{a}}k, Pavol and Murshudov, Garib N. and Pannu, Navraj S.},
  journal   = {Acta Crystallographica Section D},
  title     = {Direct incorporation of experimental phase information in model refinement},
  year      = {2004},
  pages     = {2196--2201},
  volume    = {60},
  doi       = {10.1107/S0907444904019079},
  file      = {ba5062.pdf:by-author/S/Skubak/2004_Skubak_2196.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444904019079},
}

@Article{Skubak2013,
  author    = {Skubák, Pavol and Pannu, Navraj S.},
  journal   = {Nat Commun},
  title     = {Automatic protein structure solution from weak X-ray data},
  year      = {2013},
  pages     = {2777},
  volume    = {4},
  abstract  = {Determining new protein structures from X-ray diffraction data at low resolution or with a weak anomalous signal is a difficult and often an impossible task. Here we propose a multivariate algorithm that simultaneously combines the structure determination steps. In tests on over 140 real data sets from the protein data bank, we show that this combined approach can automatically build models where current algorithms fail, including an anisotropically diffracting 3.88 Å RNA polymerase II data set. The method seamlessly automates the process, is ideal for non-specialists and provides a mathematical framework for successfully combining various sources of information in image processing.},
  comment   = {Supplementary information available for this article at http://www.nature.com/ncomms/2013/131115/ncomms3777/suppinfo/ncomms3777_S1.html},
  file      = {2013_Skubák_2777.pdf:by-author/S/Skubak/2013_Skubák_2777.pdf:PDF},
  keywords  = {AutoSol; Automated Structure Solution; BUCCANEER; CRANK; Data Management; PARROT; PHENIX; Protein Crystallography; REFMAC; X-ray Crystallography},
  owner     = {saulius},
  publisher = {Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},
  timestamp = {2013.11.25},
  creationdate = {2013-11-25T00:00:00},
  url       = {http://dx.doi.org/10.1038/ncomms3777},
}

@InProceedings{Smalley2011,
  author    = {Stephen Smalley},
  title     = {The Case for SE Android},
  year      = {2011},
  comment   = {The Case for SE Android Stephen Smalley sds@tycho.nsa.gov Trust Mechanisms (R2X) National Security Agency 1},
  file      = {:by-author/S/Smalley/2011_Smalley.pdf:PDF},
  owner     = {saulius},
  timestamp = {2013.08.10},
  creationdate = {2013-08-10T00:00:00},
}

@Article{Smart2012,
  author    = {Smart, Oliver S. and Womack, Thomas O. and Flensburg, Claus and Keller, Peter and Paciorek, W{\l}odek and Sharff, Andrew and Vonrhein, Clemens and Bricogne, G{\'{e}}rard},
  journal   = {Acta Crystallographica Section D},
  title     = {Exploiting structure similarity in refinement: automated NCS and target-structure restraints in {\it BUSTER}},
  year      = {2012},
  month     = {Apr},
  number    = {4},
  pages     = {368--380},
  volume    = {68},
  abstract  = {Maximum-likelihood X-ray macromolecular structure refinement in {\it BUSTER} has been extended with restraints facilitating the exploitation of structural similarity. The similarity can be between two or more chains within the structure being refined, thus favouring NCS, or to a distinct `target' structure that remains fixed during refinement. The~local structural similarity restraints (LSSR) approach considers all distances less than 5.5{\AA} between pairs of atoms in the chain to be restrained. For each, the difference from the distance between the corresponding atoms in the related chain is found. LSSR applies a restraint penalty on each difference. A functional form that reaches a plateau for large differences is used to avoid the restraints distorting parts of the structure that are not similar. Because LSSR are local, there is no need to separate out domains. Some restraint pruning is still necessary, but this has been automated. LSSR have been available to academic users of {\it BUSTER} since 2009 with the easy-to-use {\tt -autoncs} and {\tt -{\-}target target.pdb} options. The~use of LSSR is illustrated in the re-refinement of PDB entries 5rnt, where {\tt -target} enables the correct ligand-binding structure to be found, and 1osg, where {\tt -autoncs} contributes to the location of an additional copy of the cyclic peptide ligand.},
  doi       = {10.1107/S0907444911056058},
  file      = {2012_Smart_368.pdf:by-author/S/Smart/2012_Smart_368.pdf:PDF},
  keywords  = {BUSTER; Local Structural Similarity Restraints; Macromolecular Crystallography; NCS Restraints; Refinement Restrains; Target-structure Restraints},
  owner     = {saulius},
  timestamp = {2016.09.28},
  creationdate = {2016-09-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444911056058},
}

@Article{Smiley2006,
  author    = {Smiley, R. Derike and Hammes, Gordon G.},
  journal   = {Chemical reviews},
  title     = {Single molecule studies of enzyme mechanisms.},
  year      = {2006},
  pages     = {3080--94},
  volume    = {106},
  file      = {:by-author/S/Smiley/2006_Smiley_3080.pdf:PDF},
  keywords  = {{gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Smiley2006a,
  author    = {Smiley, R. Derike and Zhuang, Zhihao and Benkovic, Stephen J. and Hammes, Gordon G.},
  journal   = {Biochemistry},
  title     = {Single-molecule investigation of the T4 bacteriophage DNA polymerase holoenzyme: multiple pathways of holoenzyme formation.},
  year      = {2006},
  pages     = {7990--7},
  volume    = {45},
  abstract  = {In T4 bacteriophage, the DNA polymerase holoenzyme is responsible for accurate and processive DNA synthesis. The holoenzyme consists of DNA polymerase gp43 and clamp protein gp45. To form a productive holoenzyme complex, clamp loader protein gp44/62 is required for the loading of gp45, along with MgATP, and also for the subsequent binding of polymerase to the loaded clamp. Recently published evidence suggests that holoenzyme assembly in the T4 replisome may take place via more than one pathway [Zhuang, Z., Berdis, A. J., and Benkovic, S. J. (2006) Biochemistry 45, 7976-7989]. To demonstrate unequivocally whether there are multiple pathways leading to the formation of a productive holoenzyme, single-molecule fluorescence microscopy has been used to study the potential clamp loading and holoenzyme assembly pathways on a single-molecule DNA substrate. The results obtained reveal four pathways that foster the formation of a functional holoenzyme on DNA: (1) clamp loader-clamp complex binding to DNA followed by polymerase, (2) clamp loader binding to DNA followed by clamp and then polymerase, (3) clamp binding to DNA followed by clamp loader and then polymerase, and (4) polymerase binding to DNA followed by the clamp loader-clamp complex. In all cases, MgATP is required. The possible physiological significance of the various assembly pathways is discussed in the context of replication initiation and lagging strand synthesis during various stages of T4 phage replication.},
  file      = {:by-author/S/Smiley/2006_Smiley_7990.pdf:PDF},
  keywords  = {Replisoma; {gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Smith2005,
  author    = {Smith, 3rd, Amos B. and Rucker, Paul V. and Brouard, Ignacio and Freeze, B. Scott and Xia, Shujun and Horwitz, Susan Band},
  journal   = {Organic letters},
  title     = {Design, synthesis, and biological evaluation of potent discodermolide fluorescent and photoaffinity molecular probes.},
  year      = {2005},
  pages     = {5199--202},
  volume    = {7},
  abstract  = {[structure: see text] The design, synthesis, and biological evaluation of a series of (+)-discodermolide molecular probes possessing photoaffinity and fluorescent appendages has been achieved. Stereoselective olefin cross-metathesis comprised a key tactic for construction of two of the molecular probes. Three photoaffinity probes were radiolabeled with tritium.},
  file      = {:by-author/S/Smith/2005_Smith_5199.pdf:PDF},
  keywords  = {Bioconjugation},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@Article{Smith2016,
  author    = {Smith, Arfon M. and Katz, Daniel S. and Niemeyer, Kyle E.},
  journal   = {PeerJ Computer Science},
  title     = {Software citation principles},
  year      = {2016},
  issn      = {2376-5992},
  month     = sep,
  pages     = {e86},
  volume    = {2},
  abstract  = {Software is a critical part of modern research and yet there is little support across the scholarly ecosystem for its acknowledgement and citation. Inspired by the activities of the FORCE11 working group focused on data citation, this document summarizes the recommendations of the FORCE11 Software Citation Working Group and its activities between June 2015 and April 2016. Based on a review of existing community practices, the goal of the working group was to produce a consolidated set of citation principles that may encourage broad adoption of a consistent policy for software citation across disciplines and venues. Our work is presented here as a set of software citation principles, a discussion of the motivations for developing the principles, reviews of existing community practice, and a discussion of the requirements these principles would place upon different stakeholders. Working examples and possible technical solutions for how these principles can be implemented will be discussed in a separate paper.},
  doi       = {10.7717/peerj-cs.86},
  file      = {2016_Smith_e86.pdf:by-author/S/Smith/2016_Smith_e86.pdf:PDF},
  keywords  = {Attribution; Software Citation; Software Credit},
  owner     = {saulius},
  timestamp = {2016.10.16},
  creationdate = {2016-10-16T00:00:00},
  url       = {https://doi.org/10.7717/peerj-cs.86},
}

@Article{Smith1970,
  author    = {Smith, Hamilton O. and Welcox, K.W.},
  journal   = {Journal of Molecular Biology},
  title     = {A Restriction enzyme from Hemophilus influenzae. I. Purification and general properties},
  year      = {1970},
  issn      = {0022-2836},
  month     = {Jul},
  number    = {2},
  pages     = {379--391},
  volume    = {51},
  abstract  = {Extracts of Hemophilus inJEuenzue strain Rd contain an endonuclease activity which produces a rapid decrease in the specific viscosity of a variety of foreign native DNA’s; the specific viscosity of H. inJluenzae DNA is not altered under the same conditions. This “restriction” endonuclease activity has been purified approximately 2OO-fold. The purified enzyme contains no detectable exo- or endonucleolytic activity against H. influenzae DNA. However, with native phage T7 DNA as substrate, it produces about 40 double-strand 5’-phosphoryl, 3’-hydroxyl cleavages. The limit product has an average length of about 1000 nucleotide pairs and contains no single-strand breaks. The enzyme is inactive on denatured DNA and it requires no special co-factors other than magnesium ions.},
  doi       = {10.1016/0022-2836(70)90149-X},
  file      = {1970_Smith_379.pdf:by-author/S/Smith/1970_Smith_379.pdf:PDF},
  keywords  = {HindII; History; Restriction Endonucleases (REases)},
  owner     = {saulius},
  pmid      = {5312500},
  publisher = {Elsevier BV},
  pubmedurl = {https://www.ncbi.nlm.nih.gov/pubmed/5312500},
  timestamp = {2016.12.04},
  creationdate = {2016-12-04T00:00:00},
  url       = {http://dx.doi.org/10.1016/0022-2836(70)90149-X},
}

@Article{Smith1964,
  author    = {J. F. Smith and V. L. Schneider},
  journal   = {Journal of the Less Common Metals},
  title     = {Anisotropic thermal expansion of indium},
  year      = {1964},
  issn      = {0022-5088},
  pages     = {17 - 22},
  volume    = {7},
  abstract  = {The anisotropic thermal expansion of three grades of indium and dilute alloys of thallium, cadmium, tin, and lead in indium were measured over the temperature range 80°–300°K. The expansion behavior of the three grades of indium and of the indium-thallium alloy was essentially the same. The expansion coefficients of the indium-tin and indium-lead alloys were comparable but were more positive than the values for indium in the upper portion of the temperature range. The expansion of the indium-cadmium alloy was comparable to that of indium parallel to the c-direction but was significantly greater in the perpendicular direction. It is likely that electronic considerations are primarily responsible for the observed expansion behavior. Qualitative considerations show no inconsistency between this interpretation of the electronic role in the expansion of indium and the currently known details of the geometry of the Fermi surface.},
  doi       = {10.1016/0022-5088(64)90013-X},
  file      = {:by-author/S/Smith/1964_Smith_17.pdf:PDF},
  keywords  = {For COD Deposition; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2011.11.03},
  creationdate = {2011-11-03T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/002250886490013X},
}

@Article{Smith1976,
  author    = {J. Maynard Smith},
  journal   = {American Scientist},
  title     = {Evolution and the Theory of Games},
  year      = {1976},
  pages     = {41--45},
  volume    = {64},
  abstract  = {In situations characterized by conflict of interest, the best strategy to adopt depends on what others are doing},
  file      = {:by-author/S/Smith/1976_Smith_41.pdf:PDF},
  groups    = {sg/Bayesian},
  keywords  = {Bayesian Statistics},
  owner     = {saulius},
  timestamp = {2012.09.30},
  creationdate = {2012-09-30T00:00:00},
  url       = {http://www.jstor.org/stable/27847040},
}

@Article{Smith1999,
  author    = {Smith, K S and Jakubzick, C and Whittam, T S and Ferry, J G},
  journal   = {Proceedings of the National Academy of Sciences of the United States of America},
  title     = {Carbonic anhydrase is an ancient enzyme widespread in prokaryotes.},
  year      = {1999},
  pages     = {15184--9},
  volume    = {96},
  abstract  = {Carbonic anhydrases catalyze the reversible hydration of CO(2) and are ubiquitous in highly evolved eukaryotes. The recent identification of a third class of carbonic anhydrase (gamma class) in a methanoarchaeon and our present finding that the beta class also extends into thermophilic species from the Archaea domain led us to initiate a systematic search for these enzymes in metabolically and phylogenetically diverse prokaryotes. Here we show that carbonic anhydrase is widespread in the Archaea and Bacteria domains, and is an ancient enzyme. The occurrence in chemolithoautotrophic species occupying deep branches of the universal phylogenetic tree suggests a role for this enzyme in the proposed autotrophic origin of life. The presence of the beta and gamma classes in metabolically diverse species spanning the Archaea and Bacteria domains demonstrates that carbonic anhydrases have a far more extensive and fundamental role in prokaryotic biology than previously recognized.},
  file      = {1999_Smith_15184.pdf:by-author/S/Smith/1999_Smith_15184.pdf:PDF},
  groups    = {sg/reviews},
  keywords  = {Carbonic Anhydrases},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Presentation{Smith2001,
  author    = {Smith, M. A.},
  title     = {Operating Systems Introduction},
  year      = {2001},
  file      = {:by-author/S/Smith/2001_Smith_handouts.pdf:PDF},
  keywords  = {Computer Science (CS); Operating Systems},
  owner     = {saulius},
  pages     = {handouts},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Smith2008,
  author    = {Smith, Paul E.},
  journal   = {The Journal of Chemical Physics},
  title     = {On the Kirkwood–Buff inversion procedure},
  year      = {2008},
  pages     = {124509},
  volume    = {129},
  abstract  = {A general approach is presented to express the Kirkwood–Buff integrals, the central component of the Kirkwood–Buff theory of solutions, in terms of thermodynamic properties of solution mixtures. A general expression valid for any number of components is provided in terms of matrix cofactors, while explicit expressions are given for three and four component mixtures. The corresponding symmetric ideal solution values are also presented for four and higher component mixtures.},
  doi       = {10.1063/1.2982171},
  file      = {2008_Smith_124509.pdf:by-author/S/Smith/2008_Smith_124509.pdf:PDF},
  keywords  = {Kirkwood-Buff Theory; Statistical Physics; Theory of Solutions},
  owner     = {saulius},
  timestamp = {2015.03.13},
  creationdate = {2015-03-13T00:00:00},
  url       = {http://scitation.aip.org/content/aip/journal/jcp/129/12/10.1063/1.2982171},
}

@Manuscript{Smith2007,
  author       = {Ray Smith},
  title        = {An Overview of the Tesseract OCR Engine},
  year         = {2007},
  keywords     = {Algorithms; OCR; Tesseract OCR},
  organization = {Google Inc.},
  url          = {http://static.googleusercontent.com/media/research.google.com/en//pubs/archive/33418.pdf},
  abstract     = {The Tesseract OCR engine, as was the HP Research Prototype in the UNLV Fourth Annual Test of OCR Accuracy[1], is described in a comprehensive overview. Emphasis is placed on aspects that are novel or at least unusual in an OCR engine, including in particular the line finding, features/classification methods, and the adaptive classifier.},
  file         = {:by-author/S/Smith/2007_Smith.pdf:PDF},
  groups       = {sg/OCR engines},
  owner        = {saulius},
  timestamp = {2014.11.06},
  creationdate = {2014-11-06T00:00:00},
}

@Article{Smith2014,
  author    = {Smith, Rachel M. and Pernstich, Christian and Halford, Stephen E.},
  journal   = {Nucleic Acids Research},
  title     = {{TstI}, a Type {II} restriction–modification protein with {DNA} recognition, cleavage and methylation functions in a single polypeptide},
  year      = {2014},
  pages     = {5809--5822},
  volume    = {42},
  abstract  = {Type II restriction–modification systems cleave and methylate DNA at specific sequences. However, the Type IIB systems look more like Type I than conventional Type II schemes as they employ the same protein for both restriction and modification and for DNA recognition. Several Type IIB proteins, including the archetype BcgI, are assemblies of two polypeptides: one with endonuclease and methyltransferase roles, another for DNA recognition. Conversely, some IIB proteins express all three functions from separate segments of a single polypeptide. This study analysed one such single-chain protein, TstI. Comparison with BcgI showed that the one- and the two-polypeptide systems differ markedly. Unlike the heterologous assembly of BcgI, TstI forms a homotetramer. The tetramer bridges two recognition sites before eventually cutting the DNA in both strands on both sides of the sites, but at each site the first double-strand break is made long before the second. In contrast, BcgI cuts all eight target bonds at two sites in a single step. TstI also differs from BcgI in either methylating or cleaving unmodified sites at similar rates. The site may thus be modified before TstI can make the second double-strand break. TstI MTase acts best at hemi-methylated sites.},
  doi       = {10.1093/nar/gku187},
  eprint    = {http://nar.oxfordjournals.org/content/42/9/5809.full.pdf+html},
  file      = {:by-author/S/Smith/2014_Smith_5809.pdf:PDF},
  groups    = {sg/TstI},
  keywords  = {Restriction Endonucleases (REases)},
  owner     = {andrius},
  timestamp = {2014.09.04},
  creationdate = {2014-09-04T00:00:00},
  url       = {http://nar.oxfordjournals.org/content/42/9/5809.abstract},
}

@Article{Smith1981,
  author    = {T.F. Smith and M.S. Waterman},
  journal   = {Journal of Molecular Biology},
  title     = {Identification of common molecular subsequences},
  year      = {1981},
  issn      = {0022-2836},
  pages     = {195--197},
  volume    = {147},
  abstract  = {The identification of maximally homologous subsequences among sets of long sequences is an important problem in molecular sequence analysis. The problem is straightforward only if one restricts consideration to contiguous subsequences (segments)containing no internal deletions or insertions. The more general problem has its solution in an extension of sequence metrics (Sellers 1974; Waterman et al., 1976) developed to measure the minimum number of “events” required t o convert one sequence into another. These developments in the modern sequence analysis began with the heuristic homology algorithm of Needleman & Wunsch (1970) which first introduced an iterative matrix method of calculation. Numerous other heuristic algorithms have been suggested including those of Fitch (1966)and Dayhoff (1969). More mathemat- ically rigorous algorithms were suggested by Sankoff (1972), Reichert et al. (1973) and Beyer et al. (1979), but these were generally not biologically satisfying or interpretable. Success came with Sellers (1974) development of a true metric mewure of the distance between sequences. This metric was later generalized by Waterman et al. (1976) to include deletions/insertions of arbitrary length. This metric represents the minimum number of “mutational events” required to convert one sequence into another. It is of interest t o note that Smith et al. (1980) have recently shown that under some conditions the generalized Sellers metric is equivalent t o the original homology algorithm of Needleman & Wunsch (1970). In this letter we extend the above ideas to find a pair of segments, one from each of two long sequences, such that there is no other pair of segments with greater similarity (homology). The similarity measure used here allows for arbitrary length deletions and insertions.},
  doi       = {10.1016/0022-2836(81)90087-5},
  file      = {1981_Smith_195.pdf:by-author/S/Smith/1981_Smith_195.pdf:PDF},
  owner     = {saulius},
  timestamp = {2013.04.01},
  creationdate = {2013-04-01T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/0022283681900875},
}

@Article{Smrcok2013,
  author    = {Smrcok, Lubomır and Mach, Pavel and Le Bail, Armel},
  journal   = {Acta Crystallographica Section B: Structural Science, Crystal Engineering and Materials},
  title     = {Decafluorocyclohex-1-ene at 4.2 {K}-crystal structure and theoretical analysis of weak interactions},
  year      = {2013},
  pages     = {395--404},
  volume    = {69},
  file      = {[PDF] from researchgate.net:by-author/S/Smrcok/2013_Smrcok_395.pdf:application/pdf},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://scripts.iucr.org/cgi-bin/paper_yard?eb5026},
  urldate   = {2015-08-31},
}

@Article{Smrcok2013a,
  author    = {Smrčok, Lubomír and Mach, Pavel and Le Bail, Armel},
  journal   = {Acta crystallographica Section B, Structural science, crystal engineering and materials},
  title     = {Decafluorocyclohex-1-ene at 4.2 K - crystal structure and theoretical analysis of weak interactions.},
  year      = {2013},
  pages     = {395--404},
  volume    = {69},
  abstract  = {The crystal structure of 1,2,3,3,4,4,5,5,6,6-decafluorocyclohex-1-ene (decafluorocyclohex-1-ene, C6F10) was solved in direct space from neutron powder diffraction data previously collected at 4.2 K [Pawley, G. S. (1981). J. Appl. Cryst. 14, 357-361] and refined by energy minimization in the solid state. To optimize the positions of the 64 atoms in the monoclinic computational cell the PBESOL and hybrid PBE0 functionals were used. The crystal structure of the title compound, which is liquid at room temperature, is built of antiparallel pairs of molecules assembled into molecular columns stacked along the a axis. Dominating the crystal-building forces are weak intermolecular dispersion interactions. Bonding conditions in the structure were analysed by theoretical molecular calculations of representative next-neighbor molecular dimers carried out using dispersion-corrected density functional theory (DFT) functionals and the SCS-MP2 wavefunction method. The largest interaction energy is of the order of ∼ 21 kJ mol(-1), above the interaction energy of a benzene dimer (11.3 kJ mol(-1)) and close to that of a water dimer (20.9 kJ mol(-1)). The interaction energy for the second most stable dimer can be compared with either that of a benzene dimer or of a C-H...π hydrogen bond. The remaining five weakly interacting dimers (∼ 4.2-8.4 kJ mol(-1)) can be characterized as having stronger interactions than those of methane dimers (-2.2 kJ mol(-1)), but weaker than those of benzene molecule pairs or weak C-H...C interactions for instance.},
  file      = {:by-author/S/Smrčok/2013_Smrcok_395.pdf:PDF},
  owner     = {saulius},
  timestamp = {2014.03.23},
  creationdate = {2014-03-23T00:00:00},
}

@Article{Snyder2013,
  author    = {Phillip W. Snyder and Matthew R. Lockett and Demetri T. Moustakas and George M. Whitesides},
  journal   = {The European Physical Journal Special Topics},
  title     = {Is it the shape of the cavity, or the shape of the water in the cavity?},
  year      = {2013},
  pages     = {853--891},
  volume    = {223},
  abstract  = {Historical interpretations of the thermodynamics character- izing biomolecular recognition have marginalized the role of water. An important (even, perhaps, dominant) contribution to molecular recognition in water comes from the “hydrophobic effect,” in which non-polar portions of a ligand interact preferentially with non-polar regions of a protein. Water surrounds the ligand, and water fills the binding pocket of the protein: when the protein-ligand complex forms, and hydrophobic surfaces of the binding pocket and the ligand ap- proach one another, the molecules (and hydrogen-bonded networks of molecules) of water associated with both surfaces rearrange and, in part, entirely escape into the bulk solution. It is now clear that neither of the two most commonly cited rationalizations for the hydrophobic effect–an entropy-dominated hydrophobic effect, in which ordered waters at the surface of the ligand, and water at the surface of the protein, are released to the bulk upon binding, and a “lock-and-key” model, in which the surface of a ligand interacts directly with a sur- face of a protein having a complementary shape–can account for water- mediated interactions between the ligand and the protein, and neither is sufficient to account for the experimental observation of both entropy- and enthalpy-dominated hydrophobic effects. What is now clear is that there is no single hydrophobic effect, with a universally applicable, com- mon, thermodynamic description: different processes (i.e., partitioning between phases of different hydrophobicity, aggregation in water, and binding) with different thermodynamics, depend on the molecular-level details of the structures of the molecules involved, and of the aggregates that form. A “water-centric” description of the hydrophobic effect in biomolecular recognition focuses on the structures of water surrounding the ligand, and of water filling the binding pocket of the protein, both before and after binding. This view attributes the hydrophobic effect to changes in the free energy of the networks of hydrogen bonds that are formed, broken, or re-arranged when two hydrophobic surfaces approach (but do not necessarily contact) one another. The details of the molecular topography (and the polar character) of the mole- cular surfaces play an important role in determining the structure of these networks of hydrogen-bonded waters, and in the thermodynamic description of the hydrophobic effect(s). Theorists have led the for- mulation of this “water-centric view”, although experiments are now supplying support for it. It poses complex problems for would-be “de- signers” of protein-ligand interactions, and for so-called “rational drug design”.},
  doi       = {10.1140/epjst/e2013-01818-y},
  file      = {:by-author/S/Snyder/2013_snyder_853.pdf:PDF},
  owner     = {alexey},
  timestamp = {2016.03.01},
  creationdate = {2016-03-01T00:00:00},
}

@Article{Snyder2011,
  author       = {Phillip W Snyder and Jasmin Mecinovic and Demetri T Moustakas and Samuel W Thomas and Michael Harder and Eric T Mack and Matthew R Lockett and Annie Héroux and Woody Sherman and George M Whitesides},
  journal      = {Proc Natl Acad Sci U S A},
  title        = {Mechanism of the hydrophobic effect in the biomolecular recognition of arylsulfonamides by carbonic anhydrase.},
  year         = {2011},
  month        = {Nov},
  number       = {44},
  pages        = {17889--17894},
  volume       = {108},
  abstract     = {The hydrophobic effect--a rationalization of the insolubility of nonpolar molecules in water--is centrally important to biomolecular recognition. Despite extensive research devoted to the hydrophobic effect, its molecular mechanisms remain controversial, and there are still no reliably predictive models for its role in protein-ligand binding. Here we describe a particularly well-defined system of protein and ligands--carbonic anhydrase and a series of structurally homologous heterocyclic aromatic sulfonamides--that we use to characterize hydrophobic interactions thermodynamically and structurally. In binding to this structurally rigid protein, a set of ligands (also defined to be structurally rigid) shows the expected gain in binding free energy as hydrophobic surface area is added. Isothermal titration calorimetry demonstrates that enthalpy determines these increases in binding affinity, and that changes in the heat capacity of binding are negative. X-ray crystallography and molecular dynamics simulations are compatible with the proposal that the differences in binding between the homologous ligands stem from changes in the number and organization of water molecules localized in the active site in the bound complexes, rather than (or perhaps in addition to) release of structured water from the apposed hydrophobic surfaces. These results support the hypothesis that structured water molecules--including both the molecules of water displaced by the ligands and those reorganized upon ligand binding--determine the thermodynamics of binding of these ligands at the active site of the protein. Hydrophobic effects in various contexts have different structural and thermodynamic origins, although all may be manifestations of the differences in characteristics of bulk water and water close to hydrophobic surfaces.},
  creationdate = {2016-03-01T00:00:00},
  doi          = {10.1073/pnas.1114107108},
  file         = {:by-author/S/Snyder/2011_Snyder_17889.pdf:PDF},
  institution  = {Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA.},
  keywords     = {Binding Sites; Calorimetry; Carbonic Anhydrases; Crystallography; Metabolism; Molecular Dynamics Simulation; Sulfonamides; Thermodynamics; X-Ray},
  language     = {eng},
  medline-pst  = {ppublish},
  owner        = {alexey},
  pii          = {1114107108},
  pmid         = {22011572},
  timestamp    = {2016.03.01},
  url          = {http://dx.doi.org/10.1073/pnas.1114107108},
}

@Article{Soares2003,
  author    = {Soares, Alexei S. and Caspar, Donald L. D. and Weckert, Edgar and H{\'{e}}roux, Annie and H{\"{o}}lzer, Kerstin and Schroer, Klaus and Zellner, Johannes and Schneider, Dieter and Nolan, William and Sweet, Robert M.},
  journal   = {Acta Crystallographica Section D},
  title     = {Three-beam interference is a sensitive measure of the efficacy of macromolecular refinement techniques},
  year      = {2003},
  pages     = {1716--1724},
  volume    = {59},
  doi       = {10.1107/S0907444903015403},
  file      = {ea5002.pdf:by-author/S/Soares/2003_Soares_1716.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444903015403},
}

@Manuscript{Sobalvarro1993,
  author      = {Patrick G. Sobalvarro},
  title       = {A Compacting Garbage Collector for Computers Without Virtual Memory},
  year        = {1993},
  institution = {Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology},
  keywords    = {Computer Science (CS); Garbage Collection; Memory Allocation},
  month       = {July},
  abstract    = {We present a novel algorithm for compacting garbage col- lection on computers without virtual memory. The algorithm does not use Cheney-style copying 3], and does not require additional storage for forwarding pointers. The algorithm, which builds on earlier work by D. J. Edwards, uses separate spaces for objects of di erent sizes, and is intended for use on systems without virtual memory where storage is at a premium.},
  file        = {:by-author/S/Sobalvarro/1993_Sobalvarro.ps:PostScript;:by-author/S/Sobalvarro/1993_Sobalvarro.pdf:PDF},
  groups      = {sg/Garbage collectors},
  owner       = {saulius},
  timestamp = {2015.02.27},
  creationdate = {2015-02-27T00:00:00},
}

@InProceedings{Sobe2006,
  author    = {Sobe, P. and Peter, K.},
  booktitle = {Network Computing and Applications, 2006. NCA 2006. Fifth IEEE International Symposium on},
  title     = {Comparison of Redundancy Schemes for Distributed Storage Systems},
  year      = {2006},
  pages     = {196--203},
  abstract  = {Reliable distributed data storage systems have to employ redundancy codes to tolerate the loss of storages. Many appropriate codes and algorithms can be found in the literature, but efficient schemes for tolerating several storage failures and their embedding in a distributed system are still research issues. In this paper, a variety of redundancy schemes are compared that got implemented in a distributed storage system. All schemes are based on parity and Reed/Solomon and are integrated in the storage system NetRAID. This system allows to configure several user-specified layouts. A performance and reliability analysis of several data and redundancy layouts is presented that combines analytical and experimental results. In a detail, we present performance results for an optimized Reed/Solomon implementation and give an outline for speeding up encoding and recovery by reconfigurable hardware employed in the distributed storage system},
  doi       = {10.1109/NCA.2006.18},
  file      = {:by-author/S/Sobe/2006_Sobe_01659492.pdf:PDF},
  keywords  = {Data Analysis; Data Engineering; Data Storage Systems; Distributed Computing; Distributed Storage System; Fault Tolerance; Hardware; Interleaved Codes; NetRAID Storage System; Performance Analysis; RAID; Reconfigurable Hardware; Redundancy; Redundancy Schemes; Reed-Solomon Codes; Reliability Analysis; Reliability Engineering; Storage Management},
  owner     = {saulius},
  timestamp = {2013.09.10},
  creationdate = {2013-09-10T00:00:00},
  url       = {http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=1659492&tag=1},
}

@Article{Socolar1986,
  author    = {Joshua E.S. Socolar and Paul J. Steinhardt},
  title     = {Quasicrystals. {II}. Unit-cell configurations},
  year      = {1986},
  pages     = {617--647},
  volume    = {34},
  file      = {Joshua E.S. Socolar and Paul J. Steinhardt - 1986 - Quasicrystals. II. Unit-cell configurations.pdf:by-author/S/Socolar/1986_Socolar_617.pdf:application/pdf},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://physics.princeton.edu/~steinh/QuasiPartII.pdf},
  urldate   = {2015-09-08},
}

@Manual{Soeding2006,
  title     = {Quick guide to {HHsearch}},
  author    = {Johannes Söding},
  edition   = {1.5.0},
  month     = {Nov},
  year      = {2006},
  file      = {:by-author/S/Söding/2006_Söding_manual.pdf:PDF},
  keywords  = {Proteins; Structure Predicion},
  owner     = {andrius},
  timestamp = {2014.01.09},
  creationdate = {2014-01-09T00:00:00},
}

@InProceedings{Soheili2005,
  author    = {Amir Soheili and Vana Kalogeraki and Dimitrios Gunopulos},
  booktitle = {Proceedings of the 13th annual ACM international workshop on Geographic information systems},
  title     = {Spatial Queries in Sensor Networks},
  year      = {2005},
  pages     = {61--70},
  abstract  = {Spatial queries are a subset of queries in which the database or the Recent advances in low-power sensing devices coupled with the sensor network is queried by location rather than an attribute. widespread availability of wireless ad-hoc networks have fueled Spatial queries are used to answer questions, such as find the the development of sensor networks. These are typically deployed average temperature in an area or count the number of sensors over wide areas to gather data in the environment and monitor within one mile of a point of interest. In a traditional spatial events of interest. The ability to run spatial queries is extremely database, spatial indexing techniques such as R-Tree, R},
  doi       = {10.1145/1097064.1097074},
  file      = {:by-author/S/Soheili/2005_Soheili_61.pdf:PDF},
  isbn      = {1-59593-146-5},
  keywords  = {Sensor Networks; Spatial Indices; Spatial Queries},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://doi.acm.org/10.1145/1097064.1097074},
}

@InProceedings{Soicher1994,
  author    = {Leonard H. Soicher},
  booktitle = {EIDMA Minicourse, Computer Algebra with emphasis on discrete algebra and geometry},
  title     = {Coset enumeration, permutation group algorithms, and applications to graphs and geometries},
  year      = {1994},
  address   = {Eindhoven},
  abstract  = {In these notes we discuss coset enumeration and basic permutation group algorithms. To illustrate some applications to graphs and finite geometries, we classify and studey some graphs which are locally the incidence graph of the 2 -- (11,5,2) design.},
  file      = {:by-author/S/Soicher/1994_Soicher.ps:PostScript},
  owner     = {saulius},
  timestamp = {2013.03.22},
  creationdate = {2013-03-22T00:00:00},
  url       = {http://www.maths.qmul.ac.uk/~leonard/pubs.html},
}

@Article{Sokolov2008,
  author    = {Sokolov, Anatoliy N and Swenson, Dale C and MacGillivray, Leonard R},
  journal   = {Proceedings of the National Academy of Sciences of the United States of America},
  title     = {Conformational polymorphism in a heteromolecular single crystal leads to concerted movement akin to collective rack-and-pinion gears at the molecular level.},
  year      = {2008},
  pages     = {1794--7},
  volume    = {105},
  abstract  = {We describe a heteromolecular single crystal that exhibits three reversible and concerted reorganizations upon heating and cooling. The products of the reorganizations are conformational polymorphs. The reorganizations are postulated to proceed through three motions: (i) alkyl translations, (ii) olefin rotations, and (iii) rotational tilts. The motions are akin to rack-and-pinion gears at the molecular level. The rack-like movement is based on expansions and compressions of alkyl chains that are coupled with pinion-like 180 degree rotations of olefins. To accommodate the movements, phenol and thiophene components undergo rotational tilts about intermolecular hydrogen bonds. The movements are collective, being propagated in close-packed repeating units. This discovery marks a step to understanding how organic solids can support the development of crystalline molecular machines and devices through correlated and collective movements.},
  file      = {2008_Sokolov_1794.pdf:by-author/S/Sokolov/2008_Sokolov_1794.pdf:PDF},
  keywords  = {Molecular Machines},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Sokolowska2007b,
  author      = {M. Sokolowska and M. Kaus-Drobek and H. Czapinska and G. Tamulaitis and V. Siksnys and M. Bochtler},
  journal     = {Cell Mol Life Sci},
  title       = {Restriction endonucleases that resemble a component of the bacterial DNA repair machinery.},
  year        = {2007},
  month       = {Sep},
  number      = {18},
  pages       = {2351--2357},
  volume      = {64},
  abstract    = {It has long been known that most Type II restriction endonucleases share a conserved core fold and similar active-sites. The same core folding motif is also present in the MutH protein, a component of the bacterial DNA mismatch repair machinery. In contrast to most Type II restriction endonucleases, which assemble into functional dimers and catalyze double-strand breaks, MutH is a monomer and nicks hemimethylated DNA. Recent biochemical and crystallographic studies demonstrate that the restriction enzymes BcnI and MvaI share many additional features with MutH-like proteins, but not with most other restriction endonucleases. The structurally similar monomers all recognize approximately symmetric target sequences asymmetrically. Differential sensitivities to slight substrate asymmetries, which could be altered by protein engineering, determine whether the enzymes catalyze only single-strand nicks or double-strand breaks.},
  doi         = {10.1007/s00018-007-7124-9},
  file        = {2007_Sokolowska_2351.pdf:by-author/S/Sokolowska/2007_Sokolowska_2351.pdf:PDF},
  institution = {International Institute of Molecular and Cell Biology, Trojdena 4, 02-109, Warsaw, Poland.},
  keywords    = {Bacteria; Bacterial; Chemistry/metabolism; DNA; DNA Repair; DNA Restriction Enzymes; Enzymology/genetics/metabolism; Metabolism},
  language    = {eng},
  medline-pst = {ppublish},
  owner       = {em},
  pmid        = {17568994},
  timestamp = {2011.07.13},
  creationdate = {2011-07-13T00:00:00},
  url         = {http://dx.doi.org/10.1007/s00018-007-7124-9},
}

@Article{Sokolowska2007,
  author    = {Sokolowska, Monika and Kaus-Drobek, Magdalena and Czapinska, Honorata and Tamulaitis, Gintautas and Szczepanowski, Roman H. and Urbanke, Claus and Siksnys, Virginijus and Bochtler, Matthias},
  journal   = {Journal of molecular biology},
  title     = {Monomeric restriction endonuclease BcnI in the apo form and in an asymmetric complex with target DNA.},
  year      = {2007},
  pages     = {722--34},
  volume    = {369},
  abstract  = {Restriction endonuclease BcnI cleaves duplex DNA containing the sequence CC/SGG (S stands for C or G, / designates a cleavage position) to generate staggered products with single nucleotide 5'-overhangs. Here, we show that BcnI functions as a monomer that interacts with its target DNA in 1:1 molar ratio and report crystal structures of BcnI in the absence and in the presence of DNA. In the complex with DNA, BcnI makes specific contacts with all five bases of the target sequence and not just with a half-site, as the protomer of a typical dimeric restriction endonuclease. Our data are inconsistent with BcnI dimerization and suggest that the enzyme introduces double-strand breaks by sequentially nicking individual DNA strands, although this remains to be confirmed by kinetic experiments. BcnI is remotely similar to the DNA repair protein MutH and shares approximately 20% sequence identity with the restriction endonuclease MvaI, which is specific for the related sequence CC/WGG (W stands for A or T). As expected, BcnI is structurally similar to MvaI and recognizes conserved bases in the target sequence similarly but not identically. BcnI has a unique machinery for the recognition of the central base-pair.},
  file      = {:by-author/S/Sokolowska/2007_Sokolowska_722.pdf:PDF},
  keywords  = {Ecl18kI EcoRII; TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Solaja2002,
  author           = {Šolaja, Bogdan A. and Terzić, Nataša and Pocsfalvi, Gabriella and Gerena, Lucia and Tinant, Bernard and Opsenica, Dejan and Milhous, Wilbur K.},
  journal          = {Journal of Medicinal Chemistry},
  title            = {Mixed Steroidal 1,2,4,5-Tetraoxanes: Antimalarial and Antimycobacterial Activity},
  year             = {2002},
  issn             = {1520-4804},
  month            = {Jun},
  number           = {16},
  pages            = {3331--3336},
  volume           = {45},
  creationdate     = {2022-07-15T11:07:55},
  doi              = {10.1021/jm020891g},
  file             = {:by-author/Š/Šolaja/2002_Šolaja_3331.pdf:PDF},
  modificationdate = {2022-12-24T18:57:35},
  owner            = {andrius},
  publisher        = {American Chemical Society (ACS)},
  url              = {https://doi.org/10.1021/jm020891g},
}

@Article{Soldatova2011,
  author    = {Soldatova, Larisa N and Rzhetsky, Andrey},
  journal   = {Journal of Biomedical Semantics},
  title     = {Representation of research hypotheses},
  year      = {2011},
  issn      = {2041-1480},
  pages     = {S9},
  volume    = {2},
  abstract  = {Background Hypotheses are now being automatically produced on an industrial scale by computers in biology, e.g. the annotation of a genome is essentially a large set of hypotheses generated by sequence similarity programs; and robot scientists enable the full automation of a scientific investigation, including generation and testing of research hypotheses. Results This paper proposes a logically defined way for recording automatically generated hypotheses in machine amenable way. The proposed formalism allows the description of complete hypotheses sets as specified input and output for scientific investigations. The formalism supports the decomposition of research hypotheses into more specialised hypotheses if that is required by an application. Hypotheses are represented in an operational way – it is possible to design an experiment to test them. The explicit formal description of research hypotheses promotes the explicit formal description of the results and conclusions of an investigation. The paper also proposes a framework for automated hypotheses generation. We demonstrate how the key components of the proposed framework are implemented in the Robot Scientist “Adam”. Conclusions A formal representation of automatically generated research hypotheses can help to improve the way humans produce, record, and validate research hypotheses. Availability http://www.aber.ac.uk/en/cs/research/cb/projects/robotscientist/results/},
  doi       = {10.1186/2041-1480-2-S2-S9},
  file      = {Soldatova and Rzhetsky - 2011 - Representation of research hypotheses.pdf:by-author/S/Soldatova/2011_Soldatova_S9.pdf:application/pdf},
  groups    = {sg/Knowledge engineering},
  keywords  = {Artificial Intelligence (AI); Knowledge Engineering; Knowledge Representation; Prolog},
  owner     = {saulius},
  pmcid     = {PMC3102898},
  pmid      = {21624164},
  timestamp = {2015.10.23},
  creationdate = {2015-10-23T00:00:00},
  url       = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3102898/},
  urldate   = {2015-10-16},
}

@Article{SolerLopez2000,
  author    = {Montserrat Soler-Lopez and Lucy Malinina and Juan A. Subirana},
  journal   = {The Journal of Biological Chemistry},
  title     = {Solvent Organization in an Oligonucleotide Crystal},
  year      = {2000},
  pages     = {23034--23044},
  volume    = {275},
  doi       = {10.1074/jbc.M002119200},
  file      = {SolerLopez_2000_23034.pdf:by-author/S/SolerLopez/2000_SolerLopez_23034.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://www.jbc.org/content/275/30/23034.full.pdf+html},
}

@Article{Solovyev2006,
  author    = {Solovyev, I. V.},
  journal   = {arXiv},
  title     = {Lattice Distortion and Magnetism of 3d-t2g Perovskite Oxides},
  year      = {2006},
  pages     = {0602035v1},
  abstract  = {Several puzzling aspects of interplay of the experimental lattice distortion and the the magnetic properties of four narrow t2g -band perovskite oxides (YTiO3 , LaTiO3 , YVO3 , and LaVO3 ) are clarified using results of first-principles electronic structure calculations. First, we derive param- eters of the effective Hubbard-type Hamiltonian for the isolated t2g bands using newly developed downfolding method for the kinetic-energy part and a hybrid approach, based on the combina- tion of the random-phase approximation and the constraint local-density approximation, for the screened Coulomb interaction part. Apart form the above-mentioned approximation, the procedure of constructing the model Hamiltonian is totally parameter-free. The results are discussed in terms of the Wannier functions localized around transition-metal sites. The obtained Hamiltonian was solved using a number of techniques, including the mean-field Hartree-Fock (HF) approximation, the second-order perturbation theory for the correlation energy, and a variational superexchange theory, which takes into account the multiplet structure of the atomic states. We argue that the crystal distortion has a profound effect not only on the values of the crystal-field (CF) splitting, but also on the behavior of transfer integrals and even the screened Coulomb interactions. Even though the CF splitting is not particularly large to quench the orbital degrees of freedom, the crys- tal distortion imposes a severe constraint on the form of the possible orbital states, which favor the formation of the experimentally observed magnetic structures in YTiO3 , YVO3 , and LaVO3 even at the level of mean-field HF approximation. It is remarkable that for all three compounds, the main results of all-electron calculations can be successfully reproduced in our minimal model derived for the isolated t2g bands. We confirm that such an agreement is only possible when the nonsphericity of the Madelung potential is explicitly included into the model. Beyond the HF ap- proximation, the correlations effects systematically improve the agreement with the experimental data. Using the same type of approximations we could not reproduce the correct magnetic ground state of LaTiO3 . However, we expect that the situation may change by systematically improving the level of approximations for dealing with the correlation effects.},
  file      = {:by-author/S/Solovyev/2006_Solovyev.pdf:PDF},
  keywords  = {Perovskites},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Manuscript{Soma1999,
  author    = {John T. Soma and Kurt Leyendecker and Steven L. Webb},
  title     = {Software Patents: a U.S. and E.U. Comparision},
  year      = {1999},
  keywords  = {Patentai; Teise},
  file      = {:by-author/S/Soma/1999_Soma.S. AND E.U. COMPARISION.RTF:DOC},
  owner     = {saulius},
  timestamp = {2015.02.28},
  creationdate = {2015-02-28T00:00:00},
}

@Article{Sommerhalter2005,
  author    = {Monika Sommerhalter and Raquel L. Lieberman and Amy C. Rosenzweig},
  journal   = {Inorganic Chemistry},
  title     = {{X}-ray Crystallography and Biological Metal Centers: Is Seeing Believing?},
  year      = {2005},
  pages     = {770--778},
  volume    = {44},
  abstract  = {Metalloenzyme crystal structures have a major impact on our understanding of biological metal centers. They are often the starting point for mechanistic and computational studies and inspire synthetic modeling chemistry. The strengths and limitations of X-ray crystallography in determining properties of biological metal centers and their corresponding ligand spheres are explored through examples, including ribonucleotide reductase R2 and particulate methane monooxygenase. Protein crystal structures locate metal ions within a protein fold and reveal the identities and coordination geometries of amino acid ligands. Data collection strategies that exploit the anomalous scattering effect of metal ions can establish metal ion identity. The quality of crystallographic data, particularly the resolution, determines the level of detail that can be extracted from a protein crystal structure. Complementary spectroscopic techniques can provide crucial information regarding the redox state of the metal center as well as the presence, type, and protonation state of exogenous ligands. The final result of the crystallographic characterization of a metalloenzyme is a model based on crystallographic data, supported by information from biophysical and modeling studies, influenced by sample handling, and interpreted carefully by the crystallographer.},
  doi       = {10.1021/ic0485256},
  file      = {:by-author/S/Sommerhalter/2005_Sommerhalter_770.pdf:PDF},
  owner     = {antanas},
  timestamp = {2013.12.11},
  creationdate = {2013-12-11T00:00:00},
  url       = {http://pubs.acs.org/doi/abs/10.1021/ic0485256},
}

@Article{Son2009,
  author    = {Son},
  journal   = {Journal of Applied Physics},
  title     = {Terahertz electromagnetic interactions with biological matter and their applications},
  year      = {2009},
  pages     = {102033},
  volume    = {105},
  abstract  = {The characteristics of electromagnetic interactions with biological matter in the terahertz region are reviewed. The recent development of terahertz technology has made possible the study of the scientifically rich spectral region where molecular rotational and vibrational modes exist. The technology is reviewed in terms of sources, detectors, and related techniques for spectroscopy and imaging. The spectroscopic technique has been utilized for the investigation of various biological molecules including DNAs, RNAs, nucleobases, proteins, polypeptides, and biological liquids to reveal intermolecular and intramolecular dynamics. Terahertz imaging has also proven to be a potential modality of medical diagnosis using the results of preliminary researches of skin and breast cancers.},
  doi       = {10.1063/1.3116140},
  file      = {:by-author/S/Son/2009_Son_102033.pdf:PDF},
  keywords  = {Physics; Terahertz EM Waves},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@PhdThesis{Song2004,
  author    = {Song, J.},
  school    = {MIT},
  title     = {Building Robust Chemical Reaction Mechanisms: Next Generation of Automatic Model Construction Software},
  year      = {2004},
  file      = {2004_Song_phdthesis.pdf:by-author/S/Song/2004_Song_phdthesis.pdf:PDF},
  owner     = {saulius},
  timestamp = {2014.07.16},
  creationdate = {2014-07-16T00:00:00},
  url       = {http://hdl.handle.net/1721.1/30058},
}

@Article{Soofi2000,
  author           = {Soofi, Ehsan S.},
  journal          = {Journal of the American Statistical Association},
  title            = {Principal information theoretic approaches},
  year             = {2000},
  pages            = {1349--1353},
  volume           = {95},
  creationdate     = {2012-10-04T00:00:00},
  doi              = {10.1080/01621459.2000.10474346},
  eprint           = {http://www.tandfonline.com/doi/pdf/10.1080/01621459.2000.10474346},
  file             = {2000_Soofi_1349.pdf:by-author/S/Soofi/2000_Soofi_1349.pdf:PDF},
  groups           = {sg/Bayesian},
  keywords         = {Bayesian Statistics; Information Theory; Maximum Entropy},
  modificationdate = {2024-10-13T08:51:37},
  owner            = {saulius},
  timestamp        = {2012.10.04},
  url              = {http://www.tandfonline.com/doi/abs/10.1080/01621459.2000.10474346},
}

@Article{Soukup1999,
  author    = {Soukup, Garrett A. and Breaker, Ronald R.},
  journal   = {Proceedings of the National Academy of Sciences},
  title     = {Engineering precision {RNA} molecular switches},
  year      = {1999},
  issn      = {0027-8424, 1091-6490},
  pages     = {3584--3589},
  volume    = {96},
  abstract  = {Ligand-specific molecular switches composed of RNA were created by coupling preexisting catalytic and receptor domains via structural bridges. Binding of ligand to the receptor triggers a conformational change within the bridge, and this structural reorganization dictates the activity of the adjoining ribozyme. The modular nature of these tripartite constructs makes possible the rapid construction of precision RNA molecular switches that trigger only in the presence of their corresponding ligand. By using similar enzyme engineering strategies, new RNA switches can be made to operate as designer molecular sensors or as a new class of genetic control elements.},
  doi       = {10.1073/pnas.96.7.3584},
  file      = {Full Text PDF:by-author/S/Soukup/1999_Soukup_3584.pdf:application/pdf;Snapshot:by-author/S/Soukup/1999_Soukup_3584.html:text/html},
  groups    = {sg/biomolecular},
  language  = {en},
  owner     = {saulius},
  pmid      = {10097080},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://www.pnas.org/content/96/7/3584},
  urldate   = {2015-08-05},
}

@Webpage{ESS2010,
  author    = {European Spallation Source},
  retrieved = {2014-01-20},
  title     = {30 times brighter than today},
  url       = {http://europeanspallationsource.se/30-times-brighter-today},
  year      = {2010},
  file      = {:by-author/E/ESS/2010_ESS.odt:OpenDocument text},
  keywords  = {European Spallation Source; Neutron Diffraction; Neutron Source; Research Infrastructure},
  owner     = {saulius},
  timestamp = {2014.01.21},
  creationdate = {2014-01-21T00:00:00},
}

@Article{Sousa2000,
  author    = {Sousa, M. C. and Trame, C. B. and Tsuruta, H. and Wilbanks, S. M. and Reddy, V. S. and McKay, D. B.},
  journal   = {Cell},
  title     = {Crystal and solution structures of an HslUV protease-chaperone complex.},
  year      = {2000},
  pages     = {633--43},
  volume    = {103},
  abstract  = {HslUV is a "prokaryotic proteasome" composed of the HslV protease and the HslU ATPase, a chaperone of the Clp/Hsp100 family. The 3.4 A crystal structure of an HslUV complex is presented here. Two hexameric ATP binding rings of HslU bind intimately to opposite sides of the HslV protease; the HslU "intermediate domains" extend outward from the complex. The solution structure of HslUV, derived from small angle X-ray scattering data under conditions where the complex is assembled and active, agrees with this crystallographic structure. When the complex forms, the carboxy-terminal helices of HslU distend and bind between subunits of HslV, and the apical helices of HslV shift substantially, transmitting a conformational change to the active site region of the protease.},
  file      = {:by-author/S/Sousa/2000_Sousa_633.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Souvignier2006,
  author    = {Souvignier, Bernd},
  journal   = {Zeitschrift für Kristallographie - Crystalline Materials},
  title     = {The four-dimensional magnetic point and space groups},
  year      = {2006},
  issn      = {2194-4946},
  pages     = {77--82},
  volume    = {221},
  abstract  = {Abstract This paper describes the classification of magnetic point and space groups which are also referred to as antisymmetry groups or black-and-white groups. These groups play an important role in the description of discrete point sets in which the points are not only characterized by their spatial coordinates but also by an additional property taking one of two possible values (e.g. spin up or down). Each operation of a magnetic group may or may not switch the value of this additional property. In this paper, the methods for classifying magnetic groups in arbitrary dimensions are described in an algorithmic fashion. Results of the full classification in four-dimensional space are given and the application of the magnetic groups in this dimension to quasicrystals is indicated. Abstract This paper describes the classification of magnetic point and space groups which are also referred to as antisymmetry groups or black-and-white groups. These groups play an important role in the description of discrete point sets in which the points are not only characterized by their spatial coordinates but also by an additional property taking one of two possible values (e.g. spin up or down). Each operation of a magnetic group may or may not switch the value of this additional property. In this paper, the methods for classifying magnetic groups in arbitrary dimensions are described in an algorithmic fashion. Results of the full classification in four-dimensional space are given and the application of the magnetic groups in this dimension to quasicrystals is indicated.},
  booktitle = {Zeitschrift für Kristallographie - Crystalline Materials},
  doi       = {10.1524/zkri.2006.221.1.77},
  file      = {2006_Souvignier_77.pdf:by-author/S/Souvignier/2006_Souvignier_77.pdf:PDF},
  keywords  = {Crystallography; Spacegroups; Superspacegroups; Symmetry},
  owner     = {saulius},
  publisher = {Oldenbourg Wissenschaftsverlag GmbH},
  timestamp = {2013.04.19},
  creationdate = {2013-04-19T00:00:00},
  url       = {http://dx.doi.org/10.1524/zkri.2006.221.1.77},
}

@Article{Souvignier1994,
  author    = {Bernd Souvignier},
  journal   = {Mathematics of Computation},
  title     = {Irreducible Finite Integral Matrix Groups of Degree 8 and 10},
  year      = {1994},
  pages     = {335--350},
  volume    = {63},
  doi       = {10.2307/2153579},
  file      = {:by-author/S/Souvignier/1994_Souvignier_335.pdf:PDF},
  keywords  = {Algebra; Bravais Lattices; Group Theory; Integral Matrix Groups; Spacegroups; Symmetry},
  owner     = {saulius},
  timestamp = {2015.10.09},
  creationdate = {2015-10-09T00:00:00},
  url       = {http://www.jstor.org/stable/2153579},
}

@Article{Spacciapoli1994,
  author    = {Spacciapoli, P. and Nossal, N. G.},
  journal   = {The Journal of biological chemistry},
  title     = {Interaction of DNA polymerase and DNA helicase within the bacteriophage T4 DNA replication complex. Leading strand synthesis by the T4 DNA polymerase mutant A737V (tsL141) requires the T4 gene 59 helicase assembly protein.},
  year      = {1994},
  pages     = {447--55},
  volume    = {269},
  abstract  = {The bacteriophage T4 tsL141 (A737V) mutant in T4 DNA polymerase is temperature-sensitive for DNA replication and an antimutator for some types of mutations. In the accompanying paper (Spacciapoli, P., and Nossal, N. G. (1993) J. Biol. Chem. 269, 438-446), we show that the purified A737V T4 DNA polymerase is less processive than the wild type enzyme as a polymerase, but is more processive as an exonuclease. The bacteriophage T4 multienzyme replication complex reconstituted with the A737V mutant polymerase is defective in both lagging and leading strand synthesis. On lagging strand templates, the A737V polymerase is stimulated by the gene 44/62 and 45 polymerase accessory proteins and the gene 32 DNA binding protein, but is still arrested at pause sites much more frequently than the wild type. In contrast to wild type T4 DNA polymerase, the A737V polymerase does not catalyze leading strand synthesis on a forked duplex template with the polymerase accessory proteins, 32 protein, and the gene 41 protein helicase. The A737V polymerase requires the T4 gene 59 helicase assembly protein, as well as the other proteins, to carry out this reaction. Each of these defects is suppressed by the intragenic L771F mutation that suppresses the antimutator phenotype of the A737V, polymerase in vivo (Reha-Krantz, L. J., Stocki, S., Nonay, R., and Maughan, C. (1989) J. Cell. Biochem. 13D, 140).},
  file      = {:by-author/S/Spacciapoli/1994_Spacciapoli_447.pdf:PDF},
  keywords  = {{gp41} Helicase; {gp59}},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Spadaccini2012b,
  author    = {Spadaccini, Nick and Castleden, Ian R. and du Boulay, Doug and Hall, Sydney R.},
  journal   = {Journal of Chemical Information and Modeling},
  title     = {dREL: A Relational Expression Language for Dictionary Methods},
  year      = {2012},
  pages     = {1917--1925},
  volume    = {52},
  abstract  = {The provision of precise metadata is an important but a largely underrated challenge for modern science [Nature2009, 461, 145]. We describe here a dictionary methods language dREL that has been designed to enable complex data relationships to be expressed as formulaic scripts in data dictionaries written in DDLm [Spadaccini and Hall J. Chem. Inf. Model.2012 doi:10.1021/ci300075z]. dREL describes data relationships in a simple but powerful canonical form that is easy to read and understand and can be executed computationally to evaluate or validate data. The execution of dREL expressions is not a substitute for traditional scientific computation; it is to provide precise data dependency information to domain-specific definitions and a means for cross-validating data. Some scientific fields apply conventional programming languages to methods scripts but these tend to inhibit both dictionary development and accessibility. dREL removes the programming barrier and encourages the production of the metadata needed for seamless data archiving and exchange in science.},
  doi       = {10.1021/ci300076w},
  eprint    = {http://pubs.acs.org/doi/pdf/10.1021/ci300076w},
  file      = {2012_Spadaccini_1917.pdf:by-author/S/Spadaccini/2012_Spadaccini_1917.pdf:PDF},
  keywords  = {Computer Languages; Crystallographic Computing; Crystallography; Data Management; Programming Languages; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2013.08.20},
  creationdate = {2013-08-20T00:00:00},
  url       = {http://pubs.acs.org/doi/abs/10.1021/ci300076w},
}

@Article{Spadaccini2012,
  author           = {Spadaccini, Nick and Hall, Sydney R.},
  journal          = {Journal of Chemical Information and Modeling},
  title            = {DDLm: A New Dictionary Definition Language},
  year             = {2012},
  pages            = {1907--1916},
  volume           = {52},
  abstract         = {A previous paper [Spadaccini and Hall J. Chem. Inf. Model. doi:10.1021/ci300074v] details extensions to the STAR File [Hall J. Chem. Inf. Comput. Sci.1991, 31, 326–333] syntax that will improve the exchange and archiving of electronic data. This paper describes a dictionary definition language (DDLm) for defining STAR File data items in a domain dictionary. A dictionary that defines the ontology and vocabulary of a discipline is built with DDLm, which is itself implemented in STAR, and is extensible and machine parsable. The DDLm is semantically rich and highly specific; provides strong data typing, data enumerations, and ranges; enables relationship keys between data items; and uses imbedded methods written in dREL [Spadaccini et al. J. Chem. Inf. Model. doi:10.1021/ci300076w] for data validation and evaluation and for refining data definitions. It promotes the modular definition of the discipline ontology and reuse through the ability to import definitions from other local and remote dictionaries, thus encouraging the sharing of data dictionaries within and across domains.},
  creationdate     = {2013-07-17T00:00:00},
  doi              = {10.1021/ci300075z},
  eprint           = {http://pubs.acs.org/doi/pdf/10.1021/ci300075z},
  file             = {2012_Spadaccini_1907.pdf:by-author/S/Spadaccini/2012_Spadaccini_1907.pdf:PDF},
  groups           = {sg/CIF, am/CIF},
  keywords         = {CIF; Data Management; X-ray Crystallography},
  modificationdate = {2023-08-07T10:23:05},
  owner            = {saulius},
  timestamp        = {2013.07.17},
  url              = {http://pubs.acs.org/doi/abs/10.1021/ci300075z},
}

@Article{Spadaccini2012a,
  author           = {Spadaccini, Nick and Hall, Sydney R.},
  journal          = {Journal of Chemical Information and Modeling},
  title            = {Extensions to the STAR File Syntax},
  year             = {2012},
  pages            = {1901--1906},
  volume           = {52},
  abstract         = {The STAR File [Hall J. Chem. Inf. Comput. Sci.1991, 31, 326–333; Hall and Spadaccini J. Chem. Inf. Comput. Sci.1994, 34, 505–508] format represents a universal language adopted for electronic data and metadata exchange in the molecular-structure sciences [Hall et al. Acta Crystallogr. Sect. A1991, 47, 655–685; International Tables for International Tables for Crystallography. Vol. G: Definition and exchange of crystallographic data; Springer: Dordrecht, The Netherlands, 2005; Allen et al. J. Chem. Inf. Comput. Sci.1995, 35, 412–427] and used by the International Union for Crystallography for publication submissions and database depositions. This paper describes an extended STAR syntax that facilitates richer and more specific data definition and typing and a commensurate improvement in precise data description.},
  creationdate     = {2013-07-17T00:00:00},
  doi              = {10.1021/ci300074v},
  eprint           = {http://pubs.acs.org/doi/pdf/10.1021/ci300074v},
  file             = {2012_Spadaccini_1901.pdf:by-author/S/Spadaccini/2012_Spadaccini_1901.pdf:PDF},
  groups           = {sg/CIF, am/CIF},
  keywords         = {CIF; Data Management; X-ray Crystallography},
  modificationdate = {2023-08-07T10:23:05},
  owner            = {saulius},
  timestamp        = {2013.07.17},
  url              = {http://pubs.acs.org/doi/abs/10.1021/ci300074v},
}

@Article{Spadaccini1994,
  author    = {Nick Spadaccini and Sydney R. Hall},
  journal   = {J. Chem. Inf Comput. Sci.},
  title     = {Star-Base: Accessing STAR File Data},
  year      = {1994},
  pages     = {509--516},
  volume    = {34},
  abstract  = {Star-Base is ANSI C compliant software for extracting data from a STAR File. It employs a versatile query language to return data as STAR conformant data.},
  doi       = {10.1021/ci00019a006},
  file      = {1994_Spadaccini_509.pdf:by-author/S/Spadaccini/1994_Spadaccini_509.pdf:PDF},
  owner     = {saulius},
  timestamp = {2013.10.17},
  creationdate = {2013-10-17T00:00:00},
}

@Article{Spanos2007,
  author    = {Aris Spanos},
  journal   = {Philosophy of Science},
  title     = {Curve Fitting, the Reliability of Inductive Inference, and the Error-Statistical Approach},
  year      = {2007},
  pages     = {1046--1066},
  volume    = {74},
  abstract  = {The main aim of this paper is to revisit the curve fitting problem using the reliability of inductive inference as a primary criterion for the ‘fittest’ curve. Viewed from this perspective, it is argued that a crucial concern with the current framework for ad- dressing the curve fitting problem is, on the one hand, the undue influence of the mathematical approximation perspective, and on the other, the insufficient attention paid to the statistical modeling aspects of the problem. Using goodness-of-fit as the primary criterion for ‘best’, the mathematical approximation perspective undermines the reliability of inference objective by giving rise to selection rules which pay insuf- ficient attention to ‘accounting for the regularities in the data’. A more appropriate framework is offered by the error-statistical approach, where (i) statistical adequacy provides the criterion for assessing when a curve captures the regularities in the data adequately, and (ii) the relevant error probabilities can be used to assess the reliability of inductive inference. Broadly speaking, the fittest curve (statistically adequate) is not determined by the smallness if its residuals, tempered by simplicity or other pragmatic criteria, but by the nonsystematic (e.g. white noise) nature of its residuals. The advocated error-statistical arguments are illustrated by comparing the Kepler and Ptolemaic mod- els on empirical grounds.},
  file      = {2007_Spanos_1046.pdf:by-author/S/Spanos/2007_Spanos_1046.pdf:PDF},
  groups    = {sg/Bayesian},
  keywords  = {Bayesian Statistics; Curve Fitting},
  owner     = {saulius},
  timestamp = {2012.10.04},
  creationdate = {2012-10-04T00:00:00},
}

@Article{Spassov1995,
  author    = {Spassov, V Z and Karshikoff, A D and Ladenstein, R},
  journal   = {Protein science : a publication of the Protein Society},
  title     = {The optimization of protein-solvent interactions: thermostability and the role of hydrophobic and electrostatic interactions.},
  year      = {1995},
  pages     = {1516--27},
  volume    = {4},
  abstract  = {Protein-solvent interactions were analyzed using an optimization parameter based on the ratio of the solvent-accessible area in the native and the unfolded protein structure. The calculations were performed for a set of 183 nonhomologous proteins with known three-dimensional structure available in the Protein Data Bank. The dependence of the total solvent-accessible surface area on the protein molecular mass was analyzed. It was shown that there is no difference between the monomeric and oligomeric proteins with respect to the solvent-accessible area. The results also suggested that for proteins with molecular mass above some critical mass, which is about 28 kDa, a formation of domain structure or subunit aggregation into oligomers is preferred rather than a further enlargement of a single domain structure. An analysis of the optimization of both protein-solvent and charge-charge interactions was performed for 14 proteins from thermophilic organisms. The comparison of the optimization parameters calculated for proteins from thermophiles and mesophiles showed that the former are generally characterized by a high degree of optimization of the hydrophobic interactions or, in cases where the optimization of the hydrophobic interactions is not sufficiently high, by highly optimized charge-charge interactions.},
  file      = {1995_Spassov_1516.pdf:by-author/S/Spassov/1995_Spassov_1516.pdf:PDF},
  keywords  = {Noncovalent Interactions; Protein Physics; Thermostability},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Speers2004,
  author    = {Anna E. Speers and Benjamin F. Cravatt},
  journal   = {ChemBioChem},
  title     = {Chemical Strategies for Activity-Based Proteomics},
  year      = {2004},
  pages     = {41--47},
  volume    = {5},
  abstract  = {The assignment of molecular and cellular functions to the numerous protein products encoded by prokaryotic and eukaryotic genomes presents a major challenge for the field of proteomics. To address this problem, chemical approaches have been introduced that utilize small-molecule probes to profile dynamics in enzyme activity in complex proteomes. These strategies for activity-based protein profiling enable both the discovery and functional analysis of enzymes associated with human disease.},
  doi       = {10.1002/cbic.200300721},
  file      = {:by-author/S/Speers/2004_Speers_41.pdf:PDF},
  owner     = {saulius},
  timestamp = {2011.12.07},
  creationdate = {2011-12-07T00:00:00},
}

@Article{Speers2004a,
  author    = {Speers, Anna E. and Cravatt, Benjamin F.},
  journal   = {Chemistry \&amp; biology},
  title     = {Profiling enzyme activities in vivo using click chemistry methods.},
  year      = {2004},
  pages     = {535--46},
  volume    = {11},
  abstract  = {Methods for profiling the activity of enzymes in vivo are needed to understand the role that these proteins and their endogenous regulators play in physiological and pathological processes. Recently, we introduced a tag-free strategy for activity-based protein profiling (ABPP) that utilizes the copper(I)-catalyzed azide-alkyne cycloaddition reaction (&quot;click chemistry&quot;) to analyze the functional state of enzymes in living cells and organisms. Here, we report a detailed characterization of the reaction parameters that affect click chemistry-based ABPP and identify conditions that maximize the speed, sensitivity, and bioorthogonality of this approach. Using these optimized conditions, we compare the enzyme activity profiles of living and homogenized breast cancer cells, resulting in the identification of several enzymes that are labeled by activity-based probes in situ but not in vitro.},
  file      = {:by-author/S/Speers/2004_Speers_535.pdf:PDF},
  keywords  = {Bioconjugation},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@Article{Spek2009,
  author    = {Spek, Anthony L},
  journal   = {Acta crystallographica. Section D, Biological crystallography},
  title     = {Structure validation in chemical crystallography.},
  year      = {2009},
  pages     = {148--55},
  volume    = {65},
  file      = {2009_Spek_148.pdf:by-author/S/Spek/2009_Spek_148.pdf:PDF},
  keywords  = {Validation; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Spek2002,
  author    = {Spek, A. L.},
  journal   = {Journal of Applied Crystallography},
  title     = {Single-crystal Structure Validation With the Program {PLATON}},
  year      = {2003},
  pages     = {7--13},
  volume    = {36},
  file      = {:by-author/S/Spek/2002_Spek_7.pdf:PDF},
  keywords  = {X-ray Crystallography},
  owner     = {andrius},
  timestamp = {2012.05.07},
  creationdate = {2012-05-07T00:00:00},
}

@Presentation{Spek2013,
  author    = {Ton Spek},
  title     = {PLATON/SQUEEZE in the context of Twinning and SHELXL2013},
  year      = {2013},
  file      = {2013_Spek.ppt:by-author/S/Spek/2013_Spek.ppt:PowerPoint},
  owner     = {saulius},
  timestamp = {2014.03.23},
  creationdate = {2014-03-23T00:00:00},
}

@Presentation{Spek2006,
  author       = {Ton Spek},
  title        = {Crystal Structure Validation: The IUCr tool to distinguish GOOD and trustable single crystal structures from BAD and UGLY reports},
  year         = {2006},
  organization = {Utrecht University,The Netherlands},
  school       = {Bijvoet Center for Biomolecular Research},
  file         = {:by-author/S/Spek/2006_Spek.ppt:PPT},
  keywords     = {Validation; X-ray Crystallography},
  owner        = {saulius},
  timestamp = {2015.03.03},
  creationdate = {2015-03-03T00:00:00},
}

@Article{Spence2013,
  author    = {Spence, J. C. H.},
  journal   = {Acta Crystallographica Section A},
  title     = {Lawrence Bragg, microdiffraction and X-ray lasers},
  year      = {2013},
  issn      = {1600-5724},
  pages     = {25--33},
  volume    = {69},
  abstract  = {We trace the historical development of W. L. Bragg's `law' and the key experimental observation which made it possible using polychromatic radiation at a time when neither X-ray wavelengths nor cell constants were known. This led, through his phasing and solving large mineral structures (without use of a computer), to work on metals, proteins, bubble rafts and his X-ray microscope. The relationship of this to early X-ray microdiffraction is outlined, followed by a brief review of electron microdiffraction methods, where electron-probe sizes smaller than one unit cell can be formed with an interesting `failure' of Bragg's law. We end with a review of recent femtosecond X-ray `snapshot' diffraction from protein nanocrystals, using an X-ray laser which generates pulses so short that they terminate before radiation damage can commence, yet subsequently destroy the sample. In this way, using short pulses instead of freezing, the nexus between dose, resolution and crystal size has been broken, opening the way to time-resolved diffraction without damage for a stream of identical particles.},
  doi       = {10.1107/S0108767312046296},
  file      = {2013_Spence_25.pdf:by-author/S/Spence/2013_Spence_25.pdf:PDF},
  keywords  = {Bragg's Law; CBED; Convergent-beam Electron Diffraction; Microdiffraction; Time-resolved Diffraction; X-ray Crystallography; X-ray Lasers},
  owner     = {saulius},
  publisher = {International Union of Crystallography},
  timestamp = {2013.05.06},
  creationdate = {2013-05-06T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0108767312046296},
}

@Article{Spiegelhalter1980,
  author    = {Spiegelhalter, D. J.},
  journal   = {Biometrika},
  title     = {An Omnibus Test for Normality for Small Samples},
  year      = {1980},
  pages     = {493--496},
  file      = {:by-author/S/Spiegelhalter/1980_Spiegelhalter_493.pdf:PDF},
  keywords  = {Statistical Tests},
  owner     = {andrius},
  timestamp = {2012.09.17},
  creationdate = {2012-09-17T00:00:00},
  url       = {http://www.jstor.org/stable/2335498},
}

@Article{Spiegelhalter1977,
  author    = {Spiegelhalter, D. J.},
  journal   = {Biometrika},
  title     = {A Test for Normality Against Symmetric Alternatives},
  year      = {1977},
  issn      = {00063444},
  pages     = {415--418},
  volume    = {64},
  abstract  = {A tractable location and scale invariant test for normality against all symmetric alternatives is proposed. The test statistic closely approximates a combination of two traditional test statistics, and is shown to have a Bayesian interpretation. A simulation study shows that the test compares favourably with a number of other recently proposed tests.},
  file      = {:by-author/S/Spiegelhalter/1977_Spiegelhalter_415.pdf:PDF},
  groups    = {sg/Bayesian},
  keywords  = {Statistical Tests},
  language  = {English},
  owner     = {andrius},
  publisher = {Biometrika Trust},
  timestamp = {2012.09.17},
  creationdate = {2012-09-17T00:00:00},
  url       = {http://www.jstor.org/stable/2335710},
}

@Article{Spilman2013,
  author    = {Spilman, Michael and Cocozaki, Alexis and Hale, Caryn and Shao, Yaming and Ramia, Nancy and Terns, Rebeca and Terns, Michael and Li, Hong and Stalgg, Scott},
  journal   = {Molecular Cell},
  title     = {Structure of an RNA Silencing Complex of the CRISPR-Cas Immune System},
  year      = {2013},
  pages     = {146--152},
  volume    = {52},
  abstract  = {Bacterial and archaeal clustered regularly interspaced short palindromic repeat (CRISPR) loci capture virus and plasmid sequences and use them to recognize and eliminate these invaders. CRISPR RNAs (crRNAs) containing the acquired sequences are incorporated into effector complexes that destroy matching invader nucleic acids. The multicomponent Cmr effector complex cleaves RNA targets complementary to the crRNAs. Here, we report cryoelectron microscopy reconstruction of a functional Cmr complex bound with a target RNA at ~12 Å. Pairs of the Cmr4 and Cmr5 proteins form a helical core that is asymmetrically capped on each end by distinct pairs of the four remaining subunits: Cmr2 and Cmr3 at the conserved 50 crRNA tag sequence and Cmr1 and Cmr6 near the 30 end of the crRNA. The shape and organization of the RNA-targeting Cmr complex is strikingly similar to the DNA-targeting Cascade complex. Our results reveal a remarkably conserved architecture among very distantly related CRISPR-Cas complexes.},
  doi       = {10.1016/j.molcel.2013.09.008},
  file      = {:by-author/S/Spilman/2013_Spilman_146.pdf:PDF},
  groups    = {sg/CRISPR-Cas},
  keywords  = {CRISPR; Cascade; Cmr Complex; EM Structure; Effector Complex},
  owner     = {em},
  timestamp = {2014.05.26},
  creationdate = {2014-05-26T00:00:00},
}

@Article{Spinellis2004,
  author    = {Spinellis, Diomidis and Clemens Szyperski},
  journal   = {IEEE Software},
  title     = {How Is Open Source Affecting Software Development?},
  year      = {2004},
  pages     = {28},
  file      = {:by-author/S/Spinellis/2004_Spinellis_28.pdf:PDF},
  keywords  = {Computer Science (CS); Software Development},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Spolar1994,
  author    = {Spolar, R S and Record, Jr, M T},
  journal   = {Science (New York, N.Y.)},
  title     = {Coupling of local folding to site-specific binding of proteins to DNA.},
  year      = {1994},
  pages     = {777--84},
  volume    = {263},
  file      = {1994_Spolar_777.pdf:by-author/S/Spolar/1994_Spolar_777.pdf:PDF},
  keywords  = {Stacking},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Sponer2000,
  author    = {Šponer, Jirí and Florián, Jan and Ng, Ho-Leung and Šponer, Judit E. and Špacková, Nad’a},
  journal   = {Nucleic Acids Research},
  title     = {Local conformational variations observed in B-DNA crystals do not improve base stacking: computational analysis of base stacking in a d(CATGGGCCCATG)2 B↔A intermediate crystal structure},
  year      = {2000},
  pages     = {4893--4902},
  volume    = {28},
  abstract  = {The crystal structure of d(CATGGGCCCATG)2 shows unique stacking patterns of a stable B↔A-DNA intermediate. We evaluated intrinsic base stacking energies in this crystal structure using an ab initio quantum mechanical method. We found that all crystal base pair steps have stacking energies close to their values in the standard and crystal B-DNA geometries. Thus, naturally occurring stacking geometries were essentially isoenergetic while individual base pair steps differed substantially in the balance of intra-strand and inter-strand stacking terms. Also, relative dispersion, electrostatic and polarization contributions to the stability of different base pair steps were very sensitive to base composition and sequence context. A large stacking flexibility is most apparent for the CpA step, while the GpG step is characterized by weak intra-strand stacking. Hydration effects were estimated using the Langevin dipoles solvation model. These calculations showed that an aqueous environment efficiently compensates for electrostatic stacking contributions. Finally, we have carried out explicit solvent molecular dynamics simulation of the d(CATGGGCCCATG)2 duplex in water. Here the DNA conformation did not retain the initial crystal geometry, but moved from the B↔A intermediate towards the B-DNA structure. The base stacking energy improved in the course of this simulation. Our findings indicate that intrinsic base stacking interactions are not sufficient to stabilize the local conformational variations in crystals.},
  doi       = {10.1093/nar/28.24.4893},
  eprint    = {http://nar.oxfordjournals.org/content/28/24/4893.full.pdf+html},
  file      = {2000_Sponer_4893.pdf:by-author/S/Sponer/2000_Sponer_4893.pdf:PDF},
  groups    = {sg/applications},
  keywords  = {Readout; Stacking},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://nar.oxfordjournals.org/content/28/24/4893.abstract},
}

@Article{Sponer1997,
  author    = {Sponer, J and Gabb, H A and Leszczynski, J and Hobza, P},
  journal   = {Biophysical journal},
  title     = {Base-base and deoxyribose-base stacking interactions in B-DNA and Z-DNA: a quantum-chemical study.},
  year      = {1997},
  pages     = {76--87},
  volume    = {73},
  abstract  = {Base-stacking interactions in canonical and crystal B-DNA and in Z-DNA steps are studied using the ab initio quantum-chemical method with inclusion of electron correlation. The stacking energies in canonical B-DNA base-pair steps vary from -9.5 kcal/mol (GG) to -13.2 kcal/mol (GC). The many-body nonadditivity term, although rather small in absolute value, influences the sequence dependence of stacking energy. The base-stacking energies calculated for CGC and a hypothetical TAT sequence in Z-configuration are similar to those in B-DNA. Comparison with older quantum-chemical studies shows that they do not provide even a qualitatively correct description of base stacking. We also evaluate the base-(deoxy)ribose stacking geometry that occurs in Z-DNA and in nucleotides linked by 2',5'-phosphodiester bonds. Although the molecular orbital analysis does not rule out the charge-transfer n-pi* interaction of the sugar 04' with the aromatic base, the base-sugar contact is stabilized by dispersion energy similar to that of stacked bases. The stabilization amounts to almost 4 kcal/mol and is thus comparable to that afforded by normal base-base stacking. This enhancement of the total stacking interaction could contribute to the propensity of short d(CG)n sequences to adopt the Z-conformation.},
  file      = {1997_Sponer_76.pdf:by-author/S/Sponer/1997_Sponer_76.pdf:PDF},
  keywords  = {Readout; Stacking},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Spudich1998,
  author     = {Spudich, John L.},
  journal    = {Molecular Microbiology},
  title      = {Variations on a molecular switch: transport and sensory signalling by archaeal rhodopsins},
  year       = {1998},
  issn       = {1365-2958},
  pages      = {1051--1058},
  volume     = {28},
  abstract   = {The archaeal rhodopsins are a family of seven-transmembrane-helix, visual pigment-like proteins found in Halobacterium salinarum and related halophilic Archaea. Two, bacteriorhodopsin (BR) and halorhodopsin (HR), are transport rhodopsins that carry out light-driven electrogenic translocation of protons and chloride, respectively, across the cell membrane. The other two, sensory rhodopsins I and II (SRI and SRII), are phototaxis receptors that send signals to tightly bound transducer proteins that in turn control a phosphorylation cascade modulating the cell's flagellar motors. Recent progress has cast light on how nature has modified the common design of these proteins to carry out their distinctly different functions: electrogenic ion transport and non-electrogenic signal transduction. A key shared mechanism between BR and SRII appears to be an interhelical salt bridge locked conformational switch that is released by photoisomerization of retinal. In BR disruption of the lock opens a cytoplasmic half-channel that ensures uptake of the transported proton from the cytoplasmic side of the membrane at a critical time in the pumping cycle. Transducer-free SRI uses the same mechanism to carry out light-driven proton transport, but interaction with its transducer blocks the cytoplasmic half-channel thereby interrupting the transport cycle. In SRI, transducer interaction also disrupts the salt bridge in the dark, poising the receptor in an intermediate conformation able to produce opposite signals depending on the colour of the stimulus light. A model for signalling is proposed in which the salt bridge-controlled half-channel is used to modulate interaction with the Htr proteins when the receptor signalling states are formed.},
  copyright  = {Blackwell Science Ltd, Oxford},
  doi        = {10.1046/j.1365-2958.1998.00859.x},
  file       = {Full Text PDF:by-author/S/Spudich/1998_Spudich_1051.pdf:application/pdf;Snapshot:by-author/S/Spudich/1998_Spudich_1051.html:text/html},
  groups     = {sg/biomolecular},
  language   = {en},
  owner      = {saulius},
  shorttitle = {Variations on a molecular switch},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url        = {http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2958.1998.00859.x/abstract},
  urldate    = {2015-08-05},
}

@Article{Spyrakis2007,
  author    = {Spyrakis, Francesca and Cozzini, Pietro and Bertoli, Chiara and Marabotti, Anna and Kellogg, Glen E and Mozzarelli, Andrea},
  journal   = {BMC structural biology},
  title     = {Energetics of the protein-DNA-water interaction.},
  year      = {2007},
  pages     = {4},
  volume    = {7},
  file      = {2007_Spyrakis_4.pdf:by-author/S/Spyrakis/2007_Spyrakis_4.pdf:PDF},
  keywords  = {Noncovalent Interactions; Protein Physics},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Spyridaki2003,
  author    = {Spyridaki, Aspasia and Matzen, Claudia and Lanio, Thomas and Jeltsch, Albert and Simoncsits, Andras and Athanasiadis, Alekos and Scheuring-Vanamee, Eva and Kokkinidis, Michael and Pingoud, Alfred},
  journal   = {Journal of molecular biology},
  title     = {Structural and biochemical characterization of a new Mg(2+) binding site near Tyr94 in the restriction endonuclease PvuII.},
  year      = {2003},
  pages     = {395--406},
  volume    = {331},
  abstract  = {We have determined the crystal structure of the PvuII endonuclease in the presence of Mg(2+). According to the structural data, divalent metal ion binding in the PvuII subunits is highly asymmetric. The PvuII-Mg(2+) complex has two distinct metal ion binding sites, one in each monomer. One site is formed by the catalytic residues Asp58 and Glu68, and has extensive similarities to a catalytically important site found in all structurally examined restriction endonucleases. The other binding site is located in the other monomer, in the immediate vicinity of the hydroxyl group of Tyr94; it has no analogy to metal ion binding sites found so far in restriction endonucleases. To assign the number of metal ions involved and to better understand the role of Mg(2+) binding to Tyr94 for the function of PvuII, we have exchanged Tyr94 by Phe and characterized the metal ion dependence of DNA cleavage of wild-type PvuII and the Y94F variant. Wild-type PvuII cleaves both strands of the DNA in a concerted reaction. Mg(2+) binding, as measured by the Mg(2+) dependence of DNA cleavage, occurs with a Hill coefficient of 4, meaning that at least two metal ions are bound to each subunit in a cooperative fashion upon formation of the active complex. Quenched-flow experiments show that DNA cleavage occurs about tenfold faster if Mg(2+) is pre-incubated with enzyme or DNA than if preformed enzyme-DNA complexes are mixed with Mg(2+). These results show that Mg(2+) cannot easily enter the active center of the preformed enzyme-DNA complex, but that for fast cleavage the metal ions must already be bound to the apoenzyme and carried with the enzyme into the enzyme-DNA complex. The Y94F variant, in contrast to wild-type PvuII, does not cleave DNA in a concerted manner and metal ion binding occurs with a Hill coefficient of 1. These results indicate that removal of the Mg(2+) binding site at Tyr94 completely disrupts the cooperativity in DNA cleavage. Moreover, in quenched-flow experiments Y94F cleaves DNA about ten times more slowly than wild-type PvuII, regardless of the order of mixing. From these results we conclude that wild-type PvuII cleaves DNA in a fast and concerted reaction, because the Mg(2+) required for catalysis are already bound at the enzyme, one of them at Tyr94. We suggest that this Mg(2+) is shifted to the active center during binding of a specific DNA substrate. These results, for the first time, shed light on the pathway by which metal ions as essential cofactors enter the catalytic center of restriction endonucleases.},
  file      = {:by-author/S/Spyridaki/2003_Spyridaki_395.pdf:PDF},
  owner     = {em},
  timestamp = {2013.09.19},
  creationdate = {2013-09-19T00:00:00},
}

@Article{Squire2003,
  author    = {John Squire and Hind AL-Khayat and Struther Arnott and Jane Crawshaw and Richard Denny and Greg Diakun and David Dover and Trevor Forsyth and Andrew He and Carlo Knupp and Geoff Mant and Ganeshalingam Rajkumar and Matthew Rodman and Mark Shotton and Alan Windle},
  journal   = {Fibre Diffraction Review},
  title     = {New CCP13 Software and the Strategy Behind Further Developments: Stripping and Modelling of Fibre Diffraction Data},
  year      = {2003},
  pages     = {7--10},
  volume    = {11},
  abstract  = {The aim of the CCP13 project is to provide easily usable software programs for those doing fibre diffraction or solution scattering studies; in fact any studies using diffraction from non-crystalline materials. Over the last ten years CCP13 project scientists have developed a set of programs for stripping and analysing fibre diffraction patterns and also patterns from solution scattering and other low-angle diffraction methods. The suite is now being updated to keep in step with new developments in beamlines, in detectors and in computing power and, in addition, new programs are being developed to allow for systematic modelling of different kinds of structures. The present report discusses the strategy behind the approach, it describes what has been implemented so far and it outlines new developments that are in the pipeline.},
  file      = {:by-author/S/Squire/2003_Squire_7.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.09.18},
  creationdate = {2012-09-18T00:00:00},
}

@Article{Sra2012,
  author    = {Suvrit Sra},
  journal   = {Computational Statistics},
  title     = {A Short Note on Parameter Approximation for von {M}ises-{F}isher Distributions: and a Fast Implementation of $I_{s}(x)$},
  year      = {2012},
  pages     = {177–190},
  volume    = {27},
  doi       = {10.1007/s00180-011-0232-x},
  file      = {:by-author/S/Sra/2012_Sra_177.pdf:PDF},
  keywords  = {Clustering on Hyperspheres},
  owner     = {andrius},
  timestamp = {2012.08.13},
  creationdate = {2012-08-13T00:00:00},
}

@Article{Srinivasan1993,
  author    = {Srinivasan, S. and March, C. J. and Sudarsanam, S.},
  journal   = {Protein science : a publication of the Protein Society},
  title     = {An automated method for modeling proteins on known templates using distance geometry.},
  year      = {1993},
  pages     = {277--89},
  volume    = {2},
  abstract  = {We present an automated method incorporated into a software package, FOLDER, to fold a protein sequence on a given three-dimensional (3D) template. Starting with the sequence alignment of a family of homologous proteins, tertiary structures are modeled using the known 3D structure of one member of the family as a template. Homologous interatomic distances from the template are used as constraints. For nonhomologous regions in the model protein, the lower and the upper bounds for the interatomic distances are imposed by steric constraints and the globular dimensions of the template, respectively. Distance geometry is used to embed an ensemble of structures consistent with these distance bounds. Structures are selected from this ensemble based on minimal distance error criteria, after a penalty function optimization step. These structures are then refined using energy optimization methods. The method is tested by simulating the alpha-chain of horse hemoglobin using the alpha-chain of human hemoglobin as the template and by comparing the generated models with the crystal structure of the alpha-chain of horse hemoglobin. We also test the packing efficiency of this method by reconstructing the atomic positions of the interior side chains beyond C beta atoms of a protein domain from a known 3D structure. In both test cases, models retain the template constraints and any additionally imposed constraints while the packing of the interior residues is optimized with no short contacts or bond deformations. To demonstrate the use of this method in simulating structures of proteins with nonhomologous disulfides, we construct a model of murine interleukin (IL)-4 using the NMR structure of human IL-4 as the template. The resulting geometry of the nonhomologous disulfide in the model structure for murine IL-4 is consistent with standard disulfide geometry.},
  file      = {:by-author/S/Srinivasan/1993_Srinivasan_277.pdf:PDF},
  keywords  = {Distance Geometry; Protein Bioinformatics},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Srivastava2007,
  author    = {Srivastava, D K and Jude, Kevin M and Banerjee, Abir L and Haldar, Manas and Manokaran, Sumathra and Kooren, Joel and Mallik, Sanku and Christianson, David W},
  journal   = {Journal of the American Chemical Society},
  title     = {Structural analysis of charge discrimination in the binding of inhibitors to human carbonic anhydrases I and II.},
  year      = {2007},
  pages     = {5528--37},
  volume    = {129},
  abstract  = {Despite the similarity in the active site pockets of carbonic anhydrase (CA) isozymes I and II, the binding affinities of benzenesulfonamide inhibitors are invariably higher with CA II as compared to CA I. To explore the structural basis of this molecular recognition phenomenon, we have designed and synthesized simple benzenesulfonamide inhibitors substituted at the para position with positively charged, negatively charged, and neutral functional groups, and we have determined the affinities and X-ray crystal structures of their enzyme complexes. The para-substituents are designed to bind in the midsection of the 15 A deep active site cleft, where interactions with enzyme residues and solvent molecules are possible. We find that a para-substituted positively charged amino group is more poorly tolerated in the active site of CA I compared with CA II. In contrast, a para-substituted negatively charged carboxylate substituent is tolerated equally well in the active sites of both CA isozymes. Notably, enzyme-inhibitor affinity increases upon neutralization of inhibitor charged groups by amidation or esterification. These results inform the design of short molecular linkers connecting the benzenesulfonamide group and a para-substituted tail group in "two-prong" CA inhibitors: an optimal linker segment will be electronically neutral, yet capable of engaging in at least some hydrogen bond interactions with protein residues and/or solvent. Microcalorimetric data reveal that inhibitor binding to CA I is enthalpically less favorable and entropically more favorable than inhibitor binding to CA II. This contrasting behavior may arise in part from differences in active site desolvation and the conformational entropy of inhibitor binding to each isozyme active site.},
  file      = {2007_Srivastava_5528.pdf:by-author/S/Srivastava/2007_Srivastava_5528.pdf:PDF},
  groups    = {sg/inhibitors, sg/hCA1, sg/hCA2},
  keywords  = {Carbonic Anhydrases; Inhibitors},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Staals2013,
  author    = {Staals, Raymond H.J. and Agari, Yoshihiro and Maki-Yonekura, Saori and Zhu, Yifan and Taylor, David W. and van Duijn, Esther and Barendregt, Arjan and Vlot, Marnix and Koehorst, Jasper J. and Sakamoto, Keiko and Masuda, Akiko and Dohmae, Naoshi and Schaap, Peter J. and Doudna, Jennifer A. and Heck, Albert J.R. and Yonekura, Koji and van der Oost, John and Shinkai, Akeo},
  journal   = {Molecular Cell},
  title     = {Structure and Activity of the RNA-Targeting Type III-B CRISPR-Cas Complex of Thermus thermophilus},
  year      = {2013},
  pages     = {135–145},
  volume    = {52},
  abstract  = {The CRISPR-Cas system is a prokaryotic host defense system against genetic elements. The Type III-B CRISPR-Cas system of the bacterium Thermus thermophilus, the TtCmr complex, is composed of six different protein subunits (Cmr1-6) and one crRNA with a stoichiometry of Cmr112131445361: crRNA1. The TtCmr complex copurifies with crRNA species of 40 and 46 nt, originating from a distinct subset of CRISPR loci and spacers. The TtCmr com- plex cleaves the target RNA at multiple sites with 6 nt intervals via a 50 ruler mechanism. Electron micro- scopy revealed that the structure of TtCmr resem- bles a ‘‘sea worm’’ and is composed of a Cmr2-3 heterodimer ‘‘tail,’’ a helical backbone of Cmr4 subunits capped by Cmr5 subunits, and a curled ‘‘head’’ containing Cmr1 and Cmr6. Despite having a backbone of only four Cmr4 subunits and being both longer and narrower, the overall architecture of TtCmr resembles that of Type I Cascade com- plexes.},
  doi       = {10.1016/j.molcel.2013.09.013},
  file      = {:by-author/S/Staals/2013_Staals_135.pdf:PDF},
  groups    = {sg/CRISPR-Cas},
  keywords  = {CRISPR; Cascade; Cmr Complex; EM Structure; Effector Complex; III-B},
  owner     = {em},
  timestamp = {2014.05.26},
  creationdate = {2014-05-26T00:00:00},
}

@Article{Stahlberg2008,
  author    = {Stahlberg, Henning and Walz, Thomas},
  journal   = {ACS chemical biology},
  title     = {Molecular electron microscopy: state of the art and current challenges.},
  year      = {2008},
  pages     = {268--81},
  volume    = {3},
  abstract  = {The objective of molecular electron microscopy (EM) is to use electron microscopes to visualize the structure of biological molecules. This Review provides a brief overview of the methods used in molecular EM, their respective strengths and successes, and current developments that promise an even more exciting future for molecular EM in the structural investigation of proteins and macromolecular complexes, studied in isolation or in the context of cells and tissues.},
  file      = {:by-author/S/Stahlberg/2008_Stahlberg_268.pdf:PDF},
  keywords  = {CryoEM},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@Article{Stajich2006,
  author     = {Stajich, Jason E. and Lapp, Hilmar},
  journal    = {Briefings in Bioinformatics},
  title      = {Open source tools and toolkits for bioinformatics: significance, and where are we?},
  year       = {2006},
  issn       = {1467-5463, 1477-4054},
  pages      = {287--296},
  volume     = {7},
  abstract   = {This review summarizes important work in open-source bioinformatics software that has occurred over the past couple of years. The survey is intended to illustrate how programs and toolkits whose source code has been developed or released under an Open Source license have changed informatics-heavy areas of life science research. Rather than creating a comprehensive list of all tools developed over the last 2–3 years, we use a few selected projects encompassing toolkit libraries, analysis tools, data analysis environments and interoperability standards to show how freely available and modifiable open-source software can serve as the foundation for building important applications, analysis workflows and resources.},
  doi        = {10.1093/bib/bbl026},
  file       = {Full Text PDF:by-author/S/Stajich/2006_Stajich_287.pdf:application/pdf;Snapshot:by-author/S/Stajich/2006_Stajich_287.html:text/html},
  keywords   = {Bioinformatics; Genomics; Open Source; Software; Tools},
  language   = {en},
  owner      = {saulius},
  pmid       = {16899494},
  shorttitle = {Open source tools and toolkits for bioinformatics},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url        = {http://bib.oxfordjournals.org/content/7/3/287},
  urldate    = {2015.06.06},
}

@Article{Stallforth2013,
  author    = {Stallforth, Pierre and Clardy, Jon},
  journal   = {Nature},
  title     = {X-ray crystallography: One size fits most},
  year      = {2013},
  issn      = {0028-0836},
  pages     = {456--457},
  volume    = {495},
  abstract  = {Crystalline 'sponges' offer a way to impose order on small molecules so that their structures can be solved by X-ray crystallography. This enables nanogram quantities of material to be analysed using the technique. See Article p.461},
  comment   = {10.1038/495456a},
  file      = {2013_Stallforth_456.pdf:by-author/S/Stallforth/2013_Stallforth_456.pdf:PDF},
  keywords  = {Chemical Crystalography; Crystallography; Porous Materials; X-ray Crystallography},
  owner     = {saulius},
  publisher = {Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},
  timestamp = {2013.04.03},
  creationdate = {2013-04-03T00:00:00},
  url       = {http://dx.doi.org/10.1038/495456a},
}

@Article{Stamelos2003,
  author    = {Stamelos, Ioannis and Lefteris Angelis and Maurizio Morisio and Evaggelos Sakellaris and George L. Bleris},
  journal   = {Information \& Management},
  title     = {Estimating the development cost of custom software},
  year      = {2003},
  pages     = {729--741},
  volume    = {40},
  abstract  = {In this paper an approach for the estimation of software development costs is presented. The method is based on the characterization of the software to be developed in terms of project and environment attributes and comparison with some similar completed project(s) recovered from a historical database. A case study is also presented, focusing on the calibration and application of the method on 59 information systems implementing supply chain functions in industry. Various strategies are explored, the best of which predicted effort quite effectively, with a mean estimation error of 24% with respect to the actual effort.},
  file      = {:by-author/S/Stamelos/2003_Stamelos_729.pdf:PDF},
  keywords  = {Computer Science (CS); Software Costs},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Presentation{Stampf2004a,
  author           = {Dave Stampf},
  title            = {{ZINC} -- Galvanizing {CIF} to Work with {UNIX}},
  year             = {2004},
  organization     = {BNL Protein Data Bank},
  creationdate     = {2013-09-19T00:00:00},
  file             = {:by-author/S/Stampf/2004_Stampf_slides.pdf:PDF},
  keywords         = {CIF},
  modificationdate = {2023-08-07T10:23:05},
  owner            = {saulius},
  timestamp        = {2013.09.19},
  url              = {http://www.iucr.org/__data/iucr/cif/software/zinc/doc/zinc-slides.pdf},
}

@Manuscript{Stampf2004,
  author           = {David R. Stampf},
  title            = {{ZINC} -- Galvanizing {CIF} to Work with {UNIX}},
  year             = {2004},
  keywords         = {CIF},
  organization     = {Protein Data Bank, Brookhaven National Laboratory},
  url              = {http://www.iucr.org/__data/iucr/cif/software/zinc/doc/zinc-paper.pdf},
  creationdate     = {2013-09-19T00:00:00},
  file             = {:by-author/S/Stampf/2004_Stampf.pdf:PDF},
  modificationdate = {2023-08-07T10:23:05},
  owner            = {saulius},
  timestamp        = {2013.09.19},
}

@Article{Stanisic2015,
  author     = {Stanisic, Luka and Legrand, Arnaud and Danjean, Vincent},
  journal    = {SIGOPS Oper. Syst. Rev.},
  title      = {An Effective Git And Org-Mode Based Workflow For Reproducible Research},
  year       = {2015},
  issn       = {0163-5980},
  month      = jan,
  number     = {1},
  pages      = {61--70},
  volume     = {49},
  abstract   = {In this paper we address the question of developing a lightweight and effective workflow for conducting experimental research on modern parallel computer systems in a reproducible way. Our approach builds on two well-known tools (Git and Org-mode) and enables to address, at least partially, issues such as running experiments, provenance tracking, experimental setup reconstruction or replicable analysis. We have been using such a methodology for two years now and it enabled us to recently publish a fully reproducible article [12]. To fully demonstrate the effectiveness of our proposal, we have opened our two year laboratory notebook with all the attached experimental data. This notebook and the underlying Git revision control system enable to illustrate and to better understand the workflow we used.},
  acmid      = {2723881},
  address    = {New York, NY, USA},
  doi        = {10.1145/2723872.2723881},
  file       = {2015_Stanisic_61.pdf:by-author/S/Stanisic/2015_Stanisic_61.pdf:PDF},
  groups     = {sg/Methods and tools},
  issue_date = {January 2015},
  keywords   = {Executable Papers; GIT; Org-mode; Reproducible Research; Work Flows},
  numpages   = {10},
  owner      = {saulius},
  publisher  = {ACM},
  timestamp = {2016.11.17},
  creationdate = {2016-11-17T00:00:00},
  url        = {http://doi.acm.org/10.1145/2723872.2723881},
}

@Article{Stankevicius1998,
  author    = {Stankevicius, K. and Lubys, A. and Timinskas, A. and Vaitkevicius, D. and Janulaitis, A.},
  journal   = {Nucleic acids research},
  title     = {Cloning and analysis of the four genes coding for Bpu10I restriction-modification enzymes.},
  year      = {1998},
  pages     = {1084--91},
  volume    = {26},
  abstract  = {The Bpu 10I R-M system from Bacillus pumilus 10, which recognizes the asymmetric 5'-CCTNAGC sequence, has been cloned, sequenced and expressed in Escherichia coli . The system comprises four adjacent, similarly oriented genes encoding two m5C MTases and two subunits of Bpu 10I ENase (34.5 and 34 kDa). Both bpu10IR genes either in cis or trans are needed for the manifestation of R. Bpu 10I activity. Subunits of R. Bpu 10I, purified to apparent homogeneity, are both required for cleavage activity. This heterosubunit structure distinguishes the Bpu 10I restriction endonuclease from all other type II restriction enzymes described previously. The subunits reveal 25% amino acid identity. Significant similarity was also identified between a 43 amino acid region of R. Dde I and one of the regions of higher identity shared between the Bpu 10I subunits, a region that could possibly include the catalytic/Mg2+binding center. The similarity between Bpu 10I and Dde I MTases is not limited to the conserved motifs (CM) typical for m5C MTases. It extends into the variable region that lies between CMs VIII and IX. Duplication of a progenitor gene, encoding an enzyme recognizing a symmetric nucleotide sequence, followed by concerted divergent evolution, may provide a possible scenario leading to the emergence of the Bpu 10I ENase, which recognizes an overall asymmetric sequence and cleaves within it symmetrically.},
  file      = {:by-author/S/Stankevicius/1998_Stankevicius_1084.pdf:PDF},
  keywords  = {TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Starikov2010,
  author    = {Starikov},
  title     = {Many Faces of Entropy or Bayesian Statistical Mechanics},
  year      = {2010},
  abstract  = {Some 80-90 years ago, George A. Linhart, unlike A. Einstein, P. Debye, M. Planck and W. Nernst, has managed to derive a very simple, but ultimately general mathematical formula for heat capacity vs. temperature from the fundamental thermodynamical principles, using what we would nowadays dub a “Bayesian approach to probability”. Moreover, he has successfully applied his result to fit the experimental data for diverse substances in their solid state in a rather broad temperature range. Nevertheless, Linhart's work was undeservedly forgotten, although it does represent a valid and fresh standpoint on thermodynamics and statistical physics, which may have a significant implication for academic and applied science.},
  file      = {:by-author/S/Starikov/2010_Starikov.pdf:PDF},
  groups    = {sg/Bayesian},
  keywords  = {Bayesian Statistics; Mathematics},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Starr2015,
  author    = {Starr, Joan and Castro, Eleni and Crosas, Mercè and Dumontier, Michel and Downs, Robert R. and Duerr, Ruth and Haak, Laurel L. and Haendel, Melissa and Herman, Ivan and Hodson, Simon and et al.},
  journal   = {PeerJ Computer Science},
  title     = {Achieving human and machine accessibility of cited data in scholarly publications},
  year      = {2015},
  issn      = {2376-5992},
  month     = {May},
  pages     = {e1},
  volume    = {1},
  abstract  = {Reproducibility and reusability of research results is an important concern in scientific communication and science policy. A foundational element of reproducibility and reusability is the open and persistently available presentation of research data. However, many common approaches for primary data publication in use today do not achieve sufficient long-term robustness, openness, accessibility or uniformity. Nor do they permit comprehensive exploitation by modern Web technologies. This has led to several authoritative studies recommending uniform direct citation of data archived in persistent repositories. Data are to be considered as first-class scholarly objects, and treated similarly in many ways to cited and archived scientific and scholarly literature. Here we briefly review the most current and widely agreed set of principle-based recommendations for scholarly data citation, the Joint Declaration of Data Citation Principles (JDDCP). We then present a framework for operationalizing the JDDCP; and a set of initial recommendations on identifier schemes, identifier resolution behavior, required metadata elements, and best practices for realizing programmatic machine actionability of cited data. The main target audience for the common implementation guidelines in this article consists of publishers, scholarly organizations, and persistent data repositories, including technical staff members in these organizations. But ordinary researchers can also benefit from these recommendations. The guidance provided here is intended to help achieve widespread, uniform human and machine accessibility of deposited data, in support of significantly improved verification, validation, reproducibility and re-use of scholarly/scientific data.},
  doi       = {10.7717/peerj-cs.1},
  file      = {2015_Starr_e1.pdf:by-author/A/Starr/2015_Starr_e1.pdf:PDF},
  groups    = {sg/Non-reproducibility},
  keywords  = {Data Sharing; Reproducible Research},
  owner     = {saulius},
  publisher = {PeerJ},
  timestamp = {2016.10.24},
  creationdate = {2016-10-24T00:00:00},
  url       = {http://dx.doi.org/10.7717/peerj-cs.1},
}

@Article{Stassin2016,
  author    = {Timoth{\'{e}}e Stassin and Helge Reinsch and Ben Van{\hspace{0.25em}}de{\hspace{0.25em}}Voorde and Stefan Wuttke and Dana D. Medina and Norbert Stock and Thomas Bein and Rob Ameloot and Dirk De{\hspace{0.25em}}Vos},
  journal   = {{ChemSusChem}},
  title     = {Adsorption and Reactive Desorption on Metal-Organic Frameworks: A Direct Strategy for Lactic Acid Recovery},
  year      = {2016},
  month     = {nov},
  comment   = {Synthesis in the supporting information. Synthesis of numerous MOFs surveyed.},
  doi       = {10.1002/cssc.201601000},
  file      = {:by-author/S/Stassin/2016_Stassin_a.pdf:PDF;Stassin2016.pdf:by-author/S/Stassin/2016_Stassin.pdf:PDF},
  groups    = {sg/MOF, sg/MOFs, am/MOFs},
  keywords  = {Synthesis},
  owner     = {saulius},
  publisher = {Wiley-Blackwell},
  timestamp = {2017.01.31},
  creationdate = {2017-01-31T00:00:00},
  url       = {https://doi.org/10.1002%2Fcssc.201601000},
}

@Manuscript{Stata1998,
  author    = {Stata, Raymie and Martín Abadi},
  title     = {A Type System for Java Bytecode Subroutines},
  year      = {1998},
  keywords  = {Computer Science (CS); Java; Programming Languages},
  url       = {https://web.eecs.umich.edu/~bchandra/courses/papers/Abadi_JVM.pdf},
  abstract  = {Java is typically compiled into an intermediate language, JVML, that is interpreted by the Java Virtual Machine. Because mobile JVML code is not always trusted, a bytecode verifier enforces static constraints that prevent various dynamic errors. Given the importance of the bytecode verifier for security, its current descriptions are inadequate. This paper proposes using typing rules to describe the bytecode veri er because they are more precise than prose, clearer than code, and easier to reason about than either. JVML has a subroutine construct used for the compilation of Java's try-finally statement. Subroutines are a major source of complexity for the bytecode veri er because they are not obviously last-in/ rst-out and because they re- quire a kind of polymorphism. Focusing on subroutines, we isolate an interesting, small subset of JVML. We give typ- ing rules for this subset and prove their correctness. Our type system constitutes a sound basis for bytecode verification and a rational reconstruction of a delicate part of Sun's bytecode verifier.},
  file      = {:by-author/S/Stata/1998_Stata.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Manuscript{Statisticat2012,
  author    = {Statisticat, L. L. C.},
  title     = {Bayesian Inference},
  year      = {2012},
  keywords  = {Bayesian Statistics; R},
  abstract  = {The Bayesian interpretation of probability is one of two broad categories of interpretations. Bayesian inference updates knowledge about unknowns, parameters, with information from data. The LaplacesDemon package in R enables Bayesian inference, and this vignette provides an introduction to the topic. This article introduces Bayes’ theorem, model-based Bayesian inference, components of Bayesian inference, prior distributions, hierarchical Bayes, conjugacy, likelihood, numerical approximation, prediction, Bayes factors, model fit, posterior predictive checks, and ends by comparing advantages and disadvantages of Bayesian inference.},
  file      = {2012_Statisticat.pdf:by-author/S/Statisticat/2012_Statisticat.pdf:PDF},
  groups    = {sg/Bayesian},
  note      = {R package version 12.11.05},
  owner     = {saulius},
  timestamp = {2012.11.27},
  creationdate = {2012-11-27T00:00:00},
}

@Article{Stearn1935,
  author    = {Stearn, A. E.},
  journal   = {The Journal of general physiology},
  title     = {THE APPLICATION OF QUANTUM MECHANICS TO CERTAIN CASES OF HOMOGENEOUS CATALYSIS : II. CERTAIN ASPECTS OF ENZYME ACTION.},
  year      = {1935},
  pages     = {301--6},
  volume    = {18},
  file      = {:by-author/S/Stearn/1935_Stearn_301.pdf:PDF},
  keywords  = {Quantum Mechanics (QM)},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Steczkiewicz2012,
  author    = {Steczkiewicz, Kamil and Muszewska, Anna and Knizewski, Lukasz and Rychlewski, Leszek and Ginalski, Krzysztof},
  journal   = {Nucleic Acids Research},
  title     = {Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily},
  year      = {2012},
  pages     = {7016–7045},
  volume    = {40},
  abstract  = {Proteins belonging to PD-(D/E)XK phosphodiesterases constitute a functionally diverse superfamily with representatives involved in replication, restriction, DNA repair and tRNA–intron splicing. Their malfunction in humans triggers severe diseases, such as Fanconi anemia and Xeroderma pigmentosum. To date there have been several attempts to identify and classify new PD-(D/E)KK phosphodiesterases using remote homology detection methods. Such efforts are complicated, because the superfamily exhibits extreme sequence and structural divergence. Using advanced homology detection methods supported with superfamily-wide domain architecture and horizontal gene transfer analyses, we provide a comprehensive reclassification of proteins containing a PD-(D/E)XK domain. The PD-(D/E)XK phosphodiesterases span over 21 900 proteins, which can be classified into 121 groups of various families. Eleven of them, including DUF4420, DUF3883, DUF4263, COG5482, COG1395, Tsp45I, HaeII, Eco47II, ScaI, HpaII and Replic_Relax, are newly assigned to the PD-(D/E)XK superfamily. Some groups of PD-(D/E)XK proteins are present in all domains of life, whereas others occur within small numbers of organisms. We observed multiple horizontal gene transfers even between human pathogenic bacteria or from Prokaryota to Eukaryota. Uncommon domain arrangements greatly elaborate the PD-(D/E)XK world. These include domain architectures suggesting regulatory roles in Eukaryotes, like stress sensing and cell-cycle regulation. Our results may inspire further experimental studies aimed at identification of exact biological functions, specific substrates and molecular mechanisms of reactions performed by these highly diverse proteins.},
  doi       = {10.1093/nar/gks382},
  file      = {:by-author/S/Steczkiewicz/2012_Steczkiewicz_7016.pdf:PDF},
  keywords  = {PD (D/E)XK; Restriction Endonucleases (REases)},
  owner     = {em},
  timestamp = {2013.01.17},
  creationdate = {2013-01-17T00:00:00},
}

@Webpage{Steed2014,
  author    = {Jonathan Steed},
  retrieved = {2014-10-17},
  title     = {Structures with Z' > 4},
  url       = {http://zprime.co.uk/database},
  year      = {2014},
  file      = {2014_Steed.odt:by-author/S/Steed/2014_Steed.odt:OpenDocument text},
  keywords  = {Molecule Reconstruction; Z; Zprime},
  owner     = {saulius},
  timestamp = {2014.10.21},
  creationdate = {2014-10-21T00:00:00},
}

@Webpage{Steed2014a,
  author    = {Jonathan Steed},
  retrieved = {2014-10-17},
  title     = {Failures of the Z' definition},
  url       = {https://community.dur.ac.uk/zprime/not.html},
  year      = {2014},
  file      = {2014_Steed_a.odt:by-author/S/Steed/2014_Steed_a.odt:OpenDocument text},
  keywords  = {Molecule Reconstruction; Z; Zprime},
  owner     = {saulius},
  timestamp = {2014.10.21},
  creationdate = {2014-10-21T00:00:00},
}

@Manuscript{Steele2006,
  author    = {Steele, Jr., Guy L. and Richard P. Gabriel},
  title     = {The Evolution of Lisp},
  year      = {2006},
  keywords  = {Computer Languages; Computer Science (CS); Lisp},
  abstract  = {Lisp is the world’s greatest programming language—or so its proponents think. The structure of Lisp makes it easy to extend the language or even to implement entirely new dialects without starting from scratch. Overall, the evolution of Lisp has been guided more by institutional rivalry, one-upsmanship, and the glee born of technical cleverness that is characteristic of the “hacker culture” than by sober assessments of technical requirements. Nevertheless this process has eventually produced both an industrial- strength programming language, messy but powerful, and a technically pure dialect, small but powerful, that is suitable for use by programming-language theoreticians. We pick up where McCarthy’s paper in the first HOPL conference left off. We trace the development chronologically from the era of the PDP-6, through the heyday of Interlisp and MacLisp, past the ascension and decline of special purpose Lisp machines, to the present era of standardization activities. We then examine the technical evolution of a few representative language features, including both some notable successes and some notable failures, that illuminate design issues that distinguish Lisp from other programming languages. We also discuss the use of Lisp as a laboratory for designing other programming languages. We conclude with some reflections on the forces that have driven the evolution of Lisp.},
  file      = {:by-author/S/Steele/2006_Steele.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@TechReport{Steele2009,
  author      = {Russell J. Steele and Adrian E. Raftery},
  institution = {Department of Statistics University of Washington},
  title       = {Performance of {B}ayesian Model Selection Criteria for Gaussian Mixture Models},
  year        = {2009},
  abstract    = {Bayesian methods are widely used for selecting the number of components in a mixture models, in part because frequentist methods have difficulty in addressing this problem in general. Here we compare some of the Bayesianly motivated or justifiable methods for choosing the number of components in a one-dimensional Gaussian mixture model: posterior probabilities for a well-known proper prior, BIC, ICL, DIC and AIC. We also introduce a new explicit unit-information prior for mixture models, analogous to the prior to which BIC corresponds in regular statistical models. We base the comparison on a simulation study, designed to reflect published estimates of mixture model parameters from the scientific literature across a range of disciplines. We found that BIC clearly outperformed the five other methods, with the maximum a posteriori estimate from the established proper prior second.},
  file        = {:by-author/S/Steele/2009_Steele.pdf:PDF},
  groups      = {sg/Bayesian},
  keywords    = {Bayesian Statistics; Gaussian Mixture Models},
  owner       = {andrius},
  timestamp = {2013.02.15},
  creationdate = {2013-02-15T00:00:00},
  url         = {http://www.stat.washington.edu/research/reports/2009/tr559.pdf},
}

@TechReport{Steenbergen2006,
  author      = {Marco R. Steenbergen},
  institution = {Department of Political Science, University of North Carolina, Chapel Hill},
  title       = {Maximum Likelihood Programming in R},
  year        = {2006},
  file        = {:by-author/S/Steenbergen/2006_Steenbergen.pdf:PDF},
  owner       = {saulius},
  timestamp = {2012.09.18},
  creationdate = {2012-09-18T00:00:00},
}

@Article{Stein1999,
  author    = {Stein, L.D. and Thierry-Mieg, J.},
  journal   = {Computing in Science Engineering},
  title     = {AceDB: a genome database management system},
  year      = {1999},
  issn      = {1521-9615},
  pages     = {44 -52},
  volume    = {1},
  abstract  = {The Human Genome Project has spawned many databases using custom software or with conventional data management systems. Surprisingly, amidst this wealth of genome database systems, few ready-made systems are available to a group that wishes to set up its own genome database or even to an individual interested in experimenting with them to learn more about bioinformatics. Many genome database systems are unavailable for distribution or are so specialized to their task that it is impractical to adapt them for use at another site. Jean Thierry-Mieg and Richard Durbin disproved this generalization by designing AceDB-an object-oriented database system-from the ground up to represent genomes and other complex biological data. Application programmers can use its APIs to fetch, examine, and modify data maintained in a variety of AceDB genome databases},
  doi       = {10.1109/5992.764215},
  file      = {1999_Stein_44.pdf:by-author/S/Stein/1999_Stein_44.pdf:PDF},
  keywords  = {APIs; AceDB Genome Database Management System; Application Program Interfaces; Application Programmers; Bioinformatics; Biology Computing; Complex Biological Data; DNA; Data Management; Databases; Genetics; Human Genome Project; Object-oriented Database System; Object-oriented Databases; Scientific Information Systems},
  owner     = {saulius},
  timestamp = {2012.10.25},
  creationdate = {2012-10-25T00:00:00},
}

@Article{Steiner2017,
  author    = {Steiner, Roberto A. and Tucker, Julie A.},
  journal   = {Acta Crystallographica Section D Structural Biology},
  title     = {Keep it together: restraints in crystallographic refinement of macromolecule–ligand complexes},
  year      = {2017},
  issn      = {2059-7983},
  month     = {Feb},
  number    = {2},
  pages     = {93–102},
  volume    = {73},
  doi       = {10.1107/s2059798316017964},
  file      = {2017_Steiner_93.pdf:by-author/S/Steiner/2017_Steiner_93.pdf:PDF},
  owner     = {andrius},
  publisher = {International Union of Crystallography (IUCr)},
  timestamp = {2017.04.25},
  creationdate = {2017-04-25T00:00:00},
  url       = {http://dx.doi.org/10.1107/S2059798316017964},
}

@Article{Steinhardt1998,
  author    = {Paul J. Steinhardt and H.-C. Jeong and K. Saitoh and M. Tanaka and E. Abe and A. P. Tsai},
  journal   = {Nature},
  title     = {Experimental verification of the quasi-unit-cell model of quasicrystal structure},
  year      = {1998},
  pages     = {55--57},
  volume    = {396},
  doi       = {10.1038/23902},
  file      = {1998_Steinhardt_55.pdf:by-author/S/Steinhardt/1998_Steinhardt_55.pdf:PDF},
  language  = {English},
  owner     = {saulius},
  timestamp = {2015.09.08},
  creationdate = {2015-09-08T00:00:00},
}

@Article{Steipe2002,
  author    = {Steipe, Boris},
  journal   = {Acta Crystallographica Section A},
  title     = {A revised proof of the metric properties of optimally superimposed vector sets},
  year      = {2002},
  pages     = {506},
  volume    = {58},
  abstract  = {A revised proof is given that the root-mean-square deviation between more than two vector sets after optimal superposition induces a metric. This corrects an error in a previous manuscript [Kaindl & Steipe (1997). Acta Cryst. A53, 809].},
  doi       = {10.1107/S0108767302011637},
  file      = {2002_Steipe_506.pdf:by-author/S/Steipe/2002_Steipe_506.pdf:PDF},
  groups    = {sg/Molecule superposion, sg/Superposition, sg/Bioinf. Algorithms},
  keywords  = {Algorithms; Proof; RMSD; Structure Superposition},
  owner     = {saulius},
  timestamp = {2013.03.22},
  creationdate = {2013-03-22T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0108767302011637},
}

@Article{Steller1997,
  author           = {Ingo Steller and Robert Bolotovsky and Michael G. Rossmann},
  journal          = {J. Appl. Cryst.},
  title            = {An algorithm for automatic indexing of oscillation images using {F}ourier analysis},
  year             = {1997},
  pages            = {1036--1040},
  volume           = {30},
  abstract         = {A fast and reliable algorithm has been developed for auto-indexing oscillation images. The observed reflection positions are used to compute the corresponding reciprocal-lattice vectors assuming a stationary crystal. These vectors are then projected onto a chosen direction. The projections are subjected to a one-dimensional Fourier analysis. A large Fourier term will be found that has a periodicity corresponding to the interplanar distance if the chosen direction happens to be perpendi- cular to a set of widely separated reciprocal-lattice planes. Exploration of such directions over a hemisphere establishes the best potential basis vectors of the real cell. The program has successfully determined the lengths and directions of basis vectors for numerous unit cells having cell dimensions ranging from 16 to 668 A and oscillation ranges from 0.2 to 2.0 ° .},
  creationdate     = {2008-07-28T00:00:00},
  file             = {1997_Steller_1036.pdf:by-author/S/Steller/1997_Steller_1036.pdf:PDF},
  keywords         = {Algorithms; Indexing; X-ray Crystallography},
  modificationdate = {2024-08-28T11:57:04},
  owner            = {saulius},
  timestamp        = {2008.07.28},
}

@Presentation{Stepanauskas2003,
  author       = {Ramūnas Stepanauskas},
  title        = {Nekultivuoti mikroorganizmai: proga ekologų ir biotechnologų bendradarbiavimui},
  year         = {2003},
  organization = {Savannah River Ecology Laboratory},
  file         = {:by-author/S/Stepanauskas/2003_Stepanauskas.ppt:PPT},
  keywords     = {Prezentacijos},
  owner        = {saulius},
  timestamp = {2015.03.03},
  creationdate = {2015-03-03T00:00:00},
}

@Presentation{Stephan2008,
  author    = {Frank Stephan},
  title     = {Problem Solving With Computers},
  year      = {2008},
  lecture   = {3},
  file      = {:by-author/S/Stephan/2008_Stephan.ps:PostScript;:by-author/S/Stephan/2008_Stephan.pdf:PDF},
  keywords  = {Computer Science (CS); Data Types; Programming Languages},
  owner     = {saulius},
  timestamp = {2015.02.27},
  creationdate = {2015-02-27T00:00:00},
}

@Article{Stephens1965,
  author    = {Stephens, M. A.},
  journal   = {Biometrika},
  title     = {The Goodness-of-fit Statistic {Vn}: Distribution and Significance Points},
  year      = {1965},
  pages     = {309--321},
  volume    = {52},
  file      = {:by-author/S/Stephens/1965_Stephens_309.pdf:PDF},
  owner     = {andrius},
  timestamp = {2012.06.01},
  creationdate = {2012-06-01T00:00:00},
}

@Article{Sterling1959,
  author    = {Theodore D. Sterling},
  journal   = {Journal of the American Statistical Association},
  title     = {Publication Decisions and their Possible Effects on Inferences Drawn from Tests of Significance --- or Vice Versa},
  year      = {1959},
  pages     = {30--34},
  volume    = {54},
  abstract  = {Abstract There is some evidence that in fields where statistical tests of significance are commonly used, research which yields nonsignificant results is not published. Such research being unknown to other investigators may be repeated independently until eventually by chance a significant result occurs—an “error of the first kind”—and is published. Significant results published in these fields are seldom verified by independent replication. The possibility thus arises that the literature of such a field consists in substantial part of false conclusions resulting from errors of the first kind in statistical tests of significance. * The author wishes to express his thanks to Sir Ronald Fisher whose discussion on related topics stimulated this research in the first place, and to Leo Katz, Oliver Lacey, Enders Robinson, and Paul Siegel for reading and criticizing earlier drafts of this manuscript.},
  doi       = {10.1080/01621459.1959.10501497},
  eprint    = {http://dx.doi.org/10.1080/01621459.1959.10501497},
  file      = {1959_Sterling_30.pdf:by-author/S/Sterling/1959_Sterling_30.pdf:PDF},
  keywords  = {Inference; Significance; Statistics},
  owner     = {saulius},
  timestamp = {2015.06.12},
  creationdate = {2015-06-12T00:00:00},
}

@Article{Stern2010,
  author    = {Stern, Adi and Keren, Leeat and Wurtzel, Omri and Amitai, Gil and Sorek, Rotem},
  journal   = {Trends in genetics : TIG},
  title     = {Self-targeting by CRISPR: gene regulation or autoimmunity?},
  year      = {2010},
  pages     = {335--40},
  volume    = {26},
  abstract  = {The recently discovered prokaryotic immune system known as CRISPR (clustered regularly interspaced short palindromic repeats) is based on small RNAs ('spacers') that restrict phage and plasmid infection. It has been hypothesized that CRISPRs can also regulate self gene expression by utilizing spacers that target self genes. By analyzing CRISPRs from 330 organisms we found that one in every 250 spacers is self-targeting, and that such self-targeting occurs in 18% of all CRISPR-bearing organisms. However, complete lack of conservation across species, combined with abundance of degraded repeats near self-targeting spacers, suggests that self-targeting is a form of autoimmunity rather than a regulatory mechanism. We propose that accidental incorporation of self nucleic acids by CRISPR can incur an autoimmune fitness cost, and this could explain the abundance of degraded CRISPR systems across prokaryotes.},
  file      = {:by-author/S/Stern/2010_Stern_335.pdf:PDF},
  groups    = {sg/CRISPR-Cas},
  keywords  = {CRISPR},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Manuscript{Stern1995,
  author    = {Richard H. Stern},
  title     = {Solving the algorithm conundrum: after 1994 in the Federal Circuit patent law needs a radical algorithmectomy},
  year      = {1995},
  keywords  = {Patentai; Teise},
  file      = {:by-author/S/Stern/1995_Stern.doc:DOC},
  owner     = {saulius},
  timestamp = {2015.02.28},
  creationdate = {2015-02-28T00:00:00},
}

@Article{Steuer2004,
  author       = {Shawn Steuer and Vera Pingoud and Alfred Pingoud and Wolfgang Wende},
  journal      = {Chembiochem},
  title        = {Chimeras of the homing endonuclease PI-SceI and the homologous Candida tropicalis intein: a study to explore the possibility of exchanging DNA-binding modules to obtain highly specific endonucleases with altered specificity.},
  year         = {2004},
  month        = {Feb},
  number       = {2},
  pages        = {206--213},
  volume       = {5},
  abstract     = {Homing endonucleases are extremely specific endodeoxyribonucleases. In vivo, these enzymes confer mobility on their genes by inducing a very specific double-strand cut in cognate alleles that lack the cooling sequence for the homing endonuclease; the cellular repair of the double-strand break with the endonuclease-containing allele as a template leads to integration of the endonuclease gene, completing the homing process. As a result of their extreme sequence specificity, homing endonucleases are promising tools for genome engineering. For this purpose, it is desirable to design enzymes with defined new specificities. To analyse which DNA-binding elements are potential candidates for use in the design of enzymes with modified or even new specificity, we produced several chimeric proteins derived from the Saccharomyces cerevisiae VMA1 intein (PI-SceI) and the related Candida tropicalis VMA1 intein. Although the mature Candida intein is devoid of endonucleolytic activity, the exchange of two DNA-binding modules of PI-SceI with the homologous elements from the Candida intein results in an active endonuclease. The low sequence homology in these modules indicates that different protein-DNA contacts are responsible for the recognition of related DNA sequences. This flexibility in DNA recognition should, in principle, allow endonucleases to be produced with new specificities useful for genome engineering.},
  creationdate = {2016-06-16T00:00:00},
  doi          = {10.1002/cbic.200300718},
  file         = {:by-author/S/Steuer/2004_Steuer_206.pdf:PDF},
  institution  = {Justus-Liebig-Universität, Institut für Biochemie FB08, Heinrich-Buff-Ring 58, 35392 Giessen, Germany.},
  keywords     = {Amino Acid Sequence; Biosynthesis/chemistry/genetics/metabolism; Candida Tropicalis; Chemistry/genetics/metabolism; Circular Dichroism; Cloning; DNA; DNA-Binding Proteins; Deoxyribonucleases; Design; Evolution; Fungal Proteins; Genetics/metabolism; Metabolism; Models; Molecular; Molecular Sequence Data; Protein Structure; Recognition; Recombinant Fusion Proteins; Restriction Endonuclease (RE); Saccharomyces Cerevisiae Proteins; Sequence Alignment; Specificity; Substrate Specificity; Tertiary; Type II Site-Specific},
  language     = {eng},
  medline-pst  = {ppublish},
  owner        = {em},
  pmid         = {14760742},
  timestamp    = {2016.06.16},
  url          = {http://dx.doi.org/10.1002/cbic.200300718},
}

@Manuscript{Stevens2011,
  author    = {W. Richard Stevens},
  title     = {Examples of pic Macros},
  year      = {2011},
  keywords  = {Computer Science (CS); Groff; Pic; Roff; Troff; Typesetting; Unix},
  url       = {http://www.kohala.com/start/troff/troff.html},
  file      = {:by-author/S/Stevens/2011_Stevens.ps:PostScript;:by-author/S/Stevens/2011_Stevens.pdf:PDF},
  owner     = {saulius},
  timestamp = {2015.02.27},
  creationdate = {2015-02-27T00:00:00},
}

@Article{Stewart2000,
  author    = {Stewart, A. E. and Lord, J. H. and Mercer, D. L.},
  journal   = {Death studies},
  title     = {A survey of professionals' training and experiences in delivering death notifications.},
  year      = {2000},
  pages     = {611--31},
  volume    = {24},
  abstract  = {A mail survey was conducted of 240 people from different professions that routinely encountered death to assess their previous training and experiences in delivering death notifications. Nearly 40% of these persons had received neither classroom nor experiential training in death notification, although 70% of respondents had performed at least one notification. The causes of death that contributed to notifiers' distress during notification included (a) violent crime, (b) drunk driving crashes, (c) suicide, and (d) the death of a child. Survivor reactions that were the most difficult for notifiers to manage during the notification included (a) attempts to harm self or others (b) physical acting-out, and (c) intense anxiety. Notifiers indicated that they most frequently coped with the stresses of notification by (a) spending time with family, (b) talking with coworkers, and (c) spending time alone. The implications of the results and the needs for systematic death notification education were discussed.},
  file      = {:by-author/S/Stewart/2000_Stewart_611.pdf:PDF},
  keywords  = {McrBC},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Steward1972,
  author    = {David J. Stewart and Osvald Knop and Conrad Ayasse and F. W. D. Woodhams},
  journal   = {Canadian Journal of Chemistry},
  title     = {Pyrochlores. VII. The oxydes of Antimony: an X-ray and Mössbauer Study},
  year      = {1972},
  pages     = {690--700},
  volume    = {50},
  abstract  = {Antimonic acid cannot be dehydrated by heating in air to give products of constant and reproducible weight without simultaneous reduction of some of the Sb(V) to Sb(III). Neither anhydrous Sb2O5 nor the hydroxy oxide Sb3O6OH postulated by Dihlstrom and Westgren can be obtained by this method. Two well-defined products of the dehydration/decomposition are Sb2O4.35(5) = Sb6O13, which forms between 650 and 850°, and β-Sb2O4. The latter, and not Sb2O3,results on heating Sb6O13 to 935°. Sb6O13 has a cubic structure of the defect pyrochlore type, a0 = 10.303(1) A, x(O2) = 0.4304(14). Combined evidence from X-ray diffractometry, density determination, and Mossbauer spectroscopy leads to Sb3+Sb5+2O6O0.5 the most probable as structural formula. The Mossbauer parameters of β-Sb2O4 are closely similar to those reported for α-Sb2O4, but the isomer shifts (relative to InSb at 77 OK) for Sbv in antimonic acid and Sb6O13 are significantly larger than those in α- and β-Sb2O4.},
  file      = {1972_Steward_CJCh50_690.pdf:by-author/S/Steward/1972_Steward.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Stewart2004,
  author    = {Stewart, D. R. and Ohlberg, D. A. A. and Beck, P. A. and Chen, Y. and Williams, R. Stanley and Jeppesen, J. O. and Nielsen, K. A. and Stoddart, J. Fraser},
  journal   = {Nano Letters},
  title     = {Molecule-independent electrical switching in {Pt}/organic monolayer/{Ti} devices},
  year      = {2004},
  issn      = {1530-6984},
  pages     = {133--136},
  volume    = {4},
  abstract  = {Electronic devices comprising a Langmuir?Blodgett molecular monolayer sandwiched between planar platinum and titanium metal electrodes functioned as switches and tunable resistors over a 102?105 Ω range under current or voltage control. Reversible hysteretic switching and resistance tuning was qualitatively similar for three very different molecular species, indicating a generic switching mechanism dominated by electrode properties or electrode/molecule interfaces, rather than molecule-specific behavior.},
  doi       = {10.1021/nl034795u},
  file      = {Stewart et al. - 2004 - Molecule-Independent Electrical Switching in PtOr.pdf:by-author/S/Stewart/2004_Stewart_133.pdf:application/pdf;ACS Full Text Snapshot:by-author/S/Stewart/2004_Stewart_133.html:text/html},
  groups    = {sg/chemical},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://dx.doi.org/10.1021/nl034795u},
  urldate   = {2015-08-21},
}

@Article{Stinton2007,
  author    = {Stinton, Graham W. and Evans, John S. O.},
  journal   = {Journal of Applied Crystallography},
  title     = {Parametric Rietveld refinement},
  year      = {2007},
  pages     = {87--95},
  volume    = {40},
  abstract  = {In this paper the method of parametric Rietveld refinement is described, in which an ensemble of diffraction data collected as a function of time, temperature, pressure or any other variable are fitted to a single evolving structural model. Parametric refinement offers a number of potential benefits over independent or sequential analysis. It can lead to higher precision of refined parameters, offers the possibility of applying physically realistic models during data analysis, allows the refinement of 'non-crystallographic' quantities such as temperature or rate constants directly from diffraction data, and can help avoid false minima.},
  doi       = {10.1107/S0021889806043275},
  file      = {db5010.pdf:by-author/S/Stinton/2007_Stinton_87.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0021889806043275},
}

@Article{Stoesser2003,
  author    = {Stoesser, Guenter and Baker, Wendy and van den Broek, Alexandra and Garcia-Pastor, Maria and Kanz, Carola and Kulikova, Tamara and Leinonen, Rasko and Lin, Quan and Lombard, Vincent and Lopez, Rodrigo and Mancuso, Renato and Nardone, Francesco and Stoehr, Peter and Tuli, Mary Ann and Tzouvara, Katerina and Vaughan, Robert},
  journal   = {Nucleic acids research},
  title     = {The EMBL Nucleotide Sequence Database: major new developments.},
  year      = {2003},
  pages     = {17--22},
  volume    = {31},
  abstract  = {The EMBL Nucleotide Sequence Database (http://www.ebi.ac.uk/embl/) incorporates, organizes and distributes nucleotide sequences from all available public sources. The database is located and maintained at the European Bioinformatics Institute (EBI) near Cambridge, UK. In an international collaboration with DDBJ (Japan) and GenBank (USA), data are exchanged amongst the collaborating databases on a daily basis to achieve optimal synchronization. Webin is the preferred web-based submission system for individual submitters, while automatic procedures allow incorporation of sequence data from large-scale genome sequencing centres and from the European Patent Office (EPO). Database releases are produced quarterly. Network services allow free access to the most up-to-date data collection via FTP, Email and World Wide Web interfaces. EBI's Sequence Retrieval System (SRS) integrates and links the main nucleotide and protein databases plus many other specialized molecular biology databases. For sequence similarity searching, a variety of tools (e.g. Fasta, BLAST) are available which allow external users to compare their own sequences against the latest data in the EMBL Nucleotide Sequence Database and SWISS-PROT. All resources can be accessed via the EBI home page at http://www.ebi.ac.uk.},
  file      = {:by-author/S/Stoesser/2003_Stoesser_17.pdf:PDF},
  keywords  = {Databases; EMBL Nucleotide Sequence Database},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@Article{Stokes2005,
  author    = {Stokes, Harold T. and Hatch, Dorian M.},
  journal   = {Journal of Applied Crystallography},
  title     = {{\it FINDSYM}: program for identifying the space-group symmetry of a crystal},
  year      = {2005},
  pages     = {237--238},
  volume    = {38},
  doi       = {10.1107/S0021889804031528},
  file      = {2005_Stokes_237.pdf:by-author/S/Stokes/2005_Stokes_237.pdf:PDF},
  keywords  = {Algorithms; Computer Programs; Spacegroups; Standard Setting; Symmetry; Wyckoff Positions; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2015.06.15},
  creationdate = {2015-06-15T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0021889804031528},
}

@InProceedings{Stonebraker1986,
  author    = {Michael Stonebraker},
  booktitle = {Proceedings of the 1986 Data Engineering Conference},
  title     = {The Case for Shared Nothing},
  year      = {1986},
  abstract  = {There are three dominent themes in building high transaction rate multiprocessor systems, namely shared memory (e.g. Synapse, IBM/AP configurations), shared disk (e.g. VAX/cluster, any multi-ported disk system), and shared nothing (e.g. Tandem, Tolerant). This paper argues that shared nothing is the preferred approach.},
  file      = {1997_Stonebraker.pdf:by-author/S/Stonebraker/1986_Stonebraker.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Stone-Sundberg2015,
  author    = {Jennifer Stone-Sundberg and Werner Kaminsky and Trevor Snyder and Peter Moeck},
  journal   = {Cryst. Res. Technol.},
  title     = {3D printed models of small and large molecules, structures and morphologies of crystals, as well as of their anisotropic physical properties},
  year      = {2015},
  pages     = {1--11},
  doi       = {10.1002/crat.201400469},
  file      = {2015_Stone-Sundberg_1.pdf:by-author/S/Stone-Sundberg/2015_Stone-Sundberg_1.pdf:PDF},
  keywords  = {3D Printing; Citing COD; Crystallography; Models; Properties; Teaching},
  owner     = {saulius},
  timestamp = {2015.03.02},
  creationdate = {2015-03-02T00:00:00},
}

@Article{Storoni2004,
  author    = {Storoni, Laurent C and McCoy, Airlie J and Read, Randy J},
  journal   = {Acta crystallographica. Section D, Biological crystallography},
  title     = {Likelihood-enhanced fast rotation functions.},
  year      = {2004},
  pages     = {432--8},
  volume    = {60},
  file      = {2004_Storoni_432.pdf:by-author/S/Storoni/2004_Storoni_432.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Presentation{Stote2005,
  author       = {Roland H. Stote},
  title        = {Introduction to Molecular Dynamics Simulations},
  year         = {2005},
  organization = {Institut de Chimie LC3-UMR 7177, Université Louis Pasteur, Strasbourg France},
  file         = {:by-author/S/Stote/2005_Stote.pdf:PDF},
  groups       = {sg/Molecular dynamics},
  owner        = {saulius},
  timestamp = {2014.03.23},
  creationdate = {2014-03-23T00:00:00},
}

@Article{Stott1988,
  author    = {Stott, Jack W. and Jeffrey E. Kottemann},
  journal   = {Communications of the ACM},
  title     = {Auatomy of a compact user interface development tool},
  year      = {1988},
  pages     = {56--66},
  volume    = {31},
  abstract  = {Many contemporary user oriented applications require a combination of attributes from both window and forms management systems. PANES was developed as a tool to fill this niche by providing a simple, yet flexible tool for both the moderately trained, as well as the more sophisticated programmer, while allowing the development of user friendly, modeless application software.},
  file      = {:by-author/S/Stott/1988_Stott_56.pdf:PDF},
  keywords  = {Computer Science (CS); GUI},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Strelkov2002,
  author    = {Sergei V. Strelkov and Peter Burkhard},
  journal   = {Journal of Structural Biology},
  title     = {Analysis of α-Helical Coiled Coils with the Program TWISTER Reveals a Structural Mechanism for Stutter Compensation},
  year      = {2002},
  pages     = {137},
  volume    = {137},
  abstract  = {α-Helicalcoiled coils represent a widespread protein structure motif distinguished by a seven-residue periodicity of apolar residues in the primary sequence. A characteristic “knobs-into-holes” packing of these residues into a hydrophobic core results in a superhelical, usually left-handed, rope of two or more α-helices. Such a geometry can be parameterized. For this purpose, a new computer program, TWISTER, was developed. With the three-dimensional coordinates as input, TWISTER uses an original algorithm to determine the local coiled-coil parameters as a function of residue number. In addition, heptad positions are assigned based on structural criteria. It is known that frequently encountered discontinuities in the heptad repeat, such as stutters and skips, can be tolerated within a continuous coiled coil but result in a local distortion of its geometry. This was explored in detail with the help of TWISTER for several two- and three-stranded coiled coils. Depending on the particular protein, stutters were found to be compensated locally by an unwinding of the superhelix, α-helical unwinding, or both. In the first case, there is often a local switch from a left-handed to a right-handed superhelix. In general, the geometrical distortion is confined to about two α-helical turns at either side of the stutter. Furthermore, stutters result in a local increase of the coiled-coil radius.},
  doi       = {10.1006/jsbi.2002.4454},
  file      = {:by-author/S/Strelkov/2002_Strelkov_137.pdf:PDF},
  keywords  = {Coiled Coil; Computer Program; Crick Parameters; Helical Parameters; Heptad Repeat; Protein Bioinformatics; Protein Conformation; Skips; Stutters},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/S1047847702944540},
}

@TechReport{Stricker1996,
  author      = {Markus Stricker and Alexander Dimai},
  institution = {Communications Technology Laboratory, Swiss Federal Institute of Technology, ETH CH-8092 Zurich, Switzerland},
  title       = {Color Indexing with Weak Spatial Constraints},
  year        = {1996},
  file        = {:by-author/S/Stricker/1996_Stricker.pdf:PDF;:by-author/S/Stricker/1996_Stricker.ps.gz:PostScript},
  keywords    = {Color Distribution Features; Color Indexing; Fuzzy Sets},
  owner       = {saulius},
  timestamp = {2015.02.27},
  creationdate = {2015-02-27T00:00:00},
}

@Article{Strobel1995,
  author    = {Strobel, S A and Cech, T R},
  journal   = {Science (New York, N.Y.)},
  title     = {Minor groove recognition of the conserved G.U pair at the Tetrahymena ribozyme reaction site.},
  year      = {1995},
  pages     = {675--9},
  volume    = {267},
  file      = {1995_Strobel_675.pdf:by-author/S/Strobel/1995_Strobel_675.pdf:PDF},
  keywords  = {Ribozymes},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Strokopytov2009,
  author    = {Strokopytov, Boris V.},
  journal   = {Journal of Applied Crystallography},
  title     = {Efficient calculation of a normal matrix{--}vector product for anisotropic full-matrix least-squares refinement of macromolecular structures},
  year      = {2009},
  pages     = {1020--1029},
  volume    = {42},
  abstract  = {A novel algorithm is described for multiplying a normal equation matrix by an arbitrary real vector using the fast Fourier transform technique during anisotropic crystallographic refinement. The matrix-vector algorithm allows one to solve normal matrix equations using the conjugate-gradients or conjugate-directions technique without explicit calculation of a normal matrix. The anisotropic version of the algorithm has been implemented in a new version of the computer program FMLSQ. The updated program has been tested on several protein structures at high resolution. In addition, rapid methods for preconditioner and normal matrix-vector product calculations are described.},
  doi       = {10.1107/S0021889809040989},
  file      = {2009_Strokopytov_1020.pdf:by-author/S/Strokopytov/2009_Strokopytov_1020.pdf:PDF},
  keywords  = {Algorithms; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0021889809040989},
}

@Article{Stroz2007,
  author    = {Stróz, Kazimierz},
  journal   = {Acta crystallographica. Section A, Foundations of crystallography},
  title     = {Transformational space-group symbols.},
  year      = {2007},
  pages     = {77--9},
  volume    = {63},
  file      = {2007_Stroz_77.pdf:by-author/S/Stróz/2007_Stróz_77.pdf:PDF},
  keywords  = {Spacegroup Symbols; Spacegroups; Symmetry},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Stroz2007a,
  author    = {Stróz, Kazimierz},
  journal   = {Acta crystallographica. Section A, Foundations of crystallography},
  title     = {A systematic approach to the derivation of standard orientation-location parts of symmetry-operation symbols.},
  year      = {2007},
  pages     = {447--54},
  volume    = {63},
  file      = {2007_Stroz_447.pdf:by-author/S/Stróz/2007_Stróz_447.pdf:PDF},
  keywords  = {Spacegroup Symbols},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Strube2009,
  author    = {Strube},
  title     = {The Effect of Entropy on Protein Folding},
  year      = {2009},
  abstract  = {This article concerns the modern challenge of determining a pro- tein’s tertiary structure and folding mechanism based on its primary amino acid sequence. We explore the concept of entropy as an influ- ential factor in this process by describing a mathematical model for the ”attractive force” of two large macromolecules, modeled as hard spheres, immersed in a low-concentration solution of particles, repre- sented as small hard spheres. Using this model we demonstrate that the greatest entropy of the small particles occurs when the surfaces of the two large macromolecules are in contact. In addition,we describe a recent extension of this model to solutions of high small-particle concentration. Finally we discuss a current application of this model to protein research.},
  file      = {:by-author/S/Strube/2009_Strube.pdf:PDF},
  keywords  = {Protein Folding},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Stuart1998,
  author    = {Stuart},
  title     = {Complete 2-loop Quantum Electrodynamic Contributions to the Muon Lifetime in the Fermi Model},
  year      = {1998},
  file      = {:by-author/S/Stuart/1998_Stuart.pdf:PDF},
  keywords  = {QED},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Stuckey1999,
  author    = {Stuckey, J A and Dixon, J E},
  journal   = {Nature structural biology},
  title     = {Crystal structure of a phospholipase D family member.},
  year      = {1999},
  pages     = {278--84},
  volume    = {6},
  abstract  = {The first crystal structure of a phospholipase D (PLD) family member has been determined at 2.0 A resolution. The PLD superfamily is defined by a common sequence motif, HxK(x)4D(x)6GSxN, and includes enzymes involved in signal transduction, lipid biosynthesis, endonucleases and open reading frames in pathogenic viruses and bacteria. The crystal structure suggests that residues from two sequence motifs form a single active site. A histidine residue from one motif acts as a nucleophile in the catalytic mechanism, forming a phosphoenzyme intermediate, whereas a histidine residue from the other motif appears to function as a general acid in the cleavage of the phosphodiester bond. The structure suggests that the conserved lysine residues are involved in phosphate binding. Large-scale genomic sequencing revealed that there are many PLD family members. Our results suggest that all of these proteins may possess a common structure and catalytic mechanism.},
  file      = {Stuckey_1999_278-Nuc-structure.pdf:by-author/S/Stuckey/1999_Stuckey_278.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Manuscript{Sturgeon1999,
  author    = {Jess B. Sturgeon and Brian B. Laird},
  title     = {Symplectic algorithm for constant-pressure molecular dynamics using a Nose-Poincare thermostat},
  year      = {1999},
  doi       = {10.1063/1.480502},
  keywords  = {Molecular Dynamics (MD); Thermostat},
  url       = {http://arxiv.org/abs/physics/9903009v1},
  abstract  = {We present a new algorithm for isothermal-isobaric molecular-dynamics simulation. The method uses an extended Hamiltonian with an Andersen piston combined with the Nos'e-Poincar'e thermostat, recently developed by Bond, Leimkuhler and Laird [J. Comp. Phys., 151, (1999)]. This Nos'e-Poincar'e-Andersen (NPA) formulation has advantages over the Nos'e-Hoover-Andersen approach in that the NPA is Hamiltonian and can take advantage of symplectic integration schemes, which lead to enhanced stability for long-time simulations. The equations of motion are integrated using a Generalized Leapfrog Algorithm and the method is easy to implement, symplectic, explicit and time reversible. To demonstrate the stability of the method we show results for test simulations using a model for aluminum.},
  comment   = {Cite as: arXiv:physics/9903009 [physics.chem-ph]},
  file      = {1999_Sturgeon_9903009v1.pdf:by-author/S/Sturgeon/1999_Sturgeon_9903009v1.pdf:PDF},
  groups    = {sg/Molecular dynamics},
  owner     = {saulius},
  timestamp = {2016.02.23},
  creationdate = {2016-02-23T00:00:00},
}

@Article{Su1999,
  author    = {Su, P. and Im, H. and Hsieh, H. and Kang'A, S. and Dunn, N. W.},
  journal   = {Applied and environmental microbiology},
  title     = {LlaFI, a type III restriction and modification system in Lactococcus lactis.},
  year      = {1999},
  pages     = {686--93},
  volume    = {65},
  abstract  = {We describe a type III restriction and modification (R/M) system, LlaFI, in Lactococcus lactis. LlaFI is encoded by a 12-kb native plasmid, pND801, harbored in L. lactis LL42-1. Sequencing revealed two adjacent open reading frames (ORFs). One ORF encodes a 680-amino-acid polypeptide, and this ORF is followed by a second ORF which encodes an 873-amino-acid polypeptide. The two ORFs appear to be organized in an operon. A homology search revealed that the two ORFs exhibited significant similarity to type III restriction (Res) and modification (Mod) subunits. The complete amino acid sequence of the Mod subunit of LlaFI was aligned with the amino acid sequences of four previously described type III methyltransferases. Both the N-terminal regions and the C-terminal regions of the Mod proteins are conserved, while the central regions are more variable. An S-adenosyl methionine (Ado-Met) binding motif (present in all adenine methyltransferases) was found in the N-terminal region of the Mod protein. The seven conserved helicase motifs found in the previously described type III R/M systems were found at the same relative positions in the LlaFI Res sequence. LlaFI has cofactor requirements for activity that are characteristic of the previously described type III enzymes. ATP and Mg2+ are required for endonucleolytic activity; however, the activity is not strictly dependent on the presence of Ado-Met but is stimulated by it. To our knowledge, this is the first type III R/M system that has been characterized not just in lactic acid bacteria but also in gram-positive bacteria.},
  file      = {:by-author/S/Su/1999_Su_686.pdf:PDF},
  keywords  = {TypeIII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Su2004,
  author    = {Su, T-J. and Connolly, B. A. and Darlington, C. and Mallin, R. and Dryden, D. T. F.},
  journal   = {Nucleic acids research},
  title     = {Unusual 2-aminopurine fluorescence from a complex of DNA and the EcoKI methyltransferase.},
  year      = {2004},
  pages     = {2223--30},
  volume    = {32},
  abstract  = {The methyltransferase, M.EcoKI, recognizes the DNA sequence 5'-AACNNNNNNGTGC-3' and methylates adenine at the underlined positions. DNA methylation has been shown by crystallography to occur via a base flipping mechanism and is believed to be a general mechanism for all methyltransferases. If no structure is available, the fluorescence of 2-aminopurine is often used as a signal for base flipping as it shows enhanced fluorescence when its environment is perturbed. We find that 2-aminopurine gives enhanced fluorescence emission not only when it is placed at the M.EcoKI methylation sites but also at a location adjacent to the target adenine. Thus it appears that 2-aminopurine fluorescence intensity is not a clear indicator of base flipping but is a more general measure of DNA distortion. Upon addition of the cofactor S-adenosyl-methionine to the M.EcoKI:DNA complex, the 2-aminopurine fluorescence changes to that of a new species showing excitation at 345 nm and emission at 450 nm. This change requires a fully active enzyme, the correct cofactor and the 2-aminopurine located at the methylation site. However, the new fluorescent species is not a covalently modified form of 2-aminopurine and we suggest that it represents a hitherto undetected physicochemical form of 2-aminopurine.},
  file      = {:by-author/S/Su/2004_Su_2223.pdf:PDF},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Su2005a,
  author    = {Su, Tsueu-Ju and Tock, Mark R. and Egelhaaf, Stefan U. and Poon, Wilson C. K. and Dryden, David T. F.},
  journal   = {Nucleic acids research},
  title     = {DNA bending by M.EcoKI methyltransferase is coupled to nucleotide flipping.},
  year      = {2005},
  pages     = {3235--44},
  volume    = {33},
  abstract  = {The maintenance methyltransferase M.EcoKI recognizes the bipartite DNA sequence 5'-AACNNNNNNGTGC-3', where N is any nucleotide. M.EcoKI preferentially methylates a sequence already containing a methylated adenine at or complementary to the underlined bases in the sequence. We find that the introduction of a single-stranded gap in the middle of the non-specific spacer, of up to 4 nt in length, does not reduce the binding affinity of M.EcoKI despite the removal of non-sequence-specific contacts between the protein and the DNA phosphate backbone. Surprisingly, binding affinity is enhanced in a manner predicted by simple polymer models of DNA flexibility. However, the activity of the enzyme declines to zero once the single-stranded region reaches 4 nt in length. This indicates that the recognition of methylation of the DNA is communicated between the two methylation targets not only through the protein structure but also through the DNA structure. Furthermore, methylation recognition requires base flipping in which the bases targeted for methylation are swung out of the DNA helix into the enzyme. By using 2-aminopurine fluorescence as the base flipping probe we find that, although flipping occurs for the intact duplex, no flipping is observed upon introduction of a gap. Our data and polymer model indicate that M.EcoKI bends the non-specific spacer and that the energy stored in a double-stranded bend is utilized to force or flip out the bases. This energy is not stored in gapped duplexes. In this way, M.EcoKI can determine the methylation status of two adenine bases separated by a considerable distance in double-stranded DNA and select the required enzymatic response.},
  file      = {:by-author/S/Su/2005_Su_3235.pdf:PDF},
  keywords  = {MTases},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Su2006,
  author    = {Su, Xun-Cheng and Schaeffer, Patrick M. and Loscha, Karin V. and Gan, Pamela H. P. and Dixon, Nicholas E. and Otting, Gottfried},
  journal   = {The FEBS journal},
  title     = {Monomeric solution structure of the helicase-binding domain of Escherichia coli DnaG primase.},
  year      = {2006},
  pages     = {4997--5009},
  volume    = {273},
  abstract  = {DnaG is the primase that lays down RNA primers on single-stranded DNA during bacterial DNA replication. The solution structure of the DnaB-helicase-binding C-terminal domain of Escherichia coli DnaG was determined by NMR spectroscopy at near-neutral pH. The structure is a rare fold that, besides occurring in DnaG C-terminal domains, has been described only for the N-terminal domain of DnaB. The C-terminal helix hairpin present in the DnaG C-terminal domain, however, is either less stable or absent in DnaB, as evidenced by high mobility of the C-terminal 35 residues in a construct comprising residues 1-171. The present structure identifies the previous crystal structure of the E. coli DnaG C-terminal domain as a domain-swapped dimer. It is also significantly different from the NMR structure reported for the corresponding domain of DnaG from the thermophile Bacillus stearothermophilus. NMR experiments showed that the DnaG C-terminal domain does not bind to residues 1-171 of the E. coli DnaB helicase with significant affinity.},
  file      = {:by-author/S/Su/2006_Su_4997.pdf:PDF},
  keywords  = {Ecoli; {gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Subacius2002,
  author    = {Subačius, Giedrius},
  title     = {The Lithuanian Language: Traditions and Trends},
  year      = {2002},
  file      = {:by-author/S/Subačius/2002_Subačius.pdf:PDF},
  keywords  = {Lingvistika},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Subirana1997,
  author    = {Subirana, J. A. and Faria, T.},
  journal   = {Biophysical journal},
  title     = {Influence of sequence on the conformation of the B-DNA helix.},
  year      = {1997},
  pages     = {333--8},
  volume    = {73},
  abstract  = {We have tried to ascertain whether the variability found in the conformational features of the 10 base steps in B-DNA is mainly due to the flanking sequences or to interactions with the environment. From an analysis of the twist parameter of the base-pair steps available from crystals of oligonucleotides and protein/oligonucleotide complexes, we conclude that in most cases the flanking sequences show little influence: the conformation of a DNA region results from the combination of the independent intrinsic features of each base step (average conformation and intrinsic variability), modulated by their interactions with the environment. Only in some cases (YR steps, in particular CG and CA/TG) does it appear that flanking sequences have an influence on the conformation of the central base step. The values obtained allow an approximation to the parameters expected for repetitive DNA sequences. In particular, it is found that poly[d(AG/CT)] should have a strongly alternating conformation, in agreement with recently reported oligonucleotide structures.},
  file      = {:by-author/S/Subirana/1997_Subirana_333.pdf:PDF},
  keywords  = {RY; Readout},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@MastersThesis{Subramanian2002,
  author    = {Sowmya Subramanian},
  school    = {Louisiana State University and Agricultural and Mechanical College, Department of Electrical and Computer Engineerin},
  title     = {Ternary logic to binary bit conversion using multiple input floating gate mosfets in 0.5 micron n-well cmos technology},
  year      = {2002},
  file      = {:by-author/S/Subramanian/2002_Subramanian_mscthesis.pdf:PDF},
  keywords  = {Computer Science (CS); Logic Circuits; Ternary Logic},
  owner     = {saulius},
  pages     = {mscthesis},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Subuddhi2008,
  author    = {Subuddhi, Usharani and Hogg, Matthew and Reha-Krantz, Linda J.},
  journal   = {Biochemistry},
  title     = {Use of 2-aminopurine fluorescence to study the role of the beta hairpin in the proofreading pathway catalyzed by the phage T4 and RB69 DNA polymerases.},
  year      = {2008},
  pages     = {6130--7},
  volume    = {47},
  abstract  = {For DNA polymerases to proofread a misincorporated nucleotide, the terminal 3-4 nucleotides of the primer strand must be separated from the template strand before being bound in the exonuclease active center. Genetic and biochemical studies of the bacteriophage T4 DNA polymerase revealed that a prominent beta-hairpin structure in the exonuclease domain is needed to efficiently form the strand-separated exonuclease complexes. We present here further mutational analysis of the loop region of the T4 DNA polymerase beta-hairpin structure, which provides additional evidence that residues in the loop, namely, Y254 and G255, are important for DNA replication fidelity. The mechanism of strand separation was probed in in vitro reactions using the fluorescence of the base analogue 2-aminopurine (2AP) and mutant RB69 DNA polymerases that have modifications to the beta hairpin, to the exonuclease active site, or to both. We propose from these studies that the beta hairpin in the exonuclease domain of the T4 and RB69 DNA polymerases functions to facilitate strand separation, but residues in the exonuclease active center are required to capture the 3' end of the primer strand following strand separation.},
  file      = {:by-author/S/Subuddhi/2008_Subuddhi_6130.pdf:PDF},
  keywords  = {{gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Sudzius2010,
  author      = {Jurgis Sūdžius and Lina Baranauskienė and Dmitrij Golovenko and Jurgita Matulienė and Vilma Michailovienė and Jolanta Torresan and Jelena Jachno and Rasa Sukackaitė and Elena Manakova and Saulius Gražulis and Sigitas Tumkevičius and Daumantas Matulis},
  journal     = {Bioorg Med Chem},
  title       = {4-[N-(substituted 4-pyrimidinyl)amino]benzenesulfonamides as inhibitors of carbonic anhydrase isozymes I, II, VII, and XIII.},
  year        = {2010},
  pages       = {7413--7421},
  volume      = {18},
  abstract    = {A series of 4-[N-(substituted 4-pyrimidinyl)amino]benzenesulfonamides were designed and synthesised. Their binding potencies as inhibitors of selected recombinant human carbonic anhydrase (hCA) isozymes I, II, VII, and XIII were measured using isothermal titration calorimetry and the thermal shift assay. To determine the structural features of inhibitor binding, the crystal structures of several compounds in complex with hCA II were determined. Several compounds exhibited selectivity towards isozymes I, II, and XIII, and some were potent inhibitors of hCA VII.},
  doi         = {10.1016/j.bmc.2010.09.011},
  file        = {2010_Sūdžius_7413.pdf:by-author/S/Sūdžius/2010_Sūdžius_7413.pdf:PDF},
  groups      = {sg/inhibitors},
  institution = {Department of Organic Chemistry, Faculty of Chemistry, Vilnius University, Naugarduko 24, LT-03225 Vilnius, Lithuania.},
  keywords    = {Antagonists /&/ Inhibitors/genetics/metabolism; Binding Sites; Calorimetry; Carbonic Anhydrase I; Carbonic Anhydrase II; Carbonic Anhydrase Inhibitors; Carbonic Anhydrases; Chemical Synthesis/chemistry/pharmacology; Chemistry; Chemistry/genetics/metabolism; Crystallography; Humans; Protein Structure; Pyrimidines; Recombinant Proteins; Structure-activity Relationship (SAR); Sulfonamides; Tertiary; X-Ray},
  language    = {eng},
  medline-pst = {ppublish},
  owner       = {em},
  pii         = {S0968-0896(10)00826-6},
  pmid        = {20889345},
  timestamp = {2013.02.18},
  creationdate = {2013-02-18T00:00:00},
  url         = {http://dx.doi.org/10.1016/j.bmc.2010.09.011},
}

@Article{Sugar2003,
  author    = {Catherine A. Sugar and Gareth M. James},
  journal   = {Journal of the American Statistical Association},
  title     = {Finding the number of clusters in a data set: An information theoretic approach},
  year      = {2003},
  pages     = {750--763},
  volume    = {98},
  file      = {:by-author/S/Sugar/2003_Sugar_750.pdf:PDF},
  owner     = {andrius},
  timestamp = {2012.11.27},
  creationdate = {2012-11-27T00:00:00},
}

@Webpage{Suehnel2008,
  author      = {Jürgen Sühnel},
  retrieved   = {2011-02-06},
  title       = {3D Structures of Biological Macromolecules. Course Material},
  url         = {http://www.imb-jena.de/www_bioc/},
  institution = {Biocomputing Group, Leibniz Institute for Age Research - Fritz Lipmann Institute, Jena Centre for Bioinformatics},
  year        = {2008},
  file        = {:by-author/S/Sühnel/2008_Sühnel.war:WAR},
  keywords    = {Presentations},
  owner       = {saulius},
  timestamp = {2015.03.02},
  creationdate = {2015-03-02T00:00:00},
}

@Presentation{Suhnel2007,
  author       = {Jürgen Sühnel},
  title        = {3D Structures of Biological Macromolecules, Part 2: Nucleic Acids},
  year         = {2007},
  organization = {Leibniz Institute for Age Research, Fritz Lipmann Institute, Jena Centre for Bioinformatics Jena / Germany},
  file         = {:by-author/S/Sühnel/2007_Sühnel_slides.pdf:PDF},
  keywords     = {Presentations},
  owner        = {saulius},
  pages        = {slides},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Sukackaite2008,
  author    = {Sukackaite, Rasa and Grazulis, Saulius and Bochtler, Matthias and Siksnys, Virginijus},
  journal   = {Journal of molecular biology},
  title     = {The recognition domain of the BpuJI restriction endonuclease in complex with cognate DNA at 1.3-A resolution.},
  year      = {2008},
  pages     = {1084--93},
  volume    = {378},
  abstract  = {Type IIS restriction endonucleases recognize asymmetric DNA sequences and cleave both DNA strands at fixed positions downstream of the recognition site. The restriction endonuclease BpuJI recognizes the asymmetric sequence 5'-CCCGT; however, it cuts at multiple sites in the vicinity of the target sequence. BpuJI consists of two physically separate domains, with catalytic and dimerization functions in the C-terminal domain and DNA recognition functions in the N-terminal domain. Here we report the crystal structure of the BpuJI recognition domain bound to cognate DNA at 1.3-A resolution. This region folds into two winged-helix subdomains, D1 and D2, interspaced by the DL subdomain. The D1 and D2 subdomains of BpuJI share structural similarity with the similar subdomains of the FokI DNA-binding domain; however, their orientations in protein-DNA complexes are different. Recognition of the 5'-CCCGT target sequence is achieved by BpuJI through the major groove contacts of amino acid residues located on both the helix-turn-helix motifs and the N-terminal arm. The role of these interactions in DNA recognition is also corroborated by mutational analysis.},
  file      = {:by-author/S/Sukackaite/2008_Sukackaite_1084.pdf:PDF},
  keywords  = {Struct; TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Sukackaite2012,
  author    = {Sukackaite, R. and Grazulis, S. and Tamulaitis, G. and Siksnys, V.},
  journal   = {Nucleic Acids Res.},
  title     = {The recognition domain of the methyl-specific endonuclease McrBC flips out 5-methylcytosine.},
  year      = {2012},
  pages     = {7552--7562},
  volume    = {40},
  doi       = {10.1093/nar/gks332},
  file      = {:by-author/S/Sukackaite/2012_Sukackaite_suppl.pdf:PDF;:by-author/S/Sukackaite/2012_Sukackaite_7552.pdf:PDF;:by-author/S/Sukackaite/2012_Sukackaite_manuscript.pdf:PDF},
  keywords  = {McrBC},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Sukackaite2012a,
  author    = {Rasa Sukackaite and Saulius Grazulis and Gintautas Tamulaitis and Virginijus Siksnys},
  journal   = {Nucleic Acids Research},
  title     = {The recognition domain of the methyl-specific endonuclease {McrBC} flips out 5-methylcytosine},
  year      = {2012},
  pages     = {S1},
  doi       = {10.1093/nar/gks332},
  file      = {:by-author/S/Sukackaite/2012_Sukackaite_S1.pdf:PDF},
  keywords  = {McrBC},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Sukackaite2012b,
  author    = {Rasa Sukackaite and Saulius Grazulis and Gintautas Tamulaitis and Virginijus Siksnys},
  journal   = {Nucleic Acids Research},
  title     = {The recognition domain of the methyl-specific endonuclease {McrBC} flips out 5-methylcytosine},
  year      = {2012},
  pages     = {manuscript},
  doi       = {10.1093/nar/gks332},
  file      = {:by-author/S/Sukackaite/2012_Sukackaite_manuscript.pdf:PDF},
  keywords  = {McrBC},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Sukackaite2011,
  author    = {Rasa Sukackaite and Saulius Grazulis and Gintautas Tamulaitis and Virginijus Siksnys},
  journal   = {Nucleic Acids Research},
  title     = {The recognition domain of the methyl-specific endonuclease McrBC flips out 5-methylcytosine},
  year      = {2011},
  pages     = {7552--7562},
  volume    = {40},
  abstract  = {DNA cytosine methylation is a widespread epigen- etic mark. Biological effects of DNA methylation are mediated by the proteins that preferentially bind to 5-methylcytosine (5mC) in different sequence contexts. Until now two different structural mechan- isms have been established for 5mC recognition in eukaryotes; however, it is still unknown how discrimination of the 5mC modification is achieved in prokaryotes. Here we report the crystal structure of the N-terminal DNA-binding domain (McrB-N) of the methyl-specific endonuclease McrBC from Escherichia coli. The McrB-N protein shows a novel DNA-binding fold adapted for 5mC-recog- nition. In the McrB-N structure in complex with methylated DNA, the 5mC base is flipped out from the DNA duplex and positioned within a binding pocket. Base flipping elegantly explains why McrBC system restricts only T4-even phages impaired in glycosylation [Luria, S.E. and Human, M.L. (1952) A nonhereditary, host-induced variation of bacterial viruses. J. Bacteriol., 64, 557–569]: flipped out 5-hydroxymethylcytosine is accommo- dated in the binding pocket but there is no room for the glycosylated base. The mechanism for 5mC recognition employed by McrB-N is highly reminis- cent of that for eukaryotic SRA domains, despite the differences in their protein folds.},
  doi       = {10.1093/nar/gks332},
  file      = {:by-author/S/Sukackaite/2011_Sukackaite_7552.pdf:PDF},
  owner     = {em},
  timestamp = {2013.09.19},
  creationdate = {2013-09-19T00:00:00},
}

@Article{Sukackaite2007,
  author    = {Rasa Sukackaite and Arunas Lagunavicius and Kornelijus Stankevicius and Claus Urbanke and Ceslovas Venclovas and Virginijus Siksnys},
  journal   = {Nucleic Acids Research},
  title     = {Restriction endonuclease {BpuJI} specific for the {5'-CCCGT} sequence is related to the archaeal {H}olliday junction resolvase family},
  year      = {2007},
  pages     = {1--13},
  abstract  = {Type IIS restriction endonucleases (REases) recog- nize asymmetric DNA sequences and cleave both DNA strands at fixed positions downstream of the recognition site. REase BpuJI recognizes the asymmetric sequence 50 -CCCGT, however it cuts at multiple sites in the vicinity of the target sequence. We show that BpuJI is a dimer, which has two DNA binding surfaces and displays optimal catalytic activity when bound to two recognition sites. BpuJI is cleaved by chymotrypsin into an N-terminal domain (NTD), which lacks catalytic activity but binds specifically to the recognition sequence as a monomer, and a C-terminal domain (CTD), which forms a dimer with non-specific nuclease activity. Fold recognition approach reveals that the CTD of BpuJI is structurally related to archaeal Holliday junction resolvases (AHJR). We demonstrate that the isolated catalytic CTD of BpuJI possesses end-directed nuclease activity and preferentially cuts 3 nt from the 30 -terminus of blunt-ended DNA. The nuclease activity of the CTD is repressed in the apo-enzyme and becomes activated upon specific DNA binding by the NTDs. This leads to a complicated pattern of specific DNA cleavage in the vicinity of the target site. Bioinformatics analysis identifies the AHJR-like domain in the putative Type III enzymes and functionally uncharacterized proteins.},
  doi       = {10.1093/nar/gkm164},
  file      = {:by-author/S/Sukackaite/2007_Sukackaite_1.pdf:PDF},
  keywords  = {Struct; TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Sukackaite2007a,
  author    = {Sukackaite, Rasa and Lagunavicius, Arunas and Stankevicius, Kornelijus and Urbanke, Claus and Venclovas, Ceslovas and Siksnys, Virginijus},
  journal   = {Nucleic acids research},
  title     = {Restriction endonuclease BpuJI specific for the 5'-CCCGT sequence is related to the archaeal Holliday junction resolvase family.},
  year      = {2007},
  pages     = {2377--89},
  volume    = {35},
  abstract  = {Type IIS restriction endonucleases (REases) recognize asymmetric DNA sequences and cleave both DNA strands at fixed positions downstream of the recognition site. REase BpuJI recognizes the asymmetric sequence 5'-CCCGT, however it cuts at multiple sites in the vicinity of the target sequence. We show that BpuJI is a dimer, which has two DNA binding surfaces and displays optimal catalytic activity when bound to two recognition sites. BpuJI is cleaved by chymotrypsin into an N-terminal domain (NTD), which lacks catalytic activity but binds specifically to the recognition sequence as a monomer, and a C-terminal domain (CTD), which forms a dimer with non-specific nuclease activity. Fold recognition approach reveals that the CTD of BpuJI is structurally related to archaeal Holliday junction resolvases (AHJR). We demonstrate that the isolated catalytic CTD of BpuJI possesses end-directed nuclease activity and preferentially cuts 3 nt from the 3'-terminus of blunt-ended DNA. The nuclease activity of the CTD is repressed in the apo-enzyme and becomes activated upon specific DNA binding by the NTDs. This leads to a complicated pattern of specific DNA cleavage in the vicinity of the target site. Bioinformatics analysis identifies the AHJR-like domain in the putative Type III enzymes and functionally uncharacterized proteins.},
  file      = {:by-author/S/Sukackaite/2007_Sukackaite_2377.pdf:PDF},
  keywords  = {TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Sun2007,
  author    = {Sun, Junliang and Lee, Stephen and Lin, Jianhua},
  journal   = {Chemistry – An Asian Journal},
  title     = {Four-Dimensional Space Groups for Pedestrians: Composite Structures},
  year      = {2007},
  issn      = {1861-471X},
  pages     = {1204--1229},
  volume    = {2},
  abstract  = {Higher-dimensional crystals have been studied for the last thirty years. However, most practicing chemists, materials scientists, and crystallographers continue to eschew the use of higher-dimensional crystallography in their work. Yet it has become increasingly clear in recent years that the number of higher-dimensional systems continues to grow from hundreds to as many as a thousand different compounds. Part of the problem has to do with the somewhat opaque language that has developed over the past decades to describe higher-dimensional systems. This language, while well-suited to the specialist, is too sophisticated for the neophyte wishing to enter the field, and as such can be an impediment. This Focus Review hopes to address this issue. The goal of this article is to show the regular chemist or materials scientist that knowledge of regular 3D crystallography is all that is really necessary to understand 4D crystal systems. To this end, we have couched higher-dimensional composite structures in the language of ordinary 3D crystals. In particular, we developed the principle of complementarity, which allows one to identify correctly 4D space groups solely from examination of the two 3D components that make up a typical 4D composite structure.},
  doi       = {10.1002/asia.200700088},
  file      = {2007_Sun_1204.pdf:by-author/S/Sun/2007_Sun_1204.pdf:PDF},
  keywords  = {Composite Compounds; Crystallography; Host-guest Systems; Incommensurate Structures; Intermetallic Phases; Spacegroups; Superspace Group; Superspacegroups; Symmetry},
  owner     = {saulius},
  publisher = {WILEY-VCH Verlag},
  timestamp = {2013.04.19},
  creationdate = {2013-04-19T00:00:00},
  url       = {http://dx.doi.org/10.1002/asia.200700088},
}

@Article{Sun2002a,
  author    = {Sun, Peter D. and Radaev, Sergei},
  journal   = {Acta crystallographica. Section D, Biological crystallography},
  title     = {Generating isomorphous heavy-atom derivatives by a quick-soak method. Part II: phasing of new structures.},
  year      = {2002},
  pages     = {1099--103},
  volume    = {58},
  abstract  = {A quick-soak method has been applied to generate de novo heavy-atom phasing to solve two new protein structures, a type II transforming growth factor beta receptor (TBRII) and a natural killer cell receptor-ligand complex, NKG2D-ULBP3. In the case of TBRII, a crystal derivatized for only 10 min in saturated HgCl(2) provided adequate phasing for structure determination. Comparison between HgCl(2) derivatives generated by 10 min soaking and by 12 h soaking revealed similar phasing statistics. The shorter soak, however, resulted in a derivative more isomorphous to the native than the longer soak as judged by changes in the unit-cell parameter a upon derivatization as well as by the quality of a combined SIRAS electron-density map. In the case of the NKG2D-ULBP3 structure, all overnight soaks in heavy-atom solutions resulted in crystal lattice disorder and only the quick soaks preserved diffraction. Despite fragile lattice packing, the quick-soaked K(2)PtCl(4) derivative was isomorphous with the native crystal and the electron-density map calculated from combined SIR and MAD phases is better than that calculated from MAD phases alone. Combined with mass-spectrometry-assisted solution heavy-atom derivative screening and the use of synchrotron radiation, the quick-soak derivatization has the potential to transform the time-consuming conventional heavy-atom search into a real-time 'on-the-fly' derivatization process that will benefit high-throughput structural genomics.},
  file      = {:by-author/S/Sun/2002_Sun_1099.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Sun2002b,
  author    = {Sun, Peter D. and Radaev, Sergei},
  journal   = {Acta Crystallographica Section D},
  title     = {Generating isomorphous heavy-atom derivatives by a quick-soak method. Part II: phasing of new structures},
  year      = {2002},
  pages     = {1099--1103},
  volume    = {58},
  doi       = {10.1107/S0907444902006522},
  file      = {gr2239.pdf:by-author/S/Sun/2002_Sun_1099.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444902006522},
}

@Article{Sun2002,
  author    = {Sun, Peter D. and Radaev, Sergei and Kattah, Michael},
  journal   = {Acta crystallographica. Section D, Biological crystallography},
  title     = {Generating isomorphous heavy-atom derivatives by a quick-soak method. Part I: test cases.},
  year      = {2002},
  pages     = {1092--8},
  volume    = {58},
  abstract  = {Screening for heavy-atom derivatives remains a time-consuming and cumbersome process that often results in non-isomorphous derivatives whose phases cannot be combined. Using lysozyme and FcgammaRIII receptor crystals as test cases, an improved soaking method for the generation of conventional heavy-atom derivatives has been developed. The method is based on soaking crystals in heavy-atom compounds for a very brief time at near-saturation concentrations. Compared with the current heavy-atom soaking method, which often takes days to achieve a derivatization, the quick-soak method completes a derivatization within 10 min to 2 h. The bound heavy-atom sites display higher peak heights from quick soaks than from overnight soaks in all cases tested. The quick-soak derivatives also preserved native-like diffraction resolution and data quality that was better than the prolonged-soak derivatives. Furthermore, derivatives generated by brief soaks are more isomorphous to the native than those generated by overnight soaks. Short soaks not only increase the likelihood of success in heavy-atom screening by reducing the pitfalls associated with prolonged soaks, such as lack of isomorphism and overall lattice disorder, but also have the potential to transform a time-consuming derivative screening into an 'on-the-fly' real-time derivatization process.},
  file      = {:by-author/S/Sun/2002_Sun_1092.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Sun2002c,
  author    = {Sun, Peter D. and Radaev, Sergei and Kattah, Michael},
  journal   = {Acta Crystallographica Section D},
  title     = {Generating isomorphous heavy-atom derivatives by a quick-soak method. Part I: test cases},
  year      = {2002},
  pages     = {1092--1098},
  volume    = {58},
  doi       = {10.1107/S0907444902006510},
  file      = {gr2238.pdf:by-author/S/Sun/2002_Sun_1092.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444902006510},
}

@Webpage{SuperGaz2006,
  author    = {SuperGaz},
  retrieved = {2008-11-25},
  title     = {List classes in package},
  url       = {https://jcp.org/en/home/index},
  year      = {2006},
  file      = {:by-author/S/SuperGaz/2006_SuperGaz.odt:},
  keywords  = {Computer Science (CS); JAVA-object-loading},
  owner     = {saulius},
  timestamp = {2015.03.03},
  creationdate = {2015-03-03T00:00:00},
}

@Article{Supuran2015,
  author    = {Supuran, Claudiu T.},
  journal   = {Journal of Enzyme Inhibition and Medicinal Chemistry},
  title     = {How many carbonic anhydrase inhibition mechanisms exist?},
  year      = {2015},
  issn      = {1475-6374},
  month     = {Nov},
  pages     = {1–16},
  abstract  = {Six genetic families of the enzyme carbonic anhydrase (CA, EC 4.2.1.1) were described to date. Inhibition of CAs has pharmacologic applications in the field of antiglaucoma, anticonvulsant, anticancer, and anti-infective agents. New classes of CA inhibitors (CAIs) were described in the last decade with enzyme inhibition mechanisms differing considerably from the classical inhibitors of the sulfonamide or anion type. Five different CA inhibition mechanisms are known: (i) the zinc binders coordinate to the catalytically crucial Zn(II) ion from the enzyme active site, with the metal in tetrahedral or trigonal bipyramidal geometries. Sulfonamides and their isosters, most anions, dithiocarbamates and their isosters, carboxylates, and hydroxamates bind in this way; (ii) inhibitors that anchor to the zinc-coordinated water molecule/hydroxide ion (phenols, carboxylates, polyamines, 2-thioxocoumarins, sulfocoumarins); (iii) inhibitors which occlude the entrance to the active site cavity (coumarins and their isosters), this binding site coinciding with that where CA activators bind; (iv) compounds which bind out of the active site cavity (a carboxylic acid derivative was seen to inhibit CA in this manner), and (v) compounds for which the inhibition mechanism is not known, among which the secondary/tertiary sulfonamides as well as imatinib/nilotinib are the most investigated examples. As CAIs are used clinically in many pathologies, with a sulfonamide inhibitor (SLC-0111) in Phase I clinical trials for the management of metastatic solid tumors, this review updates the recent findings in the field which may be useful for a structure-based drug design approach of more selective/potent modulators of the activity of these enzymes.},
  doi       = {10.3109/14756366.2015.1122001},
  file      = {2015_Supuran_1.pdf:by-author/S/Supuran/2015_Supuran_1.pdf:PDF},
  groups    = {sg/reviews},
  keywords  = {CA; Carboni Canhydrases; Review},
  owner     = {saulius},
  publisher = {Informa Healthcare},
  timestamp = {2016.01.08},
  creationdate = {2016-01-08T00:00:00},
  url       = {http://dx.doi.org/10.3109/14756366.2015.1122001},
}

@Presentation{Supuran2008,
  author    = {Claudiu T. Supuran},
  title     = {Carbonic anhydrases: old enzymes for new applications},
  year      = {2008},
  school    = {Università degli Studi di Firenze, Italia},
  file      = {:by-author/S/Supuran/2008_Supuran.ppt:PPT},
  groups    = {sg/reviews},
  keywords  = {Prezentacijos},
  month     = {September},
  owner     = {saulius},
  timestamp = {2015.03.03},
  creationdate = {2015-03-03T00:00:00},
}

@Article{Supuran2008f,
  author      = {Claudiu T Supuran},
  journal     = {Nat Rev Drug Discov},
  title       = {Carbonic anhydrases: novel therapeutic applications for inhibitors and activators.},
  year        = {2008},
  month       = {Feb},
  number      = {2},
  pages       = {168--181},
  volume      = {7},
  abstract    = {Carbonic anhydrases (CAs), a group of ubiquitously expressed metalloenzymes, are involved in numerous physiological and pathological processes, including gluconeogenesis, lipogenesis, ureagenesis, tumorigenicity and the growth and virulence of various pathogens. In addition to the established role of CA inhibitors (CAIs) as diuretics and antiglaucoma drugs, it has recently emerged that CAIs could have potential as novel anti-obesity, anticancer and anti-infective drugs. Furthermore, recent studies suggest that CA activation may provide a novel therapy for Alzheimer's disease. This article discusses the biological rationale for the novel uses of inhibitors or activators of CA activity in multiple diseases, and highlights progress in the development of specific modulators of the relevant CA isoforms, some of which are now being evaluated in clinical trials.},
  doi         = {10.1038/nrd2467},
  file        = {2008_Supuran_168.pdf:by-author/S/Supuran/2008_Supuran_168.pdf:PDF;2008_Supuran.ppt:by-author/S/Supuran/2008_Supuran.ppt:PowerPoint},
  institution = {Laboratorio di Chimica Bioinorganica, Università degli Studi di Firenze, Rm 188, Via della Lastruccia 3, I-50019 Sesto Fiorentino, Firenze, Italy. claudiu.supuran@unifi.it},
  keywords    = {Animals; Carbonic Anhydrase Inhibitors; Carbonic Anhydrases; Chemistry/metabolism; Drug Design; Humans; Isoenzymes; Models; Molecular; Molecular Structure; Pharmacology/therapeutic Use; Structure-activity Relationship (SAR)},
  language    = {eng},
  medline-pst = {ppublish},
  owner       = {alexey},
  pii         = {nrd2467},
  pmid        = {18167490},
  timestamp = {2012.07.02},
  creationdate = {2012-07-02T00:00:00},
  url         = {http://dx.doi.org/10.1038/nrd2467},
}

@Article{Supuran2001,
  author    = {Claudiu T. Supuran and Andrea Scozzafava},
  journal   = {Curr. Med. Chem. – Imm., Endoc. \& Metab. Agents},
  title     = {Carbonic Anhydrase Inhibitors},
  year      = {2001},
  pages     = {61--97},
  volume    = {1},
  abstract  = {CAs (EC 4.2.1.1) are wide-spread zinc enzymes, present in mammals in at least 14 different isoforms. Some of these isozymes are cytosolic (CA I, CA II, CA III, CA VII), others are membrane-bound (CA IV, CA IX, CA XII and CA XIV), CA V is mitochondrial and CA VI is secreted in the saliva. Three acatalytic forms are also known (CARP VIII, CARP X and CARP XI). Several important physiological and physio-pathological functions are played by many CA isozymes, which are strongly inhibited by aromatic and heterocyclic sulfonamides. The catalytic and inhibition mechanisms of these enzymes are understood in great detail, and this greatly helped the design of potent inhibitors, some of which possess important clinical applications. The use of such enzyme inhibitors as antiglaucoma drugs will be discussed in detail, together with the recent developments that led to isozyme-specific and organ- selective inhibitors. A recent discovery is connected with the involvement of CAs and their sulfonamide inhibitors in cancer: several potent sulfonamide inhibitors inhibited the growth of a multitude of tumor cells in vitro and in vivo, constituting thus interesting leads for developing novel antitumor therapies. Furthermore, some other classes of compounds that interact with CAs have recently been discovered, some of which possess modified sulfonamide or hydroxamate moieties. Some sulfonamides have also applications as diagnostic tools, in PET and MRI. Future prospects for drug design applications for inhibitors of these ubiquitous enzymes will also be discussed.},
  file      = {2001_Supuran_61.pdf:by-author/S/Supuran/2001_Supuran_61.pdf:PDF},
  groups    = {sg/inhibitors, sg/reviews},
  keywords  = {Carbonic Anhydrases; Inhibitors},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Supuran2003,
  author    = {Supuran, Claudiu T and Scozzafava, Andrea and Casini, Angela},
  journal   = {Medicinal research reviews},
  title     = {Carbonic anhydrase inhibitors.},
  year      = {2003},
  pages     = {146--89},
  volume    = {23},
  abstract  = {At least 14 different carbonic anhydrase (CA, EC 4.2.1.1) isoforms were isolated in higher vertebrates, where these zinc enzymes play crucial physiological roles. Some of these isozymes are cytosolic (CA I, CA II, CA III, CA VII), others are membrane-bound (CA IV, CA IX, CA XII, and CA XIV), CA V is mitochondrial and CA VI is secreted in saliva. Three acatalytic forms are also known, which are denominated CA related proteins (CARP), CARP VIII, CARP X, and CARP XI. Several important physiological and physio-pathological functions are played by many CA isozymes, which are strongly inhibited by aromatic and heterocyclic sulfonamides as well as inorganic, metal complexing anions. The catalytic and inhibition mechanisms of these enzymes are understood in detail, and this helped the design of potent inhibitors, some of which possess important clinical applications. The use of such enzyme inhibitors as antiglaucoma drugs will be discussed in detail, together with the recent developments that led to isozyme-specific and organ-selective inhibitors. A recent discovery is connected with the involvement of CAs and their sulfonamide inhibitors in cancer: several potent sulfonamide inhibitors inhibited the growth of a multitude of tumor cells in vitro and in vivo, thus constituting interesting leads for developing novel antitumor therapies. Furthermore, some other classes of compounds that interact with CAs have recently been discovered, some of which possess modified sulfonamide or hydroxamate moieties. Some sulfonamides have also applications as diagnostic tools, in PET and MRI or as antiepileptics or for the treatment of other neurological disorders. Future prospects for drug design applications for inhibitors of these ubiquitous enzymes are also discussed.},
  file      = {2003_Supuran_146.pdf:by-author/S/Supuran/2003_Supuran_146.pdf:PDF},
  groups    = {sg/inhibitors, sg/reviews},
  keywords  = {Carbonic Anhydrases},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Supuran1999,
  author    = {Supuran, C T and Scozzafava, A and Menabuoni, L and Mincione, F and Briganti, F and Mincione, G},
  journal   = {Metal-based drugs},
  title     = {Carbonic Anhydrase Inhibitors Part 72 Synthesis and Antiglaucoma Properties of Metal Complexes of p-Fluorobenzolamide.},
  year      = {1999},
  pages     = {67--73},
  volume    = {6},
  abstract  = {Metal complexes of a heterocyclic sulfonamides possessing very strong carbonic anhydrase (CA) inhibitory properties, i.e., 5-(p-fluorobenzenesulfonylamido)-1,3,4-thiadiazole-2-sulfonamide (p-fluorobenzolamide) were prepared. The new complexes contained metal ions such as Zn(II), Cu(II), Co(II), Ni(II), Cd(II) and Mn(II). The new compounds were characterized by standard physico-chemical procedures, and assayed as inhibitors of three CA isozymes, CA I, II and IV. Very good inhibition has been evidenced both for the parent sulfonamides as well as for the prepared complexes, against all three investigated isozymes. Some of these new complexes as well as the parent sulfonamide, strongly lowered intraocular pressure (IOP) in normotensive rabbits when administered as a 2% solution into the eye.},
  file      = {1999_Supuran_67.pdf:by-author/S/Supuran/1999_Supuran_67.pdf:PDF},
  groups    = {sg/inhibitors, sg/reviews},
  keywords  = {Carbonic Anhydrases; Inhibitors},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Surivet2012,
  author       = {Surivet, Jean-Philippe and Lange, Roland and Hubschwerlen, Christian and Keck, Wolfgang and Specklin, Jean-Luc and Ritz, Daniel and Bur, Daniel and Locher, Hans and Seiler, Peter and Strasser, Daniel Stefan and Prade, Lars and Kohl, Christopher and Schmitt, Christine and Chapoux, Gaëlle and Ilhan, Eser and Ekambaram, Nadia and Athanasiou, Alcibiade and Knezevic, Andreja and Sabato, Daniela and Chambovey, Alain and Gaertner, Mika and Enderlin, Michel and Boehme, Maria and Sippel, Virginie and Wyss, Pierre},
  journal      = {Bioorganic \& Medicinal Chemistry Letters},
  title        = {Structure-guided design, synthesis and biological evaluation of novel {DNA} ligase inhibitors with in vitro and in vivo anti-staphylococcal activity},
  year         = {2012},
  issn         = {0960-894X},
  pages        = {6705--6711},
  volume       = {22},
  abstract     = {A series of 2-amino-[1,8]-naphthyridine-3-carboxamides (ANCs) with potent inhibition of bacterial NAD+-dependent DNA ligases (LigAs) evolved from a 2,4-diaminopteridine derivative discovered by HTS. The design was guided by several highly resolved X-ray structures of our inhibitors in complex with either Streptococcus pneumoniae or Escherichia coli LigA. The structure–activity-relationship based on the ANC scaffold is discussed. The in-depth characterization of 2-amino-6-bromo-7-(trifluoromethyl)-[1,8]-naphthyridine-3-carboxamide, which displayed promising in vitro (MIC Staphylococcus aureus 1 mg/L) and in vivo anti-staphylococcal activity, is presented.},
  creationdate = {2015-10-14T00:00:00},
  doi          = {10.1016/j.bmcl.2012.08.094},
  file         = {Surivet et al. - 2012 - Structure-guided design, synthesis and biological .pdf:by-author/S/Surivet/2012_Surivet_6705.pdf:application/pdf;ScienceDirect Snapshot:by-author/S/Surivet/2012_Surivet_6705.html:text/html},
  keywords     = {2-amino-[1, 8]-naphthyridine-3-carboxamides; Antibacterials; DNA Ligase; In Vivo Active; Selective Inhibitors},
  owner        = {saulius},
  timestamp    = {2015.10.14},
  url          = {http://www.sciencedirect.com/science/article/pii/S0960894X12011055},
  urldate      = {2015-08-27},
}

@Manuscript{Suess2006,
  author           = {Michael Süß and Claudia Leopold},
  title            = {Common mistakes in {OpenMP} and how to avoid them: a collection and of best and practices},
  year             = {2006},
  abstract         = {Few data are available on common mistakes made when us- ing OpenMP. This paper presents a study on the programming errors observed in our courses on parallel programming during the last two years, along with numbers on which compilers and tools were able to spot them. The mistakes are explained and best practices for program- mers are suggested to avoid them in the future. The best practices are presented in the form of an OpenMP checklist for novice programmers.},
  creationdate     = {2013-08-11T00:00:00},
  file             = {:by-author/S/Süß/2006_Süß.pdf:PDF},
  modificationdate = {2024-10-22T15:09:29},
  owner            = {saulius},
  timestamp        = {2013.08.11},
}

@TechReport{Sussman1988,
  author      = {Geral Jay Sussman and Jack Wisdom},
  institution = {Massachusets Institute of Technology, Artificial Intelligence Laboratory},
  title       = {Numerical Evidence that the Motion of Pluto is Chaotic},
  year        = {1988},
  month       = {April},
  note        = {AI Memo 1039},
  abstract    = {The Digital Orrery has been used to perform an integration of the motion of the outer planets for 845 million years, This integration indicates that the long-term motion of the planet Pluto is chaotic. Nearby trajectories diverge exponentially with and $e$-folding time of only about 20 million years.},
  file        = {:by-author/S/Sussman/1988_Sussman.ps:PDF},
  owner       = {saulius},
  timestamp = {2012.11.19},
  creationdate = {2012-11-19T00:00:00},
}

@Article{Sussman1977,
  author    = {Joel L. Sussman and Stephen R. Holbrook and George M. Church and Sung-hou Kim},
  journal   = {Acta Crystallographica Section A},
  title     = {A Structure-factor Least-squares Refinement Procedure for Macromolecular Structures Using Constrained {\it and} Restrained Parameters},
  year      = {1977},
  pages     = {800--804},
  volume    = {33},
  doi       = {10.1107/S0567739477001958},
  file      = {:by-author/S/Sussman/1977_Sussman_800.pdf:PDF},
  keywords  = {Refinement; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0567739477001958},
}

@Article{Sutcliffe1993,
  author    = {Michael J. Sutcliffe},
  journal   = {Profein Science},
  title     = {Representing an ensemble of NMR-derived protein structures by a single structure},
  year      = {1993},
  pages     = {936--944},
  volume    = {2},
  abstract  = {The usefulness of representing an ensemble of NMR-derived protein structures by a single structure has been investigated. Two stereochemical properties have been used to assess how a single structure relates to theensemble from which it was derived, namely the distribution of +\$ torsion angles and the distribution of x1 torsion angles. The results show that theminimized average structure derived from theensemble (a total of 11 ensembles from theBrookhaven Protein Data Bank were analyzed) does not always correspond well with this ensemble, par- ticularly for those ensembles generated with a smaller number of experimentally derived restraints per residue. An alternative methodthat selects the member of the ensemble which is closest to the“average” of the ensemble has been investigated (a total of 23 ensembles from theBrookhaven Protein Data Bank were analyzed). Although this method selected a structure that on the whole corresponded more closely to theensemble than did the mini- mized average structure, this is still not a totally reliable means of selecting a single structure to represent the ensemble. This suggests that it is advisable to study the ensemble as a whole. A study has also been made of the practice of selecting the “best” rather than most representative member of the ensemble. This too suggests that the ensemble should be studied as a whole. A study of the conformationalspace occupied by the ensemble also suggests the need to consider the ensemble as a whole, particularly for those ensembles generated with a smaller number of experimentally derived restraints per residue},
  file      = {:by-author/S/Sutcliffe/1993_Sutcliffe_936.pdf:PDF},
  owner     = {saulius},
  timestamp = {2011.12.21},
  creationdate = {2011-12-21T00:00:00},
  url       = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2142398/pdf/8318898.pdf},
}

@Article{Sutherland1992,
  author    = {Sutherland, E. and Coe, L. and Raleigh, E. A.},
  journal   = {Journal of molecular biology},
  title     = {McrBC: a multisubunit GTP-dependent restriction endonuclease.},
  year      = {1992},
  pages     = {327--48},
  volume    = {225},
  abstract  = {McrBC-mediated restriction of modified DNA has been studied extensively by genetic methods, but little is known of its molecular action. We have used overproducing plasmid constructs to facilitate purification of the McrBL and McrC proteins, and report preliminary characterization of the activity of the complex. Both proteins are required for cleavage of appropriately modified DNA in vitro, in a reaction absolutely dependent on GTP. ATP inhibits the reaction. The sequence and modification requirements for cleavage of the substrate reflect those seen in vivo. The position of cleavage was examined at the nucleotide level, revealing that cleavage occurs at multiple positions in a small region. Based upon these observations, and upon cleavage of model oligonucleotide substrates, it is proposed that the recognition site for this enzyme consists of the motif RmC(N40-80)RmC, with cleavage occurring at multiple positions on both strands, between the modified C residues. In subunit composition, cofactor requirement, and relation between cleavage and recognition site, McrBC does not fit into any of the classes (types I to IV) of restriction enzyme so far described.},
  file      = {:by-author/S/Sutherland/1992_Sutherland_327.pdf:PDF},
  keywords  = {McrBC},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Manuscript{Sutherland2000,
  author    = {Ivan E. Sutherland and Jon K. Lexau},
  title     = {Designing Fast Asynchronous Circuits},
  year      = {2000},
  keywords  = {Computer Architecture; Computer Science (CS); Hardware},
  abstract  = {A five-step design process for asynchronous circuits helps simplify their logic and speed their operation. First, assume that all logic gates in the control will have nearly uniform delay. Second, use the uniform delay assumption to simplify control logic. Third, lay out the chip to get wire length data. Fourth, choose a specific delay and calculate transistor widths to apply that specific delay uniformly to all logic gates in the control; this paper shows how. Fifth, verify correct operation with standard methods. The specific gate delay trades off speed, area, and power consumption; postponing its choice takes advantage of asynchrony to accommodate the limitations imposed by layout. The theoretical lower bound for specific delay depends on the logical effort of the most complex loop in the design and remarkably, is independent of wire capacitance, given wide enough transistors, but wire capacitance puts practical bounds on speed. The effect of wire resistance remains unexplored.},
  file      = {:by-author/S/Sutherland/2000_Sutherland.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Book{Sutton1965,
  author    = {L. E. Sutton},
  publisher = {The Chemical Society},
  title     = {Tables of Interatomic Distances and Configuration in Molecules \& Ions},
  year      = {1965},
  file      = {:by-author/S/Sutton/1965_Sutton.pdf:PDF},
  owner     = {andrius},
  timestamp = {2013.04.22},
  creationdate = {2013-04-22T00:00:00},
  url       = {http://archive.org/details/TablesOfInteratomicDistancesAndConfigurationInMoleculesIons},
}

@Article{Suzuki1997,
  author      = {M. Suzuki and C. Y. Kao and D. R. McCarty},
  journal     = {Plant Cell},
  title       = {The conserved B3 domain of VIVIPAROUS1 has a cooperative DNA binding activity.},
  year        = {1997},
  pages       = {799--807},
  volume      = {9},
  abstract    = {The biochemical activities that underlie the genetically defined activator and repressor functions of the VIVIPAROUS1 (VP1) protein have resisted in vitro analysis. Here, we show that a glutathione S-transferase (GST) fusion protein, including only the highly conserved B3 domain of VP1, has a highly cooperative, sequence-specific DNA binding activity. GST fusion proteins that include larger regions of the VP1 protein have very low activity, indicating that removal of the flanking protein sequences is necessary to elicit DNA binding in vitro. DNA competition and DNase I footprinting analyses show that B3 binds specifically to the Sph element involved in VP1 activation of the C1 gene, whereas binding to the G-box-type VP1-responsive element is of low affinity and is nonspecific. Footprint analysis of the C1 promoter revealed that sequences flanking the core TCCATGCAT motif of Sph also contribute to the recognition of the Sph element in its native context. The salient features of the in vitro GST-B3 DNA interaction are in good agreement with the protein and DNA sequence requirements defined by the functional analyses of VP1 and VP1-responsive elements in maize cells.},
  doi         = {10.1105/tpc.9.5.799},
  file        = {:by-author/S/Suzuki/1997_Suzuki_799.pdf:PDF},
  institution = {Horticultural Sciences Department, University of Florida, Gainesville 32605, USA.},
  keywords    = {Base Sequence; Binding Sites; Biosynthesis; Biosynthesis/metabolism; Cloning; Conserved Sequence; DNA Probes; DNA-Binding Proteins; Deoxyribonuclease I; Genetic; Glutathione Transferase; Metabolism; Molecular; Molecular Sequence Data; Plant Proteins; Promoter Regions; Recombinant Fusion Proteins; Trans-Activators; Transcription Factors; Zea Mays},
  language    = {eng},
  medline-pst = {ppublish},
  owner       = {em},
  pii         = {9/5/799},
  pmid        = {9165754},
  timestamp = {2013.09.04},
  creationdate = {2013-09-04T00:00:00},
  url         = {http://dx.doi.org/10.1105/tpc.9.5.799},
}

@Article{Suzuki1995,
  author    = {Masashi Suzuki and Naoto Yagi and John T. Finch},
  journal   = {FEBS Letters},
  title     = {Role of base-backbone and base-base interactions in alternating {DNA} conformations},
  year      = {1995},
  pages     = {148--152},
  file      = {:by-author/S/Suzuki/1995_Suzuki_148.pdf:PDF},
  keywords  = {Deform; Readout},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Suzuki1998,
  author    = {Suzuki, Y. and Takemoto, O. and Arai, H. and Goto, M. and Yamada, J. and Morimoto, K. and Nakayama, M. and Futagi, Y. and Yano, A.},
  journal   = {No to hattatsu. Brain and development},
  title     = {[A case of congenital toxoplasmosis confirmed by detection of Toxoplasma gondii in placenta].},
  year      = {1998},
  pages     = {411--6},
  volume    = {30},
  abstract  = {We report a case of congenital toxoplasmosis with a prenatal diagnosis of fetal hydrocephalus. A CT scan performed at birth revealed ventricular dilation with calcification. The serum and CSF Toxoplasma specific IgM were elevated. The diagnosis was confirmed by the presence of Toxoplasma cysts in the placenta, and detection of the Toxoplasma SAG1 gene by a polymerase chain reaction (PCR) (placenta, positive; CSF, negative). Signs of active central nervous system infection, such as the decreased CSF glucose, and elevated CSF protein, neuron specific enolase and LDH, resolved after initiation of treatment with pyrimethamine and sulfazoxine. A PCR test using the placental tissue may be useful for the rapid diagnosis of congenital toxoplasmosis.},
  file      = {:by-author/S/Suzuki/1998_Suzuki_411.pdf:PDF},
  keywords  = {Antirestriction},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Presentation{Svergun2010a,
  author    = {Svergun},
  title     = {Rigid body refinement (basics)},
  year      = {2010},
  file      = {:by-author/S/Svergun/2010_Svergun_slides.pdf:PDF},
  keywords  = {SASREF; SAXS},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Presentation{Svergun2010b,
  author    = {Svergun},
  title     = {Ab initio methods: how/why do they work},
  year      = {2010},
  file      = {:by-author/S/Svergun/2010_Svergun_slides2.pdf:PDF},
  keywords  = {DAMMIN; SAXS},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Svergun1995,
  author    = {D. Svergun and C. Barberato and M. H. J. Koch},
  journal   = {Journal of Applied Crystallography},
  title     = {{CRYSOL} – a Program to Evaluate X-ray Solution Scattering of Biological Macromolecules from Atomic Coordinates},
  year      = {1995},
  pages     = {768},
  file      = {:by-author/S/Svergun/1995_Svergun_768.pdf:PDF},
  keywords  = {CRYSOL; SAXS},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Presentation{Svergun2010,
  author    = {Dmitri I. Svergun},
  title     = {Solution scattering from biological macromolecules},
  year      = {2010},
  course    = {EMBO Parctical Course},
  file      = {:by-author/S/Svergun/2010_Svergun_slides3.pdf:PDF},
  keywords  = {SAXS},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Svergun2007,
  author    = {Svergun, Dmitri I.},
  journal   = {Journal of Applied Crystallography},
  title     = {Small-angle scattering studies of macromolecular solutions},
  year      = {2007},
  pages     = {s10},
  file      = {:by-author/S/Svergun/2007_Svergun_s10.pdf:PDF},
  keywords  = {DAMMIN; Phage; SASREF; SAXS},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Svergun1999,
  author    = {Svergun, D. I.},
  journal   = {Biophysical journal},
  title     = {Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing.},
  year      = {1999},
  pages     = {2879--86},
  volume    = {76},
  abstract  = {A method is proposed to restore ab initio low resolution shape and internal structure of chaotically oriented particles (e.g., biological macromolecules in solution) from isotropic scattering. A multiphase model of a particle built from densely packed dummy atoms is characterized by a configuration vector assigning the atom to a specific phase or to the solvent. Simulated annealing is employed to find a configuration that fits the data while minimizing the interfacial area. Application of the method is illustrated by the restoration of a ribosome-like model structure and more realistically by the determination of the shape of several proteins from experimental x-ray scattering data.},
  file      = {:by-author/S/Svergun/1999_Svergun_2879.pdf:PDF},
  keywords  = {DAMMIN; SAXS},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Svergun1992,
  author    = {D. I. Svergun},
  journal   = {Journal of Applied Crystallography},
  title     = {Determination of the Regularization Parameter in Indirect-transform Methods Using Perceptual Criteria},
  year      = {1992},
  pages     = {495--503},
  volume    = {25},
  abstract  = {A method is proposed for the determination of the optimum value of the regularization parameter (Lagrange multiplier) when applying indirect transform techniques in small-angle scattering data analysis. The method is based on perceptual criteria of what is the best solution. A set of simple criteria is used to construct a total estimate describing the quality of the solution. Maximization of the total estimate is straightforward. Model computations show the effectiveness of the technique. The method is implemented in the program GNOM [Svergun, Semenyuk & Feigin (1988). Acta Cryst. A44, 244-250].},
  doi       = {10.1107/S0021889892001663},
  file      = {:by-author/S/Svergun/1992_Svergun_495.pdf:PDF},
  keywords  = {GNOM; SAXS},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0021889892001663},
}

@Article{Svergun1991,
  author    = {D. I. Svergun},
  journal   = {Journal of Applied Crystallography},
  title     = {Mathematical Methods in Small-angle Scattering Data Analysis},
  year      = {1991},
  pages     = {485},
  volume    = {24},
  abstract  = {Applications of modern mathematical methods to the problems of small-angle scattering data treatment and interpretation are considered. Special possibilities in data treatment, namely simultaneous treatment of data sets obtained with different experimental conditions and joint data processing for the anomalous-dispersion experiments, are presented. The methods are further developments of the indirect method based on the regularization technique [Svergun, Semenyuk & Feigin (1988). Acta Cryst. A44, 244-250]. Recent improvements in the shape-determination technique based on the multipole expansion theory [Stuhrmann (1970). Z. Phys. Chem. (Frankfurt am Main), 72, 177-184, 185-198] are described. A new method is proposed for the determination of positioning and mutual orientation of subunits in complex particles using the spherical harmonics technique.},
  doi       = {10.1107/S0021889891001280},
  file      = {:by-author/S/Svergun/1991_Svergun_485.pdf:PDF},
  keywords  = {SAXS; Theory},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0021889891001280},
}

@Article{Svergun2003,
  author    = {Dmitri I. Svergun and Michel H. J. Koch},
  journal   = {Rep. Prog. Phys.},
  title     = {Small-angle scattering studies of biological macromolecules in solution},
  year      = {2003},
  pages     = {1735--1782},
  file      = {:by-author/S/Svergun/2003_Svergun_1735.pdf:PDF},
  keywords  = {Review; SAXS; Theory},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Svergun2001,
  author    = {Svergun, D. I. and Petoukhov, M. V. and Koch, M. H.},
  journal   = {Biophysical journal},
  title     = {Determination of domain structure of proteins from X-ray solution scattering.},
  year      = {2001},
  pages     = {2946--53},
  volume    = {80},
  abstract  = {An ab initio method for building structural models of proteins from x-ray solution scattering data is presented. Simulated annealing is employed to find a chain-compatible spatial distribution of dummy residues which fits the experimental scattering pattern up to a resolution of 0.5 nm. The efficiency of the method is illustrated by the ab initio reconstruction of models of several proteins, with known and unknown crystal structure, from experimental scattering data. The new method substantially improves the resolution and reliability of models derived from scattering data and makes solution scattering a useful technique in large-scale structural characterization of proteins.},
  file      = {:by-author/S/Svergun/2001_Svergun_2946.pdf:PDF},
  keywords  = {GASBOR; SAXS},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Svoboda2015,
  author    = {Svoboda, Roman and Bezdička, Petr and Gutwirth, Jan and Málek, Jiří},
  journal   = {Materials Research Bulletin},
  title     = {Crystallization processes in {Ge} 2 {Sb} 2 {Se} 4 {Te} glass},
  year      = {2015},
  pages     = {207--214},
  volume    = {61},
  file      = {[PDF] from researchgate.net:by-author/S/Svoboda/2015_Svoboda_207.pdf:application/pdf;Snapshot:by-author/S/Svoboda/2015_Svoboda_207.html:text/html},
  groups    = {sg/NAR2012},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/S002554081400628X},
  urldate   = {2015-08-31},
}

@Article{Svrcek2009,
  author    = {Svrcek},
  title     = {Accelerated Life Cycle Comparison of Millenniata Archival DVD},
  year      = {2009},
  pages     = {D103},
  file      = {:by-author/S/Svrcek/2009_Svrcek_D103.pdf:PDF},
  keywords  = {Data Management; Preservation},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@Article{Swaminathan2008,
  author    = {Swaminathan, Kankshita and Peterson, Kevin and Jack, Thomas},
  journal   = {Trends Plant Sci},
  title     = {The plant B3 superfamily},
  year      = {2008},
  issn      = {1360-1385},
  pages     = {647--655},
  volume    = {13},
  abstract  = {The plant-specific B3 superfamily encompasses well-characterized families, such as the auxin response factor (ARF) family and the LAV family, as well as less well understood families, such as RAV and REM. In Arabidopsis, there are 118 B3 genes, and in rice there are 91 B3 genes. The B3 domain is present in genes from gymnosperms, mosses and green algae, indicating that the B3 domain evolved on the plant lineage before multicellularity. The aim of this review is to phylogenetically characterize the members of the B3 family in Arabidopsis and rice and to review the function of the B3 genes that have been studied to date.},
  doi       = {10.1016/j.tplants.2008.09.006},
  file      = {2008_Swaminathan_647.pdf:by-author/S/Swaminathan/2008_Swaminathan_647.pdf:PDF},
  keywords  = {B3; EcoRII; Plant Transcription Factors; Pseudobarrel Fold; Restriction Endonucleases (REases)},
  owner     = {saulius},
  publisher = {Elsevier Science, Ltd.},
  refid     = {S1360-1385(08)00264-1 DOI - 10.1016/j.tplants.2008.09.006},
  timestamp = {2013.01.01},
  creationdate = {2013-01-01T00:00:00},
  url       = {http://linkinghub.elsevier.com/retrieve/pii/S1360138508002641},
}

@Article{Swan2013,
  author    = {Alma Swan and Matthew Cockerill and Douglas Sipp},
  journal   = {Nature},
  title     = {Advocacy: How to hasten open access. Time to align policy; Make indexing fast and fair; Translate local journals},
  year      = {2013},
  pages     = {442--443},
  volume    = {495},
  abstract  = {Three advocates for a universally free scholarly literature give their prescriptions for the movement's next push, from findability to translations.},
  doi       = {10.1038/495442a},
  file      = {2013_Swan_442.pdf:by-author/S/Swan/2013_Swan_442.pdf:PDF},
  keywords  = {Open Access; Scientific Publication},
  owner     = {saulius},
  timestamp = {2013.04.03},
  creationdate = {2013-04-03T00:00:00},
}

@Article{Swendsen2006,
  author    = {Robert H. Swendsen},
  journal   = {Am. J. Phys.},
  title     = {Statistical mechanics of colloids and Boltzmann’s definition of the entropy},
  year      = {2006},
  pages     = {187--190},
  volume    = {74},
  doi       = {10.1119/1.2174962},
  file      = {:by-author/S/Swendsen/2006_Swendsen_187.pdf:PDF},
  keywords  = {Entropy; Statistical Mechanics},
  owner     = {saulius},
  timestamp = {2012.04.08},
  creationdate = {2012-04-08T00:00:00},
}

@Article{vanSwieten2005,
  author    = {van Swieten, Paul F. and Leeuwenburgh, Michiel A. and Kessler, Benedikt M. and Overkleeft, Herman S.},
  journal   = {Org. Biomol. Chem.},
  title     = {Bioorthogonal organic chemistry in living cells: novel strategies for labeling biomolecules},
  year      = {2005},
  pages     = {20--27},
  volume    = {3},
  abstract  = {The chemical labeling of biomolecules continues to be an important tool for the study of their function and cellular fate. Attention is increasingly focused on labeling of biomolecules in living cells{,} since cell lysis introduces many artefacts. In addition{,} with the advances in biocompatible synthetic organic chemistry{,} a whole new field of opportunity has opened up{,} affording high diversity in the nature of the label as well as a choice of ligation reactions. In recent years{,} several different two-step labeling strategies have emerged. These rely on the introduction of a bioorthogonal attachment site into a biomolecule{,} then ligation of a reporter molecule to this site using bioorthogonal organic chemistry. This Perspective focuses on these techniques{,} their implications and future directions.},
  doi       = {10.1039/B412558D},
  file      = {:by-author/v/vanSwieten/2005_vanSwieten_20.pdf:PDF},
  issue     = {1},
  keywords  = {Bioconjugation},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
  url       = {http://dx.doi.org/10.1039/B412558D},
}

@Article{Syamal1985,
  author    = {A. Syamal},
  journal   = {Journal of Chemical Education},
  title     = {Some Improper Terms in Coordination Chemistry},
  year      = {1985},
  pages     = {143},
  volume    = {62},
  abstract  = {A listing of terms recommended to replace those employing "complex" in coordination chemistry.},
  doi       = {10.1021/ed062p143},
  file      = {:./by-author/S/Syamal/1985_Syamal_143.pdf:PDF},
  keywords  = {Coordination Complex},
  owner     = {antanas},
  timestamp = {2014.01.15},
  creationdate = {2014-01-15T00:00:00},
  url       = {http://pubs.acs.org/doi/abs/10.1021/ed062p143},
}

@Article{Szalay2000,
  author     = {Szalay, Alexander S. and Kunszt, Peter Z. and Thakar, Ani and Gray, Jim and Slutz, Don and Brunner, Robert J.},
  journal    = {SIGMOD Rec.},
  title      = {Designing And Mining Multi-terabyte Astronomy Archives: The {S}loan {D}igital {S}ky {S}urvey},
  year       = {2000},
  issn       = {0163-5808},
  pages      = {451--462},
  volume     = {29},
  abstract   = {The next-generation astronomy digital archives will cover most of the sky at fine resolution in many wavelengths, from X-rays, through ultraviolet, optical, and infrared. The archives will be stored at diverse geographical locations. One of the first of these projects, the Sloan Digital Sky Survey (SDSS) is creating a 5-wavelength catalog over 10,000 square degrees of the sky (see http://www.sdss.org/). The 200 million objects in the multi-terabyte database will have mostly numerical attributes in a 100+ dimensional space. Points in this space have highly correlated distributions. The archive will enable astronomers to explore the data interactively. Data access will be aided by multidimensional spatial and attribute indices. The data will be partitioned in many ways. Small tag objects consisting of the most popular attributes will accelerate frequent searches. Splitting the data among multiple servers will allow parallel, scalable I/O and parallel data analysis. Hashing techniques will allow efficient clustering, and pair-wise comparison algorithms that should parallelize nicely. Randomly sampled subsets will allow de-bugging otherwise large queries at the desktop. Central servers will operate a data pump to support sweep searches touching most of the data. The anticipated queries will require special operators related to angular distances and complex similarity tests of object properties, like shapes, colors, velocity vectors, or temporal behaviors. These issues pose interesting data management challenges.},
  address    = {New York, NY, USA},
  doi        = {10.1145/335191.335439},
  file       = {:by-author/S/Szalay/2000_Szalay_451.pdf:PDF},
  issue_date = {June 2000},
  owner      = {saulius},
  publisher  = {ACM},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url        = {http://doi.acm.org/10.1145/335191.335439},
}

@Article{Szczelkun2002,
  author    = {Szczelkun, Mark D.},
  journal   = {Biochemistry},
  title     = {Kinetic models of translocation, head-on collision, and DNA cleavage by type I restriction endonucleases.},
  year      = {2002},
  pages     = {2067--74},
  volume    = {41},
  abstract  = {Digestion of linear DNA by type I restriction endonucleases is generally activated following the head-on collision of two translocating enzymes. However, the resulting distributions of cleavage loci along the DNA vary with different enzymes; in some cases, cleavage is located in a discrete region midway between a pair of recognition sites while in other cases cleavage is broadly distributed and occurs at nearly every intervening locus. Statistical models for DNA translocation, collision, and cleavage are described that can account for these observations and that are generally applicable to other DNA-based motor proteins. If translocation is processive (stepping forward is significantly more likely than DNA dissociation), then the linear distribution of an ensemble of proteins can be described simply using a Poisson relationship. The pattern of cleavage sites resulting from collision between two processive type I enzymes over a distance d can then be described by a binomial distribution with a standard deviation 0.5 x d1/2. Alternatively, if translocation is nonprocessive (stepping forward or dissociating become equally likely events), the linear distribution is described by a continuum of populated states and is thus extended. Comparisons of model data to the kinetics of DNA translocation and cleavage discount the nonprocessive model. Instead, the observed differences between enzymes are due to asynchronous events that occur upon collision. Therefore, type I restriction enzymes can be described as having processive DNA translocation but, in some cases, nonprocessive DNA cleavage.},
  file      = {:by-author/S/Szczelkun/2002_Szczelkun_2067.pdf:PDF},
  keywords  = {TypeI},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Szczelkun1996,
  author    = {Szczelkun, M. D. and Dillingham, M. S. and Janscak, P. and Firman, K. and Halford, S. E.},
  journal   = {The EMBO journal},
  title     = {Repercussions of DNA tracking by the type IC restriction endonuclease EcoR124I on linear, circular and catenated substrates.},
  year      = {1996},
  pages     = {6335--47},
  volume    = {15},
  abstract  = {Type I restriction endonucleases such as EcoR124I cleave DNA at undefined loci, distant from their recognition sequences, by a mechanism that involves the enzyme tracking along the DNA between recognition and cleavage sites. This mechanism was examined on plasmids that carried recognition sites for EcoR124I and recombination sites for resolvase, the latter to create DNA catenanes. Supercoiled substrates with either one or two restriction sites were linearized by EcoR124I at similar rates, although the two-site molecule underwent further cleavage more readily than the one-site DNA. The catenane from the plasmid with one EcoR124I site, carrying the site on the smaller of the two rings, was cleaved by EcoR124I exclusively in the small ring, and this underwent multiple cleavage akin to the two-site plasmid. Linear substrates derived from the plasmids were cleaved by EcoR124I at very slow rates. The communication between recognition and cleavage sites therefore cannot stem from random looping. Instead, it must follow the DNA contour between the sites. On a circular DNA, the translocation of non-specific DNA past the specifically bound protein should increase negative supercoiling in one domain and decrease it in the other. The ensuing topological barrier may be the trigger for DNA cleavage.},
  file      = {:by-author/S/Szczelkun/1996_Szczelkun_6335.pdf:PDF},
  keywords  = {TypeI},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Szczelkun1997,
  author    = {Szczelkun, M. D. and Janscak, P. and Firman, K. and Halford, S. E.},
  journal   = {Journal of molecular biology},
  title     = {Selection of non-specific DNA cleavage sites by the type IC restriction endonuclease EcoR124I.},
  year      = {1997},
  pages     = {112--23},
  volume    = {271},
  abstract  = {The Type IC restriction endonuclease EcoR124I binds specifically to its recognition sequence but subsequently translocates non-specific DNA past the complex in an ATP-dependent mechanism. The enzyme thus has the potential to cleave DNA at loci distant from the recognition site. We have scrutinised the link between translocation and cleavage on linear and circular DNA substrates. On linear DNA carrying two recognition sites, the majority of cleavages at loci distant from the recognition site occurred between the two sites, regardless of the inter-site distance or relative orientations. On circular DNA carrying one site, distant cleavages occurred throughout the DNA but an equivalent linear molecule underwent considerably fewer cleavages at distant loci. These results agree with published models for DNA tracking. However, on every molecule investigated, discrete cleavage sites were also observed within +/-250 bp of the recognition sites. The localised cleavages were not confined to particular DNA sequences and were independent of DNA topology. We propose a model to account for both distant and localised cleavage events. The conformation of the DNA loop extruded during tracking may result in two DNA segments being held in proximity to the restriction moiety on the protein, one close to the EcoR124I site and another distant from the site: cleavage may occur in either segment. Alternatively, the cutting of DNA close to recognition sites may be the result of multiple nicks being generated in the expanding loop before any extensive translocation.},
  file      = {:by-author/S/Szczelkun/1997_Szczelkun_112.pdf:PDF},
  keywords  = {TypeI},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Szczepanowski2008,
  author       = {Roman H Szczepanowski and Michael A Carpenter and Honorata Czapinska and Mindaugas Zaremba and Gintautas Tamulaitis and Virginijus Siksnys and Ashok S Bhagwat and Matthias Bochtler},
  journal      = {Nucleic Acids Res},
  title        = {Central base pair flipping and discrimination by PspGI},
  year         = {2008},
  month        = {Nov},
  number       = {19},
  pages        = {6109--6117},
  volume       = {36},
  abstract     = {PspGI is a representative of a group of restriction endonucleases that recognize a pentameric sequence related to CCNGG. Unlike the previously investigated Ecl18kI, which does not have any specificity for the central base pair, PspGI prefers A/T over G/C in its target site. Here, we present a structure of PspGI with target DNA at 1.7 A resolution. In this structure, the bases at the center of the recognition sequence are extruded from the DNA and flipped into pockets of PspGI. The flipped thymine is in the usual anti conformation, but the flipped adenine takes the normally unfavorable syn conformation. The results of this and the accompanying manuscript attribute the preference for A/T pairs over G/C pairs in the flipping position to the intrinsically lower penalty for flipping A/T pairs and to selection of the PspGI pockets against guanine and cytosine. Our data show that flipping can contribute to the discrimination between normal bases. This adds a new role to base flipping in addition to its well-known function in base modification and DNA damage repair.},
  creationdate = {2011-11-23T00:00:00},
  doi          = {10.1093/nar/gkn622},
  file         = {:by-author/S/Szczepanowski/2008_Szczepanowski_6109.pdf:PDF},
  institution  = {International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland.},
  keywords     = {Adenine; Amino Acid Sequence; Base Pairing; CCGG; Catalytic Domain; Chemistry; Crystal Structure; Crystallization; DNA; DNA-Binding Proteins; Deoxyribonucleases; Dimerization; Flip; Models; Molecular; Molecular Sequence Data; Nucleotides; PspGI; Restriction Endonuclease (RE); Thymine; Type II Site-Specific},
  language     = {eng},
  medline-pst  = {ppublish},
  owner        = {em},
  pii          = {gkn622},
  pmid         = {18829716},
  timestamp    = {2011.11.23},
  url          = {http://dx.doi.org/10.1093/nar/gkn622},
}

@Article{Szczepek2009,
  author    = {Szczepek, Michal and Mackeldanz, Petra and Möncke-Buchner, Elisabeth and Alves, Jürgen and Krüger, Detlev H. and Reuter, Monika},
  journal   = {Molecular Microbiology},
  title     = {Molecular analysis of restriction endonuclease EcoRII from Escherichia coli reveals precise regulation of its enzymatic activity by autoinhibition},
  year      = {2009},
  pages     = {1011--1021},
  volume    = {72},
  abstract  = {Bacterial restriction endonuclease EcoRII requires two recognition sites to cleave DNA. Proteolysis of EcoRII revealed the existence of two stable domains, EcoRII-N and EcoRII-C. Reduction of the enzyme to its C-terminal domain, EcoRII-C, unleashed the enzyme activity; this truncated form no longer needed two recognition sites and cleaved DNA much more efficiently than EcoRII wild-type. The crystal structure of EcoRII showed that probably the N-terminal domain sterically occludes the catalytic site, thus apparently controlling the cleavage activity. Based on these data, EcoRII was the first restriction endonuclease for which an autoinhibition mechanism as regulatory strategy was proposed. In this study, we probed this assumption and searched for the inhibitory element that mediates autoinhibition. Here we show that repression of EcoRII-C is achieved by addition of the inhibitory domain EcoRII-N or by single soluble peptides thereof in trans. Moreover, we perturbed contacts between the N- and the C-terminal domain of EcoRII by site-directed mutagenesis and proved that β-strand B1 and α-helix H2 are essential for autoinhibition; deletion of either secondary structural element completely relieved EcoRII autoinhibition. This potent regulation principle that keeps EcoRII enzyme activity controlled might protect bacteria against suicidal restriction of rare unmodified recognition sites in the cellular genome.},
  doi       = {10.1111/j.1365-2958.2009.06702.x},
  file      = {:by-author/S/Szczepek/2009_Szczepek_1011.pdf:PDF},
  keywords  = {Ecl18kI EcoRII; Restriction Endonucleases (REases); TypeII},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
  url       = {http://dx.doi.org/10.1111/j.1365-2958.2009.06702.x},
}

@Webpage{Szepesvari2008,
  author     = {Szepesvari, Csaba},
  retrieved  = {2015-12-12},
  title      = {Musings about Machine Learning, Technology and Teaching: {Bayesian} Statistics in Medical Clinical Trials},
  url        = {http://readingsml.blogspot.lt/2008/03/bayesian-statistics-in-medical-clinical.html},
  year       = {2008},
  file       = {2008_Szepesvari.html:by-author/S/Szepesvari/2008_Szepesvari.html:URL},
  groups     = {sg/Clinical Trials},
  owner      = {saulius},
  shorttitle = {Musings about {Machine} {Learning}, {Technology} and {Teaching}},
  timestamp = {2015.12.14},
  creationdate = {2015-12-14T00:00:00},
  urldate    = {2015-12-12},
}

@Article{Szostak2010,
  author    = {Szostak, Jack W.},
  journal   = {Angewandte Chemie (International ed. in English)},
  title     = {DNA ends: just the beginning (Nobel lecture).},
  year      = {2010},
  pages     = {7386--404},
  volume    = {49},
  file      = {:by-author/S/Szostak/2010_Szostak_7386.pdf:PDF},
  keywords  = {Nobel Prize Lectures},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Szychowska2016,
  author      = {Marta Szychowska and Wojciech Siwek and Damian Pawolski and Asgar Abbas Kazrani and Krzysztof Pyrc and Matthias Bochtler},
  journal     = {Acta Biochim Pol},
  title       = {Type III CRISPR complexes from Thermus thermophilus.},
  year        = {2016},
  month       = {Jun},
  abstract    = {Pathogen-specific acquired immunity in bacteria is mediated by the CRISPR (clustered regularly interspaced short palindromic repeats)-Cas systems. Thermus thermophilus strain HB8 contains CRISPR systems of several major subtypes (type I, IIIA and IIIB), and has become a widely studied model for CRISPR biology. We have selected two highly expressed CRISPR spacers, crRNA 2.1 and crRNA 2.2, and have enriched endogenous T. thermophilus proteins that co-purify with these crRNAs. Mass spectroscopy indicates that the chromatography protocol enriches predominantly Csm complex subunits, but also Cmr subunits. After several chromatographic steps, size exclusion chromatography indicated a molecular mass of the crRNA associated complex of 265±69 kDa. In agreement with earlier work, crRNAs of different lengths (containing the selected spacers) were observed. Most of these were completely lost when several T. thermophilus csm genes were ablated.},
  doi         = {10.18388/abp.2016_1261},
  file        = {:by-author/S/Szychowska/2016_Szychowska_1261.pdf:PDF},
  institution = {International Institute of Molecular and Cell Biology, Warsaw, Polandi and Institute of Biochemistry and Biophysics PAS, Warsaw, Poland.},
  keywords    = {CRISPR; Csm; Effector Complex},
  language    = {eng},
  medline-pst = {aheadofprint},
  owner       = {em},
  pii         = {2016_1261},
  pmid        = {27299480},
  timestamp = {2016.06.16},
  creationdate = {2016-06-16T00:00:00},
  url         = {http://dx.doi.org/10.18388/abp.2016_1261},
}

@Article{Soerensen2005,
  author    = {Sørensen, Hans Peter and Mortensen, Kim Kusk},
  journal   = {Journal of biotechnology},
  title     = {Advanced genetic strategies for recombinant protein expression in Escherichia coli.},
  year      = {2005},
  pages     = {113--28},
  volume    = {115},
  abstract  = {Preparations enriched by a specific protein are rarely easily obtained from natural host cells. Hence, recombinant protein production is frequently the sole applicable procedure. The ribosomal machinery, located in the cytoplasm is an outstanding catalyst of recombinant protein biosynthesis. Escherichia coli facilitates protein expression by its relative simplicity, its inexpensive and fast high-density cultivation, the well-known genetics and the large number of compatible tools available for biotechnology. Especially the variety of available plasmids, recombinant fusion partners and mutant strains have advanced the possibilities with E. coli. Although often simple for soluble proteins, major obstacles are encountered in the expression of many heterologous proteins and proteins lacking relevant interaction partners in the E. coli cytoplasm. Here we review the current most important strategies for recombinant expression in E. coli. Issues addressed include expression systems in general, selection of host strain, mRNA stability, codon bias, inclusion body formation and prevention, fusion protein technology and site-specific proteolysis, compartment directed secretion and finally co-overexpression technology. The macromolecular background for a variety of obstacles and genetic state-of-the-art solutions are presented.},
  file      = {:by-author/S/Sørensen/2005_Sorensen_113.pdf:PDF},
  keywords  = {Microbiology},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Sorensen2005,
  author    = {Hans Peter Sørensen and Kim Kusk Mortensen},
  journal   = {Microbial Cell Factories},
  title     = {Soluble expression of recombinant proteins in the cytoplasm of {E}scherichia coli},
  year      = {2005},
  pages     = {4:1},
  doi       = {10.1186/1475-2859-4-1},
  file      = {:by-author/S/Sorensen/2005_Sorensen_4\:1.pdf:PDF},
  keywords  = {Microbiology},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
  url       = {http://www.microbialcellfactories.com/content/4/1/1},
}

@Article{T.-J.Su2004,
  author    = {T.-J. Su, B. A. Connolly, C. Darlington, R. Mallin and D. T. F. Dryden},
  journal   = {Nucleic Acids Research},
  title     = {Unusual 2-aminopurine ̄uorescence from a complex of DNA and the EcoKI methyltransferase},
  year      = {2004},
  pages     = {2223--2230},
  volume    = {32},
  abstract  = {The methyltransferase, M.EcoKI, recognizes the DNA sequence 5′‐AACNNNNNNGTGC‐3′ and methylates adenine at the underlined positions. DNA methylation has been shown by crystallography to occur via a base flipping mechanism and is believed to be a general mechanism for all methyltransferases. If no structure is available, the fluorescence of 2‐aminopurine is often used as a signal for base flipping as it shows enhanced fluorescence when its environment is perturbed. We find that 2‐aminopurine gives enhanced fluorescence emission not only when it is placed at the M.EcoKI methylation sites but also at a location adjacent to the target adenine. Thus it appears that 2‐aminopurine fluorescence intensity is not a clear indicator of base flipping but is a more general measure of DNA distortion. Upon addition of the cofactor S‐adenosyl‐methionine to the M.EcoKI:DNA complex, the 2‐aminopurine fluorescence changes to that of a new species showing excitation at 345 nm and emission at 450 nm. This change requires a fully active enzyme, the correct cofactor and the 2‐aminopurine located at the methylation site. However, the new fluorescent species is not a covalently modified form of 2‐aminopurine and we suggest that it represents a hitherto undetected physicochemical form of 2‐aminopurine.},
  doi       = {10.1093/nar/gkh531},
  file      = {:by-author/T/T-JSu/2004_T-JSu_2223.pdf:PDF},
  keywords  = {MTases},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Tabor1981,
  author    = {Tabor, S. and Richardson, C. C.},
  journal   = {Proceedings of the National Academy of Sciences of the United States of America},
  title     = {Template recognition sequence for RNA primer synthesis by gene 4 protein of bacteriophage T7.},
  year      = {1981},
  pages     = {205--9},
  volume    = {78},
  abstract  = {The gene 4 protein of bacteriophage T7 recognizes specific sequences on single-stranded DNA and then catalyzes the synthesis of tetraribonucleotide primers complementary to the template. With phi X174 DNA as a template, the gene 4 protein enables T7 DNA polymerase (deoxynucleosidetriphosphate:DNA deoxynucleotidyltransferase, EC 2.7.7.7) to initiate DNA synthesis at 13 major sites. DNA sequence analysis of the 5' termini of the newly synthesized DNA shows the predominant recognition sequences for the gene 4 protein to be 3'-C-T-G-G-G-5' or 3'-C-T-G-G-T-5'; the products of synthesis at these sites are RNA primers having the sequences pppA-C-C-C or pppA-C-C-A. The gene 4 protein can also synthesize primers at the sequences 3'-C-T-G-G-AC-5' and 3'-C-T-G-T-N-5', although these sites are used less than 10% as frequently as the predominant sites. Comparison of the utilization of primer sites suggests that the gene 4 protein binds randomly to single-stranded DNA and then translocates along the DNA in a unidirectional 5'-to-3' direction with regard to the DNA strand in search of recognition sequences. Models are presented for the role of the gene 4 protein in the initiation of lagging-strand synthesis and in the initiation of DNA replication at the origin.},
  file      = {:by-author/T/Tabor/1981_Tabor_205.pdf:PDF},
  keywords  = {T7; {gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Tackett2001,
  author    = {Tackett, A. J. and Morris, P. D. and Dennis, R. and Goodwin, T. E. and Raney, K. D.},
  journal   = {Biochemistry},
  title     = {Unwinding of unnatural substrates by a DNA helicase.},
  year      = {2001},
  pages     = {543--8},
  volume    = {40},
  abstract  = {Helicases separate double-stranded DNA into single-stranded DNA intermediates that are required during replication and recombination. These enzymes are believed to transduce free energy available from ATPase activity to unwind the duplex and translocate along the nucleic acid lattice. The nature of enzyme-substrate interactions between helicases and duplex DNA substrates has not been well-defined. Most helicases require a single-stranded DNA overhang adjacent to duplex DNA in order to initiate unwinding. The strand containing the overhang is referred to as the loading strand whereas the complementary strand is referred to as the displaced strand. We have investigated the interactions between a DNA helicase and the DNA substrate by replacing the displaced strand with a nucleic acid mimic, peptide nucleic acid (PNA). PNA is capable of forming duplex structures with DNA according to Watson-Crick base pairing rules, but contains a N-(2-aminoethyl)glycine backbone in place of the deoxyribose phosphates. The PNA-DNA hybrids had higher melting temperatures than their DNA-DNA counterparts. Dda helicase, from bacteriophage T4, was able to unwind the DNA-PNA substrates at similar rates as DNA-DNA substrates. The results indicate that the rate-limiting step for unwinding is relatively insensitive to the chemical nature of the displaced strand and the thermal stability of oligonucleotide substrates.},
  file      = {:by-author/T/Tackett/2001_Tackett_543.pdf:PDF},
  keywords  = {{gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Taheri2001,
  author    = {S.M. Taheri and J. Behboodian},
  journal   = {Fuzzy Sets and Systems},
  title     = {A Bayesian approach to fuzzy hypotheses testing},
  year      = {2001},
  pages     = {39--48},
  volume    = {123},
  abstract  = {In statistical decisions we may come across imprecise (fuzzy) concepts. One important case is a situation where we are interested in testing the hypotheses that are fuzzy rather than crisp. In this paper we consider and analyze the testing of fuzzy hypotheses on the basis of a Bayesian approach. We illustrate our method by some examples, and compare it with previous works on this topic.},
  doi       = {10.1016/S0165-0114(00)00134-2},
  file      = {2001_Taheri_39.pdf:by-author/T/Taheri/2001_Taheri_39.pdf:PDF},
  groups    = {sg/CRISPR-Cas, sg/Bayesian},
  keywords  = {Bayesian Statistics; Fuzzy Logics; Fuzzy Sets},
  owner     = {saulius},
  timestamp = {2012.10.09},
  creationdate = {2012-10-09T00:00:00},
  url       = {http://www.dss.dpem.tuc.gr/pdf/A%20Bayesian%20approach%20to%20fuzzy%20hypotheses%20testing.pdf},
}

@Article{Tait2005,
  author    = {Tait},
  title     = {Godel's Reformulation of Gentzen's First Consistency Proof for Arithmetic: the No-counterexample Interpretation},
  year      = {2005},
  file      = {:by-author/T/Tait/2005_Tait.pdf:PDF},
  keywords  = {Goedel's Theorem},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Takahashi2010,
  author    = {Takahashi},
  title     = {Relevance of Weak Hydrogen Bonds in the Conformation of Organic Compounds and Bioconjugates: Evidence from Recent Experimental Data and High-Level ab Initio MO Calculations},
  year      = {2010},
  pages     = {A},
  file      = {:by-author/T/Takahashi/2010_Takahashi_A.pdf:PDF},
  keywords  = {Noncovalent Interactions; Protein Physics},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@Article{Takahashi1998,
  author    = {Takahashi},
  journal   = {Macromolecules},
  title     = {Neutron Structure Analysis of Polyethylene-d<sub>4<\sub>},
  year      = {1998},
  pages     = {3868--3871},
  volume    = {31},
  file      = {:by-author/T/Takahashi/1998_Takahashi_3868.pdf:PDF},
  keywords  = {Polyethylene; Structures},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@Article{Takahashi2004,
  author    = {Takahashi, Yasuhiro and Kumano, Takeshi},
  journal   = {Journal of Polymer Science Part B: Polymer Physics},
  title     = {Neutron crystal structure analysis of polyethylene-d4: The application of a neutron imaging plate},
  year      = {2004},
  pages     = {3836--3839},
  volume    = {42},
  abstract  = {Neutron diffraction provides a more detailed structure than X-ray diffraction. In this study, a neutron crystal structure analysis of polyethylene-d4 was carried out with a neutron imaging plate. This was the first crystal analysis of the crystalline polymer with the neutron fiber pattern. The procedure was almost the same as that in a previous work, in which the neutron structure analysis was carried out on the basis of the equatorial reflections. The azimuthal angle of the molecule with respect to the a axis was estimated to be 46.3°. This corresponded well to the value of 45° estimated in the previous work within the accuracy of the standard deviations. © 2004 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 42: 3836–3839, 2004},
  doi       = {10.1002/polb.20245},
  file      = {:by-author/T/Takahashi/2004_Takahashi_3836.pdf:PDF},
  keywords  = {Polyethylene; Structures},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1002/polb.20245},
}

@Article{Takiyama1989,
  author    = {Ryuzo Takiyama and Naoki Ono},
  journal   = {Pattern Recognition Letters},
  title     = {A least square error estimation of the center and radii of concentric arcs},
  year      = {1989},
  pages     = {237--242},
  volume    = {10},
  abstract  = {When some concentric digital arcs are given, we show formulas for the modified least square error estimation of the common center and respective radii.},
  file      = {1989_Takiyama_237.pdf:by-author/T/Takiyama/1989_Takiyama_237.pdf:PDF},
  groups    = {sg/Arc fitting, sg/Bioinf. Algorithms},
  keywords  = {Algorithms; Arc Fitting; Computer Vision; Concentric Arcs; Digital Arc; Least Square Error Estimation; Mathematics},
  owner     = {saulius},
  timestamp = {2011.01.26},
  creationdate = {2011-01-26T00:00:00},
}

@Article{Talanov2014,
  author    = {Talanov, V. M. and Shirokov, V. B.},
  journal   = {Acta crystallographica. Section A, Foundations and advances},
  title     = {Atomic order in the spinel structure - a group-theoretical analysis.},
  year      = {2014},
  pages     = {49--63},
  volume    = {70},
  abstract  = {Group-theoretical methods of the Landau theory of phase transitions are used to investigate the structures of ordered spinels. The possibility of the existence is determined of 305 phases with different types of order in Wyckoff position 8a (including seven binary and seven ternary cation substructures), 537 phases in Wyckoff position 16d (including eight binary and 11 ternary cation substructures), 595 phases in Wyckoff position 32e (including seven binary and four ternary anion substructures) and 549 phases with simultaneous ordering in Wyckoff positions 8a and 16d (including five substructures with binary order in tetrahedral and octahedral sublattices, two substructures with ternary order in both spinel sublattices, and nine substructures with different combined types of binary and ternary order). Theoretical results and experimental data are compared. Calculated structures of the spread types of ordered low-symmetry spinel modifications are given.},
  file      = {:by-author/T/Talanov/2014_Talanov_49.pdf:PDF},
  owner     = {saulius},
  timestamp = {2014.03.23},
  creationdate = {2014-03-23T00:00:00},
}

@Article{Talibov2016,
  author      = {Vladimir O Talibov and Vaida Linkuvienė and Daumantas Matulis and U. Helena Danielson},
  journal     = {J Med Chem},
  title       = {Kinetically Selective Inhibitors of Human Carbonic Anhydrase Isozymes I, II, VII, IX, XII, and XIII.},
  year        = {2016},
  month       = {Mar},
  number      = {5},
  pages       = {2083--2093},
  volume      = {59},
  abstract    = {To get a better understanding of the possibility of developing selective carbonic anhydrase (CA) inhibitors, interactions between 17 benzenesulphonamide ligands and 6 human CAs (full-length CA I, II, VII, and XIII and catalytic domains of CA IX and XII) were characterized using surface plasmon resonance and fluorescent-based thermal shift assays. Kinetics revealed that the strongest binders had subnanomolar affinities with low dissociation rates (i.e., kd values around 1 × 10(-3) s(-1)) or were essentially irreversible. Chemodynamic analysis of the interactions highlighted an intrinsic mechanism of the CA-sulphonamide interaction kinetics and showed that slow dissociation rates were mediated by large hydrophobic contacts. The studied inhibitors demonstrated a high cross-reactivity within the protein family. However, according to chemical phylogenetic analysis developed for kinetic data, several ligands were found to be selective against certain CA isozymes, indicating that it should be possible to develop selective CA inhibitors suitable for clinical use.},
  doi         = {10.1021/acs.jmedchem.5b01723},
  file        = {2016_Talibov_2083.pdf:by-author/T/Talibov/2016_Talibov_2083.pdf:PDF},
  institution = {Science for Life Laboratory, Uppsala University , Uppsala SE-751 23, Sweden.},
  keywords    = {Antagonists /&/ Inhibitors/metabolism; Carbonic Anhydrase Inhibitors; Carbonic Anhydrases; Chemical Synthesis/chemistry/pharmacology; Dose-Response Relationship; Drug; Humans; Hydrogen-Ion Concentration; Isoenzymes; Kinetics; Metabolism; Molecular Structure; Structure-activity Relationship (SAR)},
  language    = {eng},
  medline-pst = {ppublish},
  owner       = {alexey},
  pmid        = {26805033},
  timestamp = {2016.08.30},
  creationdate = {2016-08-30T00:00:00},
  url         = {http://dx.doi.org/10.1021/acs.jmedchem.5b01723},
}

@PhdThesis{Tamulaitiene2006a,
  author    = {Giedrė Tamulaitienė},
  school    = {Vilniaus universitetas/Vilnius University},
  title     = {Crystallographic and Functional Investigations of Type II Restriction Endonucleases Eco57I and SdaI},
  year      = {2006},
  file      = {:by-author/T/Tamulaitiene/2006_Tamulaitiene_phdthesis.odt:OpenDocument text;:by-author/T/Tamulaitiene/2006_Tamulaitiene_phdthesis.sxw:OpenDocument text},
  groups    = {sg/SdaI},
  owner     = {saulius},
  timestamp = {2013.08.11},
  creationdate = {2013-08-11T00:00:00},
}

@Presentation{Tamulaitiene2004a,
  author       = {Giedrė Tamulaitienė},
  title        = {Holliday sankirtos migracijos struktūrinė analizė},
  year         = {2004},
  organization = {BNSTL},
  school       = {BTI},
  file         = {:by-author/T/Tamulaitienė/2004_Tamulaitienė.ppt:PPT},
  keywords     = {Prezentacijos},
  owner        = {saulius},
  timestamp = {2015.03.03},
  creationdate = {2015-03-03T00:00:00},
}

@Article{Tamulaitiene2004,
  author    = {Tamulaitiene, Giedre and Grazulis, Saulius and Janulaitis, Arvydas and Janowski, Robert and Bujacz, Grzegorz and Jaskolski, Mariusz},
  journal   = {Biochimica et biophysica acta},
  title     = {Crystallization and preliminary crystallographic studies of a bifunctional restriction endonuclease Eco57I.},
  year      = {2004},
  pages     = {251--4},
  volume    = {1698},
  abstract  = {Restriction endonuclease Eco57I from Escherichia coli recognizes asymmetric DNA sequence 5'-CTGAAG and has both restriction (DNA cleavage a short distance away from the recognition site) and modification (methylation) activities residing in a single polypeptide chain. Single crystals of wild-type Eco57I ternary complexes with double-stranded DNA and sinefungin, a stimulator of endonuclease activity, were obtained by the vapor diffusion technique and characterized crystallographically for different variants of the DNA component. The best data for the complex with 25-mer DNA were collected to 4.2-A resolution at 100 K using synchrotron radiation. The crystals are orthorhombic, space group P2(1)2(1)2, with a=164.3, b=293.0, c=71.1 A, and contain two to four copies of the protein in the asymmetric unit.},
  file      = {:by-author/T/Tamulaitiene/2004_Tamulaitiene_251.pdf:PDF},
  keywords  = {Struct; TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Tamulaitiene2006,
  author    = {Tamulaitiene, Giedre and Jakubauskas, Arturas and Urbanke, Claus and Huber, Robert and Grazulis, Saulius and Siksnys, Virginijus},
  journal   = {Structure (London, England : 1993)},
  title     = {The crystal structure of the rare-cutting restriction enzyme SdaI reveals unexpected domain architecture.},
  year      = {2006},
  pages     = {1389--400},
  volume    = {14},
  abstract  = {Rare-cutting restriction enzymes are important tools in genome analysis. We report here the crystal structure of SdaI restriction endonuclease, which is specific for the 8 bp sequence CCTGCA/GG (&quot;/&quot; designates the cleavage site). Unlike orthodox Type IIP enzymes, which are single domain proteins, the SdaI monomer is composed of two structural domains. The N domain contains a classical winged helix-turn-helix (wHTH) DNA binding motif, while the C domain shows a typical restriction endonuclease fold. The active site of SdaI is located within the C domain and represents a variant of the canonical PD-(D/E)XK motif. SdaI determinants of sequence specificity are clustered on the recognition helix of the wHTH motif at the N domain. The modular architecture of SdaI, wherein one domain mediates DNA binding while the other domain is predicted to catalyze hydrolysis, distinguishes SdaI from previously characterized restriction enzymes interacting with symmetric recognition sequences.},
  doi       = {10.1016/j.str.2006.07.002},
  file      = {:by-author/T/Tamulaitiene/2006_Tamulaitiene_1389.pdf:PDF},
  groups    = {sg/SdaI},
  keywords  = {Struct; TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Tamulaitiene2016,
  author    = {Tamulaitiene, Giedre and Jovaisaite, Virginija and Tamulaitis, Gintautas and Songailiene, Inga and Manakova, Elena and Zaremba, Mindaugas and Grazulis, Saulius and Xu, Shuang-yong and Siksnys, Virginijus},
  journal   = {Nucleic Acids Research},
  title     = {Restriction endonuclease AgeI is a monomer which dimerizes to cleave DNA},
  year      = {2016},
  issn      = {1362-4962},
  month     = {Dec},
  pages     = {gkw1310},
  doi       = {10.1093/nar/gkw1310},
  file      = {:by-author/T/Tamulaitiene/2016_Tamulaitiene_gkw1310.pdf:PDF},
  groups    = {sg/AgeI},
  keywords  = {AgeI; Restriction Endonucleases (REases); X-ray Crystallography},
  owner     = {saulius},
  publisher = {Oxford University Press (OUP)},
  timestamp = {2017.02.10},
  creationdate = {2017-02-10T00:00:00},
  url       = {http://dx.doi.org/10.1093/nar/gkw1310},
}

@Article{Tamulaitiene2008,
  author    = {Tamulaitiene, Giedre and Siksnys, Virginijus},
  journal   = {Structure (London, England : 1993)},
  title     = {{NotI} is not boring},
  year      = {2008},
  pages     = {497--8},
  volume    = {16},
  doi       = {10.1016/j.str.2008.03.003},
  file      = {:by-author/T/Tamulaitiene/2008_Tamulaitiene_497.pdf:PDF},
  keywords  = {Octanucleotide Site; TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Tamulaitiene2014,
  author      = {Giedre Tamulaitiene and Arunas Silanskas and Saulius Grazulis and Mindaugas Zaremba and Virginijus Siksnys},
  journal     = {Nucleic Acids Res},
  title       = {Crystal structure of the R-protein of the multisubunit ATP-dependent restriction endonuclease NgoAVII.},
  year        = {2014},
  pages       = {14022--14030},
  volume      = {42},
  abstract    = {The restriction endonuclease (REase) NgoAVII is composed of two proteins, R.NgoAVII and N.NgoAVII, and shares features of both Type II restriction enzymes and Type I/III ATP-dependent restriction enzymes (see accompanying paper Zaremba et al., 2014). Here we present crystal structures of the R.NgoAVII apo-protein and the R.NgoAVII C-terminal domain bound to a specific DNA. R.NgoAVII is composed of two domains: an N-terminal nucleolytic PLD domain; and a C-terminal B3-like DNA-binding domain identified previously in BfiI and EcoRII REases, and in plant transcription factors. Structural comparison of the B3-like domains of R.NgoAVII, EcoRII, BfiI and the plant transcription factors revealed a conserved DNA-binding surface comprised of N- and C-arms that together grip the DNA. The C-arms of R.NgoAVII, EcoRII, BfiI and plant B3 domains are similar in size, but the R.NgoAVII N-arm which makes the majority of the contacts to the target site is much longer. The overall structures of R.NgoAVII and BfiI are similar; however, whilst BfiI has stand-alone catalytic activity, R.NgoAVII requires an auxiliary cognate N.NgoAVII protein and ATP hydrolysis in order to cleave DNA at the target site. The structures we present will help formulate future experiments to explore the molecular mechanisms of intersubunit crosstalk that control DNA cleavage by R.NgoAVII and related endonucleases.},
  doi         = {10.1093/nar/gku1237},
  file        = {2014_Tamulaitiene_1.pdf:by-author/T/Tamulaitiene/2014_Tamulaitiene_1.pdf:PDF},
  institution = {Department of Protein-DNA Interactions, Institute of Biotechnology, Vilnius University, Graiciuno 8, LT-02241 Vilnius, Lithuania zare@ibt.lt.},
  language    = {eng},
  medline-pst = {ppublish},
  owner       = {em},
  pii         = {gku1237},
  pmid        = {25429979},
  timestamp = {2015.01.02},
  creationdate = {2015-01-02T00:00:00},
  url         = {http://dx.doi.org/10.1093/nar/gku1237},
}

@Article{Tamulaitis2014,
  author    = {Gintautas Tamulaitis and Migle Kazlauskiene and Elena Manakova and Ceslovas Venclovas and Alison O. Nwokeoji and Mark J. Dickman and Philippe Horvath and Virginijus Siksnys},
  journal   = {Molecular Cell},
  title     = {Programmable RNA Shredding by the Type III-A CRISPR-Cas System of Streptococcus thermophilus},
  year      = {2014},
  pages     = {1--12},
  volume    = {56},
  abstract  = {Immunity against viruses and plasmids provided by CRISPR-Cas systems relies on a ribonucleoprotein effector complex that triggers the degradation of invasive nucleic acids (NA). Effector complexes of type I (Cascade) and II (Cas9-dual RNA) target foreign DNA. Intriguingly, the genetic evidence suggests that the type III-A Csm complex targets DNA, whereas biochemical data show that the type III-B Cmr complex cleaves RNA. Here we aimed to investigate NA specificity and mechanism of CRISPR interference for the Streptococcus thermophilus Csm (III-A) complex (StCsm). When expressed in Escherichia coli, two complexes of different stoichiometry copurified with 40 and 72 nt crRNA species, respectively. Both complexes targeted RNA and generated multiple cuts at 6 nt intervals. The Csm3 protein, present in multiple copies in both Csm complexes, acts as endoribonuclease. In the heterologous E. coli host, StCsm restricts MS2 RNA phage in a Csm3 nuclease-dependent manner. Thus, our results demonstrate that the type III-A StCsm complex guided by crRNA targets RNA and not DNA.},
  comment   = {ACKNOWLEDGMENTS !!! no acknowledgements to DESY in this section Experimental procedures: SAXS data for Csm-40 and Csm-72 were collected at P12 EMBL beam-line at PETRAIII storage ring of DESY synchrotron in Hamburg (Germany).},
  doi       = {10.1016/j.molcel.2014.09.027},
  file      = {:by-author/T/Tamulaitis/2014_Tamulaitis_506.pdf:PDF},
  groups    = {sg/CRISPR-Cas},
  keywords  = {CRISPR; Csm; III-A; S. thermophilus; SAXS},
  owner     = {em},
  timestamp = {2014.11.21},
  creationdate = {2014-11-21T00:00:00},
  url       = {http://dx.doi.org/10.1016/j.molcel.2014.09.027},
}

@Article{Tamulaitis2000,
  author    = {Tamulaitis, G. and Lagunavičius, A.},
  journal   = {Biologija},
  title     = {{DNA} bending induced by {MunI} restriction endonuclease},
  year      = {2000},
  pages     = {11},
  file      = {:by-author/T/Tamulaitis/2000_Tamulaitis_11.pdf:PDF},
  keywords  = {Ecl18kI; EcoRII; TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Tamulaitis2006b,
  author    = {Tamulaitis, Gintautas and Mucke, Merlind and Siksnys, Virginijus},
  journal   = {FEBS letters},
  title     = {Biochemical and mutational analysis of EcoRII functional domains reveals evolutionary links between restriction enzymes.},
  year      = {2006},
  pages     = {1665--71},
  volume    = {580},
  abstract  = {The archetypal Type IIE restriction endonuclease EcoRII is a dimer that has a modular structure. DNA binding studies indicate that the isolated C-terminal domain dimer has an interface that binds a single cognate DNA molecule whereas the N-terminal domain is a monomer that also binds a single copy of cognate DNA. Hence, the full-length EcoRII contains three putative DNA binding interfaces: one at the C-terminal domain dimer and two at each of the N-terminal domains. Mutational analysis indicates that the C-terminal domain shares conserved active site architecture and DNA binding elements with the tetrameric restriction enzyme NgoMIV. Data provided here suggest possible evolutionary relationships between different subfamilies of restriction enzymes.},
  file      = {:by-author/T/Tamulaitis/2006_Tamulaitis_1665.pdf:PDF},
  groups    = {sg/NgoMIV},
  keywords  = {Ecl18kI; EcoRII; TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Tamulaitis2006c,
  author       = {Gintautas Tamulaitis and Merlind Mucke and Virginijus Siksnys},
  journal      = {FEBS Lett},
  title        = {Biochemical and mutational analysis of EcoRII functional domains reveals evolutionary links between restriction enzymes.},
  year         = {2006},
  month        = {Mar},
  number       = {6},
  pages        = {1665--1671},
  volume       = {580},
  abstract     = {The archetypal Type IIE restriction endonuclease EcoRII is a dimer that has a modular structure. DNA binding studies indicate that the isolated C-terminal domain dimer has an interface that binds a single cognate DNA molecule whereas the N-terminal domain is a monomer that also binds a single copy of cognate DNA. Hence, the full-length EcoRII contains three putative DNA binding interfaces: one at the C-terminal domain dimer and two at each of the N-terminal domains. Mutational analysis indicates that the C-terminal domain shares conserved active site architecture and DNA binding elements with the tetrameric restriction enzyme NgoMIV. Data provided here suggest possible evolutionary relationships between different subfamilies of restriction enzymes.},
  creationdate = {2011-06-10T00:00:00},
  doi          = {10.1016/j.febslet.2006.02.010},
  file         = {2006_Tamulaitis_preprint.pdf:by-author/T/Tamulaitis/2006_Tamulaitis_preprint.pdf:PDF;2006_Tamulaitis_1665.pdf:by-author/T/Tamulaitis/2006_Tamulaitis_1665.pdf:PDF},
  institution  = {Institute of Biotechnology, Graiciuno 8, Vilnius LT-02241, Lithuania.},
  keywords     = {Amino Acid Motifs; Binding Sites; Catalytic Domain; Chemistry; Chemistry/genetics; Chromatography; Conserved Sequence; DNA; DNA Mutational Analysis; DNA Restriction Enzymes; Deoxyribonucleases; Evolution; Gel; Genetics/physiology; Molecular; Molecular Sequence Data; Protein Structure; Tertiary; Type II Site-Specific},
  language     = {eng},
  medline-pst  = {ppublish},
  owner        = {em},
  pii          = {S0014-5793(06)00198-0},
  pmid         = {16497303},
  timestamp    = {2011.06.10},
  url          = {http://dx.doi.org/10.1016/j.febslet.2006.02.010},
}

@Article{Tamulaitis2015,
  author       = {Gintautas Tamulaitis and Marius Rutkauskas and Mindaugas Zaremba and Saulius Grazulis and Giedre Tamulaitiene and Virginijus Siksnys},
  journal      = {Nucleic Acids Res},
  title        = {Functional significance of protein assemblies predicted by the crystal structure of the restriction endonuclease BsaWI.},
  year         = {2015},
  month        = {Sep},
  number       = {16},
  pages        = {8100--8110},
  volume       = {43},
  abstract     = {Type II restriction endonuclease BsaWI recognizes a degenerated sequence 5'-W/CCGGW-3' (W stands for A or T, '/' denotes the cleavage site). It belongs to a large family of restriction enzymes that contain a conserved CCGG tetranucleotide in their target sites. These enzymes are arranged as dimers or tetramers, and require binding of one, two or three DNA targets for their optimal catalytic activity. Here, we present a crystal structure and biochemical characterization of the restriction endonuclease BsaWI. BsaWI is arranged as an 'open' configuration dimer and binds a single DNA copy through a minor groove contacts. In the crystal primary BsaWI dimers form an indefinite linear chain via the C-terminal domain contacts implying possible higher order aggregates. We show that in solution BsaWI protein exists in a dimer-tetramer-oligomer equilibrium, but in the presence of specific DNA forms a tetramer bound to two target sites. Site-directed mutagenesis and kinetic experiments show that BsaWI is active as a tetramer and requires two target sites for optimal activity. We propose BsaWI mechanism that shares common features both with dimeric Ecl18kI/SgrAI and bona fide tetrameric NgoMIV/SfiI enzymes.},
  creationdate = {2016-06-09T00:00:00},
  doi          = {10.1093/nar/gkv768},
  file         = {2015_Tamulaitis_8100.pdf:by-author/T/Tamulaitis/2015_Tamulaitis_8100.pdf:PDF},
  institution  = {Department of Protein-DNA Interactions, Institute of Biotechnology, Vilnius University, Graiciuno 8, LT-02241 Vilnius, Lithuania siksnys@ibt.lt.},
  keywords     = {Bacterial Proteins; Catalytic Domain; Chemistry/metabolism; Crystallography; DNA; DNA Cleavage; Deoxyribonucleases; Enzymology; Geobacillus Stearothermophilus; Models; Molecular; Protein Binding; Protein Multimerization; Type II Site-Specific; X-Ray},
  language     = {eng},
  medline-pst  = {ppublish},
  owner        = {em},
  pii          = {gkv768},
  pmid         = {26240380},
  timestamp    = {2016.06.09},
  url          = {http://dx.doi.org/10.1093/nar/gkv768},
}

@Article{Tamulaitis2006,
  author      = {Gintautas Tamulaitis and Giedrius Sasnauskas and Merlind Mucke and Virginijus Siksnys},
  journal     = {J Mol Biol},
  title       = {Simultaneous binding of three recognition sites is necessary for a concerted plasmid DNA cleavage by EcoRII restriction endonuclease.},
  year        = {2006},
  month       = {Apr},
  number      = {2},
  pages       = {406--419},
  volume      = {358},
  abstract    = {According to the current paradigm type IIE restriction endonucleases are homodimeric proteins that simultaneously bind to two recognition sites but cleave DNA at only one site per turnover: the other site acts as an allosteric locus, activating the enzyme to cleave DNA at the first. Structural and biochemical analysis of the archetypal type IIE restriction enzyme EcoRII suggests that it has three possible DNA binding interfaces enabling simultaneous binding of three recognition sites. To test if putative synapsis of three binding sites has any functional significance, we have studied EcoRII cleavage of plasmids containing a single, two and three recognition sites under both single turnover and steady state conditions. EcoRII displays distinct reaction patterns on different substrates: (i) it shows virtually no activity on a single site plasmid; (ii) it yields open-circular DNA form nicked at one strand as an obligatory intermediate acting on a two-site plasmid; (iii) it cleaves concertedly both DNA strands at a single site during a single turnover on a three site plasmid to yield linear DNA. Cognate oligonucleotide added in trans increases the reaction velocity and changes the reaction pattern for the EcoRII cleavage of one and two-site plasmids but has little effect on the three-site plasmid. Taken together the data indicate that EcoRII requires simultaneous binding of three rather than two recognition sites in cis to achieve concerted DNA cleavage at a single site. We show that the orthodox type IIP enzyme PspGI which is an isoschisomer of EcoRII, cleaves different plasmid substrates with equal rates. Data provided here indicate that type IIE restriction enzymes EcoRII and NaeI follow different mechanisms. We propose that other type IIE restriction enzymes may employ the mechanism suggested here for EcoRII.},
  doi         = {10.1016/j.jmb.2006.02.024},
  file        = {2006_Tamulaitis_preprint.pdf:by-author/T/Tamulaitis/2006_Tamulaitis_preprint.pdf:PDF;2006_Tamulaitis_1665.pdf:by-author/T/Tamulaitis/2006_Tamulaitis_1665.pdf:PDF},
  groups      = {sg/NgoMIV},
  institution = {Institute of Biotechnology, Graiciuno 8, Vilnius, LT-02241, Lithuania.},
  keywords    = {Allosteric Site; Archaea; Binding Sites; Chemistry; Chemistry/genetics/metabolism/physiology; DNA; Deoxyribonucleases; Genetics; Hydrolysis; Kinetics; Metabolism; Plasmids; Protein Binding; Type II Site-Specific},
  language    = {eng},
  medline-pst = {ppublish},
  owner       = {em},
  pii         = {S0022-2836(06)00208-7},
  pmid        = {16529772},
  timestamp = {2011.06.10},
  creationdate = {2011-06-10T00:00:00},
  url         = {http://dx.doi.org/10.1016/j.jmb.2006.02.024},
}

@Article{Tamulaitis2006a,
  author    = {Gintautas Tamulaitis and Giedrius Sasnauskas and Merlind Mucke and Virginijus Siksnys},
  journal   = {J. Mol. Biol.},
  title     = {Simultaneous Binding of Three Recognition Sites is Necessary for a Concerted Plasmid {DNA} Cleavage by {EcoRII} Restriction Endonuclease},
  year      = {2006},
  pages     = {preprint},
  doi       = {10.1016/j.jmb.2006.02.024},
  file      = {:by-author/T/Tamulaitis/2006_Tamulaitis_preprint.pdf:PDF},
  keywords  = {Ecl18kI; EcoRII; TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Tamulaitis2002,
  author    = {Tamulaitis, Gintautas and Solonin, Alexander S. and Siksnys, Virginijus},
  journal   = {FEBS letters},
  title     = {Alternative arrangements of catalytic residues at the active sites of restriction enzymes.},
  year      = {2002},
  pages     = {17--22},
  volume    = {518},
  abstract  = {A catalytic sequence motif PDX10-30(E/D)XK is found in many restriction enzymes. On the basis of sequence similarities and mapping of the conserved residues to the crystal structure of NgoMIV we suggest that residues D160, K182, R186, R188 and E195 contribute to the catalytic/DNA binding site of the Ecl18kI restriction endonuclease. Mutational analysis confirms the functional significance of the conserved residues of Ecl18kI. Therefore, we conclude that the active site motif 159VDX21KX12E of Ecl18kI differs from the canonical PDX10-30(E/D)XK motif characteristic for most of the restriction enzymes. Moreover, we propose that two subfamilies of endonucleases Ecl18kI/PspGI/EcoRII and Cfr10I/Bse634I/NgoMIV, specific, respectively, for CCNGG/CCWGG and RCCGGY/GCCGGC sites, share conserved active site architecture and DNA binding elements.},
  file      = {:by-author/T/Tamulaitis/2002_Tamulaitis_17.pdf:PDF},
  groups    = {sg/Cfr10I, sg/NgoMIV, sg/Bse634I structures, sg/Bse634I},
  keywords  = {Ecl18kI; EcoRII; TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Tamulaitis2002a,
  author      = {Gintautas Tamulaitis and Alexander S Solonin and Virginijus Siksnys},
  journal     = {FEBS Lett},
  title       = {Alternative arrangements of catalytic residues at the active sites of restriction enzymes.},
  year        = {2002},
  month       = {May},
  number      = {1-3},
  pages       = {17--22},
  volume      = {518},
  abstract    = {A catalytic sequence motif PDX10-30(E/D)XK is found in many restriction enzymes. On the basis of sequence similarities and mapping of the conserved residues to the crystal structure of NgoMIV we suggest that residues D160, K182, R186, R188 and E195 contribute to the catalytic/DNA binding site of the Ecl18kI restriction endonuclease. Mutational analysis confirms the functional significance of the conserved residues of Ecl18kI. Therefore, we conclude that the active site motif 159VDX21KX12E of Ecl18kI differs from the canonical PDX10-30(E/D)XK motif characteristic for most of the restriction enzymes. Moreover, we propose that two subfamilies of endonucleases Ecl18kI/PspGI/EcoRII and Cfr10I/Bse634I/NgoMIV, specific, respectively, for CCNGG/CCWGG and RCCGGY/GCCGGC sites, share conserved active site architecture and DNA binding elements.},
  file        = {2002_Tamulaitis_17.pdf:by-author/T/Tamulaitis/2002_Tamulaitis_17.pdf:PDF},
  groups      = {sg/Cfr10I, sg/NgoMIV, sg/Bse634I structures, sg/Bse634I},
  institution = {Institute of Biotechnology, Graiciuno 8, 2028, Vilnius, Lithuania.},
  keywords    = {Amino Acid Motifs; Amino Acid Sequence; Amino Acids; Animals; Base Sequence; Binding Sites; Catalytic Domain; Conserved Sequence; DNA; Deoxyribonucleases; Models; Molecular; Molecular Sequence Data; Mutation; Sequence Alignment; Type II Site-Specific},
  owner       = {em},
  pii         = {S0014579302026212},
  pmid        = {11997010},
  timestamp = {2011.06.10},
  creationdate = {2011-06-10T00:00:00},
}

@Article{Tamulaitis2008,
  author      = {Gintautas Tamulaitis and Mindaugas Zaremba and Roman H Szczepanowski and Matthias Bochtler and Virginijus Siksnys},
  journal     = {Nucleic Acids Res},
  title       = {How PspGI, catalytic domain of EcoRII and Ecl18kI acquire specificities for different DNA targets},
  year        = {2008},
  month       = {Nov},
  number      = {19},
  pages       = {6101--6108},
  volume      = {36},
  abstract    = {Restriction endonucleases Ecl18kI and PspGI/catalytic domain of EcoRII recognize CCNGG and CCWGG sequences (W stands for A or T), respectively. The enzymes are structurally similar, interact identically with the palindromic CC:GG parts of their recognition sequences and flip the nucleotides at their centers. Specificity for the central nucleotides could be influenced by the strength/stability of the base pair to be disrupted and/or by direct interactions of the enzymes with the flipped bases. Here, we address the importance of these contributions. We demonstrate that wt Ecl18kI cleaves oligoduplexes containing canonical, mismatched and abasic sites in the central position of its target sequence CCNGG with equal efficiencies. In contrast, substitutions in the binding pocket for the extrahelical base alter the Ecl18kI preference for the target site: the W61Y mutant prefers only certain mismatched substrates, and the W61A variant cuts exclusively at abasic sites, suggesting that pocket interactions play a major role in base discrimination. PspGI and catalytic domain of EcoRII probe the stability of the central base pair and the identity of the flipped bases in the pockets. This 'double check' mechanism explains their extraordinary specificity for an A/T pair in the flipping position.},
  doi         = {10.1093/nar/gkn621},
  file        = {:by-author/T/Tamulaitis/2008_Tamulaitis_6101.pdf:PDF},
  institution = {Institute of Biotechnology, Graiciuno 8, LT-02241, Vilnius, Lithuania.},
  keywords    = {Amino Acid Substitution; Base Pairing; Binding Sites; CCG; Catalytic Domain; Chemistry/genetics/metabolism; Chemistry/metabolism; DNA; Deoxyribonucleases; Electrophoretic Mobility Shift Assay; Flip; Models; Molecular; PspGI; Recognition; Restriction Endonuclease (RE); Substrate Specificity; Type II Site-Specific},
  language    = {eng},
  medline-pst = {ppublish},
  owner       = {em},
  pii         = {gkn621},
  pmid        = {18820295},
  timestamp = {2011.06.10},
  creationdate = {2011-06-10T00:00:00},
  url         = {http://dx.doi.org/10.1093/nar/gkn621},
}

@Article{Tamulaitis2007,
  author    = {Tamulaitis, Gintautas and Zaremba, Mindaugas and Szczepanowski, Roman H. and Bochtler, Matthias and Siksnys, Virginijus},
  journal   = {Nucleic acids research},
  title     = {Nucleotide flipping by restriction enzymes analyzed by 2-aminopurine steady-state fluorescence.},
  year      = {2007},
  pages     = {4792--9},
  volume    = {35},
  abstract  = {Many DNA modification and repair enzymes require access to DNA bases and therefore flip nucleotides. Restriction endonucleases (REases) hydrolyze the phosphodiester backbone within or in the vicinity of the target recognition site and do not require base extrusion for the sequence readout and catalysis. Therefore, the observation of extrahelical nucleotides in a co-crystal of REase Ecl18kI with the cognate sequence, CCNGG, was unexpected. It turned out that Ecl18kI reads directly only the CCGG sequence and skips the unspecified N nucleotides, flipping them out from the helix. Sequence and structure conservation predict nucleotide flipping also for the complexes of PspGI and EcoRII with their target DNAs (/CCWGG), but data in solution are limited and indirect. Here, we demonstrate that Ecl18kI, the C-terminal domain of EcoRII (EcoRII-C) and PspGI enhance the fluorescence of 2-aminopurines (2-AP) placed at the centers of their recognition sequences. The fluorescence increase is largest for PspGI, intermediate for EcoRII-C and smallest for Ecl18kI, probably reflecting the differences in the hydrophobicity of the binding pockets within the protein. Omitting divalent metal cations and mutation of the binding pocket tryptophan to alanine strongly increase the 2-AP signal in the Ecl18kI-DNA complex. Together, our data provide the first direct evidence that Ecl18kI, EcoRII-C and PspGI flip nucleotides in solution.},
  file      = {:by-author/T/Tamulaitis/2007_Tamulaitis_4792.pdf:PDF},
  keywords  = {Ecl18kI; EcoRII; TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Tamulaitis2007a,
  author       = {Gintautas Tamulaitis and Mindaugas Zaremba and Roman H Szczepanowski and Matthias Bochtler and Virginijus Siksnys},
  journal      = {Nucleic Acids Res},
  title        = {Nucleotide flipping by restriction enzymes analyzed by 2-aminopurine steady-state fluorescence},
  year         = {2007},
  number       = {14},
  pages        = {4792--4799},
  volume       = {35},
  abstract     = {Many DNA modification and repair enzymes require access to DNA bases and therefore flip nucleotides. Restriction endonucleases (REases) hydrolyze the phosphodiester backbone within or in the vicinity of the target recognition site and do not require base extrusion for the sequence readout and catalysis. Therefore, the observation of extrahelical nucleotides in a co-crystal of REase Ecl18kI with the cognate sequence, CCNGG, was unexpected. It turned out that Ecl18kI reads directly only the CCGG sequence and skips the unspecified N nucleotides, flipping them out from the helix. Sequence and structure conservation predict nucleotide flipping also for the complexes of PspGI and EcoRII with their target DNAs (/CCWGG), but data in solution are limited and indirect. Here, we demonstrate that Ecl18kI, the C-terminal domain of EcoRII (EcoRII-C) and PspGI enhance the fluorescence of 2-aminopurines (2-AP) placed at the centers of their recognition sequences. The fluorescence increase is largest for PspGI, intermediate for EcoRII-C and smallest for Ecl18kI, probably reflecting the differences in the hydrophobicity of the binding pockets within the protein. Omitting divalent metal cations and mutation of the binding pocket tryptophan to alanine strongly increase the 2-AP signal in the Ecl18kI-DNA complex. Together, our data provide the first direct evidence that Ecl18kI, EcoRII-C and PspGI flip nucleotides in solution.},
  creationdate = {2011-06-10T00:00:00},
  doi          = {10.1093/nar/gkm513},
  file         = {2007_Tamulaitis_4792.pdf:by-author/T/Tamulaitis/2007_Tamulaitis_4792.pdf:PDF},
  institution  = {Institute of Biotechnology, Graiciuno 8, LT-02241, Vilnius, Lithuania.},
  keywords     = {2-Aminopurine; Calcium; Chemistry; Chemistry/genetics; Deoxyribonucleases; Fluorescent Dyes; Models; Molecular; Mutation; Nucleotides; Oligonucleotide Probes; Protein Structure; Tertiary; Type II Site-Specific},
  language     = {eng},
  medline-pst  = {ppublish},
  owner        = {em},
  pii          = {gkm513},
  pmid         = {17617640},
  timestamp    = {2011.06.10},
  url          = {http://dx.doi.org/10.1093/nar/gkm513},
}

@InProceedings{Tamura1997,
  author    = {Tamura, Takayuki and Oguchi, Masato and Kitsuregawa, Masaru},
  booktitle = {Proceedings of the 1997 ACM/IEEE conference on Supercomputing (CDROM)},
  title     = {Parallel database processing on a 100 Node PC cluster: cases for decision support query processing and data mining},
  year      = {1997},
  pages     = {1--16},
  abstract  = {We developed a PC cluster system consists of 100 PCs. Each PC employs the 200MHz Pentium Pro CPU and is connected with others through an ATM switch. We picked up two kinds of data intensive applications. One is decision support query processing. And the other is data mining, specifically, association rule mining. As a high speed network, ATM technology has recently come to be a de facto standard. While other high performance network standards are also available, ATM networks are widely used from local area to widely distributed environments. One of the problems of the ATM networks is its high latencies, in contrast to their higher bandwidths. This is usually considered a serious flaw of ATM in composing high performance massively parallel processors. However, applications such as large scale database analyses are insensitive to the communication latency, requiring only the bandwidth. On the other hand, the performance of personal computers is increasing rapidly these days while the prices of PCs continue to fall at a much faster rate than workstations’. The 200MHz Pentium Pro CPU is competitive in integer performance to the processor chips found in workstations. Although it is still weak at floating point operations, they are not frequently used in database applications. Thus, by combining PCs and ATM switches we can construct a large scale parallel platform very easily and very inexpensively. In this paper, we examine how such a system can help the data warehouse processing, which currently runs on expensive high-end mainframes and/or workstation servers. In our first experiment, we used the most complex query of the standard benchmark, TPC-D, on a 100 GB database to evaluate the system compared with commercial parallel systems. Our PC cluster exhibited much higher performance compared with those in current TPC benchmark reports. Second, we parallelized association rule mining and ran large scale data mining on the PC cluster. Sufficiently high linearity was obtained. Thus we believe that such commodity based PC clusters will play a very important role in large scale database processing.},
  doi       = {10.1145/509593.509642},
  file      = {:by-author/T/Tamura/1997_Tamura_1.pdf:PDF},
  isbn      = {0-89791-985-8},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://doi.acm.org/10.1145/509593.509642},
}

@Article{Tanenbaum1978,
  author    = {Tanenbaum, A. S.},
  journal   = {The Computer Journal},
  title     = {A comparison of PASCAL and ALGOL 68},
  year      = {1978},
  pages     = {316--323},
  volume    = {21},
  abstract  = {PASCAL and ALGOL 68 language features are critically examined, compared and contrasted with each other. The emphasis is on the differences between the two languages, primarily in the areas of data types and statement types. Shortcomings in both languages are pointed out.},
  doi       = {10.1093/comjnl/21.4.316},
  eprint    = {http://comjnl.oxfordjournals.org/content/21/4/316.full.pdf+html},
  file      = {1978_Tanenbaum_316.pdf:by-author/T/Tanenbaum/1978_Tanenbaum_316.pdf:PDF},
  keywords  = {Algol; Algol 68; Computer Science (CS); Pascal; Programming Languages},
  owner     = {saulius},
  timestamp = {2015.04.10},
  creationdate = {2015-04-10T00:00:00},
  url       = {http://comjnl.oxfordjournals.org/content/21/4/316.abstract},
}

@Article{Tanenbaum1977,
  author    = {Tanenbaum, Andrew S.},
  journal   = {Computing Surveys},
  title     = {A Tutorial on Algol 68: Corrigendum},
  year      = {1977},
  pages     = {255--256},
  volume    = {9},
  file      = {:by-author/T/Tanenbaum/1977_Tanenbaum_255.pdf:PDF},
  keywords  = {Algol; Algol 68; Computer Science (CS); Programming Languages},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Tanenbaum1976,
  author    = {Andrew S. Tanenbaum},
  journal   = {Computing Surveys},
  title     = {A Tutorial on Algols 68},
  year      = {1976},
  pages     = {155--190},
  volume    = {8},
  abstract  = {This paper is an introduction to the main features of ALGOL68, emphasizing the novel features not found in many other programming languages. The topics, data types (modes), type conversion (coercion), generalized expressions (units), procedures, operators, the standard prelude, and input/output, form the basis of the paper. The approach is informal, relying heavily on many short examples. The paper applies to the Revised Report, published in 1975, rather than to the original report, published in 1969.},
  file      = {:by-author/T/Tanenbaum/1976_Tanenbaum_155.pdf:PDF},
  keywords  = {Algol; Algol 68; Computer Science (CS); Programming Languages},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@InProceedings{Tanin2004,
  author    = {Tanin, Egemen and Harwood, Aaron and Samet, Hanan and Nutanong, Sarana and Truong, Minh Tri},
  booktitle = {Proceedings of the 12th annual ACM international workshop on Geographic information systems},
  title     = {A Serverless {3D} World},
  year      = {2004},
  address   = {New York, NY, USA},
  pages     = {157--165},
  publisher = {ACM},
  series    = {GIS '04},
  abstract  = {Online multi-participant virtual-world systems have at- tracted significant interest from the Internet community but are hindered by their inability to efficiently support interactivity for a large number of participants. Current solutions divide a large virtual-world into a few mutually exclusive zones, with each zone controlled by a different server, and/or limit the number of participants per server or per virtual-world. Peer-to-Peer (P2P) systems are known to provide excellent scalability in a networked environment (one peer is introduced to the system by each participant), however current P2P applications can only provide file sharing and other forms of relatively simple data communi- cations. In this paper, we present a generic 3D virtual-world application that runs on a P2P network with no central administration or server. Two issues are addressed by this paper to enable such a spatial application on a P2P network. First, we demonstrate how to index and query a 3D space on a dynamic distributed network. Second, we show how to build such a complex application from the ground level of a P2P routing algorithm. Our work leads to new directions for the development of online virtual-worlds that we believe can be used for many government, industry, and public domain applications.},
  doi       = {10.1145/1032222.1032246},
  file      = {2004_Tanin_157.pdf:by-author/T/Tanin/2004_Tanin_157.pdf:PDF},
  isbn      = {1-58113-979-9},
  location  = {Washington DC, USA},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://doi.acm.org/10.1145/1032222.1032246},
}

@Article{Tanley2013,
  author    = {Tanley, Simon W. M. and Schreurs, Antoine M. M. and Helliwell, John R. and Kroon-Batenburg, Loes M. J.},
  journal   = {Journal of Applied Crystallography},
  title     = {Experience with exchange and archiving of raw data: comparison of data from two diffractometers and four software packages on a series of lysozyme crystals},
  year      = {2013},
  pages     = {108--119},
  volume    = {46},
  abstract  = {The International Union of Crystallography has for many years been advocating archiving of raw data to accompany structural papers. Recently, it initiated the formation of the Diffraction Data Deposition Working Group with the aim of developing standards for the representation of these data. A means of studying this issue is to submit exemplar publications with associated raw data and metadata. A recent study on the effects of dimethyl sulfoxide on the binding of cisplatin and carboplatin to histidine in 11 different lysozyme crystals from two diffractometers led to an investigation of the possible effects of the equipment and X-ray diffraction data processing software on the calculated occupancies and {\it B} factors of the bound Pt compounds. 35.3Gb of data were transferred from Manchester to Utrecht to be processed with {\it EVAL}. A systematic comparison shows that the largest differences in the occupancies and {\it B} factors of the bound Pt compounds are due to the software, but the equipment also has a noticeable effect. A detailed description of and discussion on the availability of metadata is given. By making these raw diffraction data sets available {\it via} a local depository, it is possible for the diffraction community to make their own evaluation as they may wish.},
  doi       = {10.1107/S0021889812044172},
  file      = {2013_Tanley_108.pdf:by-author/T/Tanley/2013_Tanley_108.pdf:PDF},
  keywords  = {Data Archiving; Data Exchange; Data Management; Data Processing; Image Formats; Metadata; X-ray Crystallography; XRD},
  owner     = {saulius},
  timestamp = {2015.08.28},
  creationdate = {2015-08-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0021889812044172},
}

@Article{Tao2006,
  author    = {Tao, N. J.},
  journal   = {Nature Nanotechnology},
  title     = {Electron transport in molecular junctions},
  year      = {2006},
  issn      = {1748-3387},
  pages     = {173--181},
  volume    = {1},
  abstract  = {Building an electronic device using individual molecules is one of the ultimate goals in nanotechnology. To achieve this it will be necessary to measure, control and understand electron transport through molecules attached to electrodes. Substantial progress has been made over the past decade and we present here an overview of some of the recent advances. Topics covered include molecular wires, two-terminal switches and diodes, three-terminal transistor-like devices and hybrid devices that use various different signals (light, magnetic fields, and chemical and mechanical signals) to control electron transport in molecules. We also discuss further issues, including molecule–electrode contacts, local heating- and current-induced instabilities, stochastic fluctuations and the development of characterization tools.},
  copyright = {© 2006 Nature Publishing Group},
  doi       = {10.1038/nnano.2006.130},
  file      = {Full Text PDF:by-author/T/Tao/2006_Tao_173.pdf:application/pdf;Snapshot:by-author/T/Tao/2006_Tao_173.html:text/html},
  groups    = {sg/chemical},
  language  = {en},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://www.nature.com/nnano/journal/v1/n3/abs/nnano.2006.130.html},
  urldate   = {2015-08-05},
}

@Article{Tarashima2015,
  author    = {Tarashima, Noriko and Komatsu, Yasuo and Furukawa, Kazuhiro and Minakawa, Noriaki},
  journal   = {Chem. Eur. J.},
  title     = {Faithful PCR Amplification of an Unnatural Base-Pair Analogue with Four Hydrogen Bonds},
  year      = {2015},
  issn      = {0947-6539},
  month     = {Jun},
  number    = {30},
  pages     = {10688--10695},
  volume    = {21},
  doi       = {10.1002/chem.201501484},
  file      = {:by-author/T/Tarashima/2015_Tarashima_10688.pdf:PDF},
  groups    = {am/Expanded genetic code},
  owner     = {andrius},
  publisher = {Wiley-Blackwell},
  timestamp = {2016.05.18},
  creationdate = {2016-05-18T00:00:00},
  url       = {http://dx.doi.org/10.1002/chem.201501484},
}

@Article{Tarumi1995,
  author    = {Tarumi, K. and Yonesaki, T.},
  journal   = {The Journal of biological chemistry},
  title     = {Functional interactions of gene 32, 41, and 59 proteins of bacteriophage T4.},
  year      = {1995},
  pages     = {2614--9},
  volume    = {270},
  abstract  = {Genes 41 and 59 of bacteriophage T4 are involved in DNA recombination as well as in DNA replication. The 41 protein has a DNA helicase activity. The 59 protein has been recently purified and found to have a specific affinity for both 32 protein (single-stranded DNA-binding protein) and 41 protein (Yonesaki 1994, J. Biol. Chem. 269, 1284-1289). We examined the effects of 59 protein on ssDNA-dependent ATPase activity and DNA helicase activity of 41 protein in the presence or absence of 32 protein. The ATPase activity of 41 protein was strongly inhibited by 32 protein over a wide range of amounts from subsaturation to oversaturation of ssDNA. The 32 protein was also inhibitory toward DNA helicase activity. Addition of 59 protein effectively eliminated these inhibitory effects of 32 protein. Moreover, 59 protein facilitated 41 protein to overcome the barrier to initiate the unwinding reaction with a duplex flanking a single-stranded DNA gap. Intriguingly, 32 protein at an amount optimal for saturation of ssDNA stimulated the overcoming of the barrier when 59 protein was present. For the best circumvention of this initiation barrier, only eight monomers of 59 protein/one DNA substrate molecule containing 2900 nucleotides of ssDNA were required. These results strongly suggest that 59 protein modulates 41 protein activities by forming a complex with 41 protein and that 41 protein can produce recombinogenic ssDNA with the aid of 32 and 59 proteins.},
  file      = {:by-author/T/Tarumi/1995_Tarumi_2614.pdf:PDF},
  keywords  = {{gp41}; {gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Manuscript{Taubenfeld2008,
  author    = {Taubenfeld, Gadi},
  title     = {Concurrent Programming, Mutual Exclusion (1965; Dijkstra)},
  year      = {2008},
  keywords  = {Computer Science (CS); Concurrent Programming},
  file      = {:by-author/T/Taubenfeld/2008_Taubenfeld.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Taylor2003,
  author    = {Taylor, Garry},
  journal   = {Acta Crystallographica Section D},
  title     = {The phase problem},
  year      = {2003},
  pages     = {1881--1890},
  volume    = {59},
  doi       = {10.1107/S0907444903017815},
  file      = {ba5050.pdf:by-author/T/Taylor/2003_Taylor_1881.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444903017815},
}

@Article{Taylor2012,
  author    = {Taylor, Gregory K. and Stoddard, Barry L.},
  journal   = {Nucleic Acids Research},
  title     = {Structural, functional and evolutionary relationships between homing endonucleases and proteins from their host organisms},
  year      = {2012},
  pages     = {5189–5200},
  volume    = {40},
  abstract  = {Homing endonucleases (HEs) are highly specific DNA-cleaving enzymes that are encoded by invasive DNA elements (usually mobile introns or inteins) within the genomes of phage, bacteria, archea, protista and eukaryotic organelles. Six unique structural HE families, that collectively span four distinct nuclease catalytic motifs, have been characterized to date. Members of each family display structural homology and functional relationships to a wide variety of proteins from various organisms. The biological functions of those proteins are highly disparate and include non-specific DNA-degradation enzymes, restriction endonucleases, DNA-repair enzymes, resolvases, intron splicing factors and transcription factors. These relationships suggest that modern day HEs share common ancestors with proteins involved in genome fidelity, maintenance and gene expression. This review summarizes the results of structural studies of HEs and corresponding proteins from host organisms that have illustrated the manner in which these factors are related.},
  doi       = {10.1093/nar/gks226},
  file      = {:by-author/T/Taylor/2012_Taylor_5189.pdf:PDF},
  keywords  = {Evolution; Homing Endonucleases; Review},
  owner     = {em},
  timestamp = {2013.01.17},
  creationdate = {2013-01-17T00:00:00},
}

@Article{Taylor1994,
  author    = {Taylor, I. A. and Davis, K. G. and Watts, D. and Kneale, G. G.},
  journal   = {The EMBO journal},
  title     = {DNA-binding induces a major structural transition in a type I methyltransferase.},
  year      = {1994},
  pages     = {5772--8},
  volume    = {13},
  abstract  = {The type IC DNA methyltransferase M.EcoR124I is a complex multisubunit enzyme that recognizes the non-palindromic DNA sequence GAAN6RTCG. Small angle X-ray scattering has been used to investigate the solution structure of the methyltransferase and of complexes of the enzyme with unmethylated and hemimethylated 30 bp DNA duplexes containing the specific recognition sequence. A major change in the quaternary structure of the enzyme is observed following DNA binding, based on a decrease in the radius of gyration from 56 to 40 A and a reduction in the maximum dimension of the enzyme from 180 to 112 A. The structural transition observed is independent of the methylation state of the DNA. CD shows that there is no change in the secondary structure of the protein subunits when DNA is bound. In contrast, there is a large increase in the CD signal arising from the DNA, suggesting considerable structural distortion which may allow access to the bases targeted for methylation. We propose that DNA binding induces a large rotation of the two HsdM subunits towards the DNA, mediated by hinge bending domains in the specificity subunit HsdS.},
  file      = {:by-author/T/Taylor/1994_Taylor_5772.pdf:PDF},
  keywords  = {TypeI},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Taylor1991,
  author    = {Taylor, Ian and Patel, Jaynish and Firman, Keith and Kneale, Geoff},
  journal   = {Nucleic Acids Research},
  title     = {Purification and biochemical characterisation of the {EcoR124} type {I} modification methylase},
  year      = {1991},
  pages     = {179--186},
  file      = {:by-author/T/Taylor/1991_Taylor_179.pdf:PDF},
  keywords  = {TypeI},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Taylor1996,
  author    = {Taylor, J. L. and McCloskey, D. I.},
  journal   = {Experimental brain research. Experimentelle Hirnforschung. Expérimentation cérébrale},
  title     = {Selection of motor responses on the basis of unperceived stimuli.},
  year      = {1996},
  pages     = {62--6},
  volume    = {110},
  abstract  = {In a previous study, the sensory phenomenon of &quot;backward masking&quot; was used to demonstrate that subjects can preprogram a single stereotyped voluntary movement or movement-sequence and that such a movement can be triggered in response to a stimulus that is not perceived (that is, a stimulus of which the subject is unaware). In the present study, visual stimuli were presented at random in one of two different locations to normal human subjects in a choice reaction-time (RT) task. When the stimulus appeared in one of the locations, subjects made a motor response. When the stimulus appeared in the other location, subjects made a different motor response. Large and small stimuli were presented in either location. In some trials, the small stimulus was followed 50 ms later by the large stimulus. The small stimulus was then &quot;masked&quot; by the large stimulus and could not be perceived on forced-choice testing. Despite not perceiving the test stimulus in either of its randomly selected locations, subjects were able to select and execute the motor response appropriate for each location. The RTs for responses to the masked stimulus and to the same stimulus presented without masking (and so, easily perceived) were the same. This result implies that appropriate programs for two separate movements can be simultaneously held ready for use, and that either one can be executed when triggered by specific stimuli without subjective awareness of such stimuli and so without further voluntary elaboration in response to such awareness.},
  file      = {:by-author/T/Taylor/1996_Taylor_62.pdf:PDF},
  keywords  = {TypeI},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Lecture{Taylor2016,
  author    = {Michael E. Taylor},
  title     = {Differential Geometry},
  year      = {2016},
  comment   = {Author's web site: http://www.unc.edu/math/Faculty/met/},
  file      = {2016_Taylor.pdf:by-author/T/Taylor/2016_Taylor.pdf:PDF;2016_Taylor_figures.pdf:by-author/T/Taylor/2016_Taylor_figures.pdf:PDF},
  keywords  = {Differential Geometry; Riemann},
  owner     = {saulius},
  timestamp = {2016.02.27},
  creationdate = {2016-02-27T00:00:00},
  url       = {http://www.unc.edu/math/Faculty/met/DGEOM.pdf},
}

@Lecture{Taylor2015,
  author    = {Michael E. Taylor},
  title     = {Elementary Differential Geometry},
  year      = {2015},
  comment   = {Author's web site: http://www.unc.edu/math/Faculty/met/},
  file      = {2015_Taylor.pdf:by-author/T/Taylor/2015_Taylor.pdf:PDF},
  keywords  = {Differential Geometry; Riemann},
  owner     = {saulius},
  timestamp = {2016.02.27},
  creationdate = {2016-02-27T00:00:00},
  url       = {http://www.unc.edu/math/Faculty/met/M180.pdf},
}

@Lecture{Taylor2010,
  author    = {Michael E. Taylor},
  title     = {Connections and Curvature},
  year      = {2010},
  comment   = {Author's web site: http://www.unc.edu/math/Faculty/met/},
  file      = {2010_Taylor.pdf:by-author/T/Taylor/2010_Taylor.pdf:PDF},
  keywords  = {Differential Geometry; Riemann},
  owner     = {saulius},
  timestamp = {2016.02.27},
  creationdate = {2016-02-27T00:00:00},
  url       = {http://www.unc.edu/math/Faculty/met/appendc.pdf},
}

@Lecture{Taylor2009,
  author    = {Michael E. Taylor},
  title     = {Notes on Compact Riemann Surfaces},
  year      = {2009},
  comment   = {Author's web site: http://www.unc.edu/math/Faculty/met/},
  file      = {2009_Taylor.pdf:by-author/T/Taylor/2009_Taylor.pdf:PDF},
  keywords  = {Differential Geometry; Riemann},
  owner     = {saulius},
  timestamp = {2016.02.27},
  creationdate = {2016-02-27T00:00:00},
  url       = {http://www.unc.edu/math/Faculty/met/RSURF.pdf},
}

@Article{Taylor2002a,
  author    = {Taylor, Robin},
  journal   = {Acta crystallographica. Section D, Biological crystallography},
  title     = {Life-science applications of the Cambridge Structural Database.},
  year      = {2002},
  pages     = {879--88},
  volume    = {58},
  abstract  = {Several studies show that the molecular geometries and intermolecular interactions observed in small-molecule crystal structures are relevant to the modelling of in vivo situations, although the influence of crystal packing is sometimes important and should always be borne in mind. Torsional distributions derived from the Cambridge Structural Database (CSD) can be used to map out potential-energy surfaces and thereby help identify experimentally validated conformational minima of molecules with several rotatable bonds. The use of crystallographic data in this way is complementary to in vacuo theoretical calculations since it gives insights into conformational preferences in condensed-phase situations. Crystallographic data also underpin many molecular-fragment libraries and programs for generating three-dimensional models from two-dimensional chemical structures. The modelling of ligand binding to metalloenzymes is assisted by information in the CSD on preferred coordination numbers and geometries. CSD data on intermolecular interactions are useful in structure-based inhibitor design both in indicating how probable a protein-ligand interaction is and what its geometry is likely to be. They can also be used to guide searches for bioisosteric replacements. Crystallographically derived information has contributed to many life-science software applications, including programs for locating binding 'hot spots' on proteins, docking ligands into enzyme active sites, de novo ligand design, molecular superposition and three-dimensional QSAR. Overall, crystallographic data in general, and the CSD in particular, are very significant tools for the rational design of biologically active molecules.},
  file      = {:by-author/T/Taylor/2002_Taylor_879.pdf:PDF},
  owner     = {saulius},
  timestamp = {2013.03.22},
  creationdate = {2013-03-22T00:00:00},
}

@Article{Taylor2014a,
  author    = {Taylor, Robin and Cole, Jason and Korb, Oliver and McCabe, Patrick},
  journal   = {Journal of Chemical Information and Modeling},
  title     = {Knowledge-Based Libraries for Predicting the Geometric Preferences of Druglike Molecules},
  year      = {2014},
  issn      = {1549-960X},
  month     = {Sep},
  number    = {9},
  pages     = {2500–2514},
  volume    = {54},
  doi       = {10.1021/ci500358p},
  file      = {2014_Taylor_2500.pdf:by-author/T/Taylor/2014_Taylor_2500.pdf:PDF},
  groups    = {sg/Crystallography, am/Crystallography},
  owner     = {andrius},
  publisher = {American Chemical Society (ACS)},
  timestamp = {2016.12.21},
  creationdate = {2016-12-21T00:00:00},
  url       = {http://dx.doi.org/10.1021/ci500358p},
}

@Article{Taylor2002,
  author    = {R. D. Taylor and P. J. Jewsbury and J. W. Essex},
  journal   = {Journal of Computer-Aided Molecular Design},
  title     = {A Review of Protein-Small Molecule Docking Methods},
  year      = {2002},
  pages     = {151},
  abstract  = {The binding of small molecule ligands to large protein targets is central to numerous biological processes. The accurate prediction of the binding modes between the ligand and protein, (the docking problem) is of fundamental importance in modern structure-based drug design. An overview of current docking techniques is presented with a description of applications including single docking experiments and the virtual screening of databases.},
  file      = {:by-author/T/Taylor/2002_Taylor_151.pdf:PDF},
  keywords  = {Forcefields},
  owner     = {andrius},
  timestamp = {2012.05.07},
  creationdate = {2012-05-07T00:00:00},
}

@Article{Taylor2014,
  author    = {Richard H. Taylor and Frisco Rose and Cormac Toher and Ohad Levy and Kesong Yang and Marco Buongiorno Nardelli and Stefano Curtarolo},
  journal   = {Computational Materials Science},
  title     = {A \{RESTful\} \{API\} for exchanging materials data in the AFLOWLIB.org consortium},
  year      = {2014},
  issn      = {0927-0256},
  pages     = {178--192},
  volume    = {93},
  abstract  = {Abstract The continued advancement of science depends on shared and reproducible data. In the field of computational materials science and rational materials design this entails the construction of large open databases of materials properties. To this end, an Application Program Interface (API) following \{REST\} principles is introduced for the AFLOWLIB.org materials data repositories consortium. \{AUIDs\} (Aflowlib Unique IDentifier) and \{AURLs\} (Aflowlib Uniform Resource Locator) are assigned to the database resources according to a well-defined protocol described herein, which enables the client to access, through appropriate queries, the desired data for post-processing. This introduces a new level of openness into the \{AFLOWLIB\} repository, allowing the community to construct high-level work-flows and tools exploiting its rich data set of calculated structural, thermodynamic, and electronic properties. Furthermore, federating these tools will open the door to collaborative investigations of unprecedented scope that will dramatically accelerate the advancement of computational materials design and development.},
  doi       = {http://dx.doi.org/10.1016/j.commatsci.2014.05.014},
  file      = {:by-author/T/Taylor/2014_Taylor_178.pdf:PDF},
  owner     = {andrius},
  timestamp = {2015.07.27},
  creationdate = {2015-07-27T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/S0927025614003322},
}

@InProceedings{Paradise1995,
  author    = {The Paradise Team},
  booktitle = {Proceedings of the 1995 ACM SIGMOD international conference on Management of data},
  title     = {Paradise: a database system for {GIS} applications},
  year      = {1995},
  pages     = {485},
  series    = {SIGMOD '95},
  doi       = {10.1145/223784.223898},
  file      = {:by-author/T/Team/1995_Team_485.pdf:PDF},
  isbn      = {0-89791-731-6},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://doi.acm.org/10.1145/223784.223898},
}

@Article{Telksnys1999,
  author    = {Telksnys, L. and Zilinskas, A.},
  journal   = {Annals of the History of Computing, IEEE},
  title     = {Computers in Lithuania},
  year      = {1999},
  issn      = {1058-6180},
  pages     = {31--37},
  volume    = {21},
  abstract  = {Computers, computer science, and computer engineering have more than 50 years of history in Lithuania. We describe the main directions of research and industrial applications. Also, we present the development of education in computer science and engineering, called informatics in Europe and Lithuania.},
  doi       = {10.1109/85.778980},
  file      = {:by-author/T/Telksnys/1999_Telksnys_31.pdf:PDF},
  keywords  = {History},
  owner     = {andrius},
  timestamp = {2015.07.24},
  creationdate = {2015-07-24T00:00:00},
}

@Manual{Tellechea2012,
  title     = {{ChemFig}: A {TEX} package for drawing molecules},
  author    = {Christian Tellechea},
  year      = {2012},
  file      = {:by-author/T/Tellechea/2012_Tellechea_manual.pdf:PDF},
  keywords  = {Latex},
  owner     = {andrius},
  timestamp = {2013.01.13},
  creationdate = {2013-01-13T00:00:00},
  url       = {http://mirrors.ctan.org/macros/generic/chemfig/chemfig_doc_en.pdf},
}

@Manuscript{Templeman2012,
  author    = {Robert Templeman and Zahid Rahman and David Crandall and Apu Kapadia},
  title     = {{PlaceRaider}: Virtual Theft in Physical Spaces with Smartphones},
  year      = {2012},
  abstract  = {As smartphones become more pervasive, they are increasingly targeted by malware. At the same time, each new generation of smartphone features increasingly powerful onboard sensor suites. A new strain of ‘sensor malware’ has been developing that leverages these sensors to steal information from the physical environment — e.g., researchers have recently demonstrated how malware can ‘listen’ for spoken credit card numbers through the microphone, or ‘feel’ keystroke vibrations using the accelerometer. Yet the possibilities of what malware can ‘see’ through a camera have been understudied. This paper introduces a novel ‘visual malware’ called PlaceRaider, which allows remote at- tackers to engage in remote reconnaissance and what we call “virtual theft.” Through completely opportunistic use of the phone’s camera and other sensors, PlaceRaider constructs rich, three dimensional models of indoor environments. Remote burglars can thus ‘download’ the physical space, study the environment carefully, and steal virtual objects from the environment (such as financial documents, information on computer monitors, and personally identifiable information). Through two human subject studies we demonstrate the effectiveness of using mobile devices as powerful surveillance and virtual theft platforms, and we suggest several possible defenses against visual malware.},
  file      = {:by-author/T/Templeman/2012_Templeman_1.pdf:PDF},
  owner     = {andrius},
  timestamp = {2012.10.30},
  creationdate = {2012-10-30T00:00:00},
}

@Article{Templeton1999,
  author    = {Templeton},
  journal   = {Acta crystallographica. Section A, Foundations of crystallography},
  title     = {Faster calculation of the full matrix for least-squares refinement},
  year      = {1999},
  pages     = {695--699},
  volume    = {55},
  abstract  = {Equations derived from a statistical model and valid for all space groups give estimates of the elements of the matrix for least-squares refinement of atomic coordinates and isotropic thermal parameters for a large crystal structure with many diffraction data. The elements are functions of the lengths and directions of Patterson vectors and the distribution of weights as a function of Bragg angle. For a large data set, this matrix, or a portion of it, can be calculated in a time that is approximately proportional to the number of elements calculated and independent of the number of reflections.},
  file      = {:by-author/T/Templeton/1999_Templeton_695.pdf:PDF},
  keywords  = {Refinement; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Tenno2004,
  author    = {Tenno, Takeshi and Fujiwara, Kenichiro and Tochio, Hidehito and Iwai, Kazuhiro and Morita, E. Hayato and Hayashi, Hidenori and Murata, Shigeo and Hiroaki, Hidekazu and Sato, Mamoru and Tanaka, Keiji and Shirakawa, Masahiro},
  journal   = {Genes to cells : devoted to molecular \&amp; cellular mechanisms},
  title     = {Structural basis for distinct roles of Lys63- and Lys48-linked polyubiquitin chains.},
  year      = {2004},
  pages     = {865--75},
  volume    = {9},
  abstract  = {Ubiquitination, a modification in which single or multiple ubiquitin molecules are attached to a protein, serves as a signalling function that controls a wide variety of cellular processes. To date, two major forms of polyubiquitin chain have been functionally characterized, in which the isopeptide bond linkages involve Lys48 or Lys63. Lys48-linked polyubiquitin tagging is mostly used to target proteins for degradation by the proteasome, whereas Lys63-linked polyubiquitination has been linked to numerous cellular events that do not rely on degradative signalling via the proteasome. Apparently linkage-specific conformations of polyubiquitin chains are important for these cellular functions, but the structural bases distinguishing Lys48- and Lys63-linked chains remain elusive. Here, we report NMR and small-angle X-ray scattering (SAXS) studies on the intersubunit interfaces and conformations of Lys63- and Lys48-linked di- and tetraubiquitin chains. Our results indicate that, in marked contrast to Lys48-linked chains, Lys63-linked chains are elongated molecules with no stable non-covalent intersubunit interfaces and thus adopt a radically different conformation from that of Lys48-linked chains.},
  file      = {:by-author/T/Tenno/2004_Tenno_865.pdf:PDF},
  keywords  = {Struct; TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Terns2011,
  author    = {Terns, Michael P. and Terns, Rebecca M.},
  journal   = {Current opinion in microbiology},
  title     = {CRISPR-based adaptive immune systems.},
  year      = {2011},
  pages     = {321--7},
  volume    = {14},
  abstract  = {CRISPR-Cas systems are recently discovered, RNA-based immune systems that control invasions of viruses and plasmids in archaea and bacteria. Prokaryotes with CRISPR-Cas immune systems capture short invader sequences within the CRISPR loci in their genomes, and small RNAs produced from the CRISPR loci (CRISPR (cr)RNAs) guide Cas proteins to recognize and degrade (or otherwise silence) the invading nucleic acids. There are multiple variations of the pathway found among prokaryotes, each mediated by largely distinct components and mechanisms that we are only beginning to delineate. Here we will review our current understanding of the remarkable CRISPR-Cas pathways with particular attention to studies relevant to systems found in the archaea.},
  file      = {:by-author/T/Terns/2011_Terns_321.pdf:PDF},
  groups    = {sg/CRISPR-Cas},
  keywords  = {CRISPR},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Presentation{Terry2006,
  author       = {Robert Terry},
  title        = {Open access and the Wellcome Trust},
  year         = {2006},
  organization = {Wellcome Trust},
  file         = {:by-author/T/Terry/2006_Terry_slides.pdf:PDF},
  owner        = {saulius},
  pages        = {slides},
  timestamp = {2015.02.17},
  creationdate = {2015-02-17T00:00:00},
  url          = {http://www.med.lu.se/content/download/9356/80442/file/Terry%20Wellcome%20Trust.pdf#search=%22terry%20wellcome%22},
}

@Article{Terwilliger2003,
  author    = {Terwilliger, Thomas C.},
  journal   = {Acta Crystallographica Section D},
  title     = {Automated main-chain model building by template matching and iterative fragment extension},
  year      = {2003},
  pages     = {38--44},
  volume    = {59},
  doi       = {10.1107/S0907444902018036},
  file      = {gr2291.pdf:by-author/T/Terwilliger/2003_Terwilliger_38.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444902018036},
}

@Article{Terwilliger2003a,
  author    = {Terwilliger, Thomas C.},
  journal   = {Acta Crystallographica Section D},
  title     = {Improving macromolecular atomic models at moderate resolution by automated iterative model building, statistical density modification and refinement},
  year      = {2003},
  pages     = {1174--1182},
  volume    = {59},
  doi       = {10.1107/S0907444903009922},
  file      = {dz0002.pdf:by-author/T/Terwilliger/2003_Terwilliger_1174.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444903009922},
}

@Article{Terwilliger2003b,
  author    = {Terwilliger, Thomas C.},
  journal   = {Acta Crystallographica Section D},
  title     = {Statistical density modification using local pattern matching},
  year      = {2003},
  pages     = {1688--1701},
  volume    = {59},
  doi       = {10.1107/S0907444903015142},
  file      = {dz5004.pdf:by-author/T/Terwilliger/2003_Terwilliger_1688.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444903015142},
}

@Article{Terwilliger2003c,
  author    = {Thomas C. Terwilliger},
  journal   = {Acta Crystallographica Section D},
  title     = {Automated side-chain model building and sequence assignment by template matching},
  year      = {2003},
  pages     = {45--49},
  volume    = {59},
  abstract  = {An algorithm is described for automated building of side chains in an electron-density map once a main-chain model is built and for alignment of the protein sequence to the map. The procedure is based on a comparison of electron density at the expected side-chain positions with electron-density templates. The templates are constructed from average amino-acid side-chain densities in 574 refined protein structures. For each contiguous segment of main chain, a matrix with entries corresponding to an estimate of the probability that each of the 20 amino acids is located at each position of the main-chain model is obtained. The probability that this segment corresponds to each possible alignment with the sequence of the protein is estimated using a Bayesian approach and high-confidence matches are kept. Once side-chain identities are determined, the most probable rotamer for each side chain is built into the model. The automated procedure has been implemented in the RESOLVE software. Combined with automated main-chain model building, the procedure produces a preliminary model suitable for refinement and extension by an experienced crystallographer.},
  doi       = {10.1107/S0907444902018048},
  file      = {:by-author/T/Terwilliger/2003_Terwilliger_45.pdf:PDF},
  groups    = {sg/Bayesian},
  owner     = {saulius},
  timestamp = {2011.12.14},
  creationdate = {2011-12-14T00:00:00},
}

@Article{Terwilliger2001,
  author    = {Terwilliger, Thomas C.},
  journal   = {Acta Crystallographica Section D},
  title     = {Maximum-likelihood density modification using pattern recognition of structural motifs},
  year      = {2001},
  pages     = {1755--1762},
  volume    = {57},
  doi       = {10.1107/S0907444901013737},
  file      = {gr2164.pdf:by-author/T/Terwilliger/2001_Terwilliger_1755.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444901013737},
}

@Article{TerwisschavanScheltinga2003,
  author    = {Terwisscha van Scheltinga, Anke C. and Valeg{\aa}rd, Karin and Hajdu, Janos and Andersson, Inger},
  journal   = {Acta Crystallographica Section D},
  title     = {MIR phasing using merohedrally twinned crystals},
  year      = {2003},
  pages     = {2017--2022},
  volume    = {59},
  doi       = {10.1107/S090744490302122X},
  file      = {ba5046.pdf:by-author/T/TerwisschavanScheltinga/2003_TerwisschavanScheltinga_2017.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S090744490302122X},
}

@Article{TerwisschavanScheltinga2001,
  author    = {Terwisscha van Scheltinga, Anke C. and Valeg{\aa}rd, Karin and Ramaswamy, S. and Hajdu, Janos and Andersson, Inger},
  journal   = {Acta Crystallographica Section D},
  title     = {Multiple isomorphous replacement on merohedral twins: structure determination of deacetoxycephalosporin C synthase},
  year      = {2001},
  pages     = {1776--1785},
  volume    = {57},
  doi       = {10.1107/S0907444901014081},
  file      = {gr2135.pdf:by-author/T/TerwisschavanScheltinga/2001_TerwisschavanScheltinga_1776.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444901014081},
}

@Article{Thall1998,
  author    = {Peter F. Thall and Hsi-Guang Sung},
  title     = {Some Extensions and Applications of a {Bayesian} Strategy for Monitoring Multiple Outcomes in Clinical Trials},
  year      = {1998},
  pages     = {1563--1580},
  volume    = {17},
  file      = {Peter F. Thall and Hsi-Guang Sung - 1998 - Some Extensions and Applications of a Bayesian Str.pdf:by-author/T/Thall/1998_Thall_1563.pdf:application/pdf},
  groups    = {sg/Clinical Trials},
  language  = {English},
  owner     = {saulius},
  timestamp = {2015.12.14},
  creationdate = {2015-12-14T00:00:00},
  url       = {http://odin.mdacc.tmc.edu/~pfthall/main/SIM_07_1998.pdf},
  urldate   = {2015-12-12},
}

@Presentation{Thalmann2008,
  author    = {Lars Thalmann and Mats Kindahl},
  title     = {MySQL Replication Tutorial},
  year      = {2008},
  file      = {2008_Thalmann.pdf:by-author/T/Thalmann/2008_Thalmann.pdf:PDF},
  groups    = {sg/MySQL, sg/replication},
  keywords  = {Databases; Master-slave Replication; Multi-master Replication; MySQL; Replication; SQL},
  owner     = {saulius},
  timestamp = {2016.03.05},
  creationdate = {2016-03-05T00:00:00},
  url       = {http://assets.en.oreilly.com/1/event/2/MySQL%20Replication%20Tutorial%20Presentation%202.pdf},
}

@Article{Than2005,
  author    = {Than, Manuel E. and Henrich, Stefan and Bourenkov, Gleb P. and Bartunik, Hans D. and Huber, Robert and Bode, Wolfram},
  journal   = {Acta crystallographica. Section D, Biological crystallography},
  title     = {The endoproteinase furin contains two essential Ca2+ ions stabilizing its N-terminus and the unique S1 specificity pocket.},
  year      = {2005},
  pages     = {505--12},
  volume    = {61},
  abstract  = {The mammalian prohormone/proprotein convertase (PC) furin is responsible for the maturation of a great variety of homeostatic but also many pathogenic proteins within the secretory pathway and the endosomal pathway and at the cell surface. Similar to other members of the PC family, furin requires calcium for catalytic activity. In a previous paper, the structural association of the catalytic and the P-domain of furin was shown and data were presented indicating two or three calcium-binding sites. The exact number and the three-dimensional localization of the essential calcium sites within furin have now been determined by collecting X-ray diffraction data on either side of the Ca K absorption edge and by calculating a novel type of double difference map from these anomalous scattering data. Two calcium ions were unambiguously identified: the purely structural Ca-1 also conserved in the bacterial digestive subtilisins and the Ca-2 site specific to PCs and essential for the formation of the P1 specificity-determining S1-binding pocket. In addition, these anomalous diffraction data show that no tightly bound K(+) sites exist in furin.},
  file      = {:by-author/T/Than/2005_Than_505.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Theobald2005,
  author           = {Douglas L. Theobald},
  journal          = {Acta Crystallographica Section A},
  title            = {Rapid calculation of {RMSD}s using a quaternion-based characteristic polynomial},
  year             = {2005},
  pages            = {478--480},
  volume           = {A61},
  creationdate     = {2014-10-29T00:00:00},
  doi              = {10.1107/S0108767305015266},
  file             = {:by-author/T/Theobald/2005_Theobald_478.pdf:PDF},
  keywords         = {Characteristic Equation; Quartic Polynomial; Quaternion; RMSD; Rotational Superposition; Structure Superposition; Superposition},
  modificationdate = {2024-05-12T11:36:04},
  owner            = {antanas},
  timestamp        = {2014.10.29},
}

@Article{Theobald2011,
  author           = {Douglas L. Theobald and Kanti V. Mardia},
  title            = {Full {B}ayesian analysis of the generalized non-isotropic {P}rocrustes problem with scaling},
  year             = {2011},
  pages            = {41--44},
  creationdate     = {2012-05-15T00:00:00},
  file             = {:by-author/T/Theobald/2011_Theobald_41.pdf:PDF},
  groups           = {sg/Molecule superposion, sg/Superposition, sg/Bayesian, sg/Bioinf. Algorithms},
  keywords         = {Procrustes; Structure Superposition},
  modificationdate = {2024-05-12T16:53:29},
  owner            = {saulius},
  timestamp        = {2012.05.15},
}

@Article{Theobald2012,
  author           = {Theobald, Douglas L. and Steindel, Phillip A.},
  journal          = {Bioinformatics},
  title            = {Optimal simultaneous superpositioning of multiple structures with missing data},
  year             = {2012},
  issn             = {1367-4803},
  pages            = {1972--1979},
  volume           = {28},
  address          = {Oxford, UK},
  creationdate     = {2012-05-15T00:00:00},
  doi              = {10.1093/bioinformatics/bts243},
  file             = {:by-author/T/Theobald/2012_Theobald.pdf:PDF},
  groups           = {sg/Molecule superposion, sg/Superposition, sg/Bioinf. Algorithms},
  keywords         = {Structure Superposition},
  modificationdate = {2024-05-12T16:49:08},
  owner            = {saulius},
  publisher        = {Oxford University Press},
  timestamp        = {2012.05.15},
  url              = {http://dx.doi.org/10.1093/bioinformatics/bts243},
}

@Article{Theobald2006,
  author           = {Theobald, Douglas L. and Wuttke, Deborah S.},
  journal          = {Bioinformatics (Oxford, England)},
  title            = {{THESEUS}: maximum likelihood superpositioning and analysis of macromolecular structures},
  year             = {2006},
  issn             = {1367-4803},
  month            = jun,
  number           = {17},
  pages            = {2171--2},
  volume           = {22},
  abstract         = {THESEUS is a command line program for performing maximum likelihood (ML) superpositions and analysis of macromolecular structures. While conventional superpositioning methods use ordinary least-squares (LS) as the optimization criterion, ML superpositions provide substantially improved accuracy by down-weighting variable structural regions and by correcting for correlations among atoms. ML superpositioning is robust and insensitive to the specific atoms included in the analysis, and thus it does not require subjective pruning of selected variable atomic coordinates. Output includes both likelihood-based and frequentist statistics for accurate evaluation of the adequacy of a superposition and for reliable analysis of structural similarities and differences. THESEUS performs principal components analysis for analyzing the complex correlations found among atoms within a structural ensemble. AVAILABILITY: ANSI C source code and selected binaries for various computing platforms are available under the GNU open source license from http://monkshood.colorado.edu/theseus/ or http://www.theseus3d.org.},
  creationdate     = {2012-05-15T00:00:00},
  doi              = {10.1093/bioinformatics/btl332},
  file             = {:by-author/T/Theobald/2006_Theobald_2171.pdf:PDF},
  groups           = {sg/Molecule superposion, sg/Superposition, sg/Bioinf. Algorithms},
  keywords         = {Structure Superposition},
  modificationdate = {2024-05-12T13:59:45},
  owner            = {saulius},
  publisher        = {Oxford University Press (OUP)},
  timestamp        = {2012.05.15},
}

@Article{Thessen2011,
  author    = {Thessen, Anne E. and Patterson, David J.},
  journal   = {ZooKeys},
  title     = {Data issues in the life sciences},
  year      = {2011},
  pages     = {15--51},
  volume    = {150},
  abstract  = {We review technical and sociological issues facing the Life Sciences as they transform into more data-centric disciplines - the “Big New Biology”. Three major challenges are: 1) lack of comprehensive standards; 2) lack of incentives for individual scientists to share data; 3) lack of appropriate infrastructure and support. Technological advances with standards, bandwidth, distributed computing, exemplar successes, and a strong presence in the emerging world of Linked Open Data are sufficient to conclude that technical issues will be overcome in the foreseeable future. While motivated to have a shared open infrastructure and data pool, and pressured by funding agencies in move in this direction, the sociological issues determine progress. Major sociological issues include our lack of understanding of the heterogeneous data cultures within Life Sciences, and the impediments to progress include a lack of incentives to build appropriate infrastructures into projects and institutions or to encourage scientists to make data openly available.},
  doi       = {10.3897/zookeys.150.1766},
  file      = {:by-author/T/Thesen/2011_Thesen_15.pdf:PDF},
  keywords  = {Data Issues; Data Support; Databases; Life Science},
  owner     = {antanas},
  timestamp = {2015.05.14},
  creationdate = {2015-05-14T00:00:00},
}

@Article{Thiagarajan2008,
  author    = {Arvind Thiagarajan and Sammuel Madden},
  title     = {Querying Continuous Functions in a Database System},
  year      = {2008},
  pages     = {791--804},
  abstract  = {Many scientific, financial, data mining and sensor network applications need to work with continuous, rather than discrete data e.g., temperature as a function of location, or stock prices or vehicle trajectories as a function of time. Querying raw or discrete data is unsatisfactory for these applications – e.g., in a sensor network, it is necessary to interpolate sensor readings to predict values at locations where sensors are not deployed. In other situations, raw data can be inaccurate owing to measurement errors, and it is useful to fit continuous functions to raw data and query the functions, rather than raw data itself – e.g., fitting a smooth curve to noisy sensor readings, or a smooth trajectory to GPS data containing gaps or outliers. Existing databases do not support storing or querying continuous functions, short of brute-force discretization of functions into a collection of tuples. We present FunctionDB, a novel database},
  file      = {:by-author/T/Thiagarajan/2008_Thiagarajan_791.pdf:PDF},
  keywords  = {Computer Science (CS); Continuous; Databases},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Thirlway2004,
  author    = {Thirlway, Jenny and Turner, Ian J. and Gibson, Christopher T. and Gardiner, Laurence and Brady, Kevin and Allen, Stephanie and Roberts, Clive J. and Soultanas, Panos},
  journal   = {Nucleic acids research},
  title     = {DnaG interacts with a linker region that joins the N- and C-domains of DnaB and induces the formation of 3-fold symmetric rings.},
  year      = {2004},
  pages     = {2977--86},
  volume    = {32},
  abstract  = {Loading of the replicative ring helicase onto the origin of replication (oriC) is the final outcome of a well coordinated series of events that collectively constitute a primosomal cascade. Once the ring helicase is loaded, it recruits the primase and signals the switch to the polymerization mode. The transient nature of the helicase-primase (DnaB-DnaG) interaction in the Escherichia coli system has hindered our efforts to elucidate its structure and function. Taking advantage of the stable DnaB-DnaG complex in Bacillus stearothermophilus, we have reviewed conflicting mutagenic data from other bacterial systems and shown that DnaG interacts with the flexible linker that connects the N- and C-terminal domains of DnaB. Furthermore, atomic force microscopy (AFM) imaging experiments show that binding of the primase to the helicase induces predominantly a 3-fold symmetric morphology to the hexameric ring. Overall, three DnaG molecules appear to interact with the hexameric ring helicase but a small number of complexes with two and even one DnaG molecule bound to DnaB were also detected. The structural/functional significance of these data is discussed and a speculative structural model for this complex is suggested.},
  file      = {:by-author/T/Thirlway/2004_Thirlway_2977.pdf:PDF},
  keywords  = {Ecoli; {gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Thomas2003,
  author    = {Thomas, Angela T. and Brammar, William J. and Wilkins, Brian M.},
  journal   = {Journal of bacteriology},
  title     = {Plasmid R16 ArdA protein preferentially targets restriction activity of the type I restriction-modification system EcoKI.},
  year      = {2003},
  pages     = {2022--5},
  volume    = {185},
  abstract  = {The ArdA antirestriction protein of the IncB plasmid R16 selectively inhibited the restriction activity of EcoKI, leaving significant levels of modification activity under conditions in which restriction was almost completely prevented. The results are consistent with the hypothesis that ArdA functions in bacterial conjugation to allow an unmodified plasmid to evade restriction in the recipient bacterium and yet acquire cognate modification.},
  file      = {:by-author/T/Thomas/2003_Thomas_2022.pdf:PDF},
  keywords  = {Antirestriction},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Thomas2010,
  author    = {Thomas, Ian R. and Bruno, Ian J. and Cole, Jason C. and Macrae, Clare F. and Pidcock, Elna and Wood, Peter A.},
  journal   = {Journal of Applied Crystallography},
  title     = {WebCSD: the online portal to the Cambridge Structural Database.},
  year      = {2010},
  pages     = {362--366},
  volume    = {43},
  abstract  = {WebCSD, a new web-based application developed by the Cambridge Crystallographic Data Centre, offers fast searching of the Cambridge Structural Database using only a standard internet browser. Search facilities include two-dimensional substructure, molecular similarity, text/numeric and reduced cell searching. Text, chemical diagrams and three-dimensional structural information can all be studied in the results browser using the efficient entry summaries and embedded three-dimensional viewer.},
  file      = {:by-author/T/Thomas/2010_Thomas_362.pdf:PDF},
  keywords  = {Data Presentation; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Manuscript{Thomas1999,
  author    = {John R. Thomas},
  title     = {The patenting of the liberal professions},
  year      = {1999},
  keywords  = {Patentai; Teise},
  file      = {:by-author/T/Thomas/1999_Thomas.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Manuscript{Thomas1998,
  author    = {Thomas, Reuben},
  title     = {Mite: a fast and exible virtual machine},
  year      = {1998},
  keywords  = {Computer Science (CS); Virtual Machines},
  month     = {August},
  abstract  = {Recent interest in virtual machines has been due mainly to the need to distribute executable content over the World Wide Web, where security and standardization are the key concerns. To ful l the potential of distributed network computing virtual machines must be built into the OS kernel where speed and exibility are of the essence. Mite is a virtual machine designed to allow optimising compilers to produce compact portable binaries which can be quickly translated at load-time into fast code. Its minimal core can be extended with support for language, machine or OS-speci c features. Mite's design and current and planned implementation work are described, along with reasons why it should be of particular interest to Forth programmers.},
  file      = {:by-author/T/Thomas/1998_Thomas.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Thomas1988,
  author    = {Samuel M. Thomas},
  title     = {A simple approach for the estimation of circular arc center and its radius},
  year      = {1988},
  pages     = {369},
  abstract  = {A simple exact solution for estimating the location of the center of a circular arc and its radius is suggested. Its features are demonstrated with the help of a computer program.},
  file      = {1988_Thomas_369.pdf:by-author/T/Thomas/1988_Thomas_369.pdf:PDF},
  groups    = {sg/Arc fitting, sg/Bioinf. Algorithms},
  keywords  = {Algorithms; Arc Fitting; Mathematics},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Thompson2001,
  author    = {Thompson, P R and Cole, P A},
  journal   = {Proceedings of the National Academy of Sciences of the United States of America},
  title     = {Probing the mechanism of enzymatic phosphoryl transfer with a chemical trick.},
  year      = {2001},
  pages     = {8170--1},
  volume    = {98},
  file      = {Thompson_2001_8170.pdf:by-author/T/Thompson/2001_Thompson_8170.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Thompson1988,
  author    = {Thompson, Richard B.},
  journal   = {Mathematics Magazine},
  title     = {Global positioning system: The mathematics of {GPS} receivers},
  year      = {1988},
  pages     = {260--269},
  volume    = {71},
  file      = {:by-author/T/Thompson/1988_Thompson_260.pdf:PDF},
  keywords  = {Algorithms; GPS},
  owner     = {saulius},
  timestamp = {2014.11.06},
  creationdate = {2014-11-06T00:00:00},
  url       = {http://www.maa.org/sites/default/files/pdf/cms_upload/Thompson07734.pdf},
}

@Presentation{Thomsen2004,
  author       = {Bent Thomsen},
  title        = {Languages and Compilers (SProg og Oversættere): Abstract Data Types and Object Oriented Features},
  year         = {2004},
  organization = {Department of Computer Science},
  school       = {Aalborg University},
  file         = {:by-author/T/Thomsen/2004_Thomsen.ppt:PPT},
  keywords     = {Prezentacijos},
  owner        = {saulius},
  timestamp = {2015.03.03},
  creationdate = {2015-03-03T00:00:00},
}

@Presentation{Thomsen2003,
  author       = {Bent Thomsen},
  title        = {Languages and Compilers (SProg og Oversættere)},
  year         = {2003},
  organization = {Department of Computer Science},
  school       = {Aalborg University},
  file         = {:by-author/T/Thomsen/2003_Thomsen.ppt:PPT},
  keywords     = {Prezentacijos},
  owner        = {saulius},
  timestamp = {2015.03.03},
  creationdate = {2015-03-03T00:00:00},
}

@Article{Thomson2014,
  author    = {Thomson, Andrew R. and Wood, Christopher W. and Burton, Antony J. and Bartlett, Gail J. and Sessions, Richard B. and Brady, R. Leo and Woolfson, Derek N.},
  journal   = {Science},
  title     = {Computational design of water-soluble α-helical barrels},
  year      = {2014},
  issn      = {0036-8075},
  number    = {6208},
  pages     = {485--488},
  volume    = {346},
  abstract  = {The design of protein sequences that fold into prescribed de novo structures is challenging. General solutions to this problem require geometric descriptions of protein folds and methods to fit sequences to these. The α-helical coiled coils present a promising class of protein for this and offer considerable scope for exploring hitherto unseen structures. For α-helical barrels, which have more than four helices and accessible central channels, many of the possible structures remain unobserved. Here, we combine geometrical considerations, knowledge-based scoring, and atomistic modeling to facilitate the design of new channel-containing α-helical barrels. X-ray crystal structures of the resulting designs match predicted in silico models. Furthermore, the observed channels are chemically defined and have diameters related to oligomer state, which present routes to design protein function.},
  doi       = {10.1126/science.1257452},
  eprint    = {http://science.sciencemag.org/content/346/6208/485.full.pdf},
  file      = {2014_Thomson_485.pdf:by-author/T/Thomson/2014_Thomson_485.pdf:PDF},
  keywords  = {Bioinformatics; Protein Design},
  owner     = {saulius},
  publisher = {American Association for the Advancement of Science},
  timestamp = {2016.03.09},
  creationdate = {2016-03-09T00:00:00},
  url       = {http://science.sciencemag.org/content/346/6208/485},
}

@Article{Thomson2016,
  author    = {Thomson, Daniel W. and Dinger, Marcel E.},
  journal   = {Nature Reviews Genetics},
  title     = {Endogenous {microRNA} sponges: evidence and controversy},
  year      = {2016},
  issn      = {1471-0064},
  month     = {Apr},
  number    = {5},
  pages     = {272–283},
  volume    = {17},
  doi       = {10.1038/nrg.2016.20},
  file      = {:by-author/T/Thompson/2016_Thompson_272.pdf:PDF},
  groups    = {am/RNA activation},
  owner     = {andrius},
  publisher = {Nature Publishing Group},
  timestamp = {2016.08.22},
  creationdate = {2016-08-22T00:00:00},
  url       = {http://dx.doi.org/10.1038/nrg.2016.20},
}

@Presentation{Thomson2011,
  author    = {Mark Thomson},
  title     = {Fitting and Hypothesis testing},
  year      = {2011},
  course    = {Statistics},
  lecture   = {3},
  comment   = {Nice treatement of chi**2},
  file      = {:by-author/T/Thomson/2011_Thomson_presentation.pdf:PDF},
  owner     = {saulius},
  pages     = {presentation},
  timestamp = {2012.09.18},
  creationdate = {2012-09-18T00:00:00},
}

@InProceedings{Thorp1998,
  author    = {Thorp, Edward O.},
  booktitle = {Proceedings of the 2nd IEEE International Symposium on Wearable Computers},
  title     = {The Invention of the First Wearable Computer},
  year      = {1998},
  address   = {Washington, DC, USA},
  pages     = {4},
  publisher = {IEEE Computer Society},
  series    = {ISWC '98},
  abstract  = {aThe first wearable computer was conceived in 1955 by the author to predict roulette, culminating in a joint effort at M.I.T. with Claude Shannon in 1960-61. The final operating version was tested in Shannon’s basement home lab in June of 1961. The cigarette pack sized analog device yielded an expected gain of +44% when betting on the most favored “octant.” The Shannons and Thorps tested the computer in Las Vegas in the summer of 1961. The predictions there were consistent with the laboratory expected gain of 44% but a minor hardware problem deferred sustained serious betting. We kept the method and the existence of the computer secret until 1966.},
  acmid     = {858031},
  file      = {1998_Thorp_4.pdf:by-author/T/Thorp/1998_Thorp_4.pdf:PDF},
  isbn      = {0-8186-9074-7},
  keywords  = {Casino; Games of Chance; Predicion; Roulette; Statistics},
  owner     = {saulius},
  timestamp = {2012.10.26},
  creationdate = {2012-10-26T00:00:00},
  url       = {http://dl.acm.org/citation.cfm?id=857199.858031},
}

@Article{Thukral2012,
  author    = {R. Thukral},
  journal   = {American Journal of Computational and Applied M athematics},
  title     = {A New Fifth-Order Iterative Method for Finding MultipleRoots of Nonlinear Equations},
  year      = {2012},
  pages     = {260},
  volume    = {2},
  abstract  = {In this paper, we present a fifth-order method for finding multiple zeros of nonlinear equations. Per iteration, the new method requires two evaluations of functions and two of its first derivative. It is proved that the method has a convergence of order five. Finally, some numerical examples are given to show the performance of the presented method, and compared with some known methods.},
  doi       = {10.5923/j.ajcam.20120206.04},
  file      = {:by-author/T/Thukral/2012_Thukral_260.pdf:PDF},
  keywords  = {Algorithms},
  owner     = {saulius},
  timestamp = {2013.03.22},
  creationdate = {2013-03-22T00:00:00},
}

@Article{Tian2007,
  author    = {Tian, Feifei and Zhou, Peng and Lv, Fenglin and Song, Rong and Li, Zhiliang},
  journal   = {Journal of peptide science : an official publication of the European Peptide Society},
  title     = {Three-dimensional holograph vector of atomic interaction field (3D-HoVAIF): a novel rotation-translation invariant 3D structure descriptor and its applications to peptides.},
  year      = {2007},
  pages     = {549--66},
  volume    = {13},
  abstract  = {Quantitative structure-activity relationship (QSAR) study, important in drug design, mainly involves two aspects, molecular structural characterization (MSC) and construction of a statistical model. MSC focuses on transforming molecular structural and property characteristics into a group of numerical codes, dedicated to minimizing information loss during this process. In this context, common atoms in organic compounds are classified according to their families in the periodic table, and hybridization states, and on the basis of these, three nonbonding interactions (i.e. electrostatic, van der Waals and hydrophobic) are calculated, ultimately resulting in a new rotation-translation invariant, 3D-MSC, as a three-dimensional holograph vector of atomic interaction field (3D-HoVAIF). By applying 3D-HoVAIF to QSAR studies on two classical peptides including 58 angiotensin-converting enzyme (ACE) inhibitors and 48 bitter-tasting dipeptides, we get two excellent genetic algorithm-partial least squares (GA-PLS) models, with statistics r(2), q(2), root mean square error (RMSEE), and root mean square error of cross-validation (RMSCV) of 0.857, 0.811, 0.376, and 0.432 for ACE inhibitors and 0.940, 0.892, 0.153 and 0.205 for bitter-tasting dipeptides, respectively. By equally dividing the two datasets into training and test sets by D-optimal, the 3D-HoVAIF approach undergoes rigorous statistical validation. Furthermore, the superior performance of 3D-HoVAIF is confirmed in comparison with two other peptide MSC approaches referring to z-scale and ISA-ECI. For 58 ACE inhibitors, the GA-PLS model yields two principal components, with the following statistics: r(2) = 0.893, q(2) = 0.824, RMSEE = 0.349, RMSCV = 0.425, q2(ext) = 0.739, r2(ext)= 0.784, r2(0.ext) = 0.781, rf2(0.ext) = 0.77, k = 0.962, k' = 1.019, and RMSEP = 0.460; for 48 bitter-tasting dipeptides, three principal components resulted, with the statistics as: r(2) = 0.950, q(2) = 0.893, RMSEE = 0.152, RMSCV = 0.222, q2(ext)= 0.875, r2(ext) = 0.919, r2(0.ext)= 0.919, rf2(0.ext)= 0.919, k = 1.018, k' = 0.974, and RMSEP = 0.198. In addition, the relationship of ACE-inhibiting activities with bitter-tasting thresholds has been investigated by applying the above-constructed models to predictions on 400 theoretically possible dipeptides. Through analysis, the ACE-inhibiting activities are found to be prominently related to bitter-tasting intensities. Thus, it is deemed to be difficult to find such dipeptides that simultaneously satisfy pharmacodynamic action (high ACE-inhibiting activities) and comfortable tastes, suggesting that active components of dipeptides that are served as functional food to lower blood pressure are not very ideal.},
  file      = {:by-author/T/Tian/2007_Tian_549.pdf:PDF},
  keywords  = {Protein Bioinformatics; Quantitative Structure-activity Relationship (QSAR)},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Tidow2007,
  author    = {Tidow, Henning and Melero, Roberto and Mylonas, Efstratios and Freund, Stefan M. V. and Grossmann, J. Guenter and Carazo, José María and Svergun, Dmitri I. and Valle, Mikel and Fersht, Alan R.},
  journal   = {Proceedings of the National Academy of Sciences of the United States of America},
  title     = {Quaternary structures of tumor suppressor p53 and a specific p53 DNA complex.},
  year      = {2007},
  pages     = {12324--9},
  volume    = {104},
  abstract  = {The homotetrameric tumor suppressor p53 consists of folded core and tetramerization domains, linked and flanked by intrinsically disordered segments that impede structure analysis by x-ray crystallography and NMR. Here, we solved the quaternary structure of human p53 in solution by a combination of small-angle x-ray scattering, which defined its shape, and NMR, which identified the core domain interfaces and showed that the folded domains had the same structure in the intact protein as in fragments. We combined the solution data with electron microscopy on immobilized samples that provided medium resolution 3D maps. Ab initio and rigid body modeling of scattering data revealed an elongated cross-shaped structure with a pair of loosely coupled core domain dimers at the ends, which are accessible for binding to DNA and partner proteins. The core domains in that open conformation closed around a specific DNA response element to form a compact complex whose structure was independently determined by electron microscopy. The structure of the DNA complex is consistent with that of the complex of four separate core domains and response element fragments solved by x-ray crystallography and contacts identified by NMR. Electron microscopy on the conformationally mobile, unbound p53 selected a minor compact conformation, which resembled the closed conformation, from the ensemble of predominantly open conformations. A multipronged structural approach could be generally useful for the structural characterization of the rapidly growing number of multidomain proteins with intrinsically disordered regions.},
  file      = {:by-author/T/Tidow/2007_Tidow_12324.pdf:PDF;2007_Tidow_Fig6.jpg:by-author/T/Tidow/2007_Tidow_Fig6.jpg:JPG image;2007_Tidow_Fig7.html:by-author/T/Tidow/2007_Tidow_Fig7.html:URL;:by-author/T/Tidow/2007_Tidow_Fig8.pdf:PDF;:by-author/T/Tidow/2007_Tidow_Fig9.pdf:PDF;2007_Tidow_Fig10.jpg:by-author/T/Tidow/2007_Tidow_Fig10.jpg:JPG image;2007_Tidow_Fig11.jpg:by-author/T/Tidow/2007_Tidow_Fig11.jpg:JPG image},
  keywords  = {DAMMIN; Experiment; SASREF; SAXS},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Presentation{Tierney2007,
  author    = {Luke Tierney},
  title     = {Brief Introduction to OpenMP},
  year      = {2007},
  file      = {:by-author/T/Tierney/2007_Tierney.pdf:PDF},
  month     = {oct},
  owner     = {saulius},
  timestamp = {2013.08.11},
  creationdate = {2013-08-11T00:00:00},
}

@Presentation{Tighiouart2014,
  author    = {Mourad Tighiouart},
  title     = {Adaptive Designs In Clinical Trials},
  year      = {2014},
  file      = {2014_Tighiouart.pdf:by-author/T/Tighiouart/2014_Tighiouart.pdf:PDF},
  groups    = {sg/Clinical Trials},
  owner     = {saulius},
  timestamp = {2015.12.14},
  creationdate = {2015-12-14T00:00:00},
  url       = {http://www.cedars-sinai.edu/Patients/Programs-and-Services/Samuel-Oschin-Comprehensive-Cancer-Institute-/For-Medical-Professionals/Conferences-and-Workshops/Documents/Adaptive-Designs-in-Clinical-Trials-12-3-14.pdf},
  urldate   = {2015-12-12},
}

@Article{Tilley2006,
  author    = {Tilley, S. David and Francis, Matthew B.},
  journal   = {Journal of the American Chemical Society},
  title     = {Tyrosine-selective protein alkylation using pi-allylpalladium complexes.},
  year      = {2006},
  pages     = {1080--1},
  volume    = {128},
  abstract  = {A new protein modification reaction has been developed based on a palladium-catalyzed allylic alkylation of tyrosine residues. This technique employs electrophilic pi-allyl intermediates derived from allylic acetate and carbamate precursors and can be used to modify proteins in aqueous solution at room temperature. To facilitate the detection of modified proteins using SDS-PAGE analysis, a fluorescent allyl acetate was synthesized and coupled to chymotrypsinogen A and bacteriophage MS2. The tyrosine selectivity of the reaction was confirmed through trypsin digest analysis. The utility of the reaction was demonstrated by using taurine-derived carbamates as water solubilizing groups that are cleaved upon protein functionalization. This solubility switching technique was used to install hydrophobic farnesyl and C(17) chains on chymotrypsinogen A in water using little or no cosolvent. Following this, the C(17) alkylated proteins were found to associate with lipid vesicles. In addition to providing a new protein modification strategy targeting an under-utilized amino acid side chain, this method provides convenient access to synthetic lipoproteins.},
  file      = {:by-author/T/Tilley/2006_Tilley_1080.pdf:PDF},
  keywords  = {Bioconjugation},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@Article{Timinskas1995,
  author    = {Albertas Timinskas and Viktoras Butkus and Arvydas Janulaitis},
  journal   = {Gene},
  title     = {Sequence motifs characteristic for {DNA} [cytosine-{N4}] and {DNA} [adenine-{N6}] methyltransferases. Classification of all {DNA} methyltransferases},
  year      = {1995},
  pages     = {3--11},
  volume    = {157},
  doi       = {10.1016/0378-1119(94)00783-O},
  file      = {:by-author/T/Timinskas/1995_Timinskas_3.pdf:PDF},
  owner     = {andrius},
  timestamp = {2014.09.11},
  creationdate = {2014-09-11T00:00:00},
}

@Article{Timpte2001,
  author    = {Timpte, C},
  journal   = {Trends in plant science},
  title     = {Auxin binding protein: curiouser and curiouser.},
  year      = {2001},
  pages     = {586--90},
  volume    = {6},
  abstract  = {Auxin is implicated in a variety of plant developmental processes, yet the molecular mechanism of auxin response remains largely unknown. Auxin binding protein 1 (ABP1) mediates cell expansion and might be involved in cell cycle control. Structural modeling shows that it is a beta-barrel dimer, with the C terminus free to interact with other proteins. We do not know where ABP1 performs its receptor function. Most ABP1 is detected within the endoplasmic reticulum but the evidence indicates that it functions at the plasma membrane. ABP1 is established as a crucial component of auxin signaling, but its precise mechanism remains unclear.},
  file      = {Timpte_2001_586_auxin_binding_p.pdf:by-author/T/Timpte/2001_Timpte_586.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Tischer2010,
  author    = {Tischer, Alexander and Lilie, Hauke and Rudolph, Rainer and Lange, Christian},
  journal   = {PROTEIN SCIENCE},
  title     = {L-Arginine hydrochloride increases the solubility of folded and unfolded recombinant plasminogen activator rPA},
  year      = {2010},
  pages     = {1783—1795},
  volume    = {19},
  abstract  = {L-Arginine hydrochloride (L-ArgHCl) was found to be an effective enhancer for in vitro protein refolding more than two decades ago. A detailed understanding of the mechanism of action, by which L-ArgHCl as co-solvent is capable to effectively suppress protein aggregation, while protein stability is preserved, has remained elusive. Concepts for the effects of co-solvents, which have been established over the last decades, were found to be insufficient to completely explain the effects of L-ArgHCl on protein refolding. In this article, we present data, which clearly establish that L-ArgHCl acts on the equilibrium solubility of the native model protein recombinant plasminogen activator (rPA), while for S-carboxymethylated rPA (IAA-rPA) that served as a model protein for denatured protein states, equilibrium solubilities could not be obtained. Solid to solute free transfer energies for native rPA were lowered by up to 14 kJ mol-1 under the tested conditions. This finding is in marked contrast to a previously proposed model in which L-ArgHCl acts as a neutral crowder which exclusively has an influence on the stability of the transition state of aggregation. The effects on the apparent solubility of IAA-rPA, as well as on the aggregation kinetics of all studied protein species, that were observed in the present work could tentatively be explained within the framework of a nucleation-aggregation scheme, in which L-ArgHCl exerts a strong effect on the pre-equilibria leading to formation of the aggregation seed.},
  doi       = {10.1002/pro.465},
  file      = {:by-author/T/Tischer/2010_Tischer_1783.pdf:PDF},
  keywords  = {Aggregation; Arginine; Equilibrium Solubility; Folding; IAA-rPA; Protein Crystallization; RPA},
  owner     = {em},
  timestamp = {2014.05.26},
  creationdate = {2014-05-26T00:00:00},
}

@Article{Titheradge2001,
  author    = {Titheradge, A. J. and King, J. and Ryu, J. and Murray, N. E.},
  journal   = {Nucleic acids research},
  title     = {Families of restriction enzymes: an analysis prompted by molecular and genetic data for type ID restriction and modification systems.},
  year      = {2001},
  pages     = {4195--205},
  volume    = {29},
  abstract  = {Current genetic and molecular evidence places all the known type I restriction and modification systems of Escherichia coli and Salmonella enterica into one of four discrete families: type IA, IB, IC or ID. StySBLI is the founder member of the ID family. Similarities of coding sequences have identified restriction systems in E.coli and Klebsiella pneumoniae as probable members of the type ID family. We present complementation tests that confirm the allocation of EcoR9I and KpnAI to the ID family. An alignment of the amino acid sequences of the HsdS subunits of StySBLI and EcoR9I identify two variable regions, each predicted to be a target recognition domain (TRD). Consistent with two TRDs, StySBLI was shown to recognise a bipartite target sequence, but one in which the adenine residues that are the substrates for methylation are separated by only 6 bp. Implications of family relationships are discussed and evidence is presented that extends the family affiliations identified in enteric bacteria to a wide range of other genera.},
  file      = {:by-author/T/Titheradge/2001_Titheradge_4195.pdf:PDF},
  keywords  = {TypeI},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@PhdThesis{Titzer2007,
  author    = {Benjamin Lawrence Titzer},
  school    = {University of California, Los Angeles},
  title     = {Objects to Bits: Efficient Implementation of Object-oriented Languages on Very Small Devices},
  year      = {2007},
  file      = {:by-author/T/Titzer/2007_Titzer_phdthesis.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.06.04},
  creationdate = {2012-06-04T00:00:00},
  url       = {http://compilers.cs.ucla.edu/virgil/titzer-dissertation.pdf},
}

@Presentation{Toby2010,
  author       = {Brian H. Toby},
  title        = {Getting Started with Rietveld},
  year         = {2010},
  organization = {Argonne National Laboratory},
  file         = {:by-author/T/Toby/2010_Toby_slides.pdf:PDF},
  owner        = {saulius},
  pages        = {slides},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Toby2003a,
  author           = {Brian H. Toby},
  journal          = {Journal of Applied Crystallography},
  title            = {{CIF} applications. {XIII}. {\it CIFEDIT}, a program for viewing and editing {CIF}s},
  year             = {2003},
  pages            = {1288--1289},
  volume           = {36},
  abstract         = {The CIFEDIT program displays the contents of single- or multi-block crystallographic information files (CIF). The program can also be used to edit the data values for CIF items, including adding or deleting sets of entries in a loop. CIF dictionaries are used to display definitions for data names and units. In the case of DDL 1.4 dictionaries, validation information is used to check numerical values. The program is written using the cross-platform scripting language Tcl/Tk and thus is largely platform-independent. It has been tested under Windows, Mac OS X and Unix.},
  creationdate     = {2012-10-21T00:00:00},
  doi              = {10.1107/S0021889803016790},
  file             = {:by-author/T/Toby/2003_Toby_1288.pdf:PDF},
  keywords         = {CIF; CIF Applications; CIFEDIT; Computer Programs; Data Quality},
  modificationdate = {2023-08-07T10:23:05},
  owner            = {saulius},
  timestamp        = {2012.10.21},
  url              = {http://dx.doi.org/10.1107/S0021889803016790},
}

@Article{Toby2003,
  author           = {Toby, Brian H. and Von Dreele, Robert B. and Larson, Allen C.},
  journal          = {Journal of Applied Crystallography},
  title            = {{CIF} applications. {XIV}. Reporting of {R}ietveld results using {pdCIF}: {GSAS2CIF}},
  year             = {2003},
  pages            = {1290--1294},
  volume           = {36},
  abstract         = {A discussion of the process of creating powder diffraction CIF documents (pdCIF) from Rietveld results is presented, with particular focus on the computer program GSAS2CIF. The data structures used within GSAS2CIF are described, as well as how the program implements template ®les for descriptive information. Two graphical user interface utilities are also discussed.},
  creationdate     = {2008-07-28T00:00:00},
  doi              = {10.1107/S0021889803016819},
  file             = {2003_Toby_1290.pdf:by-author/T/Toby/2003_Toby_1290.pdf:PDF;2003_Toby_1290suppl1.pdf:by-author/T/Toby/2003_Toby_1290suppl1.pdf:PDF;2003_Toby_1290suppl2.pdf:by-author/T/Toby/2003_Toby_1290suppl2.pdf:PDF},
  keywords         = {CIF; Data Quality; Powder Diffraction; Rietveld Refinement; X-ray Crystallography},
  modificationdate = {2024-05-20T16:52:11},
  owner            = {saulius},
  timestamp        = {2008.07.28},
  url              = {http://www.ncnr.nist.gov/xtal/software/cif/gsas2cif.pdf},
}

@Article{Tock2005,
  author    = {Tock, Mark R. and Dryden, David T. F.},
  journal   = {Current opinion in microbiology},
  title     = {The biology of restriction and anti-restriction.},
  year      = {2005},
  pages     = {466--72},
  volume    = {8},
  abstract  = {The phenomena of prokaryotic restriction and modification, as well as anti-restriction, were first discovered five decades ago but have yielded only gradually to rigorous analysis. Work presented at the 5th New England Biolabs Meeting on Restriction-Modification (available on REBASE, http://www.rebase.com) and several recently published genetic, biochemical and biophysical analyses indicate that these fields continue to contribute significantly to basic science. Recently, there have been several studies that have shed light on the still developing field of restriction-modification and on the newly re-emerging field of anti-restriction.},
  file      = {:by-author/T/Tock/2005_Tock_466.pdf:PDF},
  keywords  = {Antirestriction},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Todd1936,
  author    = {Todd,J. A. and Coxeter,H. S. M.},
  journal   = {Proceedings of the Edinburgh Mathematical Society (Series 2)},
  title     = {A practical method for enumerating cosets of a finite abstract group},
  year      = {1936},
  issn      = {1464-3839},
  pages     = {26--34},
  volume    = {5},
  abstract  = {An important problem in finite-group theory is the determination of an abstract definition for a given group , that is, a set of relationsbetween k generating operations S1, …., Sk of , such that every other relation between S1, …., Sk is an algebraic consequence of (1).The number of groups for which abstract definitions are actually known is relatively small, but a remarkable feature of the results already obtained is the extreme simplicity of the relations (1) in the case of several groups of quite high order. This fact constitutes an additional incentive to the search for abstract definitions, and many elegant results have doubtless yet to be discovered.},
  doi       = {10.1017/S0013091500008221},
  file      = {:by-author/T/Todd/1936_Todd_26.pdf:PDF},
  issue     = {01},
  numpages  = {9},
  owner     = {saulius},
  timestamp = {2013.03.22},
  creationdate = {2013-03-22T00:00:00},
  url       = {http://journals.cambridge.org/article_S0013091500008221},
}

@Article{Todd2008,
  author    = {Todd, Peter A. and Ladle, Richard J.},
  journal   = {Ethics in Science and Environmental Politics},
  title     = {Hidden dangers of a `citation culture'},
  year      = {2008},
  pages     = {13--16},
  volume    = {8},
  abstract  = {The influence of the journal impact factor and the effect of a ‘citation culture’ on science and scientists have been discussed extensively (Lawrence 2007; Curr Biol 17:R583–585). Neverthe- less, many still believe that the number of citations a paper receives provides some measure of its quality. This belief may be unfounded, however, as there are 2 substantial areas of error that can dis- tort a citation count or any metric based on a citation count. One is the deliberate manipulation of the system by scientists trying to ensure the highest possible number of cites to their papers; this has been examined elsewhere (Lawrence 2003; Nature 422:259–261). The second area of inaccuracy is inherent to how papers are cited, indexed and searched for. It is this latter, lesser known, source of error that we will investigate here.},
  doi       = {10.3354/esep00091},
  file      = {:by-author/T/Todd/2008_Todd_13.pdf:PDF},
  groups    = {sg/Bibliometrics},
  keywords  = {Assessment; Bibliometrics; Citation Counts; G Index; H Index; Impact Factors; Scientists},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Todorov2008,
  author           = {Todorov, Georgi and Bernstein, Herbert J.},
  journal          = {Journal of Applied Crystallography},
  title            = {{\it VCIF2}: extended {CIF} validation software},
  year             = {2008},
  pages            = {808--810},
  volume           = {41},
  abstract         = {Recent revisions to the CIF standard, the growing number of dictionaries and the critical role played by CIF in the IUCr publication process led the IUCr to fund a two-year project to upgrade portions of the existing CIF software base to support longer lines and more rigorous validation of CIFs against multiple layered dictionaries. A database-based approach to validation to ensure compliance with data-range and enumeration specifications, to ensure compliance with parent-child relationships, and to detect missing and duplicated tags is presented here. This approach to validation is being extended to support the handling of binary synchrotron imgCIF data.},
  creationdate     = {2008-07-28T00:00:00},
  doi              = {10.1107/S002188980801385X},
  file             = {2008_Todorov_808.pdf:by-author/T/Todorov/2008_Todorov_808.pdf:PDF},
  keywords         = {CIF; Data Quality; X-ray Crystallography},
  modificationdate = {2023-08-07T10:23:05},
  owner            = {saulius},
  timestamp        = {2008.07.28},
  url              = {http://dx.doi.org/10.1107/S002188980801385X},
}

@Presentation{Todorov2006,
  author           = {Georgi Todorov and Kostadin Z. Mitev and Herbert J. Bernstein},
  title            = {Extended {CIF} Validation Software},
  year             = {2006},
  organization     = {Dowling College},
  creationdate     = {2012-04-05T00:00:00},
  file             = {:by-author/T/Todorov/2006_Todorov_slides.pdf:PDF},
  keywords         = {CIF},
  modificationdate = {2023-08-07T10:23:05},
  owner            = {saulius},
  pages            = {slides},
  timestamp        = {2012.04.05},
}

@Webpage{Toffoli2004,
  author    = {Tommaso Toffoli},
  retrieved = {2008-07-28},
  title     = {Honesty in Inference},
  url       = {http://www.americanscientist.org/template/BookReviewTypeDetail/assetid/31352;jsessionid=aaafUfFE59g_3X},
  year      = {2004},
  file      = {:by-author/T/Toffoli/2004_Toffoli.war:},
  groups    = {sg/Bayesian},
  journal   = {American Scientist},
  keywords  = {Bayesian Statistics; Mathematics},
  owner     = {saulius},
  timestamp = {2015.03.02},
  creationdate = {2015-03-02T00:00:00},
}

@Electronic{Togo2012,
  author    = {Togo, Atsushi},
  title     = {Niggli cell — niggli 0.1 documentation},
  url       = {http://atztogo.github.io/niggli},
  year      = {2012},
  file      = {:by-author/T/Togo/2012_Togo.pdf:PDF},
  owner     = {andrius},
  timestamp = {2014.11.04},
  creationdate = {2014-11-04T00:00:00},
}

@Manuscript{Togo2015,
  author           = {Atsushi Togo and Isao Tanaka},
  title            = {{spglib}: a {C} library of crystal symmetry toolbox},
  year             = {2015},
  keywords         = {Algorithms; C Library; Crystallography; Spacegroup Determination; Spacegroups; Spglib; Symmetry Determination},
  creationdate     = {2015-06-04T00:00:00},
  file             = {:by-author/T/Togo/2015_Togo_manuscript.pdf:PDF},
  modificationdate = {2024-06-02T17:43:57},
  owner            = {andrius},
  timestamp        = {2015.06.04},
}

@Article{Tolman1928,
  author    = {Tolman, R. C.},
  journal   = {Proceedings of the National Academy of Sciences of the United States of America},
  title     = {On the Equilibrium between Radiation and Matter in Einstein's Closed Universe.},
  year      = {1928},
  pages     = {353--6},
  volume    = {14},
  file      = {:by-author/T/Tolman/1928_Tolman_353.pdf:PDF},
  keywords  = {General Reliativity},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Tolman1928a,
  author    = {Tolman, R. C.},
  journal   = {Proceedings of the National Academy of Sciences of the United States of America},
  title     = {On the Energy and Entropy of Einstein's Closed Universe.},
  year      = {1928},
  pages     = {348--53},
  volume    = {14},
  file      = {:by-author/T/Tolman/1928_Tolman_348.pdf:PDF},
  keywords  = {General Reliativity},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Tompa2005,
  author    = {Tompa, Peter},
  journal   = {FEBS letters},
  title     = {The interplay between structure and function in intrinsically unstructured proteins.},
  year      = {2005},
  pages     = {3346--54},
  volume    = {579},
  abstract  = {Intrinsically unstructured proteins (IUPs) are common in various proteomes and occupy a unique structural and functional niche in which function is directly linked to structural disorder. The evidence that these proteins exist without a well-defined folded structure in vitro is compelling, and justifies considering them a separate class within the protein world. In this paper, novel advances in the rapidly advancing field of IUPs are reviewed, with the major attention directed to the evidence of their unfolded character in vivo, the interplay of their residual structure and their various functional modes and the functional benefits their malleable structural state provides. Via all these details, it is demonstrated that in only a couple of years after its conception, the idea of protein disorder has already come of age and transformed our basic concepts of protein structure and function.},
  file      = {:by-author/T/Tompa/2005_Tompa_3346.pdf:PDF},
  keywords  = {Intrinsically Unfolded Prot},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Tompa2002,
  author    = {Tompa, Peter},
  journal   = {Trends in biochemical sciences},
  title     = {Intrinsically unstructured proteins.},
  year      = {2002},
  pages     = {527--33},
  volume    = {27},
  abstract  = {The recent suggestion that the classical structure-function paradigm should be extended to proteins and protein domains whose native and functional state is intrinsically unstructured has received a great deal of support. There is ample evidence that the unstructured state, common to all living organisms, is essential for basic cellular functions; thus it deserves to be recognized as a separate functional and structural category within the protein kingdom. In this review, recent findings are surveyed to illustrate that this novel but rapidly advancing field has reached a point where these proteins can be comprehensively classified on the basis of structure and function.},
  file      = {:by-author/T/Tompa/2002_Tompa_527.pdf:PDF},
  keywords  = {Intrinsically Unfolded Prot},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Tong2000,
  author    = {Tong, C K and Brion, L P and Suarez, C and Chesler, M},
  journal   = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
  title     = {Interstitial carbonic anhydrase (CA) activity in brain is attributable to membrane-bound CA type IV.},
  year      = {2000},
  pages     = {8247--53},
  volume    = {20},
  abstract  = {We tested the hypothesis that extracellular membrane-bound carbonic anhydrase (CA) type IV is responsible for the regulation of interstitial pH (pH(o)) transients in brain. Rat hippocampal slices were incubated in phosphatidylinositol-specific phospholipase C (PI-PLC), which cleaves the link of CA IV to the external face of plasma membranes. Then evoked alkaline pH(o) shifts were studied in a recording chamber, using pH microelectrodes. Incubation fluid was saved for later analysis. The ability to buffer a rapid alkaline load was reduced markedly in PI-PLC-treated tissue as compared with adjacent, paired control slices. The effect of benzolamide (a poorly permeant CA inhibitor) on evoked pH(o) shifts was diminished greatly in the PI-PLC-treated tissue, consistent with the washout of interstitial CA. Treatment of the incubation fluid with SDS abolished nearly all of the CA activity in fluid from controls, whereas an SDS-insensitive component remained in the fluid from PI-PLC-treated slices. These data suggested that CA type II (which is blocked by SDS) leaked from injured glial cells in both slice preparations, whereas CA type IV (which is insensitive to SDS) was liberated selectively into the fluid from PI-PLC-treated tissue. Western blot analysis was consistent with this interpretation, demonstrating a predominance of CA IV in the incubation fluid from PI-PLC-treated tissue and variable amounts of CA II in fluid from PI-PLC-treated and control slices. These results demonstrate that interstitial CA activity brain is attributable principally to membrane-bound CA IV.},
  file      = {2000_Tong_8247.pdf:by-author/T/Tong/2000_Tong_8247.pdf:PDF},
  groups    = {sg/physiology, sg/hCA4},
  keywords  = {Carbonic Anhydrases},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Tong2001,
  author    = {Tong, L},
  journal   = {Acta crystallographica. Section D, Biological crystallography},
  title     = {How to take advantage of non-crystallographic symmetry in molecular replacement: 'locked' rotation and translation functions.},
  year      = {2001},
  pages     = {1383--9},
  volume    = {57},
  file      = {2001_Tong_1383.pdf:by-author/T/Tong/2001_Tong_1383.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Tong1997,
  author    = {Tong, W. and Perkins, R. and Strelitz, R. and Collantes, E. R. and Keenan, S. and Welsh, W. J. and Branham, W. S. and Sheehan, D. M.},
  journal   = {Environmental health perspectives},
  title     = {Quantitative structure-activity relationships (QSARs) for estrogen binding to the estrogen receptor: predictions across species.},
  year      = {1997},
  pages     = {1116--24},
  volume    = {105},
  abstract  = {The recognition of adverse effects due to environmental endocrine disruptors in humans and wildlife has focused attention on the need for predictive tools to select the most likely estrogenic chemicals from a very large number of chemicals for subsequent screening and/or testing for potential environmental toxicity. A three-dimensional quantitative structure-activity relationship (QSAR) model using comparative molecular field analysis (CoMFA) was constructed based on relative binding affinity (RBA) data from an estrogen receptor (ER) binding assay using calf uterine cytosol. The model demonstrated significant correlation of the calculated steric and electrostatic fields with RBA and yielded predictions that agreed well with experimental values over the entire range of RBA values. Analysis of the CoMFA three-dimensional contour plots revealed a consistent picture of the structural features that are largely responsible for the observed variations in RBA. Importantly, we established a correlation between the predicted RBA values for calf ER and their actual RBA values for human ER. These findings suggest a means to begin to construct a more comprehensive estrogen knowledge base by combining RBA assay data from multiple species in 3D-QSAR based predictive models, which could then be used to screen untested chemicals for their potential to bind to the ER. Another QSAR model was developed based on classical physicochemical descriptors generated using the CODESSA (Comprehensive Descriptors for Structural and Statistical Analysis) program. The predictive ability of the CoMFA model was superior to the corresponding CODESSA model.},
  file      = {:by-author/T/Tong/1997_Tong_1116.pdf:PDF},
  keywords  = {Receptor Binding},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Tonouchi2007,
  author    = {Tonouchi},
  title     = {Cutting-edge terahertz technology},
  year      = {2007},
  pages     = {97},
  file      = {:by-author/T/Tonouchi/2007_Tonouchi_97.pdf:PDF},
  keywords  = {Physics; Terahertz EM Waves},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@Article{Toofan1994,
  author    = {Jahansooz Toofan},
  journal   = {Journal of Chemical Education},
  title     = {A Simple Expression between Critical Radius Ratio and Coordination Numbers},
  year      = {1994},
  pages     = {147},
  volume    = {71},
  abstract  = {Critical radius ratios for common coordination numbers and their derivation.},
  doi       = {10.1021/ed071p147},
  file      = {:./by-author/T/Toofan/1994_Toofan_147.pdf:PDF},
  keywords  = {Coordination Complex},
  owner     = {antanas},
  timestamp = {2014.01.15},
  creationdate = {2014-01-15T00:00:00},
  url       = {http://pubs.acs.org/doi/abs/10.1021/ed071p147},
}

@Article{Topf2008,
  author    = {Topf, Maya and Lasker, Keren and Webb, Ben and Wolfson, Haim and Chiu, Wah and Sali, Andrej},
  journal   = {Structure (London, England : 1993)},
  title     = {Protein structure fitting and refinement guided by cryo-EM density.},
  year      = {2008},
  pages     = {295--307},
  volume    = {16},
  abstract  = {For many macromolecular assemblies, both a cryo-electron microscopy map and atomic structures of its component proteins are available. Here we describe a method for fitting and refining a component structure within its map at intermediate resolution (&lt;15 A). The atomic positions are optimized with respect to a scoring function that includes the crosscorrelation coefficient between the structure and the map as well as stereochemical and nonbonded interaction terms. A heuristic optimization that relies on a Monte Carlo search, a conjugate-gradients minimization, and simulated annealing molecular dynamics is applied to a series of subdivisions of the structure into progressively smaller rigid bodies. The method was tested on 15 proteins of known structure with 13 simulated maps and 3 experimentally determined maps. At approximately 10 A resolution, Calpha rmsd between the initial and final structures was reduced on average by approximately 53%. The method is automated and can refine both experimental and predicted atomic structures.},
  file      = {:by-author/T/Topf/2008_Topf_295.pdf:PDF},
  groups    = {sg/applications},
  keywords  = {CryoEM; Structure Solution Methods},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Torp2004,
  author    = {Torp, Kristian and Jensen, Christian S. and Snodgrass, Richard T.},
  journal   = {Information Systems},
  title     = {Modification semantics in now-relative databases},
  year      = {2004},
  issn      = {0306-4379},
  month     = {Dec},
  number    = {8},
  pages     = {653--683},
  volume    = {29},
  abstract  = {Most real-world databases record time-v arying information. In such databases, theMost real-world databases record time-varying information. In such databases, the notion of “the current time,” or NOW, occurs naturally and prominently. For example, when capturing the past states of a relation using begin and end time columns, tuples that are part of the current state have some past time as their begin time and NOW as their end time. While the semantics of such variable databases has been described in detail and is well understood, the modification of variable databases remains une xplored. This paper defines the semantics of modifications involving the variable NOW. More specifically, the problems with modifications in the presence of NO W are explored, illustrating that the main problems are with modifications of tuples that reach into the future. The paper defines the semantics of modifications—including insertions, deletions, and updates—of databases without NOW, with NOW, and with values of the type NOW + $\Delta$, where $\Delta$
 is a non-variable time duration. To accommodate these semantics, three new timestamp values are introduced. Finally, implementation is explored. We sho w how to represent the variable NOW with columns of standard SQL data types and give a mapping from SQL on now-relative data to standard SQL on these columns. The paper thereby completes the semantics, the querying, and the modification of now-relative databases.},
  doi       = {10.1016/s0306-4379(03)00047-4},
  file      = {2004_Torp_653.pdf:by-author/T/Torp/2004_Torp_653.pdf:PDF},
  keywords  = {Computer Science (CS); Database Versioning; Temporal Databases},
  owner     = {saulius},
  publisher = {Elsevier BV},
  timestamp = {2016.11.17},
  creationdate = {2016-11-17T00:00:00},
  url       = {http://dx.doi.org/10.1016/S0306-4379(03)00047-4},
}

@Article{Torp2000,
  author    = {Kristian Torp and Christian S. Jensen and Richard T. Snodgrass},
  journal   = {International Journal on Very Large Databases},
  title     = {Effective Timestamping in Databases},
  year      = {2000},
  month     = {February},
  pages     = {267--288},
  volume    = {8},
  abstract  = {Many existing database applications place various timestamps on their data, rendering temporal values such as dates and times prevalent in database tables. During the past two decades, several dozen temporal data models have appeared, all with timestamps being integral components. The models have used timestamps for encoding two specific temporal aspects of database facts, namely transac- tion time, when the facts are current in the database, and valid time, when the facts are true in the modeled reality. However, with few exceptions, the assignment of timestamp values has been considered only in the context of individual modification statements. This paper takes the next logical step: It considers the use of timestamping for capturing transaction and valid time in the context of transactions. The paper initially identifies and analyzes several problems with straightforward time- stamping, then proceeds to propose a variety of techniques aimed at solving these problems. Timestamping the results of a transaction with the commit time of the transaction is a promising approach. The paper studies how this time-stamping may be done using a spectrum of techniques. While many database facts are valid until now, the current time, this value is absent from the existing temporal types. Techniques that address this problem using different substitute values are presented. Using a stratum architecture, the performance of the different proposed techniques are studied. Although querying and modifying time-varying data is accompanied by a number of subtle problems, we present a comprehensive approach that provides application programmers with sim- ple, consistent, and efficient support for modifying bitemporal databases in the context of user transactions.},
  file      = {2000_Torp_267.pdf:by-author/T/Torp/2000_Torp_267.pdf:PDF},
  issue     = {3+4},
  keywords  = {Computer Science (CS); Database Versioning; Temporal Databases},
  owner     = {saulius},
  timestamp = {2016.11.17},
  creationdate = {2016-11-17T00:00:00},
  url       = {http://www.cs.arizona.edu/people/rts/pubs/VLDBJ99.pdf},
}

@Article{Torre1998,
  author    = {de la Torre, J. García and B. Carrasco},
  journal   = {Eur. Biophys. J.},
  title     = {Intrinsic viscosity and rotational diffusion of bead models for rigid macromolecules and bioparticles},
  year      = {1998},
  pages     = {549--557},
  volume    = {27},
  abstract  = {The conventional Kirkwood-Riseman (K-R) treatment of the intrinsic viscosity of macromolecular bead models shows a deficiency when it is applied to models with few beads, whose sizes are not much smaller than of the modelled particle. We present a complete derivation of the intrinsic viscosity up to first order in interbead dis- tances (Oseen-type hydrodynamic interaction), finding that a term that belongs to the zeroth-order contribution is missing in the usual description. This term is simply pro- portional to the total volume of the bead model. The na- ture of this correction for viscosity is similar to a previ- ously described correction for rotational coefficients. We discuss the performance of these corrections for various simple models, including ellipsoids as well as oligomeric structures in rodlike, chainlike and polyhedral conforma- tions.},
  file      = {Torre_1998_549.pdf:by-author/T/Torre/1998_Torre_549.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@InProceedings{Torres-Salinas2014a,
  author    = {Torres-Salinas, Daniel and Jiménez-Contreras, Evaristo and Robinson-García, Nicolas},
  title     = {How many citations are there in the Data Citation Index?},
  year      = {2014},
  file      = {:by-author/T/Torres-Salinas/2014_Torres-Salinas.pdf:PDF},
  keywords  = {COD; Data Citation Index},
  owner     = {antanas},
  timestamp = {2015.03.04},
  creationdate = {2015-03-04T00:00:00},
}

@Article{Torres-Salinas2014,
  author    = {Torres-Salinas, Daniel and Martín-Martín, Alberto and Fuente-Gutiérrez, Enrique},
  journal   = {Revista Española de Documentación Científica},
  title     = {Analysis of the coverage of the Data Citation Index -- Thomson Reuters: disciplines, document types and repositories},
  year      = {2014},
  pages     = {e036},
  volume    = {37},
  abstract  = {In the past years, the movement of data sharing has been enjoying great popularity. Within this context, Thomson Reuters launched at the end of 2012 a new product inside the Web of Knowledge family: the Data Citation Index. The aim of this new database is to enable discovery and access, from a single place, to data from a variety of data repositories from different subject areas and from around the world. In short note we present some results from the analysis of the Data Citation Index. Specifically, we address the following issues: discipline coverage, data types present in the database and repositories that were included at the time of the study.},
  doi       = {10.3989/redc.2014.1.1114},
  file      = {:./by-author/T/Torres-Salinas/2014_Torres-Salinas_e036.pdf:PDF},
  owner     = {antanas},
  timestamp = {2015.02.11},
  creationdate = {2015-02-11T00:00:00},
}

@Periodical{Torres-Salinas2013,
  title        = {An introduction to the coverage of the Data Citation Index (Thomson-Reuters): disciplines, document types and repositories},
  year         = {2013},
  month        = {June},
  note         = {Versión 1.0},
  organization = {EC3 Research Group \& EC3 metricsSpin-Off, Universidad de Navarra, Pamplona;},
  series       = {EC3 Working Papers},
  url          = {http://arxiv.org/ftp/arxiv/papers/1306/1306.6584.pdf},
  volume       = {11},
  abstract     = {In the past years, the movement of data sharing has been enjoying great popularity. Within this context, Thomson Reuters launched at the end of 2012 a new product inside the Web of Knowledge family: the Data Citation Index. The aim of this tool is to enab le discovery and access, from a single place, to data from a variety of data repositories from different subject areas and from around the world. In this working paper we present some preliminary results from the analysis of the D ata C itation I ndex . Specif ically, we address the following issues: discipline coverage, data types present in the database, and repositories that were included at the time of the study.},
  author       = {Daniel Torres-Salinas and Alberto Martín-Martín and Enrique Fuente-Gutiérrez},
  comment      = {A working paper about the TR Data Citation Index; mentions COD as the fith-largest repository},
  file         = {:by-author/T/Torres-Salinas/2013_Torres-Salinas.pdf:PDF},
  keywords     = {Citation Indexes; Data; Data Access Policy; Data Management; Data Sharing; Databases; Information Sources Repository; Open Access; Research Data; Scientific Communication; Thomson Reuters; Web of Science},
  owner        = {saulius},
  timestamp = {2013.07.31},
  creationdate = {2013-07-31T00:00:00},
  version      = {1.0},
}

@Article{Torshin2002,
  author          = {Torshin, Ivan Y.},
  journal         = {Medical science monitor : international medical journal of experimental and clinical research},
  title           = {Functional maps of the junctions between interglobular contacts and active sites in glycolytic enzymes -- a comparative analysis of the biochemical and structural data.},
  year            = {2002},
  issn            = {1234-1010},
  month           = apr,
  pages           = {BR123--BR135},
  volume          = {8},
  abstract        = {Oligomers and separate subunits of the glycolytic enzymes often have different catalytic properties. However, spectral data show an apparent lack of significant conformational changes during oligomerization. Since the conformation of an enzyme determines its catalytic properties, the structural mechanism(s) influencing the activity is of considerable interest. Analysis of the spatial structures of the junctions between interglobular contacts and binding sites may give a clue to the mechanism(s) of the activation. In this work, the problem was studied using available structural and biochemical data for the oligomeric enzymes of glycolysis. Computational analysis of the structures of the junctions has identified three structurally distinct types of junctions: 1. interglobular binding site (2 of 8 enzymes); 2. domain-domain stabilization (5 of 8); and 3. 'sequence overlap' or a local conformational change (all enzymes). Thus the catalytic activity may be influenced through the shifts of the modules of protein structure (types 1, 2) and/or due to a slight change in the local structure (type 3). The more common junctions of types 2 and 3 are well conserved among eukaryotic enzymes, which suggests their biological importance. The results suggest that a profound and a complex change in conformation in subunits of an oligomeric enzyme may not be necessary for a significant change in the catalytic properties. The analysis maps the residues important for the junctions and thus for the link between the catalytic activity and the oligomeric state of the enzymes.},
  chemicals       = {Escherichia coli Proteins, Holoenzymes, Protein Subunits, Saccharomyces cerevisiae Proteins, Glyceraldehyde-3-Phosphate Dehydrogenases, Phosphofructokinases, Pyruvate Kinase, Fructose-Bisphosphate Aldolase, Phosphopyruvate Hydratase, Triose-Phosphate Isomerase, Glucose-6-Phosphate Isomerase, Phosphoglycerate Mutase},
  citation-subset = {IM},
  completed       = {2002-09-26},
  country         = {United States},
  creationdate    = {2012-10-21T00:00:00},
  file            = {:by-author/T/Torshin/2002_Torshin_BR123.pdf:PDF},
  issn-linking    = {1234-1010},
  issue           = {4},
  keywords        = {Animals; Binding Sites; Catalysis; Chemistry; Computational Biology; Enzyme Activation; Escherichia Coli Proteins; Fructose-Bisphosphate Aldolase; Glucose-6-Phosphate Isomerase; Glyceraldehyde-3-Phosphate Dehydrogenases; Glycolysis; Holoenzymes; Humans; MSM; Models; Molecular; Nephropidae; Phosphofructokinases; Phosphoglycerate Mutase; Phosphopyruvate Hydratase; Protein Conformation; Protein Interaction Mapping; Protein Structure; Protein Subunits; Pyruvate Kinase; Rabbits; Rats; Saccharomyces Cerevisiae Proteins; Structure-activity Relationship (SAR); Tertiary; Triose-Phosphate Isomerase},
  nlm-id          = {9609063},
  owner           = {saulius},
  pii             = {2397},
  pmid            = {11951058},
  pubmodel        = {Print},
  pubstate        = {ppublish},
  timestamp       = {2012.10.21},
}

@Article{Toth2003,
  author    = {Toth, Eric A. and Li, Ying and Sawaya, Michael R. and Cheng, Yifan and Ellenberger, Tom},
  journal   = {Molecular cell},
  title     = {The crystal structure of the bifunctional primase-helicase of bacteriophage T7.},
  year      = {2003},
  pages     = {1113--23},
  volume    = {12},
  abstract  = {Within minutes after infecting Escherichia coli, bacteriophage T7 synthesizes many copies of its genomic DNA. The lynchpin of the T7 replication system is a bifunctional primase-helicase that unwinds duplex DNA at the replication fork while initiating the synthesis of Okazaki fragments on the lagging strand. We have determined a 3.45 A crystal structure of the T7 primase-helicase that shows an articulated arrangement of the primase and helicase sites. The crystallized primase-helicase is a heptamer with a crown-like shape, reflecting an intimate packing of helicase domains into a ring that is topped with loosely arrayed primase domains. This heptameric isoform can accommodate double-stranded DNA in its central channel, which nicely explains its recently described DNA remodeling activity. The double-jointed structure of the primase-helicase permits a free range of motion for the primase and helicase domains that suggests how the continuous unwinding of DNA at the replication fork can be periodically coupled to Okazaki fragment synthesis.},
  file      = {:by-author/T/Toth/2003_Toth_1113.pdf:PDF},
  keywords  = {T7; {gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Tougu1996,
  author    = {Tougu, K. and Marians, K. J.},
  journal   = {The Journal of biological chemistry},
  title     = {The extreme C terminus of primase is required for interaction with DnaB at the replication fork.},
  year      = {1996},
  pages     = {21391--7},
  volume    = {271},
  abstract  = {We have shown previously that a protein-protein interaction between DnaG and DnaB is required to attract the primase to the replication fork. This interaction was mediated by the C-terminal 16-kDa domain (p16) of the primase. A screen was developed that allowed the detection of mutant p16 proteins that did not interact with DnaB. Various mutagenesis protocols were used to localize this interaction domain to the extreme C terminus of the primase. A mutant primase missing only the C-terminal 16 amino acids was isolated and its activities examined. This mutant enzyme was fully active as a primase, but was incapable of interacting with DnaB. Thus, the mutant primase could not support DNA synthesis in either the general priming reaction or during phiX174 complementary strand DNA replication. Alanine cluster mutagenesis and deletion analysis in p16 allowed the further localization of the interaction domain to the extreme C-terminal 8 amino acids in primase.},
  file      = {:by-author/T/Tougu/1996_Tougu_21391.pdf:PDF},
  keywords  = {Ecoli; {gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Tougu1996a,
  author    = {Tougu, K. and Marians, K. J.},
  journal   = {The Journal of biological chemistry},
  title     = {The interaction between helicase and primase sets the replication fork clock.},
  year      = {1996},
  pages     = {21398--405},
  volume    = {271},
  abstract  = {The synthesis of an Okazaki fragment occurs once every 1-2 s at the Escherichia coli replication fork and requires precise coordination of the enzymatic activities required. We have shown previously that the primase is recruited anew from solution for each cycle of Okazaki fragment synthesis and that association of primase with the replication fork is via a protein-protein interaction with the helicase, DnaB. We describe here mutant primases that have an altered interaction with DnaB and that direct the synthesis of Okazaki fragments of altered length compared to the wild-type. The mutant primases were deficient only in their ability to participate in replication reactions where their entry to the DNA was provided by the initial protein-protein interaction with DnaB. The primer synthesis capacity of these proteins remained unaffected, as was their ability to interact with the DNA polymerase III holoenzyme. Neither replication fork rate nor the efficiency of primer utilization was affected at replication forks programmed by the mutant enzymes. Thus, the interaction between DnaG and DnaB at the replication fork is the primary regulator of the cycle of Okazaki fragment synthesis.},
  file      = {:by-author/T/Tougu/1996_Tougu_21398.pdf:PDF},
  keywords  = {Ecoli; {gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Touw2016,
  author    = {Touw, Wouter G. and van Beusekom, Bart and Evers, Jochem M. G. and Vriend, Gert and Joosten, Robbie P.},
  journal   = {Acta Crystallographica Section D Structural Biology},
  title     = {Validation and correction of Zn–CysxHisycomplexes},
  year      = {2016},
  issn      = {2059-7983},
  month     = {Sep},
  number    = {10},
  pages     = {1110–1118},
  volume    = {72},
  doi       = {10.1107/s2059798316013036},
  file      = {2016_Touw_1110.pdf:by-author/T/Touw/2016_Touw_1110.pdf:PDF},
  groups    = {sg/Crystallography, am/Crystallography},
  owner     = {andrius},
  publisher = {International Union of Crystallography (IUCr)},
  timestamp = {2016.11.14},
  creationdate = {2016-11-14T00:00:00},
  url       = {http://dx.doi.org/10.1107/S2059798316013036},
}

@Article{Touw2010,
  author    = {Wouter G. Touw and Gert Vriend},
  journal   = {Acta Crystallographica Section D},
  title     = {On the Complexity of {E}ngh and {H}uber Refinement Restraints: The Angle $\tau$ as Example},
  year      = {2010},
  pages     = {1341--1350},
  volume    = {66},
  abstract  = {The Engh and Huber parameters for bond lengths and bond angles have been used uncontested in macromolecular structure refinement from 1991 until very recently, despite critical discussion of their ubiquitous validity by many authors. An extensive analysis of the backbone angle $\tau$ (N—C$^{\alpha}$—C) illustrates that the Engh and Huber parameters can indeed be improved and a recent study [Tronrud et al. (2010), Acta Cryst. D66, 834–842] confirms these ideas. However, the present study of $\tau$ shows that improving the Engh and Huber parameters will be considerably more complex than simply making the parameters a function of the backbone $phi$,$psi$ angles. Many other aspects, such as the cooperativity of hydrogen bonds, the bending of secondary-structure elements and a series of biophysical aspects of the 20 amino-acid types, will also need to be taken into account. Different sets of Engh and Huber parameters will be needed for conceptually different refinement programs.},
  doi       = {10.1107/S0907444910040928},
  file      = {:by-author/T/Touw/2010_Touw_1341.pdf:PDF},
  keywords  = {Restrains; X-ray Crystallography},
  owner     = {andrius},
  timestamp = {2012.05.07},
  creationdate = {2012-05-07T00:00:00},
}

@PhdThesis{Townsend2007,
  author    = {Townsend, Joseph Andrew},
  school    = {University of Cambridge},
  title     = {Automated Analysis and Validation of Chemical Literature},
  year      = {2007},
  file      = {:by-author/T/Townsend/2007_Townsend_phdthesis.pdf:PDF},
  owner     = {andrius},
  timestamp = {2015.03.31},
  creationdate = {2015-03-31T00:00:00},
  url       = {http://www.dspace.cam.ac.uk/handle/1810/197570},
}

@Article{Townsend2011,
  author    = {Townsend, Joe and Murray-Rust, Peter},
  journal   = {Journal of Cheminformatics},
  title     = {CMLLite: a design philosophy for CML},
  year      = {2011},
  issn      = {1758-2946},
  pages     = {39},
  volume    = {3},
  abstract  = {CMLLite is a collection of definitions and processes which provide strong and flexible validation for a document in Chemical Markup Language (CML). It consists of an updated CML schema (schema3), conventions specifying rules in both human and machine-understandable forms and a validator available both online and offline to check conformance. This article explores the rationale behind the changes which have been made to the schema, explains how conventions interact and how they are designed, formulated, implemented and tested, and gives an overview of the validation service.},
  doi       = {10.1186/1758-2946-3-39},
  file      = {2011_Townsend_39.pdf:by-author/T/Townsend/2011_Townsend_39.pdf:PDF},
  owner     = {saulius},
  pubmedid  = {21999395},
  timestamp = {2014.06.23},
  creationdate = {2014-06-23T00:00:00},
  url       = {http://www.jcheminf.com/content/3/1/39},
}

@Article{Townson2007,
  author    = {Townson, Sharon A. and Samuelson, James C. and Bao, Yongming and Xu, Shuang-Yong and Aggarwal, Aneel K.},
  journal   = {Structure (London, England : 1993)},
  title     = {BstYI bound to noncognate DNA reveals a \&quot;hemispecific\&quot; complex: implications for DNA scanning.},
  year      = {2007},
  pages     = {449--59},
  volume    = {15},
  abstract  = {DNA recognition by proteins is essential for specific expression of genes in a living organism. En route to a target DNA site, a protein will often sample noncognate DNA sites through nonspecific protein-DNA interactions, resulting in a variety of conformationally different binding states. We present here the crystal structure of endonuclease BstYI bound to a noncognate DNA. Surprisingly, the structure reveals the enzyme in a &quot;hemispecific&quot; binding state on the pathway between nonspecific and specific recognition. A single base pair change in the DNA abolishes binding of only one monomer, with the second monomer bound specifically. We show that the enzyme binds essentially as a rigid body, and that one end of the DNA is accommodated loosely in the binding cleft while the other end is held tightly. Another intriguing feature of the structure is Ser172, which has a dual role in establishing nonspecific and specific contacts. Taken together, the structure provides a snapshot of an enzyme in a &quot;paused&quot; intermediate state that may be part of a more general mechanism of scanning DNA.},
  file      = {:by-author/T/Townson/2007_Townson_449.pdf:PDF},
  keywords  = {Struct; TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Townson2004,
  author    = {Townson, Sharon A and Samuelson, James C and Vanamee, Eva Scheuring and Edwards, Thomas A and Escalante, Carlos R and Xu, Shuang-Yong and Aggarwal, Aneel K},
  journal   = {Journal of molecular biology},
  title     = {Crystal structure of BstYI at 1.85A resolution: a thermophilic restriction endonuclease with overlapping specificities to BamHI and BglII.},
  year      = {2004},
  pages     = {725--33},
  volume    = {338},
  abstract  = {We report here the structure of BstYI, an "intermediate" type II restriction endonuclease with overlapping sequence specificities to BamHI and BglII. BstYI, a thermophilic endonuclease, recognizes and cleaves the degenerate hexanucleotide sequence 5'-RGATCY-3' (where R=A or G and Y=C or T), cleaving DNA after the 5'-R on each strand to produce four-base (5') staggered ends. The crystal structure of free BstYI was solved at 1.85A resolution by multi-wavelength anomalous dispersion (MAD) phasing. Comparison with BamHI and BglII reveals a strong structural consensus between all three enzymes mapping to the alpha/beta core domain and residues involved in catalysis. Unexpectedly, BstYI also contains an additional "arm" substructure outside of the core protein, which enables the enzyme to adopt a more compact, intertwined dimer structure compared with BamHI and BglII. This arm substructure may underlie the thermostability of BstYI. We identify putative DNA recognition residues and speculate as to how this enzyme achieves a "relaxed" DNA specificity.},
  file      = {Townson_2004_725-BstYI_structure.pdf:by-author/T/Townson/2004_Townson_725.pdf:PDF},
  keywords  = {Struct; TypeII},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Townson2005,
  author    = {Townson, Sharon A. and Samuelson, James C. and Xu, Shuang-Yong and Aggarwal, Aneel K.},
  journal   = {Structure (London, England : 1993)},
  title     = {Implications for switching restriction enzyme specificities from the structure of BstYI bound to a BglII DNA sequence.},
  year      = {2005},
  pages     = {791--801},
  volume    = {13},
  abstract  = {The type II restriction endonuclease BstYI recognizes the degenerate sequence 5'-RGATCY-3' (where R = A/G and Y = C/T), which overlaps with both BamHI (GGATCC) and BglII (AGATCT), and thus raises the question of whether BstYI DNA recognition will be more BamHI-like or BglII-like. We present here the structure of BstYI bound to a cognate DNA sequence (AGATCT). We find the complex to be more BglII-like with similarities mapping to DNA conformation, domain organization, and residues involved in catalysis. However, BstYI is unique in containing an extended arm subdomain, and the mechanism of DNA capture has both BglII-like and BamHI-like elements. Further, DNA recognition is more minimal than BglII and BamHI, where only two residues mediate recognition of the entire core sequence. Taken together, the structure reveals a mechanism of degenerate DNA recognition and offers insights into the possibilities and limitations in altering specificities of closely related restriction enzymes.},
  file      = {:by-author/T/Townson/2005_Townson_791.pdf:PDF},
  keywords  = {Struct; TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Trabi2002,
  author    = {Manuela Trabi and David J. Craik},
  journal   = {TRENDS in Biochemical Sciences},
  title     = {Circular proteins – no end in sight},
  year      = {2002},
  pages     = {132--138},
  volume    = {27},
  file      = {Trabi_TIBS_2002_132.pdf:by-author/T/Trabi/XXXX_Trabi_2002.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Trakselis2001,
  author    = {Trakselis, M. A. and Mayer, M. U. and Ishmael, F. T. and Roccasecca, R. M. and Benkovic, S. J.},
  journal   = {Trends in biochemical sciences},
  title     = {Dynamic protein interactions in the bacteriophage T4 replisome.},
  year      = {2001},
  pages     = {566--72},
  volume    = {26},
  abstract  = {The bacteriophage T4 DNA replisome is a complex dynamic system employing a variety of proteins to orchestrate the synthesis of DNA on both the leading and lagging strands. Assembly of the protein complexes responsible for DNA synthesis and priming requires the coordination of transient biomolecular interactions. This interplay of proteins has been dissected through the use of small molecules including fluorescent probes and crosslinkers, enabling the development of a complex dynamic structural and kinetic model for DNA polymerase holoenzyme assembly and primosome formation.},
  file      = {:by-author/T/Trakselis/2001_Trakselis_566.pdf:PDF},
  keywords  = {Replisoma; {gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Trakselis2003,
  author    = {Trakselis, Michael A. and Roccasecca, Rosa Maria and Yang, Jingsong and Valentine, Ann M. and Benkovic, Stephen J.},
  journal   = {The Journal of biological chemistry},
  title     = {Dissociative properties of the proteins within the bacteriophage T4 replisome.},
  year      = {2003},
  pages     = {49839--49},
  volume    = {278},
  abstract  = {DNA replication is a highly processive and efficient process that involves the coordination of at least eight proteins to form the replisome in bacteriophage T4. Replication of DNA occurs in the 5' to 3' direction resulting in continuous replication on the leading strand and discontinuous replication on the lagging strand. A key question is how a continuous and discontinuous replication process is coordinated. One solution is to avoid having the completion of one Okazaki fragment to signal the start of the next but instead to have a key step such as priming proceed in parallel to lagging strand replication. Such a mechanism requires protein elements of the replisome to readily dissociate during the replication process. Protein trapping experiments were performed to test for dissociation of the clamp loader and primase from an active replisome in vitro whose template was both a small synthetic DNA minicircle and a larger DNA substrate. The primase, clamp, and clamp loader are found to dissociate from the replisome and are continuously recruited from solution. The effect of varying protein concentrations (dilution) on the size of Okazaki fragments supported the protein trapping results. These findings are in accord with previous results for the accessory proteins but, importantly now, identify the primase as dissociating from an active replisome. The recruitment of the primase from solution during DNA synthesis has also been found for Escherichia coli but not bacteriophage T7. The implications of these results for RNA priming and extension during the repetitive synthesis of Okazaki fragments are discussed.},
  file      = {:by-author/T/Trakselis/2003_Trakselis_49839.pdf:PDF},
  keywords  = {Replisoma; {gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Trauner2012,
  author    = {Trauner, Dirk},
  journal   = {Beilstein Journal of Organic Chemistry},
  title     = {Molecular switches and cages},
  year      = {2012},
  issn      = {1860-5397},
  pages     = {870--871},
  volume    = {8},
  doi       = {10.3762/bjoc.8.97},
  file      = {Trauner - 2012 - Molecular switches and cages.pdf:by-author/T/Trauner/2012_Trauner_870.pdf:application/pdf},
  groups    = {sg/chemical},
  language  = {en},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://www.beilstein-journals.org/bjoc/content/8/1/97},
  urldate   = {2015-10-09},
}

@Presentation{Trewhella2010,
  author    = {Trewhella, Jill},
  title     = {Complementary use of {SAXS} and {SANS}},
  year      = {2010},
  file      = {:by-author/T/Trewhella/2010_Trewhella_slides.pdf:PDF},
  keywords  = {SAXS},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Trifonov2002,
  author    = {A. Trifonov and Björk and J. Söderholm and T. Tsegaye},
  journal   = {Eur. Phys. J. D},
  title     = {Comprehensive experimental test of quantum erasure},
  year      = {2002},
  pages     = {251--258},
  volume    = {18},
  abstract  = {In an interferometer, path information and interference visibility are incompatible quantities. Complete determination of the path will exclude any possibility of interference, rendering zero visibility. However, it is, under certain conditions, possible to trade the path information for improved (conditioned) visibility. This procedure is called quantum erasure. We have performed such experiments with polarization-entangled photon pairs. Using a partial polarizer, we could vary the degree of entanglement between the object and the probe. We could also vary the interferometer splitting ratio and thereby vary the a priori path predictability. This allowed us to test quantum erasure under a number of different experimental conditions. All experiments were in good agreement with theory.},
  doi       = {10.1140/epjd/e20020030},
  file      = {2002_Trifonov_251.pdf:by-author/T/Trifonov/2002_Trifonov_251.pdf:PDF},
  keywords  = {Quantum Erasure; Quantum Mechanics (QM); Wave Particle Duality},
  owner     = {saulius},
  timestamp = {2012.11.02},
  creationdate = {2012-11-02T00:00:00},
  url       = {http://epjd.epj.org/index.php?option=com_article&access=standard&Itemid=129&url=/articles/epjd/ref/2002/02/d01180/d01180.html},
}

@Article{Tripp2001,
  author    = {Tripp, B C and Smith, K and Ferry, J G},
  journal   = {The Journal of biological chemistry},
  title     = {Carbonic anhydrase: new insights for an ancient enzyme.},
  year      = {2001},
  pages     = {48615--8},
  volume    = {276},
  file      = {Tripp_2001_48615.pdf:by-author/T/Tripp/2001_Tripp_48615.pdf:PDF},
  groups    = {sg/reviews},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Tronrud2010,
  author    = {Tronrud},
  journal   = {Acta Crystallographica Section D},
  title     = {Using a Conformation-dependent Stereochemical Library Improves Crystallographic Refinement of Proteins},
  year      = {2010},
  pages     = {834},
  volume    = {66},
  file      = {:by-author/T/Tronrud/2010_Tronrud_834.pdf:PDF},
  keywords  = {X-ray Crystallography},
  owner     = {andrius},
  timestamp = {2012.05.07},
  creationdate = {2012-05-07T00:00:00},
}

@Article{Tronrud2004,
  author    = {Tronrud, Dale E.},
  journal   = {Acta Crystallographica Section D},
  title     = {Introduction to macromolecular refinement},
  year      = {2004},
  pages     = {2156--2168},
  volume    = {60},
  doi       = {10.1107/S090744490402356X},
  file      = {ba5072.pdf:by-author/T/Tronrud/2004_Tronrud_2156.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S090744490402356X},
}

@Manuscript{Trosset1997,
  author    = {Michael W. Trosset},
  title     = {Distance Matrix Completion by Numerical Optimization},
  year      = {1997},
  month     = {June},
  file      = {:by-author/T/Trosset/1997_Trosset.ps:PostScript;:by-author/T/Trosset/1997_Trosset.pdf:PDF},
  owner     = {saulius},
  timestamp = {2015.02.27},
  creationdate = {2015-02-27T00:00:00},
}

@Article{Trueblood1996,
  author    = {Trueblood, K. N. and B{\"{u}}rgi, H.-B. and Burzlaff, H. and Dunitz, J. D. and Gramaccioli, C. M. and Schulz, H. H. and Shmueli, U. and Abrahams, S. C.},
  journal   = {Acta Crystallographica Section A},
  title     = {Atomic Dispacement Parameter Nomenclature. Report of a Subcommittee on Atomic Displacement Parameter Nomenclature},
  year      = {1996},
  pages     = {770--781},
  volume    = {52},
  abstract  = {Modern X-ray and neutron diffraction techniques can give precise parameters that describe dynamic or static displacements of atoms in crystals. However, confusing and inconsistent terms and symbols for these quanti- ties occur in the crystallographic literature. This report discusses various forms of these quantities, derived from probability density functions and based on Bragg diffraction data, both when the Gaussian approxima- tion is appropriate and when it is not. The focus is especially on individual atomic anisotropic displacement parameters (ADPs), which may represent atomic motion and possible static displacive disorder. The first of the four sections gives background information, including definitions. The second concerns the kinds of parameter describing atomic displacements that have most often been used in crystal structure analysis and hence are most commonly found in the literature on the subject. It includes a discussion of graphical representations of the Gaussian mean-square displacement matrix. The third section considers the expressions used when the Gauss- Jan approximation is not adequate. The final section gives recommendations for symbols and nomenclature.},
  doi       = {10.1107/S0108767396005697},
  file      = {:by-author/T/Trueblood/1996_Trueblood_770.pdf:PDF},
  owner     = {alexey},
  timestamp = {2014.04.16},
  creationdate = {2014-04-16T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0108767396005697},
}

@Article{Truflandier2010,
  author    = {Truflandier, Lionel A. and Boucher, Florent and Payen, Christophe and Hajjar, Redouane and Millot, Yannick and Bonhomme, Christian and Steunou, Nathalie},
  journal   = {Journal of the American Chemical Society},
  title     = {DFT-NMR Investigation and 51V 3QMAS Experiments for Probing Surface OH Ligands and the Hydrogen-Bond Network in a Polyoxovanadate Cluster: The Case of Cs4[H2V10O28]·4H2O},
  year      = {2010},
  pages     = {4653--4668},
  volume    = {132},
  abstract  = {This work shows that the combination of first-principles calculations and 51V NMR experiments is a powerful tool to elucidate the location of surface hydroxyl groups and to precisely describe the hydrogen bond network in the complex decavanadate cluster Cs4[H2V10O28].4H2O, enhancing the strength of NMR crystallography. The detailed characterization of H-bond networks for these kinds of inorganic compounds is of primary importance and should benefit from the DFT-NMR predictions by considering explicitly the periodic boundary conditions. The determination of the Cs4[H2V10O28]·4H2O structure by single-crystal X-ray diffraction was not sufficiently accurate to provide the location of protons. From available diffraction data, five different protonated model structures have been built and optimized using DFT-based methods. The possible interconversion of two decavanadate isomers through a proton exchange is evaluated by calculating the energy barrier and recording variable-temperature 1H MAS NMR spectra. First-principles calculations of 51V NMR parameters clearly indicate that these parameters are very sensitive to the local intermolecular hydrogen-bonding interactions. Considering the DFT error limits, the fairly good agreement between calculated and experimental NMR parameters arising from the statistical modeling of the data allows the unambiguous assignment of the five 51V NMR signals and, thus, the location of OH surface ligands in the decavanadate cluster. In particular, first-principles calculations accurately reproduce the 51V quadrupolar parameters. These results are fully consistent with 51V 3QMAS NMR spectra recorded with and without 1H decoupling. Finally, correlations are established between local octahedral VO6 deformations and 51V NMR parameters (Cq and Δδ), which will be useful for the characterization of a wide range of chemical species containing vanadium(V).},
  doi       = {10.1021/ja908973y},
  eprint    = {http://pubs.acs.org/doi/pdf/10.1021/ja908973y},
  file      = {2010_Truflandier_4653.pdf:by-author/T/Truflandier/2010_Truflandier_4653.pdf:PDF;2010_Truflandier_4653suppl.pdf:by-author/T/Truflandier/2010_Truflandier_4653suppl.pdf:PDF},
  keywords  = {Computational Chemistry; Density Functional Theory (DFT); NMR; Quantum Chemistry},
  owner     = {saulius},
  timestamp = {2014.07.22},
  creationdate = {2014-07-22T00:00:00},
  url       = {http://pubs.acs.org/doi/abs/10.1021/ja908973y},
}

@Article{Tryon1973,
  author    = {Edward P. Tryon},
  journal   = {Nature},
  title     = {Is the Universe a Vacuum Fluctuation?},
  year      = {1973},
  pages     = {396--397},
  volume    = {246},
  file      = {1973_Tryon_396.pdf:by-author/T/Tryon/1973_Tryon_396.pdf:PDF},
  owner     = {saulius},
  timestamp = {2015.05.27},
  creationdate = {2015-05-27T00:00:00},
}

@TechReport{Tsao1993,
  author      = {A. Tsao and T. Turnbull},
  institution = {Supercomputing Research Center, 17100 Science Drive, Bowie, MD 20715-4300},
  title       = {A Comparison of Algorithms for Banded Matrix Multiplication},
  year        = {1993},
  abstract    = {We present and compare several methods for multiplying banded square matrices. Various storage schemes and their implementations are discussed. Of particular interest is an algorithm for multiplying matrices by diagonals, which always references contiguous matrix elements. Two blocked implementations also are presented. These specialized routines are attractive for multiplying matrices whose bandwidths are known to be small relative to the size of the matrices. Results from tests performed on a Cray-2, Cray Y-MP, and RS/6000 are given. It is shown that, for specialized applications, a substantial savings can be realized over the standard three-loop multiplication algorithm.},
  file        = {:by-author/T/Tsao/1993_Tsao.ps:PostScript;:by-author/T/Tsao/1993_Tsao.pdf:PDF},
  keywords    = {Bamded Matrices; Computer Science (CS); Linear Algebra; Matrix Multiplication},
  owner       = {saulius},
  timestamp = {2015.02.27},
  creationdate = {2015-02-27T00:00:00},
}

@Article{Tsao2005,
  author    = {Tsao, Meng-Lin and Tian, Feng and Schultz, Peter G.},
  journal   = {Chembiochem: a European Journal of Chemical Biology},
  title     = {Selective Staudinger modification of proteins containing p-azidophenylalanine.},
  year      = {2005},
  pages     = {2147--9},
  volume    = {6},
  file      = {:by-author/T/Tsao/2005_Tsao_2147.pdf:PDF},
  keywords  = {Bioconjugation},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@InProceedings{Tschantz2005,
  author    = {Matthew S. Tschantz and Michael D. Ernst},
  booktitle = {OOPSLA’05},
  title     = {Javari: Adding Reference Immutability to Java},
  year      = {2005},
  pages     = {211--230},
  abstract  = {This paper describes a type system that is capable of ex- pressing and enforcing immutability constraints. The spe- cific constraint expressed is that the abstract state of the object to which an immutable reference refers cannot be modified using that reference. The abstract state is (part of) the transitively reachable state: that is, the state of the object and all state reachable from it by following references. The type system permits explicitly excluding fields from the abstract state of an object. For a statically type-safe lan- guage, the type system guarantees reference immutability. If the language is extended with immutability downcasts, then run-time checks enforce the reference immutability constraints. This research builds upon previous research in language support for reference immutability. Improvements that are new in this paper include distinguishing the notions of as- signability and mutability; integration with Java 5’s generic types and with multi-dimensional arrays; a mutability poly- morphism approach to avoiding code duplication; type-safe support for reflection and serialization; and formal type rules and type soundness proof for a core calculus. Furthermore, it retains the valuable features of the previous dialect, in- cluding usability by humans (as evidenced by experience with 160,000 lines of Javari code) and interoperability with Java and existing JVMs.},
  file      = {:by-author/T/Tschantz/2005_Tschantz_OOPSLA.pdf:PDF},
  keywords  = {Computer Science (CS); Type Systems},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Tseng2000,
  author    = {Tseng, T. Y. and Frick, D. N. and Richardson, C. C.},
  journal   = {Biochemistry},
  title     = {Characterization of a novel DNA primase from the Salmonella typhimurium bacteriophage SP6.},
  year      = {2000},
  pages     = {1643--54},
  volume    = {39},
  abstract  = {The gene for the DNA primase encoded by Salmonella typhimurium bacteriophage SP6 has been cloned and expressed in Escherichia coli and its 74-kDa protein product purified to homogeneity. The SP6 primase is a DNA-dependent RNA polymerase that synthesizes short oligoribonucleotides containing each of the four canonical ribonucleotides. GTP and CTP are both required for the initiation of oligoribonucleotide synthesis. In reactions containing only GTP and CTP, SP6 primase incorporates GTP at the 5'-end of oligoribonucleotides and CMP at the second position. On synthetic DNA templates, pppGpC dinucleotides are synthesized most rapidly in the presence of the sequence 5'-GCA-3'. This trinucleotide sequence, containing a cryptic dA at the 3'-end, differs from other known bacterial and phage primase recognition sites. SP6 primase shares some properties with the well-characterized E. colibacteriophage T7 primase. The T7 DNA polymerase can use oligoribonucleotides synthesized by SP6 primase as primers for DNA synthesis. However, oligoribonucleotide synthesis by SP6 primase is not stimulated by either the E. coli- or the T7-encoded ssDNA binding protein. An amino acid sequence alignment of the SP6 and T7 primases, which share only 22.4% amino acid identity, indicates amino acids likely critical for oligoribonucleotide synthesis as well as a putative Cys(3)His zinc finger motif that may be involved in DNA binding.},
  file      = {:by-author/T/Tseng/2000_Tseng_1643.pdf:PDF},
  keywords  = {Primase; {gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Manuscript{TseytlinXXXX,
  author    = {Eugene Tseytlin and Shi-Kuo Chang},
  title     = {A Visual Shell Scripting Tool},
  year      = {XXXX},
  keywords  = {Computer Science (CS); Visual Programming},
  file      = {:by-author/T/Tseytlin/XXXX_Tseytlin.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Manual{Tubert-Brohman2009,
  title     = {Chemistry::Ring::Find - Find the rings (cycles) in a molecule. Note on Figueras, J. Ring perception using breadth-first search. J. Chem. Inf. Comput. Sci. 1996, 36, 986-991},
  author    = {Ivan Tubert-Brohman},
  year      = {2009},
  file      = {2009_Tubert-Brohman.txt:by-author/T/Tubert-Brohman/2009_Tubert-Brohman.txt:Text},
  keywords  = {Computational Chemistry; Perl; Ring Perception; SSSR},
  owner     = {saulius},
  timestamp = {2015.03.10},
  creationdate = {2015-03-10T00:00:00},
  url       = {http://search.cpan.org/~itub/Chemistry-Ring-0.20/lib/Chemistry/Ring/Find.pm},
}

@Article{Tumkevicius2003,
  author    = {Sigitas Tumkevicius and Linas Labanauskas and Virginija Bucinskaite and Algirdas Brukstus and Gintaras Urbelis},
  journal   = {Tetrahedron Letters},
  title     = {Synthesis and structure of benzimidazo[1,2-c][1,2,3]thiadiazoles: first examples of a novel ring system},
  year      = {2003},
  month     = {Aug},
  note      = {Virginija Bucinskaite-Dudutienė},
  number    = {35},
  pages     = {6635--6638},
  volume    = {44},
  abstract  = {(1-Amino-1H-benzimidazol-2-yl)methanol 1 with thionyl chloride at reflux afforded 3-chlorobenzimidazo[1,2-c][1,2,3]thiadiazole 4, which reacted with various nucleophiles to give different products depending on the nature of the solvent. The structures of 4 and di(benzimidazo[1,2-c][1,2,3]thiadiazol-3-yl)sulfide 8 were confirmed by single-crystal X-ray analysis.},
  doi       = {10.1016/S0040-4039(03)01672-1},
  file      = {2003_Tumkevicius_6635.pdf:by-author/T/Tumkevicius/2003_Tumkevicius_6635.pdf:PDF},
  groups    = {sg/inhibitors},
  keywords  = {Carbonic Anhydrases; Inhibitors},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/S0040403903016721},
}

@Article{Turing1937,
  author    = {A. M. Turing},
  journal   = {J. Symb. Log.},
  title     = {Computability and $\lambda$-definability.},
  year      = {1937},
  issn      = {0022-4812; 1943-5886/e},
  pages     = {153--163},
  volume    = {2},
  doi       = {10.2307/2268280},
  file      = {1937_Turing_153.pdf:by-author/T/Turing/1937_Turing_153.pdf:PDF},
  fjournal  = {The Journal of Symbolic Logic},
  keywords  = {Computability; Foundations of Mathematics; Lambda-calculus},
  language  = {English},
  owner     = {saulius},
  publisher = {Cambridge University Press, West Nyack, NY; Association for Symbolic Logic (ASL), Poughkeepsie, NY},
  timestamp = {2016.11.11},
  creationdate = {2016-11-11T00:00:00},
  zbl       = {63.0824.03},
}

@Article{Turner2014,
  author    = {Turner, Michael and Jiao, Alan and Slack, Frank J.},
  journal   = {Cell Cycle},
  title     = {Autoregulation of lin-4 microRNA transcription by RNA activation (RNAa) in C. elegans},
  year      = {2014},
  issn      = {1551-4005},
  month     = {Jan},
  number    = {5},
  pages     = {772–781},
  volume    = {13},
  doi       = {10.4161/cc.27679},
  file      = {2014_Turner_772.pdf:by-author/T/Turner/2014_Turner_772.pdf:PDF},
  groups    = {am/RNA activation},
  owner     = {andrius},
  publisher = {Informa UK Limited},
  timestamp = {2016.09.10},
  creationdate = {2016-09-10T00:00:00},
  url       = {http://dx.doi.org/10.4161/cc.27679},
}

@Article{Turner2002,
  author    = {Trevor Turner},
  journal   = {BMJ},
  title     = {Is mass dysmorphophobia a better term?},
  year      = {2002},
  pages     = {672},
  volume    = {324},
  doi       = {10.1136/bmj.324.7338.679/a},
  file      = {2002_Turner_672.pdf:by-author/T/Turner/2002_Turner_672.pdf:PDF},
  keywords  = {Redisorganisation},
  owner     = {saulius},
  timestamp = {2016.05.14},
  creationdate = {2016-05-14T00:00:00},
}

@Presentation{Turner2010,
  author       = {William J. Turner},
  title        = {Exact Arithmetic on a Computer: Symbolic Computation and Computer Algebra},
  year         = {2010},
  organization = {Department of Mathematics \& Computer Science, Wabash College},
  file         = {2010_Turner.pdf:by-author/T/Turner/2010_Turner.pdf:PDF},
  keywords     = {Compuer Algebra; Computer Science (CS); Exact Computations},
  month        = {September},
  owner        = {saulius},
  timestamp = {2016.06.13},
  creationdate = {2016-06-13T00:00:00},
  url          = {http://persweb.wabash.edu/facstaff/turnerw/presentations/colloquium-2010-handout.pdf},
}

@MastersThesis{Turnovsky2004,
  author    = {Petra Turnovsky},
  school    = {Donau-Universität Krems},
  title     = {Die Open Access – Bewegung und ihre Rezeption an wissenschaftlichen Bibliotheken in Österreich},
  year      = {2004},
  abstract  = {As a reaction to the serials crisis a movement has formed, which aims at open and charge free access to scientific literature in the internet. Open Access can be achieved by selfarchiving or by open access journals, which are financed by author payments. This master thesis provides a survey about the current state of the art of the movement, about the different conditions in the scientific disciplines and the networked initiatives. The situation is considered from the libraries’ point of view. The instruments for retrieval were identified as a week point. An additional obstacle for Open Access is the importance of the citation rate when scientific publications are evaluated. Due to the installation of e-print-servers a new assignment for libraries has developed. The evaluation of the websites of scientific libraries in Austria shows that the Open Access movement has not met much notice in Austria so far. The websites of several libraries in Germany, Switzerland and anglophone countries are used as comparisons. Consequential suggestions for dealing with Open Access in libraries were derivated.},
  file      = {:by-author/T/Turnovsky/2004_Turnovsky_dissertation.pdf:PDF},
  owner     = {saulius},
  pages     = {dissertation},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Tuschl1994,
  author    = {Tuschl, T and Gohlke, C and Jovin, T M and Westhof, E and Eckstein, F},
  journal   = {Science (New York, N.Y.)},
  title     = {A three-dimensional model for the hammerhead ribozyme based on fluorescence measurements.},
  year      = {1994},
  pages     = {785--9},
  volume    = {266},
  file      = {1994_Tuschl_785.pdf:by-author/T/Tuschl/1994_Tuschl_785.pdf:PDF},
  keywords  = {Ribozymes},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Tuyl2009,
  author    = {Tuyl},
  journal   = {Bayesian Analysis},
  title     = {Posterior predictive arguments in favor of the Bayes-Laplace prior as the consensus prior for binomial and multinomial parameters},
  year      = {2009},
  pages     = {151--158},
  volume    = {4},
  abstract  = {It is argued that the posterior predictive distribution for the binomial and multinomial distributions, when viewed via a hypergeometric-like representation, suggests the uniform prior on the parameters for these models. The argument is supported by studying variations on an example by Fisher, and complements Bayes' original argument for a uniform prior predictive distribution for the binomial. The fact that both arguments lead to invariance under transformation is also discussed.},
  doi       = {10.1214/09-BA405},
  file      = {:by-author/T/Tuyl/2009_Tuyl_151.pdf:PDF},
  groups    = {sg/Bayesian},
  keywords  = {Bayesian Inference; Bayesian Statistics; Binomial Distribution; Invariance; Jeffreys Prior; Mathematics; Noninformative Priors},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Tzeng1991,
  author    = {Tzeng, Chun-Hung},
  journal   = {Annals of Mathematics and Artificial Intelligence},
  title     = {A mathematical formulation of uncertain information},
  year      = {1991},
  issn      = {1012-2443, 1573-7470},
  pages     = {69--87},
  volume    = {4},
  abstract  = {This paper introduces a mathematical model of uncertain information. Each body of uncertain information is an information quadruplet, consisting of a code space, a message space, an interpretation function, and an evidence space. Each information quadruplet contains prior information as well as possible new evidence which may appear later. The definitions of basic probability and belief function are based on the prior information. Given new evidence, Bayes' rule is used to update the prior information. This paper also introduces an idea of independent information and its combination. A combination formula is derived for combining independent information. Both the conventional Bayesian approach and Dempster-Shafer's approach belong to this mathematical model. A Bayesian prior probability measure is the prior information of a special information quadruplet; Bayesian conditioning is the combination of special independent information. A Dempster's belief function is the belief function of a different information quadruplet; the Dempster combination rule is the combination rule of independent quadruplets. This paper is a mathematical study of handling uncertainty and shows that both the conventional Bayesian approach and Dempster-Shafer's approach originate from the same mathematical theory.},
  doi       = {10.1007/BF01531173},
  file      = {Tzeng - 1991 - A mathematical formulation of uncertain informatio.pdf:by-author/T/Tzeng/1991_Tzeng_69.pdf:application/pdf;Snapshot:by-author/T/Tzeng/1991_Tzeng_69.html:text/html},
  groups    = {sg/Probability theory, sg/Bayesian},
  keywords  = {Artificial Intelligence (incl. Robotics); Chaos; Complex Systems; Computer Science (CS); General; Mathematics; Neural Networks (NN); Nonlinear Dynamics},
  language  = {en},
  owner     = {saulius},
  timestamp = {2015.12.07},
  creationdate = {2015-12-07T00:00:00},
  url       = {http://link.springer.com/article/10.1007/BF01531173},
  urldate   = {2015-12-07},
}

@Webpage{UCL1996,
  author    = {UCL},
  retrieved = {2008-07-28},
  title     = {Statistical Science: Abstracts of research reports - 1996},
  url       = {http://www.ucl.ac.uk/Stats/research/Resrprts/abs96.html},
  year      = {1996},
  file      = {:by-author/U/UCL/1996_UCL.war:},
  groups    = {sg/Bayesian},
  keywords  = {Bayesian Statistics; Mathematics},
  owner     = {saulius},
  timestamp = {2015.03.02},
  creationdate = {2015-03-02T00:00:00},
}

@Article{Uekusa1992,
  author    = {Uekusa, H. and Ohba, S. and Tokii, T. and Muto, Y. and Kato, M. and Husebye, S. and Steward, O. W. and Chang, S.-C. and Rose, J. P. and Pletcher, J. F. and Suzuki, I.},
  journal   = {Acta Crystallographica Section B},
  title     = {Magneto-structural corrections of dimeric copper(II) trichloroacetates},
  year      = {1992},
  pages     = {650--667},
  volume    = {48},
  doi       = {10.1107/S0108768192002908},
  file      = {:by-author/U/Uekusa/1992_Uekusa_650.pdf:PDF},
  owner     = {antanas},
  timestamp = {2013.04.11},
  creationdate = {2013-04-11T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0108768192002908},
}

@Article{Uesugi2005,
  author    = {Uesugi, Yoshiko and Mori, Koichi and Arima, Jiro and Iwabuchi, Masaki and Hatanaka, Tadashi},
  journal   = {The Journal of biological chemistry},
  title     = {Recognition of phospholipids in Streptomyces phospholipase D.},
  year      = {2005},
  pages     = {26143--51},
  volume    = {280},
  abstract  = {To investigate the contribution of amino acid residues to the enzyme reaction of Streptomyces phospholipase D (PLD), we constructed a chimeric gene library between two highly homologous plds, which indicated different activity in transphosphatidylation, using RIBS (repeat-length independent and broad spectrum) in vivo DNA shuffling. By comparing the activities of chimeras, six candidate residues related to transphosphatidylation activity were shown. Based on the above result, we constructed several mutants to identify the key residues involved in the recognition of phospholipids. By kinetic analysis, we identified that Gly188 and Asp191 of PLD from Streptomyces septatus TH-2, which are not present in the highly conserved catalytic HXKXXXXD (HKD) motifs, are key amino acid residues related to the transphosphatidylation activity. To investigate the role of two residues in the recognition of phospholipids, the effects of these residues on binding to substrates were analyzed by surface plasmon spectroscopy. The result suggests that Gly188 and Asp191 are involved in the recognition of phospholipids in correlation with the N-terminal HKD motif. Furthermore, this study also provides experimental evidence that the N-terminal HKD motif contains the catalytic nucleophile, which attacks the phosphatidyl group of the substrate.},
  file      = {Uesugi_2005_26143-PLD-chimeras.pdf:by-author/U/Uesugi/2005_Uesugi_26143.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@TechReport{Uffink1997,
  author      = {Jos Uffink},
  institution = {Institute for History and Foundations of Science, Utrecht University (NL)},
  title       = {Can the maximum entropy principle be explained as a consistency requirement?},
  year        = {1997},
  abstract    = {The principle of maximum entropy is a general method to assign values to probability distributions on the basis of partial information. This principle, introduced by Jaynes in 1957, forms an extension of the classical principle of insufficient reason. It has been further generalized, both in mathematical formulation and in intended scope, into the principle of maximum relative entropy or of minimum information. It has been claimed that these principles are singled out as unique methods of statistical inference that agree with certain compelling consistency requirements. This paper reviews these consistency arguments and the surrounding controversy. It is shown that the uniqueness proofs are flawed, or rest on unreasonably strong assumptions. A more general class of inference rules, maximizing the so-called Rényi entropies, is exhibited which also fulfill the reasonable part of the consistency assumptions.},
  file        = {PS:by-author/U/Uffink/1997_Uffink.ps.gz:PostScript;1997_Uffink.pdf:by-author/U/Uffink/1997_Uffink.pdf:PDF},
  groups      = {sg/Bayesian},
  keywords    = {Bayesian Statistics},
  owner       = {saulius},
  timestamp = {2012.10.04},
  creationdate = {2012-10-04T00:00:00},
  url         = {http://www.phys.uu.nl/~wwwgrnsl/jos/mepabst/mepabst.html},
}

@TechReport{Uffink1997a,
  author      = {Jos Uffink},
  institution = {Institute for History and Foundations of Science, Utrecht University (NL)},
  title       = {The constraint rule of the maximum entropy principle},
  year        = {1997},
  month       = {feb},
  abstract    = {The principle of maximum entropy is a method for assigning values to probability distributions on the basis of partial information. In usual formulations of this and related methods of inference one assumes that this partial information takes the form of a constraint on allowed probability distributions. In practical applications, however, the information consists of empirical data. A constraint rule is then employed to these data. Usually one adopts the rule to equate the expectation values of certain functions with their empirical averages. There are, however, various other ways in which one can construct constraints from empirical data, which makes the maximum entropy principle lead to very different probability assignments. This paper shows that an argument by Jaynes to justify the usual constraint rule is unsatisfactory and investigates several alternative choices. The choice of a constraint rule is also shown to be of crucial importance to the debate on the question whether there is a conflict between the methods of inference based on maximum entropy and Bayesian conditionalization.},
  file        = {PS:by-author/U/Uffink/1997_Uffink_tr2.ps.gz:PostScript;1997_Uffink_tr2.pdf:by-author/U/Uffink/1997_Uffink_tr2.pdf:PDF},
  groups      = {sg/Bayesian},
  keywords    = {Bayesian Statistics; Maximum Emtropy},
  owner       = {saulius},
  timestamp = {2012.10.04},
  creationdate = {2012-10-04T00:00:00},
  url         = {http://www.projects.science.uu.nl/igg/jos/mep2def/mep2def.html},
}

@TechReport{UKRDS2007,
  author      = {UKRDS},
  institution = {UKRDS},
  title       = {The data imperative: Managing the UK’s research data for future use},
  year        = {2007},
  file        = {:by-author/u/ukrds/2007_ukrds.pdf:PDF},
  keywords    = {Data Management; Preservation},
  owner       = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Ullmann1976,
  author    = {Ullmann, J. R.},
  journal   = {J. ACM},
  title     = {An Algorithm for Subgraph Isomorphism},
  year      = {1976},
  pages     = {31--42},
  volume    = {23},
  abstract  = {Subgraph isomorphism can be determined by means of a brute-force tree-search enumeration procedure. In this paper a new algorithm is introduced that attains efficiencyby inferentially eliminatingsuccessor nodes in the tree search. To assess the time actually taken by the new algomthm, subgraph isomorphism, chque detection, graph isomorphism, and directed graph isomorphism ex- periments have been carried out with random and with various nonrandom graphs. A parallel asynchronous logic-in-memory implementation of a vital part of the algorithm is also described, although this hardware has not actually been bmlt The hardware implementation would allow very rapid determination of isomorphism.},
  doi       = {10.1145/321921.321925},
  file      = {:by-author/U/Ullmann/1976_Ullmann_31.pdf:PDF},
  keywords  = {Chemical Graph Matching},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
  url       = {http://doi.acm.org/10.1145/321921.321925},
}

@Article{Ulmasov2000,
  author    = {Ulmasov, B and Waheed, A and Shah, G N and Grubb, J H and Sly, W S and Tu, C and Silverman, D N},
  journal   = {Proceedings of the National Academy of Sciences of the United States of America},
  title     = {Purification and kinetic analysis of recombinant CA XII, a membrane carbonic anhydrase overexpressed in certain cancers.},
  year      = {2000},
  pages     = {14212--7},
  volume    = {97},
  abstract  = {Carbonic anhydrase XII (CA XII) is a transmembrane glycoprotein with an active extracellular CA domain that is overexpressed on cell surfaces of certain cancers. Its expression has been linked to tumor invasiveness. To characterize its catalytic properties, we purified recombinant secretory forms of wild-type and mutant CA XIIs. The catalytic properties of these enzymes in the hydration of CO(2) were measured at steady state by stopped-flow spectrophotometry and at chemical equilibrium by the exchange of (18)O between CO(2) and water determined by mass spectrometry. The catalysis of CO(2) hydration by soluble CA XII has a maximal value of k(cat)/K(m) at 34 microM(-1) small middle dots(-1), which is similar to those of the membrane-associated CA IV and to soluble CA I. The pH profiles of this catalysis and the catalyzed hydrolysis of 4-nitrophenylacetate indicate that the pK(a) of the zinc-bound water in CA XII is 7.1. His64 in CA XII acts as a proton shuttle residue, as evidenced by the reduced rate constant for proton transfer in the mutants containing the replacements His64 --&gt; Ala and His64 --&gt; Arg, as well as by the selective inhibition of the proton transfer step by cupric ions in wild-type CA XII. The catalytic rate of CO(2) hydration by the soluble form of CA XII is identical with that of the membrane-bound enzyme. These observations suggest a role for CA XII in CO(2)/HCO(3)(-) homeostasis in cells in which it is normally expressed. They are also compatible with a role for CA XII in acidifying the microenvironment of cancer cells in which CA XII is overexpressed, providing a mechanism for CA XII to augment tumor invasiveness and suggesting CA XII as a potential target for chemotherapeutic agents.},
  file      = {2000_Ulmasov_14212.pdf:by-author/U/Ulmasov/2000_Ulmasov_14212.pdf:PDF},
  groups    = {sg/cancer, sg/hCA12},
  keywords  = {CA12; Carbonic Anhydrases},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Ulmasov1997b,
  author      = {T. Ulmasov and G. Hagen and T. J. Guilfoyle},
  journal     = {Science},
  title       = {ARF1, a transcription factor that binds to auxin response elements.},
  year        = {1997},
  pages       = {1865--1868},
  volume      = {276},
  abstract    = {The plant hormone auxin regulates plant physiology by modulating the interaction of transcription factors with auxin response elements (AuxREs) of the affected genes. A transcription factor, Auxin Response Factor 1 (ARF1), that binds to the sequence TGTCTC in AuxREs was cloned from Arabidopsis by using a yeast one-hybrid system. ARF1 has an amino-terminal DNA-binding domain related to the carboxyl terminus of the maize transactivator Viviparous-1. Sequence requirements for ARF1 binding in vitro are identical to those that confer auxin responsiveness in vivo. The carboxyl terminus of ARF1 contains two motifs found in the Aux/IAA class of proteins and appears to mediate protein-protein interactions.},
  file        = {:by-author/U/Ulmasov/1997_Ulmasov_1865.pdf:PDF},
  institution = {Department of Biochemistry, University of Missouri, 117 Schweitzer Hall, Columbia, MO 65211, USA.},
  keywords    = {Amino Acid Sequence; Arabidopsis; Arabidopsis Proteins; Base Sequence; Binding Sites; Chemistry/genetics/metabolism; Cloning; DNA; DNA-Binding Proteins; Genes; Genetic; Genetics; Genetics/metabolism; Indoleacetic Acids; Molecular; Molecular Sequence Data; Mutation; Nucleic Acid; Pharmacology; Plant; Plant Proteins; Promoter Regions; Repetitive Sequences; Transcription Factors},
  language    = {eng},
  medline-pst = {ppublish},
  owner       = {em},
  pmid        = {9188533},
  timestamp = {2013.09.04},
  creationdate = {2013-09-04T00:00:00},
}

@MastersThesis{Ulusoy1996,
  author    = {Hasan Ulusoy and Selcuk Senkul},
  title     = {A Constraint System for Solving Alphametic Puzzles \& Paint by Numbers Puzzle},
  year      = {1996},
  month     = {June},
  file      = {:by-author/U/Ulusoy/1996_Ulusoy.pdf:PDF},
  keywords  = {Alphametics; Computer Science (CS)},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Ulyanov1984,
  author      = {N. B. Ulyanov and V. B. Zhurkin},
  journal     = {J Biomol Struct Dyn},
  title       = {Sequence-dependent anisotropic flexibility of B-DNA. A conformational study.},
  year        = {1984},
  month       = {Oct},
  number      = {2},
  pages       = {361--385},
  volume      = {2},
  abstract    = {Bending flexibility of the six tetrameric duplexes was investigated d(AAAA):d(TTTT), d(AATT)2, d(TTAA)2, d(GGGG):d(CCCC), d(GGCC)2 and d(CCGG)2,. The tetramers were extended in the both directions by regular double helices. The stiffness of the B-DNA double helix when bent into the both grooves proved to be less than that in the perpendicular direction by an order of magnitude. Such an anisotropy is a property of the sugar-phosphate backbone structure. The calculated fluctuations of the DNA bending along the dyad axis, 5-7 degree, are in agreement with experimental value of the DNA persistence length. Anisotropy of the double helix is sequence-dependent: most easily bent into the minor groove are the tetramers with purine-pyrimidine dimer (RY) in the middle. In contrast, YR dinucleotides prefer bending into the major groove. Moreover, they have an equilibrium bend of 6-12 degree into this groove. The above inequality is caused by stacking interaction of the bases. The bend in the central dimer is distributed to some extent between the adjacent links, though the main fraction of the bend remains within the central link. Variation of the sugar-phosphate geometry in the bent helix is inessential, so that DNA remains within the B-family of forms: namely, when the helical axis is bent by 20 degree. the backbone dihedral angles vary by no more than 15 degree. The obtained results are in accord with x-ray structure of the B-DNA dodecamer; they further substantiate our early model of DNA wrapping in the nucleosome by means of "mini-kinks" separated by a half-pitch of the double helix, i.e. by 5-6 b.p. Sequence-dependent anisotropy of DNA presumably dictates the three-dimensional structure of DNA in solution as well. We have found that nonrandom allocation of YR dimers leads to the systematic bends in equilibrium structure of certain DNA fragments.},
  file        = {1984_Ulyanov_361.pdf:by-author/U/Ulyanov/1984_Ulyanov_361.pdf:PDF},
  groups      = {sg/applications},
  institution = {Institute of Molecular Biology, Academy of Science of the USSR, Moscow.},
  keywords    = {Algorithms; Base Sequence; DNA; Nucleic Acid Conformation; Nucleosomes; Oligodeoxyribonucleotides; Thermodynamics},
  language    = {eng},
  medline-pst = {ppublish},
  owner       = {em},
  pmid        = {6400941},
  timestamp = {2011.11.25},
  creationdate = {2011-11-25T00:00:00},
}

@Article{Ulyanov1984a,
  author    = {Nikolai B. Ulyanov and Victor B. Zhurkin},
  journal   = {Journal of Biomolecular Structure and Dynamics},
  title     = {Sequence-Dependent Anisotropic Flexibility of {B-DNA}. A Conformational Study},
  year      = {1984},
  pages     = {361--385},
  volume    = {2},
  abstract  = {Bending flexibility of the six tetrameric duplexes was investigated d(AAAA):d(TTTT), d(AATT)2, d(TTAA) 2, d(GGGG):d(CCCC), d(GGCC) 2 and d(CCGG) 2. The tetramers were extended in the both directions by regular double helices. The stiffness of the B-DNA double helix when bent into the both grooves proved to be less than that in the perpendicular direction by an order of magnitude. Such an anisotropy is a property of the sugar-phosphate backbone structure. The calculated fluctuations of the DNA bending along the dyad axis, 5–7°, are in agreement with experimental value of the DNA persistence length. Anisotropy of the double helix is sequence-dependent: most easily bent into the minor groove are the tetramers with purine-pyrimidine dimer (RY) in the middle. In contrast, YR dinucleotides prefer bending into the major groove. Moreover, they have an equilibrium bend of 6–12° into this groove. The above inequality is caused by stacking interaction of the bases. The bend in the central dimer is distributed to some extent between the adjacent links, though the main fraction of the bend remains within the central link. Variation of the sugar-phosphate geometry in the bent helix is inessential, so that DNA remains within the B-family of forms: namely, when the helical axis is bent by 20°, the backbone dihedral angles vary by no more than 15°. The obtained results are in accord with x-ray structure of the B-DNA dodecamer; they further substantiate our early model of DNA wrapping in the nucleosome by means of “mini-kinks” separated by a half-pitch of the double helix, i.e. by 5–6 b.p. Sequence-dependent anisotropy of DNA presumably dictates the three-dimentional structure of DNA in solution as well. We have found that nonrandom allocation of YR dimers leads to the systematic bends in equilibrium structure of certain DNA fragments.},
  doi       = {10.1080/07391102.1984.10507573},
  file      = {1984_Ulyanov_361.pdf:by-author/U/Ulyanov/1984_Ulyanov_361.pdf:PDF},
  groups    = {sg/applications},
  keywords  = {DNA; DNA Bases; DNA Conformation; RY; Readout; Stacking},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://www.tandfonline.com/doi/abs/10.1080/07391102.1984.10507573},
}

@Article{Umeyama1991,
  author           = {Shinji Umeyama},
  journal          = {IEEE Trans. Pattern Anal. Mach. Intell.},
  title            = {Least squares estimation of transformation parameters between two point sets},
  year             = {1991},
  issn             = {0162-8828},
  month            = apr,
  number           = {4},
  pages            = {376--380},
  volume           = {13},
  comment          = {Cited by Chen2004. Same proof for translations as in Horn1987. How does this align with Chen2004, even though they cite Umeyama1991? Contradicts Chen2004?},
  creationdate     = {2012-05-16T00:00:00},
  doi              = {10.1109/34.88573},
  file             = {1991_Umeyama_376.pdf:by-author/U/Umeyama/1991_Umeyama_376.pdf:PDF},
  groups           = {sg/Molecule superposion, sg/Superposition, sg/Bioinf. Algorithms},
  keywords         = {Algorithms; Structure Superposition},
  modificationdate = {2024-05-12T19:10:59},
  owner            = {saulius},
  publisher        = {Institute of Electrical and Electronics Engineers (IEEE)},
  timestamp        = {2012.05.16},
}

@Article{Umezawa2000,
  author    = {Umezawa, Y and Nishio, M},
  journal   = {Bioorganic \&amp; medicinal chemistry},
  title     = {CH/pi interactions in the crystal structure of TATA-box binding protein/DNA complexes.},
  year      = {2000},
  pages     = {2643--50},
  volume    = {8},
  file      = {Umezawa_2000_2643.pdf:by-author/U/Umezawa/2000_Umezawa_2643.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Umezawa1998,
  author    = {Yoji Umezawa and Motohiro Nishio},
  journal   = {Bioorganic \& Medicinal Chemistry},
  title     = {CH/pi interactions as demonstrated in the crystal structure of guanine-nucleotide binding proteins, Src homology-2 domains and human growth hormone in complex with their specific ligands.},
  year      = {1998},
  pages     = {493--504},
  volume    = {6},
  abstract  = {The CH/pi interaction is a weak attractive molecular force occurring between CH groups and pi-systems. Possibility has been examined for the role of CH/pi interaction, by use of a computer program, in the crystallographic data of several guanine-nucleotide binding proteins, src homology-2 domains and human growth hormone complexed with their specific ligands. Short CH/pi contacts have been found in every case where cohesive forces are expected. Comparison of the structures of functionary related proteins has shown that mutation may occur but necessary CH/pi interactions are conserved. A considerable part of the non-polar interactions, broadly ascribed in the past to the van der Waals interaction or the so-called hydrophobic effect, has been suggested to be attributed to a more specific attractive force, the CH/pi interaction.},
  doi       = {10.1016/S0968-0896(98)00002-9},
  file      = {1998_Umezawa_493.pdf:by-author/U/Umezawa/1998_Umezawa_493.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/S0968089698000029},
}

@Webpage{pic2html,
  author    = {unknown},
  retrieved = {2011-10-31},
  title     = {Turning PIC into HTML},
  url       = {http://www.kohala.com/start/troff/pic2html.html},
  file      = {:by-author/u/unknown/XXXX_unknown.odt:},
  keywords  = {Computer Science (CS); Troff; Typesetting},
  owner     = {saulius},
  timestamp = {2015.03.03},
  creationdate = {2015-03-03T00:00:00},
}

@Webpage{unknown,
  author    = {unknown},
  retrieved = {2011-06-14},
  title     = {Bond Lengths and Energies},
  url       = {http://www.doe-mbi.ucla.edu/CHEM125/bonds.html},
  file      = {:by-author/u/unknown/XXXX_unknown.html:},
  keywords  = {Noncovalent-interactions; Protein-physics},
  owner     = {saulius},
  timestamp = {2015.03.03},
  creationdate = {2015-03-03T00:00:00},
}

@Electronic{ComputationalGeometryCode2008,
  author    = {unknown},
  title     = {Computational Geometry Code},
  url       = {http://web.engr.illinois.edu/~jeffe/compgeom/code.html},
  year      = {XXXX},
  file      = {:by-author/u/unknown/XXXX_unknown_a.odt:},
  keywords  = {Computer Science (CS); Geometric-algorithms; Programs},
  owner     = {saulius},
  retrieved = {2008-10-28},
  timestamp = {2015.03.03},
  creationdate = {2015-03-03T00:00:00},
}

@Presentation{unknownXXXXa,
  author    = {unknown},
  title     = {Lecture 20 Precise and Certifiable Arithmetic},
  year      = {XXXX},
  file      = {:by-author/u/unknown/XXXX_unknown.pdf:PDF},
  owner     = {saulius},
  timestamp = {2015.02.25},
  creationdate = {2015-02-25T00:00:00},
}

@Lecture{unknownXXXXb,
  author    = {unknown},
  title     = {Assignment 14: Advanced Exercises in Molecular Dynamics},
  year      = {XXXX},
  file      = {:by-author/u/unknown/XXXX_unknown.pdf:PDF},
  groups    = {sg/applications},
  keywords  = {Molecular Dynamics (MD)},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Lecture{unknownXXXXc,
  author    = {unknown},
  title     = {Particle in a box},
  year      = {XXXX},
  lecture   = {Lecture 10},
  file      = {:by-author/u/unknown/XXXX_unknown_lecture10.pdf:PDF},
  keywords  = {Quantum Mechanics (QM)},
  owner     = {saulius},
  pages     = {lecture10},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Presentation{unknownXXXXd,
  author    = {unknown},
  title     = {Spontaneous Processes. Entropy and the Second Law of Thermodynamics},
  year      = {XXXX},
  file      = {:by-author/u/unknown/XXXX_unknown_slides.pdf:PDF},
  keywords  = {Thermodynamics},
  owner     = {saulius},
  pages     = {slides},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Webpage{unknown2012,
  author    = {unknown},
  retrieved = {2012-12-26},
  title     = {TLSView Manual},
  url       = {http://pymmlib.sourceforge.net/tlsview/tlsview.html},
  year      = {2012},
  file      = {:by-author/u/unknown/2012_unknown.odt:PDF},
  owner     = {saulius},
  timestamp = {2013.03.22},
  creationdate = {2013-03-22T00:00:00},
}

@Presentation{unknown2012a,
  author    = {unknown},
  title     = {Introduction to MPI (Message-Passing Interface)},
  year      = {2012},
  file      = {:by-author/u/unknown/2012_unknown_slides.pdf:PDF},
  owner     = {saulius},
  pages     = {slides},
  timestamp = {2013.07.02},
  creationdate = {2013-07-02T00:00:00},
}

@Webpage{2011,
  author    = {unknown},
  retrieved = {2011-07-21},
  title     = {Physics of Billiards},
  url       = {http://www.real-world-physics-problems.com/physics-of-billiards.html},
  year      = {2011},
  file      = {:by-author/u/unknown/2011_unknown.odt:},
  groups    = {sg/Molecular dynamics},
  keywords  = {Hard-spheres; Molecular-dynamics},
  owner     = {saulius},
  timestamp = {2015.03.03},
  creationdate = {2015-03-03T00:00:00},
}

@Manuscript{unknown2011,
  author    = {unknown},
  title     = {Analysis of Environmental Data. Conceptual Foundations: Bayesian Inference},
  year      = {2011},
  file      = {:by-author/u/unknown/2011_unknown_slides.pdf:PDF},
  groups    = {sg/Bayesian},
  owner     = {saulius},
  pages     = {slides},
  timestamp = {2012.09.30},
  creationdate = {2012-09-30T00:00:00},
}

@Article{unknown2010,
  author    = {unknown},
  title     = {The Entropy of the Classical Ideal Gas},
  year      = {2010},
  file      = {:by-author/u/unknown/2010_unknown.pdf:PDF},
  keywords  = {Entropy},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Misc{anonymous2008,
  author    = {unknown},
  title     = {Lecture 12 - Eigenvalue methods},
  year      = {2008},
  file      = {2008_unknown_lecture12.pdf:by-author/u/unknown/2008_unknown.pdf:PDF},
  owner     = {saulius},
  timestamp = {2011.12.13},
  creationdate = {2011-12-13T00:00:00},
}

@Misc{Methods,
  author    = {unknown},
  title     = {Lecture 7 - Iteratives methods, Jacobi + Gauss Seidel+ SOR},
  year      = {2008},
  file      = {2008_unknown_lecture07.pdf:by-author/u/unknown/2008_unknown.pdf:PDF},
  owner     = {saulius},
  timestamp = {2011.12.13},
  creationdate = {2011-12-13T00:00:00},
}

@Presentation{unknown2008,
  author    = {unknown},
  title     = {The Shortest Vector Problem (Lattice Reduction Algorithms)},
  year      = {2008},
  file      = {:by-author/u/unknown/2008_unknown_slides.pdf:PDF},
  keywords  = {Closest Vector Problem; Simulations},
  owner     = {saulius},
  pages     = {slides},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Presentation{unknown2007,
  author    = {unknown},
  title     = {CHM 404},
  year      = {2007},
  file      = {:by-author/u/unknown/2007_unknown_slides.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{unknown2006,
  author    = {unknown},
  title     = {Unit Cell Determination and Refinement},
  year      = {2006},
  pages     = {chapter5},
  file      = {:by-author/u/unknown/2006_unknown_chapter5.pdf:PDF},
  keywords  = {Crystal Cell; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Manuscript{unknown2005,
  author    = {unknown},
  title     = {Memetikos ištakos},
  year      = {2005},
  keywords  = {SocialSci},
  file      = {:by-author/u/unknown/2005_unknown.doc:DOC},
  owner     = {saulius},
  timestamp = {2015.02.28},
  creationdate = {2015-02-28T00:00:00},
}

@Lecture{unknown2005a,
  author    = {unknown},
  title     = {Hydrogen Bonds. The electrostatic nature of hydrogen bonds},
  year      = {2005},
  file      = {:by-author/u/unknown/2005_unknown.pdf:PDF},
  keywords  = {Computer Science (CS); Logic Circuits; Ternary},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{unknown2005b,
  author    = {unknown},
  title     = {Hydrogen Bonds},
  year      = {2005},
  file      = {:by-author/u/unknown/2005_unknown.pdf:PDF},
  keywords  = {H Bonds; Protein Physics},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Presentation{unknown2005c,
  author    = {unknown},
  title     = {Synthesis: Verilog → Gates},
  year      = {2005},
  file      = {:by-author/u/unknown/2005_unknown_slides.pdf:PDF},
  keywords  = {Computer Architecture; Computer Science (CS); Hardware; Logic Gates},
  owner     = {saulius},
  pages     = {slides},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Presentation{unknown2004,
  author    = {unknown},
  title     = {Code Generation and Optimization},
  year      = {2004},
  file      = {:by-author/u/unknown/2004_unknown_slides.pdf:PDF},
  keywords  = {Code Generation; Compiler Design; Computer Science (CS)},
  owner     = {saulius},
  pages     = {slides},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Presentation{unknown2004a,
  author    = {unknown},
  title     = {Instruction set architectures},
  year      = {2004},
  file      = {:by-author/u/unknown/2004_unknown.pdf:PDF;:by-author/u/unknown/2004_unknown.ps:PostScript},
  owner     = {saulius},
  timestamp = {2015.02.25},
  creationdate = {2015-02-25T00:00:00},
}

@Presentation{unknown2003,
  author    = {unknown},
  title     = {Collision Dynamics},
  year      = {2003},
  file      = {:by-author/u/unknown/2003_unknown_b.pdf:PDF},
  owner     = {saulius},
  timestamp = {2015.02.27},
  creationdate = {2015-02-27T00:00:00},
}

@Manuscript{unknown2003a,
  author    = {unknown},
  title     = {OpenMP},
  year      = {2003},
  url       = {https://computing.llnl.gov/tutorials/openMP},
  file      = {:by-author/u/unknown/2003_unknown_a.pdf:PDF},
  owner     = {saulius},
  timestamp = {2013.07.02},
  creationdate = {2013-07-02T00:00:00},
}

@InBook{unknown2002,
  author    = {unknown},
  pages     = {111--183},
  title     = {Logic Gates},
  year      = {2002},
  file      = {:by-author/u/unknown/2002_unknown_111.pdf:PDF},
  keywords  = {Boolean Algebra; Computer Architecture; Computer Science (CS)},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Presentation{unknown2001,
  author    = {unknown},
  title     = {Weakest-Precondition Reasoning},
  year      = {2001},
  file      = {:by-author/u/unknown/2001_unknown_slides.pdf:PDF},
  groups    = {sg/Correctness proofs},
  keywords  = {Computer Science (CS); Correctness Proofs},
  owner     = {saulius},
  pages     = {slides},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@InBook{Rabaey2000,
  author    = {Jan M. Rabaey},
  chapter   = {6},
  pages     = {197--261},
  publisher = {Prentice-Hall},
  title     = {Designing combinational logic gates in {CMOS}},
  year      = {2000},
  booktitle = {Digital Integrated Circuits},
  comment   = {Explains why NMOS are to be used for pull-down networks (PDNs), and PMOS should be used for pull-up networks (PUNs).

Bibliography restored by scanning materials in http://bwrcs.eecs.berkeley.edu/Classes/icdesign/ee141_f01/notes.html and http://bwrcs.eecs.berkeley.edu/Classes/IcBook/index.html},
  file      = {:by-author/u/unknown/2000_unknown.pdf:PDF},
  keywords  = {Computer Architecture; Computer Science (CS); Hardware},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
  url       = {http://bwrcs.eecs.berkeley.edu/Classes/icdesign/ee141_f01/Notes/chapter6.pdf},
}

@Article{unknown2000a,
  author    = {unknown},
  title     = {Brownian Dynamics},
  year      = {2000},
  pages     = {91},
  file      = {:by-author/u/unknown/2000_unknown_91.pdf:PDF},
  keywords  = {Brownian Dynamics},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@InBook{unknown1999,
  author    = {unknown},
  chapter   = {18},
  pages     = {255--266},
  title     = {Arrays},
  year      = {1999},
  file      = {:by-author/u/unknown/1999_unknown_chapter18.pdf:PDF},
  keywords  = {Computer Science (CS); Programming Language Design},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Presentation{unknown1984,
  author    = {unknown},
  title     = {Local/Distributed Garbage Collection in Renaissance},
  year      = {1984},
  file      = {:by-author/u/unknown/1984_unknown.ps:PostScript;:by-author/u/unknown/1984_unknown.pdf:PDF},
  groups    = {sg/Garbage collectors},
  owner     = {saulius},
  timestamp = {2015.02.25},
  creationdate = {2015-02-25T00:00:00},
}

@InProceedings{Unten2004,
  author    = {Hiroki Unten and Katsushi Ikeuchi},
  booktitle = {10th International Conference on Virtual Systems and Multimedia(VSMM2004)},
  title     = {Virtual Reality Model of Koumokuten Generated from Measurement},
  year      = {2004},
  pages     = {665},
  abstract  = {Contents generation from measurement is an effective approach to automatic modeling of real world objects. In this paper, we present a system to create virtual reality model automatically from measurement of real object and present a virtual reality model of Koumokuten clay figure, which is a great treasure at Nara Toudaiji Temple, generated from the system. 3D geometric model of Koumokuten is generated from range image measured by range sensor and color images of it are acquired by digital camera. In the measurement digital camera is mounted on the range sensor and camera parameters between range image and color images are estimated from calibration techniques utilizing calibration box before data acquisition. We get textured model by mapping the images onto the 3D geometric model using the camera parameters estimated from the calibration. And we show several example applications of the virtual reality model of Koumokuten. By utilizing the virtual reality model we get different appearance of Koumokuten.},
  file      = {2004_Unten_665.pdf:by-author/U/Unten/2004_Unten_665.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://130.203.133.150/viewdoc/download?doi=10.1.1.61.1370&rep=rep1&type=pdf},
}

@Article{Urban1998,
  author    = {Knut W. Urban},
  journal   = {Nature},
  title     = {From tilings to coverings},
  year      = {1998},
  pages     = {14--15},
  volume    = {396},
  doi       = {10.1038/23806},
  file      = {1998_Urban_14.pdf:by-author/U/Urban/1998_Urban_14.pdf:PDF},
  language  = {English},
  owner     = {saulius},
  timestamp = {2015.09.08},
  creationdate = {2015-09-08T00:00:00},
}

@Manuscript{Urbanek2011,
  author    = {Simon Urbanek},
  title     = {Plots eXtreme - Next-generation Interactive Graphics Design and Implementation of Modern Interactive Graphics},
  year      = {2011},
  keywords  = {Computer Graphics; Data Analysis; Interactive Graphics; Software},
  abstract  = {Interactive graphics provide a very important tool that facilitates the process of exploratory data and model analysis which is a crucial step in real-world applied statistics. Only a very limited set of software exists that provides truly interactive graphics for data analysis, partially because it is not easy to implement. Very often specialized software is created to offer graphics for a particular problem, but many fundamental plots are omitted since it is not considered new research. In this paper we discuss a general framework that allows to create interactive graphics software on a sound foundation that offers consistent user interface, fast prototyping of new plots and extensibility to support interactive models. In addition, we also discuss one implementation of the general framework: iPlots eXtreme - next-generation interactive graphics for analysis of large data in R. It provides most fundamental plot types and allows new interactive plots to be created. The implementation raises interactive graphics performance to an entirely new level. We will discuss briefly several methods that allowed us to achieve this goal and illustrate the use of advanced programmability features in conjunction with R.},
  file      = {:by-author/U/Urbanek/2011_Urbanek.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.09.30},
  creationdate = {2012-09-30T00:00:00},
}

@Article{Urzhumtsev1996a,
  author      = {A. G. Urzhumtsev},
  journal     = {Joint CCP4 and ESF-EACBM newsletter on protein crystallography},
  title       = {Relationships between some rotation descriptions for molecular replacement procedure},
  year        = {1996},
  month       = {Jun},
  number      = {32},
  pages       = {1--4},
  file        = {:by-author/c/ccp4-newsletter/1996_ccp4-newsletter.pdf:PDF},
  institution = {Collaborative Computational Project No. 4},
  keywords    = {CCP4; X-ray Crystallography},
  owner       = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Urzhumtsev1996,
  author    = {Urzhumtsev, A. G. and Vernoslova, E. A. and Podjarny, A. D.},
  journal   = {Acta crystallographica. Section D, Biological crystallography},
  title     = {Approaches to very low resolution phasing of the ribosome 50S particle from Thermus thermophilus by the few-atoms-models and molecular-replacement methods.},
  year      = {1996},
  pages     = {1092--7},
  volume    = {52},
  abstract  = {Estimates for the phases of the X-ray diffraction data from the 50S ribosomal particle of Thermus thermophilus has been made to an effective resolution around 80 A using the few-atoms-modes ab initio technique [Lunin, Lunina, Petrova, Vernoslova, Urzhumtsev &amp; Podjarny (1995). Acta Cryst. D51, 896-903]. This technique models the density with a small number of Gaussian spheres to generate a large number of possible phase sets and then uses clustering algorithms to identify the best ones. Independently, an envelope obtained from electron-micrograph image reconstruction [Yonath, Leonard &amp; Wittmann (1987). Science, 236, 813-816] was oriented and positioned using the molecular-replacement technique, specially adapted to the very low resolution case [Urzhumtsev &amp; Podjarny (1995). Acta Cryst. D51, 888-895]. The two methods show similar packing arrangements. The electron density calculated by the few-atoms-models technique without any assumption on the number of molecules in asymmetric unit or on their shape shows recognizable features of the particle.},
  file      = {:by-author/U/Urzhumtsev/1996_Urzhumtsev_1092.pdf:PDF},
  keywords  = {Ribosome Structure},
  owner     = {saulius},
  timestamp = {2012.06.25},
  creationdate = {2012-06-25T00:00:00},
}

@Article{Uson2003,
  author    = {Us{\'{o}}n, Isabel and Schmidt, Bernhard and von B{\"{u}}low, Rixa and Grimme, Susanne and von Figura, Kurt and Dauter, Miroslawa and Rajashankar, Kanagalaghatta R. and Dauter, Zbigniew and Sheldrick, George M.},
  journal   = {Acta Crystallographica Section D},
  title     = {Locating the anomalous scatterer substructures in halide and sulfur phasing},
  year      = {2003},
  pages     = {57--66},
  volume    = {59},
  doi       = {10.1107/S090744490201884X},
  file      = {fw0021.pdf:by-author/U/Uson/2003_Uson_57.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S090744490201884X},
}

@Article{Uson2007,
  author    = {Us{\'{o}}n, Isabel and Stevenson, Clare E. M. and Lawson, David M. and Sheldrick, George M.},
  journal   = {Acta Crystallographica Section D},
  title     = {Structure determination of the {\it O}-methyltransferase NovP using the `free lunch algorithm' as implemented in {\it SHELXE}},
  year      = {2007},
  pages     = {1069--1074},
  volume    = {63},
  doi       = {10.1107/S0907444907042230},
  file      = {dz5108.pdf:by-author/U/Uson/2007_Uson_1069.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444907042230},
}

@Article{Uversky2002,
  author    = {Uversky, Vladimir N.},
  journal   = {Protein science : a publication of the Protein Society},
  title     = {Natively unfolded proteins: a point where biology waits for physics.},
  year      = {2002},
  pages     = {739--56},
  volume    = {11},
  abstract  = {The experimental material accumulated in the literature on the conformational behavior of intrinsically unstructured (natively unfolded) proteins was analyzed. Results of this analysis showed that these proteins do not possess uniform structural properties, as expected for members of a single thermodynamic entity. Rather, these proteins may be divided into two structurally different groups: intrinsic coils, and premolten globules. Proteins from the first group have hydrodynamic dimensions typical of random coils in poor solvent and do not possess any (or almost any) ordered secondary structure. Proteins from the second group are essentially more compact, exhibiting some amount of residual secondary structure, although they are still less dense than native or molten globule proteins. An important feature of the intrinsically unstructured proteins is that they undergo disorder-order transition during or prior to their biological function. In this respect, the Protein Quartet model, with function arising from four specific conformations (ordered forms, molten globules, premolten globules, and random coils) and transitions between any two of the states, is discussed.},
  file      = {:by-author/U/Uversky/2002_Uversky_739.pdf:PDF},
  keywords  = {Intrinsically Unfolded Prot},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Presentation{Vaart2006,
  author    = {Aad van der Vaart},
  title     = {Some Results in Nonparametric Bayesian Inference},
  year      = {2006},
  school    = {Vrije Universiteit Amsterdam},
  file      = {:by-author/V/Vaart/2006_Vaart_slides.pdf:PDF},
  groups    = {sg/Bayesian},
  keywords  = {Bayesian Statistics},
  owner     = {saulius},
  pages     = {slides},
  timestamp = {2012.09.30},
  creationdate = {2012-09-30T00:00:00},
}

@Presentation{Vachette2010,
  author    = {Vachette, P.},
  title     = {Scattering of X-rays},
  year      = {2010},
  file      = {:by-author/V/Vachette/2010_Vachette_slides.pdf:PDF},
  keywords  = {SAXS},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Vagin2004,
  author    = {Vagin, Alexei A. and Steiner, Roberto A. and Lebedev, Andrey A. and Potterton, Liz and McNicholas, Stuart and Long, Fei and Murshudov, Garib N.},
  journal   = {Acta Crystallographica Section D},
  title     = {{\it REFMAC}5 dictionary: organization of prior chemical knowledge and guidelines for its use},
  year      = {2004},
  month     = {Dec},
  number    = {12},
  pages     = {2184--2195},
  volume    = {60},
  abstract  = {One of the most important aspects of macromolecular structure refinement is the use of prior chemical knowledge. Bond lengths, bond angles and other chemical properties are used in restrained refinement as subsidiary conditions. This contribution describes the organization and some aspects of the use of the flexible and human/machine-readable dictionary of prior chemical knowledge used by the maximum-likelihood macromolecular-refinement program REFMAC5. The dictionary stores information about monomers which represent the constitutive building blocks of biological macromolecules (amino acids, nucleic acids and saccharides) and about numerous organic/inorganic compounds commonly found in macromolecular crystallography. It also describes the modifications the building blocks undergo as a result of chemical reactions and the links required for polymer formation. More than 2000 monomer entries, 100 modification entries and 200 link entries are currently available. Algorithms and tools for updating and adding new entries to the dictionary have also been developed and are presented here. In many cases, the REFMAC5 dictionary allows entirely automatic generation of restraints within REFMAC5 refinement runs.},
  address   = {Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5YW, England.},
  doi       = {10.1107/S0907444904023510},
  file      = {2004_Vagin_2184.pdf:by-author/V/Vagin/2004_Vagin_2184.pdf:PDF},
  isbn      = {0907-4449},
  owner     = {em},
  timestamp = {2016.06.16},
  creationdate = {2016-06-16T00:00:00},
  url       = {http://view.ncbi.nlm.nih.gov/pubmed/15572771},
}

@Article{Vagin1997,
  author           = {Vagin, A. and Teplyakov, A.},
  journal          = {J. Appl. Cryst.},
  title            = {MOLREP: an Automated Program for Molecular Replacement.},
  year             = {1997},
  pages            = {1022--1025},
  volume           = {30},
  abstract         = {Abstract: MOLREP is an automated program for molecular replacement which utilizes effective new approaches in data processing and rotational and translational searching. These include an automatic choice of all parameters, scaling by Patterson origin peaks and soft resolution cut-off. One of the cornerstones of the program is an original full-symmetry translation function combined with a packing function. Information from the model already placed in the cell is incorporated in both translation and packing functions. A number of tests using experimental data proved the ability of the program to find the correct solution in difficult cases.},
  creationdate     = {2013-05-27T00:00:00},
  doi              = {10.1107/S0021889897006766},
  file             = {:by-author/V/Vagin/1997_Vagin_1022.pdf:PDF},
  keywords         = {CCP4; MOLREP; Molrep; Protein Crystallography},
  modificationdate = {2022-11-04T22:27:50},
  owner            = {em},
  timestamp        = {2013.05.27},
}

@Presentation{Vaitkus2017,
  author    = {Antanas Vaitkus},
  title     = {Chemical information extraction from the crystallographic data},
  year      = {2017},
  file      = {:by-author/V/Vaitkus/Vaitkus_2017-03-16.pdf:PDF},
  owner     = {antanas},
  timestamp = {2017.03.20},
  creationdate = {2017-03-20T00:00:00},
  url       = {svn+ssh://saulius-grazulis.lt/home/saulius/svn-repositories/Antanas-Vaitkus/presentations/BTI/2017-cif2molecule},
}

@Article{Vaitkus2021,
  author           = {Vaitkus, Antanas and Merkys, Andrius and Gražulis, Saulius},
  journal          = {Journal of Applied Crystallography},
  title            = {Validation of the {C}rystallography {O}pen {D}atabase using the {C}rystallographic {I}nformation {F}ramework},
  year             = {2021},
  issn             = {1600-5767},
  month            = {Feb},
  number           = {2},
  pages            = {1--12},
  volume           = {54},
  creationdate     = {2021-03-22T00:00:00},
  doi              = {10.1107/s1600576720016532},
  file             = {:by-author/V/Vaitkus/2021_Vaitkus_1.pdf:PDF},
  keywords         = {CIF; COD; Chemical Crystallography; Crystallography; Databases; Validation},
  modificationdate = {2024-01-12T09:20:36},
  owner            = {andrius},
  publisher        = {International Union of Crystallography (IUCr)},
  timestamp        = {2021.03.22},
  url              = {https://doi.org/10.1107/S1600576720016532},
}

@Article{Vale1996,
  author     = {Ronald D. Vale},
  journal    = {The Journal of Cell Biology},
  title      = {Switches, latches, and amplifiers: common themes of {G} proteins and molecular motors},
  year       = {1996},
  issn       = {0021-9525},
  pages      = {291--302},
  volume     = {135},
  file       = {PubMed Central Full Text PDF:by-author/V/Vale/1996_Vale_291.pdf:application/pdf},
  groups     = {sg/biomolecular},
  owner      = {saulius},
  pmcid      = {PMC2121043},
  pmid       = {8896589},
  shorttitle = {Switches, latches, and amplifiers},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url        = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2121043/},
  urldate    = {2015-08-05},
}

@Article{Vale2000,
  author     = {Vale, Ronald D. and Milligan, Ronald A.},
  journal    = {Science},
  title      = {The way things move: looking under the hood of molecular motor proteins},
  year       = {2000},
  issn       = {0036-8075, 1095-9203},
  pages      = {88--95},
  volume     = {288},
  abstract   = {The microtubule-based kinesin motors and actin-based myosin motors generate motions associated with intracellular trafficking, cell division, and muscle contraction. Early studies suggested that these molecular motors work by very different mechanisms. Recently, however, it has become clear that kinesin and myosin share a common core structure and convert energy from adenosine triphosphate into protein motion using a similar conformational change strategy. Many different types of mechanical amplifiers have evolved that operate in conjunction with the conserved core. This modular design has given rise to a remarkable diversity of kinesin and myosin motors whose motile properties are optimized for performing distinct biological functions.},
  doi        = {10.1126/science.288.5463.88},
  file       = {Vale and Milligan - 2000 - The Way Things Move Looking Under the Hood of Mol.pdf:by-author/V/Vale/2000_Vale_88.pdf:application/pdf;Snapshot:by-author/V/Vale/2000_Vale_88.html:text/html},
  groups     = {sg/biomolecular},
  language   = {en},
  owner      = {saulius},
  pmid       = {10753125},
  shorttitle = {The way things move},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url        = {http://www.sciencemag.org/content/288/5463/88},
  urldate    = {2015-08-05},
}

@Manuscript{Valentinavicius2008,
  author    = {Saulius Valentinavičius},
  title     = {Objektiškai orientuota analizė},
  year      = {2008},
  keywords  = {Computer Science (CS); Objektiškai-orientuota-analizė},
  file      = {:by-author/V/Valentinavičius/2008_Valentinavičius.doc:DOC},
  owner     = {saulius},
  timestamp = {2015.02.28},
  creationdate = {2015-02-28T00:00:00},
}

@Article{Valentine2001,
  author    = {Valentine, A. M. and Ishmael, F. T. and Shier, V. K. and Benkovic, S. J.},
  journal   = {Biochemistry},
  title     = {A zinc ribbon protein in DNA replication: primer synthesis and macromolecular interactions by the bacteriophage T4 primase.},
  year      = {2001},
  pages     = {15074--85},
  volume    = {40},
  abstract  = {The gene product 61 primase protein from bacteriophage T4 was expressed as an intein fusion and purified to homogeneity. The primase binds one zinc ion, which is coordinated by four cysteine residues to form a zinc ribbon motif. Factors that influence the rate of priming were investigated, and a physiologically relevant priming rate of approximately 1 primer per second per primosome was achieved. Primase binding to the single-stranded binding protein (1 primase:4 gp32 monomers; K(d) approximately 860 nM) and to the helicase protein in the presence of DNA and ATP-gamma-S (1 primase:1 helicase monomer; K(d) approximately 100 nM) was investigated by isothermal titration calorimetry (ITC). Because the helicase is hexameric, the inferred stoichiometry of primase binding as part of the primosome is helicase hexamer:primase in a ratio of 1:6, suggesting that the active primase, like the helicase, might have a ring-like structure. The primase is a monomer in solution but binds to single-stranded DNA (ssDNA) primarily as a trimer (K(d) approximately 50-100 nM) as demonstrated by ITC and chemical cross-linking. Magnesium is required for primase-ssDNA binding. The minimum length of ssDNA required for stable binding is 22-24 bases, although cross-linking reveals transient interactions on oligonucleotides as short as 8 bases. The association is endothermic at physiologically relevant temperatures, which suggests an overall gain in entropy upon binding. Some possible sources of this gain in entropy are discussed.},
  file      = {:by-author/V/Valentine/2001_Valentine_15074.pdf:PDF},
  keywords  = {Primase; {gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Valentine2004,
  author    = {Valentine, M T and Perlman, Z E and Gardel, M L and Shin, J H and Matsudaira, P and Mitchison, T J and Weitz, D A},
  journal   = {Biophysical journal},
  title     = {Colloid surface chemistry critically affects multiple particle tracking measurements of biomaterials.},
  year      = {2004},
  pages     = {4004--14},
  volume    = {86},
  abstract  = {Characterization of the properties of complex biomaterials using microrheological techniques has the promise of providing fundamental insights into their biomechanical functions; however, precise interpretations of such measurements are hindered by inadequate characterization of the interactions between tracers and the networks they probe. We here show that colloid surface chemistry can profoundly affect multiple particle tracking measurements of networks of fibrin, entangled F-actin solutions, and networks of cross-linked F-actin. We present a simple protocol to render the surface of colloidal probe particles protein-resistant by grafting short amine-terminated methoxy-poly(ethylene glycol) to the surface of carboxylated microspheres. We demonstrate that these poly(ethylene glycol)-coated tracers adsorb significantly less protein than particles coated with bovine serum albumin or unmodified probe particles. We establish that varying particle surface chemistry selectively tunes the sensitivity of the particles to different physical properties of their microenvironments. Specifically, particles that are weakly bound to a heterogeneous network are sensitive to changes in network stiffness, whereas protein-resistant tracers measure changes in the viscosity of the fluid and in the network microstructure. We demonstrate experimentally that two-particle microrheology analysis significantly reduces differences arising from tracer surface chemistry, indicating that modifications of network properties near the particle do not introduce large-scale heterogeneities. Our results establish that controlling colloid-protein interactions is crucial to the successful application of multiple particle tracking techniques to reconstituted protein networks, cytoplasm, and cells.},
  file      = {2004_Valentine_4004.pdf:by-author/V/Valentine/2004_Valentine_4004.pdf:PDF},
  keywords  = {Poisson-Boltzmann eq; Protein Physics; Solvatation},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Valiev2010,
  author    = {M. Valiev and E.J. Bylaska and N. Govind and K. Kowalski and T.P. Straatsma and H.J.J. Van Dam and D. Wang and J. Nieplocha and E. Apra and T.L. Windus and W.A. de Jong},
  journal   = {Computer Physics Communications},
  title     = {{NWChem}: A comprehensive and scalable open-source solution for large scale molecular simulations},
  year      = {2010},
  pages     = {1477--1489},
  volume    = {181},
  doi       = {10.1016/j.cpc.2010.04.018},
  file      = {:by-author/V/Valiev/2010_Valiev_1477.pdf:PDF},
  owner     = {andrius},
  timestamp = {2015.11.10},
  creationdate = {2015-11-10T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/S0010465510001438},
}

@Presentation{Valle2015,
  author      = {Valle, Mario},
  title       = {Few Ideas about Linked Data for Material Databases},
  year        = {2015},
  file        = {:by-author/V/Valle/2015_Valle_slides.pdf:PDF},
  institution = {CSCS},
  owner       = {andrius},
  timestamp = {2015.07.21},
  creationdate = {2015-07-21T00:00:00},
}

@TechReport{Valle2015b,
  author      = {Valle, Mario},
  institution = {CSCS and EPFL},
  title       = {Brainstorming on Linked Data relevance for Material Database},
  year        = {2015},
  file        = {:by-author/V/Valle/2015_Valle_techreport.pdf:PDF},
  owner       = {andrius},
  timestamp = {2015.07.22},
  creationdate = {2015-07-22T00:00:00},
}

@TechReport{Valle2015a,
  author           = {Valle, Mario and Merkys, Andrius and Mounet, Nicolas},
  institution      = {CSCS and EPFL},
  title            = {Metadata and ontologies for {AiiDA} database – {EPFL} working meeting report},
  year             = {2015},
  month            = {October},
  creationdate     = {2015-11-04T00:00:00},
  file             = {:by-author/V/Valle/2015_Valle_techreport2.pdf:PDF},
  modificationdate = {2023-10-29T18:51:28},
  owner            = {andrius},
  timestamp        = {2015.11.04},
}

@Article{Duyne1993,
  author    = {Van Duyne, G. D. and Standaert, R. F. and Karplus, P. A. and Schreiber, S. L. and Clardy, J.},
  journal   = {Journal of molecular biology},
  title     = {Atomic structures of the human immunophilin FKBP-12 complexes with FK506 and rapamycin.},
  year      = {1993},
  pages     = {105--24},
  volume    = {229},
  abstract  = {High resolution structures for the complexes formed by the immunosuppressive agents FK506 and rapamycin with the human immunophilin FKBP-12 have been determined by X-ray diffraction. FKBP-12 has a novel fold comprised of a five-stranded beta-sheet wrapping around a short alpha-helix with an overall conical shape. Both FK506 and rapamycin bind in the cavity defined by the beta-sheet, alpha-helix and three loops. Both FK506 and rapamycin bind in similar fashions with a set of hydrogen bonds and an unusual carbonyl binding pocket. Bound FK506 has a different conformation than free (crystalline) FK506 while rapamycin's bound conformation is virtually identical to that of unbound rapamycin. FKBP-12 is a peptidyl-prolyl isomerase (PPIase), and the structures of the complexes suggest ways in which this catalytic activity could operate. The different complexes are active in suppressing different steps of T cell activation, an activity seemingly unconnected with the PPIase activity.},
  file      = {:by-author/V/VanDuyne/1993_Duyne_105.pdf:PDF},
  keywords  = {Microbiology},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@PhdThesis{VanRenssen2005,
  author    = {Van Renssen, Andries Simon Hendrik Paul},
  school    = {TU Delft, Faculty of Electrical Engineering, Mathematics and Computer Science},
  title     = {Gellish: a generic extensible ontological language - design and application of a universal data structure},
  year      = {2005},
  month     = {September},
  abstract  = {Since long data storage and data communication lack a common standard universal data model as well as a common data language for the application domains of database users. This hampers data communication between systems and causes costly data conversion processes. Various solutions have been proposed. However, those solutions either have a limited scope and are mutually incompatible or are difficult to implement. This thesis presents an integral solution to this problem in the form of the semantically rich standard Open Source Gellish English language. Gellish enables electronic data storage and data exchange in a neutral and system independent way. Gellish is relatively easy to implement. Gellish English is the English variant of Gellish and is a structured subset of natural English. Variants for other languages are under development. Gellish enables automated translations between language variants. This means that Gellish English messages can be displayed in any other language variant. Gellish is an extension and integration of the concepts defined in various ISO and non-ISO standard data models and dictionary standards. The Gellish language can replace data models, and provides an extendable ontology with standard reference data for customization and harmonization of systems. A Gellish implementation typically uses the Gellish Table, which is a single table, based on an object-relation-object structure, that is sufficient to express any kind of factual information. The Gellish Dictionary / Taxonomy / Ontology can be used among others to harmonize the content of existing systems, such as data in Design systems, ERP systems and Procurement systems. It also enables the integration of data from different sources, such as data from various engineering and E-Business applications. For example, it enables to describe product catalogues in a system independent way or to describe product requirements, equipment designs, equipment performance, business processes and business transactions so that they can be exchanged between different systems from different parties without the need to convert or translate the data. Usage of Gellish is supported by an Open Source website on http://sourceforge.net/projects/gellish/.},
  file      = {:by-author/V/VanRenssen/2005_VanRenssen.pdf:PDF},
  groups    = {sg/Gellish, sg/Conrolled vocabularies},
  isbn      = {90-407-2597-4},
  keywords  = {Artificial Languages; Controlled Wocabulary; Gellish; Ontologies},
  owner     = {saulius},
  publisher = {Delft University Press},
  timestamp = {2016.02.23},
  creationdate = {2016-02-23T00:00:00},
  url       = {http://repository.tudelft.nl/view/ir/uuid:de26132b-6f03-41b9-b882-c74b7e34a07d/},
}

@Article{Vanamee2003,
  author    = {Vanamee, Eva Scheuring and Hsieh, Pei chung and Zhu, Zhenyu and Yates, David and Garman, Elspeth and Xu, Shuang yong and Aggarwal, Aneel K.},
  journal   = {Journal of molecular biology},
  title     = {Glucocorticoid receptor-like Zn(Cys)4 motifs in BslI restriction endonuclease.},
  year      = {2003},
  pages     = {595--603},
  volume    = {334},
  abstract  = {BslI restriction endonuclease cleaves the symmetric sequence CCN(7)GG (where N=A, C, G or T). The enzyme is composed of two subunits, alpha and beta, that form a heterotetramer (alpha(2)beta(2)) in solution. The alpha subunit is believed to be responsible for DNA recognition, while the beta subunit is thought to mediate cleavage. Here, for the first time, we provide experimental evidence that BslI binds Zn(II). Specifically, using X-ray absorption spectroscopic analysis we show that the alpha subunit of BslI contains two Zn(Cys)(4)-type zinc motifs similar to those in the DNA-binding domain of the glucocorticoid receptor. This conclusion is supported by genetic analysis of the zinc-binding motifs, whereby amino acid substitutions in the zinc finger motifs are demonstrated to abolish or impair cleavage activity. An additional putative zinc-binding motif was identified in the beta subunit, consistent with the X-ray absorption data. These data were corroborated by proton induced X-ray emission measurements showing that full BslI contains at least three fully occupied Zn sites per alpha/beta heterodimer. On the basis of these data, we propose a role for the BslI Zn motifs in protein-DNA as well as protein-protein interactions.},
  file      = {:by-author/V/Vanamee/2003_Vanamee_595.pdf:PDF},
  keywords  = {TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Vanamee2005,
  author    = {Vanamee, Eva Scheuring and Viadiu, Hector and Kucera, Rebecca and Dorner, Lydia and Picone, Stephen and Schildkraut, Ira and Aggarwal, Aneel K.},
  journal   = {The EMBO journal},
  title     = {A view of consecutive binding events from structures of tetrameric endonuclease SfiI bound to DNA.},
  year      = {2005},
  pages     = {4198--208},
  volume    = {24},
  abstract  = {Many reactions in cells proceed via the sequestration of two DNA molecules in a synaptic complex. SfiI is a member of a growing family of restriction enzymes that can bind and cleave two DNA sites simultaneously. We present here the structures of tetrameric SfiI in complex with cognate DNA. The structures reveal two different binding states of SfiI: one with both DNA-binding sites fully occupied and the other with fully and partially occupied sites. These two states provide details on how SfiI recognizes and cleaves its target DNA sites, and gives insight into sequential binding events. The SfiI recognition sequence (GGCCNNNN[downward arrow]NGGCC) is a subset of the recognition sequence of BglI (GCCNNNN[downward arrow]NGGC), and both enzymes cleave their target DNAs to leave 3-base 3' overhangs. We show that even though SfiI is a tetramer and BglI is a dimer, and there is little sequence similarity between the two enzymes, their modes of DNA recognition are unusually similar.},
  file      = {:by-author/V/Vanamee/2005_Vanamee_4198.pdf:PDF},
  keywords  = {Struct; TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Vanclay2012,
  author     = {Vanclay, Jerome K.},
  journal    = {Scientometrics},
  title      = {Impact factor: outdated artefact or stepping-stone to journal certification?},
  year       = {2012},
  issn       = {0138-9130, 1588-2861},
  pages      = {211--238},
  volume     = {92},
  abstract   = {A review of Garfield's journal impact factor and its specific implementation as the Thomson Reuters Impact Factor reveals several weaknesses in this commonly-used indicator of journal standing. Key limitations include the mismatch between citing and cited documents, the deceptive display of three decimals that belies the real precision, and the absence of confidence intervals. These are minor issues that are easily amended and should be corrected, but more substantive improvements are needed. There are indications that the scientific community seeks and needs better certification of journal procedures to improve the quality of published science. Comprehensive certification of editorial and review procedures could help ensure adequate procedures to detect duplicate and fraudulent submissions.},
  annote     = {Comment: 25 pages, 12 figures, 6 tables},
  doi        = {10.1007/s11192-011-0561-0},
  file       = {arXiv\:1201.3076 PDF:by-author/V/Vanclay/2012_Vanclay_211.pdf:application/pdf;arXiv.org Snapshot:by-author/V/Vanclay/2012_Vanclay_211.html:text/html},
  groups     = {sg/Bibliometrics},
  keywords   = {Computer Science - Digital Libraries},
  owner      = {saulius},
  shorttitle = {Impact factor},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url        = {http://arxiv.org/abs/1201.3076},
  urldate    = {2015-07-06},
}

@Article{VanLeeuwen2014,
  author    = {VanLeeuwen, Brian K. and Gopalan, Venkatraman and Litvin, Daniel B.},
  journal   = {Acta crystallographica. Section A, Foundations and advances},
  title     = {Double antisymmetry and the rotation-reversal space groups.},
  year      = {2014},
  pages     = {24--38},
  volume    = {70},
  abstract  = {Rotation-reversal symmetry was recently introduced to generalize the symmetry classification of rigid static rotations in crystals such as tilted octahedra in perovskite structures and tilted tetrahedra in silica structures. This operation has important implications for crystallographic group theory, namely that new symmetry groups are necessary to properly describe observations of rotation-reversal symmetry in crystals. When both rotation-reversal symmetry and time-reversal symmetry are considered in conjunction with space-group symmetry, it is found that there are 17,803 types of symmetry which a crystal structure can exhibit. These symmetry groups have the potential to advance understanding of polyhedral rotations in crystals, the magnetic structure of crystals and the coupling thereof. The full listing of the double antisymmetry space groups can be found in the supplementary materials of the present work and at http://sites.psu.edu/gopalan/research/symmetry/.},
  file      = {:by-author/V/VanLeeuwen/2014_VanLeeuwen_24.pdf:PDF},
  owner     = {saulius},
  timestamp = {2014.03.23},
  creationdate = {2014-03-23T00:00:00},
}

@InProceedings{VanNorman1990,
  author    = {Rick VanNorman and Koopman, Phil},
  booktitle = {Proceedings of the 1990 Roschester Forth Conference},
  title     = {Adding a Third Stack to a Forth Engine},
  year      = {1990},
  pages     = {150},
  file      = {1990_VanNorman_150.pdf:by-author/V/VanNorman/1990_VanNorman_150.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@Article{Vansteelandt2006,
  author    = {Stijn Vansteelandt and Els Goetghebeur and Michael G. Kenward and Geert Molenberghs},
  journal   = {Statistica Sinica},
  title     = {Ignorance and uncertainty regions as inferential tools in a sensitivity analysis},
  year      = {2006},
  pages     = {953--980},
  volume    = {16},
  abstract  = {It has long been recognised that most standard point estimators lean heavily on untestable assumptions when missing data are encountered. Statisticians have therefore advocated the use of sensitivity analysis, but paid relatively little attention to strategies for summarizing the results from such analyses, summaries that have clear interpretation, verifiable properties and feasible implementation. As a step in this direction, several authors have proposed to shift the focus of inference from point estimators to estimated intervals or regions of ignorance. These regions combine standard point estimates obtained under all possible/plausible missing data models that yield identified parameters of interest. They thus reflect the achievable information from the given data generation structure with its missing data component. The standard framework of inference needs extension to allow for a transparent study of statistical properties of such regions. In this paper we propose a definition of consistency for a region and introduce the concepts of pointwise, weak and strong coverage for larger regions which ac- knowledge sampling imprecision in addition to the structural lack of information. The larger regions are called uncertainty regions and quantify an overall level of information by adding imprecision due to sampling error to the estimated region of ignorance. The distinction between ignorance and sampling error is often useful, for instance when sample size considerations are made. The type of coverage required depends on the analysis goal. We provide algorithms for constructing several types of uncertainty regions, and derive general relationships between them. Based on the estimated uncertainty regions, we show how classical hypothesis tests can be performed without untestable assumptions on the missingness mechanism.},
  file      = {2006_Vansteelandt_953.pdf:by-author/V/Vansteelandt/2006_Vansteelandt_953.pdf:PDF},
  groups    = {sg/Bayesian},
  keywords  = {Bayesian Statistics; Bounds; Identifiability; Incomplete Data; Inference; Pattern-mixture Model; Selection Mode},
  owner     = {saulius},
  timestamp = {2013.01.02},
  creationdate = {2013-01-02T00:00:00},
  url       = {http://www3.stat.sinica.edu.tw/statistica/oldpdf/A16n315.pdf},
}

@Article{Velkov1999,
  author    = {Velkov, Vassili V.},
  journal   = {Journal of Biosciences},
  title     = {How environmental factors regulate mutagenesis and gene transfer in microorganisms},
  year      = {1999},
  issn      = {0250-5991},
  pages     = {529--559},
  volume    = {24},
  doi       = {10.1007/BF02942664},
  file      = {1999_Velkov_529.html:by-author/V/Velkov/1999_Velkov_529.html:URL},
  keywords  = {Adaptive Mutagenesis; Evolution; General Resistance; Inter-species Gene Transfer; Microorganisms; Sigma-S; Speciation; Stationary Phase},
  language  = {English},
  owner     = {em},
  publisher = {Springer India},
  timestamp = {2013.08.11},
  creationdate = {2013-08-11T00:00:00},
  url       = {http://dx.doi.org/10.1007/BF02942664},
}

@InBook{Venclovas2012,
  author    = {Česlovas Venclovas},
  chapter   = {Methods for Sequence–Structure Alignment},
  editor    = {Andrew J.W. Orry and Ruben Abagyan},
  pages     = {55--82},
  publisher = {Springer Science+Business Media},
  title     = {Homology Modeling: Methods and Protocols},
  year      = {2012},
  volume    = {857},
  comment   = {Homology modeling is based on the observation that related protein sequences adopt similar three-dimensional structures. Hence, a homology model of a protein can be derived using related protein structure(s) as modeling template(s). A key step in this approach is the establishment of correspondence between residues of the protein to be modeled and those of modeling template(s). This step, often referred to as sequence-structure alignment, is one of the major determinants of the accuracy of a homology model. This chapter gives an overview of methods for deriving sequence–structure alignments and discusses recent methodological developments leading to improved performance. However, no method is perfect. How to find alignment regions that may have errors and how to make improvements? This is another focus of this chapter. Finally, the chapter provides a practical guidance of how to get the most of the available tools in maximizing the accuracy of sequence-structure alignments.},
  doi       = {10.1007/978-1-61779-588-6_3},
  file      = {:by-author/V/Venclovas/2012_Venclovas_55.pdf:PDF},
  keywords  = {Bioinformatics; Proteins; Structure Prediction},
  owner     = {andrius},
  timestamp = {2013.11.21},
  creationdate = {2013-11-21T00:00:00},
}

@Article{Venclovas2009,
  author    = {Venclovas, Č. and Margelevičius, M.},
  journal   = {Proteins},
  title     = {The use of automatic tools and human expertise in template-based modeling of {CASP8} target proteins},
  year      = {2009},
  pages     = {81--88},
  volume    = {77},
  abstract  = {Here, we describe our template-based protein modeling approach and its performance during the eighth community-wide experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP8, http://predictioncenter.org/casp8). In CASP8, our modeling approach was supplemented by the newly developed distant homology detection method based on sequence profile–profile comparison. Detection of structural homologs that could be used as modeling templates was largely achieved by automated profile-based searches. However, the other two major steps in template-based modeling (TBM) (selection of the best template(s) and construction of the optimal sequence-structure alignment) to a large degree relied on the combination of automatic tools and manual input. The analysis of 64 domains categorized by CASP8 assessors as TBM domains revealed that we missed correct structural templates for only four of them. The use of multiple templates or their fragments enabled us to improve over the structure of the single best PDB template in about 1/3 of our models for TBM domains. Our results for sequence-structure alignments are mixed. Although many models have optimal or near optimal sequence mapping, a large fraction contains one or more misaligned regions. Strikingly, in spite of this, our TBM models have the best overall alignment accuracy scores. This clearly suggests that the correct mapping of protein sequence onto three-dimensional structure remains one of the big challenges in protein structure prediction.},
  doi       = {10.1002/prot.22515},
  file      = {:by-author/V/Venclovas/2009_Venclovas_81.pdf:PDF},
  keywords  = {Proteins; Structure Prediction},
  owner     = {andrius},
  timestamp = {2013.11.22},
  creationdate = {2013-11-22T00:00:00},
}

@Article{Venclovas2005,
  author    = {Venclovas, Česlovas and Margelevičius, Mindaugas},
  journal   = {Proteins},
  title     = {Comparative Modeling in {CASP6} Using Consensus Approach to Template Selection, Sequence-Structure Alignment, and Structure Assessment},
  year      = {2005},
  pages     = {99--105},
  volume    = {7},
  comment   = {Along with over 150 other groups we have tested our template-based protein structure prediction approach by submitting models for 30 target proteins to the sixth round of the Critical Assessment of Protein Structure Prediction Methods (CASP6, http://predictioncenter.org). Most of our modeled proteins fall into the comparative or homology modeling (CM) category, and some are fold recognition (FR) targets. The key feature of our structure prediction strategy in CASP6 was an attempt to optimally select structural templates and to make accurate sequence-structure alignments. Template selection was based mainly on consensus results of multiple sequence searches. Likewise, the consensus of multiple alignment variants (or lack of it) was used to initially delineate reliable and unreliable alignment regions. Structure evaluation approaches were then used to identify the correct sequence-structure mapping. Our results suggest that in many cases use of multiple templates is advantageous. Selecting correct alignments even within the context of a three-dimensional structure remains a challenge. Together with more effective energy evaluation methods the simultaneous relaxation/refinement of a "frozen" backbone inherited from the template is likely needed to see a clear progress in tackling this problem. Our analysis also suggests that human input has little to contribute to automatic methods in modeling high homology targets. On the other hand, human expertise can be very valuable in modeling distantly related proteins and critical in cases of unexpected evolutionary changes in protein structure.},
  file      = {:by-author/V/Venclovas/2005_Venclovas_99.pdf:PDF},
  keywords  = {Proteins; Structure Prediction},
  owner     = {andrius},
  timestamp = {2013.11.27},
  creationdate = {2013-11-27T00:00:00},
}

@Article{Venclovas1995,
  author       = {Venclovas, Česlovas and Siksnys, Virginijus},
  journal      = {Nature Structural Biology},
  title        = {Different enzymes with similar structures involved in Mg2+-mediated polynucleotidyl transfer},
  year         = {1995},
  issn         = {1072-8368},
  month        = {Oct},
  number       = {10},
  pages        = {838--841},
  volume       = {2},
  abstract     = {Comparison of X-ray structures of restriction endonucleases and polynucleotidyl transferase superfamily enzymes reveals a structural resemblance.},
  creationdate = {2016-06-25T00:00:00},
  doi          = {10.1038/nsb1095-838},
  file         = {1995_Venclovas_838.pdf:by-author/V/Venclovas/1995_Venclovas_838.pdf:PDF},
  keywords     = {Binding Sites; Chemistry; Chemistry/metabolism; Chemistry/metabolism/physiology; Crystallography; DNA Nucleotidyltransferases; DNA Restriction Enzymes; Deoxyribonucleases; Integrases; Magnesium; Metabolism; Models; Molecular; Polynucleotides; Protein Conformation; Protein Folding; Type II Site-Specific; X-Ray},
  owner        = {saulius},
  publisher    = {Nature Publishing Group},
  timestamp    = {2016.06.25},
  url          = {http://dx.doi.org/10.1038/nsb1095-838},
}

@Article{Venclovas1994,
  author       = {C. Venclovas and A. Timinskas and V. Siksnys},
  journal      = {Proteins},
  title        = {Five-stranded beta-sheet sandwiched with two alpha-helices: a structural link between restriction endonucleases EcoRI and EcoRV.},
  year         = {1994},
  month        = {Nov},
  number       = {3},
  pages        = {279--282},
  volume       = {20},
  abstract     = {Examination of crystal structures of restriction endonucleases EcoRI and EcoRV complexes with their cognate DNA revealed a common structural element, which forms the core of both proteins. This element consists of a five-stranded beta-sheet and two alpha-helices packed against it and could be described as alpha-beta sandwich in which helices and beta-strands lie in two stacked layers. While the spatial structure of this alpha-beta sandwich is conserved in both enzymes, there are not detectable similarities between amino acid sequences except of a few residues involved in active site formation. Probably, other restriction endonucleases which have similar organization of the active site might possess similar structural element regardless of DNA sequence recognized and recognition elements in the enzyme used.},
  creationdate = {2016-06-09T00:00:00},
  doi          = {10.1002/prot.340200308},
  file         = {1994_Venclovas_279.pdf:by-author/V/Venclovas/1994_Venclovas_279.pdf:PDF},
  institution  = {Institute of Biotechnology Fermentas, Vilnius, Lithuania.},
  keywords     = {Amino Acid Sequence; Binding Sites; Chemistry/genetics; Deoxyribonuclease EcoRI; Deoxyribonucleases; Enzymology/genetics; Escherichia Coli; Models; Molecular; Molecular Sequence Data; Mutagenesis; Protein Structure; Secondary; Site-Directed; Type II Site-Specific},
  language     = {eng},
  medline-pst  = {ppublish},
  owner        = {em},
  pmid         = {7892176},
  timestamp    = {2016.06.09},
  url          = {http://dx.doi.org/10.1002/prot.340200308},
}

@Article{Venclovas1994a,
  author    = {Venclovas, C. and Timinskas, A. and Siksnys, V.},
  journal   = {Proteins},
  title     = {Five-stranded beta-sheet sandwiched with two alpha-helices: a structural link between restriction endonucleases EcoRI and EcoRV.},
  year      = {1994},
  pages     = {279--82},
  volume    = {20},
  abstract  = {Examination of crystal structures of restriction endonucleases EcoRI and EcoRV complexes with their cognate DNA revealed a common structural element, which forms the core of both proteins. This element consists of a five-stranded beta-sheet and two alpha-helices packed against it and could be described as alpha-beta sandwich in which helices and beta-strands lie in two stacked layers. While the spatial structure of this alpha-beta sandwich is conserved in both enzymes, there are not detectable similarities between amino acid sequences except of a few residues involved in active site formation. Probably, other restriction endonucleases which have similar organization of the active site might possess similar structural element regardless of DNA sequence recognized and recognition elements in the enzyme used.},
  file      = {:by-author/V/Venclovas/1994_Venclovas_279.pdf:PDF},
  keywords  = {Evolution; TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Venkataraman2006,
  author    = {Venkataraman, Latha and Klare, Jennifer E. and Nuckolls, Colin and Hybertsen, Mark S. and Steigerwald, Michael L.},
  journal   = {Nature},
  title     = {Dependence of single-molecule junction conductance on molecular conformation},
  year      = {2006},
  issn      = {0028-0836},
  pages     = {904--907},
  volume    = {442},
  abstract  = {Since it was first suggested that a single molecule might function as an active electronic component, a number of techniques have been developed to measure the charge transport properties of single molecules. Although scanning tunnelling microscopy observations under high vacuum conditions can allow stable measurements of electron transport, most measurements of a single molecule bonded in a metal–molecule–metal junction exhibit relatively large variations in conductance. As a result, even simple predictions about how molecules behave in such junctions have still not been rigorously tested. For instance, it is well known that the tunnelling current passing through a molecule depends on its conformation; but although some experiments have verified this effect, a comprehensive mapping of how junction conductance changes with molecular conformation is not yet available. In the simple case of a biphenyl—a molecule with two phenyl rings linked by a single C–C bond—conductance is expected to change with the relative twist angle between the two rings, with the planar conformation having the highest conductance. Here we use amine link groups to form single-molecule junctions with more reproducible current–voltage characteristics. This allows us to extract average conductance values from thousands of individual measurements on a series of seven biphenyl molecules with different ring substitutions that alter the twist angle of the molecules. We find that the conductance for the series decreases with increasing twist angle, consistent with a cosine-squared relation predicted for transport through -conjugated biphenyl systems.},
  copyright = {© 2006 Nature Publishing Group},
  doi       = {10.1038/nature05037},
  file      = {Full Text PDF:by-author/V/Venkataraman/2006_Venkataraman_904.pdf:application/pdf;Snapshot:by-author/V/Venkataraman/2006_Venkataraman_904.html:text/html},
  groups    = {sg/chemical},
  language  = {en},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://www.nature.com/nature/journal/v442/n7105/full/nature05037.html},
  urldate   = {2015-08-05},
}

@Article{Venkatesan1982,
  author    = {Venkatesan, M. and Silver, L. L. and Nossal, N. G.},
  journal   = {The Journal of biological chemistry},
  title     = {Bacteriophage T4 gene 41 protein, required for the synthesis of RNA primers, is also a DNA helicase.},
  year      = {1982},
  pages     = {12426--34},
  volume    = {257},
  abstract  = {Bacteriophage T4 gene 41 protein is one of the two phage proteins previously shown to be required for the synthesis of the pentaribonucleotide primers which initiate the synthesis of new chains in the T4 DNA replication system. We now show that a DNA helicase activity which can unwind short fragments annealed to complementary single-stranded DNA copurifies with the gene 41 priming protein. T4 gene 41 is essential for both the priming and helicase activities, since both are absent after infection by T4 phage with an amber mutation in gene 41. A complete gene 41 product is also required for two other activities previously found in purified preparations of the priming activity: a single-stranded DNA-dependent GTPase (ATPase) and an activity which stimulates strand displacement synthesis catalyzed by T4 DNA polymerase, the T4 gene 44/62 and 45 polymerase accessory proteins, and the T4 gene 32 helix-destabilizing protein (five-protein reaction). The 41 protein helicase requires a single-stranded DNA region adjoining the duplex region and begins unwinding at the 3' terminus of the fragment. There is a sigmoidal dependence on both nucleotide (rGTP, rATP) and protein concentration for this reaction. 41 Protein helicase activity is stimulated by our purest preparation of the T4 gene 61 priming protein, and by the T4 gene 44/62 and 45 polymerase accessory proteins. The direction of unwinding is consistent with the idea that 41 protein facilitates DNA synthesis on duplex templates by destabilizing the helix as it moves 5' to 3' on the displaced strand.},
  file      = {:by-author/V/Venkatesan/1982_Venkatesan_12426.pdf:PDF},
  keywords  = {{gp41}; {gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Webpage{Venners1996,
  author    = {Bill Venners},
  retrieved = {2015-03-11},
  title     = {Eternal Math: A Simulation of the Java Virtual Machine},
  url       = {http://www.artima.com/insidejvm/applets/JVMSimulators/EternalMath.java},
  year      = {1996},
  file      = {:by-author/V/Venners/1996_Venners.odt:OpenDocument text;:by-author/V/Venners/1996_Venners/EternalMath.java:Text},
  keywords  = {Bytecode; Computer Science (CS); Interpreters; Java; Programing Languages; Virtual Machines},
  owner     = {saulius},
  timestamp = {2015.03.11},
  creationdate = {2015-03-11T00:00:00},
}

@Article{Verbeek2006,
  author    = {Jakob J. Verbeek and Jan R.J. Nunnink and Nikos Vlassis},
  journal   = {Data Mining and Knowledge Discovery},
  title     = {Accelerated {EM}-based clustering of large data sets},
  year      = {2006},
  pages     = {291--307},
  volume    = {13},
  abstract  = {Motivated by the poor performance (linear complexity) of the EM algorithm in clustering large data sets, and inspired by the successful accelerated versions of related algorithms like k-means, we derive an accelerated variant of the EM algorithm for Gaussian mixtures that: (1) offers speedups that are at least linear in the number of data points, (2) ensures convergence by strictly increasing a lower bound on the data log-likelihood in each learning step, and (3) allows ample freedom in the design of other accelerated variants. We also derive a similar accelerated algorithm for greedy mixture learning, where very satisfactory results are obtained. The core idea is to define a lower bound on the data log-likelihood based on a grouping of data points. The bound is maximized by computing in turn (i) optimal assignments of groups of data points to the mixture components, and (ii) optimal re-estimation of the model parameters based on average sufficient statistics computed over groups of data points. The proposed method naturally generalizes to mixtures of other members of the exponential family. Experimental results show the potential of the proposed method over other state-of-the-art acceleration techniques.},
  doi       = {10.1007/s10618-005-0033-3},
  file      = {:by-author/V/Verbeek/2006_Verbeek_291.pdf:PDF},
  groups    = {am/Expectation maximisation},
  keywords  = {Expectation Maximisation; Gaussian Mixture Models},
  owner     = {andrius},
  timestamp = {2013.02.28},
  creationdate = {2013-02-28T00:00:00},
}

@MastersThesis{VergaraLarrea2011,
  author           = {Vergara Larrea, Ver{\'{o}}nica G.},
  school           = {Florida State University},
  title            = {Construction of {D}elaunay Triangulations on the Sphere: A Parallel Approach},
  year             = {2011},
  type             = {Master thesis},
  comment          = {This thesis explores possible improvements in the construction of Delaunay Trian- gulations on the Sphere by designing and implementing a parallel alternative to the software package STRIPACK. First, it gives an introduction to Delaunay Triangu- lations on the plane and presents current methods available for their construction. Then, these concepts are mapped to the spherical case: Spherical Delaunay Triangu- lation (SDT). To provide a better understanding of the design choices, this document includes a brief overview of parallel programming, that is followed by the details of the implementation of the SDT generation code. In addition, it provides examples of resulting SDTs as well as benchmarks to analyze its performance. This project was inspired by the concepts presented in Robert Renka’s work [26] and was implemented in C++ using MPI.},
  creationdate     = {2014-09-16T00:00:00},
  file             = {:by-author/V/VergaraLarrea/2011_VergaraLarrea.pdf:PDF},
  keywords         = {Algorithms},
  modificationdate = {2024-05-16T08:43:57},
  owner            = {andrius},
  timestamp        = {2014.09.16},
  url              = {http://diginole.lib.fsu.edu/cgi/viewcontent.cgi?article=5571&context=etd},
}

@Article{Vergara2003,
  author    = {Vergara, Alessandro and Lorber, Bernard and Zagari, Adriana and Gieg{\'{e}}, Richard},
  journal   = {Acta Crystallographica Section D},
  title     = {Physical aspects of protein crystal growth investigated with the Advanced Protein Crystallization Facility in reduced-gravity environments},
  year      = {2003},
  pages     = {2--15},
  volume    = {59},
  doi       = {10.1107/S0907444902021443},
  file      = {gr2290.pdf:by-author/V/Vergara/2003_Vergara_2.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444902021443},
}

@Manuscript{Verkuil2013,
  author    = {Steven Verkuil},
  title     = {A Comparison of Fault-Tolerant Cloud Storage File Systems},
  year      = {2013},
  keywords  = {Apache Hadoop File System (HDFS); Computer Science (CS); Fault-tollerant File Systems; GlusterFS; Redundant Storage; Replicated Storage; XtreemFS},
  language  = {English},
  url       = {http://referaat.cs.utwente.nl/conference/19/paper/7390/a-comparison-of-fault-tolerant-cloud-storage-file-systems.pdf},
  abstract  = {There are many cloud storage file systems that guar antee fault-tolerance. Implementation of fault-tolerance in a cloud storage file system is achieved in several differen t ways. This paper aims to find the benefits and drawbacks of ex isting fault-tolerant file systems by defining criteria o n which fault- tolerant file systems can be graded. Several distri buted file systems will be compared to discover how the criter ia are satisfied. The research concludes with an overview of how the different file systems, each powered by their own d istinct architecture , perform in an environment that is prone to errors. It is shown that not all file systems perform evenl y well regarding the criteria, therefore underlining the n eed to evaluate fault-tolerance behavior when choosing a f ile system.},
  file      = {2013_Verkuil.pdf:by-author/V/Verkuil/2013_Verkuil.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.02},
  creationdate = {2016-12-02T00:00:00},
}

@Presentation{Verma2011,
  author    = {Sandeep Verma},
  title     = {Metal‐Organic Frameworks on CNTs: Covalent Conjugates and Catalysis},
  year      = {2011},
  file      = {:by-author/V/Verma/2011_Verma_slides.pdf:PDF},
  keywords  = {Adenine; Metal-Organic Frameworks (MOF)},
  owner     = {saulius},
  pages     = {slides},
  timestamp = {2013.01.05},
  creationdate = {2013-01-05T00:00:00},
}

@Presentation{Vestergaard2010,
  author    = {Vestergaard},
  title     = {Structural Investigation of Protein Fibrillation without disturbing the inherent equilibriums - Towards structural and Biophysical Analysis of the Autocatalytic Effect of Fibrillogenesis},
  year      = {2010},
  file      = {:by-author/V/Vestergaard/2010_Vestergaard_slides.pdf:PDF},
  keywords  = {SAXS},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Vetter2001,
  author    = {Vetter, Ingrid R. and Wittinghofer, Alfred},
  journal   = {Science},
  title     = {The guanine nucleotide-binding switch in three dimensions},
  year      = {2001},
  issn      = {0036-8075, 1095-9203},
  pages     = {1299--1304},
  volume    = {294},
  abstract  = {Guanine nucleotide–binding proteins regulate a variety of processes, including sensual perception, protein synthesis, various transport processes, and cell growth and differentiation. They act as molecular switches and timers that cycle between inactive guanosine diphosphate (GDP)–bound and active guanosine triphosphate (GTP)–bound states. Recent structural studies show that the switch apparatus itself is a conserved fundamental module but that its regulators and effectors are quite diverse in their structures and modes of interaction. Here we will try to define some underlying principles.},
  doi       = {10.1126/science.1062023},
  file      = {Full Text PDF:by-author/V/Vetter/2001_Vetter_1299.pdf:application/pdf;Snapshot:by-author/V/Vetter/2001_Vetter_1299.html:text/html},
  groups    = {sg/biomolecular},
  language  = {en},
  owner     = {saulius},
  pmid      = {11701921},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://www.sciencemag.org/content/294/5545/1299},
  urldate   = {2015-08-05},
}

@Article{Viadiu1998,
  author    = {Viadiu, H. and Aggarwal, A. K.},
  journal   = {Nature structural biology},
  title     = {The role of metals in catalysis by the restriction endonuclease BamHI.},
  year      = {1998},
  pages     = {910--6},
  volume    = {5},
  abstract  = {Type II restriction enzymes are characterized by their remarkable specificity and simplicity. They require only divalent metals (such as Mg2+ or Mn2+) as cofactors to catalyze the hydrolysis of DNA. However, most of the structural work on endonucleases has been performed in the absence of metals, leaving unanswered questions about their mechanisms of DNA cleavage. Here we report structures of the endonuclease BamHI-DNA complex, determined in the presence of Mn2+ and Ca2+, that describe the enzyme at different stages of catalysis. Overall, the results support a two-metal mechanism of DNA cleavage for BamHI which is distinct from that of EcoRV.},
  file      = {:by-author/V/Viadiu/1998_Viadiu_910.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Manuscript{Vicig2012,
  author    = {Paolo Vicig and Teddy Seidenfeld},
  title     = {Bruno de Finetti and Imprecision: Imprecise Probability Does not Exist!},
  year      = {2012},
  url       = {http://www.hss.cmu.edu/philosophy/seidenfeld/relating%20to%20coherence%20and%20decision%20theory/De%20Finetti%20and%20Imprecise%20Probabilities.pdf},
  file      = {2012_Vicig.pdf:by-author/V/Vicig/2012_Vicig.pdf:PDF},
  journal   = {International Journal of Approximate Reasoning},
  owner     = {saulius},
  timestamp = {2012.11.23},
  creationdate = {2012-11-23T00:00:00},
}

@Article{Vickers2006,
  author    = {Vickers},
  title     = {Whose Data Set is It Anyway? Sharing Raw Data from Randomized Trials},
  year      = {2006},
  pages     = {1745-6215-7-15},
  file      = {:by-author/V/Vickers/2006_Vickers_1745.pdf:PDF},
  keywords  = {Data Sharing; Scientific Publications},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@Presentation{Vidakovic2005,
  author    = {Brani Vidakovic},
  title     = {Priors},
  year      = {2005},
  file      = {:by-author/V/Vidakovic/2005_Vidakovic_handouts.pdf:PDF},
  groups    = {sg/Bayesian},
  keywords  = {Bayesian Statistics; Mathematics},
  owner     = {saulius},
  pages     = {handouts},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Vilenkin1982,
  author    = {Alexander Vilenkin},
  journal   = {Physics Letters B},
  title     = {Creation of Universes from Nothing},
  year      = {1982},
  pages     = {25--28},
  volume    = {117},
  file      = {1982_Vilenkin_25.pdf:by-author/V/Vilenkin/1982_Vilenkin_25.pdf:PDF},
  owner     = {saulius},
  timestamp = {2015.05.27},
  creationdate = {2015-05-27T00:00:00},
}

@Article{Vilkaitis2000,
  author    = {Vilkaitis, G. and Dong, A. and Weinhold, E. and Cheng, X. and Klimasauskas, S.},
  journal   = {The Journal of biological chemistry},
  title     = {Functional roles of the conserved threonine 250 in the target recognition domain of HhaI DNA methyltransferase.},
  year      = {2000},
  pages     = {38722--30},
  volume    = {275},
  abstract  = {DNA cytosine-5-methyltransferase HhaI recognizes the GCGC sequence and flips the inner cytosine out of DNA helix and into the catalytic site for methylation. The 5'-phosphate of the flipped out cytosine is in contact with the conserved Thr-250 from the target recognition domain. We have produced 12 mutants of Thr-250 and examined their methylation potential in vivo. Six active mutants were subjected to detailed biochemical and structural studies. Mutants with similar or smaller side chains (Ser, Cys, and Gly) are very similar to wild-type enzyme in terms of steady-state kinetic parameters k(cat), K(m)(DNA), K(m)(AdoMet). In contrast, the mutants with bulkier side chains (Asn, Asp, and His) show increased K(m) values for both substrates. Fluorescence titrations and stopped-flow kinetic analysis of interactions with duplex oligonucleotides containing 2-aminopurine at the target base position indicate that the T250G mutation leads to a more polar but less solvent-accessible position of the flipped out target base. The x-ray structure of the ternary M. HhaI(T250G).DNA.AdoHcy complex shows that the target cytosine is locked in the catalytic center of enzyme. The space created by the mutation is filled by water molecules and the adjacent DNA backbone atoms dislocate slightly toward the missing side chain. In aggregate, our results suggest that the side chain of Thr-250 is involved in constraining the conformation the DNA backbone and the target base during its rotation into the catalytic site of enzyme.},
  file      = {:by-author/V/Vilkaitis/2000_Vilkaitis_38722.pdf:PDF},
  keywords  = {HhaI},
  owner     = {saulius},
  timestamp = {2012.11.05},
  creationdate = {2012-11-05T00:00:00},
}

@Article{Vilkaitis2001,
  author    = {Vilkaitis, G. and Merkiene, E. and Serva, S. and Weinhold, E. and Klimasauskas, S.},
  journal   = {The Journal of biological chemistry},
  title     = {The mechanism of DNA cytosine-5 methylation. Kinetic and mutational dissection of Hhai methyltransferase.},
  year      = {2001},
  pages     = {20924--34},
  volume    = {276},
  abstract  = {Kinetic and binding studies involving a model DNA cytosine-5-methyltransferase, M.HhaI, and a 37-mer DNA duplex containing a single hemimethylated target site were applied to characterize intermediates on the reaction pathway. Stopped-flow fluorescence studies reveal that cofactor S-adenosyl-l-methionine (AdoMet) and product S-adenosyl-l-homocysteine (AdoHcy) form similar rapidly reversible binary complexes with the enzyme in solution. The M.HhaI.AdoMet complex (k(off) = 22 s(-)1, K(D) = 6 microm) is partially converted into products during isotope-partitioning experiments, suggesting that it is catalytically competent. Chemical formation of the product M.HhaI.(Me)DNA.AdoHcy (k(chem) = 0.26 s(-)1) is followed by a slower decay step (k(off) = 0.045 s(-)1), which is the rate-limiting step in the catalytic cycle (k(cat) = 0.04 s(-)1). Analysis of reaction products shows that the hemimethylated substrate undergoes complete (&gt;95\%) conversion into fully methylated product during the initial burst phase, indicating that M.HhaI exerts high binding selectivity toward the target strand. The T250N, T250D, and T250H mutations, which introduce moderate perturbation in the catalytic site, lead to substantially increased K(D)(DNA(ternary)), k(off)(DNA(ternary)), K(M)(AdoMet(ternary)) values but small changes in K(D)(DNA(binary)), K(D)(AdoMet(binary)), k(chem), and k(cat). When the target cytosine is replaced with 5-fluorocytosine, the chemistry step leading to an irreversible covalent M.HhaI.DNA complex is inhibited 400-fold (k(chem)(5FC) = 0.7 x 10(-)3 s(-)1), and the Thr-250 mutations confer further dramatic decrease of the rate of the covalent methylation k(chem). We suggest that activation of the pyrimidine ring via covalent addition at C-6 is a major contributor to the rate of the chemistry step (k(chem)) in the case of cytosine but not 5-fluorocytosine. In contrast to previous reports, our results imply a random substrate binding order mechanism for M.HhaI.},
  file      = {:by-author/V/Vilkaitis/2001_Vilkaitis_20924.pdf:PDF},
  keywords  = {HhaI},
  owner     = {saulius},
  timestamp = {2012.11.05},
  creationdate = {2012-11-05T00:00:00},
}

@Article{Villars2004a,
  author    = {P. Villars and M. Berndt and K. Brandenburg and K. Cenzual and J. Daams and F. Hulliger and T. Massalski and H. Okamoto and K. Osaki and A. Prince and H. Putz and S. Iwata},
  journal   = {Journal of Alloys and Compounds},
  title     = {The Pauling File, Binaries Edition},
  year      = {2004},
  issn      = {0925-8388},
  note      = {Proceedings of the \{VIII\} International Conference on Crystal Chemistry of Intermetallic Compounds},
  number    = {1–2},
  pages     = {293 - 297},
  volume    = {367},
  abstract  = {The Pauling File project was launched in 1995 with the aim to create tools for scientists working with inorganic compounds, with particular focus on materials design. As a first step, a comprehensive, phase-oriented database is being built up. It groups four categories of data under the retrieval software: constitution data, crystal structure data, powder diffraction data, and a broad range of physical properties. The project will cover all binary, ternary and multinary, non-organic compounds (no CH bonds), but the first edition is limited to binary compounds.},
  doi       = {10.1016/j.jallcom.2003.08.058},
  file      = {2004_Villars_293.pdf:by-author/V/Villars/2004_Villars_293.pdf:PDF},
  keywords  = {Pauling File},
  owner     = {saulius},
  timestamp = {2014.09.07},
  creationdate = {2014-09-07T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/S0925838803008429},
}

@Article{Villars2001,
  author    = {P Villars and K Brandenburg and M Berndt and S LeClair and A Jackson and Y.-H Pao and B Igelnik and M Oxley and B Bakshi and P Chen and S Iwata},
  journal   = {Journal of Alloys and Compounds},
  title     = {Binary, ternary and quaternary compound former/nonformer prediction via Mendeleev number},
  year      = {2001},
  issn      = {0925-8388},
  note      = {The 13th International Conference on Solid Compounds of Transition Elements},
  number    = {0},
  pages     = {26 - 38},
  volume    = {317–318},
  abstract  = {A significant breakthrough has been achieved in the design of new materials by using materials databases, semiempirical approaches and neural networks. It was found in the present work that a nonlinear expression involving one elemental property parameter can be used to predict, with an overall accuracy exceeding 99%, the occurrence of a compound for any binary, ternary or quaternary system. This elemental property parameter, referred to as the Mendeleev number, was conceived by D.G. Pettifor in 1983 to group binary compounds by crystal structures. The immediate profit of this discovery is the obvious savings, in time and resources, relative to the investigation of yet-to-be-studied, materials systems. In the longer term the relation found here will make it possible to better define the search space for the development of new materials and encourage attempts to predict more specific information such as stoichiometries, crystal structures and physical properties.},
  doi       = {10.1016/S0925-8388(00)01410-9},
  file      = {2001_Villars_26.pdf:by-author/V/Villars/2001_Villars_26.pdf:PDF},
  keywords  = {Materials Design},
  owner     = {saulius},
  timestamp = {2014.09.07},
  creationdate = {2014-09-07T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/S0925838800014109},
}

@Article{Villars2000,
  author    = {P Villars and K Brandenburg and M Berndt and S LeClair and A Jackson and Y.-H Paod and B Igelnik and M Oxley and B Bakshi and P Chen and S Iwata},
  journal   = {Engineering Applications of Artificial Intelligence},
  title     = {Interplay of large materials databases, semi-empirical methods, neuro-computing and first principle calculations for ternary compound former/nonformer prediction},
  year      = {2000},
  issn      = {0952-1976},
  pages     = {497 - 505},
  volume    = {13},
  abstract  = {A significant breakthrough has been achieved using materials databases, semi-empirical methods and neural networks to aid in the design of new materials. A collaborative, international, team discovered that a non-linear expression involving one elemental property parameter could be used to predict, with 99+% accuracy, the occurrence of a compound for any ternary materials system. This elemental property parameter, referred to as the Mendeleev Number, was conceived by D.G. Pettifor in 1984 to group binary compounds by structure type. The near term significance of this discovery is the obvious savings, in time and resources, relative to assessing the merits of future, yet-to-be-realized, materials systems. In longer term this breakthrough is the basis for both narrowing the search space for potentially beneficial new materials and enabeling the prediction of even more specific materials information such as stoichiometries, crystal structures and intrinsic properties.},
  doi       = {10.1016/S0952-1976(00)00028-2},
  file      = {2000_Villars_497.pdf:by-author/V/Villars/2000_Villars_497.pdf:PDF},
  keywords  = {Materials Design},
  owner     = {saulius},
  timestamp = {2014.09.07},
  creationdate = {2014-09-07T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/S0952197600000282},
}

@Article{Villars2004,
  author    = {P. Villars and K. Cenzual and J. Daams and Y. Chen and S. Iwata},
  journal   = {Journal of Alloys and Compounds},
  title     = {Data-driven atomic environment prediction for binaries using the Mendeleev number: Part 1. Composition \{AB\}},
  year      = {2004},
  issn      = {0925-8388},
  note      = {Proceedings of the \{VIII\} International Conference on Crystal Chemistry of Intermetallic Compounds},
  number    = {1–2},
  pages     = {167 - 175},
  volume    = {367},
  abstract  = {The atomic environment types (AETs) (coordination polyhedra) realized by each chemical element in binary compounds at the equi-atomic composition were analyzed based on a comprehensive set of literature data. The Mendeleev number (MN) (ordering number listing the chemical elements column by column through the periodic system) was successfully used to classify the chemical systems. An atomic environment type map, using as coordinates the maximum Mendeleev number versus the ratio between the minimum and the maximum Mendeleev number, sub-divided the chemical systems where different atomic environment types occur in distinct stability domains. The same maps also showed a clear separation between chemical systems where intermediate compounds form and those where no compounds form. These maps make it possible to predict the existence of compound that have not yet been investigated with a particular atomic environment.},
  doi       = {10.1016/j.jallcom.2003.08.060},
  file      = {2004_Villars_167.pdf:by-author/V/Villars/2004_Villars_167.pdf:PDF},
  keywords  = {Atomic Environment; Data Mining; Mendeleev Number},
  owner     = {saulius},
  timestamp = {2014.09.07},
  creationdate = {2014-09-07T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/S0925838803008004},
}

@Article{Villars1998,
  author    = {P. Villars and N. Onodera and S. Iwata},
  journal   = {Journal of Alloys and Compounds},
  title     = {The Linus Pauling file (LPF) and its application to materials design},
  year      = {1998},
  issn      = {0925-8388},
  pages     = {1 - 7},
  volume    = {279},
  abstract  = {The \{LPF\} is a database which consists of a data part, as well as a smart software part. The data part covers all non-organic (e.g., alloys, intermetallics, ceramics, minerals, etc.) ordered solid state materials (systems) and consists of structure, diffraction, constitution, intrinsic property and bibliographic information. In materials science, the crystal structure of a compound holds the key-position, and is governed by five elemental factors: size, atomic-number, electrochemical, valence-electron and angular valence-orbital. The relations between these factors and the crystal structure are very complex, but the many regularities found to date prove that these relations are not only of a qualitative but, as well, a quantitative nature with an acceptable accuracy. The authors are completely convinced that, in the future, if one wishes to find, efficiently and systematically, novel multinary materials, the process will involve linking large databases such as the \{LPF\} (information) in a clever way with already known principles (knowledge), and thus creating an information-knowledge system, preferably via international collaboration.},
  doi       = {10.1016/S0925-8388(98)00605-7},
  file      = {1998_Villars_1.pdf:by-author/V/Villars/1998_Villars_1.pdf:PDF},
  keywords  = {Materials Database; Materials Design; Materials Structure Prediction; Regularities},
  owner     = {saulius},
  timestamp = {2014.09.07},
  creationdate = {2014-09-07T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/S0925838898006057},
}

@Article{Villegas2013,
  author    = {Villegas, Edward},
  title     = {Diseno de nuevos materiales duros por métodos ab initio},
  year      = {2013},
  file      = {[PDF] from researchgate.net:by-author/V/Villegas/2013_Villegas.pdf:application/pdf},
  groups    = {sg/NAR2012},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://www.researchgate.net/profile/Edward_Villegas/publication/260247790_Diseo_de_nuevos_materiales_duros_por_mtodos_ab_initio/links/00b7d5304fa86dfcad000000.pdf},
  urldate   = {2015-08-31},
}

@Article{Villemain2000,
  author    = {Villemain, J. L. and Ma, Y. and Giedroc, D. P. and Morrical, S. W.},
  journal   = {The Journal of biological chemistry},
  title     = {Mutations in the N-terminal cooperativity domain of gene 32 protein alter properties of the T4 DNA replication and recombination systems.},
  year      = {2000},
  pages     = {31496--504},
  volume    = {275},
  abstract  = {The gene 32 protein (gp32) of bacteriophage T4 is the essential single-stranded DNA (ssDNA)-binding protein required for phage DNA replication and recombination. gp32 binds ssDNA with high affinity and cooperativity, forming contiguous clusters that optimally configure the ssDNA for recognition by DNA polymerase or recombination enzymes. The precise roles of gp32 affinity and cooperativity in promoting replication and recombination have yet to be defined, however. Previous work established that the N-terminal "B-domain" of gp32 is essential for cooperativity and that point mutations at Arg(4) and Lys(3) positions have varying and dramatic effects on gp32-ssDNA interactions. Therefore, we examined the effects of six different gp32 B-domain mutants on T4 in vitro systems for DNA synthesis and homologous pairing. We find that the B-domain is essential for gp32's stimulation of these reactions. The stimulatory efficacy of gp32 B-domain mutants generally correlates with the hierarchy of relative ssDNA binding affinities, i.e. wild-type gp32 approximately R4K &gt; K3A approximately R4Q &gt; R4T &gt; R4G gp32-B. However, the functional defect of a particular mutant is often greater than can be explained simply by its ability to saturate the ssDNA at equilibrium, suggesting additional defects in the proper assembly and activity of DNA polymerase and recombinase complexes on ssDNA, which may derive from a decreased lifetime of gp32-ssDNA clusters.},
  file      = {:by-author/V/Villemain/2000_Villemain_31496.pdf:PDF},
  keywords  = {Solid-state Batteries (SSB); {gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Manuscript{Vincent2002,
  author    = {Etienne Vincent and Robert Laganiere},
  title     = {Detecting Planar Homographies in an Image Pair},
  year      = {2002},
  keywords  = {Algorithms; Homography},
  url       = {http://www.site.uottawa.ca/research/viva/papers/homographie.pdf},
  comment   = {This paper proposes an algorithm that detects planar ho- mographies in uncalibrated image pairs. It then demon- strates how this plane identification method can be used as a first step in an image analysis process, when point matching between images is unreliable. The detection is performed using a RANSAC scheme based on the linear computation of the homography matrix elements using four points. Results are shown on real image pairs.},
  file      = {:by-author/V/Vincent/2002_Vincent.pdf:PDF},
  owner     = {andrius},
  timestamp = {2013.01.24},
  creationdate = {2013-01-24T00:00:00},
}

@Article{Vitkute1998,
  author    = {Vitkute, J. and Maneliene, Z. and Petrusyte, M. and Janulaitis, A.},
  journal   = {Nucleic acids research},
  title     = {BfiI, a restriction endonuclease from Bacillus firmus S8120, which recognizes the novel non-palindromic sequence 5'-ACTGGG(N)5/4-3'.},
  year      = {1998},
  pages     = {3348--9},
  volume    = {26},
  abstract  = {A new type IIS restriction endonuclease Bfi I hasbeen partially purified from Bacillus firmus S8120. Bfi I recognizes the non-palindromic hexanucleotide sequence 5'-ACTGGG(N)5/4-3' and makes a staggered cut at the fifth base pair downstream of the recognition sequence on the upper strand, producing a single base 3' protruding end.},
  file      = {:by-author/V/Vitkute/1998_Vitkute_3348.pdf:PDF},
  keywords  = {BfiI; TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Vitkute2001,
  author    = {Vitkute, J. and Stankevicius, K. and Tamulaitiene, G. and Maneliene, Z. and Timinskas, A. and Berg, D. E. and Janulaitis, A.},
  journal   = {Journal of bacteriology},
  title     = {Specificities of eleven different DNA methyltransferases of Helicobacter pylori strain 26695.},
  year      = {2001},
  pages     = {443--50},
  volume    = {183},
  abstract  = {Methyltransferases (MTases) of procaryotes affect general cellular processes such as mismatch repair, regulation of transcription, replication, and transposition, and in some cases may be essential for viability. As components of restriction-modification systems, they contribute to bacterial genetic diversity. The genome of Helicobacter pylori strain 26695 contains 25 open reading frames encoding putative DNA MTases. To assess which MTase genes are active, strain 26695 genomic DNA was tested for cleavage by 147 restriction endonucleases; 24 were found that did not cleave this DNA. The specificities of 11 expressed MTases and the genes encoding them were identified from this restriction data, combined with the known sensitivities of restriction endonucleases to specific DNA modification, homology searches, gene cloning and genomic mapping of the methylated bases m(4)C, m(5)C, and m(6)A.},
  file      = {:by-author/V/Vitkute/2001_Vitkute_443.pdf:PDF},
  keywords  = {Methylase; TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Vivares2002,
  author    = {Vivar{\`{e}}s, D. and Bonnet{\'{e}}, F.},
  journal   = {Acta Crystallographica Section D},
  title     = {X-ray scattering studies of {\it Aspergillus flavus} urate oxidase: towards a better understanding of PEG effects on the crystallization of large proteins},
  year      = {2002},
  pages     = {472--479},
  volume    = {58},
  doi       = {10.1107/S0907444902000124},
  file      = {en0057.pdf:by-author/V/Vivares/2002_Vivares_472.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444902000124},
}

@Article{Vocadlo2004,
  author    = {Vocadlo, David J. and Bertozzi, Carolyn R.},
  journal   = {Angewandte Chemie (International ed. in English)},
  title     = {A strategy for functional proteomic analysis of glycosidase activity from cell lysates.},
  year      = {2004},
  pages     = {5338--42},
  volume    = {43},
  file      = {:by-author/V/Vocadlo/2004_Vocadlo_5338.pdf:PDF},
  keywords  = {Bioconjugation},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@Article{Volkov2003,
  author    = {Volkov, Vladimir V. and Svergun, Dmitri I.2},
  journal   = {Journal of Applied Crystallography},
  title     = {Uniqueness of {\it ab initio} shape determination in small-angle scattering},
  year      = {2003},
  pages     = {860--864},
  volume    = {36},
  abstract  = {Scattering patterns from geometrical bodies with different shapes and anisometry (solid and hollow spheres, cylinders, prisms) are computed and the shapes are reconstructed ab initio using envelope function and bead modelling methods. A procedure is described to analyze multiple solutions provided by bead modeling methods and to estimate stability and reliability of the shape reconstruction. It is demonstrated that flat shapes are more difficult to restore than elongated ones and types of shapes are indicated, which require additional information for reliable shape reconsrtuction from the scattering data.},
  doi       = {10.1107/S0021889803000268},
  file      = {2003_Volkov_860.pdf:by-author/V/Volkov/2003_Volkov_860.pdf:PDF},
  keywords  = {DAMAVER; SAXS; Shape},
  owner     = {em},
  timestamp = {2013.01.02},
  creationdate = {2013-01-02T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0021889803000268},
}

@Article{Volodin2014,
  author    = {Volodin, A. A. and Fursikov, P. V. and Belmesov, A. A. and Shul’ga, Yu M. and Khodos, I. I. and Abdusalyamova, M. N. and Tarasov, B. P.},
  journal   = {Inorganic Materials},
  title     = {Electrical conductivity of lanthanum oxide based composites containing carbon nanofibers},
  year      = {2014},
  pages     = {673--681},
  volume    = {50},
  file      = {[PDF] from researchgate.net:by-author/V/Volodin/2014_Volodin_673.pdf:application/pdf;Snapshot:by-author/V/Volodin/2014_Volodin_673.html:text/html},
  groups    = {sg/JAC2009},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://link.springer.com/article/10.1134/S0020168514070164},
  urldate   = {2015-08-31},
}

@Article{Vondrous,
  author    = {Vondrous, A. and Jejkal, T. and Ressmann, D. and Mexner, W. and Stotzka, R.},
  title     = {{BEAMLINE} {DATA} {MANAGEMENT} {AT} {THE} {SYNCHROTRON} {ANKA}},
  file      = {[PDF] from kek.jp:by-author/V/Vondrous/XXXX_Vondrous.pdf:application/pdf},
  groups    = {sg/NAR2012},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://epaper.kek.jp/PCaPAC2014/papers/fpo034.pdf},
  urldate   = {2015-08-31},
}

@PhdThesis{Votsis2004,
  author    = {Votsis},
  school    = {London School of Economics And Political Science},
  title     = {The Epistemological Status of Scientific Theories: An Investigation of The Structural Realist Account},
  year      = {2004},
  abstract  = {In this dissertation, I examine a view called ‘Epistemic Structural Realism’, which holds that we can, at best, have knowledge of the structure of the physical world. Put crudely, we can know physical objects only to the extent that they are nodes in a structure. In the spirit of Occam’s razor, I argue that, given certain minimal assumptions, epistemic structural realism provides a viable and reasonable scientific realist position that is less vulnerable to anti-realist arguments than any of its rivals.},
  file      = {:by-author/V/Votsis/2004_Votsis_phdthesis.pdf:PDF},
  keywords  = {Epistemology; Philosophy},
  owner     = {saulius},
  pages     = {phdthesis},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Voutsas1982,
  author    = {G. P. Voutsas and P. J. Rentzeperis},
  journal   = {Zeitschrift fur Kristallographie},
  title     = {The Crystal Structure of Antimony Selenoiodide, {ShSeI}},
  year      = {1982},
  pages     = {111},
  file      = {:by-author/V/Voutsas/1982_Voutsas_111.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Voziyan2005,
  author    = {Voziyan, Paul A. and Johnston, Mary and Chao, Angela and Bomhoff, Greg and Fisher, Mark T.},
  journal   = {Journal of structural and functional genomics},
  title     = {Designing a high throughput refolding array using a combination of the GroEL chaperonin and osmolytes.},
  year      = {2005},
  pages     = {183--8},
  volume    = {6},
  abstract  = {Although GroE chaperonins and osmolytes had been used separately as protein folding aids, combining these two methods provides a considerable advantage for folding proteins that cannot fold with either osmolytes or chaperonins alone. This technique rapidly identifies superior folding solution conditions for a broad array of proteins that are difficult or impossible to fold by other methods. While testing the broad applicability of this technique, we have discovered that osmolytes greatly simplify the chaperonin reaction by eliminating the requirement for the co-chaperonin GroES which is normally involved in encapsulating folding proteins within the GroEL-GroES cavity. Therefore, combinations of soluble or immobilized GroEL, osmolytes and ATP or even ADP are sufficient to refold the test proteins. The first step in the chaperonin/osmolyte process is to form a stable long-lived chaperonin-substrate protein complex in the absence of nucleotide. In the second step, different osmolyte solutions are added along with nucleotides, thus forming a 'folding array' to identify superior folding conditions. The stable chaperonin-substrate protein complex can be concentrated or immobilized prior to osmolyte addition. This procedure prevents-off pathway aggregation during folding/refolding reactions and more importantly allows one to refold proteins at concentrations (approximately mg/ml) that are substantially higher than the critical aggregation concentration for given protein. This technique can be used for successful refolding of proteins from purified inclusion bodies. Recently, other investigators have used our chaperonin/osmolyte method to demonstrate that a mutant protein that misfolds in human disease can be rescued by GroEL/osmolyte system. Soluble or immobilized GroEL can be easily removed from the released folded protein using simple separation techniques. The method allows for isolation of folded monomeric or oligomeric proteins in quantities sufficient for X-ray crystallography or NMR structural determinations.},
  file      = {:by-author/V/Voziyan/2005_Voziyan_183.pdf:PDF},
  keywords  = {Grow Krystal},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Vreshch2011,
  author    = {Vreshch, Volodimir},
  journal   = {Journal of Applied Crystallography},
  title     = {{\it DiffractWD}: an open-source program for powder pattern comparison and visualization},
  year      = {2011},
  month     = {Feb},
  number    = {1},
  pages     = {219--220},
  volume    = {44},
  abstract  = {A new program for basic powder pattern manipulations and visualization is described. It provides a user-friendly interface for comparison of spectra with each other and with simulated patterns based on single-crystal data. The program contains all necessary tools for the preparation of routine images for qualitative phase analysis and can be downloaded free of charge from http://diffractwd.com.},
  doi       = {10.1107/S0021889810044614},
  file      = {2011_Vreshch_219.pdf:by-author/V/Vreshch/2011_Vreshch_219.pdf:PDF},
  keywords  = {Computer Programs; DiffractWD; Phase Analysis; Powder Patterns},
  owner     = {saulius},
  timestamp = {2016.07.22},
  creationdate = {2016-07-22T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0021889810044614},
}

@Article{Vukicevic2009,
  author    = {Damir Vukičević},
  journal   = {Kragujevac J. Math.},
  title     = {On the rules for the elimination of the non-canonical Morgan trees},
  year      = {2009},
  pages     = {117--122},
  abstract  = {The concept of Morgan tree [6] is shown to be useful in generation of all non- isomorphic trees. Namely, to each tree one can assign canonical Morgan tree. Since, the number of Morgan trees [5, 1] is much larger then number of canonical Morgan trees, it is of interest to create an efficient algorithm that creates only a fraction of Morgan trees not eliminating the single canonical Morgan tree. Then, in the second step, non-canonical trees are eliminated. The rules for the recognition of non-canonical trees are proposed in [4, 3]. However, it seems that Rule 3 in [4] and Rule 1se in paper [3] are not correct. In this paper, we present the counter-examples to these rules.},
  file      = {:by-author/V/Vukičević/2009_Vukicevic_117.pdf:PDF},
  owner     = {saulius},
  timestamp = {2014.01.26},
  creationdate = {2014-01-26T00:00:00},
  url       = {http://www.kjm.pmf.kg.ac.rs/pub/12614768414947_kjom3211.pdf},
}

@Article{Vullo2005,
  author    = {Vullo, Daniela and Innocenti, Alessio and Nishimori, Isao and Pastorek, Jaromír and Scozzafava, Andrea and Pastoreková, Silvia and Supuran, Claudiu T},
  journal   = {Bioorganic \&amp; medicinal chemistry letters},
  title     = {Carbonic anhydrase inhibitors. Inhibition of the transmembrane isozyme XII with sulfonamides-a new target for the design of antitumor and antiglaucoma drugs?},
  year      = {2005},
  pages     = {963--9},
  volume    = {15},
  file      = {2005_Vullo_963.pdf:by-author/V/Vullo/2005_Vullo_963.pdf:PDF},
  groups    = {sg/inhibitors, sg/hCA12},
  keywords  = {Carbonic Anhydrases},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Vullo2005a,
  author    = {Vullo, Daniela and Voipio, Juha and Innocenti, Alessio and Rivera, Claudio and Ranki, Harri and Scozzafava, Andrea and Kaila, Kai and Supuran, Claudiu T},
  journal   = {Bioorganic \&amp; medicinal chemistry letters},
  title     = {Carbonic anhydrase inhibitors. Inhibition of the human cytosolic isozyme VII with aromatic and heterocyclic sulfonamides.},
  year      = {2005},
  pages     = {971--6},
  volume    = {15},
  file      = {2005_Vullo_971.pdf:by-author/V/Vullo/2005_Vullo_971.pdf:PDF},
  groups    = {sg/inhibitors, sg/hCA7},
  keywords  = {Carbonic Anhydrases},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@InProceedings{Vyas,
  author    = {Dhaval Vyas and Olga Kulyk and Paul van der Vet and Anton Nijholt and Gerrit C. van der Veer},
  booktitle = {Proceedings of the 15th European Conference on Cognitive Ergonomics: The Ergonomics of Cool Interaction},
  title     = {Structures of Life: The Role of Molecular Structures in Scientists’ Work},
  year      = {2008},
  pages     = {12:1--12:4},
  series    = {ECCE '08},
  doi       = {10.1145/1473018.1473034},
  file      = {:by-author/V/Vyas/2008_Vyas_1.pdf:PDF},
  isbn      = {978-1-60558-399-0},
  journal   = {Structures of Life},
  owner     = {antanas},
  timestamp = {2013.12.12},
  creationdate = {2013-12-12T00:00:00},
  url       = {http://doi.acm.org/10.1145/1473018.1473034},
}

@TechReport{Wadler1990,
  author      = {Philip Wadler},
  institution = {University of Glasgow},
  title       = {Linear types can change the world!},
  year        = {1990},
  abstract    = {The linear logic of J.-Y. Girard suggests a new type system for functional languages, one which supports operations that \change the world". Values be- longing to a linear type must be used exactly once: like the world, they cannot be duplicated or destroyed. Such values require no reference counting or garbage collection, and safely admit destructive array update. Linear types extend Schmidt's notion of single threading; provide an alternative to Hudak and Bloss' update analysis; and o er a practical complement to Lafont and Holmstrom's elegant linear languages.},
  file        = {:by-author/W/Wadler/1990_Wadler.ps.gz:PostScript;:by-author/W/Wadler/1990_Wadler.pdf:PDF},
  groups      = {sg/Garbage collectors},
  owner       = {saulius},
  timestamp = {2015.02.27},
  creationdate = {2015-02-27T00:00:00},
}

@Article{Wagenfuehr2007,
  author    = {Katja Wagenführ and Stefan Pieper and Petra Mackeldanz and Michael Linscheid and Detlev H. Krüger and Monika Reuter},
  journal   = {J. Mol. Biol.},
  title     = {Structural Domains in the Type {III} Restriction Endonuclease {EcoP15I}: Characterization by Limited Proteolysis, Mass Spectrometry and Insertional Mutagenesis},
  year      = {2007},
  pages     = {93--102},
  doi       = {10.1016/j.jmb.2006.10.087},
  file      = {:by-author/W/Wagenfuehr/2007_Wagenfuehr_93.pdf:PDF},
  keywords  = {TypeIII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Wagenfuhr2007,
  author    = {Wagenführ, Katja and Pieper, Stefan and Mackeldanz, Petra and Linscheid, Michael and Krüger, Detlev H. and Reuter, Monika},
  journal   = {Journal of molecular biology},
  title     = {Structural domains in the type III restriction endonuclease EcoP15I: characterization by limited proteolysis, mass spectrometry and insertional mutagenesis.},
  year      = {2007},
  pages     = {93--102},
  volume    = {366},
  abstract  = {The Type III restriction endonuclease EcoP15I forms a hetero-oligomeric enzyme complex that consists of two modification (Mod) subunits and two restriction (Res) subunits. Structural data on Type III restriction enzymes in general are lacking because of their remarkable size of more than 400 kDa and the laborious and low-yield protein purification procedures. We took advantage of the EcoP15I-overexpressing vector pQEP15 and affinity chromatography to generate a quantity of EcoP15I high enough for comprehensive proteolytic digestion studies and analyses of the proteolytic fragments by mass spectrometry. We show here that in the presence of specific DNA the entire Mod subunit is protected from trypsin digestion, whereas in the absence of DNA stable protein domains of the Mod subunit were not detected. In contrast, the Res subunit is comprised of two trypsin-resistant domains of approximately 77-79 kDa and 27-29 kDa, respectively. The cofactor ATP and the presence of DNA, either specific or unspecific, are important stabilizers of the Res subunit. The large N-terminal domain of Res contains numerous functional motifs that are predicted to be involved in ATP-binding and hydrolysis and/or DNA translocation. The C-terminal small domain harbours the catalytic center. Based on our data, we conclude that both structural Res domains are connected by a flexible linker region that spans 23 amino acid residues. To confirm this conclusion, we have investigated several EcoP15I enzyme mutants obtained by insertion mutagenesis in and around the predicted linker region within the Res subunit. All mutants tolerated the genetic manipulation and did not display loss of function or alteration of the DNA cleavage position.},
  file      = {:by-author/W/Wagenführ/2007_Wagenführ_93.pdf:PDF},
  keywords  = {TypeIII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Wagenmakers2007,
  author    = {Eric-Jan Wagenmakers},
  journal   = {Psychonomic Bulletin \& Review},
  title     = {A practical solution to the pervasive problems of P values},
  year      = {2007},
  pages     = {779--804},
  volume    = {14},
  file      = {2007_Wagenmakers_779.pdf:by-author/W/Wagenmakers/2007_Wagenmakers_779.pdf:PDF;2007_Wagenmakers_779corrigendum.pdf:by-author/W/Wagenmakers/2007_Wagenmakers_779corrigendum.pdf:PDF},
  groups    = {sg/Bayesian},
  keywords  = {Bayesian Statistics; Hypothesis Testing},
  owner     = {saulius},
  timestamp = {2015.12.18},
  creationdate = {2015-12-18T00:00:00},
  url       = {http://www.ejwagenmakers.com/2007/pValueProblems.pdf},
}

@Article{Wagenmakers2007a,
  author    = {Eric-Jan Wagenmakers},
  journal   = {Psychonomic Bulletin \& Review},
  title     = {A practical solution to the pervasive problems of P values (corrigendum)},
  year      = {2007},
  pages     = {779--804},
  volume    = {14},
  file      = {2007_Wagenmakers_779corrigendum.pdf:by-author/W/Wagenmakers/2007_Wagenmakers_779corrigendum.pdf:PDF},
  groups    = {sg/Bayesian},
  keywords  = {Bayesian Statistics; Hypothesis Testing},
  owner     = {saulius},
  timestamp = {2015.12.18},
  creationdate = {2015-12-18T00:00:00},
  url       = {http://www.ejwagenmakers.com/2007/CorrigendumPvalues.pdf},
}

@Manuscript{Wagenmakers2010,
  author    = {Eric-Jan Wagenmakers and Michael Lee and Tom Lodewyckx and Geoffrey J. Iverson},
  title     = {Bayesian Versus Frequentist Inference},
  year      = {2010},
  keywords  = {Bayesian Statistics; Frequentist Statistics Criticism},
  file      = {:by-author/W/Wagenmakers/2010_Wagenmakers_181.pdf:PDF},
  groups    = {sg/Bayesian},
  owner     = {saulius},
  pages     = {181},
  timestamp = {2012.09.30},
  creationdate = {2012-09-30T00:00:00},
}

@Article{Wagner2010,
  author    = {Wagner, Jason and Avvaru, Balendu Sankara and Robbins, Arthur H and Scozzafava, Andrea and Supuran, Claudiu T and McKenna, Robert},
  journal   = {Bioorganic \&amp; medicinal chemistry},
  title     = {Coumarinyl-substituted sulfonamides strongly inhibit several human carbonic anhydrase isoforms: solution and crystallographic investigations.},
  year      = {2010},
  pages     = {4873--8},
  volume    = {18},
  file      = {2010_Wagner_4873.pdf:by-author/W/Wagner/2010_Wagner_4873.pdf:PDF},
  groups    = {sg/inhibitors},
  keywords  = {Carbonic Anhydrases; Inhibitors},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@InProceedings{Wagner1988,
  author       = {Kenneth D. Wagner},
  booktitle    = {IEEE Design \& Test of Computers},
  title        = {Clock System Design},
  year         = {1988},
  month        = {October},
  organization = {IBM Corp.},
  pages        = {8--27},
  file         = {1988_Wagner_8.pdf:by-author/W/Wagner/1988_Wagner_8.pdf:PDF},
  keywords     = {CPU Design; Computer Science (CS); Electronics},
  owner        = {saulius},
  timestamp = {2015.03.11},
  creationdate = {2015-03-11T00:00:00},
  url          = {http://web.ece.ucdavis.edu/~vojin/CLASSES/EEC280/Web-page/papers/Clocking/clk-dsgn-Wagner88.pdf},
}

@Article{Wah1998,
  author    = {Wah, D. A. and Bitinaite, J. and Schildkraut, I. and Aggarwal, A. K.},
  journal   = {Proceedings of the National Academy of Sciences of the United States of America},
  title     = {Structure of FokI has implications for DNA cleavage.},
  year      = {1998},
  pages     = {10564--9},
  volume    = {95},
  abstract  = {FokI is a member an unusual class of restriction enzymes that recognize a specific DNA sequence and cleave nonspecifically a short distance away from that sequence. FokI consists of an N-terminal DNA recognition domain and a C-terminal cleavage domain. The bipartite nature of FokI has led to the development of artificial enzymes with novel specificities. We have solved the structure of FokI to 2.3 A resolution. The structure reveals a dimer, in which the dimerization interface is mediated by the cleavage domain. Each monomer has an overall conformation similar to that found in the FokI-DNA complex, with the cleavage domain packing alongside the DNA recognition domain. In corroboration with the cleavage data presented in the accompanying paper in this issue of Proceedings, we propose a model for FokI DNA cleavage that requires the dimerization of FokI on DNA to cleave both DNA strands.},
  file      = {:by-author/W/Wah/1998_Wah_10564.pdf:PDF},
  keywords  = {Octanucleotide Site; TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Wah1997,
  author    = {Wah, D A and Hirsch, J A and Dorner, L F and Schildkraut, I and Aggarwal, A K},
  journal   = {Nature},
  title     = {Structure of the multimodular endonuclease FokI bound to DNA.},
  year      = {1997},
  pages     = {97--100},
  volume    = {388},
  abstract  = {FokI is a member of an unusual class of bipartite restriction enzymes that recognize a specific DNA sequence and cleave DNA nonspecifically a short distance away from that sequence. Because of its unusual bipartite nature, FokI has been used to create artificial enzymes with new specificities. We have determined the crystal structure at 2.8A resolution of the complete FokI enzyme bound to DNA. As anticipated, the enzyme contains amino- and carboxy-terminal domains corresponding to the DNA-recognition and cleavage functions, respectively. The recognition domain is made of three smaller subdomains (D1, D2 and D3) which are evolutionarily related to the helix-turn-helix-containing DNA-binding domain of the catabolite gene activator protein CAP. The CAP core has been extensively embellished in the first two subdomains, whereas in the third subdomain it has been co-opted for protein-protein interactions. Surprisingly, the cleavage domain contains only a single catalytic centre, raising the question of how monomeric FokI manages to cleave both DNA strands. Unexpectedly, the cleavage domain is sequestered in a 'piggyback' fashion by the recognition domain. The structure suggests a new mechanism for nuclease activation and provides a framework for the design of chimaeric enzymes with altered specificities.},
  file      = {Wah_1997_97_Nature-Structure_monomeric_FokI_DNA.pdf:by-author/W/Wah/1997_Wah_97.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@TechReport{Wain2006,
  author      = {Richard Wain and Ian Bush and Martyn Guest and Miles Deegan and Igor Kozin and Christine Kitchen},
  institution = {Computational Science and Engineering Department, CCLRC Daresbury Laboratory, Daresbury, Warrington, Cheshire, WA4 4AD, UK},
  title       = {An overview of FPGAs and FPGA programming; Initial experiences at Daresbury},
  year        = {2006},
  month       = {November},
  abstract    = {This report will provide a brief introduction to Field Programmable Gate Arrays (FPGAs), the key reasons for their emergence into the High Performance Computing (HPC) market and the difficulties of assessing their performance against that of conventional microprocessors. It will also discuss FPGA programming tools and the key challenges involved in programming these devices. As well as providing some background information on FPGAs and FPGA programming this report will cover our initial experiences of FPGA programming with specific reference to the Cray XD1 system.},
  file        = {:by-author/W/Wain/2006_Wain.pdf:PDF},
  keywords    = {Computer Science (CS); FPGA},
  owner       = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Wakelin2005,
  author    = {Wakelin, J. and Murray-Rust, P. and Tyrrell, S. and Zhang, Y. and Rzepa, H. S. and García, A.},
  journal   = {Molecular Simulation},
  title     = {CML tools and information flow in atomic scale simulations},
  year      = {2005},
  pages     = {315--322},
  volume    = {31},
  abstract  = {High-throughput computation of molecules and crystals is supported through an XML infrastructure based on Chemical Markup Language (CML). Tools have been developed for the automatic creation of job input and the extraction of structured XML information from the output. The approach is generic and supports several languages (Java, C++, Python, FORTRAN) so that “black-box” modules can be created.},
  doi       = {10.1080/08927020500065850},
  eprint    = {http://dx.doi.org/10.1080/08927020500065850},
  file      = {2005_Wakelin_315.pdf:by-author/W/Wakelin/2005_Wakelin_315.pdf:PDF},
  keywords  = {CML; Chemoinformatics; Computational Chemistry; Crystallography; Data Formats; Data Management; X-ray Crystallography; XML},
  owner     = {saulius},
  timestamp = {2014.06.24},
  creationdate = {2014-06-24T00:00:00},
  url       = {http://dx.doi.org/10.1080/08927020500065850},
}

@Article{Waldrop1992,
  author    = {Waldrop, M M},
  journal   = {Science (New York, N.Y.)},
  title     = {Finding RNA makes proteins gives 'RNA world' a big boost.},
  year      = {1992},
  pages     = {1396--7},
  volume    = {256},
  file      = {1992_Waldrop_1396.pdf:by-author/W/Waldrop/1992_Waldrop_1396.pdf:PDF},
  keywords  = {RNA World; Ribozymes},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Waldrop1989,
  author    = {Waldrop, M M},
  journal   = {Science (New York, N.Y.)},
  title     = {Did life really start out in an RNA world?},
  year      = {1989},
  pages     = {1248--9},
  volume    = {246},
  file      = {1989_Waldrop_1248.pdf:by-author/W/Waldrop/1989_Waldrop_1248.pdf:PDF},
  keywords  = {RNA World; Ribozymes},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Manuscript{Walker2000,
  author    = {Walker, David and Greg Morrisett},
  title     = {Alias Types for Recursive Data Structures},
  year      = {2000},
  keywords  = {Computer Science (CS); Type Systems},
  abstract  = {Linear type systems permit programmers to deallocate or explicitly recycle memory, but are severely restricted by the fact that they admit no aliasing. This paper describes a pseudo-linear type system that allows a degree of aliasing and memory reuse as well as the ability to de ne complex recursive data structures. Our type system can encode con- ventional linear data structures such as linear lists and trees as well as more sophisticated data structures including cyclic and doubly-linked lists and trees. In the latter cases, our type system is expressive enough to represent pointer aliasing and yet safely permit destructive operations such as object deallocation. We demonstrate the exibility of our type system by encoding two common space-conscious algo- rithms: destination-passing style and Deutsch-Schorr-Waite or "link-reversal" traversal algorithms.},
  file      = {:by-author/W/Walker/2000_Walker.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Walkinshaw2002,
  author    = {Walkinshaw, M. D. and Taylor, P. and Sturrock, S. S. and Atanasiu, C. and Berge, T. and Henderson, R. M. and Edwardson, J. M. and Dryden, D. T. F.},
  journal   = {Molecular cell},
  title     = {Structure of Ocr from bacteriophage T7, a protein that mimics B-form DNA.},
  year      = {2002},
  pages     = {187--94},
  volume    = {9},
  abstract  = {We have solved, by X-ray crystallography to a resolution of 1.8 A, the structure of a protein capable of mimicking approximately 20 base pairs of B-form DNA. This ocr protein, encoded by gene 0.3 of bacteriophage T7, mimics the size and shape of a bent DNA molecule and the arrangement of negative charges along the phosphate backbone of B-form DNA. We also demonstrate that ocr is an efficient inhibitor in vivo of all known families of the complex type I DNA restriction enzymes. Using atomic force microscopy, we have also observed that type I enzymes induce a bend in DNA of similar magnitude to the bend in the ocr molecule. This first structure of an antirestriction protein demonstrates the construction of structural mimetics of long segments of B-form DNA.},
  file      = {:by-author/W/Walkinshaw/2002_Walkinshaw_187.pdf:PDF},
  keywords  = {Antirestriction},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@TechReport{Wall1999,
  author      = {David W. Wall and Michael L. Powell},
  institution = {Digital Equipment Corporation, Western Research Laboratory},
  title       = {The Mahler Experience: Using an Intermediate Language as the Machine Description},
  year        = {1999},
  abstract    = {Division of a compiler into a front end and a back end that communicate via an intermediate language is a well-known technique. We go farther and use the intermediate language as the official description of a family of machines with simple instruction sets and addressing capabilities, hiding some of the inconvenient details of the real machine from the users and the front end compilers. Then we can implement each machine in this family with whatever technology is appropriate, without having to make the details match those of other machines in the family. Each machine can therefore be faster than it would be if we required the machines to be object- code compatible, but the front end compilers need not change to accommodate that flexibility. To do this credibly, we have had to hide not only the existence of the details but also the performance conse- quences of hiding them. The back end that compiles and links the intermediate language tries to produce code that does not suffer a performance penalty because of the details that were hidden from the front end compiler. To accomplish this, we have used a number of link-time optimizations, including instruction scheduling and interprocedural register allocation, to hide the existence of such idiosyncracies as delayed branches and noninfinite register sets. For the most part we have been successful.},
  file        = {:by-author/W/Wall/1999_Wall.pdf:PDF},
  keywords    = {Compiler Design; Computer Science (CS)},
  owner       = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Waller1923,
  author    = {Waller, Ivar},
  journal   = {Zeitschrift für Physik},
  title     = {Zur Frage der Einwirkung der Wärmebewegung auf die Interferenz von Röntgenstrahlen},
  year      = {1923},
  issn      = {0044-3328},
  pages     = {398--408},
  volume    = {17},
  doi       = {10.1007/BF01328696},
  file      = {1923_Waller_398.pdf:by-author/W/Waller/1923_Waller_398.pdf:PDF},
  keywords  = {Atomic Displacement Parameters; Crystallography; Debye-Waller Factor; X-ray Crystallography},
  language  = {German},
  owner     = {saulius},
  publisher = {Springer-Verlag},
  timestamp = {2013.05.03},
  creationdate = {2013-05-03T00:00:00},
  url       = {http://dx.doi.org/10.1007/BF01328696},
}

@Article{Wang2005a,
  author    = {Caihua Wang and Scott Leffler and David H. Thompson and Christine A. Hrycyna},
  journal   = {Biochemical and Biophysical Research Communications},
  title     = {A general fluorescence-based coupled assay for S-adenosylmethionine-dependent methyltransferases},
  year      = {2005},
  pages     = {351--356},
  volume    = {331},
  abstract  = {We have developed a simple and sensitive fluorescence-based two-step coupled enzyme assay to report the activity of S-adenosylmethionine-dependent methyltransferases. This assay relies on a fluorescein–cystamine–methyl red (FL-S-S-MR) reporter molecule that can be activated by thiols. In the absence of thiols, fluorescence from the reporter is quenched through fluorescence resonance energy transfer between the two chromophores. In this report, we use catechol-O-methyltransferase with the addition of S-adenosylhomocysteine hydrolase to produce the thiol homocysteine. The presence of homocysteine leads to disulfide bond cleavage in the cystamine tether and fluorescence dequenching as the uncoupled chromophores are diluted into the surrounding media. The sensitivity and specificity of FL-S-S-MR to thiols enabled detection of ⩽1 μM concentrations of homocysteine, suggesting that this assay is sensitive enough to detect biologically relevant amounts of homocysteine. We believe that this fluorescence reporter approach may be generalizable to all enzymatic or chemical assays that produce thiols.},
  doi       = {10.1016/j.bbrc.2005.03.170},
  file      = {:by-author/W/Wang/2005_Wang_351.pdf:PDF},
  keywords  = {Assay; Fluorescence; Methyltransferases; S Adenosylmethionine},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Wang2001a,
  author    = {Wang, Jimin},
  journal   = {Journal of Structural Biology},
  title     = {A Corrected Quaternary Arrangement of the Peptidase HslV and ATPase HslU in a Cocrystal Structure},
  year      = {2001},
  pages     = {15--24},
  volume    = {134},
  doi       = {10.1006/jsbi.2001.4347},
  file      = {2001_Wang_15.pdf:by-author/W/Wang/2001_Wang_15.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@Article{Wang2000,
  author    = {J. Wang and J. Denny and C. Tian and S. Kim and Y. Mo and F. Kovacs and Z. Song and K. Nishimura and Z. Gan and R. Fu and J.R. Quine and T.A. Cross},
  journal   = {Journal of Magnetic Resonance},
  title     = {Imaging Membrane Protein Helical Wheels},
  year      = {2000},
  pages     = {162–167},
  volume    = {144},
  abstract  = {Resonance patterns have been observed in 2D solid-state NMR spectra of the transmembrane segment of M2 protein from Influenza A virus in oriented samples reflecting the helical wheel of this α-helix. The center of this pattern uniquely defines the helical tilt with respect to the bilayer normal without a need for resonance assignments. The distribution of resonances from amino acid specific labels around the “PISA wheel” defines the rotational orientation of the helix and yields preliminary site-specific assignments. With assignments high-resolution structural detail, such as differences in tilt and rotational orientation along the helical axis leading to an assessment of helical coiling, can be obtained.},
  doi       = {10.1006/jmre.2000.2037},
  file      = {:by-author/W/Wang/2000_Wang_162–167.pdf:PDF},
  keywords  = {Helical Wheel; Membrane Proteins; Orientational Constraints; Oriented Samples; PISEMA; Protein Structures},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/S1090780700920378},
}

@Article{Wang2005b,
  author    = {Jimin Wang and Satwik Kamtekar and Andrea J. Berman and Thomas A. Steitz},
  journal   = {Acta Cryst. D},
  title     = {Correction of X-ray intensities from single crystals containing lattice-translocation defects},
  year      = {2005},
  pages     = {67--74},
  volume    = {61},
  doi       = {10.1107/S0907444904026721},
  file      = {2005_Wang_67.pdf:by-author/W/Wang/2005_Wang_67.pdf:PDF},
  keywords  = {Disordered Crystals; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Wang2015,
  author    = {Wang, Ji and Place, Robert F and Portnoy, Victoria and Huang, Vera and Kang, Moo Rim and Ho, Maurice Kwok Chung and LI, Long-Cheng},
  journal   = {Journal of Biological Methods},
  title     = {Inducing gene expression by targeting promoter sequences using small activating {RNAs}},
  year      = {2015},
  issn      = {2326-9901},
  month     = {Mar},
  number    = {1},
  pages     = {e14},
  volume    = {2},
  doi       = {10.14440/jbm.2015.39},
  file      = {2015_Wang_e14.pdf:by-author/W/Wang/2015_Wang_e14.pdf:PDF},
  groups    = {am/RNA activation},
  owner     = {andrius},
  publisher = {Journal of Biological Methods},
  timestamp = {2016.09.15},
  creationdate = {2016-09-15T00:00:00},
  url       = {http://dx.doi.org/10.14440/jbm.2015.39},
}

@Article{Wang2006,
  author    = {Wang, Jiangyun and Xie, Jianming and Schultz, Peter G.},
  journal   = {Journal of the American Chemical Society},
  title     = {A genetically encoded fluorescent amino acid.},
  year      = {2006},
  pages     = {8738--9},
  volume    = {128},
  abstract  = {The fluorescent amino acid l-(7-hydroxycoumarin-4-yl) ethylglycine 1 has been genetically encoded in E. coli in response to the amber TAG codon. Because of its high fluorescence quantum yield, relatively large Stoke's shift, and sensitivity to both pH and polarity, this amino acid should provide a useful probe of protein localization and trafficking, protein conformation changes, and protein-protein interactions.},
  file      = {:by-author/W/Wang/2006_Wang_8738.pdf:PDF},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Wang1992,
  author    = {Wang, J F and Cech, T R},
  journal   = {Science (New York, N.Y.)},
  title     = {Tertiary structure around the guanosine-binding site of the Tetrahymena ribozyme.},
  year      = {1992},
  pages     = {526--9},
  volume    = {256},
  file      = {1992_Wang_526.pdf:by-author/W/Wang/1992_Wang_526.pdf:PDF},
  keywords  = {Ribozymes},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Wang2007,
  author    = {Wang, Kaihang and Neumann, Heinz and Peak-Chew, Sew Y and Chin, Jason W},
  journal   = {Nature Biotechnology},
  title     = {Evolved orthogonal ribosomes enhance the efficiency of synthetic genetic code expansion},
  year      = {2007},
  issn      = {1087-0156},
  month     = {Jun},
  number    = {7},
  pages     = {770--777},
  volume    = {25},
  doi       = {10.1038/nbt1314},
  file      = {:by-author/W/Wang/2007_Wang_770.pdf:PDF},
  groups    = {am/Expanded genetic code},
  owner     = {andrius},
  publisher = {Nature Publishing Group},
  timestamp = {2016.05.17},
  creationdate = {2016-05-17T00:00:00},
  url       = {http://dx.doi.org/10.1038/nbt1314},
}

@InProceedings{Wang2002,
  author    = {Min Wang and X. Sean Wang},
  booktitle = {SAC 2002, Madrid, Spain},
  title     = {Optimizing Relational Store for E-Catalog Queries: a Data Mining Approach},
  year      = {2002},
  pages     = {1147--1152},
  abstract  = {A frequent use of database management systems in electronic commerce is to provide electronic product catalogs (e-cataiogs) that allow users to search for products of interest via constraints on attributes. A n intuitively straightforward representation of e- catalogs is to use one table for the whole e-catalog as it is conceptually easy to maintain and query. How- ever, for any e-commerce business with a reasonably large n u m b e r of products and product types, its e- catalog usually involves a large number of attributes due to the great variety of the products, and at the same time, contains a large number of null values due to the fact that each product only has values under a relatively small number of attributes. Be- cause of these properties, the above intuitive method does not work well in current relational ctatabase systems. Techniques have been proposed in the lit- erature to deal with this problem, namely binary mad vertical schemas. However, these techniques fail to take advantage of inherent properties of realis- tic e-catalogs to provide superior performance. This paper proposes a novel decomposition method for e- catalogs based on association rule discovery, a data mining technique. The method discovers groups of attributes that frequently appear together, i.e., are frequently used together to describe products, and generates schemas that contain these groups. This paper also reports experimental results showing the efficiency of the method.},
  file      = {:by-author/W/Wang/2002_Wang_1147.pdf:PDF},
  keywords  = {Computer Science (CS); Data; Databases},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Wang2003,
  author    = {Wang, Qian and Chan, Timothy R. and Hilgraf, Robert and Fokin, Valery V. and Sharpless, K. Barry and Finn, M. G.},
  journal   = {Journal of the American Chemical Society},
  title     = {Bioconjugation by copper(I)-catalyzed azide-alkyne [3 + 2] cycloaddition.},
  year      = {2003},
  pages     = {3192--3},
  volume    = {125},
  abstract  = {The copper-catalyzed cycloaddition reaction between azides and alkynes functions efficiently in aqueous solution in the presence of a tris(triazolyl)amine ligand. The process has been employed to make rapid and reliable covalent connections to micromolar concentrations of protein decorated with either of the reactive moieties. The chelating ligand plays a crucial role in stabilizing the Cu(I) oxidation state and protecting the protein from Cu(triazole)-induced denaturation. Because the azide and alkyne groups themselves are unreactive with protein residues or other biomolecules, their ligation is of potential utility as a general bioconjugation method.},
  file      = {:by-author/W/Wang/2003_Wang_3192.pdf:PDF},
  keywords  = {Bioconjugation},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@Article{Wang2012a,
  author           = {Xueyi Wang and Jianmin Dong},
  journal          = {2012 2nd International Conference on Biomedical Engineering and Technology IPCBEE},
  title            = {A normalized weighted {RMSD} for measuring protein structure superposition},
  year             = {2012},
  pages            = {68--72},
  volume           = {34},
  abstract         = {Root-mean-square-deviation (RMSD) is the most widely used measure of the similarity of superimposed protein structures, but it is sensitive to outliers anda smaller RMSD value may not correspond to a better structure superposition. Many alternative measures have been proposed to overcome the deficiency in RMSD. In this paper, we extend the RMSD to normalized weighted RMSD (nwRMSD) to measure the quality of superimposed structures, where the nwRMSD assigns a normalized weight to eachsuperimposed position. We present an iterative algorithm to minimize nwRMSD for structure superposition and propose a new weight function for structure superposition. We show that NMR ensembles minimized by the nwRMSD measure can clearly display structurally conserved and flexible regions, which are better than the superposition in original structures.},
  creationdate     = {2014-12-02T00:00:00},
  file             = {:by-author/W/Wang/2012_Wang_68.pdf:PDF},
  groups           = {sg/Molecule superposion, sg/Superposition, sg/Bioinf. Algorithms},
  keywords         = {Normalized Weighted RMSD; Position Weight; Structure Superposition},
  modificationdate = {2024-05-12T22:02:18},
  owner            = {antanas},
  timestamp        = {2014.12.02},
}

@Manuscript{Wang2005,
  author    = {Xiaoyun Wang and Hongbo Yu},
  title     = {How to Break MD5 and Other Hash Functions},
  year      = {2005},
  keywords  = {Computer Science (CS); Cryptography},
  abstract  = {MD5 is one of the most widely used cryptographic hash func- tions nowadays. It was designed in 1992 as an improvement of MD4, and its security was widely studied since then by several authors. The best known result so far was a semi free-start collision, in which the initial value of the hash function is replaced by a non-standard value, which is the result of the attack. In this paper we present a new powerful attack on MD5 which allows us to find collisions efficiently. We used this attack to find collisions of MD5 in about 15 minutes up to an hour computation time. The attack is a differential attack, which unlike most differential attacks, does not use the exclusive-or as a measure of difference, but instead uses modular integer subtraction as the measure. We call this kind of differential a modular differential. An application of this attack to MD4 can find a collision in less than a fraction of a second. This attack is also applicable to other hash functions, such as RIPEMD and HAVAL.},
  file      = {:by-author/W/Wang/2005_Wang.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Wang2012b,
  author    = {Wang, Yijun and Deng, Dexiang and Zhang, Rong and Wang, Suxin and Bian, Yunlong and Yin, Zhitong},
  journal   = {Molecular Biology Reports},
  title     = {Systematic analysis of plant-specific B3 domain-containing proteins based on the genome resources of 11 sequenced species},
  year      = {2012},
  pages     = {6267–6282},
  volume    = {39},
  abstract  = {B3 domain-containing proteins constitute a large transcription factor superfamily. The plant-specific B3 super- family consists of four family members, i.e., LAV (LEC2 [LEAFY COTYLEDON 2]/ABI3 [ABSCISIC ACID INSEN SITIVE 3] - VAL [VP1/ABI3-LIKE]), RAV (RELATED to ABI3/VP1), ARF (AUXIN RESPONSE FACTOR) and REM (REPRODUCTIVE MERISTEM) families. The B3 super- family plays a central role in plant life, from embryogenesis to seed maturation and dormancy. In previous research, we have characterized ARF family, member of the B3 superfamily in silico (Wang et al., Mol Biol Rep, 2011, doi:10.1007/s11033- 011-0991-z). In this study, we systematically analyzed the diversity, phylogeny and evolution of B3 domain-containing proteins based on genomic resources of 11 sequenced species. A total of 865 B3 domain-containing genes were identified from 11 sequenced species through an iterative strategy. The number of B3 domain-containing genes varies not only between species but between gene families. B3 domain-con- taining genes are unevenly distributed in chromosomes and tend to cluster in the genome. Numerous combinations of B3 domains and their partner domains contribute to the sequences and structural diversification of the B3 superfamiy. Phyloge- netic results showed that moss VAL proteins are related to LEC2/ABI3 instead of VAL proteins from higher plants. Lineage-specific expansion of ARF and REM proteins was observed. The REM family is the most diversified member among the B3 superfamily and experiences a rapid divergence during selective sweep. Based on structural and phylogenetic analysis results, two possible evolutional modes of the B3 superfamily were presented. Results presented here provide a resource for further characterization of the B3 superfamily.},
  doi       = {10.1007/s11033-012-1448-8},
  file      = {:by-author/W/Wang/2012_Wang_6267.pdf:PDF},
  keywords  = {B3 Domain; B3 Domain-containing Protein; BfiI; DBD; Diversity; EcoRII; Evolution; Phylogeny},
  owner     = {em},
  timestamp = {2014.05.26},
  creationdate = {2014-05-26T00:00:00},
}

@Article{Wang2012,
  author    = {Wang, Yan and Li, Quan},
  journal   = {Advanced Materials},
  title     = {Light-driven chiral molecular switches or motors in liquid crystals},
  year      = {2012},
  issn      = {1521-4095},
  pages     = {1926--1945},
  volume    = {24},
  abstract  = {The ability to tune molecular self-organization with an external stimulus is a main driving force in the bottom-up nanofabrication of molecular devices. Light-driven chiral molecular switches or motors in liquid crystals that are capable of self-organizing into optically tunable helical superstructures undoubtedly represent a striking example, owing to their unique property of selective light reflection and which may lead to applications in the future. In this review, we focus on different classes of light-driven chiral molecular switches or motors in liquid crystal media for the induction and manipulation of photoresponsive cholesteric liquid crystal systems and their consequent applications. Moreover, the change of helical twisting powers of chiral dopants and their capability of helix inversion in the induced cholesteric phases are highlighted and discussed in the light of their molecular geometric changes.},
  doi       = {10.1002/adma.201200241},
  file      = {Wang and Li - 2012 - Light-Driven Chiral Molecular Switches or Motors i.pdf:by-author/W/Wang/2012_Wang_1926.pdf:application/pdf;Snapshot:by-author/W/Wang/2012_Wang_1926.html:text/html},
  groups    = {sg/chemical},
  keywords  = {Cholesteric Liquid Crystals; Helical Twisting Power; Light-driven Chiral; Motors; Photo Addressed Displays; Self-organized Helical Superstructures; Switches},
  language  = {en},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://onlinelibrary.wiley.com/doi/10.1002/adma.201200241/abstract},
  urldate   = {2015-08-21},
}

@InProceedings{Wang2013,
  author    = {Ziyu Wang and Shakir Mohamed and Nando de Freitas},
  booktitle = {Proceedings of the 30th International Conference on Machine Learning},
  title     = {Adaptive Hamiltonian and Riemann Manifold Monte Carlo Samplers},
  year      = {2013},
  abstract  = {In this paper we address the widely- experienced difficulty in tuning Monte Carlo sampler based on simulating Hamiltonian dy- namics. We develop an algorithm that al- lows for the adaptation of Hamiltonian and Riemann manifold Hamiltonian Monte Carlo samplers using Bayesian optimization that al- lows for infinite adaptation of the parameters of these samplers. We show that the resulting samplers are ergodic, and that the use of our adaptive algorithms makes it easy to obtain more efficient samplers, in some cases pre- cluding the need for more complex solutions. Hamiltonian-based Monte Carlo samplers are widely known to be an excellent choice of MCMC method, and we aim with this paper to remove a key obstacle towards the more widespread use of these samplers in practice.},
  file      = {2013_Wang.pdf:by-author/W/Wang/2013_Wang.pdf:PDF},
  groups    = {sg/Monte Carlo, sg/Hamiltonian Monte-Carlo, sg/Bioinf. Algorithms},
  keywords  = {Algorithm; Hamiltonian; MCMC; Monte-Carlo Sampler},
  owner     = {saulius},
  timestamp = {2016.06.02},
  creationdate = {2016-06-02T00:00:00},
  url       = {http://jmlr.org/proceedings/papers/v28/wang13e.pdf},
}

@Presentation{Wanigasekera2003,
  author    = {Chandana Praneeth Wanigasekera},
  title     = {Trusted Computing},
  year      = {2003},
  file      = {:by-author/W/Wanigasekera/2003_Wanigasekera.ppt:PPT},
  keywords  = {Computer Science (CS)},
  owner     = {saulius},
  timestamp = {2015.03.03},
  creationdate = {2015-03-03T00:00:00},
}

@Presentation{Ward2003,
  author    = {Steve Ward and Chris Terman},
  title     = {Building the Beta},
  year      = {2003},
  course    = {Computation Structures},
  file      = {:by-author/W/Ward/2003_Ward.pdf:PDF},
  keywords  = {CPU-design; Computer Architecture; Computer Science (CS); RISC},
  owner     = {saulius},
  timestamp = {2015.03.11},
  creationdate = {2015-03-11T00:00:00},
  url       = {http://6004.csail.mit.edu/Spring02/handouts/L15-4up.pdf},
}

@Article{Warr2015,
  author    = {Warr, Wendy A.},
  journal   = {Journal of Computer-Aided Molecular Design},
  title     = {Many {InChIs} and quite some feat},
  year      = {2015},
  issn      = {1573-4951},
  month     = {Jun},
  number    = {8},
  pages     = {681--694},
  volume    = {29},
  doi       = {10.1007/s10822-015-9854-3},
  file      = {:by-author/W/Warr/2015_Warr_681.pdf:PDF},
  publisher = {Springer Science and Business Media LLC},
  url       = {https://link.springer.com/article/10.1007/s10822-015-9854-3},
  owner     = {andrius},
  creationdate = {2021-11-04T12:31:29},
  modificationdate = {2022-12-24T18:49+02:00},
}

@Presentation{Warr2010,
  author    = {Wendy A. Warr},
  title     = {Tautomerism in chemical information management systems},
  year      = {2010},
  file      = {:by-author/W/Warr/2010_Warr_slides.pdf:PDF},
  owner     = {saulius},
  pages     = {slides},
  timestamp = {2014.01.26},
  creationdate = {2014-01-26T00:00:00},
  url       = {http://www.warr.com},
}

@Presentation{Warr2005,
  author    = {Wendy A. Warr},
  title     = {Twenty Five Years of Progress in Cheminformatics},
  year      = {2005},
  file      = {:by-author/W/Warr/2005_Warr_slides.pdf:PDF},
  owner     = {saulius},
  pages     = {slides},
  timestamp = {2014.01.26},
  creationdate = {2014-01-26T00:00:00},
  url       = {http://www.warr.com},
}

@Article{Waser1963,
  author    = {J{\"{u}}rg Waser},
  journal   = {Acta Crystallographica},
  title     = {Least-Squares Refinement with Subsidiary Conditions},
  year      = {1963},
  pages     = {1091--1094},
  volume    = {16},
  abstract  = {A method of least-squares refinement is described in which the subsidiary conditions are treated like observational equations. The advantages of the method are its generality, its adaptability to machine computing, and the possibility of relaxing the subsidiary conditions to any desired degree by appropriate changes in the weighting. In suitable cases the method extends the range for which least-squares refinements converge to the correct solution.},
  doi       = {10.1107/S0365110X63002929},
  file      = {:by-author/W/Waser/1963_Waser_1091.pdf:PDF},
  owner     = {andrius},
  timestamp = {2013.04.26},
  creationdate = {2013-04-26T00:00:00},
}

@Article{Waser2007,
  author    = {Waser, Rainer and Aono, Masakazu},
  journal   = {Nature Materials},
  title     = {Nanoionics-based resistive switching memories},
  year      = {2007},
  issn      = {1476-1122},
  pages     = {833--840},
  volume    = {6},
  abstract  = {Many metal–insulator–metal systems show electrically induced resistive switching effects and have therefore been proposed as the basis for future non-volatile memories. They combine the advantages of Flash and DRAM (dynamic random access memories) while avoiding their drawbacks, and they might be highly scalable. Here we propose a coarse-grained classification into primarily thermal, electrical or ion-migration-induced switching mechanisms. The ion-migration effects are coupled to redox processes which cause the change in resistance. They are subdivided into cation-migration cells, based on the electrochemical growth and dissolution of metallic filaments, and anion-migration cells, typically realized with transition metal oxides as the insulator, in which electronically conducting paths of sub-oxides are formed and removed by local redox processes. From this insight, we take a brief look into molecular switching systems. Finally, we discuss chip architecture and scaling issues.},
  copyright = {© 2007 Nature Publishing Group},
  doi       = {10.1038/nmat2023},
  file      = {Waser and Aono - 2007 - Nanoionics-based resistive switching memories.pdf:by-author/W/Waser/2007_Waser_833.pdf:application/pdf;Snapshot:by-author/W/Waser/2007_Waser_833.html:text/html},
  groups    = {sg/chemical},
  language  = {en},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://www.nature.com/nmat/journal/v6/n11/abs/nmat2023.html},
  urldate   = {2015-08-21},
}

@Manuscript{Washburn2006,
  author    = {Geoffrey Washburn and Stephanie Weirich},
  title     = {Good Advice for Type-directed Programming Aspect-oriented Programming and Extensible Generic Functions},
  year      = {2006},
  keywords  = {Compiler Design; Computer Science (CS); Programming Languages; Type Systems},
  abstract  = {Type-directed programming is an important idiom for software design. In type-directed programming the behavior of programs is guided by the type structure of data. It makes it possible to implement many sorts of operations, such as serialization, traversals, and queries, only once and without needing to continually revise their implementations as new data types are defined. Type-directed programming is the basis for recent research into “scrapping” tedious boilerplate code that arises in functional pro- gramming with algebraic data types. This research has primarily focused on writing type-directed functions that are closed to ex- tension. However, Lämmel and Peyton Jones recently developed a technique for writing openly extensible type-directed functions in Haskell by making clever use of type classes. Unfortunately, this technique has a number of limitations such as the inability to write specialized cases for existential or nested data types and function types becoming too constrained to be used as first-class functions. We present an alternate approach to writing openly extensible type-directed functions by using the aspect-oriented programming features provided by the language AspectML. Our solution not only avoids the limitations present in Lämmel and Peyton Jones’s technique, but also allows type-directed functions to be extended at any time with cases for types that were not even known at compile- time. This capability is critical to writing programs that make use of dynamic loading or runtime type generativity.},
  file      = {:by-author/W/Washburn/2006_Washburn_WGP06.pdf:PDF},
  owner     = {saulius},
  pages     = {WGP06},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Wasserman2006,
  author    = {Larry Wasserman},
  journal   = {Bayesian Analysis},
  title     = {Frequentist Bayes is objective},
  year      = {2006},
  pages     = {451--456},
  volume    = {1},
  abstract  = {In this comment, I argue that Bayes procedures with good frequentist properties are objective. I introduce the idea with a short play, followed by some commentary.},
  file      = {2006_Wasserman_451.pdf:by-author/W/Wasserman/2006_Wasserman_451.pdf:PDF},
  groups    = {sg/Bayesian},
  owner     = {saulius},
  timestamp = {2013.01.02},
  creationdate = {2013-01-02T00:00:00},
  url       = {http://ba.stat.cmu.edu/journal/2006/vol01/issue03/wasserman.pdf},
}

@Article{Wasserstein2016,
  author    = {Ronald L. Wasserstein and Nicole A. Lazar},
  journal   = {The American Statistician},
  title     = {The ASA's statement on p-values: context, process, and purpose},
  year      = {2016},
  number    = {ja},
  doi       = {10.1080/00031305.2016.1154108},
  eprint    = {http://dx.doi.org/10.1080/00031305.2016.1154108},
  file      = {2016_Wasserstein.pdf:by-author/W/Wasserstein/2016_Wasserstein.pdf:PDF},
  keywords  = {Criticism; P-values; Statistics},
  owner     = {saulius},
  timestamp = {2016.03.09},
  creationdate = {2016-03-09T00:00:00},
  url       = {http://dx.doi.org/10.1080/00031305.2016.1154108},
}

@Article{Wassman2004,
  author    = {Wassman, Christopher D. and Tam, Phillip Y. and Lathrop, Richard H. and Weiss, Gregory A.},
  journal   = {Nucleic acids research},
  title     = {Predicting oligonucleotide-directed mutagenesis failures in protein engineering.},
  year      = {2004},
  pages     = {6407--13},
  volume    = {32},
  abstract  = {Protein engineering uses oligonucleotide-directed mutagenesis to modify DNA sequences through a two-step process of hybridization and enzymatic synthesis. Inefficient reactions confound attempts to introduce mutations, especially for the construction of vast combinatorial protein libraries. This paper applied computational approaches to the problem of inefficient mutagenesis. Several results implicated oligonucleotide annealing to non-target sites, termed 'cross-hybridization', as a significant contributor to mutagenesis reaction failures. Test oligonucleotides demonstrated control over reaction outcomes. A novel cross-hybridization score, quickly computable for any plasmid and oligonucleotide mixture, directly correlated with yields of deleterious mutagenesis side products. Cross-hybridization was confirmed conclusively by partial incorporation of an oligonucleotide at a predicted cross-hybridization site, and by modification of putative template secondary structure to control cross-hybridization. Even in low concentrations, cross-hybridizing species in mixtures poisoned reactions. These results provide a basis for improved mutagenesis efficiencies and increased diversities of cognate protein libraries.},
  file      = {:by-author/W/Wassman/2004_Wassman_6407.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Watkin2008,
  author    = {Watkin, David},
  journal   = {Journal of Applied Crystallography},
  title     = {Structure refinement: some background theory and practical strategies},
  year      = {2008},
  issn      = {0021-8898},
  month     = {Apr},
  number    = {3},
  pages     = {491–522},
  volume    = {41},
  doi       = {10.1107/s0021889808007279},
  file      = {2008_Watkin_491.pdf:by-author/W/Watkin/2008_Watkin_491.pdf:PDF},
  groups    = {sg/Crystallography, am/Crystallography},
  owner     = {andrius},
  publisher = {International Union of Crystallography (IUCr)},
  timestamp = {2016.12.19},
  creationdate = {2016-12-19T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0021889808007279},
}

@Article{Watkin2000,
  author    = {Watkin, D},
  journal   = {Acta crystallographica. Section B, Structural science},
  title     = {Uequiv: its past, present and future.},
  year      = {2000},
  pages     = {747--9},
  volume    = {56 ( Pt 5)},
  file      = {2000_Watkin_747.pdf:by-author/W/Watkin/2000_Watkin_747.pdf:PDF},
  keywords  = {Uequiv; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Conference{Watkin2012,
  author    = {David Watkin and Richard Cooper and Anna Collins},
  booktitle = {Transformations and Structural Oddities in Molecular Crystals: In Honor of Bruce M. Foxman},
  title     = {Z'>1 Structures. Just a Nuisance or Something more Interesting?},
  year      = {2012},
  pages     = {1--19},
  volume    = {43},
  file      = {2012_Watkin_1.pdf:by-author/W/Watkin/2012_Watkin_1.pdf:PDF},
  keywords  = {Crystal Packing; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2014.07.02},
  creationdate = {2014-07-02T00:00:00},
  url       = {http://www.amercrystalassn.org/documents/2012%20Transactions/Watkin%201-19.pdf},
}

@Article{Watson1953,
  author    = {Watson, J. D. and Crick, F. H.},
  journal   = {Nature},
  title     = {Genetical implications of the structure of deoxyribonucleic acid.},
  year      = {1953},
  pages     = {964--7},
  volume    = {171},
  file      = {:by-author/W/Watson/1953_Watson_964.pdf:PDF},
  keywords  = {DNA Structure},
  owner     = {saulius},
  timestamp = {2012.11.21},
  creationdate = {2012-11-21T00:00:00},
  url       = {http://www.nature.com/nature/dna50/watsoncrick2.pdf},
}

@Article{Watson1953a,
  author    = {Watson, J. D. and Crick, F. H.},
  journal   = {Nature},
  title     = {Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid.},
  year      = {1953},
  pages     = {737--8},
  volume    = {171},
  file      = {:by-author/W/Watson/1953_Watson_737.pdf:PDF},
  keywords  = {DNA Structure},
  owner     = {saulius},
  timestamp = {2012.11.21},
  creationdate = {2012-11-21T00:00:00},
  url       = {http://www.nature.com/nature/dna50/watsoncrick.pdf},
}

@Article{Watzke2006,
  author    = {Watzke, Anja and Köhn, Maja and Gutierrez-Rodriguez, Marta and Wacker, Ron and Schröder, Hendrik and Breinbauer, Rolf and Kuhlmann, Jürgen and Alexandrov, Kirill and Niemeyer, Christof M. and Goody, Roger S. and Waldmann, Herbert},
  journal   = {Angewandte Chemie (International ed. in English)},
  title     = {Site-selective protein immobilization by Staudinger ligation.},
  year      = {2006},
  pages     = {1408--12},
  volume    = {45},
  file      = {:by-author/W/Watzke/2006_Watzke_1408.pdf:PDF},
  keywords  = {Bioconjugation},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@Manuscript{Way2008,
  author    = {Thomas Way and Rushikesh Katikar and Purushotham Ch},
  title     = {Nanocompilation for the Cell Matrix Architecture},
  year      = {2008},
  keywords  = {Cell Matrix; Computer Science (CS)},
  file      = {:by-author/W/Way/2008_Way_techreport.pdf:PDF},
  groups    = {sg/Cell Matrix},
  owner     = {saulius},
  pages     = {techreport},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Webb2014,
  author    = {Webb, Benjamin and Šali, Andrej},
  journal   = {Current Protocols in Bioinformatics},
  title     = {Comparative Protein Structure Modeling Using {MODELLER}},
  year      = {2014},
  month     = {Sep},
  pages     = {5.6.1–5.6.32},
  abstract  = {Functional characterization of a protein sequence is one of the most frequent problems in biology. This task is usually facilitated by accurate three-dimensional (3-D) structure of the studied protein. In the absence of an experimentally determined structure, comparative or homology modeling can sometimes provide a useful 3-D model for a protein that is related to at least one known protein structure. Comparative modeling predicts the 3-D structure of a given protein sequence (target) based primarily on its alignment to one or more proteins of known structure (templates). The prediction process consists of fold assignment, target-template alignment, model building, and model evaluation. This unit describes how to calculate comparative models using the program MODELLER and discusses all four steps of comparative modeling, frequently observed errors, and some applications. Modeling lactate dehydrogenase from Trichomonas vaginalis (TvLDH) is described as an example. The download and installation of the MODELLER software is also described.},
  doi       = {10.1002/0471250953.bi0506s47},
  file      = {2014_Webb_5.6.1.pdf:by-author/W/Webb/2014_Webb_5.6.1.pdf:PDF},
  isbn      = {http://id.crossref.org/isbn/9780471250951},
  owner     = {andrius},
  publisher = {Wiley-Blackwell},
  timestamp = {2017.01.17},
  creationdate = {2017-01-17T00:00:00},
  url       = {http://dx.doi.org/10.1002/0471250953.bi0506s47},
}

@Article{Weber2006,
  author    = {Weber, Alexander and Böhm, Markus and Supuran, Claudiu T and Scozzafava, Andrea and Sotriffer, Christoph A and Klebe, Gerhard},
  journal   = {Journal of chemical information and modeling},
  title     = {3D QSAR selectivity analyses of carbonic anhydrase inhibitors: insights for the design of isozyme selective inhibitors.},
  year      = {2006},
  pages     = {2737--60},
  volume    = {46},
  abstract  = {A 3D QSAR selectivity analysis of carbonic anhydrase (CA) inhibitors using a data set of 87 CA inhibitors is reported. After ligand minimization in the binding pockets of CA I, CA II, and CA IV isoforms, selectivity CoMFA and CoMSIA 3D QSAR models have been derived by taking the affinity differences (DeltapKi) with respect to two CA isozymes as independent variables. Evaluation of the developed 3D QSAR selectivity models allows us to determine amino acids in the respective CA isozymes that possibly play a crucial role for selective inhibition of these isozymes. We further combined the ligand-based 3D QSAR models with the docking program AUTODOCK in order to screen for novel CA inhibitors. Correct binding modes are predicted for various CA inhibitors with respect to known crystal structures. Furthermore, in combination with the developed 3D QSAR models we could successfully estimate the affinity of CA inhibitors even in cases where the applied scoring function failed. This novel strategy to combine AUTODOCK poses with CoMFA/CoMSIA 3D QSAR models can be used as a guideline to assess the relevance of generated binding modes and to accurately predict the binding affinity of newly designed CA inhibitors that could play a crucial role in the treatment of pathologies such as tumors, obesity, or glaucoma.},
  file      = {2006_Weber_2737.pdf:by-author/W/Weber/2006_Weber_2737.pdf:PDF},
  groups    = {sg/inhibitors, sg/modelling},
  keywords  = {Carbonic Anhydrases},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@InBook{Weerasinghe2010,
  author    = {Weerasinghe, Samantha and Gee, Moon Bae and Kang, Myungshim and Bentenitis, Nikolaos and Smith, Paul E.},
  pages     = {55--76},
  publisher = {Wiley-VCH Verlag GmbH \& Co. KGaA},
  title     = {Developing Force Fields from the Microscopic Structure of Solutions: The Kirkwood–Buff Approach},
  year      = {2010},
  isbn      = {9783527629251},
  abstract  = {What is the structure of a solution? How can we understand and predict the effects of solvation at the atomic level? These are important issues that need to be addressed if we are to develop accurate and useful models of solution mixture s. In principle, computer simulation can provide this information in exquisite detail. However, the results of computer simulations are determined by the quality of the force field (FF), and the extent of sampling achieved during the simulation. The latter is not usually a problem for the majority of solution mixtures using currently available computational resources. On the other hand, the quality of the force fi eld s used to represent solution mixtures is debatable. Current force fi elds for small molecule s reproduce many of the properties of solution quite well. However, recently, we have found that they do a relatively poor job in reproducing other important characteristics of solution mixtures, in particular, the activity of a cosolvent in a solvent.},
  booktitle = {Modeling Solvent Environments},
  doi       = {10.1002/9783527629251.ch3},
  file      = {2010_Weerasinghe_55.pdf:by-author/W/Weerasinghe/2010_Weerasinghe_55.pdf:PDF},
  keywords  = {Activity; Cosolvents; KBFF; Kirkwood-Buff Theory; Solvation; Statistical Physics; Theory of Solutions; Urea},
  owner     = {saulius},
  timestamp = {2015.03.13},
  creationdate = {2015-03-13T00:00:00},
  url       = {http://dx.doi.org/10.1002/9783527629251.ch3},
}

@Article{Wei2008,
  author    = {Wei, Hua and Therrien, Caitlin and Blanchard, Aine and Guan, Shengxi and Zhu, Zhenyu},
  journal   = {Nucleic acids research},
  title     = {The Fidelity Index provides a systematic quantitation of star activity of DNA restriction endonucleases.},
  year      = {2008},
  pages     = {e50},
  volume    = {36},
  abstract  = {Restriction endonucleases are the basic tools of molecular biology. Many restriction endonucleases show relaxed sequence recognition, called star activity, as an inherent property under various digestion conditions including the optimal ones. To quantify this property we propose the concept of the Fidelity Index (FI), which is defined as the ratio of the maximum enzyme amount showing no star activity to the minimum amount needed for complete digestion at the cognate recognition site for any particular restriction endonuclease. Fidelity indices for a large number of restriction endonucleases are reported here. The effects of reaction vessel, reaction volume, incubation mode, substrate differences, reaction time, reaction temperature and additional glycerol, DMSO, ethanol and Mn(2+) on the FI are also investigated. The FI provides a practical guideline for the use of restriction endonucleases and defines a fundamental property by which restriction endonucleases can be characterized.},
  file      = {:by-author/W/Wei/2008_Wei_e50.pdf:PDF},
  keywords  = {TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Wei2008l,
  author       = {Hua Wei and Caitlin Therrien and Aine Blanchard and Shengxi Guan and Zhenyu Zhu},
  journal      = {Nucleic Acids Res},
  title        = {The Fidelity Index provides a systematic quantitation of star activity of DNA restriction endonucleases.},
  year         = {2008},
  month        = {May},
  number       = {9},
  pages        = {e50},
  volume       = {36},
  abstract     = {Restriction endonucleases are the basic tools of molecular biology. Many restriction endonucleases show relaxed sequence recognition, called star activity, as an inherent property under various digestion conditions including the optimal ones. To quantify this property we propose the concept of the Fidelity Index (FI), which is defined as the ratio of the maximum enzyme amount showing no star activity to the minimum amount needed for complete digestion at the cognate recognition site for any particular restriction endonuclease. Fidelity indices for a large number of restriction endonucleases are reported here. The effects of reaction vessel, reaction volume, incubation mode, substrate differences, reaction time, reaction temperature and additional glycerol, DMSO, ethanol and Mn(2+) on the FI are also investigated. The FI provides a practical guideline for the use of restriction endonucleases and defines a fundamental property by which restriction endonucleases can be characterized.},
  creationdate = {2012-03-12T00:00:00},
  doi          = {10.1093/nar/gkn182},
  file         = {2008_Wei_e50.pdf:by-author/W/Wei/2008_Wei_e50.pdf:PDF},
  institution  = {New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA.},
  keywords     = {Analysis/classification/metabolism; Buffers; Chemistry/metabolism; DNA; DNA Restriction Enzymes; Metabolism; Polymerase Chain Reaction; Substrate Specificity; Superhelical; Temperature; Terminology as Topic},
  language     = {eng},
  medline-pst  = {ppublish},
  owner        = {em},
  pii          = {gkn182},
  pmid         = {18413342},
  timestamp    = {2012.03.12},
  url          = {http://dx.doi.org/10.1093/nar/gkn182},
}

@Article{Weigelt1999,
  author    = {Weigelt, J. and Brown, S. E. and Miles, C. S. and Dixon, N. E. and Otting, G.},
  journal   = {Structure (London, England : 1993)},
  title     = {NMR structure of the N-terminal domain of E. coli DnaB helicase: implications for structure rearrangements in the helicase hexamer.},
  year      = {1999},
  pages     = {681--90},
  volume    = {7},
  file      = {:by-author/W/Weigelt/1999_Weigelt_681.pdf:PDF},
  keywords  = {{gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Weinberg1996,
  author        = {Weinberg, Steven},
  journal       = {arXiv},
  title         = {What is quantum field theory, and what did we think it is?},
  year          = {1997},
  pages         = {9702027v1},
  archiveprefix = {arXiv},
  eprint        = {hep-th/9702027},
  file          = {1997_Weinberg_9702027v1.pdf:by-author/W/Weinberg/1997_Weinberg_9702027v1.pdf:PDF},
  keywords      = {Quantum Mechanics (QM)},
  owner         = {saulius},
  primaryclass  = {hep-th},
  reportnumber  = {UTTG-05-97},
  slaccitation  = {%%CITATION = HEP-TH/9702027;%%},
  timestamp = {2013.01.02},
  creationdate = {2013-01-02T00:00:00},
  url           = {http://arxiv.org/abs/hep-th/9702027},
}

@Article{Weiserova2000,
  author    = {Weiserova, M. and Dutta, C. F. and Firman, K.},
  journal   = {Journal of molecular biology},
  title     = {A novel mutant of the type I restriction-modification enzyme EcoR124I is altered at a key stage of the subunit assembly pathway.},
  year      = {2000},
  pages     = {301--10},
  volume    = {304},
  abstract  = {The HsdS subunit of a type I restriction-modification (R-M) system plays an essential role in the activity of both the modification methylase and the restriction endonuclease. This subunit is responsible for DNA binding, but also contains conserved amino acid sequences responsible for protein-protein interactions. The most important protein-protein interactions are those between the HsdS subunit and the HsdM (methylation) subunit that result in assembly of an independent methylase (MTase) of stoichiometry M(2)S(1). Here, we analysed the impact on the restriction and modification activities of the change Trp(212)--&gt;Arg in the distal border of the central conserved region of the EcoR124I HsdS subunit. We demonstrate that this point mutation significantly influences the ability of the mutant HsdS subunit to assemble with the HsdM subunit to produce a functional MTase. As a consequence of this, the mutant MTase has drastically reduced DNA binding, which is restored only when the HsdR (restriction) subunit binds with the MTase. Therefore, HsdR acts as a chaperon allowing not only binding of the enzyme to DNA, but also restoring the methylation activity and, at sufficiently high concentrations in vitro of HsdR, restoring restriction activity.},
  file      = {:by-author/W/Weiserova/2000_Weiserova_301.pdf:PDF},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Weiserova1998,
  author    = {Weiserova, M. and Firman, K.},
  journal   = {Biological chemistry},
  title     = {Isolation of a non-classical mutant of the DNA recognition subunit of the type I restriction endonuclease R.EcoR124I.},
  year      = {1998},
  pages     = {585--9},
  volume    = {379},
  abstract  = {We have used deletion mutagenesis and PCR-based misincorporation mutagenesis to produce a collection of mutations in the central conserved region of the DNA binding subunit of the type IC restriction endonuclease EcoR124I. It has been proposed that this domain is involved in protein-protein interactions during the assembly of the endonuclease. While a large percentage of these mutations gave a classical Res- Mod- phenotype, one mutant was isolated with a nonclassical Res- Mod+ phenotype. The loss of restriction activity, but retention of the ability to modify indicates that this mutation cannot affect DNA binding and must alter the assembly of the endonuclease in such a way as to prevent DNA cleavage but allow methylation. This mutant resulted from a single amino acid change Trp212--&gt;Arg. The location of the single amino acid change is at the border of the central conserved region and the second target recognition domain (TRD2) and suggests that this region is extremely important for the assembly of the methylase with the HsdR subunit into a functional restriction endonuclease.},
  file      = {:by-author/W/Weiserova/1998_Weiserova_585.pdf:PDF},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Weiserova1993,
  author    = {Weiserova, M. and Janscak, P. and Benada, O. and Hubácek, J. and Zinkevich, V. E. and Glover, S. W. and Firman, K.},
  journal   = {Nucleic acids research},
  title     = {Cloning, production and characterisation of wild type and mutant forms of the R.EcoK endonucleases.},
  year      = {1993},
  pages     = {373--9},
  volume    = {21},
  abstract  = {The hsdR, hsdM and hsdS genes coding for R.EcoK restriction endonuclease, both with and without a temperature sensitive mutation (ts-1) in the hsdS gene, were cloned in pBR322 plasmid and introduced into E.coli C3-6. The presence of the hsdSts-1 mutation has no effect on the R-M phenotype of this construct in bacteria grown at 42 degrees C. However, DNA sequencing indicates that the mutation is still present on the pBR322-hsdts-1 operon. The putative temperature-sensitive endonuclease was purified from bacteria carrying this plasmid and the ability to cleave and methylate plasmid DNA was investigated. The mutant endonuclease was found to show temperature-sensitivity for restriction. Modification was dramatically reduced at both the permissive and non-permissive temperatures. The wild type enzyme was found to cleave circular DNA in a manner which strongly suggests that only one endonuclease molecule is required per cleavage event. Circular and linear DNA appear to be cleaved using different mechanisms, and cleavage of linear DNA may require a second endonuclease molecule. The subunit composition of the purified endonucleases was investigated and compared to the level of subunit production in minicells. There is no evidence that HsdR is prevented from assembling with HsdM and HsdSts-1 to produce the mutant endonuclease. The data also suggests that the level of HsdR subunit may be limiting within the cell. We suggest that an excess of HsdM and HsdS may produce the methylase in vivo and that assembly of the endonuclease may be dependent upon the prior production of this methylase.},
  file      = {:by-author/W/Weiserova/1993_Weiserova_373.pdf:PDF},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Weiss200X,
  author    = {Weiss},
  title     = {A New Procedure for Automated Protein Structure Determination involving the use of soft X-rays},
  year      = {200X},
  pages     = {28},
  file      = {:by-author/W/Weiss/200X_Weiss_28.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Weiss2001,
  author    = {Weiss, Manfred S.},
  journal   = {Journal of Applied Crystallography},
  title     = {Global indicators of X-ray data quality},
  year      = {2001},
  pages     = {130--135},
  volume    = {34},
  doi       = {10.1107/S0021889800018227},
  file      = {2001_Weiss_130.pdf:by-author/W/Weiss/2001_Weiss_130.pdf:PDF},
  keywords  = {Data Processing; Data Quality; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2011.10.13},
  creationdate = {2011-10-13T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0021889800018227},
}

@Article{Weiss2004,
  author    = {Weiss, Manfred S and Mander, Gerd and Hedderich, Reiner and Diederichs, Kay and Ermler, Ulrich and Warkentin, Eberhard},
  journal   = {Acta crystallographica. Section D, Biological crystallography},
  title     = {Determination of a novel structure by a combination of long-wavelength sulfur phasing and radiation-damage-induced phasing.},
  year      = {2004},
  pages     = {686--95},
  volume    = {60},
  file      = {Weiss_2004_686_sulphur-damage-phasing.pdf:by-author/W/Weiss/2004_Weiss_686.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Weiss2004a,
  author    = {Weiss, Manfred S. and Mander, Gerd and Hedderich, Reiner and Diederichs, Kay and Ermler, Ulrich and Warkentin, Eberhard},
  journal   = {Acta Crystallographica Section D},
  title     = {Determination of a novel structure by a combination of long-wavelength sulfur phasing and radiation-damage-induced phasing},
  year      = {2004},
  pages     = {686--695},
  volume    = {60},
  doi       = {10.1107/S0907444904003002},
  file      = {he5281.pdf:by-author/W/Weiss/2004_Weiss_686.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444904003002},
}

@Manuscript{Weissman1995,
  author    = {Peter Weissman},
  title     = {Computer software as patentable subject matter: contrasting United States, japanese, and european laws},
  year      = {1995},
  keywords  = {Patentai; Teise},
  file      = {:by-author/W/Weissman/1995_Weissman.doc:DOC},
  owner     = {saulius},
  timestamp = {2015.02.28},
  creationdate = {2015-02-28T00:00:00},
}

@Article{Weng:db5040,
  author    = {Weng, Ze F. and Motherwell, W. D. Sam and Cole, Jacqueline M.},
  journal   = {Journal of Applied Crystallography},
  title     = {{\it Tormat}: a program for the automated structural alignment of molecular conformations},
  year      = {2008},
  pages     = {955--957},
  volume    = {41},
  doi       = {10.1107/S002188980802308X},
  file      = {2008_Weng_955.pdf:by-author/W/Weng/2008_Weng_955.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
  url       = {http://dx.doi.org/10.1107/S002188980802308X},
}

@Article{Wenk2014,
  author    = {Wenk, Hans-Rudolf and Lutterotti, Luca and Kaercher, Pamela and Kanitpanyacharoen, Waruntorn and Miyagi, Lowell and Vasin, Roman},
  journal   = {Powder Diffraction},
  title     = {Rietveld texture analysis from synchrotron diffraction images. {II}. complex multiphase materials and diamond anvil cell experiments},
  year      = {2014},
  pages     = {220--232},
  volume    = {29},
  file      = {[PDF] from researchgate.net:by-author/W/Wenk/2014_Wenk_220.pdf:application/pdf;Snapshot:by-author/W/Wenk/2014_Wenk_220.html:text/html},
  groups    = {sg/JAC2009},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://journals.cambridge.org/abstract_S0885715614000360},
  urldate   = {2015-08-31},
}

@Article{Wenz1996,
  author    = {Wenz, C. and Jeltsch, A. and Pingoud, A.},
  journal   = {The Journal of biological chemistry},
  title     = {Probing the indirect readout of the restriction enzyme EcoRV. Mutational analysis of contacts to the DNA backbone.},
  year      = {1996},
  pages     = {5565--73},
  volume    = {271},
  abstract  = {According to the crystal structure of the specific EcoRV.DNA complex, not only the functional groups of the nucleobases but also the phosphate groups of the DNA backbone are contacted by the enzyme. To examine the contribution of backbone contacts to substrate recognition and catalysis by EcoRV, we exchanged 12 amino acids residues located close to phosphate groups by site-directed mutagenesis. We purified the resulting EcoRV mutants and characterized them with respect to their DNA binding and cleavage activity. According to our steady state kinetic analysis, there are strong interactions between three basic amino acid residues (Lys-119, Arg-140, and Arg-226) and the phosphate backbone that support specific binding presumably by inducing and maintaining the kinked conformation of the DNA observed in the specific EcoRV.DNA complex. These contacts are important in both the ground state and the transition state. Other, uncharged residues (Thr-93 and Ser-112), which could be involved in hydrogen bonds to the phosphate groups, are needed primarily to stabilize the transition state. An especially important amino acid residue is Thr-37, which seems to couple recognition to catalysis by indirect readout.},
  file      = {:by-author/W/Wenz/1996_Wenz_5565.pdf:PDF},
  keywords  = {Readout},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@PhdThesis{Wesolowski2012,
  author    = {Wesolowski, Michal John},
  school    = {University of Waterloo},
  title     = {Properties of carbon nanomaterials produced by ultrashort pulsed laser irradiation},
  year      = {2012},
  file      = {[PDF] from uwaterloo.ca:by-author/W/Wesolowski/2012_Wesolowski.pdf:application/pdf;Snapshot:by-author/W/Wesolowski/2012_Wesolowski.html:text/html},
  groups    = {sg/JAC2009},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {https://uwspace.uwaterloo.ca/handle/10012/6904},
  urldate   = {2015-08-31},
}

@Article{Westbrook2000,
  author           = {Westbrook, J D and Bourne, P E},
  journal          = {Bioinformatics (Oxford, England)},
  title            = {STAR/mmCIF: an ontology for macromolecular structure.},
  year             = {2000},
  pages            = {159--68},
  volume           = {16},
  creationdate     = {2008-07-28T00:00:00},
  file             = {2000_Westbrook_159.pdf:by-author/W/Westbrook/2000_Westbrook_159.pdf:PDF},
  keywords         = {CIF; Databases; PDB; {mmCIF}},
  modificationdate = {2023-08-07T10:23:05},
  owner            = {saulius},
  timestamp        = {2008.07.28},
}

@InCollection{Westbrook2005,
  author           = {J. D. Westbrook and K. H Enrick and E. L. Ulrich and H. M. Berman},
  booktitle        = {International Tables for Crystallography},
  title            = {The {P}rotein {D}ata {B}ank Exchange Data Dictionary},
  year             = {2005},
  chapter          = {Appendix 3.6.2},
  pages            = {195},
  creationdate     = {2012-11-20T00:00:00},
  file             = {2005_Westbrook_195.pdf:by-author/W/Westbrook/2005_Westbrook_195.pdf:PDF},
  groups           = {am/PDB},
  keywords         = {CIF; Databases; PDB; {mmCIF}},
  modificationdate = {2023-08-07T10:23:05},
  owner            = {saulius},
  timestamp        = {2012.11.20},
}

@Manuscript{Weston2003,
  author    = {Tom Weston},
  title     = {The {Banach}-{Tarski} paradox},
  year      = {2003},
  language  = {English},
  url       = {http://people.math.umass.edu/~weston/oldpapers/banach.pdf},
  file      = {Tom Weston - The Banach-Tarski paradox.pdf:by-author/W/Weston/2003_Weston.pdf:PDF},
  owner     = {saulius},
  timestamp = {2015.12.07},
  creationdate = {2015-12-07T00:00:00},
  urldate   = {2015-12-07},
}

@Article{Westra2012a,
  author    = {Edze R. Westra and Paul B.G. van Erp and Tim Künne and Shi Pey Wong and Raymond H.J. Staals and Christel L.C. Seegers and Sander Bollen and Matthijs M. Jore and Ekaterina Semenova and Konstantin Severinov and Willem M. de Vos and Remus T. Dame and Renko de Vries and Stan J.J. Brouns and John van der Oost},
  journal   = {Molecular Cell},
  title     = {{CRISPR} Immunity Relies on the Consecutive Binding and Degradation of Negatively Supercoiled Invader {DNA} by {C}ascade and {Cas3}},
  year      = {2012},
  pages     = {suppl2},
  volume    = {46},
  file      = {:by-author/W/Westra/2012_Westra_suppl2.pdf:PDF},
  groups    = {sg/CRISPR-Cas},
  keywords  = {CRISPR},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Westra2012,
  author    = {Westra, Lubbert Y. T. and Maas, Paul J. M.},
  journal   = {PhytoKeys},
  title     = {Tetrameranthus (Annonaceae) revisited including a new species.},
  year      = {2012},
  number    = {12},
  pages     = {1--21},
  abstract  = {The taxonomic revision of the infrequently collected genus Tetrameranthus by Westra (1985) is updated. A new species is described from French Guiana and Amapá, Brazil, increasing the number of species in this genus to seven.},
  file      = {:by-author/W/Westra/2012_Westra_1.pdf:PDF},
  groups    = {sg/CRISPR-Cas},
  keywords  = {CRISPR},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Wetzel2009,
  author    = {Wetzel, Stefan and Klein, Karsten and Renner, Steffen and Rauh, Daniel and Oprea, Tudor I and Mutzel, Petra and Waldmann, Herbert},
  journal   = {Nat. Chem. Biol.},
  title     = {Interactive exploration of chemical space with Scaffold Hunter},
  year      = {2009},
  issn      = {1552-4450},
  pages     = {581--583},
  volume    = {5},
  abstract  = {We describe Scaffold Hunter, a highly interactive computer-based tool for navigation in chemical space that fosters intuitive recognition of complex structural relationships associated with bioactivity. The program reads compound structures and bioactivity data, generates compound scaffolds, correlates them in a hierarchical tree-like arrangement, and annotates them with bioactivity. Brachiation along tree branches from structurally complex to simple scaffolds allows identification of new ligand types. We provide proof of concept for pyruvate kinase.},
  comment   = {10.1038/nchembio.187},
  file      = {2009_Wetzel_581.pdf:by-author/W/Wetzel/2009_Wetzel_581.pdf:PDF},
  owner     = {saulius},
  publisher = {Nature Publishing Group},
  timestamp = {2013.04.01},
  creationdate = {2013-04-01T00:00:00},
  url       = {http://dx.doi.org/10.1038/nchembio.187},
}

@Article{Whelan2008,
  author    = {Whelan, K. E. and King, R. D.},
  journal   = {BMC bioinformatics},
  title     = {Using a logical model to predict the growth of yeast},
  year      = {2008},
  issn      = {1471-2105},
  pages     = {97},
  volume    = {9},
  abstract  = {BACKGROUND: A logical model of the known metabolic processes in S. cerevisiae was constructed from iFF708, an existing Flux Balance Analysis (FBA) model, and augmented with information from the KEGG online pathway database. The use of predicate logic as the knowledge representation for modelling enables an explicit representation of the structure of the metabolic network, and enables logical inference techniques to be used for model identification/improvement. RESULTS: Compared to the FBA model, the logical model has information on an additional 263 putative genes and 247 additional reactions. The correctness of this model was evaluated by comparison with iND750 (an updated FBA model closely related to iFF708) by evaluating the performance of both models on predicting empirical minimal medium growth data/essential gene listings. CONCLUSION: ROC analysis and other statistical studies revealed that use of the simpler logical form and larger coverage results in no significant degradation of performance compared to iND750.},
  doi       = {10.1186/1471-2105-9-97},
  file      = {Whelan and King - 2008 - Using a logical model to predict the growth of yea.pdf:by-author/W/Whelan/2008_Whelan_97.pdf:application/pdf;Snapshot:by-author/W/Whelan/2008_Whelan_97.html:text/html},
  groups    = {sg/Knowledge engineering},
  keywords  = {Artificial Intelligence (AI); Biological; Cell Proliferation; Computer Simulation; Knowledge Engineering; Knowledge Representation; Logistic Models; Models; Prolog; Saccharomyces Cerevisiae; Saccharomyces Cerevisiae Proteins; Signal Transduction},
  language  = {eng},
  owner     = {saulius},
  pmcid     = {PMC2335308},
  pmid      = {18269749},
  timestamp = {2015.10.23},
  creationdate = {2015-10-23T00:00:00},
}

@Article{White2002,
  author    = {White, Peter S. and Rodgers, John R. and Le Page, Yvon},
  journal   = {Acta Crystallographica Section B},
  title     = {{CRYSTMET}: a database of the structures and powder patterns of metals and intermetallics},
  year      = {2002},
  pages     = {343--348},
  volume    = {58},
  abstract  = {CRYSTMET is a database of critically evaluated crystallographic data for metals (including alloys, intermetallics and minerals) and associated bibliographic, chemical and physical information. Also included are simulated powder diffraction patterns for all of the entries. The database currently contains almost 70000 entries and covers the literature exhaustively from 1922 to the present. The database is available on CD-ROM with search/analysis software for use on personal computers. This software can be used with any database in the appropriate format; currently CRYSTMET and the ICSD databases are available. This paper describes the database content, the procedures used in its construction, the software made available to the user and a number of potential uses for the data.},
  doi       = {10.1107/S0108768102002902},
  file      = {2002_White_343.pdf:by-author/W/White/2002_White_343.pdf:PDF},
  groups    = {am/CRYSTMET},
  keywords  = {CRYSTMET; Crystallographic Databases; Database of Structures and Powder Patterns},
  owner     = {saulius},
  timestamp = {2015.12.18},
  creationdate = {2015-12-18T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0108768102002902},
}

@Presentation{Whiteley2011,
  author    = {Nick Whiteley},
  title     = {The Metropolis-Hastings Algorithm},
  year      = {2011},
  lecture   = {lecture 7},
  school    = {University of Bristol},
  file      = {:by-author/W/Whiteley/2011_Whiteley_slides.pdf:PDF},
  keywords  = {Metropolis Hastings; Monte Carlo},
  owner     = {saulius},
  pages     = {slides},
  timestamp = {2012.10.04},
  creationdate = {2012-10-04T00:00:00},
}

@Article{Whittington2004,
  author    = {Whittington, Douglas A and Grubb, Jeffrey H and Waheed, Abdul and Shah, Gul N and Sly, William S and Christianson, David W},
  journal   = {The Journal of biological chemistry},
  title     = {Expression, assay, and structure of the extracellular domain of murine carbonic anhydrase XIV: implications for selective inhibition of membrane-associated isozymes.},
  year      = {2004},
  pages     = {7223--8},
  volume    = {279},
  abstract  = {Carbonic anhydrase (CA) XIV is the most recently identified mammalian carbonic anhydrase isozyme, and its presence has been demonstrated in a number of tissues. Full-length CA XIV is a transmembrane protein composed of an extracellular catalytic domain, a single transmembrane helix, and a short intracellular polypeptide segment. The amino acid sequence identity of human CA XIV relative to the other membrane-associated isozymes (CA IV, CA IX, and CA XII) is 34-46%. We report here the expression and purification of both the full-length enzyme and a truncated, secretory form of murine CA XIV. Both forms of this isozyme are highly active, and both show an abrogation of activity in the presence of 0.2% SDS, in contrast to the behavior of murine CA IV. We also report the crystal structure of the extracellular domain of murine CA XIV at 2.8 A resolution and of an enzyme-acetazolamide complex at 2.9 A resolution. The structure shows a monomeric glycoprotein with a topology similar to that of other mammalian CA isozymes. Based on the x-ray crystallographic results, we compare and contrast known structures of membrane-associated CA isozymes to rationalize the structural elements responsible for the SDS resistance of CA IV and to discuss prospects for the design of selective inhibitors of membrane-associated CA isozymes.},
  file      = {2004_Whittington_7223.pdf:by-author/W/Whittington/2004_Whittington_7223.pdf:PDF},
  groups    = {sg/mCA14},
  keywords  = {CA14; Carbonic Anhydrases},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Wichmann1999,
  author    = {B. A. Wichmann},
  title     = {Ackermann's function: a study in the efficiency of calling procedures},
  year      = {1999},
  month     = {March},
  abstract  = {A six line recursive procedure is used to assess the efficiency of the proce- dure calling mechanism in ALGOL-like languages. The results from some 40 systems varying from ALGOL 68 and PL/I to System Implementation Lan- guages for minicomputers are presented and compared. A hundred to one variation in performance occurs with this test, the major reasons for which are given.},
  file      = {:by-author/W/Wichmann/1999_Wichmann.pdf:PDF},
  keywords  = {Ackermann Function; Computer Architecture; Computer Science (CS); Performance Comparison},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Wickelgren2003,
  author    = {Ingrid Wickelgren},
  journal   = {Science},
  title     = {Spinning Junk Into Gold},
  year      = {2003},
  pages     = {1649},
  doi       = {10.1126/science.300.5626.1646},
  file      = {Wickelgren_2003_1649.pdf:by-author/W/Wickelgren/2003_Wickelgren_1649.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Widdifield2010,
  author    = {Cory M. Widdifield and David L. Bryce},
  title     = {upporting Information for: Solid-State 127I NMR and GIPAW DFT Study of Metal Iodides and their Hydrates: Structure, Symmetry, and Higher-Order Quadrupole-Induced Effects},
  year      = {2010},
  pages     = {S1},
  file      = {:by-author/W/Widdifield/2010_Widdifield_S1.pdf:PDF},
  keywords  = {For COD Deposition; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@Article{Widlak2003,
  author    = {Widlak, Piotr and Lanuszewska, Joanna and Cary, Robert B and Garrard, William T},
  journal   = {The Journal of biological chemistry},
  title     = {Subunit structures and stoichiometries of human DNA fragmentation factor proteins before and after induction of apoptosis.},
  year      = {2003},
  pages     = {26915--22},
  volume    = {278},
  abstract  = {DNA fragmentation factor (DFF) is one of the major endonucleases responsible for internucleosomal DNA cleavage during apoptosis. Understanding the regulatory checkpoints involved in safeguarding non-apoptotic cells against accidental activation of this nuclease is as important as elucidating its activation mechanisms during apoptosis. Here we address these issues by determining DFF native subunit structures and stoichiometries in human cells before and after induction of apoptosis using the technique of native pore-exclusion limit electrophoresis in combination with Western analyses. For comparison, we employed similar techniques with recombinant proteins in conjunction with atomic force microscopy. Before induction of apoptosis, the expression of DFF subunits varied widely among the cell types studied, and the chaperone/inhibitor subunits DFF45 and DFF35 unexpectedly existed primarily as monomers in vast excess of the latent nuclease subunit, DFF40, which was stoichiometrically associated with DFF45 to form heterodimers. DFF35 was exclusively cytoplasmic as a monomer. Nuclease activation upon caspase-3 cleavage of DFF45/DFF35 was accompanied by DFF40 homo-oligomer formation, with a tetramer being the smallest unit. Interestingly, intact DFF45 can inhibit nuclease activity by associating with these homo-oligomers without mediating their disassembly. We conclude that DFF nuclease is regulated by multiple pre- and post-activation fail-safe steps.},
  file      = {Widlak_2003_26915-DFF_subunit_structures.pdf:by-author/W/Widlak/2003_Widlak_26915.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Wiedenheft2011a,
  author    = {Wiedenheft, Blake and van Duijn, Esther and Bultema, Jelle B. and Bultema, Jelle and Waghmare, Sakharam P. and Waghmare, Sakharam and Zhou, Kaihong and Barendregt, Arjan and Westphal, Wiebke and Heck, Albert J. R. and Heck, Albert and Boekema, Egbert J. and Boekema, Egbert and Dickman, Mark J. and Dickman, Mark and Doudna, Jennifer A.},
  journal   = {Proceedings of the National Academy of Sciences of the United States of America},
  title     = {RNA-guided complex from a bacterial immune system enhances target recognition through seed sequence interactions.},
  year      = {2011},
  pages     = {10092--7},
  volume    = {108},
  abstract  = {Prokaryotes have evolved multiple versions of an RNA-guided adaptive immune system that targets foreign nucleic acids. In each case, transcripts derived from clustered regularly interspaced short palindromic repeats (CRISPRs) are thought to selectively target invading phage and plasmids in a sequence-specific process involving a variable cassette of CRISPR-associated (cas) genes. The CRISPR locus in Pseudomonas aeruginosa (PA14) includes four cas genes that are unique to and conserved in microorganisms harboring the Csy-type (CRISPR system yersinia) immune system. Here we show that the Csy proteins (Csy1-4) assemble into a 350 kDa ribonucleoprotein complex that facilitates target recognition by enhancing sequence-specific hybridization between the CRISPR RNA and complementary target sequences. Target recognition is enthalpically driven and localized to a &quot;seed sequence&quot; at the 5' end of the CRISPR RNA spacer. Structural analysis of the complex by small-angle X-ray scattering and single particle electron microscopy reveals a crescent-shaped particle that bears striking resemblance to the architecture of a large CRISPR-associated complex from Escherichia coli, termed Cascade. Although similarity between these two complexes is not evident at the sequence level, their unequal subunit stoichiometry and quaternary architecture reveal conserved structural features that may be common among diverse CRISPR-mediated defense systems.},
  file      = {:by-author/W/Wiedenheft/2011_Wiedenheft_10092.pdf:PDF},
  groups    = {sg/CRISPR-Cas},
  keywords  = {CRISPR},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Wiedenheft2011,
  author    = {Wiedenheft, Blake and Lander, Gabriel C. and Zhou, Kaihong and Jore, Matthijs M. and Brouns, Stan J. J. and van der Oost, John and Doudna, Jennifer A. and Nogales, Eva},
  journal   = {Nature},
  title     = {Structures of the RNA-guided surveillance complex from a bacterial immune system.},
  year      = {2011},
  pages     = {486--489},
  volume    = {477},
  abstract  = {Bacteria and archaea acquire resistance to viruses and plasmids by integrating short fragments of foreign DNA into clustered regularly interspaced short palindromic repeats (CRISPRs). These repetitive loci maintain a genetic record of all prior encounters with foreign transgressors. CRISPRs are transcribed and the long primary transcript is processed into a library of short CRISPR-derived RNAs (crRNAs) that contain a unique sequence complementary to a foreign nucleic-acid challenger. In Escherichia coli, crRNAs are incorporated into a multisubunit surveillance complex called Cascade (CRISPR-associated complex for antiviral defence), which is required for protection against bacteriophages. Here we use cryo-electron microscopy to determine the subnanometre structures of Cascade before and after binding to a target sequence. These structures reveal a sea-horse-shaped architecture in which the crRNA is displayed along a helical arrangement of protein subunits that protect the crRNA from degradation while maintaining its availability for base pairing. Cascade engages invading nucleic acids through high-affinity base-pairing interactions near the 5' end of the crRNA. Base pairing extends along the crRNA, resulting in a series of short helical segments that trigger a concerted conformational change. This conformational rearrangement may serve as a signal that recruits a trans-acting nuclease (Cas3) for destruction of invading nucleic-acid sequences.},
  doi       = {10.1038/nature10402},
  file      = {:by-author/W/Wiedenheft/2011_Wiedenheft_486.pdf:PDF},
  groups    = {sg/CRISPR-Cas},
  keywords  = {CRISPR},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Wiederstein2007,
  author    = {Wiederstein, Markus and Sippl, Manfred J.},
  journal   = {Nucleic Acids Research},
  title     = {{ProSA-web}: interactive web service for the recognition of errors in three-dimensional structures of proteins},
  year      = {2007},
  pages     = {W407-W410},
  volume    = {35},
  abstract  = {A major problem in structural biology is the recognition of errors in experimental and theoretical models of protein structures. The ProSA program (Protein Structure Analysis) is an established tool which has a large user base and is frequently employed in the refinement and validation of experimental protein structures and in structure prediction and modeling. The analysis of protein structures is generally a difficult and cumbersome exercise. The new service presented here is a straightforward and easy to use extension of the classic ProSA program which exploits the advantages of interactive web-based applications for the display of scores and energy plots that highlight potential problems spotted in protein structures. In particular, the quality scores of a protein are displayed in the context of all known protein structures and problematic parts of a structure are shown and highlighted in a 3D molecule viewer. The service specifically addresses the needs encountered in the validation of protein structures obtained from X-ray analysis, NMR spectroscopy and theoretical calculations. ProSA-web is accessible at https://prosa.services.came.sbg.ac.at},
  doi       = {10.1093/nar/gkm290},
  file      = {:by-author/W/Wiederstein/2007_Wiederstein_W407.pdf:PDF},
  keywords  = {Proteins; Structure Predicion},
  owner     = {andrius},
  timestamp = {2014.03.11},
  creationdate = {2014-03-11T00:00:00},
  url       = {http://nar.oxfordjournals.org/content/35/suppl_2/W407.abstract},
}

@Article{Wiener1985,
  author     = {Wiener, Richard S. and Sincovec, Richard F.},
  journal    = {SIGPLAN Not.},
  title      = {Two Approaches to Implementing Generic Data Structures in Modula-2},
  year       = {1985},
  issn       = {0362-1340},
  pages      = {56--64},
  volume     = {20},
  acmid      = {988344},
  address    = {New York, NY, USA},
  doi        = {10.1145/988336.988344},
  file       = {1985_Wiener_56.pdf:by-author/W/Wiener/1985_Wiener_56.pdf:PDF},
  groups     = {sg/Generic types, sg/Modula-2},
  issue_date = {June 1985},
  numpages   = {9},
  owner      = {saulius},
  publisher  = {ACM},
  timestamp = {2015.12.16},
  creationdate = {2015-12-16T00:00:00},
  url        = {http://doi.acm.org/10.1145/988336.988344},
}

@Article{Wijnberg2004,
  author    = {Nachoem M. Wijnberg},
  journal   = {Organization Studies},
  title     = {Innovation and Organization: Value and Competition in Selection Systems},
  year      = {2004},
  pages     = {1413--1433},
  volume    = {25},
  abstract  = {New definitions are proposed for the concepts ‘innovation’ and ‘organization’ by looking at the concepts in terms of value and competition and using the framework of the selection system. Also, new definitions are proposed for ‘importance of an innovation’ and ‘stylistic innovation’. Some results can be directly derived from the definitions, such as that economic entities can exist that are organizations in the perception of the individual members and groups of competing actors in the perception of others. Together the new definitions provide a foundation for a better understanding of not just the concepts themselves but also of the relationships between the type and importance of innovations and the most likely characteristics of successful innovators.},
  doi       = {10.1177/0170840604046350},
  eprint    = {http://oss.sagepub.com/content/25/8/1413.full.pdf+html},
  file      = {2004_Wijnberg_1413.pdf:by-author/W/Wijnberg/2004_Wijnberg_1413.pdf:PDF},
  keywords  = {Economy},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://oss.sagepub.com/content/25/8/1413.abstract},
}

@Webpage{Wikipedia2016,
  author    = {Authors of Wikipedia},
  retrieved = {2016-02-22},
  title     = {Gellish},
  url       = {https://en.wikipedia.org/wiki/Gellish},
  year      = {2016},
  file      = {2016_Wikipedia_Gellish.pdf:by-author/W/Wikipedia/2016_Wikipedia_Gellish.pdf:PDF},
  groups    = {sg/Gellish, sg/Conrolled vocabularies},
  keywords  = {Artificial Languages; Controlled Vocabularies; Gellish; Ontologies},
  owner     = {saulius},
  timestamp = {2016.02.23},
  creationdate = {2016-02-23T00:00:00},
}

@Webpage{Wikipedia2015,
  author    = {Authors of Wikipedia},
  retrieved = {2015-03-27},
  title     = {Gibbs paradox},
  url       = {http://en.wikipedia.org/wiki/Gibbs_paradox},
  year      = {2015},
  abstract  = {In statistical mechanics, a semi-classical derivation of the entropy that does not take into account the indistinguishability of particles, yields an expression for the entropy which is not extensive (is not proportional to the amount of substance in question). This leads to a paradox known as the Gibbs paradox, after Josiah Willard Gibbs. The paradox allows for the entropy of closed systems to decrease, violating the second law of thermodynamics. A related paradox is the "mixing paradox". If one takes the perspective that the definition of entropy must be changed so as to ignore particle permutation, the paradox is averted.},
  file      = {:by-author/W/Wikipedia/2015_Wikipedia.odt:OpenDocument text},
  owner     = {saulius},
  timestamp = {2015.03.27},
  creationdate = {2015-03-27T00:00:00},
}

@Webpage{Wikipedia2014,
  author    = {Authors of Wikipedia},
  retrieved = {2015-03-18},
  title     = {Microcanonical ensemble},
  url       = {https://en.wikipedia.org/wiki/Microcanonical_ensemble},
  year      = {2014},
  abstract  = {In statistical mechanics, a microcanonical ensemble is the statistical ensemble that is used to represent the possible states of a mechanical system which has an exactly specified total energy.[1] The system is assumed to be isolated in the sense that the system cannot exchange energy or particles with its environment, so that (by conservation of energy) the energy of the system remains exactly known as time goes on. The system's energy, composition, volume, and shape are kept the same in all possible states of the system.},
  file      = {:by-author/W/Wikipedia/2014_Wikipedia.odt:OpenDocument text},
  owner     = {saulius},
  timestamp = {2015.03.18},
  creationdate = {2015-03-18T00:00:00},
}

@Webpage{Wikipedia2012,
  author    = {Authors of Wikipedia},
  retrieved = {2012-01-12},
  title     = {Periodic boundary conditions},
  url       = {http://en.wikipedia.org/wiki/Periodic_boundary_conditions},
  year      = {2012},
  file      = {:by-author/W/Wikipedia/2012_Wikipedia.odt:},
  keywords  = {Periodic-boundary-conditions; Simulations},
  owner     = {saulius},
  timestamp = {2015.03.03},
  creationdate = {2015-03-03T00:00:00},
}

@Webpage{Wikipedia2011,
  author    = {Authors of Wikipedia},
  retrieved = {2011-12-04},
  title     = {Spin (physics)},
  url       = {http://en.wikipedia.org/wiki/Spin_(physics)},
  year      = {2011},
  file      = {:by-author/W/Wikipedia/2011_Wikipedia.pdf:;:by-author/W/Wikipedia/2011_Wikipedia.odt:},
  keywords  = {Mathematics; Spin-and-spinors},
  owner     = {saulius},
  timestamp = {2015.03.03},
  creationdate = {2015-03-03T00:00:00},
}

@Webpage{Wikipedia2009,
  author    = {Authors of Wikipedia},
  retrieved = {2009-02-07},
  title     = {Test-driven development},
  url       = {http://en.wikipedia.org/wiki/Test-driven_development},
  month     = {February},
  year      = {2009},
  file      = {:by-author/W/Wikipedia/2009_Wikipedia.war:},
  keywords  = {Computer Science (CS); Test Driven Development},
  owner     = {saulius},
  timestamp = {2015.03.02},
  creationdate = {2015-03-02T00:00:00},
}

@Webpage{Wikipedia2006,
  author    = {Authors of Wikipedia},
  retrieved = {2008-07-28},
  title     = {Gödel's incompleteness theorem},
  url       = {http://en.wikipedia.org/wiki/G%C3%B6del%27s_incompleteness_theorems},
  month     = {February},
  year      = {2006},
  file      = {:by-author/W/Wikipedia/2006_Wikipedia.war:WAR},
  keywords  = {Goedel's Theorem},
  owner     = {saulius},
  timestamp = {2015.03.02},
  creationdate = {2015-03-02T00:00:00},
}

@Webpage{Wikipedia2006a,
  author    = {Authors of Wikipedia},
  retrieved = {2008-07-28},
  title     = {Self-verifying theories},
  url       = {http://en.wikipedia.org/wiki/Self-verifying_theories},
  month     = {January},
  year      = {2006},
  file      = {:by-author/W/Wikipedia/2006_Wikipedia_a.war:},
  keywords  = {Goedel's Theorem},
  owner     = {saulius},
  timestamp = {2015.03.02},
  creationdate = {2015-03-02T00:00:00},
}

@Webpage{Wikipedia2006b,
  author    = {Authors of Wikipedia},
  retrieved = {2008-07-28},
  title     = {Method of analytic tableaux},
  url       = {http://en.wikipedia.org/wiki/Analytic_tableaux},
  month     = {February},
  year      = {2006},
  file      = {:by-author/W/Wikipedia/2006_Wikipedia_b.war:},
  keywords  = {Philosophy},
  owner     = {saulius},
  timestamp = {2015.03.02},
  creationdate = {2015-03-02T00:00:00},
}

@Webpage{Wikipedia2006c,
  author    = {Authors of Wikipedia},
  retrieved = {2008-07-28},
  title     = {Redundancy theory of truth},
  url       = {http://en.wikipedia.org/wiki/Disquotationalism},
  month     = {January},
  year      = {2006},
  file      = {:by-author/W/Wikipedia/2006_Wikipedia_c.war:},
  keywords  = {Philosophy},
  owner     = {saulius},
  timestamp = {2015.03.02},
  creationdate = {2015-03-02T00:00:00},
}

@Webpage{Wikipedia2006d,
  author    = {Authors of Wikipedia},
  retrieved = {2008-07-28},
  title     = {Intuitionistic logic},
  url       = {http://en.wikipedia.org/wiki/Intuitionistic_logic},
  month     = {February},
  year      = {2006},
  file      = {:by-author/W/Wikipedia/2006_Wikipedia_d.war:},
  keywords  = {Philosophy},
  owner     = {saulius},
  timestamp = {2015.03.02},
  creationdate = {2015-03-02T00:00:00},
}

@Webpage{Wikipedia2016a,
  author    = {Users of Wikipedia},
  retrieved = {2016-07-17},
  title     = {Firing squad synchronization problem},
  url       = {https://en.wikipedia.org/wiki/Firing_squad_synchronization_problem},
  year      = {2016},
  file      = {2016_Wikipedia_FSSyncP.odt:by-author/W/Wikipedia/2016_Wikipedia_FSSyncP.odt:OpenDocument text;2016_Wikipedia_FSSyncP.pdf:by-author/W/Wikipedia/2016_Wikipedia_FSSyncP.pdf:PDF},
  keywords  = {Celular Automata; Computer Science (CS)},
  owner     = {saulius},
  timestamp = {2016.07.17},
  creationdate = {2016-07-17T00:00:00},
}

@Article{Wilbanks2013,
  author    = {Wilbanks, John},
  journal   = {Nature},
  title     = {Licence restrictions: A fool's errand},
  year      = {2013},
  issn      = {0028-0836},
  pages     = {440--441},
  volume    = {495},
  abstract  = {Copyright licensing is a topic usually left to law review articles, or obscure terms of service on websites, or agreements between publishers and libraries. But it is an essential element of the move towards open access — the free, immediate online availability of scholarly articles coupled with the right to use them fully in the digital environment. An article that is free to read is not necessarily open for all uses — often, it cannot be reused for text mining or in derivative works, for example. The permitted uses depend on the copyright licence used by the author.},
  comment   = {10.1038/495440a},
  file      = {2013_Wilbanks_440.pdf:by-author/W/Wilbanks/2013_Wilbanks_440.pdf:PDF},
  keywords  = {Communication Policy; Open Access; Publishing; Research Management; Scientific Publication},
  owner     = {saulius},
  publisher = {Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},
  timestamp = {2013.04.03},
  creationdate = {2013-04-03T00:00:00},
  url       = {http://dx.doi.org/10.1038/495440a},
}

@InProceedings{WilcoxOHearn2008,
  author    = {Wilcox-O'Hearn, Zooko and Warner, Brian},
  booktitle = {Proceedings of the 4th ACM International Workshop on Storage Security and Survivability},
  title     = {Tahoe: The Least-authority Filesystem},
  year      = {2008},
  address   = {New York, NY, USA},
  pages     = {21--26},
  publisher = {ACM},
  series    = {StorageSS '08},
  abstract  = {Tahoe is a system for secure, distributed storage. It uses ca- pabilities for access control, cryptography for confidentiality and integrity, and erasure coding for fault-tolerance. It has been deployed in a commercial backup service and is currently operational. The implementation is Open Source},
  acmid     = {1456474},
  comment   = {ACM 978-1-60558-299-3/08/10 http://dl.acm.org/citation.cfm?doid=1456469.1456474 http://doi.acm.org/10.1145/1456469.1456474},
  doi       = {10.1145/1456469.1456474},
  file      = {:by-author/W/Wilcox-OHearn/2008_Wilcox-OHearn_524.pdf:PDF},
  isbn      = {978-1-60558-299-3},
  keywords  = {Capabilities; Fault-tolerance; Open Source; Peer-to-peer},
  location  = {Alexandria, Virginia, USA},
  numpages  = {6},
  owner     = {saulius},
  timestamp = {2014.09.23},
  creationdate = {2014-09-23T00:00:00},
  url       = {https://gnunet.org/sites/default/files/lafs.pdf},
}

@Article{Wilhite2012,
  author    = {Wilhite, Allen W. and Fong, Eric A.},
  journal   = {Science},
  title     = {Coercive Citation in Academic Publishing},
  year      = {2012},
  pages     = {542--543},
  volume    = {335},
  abstract  = {Despite their shortcomings (1–4), impact factors continue to be a primary means by which academics “quantify the quality of science” (5). One side effect of impact factors is the incentive they create for editors to coerce authors to add citations to their journal. Coercive self-citation does not refer to the normal citation directions, given during a peer-review process, meant to improve a paper. Coercive self-citation refers to requests that (i) give no indication that the manuscript was lacking in attribution; (ii) make no suggestion as to specific articles, authors, or a body of work requiring review; and (iii) only guide authors to add citations from the editor's journal. This quote from an editor as a condition for publication highlights the problem: “you cite Leukemia [once in 42 references]. Consequently, we kindly ask you to add references of articles published in Leukemia to your present article” (6). Gentler language may be used, but the message is clear: Add citations or risk rejection.},
  doi       = {10.1126/science.1212540},
  eprint    = {http://www.sciencemag.org/content/335/6068/542.full.pdf},
  file      = {2012_Wilhite_542.pdf:by-author/W/Wilhite/2012_Wilhite_542.pdf:PDF},
  groups    = {sg/Bibliometrics},
  keywords  = {Bibliometrics; Citations; Impact Factor (IF); Publication; Publishing; Self Citation},
  owner     = {saulius},
  timestamp = {2013.04.03},
  creationdate = {2013-04-03T00:00:00},
  url       = {http://www.sciencemag.org/content/335/6068/542.short},
}

@Article{Wilkins2002,
  author    = {Wilkins, Brian M.},
  journal   = {Environmental microbiology},
  title     = {Plasmid promiscuity: meeting the challenge of DNA immigration control.},
  year      = {2002},
  pages     = {495--500},
  volume    = {4},
  file      = {:by-author/W/Wilkins/2002_Wilkins_495.pdf:PDF},
  keywords  = {Antirestriction},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Wilkins1970,
  author    = {Wilkins, M. H. and Arnott, S. and Marvin, D. A. and Hamilton, L. D.},
  journal   = {Science (New York, N.Y.)},
  title     = {Some misconceptions on Fourier analysis and Watson-Crick base pairing.},
  year      = {1970},
  pages     = {1693--4},
  volume    = {167},
  file      = {:by-author/W/Wilkins/1970_Wilkins_1693.pdf:PDF},
  keywords  = {DNA Structure},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Wilkins1953,
  author    = {Wilkins, M. H. F. and Stokes, A. R. and Wilson, H. R.},
  journal   = {Nature},
  title     = {Molecular structure of deoxypentose nucleic acids.},
  year      = {1953},
  pages     = {738--40},
  volume    = {171},
  file      = {:by-author/W/Wilkins/1953_Wilkins_738.pdf:PDF},
  keywords  = {DNA Structure},
  owner     = {saulius},
  timestamp = {2012.11.21},
  creationdate = {2012-11-21T00:00:00},
  url       = {http://www.nature.com/nature/dna50/wilkins.pdf},
}

@Article{Wilkinson2006,
  author    = {Brendan L. Wilkinson and Laurent F. Bornaghi and Sally-Ann Poulsen and Todd A. Houston},
  journal   = {Tetrahedron},
  title     = {Synthetic utility of glycosyl triazoles in carbohydrate chemistry},
  year      = {2006},
  pages     = {8115},
  volume    = {62},
  abstract  = {We report herein a study of the synthetic utility of the glucosyl triazole moiety in carbohydrate chemistry. A model glucosyl triazole was prepared by a modified Huisgen 1,3-dipolar cycloaddition reaction. The relative rate of cycloaddition was investigated using a variety of alcohol co-solvents and reaction temperatures. It was found that the reaction proceeded with similar efficiency irrespective of co-solvent, however mildly elevated temperatures (40&#xa0;°C cf. rt) increased the speed of reaction significantly (2&#xa0;h cf. 8&#xa0;h). The robustness of the triazole moiety was then interrogated under conditions typically encountered in carbohydrate chemistry reaction sequences—alcohol group protection/deprotection, nucleophilic displacement, and O-glycosylation. The triazole integrity was retained in all cases studied as evidenced from full compound characterization. Finally, a diverse set of triazole-linked glycoconjugates was synthesized. Collectively, our results demonstrated that the glucosyl triazole moiety was indeed a robust entity for carbohydrate chemistry.},
  doi       = {10.1016/j.tet.2006.06.001},
  file      = {:by-author/W/Wilkinson/2006_Wilkinson_8115.pdf:PDF},
  keywords  = {Bioconjugation; Carbohydrate; Click Chemistry; Glycoconjugate; Huisgen Reaction},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/S0040402006008891},
}

@Article{Wille1972,
  author    = {Wille, Friedrich},
  journal   = {Math. Z.},
  title     = {Galerkins L6sungsn iherungen bei rnonotonen Abbildungen},
  year      = {1972},
  pages     = {10--16},
  volume    = {127},
  abstract  = {Gar mancher hatte Mtihe schon mit seiner L6sungskonstruktion. Drum haben wir uns ausgedacht wie man es mit Galerkin macht.},
  file      = {:by-author/W/Wille/1972_Wille_10.pdf:PDF},
  keywords  = {Mathematics; Poetry},
  owner     = {em},
  timestamp = {2013.12.30},
  creationdate = {2013-12-30T00:00:00},
}

@Article{Williams2012,
  author    = {Williams, Antony John and Yerin, Andrey},
  journal   = {Wiley Interdisciplinary Reviews: Computational Molecular Science},
  title     = {Automated systematic nomenclature generation for organic compounds},
  year      = {2012},
  issn      = {1759-0876},
  month     = {Sep},
  number    = {2},
  pages     = {150--160},
  volume    = {3},
  doi       = {10.1002/wcms.1118},
  file      = {:by-author/W/Williams/2012_Williams_150.pdf:PDF},
  publisher = {Wiley},
  url       = {https://doi.org/10.1002/wcms.1118},
  owner     = {andrius},
  creationdate = {2021-11-05T16:55:22},
  modificationdate = {2022-12-24T18:51+02:00},
}

@Article{Williams2011,
  author    = {Williams, Antony J. and Ekins, Sean},
  journal   = {Drug Discovery Today},
  title     = {A quality alert and call for improved curation of public chemistry databases},
  year      = {2011},
  issn      = {1359-6446},
  month     = {Sep},
  number    = {17-18},
  pages     = {747–750},
  volume    = {16},
  abstract  = {In the last ten years, public online databases have rapidly become trusted valuable resources upon which researchers rely for their chemical structures and data for use in cheminformatics, bioinformatics, systems biology, translational medicine and now drug repositioning or repurposing efforts. Their utility depends on the quality of the underlying molecular structures used. Unfortunately, the quality of much of the chemical structure-based data introduced to the public domain is poor. As an example we describe some of the errors found in the recently released NIH Chemical Genomics Center ‘NPC browser’ database as an example. There is an urgent need for government funded data curation to improve the quality of internet chemistry and to limit the proliferation of errors and wasted efforts.},
  doi       = {10.1016/j.drudis.2011.07.007},
  file      = {2011_Williams_747.pdf:by-author/W/Williams/2011_Williams_747.pdf:PDF},
  groups    = {am/Data quality},
  owner     = {andrius},
  publisher = {Elsevier BV},
  timestamp = {2016.12.28},
  creationdate = {2016-12-28T00:00:00},
  url       = {http://dx.doi.org/10.1016/j.drudis.2011.07.007},
}

@Presentation{WilliamsXXXX,
  author    = {Chris Williams},
  title     = {The Gaussian Distribution},
  year      = {XXXX},
  file      = {:by-author/W/Williams/XXXX_Williams_slides.pdf:PDF},
  owner     = {saulius},
  pages     = {slides},
  timestamp = {2013.03.22},
  creationdate = {2013-03-22T00:00:00},
  url       = {http://homepages.inf.ed.ac.uk/ckiw/},
}

@Manuscript{Williams2008,
  author       = {David N. Williams},
  title        = {The {Dirac} algebra for any spin},
  year         = {2008},
  keywords     = {Mathematics; Spin; Spinors},
  organization = {Eidgenössiche Technische Hochschule Zürich},
  url          = {http://www-personal.umich.edu/~williams/papers/diracalg.pdf},
  file         = {:by-author/W/Williams/2008_Williams_1.pdf:PDF},
  owner        = {saulius},
  pages        = {1--29},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Williams1969,
  author    = {Williams, D. E.},
  journal   = {Acta Crystallographica Section A},
  title     = {A method of calculating molecular crystal structures},
  year      = {1969},
  pages     = {464--470},
  volume    = {25},
  abstract  = {A novel method of calculating the molecular position in a lattice of known dimensions is presented. The repulsive lattice energy is approximated by a sum of quadratic nonbonded interatomic potential functions and the lattice energy sum is minimized by full-matrix least squares. The convergence range from arbitrary trial models is greater than the previously used steepest descent method using (exp-6) nonbonded potentials. Greatly increased speed of convergence is also obtained because of the inclusion of off-diagonal terms and the small number of repulsive interactions which are considered. The calculated packing models are sufficiently accurate to serve as a starting point for structure factor least-squares refinement based on diffraction data.},
  doi       = {10.1107/S0567739469000933},
  file      = {:by-author/W/Williams/1969_Williams_464.pdf:PDF},
  groups    = {sg/Crystal structure prediction},
  keywords  = {Crystal Structure Prediction (CSP)},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0567739469000933},
}

@Article{Williams2001,
  author    = {Williams, S. A. and Halford, S. E.},
  journal   = {Nucleic acids research},
  title     = {SfiI endonuclease activity is strongly influenced by the non-specific sequence in the middle of its recognition site.},
  year      = {2001},
  pages     = {1476--83},
  volume    = {29},
  abstract  = {The SfiI endonuclease cleaves DNA at the sequence GGCCNNNN NGGCC, where N is any base and downward arrow is the point of cleavage. Proteins that recognise discontinuous sequences in DNA can be affected by the unspecified sequence between the specified base pairs of the target site. To examine whether this applies to SFII, a series of DNA duplexes were made with identical sequences apart from discrete variations in the 5 bp spacer. The rates at which SFII cleaved each duplex were measured under steady-state conditions: the steady-state rates were determined by the DNA cleavage step in the reaction pathway. SFII cleaved some of these substrates at faster rates than other substrates. For example, the change in spacer sequence from AACAA to AAACA caused a 70-fold increase in reaction rate. In general, the extrapolated values for k(cat) and K(m) were both higher on substrates with inflexible spacers than those with flexible structures. The dinucleotide at the site of cleavage was largely immaterial. SFII activity is thus highly dependent on conformational variations in the spacer DNA.},
  file      = {:by-author/W/Williams/2001_Williams_1476.pdf:PDF},
  keywords  = {Readout},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Manuscript{Wills2007,
  author    = {John M. Wills and Olle Eriksson and Mebarek Alouani and David L. Price},
  title     = {Full-Potential {LMTO} Total Energy and Force Calculations},
  year      = {2007},
  url       = {http://gurka.fysik.uu.se/esp/FPLMTO.pdf},
  abstract  = {The essential features of a full potential electronic structure method using Linear Muffin-Tin Orbitals (LMTOs) are presented. The electron density and potential in this method are represented with no inherent geometrical approximation. This method allows the calculation of total energies and forces with arbitrary accuracy while sacrifiicng much of the efficiency and physical content of approximate methods such as LMTO-ASA method.},
  file      = {2007_Wills_manuscript.pdf:by-author/W/Wills/2007_Wills_manuscript.pdf:PDF},
  owner     = {saulius},
  timestamp = {2014.07.31},
  creationdate = {2014-07-31T00:00:00},
}

@Presentation{Willumeit2010,
  author    = {Willumeit, Regine},
  title     = {Scattering of Neutrons Basics},
  year      = {2010},
  file      = {:by-author/W/Willumeit/2010_Willumeit_slides.pdf:PDF},
  keywords  = {SAXS},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Wilson1950,
  author    = {Wilson, A. J. C.},
  journal   = {Acta Crystallographica},
  title     = {Largest likely values for the reliability index},
  year      = {1950},
  pages     = {397--398},
  volume    = {3},
  doi       = {10.1107/S0365110X50001129},
  file      = {1950_Wilson_397.pdf:by-author/W/Wilson/1950_Wilson_397.pdf:PDF},
  keywords  = {Data Quality; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2014.03.24},
  creationdate = {2014-03-24T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0365110X50001129},
}

@Article{Wilson1950a,
  author    = {Wilson, A. J. C.},
  journal   = {Acta Crystallographica},
  title     = {The probability distribution of X-ray intensities. III. Effects of symmetry elements on zones and rows},
  year      = {1950},
  pages     = {258--261},
  volume    = {3},
  abstract  = {A symmetry element that causes equivalent atoms to coincide in groups of n in a plane (or line) projection produces a zone (or row) of reflexions whose average intensity is n$\Sigma$ , where $\Sigma$ is the sum of the squares of the scattering factors of the atoms in the unit cell. The average for the general reflexions is $\Sigma$; the difference between the zone (or row) average and the general average may be useful in the purely X-ray determination of space groups. The effects of simple symmetry elements on the probability distribution of the intensities are summarized in two tables.},
  doi       = {10.1107/S0365110X50000677},
  file      = {1950_Wilson_258.pdf:by-author/W/Wilson/1950_Wilson_258.pdf:PDF},
  keywords  = {X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2014.03.24},
  creationdate = {2014-03-24T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0365110X50000677},
}

@Article{Wilson1949,
  author    = {Wilson, A. J. C.},
  journal   = {Acta Crystallographica},
  title     = {The probability distribution of X-ray intensities},
  year      = {1949},
  pages     = {318--321},
  volume    = {2},
  doi       = {10.1107/S0365110X49000813},
  file      = {1949_Wilson_318.pdf:by-author/W/Wilson/1949_Wilson_318.pdf:PDF},
  keywords  = {X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2014.03.24},
  creationdate = {2014-03-24T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0365110X49000813},
}

@Article{Wilson1968,
  author    = {Wilson, Fred L.},
  journal   = {American Journal of Physics},
  title     = {Fermi’s Theory of Beta Decay},
  year      = {1968},
  issn      = {0002-9505},
  number    = {12},
  pages     = {1150--1160},
  volume    = {36},
  doi       = {10.1119/1.1974382},
  file      = {1968_Wilson_1150.pdf:by-author/W/Wilson/1968_Wilson_1150.pdf:PDF},
  owner     = {saulius},
  publisher = {American Association of Physics Teachers (AAPT)},
  timestamp = {2016.03.19},
  creationdate = {2016-03-19T00:00:00},
  url       = {http://dx.doi.org/10.1119/1.1974382},
}

@Article{Wilson2008,
  author    = {Paul R. Wilson},
  journal   = {ACM Computing Surveys},
  title     = {Uniprocessor Garbage Collection Techniques},
  year      = {2008},
  file      = {:by-author/W/Wilson/2008_Wilson.pdf:PDF;:by-author/W/Wilson/2008_Wilson.ps:PostScript},
  groups    = {sg/Garbage collectors},
  owner     = {saulius},
  timestamp = {2015.02.25},
  creationdate = {2015-02-25T00:00:00},
}

@InProceedings{Wilson1991,
  author    = {Paul R. Wilson and Barry Hayes},
  title     = {The 1991 Workshop on Garbage Collection in Object-Oriented Systems},
  year      = {1991},
  file      = {:by-author/W/Wilson/1991_Wilson.pdf:PDF;:by-author/W/Wilson/1991_Wilson.ps:PostScript},
  groups    = {sg/Garbage collectors},
  owner     = {saulius},
  timestamp = {2015.02.25},
  creationdate = {2015-02-25T00:00:00},
}

@TechReport{Wilson1995,
  author      = {Paul~R. Wilson and Mark~S. Johnstone and Michael Neely and David Boles},
  institution = {Department of Computer Sciences, University of Texas at Austin},
  title       = {Dynamic Storage Allocation: A Survey and Critical Review},
  year        = {1995},
  file        = {:by-author/W/Wilson/1995_Wilson.ps:PostScript;:by-author/W/Wilson/1995_Wilson.pdf:PDF},
  groups      = {sg/Garbage collectors},
  keywords    = {Computer Science (CS); Garbage Collection; Memory Allocation},
  owner       = {saulius},
  timestamp = {2015.02.27},
  creationdate = {2015-02-27T00:00:00},
}

@Article{Wilson2009,
  author    = {Wilson, Timothy J and Lilley, David M J},
  journal   = {Science (New York, N.Y.)},
  title     = {Biochemistry. The evolution of ribozyme chemistry.},
  year      = {2009},
  pages     = {1436--8},
  volume    = {323},
  file      = {2009_Wilson_1436.pdf:by-author/W/Wilson/2009_Wilson_1436.pdf:PDF},
  keywords  = {Ribozymes},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Wiltschi2016,
  author    = {Birgit Wiltschi},
  journal   = {Fungal Genetics and Biology},
  title     = {Incorporation of non-canonical amino acids into proteins in yeast},
  year      = {2016},
  issn      = {1087-1845},
  note      = {The Era of Synthetic Biology in Yeast and Filamentous Fungi},
  pages     = {137--156},
  volume    = {89},
  abstract  = {Abstract Non-canonical amino acids add extraordinary chemistries to proteins when they gain access to translation. In yeast, they can be incorporated into proteins by replacing a canonical amino acid or in a site-specific manner in response to an amber stop codon. The first approach simply exploits the natural substrate tolerance of the aminoacyl-tRNA synthetases in an auxotrophic host. The latter requires the co-expression of an orthogonal aminoacyl-tRNA synthetase that is specific for the non-canonical amino acid together with an amber suppressor tRNA. This review briefly recaps the residue- and site-specific incorporation techniques for non-canonical amino acids in yeast. It describes the selection system for orthogonal aminoacyl-tRNA synthetase/suppressor tRNA pairs and compares the different expression systems for these pairs. Numerous examples illustrate the application of non-canonical amino acids for protein engineering in yeast. The compilation includes the chemical structures of the amino acid analogs, the orthogonal pairs that were used for their incorporation and the titers of the labeled variant proteins.},
  doi       = {10.1016/j.fgb.2016.02.002},
  file      = {:by-author/W/Wiltschi/2016_Wiltschi_137.pdf:PDF},
  groups    = {am/Expanded genetic code},
  owner     = {andrius},
  timestamp = {2016.05.04},
  creationdate = {2016-05-04T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/S1087184516300160},
}

@TechReport{Winchenbach2004,
  author      = {Samuel Winchenbach and Mohammed Driss},
  institution = {University of Maine},
  title       = {8-Bit Arithmetic Logic Unit},
  year        = {2004},
  file        = {:by-author/W/Winchenbach/2004_Winchenbach.pdf:PDF},
  keywords    = {ALU; CPU Design; Computer Science (CS)},
  owner       = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Wing2008,
  author    = {Richard A. Wing and Scott Bailey and Thomas A. Steitz},
  journal   = {Journal of Molecular Biology},
  title     = {Insights into the Replisome from the Structure of a Ternary Complex of the DNA Polymerase III α-Subunit},
  year      = {2008},
  issn      = {0022-2836},
  pages     = {859 - 869},
  volume    = {382},
  abstract  = {The crystal structure of the catalytic α−subunit of the DNA polymerase III (PolIIIα) holoenzyme bound to primer–template DNA and an incoming deoxy-nucleoside 5′-triphosphate has been determined at 4.6-Å resolution. The polymerase interacts with the sugar–phosphate backbone of the DNA across its minor groove, which is made possible by significant movements of the thumb, finger, and β-binding domains relative to their orientations in the unliganded polymerase structure. Additionally, the DNA and incoming nucleotide are bound to the active site of PolIIIα nearly identically as they are in their complex with DNA polymerase β, thereby proving that the eubacterial replicating polymerase, but not the eukaryotic replicating polymerase, is homologous to DNA polymerase β. Finally, superimposing a recent structure of the clamp bound to DNA on this PolIIIα complex with DNA places a loop of the β-binding domain into the appropriate clamp cleft and supports a mechanism of polymerase switching.},
  doi       = {10.1016/j.jmb.2008.07.058},
  file      = {2008_Wing_859.pdf:by-author/W/Wing/2008_Wing_859.pdf:PDF;mmc1.doc:by-author/W/Wing/2008_Wing_859_suppl/mmc1.doc:Word;mmc2.doc:by-author/W/Wing/2008_Wing_859_suppl/mmc2.doc:Word;mmc3.doc:by-author/W/Wing/2008_Wing_859_suppl/mmc3.doc:Word;mmc4.doc:by-author/W/Wing/2008_Wing_859_suppl/mmc4.doc:Word;mmc5.doc:by-author/W/Wing/2008_Wing_859_suppl/mmc5.doc:Word;mmc6.doc:by-author/W/Wing/2008_Wing_859_suppl/mmc6.doc:Word;mmc7.doc:by-author/W/Wing/2008_Wing_859_suppl/mmc7.doc:Word;mmc8.doc Omit Electron Density Maps:by-author/W/Wing/2008_Wing_859_suppl/mmc8.doc:Word},
  keywords  = {DNA; Eubacteria; PolIII; Replication},
  owner     = {saulius},
  timestamp = {2012.10.24},
  creationdate = {2012-10-24T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/S0022283608009121},
}

@Article{Winiarski2014,
  author    = {Winiarski, Micha{\textbackslash}l J. and Szreder, Natalia A. and Barczyński, Ryszard J. and Klimczuk, Tomasz},
  journal   = {Journal of Alloys and Compounds},
  title     = {Synthesis, single crystal growth and properties of {Sr} 5 {Pb} 3 {ZnO} 12},
  year      = {2014},
  pages     = {63--68},
  volume    = {617},
  file      = {[PDF] from arxiv.org:by-author/W/Winiarski/2014_Winiarski_63.pdf:application/pdf;Snapshot:by-author/W/Winiarski/2014_Winiarski_63.html:text/html},
  groups    = {sg/JAC2009},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/S0925838814017496},
  urldate   = {2015-08-31},
}

@Article{Winkler1996,
  author    = {Winkler, R. L. and Muñoz, Javier and Cervera, José L. and Bernardo, José M. and Blattenberger, Gail and Kadane, Joseph B. and Lindley, Dennis V. and Murphy, Allan H. and Oliver, Robert M. and Ríos-Insua, David},
  journal   = {Test},
  title     = {Scoring rules and the evaluation of probabilities},
  year      = {1996},
  issn      = {1133-0686, 1863-8260},
  pages     = {1--60},
  volume    = {5},
  abstract  = {Summary In Bayesian inference and decision analysis, inferences and predictions are inherently probabilistic in nature. Scoring rules, which involve the computation of a score based on probability forecasts and what actually occurs, can be used to evaluate probabilities and to provide appropriate incentives for “good” probabilities. This paper review scoring rules and some related measures for evaluating probabilities, including decompositions of scoring rules and attributes of “goodness” of probabilites, comparability of scores, and the design of scoring rules for specific inferential and decision-making problems},
  doi       = {10.1007/BF02562681},
  file      = {Winkler et al. - 1996 - Scoring rules and the evaluation of probabilities.pdf:by-author/W/Winkler/1996_Winkler_1.pdf:application/pdf;Snapshot:by-author/W/Winkler/1996_Winkler_1.html:text/html},
  groups    = {sg/Probability theory, sg/Bayesian},
  keywords  = {Attributes of “Good” Probabilities; Decomposition of Expected Scores; Evaluation of Probabilities; General; Probability Assessment; Probability Forecasts; Scoring Rules; Statistical Theory and Methods; Statistics; Statistics for Business/Economics/Mathematical Finance/Insurance},
  language  = {en},
  owner     = {saulius},
  timestamp = {2015.12.07},
  creationdate = {2015-12-07T00:00:00},
  url       = {http://link.springer.com/article/10.1007/BF02562681},
  urldate   = {2015-12-07},
}

@Article{Winn2001,
  author    = {Winn, M. D. and Isupov, M. N. and Murshudov, G. N.},
  journal   = {Acta Crystallographica Section D},
  title     = {Use of TLS parameters to model anisotropic displacements in macromolecular refinement},
  year      = {2001},
  pages     = {122--133},
  volume    = {57},
  abstract  = {An essential step in macromolecular refinement is the selection of model parameters which give as good a description of the experimental data as possible while retaining a realistic data-to-parameter ratio. This is particularly true of the choice of atomic displacement parameters, where the move from individual isotropic to individual anisotropic refinement involves a sixfold increase in the number of required displacement parameters. The number of refinement parameters can be reduced by using collective variables rather than independent atomic variables and one of the simplest examples of this is the TLS parameterization for describing the translation, libration and screw-rotation displacements of a pseudo-rigid body. This article describes the implementation of the TLS parameterization in the macromolecular refinement program REFMAC. Derivatives of the residual with respect to the TLS parameters are expanded in terms of the derivatives with respect to individual anisotropic U values, which in turn are calculated using a fast Fourier transform technique. TLS refinement is therefore fast and can be used routinely. Examples of TLS refinement are given for glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and a transcription activator GerE, for both of which there is data to only 2.0 Å, so that individual anisotropic refinement is not feasible. GAPDH has been refined with between one and four TLS groups in the asymmetric unit and GerE with six TLS groups. In both cases, inclusion of TLS parameters gives improved refinement statistics and in particular an improvement in R and free R values of several percent. Furthermore, GAPDH and GerE have two and six molecules in the asymmetric unit, respectively, and in each case the displacement parameters differ significantly between molecules. These differences are well accounted for by the TLS parameterization, leaving residual local displacements which are very similar between molecules and to which NCS restraints can be applied.},
  doi       = {10.1107/S0907444900014736},
  file      = {2001_Winn_122.pdf:by-author/W/Winn/2001_Winn_122.pdf:PDF},
  keywords  = {Algorithms; Anisotropic Refinement; Crystallography; REFMAC; TLS Parameterization; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2012.12.26},
  creationdate = {2012-12-26T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444900014736},
}

@Article{Winquist2013,
  author       = {Johan Winquist and Stefan Geschwindner and Yafeng Xue and Lars Gustavsson and Djordje Musil and Johanna Deinum and U. Helena Danielson},
  journal      = {Biochemistry},
  title        = {Identification of structural-kinetic and structural-thermodynamic relationships for thrombin inhibitors.},
  year         = {2013},
  month        = {Jan},
  number       = {4},
  pages        = {613--626},
  volume       = {52},
  abstract     = {To improve our understanding of drug-target interactions, we explored the effect of introducing substituted amine residues with increased chain length in the P3 residue of the thrombin inhibitor melagatran. Inhibition, kinetic, and thermodynamic data obtained via stopped-flow spectroscopy (SF), isothermal microcalorimetry (ITC), and surface plasmon resonance (SPR) biosensor analysis were interpreted with the help of X-ray crystal structures of the enzyme-inhibitor complexes. The association rate became faster when the lipophilicity of the inhibitors was increased. This was coupled to an increased enthalpic component and a corresponding decreased entropic component. The dissociation rates were reduced with an increase in chain length, with only a smaller increase and a decrease in the enthalpic and entropic components, respectively. Overall, the affinity increased with an increase in chain length, with similar changes in the enthalpic and entropic components. ITC analysis confirmed the equilibrium data from SPR analysis, showing that the interaction of melagatran was the most enthalpy-driven interaction. Structural analysis of the thrombin-inhibitor complex showed that the orientation of the P1 and P2 parts of the molecules was very similar, but that there were significant differences in the interaction between the terminal part of the P3 side chain and the binding pocket. A combination of charge repulsion, H-bonds, and hydrophobic interactions could be used to explain the observed kinetic and thermodynamic profiles for the ligands. In conclusion, changes in the structure of a lead compound can have significant effects on its interaction with the target that translate directly into kinetic and thermodynamic effects. In contrast to what may be intuitively expected, hydrogen bond formation and breakage are not necessarily reflected in enthalpy gains and losses, respectively.},
  creationdate = {2016-06-06T00:00:00},
  doi          = {10.1021/bi301333z},
  file         = {2013_Winquist_613.pdf:by-author/W/Winquist/2013_Winquist_613.pdf:PDF},
  institution  = {Department of Chemistry-BMC, Uppsala University, SE-751 23 Uppsala, Sweden.},
  keywords     = {Antagonists /&/ Inhibitors/chemistry; Antithrombins; Azetidines; Benzylamines; Catalytic Domain; Chemistry; Crystallography; Drug Discovery; Hirudins; Humans; Hydrogen Bonding; Hydrophobic and Hydrophilic Interactions; Kinetics; Models; Molecular; Protein Binding; Surface Properties; Thermodynamics; Thrombin; X-Ray},
  language     = {eng},
  medline-pst  = {ppublish},
  owner        = {alexey},
  pmid         = {23290007},
  timestamp    = {2016.06.06},
  url          = {http://dx.doi.org/10.1021/bi301333z},
}

@Manuscript{Winroth1993a,
  author    = {Harald Winroth},
  title     = {Exception Handling in ANSI and C},
  year      = {1993},
  keywords  = {C; Exception; Signal; Unwind},
  file      = {:by-author/W/Winroth/1993_Winroth.ps:PostScript;:by-author/W/Winroth/1993_Winroth.pdf:PDF},
  owner     = {saulius},
  timestamp = {2013.08.10},
  creationdate = {2013-08-10T00:00:00},
}

@Article{Winroth1993,
  author    = {Harald Winroth and Matti Rendahl},
  journal   = {The C Users Journal},
  title     = {Exception Handling In C},
  year      = {1993},
  month     = {oct},
  pages     = {33--46},
  file      = {:by-author/W/Winroth/1993_Winroth_33.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.06.04},
  creationdate = {2012-06-04T00:00:00},
}

@Webpage{Winterbottom1997,
  author    = {Phil Winterbottom and Rob Pike},
  retrieved = {2015-03-06},
  title     = {The design of the Inferno virtual machine},
  url       = {http://herpolhode.com/rob/hotchips.html},
  year      = {1997},
  abstract  = {Virtual machines are an important component of modern portable environments such as Inferno and Java because they provide an architecture-independent representation of executable code. Their performance is critical to the success of such environments, but they are difficult to design well because they are subject to conflicting goals. On the one hand, they offer a way to hide the differences between instruction architectures; on the other, they must be implemented efficiently on a variety of underlying machines. A comparison of the engineering and evolution of the Inferno and Java virtual machines provides insight into the tradeoffs in their design and implementation. We argue that the design of virtual machines should be rooted in the nature of modern processors, not language interpreters, with an eye towards on-the-fly compilation rather than interpretation or special-purpose silicon.},
  file      = {:by-author/W/Winterbottom/1997_Winterbottom.html:URL},
  keywords  = {Computer Science (CS); Virtual Machines},
  owner     = {saulius},
  timestamp = {2015.03.03},
  creationdate = {2015-03-03T00:00:00},
}

@TechReport{Winterstein1995,
  author      = {S. R. Winterstein and C. H. Lange and S. Kumar},
  institution = {Civil Engineering Department, Stanford University, Stanford, CA 94305},
  title       = {Fitting: A Subroutine to Fit Four-Moment Probability Distributions to Data},
  year        = {1995},
  abstract    = {'fitting' is a Fortran subroutine that constructs a smooth, generalized four- parameter probability distribution model. It is fit to the first four statistical moments of the random variable X (i.e., average values of X, X2, X3, and X4) which can be calculated from data using the associated subroutine calmom. The generalized model is produced from a cubic distortion of the parent model, calibrated to match the first four moments of the data. This four-moment matching is intended to provide models that are more faithful to the data in the upper tail of the distribution. Examples are shown for two specific cases.},
  file        = {1995_Winterstein_tr.pdf:by-author/W/Winterstein/1995_Winterstein_tr.pdf:PDF},
  owner       = {saulius},
  timestamp = {2012.09.18},
  creationdate = {2012-09-18T00:00:00},
}

@Article{Winum2005,
  author    = {Winum, Jean-Yves and Cecchi, Alessandro and Montero, Jean-Louis and Innocenti, Alessio and Scozzafava, Andrea and Supuran, Claudiu T},
  journal   = {Bioorganic \&amp; medicinal chemistry letters},
  title     = {Carbonic anhydrase inhibitors. Synthesis and inhibition of cytosolic/tumor-associated carbonic anhydrase isozymes I, II, and IX with boron-containing sulfonamides, sulfamides, and sulfamates: toward agents for boron neutron capture therapy of hypoxic tumors.},
  year      = {2005},
  pages     = {3302--6},
  volume    = {15},
  file      = {2005_Winum_3302.pdf:by-author/W/Winum/2005_Winum_3302.pdf:PDF},
  groups    = {sg/inhibitors, sg/hCA1, sg/hCA2, sg/hCA9},
  keywords  = {Carbonic Anhydrases},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Winum2005a,
  author    = {Winum, Jean-Yves and Scozzafava, Andrea and Montero, Jean-Louis and Supuran, Claudiu T},
  journal   = {Medicinal research reviews},
  title     = {Sulfamates and their therapeutic potential.},
  year      = {2005},
  pages     = {186--228},
  volume    = {25},
  abstract  = {Starting from the very simple molecule sulfamic acid, O-substituted-, N-substituted-, or di-/tri-substituted sulfamates may be obtained, which show specific biological activities which were or started to be exploited for the design of many types of therapeutic agents. Among them, sulfamate inhibitors of aminoacyl-tRNA synthetases (aaRSs) were recently reported, constituting completely new classes of antibiotics, useful in the fight of drug-resistant infections. Anti-viral agents incorporating sulfamate moieties have also been obtained, with at least two types of such derivatives investigated: the nucleoside/nucleotide human immunodeficiency virus (HIV) reverse transcriptase inhibitors, and the HIV protease inhibitors (PIs). In the increasing armamentarium of anti-cancer drugs, the sulfamates occupy a special position, with at least two important targets evidenced so far: the steroid sulfatases (STSs) and the carbonic anhydrases (CAs). An impressing number of inhibitors of STSs of the sulfamate type have been reported in the last years, with several compounds, such as 667COUMATE among others, progressing to clinical trials for the treatment of hormone-dependent tumors (breast and prostate cancers). This field is rapidly evolving, with many types of new inhibitors being constantly reported and designed in such a way as to increase their anti-tumor properties, and decrease undesired features (for example, estrogenicity, a problem encountered with the first generation such inhibitors, such as EMATE). Among the many isozymes of CAs, at least two, CA IX and CA XII, are highly overexpressed in tumors, being generally absent in the normal tissues. Inhibition of tumor-associated CAs was hypothesized to lead to novel therapeutic approaches for the treatment of cancer. Many sulfamates act as very potent (low nanomolar) CA inhibitors. The X-ray crystal structure of the best-studied isozyme, CA II, with three sulfamates (sulfamic acid, topiramate, and EMATE) has recently been reported, which allowed for a rationale drug design of new inhibitors. Indeed, low nanomolar CA IX inhibitors of the sulfamate type have been reported, although such compounds also act as efficient inhibitors of isozymes CA I and II, which are not associated with tumors. A large number of anti-convulsant sulfamates have been described, with one such compound, topiramate, being widely used clinically as anti-epileptic drug. By taking into consideration a side effect of topiramate, an anti-epileptic drug leading to weight loss in some patients, it has recently been proposed to use this drug and related sulfamates for the treatment of obesity. The rationale of this use is based on the inhibition of the mitochondrial CA isozyme, CA V, involved in lipogenesis. Some sulfamates were also shown to possess potent inhibitory activity against acyl coenzyme A:cholesterol acyltransferase, an enzyme involved in cholesterol metabolism. One such agent, avasimibe, is in advanced clinical trials for the treatment of hyperlipidemia and atherosclerosis. Thus, the sulfamate moiety offers very attractive possibilities for the drug design of various pharmacological agents, which are on one hand due to the relative ease with which such compounds are synthesized, and on the other one, due to the fact that biological activity of most of them is impressive.},
  file      = {2005_Winum_186.pdf:by-author/W/Winum/2005_Winum_186.pdf:PDF},
  groups    = {sg/inhibitors, sg/medicine},
  keywords  = {Carbonic Anhydrases},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Wishart2008,
  author    = {Wishart, David S. and Knox, Craig and Guo, An Chi and Cheng, Dean and Shrivastava, Savita and Tzur, Dan and Gautam, Bijaya and Hassanali, Murtaza},
  journal   = {Nucleic Acids Research},
  title     = {DrugBank: a knowledgebase for drugs, drug actions and drug targets},
  year      = {2008},
  pages     = {D901-D906},
  volume    = {36},
  abstract  = {DrugBank is a richly annotated resource that combines detailed drug data with comprehensive drug target and drug action information. Since its first release in 2006, DrugBank has been widely used to facilitate in silico drug target discovery, drug design, drug docking or screening, drug metabolism prediction, drug interaction prediction and general pharmaceutical education. The latest version of DrugBank (release 2.0) has been expanded significantly over the previous release. With ∼4900 drug entries, it now contains 60% more FDA-approved small molecule and biotech drugs including 10% more ‘experimental’ drugs. Significantly, more protein target data has also been added to the database, with the latest version of DrugBank containing three times as many non-redundant protein or drug target sequences as before (1565 versus 524). Each DrugCard entry now contains more than 100 data fields with half of the information being devoted to drug/chemical data and the other half devoted to pharmacological, pharmacogenomic and molecular biological data. A number of new data fields, including food–drug interactions, drug–drug interactions and experimental ADME data have been added in response to numerous user requests. DrugBank has also significantly improved the power and simplicity of its structure query and text query searches. DrugBank is available at http://www.drugbank.ca},
  doi       = {10.1093/nar/gkm958},
  eprint    = {http://nar.oxfordjournals.org/content/36/suppl_1/D901.full.pdf+html},
  file      = {:by-author/W/Wishart/2008_Wishart_901.pdf:PDF},
  keywords  = {DrugBank},
  owner     = {antanas},
  timestamp = {2014.07.02},
  creationdate = {2014-07-02T00:00:00},
  url       = {http://nar.oxfordjournals.org/content/36/suppl_1/D901.abstract},
}

@Article{Wishart2006,
  author    = {Wishart, David S. and Knox, Craig and Guo, An Chi and Shrivastava, Savita and Hassanali, Murtaza and Stothard, Paul and Chang, Zhan and Woolsey, Jennifer},
  journal   = {Nucleic Acids Research},
  title     = {DrugBank: a comprehensive resource for in silico drug discovery and exploration},
  year      = {2006},
  pages     = {D668-D672},
  volume    = {34},
  abstract  = {DrugBank is a unique bioinformatics/cheminformatics resource that combines detailed drug (i.e. chemical) data with comprehensive drug target (i.e. protein) information. The database contains >4100 drug entries including >800 FDA approved small molecule and biotech drugs as well as >3200 experimental drugs. Additionally, >14 000 protein or drug target sequences are linked to these drug entries. Each DrugCard entry contains >80 data fields with half of the information being devoted to drug/chemical data and the other half devoted to drug target or protein data. Many data fields are hyperlinked to other databases (KEGG, PubChem, ChEBI, PDB, Swiss-Prot and GenBank) and a variety of structure viewing applets. The database is fully searchable supporting extensive text, sequence, chemical structure and relational query searches. Potential applications of DrugBank include in silico drug target discovery, drug design, drug docking or screening, drug metabolism prediction, drug interaction prediction and general pharmaceutical education. DrugBank is available at http://redpoll.pharmacy.ualberta.ca/drugbank/.},
  doi       = {10.1093/nar/gkj067},
  eprint    = {http://nar.oxfordjournals.org/content/34/suppl_1/D668.full.pdf+html},
  file      = {:by-author/W/Wishart/2006_Wishart_D668.pdf:PDF},
  keywords  = {DrugBank},
  owner     = {antanas},
  timestamp = {2014.07.02},
  creationdate = {2014-07-02T00:00:00},
  url       = {http://nar.oxfordjournals.org/content/34/suppl_1/D668.abstract},
}

@Article{Wisz2003,
  author    = {Wisz, Michael S and Hellinga, Homme W},
  journal   = {Proteins},
  title     = {An empirical model for electrostatic interactions in proteins incorporating multiple geometry-dependent dielectric constants.},
  year      = {2003},
  pages     = {360--77},
  volume    = {51},
  abstract  = {Here we introduce an electrostatic model that treats the complexity of electrostatic interactions in a heterogeneous protein environment by using multiple parameters that take into account variations in protein geometry, local structure, and the type of interacting residues. The optimal values for these parameters were obtained by fitting the model to a large dataset of 260 experimentally determined pK(a) values distributed over 41 proteins. We obtain fits between the calculated and observed values that are significantly better than the null model. The model performs well on the groups that exhibit large pK(a) shifts from solution values in response to the protein environment and compares favorably with other, successful continuum models. The empirically determined values of the parameters correlate well with experimentally observed contributions of hydrogen bonds and ion pairs as well as theoretically predicted magnitudes of charge-charge and charge-polar interactions. The magnitudes of the dielectric constants assigned to different regions of the protein rank according to the strength of the relaxation effects expected for the core, boundary, and surface. The electrostatic interactions in this model are pairwise decomposable and can be calculated rapidly. This model is therefore well suited for the large computations required for simulating protein properties and especially for prediction of mutations for protein design.},
  file      = {2003_Wisz_360.pdf:by-author/W/Wisz/2003_Wisz_360.pdf:PDF},
  keywords  = {Noncovalent Interactions; Protein Physics},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Manuscript{Wittenberger2002,
  author    = {Jorg F. Wittenberger},
  title     = {Askemos - a distributed settlement},
  year      = {2002},
  keywords  = {Computer Science (CS); Reliable Computing},
  abstract  = {This paper presents Askemos[1], an autonomous, distributed operating system on top of peer to peer networks which significantly raises the level of abstraction in comparison with today’s operating systems. Askemos addresses safe, secure and correct (forge proof) information processing while securing intellec- tual property in an innovative way. Askemos defines a virtual machine on document level, which is defined in terms of abstract trees and pure functional transformation of them, both described in XML. This virtual machine has no physical representation at any single machine. Instead it works distributed among independent components which appear as if they observed it. To achieve that effect, the participat- ing machines compute the process steps of the virtual machine independent and vote among each other about the correct result. To prevent illegal attacks, there exists no concept of unique resources like superuser rights or unique name spaces.},
  file      = {:by-author/W/Wittenberger/2002_Wittenberger.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Wlodawer2008,
  author    = {Alexander Wlodawer and Wladek Minor and Zbigniew Dauter and Mariusz Jaskolski},
  journal   = {FEBS Journal},
  title     = {Protein crystallography for non-crystallographers, or how to get the best (but not more) from published macromolecular structures},
  year      = {2008},
  pages     = {1--21},
  volume    = {275},
  abstract  = {The number of macromolecular structures deposited in the Protein Data Bank now exceeds 45 000, with the vast majority determined using crystal- lographic methods. Thousands of studies describing such structures have been published in the scientific literature, and 14 Nobel prizes in chemistry or medicine have been awarded to protein crystallographers. As important as these structures are for understanding the processes that take place in living organisms and also for practical applications such as drug design, many non-crystallographers still have problems with critical evaluation of the structural literature data. This review attempts to provide a brief out- line of technical aspects of crystallography and to explain the meaning of some parameters that should be evaluated by users of macromolecular structures in order to interpret, but not over-interpret, the information present in the coordinate files and in their description. A discussion of the extent of the information that can be gleaned from the coordinates of structures solved at different resolution, as well as problems and pitfalls encountered in structure determination and interpretation are also covered.},
  doi       = {10.1111/j.1742-4658.2007.06178.x},
  file      = {:by-author/W/Wlodawer/2008_Wlodawer_1.pdf:PDF},
  owner     = {antanas},
  timestamp = {2013.12.12},
  creationdate = {2013-12-12T00:00:00},
  url       = {http://dx.doi.org/10.1111/j.1742-4658.2007.06178.x},
}

@Article{Woerd2001a,
  author    = {van der Woerd, M. J. and Pelletier, J. J. and Xu, S. and Friedman, A. M.},
  journal   = {Structure (London, England : 1993)},
  title     = {Restriction enzyme BsoBI-DNA complex: a tunnel for recognition of degenerate DNA sequences and potential histidine catalysis.},
  year      = {2001},
  pages     = {133--44},
  volume    = {9},
  file      = {:by-author/v/vanderWoerd/2001_Woerd_133.pdf:PDF},
  keywords  = {Struct; TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Wojciechowski2011,
  author    = {Wojciechowski, Filip and Leumann, Christian J.},
  journal   = {Chem. Soc. Rev.},
  title     = {Alternative DNA base-pairs: from efforts to expand the genetic code to potential material applications},
  year      = {2011},
  issn      = {1460-4744},
  number    = {12},
  pages     = {5669},
  volume    = {40},
  doi       = {10.1039/c1cs15027h},
  file      = {:by-author/W/Wojciechowski/2011_Wojciechowski_5669.pdf:PDF},
  groups    = {am/Expanded genetic code},
  owner     = {andrius},
  publisher = {Royal Society of Chemistry (RSC)},
  timestamp = {2016.05.06},
  creationdate = {2016-05-06T00:00:00},
  url       = {http://dx.doi.org/10.1039/c1cs15027h},
}

@Presentation{Wolber2006,
  author           = {Gerhard Wolber and Alois A. Dornhofer and Thierry Langer},
  title            = {Efficient overlay of molecular 3-{D} pharmacophores},
  year             = {2006},
  creationdate     = {2012-05-15T00:00:00},
  file             = {:by-author/W/Wolber/2006_Wolber_slides.pdf:PDF},
  groups           = {sg/Molecule superposion, sg/Superposition, sg/Bioinf. Algorithms},
  keywords         = {Structure Superposition},
  modificationdate = {2024-05-12T17:09:43},
  owner            = {saulius},
  pages            = {slides},
  timestamp        = {2012.05.15},
  url              = {https://www.inteligand.com/pubs/060225_wolber_pharmacophore_overlay.pdf},
}

@Article{Wold1981,
  author    = {Wold, Finn},
  journal   = {Ann. Rev. Biochem.},
  title     = {In Vivo Chemical Modification Of Proteins (post-translational Modification)},
  year      = {1981},
  pages     = {783--814},
  volume    = {50},
  file      = {1981_Wold_783.pdf:by-author/W/Wold/1981_Wold_783.pdf:PDF},
  keywords  = {Chemical Modification; Post Translational Modification},
  owner     = {em},
  timestamp = {2013.01.07},
  creationdate = {2013-01-07T00:00:00},
}

@Article{Wolfe-Simon2011,
  author    = {Wolfe-Simon, Felisa and Switzer Blum, Jodi and Kulp, Thomas R. and Gordon, Gwyneth W. and Hoeft, Shelley E. and Pett-Ridge, Jennifer and Stolz, John F. and Webb, Samuel M. and Weber, Peter K. and Davies, Paul C. W. and Anbar, Ariel D. and Oremland, Ronald S.},
  journal   = {Science (New York, N.Y.)},
  title     = {A bacterium that can grow by using arsenic instead of phosphorus.},
  year      = {2011},
  pages     = {1163--6},
  volume    = {332},
  abstract  = {Life is mostly composed of the elements carbon, hydrogen, nitrogen, oxygen, sulfur, and phosphorus. Although these six elements make up nucleic acids, proteins, and lipids and thus the bulk of living matter, it is theoretically possible that some other elements in the periodic table could serve the same functions. Here, we describe a bacterium, strain GFAJ-1 of the Halomonadaceae, isolated from Mono Lake, California, that is able to substitute arsenic for phosphorus to sustain its growth. Our data show evidence for arsenate in macromolecules that normally contain phosphate, most notably nucleic acids and proteins. Exchange of one of the major bio-elements may have profound evolutionary and geochemical importance.},
  file      = {:by-author/W/Wolfe-Simon/2011_Wolfe-Simon_1163.pdf:PDF},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{deWolff:a24271,
  author    = {de Wolff, P. M. and Belov, N. V. and Bertaut, E. F. and Buerger, M. J. and Donnay, J. D. H. and Fischer, W. and Hahn, Th. and Koptsik, V. A. and Mackay, A. L. and Wondratschek, H. and Wilson, A. J. C. and Abrahams, S. C.},
  journal   = {Acta Crystallographica Section A},
  title     = {Nomenclature for crystal families, Bravais-lattice types and arithmetic classes. Report of the International Union of Crystallography {\it Ad-Hoc} Committee on the Nomenclature of Symmetry},
  year      = {1985},
  pages     = {278--280},
  volume    = {41},
  abstract  = {Standard symbols representing crystal families, two- and three-dimensional Bravais-lattice types and arithmetic classes are recommended for use by the IUCr. The six crystal families are designated by lower-case letters. The family letter in the symbol of each of the 14 lattice types is followed by an upper-case letter to distinguish different lattice types within the family. Arithmetic classes are indicated by modified symbols of the corresponding symmorphic space groups.},
  doi       = {10.1107/S0108767385000587},
  file      = {1985_Wolff_278.pdf:by-author/W/Wolff/1985_Wolff_278.pdf:PDF},
  groups    = {sg/Cell reduction},
  keywords  = {Nomenclature; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2014.06.26},
  creationdate = {2014-06-26T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0108767385000587},
}

@Article{Wolff1989,
  author    = {de Wolff, P. M. and Billiet, Y. and Donnay, J. D. H. and Fischer, W. and Galiulin, R. B. and Glazer, A. M. and Senechal, M. and Shoemaker, D. P. and Wondratschek, H. and Hahn, Th. and Wilson, A. J. C. and Abrahams, S. C.},
  journal   = {Acta Crystallographica Section A},
  title     = {Definition of symmetry elements in space groups and point groups. Report of the International Union of Crystallography {\it Ad}-{\it Hoc} Committee on the Nomenclature of Symmetry},
  year      = {1989},
  pages     = {494--499},
  volume    = {45},
  abstract  = {A 'geometric element' is defined, for any given symmetry operation, as a geometric item that allows the operation (after removing any intrinsic translation) to be located and oriented. In the case of an inversion, a (screw-) rotation or a (glide-) reflection, it is respectively a point, line or plane. In the case of a rotoinversion, the geometric element consists of the axis of the rotation part and the center of the inversion part. As a general concept, the geometric element may be justified by a mathematical definition (as given in the Appendix). A "symmetry element" (of a given crystal structure or object) is defined as a concept with a double meaning, namely the combination of a geometric element with the set of symmetry operations having this geometric element in common ('element set'). There is no overlap between element sets of a given structure. Together with the identity and the translations, for which a geometric element is not defined, the element sets cover all symmetry operations.},
  doi       = {10.1107/S0108767389002230},
  file      = {1989_Wolff_494.pdf:by-author/W/Wolff/1989_Wolff_494.pdf:PDF},
  keywords  = {Spacegroups; Symmetry; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2014.05.08},
  creationdate = {2014-05-08T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0108767389002230},
}

@Article{deWolff1991,
  author    = {de Wolff, P. M. and Gruber, B.},
  journal   = {Acta Crystallographica Section A},
  title     = {Niggli lattice characters: definition and graphical representation},
  year      = {1991},
  pages     = {29--36},
  volume    = {47},
  abstract  = {An exact definition of the 44 lattice characters listed by Niggli is thoroughly discussed and is elucidated by examples. In order to represent the characters graphically, use is made of the projection of the Niggli-reduced basis vector c on the a, b plane. Not only is the projected end point of c restricted to certain domains in the plane by the reduction rules - cf. International Tables for Crystallography (1987), ch. 9.3 (Dordrecht: Kluwer) - but for given constants A, B and F in the Niggli-reduced form this polygonal domain contains the locus of each of the characters as a vertex or an edge or the area of the polygon. For each of the cases a = b = c, a = b < c, a < b = c and a < b < c, nine figures fully cover all alternatives determined by five special values F = A/2, 0, -A/4, -A/3 and -A/2 and the four open intervals between them. Also, all normalized Buerger bases which are not Niggli-reduced bases are shown in the same figures.},
  comment   = {44 entry table},
  doi       = {10.1107/S0108767390009485},
  file      = {:by-author/d/deWolff/1991_deWolff_29.pdf:PDF},
  groups    = {sg/Cell sg/Reduction, sg/Cell reduction},
  keywords  = {Crystal Cell; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0108767390009485},
}

@Article{Wolfram1985,
  author    = {Stephen Wolfram},
  journal   = {Physica Scripta},
  title     = {Twenty Problems in the Theory of Cellular Automata},
  year      = {1985},
  pages     = {170--183},
  volume    = {T9},
  file      = {1985_Wolfram_170.pdf:by-author/W/Wolfram/1985_Wolfram_170.pdf:PDF},
  groups    = {sg/Cellular automata},
  keywords  = {Cellular Automata},
  owner     = {saulius},
  timestamp = {2015.10.23},
  creationdate = {2015-10-23T00:00:00},
  url       = {http://www.stephenwolfram.com/publications/academic/problems-theory-cellular-automata.pdf},
}

@Manuscript{Wolpert1994,
  author    = {David H. Wolpert},
  title     = {On the Bayesian “Occam Factors” Argument for Occam’s Razor},
  year      = {1994},
  keywords  = {Bayesian Statistics; Occam’s Razor; Ockham's Razor},
  url       = {http://www.denizyuret.com/ref/wolpert/papers/55.pdf},
  abstract  = {This paper discusses some of the problematic aspects of the Bayesian first-principles “proof” of Occam’s razor which involves Occam factors. Although it is true that the posterior for a model is reduced due to Occam factors if that model is capable of expressing many functions, the phenomenon need not have anything to do with Occam’s razor. This paper shows this by i) per- forming reductio ad absurdum on the argument that the Occam factors effect implies Occam’s ra- zor; ii) presenting an alternative Bayesian approach which explicitly does not result in Occam’s razor; and finally iii) disentangling the underlying problem with viewing the Occam factors argu- ment as a proof or “automatic embodiment” of Occam’s razor.},
  file      = {:by-author/W/Wolpert/1994_Wolpert_manuscript.pdf:PDF},
  groups    = {sg/Bayesian},
  owner     = {saulius},
  timestamp = {2012.11.24},
  creationdate = {2012-11-24T00:00:00},
}

@Article{Wolverton1974,
  author    = {Ray W. Wolverton},
  journal   = {IEEE Transactions on Computers},
  title     = {The Cost of Developing Large-Scale Software},
  year      = {1974},
  pages     = {615--636},
  volume    = {c-23},
  abstract  = {The work of software cost forecasting falls into two parts. First we make what we call structural forecasts, and then we calculate the absolute dollar-volume forecasts. Structural forecasts describe the technology and function of a software project, but not its size. We allocate resources (costs) over the project's life cycle from the structural forecasts. Judgment, technical knowledge, and econometric research should combine in making the structural fore- casts. A methodology based on a 25 X 7 structural forecast matrix that has been used by TRW with good results over the past few years is presented in this paper. With the structural forecast in hand, we go on to calculate the absolute dollar-volume forecasts. The general logic followed in "absolute" cost estimating can be based on either a mental process or an explicit algorithm. A cost estimating algorithm is presented and five tradition methods of software cost forecasting are described: top-down estimating, similarities and differences estimating, ratio estimating, standards estimating, and bottom-up estimating. All forecasting methods suffer from the need for a valid cost data base for many estimating situations. Software information elements that experience has shown to be useful in establishing such a data base are given in the body of the paper. Major pricing pitfalls are identified. Two case studies are presented that illustrate the software cost forecasting methodology and his- torical results. Topics for further work and study are suggested.},
  file      = {1974_Wolverton_615.pdf:by-author/W/Wolverton/1974_Wolverton_615.pdf:PDF},
  owner     = {saulius},
  timestamp = {2015.11.22},
  creationdate = {2015-11-22T00:00:00},
  url       = {http://www.computer.org/csdl/trans/tc/1974/06/01672595.pdf},
}

@Article{Woo2003,
  author    = {Eui-Jeon Woo and Yeon-Gil Kim and Min-Sung Kim and Won-Deok Han and Sejeong Shin and Howard Robinson and Sam-Yong Park and Byung-Ha Oh},
  journal   = {Molecular Cell},
  title     = {Structural Mechanism for Inactivation and Activation of {CAD/DFF40} in the Apoptotic Pathway},
  year      = {2003},
  issn      = {1097-2765},
  pages     = {531--539},
  volume    = {14},
  doi       = {10.1016/S1097-2765(04)00258-8},
  file      = {Woo_2003_531-DFF40_structure.pdf:by-author/W/Woo/2003_Woo.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/S1097276504002588},
}

@InProceedings{Woo2000,
  author    = {Woo, Sung-Ho and Yang, Sung-Bong},
  booktitle = {Proceedings of the 8th ACM international symposium on Advances in geographic information systems},
  title     = {An Improved Network Clustering Method for {I/O}-Efficient Query Processing},
  year      = {2000},
  address   = {New York, NY, USA},
  pages     = {62--68},
  publisher = {ACM},
  series    = {GIS '00},
  abstract  = {Efficient network query processing is extremely important in Geographical Information Systems (GIS) and Intelligent Transportation Systems (ITS) which include various applications of transportation, utility and communication networks, etc. In order to reduce the I/O cost in network query processing a given network should be stored with high disk-space utilization and a low edge-cut ratio. To do so the nodes in the network should be clustered in such a way that each cluster fits in a disk page with as small number of edge-cuts as possible. This is known as the network clustering problem which is NP-complete. In this paper we present a network clustering method, called Network-Traversal Clustering (NTC) method, which assigns the nodes of a given network to disk pages with optimal disk-space utilization and a low edge-cut ratio. NTC is suitable for the bulk loading operation into a network indexing structure. In the experimental results NTC outperformed the Connectivity-Clustered Access Method, the Spatial Partition Clustering (SPC) and SPC-R which is a modification of SPC on various networks.},
  doi       = {10.1145/355274.355283},
  file      = {:by-author/W/Woo/2000_Woo_62.pdf:PDF},
  isbn      = {1-58113-319-7},
  location  = {Washington, D.C., United States},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://doi.acm.org/10.1145/355274.355283},
}

@Article{Woo2005,
  author    = {Woo, Youn-Hi and Rajagopalan, P. T. Ravi and Benkovic, Stephen J.},
  journal   = {Analytical biochemistry},
  title     = {A nonradioactive DNA methyltransferase assay adaptable to high-throughput screening.},
  year      = {2005},
  pages     = {336--40},
  volume    = {340},
  abstract  = {We have developed a nonradioactive assay method for DNA methyltransferases based on the ability to protect substrate DNA from restriction. DNA immobilized to a microplate well was treated sequentially with methyltransferase and an appropriate endonuclease. The amount of methylated DNA product is reflected by a proportional decrease in endonuclease cleavage, which is in turn reflected by increased retention of the end-labeled affinity probe. A single universal substrate was designed to assay multiple methyltransferases including those that do not have a cognate endonuclease. The methodology developed is suited to screen a large number of compounds for inhibitors of various methyltransferases.},
  file      = {:by-author/W/Woo/2005_Woo_336.pdf:PDF},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Wood1947,
  author    = {Wood, Elizabeth Armstrong},
  journal   = {Journal of Applied Physics},
  title     = {The Conversion Factor for kX Units to Angström Units},
  year      = {1947},
  issn      = {0021-8979},
  number    = {10},
  pages     = {929},
  volume    = {18},
  doi       = {10.1063/1.1697570},
  file      = {:./by-author/W/Wood/1947_Wood_929.pdf:PDF},
  keywords  = {Angström; Unit Conversion; {kX}},
  owner     = {antanas},
  publisher = {AIP Publishing},
  timestamp = {2016.04.08},
  creationdate = {2016-04-08T00:00:00},
  url       = {http://dx.doi.org/10.1063/1.1697570},
}

@Article{Wood1996,
  author    = {Gordon H. Wood and John R and S. Roger Gough and Pierre Villars},
  journal   = {Journal of Research of the National Institute of Standards and Technology},
  title     = {CRYSTMET—The NRCC Metals Crystallographic Data File},
  year      = {1996},
  pages     = {205--215},
  volume    = {101},
  abstract  = {CRYSTMET, the National Research Council of Canada Metals Crystallographic Data File, is a computer-readable database of critically evaluated crystallographic data for metals (including alloys, intermetallics and minerals) accompanied by pertinent chemical, physical and bibliographic information. It currently contains about 60 000 entries and covers the literature exhaustively from 1913.},
  doi       = {10.6028/jres.101.021},
  file      = {1996_Wood_205.pdf:by-author/W/Wood/1996_Wood_205.pdf:PDF},
  groups    = {am/CRYSTMET},
  owner     = {saulius},
  timestamp = {2015.12.18},
  creationdate = {2015-12-18T00:00:00},
  url       = {http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.95.7549},
}

@Article{Wood2005,
  author    = {Wood, Katie M. and Daniels, Lucy E. and Halford, Stephen E.},
  journal   = {Journal of molecular biology},
  title     = {Long-range communications between DNA sites by the dimeric restriction endonuclease SgrAI.},
  year      = {2005},
  pages     = {240--53},
  volume    = {350},
  abstract  = {The SgrAI endonuclease displays its maximal activity on DNA with two copies of its recognition sequence, cleaving both sites concertedly. While most restriction enzymes that act concurrently at two sites are tetramers, SgrAI is a dimer in solution. Its reaction at two cognate sites involves the association of two DNA-bound dimers. SgrAI can also bridge cognate and secondary sites, the latter being certain sequences that differ from the cognate by one base-pair. The mechanisms for cognate-cognate and cognate-secondary communications were examined for sites in the following topological relationships: in cis, on plasmids with two sites in a single DNA molecule; on catenanes containing two interlinked rings of DNA with one site in each ring; and in trans, on oligoduplexes carrying either a single site or the DNA termini generated by SgrAI. Both cognate-cognate and cognate-secondary interactions occur through 3-D space and not by 1-D tracking along the DNA. Both sorts of communication arise more readily when the sites are tethered to each other, either in cis on the same molecule of DNA or by the interlinking of catenane rings, than when released from the tether. However, the dimer bound to an oligoduplex carrying either a cognate or a secondary site could be activated to cleave that duplex by interacting with a second dimer bound to the recognition site, provided both duplexes are at least 30 base-pairs long: the second dimer could alternatively be bound to the two duplexes that correspond to the products of DNA cleavage by SgrAI.},
  file      = {:by-author/W/Wood/2005_Wood_240.pdf:PDF},
  keywords  = {Tetra; TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@InProceedings{Wood1959,
  author    = {Wood, W. W. and Jacobson, J. D.},
  booktitle = {Papers presented at the the March 3-5, 1959, western joint computer conference},
  title     = {Monte Carlo calculations in statistical mechanics},
  year      = {1959},
  address   = {New York, NY, USA},
  pages     = {261--269},
  publisher = {ACM},
  series    = {IRE-AIEE-ACM '59 (Western)},
  acmid     = {1457887},
  doi       = {10.1145/1457838.1457887},
  file      = {1959_Wood_261.pdf:by-author/W/Wood/1959_Wood_261.pdf:PDF},
  groups    = {sg/Molecular dynamics},
  keywords  = {Hard Spheres; Molecular Dynamics (MD)},
  location  = {San Francisco, California},
  numpages  = {9},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://doi.acm.org/10.1145/1457838.1457887},
}

@Article{Wood1957,
  author    = {W. W. Wood and J. D. Jacobson},
  journal   = {Journal of Chemical Physics},
  title     = {Preliminary Results from a Recalculation of the Monte Carlo Equation of State of Hard Spheres},
  year      = {1957},
  pages     = {1207--1208},
  volume    = {27},
  doi       = {10.1063/1.1743956},
  file      = {1957_Wood_1207.pdf:by-author/W/Wood/1957_Wood_1207.pdf:PDF},
  groups    = {sg/Molecular dynamics},
  keywords  = {Hard Spheres; Molecular Dynamics (MD)},
  owner     = {saulius},
  timestamp = {2011.10.21},
  creationdate = {2011-10-21T00:00:00},
  url       = {http://jcp.aip.org/resource/1/jcpsa6/v27/i5/p1207_s1},
}

@PhdThesis{Woods1985,
  author    = {Woods, Daniel John},
  school    = {Rice University},
  title     = {An Interactive Approach For Solving Multi-objective Optimization Problems},
  year      = {1985},
  abstract  = {Multi-objective optimization problems are characterized by the need to consider multiple, and possibly conflicting, objectives in the solution process. We present an approach based on the use of interactive computer graphics to obtain qualitative information from a user about approximate solutions. We then use this qualitative information to transform the multi-objective optimization problem into a single-objective optimization problem that we may solve using standard techniques. Preliminary convergence results for the Nelder-Mead simplex algorithm are presented. Techniques for updating the single-objective problem after each piece of information is obtained from the user are described. These techniques are based on the duality theory for linear and quadratic programming. A software system for the subclass of 1-dimensional curve-fitting problems is also described.},
  file      = {:by-author/W/Woods/1985_Woods_phdthesis.PDF:PDF},
  owner     = {andrius},
  timestamp = {2012.11.29},
  creationdate = {2012-11-29T00:00:00},
  url       = {http://hdl.handle.net/1911/15945},
}

@Presentation{Woodward2005,
  author    = {Patrick M. Woodward},
  title     = {X-ray Powder Diffraction Peak Intensities},
  year      = {2005},
  course    = {Chemistry 754},
  lecture   = {Lecture #10},
  school    = {OSU},
  file      = {2005_Woodward_slides.pdf:by-author/W/Woodward/2005_Woodward_slides.pdf:PDF},
  keywords  = {Diffraction Peak Multiplicities; Intensity Calculation; Powder Diffraction},
  owner     = {saulius},
  timestamp = {2014.09.16},
  creationdate = {2014-09-16T00:00:00},
  url       = {https://chemistry.osu.edu/~woodward/ch754/lect2003/xrd_peakintensities.pdf},
}

@Article{Woolf1989,
  author    = {A. A. Woolf},
  journal   = {Journal of Chemical Education},
  title     = {Coordination and Radius Ratio: A Graphical Representation},
  year      = {1989},
  pages     = {509},
  volume    = {66},
  abstract  = {A graphical representation of and explanations for radius ratio limits for given coordinations.},
  doi       = {10.1021/ed066p509},
  file      = {:./by-author/W/Woolf/1989_Woolf_509.pdf:PDF},
  keywords  = {Coordination Complex},
  owner     = {antanas},
  timestamp = {2014.01.15},
  creationdate = {2014-01-15T00:00:00},
  url       = {http://pubs.acs.org/doi/abs/10.1021/ed066p509},
}

@Article{Word1999,
  author    = {Word, J. M. and Lovell, S. C. and Richardson, J. S. and Richardson, D. C.},
  journal   = {Journal of molecular biology},
  title     = {Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation.},
  year      = {1999},
  pages     = {1735--47},
  volume    = {285},
  abstract  = {Small-probe contact dot surface analysis, with all explicit hydrogen atoms added and their van der Waals contacts included, was used to choose between the two possible orientations for each of 1554 asparagine (Asn) and glutamine (Gln) side-chain amide groups in a dataset of 100 unrelated, high-quality protein crystal structures at 0.9 to 1.7 A resolution. For the movable-H groups, each connected, closed set of local H-bonds was optimized for both H-bonds and van der Waals overlaps. In addition to the Asn/Gln "flips", this process included rotation of OH, SH, NH3+, and methionine methyl H atoms, flip and protonation state of histidine rings, interaction with bound ligands, and a simple model of water interactions. However, except for switching N and O identity for amide flips (or N and C identity for His flips), no non-H atoms were shifted. Even in these very high-quality structures, about 20 % of the Asn/Gln side-chains required a 180 degrees flip to optimize H-bonding and/or to avoid NH2 clashes with neighboring atoms (incorporating a conservative score penalty which, for marginal cases, favors the assignment in the original coordinate file). The programs Reduce, Probe, and Mage provide not only a suggested amide orientation, but also a numerical score comparison, a categorization of the marginal cases, and a direct visualization of all relevant interactions in both orientations. Visual examination allowed confirmation of the raw score assignment for about 40 % of those Asn/Gln flips placed within the "marginal" penalty range by the automated algorithm, while uncovering only a small number of cases whose automated assignment was incorrect because of special circumstances not yet handled by the algorithm. It seems that the H-bond and the atomic-clash criteria independently look at the same structural realities: when both criteria gave a clear answer they agreed every time. But consideration of van der Waals clashes settled many additional cases for which H-bonding was either absent or approximately equivalent for the two main alternatives. With this extra information, 86 % of all side-chain amide groups could be oriented quite unambiguously. In the absence of further experimental data, it would probably be inappropriate to assign many more than this. Some of the remaining 14 % are ambiguous because of coordinate error or inadequacy of the theoretical model, but the great majority of ambiguous cases probably occur as a dynamic mix of both flip states in the actual protein molecule. The software and the 100 coordinate files with all H atoms added and optimized and with amide flips corrected are publicly available.},
  file      = {:by-author/W/Word/1999_Word_1735.pdf:PDF},
  keywords  = {Grow Krystal},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Woude2004,
  author    = {van der Woude, Marjan W. and Bäumler, Andreas J.},
  journal   = {Clinical microbiology reviews},
  title     = {Phase and antigenic variation in bacteria.},
  year      = {2004},
  pages     = {581-611, table of contents},
  volume    = {17},
  abstract  = {Phase and antigenic variation result in a heterogenic phenotype of a clonal bacterial population, in which individual cells either express the phase-variable protein(s) or not, or express one of multiple antigenic forms of the protein, respectively. This form of regulation has been identified mainly, but by no means exclusively, for a wide variety of surface structures in animal pathogens and is implicated as a virulence strategy. This review provides an overview of the many bacterial proteins and structures that are under the control of phase or antigenic variation. The context is mainly within the role of the proteins and variation for pathogenesis, which reflects the main body of literature. The occurrence of phase variation in expression of genes not readily recognizable as virulence factors is highlighted as well, to illustrate that our current knowledge is incomplete. From recent genome sequence analysis, it has become clear that phase variation may be more widespread than is currently recognized, and a brief discussion is included to show how genome sequence analysis can provide novel information, as well as its limitations. The current state of knowledge of the molecular mechanisms leading to phase variation and antigenic variation are reviewed, and the way in which these mechanisms form part of the general regulatory network of the cell is addressed. Arguments both for and against a role of phase and antigenic variation in immune evasion are presented and put into new perspective by distinguishing between a role in bacterial persistence in a host and a role in facilitating evasion of cross-immunity. Finally, examples are presented to illustrate that phase-variable gene expression should be taken into account in the development of diagnostic assays and in the interpretation of experimental results and epidemiological studies.},
  file      = {:by-author/v/vanderWoude/2004_Woude_581.pdf:PDF},
  keywords  = {Obzor},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@TechReport{Wright1992,
  author      = {Andrew K. Wright and Matthias Felleisen},
  institution = {Department of Computer Science, Rice University, Houston, TX 77251-1892},
  title       = {A Syntactic Approach to Type Soundness},
  year        = {1992},
  month       = {June},
  number      = {TR91-160},
  abstract    = {We present a new approach to proving type soundness for Hindley/Milner-style polymorphic type systems. The keys to our approach are (1) an adaptation of subject reduction theorems from combinatory logic to programming languages, and (2) the use of rewriting techniques for the speci cation of the language semantics. The approach easily extends from polymorphic functional languages to imperative languages that provide references, exceptions, continuations, and similar features. We illustrate the technique with a type soundness theorem for the core of Standard ML, which includes the rst type soundness proof for polymorphic exceptions and continuations.},
  file        = {:by-author/W/Wright/1992_Wright.ps.gz:PostScript;:by-author/W/Wright/1992_Wright.pdf:PDF},
  owner       = {saulius},
  timestamp = {2015.02.27},
  creationdate = {2015-02-27T00:00:00},
}

@Article{Wright2015,
  author       = {Wright, J. S. and Vitórica-Yrezábal, I. J. and Adams, H. and Thompson, S. P. and Hill, A. H. and Brammer, L.},
  journal      = {{IUCrJ}},
  title        = {Solvent-vapour-assisted pathways and the role of pre-organization in solid-state transformations of coordination polymers},
  year         = {2015},
  issn         = {2052-2525},
  number       = {2},
  pages        = {188--197},
  volume       = {2},
  abstract     = {A family of one-dimensional coordination polymers, [Ag4(O2C({CF}2)2CF3)4(phenazine)2(arene)n]·m(arene), 1 (arene = toluene or xylene), have been synthesized and crystallographically characterized. Arene guest loss invokes structural transformations to yield a pair of polymorphic coordination polymers [Ag4(O2C({CF}2)2CF3)4(phenazine)2], 2a and/or 2b, with one- and two-dimensional architectures, respectively. The role of pre-organization of the polymer chains of 1 in the selectivity for formation of either polymorph is explored, and the templating effect of toluene and p-xylene over o-xylene or m-xylene in the formation of arene-containing architecture 1 is also demonstrated. The formation of arene-free phase 2b, not accessible in a phase-pure form through other means, is shown to be the sole product of loss of toluene from 1-tol·tol [Ag4(O2C({CF}2)2CF3)4(phenazine)2(toluene)]·2(toluene), a phase containing toluene coordinated to Ag(I) in an unusual μ:η1,η1 manner. Solvent-vapour-assisted conversion between the polymorphic coordination polymers and solvent-vapour influence on the conversion of coordination polymers 1 to 2a and 2b is also explored. The transformations have been examined and confirmed by X-ray diffraction, {NMR} spectroscopy and thermal analyses, including in situ diffraction studies of some transformations.},
  date         = {2015-03-01},
  doi          = {10.1107/S2052252515000147},
  file         = {Full Text PDF:by-author/W/Wright/2015_Wright_188.pdf:PDF;Snapshot:by-author/W/Wright/2015_Wright_188.html:URL},
  groups       = {sg/MOF, sg/MOFs, am/MOFs},
  journaltitle = {{IUCrJ}},
  keywords     = {Coordination Polymers; Solid-state Transformation; Solvent-vapour-assisted Conversion},
  langid       = {english},
  owner        = {saulius},
  rights       = {http://creativecommons.org/licenses/by/2.0/uk},
  shortjournal = {{IUCrJ}},
  timestamp = {2017.01.29},
  creationdate = {2017-01-29T00:00:00},
  url          = {http://scripts.iucr.org/cgi-bin/paper?bi5040},
  urldate      = {2017-01-29},
}

@Article{Wu1992,
  author    = {Wu, C. A. and Zechner, E. L. and Marians, K. J.},
  journal   = {The Journal of biological chemistry},
  title     = {Coordinated leading- and lagging-strand synthesis at the Escherichia coli DNA replication fork. I. Multiple effectors act to modulate Okazaki fragment size.},
  year      = {1992},
  pages     = {4030--44},
  volume    = {267},
  abstract  = {The coordinated action of many enzymatic activities is required at the DNA replication fork to ensure the error-free, efficient, and simultaneous synthesis of the leading and lagging strands of DNA. In order to define the essential protein-protein interactions and model the regulatory pathways that control Okazaki fragment synthesis, we have reconstituted the replication fork of Escherichia coli in vitro in a rolling circle-type DNA replication system. In this system, in the presence of the single-stranded DNA binding protein, the helicase/primase function on the lagging-strand template is provided by the primosome, and the synthesis of DNA strands is catalyzed by the DNA polymerase III holoenzyme. These reconstituted replication forks synthesize equivalent amounts of leading- and lagging-strand DNA, move at rates comparable to those measured in vivo (600-800 nucleotides/s at 30 degrees C), and can synthesize leading strands in the range of 150-500 kilobases in length. Using this system, we have studied the cycle of Okazaki fragment synthesis at the replication fork. This cycle is likely to have several well defined decision points, steps in the cycle where incorrect execution by the enzymatic machinery will result in an alteration in the product of the reaction, i.e. in the size of the Okazaki fragments. Since identification of these decision points should aid in the determination of which of the enzymes acting at the replication fork control the cycle, we have endeavored to identify those reaction parameters that, when varied, alter the size of the Okazaki fragments synthesized. Here we demonstrate that some enzymes, such as the DnaB helicase, remain associated continuously with the fork while others, such as the primase, must be recruited from solution each time synthesis of an Okazaki fragment is initiated. We also show that variation of the concentration of the ribonucleoside triphosphates and the deoxyribonucleoside triphosphates affects Okazaki fragment size, that the control mechanisms acting at the fork to control Okazaki fragment size are not fixed at the time the fork is assembled but can be varied during the lifetime of the fork, and that alteration in the rate of the leading-strand DNA polymerase cannot account for the effect of the deoxyribonucleoside triphosphates.},
  file      = {:by-author/W/Wu/1992_Wu_4030.pdf:PDF},
  keywords  = {Ecoli; {gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Wu,
  author    = {Di Wu and Zhijun Wu},
  journal   = {Journal of Global Optimization},
  title     = {An updated geometric build-up algorithm for solving the molecular distance geometry problems with sparse distance data},
  year      = {2007},
  pages     = {661--673},
  volume    = {37},
  abstract  = {An updated geometric build-up algorithm is developed for solving the molecular distance geometry problem with a sparse set of inter-atomic distances. Different from the general geometric build-up algorithm, the updated algorithm recomputes the coordinates of the base atoms whenever necessary and possible. In this way, the errors introduced in solving the algebraic equations for the determination of the coordinates of the atoms are controlled in the intermediate computational steps. The method for re-computing the coordinates of the base atoms based on the estimation on the root-mean-square deviation (RMSD) is described. The results of applying the updated algorithm to a set of protein structure problems are presented. In many cases, the updated algorithm solves the problems with high accuracy when the results of the general algorithm are inadequate.},
  file      = {:by-author/W/Wu/2007_Wu_661.pdf:PDF},
  owner     = {saulius},
  timestamp = {2011.12.14},
  creationdate = {2011-12-14T00:00:00},
}

@Article{Wu2001,
  author    = {Guang-Wen Wu and Richard J. Sadus},
  journal   = {Journal of Chemical Physics},
  title     = {Liquid-crystal behavior of hard ellipsoid dimers},
  year      = {2001},
  pages     = {5432--5434},
  volume    = {114},
  file      = {2001_Wu_5432.pdf:by-author/W/Wu/2001_Wu_5432.pdf:PDF},
  groups    = {sg/Molecular dynamics},
  keywords  = {Hard Spheres; Molecular Dynamics (MD)},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Wu1987,
  author    = {Wu, J. C. and Santi, D. V.},
  journal   = {The Journal of biological chemistry},
  title     = {Kinetic and catalytic mechanism of HhaI methyltransferase.},
  year      = {1987},
  pages     = {4778--86},
  volume    = {262},
  abstract  = {Kinetic and catalytic properties of the DNA (cytosine-5)-methyltransferase HhaI are described. With poly(dG-dC) as substrate, the reaction proceeds by an equilibrium (or processive) ordered Bi-Bi mechanism in which DNA binds to the enzyme first, followed by S-adenosylmethionine (AdoMet). After methyl transfer, S-adenosylhomocysteine (AdoHcy) dissociates followed by methylated DNA. AdoHcy is a potent competitive inhibitor with respect to AdoMet (Ki = 2.0 microM) and its generation during reactions results in non-linear kinetics. AdoMet and AdoHcy significantly interact with only the substrate enzyme-DNA complex; they do not bind to free enzyme and bind poorly to the methylated enzyme-DNA complex. In the absence of AdoMet, HhaI methylase catalyzes exchange of the 5-H of substrate cytosines for protons of water at about 7-fold the rate of methylation. The 5-H exchange reaction is inhibited by AdoMet or AdoHcy. In the enzyme-DNA-AdoHcy complex, AdoHcy also suppresses dissociation of DNA and reassociation of the enzyme with other substrate sequences. Our studies reveal that the catalytic mechanism of DNA (cytosine-5)-methyltransferases involves attack of the C6 of substrate cytosines by an enzyme nucleophile and formation of a transient covalent adduct. Based on precedents of other enzymes which catalyze similar reactions and the susceptibility of HhaI to inactivation by N-ethylmaleimide, we propose that the sulfhydryl group of a cysteine residue is the nucleophilic catalyst. Furthermore, we propose that Cys-81 is the active-site catalyst in HhaI. This residue is found in a Pro-Cys doublet which is conserved in all DNA (cytosine-5)-methyltransferases whose sequences have been determined to date and is found in related enzymes. Finally, we discuss the possibility that covalent adducts between C6 of pyrimidines and nucleophiles of proteins may be important general components of protein-nucleic acid interactions.},
  file      = {:by-author/W/Wu/1987_Wu_4778.pdf:PDF},
  keywords  = {HhaI},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@InCollection{Wu2013,
  author    = {Wu, Xinyuan and You, Xiong and Wang, Bin},
  booktitle = {Structure-Preserving Algorithms for Oscillatory Differential Equations},
  publisher = {Springer Berlin Heidelberg},
  title     = {Energy-Preserving ERKN Methods},
  year      = {2013},
  isbn      = {978-3-642-35337-6},
  pages     = {173--184},
  abstract  = {Chapter 7 is concerned with the energy-preserving numerical integration for the system of oscillatory second-order differential equations q¨+Mq=f(q) , where M is a symmetric positive semi-definite matrix and f(q)=−∇U(q). Based on the traditional average-vector-field (AVF) methods, adapted average-vector-field (AAVF) methods are developed. A discretization with a quadrature formula leads to a highly accurate energy-preserving ERKN-type AAVF integrator. This integrator is symmetric and is shown to preserve the Hamiltonian H if U(q) is a polynomial of degree s≤6. In the long-term integration of the well-known Fermi–Pasta–Ulam problem, the integrator is shown to preserve the energy more accurately than some existing methods in the literature. Resonance instabilities and energy exchange between stiff components are also illustrated.},
  doi       = {10.1007/978-3-642-35338-3_7},
  file      = {2013_Wu_173.pdf:by-author/W/Wu/2013_Wu_173.pdf:PDF},
  groups    = {sg/Molecular dynamics},
  keywords  = {Energy Preserving; Molecular Dynamics (MD); Numerical Integrations},
  language  = {English},
  owner     = {saulius},
  timestamp = {2015.03.20},
  creationdate = {2015-03-20T00:00:00},
  url       = {http://dx.doi.org/10.1007/978-3-642-35338-3_7},
}

@Article{Wu1994,
  author    = {Wu, X. C. and Richards, N. T. and Michael, J. and Johns, E.},
  journal   = {British journal of pharmacology},
  title     = {Relative roles of nitric oxide and cyclo-oxygenase and lipoxygenase products of arachidonic acid in the contractile responses of rat renal arcuate arteries.},
  year      = {1994},
  pages     = {369--76},
  volume    = {112},
  abstract  = {1. We have examined the effects of inhibition of nitric oxide synthase, cyclo-oxygenase and lipoxygenase on the responses of renal arcuate arteries of Wistar rats, with and without endothelium, to noradrenaline, potassium chloride, endothelin-1, acetylcholine and sodium nitroprusside. 2. Noradrenaline, potassium chloride and endothelin-1 caused concentration-dependent contraction of the vessels. Indomethacin (14 microM) attenuated the contractile response to noradrenaline and to potassium chloride. The inhibitory effect of indomethacin persisted following endothelial removal. 3. Acetylcholine produced concentration-dependent relaxation of the vessels which was potentiated by indomethacin (14 microM). 4. NG-nitro-L-arginine methyl ester (L-NAME, 100 microM) did not affect the contractile response to either noradrenaline or potassium chloride but abolished relaxation to acetylcholine. In addition, L-NAME abolished the affects of indomethacin on acetylcholine-induced relaxation and noradrenaline- and potassium chloride-induced contraction. 5. BWC755C attenuated noradrenaline and potassium chloride-induced contraction. This effect persisted in the presence of indomethacin. 6. In vessels pretreated with CHAPS, BW755C inhibited both noradrenaline and potassium chloride-induced contraction. In these vessels BW755C had no additional inhibitory effect to indomethacin on noradrenaline- and potassium-induced contraction. 7. Inhibition of nitric oxide synthase with L-NAME (100 microM) attenuated the effect of BW755C on noradrenaline- and potassium-induced contraction. 8. BW755C alone did not affect endothelium-dependent relaxation as assessed by the response to acetylcholine. However, in the presence of indomethacin, BW755C inhibited acetylcholine-induced relaxation. 9. BW755C did not affect endothelium-independent relaxation as assessed by the response to sodium nitroprusside in vessels with or without endothelium. 10. These data support the existence of two vasoconstrictor products of arachidonic acid released during contraction of renal arcuate arteries with noradrenaline and potassium chloride. A cyclooxygenase product which appears to be endothelium-independent and the other an endothelium dependent lipoxygenase product.},
  file      = {:by-author/W/Wu/1994_Wu_369.pdf:PDF},
  keywords  = {Protein Subdomains},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Wu1990,
  author    = {X. W. Wu and F. P. Prosser},
  journal   = {{IEE} Proceedings {G} Circuits, Devices and Systems},
  title     = {{CMOS} ternary logic circuits},
  year      = {1990},
  number    = {1},
  pages     = {21--27},
  volume    = {137},
  doi       = {10.1049/ip-g-2.1990.0005},
  file      = {:by-author/W/Wu/1990_Wu_21.pdf:PDF},
  keywords  = {Computer Science (CS); Logic Circuits; Ternary},
  owner     = {saulius},
  publisher = {Institution of Engineering and Technology ({IET})},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Wu1991,
  author    = {Wu, X.-J. and Horiuchi, S.},
  journal   = {Acta Crystallographica Section A},
  title     = {Diffraction streaks due to phase disorder in one-dimensional displacive modulation},
  year      = {1991},
  pages     = {11--16},
  volume    = {47},
  abstract  = {It can be proved mathematically that the initial phase disorder in the wave of a one-dimensional displacive modulation introduces additional variations in the structure of reciprocal space and, as a result, causes characteristic diffraction streaks. Using a simple two- dimensional model, the occurrence of such streaks is confirmed in optical diffraction patterns. Electron diffraction streaks from two crystals with incom- mensurately modulated structures are presented and explained as the diffraction effect of the phase dis- order.},
  doi       = {10.1107/S0108767390009059},
  file      = {:by-author/W/Wu/1991_Wu_11.pdf:PDF},
  keywords  = {Disordered Crystals; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0108767390009059},
}

@Article{Wulff1913,
  author    = {Georg Wulff},
  journal   = {Physikalische Zeitschrift},
  title     = {Über die Kristallröntgenogramme},
  year      = {1913},
  pages     = {217--220},
  volume    = {14},
  file      = {1913_Wulff_217.pdf:by-author/W/Wulff/1913_Wulff_217.pdf:PDF},
  keywords  = {Brag-Wulff Law; Bragg's Law; History; History of Science; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2015.03.02},
  creationdate = {2015-03-02T00:00:00},
  url       = {http://babel.hathitrust.org/cgi/pt?id=mdp.39015021268936},
}

@Article{Wuthrich2002,
  author    = {Wüthrich},
  title     = {NMR Studies of Structure and Function of Biologiccal Macromolecules},
  year      = {2002},
  file      = {:by-author/W/Wüthrich/2002_Wüthrich.pdf:PDF},
  keywords  = {Nobel Prize Lectures},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Wynveen2008,
  author    = {Wynveen, Aaron and Lee, Dominic J and Kornyshev, Alexei A and Leikin, Sergey},
  journal   = {Nucleic acids research},
  title     = {Helical coherence of DNA in crystals and solution.},
  year      = {2008},
  pages     = {5540--51},
  volume    = {36},
  abstract  = {The twist, rise, slide, shift, tilt and roll between adjoining base pairs in DNA depend on the identity of the bases. The resulting dependence of the double helix conformation on the nucleotide sequence is important for DNA recognition by proteins, packaging and maintenance of genetic material, and other interactions involving DNA. This dependence, however, is obscured by poorly understood variations in the stacking geometry of the same adjoining base pairs within different sequence contexts. In this article, we approach the problem of sequence-dependent DNA conformation by statistical analysis of X-ray and NMR structures of DNA oligomers. We evaluate the corresponding helical coherence length--a cumulative parameter quantifying sequence-dependent deviations from the ideal double helix geometry. We find, e.g. that the solution structure of synthetic oligomers is characterized by 100-200 A coherence length, which is similar to approximately 150 A coherence length of natural, salmon-sperm DNA. Packing of oligomers in crystals dramatically alters their helical coherence. The coherence length increases to 800-1200 A, consistent with its theoretically predicted role in interactions between DNA at close separations.},
  file      = {2008_Wynveen_5540.pdf:by-author/W/Wynveen/2008_Wynveen_5540.pdf:PDF},
  keywords  = {Stacking},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Wyszomirski2012,
  author    = {Wyszomirski, Karol H. and Curth, Ute and Alves, Jürgen and Mackeldanz, Petra and Möncke-Buchner, Elisabeth and Schutkowski, Mike and Krüger, Detlev H. and Reuter, Monika},
  journal   = {Nucleic acids research},
  title     = {Type III restriction endonuclease EcoP15I is a heterotrimeric complex containing one Res subunit with several DNA-binding regions and ATPase activity.},
  year      = {2012},
  pages     = {3610--22},
  volume    = {40},
  abstract  = {For efficient DNA cleavage, the Type III restriction endonuclease EcoP15I communicates with two inversely oriented recognition sites in an ATP-dependent process. EcoP15I consists of methylation (Mod) and restriction (Res) subunits forming a multifunctional enzyme complex able to methylate or to cleave DNA. In this study, we determined by different analytical methods that EcoP15I contains a single Res subunit in a Mod(2)Res stoichiometry. The Res subunit comprises a translocase (Tr) domain carrying functional motifs of superfamily 2 helicases and an endonuclease domain with a PD..D/EXK motif. We show that the isolated Tr domain retains ATP-hydrolyzing activity and binds single- and double-stranded DNA in a sequence-independent manner. To localize the regions of DNA binding, we screened peptide arrays representing the entire Res sequence for their ability to interact with DNA. We discovered four DNA-binding regions in the Tr domain and two DNA-binding regions in the endonuclease domain. Modelling of the Tr domain shows that these multiple DNA-binding regions are located on the surface, free to interact with DNA. Interestingly, the positions of the DNA-binding regions are conserved among other Type III restriction endonucleases.},
  file      = {:by-author/W/Wyszomirski/2012_Wyszomirski_3610.pdf:PDF},
  keywords  = {TypeIII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Xenides2006,
  author    = {D. Xenides and B.R. Randolf and B.M. Rode},
  journal   = {Journal of Molecular Liquids},
  title     = {Hydrogen Bonding in Liquid Water: An ab initio {QM/MM} {MD} Simulation Study},
  year      = {2006},
  issn      = {0167-7322},
  pages     = {61--67},
  volume    = {123},
  abstract  = {Pattern and dynamics of hydrogen bonds in liquid water were investigated by a quantum mechanical/molecular mechanical molecular dynamics (QM/MM MD) simulation at Hartree–Fock (HF) level of theory. A large subregion of the whole system comprising two complete coordination shells was treated quantum mechanically in order to include all polarization and charge transfer effects and to obtain accurate data about structure and dynamics of the intermolecular bonds. The results of this investigation are in agreement with recent experimental findings and suggest that in liquid water every molecule forms in average 2.8, but almost as a rule less than four intermolecular hydrogen bonds.},
  doi       = {10.1016/j.molliq.2005.06.002},
  file      = {2006_Xenides_61.pdf:by-author/X/Xenides/2006_Xenides_61.pdf:PDF},
  groups    = {sg/applications},
  keywords  = {Quantum Chemistry},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/S0167732205001054},
}

@Article{Xi2005,
  author    = {Xi, Jun and Zhang, Zhiquan and Zhuang, Zhihao and Yang, Jingsong and Spiering, Michelle M. and Hammes, Gordon G. and Benkovic, Stephen J.},
  journal   = {Biochemistry},
  title     = {Interaction between the T4 helicase loading protein (gp59) and the DNA polymerase (gp43): unlocking of the gp59-gp43-DNA complex to initiate assembly of a fully functional replisome.},
  year      = {2005},
  pages     = {7747--56},
  volume    = {44},
  abstract  = {Single-molecule fluorescence resonance energy transfer and functional assays have been used to study the initiation and regulation of the bacteriophage T4 DNA replication system. Previous work has demonstrated that a complex of the helicase loading protein (gp59) and the DNA polymerase (gp43) on forked DNA totally inhibits the polymerase and exonuclease activities of gp43 by a molecular locking mechanism (Xi, J., Zhuang, Z., Zhang, Z., Selzer, T., Spiering, M. M., Hammes, G. G., and Benkovic, S. J. (2005) Biochemistry 44, 2305-2318). We now show that this complex is "unlocked" by the addition of the helicase (gp41) with restoration of the DNA polymerase activity. Gp59 retains its ability to load the helicase while forming a gp59-gp43 complex at a DNA fork in the presence of the single-stranded DNA binding protein (gp32). Upon the addition of gp41 and MgATP, gp59 dissociates from the complex, and the DNA-bound gp41 is capable of recruiting the primase (gp61) to form a functional primosome and, subsequently, a fully active replisome. Functional assays of leading- and lagging-strand synthesis on an active replication fork show that the absence of gp59 has no effect on the coupling of leading- and lagging-strand synthesis or on the size of the Okazaki DNA fragments. We conclude that gp59 acts in a manner similar to the clamp loader to ensure proper assembly of the replisome and does not remain as a replisome component during active replication.},
  file      = {:by-author/X/Xi/2005_Xi_7747.pdf:PDF},
  keywords  = {Replisoma; {gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Xi2005a,
  author    = {Xi, Jun and Zhuang, Zhihao and Zhang, Zhiquan and Selzer, Tzvia and Spiering, Michelle M. and Hammes, Gordon G. and Benkovic, Stephen J.},
  journal   = {Biochemistry},
  title     = {Interaction between the T4 helicase-loading protein (gp59) and the DNA polymerase (gp43): a locking mechanism to delay replication during replisome assembly.},
  year      = {2005},
  pages     = {2305--18},
  volume    = {44},
  abstract  = {The T4 helicase-loading protein (gp59) has been proposed to coordinate leading- and lagging-strand DNA synthesis by blocking leading-strand synthesis during the primosome assembly. In this work, we unambiguously demonstrate through a series of biochemical and biophysical experiments, including single-molecule fluorescence microscopy, that the inhibition of leading-strand holoenzyme progression by gp59 is the result of a complex formed between gp59 and leading-strand polymerase (gp43) on DNA that is instrumental in preventing premature replication during the assembly of the T4 replisome. We find that both the polymerization and 3' --&gt; 5' exonuclease activities of gp43 are totally inhibited within this complex. Chemical cross-linking of the complex followed by tryptic digestion and peptide identification through matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) mass spectrometry identified Cys169 of gp43 and Cys215 of gp59 as residues in a region of a protein-protein contact. With the available crystal structures for both gp43 and gp59, a model of the complex was constructed based on shape complementarity, revealing that parts of the C-terminal domain from gp59 insert into the interface created by the thumb and exonuclease domains of gp43. This insertion effectively locks the polymerase into a conformation where switching between the pol and editing modes is prevented. Thus, continued assembly of the replisome through addition of the primosome components and elements of the lagging-strand holoenzyme can occur without leading-strand DNA replication.},
  file      = {:by-author/X/Xi/2005_Xi_2305.pdf:PDF},
  keywords  = {Replisoma; {gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Xi2005b,
  author    = {Xi, Jun and Zhuang, Zhihao and Zhang, Zhiquan and Selzer, Tzvia and Spiering, Michelle M. and Hammes, Gordon G. and Benkovic, Stephen J.},
  journal   = {Biochemistry},
  title     = {The Interaction between the T4 Helicase Loading Protein (gp59) and the DNA Polymerase (gp43):  a Locking Mechanism to Delay Replication during Replisome Assembly},
  year      = {2005},
  pages     = {12264--12264},
  volume    = {44},
  doi       = {10.1021/bi058024b},
  eprint    = {http://pubs.acs.org/doi/pdf/10.1021/bi058024b},
  file      = {:by-author/Z/Zhuang/2005_Zhuang_12264.pdf:PDF},
  keywords  = {{gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://pubs.acs.org/doi/abs/10.1021/bi058024b},
}

@Article{Xi2005c,
  author    = {Xi, Jun and Zhuang, Zhihao and Zhang, Zhiquan and Selzer, Tzvia and Spiering, Michelle M. and Hammes, Gordon G. and Benkovic, Stephen J.},
  journal   = {Biochemistry},
  title     = {Interaction between the T4 Helicase-Loading Protein (gp59) and the DNA Polymerase (gp43):  A Locking Mechanism to Delay Replication during Replisome Assembly†},
  year      = {2005},
  pages     = {2305--2318},
  volume    = {44},
  abstract  = {The T4 helicase-loading protein (gp59) has been proposed to coordinate leading- and lagging-strand DNA synthesis by blocking leading-strand synthesis during the primosome assembly. In this work, we unambiguously demonstrate through a series of biochemical and biophysical experiments, including single-molecule fluorescence microscopy, that the inhibition of leading-strand holoenzyme progression by gp59 is the result of a complex formed between gp59 and leading-strand polymerase (gp43) on DNA that is instrumental in preventing premature replication during the assembly of the T4 replisome. We find that both the polymerization and 3‘ → 5‘ exonuclease activities of gp43 are totally inhibited within this complex. Chemical cross-linking of the complex followed by tryptic digestion and peptide identification through matrix-assisted laser desorption/ionization−time-of-flight (MALDI-TOF) mass spectrometry identified Cys169 of gp43 and Cys215 of gp59 as residues in a region of a protein−protein contact. With the available crystal structures for both gp43 and gp59, a model of the complex was constructed based on shape complementarity, revealing that parts of the C-terminal domain from gp59 insert into the interface created by the thumb and exonuclease domains of gp43. This insertion effectively locks the polymerase into a conformation where switching between the pol and editing modes is prevented. Thus, continued assembly of the replisome through addition of the primosome components and elements of the lagging-strand holoenzyme can occur without leading-strand DNA replication.},
  doi       = {10.1021/bi0479508},
  eprint    = {http://pubs.acs.org/doi/pdf/10.1021/bi0479508},
  file      = {:by-author/Z/Zhuang/2005_Zhuang_2305.pdf:PDF},
  keywords  = {Replisoma; {gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://pubs.acs.org/doi/abs/10.1021/bi0479508},
}

@Article{Xia1998,
  author    = {Tianbing Xia and John SantaLucia, Jr. and Mark E. Burkard and Ryszard Kierzek and Susan J. Schroeder and Xiaoqi Jiao and Christopher Cox and Douglas H. Turner},
  journal   = {Biochemistry},
  title     = {Thermodynamic Parameters for an Expanded Nearest-Neighbor Model for Formation of {RNA} Duplexes with {W}atson-{C}rick Base Pairs},
  year      = {1998},
  pages     = {14719--14735},
  volume    = {37},
  doi       = {10.1021/bi9809425},
  file      = {1998_Xia_14719.pdf:by-author/X/Xia/1998_Xia_14719.pdf:PDF},
  owner     = {andrius},
  timestamp = {2016.09.20},
  creationdate = {2016-09-20T00:00:00},
}

@InProceedings{Xia2005,
  author    = {Xia, Tian and Zhang, Donghui and Kanoulas, Evangelos and Du, Yang},
  booktitle = {Proceedings of the 31st international conference on Very large data bases},
  title     = {On Computing Top-t Most Influential Spatial Sites},
  year      = {2005},
  pages     = {946--957},
  publisher = {VLDB Endowment},
  series    = {VLDB '05},
  abstract  = {Given a set O of weighted objects, a set S of sites, and a query site s, the bichromatic RNN query computes the influence set of s, or the set of objects in O that consider s as the nearest site among all sites in S. The influence of a site s can be defined as the total weight of its RNNs. This paper addresses the new and interesting problem of finding the top-t most influential sites from S, inside a given spatial region Q. A straightforward approach is to find the sites in Q, and compute the RNNs of every such site. This approach is not efficient for two reasons. First, all sites in Q need to be identified whatsoever, and the number may be large. Second, both the site R-tree and the object R-tree need to be browsed a large number of times. For each site in Q, the R-tree of sites is browsed to identify the influence region -- a polygonal region that may contain RNNs, and then the R-tree of objects is browsed to find the RNN set. This paper proposes an algorithm called TopInfluential-Sites, which finds the top-t most influential sites by browsing both trees once systematically. Novel pruning techniques are provided, based on a new metric called minExistDNN. There is no need to compute the influence for all sites in Q, or even to visit all sites in Q. Experimental results verify that our proposed method outperforms the straightforward approach.},
  file      = {:by-author/X/Xia/2005_Xia_946.pdf:PDF},
  isbn      = {1-59593-154-6},
  location  = {Trondheim, Norway},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dl.acm.org/citation.cfm?id=1083592.1083701},
}

@Article{Xiao2013,
  author    = {Xiao, Juan and Wu, Yuan and Li, Mian and Liu, Bao-Yu and Huang, Xiao-Chun and Li, Dan},
  journal   = {Chemistry – A European Journal},
  title     = {Crystalline Structural Intermediates of a Breathing Metal–Organic Framework That Functions as a Luminescent Sensor and Gas Reservoir},
  year      = {2013},
  issn      = {1521-3765},
  pages     = {manuscript},
  doi       = {10.1002/chem.201203515},
  file      = {:by-author/X/Xiao/2013_Xiao_manuscript.pdf:PDF},
  keywords  = {Breathing Effect; Metal-Organic Frameworks (MOF); Photoluminescence; Sensors; Structural Elucidation},
  owner     = {saulius},
  publisher = {WILEY-VCH Verlag},
  timestamp = {2013.01.05},
  creationdate = {2013-01-05T00:00:00},
  url       = {http://dx.doi.org/10.1002/chem.201203515},
}

@Article{Xie2005,
  author    = {Xie, Jianming and Schultz, Peter G.},
  journal   = {Current opinion in chemical biology},
  title     = {Adding amino acids to the genetic repertoire.},
  year      = {2005},
  pages     = {548--54},
  volume    = {9},
  abstract  = {Considerable progress has been made in expanding the number and nature of genetically encoded amino acids in Escherichia coli, yeast and mammalian cells in the past four years. To date, over 30 unnatural amino acids have been cotranslationally incorporated into proteins with high fidelity and efficiency by means of a unique codon and corresponding orthogonal tRNA-aminoacyl-tRNA synthetase pair. The incorporated amino acids contain spectroscopic probes, post-translational modifications, metal chelators, photoaffinity labels and unique functional groups. The ability to genetically encode additional amino acids, beyond the common 20, provides a powerful approach for probing protein structure and function both in vitro and in vivo, as well as generating proteins with new or enhanced properties.},
  file      = {:by-author/X/Xie/2005_Xie_548.pdf:PDF},
  keywords  = {Bioconjugation},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@Manuscript{Xie2012,
  author    = {Minge Xie and Regina Y. Liu and C. V. Damaraju and William H. Olson},
  title     = {Incorporating External Information in Analyses of Clinical Trials with Binary Outcomes},
  year      = {2012},
  url       = {http://stat.rutgers.edu/home/mxie/RCPapers/expertopinions-final.pdf},
  file      = {2012_Xie.pdf:by-author/X/Xie/2012_Xie.pdf:PDF},
  groups    = {sg/Clinical Trials},
  owner     = {saulius},
  timestamp = {2015.12.14},
  creationdate = {2015-12-14T00:00:00},
  urldate   = {2015-12-12},
}

@Article{Xu2001,
  author    = {Xu, H. and Wang, Y. and Bleuit, J. S. and Morrical, S. W.},
  journal   = {Biochemistry},
  title     = {Helicase assembly protein Gp59 of bacteriophage T4: fluorescence anisotropy and sedimentation studies of complexes formed with derivatives of Gp32, the phage ssDNA binding protein.},
  year      = {2001},
  pages     = {7651--61},
  volume    = {40},
  abstract  = {The gene 59 protein (gp59) of bacteriophage T4 performs a vital function in phage DNA replication by directing the assembly of gp41, the DNA helicase component of the T4 primosome, onto lagging strand ssDNA at nascent replication forks. The helicase assembly activity of gp59 is required for optimum efficiency of helicase acquisition by the replication fork during strand displacement DNA synthesis and is essential for helicase and primosome assembly during T4 recombination-dependent DNA replication transactions. Of central importance is the ability of gp59 to load the gp41 helicase onto ssDNA previously coated with cooperatively bound molecules of gp32, the T4 ssDNA binding protein. Gp59 heteroassociations with ssDNA, gp32, and gp41 all appear to be essential for this loading reaction. Previous studies demonstrated that a tripartite complex containing gp59 and gp32 simultaneously cooccupying ssDNA is an essential intermediate in gp59-dependent helicase loading; however, the biochemical and structural parameters of gp59-gp32 complexes with or without ssDNA are currently unknown. To better understand gp59-gp32 interactions, we performed fluorescence anisotropy and analytical ultracentrifugation experiments employing native or rhodamine-labeled gp59 species in combination with altered forms of gp32, allowing us to determine their binding parameters, shape parameters, and other hydrodynamic properties. Two truncated forms of gp32 were used: gp32-B, which lacks the N-terminal B-domain required for cooperative binding to ssDNA and for stable self-association, and A-domain fragment, which is the C-terminal peptide of gp32 lacking ssDNA binding ability. Results indicate that gp59 binds with high affinity to either gp32 derivative to form a 1:1 heterodimer. In both cases, heterodimer formation is accompanied by a conformational change in gp59 which correlates with decreased gp59-DNA binding affinity. Hydrodynamic modeling suggests an asymmetric prolate ellipsoid shape for gp59, consistent with its X-ray crystallographic structure, and this asymmetry appears to increase upon binding of gp32 derivatives. Implications of our findings for the structure and function of gp59 and gp59-gp32 complexes in T4 replication are discussed.},
  file      = {:by-author/X/Xu/2001_Xu_7651.pdf:PDF},
  keywords  = {{gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Xu2001a,
  author    = {Jun Xu and Zbigniew Kalbarczyk and Ravishankar K. Iyer},
  title     = {Networked Windows NT System Field Failure Data Analysis},
  year      = {2001},
  abstract  = {This paper presents a measurement-based depend- ability study of a Networked Windows NT system based on field data collected from NT System Logs from 503 servers running in a production environment over a four-month period. The event logs at hand contains only system reboot information. We study individual server failures and domain behavior in order to characterize failure behavior and explore error propagation between servers. The key observations from this study are: (1) system software and hardware failures are the two ma- jor contributors to the total system downtime (22% and 10%), (2) recovery from application software failures are usually quick, (3) in many cases, more than one re- boots are required to recover from a failure, (4) the av- erage availability of an individual server is over 99%,(5) there is a strong indication of error dependency or error propagation across the network, (6) most (58%) reboots are unclassified indicating the need for better logging techniques, (7) maintenance and configuration contrib- ute to 24% of system downtime.},
  file      = {:by-author/X/Xu/2001_Xu.pdf:PDF},
  keywords  = {Computer Science (CS); Networks},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Xu2007,
  author      = {Lan Xu and Stacy D Benson and Roger M Burnett},
  journal     = {J Struct Biol},
  title       = {Nanoporous crystals of chicken embryo lethal orphan (CELO) adenovirus major coat protein, hexon.},
  year        = {2007},
  pages       = {424--431},
  volume      = {157},
  abstract    = {CELO (chicken embryo lethal orphan) virus is an avian adenovirus that is being developed as a gene transfer vector. Its trimeric major coat protein (942 residues, 106,709 Da) has 42\% sequence identity to human adenovirus type 2 (AdH2) hexon and 45\% to AdH5 hexon. For structural studies, the growth of CELO virus has been optimized, and its hexon purified and crystallized. The hexon crystals, the first non-human example, diffract to 3.9 A resolution. Molecular replacement using the AdH5 model was used to identify the location of the CELO hexon within the unit cell. There is one hexon monomer in the asymmetric unit of the trigonal space group P321 (a=b=157.8 A, c=114.2 A, gamma=120 degrees) and the solvent content is 67.8\%. The hexons pack in a hexagonal honeycomb so that large approximately 100 A diameter channels run through the entire crystal. This remarkable property of the crystals lends itself to their exploitation as a nanomaterial. Structural studies on CELO will elucidate the differences between avian and human adenoviruses and contribute to a better understanding of adenoviruses with non-human hosts.},
  doi         = {10.1016/j.jsb.2006.08.017},
  file        = {:by-author/X/Xu/2007_Xu_424.pdf:PDF},
  institution = {The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA.},
  keywords    = {Amino Acid; Amino Acid Sequence; Animals; Capsid Proteins; Chemistry; Chemistry/isolation /&/ Purification; Chick Embryo; Crystallization; Fowl Adenovirus A; Growth /&/ Development/ultrastructure; Models; Molecular; Molecular Sequence Data; Nanoparticles; Nanotechnology; Protein Structure; Quaternary; Sequence Homology},
  language    = {eng},
  medline-pst = {ppublish},
  owner       = {alexey},
  pii         = {S1047-8477(06)00272-3},
  pmid        = {17071105},
  timestamp = {2013.04.16},
  creationdate = {2013-04-16T00:00:00},
  url         = {http://dx.doi.org/10.1016/j.jsb.2006.08.017},
}

@Article{Xu2004a,
  author    = {Xu, Qian Steven and Kucera, Rebecca B. and Roberts, Richard J. and Guo, Hwai-Chen},
  journal   = {Structure (London, England : 1993)},
  title     = {An asymmetric complex of restriction endonuclease MspI on its palindromic DNA recognition site.},
  year      = {2004},
  pages     = {1741--7},
  volume    = {12},
  abstract  = {Most well-known restriction endonucleases recognize palindromic DNA sequences and are classified as Type IIP. Due to the recognition and cleavage symmetry, Type IIP enzymes are usually found to act as homodimers in forming 2-fold symmetric enzyme-DNA complexes. Here we report an asymmetric complex of the Type IIP restriction enzyme MspI in complex with its cognate recognition sequence. Unlike any other Type IIP enzyme reported to date, an MspI monomer and not a dimer binds to a palindromic DNA sequence. The enzyme makes specific contacts with all 4 base pairs in the recognition sequence, by six direct and five water-mediated hydrogen bonds and numerous van der Waal contacts. This MspI-DNA structure represents the first example of asymmetric recognition of a palindromic DNA sequence by two different structural motifs in one polypeptide. A few possible pathways are discussed for MspI to cut both strands of DNA, either as a monomer or dimer.},
  file      = {:by-author/X/Xu/2004_Xu_1741.pdf:PDF},
  keywords  = {TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Manuscript{Xu2004,
  author    = {Qian Steven Xu and Rebecca B. Kucera and Richard J. Roberts and Hwai-Chen Guo1},
  title     = {An asymmetric complex of restriction endonuclease MspI on its palindromic DNA recognition site},
  year      = {2004},
  file      = {:by-author/X/Xu/2004_Xu_manuscript.pdf:PDF},
  owner     = {saulius},
  pages     = {manuscript},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Manuscript{Yablo2003,
  author    = {Yablo},
  title     = {New Grounds for Naïve Truth Theory},
  year      = {2003},
  keywords  = {Philosophy},
  file      = {:by-author/Y/Yablo/2003_Yablo.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Presentation{Yagi2010,
  author    = {Yagi, Naoto},
  title     = {Time resolved biological {SAXS} at {SPring-8}},
  year      = {2010},
  file      = {:by-author/Y/Yagi/2010_Yagi_slides.pdf:PDF},
  keywords  = {SAXS},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Yamasaki2004,
  author    = {Yamasaki, Kazuhiko and Kigawa, Takanori and Inoue, Makoto and Tateno, Masaru and Yamasaki, Tomoko and Yabuki, Takashi and Aoki, Masaaki and Seki, Eiko and Matsuda, Takayoshi and Tomo, Yasuko and Hayami, Nobuhiro and Terada, Takaho and Shirouzu, Mikako and Osanai, Takashi and Tanaka, Akiko and Seki, Motoaki and Shinozaki, Kazuo and Yokoyama, Shigeyuki},
  journal   = {The Plant cell},
  title     = {Solution structure of the B3 DNA binding domain of the Arabidopsis cold-responsive transcription factor RAV1.},
  year      = {2004},
  pages     = {3448--59},
  volume    = {16},
  abstract  = {The B3 DNA binding domain is shared amongst various plant-specific transcription factors, including factors involved in auxin-regulated and abscisic acid-regulated transcription. Herein, we report the NMR solution structure of the B3 domain of the Arabidopsis thaliana cold-responsive transcription factor RAV1. The structure consists of a seven-stranded open beta-barrel and two alpha-helices located at the ends of the barrel and is significantly similar to the structure of the noncatalytic DNA binding domain of the restriction enzyme EcoRII. An NMR titration experiment revealed a DNA recognition interface that enabled us to propose a structural model of the protein-DNA complex. The locations of the DNA-contacting residues are also likely to be similar to those of the EcoRII DNA binding domain.},
  file      = {Yamasaki_2004_3448-Transcription-Factor-RAV1.pdf:by-author/Y/Yamasaki/2004_Yamasaki_3448.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Yamasaki2012,
  author    = {Kazuhiko Yamasaki and Takanori Kigawa and Motoaki Seki and Kazuo Shinozaki and Shigeyuki Yokoyama},
  journal   = {Trends in Plant Science},
  title     = {DNA-binding domains of plant-specific transcription factors: structure, function, and evolution},
  year      = {2012},
  issn      = {1360-1385},
  pages     = {-},
  abstract  = {The families of the plant-specific transcription factors (TFs) are defined by their characteristic DNA-binding domains (DBDs), such as AP2/ERF, B3, NAC, SBP, and WRKY. Recently, three-dimensional structures of the DBDs, including those in complexes with DNA, were determined by NMR spectroscopy and X-ray crystallography. In this review we summarize the functional and evolutionary implications arising from structure analyses. The unexpected structural similarity between B3 and the noncatalytic DBD of the restriction endonuclease EcoRII allowed us to build structural models of the B3/DNA complex. Most of the DBDs of plant-specific TFs are likely to have originated from endonucleases associated with transposable elements. After the DBDs have been established in unicellular eukaryotes, they experienced extensive plant-specific expansion, by acquiring new functions.},
  doi       = {10.1016/j.tplants.2012.09.001},
  file      = {2012_Yamasaki_preprint.PDF:by-author/Y/Yamasaki/2012_Yamasaki_preprint.PDF:PDF},
  keywords  = {BfiI; DNA Binding; Plant Transcription Factors},
  owner     = {saulius},
  timestamp = {2012.10.09},
  creationdate = {2012-10-09T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/S1360138512001963},
}

@Article{Yang1957,
  author    = {Chenning Yang},
  title     = {The Law of Parity Conservation and Other Symmetry Laws of Physics},
  year      = {1957},
  file      = {:by-author/Y/Yang/1957_Yang.pdf:PDF},
  keywords  = {Quantum Mechanics (QM)},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Yang2001,
  author    = {Yang, C and Pflugrath, J W},
  journal   = {Acta crystallographica. Section D, Biological crystallography},
  title     = {Applications of anomalous scattering from S atoms for improved phasing of protein diffraction data collected at Cu Kalpha wavelength.},
  year      = {2001},
  pages     = {1480--90},
  volume    = {57},
  file      = {2001_Yang_1480.pdf:by-author/Y/Yang/2001_Yang_1480.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Yang2003,
  author    = {Yang, Cheng and Pflugrath, J. W. and Courville, D. A. and Stence, C. N. and Ferrara, Joseph D.},
  journal   = {Acta Crystallographica Section D},
  title     = {Away from the edge: SAD phasing from the sulfur anomalous signal measured in-house with chromium radiation},
  year      = {2003},
  pages     = {1943--1957},
  volume    = {59},
  doi       = {10.1107/S0907444903018547},
  file      = {ba5049.pdf:by-author/Y/Yang/2003_Yang_1943.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444903018547},
}

@Article{Yang2002,
  author    = {Yang, Guangwei and Franklin, Matthew and Li, Jing and Lin, T-C. and Konigsberg, William},
  journal   = {Biochemistry},
  title     = {Correlation of the kinetics of finger domain mutants in RB69 DNA polymerase with its structure.},
  year      = {2002},
  pages     = {2526--34},
  volume    = {41},
  abstract  = {We have estimated pre-steady-state kinetic parameters for the addition of a single nucleotide residue by a set of RB69 DNA polymerase mutants in which four highly conserved residues in the fingers domain have been replaced by Ala. The relationship between the kinetic constants exhibited by the mutants and the structure of the ternary complex [Franklin, M., Wang, J., and Steitz T. (2001) Cell 105, 657-667] was consistent with the following sets of interactions between the conserved residues and oxygen atoms in the triphosphate portion of the incoming dNTP: (i) the epsilon-amino group of K560 contacts oxygen atoms of the alpha- and gamma-phosphates, (ii) the amide side chain of Asn 564 forms a hydrogen bond via a water molecule with the nonbridging oxygen of the beta-phosphate, and (iii) the epsilon-amino and delta-guanidino groups of K486 and R482, respectively, contact the nonbridging oxygens of the gamma-phosphate. We have also determined the pre-steady-state kinetic parameters for the addition of both dCTP and dCDP onto a 13/20mer primer/template with an exo(-) derivative of RB69 DNA polymerase and have shown that the deoxynucleoside diphosphate can be incorporated, in contrast to the behavior of the Klenow fragment which cannot use dCDP as a substrate. We have shown that, with RB69 DNA polymerase, in contrast to the Klenow fragment, there is no inhibition of the primer-extension reaction by incoming NTPs having either noncomplementary bases or ribo- instead of a deoxyribose moieties. This implies that the mode of recognition of incoming dNTPs and triggering of the conformational change, which is thought to occur prior to the chemical step, differs between these two enzymes.},
  file      = {:by-author/Y/Yang/2002_Yang_2526.pdf:PDF},
  keywords  = {Struktur; {gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Yang2005a,
  author    = {Yang, Jingsong and Xi, Jun and Zhuang, Zhihao and Benkovic, Stephen J.},
  journal   = {The Journal of biological chemistry},
  title     = {The oligomeric T4 primase is the functional form during replication.},
  year      = {2005},
  pages     = {25416--23},
  volume    = {280},
  abstract  = {Replisome DNA primases are responsible for the synthesis of short RNA primers required for the initiation of repetitive Okazaki fragment synthesis on the lagging strand during DNA replication. In bacteriophage T4, the primase (gp61) interacts with the helicase (gp41) to form the primosome complex, an interaction that greatly stimulates the priming activity of gp61. Because gp41 is hexameric, a question arises as to whether gp61 also forms a hexameric structure during replication. Several results from this study support such a structure. Titration of the primase/single-stranded DNA binding followed by fluorescence anisotropy implicated a 6:1 stoichiometry. The observed rate constant, k(cat), for priming was found to increase with the primase concentration, implicating an oligomeric form of the primase as the major functional species. The generation of hetero-oligomeric populations of the hexameric primase by controlled mixing of wild type and an inactive mutant primase confirmed the oligomeric nature of the most active primase form. Mutant primases defective in either the N- or C-terminal domains and catalytically inactive could be mixed to create oligomeric primases with restored catalytic activity suggesting an active site shared between subunits. Collectively, these results provide strong evidence for the functional oligomerization of gp61. The potential roles of gp61 oligomerization during lagging strand synthesis are discussed.},
  file      = {:by-author/Y/Yang/2005_Yang_25416.pdf:PDF},
  keywords  = {{gp41}; {gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Yang2011,
  author    = {Yang, Linlin and Guo, Lianshun and Chen, Qianqian and Sun, Huafei and Liu, Jie and Zhang, Xianxi and Pan, Xu and Dai, Songyuan},
  journal   = {Journal of molecular graphics \&amp; modelling},
  title     = {Theoretical design and screening of panchromatic phthalocyanine sensitizers derived from TT1 for dye-sensitized solar cells.},
  year      = {2012},
  pages     = {1--9},
  volume    = {34},
  abstract  = {Computational screening of new dyes is becoming an extremely powerful tool, especially when associated with experimental synthetic efforts that might eventually lead to new and more efficient products. Nine novel unsymmetrical zinc phthalocyanine complexes derived from TT1 were designed as sensitizer candidates for dye-sensitized solar cells with three peripheral -CH₃, -OH, -OCH₃, -OPh, -NH₂, -NHCH₃, -N(CH₃)₂, -NHPh and -N(Ph)₂ substituents as the donors and a carboxyl group as the acceptor. The molecular orbital and the electronic absorption spectra properties of these compounds were studied and compared to those of TT1 using the density functional theory and time-dependent density functional theory calculations at B3LYP level with the LANL2DZ basis set. The novel candidates bearing the -NH₂, -NHCH₃, -N(CH₃)₂, -NHPh and -N(Ph)₂ moieties as the donors were found to be very promising for providing higher efficiencies than that of TT1 or even the current 4.6% efficiency record held by PcS6. They have higher LUMO levels, smaller energy gaps and red-shifted absorption bands compared to those of TT1. The new absorption bands emerging in 450-600 nm regions may promote ZnPcL-NH₂, ZnPcL-NHCH₃, ZnPcL-N(CH₃)₂, ZnPcL-NHPh and ZnPcL-N(Ph)₂ from near infrared to panchromatic sensitizers. Further experimental synthetic efforts are in progress in our group to validate the predictions in this report.},
  file      = {:by-author/Y/Yang/2011_Yang_1.pdf:PDF},
  keywords  = {Obzor},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Yang2009,
  author    = {Lei Yang and Guang Song and Alicia Carriquiry and Robert L. Jernigan},
  journal   = {Structure},
  title     = {Close Correspondence between the Motions from Principal Component Analysis of Multiple {HIV}-1 Protease Structures and Elastic Network Modes},
  year      = {2009},
  issn      = {0969-2126},
  pages     = {321--330},
  volume    = {16},
  abstract  = {The large number of available HIV-1 protease structures provides a remarkable sampling of conformations of the different conformational states, which can be viewed as direct structural information about the dynamics of the HIV-1 protease. After structure matching, we apply principal component analysis (PCA) to obtain the important apparent motions for both bound and unbound structures. There are significant similarities between the first few key motions and the first few low-frequency normal modes calculated from a static representative structure with an elastic network model (ENM), strongly suggesting that the variations among the observed structures and the corresponding conformational changes are facilitated by the low-frequency, global motions intrinsic to the structure. Similarities are also found when the approach is applied to an NMR ensemble, as well as to molecular dynamics (MD) trajectories. Thus, a sufficiently large number of experimental structures can directly provide important information about protein dynamics, but ENM can also provide similar sampling of conformations.},
  doi       = {10.1016/j.str.2007.12.011},
  file      = {2008_Yang_321.pdf:by-author/Y/Yang/2009_Yang.pdf:PDF},
  keywords  = {Principle Component Analysis},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/S0969212608000117},
}

@Article{Yang2010,
  author    = {Yang, Rui and Li, Lei and Xiong, Ying and Li, Jian-Rong and Zhou, Hong-Cai and Su, Cheng-Yong},
  journal   = {Chemistry - An Asian Journal},
  title     = {Two Robust Porous Metal-Organic Frameworks Sustained by Distinct Catenation: Selective Gas Sorption and Single-Crystal-to-Single-Crystal Guest Exchange},
  year      = {2010},
  issn      = {1861-4728},
  month     = {Aug},
  number    = {11},
  pages     = {2358--2368},
  volume    = {5},
  comment   = {cited by Inokuma2016 (DOI:10.1002/asia.201601551)},
  doi       = {10.1002/asia.201000218},
  file      = {2010_Yang_2358.pdf:by-author/Y/Yang/2010_Yang_2358.pdf:PDF},
  groups    = {sg/MOF, sg/MOFs, am/MOFs},
  keywords  = {Metal-Organic Frameworks (MOF); Synthesis},
  owner     = {saulius},
  publisher = {Wiley-Blackwell},
  timestamp = {2017.02.13},
  creationdate = {2017-02-13T00:00:00},
  url       = {http://dx.doi.org/10.1002/asia.201000218},
}

@Article{Yang2002a,
  author    = {Yang, Shixin and Yu, Xiong and VanLoock, Margaret S. and Jezewska, Maria J. and Bujalowski, Wlodzimierz and Egelman, Edward H.},
  journal   = {Journal of molecular biology},
  title     = {Flexibility of the rings: structural asymmetry in the DnaB hexameric helicase.},
  year      = {2002},
  pages     = {839--49},
  volume    = {321},
  abstract  = {DnaB is the primary replicative helicase in Escherichia coli and the hexameric DnaB ring has previously been shown to exist in two states in the presence of nucleotides. In one, all subunits are equivalent, while in the other, there are two different subunit conformations resulting in a trimer of dimers. Under all conditions that we have used for electron microscopy, including the absence of nucleotide, some rings exist as trimers of dimers, showing that the symmetry of the DnaB hexamer can be broken prior to nucleotide binding. Three-dimensional reconstructions reveal that the N-terminal domain of DnaB makes two very different contacts with neighboring subunits in the trimer of dimers, but does not form a predicted dimer with a neighboring N-terminal domain. Within the trimer of dimers, the helicase domain exists in two alternate conformations, each of which can form symmetrical hexamers depending upon the nucleotide cofactor used. These results provide new information about the modular architecture and domain dynamics of helicases, and suggest, by comparison with the hexameric bacteriophage T7 gp4 and SV40 large T-antigen helicases, that a great structural and mechanistic diversity may exist among the hexameric helicases.},
  file      = {:by-author/Y/Yang/2002_Yang_839.pdf:PDF},
  keywords  = {Ecoli; {gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Yang2005b,
  author    = {Yang Yang and Shuman Liu and Keisaku Kimura},
  journal   = {Chemistry Letters},
  title     = {Synthesis of Well-dispersed CuI Nanoparticles from an Available Solution Precursor},
  year      = {2005},
  pages     = {1158--1159},
  volume    = {34},
  file      = {:by-author/Y/Yang/2005_Yang_1158.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Yang2005,
  author    = {Yang, Zhe and Horton, John R. and Maunus, Robert and Wilson, Geoffrey G. and Roberts, Richard J. and Cheng, Xiaodong},
  journal   = {Nucleic acids research},
  title     = {Structure of HinP1I endonuclease reveals a striking similarity to the monomeric restriction enzyme MspI.},
  year      = {2005},
  pages     = {1892--901},
  volume    = {33},
  abstract  = {HinP1I, a type II restriction endonuclease, recognizes and cleaves a palindromic tetranucleotide sequence (G/CGC) in double-stranded DNA, producing 2 nt 5' overhanging ends. Here, we report the structure of HinP1I crystallized as one protein monomer in the crystallographic asymmetric unit. HinP1I displays an elongated shape, with a conserved catalytic core domain containing an active-site motif of SDX18QXK and a putative DNA-binding domain. Without significant sequence homology, HinP1I displays striking structural similarity to MspI, an endonuclease that cleaves a similar palindromic DNA sequence (C/CGG) and binds to that sequence crystallographically as a monomer. Almost all the structural elements of MspI can be matched in HinP1I, including both the DNA recognition and catalytic elements. Examining the protein-protein interactions in the crystal lattice, HinP1I could be dimerized through two helices located on the opposite side of the protein to the active site, generating a molecule with two active sites and two DNA-binding surfaces opposite one another on the outer surfaces of the dimer. A possible functional link between this unusual dimerization mode and the tetrameric restriction enzymes is discussed.},
  file      = {:by-author/Y/Yang/2005_Yang_1892.pdf:PDF},
  keywords  = {Struct; TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Yanson1994,
  author    = {Yanson, T. I. and Manyako, M. B. and Bodak, O. I. and Zarechnyuk, O. S. and Gladyshevskii, R. E. and Cern{\'{y}}, R. and Yvon, K.},
  journal   = {Acta Crystallographica Section C},
  title     = {Hexagonal Yb${\sb 6}$Cr${\sb 4+{\it x}}$Al${\sb 43{$-$}{\it x}}$ ({\it x} = 1.76) with a new structure type},
  year      = {1994},
  pages     = {1529--1531},
  volume    = {50},
  doi       = {10.1107/S010827019400377X},
  file      = {:by-author/Y/Yanson/1994_Yanson_1529.pdf:PDF},
  owner     = {antanas},
  timestamp = {2013.04.11},
  creationdate = {2013-04-11T00:00:00},
  url       = {http://dx.doi.org/10.1107/S010827019400377X},
}

@Article{Yao2004,
  author    = {Yao, Min and Yasutake, Yoshiaki and Tanaka, Isao},
  journal   = {Acta Crystallographica Section D},
  title     = {Flash-cooling of macromolecular crystals in a capillary to overcome increased mosaicity},
  year      = {2004},
  pages     = {39--45},
  volume    = {60},
  doi       = {10.1107/S0907444903021188},
  file      = {dz5009.pdf:by-author/Y/Yao/2004_Yao_39.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444903021188},
}

@Article{Yao1997,
  author    = {Shao Yao and Indraneel Ghosh and Reena Zutshi and Jean Chmielewsk},
  journal   = {J. Am. Chem. Soc.},
  title     = {A pH-Modulated, Self-Replicating Peptide},
  year      = {1997},
  pages     = {10559--10560},
  volume    = {119},
  file      = {1997_Yao_10559.pdf:by-author/Y/Yao/1997_Yao_10559.pdf:PDF},
  keywords  = {Chemical Prebiotic; Evolution},
  owner     = {saulius},
  timestamp = {2012.11.20},
  creationdate = {2012-11-20T00:00:00},
}

@Article{Yao1999,
  author    = {Shao Yao and Indraneel Ghosh and Reena Zutshi and Jean Chmielewski},
  journal   = {J. Am. Chem. Soc.},
  title     = {A pH-Modulated, Self-Replicating Peptide: Additions and Corrections},
  year      = {1999},
  pages     = {8132},
  doi       = {10.1021/ja995525+},
  file      = {1999_Yao_8132.pdf:by-author/Y/Yao/1999_Yao_8132.pdf:PDF},
  keywords  = {Chemical Prebiotic; Evolution},
  owner     = {saulius},
  timestamp = {2012.11.20},
  creationdate = {2012-11-20T00:00:00},
}

@Article{Yao1998,
  author    = {Yao, S and Ghosh, I and Zutshi, R and Chmielewski, J},
  journal   = {Nature},
  title     = {Selective amplification by auto- and cross-catalysis in a replicating peptide system.},
  year      = {1998},
  pages     = {447--50},
  volume    = {396},
  abstract  = {Self-replication has been demonstrated in synthetic chemical systems based on oligonucleotides, peptides and complementary molecules without natural analogues. However, within a living cell virtually no molecule catalyses its own formation, and the search for chemical systems in which both auto- and cross-catalysis can occur has therefore attracted wide interest. One such system, consisting of two self-replicating peptides that catalyse each other's production, has been reported. Here we describe a four-component peptide system that is capable of auto- and cross-catalysis and allows for the selective amplification of one or more of the products by changing the reaction conditions. The ability of this system selectively to amplify one or more molecules in response to changes in environmental conditions such as pH or salt concentration supports the suggestions that self-replicating peptides may have played a role in the origin of life.},
  file      = {1998_Yao_447.pdf:by-author/Y/Yao/1998_Yao_447.pdf:PDF},
  keywords  = {Chemical Prebiotic; Evolution},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Yashima2001,
  author    = {Yashima, Eiji and Maeda, Katsuhiro and Sato, Osamu},
  journal   = {Journal of the American Chemical Society},
  title     = {Switching of a macromolecular helicity for visual distinction of molecular recognition events},
  year      = {2001},
  issn      = {0002-7863},
  pages     = {8159--8160},
  volume    = {123},
  doi       = {10.1021/ja016393z},
  file      = {Yashima et al. - 2001 - Switching of a Macromolecular Helicity for Visual .pdf:by-author/Y/Yashima/2001_Yashima_8159.pdf:PDF;ACS Full Text Snapshot:by-author/Y/Yashima/2001_Yashima_8159.html:URL},
  groups    = {sg/chemical},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://dx.doi.org/10.1021/ja016393z},
  urldate   = {2015-08-21},
}

@MastersThesis{Yatsenko2003,
  author    = {Dimitri V. Yatsenko},
  school    = {Utah State University},
  title     = {Automated Placement And Routing Of Cell Matrix Circuits},
  year      = {2003},
  file      = {:by-author/Y/Yatsenko/2003_Yatsenko_mscthesis.pdf:PDF},
  groups    = {sg/Cell Matrix},
  keywords  = {Cell Matrix; Computer Science (CS)},
  owner     = {saulius},
  pages     = {mscthesis},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@InProceedings{Yeh1999,
  author    = {Yeh, Tsin Shu},
  booktitle = {Proceedings of the 7th ACM international symposium on Advances in geographic information systems},
  title     = {Spot: distance based join indices for spatial data},
  year      = {1999},
  address   = {New York, NY, USA},
  pages     = {103--109},
  publisher = {ACM},
  series    = {GIS '99},
  abstract  = {Recently, distance based spatial queries have become more and more important for spatial data analysis, data-mining, and geo marketing. Such queries capture metric relationships between spatial entities. They need the computation of spatial join with a metric distance criterion, which is extremely expensive in I/O disk cost. Indeed this is equivalent to make a cartesian product between all entities. Processing these queries is a challenging task due to the huge amount of spatial data and to the conceptual nature of the problems. Distance based spatial queries is a common problem in Geographical Information Systems (GIS). Several approaches have been presented in recent years, almost all of them based on structures called join indices. Such structures transform the complexity of the spatial join into a traditional problem that can be processed with basic operators of relational data model. However, a join indices file contains the cartesian product of couples of spatial objects with their distances. Consequently, it is properly working only on few amounts of data. In this paper, we propose a distance based join indices approach for spatial data in order to reduce the cost of storage and processing. The idea is to store only distances of spatial data linked to virtual points called "spots" which avoids storing all combinations of distances two by two. A spot is a roundup of a set of spatial objects. We propose a data structure on disk that uses a clustering method to reduce the disk I/O during the join computation. In theory, and confirmed by empirical studies, this approach outperforms the traditional distance join method by at least one order of magnitude, especially when the data set is large.},
  doi       = {10.1145/320134.320161},
  file      = {:by-author/Y/Yeh/1999_Yeh_103.pdf:PDF},
  isbn      = {1-58113-235-2},
  location  = {Kansas City, Missouri, United States},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://doi.acm.org/10.1145/320134.320161},
}

@Presentation{Yelick2001,
  author    = {Kathy Yelick},
  title     = {Message Passing Programming (MPI)},
  year      = {2001},
  file      = {:by-author/Y/Yelick/2001_Yelick_slides.pdf:PDF},
  owner     = {saulius},
  pages     = {slides},
  timestamp = {2013.07.02},
  creationdate = {2013-07-02T00:00:00},
  url       = {http://cseweb.ucsd.edu/~carter/260/yelickMPI.pdf},
}

@MastersThesis{Yerushalmi1997,
  author    = {Yoav Yerushalmi},
  school    = {Massachusetts Institute Of Technology},
  title     = {Incremental Cryptography},
  year      = {1997},
  type      = {BSc thesis},
  abstract  = {Given a cryptographic operation and data to be operated upon, standard schemes compute the cryptographic operation from scratch. Incremental schemes instead at- tempt to use a previously computed result if available on a previous version of the document, along with a list of changes performed to obtain the later document. The goal is to yield a faster computation. This technique can be applied to a wide variety of situations. Examples include creating dynamically updated MACs, digital signatures, or encryptions. Ideally, the apparent speed improvements will make integrating this feature into a system as a default viable. Users will not notice the delays inherent in traditional cryptography, and so will accept it. The problem of efficiency of computation of ciphers will be analyzed in terms of perceived speed. A solution for the long delays after editing a document and waiting for a cryptographic operation to complete will be proposed. Finally, a testbed implementation of both a MAC generator and a public-key encryptor for emacs is written and analyzed.},
  file      = {1997_Yerushalmi_1.pdf:by-author/Y/Yerushalmi/1997_Yerushalmi_1.pdf:PDF},
  keywords  = {Computer Science (CS); Cryptography; Incremental Cryptography},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Manuscript{Yi2006,
  author    = {Chuang Yi},
  title     = {Metropolis Hastings Markov Chain Monte Carlo},
  year      = {2006},
  keywords  = {Metropolis Hastings; Monte Carlo},
  file      = {:by-author/Y/Yi/2006_Yi.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.10.04},
  creationdate = {2012-10-04T00:00:00},
}

@Article{Yodh2010,
  author    = {Yodh, Jaya G. and Schlierf, Michael and Ha, Taekjip},
  journal   = {Quarterly reviews of biophysics},
  title     = {Insight into helicase mechanism and function revealed through single-molecule approaches.},
  year      = {2010},
  pages     = {185--217},
  volume    = {43},
  abstract  = {Helicases are a class of nucleic acid (NA) motors that catalyze NTP-dependent unwinding of NA duplexes into single strands, a reaction essential to all areas of NA metabolism. In the last decade, single-molecule (sm) technology has proven to be highly useful in revealing mechanistic insight into helicase activity that is not always detectable via ensemble assays. A combination of methods based on fluorescence, optical and magnetic tweezers, and flow-induced DNA stretching has enabled the study of helicase conformational dynamics, force generation, step size, pausing, reversal and repetitive behaviors during translocation and unwinding by helicases working alone and as part of multiprotein complexes. The contributions of these sm investigations to our understanding of helicase mechanism and function will be discussed.},
  file      = {:by-author/Y/Yodh/2010_Yodh_185.pdf:PDF},
  keywords  = {{gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Yogavel2007,
  author    = {Yogavel, Manickam and Gill, Jasmita and Mishra, Prakash Chandra and Sharma, Amit},
  journal   = {Acta crystallographica. Section D, Biological crystallography},
  title     = {SAD phasing of a structure based on cocrystallized iodides using an in-house Cu Kalpha X-ray source: effects of data redundancy and completeness on structure solution.},
  year      = {2007},
  pages     = {931--4},
  volume    = {63},
  abstract  = {Superoxide dismutase (SOD) from Potentilla atrosanguinea (Wall. ex. Lehm.) was crystallized using 20% PEG 3350 and 0.2 M ammonium iodide and diffraction data were collected to 2.36 A resolution using an in-house Cu Kalpha X-ray source. Analyses show that data with a redundancy of 3.2 were sufficient to determine the structure by the SAD technique using the iodine anomalous signal. This redundancy is lower than that in previous cases in which protein structures were determined using iodines for phasing and in-house copper X-ray sources. Cocrystallization of proteins with halide salts such as ammonium iodide in combination with copper-anode X-ray radiation can therefore serve as a powerful and easy avenue for structure solution.},
  doi       = {10.1107/S0907444907029174},
  file      = {:by-author/Y/Yogavel/2007_Yogavel_931.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Yonath1983,
  author    = {Yonath, A. and Tesche, B. and Lorenz, S. and Müssig, J. and Erdmann, V. A. and Wittmann, H. G.},
  journal   = {FEBS letters},
  title     = {Several crystal forms of the Bacillus stearothermophilus 50 S ribosomal particles.},
  year      = {1983},
  pages     = {15--20},
  volume    = {154},
  file      = {:by-author/Y/Yonath/1983_Yonath_15.pdf:PDF},
  keywords  = {Ribosome Structure},
  owner     = {saulius},
  timestamp = {2012.06.25},
  creationdate = {2012-06-25T00:00:00},
}

@Article{Yong1996,
  author    = {Yong, Yongqi and Romano, Louis J.},
  journal   = {Chemical Research in Toxicology},
  title     = {Benzo[a]pyrene−DNA Adducts Inhibit the DNA Helicase Activity of the Bacteriophage T7 Gene 4 Protein},
  year      = {1996},
  pages     = {179--187},
  volume    = {9},
  abstract  = {The gene 4 protein of bacteriophage T7 provides the essential helicase and primase activities for the replication of the T7 genome. In addition, it also displays a DNA-dependent deoxyribonucleoside triphosphatase activity, the preferred substrate of which is dTTP. Previous investigations have demonstrated that the translocation of the gene 4 protein along single-stranded DNA is blocked by the presence of benzo[a]pyrene−DNA adducts and that the gene 4 protein is likely to be sequestered at the sites of these adducts. In the present study, we directly show that the helicase activity of the gene 4 protein is also profoundly inhibited by the benzo[a]pyrene−DNA adducts. The inhibitory effects of these adducts are strand-specific in that they block the DNA helicase activity of the gene 4 protein only when they are located in the DNA strand where the gene 4 protein translocates when it unwinds double-stranded DNA. Consistent with the hypothesis that the gene 4 protein is sequestered at the adduct site, we also show that the complexes formed by the gene 4 protein and benzo[a]pyrene-modified DNA are far more stable than those formed by the gene 4 protein and unmodified DNA.},
  doi       = {10.1021/tx950112h},
  eprint    = {http://pubs.acs.org/doi/pdf/10.1021/tx950112h},
  file      = {1996_Yong_179.pdf:by-author/Y/Yong/1996_Yong_179.pdf:PDF;Supplementary information:by-author/Y/Yong/1996_Yong_179suppl.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://pubs.acs.org/doi/abs/10.1021/tx950112h},
}

@Article{Yoon2014,
  author     = {Yoon, Hyo Jae and Liao, Kung-Ching and Lockett, Matthew R. and Kwok, Sen Wai and Baghbanzadeh, Mostafa and Whitesides, George M.},
  journal    = {Journal of the American Chemical Society},
  title      = {Rectification in tunneling junctions: 2, 2′-bipyridyl-terminated n-alkanethiolates},
  year       = {2014},
  pages      = {17155--17162},
  volume     = {136},
  file       = {[PDF] from harvard.edu:by-author/Y/Yoon/2014_Yoon_17155.pdf:PDF;Snapshot:by-author/Y/Yoon/2014_Yoon_17155.html:URL},
  groups     = {sg/JAC2009, sg/NAR2012},
  owner      = {saulius},
  shorttitle = {Rectification in tunneling junctions},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url        = {http://pubs.acs.org/doi/abs/10.1021/ja509110a},
  urldate    = {2015-08-31},
}

@PhdThesis{Yoon2008,
  author    = {Yoon, Ji Won},
  school    = {Department of Engineering University of Cambridge},
  title     = {Bayesian Inference for Biophysical and Chemical Signals},
  year      = {2008},
  file      = {2008_Yoon_phdthesis.pdf:by-author/Y/Yoon/2008_Yoon_phdthesis.pdf:PDF},
  groups    = {sg/Bayesian},
  owner     = {saulius},
  timestamp = {2012.09.18},
  creationdate = {2012-09-18T00:00:00},
}

@Article{Yoon2000,
  author    = {Jeong-Mi Yoon and Yash Gad and Zhijun Wu},
  title     = {Mathematical Modeling of Protein Structure Using Distance Geometry},
  year      = {2000},
  pages     = {TR00-24},
  abstract  = {This paper reviews methods for structure determination with interatomic distances and explores possible improvement of the methods and ways of combining them with potential energy minimization.},
  file      = {:by-author/Y/Yoon/2000_Yoon_TR00.pdf:PDF},
  keywords  = {Distance Geometry; Protein Bioinformatics},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Yoshioka2007,
  author    = {Yoshioka, Craig and Pulokas, James and Fellmann, Denis and Potter, Clinton S and Milligan, Ronald A and Carragher, Bridget},
  journal   = {Journal of structural biology},
  title     = {Automation of random conical tilt and orthogonal tilt data collection using feature-based correlation.},
  year      = {2007},
  pages     = {335--46},
  volume    = {159},
  abstract  = {Visualization by electron microscopy has provided many insights into the composition, quaternary structure, and mechanism of macromolecular assemblies. By preserving samples in stain or vitreous ice it is possible to image them as discrete particles, and from these images generate three-dimensional structures. This 'single-particle' approach suffers from two major shortcomings; it requires an initial model to reconstitute 2D data into a 3D volume, and it often fails when faced with conformational variability. Random conical tilt (RCT) and orthogonal tilt (OTR) are methods developed to overcome these problems, but the data collection required, particularly for vitreous ice specimens, is difficult and tedious. In this paper, we present an automated approach to RCT/OTR data collection that removes the burden of manual collection and offers higher quality and throughput than is otherwise possible. We show example datasets collected under stain and cryo conditions and provide statistics related to the efficiency and robustness of the process. Furthermore, we describe the new algorithms that make this method possible, which include new calibrations, improved targeting and feature-based tracking.},
  file      = {2007_Yoshioka_335.pdf:by-author/Y/Yoshioka/2007_Yoshioka_335.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Young2010,
  author    = {Derek S. Young},
  journal   = {Journal of Statistical Software},
  title     = {{tolerance}: An {R} Package for Estimating Tolerance Intervals},
  year      = {2010},
  volume    = {36},
  file      = {:by-author/Y/Young/2010_Young.pdf:PDF},
  keywords  = {Statistics},
  owner     = {andrius},
  timestamp = {2014.05.04},
  creationdate = {2014-05-04T00:00:00},
  url       = {http://www.jstatsoft.org/v36/i05},
}

@TechReport{Young2012,
  author      = {Jasmine Young},
  institution = {wwPDB},
  title       = {Protein Data Bank Contents Guide: Atomic Coordinate Entry Format Description. Version 3.30},
  year        = {2012},
  abstract    = {The Protein Data Bank (PDB) is an archive of experimentally determined three-dimensional structures of biological macromolecules that serves a global community of researchers, educators, and students. The data contained in the archive include atomic coordinates, crystallographic structure factors and NMR experimental data. Aside from coordinates, each deposition also includes the names of molecules, primary and secondary structure information, sequence database references, where appropriate, and ligand and biological assembly information, details about data collection and structure solution, and bibliographic citations. This comprehensive guide describes the "PDB format" used by the members of the worldwide Protein Data Bank (wwPDB; Berman, H.M., Henrick, K. and Nakamura, H. Announcing the worldwide Protein Data Bank. Nat Struct Biol 10, 980 (2003)). Questions should be sent to info@wwpdb.org},
  file        = {:by-author/Y/Young/2012_Young.pdf:PDF},
  groups      = {am/PDB},
  keywords    = {Data Management; File Formats; PDB; PDB File Format},
  owner       = {saulius},
  timestamp = {2014.03.24},
  creationdate = {2014-03-24T00:00:00},
  url         = {ftp://ftp.wwpdb.org/pub/pdb/doc/format_descriptions/Format_v33_A4.pdf},
}

@Article{Young1995,
  author    = {Young, M. A. and Ravishanker, G. and Beveridge, D. L. and Berman, H. M.},
  journal   = {Biophysical journal},
  title     = {Analysis of local helix bending in crystal structures of DNA oligonucleotides and DNA-protein complexes.},
  year      = {1995},
  pages     = {2454--68},
  volume    = {68},
  abstract  = {Sequence-dependent bending of the helical axes in 112 oligonucleotide duplex crystal structures resident in the Nucleic Acid Database have been analyzed and compared with the use of bending dials, a computer graphics tool. Our analysis includes structures of both A and B forms of DNA and considers both uncomplexed forms of the double helix as well as those bound to drugs and proteins. The patterns in bending preferences in the crystal structures are analyzed by base pair steps, and emerging trends are noted. Analysis of the 66 B-form structures in the Nucleic Acid Database indicates that uniform trends within all pyrimidine-purine and purine-pyrimidine steps are not necessarily observed but are found particularly at CG and GC steps of dodecamers. The results support the idea that AA steps are relatively straight and that larger roll bends occur at or near the junctions of these A-tracts with their flanking sequences. The data on 16 available crystal structures of protein-DNA complexes indicate that the majority of the DNA bends induced via protein binding are sharp localized kinks. The analysis of the 30 available A-form DNA structures indicates that these structures are also bent and show a definitive preference for bending into the deep major groove over the shallow minor groove.},
  file      = {:by-author/Y/Young/1995_Young_2454.pdf:PDF},
  keywords  = {RY; Readout},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Yu1999,
  author    = {Yu, Hongtao},
  journal   = {Proc. Natl. Acad. Sci. USA},
  title     = {Extending the size limit of protein nuclear magnetic resonance},
  year      = {1999},
  pages     = {332--334},
  volume    = {96},
  file      = {:by-author/Y/Yu/1999_Yu_332.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@Article{Yu1996,
  author    = {Yu, X. and Jezewska, M. J. and Bujalowski, W. and Egelman, E. H.},
  journal   = {Journal of molecular biology},
  title     = {The hexameric E. coli DnaB helicase can exist in different Quaternary states.},
  year      = {1996},
  pages     = {7--14},
  volume    = {259},
  abstract  = {The DnaB protein is the primary replicative helicase in Escherichia coli, and the active form of the protein is a hexamer. It has been reported that the protein forms a ring with strong 3-fold symmetry, which was suggested to be a trimer of dimers. We show that under different conditions, using either ATP, ATP gamma S, AMP-PNP or ADP as nucleotide cofactors, we always find two different forms of the DnaB ring; one with a 3-fold symmetry and one with 6-fold symmetry. We have used scanning transmission electron microscopy for mass analysis, and have found that both forms are hexamers, excluding the possibility that the 3-fold form is in fact a trimer of the 52 kDa monomer. We have also found rings that are in an intermediate state between these two. The existence of hexamers in discrete states shows that the transitions between these states must be cooperative. These observations suggest that there may be an equilibrium between two different conformations of the hexameric ring. The role of these two states in the mechanism of helicase action remains to be determined.},
  file      = {:by-author/Y/Yu/1996_Yu_7.pdf:PDF},
  keywords  = {Ecoli; {gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Yuan2010,
  author    = {Gary Yuan and François Gygi},
  journal   = {Computational Science \& Discovery},
  title     = {ESTEST: a framework for the validation and verification of electronic structure codes},
  year      = {2010},
  pages     = {015004},
  volume    = {3},
  abstract  = {We present a framework for the verification and validation (V&V) of electronic structure simulation software. Electronic structure computations involve numerous parameters and approximations that determine their accuracy and reliability. As a large number of simulation data coming from several electronic structure codes are becoming available, the associated V&V process is becoming increasingly complex. We introduce ESTEST as a framework for facilitating the verification and validation of electronic structure computations. ESTEST software enables the V&V, comparison and sharing of simulation data by constructing a unified representation of code outputs, populating and organizing a query database with these representations and interfacing the data through a web service that offers ways to search, view, compare, visualize and post-process the data. We present examples of V&V as well as comparison and analysis from our implementation, and justify the details of each of the innovative features of this software. The present implementation supports electronic structure codes such as Qbox, Quantum Espresso, ABINIT, and the Exciting code. An online demonstration is available at http://estest.ucdavis.edu [http://estest.ucdavis.edu] .},
  doi       = {10.1088/1749-4699/3/1/015004},
  file      = {:by-author/Y/Yuan/2010_Yuan_015004.pdf:PDF},
  keywords  = {Chemoinformatics; Code Valudation; Computational Chemistry; Quantum Chemistry; XML},
  owner     = {saulius},
  timestamp = {2014.07.17},
  creationdate = {2014-07-17T00:00:00},
  url       = {http://stacks.iop.org/1749-4699/3/i=1/a=015004},
}

@Article{Yuan2017,
  author    = {Yutao Yuan and Yanqiang Zhang and Long Liu and Nianming Jiao and Kun Dong and Suojiang Zhang},
  journal   = {{RSC} Adv.},
  title     = {Bicyclic ammonium ionic liquids as dense hypergolic fuels},
  year      = {2017},
  number    = {35},
  pages     = {21592--21599},
  volume    = {7},
  doi       = {10.1039/c7ra03090h},
  file      = {2017_Yuan_21592.pdf:by-author/Y/Yuan/2017_Yuan_21592.pdf:PDF;Supplementary info:by-author/Y/Yuan/2017_Yuan_21592a.pdf:PDF},
  groups    = {Structre-property relations},
  owner     = {saulius},
  publisher = {Royal Society of Chemistry ({RSC})},
  timestamp = {2017.04.19},
  creationdate = {2017-04-19T00:00:00},
}

@Article{Yuen1996,
  author    = {P.C. Yuen and G.C. Feng},
  journal   = {Pattern Recognition Letters},
  title     = {A novel method for parameter estimation of digital arc},
  year      = {1996},
  pages     = {929--938},
  volume    = {17},
  abstract  = {A novel algorithm for parameter estimation of circular arcs is developed and reported in this letter. The proposed method is unbiased and consistent. Experimental results show that our method provides a better accuracy than certain existing methods.},
  file      = {1996_Yuen_929.pdf:by-author/Y/Yuen/1996_Yuen_929.pdf:PDF},
  groups    = {sg/Arc fitting},
  keywords  = {Arc Fitting; Mathematics},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Manuscript{Yung1999,
  author    = {Kwong Hiu Yung},
  title     = {Explaining the Stein Paradox Kwong Hiu Yung},
  year      = {1999},
  keywords  = {Bayesian Statistics},
  url       = {http://www.cs.nyu.edu/~roweis/csc2515-2006/readings/stein_paradox.pdf},
  abstract  = {This report offers several rationale for the Stein para- dox. Sections 1 and 2 defines the multivariate nor- mal mean estimation problem and introduces Stein’s paradox. Sections 3–8 advances the Galtonian per- spective and explains Stein’s paradox using regres- sion analysis. Sections 9 and 10 approaches Stein’s paradox through the conventional empirical Bayes approach. The closing sections 11 and 12 compares admissibility to equivariance and to minimaxity as criteria for simultaneous estimation.},
  file      = {:by-author/Y/Yung/1999_Yung.pdf:PDF},
  groups    = {sg/Bayesian},
  owner     = {saulius},
  timestamp = {2012.10.10},
  creationdate = {2012-10-10T00:00:00},
}

@Article{Yunusova2006,
  author    = {A. K. Yunusova and E. A. Rogulin and R. I. Artyukh and L. A. Zheleznaya and N. I. Matvienko/home/saulius/papers/BspD6I/Bsp_savybes2001.pdf},
  journal   = {Biochemistry (Moscow)},
  title     = {Nickase and a Protein Encoded by an Open Reading Frame Downstream from the Nickase BspD6I Gene Form a Restriction Endonuclease Complex},
  year      = {2006},
  pages     = {815--820},
  volume    = {71},
  abstract  = {We are the first to have isolated a protein (186 amino acid residues) encoded by the open reading frame adjacent to the end of the BspD6I nickase (N.BspD6I) gene. Cleavage of both DNA strands near the sequence recognized by nickase (5′-GAGTC/5′-GACTC) occurs when this protein is added to the reaction mixture containing N.BspD6I. The protein encoded by the open reading frame and the nickase are suggested to be subunits of heterodimeric restriction endonuclease R.BspD6I.},
  doi       = {10.1134/S0006297906070157},
  file      = {:by-author/Y/Yunusova/2006_Yunusova_815.pdf:PDF},
  owner     = {saulius},
  timestamp = {2011.12.07},
  creationdate = {2011-12-07T00:00:00},
}

@Article{Yurke2000,
  author    = {Yurke, Bernard and Turberfield, Andrew J. and Mills, Allen P. and Simmel, Friedrich C. and Neumann, Jennifer L.},
  journal   = {Nature},
  title     = {A {DNA}-fuelled molecular machine made of {DNA}},
  year      = {2000},
  issn      = {0028-0836},
  pages     = {605--608},
  volume    = {406},
  abstract  = {Molecular recognition between complementary strands of DNA allows construction on a nanometre length scale. For example, DNA tags may be used to organize the assembly of colloidal particles, and DNA templates can direct the growth of semiconductor nanocrystals and metal wires. As a structural material in its own right, DNA can be used to make ordered static arrays of tiles, linked rings and polyhedra. The construction of active devices is also possible—for example, a nanomechanical switch, whose conformation is changed by inducing a transition in the chirality of the DNA double helix. Melting of chemically modified DNA has been induced by optical absorption, and conformational changes caused by the binding of oligonucleotides or other small groups have been shown to change the enzymatic activity of ribozymes. Here we report the construction of a DNA machine in which the DNA is used not only as a structural material, but also as 'fuel'. The machine, made from three strands of DNA, has the form of a pair of tweezers. It may be closed and opened by addition of auxiliary strands of 'fuel' DNA; each cycle produces a duplex DNA waste product.},
  copyright = {© 2000 Nature Publishing Group},
  doi       = {10.1038/35020524},
  file      = {Full Text PDF:by-author/Y/Yurke/2000_Yurke_605.pdf:application/pdf;Snapshot:by-author/Y/Yurke/2000_Yurke_605.html:text/html},
  groups    = {sg/biomolecular},
  language  = {en},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://www.nature.com/nature/journal/v406/n6796/abs/406605a0.html},
  urldate   = {2015-08-05},
}

@Article{Yvon1977,
  author    = {Yvon, K. and Jeitschko, W. and Parth{\'{e}}, E.},
  journal   = {Journal of Applied Crystallography},
  title     = {{\it LAZY PULVERIX}, a computer program, for calculating X-ray and neutron diffraction powder patterns},
  year      = {1977},
  pages     = {73--74},
  volume    = {10},
  abstract  = {A computer program has been written with the aim of calculating powder patterns without the use of crystallographic tables. This has been achieved by deriving all symmetry information such as general equivalent positions from the Hermann-Mauguin space-group symbols, by calculating automatically the multiplicities of special positions and by storing the necessary constants, such as scattering factor tables, anomalous dispersion correction terms and X-ray wavelengths in the program. Owing to the very restricted amount of input data this program is especially suited for users with a limited knowledge of crystallography.},
  doi       = {10.1107/S0021889877012898},
  file      = {1977_Yvon_73.pdf:by-author/Y/Yvon/1977_Yvon_73.pdf:PDF},
  keywords  = {Algorithms; Crystallography; Powder Diffraction; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2013.05.03},
  creationdate = {2013-05-03T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0021889877012898},
}

@Article{zadeh_is_2008,
  author    = {Zadeh, Lotfi A.},
  journal   = {Information Sciences},
  title     = {Is there a need for fuzzy logic?},
  year      = {2008},
  issn      = {0020-0255},
  pages     = {2751--2779},
  volume    = {178},
  abstract  = {“Is there a need for fuzzy logic?” is an issue which is associated with a long history of spirited discussions and debate. There are many misconceptions about fuzzy logic. Fuzzy logic is not fuzzy. Basically, fuzzy logic is a precise logic of imprecision and approximate reasoning. More specifically, fuzzy logic may be viewed as an attempt at formalization/mechanization of two remarkable human capabilities. First, the capability to converse, reason and make rational decisions in an environment of imprecision, uncertainty, incompleteness of information, conflicting information, partiality of truth and partiality of possibility – in short, in an environment of imperfect information. And second, the capability to perform a wide variety of physical and mental tasks without any measurements and any computations [L.A. Zadeh, From computing with numbers to computing with words – from manipulation of measurements to manipulation of perceptions, IEEE Transactions on Circuits and Systems 45 (1999) 105–119; L.A. Zadeh, A new direction in AI – toward a computational theory of perceptions, AI Magazine 22 (1) (2001) 73–84]. In fact, one of the principal contributions of fuzzy logic – a contribution which is widely unrecognized – is its high power of precisiation. Fuzzy logic is much more than a logical system. It has many facets. The principal facets are: logical, fuzzy-set-theoretic, epistemic and relational. Most of the practical applications of fuzzy logic are associated with its relational facet. In this paper, fuzzy logic is viewed in a nonstandard perspective. In this perspective, the cornerstones of fuzzy logic – and its principal distinguishing features – are: graduation, granulation, precisiation and the concept of a generalized constraint. A concept which has a position of centrality in the nontraditional view of fuzzy logic is that of precisiation. Informally, precisiation is an operation which transforms an object, p, into an object, p∗, which in some specified sense is defined more precisely than p. The object of precisiation and the result of precisiation are referred to as precisiend and precisiand, respectively. In fuzzy logic, a differentiation is made between two meanings of precision – precision of value, v-precision, and precision of meaning, m-precision. Furthermore, in the case of m-precisiation a differentiation is made between mh-precisiation, which is human-oriented (nonmathematical), and mm-precisiation, which is machine-oriented (mathematical). A dictionary definition is a form of mh-precisiation, with the definiens and definiendum playing the roles of precisiend and precisiand, respectively. Cointension is a qualitative measure of the proximity of meanings of the precisiend and precisiand. A precisiand is cointensive if its meaning is close to the meaning of the precisiend. A concept which plays a key role in the nontraditional view of fuzzy logic is that of a generalized constraint. If X is a variable then a generalized constraint on X, GC(X), is expressed as X isr R, where R is the constraining relation and r is an indexical variable which defines the modality of the constraint, that is, its semantics. The primary constraints are: possibilistic, (r = blank), probabilistic (r = p) and veristic (r = v). The standard constraints are: bivalent possibilistic, probabilistic and bivalent veristic. In large measure, science is based on standard constraints. Generalized constraints may be combined, qualified, projected, propagated and counterpropagated. The set of all generalized constraints, together with the rules which govern generation of generalized constraints, is referred to as the generalized constraint language, GCL. The standard constraint language, SCL, is a subset of GCL. In fuzzy logic, propositions, predicates and other semantic entities are precisiated through translation into GCL. Equivalently, a semantic entity, p, may be precisiated by representing its meaning as a generalized constraint. By construction, fuzzy logic has a much higher level of generality than bivalent logic. It is the generality of fuzzy logic that underlies much of what fuzzy logic has to offer. Among the important contributions of fuzzy logic are the following: 1. FL-generalization. Any bivalent-logic-based theory, T, may be FL-generalized, and hence upgraded, through addition to T of concepts and techniques drawn from fuzzy logic. Examples: fuzzy control, fuzzy linear programming, fuzzy probability theory and fuzzy topology. 2. Linguistic variables and fuzzy if–then rules. The formalism of linguistic variables and fuzzy if–then rules is, in effect, a powerful modeling language which is widely used in applications of fuzzy logic. Basically, the formalism serves as a means of summarization and information compression through the use of granulation. 3. Cointensive precisiation. Fuzzy logic has a high power of cointensive precisiation. This power is needed for a formulation of cointensive definitions of scientific concepts and cointensive formalization of human-centric fields such as economics, linguistics, law, conflict resolution, psychology and medicine. 4. NL-Computation (computing with words). Fuzzy logic serves as a basis for NL-Computation, that is, computation with information described in natural language. NL-Computation is of direct relevance to mechanization of natural language understanding and computation with imprecise probabilities. More generally, NL-Computation is needed for dealing with second-order uncertainty, that is, uncertainty about uncertainty, or uncertainty2 for short. In summary, progression from bivalent logic to fuzzy logic is a significant positive step in the evolution of science. In large measure, the real-world is a fuzzy world. To deal with fuzzy reality what is needed is fuzzy logic. In coming years, fuzzy logic is likely to grow in visibility, importance and acceptance.},
  doi       = {10.1016/j.ins.2008.02.012},
  file      = {Zadeh - 2008 - Is there a need for fuzzy logic.pdf:by-author/Z/Zadeh/2008_Zadeh_2751.pdf:application/pdf;ScienceDirect Snapshot:by-author/Z/Zadeh/2008_Zadeh_2751.html:text/html},
  groups    = {sg/Fuzzy sg/Logic},
  keywords  = {Approximate Reasoning; Computing With Perceptions; Computing With Words; Fuzzy Logic; Fuzzy Sets; Generalized Theory of Uncertainty},
  owner     = {saulius},
  timestamp = {2015.12.07},
  creationdate = {2015-12-07T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/S0020025508000716},
  urldate   = {2015-12-07},
}

@Article{zadeh_generalized_2006,
  author    = {Zadeh, Lotfi A.},
  journal   = {Computational Statistics \& Data Analysis},
  title     = {Generalized theory of uncertainty ({GTU})—principal concepts and ideas},
  year      = {2006},
  issn      = {0167-9473},
  pages     = {15--46},
  volume    = {51},
  abstract  = {Uncertainty is an attribute of information. The path-breaking work of Shannon has led to a universal acceptance of the thesis that information is statistical in nature. Concomitantly, existing theories of uncertainty are based on probability theory. The generalized theory of uncertainty (GTU) departs from existing theories in essential ways. First, the thesis that information is statistical in nature is replaced by a much more general thesis that information is a generalized constraint, with statistical uncertainty being a special, albeit important case. Equating information to a generalized constraint is the fundamental thesis of GTU. Second, bivalence is abandoned throughout GTU, and the foundation of GTU is shifted from bivalent logic to fuzzy logic. As a consequence, in GTU everything is or is allowed to be a matter of degree or, equivalently, fuzzy. Concomitantly, all variables are, or are allowed to be granular, with a granule being a clump of values drawn together by a generalized constraint. And third, one of the principal objectives of GTU is achievement of NL-capability, that is, the capability to operate on information described in natural language. NL-capability has high importance because much of human knowledge, including knowledge about probabilities, is described in natural language. NL-capability is the focus of attention in the present paper. The centerpiece of GTU is the concept of a generalized constraint. The concept of a generalized constraint is motivated by the fact that most real-world constraints are elastic rather than rigid, and have a complex structure even when simple in appearance. The paper concludes with examples of computation with uncertain information described in natural language.},
  doi       = {10.1016/j.csda.2006.04.029},
  file      = {Zadeh - 2006 - Generalized theory of uncertainty (GTU)—principal .pdf:by-author/Z/Zadeh/2006_Zadeh_15.pdf:application/pdf;ScienceDirect Snapshot:by-author/Z/Zadeh/2006_Zadeh_15.html:text/html},
  groups    = {sg/Fuzzy sg/Logic},
  keywords  = {Fuzzy Logic; Generalized Constraint-based Computation; Natural Language Computation; Precisiation; Statistics},
  owner     = {saulius},
  series    = {The {Fuzzy} {Approach} to {Statistical} {Analysis}},
  timestamp = {2015.12.07},
  creationdate = {2015-12-07T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/S0167947306001290},
  urldate   = {2015-12-07},
}

@MastersThesis{Zagorskaite2011,
  author    = {Zagorskaitė, Evelina},
  school    = {Vilniaus universitetas},
  title     = {{III} tipo restrikcijos fermentų nukleazinio centro sandaros tyrimai},
  year      = {2011},
  file      = {:by-author/Z/Zagorskaitė/2011_Zagorskaitė_bscthesis.pdf:PDF},
  keywords  = {TypeIII},
  owner     = {em},
  pages     = {bscthesis},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Zahara2009,
  author    = {Erwie Zahara and Yi-Tung Kao},
  journal   = {Expert Systems with Applications},
  title     = {Hybrid Nelder-Mead simplex search and particle swarm optimization for constrained engineering design problems},
  year      = {2009},
  pages     = {3880--3886},
  file      = {:by-author/Z/Zahara/2009_Zahara_3880.pdf:PDF},
  keywords  = {Computer Science (CS); Minimisation; Simplex Method},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Webpage{Zaitsev2006,
  author    = {Peter Zaitsev},
  retrieved = {2009-04-24},
  title     = {MySQL Query Cache (MySQL Performance Blog)},
  url       = {http://www.percona.com/blog/2006/07/27/mysql-query-cache/},
  year      = {2006},
  file      = {:by-author/Z/Zaitsev/2006_Zaitsev.odt:},
  keywords  = {Computer Science (CS); Databases; Query_cache},
  owner     = {saulius},
  timestamp = {2015.03.03},
  creationdate = {2015-03-03T00:00:00},
}

@InProceedings{Zakai2011,
  author    = {Zakai, Alon},
  booktitle = {Proceedings of the ACM International Conference Companion on Object Oriented Programming Systems Languages and Applications Companion},
  title     = {Emscripten: An LLVM-to-JavaScript Compiler},
  year      = {2011},
  address   = {New York, NY, USA},
  pages     = {301--312},
  publisher = {ACM},
  series    = {OOPSLA '11},
  abstract  = {We present Emscripten, a compiler from LLVM (Low Level Virtual Machine) assembly to JavaScript. This opens up two avenues for running code written in languages other than JavaScript on the web: (1) Compile code directly into LLVM assembly, and then compile that into JavaScript using Emscripten, or (2) Compile a language's entire runtime into LLVM and then JavaScript, as in the previous approach, and then use the compiled runtime to run code written in that language. For example, the former approach can work for C and C++, while the latter can work for Python; all three examples open up new opportunities for running code on the web. Emscripten itself is written in JavaScript and is available under the MIT license (a permissive open source license), at http://www.emscripten.org. As a compiler from LLVM to JavaScript, the challenges in designing Emscripten are somewhat the reverse of the norm - one must go from a low-level assembly into a high-level language, and recreate parts of the original high-level structure of the code that were lost in the compilation to low-level LLVM. We detail the methods used in Emscripten to deal with those challenges, and in particular present and prove the validity of Emscripten's Relooper algorithm, which recreates high-level loop structures from low-level branching data.},
  acmid     = {2048224},
  doi       = {10.1145/2048147.2048224},
  file      = {2011_Zakai_301.pdf:by-author/Z/Zakai/2011_Zakai_301.pdf:PDF},
  isbn      = {978-1-4503-0942-4},
  keywords  = {Compiler Design; Decompiler; Javascript; LLVM},
  location  = {Portland, Oregon, USA},
  numpages  = {12},
  owner     = {saulius},
  timestamp = {2016.10.05},
  creationdate = {2016-10-05T00:00:00},
  url       = {http://doi.acm.org/10.1145/2048147.2048224},
}

@Article{Zakharova2004,
  author    = {Zakharova, E. and Wang, J. and Konigsberg, W.},
  journal   = {Biochemistry},
  title     = {The activity of selected RB69 DNA polymerase mutants can be restored by manganese ions: the existence of alternative metal ion ligands used during the polymerization cycle.},
  year      = {2004},
  pages     = {6587--95},
  volume    = {43},
  abstract  = {Site specific mutants in the pol active center of RB69 DNA polymerase have been produced and studied using rapid chemical-quench techniques. Pre-steady-state kinetic analysis carried out with Mg(2+) and Mn(2+) has enabled us to divide the mutants into two groups. One group had greatly reduced k(pols) values in the presence of Mg(2+) but responded to Mn(2+) which restored the k(pol) values for the nucleotidyl transfer reaction to near wild-type levels. The other group of mutants also had lower k(pol) values, relative to that of the wild-type polymerase, but could not be rescued by Mn(2+). The behavior of these mutants was interpreted in terms of the crystal structures of the available RB69 pol complexes. Our results on the metal ion dependence of the D621A and E686A mutants, together with knowledge of the position of their side chains in two different RB69 pol conformations, suggest that these acidic residues serve as alternative ligands for the metal ions destined to occupy the A and B catalytic sites. We infer that this occurs prior to the conformational change that produces the ternary RB69 pol complex in which the A and B metal ions are ligated by D623 and D411 as the enzyme is poised for phosphoryl transfer.},
  file      = {:by-author/Z/Zakharova/2004_Zakharova_6587.pdf:PDF},
  keywords  = {{gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Zamora1976,
  author    = {Antonio Zamora},
  journal   = {Journal of Chemical Information and Computer Sciences},
  title     = {An Algorithm for Finding the Smallest Set of Smallest Rings},
  year      = {1976},
  pages     = {40--43},
  volume    = {16},
  abstract  = {This paper describes an algorithm which finds the smallest set of smallest rings of a ring system without the necessity of finding all rings in the ring system. The algorithm first finds the smallest rings in which unused atoms occur and then progresses to find the smallest rings in which unused edges and faces occur until the smallest set of rings required to describe the complete ring system is found. The algorithm converges quickly because the lengths of the paths that need to be scanned to discover each new ring decrease when a smaller ring is found.},
  file      = {1976_Zamora_40.pdf:by-author/Z/Zamora/1976_Zamora_40.pdf:PDF},
  keywords  = {Ring Perception},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Zaremba2010,
  author    = {Zaremba, Mindaugas and Owsicka, Amelia and Tamulaitis, Gintautas and Sasnauskas, Giedrius and Shlyakhtenko, Luda S. and Lushnikov, Alexander Y. and Lyubchenko, Yuri L. and Laurens, Niels and van den Broek, Bram and Wuite, Gijs J. L. and Siksnys, Virginijus},
  journal   = {Nucleic acids research},
  title     = {DNA synapsis through transient tetramerization triggers cleavage by Ecl18kI restriction enzyme.},
  year      = {2010},
  pages     = {7142--54},
  volume    = {38},
  abstract  = {To cut DNA at their target sites, restriction enzymes assemble into different oligomeric structures. The Ecl18kI endonuclease in the crystal is arranged as a tetramer made of two dimers each bound to a DNA copy. However, free in solution Ecl18kI is a dimer. To find out whether the Ecl18kI dimer or tetramer represents the functionally important assembly, we generated mutants aimed at disrupting the putative dimer-dimer interface and analysed the functional properties of Ecl18kI and mutant variants. We show by atomic force microscopy that on two-site DNA, Ecl18kI loops out an intervening DNA fragment and forms a tetramer. Using the tethered particle motion technique, we demonstrate that in solution DNA looping is highly dynamic and involves a transient interaction between the two DNA-bound dimers. Furthermore, we show that Ecl18kI cleaves DNA in the synaptic complex much faster than when acting on a single recognition site. Contrary to Ecl18kI, the tetramerization interface mutant R174A binds DNA as a dimer, shows no DNA looping and is virtually inactive. We conclude that Ecl18kI follows the association model for the synaptic complex assembly in which it binds to the target site as a dimer and then associates into a transient tetrameric form to accomplish the cleavage reaction.},
  doi       = {10.1093/nar/gkq560},
  file      = {:by-author/Z/Zaremba/2010_Zaremba_7142.pdf:PDF},
  keywords  = {Ecl18kI EcoRII; TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Zaremba2010a,
  author      = {Mindaugas Zaremba and Amelia Owsicka and Gintautas Tamulaitis and Giedrius Sasnauskas and Luda S Shlyakhtenko and Alexander Y Lushnikov and Yuri L Lyubchenko and Niels Laurens and Bram van den Broek and Gijs J L Wuite and Virginijus Siksnys},
  journal     = {Nucleic Acids Res},
  title       = {DNA synapsis through transient tetramerization triggers cleavage by Ecl18kI restriction enzyme.},
  year        = {2010},
  month       = {Nov},
  number      = {20},
  pages       = {7142--7154},
  volume      = {38},
  abstract    = {To cut DNA at their target sites, restriction enzymes assemble into different oligomeric structures. The Ecl18kI endonuclease in the crystal is arranged as a tetramer made of two dimers each bound to a DNA copy. However, free in solution Ecl18kI is a dimer. To find out whether the Ecl18kI dimer or tetramer represents the functionally important assembly, we generated mutants aimed at disrupting the putative dimer-dimer interface and analysed the functional properties of Ecl18kI and mutant variants. We show by atomic force microscopy that on two-site DNA, Ecl18kI loops out an intervening DNA fragment and forms a tetramer. Using the tethered particle motion technique, we demonstrate that in solution DNA looping is highly dynamic and involves a transient interaction between the two DNA-bound dimers. Furthermore, we show that Ecl18kI cleaves DNA in the synaptic complex much faster than when acting on a single recognition site. Contrary to Ecl18kI, the tetramerization interface mutant R174A binds DNA as a dimer, shows no DNA looping and is virtually inactive. We conclude that Ecl18kI follows the association model for the synaptic complex assembly in which it binds to the target site as a dimer and then associates into a transient tetrameric form to accomplish the cleavage reaction.},
  doi         = {10.1093/nar/gkq560},
  file        = {2010_Zaremba_7142.pdf:by-author/Z/Zaremba/2010_Zaremba_7142.pdf:PDF},
  institution = {Institute of Biotechnology, Graiciuno 8, LT-02241, Vilnius, Lithuania.},
  keywords    = {Atomic Force; Chemistry/genetics/metabolism; Chemistry/metabolism/ultrastructure; DNA; DNA Cleavage; Deoxyribonucleases; Microscopy; Models; Molecular; Mutation; Protein Binding; Protein Multimerization; Type II Site-Specific},
  language    = {eng},
  medline-pst = {ppublish},
  owner       = {em},
  pii         = {gkq560},
  pmid        = {20571089},
  timestamp = {2011.12.09},
  creationdate = {2011-12-09T00:00:00},
  url         = {http://dx.doi.org/10.1093/nar/gkq560},
}

@Article{Zaremba2012,
  author    = {Mindaugas Zaremba and Giedrius Sasnauskas and Virginijus Siksnys},
  journal   = {FEBS Letters},
  title     = {The link between restriction endonuclease fidelity and oligomeric state: A study with Bse634I},
  year      = {2012},
  issn      = {0014-5793},
  pages     = {3324 - 3329},
  volume    = {586},
  abstract  = {Type II restriction endonucleases (REases) exist in multiple oligomeric forms. The tetrameric REases have two DNA binding interfaces and must synapse two recognition sites to achieve cleavage. It was hypothesised that binding of two recognition sites by tetrameric enzymes contributes to their fidelity. Here, we experimentally determined the fidelity for Bse634I REase in different oligomeric states. Surprisingly, we find that tetramerisation does not increase REase fidelity in comparison to the dimeric variant. Instead, an inherent ability to act concertedly at two sites provides tetrameric REase with a safety-catch to prevent host DNA cleavage if a single unmodified site becomes available.},
  doi       = {10.1016/j.febslet.2012.07.009},
  file      = {2012_Zaremba_3324.pdf:by-author/Z/Zaremba/2012_Zaremba_3324.pdf:PDF},
  groups    = {sg/Bse634I structures, sg/Bse634I},
  keywords  = {Bse634I; Protein-DNA Interaction; R/M Systems; Restriction Endonucleases (REases)},
  owner     = {saulius},
  timestamp = {2012.12.05},
  creationdate = {2012-12-05T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/S0014579312005777},
}

@Article{Zaremba2012a,
  author       = {Mindaugas Zaremba and Giedrius Sasnauskas and Virginijus Siksnys},
  journal      = {FEBS Lett},
  title        = {The link between restriction endonuclease fidelity and oligomeric state: a study with Bse634I.},
  year         = {2012},
  month        = {Sep},
  number       = {19},
  pages        = {3324--3329},
  volume       = {586},
  abstract     = {Type II restriction endonucleases (REases) exist in multiple oligomeric forms. The tetrameric REases have two DNA binding interfaces and must synapse two recognition sites to achieve cleavage. It was hypothesised that binding of two recognition sites by tetrameric enzymes contributes to their fidelity. Here, we experimentally determined the fidelity for Bse634I REase in different oligomeric states. Surprisingly, we find that tetramerisation does not increase REase fidelity in comparison to the dimeric variant. Instead, an inherent ability to act concertedly at two sites provides tetrameric REase with a safety-catch to prevent host DNA cleavage if a single unmodified site becomes available.},
  creationdate = {2016-06-09T00:00:00},
  doi          = {10.1016/j.febslet.2012.07.009},
  file         = {2012_Zaremba_3324.pdf:by-author/Z/Zaremba/2012_Zaremba_3324.pdf:PDF},
  groups       = {sg/Bse634I structures, sg/Bse634I},
  institution  = {Institute of Biotechnology, Vilnius University, Vilnius, Lithuania.},
  keywords     = {Allosteric Regulation; Amino Acid Substitution; Bacteriophage Lambda; Base Sequence; Catalytic Domain; Chemistry/genetics/metabolism; DNA; Deoxyribonucleases; Genetics/metabolism; Mutagenesis; Plasmids; Protein Multimerization; Protein Structure; Quaternary; Recombinant Proteins; Site-Directed; Type II Site-Specific; Viral},
  language     = {eng},
  medline-pst  = {ppublish},
  owner        = {em},
  pii          = {S0014-5793(12)00577-7},
  pmid         = {22828280},
  timestamp    = {2016.06.09},
  url          = {http://dx.doi.org/10.1016/j.febslet.2012.07.009},
}

@Article{Zaremba2006,
  author    = {Zaremba, Mindaugas and Sasnauskas, Giedrius and Urbanke, Claus and Siksnys, Virginijus},
  journal   = {Journal of molecular biology},
  title     = {Allosteric communication network in the tetrameric restriction endonuclease Bse634I.},
  year      = {2006},
  pages     = {800--12},
  volume    = {363},
  abstract  = {Restriction endonuclease Bse634I is a homotetramer arranged as a dimer of two primary dimers. Bse634I displays its maximum catalytic efficiency upon binding of two copies of cognate DNA, one per each primary dimer. The catalytic activity of Bse634I on a single DNA copy is down-regulated due to the cross-talking interactions between the primary dimers. The mechanism of signal propagation between the individual active sites of Bse634I remains unclear. To identify communication pathways involved in the catalytic activity regulation of Bse634I tetramer we mutated a selected set of amino acid residues at the dimer-dimer interface and analysed the oligomeric state and catalytic properties of the mutant proteins. We demonstrate that alanine replacement of N262 and V263 residues located in the loop at the tetramerisation interface did not inhibit tetramer assembly but dramatically altered the catalytic properties of Bse634I despite of the distal location from the active site. Kinetic analysis using cognate hairpin oligonucleotide and one and two-site plasmids as substrates allowed us to identify two types of communication signals propagated through the dimer-dimer interface in the Bse634I tetramer: the inhibitory, or &quot;stopper&quot; and the activating, or &quot;sync&quot; signal. We suggest that the interplay between the two signals determines the catalytic and regulatory properties of the Bse634I and mutant proteins.},
  file      = {:by-author/Z/Zaremba/2006_Zaremba_800.pdf:PDF},
  groups    = {sg/Bse634I structures, sg/Bse634I},
  keywords  = {Bse634I; TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Zaremba2006a,
  author       = {Mindaugas Zaremba and Giedrius Sasnauskas and Claus Urbanke and Virginijus Siksnys},
  journal      = {J Mol Biol},
  title        = {Allosteric communication network in the tetrameric restriction endonuclease Bse634I},
  year         = {2006},
  month        = {Nov},
  number       = {4},
  pages        = {800--812},
  volume       = {363},
  abstract     = {Restriction endonuclease Bse634I is a homotetramer arranged as a dimer of two primary dimers. Bse634I displays its maximum catalytic efficiency upon binding of two copies of cognate DNA, one per each primary dimer. The catalytic activity of Bse634I on a single DNA copy is down-regulated due to the cross-talking interactions between the primary dimers. The mechanism of signal propagation between the individual active sites of Bse634I remains unclear. To identify communication pathways involved in the catalytic activity regulation of Bse634I tetramer we mutated a selected set of amino acid residues at the dimer-dimer interface and analysed the oligomeric state and catalytic properties of the mutant proteins. We demonstrate that alanine replacement of N262 and V263 residues located in the loop at the tetramerisation interface did not inhibit tetramer assembly but dramatically altered the catalytic properties of Bse634I despite of the distal location from the active site. Kinetic analysis using cognate hairpin oligonucleotide and one and two-site plasmids as substrates allowed us to identify two types of communication signals propagated through the dimer-dimer interface in the Bse634I tetramer: the inhibitory, or "stopper" and the activating, or "sync" signal. We suggest that the interplay between the two signals determines the catalytic and regulatory properties of the Bse634I and mutant proteins.},
  creationdate = {2011-06-10T00:00:00},
  doi          = {10.1016/j.jmb.2006.08.050},
  file         = {2006_Zaremba_800.pdf:by-author/Z/Zaremba/2006_Zaremba_800.pdf:PDF},
  groups       = {sg/Bse634I structures, sg/Bse634I},
  institution  = {Institute of Biotechnology, Graiciuno 8, Vilnius, LT-02241, Lithuania.},
  keywords     = {Allosteric Regulation; DNA; DNA Cleavage; DNA Restriction Enzymes; Enzyme Stability; Guanidine; Kinetics; Models; Molecular; Mutagenesis; Nucleic Acid Conformation; Plasmids; Protein Folding; Protein Structure; Quaternary; Secondary},
  owner        = {em},
  pii          = {S0022-2836(06)01089-8},
  pmid         = {16987525},
  timestamp    = {2011.06.10},
  url          = {http://dx.doi.org/10.1016/j.jmb.2006.08.050},
}

@Article{Zaremba2005,
  author    = {Zaremba, M. and Sasnauskas, G. and Urbanke, C. and Siksnys, V.},
  journal   = {Journal of molecular biology},
  title     = {Conversion of the tetrameric restriction endonuclease Bse634I into a dimer: oligomeric structure-stability-function correlations.},
  year      = {2005},
  pages     = {459--78},
  volume    = {348},
  abstract  = {The Bse634I restriction endonuclease is a tetramer and belongs to the type IIF subtype of restriction enzymes. It requires two recognition sites for its optimal activity and cleaves plasmid DNA with two sites much faster than a single-site DNA. We show that disruption of the tetramerisation interface of Bse634I by site-directed mutagenesis converts the tetrameric enzyme into a dimer. Dimeric W228A mutant cleaves plasmid DNA containing one or two sites with the same efficiency as the tetramer cleaves the two-site plasmid. Hence, the catalytic activity of the Bse634I tetramer on a single-site DNA is down-regulated due to the cross-talking interactions between the individual dimers. The autoinhibition within the Bse634I tetramer is relieved by bridging two DNA copies into the synaptic complex that promotes fast and concerted cleavage at both sites. Cleavage analysis of the oligonucleotide attached to the solid support revealed that Bse634I is able to form catalytically competent synaptic complexes by bridging two molecules of the cognate DNA, cognate DNA-miscognate DNA and cognate DNA-product DNA. Taken together, our data demonstrate that a single W228A mutation converts a tetrameric type IIF restriction enzyme Bse634I into the orthodox dimeric type IIP restriction endonuclease. However, the stability of the dimer towards chemical denaturants, thermal inactivation and proteolytic degradation are compromised.},
  file      = {:by-author/Z/Zaremba/2005_Zaremba_459.pdf:PDF},
  groups    = {sg/Bse634I structures, sg/Bse634I},
  keywords  = {Bse634I; TypeII},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Zaremba2005a,
  author      = {M. Zaremba and G. Sasnauskas and C. Urbanke and V. Siksnys},
  journal     = {J Mol Biol},
  title       = {Conversion of the tetrameric restriction endonuclease Bse634I into a dimer: oligomeric structure-stability-function correlations},
  year        = {2005},
  month       = {Apr},
  number      = {2},
  pages       = {459--478},
  volume      = {348},
  abstract    = {The Bse634I restriction endonuclease is a tetramer and belongs to the type IIF subtype of restriction enzymes. It requires two recognition sites for its optimal activity and cleaves plasmid DNA with two sites much faster than a single-site DNA. We show that disruption of the tetramerisation interface of Bse634I by site-directed mutagenesis converts the tetrameric enzyme into a dimer. Dimeric W228A mutant cleaves plasmid DNA containing one or two sites with the same efficiency as the tetramer cleaves the two-site plasmid. Hence, the catalytic activity of the Bse634I tetramer on a single-site DNA is down-regulated due to the cross-talking interactions between the individual dimers. The autoinhibition within the Bse634I tetramer is relieved by bridging two DNA copies into the synaptic complex that promotes fast and concerted cleavage at both sites. Cleavage analysis of the oligonucleotide attached to the solid support revealed that Bse634I is able to form catalytically competent synaptic complexes by bridging two molecules of the cognate DNA, cognate DNA-miscognate DNA and cognate DNA-product DNA. Taken together, our data demonstrate that a single W228A mutation converts a tetrameric type IIF restriction enzyme Bse634I into the orthodox dimeric type IIP restriction endonuclease. However, the stability of the dimer towards chemical denaturants, thermal inactivation and proteolytic degradation are compromised.},
  doi         = {10.1016/j.jmb.2005.02.037},
  file        = {2005_Zaremba_459.pdf:by-author/Z/Zaremba/2005_Zaremba_459.pdf:PDF},
  groups      = {sg/Bse634I structures, sg/Bse634I},
  institution = {Institute of Biotechnology, Graiciuno 8, Vilnius LT-02241, Lithuania.},
  keywords    = {Chromatography; DNA; DNA Restriction Enzymes; Dimerization; Enzyme Stability; Gel; Geobacillus Stearothermophilus; Models; Molecular; Mutation; Plasmids; Protein Denaturation; Protein Folding; Protein Structure; Quaternary; Temperature; Tryptophan; Ultracentrifugation},
  owner       = {em},
  pii         = {S0022-2836(05)00203-2},
  pmid        = {15811381},
  timestamp = {2011.06.10},
  creationdate = {2011-06-10T00:00:00},
  url         = {http://dx.doi.org/10.1016/j.jmb.2005.02.037},
}

@Article{Zaremba2014,
  author      = {Mindaugas Zaremba and Paulius Toliusis and Rokas Grigaitis and Elena Manakova and Arunas Silanskas and Giedre Tamulaitiene and Mark D Szczelkun and Virginijus Siksnys},
  journal     = {Nucleic Acids Res},
  title       = {DNA cleavage by CgII and NgoAVII requires interaction between N- and R-proteins and extensive nucleotide hydrolysis.},
  year        = {2014},
  pages       = {13887--13896},
  volume      = {42},
  abstract    = {The stress-sensitive restriction-modification (RM) system CglI from Corynebacterium glutamicum and the homologous NgoAVII RM system from Neisseria gonorrhoeae FA1090 are composed of three genes: a DNA methyltransferase (M.CglI and M.NgoAVII), a putative restriction endonuclease (R.CglI and R.NgoAVII, or R-proteins) and a predicted DEAD-family helicase/ATPase (N.CglI and N.NgoAVII or N-proteins). Here we report a biochemical characterization of the R- and N-proteins. Size-exclusion chromatography and SAXS experiments reveal that the isolated R.CglI, R.NgoAVII and N.CglI proteins form homodimers, while N.NgoAVII is a monomer in solution. Moreover, the R.CglI and N.CglI proteins assemble in a complex with R2N2 stoichiometry. Next, we show that N-proteins have ATPase activity that is dependent on double-stranded DNA and is stimulated by the R-proteins. Functional ATPase activity and extensive ATP hydrolysis (∼170 ATP/s/monomer) are required for site-specific DNA cleavage by R-proteins. We show that ATP-dependent DNA cleavage by R-proteins occurs at fixed positions (6-7 nucleotides) downstream of the asymmetric recognition sequence 5'-GCCGC-3'. Despite similarities to both Type I and II restriction endonucleases, the CglI and NgoAVII enzymes may employ a unique catalytic mechanism for DNA cleavage.},
  doi         = {10.1093/nar/gku1236},
  file        = {:by-author/Z/Zaremba/2014_Zaremba_13887.pdf:PDF},
  institution = {Department of Protein-DNA Interactions, Institute of Biotechnology, Vilnius University, Graiciuno 8, LT-02241 Vilnius, Lithuania siksnys@ibt.lt.},
  keywords    = {CglI; NgoAVII; Restriction Endonuclease (RE); Restriction Endonucleases (REases); SAXS},
  language    = {eng},
  medline-pst = {ppublish},
  owner       = {em},
  pii         = {gku1236},
  pmid        = {25429977},
  timestamp = {2015.01.21},
  creationdate = {2015-01-21T00:00:00},
  url         = {http://dx.doi.org/10.1093/nar/gku1236},
}

@Article{Zaremba2004,
  author    = {Zaremba, Mindaugas and Urbanke, Claus and Halford, Stephen E and Siksnys, Virginijus},
  journal   = {Journal of molecular biology},
  title     = {Generation of the BfiI restriction endonuclease from the fusion of a DNA recognition domain to a non-specific nuclease from the phospholipase D superfamily.},
  year      = {2004},
  pages     = {81--92},
  volume    = {336},
  abstract  = {The BfiI endonuclease cleaves DNA at fixed positions downstream of an asymmetric sequence. Unlike other restriction enzymes, it functions without metal ions. The N-terminal half of BfiI is similar to Nuc, an EDTA-resistant nuclease from Salmonella typhimurium that belongs to the phosphoplipase D superfamily. Nuc is a dimer with one active site at its subunit interface, as is BfiI, but it cuts DNA non-specifically. BfiI was cleaved by thermolysin into an N-terminal domain, which forms a dimer with non-specific nuclease activity, and a C-terminal domain, which lacks catalytic activity but binds specifically to the recognition sequence as a monomer. On denaturation with guanidinium, BfiI underwent two unfolding transitions: one at a relatively low concentration of guanidinium, to a dimeric non-specific nuclease; a second at a higher concentration, to an inactive monomer. The isolated C-terminal domain unfolded at the first (relatively low) concentration, the isolated N-terminal at the second. Hence, BfiI consists of two physically separate domains, with catalytic and dimerisation functions in the N terminus and DNA recognition functions in the C terminus. It is the first example of a restriction enzyme generated by the evolutionary fusion of a DNA recognition domain to a phosphodiesterase from the phospholipase D superfamily. BfiI may consist of three structural units: a stable central core with the active site, made from two copies of the N-terminal domain, flanked by relatively unstable C-terminal domains, that each bind a copy of the recognition sequence.},
  file      = {Zaremba_2004_81-bfiI_domains.pdf:by-author/Z/Zaremba/2004_Zaremba_81.pdf:PDF},
  keywords  = {BfiI; TypeII},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Zarrin2007,
  author    = {Zarrin, Ali A. and Del Vecchio, Catherine and Tseng, Eva and Gleason, Megan and Zarin, Payam and Tian, Ming and Alt, Frederick W.},
  journal   = {Science (New York, N.Y.)},
  title     = {Antibody class switching mediated by yeast endonuclease-generated DNA breaks.},
  year      = {2007},
  pages     = {377--81},
  volume    = {315},
  abstract  = {Antibody class switching in activated B cells uses class switch recombination (CSR), which joins activation-induced cytidine deaminase (AID)-dependent double-strand breaks (DSBs) within two large immunoglobulin heavy chain (IgH) locus switch (S) regions that lie up to 200 kilobases apart. To test postulated roles of S regions and AID in CSR, we generated mutant B cells in which donor Smu and accepter Sgamma1 regions were replaced with yeast I-SceI endonuclease sites. We found that site-specific I-SceI DSBs mediate recombinational IgH locus class switching from IgM to IgG1 without S regions or AID. We propose that CSR evolved to exploit a general DNA repair process that promotes joining of widely separated DSBs within a chromosome.},
  file      = {:by-author/Z/Zarrin/2007_Zarrin_377.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Zarychta2007,
  author    = {Zarychta, Bartosz and Pichon-Pesme, Virginie and Guillot, Benoît and Lecomte, Claude and Jelsch, Christian},
  journal   = {Acta crystallographica. Section A, Foundations of crystallography},
  title     = {On the application of an experimental multipolar pseudo-atom library for accurate refinement of small-molecule and protein crystal structures.},
  year      = {2007},
  pages     = {108--25},
  volume    = {63},
  abstract  = {With an increasing number of biomacromolecular crystal structures being measured to ultra-high resolution, it has become possible to extend to large systems experimental charge-density methods that are usually applied to small molecules. A library has been built of average multipole populations describing the electron density of chemical groups in all 20 amino acids found in proteins. The library uses the Hansen &amp; Coppens multipolar pseudo-atom model to derive molecular electron density and electrostatic potential distributions. The library values are obtained from several small peptide or amino acid crystal structures refined against ultra-high-resolution X-ray diffraction data. The library transfer is applied automatically in the MoPro software suite to peptide and protein structures measured at atomic resolution. The transferred multipolar parameters are kept fixed while the positional and thermal parameters are refined. This enables a proper deconvolution of thermal motion and valence-electron-density redistributions, even when the diffraction data do not extend to subatomic resolution. The use of the experimental library multipolar atom model (ELMAM) also has a major impact on crystallographic structure modelling in the case of small-molecule crystals at atomic resolution. Compared to a spherical-atom model, the library transfer results in a more accurate crystal structure, notably in terms of thermal displacement parameters and bond distances involving H atoms. Upon transfer, crystallographic statistics of fit are improved, particularly free R factors, and residual electron-density maps are cleaner.},
  doi       = {10.1107/S0108767306053748},
  file      = {:by-author/Z/Zarychta/2007_Zarychta_108.pdf:PDF},
  keywords  = {Protein Crystallography; Ultra High Resolution; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2013.02.12},
  creationdate = {2013-02-12T00:00:00},
}

@Article{Zass1996,
  author    = {Zass, Engelbert},
  journal   = {Journal of Chemical Information and Computer Sciences},
  title     = {From Handbooks to Databases on the Net:  New Solutions and Old Problems in Information Retrieval for Chemists},
  year      = {1996},
  pages     = {942--948},
  volume    = {36},
  abstract  = {Sources for chemical information are becoming ever more powerful and varied:  besides the still important printed sources, there are public databases, large in-house systems, and databases on PCs/CD-ROMs. The price to pay for this information cornucopia, however, is increased complexity for users. Improved front-ends and the change from terminal-mainframe to client-server systems ease the burden of searching, but such means are not yet sufficient to make chemical information retrieval a reliable routine operation of every chemist. We need even more improved database quality, better goal-oriented marketing and training by producers and hosts, and problem-oriented education for chemical information retrieval as an obligatory part of chemistry syllabi.},
  doi       = {10.1021/ci950249d},
  file      = {:by-author/Z/Zass/1996_Zass_942.pdf:PDF},
  keywords  = {Chemical Databases},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
  url       = {http://pubs.acs.org/doi/abs/10.1021/ci950249d},
}

@Article{Zavadova2005,
  author    = {Zavadova, Zuzana and Zavada, Jan},
  journal   = {Oncology reports},
  title     = {Carbonic anhydrase IX (CA IX) mediates tumor cell interactions with microenvironment.},
  year      = {2005},
  pages     = {977--82},
  volume    = {13},
  abstract  = {Expression of CA IX is normally restricted to the mucosa of alimentary tract, but on the other hand, it takes place in a high percentage of human cancers derived from tissues which are normally CA IX-negative. It is a transmembrane protein with two extracellular domains: carbonic anhydrase (CA) with a high catalytic activity and a proteoglycan-like segment (PG), mediating cell-cell adhesion. Both CA and PG domains interact with the microenvironment and they could play a role in tumorigenesis, but their roles are poorly understood. The present work characterizes some newly recognized properties of the PG. One of them is a prevalently negative charge, caused by a high proportion of dicarboxylic amino acids. This is reflected by easy dissociation of complexes formed by PG either with monoclonal antibody M75 or with the cell surface receptor already at slightly acidic pH. This property might facilitate separation of cells from the primary tumor. Released cells may subsequently attach elsewhere in the organism and eventually start metastatic growth. Another aim of the present study was to identify human tumor cell lines which are expressing the presumed CA IX receptor molecule. The same cell lines were also tested for the presence of CA IX protein; we found that expression of CA IX and of the receptor is independent of each other. In addition, we examined the species specificity of CA IX receptors. The PG domain, which contains the epitope of mAb M75 -PGEEDLP- overlapping with the binding site for putative receptor is relatively conserved in evolution: human and rat CA IX cross-react with M75 antibody on western blots. Consistently with this, human and rat cells can attach to purified human CA IX protein. On the other hand, murine CA IX contains an entirely different equivalent of PG sequence and it does not react with M75 antibody or attach to human CA IX protein. This is suggestive of the co-evolution of CA IX protein together with its receptor.},
  file      = {2005_Zavadova_977.pdf:by-author/Z/Zavadova/2005_Zavadova_977.pdf:PDF},
  groups    = {sg/cancer, sg/hCA9},
  keywords  = {CA9; Carbonic Anhydrases},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Zechner1992,
  author    = {Zechner, E. L. and Wu, C. A. and Marians, K. J.},
  journal   = {The Journal of biological chemistry},
  title     = {Coordinated leading- and lagging-strand synthesis at the Escherichia coli DNA replication fork. III. A polymerase-primase interaction governs primer size.},
  year      = {1992},
  pages     = {4054--63},
  volume    = {267},
  abstract  = {Studies with a rolling-circle DNA replication system reconstituted in vitro with a tailed form II DNA template, the DNA polymerase III holoenzyme (Pol III HE), the Escherichia coli single-stranded DNA binding protein, and the primosome, showed that within the context of a replication fork, the oligoribonucleotide primers that were formed were limited to a length in the range of 9 to 14 nucleotides, regardless of whether they were subsequently elongated by the lagging-strand DNA polymerase. This is in contrast to the 8-60-nucleotide-long primers synthesized by the primosome in the absence of DNA replication on a bacteriophage phi X174 DNA template, although when primer synthesis and DNA replication were catalyzed concurrently in this system, the extent of RNA polymerization decreased. As described in this report, we therefore examined the effect of the DNA Pol III HE on the length of primers synthesized by primase in vitro in the absence of DNA replication. When primer synthesis was catalyzed either: i) by the primosome on a phi X174 DNA template, ii) by primase on naked DNA with the aid of the DnaB protein (general priming), or iii) by primase alone at the bacteriophage G4 origin, the presence of the DNA Pol III HE in the reaction mixtures resulted in a universal reduction in the length of the heterogeneous RNA products to a uniform size of approximately 10 nucleotides. dNTPs were not required, and the addition of dGMP, an inhibitor of the 3'----5' exonuclease of the DNA Pol III HE, did not alter the effect; therefore, neither the 5'----3' DNA polymerase activity nor the 3'----5' exonuclease activity of the DNA Pol III HE was involved. E. coli DNA polymerase I, and the DNA polymerases of bacteriophages T4 and T7 could not substitute for the DNA Pol III HE. The Pol III core plays a crucial role in mediating this effect, although other subunits of the DNA Pol III HE are also required. These observations suggest that the association of primase with the DNA Pol III HE during primer synthesis regulates its catalytic activity and that this regulatory interaction occurs independently of, and prior to, formation of a preinitiation complex of the DNA Pol III HE on the primer terminus.},
  file      = {:by-author/Z/Zechner/1992_Zechner_4054.pdf:PDF},
  keywords  = {Ecoli; {gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Zeh1993,
  author    = {H. D. Zeh},
  title     = {There are no Quantum Jumps, nor are there Particles!},
  year      = {1993},
  pages     = {preprint},
  abstract  = {Quantum theory does not require the existence of discontinuities: neither in time (quantum jumps), nor in space (particles), nor in spacetime (quantum events). These apparent discontinuities are readily described objectively by the continuous process of decoherence occurring locally on a very short time scale according to the Schršdinger equation for interacting systems, while the observerÕs Ôincrease of informationÕ is appropriately represented by the resulting dynamical decoupling of the corresponding components of the global wave function.},
  file      = {:by-author/Z/Zeh/1993_Zeh_preprint.pdf:PDF},
  keywords  = {Quantum Mechanics (QM)},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Zelikovich1995,
  author    = {Zelikovich, Lior and Libman, Jacqueline and Shanzer, Abraham},
  journal   = {Nature},
  title     = {Molecular redox switches based on chemical triggering of iron translocation in triple-stranded helical complexes},
  year      = {1995},
  pages     = {790--792},
  volume    = {374},
  copyright = {© 1995 Nature Publishing Group},
  doi       = {10.1038/374790a0},
  file      = {Zelikovich et al. - 1995 - Molecular redox switches based on chemical trigger.pdf:by-author/Z/Zelikovich/1995_Zelikovich_790.pdf:application/pdf;Snapshot:by-author/Z/Zelikovich/1995_Zelikovich_790.html:text/html},
  groups    = {sg/chemical, sg/electronics},
  language  = {en},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://www.nature.com/nature/journal/v374/n6525/abs/374790a0.html},
  urldate   = {2015-08-26},
}

@Article{Zeng1994,
  author           = {Zeng, G.-F. and Qin, M. and Lin, Y.-H. and Xi, S.-Q.},
  journal          = {Acta Crystallographica Section C},
  title            = {Tribenzylammonium dibenzylammonium tetrachlorocuprate},
  year             = {1994},
  pages            = {200--202},
  volume           = {50},
  creationdate     = {2013-04-08T00:00:00},
  doi              = {10.1107/S0108270193007735},
  file             = {:by-author/Z/Zeng/1994_Zeng_200.pdf:PDF},
  keywords         = {CIF; CIF Files},
  modificationdate = {2023-08-07T10:23:05},
  owner            = {antanas},
  timestamp        = {2013.04.08},
  url              = {http://dx.doi.org/10.1107/S0108270193007735},
}

@Article{Zewail2010,
  author    = {Zewail, Ahmed},
  journal   = {Nature},
  title     = {Curiouser and curiouser: managing discovery making.},
  year      = {2010},
  pages     = {347},
  volume    = {468},
  file      = {:by-author/Z/Zewail/2010_Zewail_347.pdf:PDF},
  keywords  = {Science Policy},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@InProceedings{Zhang2006a,
  author    = {Zhang, Donghui and Du, Yang and Xia, Tian and Tao, Yufei},
  booktitle = {Proceedings of the 32nd international conference on Very large data bases},
  title     = {Progressive Computation Of The Min-dist Optimal-location Query},
  year      = {2006},
  pages     = {643--654},
  publisher = {VLDB Endowment},
  series    = {VLDB '06},
  abstract  = {This paper proposes and solves the min-dist optimal-location query in spatial databases. Given a set S of sites, a set O of weighted objects, and a spatial region Q, the min-dist optimal-location query returns a location in Q which, if a new site is built there, minimizes the average distance from each object to its closest site. This query can help a franchise (e.g. McDonald’s) decide where to put a new store in order to maximize the benefit to its customers. To solve this problem is challenging, for there are theoretically infinite number of locations in Q, all of which could be candidates. This paper first provides a theorem that limits the number of candidate locations without losing the power to find exact answers. Then it provides a progressive algorithm that quickly suggests a location, tells the maximum error it may have, and keeps refining the result. When the algorithm finishes, the exact answer can be found. The intermediate result of early runs can be used to prune the search space for later runs. Crucial to the pruning technique are novel lower-bound estimators. The proposed algorithm, the effect of several optimizations, and the progressiveness are experimentally evaluated.},
  file      = {:by-author/Z/Zhang/2006_Zhang_643.pdf:PDF},
  location  = {Seoul, Korea},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dl.acm.org/citation.cfm?id=1182635.1164183},
}

@InProceedings{Zhang2004a,
  author    = {Zhang, Donghui and Xia, Tian},
  booktitle = {Proceedings of the 12th annual ACM international workshop on Geographic information systems},
  title     = {A Novel Improvement to the R*-tree Spatial Index using Gain/Loss Metrics},
  year      = {2004},
  address   = {New York, NY, USA},
  pages     = {204--213},
  publisher = {ACM},
  series    = {GIS '04},
  abstract  = {The R*-tree is a state-of-the-art spatial index structure. It has already found its way into commercial systems. The most important improvement of the R*-tree over the original R-tree is that it utilizes forced reinsertion. That is, if a disk page overflows, some objects are removed from the page and reinserted into the index. The goals are: (a) to reduce the MBR area; and (b) to keep the shape of the MBR close to a square. However, no existing work consists of a unified metric which can be used to balance the two criteria. For example, if there are two methods to remove objects from a rectangle, and one results in a rectangle with smaller area, while the other results in a square with slightly larger area, which method shall we choose? The R*-tree algorithm selects objects whose distances to the center of the page's MBR are the largest. However, this is not optimal. In this paper, we formally define the quality of a rectangle and the gain to shrink a rectangle. Then we provide algorithms to shrink the MBRs with the goal to maximize the gain. The algorithms are experimentally compared with the R*-tree's reinsertion algorithm. Furthermore, as the opposite of gain, we define the loss of expanding a rectangle. While inserting an object into the R*-tree, we need to choose a sub-tree to put the object in. With the new metric, we can choose the sub-tree with the least loss. Finally, we integrate the new algorithms into the R*-tree.},
  doi       = {10.1145/1032222.1032253},
  file      = {:by-author/Z/Zhang/2004_Zhang_204.pdf:PDF},
  isbn      = {1-58113-979-9},
  location  = {Washington DC, USA},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://doi.acm.org/10.1145/1032222.1032253},
}

@Manuscript{Zhang,
  author    = {Hantao Zhang and Xin Hua},
  title     = {Proving Ramsey's Theorem by the Cover Set Induction: A Case and Comparison Study},
  keywords  = {Automated Reasoning; Computer Science (CS); Cover Set Induction; Program Verification},
  file      = {:by-author/Z/Zhang/XXXX_Zhang.dvi:DVI},
  owner     = {saulius},
  timestamp = {2015.03.03},
  creationdate = {2015-03-03T00:00:00},
}

@Manuscript{Zhanga,
  author    = {Hantao Zhang and Zin Hua},
  title     = {Proving the Chinese Reminder Theorem by the Cover Set Induction},
  keywords  = {Automated Reasoning; Computer Science (CS); Cover Set Induction; Program Verification},
  file      = {:by-author/Z/Zhang/XXXX_Zhang_a.dvi:DVI},
  owner     = {saulius},
  timestamp = {2015.03.03},
  creationdate = {2015-03-03T00:00:00},
}

@Article{Zhang2011,
  author    = {Zhang, Jian and Liang, Yu and Zhang, Yang},
  journal   = {Structure (London, England : 1993)},
  title     = {Atomic-level protein structure refinement using fragment-guided molecular dynamics conformation sampling.},
  year      = {2011},
  number    = {12},
  pages     = {1784--1795},
  volume    = {19},
  abstract  = {One of critical difficulties of molecular dynamics (MD) simulations in protein structure refinement is that the physics-based energy landscape lacks a middle-range funnel to guide nonnative conformations toward near-native states. We propose to use the target model as a probe to identify fragmental analogs from PDB. The distance maps are then used to reshape the MD energy funnel. The protocol was tested on 181 benchmarking and 26 CASP targets. It was found that structure models of correct folds with TM-score &gt;0.5 can be often pulled closer to native with higher GDT-HA score, but improvement for the models of incorrect folds (TM-score &lt;0.5) are much less pronounced. These data indicate that template-based fragmental distance maps essentially reshaped the MD energy landscape from golf-course-like to funnel-like ones in the successfully refined targets with a radius of TM-score ∼0.5. These results demonstrate a new avenue to improve high-resolution structures by combining knowledge-based template information with physics-based MD simulations.},
  doi       = {10.1016/j.str.2011.09.022},
  file      = {:by-author/Z/Zhang/2011_Zhang_1784.pdf:pdf},
  keywords  = {Structure Refinement; Validation; X-ray Crystallography},
  mid       = {NIHMS331932},
  owner     = {saulius},
  pii       = {S0969-2126(11)00337-6},
  pmc       = {PMC3240822},
  pubmed    = {22153501},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Article{Zhang2012,
  author    = {Zhang, Jing and Rouillon, Christophe and Kerou, Melina and Reeks, Judith and Brugger, Kim and Graham, Shirley and Reimann, Julia and Cannone, Giuseppe and Liu, Huanting and Albers, Sonja-Verena and Naismith, James H. and Spagnolo, Laura and White, Malcolm F.},
  journal   = {Mol. Cell},
  title     = {Structure and Mechanism of the CMR Complex for CRISPR-Mediated Antiviral Immunity},
  year      = {2012},
  pages     = {303–313},
  volume    = {45},
  abstract  = {The prokaryotic clusters of regularly interspaced palindromic repeats (CRISPR) system utilizes ge- nomically encoded CRISPR RNA (crRNA), derived from invading viruses and incorporated into ribonu- cleoprotein complexes with CRISPR-associated (CAS) proteins, to target and degrade viral DNA or RNA on subsequent infection. RNA is targeted by the CMR complex. In Sulfolobus solfataricus, this complex is composed of seven CAS protein subunits (Cmr1-7) and carries a diverse ‘‘payload’’ of targeting crRNA. The crystal structure of Cmr7 and low-resolu- tion structure of the complex are presented. S. solfataricus CMR cleaves RNA targets in an endo- nucleolytic reaction at UA dinucleotides. This activity is dependent on the 8 nt repeat-derived 50 sequence in the crRNA, but not on the presence of a proto- spacer-associated motif (PAM) in the target. Both target and guide RNAs can be cleaved, although a single molecule of guide RNA can support the degra- dation of multiple targets.},
  doi       = {10.1016/j.molcel.2011.12.013},
  file      = {:by-author/Z/Zhang/2012_Zhang_303.pdf:PDF},
  groups    = {sg/CRISPR-Cas},
  keywords  = {CRISPR; Cas Complex; Cmr Complex; Cmr7; EM Structure; RNA Cleavage},
  owner     = {em},
  timestamp = {2013.10.01},
  creationdate = {2013-10-01T00:00:00},
}

@Article{Zhang2017a,
  author    = {Miao Zhang and Lin Liu and Teng He and Zhao Li and Guotao Wu and Ping Chen},
  journal   = {Chemistry - An Asian Journal},
  title     = {Microporous Crystalline $\upgamma$-Al2 O3 Replicated from Microporous Covalent Triazine Framework and Its Application as Support for Catalytic Hydrolysis of Ammonia Borane},
  year      = {2017},
  month     = {jan},
  comment   = {Contains synthesis descriptin but seems complicated (S.G.)},
  doi       = {10.1002/asia.201601631},
  file      = {:by-author/Z/Zhang/2017_Zhang.pdf:PDF},
  groups    = {sg/MOF, sg/MOFs, am/MOFs},
  keywords  = {Synthesis},
  owner     = {saulius},
  publisher = {Wiley-Blackwell},
  timestamp = {2017.01.31},
  creationdate = {2017-01-31T00:00:00},
  url       = {https://doi.org/10.1002%2Fasia.201601631},
}

@InProceedings{Zhang2007,
  author    = {Zhang, Wei and Xue, Xiangyang and Sun, Zichen and Guo, Yue-Fei and Lu, Hong},
  booktitle = {Proceedings of the 24th international conference on Machine learning},
  title     = {Optimal Dimensionality of Metric Space for Classification},
  year      = {2007},
  address   = {New York, NY, USA},
  pages     = {1135--1142},
  publisher = {ACM},
  series    = {ICML '07},
  abstract  = {In many real-world applications, Euclidean distance in the original space is not good due to the curse of dimensionality. In this paper, we propose a new method, called Discriminant Neighborhood Embedding (DNE), to learn an appropriate metric space for classification given finite training samples. We define a discriminant adjacent matrix in favor of classification task, i.e., neighboring samples in the same class are squeezed but those in different classes are separated as far as possible. The optimal dimensionality of the metric space can be estimated by spectral analysis in the proposed method, which is of great significance for high-dimensional patterns. Experiments with various datasets demonstrate the effectiveness of our method.},
  doi       = {10.1145/1273496.1273639},
  file      = {:by-author/Z/Zhang/2007_Zhang_1135.pdf:PDF},
  isbn      = {978-1-59593-793-3},
  location  = {Corvalis, Oregon},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://doi.acm.org/10.1145/1273496.1273639},
}

@Article{Zhang2006,
  author    = {Zhang, Xiaodong and Bruice, Thomas C.},
  journal   = {Proceedings of the National Academy of Sciences of the United States of America},
  title     = {The mechanism of M.HhaI DNA C5 cytosine methyltransferase enzyme: a quantum mechanics/molecular mechanics approach.},
  year      = {2006},
  pages     = {6148--53},
  volume    = {103},
  abstract  = {The mechanism of DNA cytosine-5-methylation catalyzed by the bacterial M.HhaI enzyme has been considered as a stepwise nucleophilic addition of Cys-81-S- to cytosine C6 followed by C5 nucleophilic replacement of the methyl of S-adenosyl-L-methionine to produce 5-methyl-6-Cys-81-S-5,6-dihydrocytosine. In this study, we show that the reaction is concerted from a series of energy calculations by using the quantum mechanical/molecular mechanical hybrid method. Deprotonation of 5-methyl-6-Cys-81-S-5,6-dihydrocytosine and expulsion of Cys-81-S- provides the product DNA 5-methylcytosine. A required base catalyst for this deprotonation is not available as a member of the active site structure. A water channel between the active site and bulk water allows entrance of solvent to the active site. Hydroxide at 10(-7) mole fraction (pH = 7) is shown to be sufficient for the required catalysis. We also show that Glu-119-CO2H can divert the reaction by protonating cytosine N3 when Cys-81-S- attacks cytosine, to form the 6-Cys-81-S-3-hydrocytosine. The reactants and 6-Cys-81-S-3-hydrocytosine product are in rapid equilibrium, and this explains the observed hydrogen exchange of cytosine with solvent.},
  file      = {:by-author/Z/Zhang/2006_Zhang_6148.pdf:PDF},
  keywords  = {HhaI},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Zhang2014,
  author    = {Zhang, Xizhe and Li, Haitang and Burnett, John C. and Rossi, John J.},
  journal   = {RNA},
  title     = {The role of antisense long noncoding RNA in small RNA-triggered gene activation},
  year      = {2014},
  issn      = {1469-9001},
  month     = {Oct},
  number    = {12},
  pages     = {1916–1928},
  volume    = {20},
  doi       = {10.1261/rna.043968.113},
  file      = {2014_Zhang_1916.pdf:by-author/Z/Zhang/2014_Zhang_1916.pdf:PDF},
  groups    = {am/RNA activation},
  owner     = {andrius},
  publisher = {Cold Spring Harbor Laboratory Press},
  timestamp = {2016.10.03},
  creationdate = {2016-10-03T00:00:00},
  url       = {http://dx.doi.org/10.1261/rna.043968.113},
}

@Article{Zhang2017,
  author    = {Zhang, Yorke and Lamb, Brian M. and Feldman, Aaron W. and Zhou, Anne Xiaozhou and Lavergne, Thomas and Li, Lingjun and Romesberg, Floyd E.},
  journal   = {Proceedings of the National Academy of Sciences},
  title     = {A semisynthetic organism engineered for the stable expansion of the genetic alphabet},
  year      = {2017},
  issn      = {1091-6490},
  month     = {Jan},
  pages     = {201616443},
  abstract  = {All natural organisms store genetic information in a four-letter, two- base-pair genetic alphabet. The expansion of the genetic alphabet with two synthetic unnatural nucleotides that selectively pair to form an unnatural base pair (UBP) would increase the information storage potential of DNA, and semisynthetic organisms (SSOs) that stably harbor this expanded alphabet would thereby have the potential to store and retrieve increased information. Toward this goal, we previously reported that Escherichia coli grown in the presence of the unnatural nucleoside triphosphates dNaMTP and d5SICSTP, and provided with the means to import them via expres- sion of a plasmid-borne nucleoside triphosphate transporter, repli- cates DNA containing a single dNaM-d5SICS UBP. Although this represented an important proof-of-concept, the nascent SSO grew poorly and, more problematically, required growth under controlled conditions and even then was unable to indefinitely store the unnat- ural information, which is clearly a prerequisite for true semisynthetic life. Here, to fortify and vivify the nascent SSO, we engineered the transporter, used a more chemically optimized UBP, and harnessed the power of the bacterial immune response by using Cas9 to elimi- nate DNA that had lost the UBP. The optimized SSO grows robustly, constitutively imports the unnatural triphosphates, and is able to in- definitely retain multiple UBPs in virtually any sequence context. This SSO is thus a form of life that can stably store genetic information using a six-letter, three-base-pair alphabet.},
  doi       = {10.1073/pnas.1616443114},
  file      = {2017_Zhang_201616443.pdf:by-author/Z/Zhang/2017_Zhang_201616443.pdf:PDF},
  keywords  = {Artificial Bases; DNA; Origin of Life},
  owner     = {saulius},
  publisher = {Proceedings of the National Academy of Sciences},
  timestamp = {2017.01.27},
  creationdate = {2017-01-27T00:00:00},
  url       = {http://dx.doi.org/10.1073/pnas.1616443114},
}

@Article{Zhang2005a,
  author    = {Zhang, Yang and Skolnick, Jeffrey},
  journal   = {Nucleic acids research},
  title     = {TM-align: a protein structure alignment algorithm based on the TM-score.},
  year      = {2005},
  pages     = {2302--9},
  volume    = {33},
  abstract  = {We have developed TM-align, a new algorithm to identify the best structural alignment between protein pairs that combines the TM-score rotation matrix and Dynamic Programming (DP). The algorithm is approximately 4 times faster than CE and 20 times faster than DALI and SAL. On average, the resulting structure alignments have higher accuracy and coverage than those provided by these most often-used methods. TM-align is applied to an all-against-all structure comparison of 10 515 representative protein chains from the Protein Data Bank (PDB) with a sequence identity cutoff &lt;95%: 1996 distinct folds are found when a TM-score threshold of 0.5 is used. We also use TM-align to match the models predicted by TASSER for solved non-homologous proteins in PDB. For both folded and misfolded models, TM-align can almost always find close structural analogs, with an average root mean square deviation, RMSD, of 3 A and 87% alignment coverage. Nevertheless, there exists a significant correlation between the correctness of the predicted structure and the structural similarity of the model to the other proteins in the PDB. This correlation could be used to assist in model selection in blind protein structure predictions. The TM-align program is freely downloadable at http://bioinformatics.buffalo.edu/TM-align.},
  file      = {:by-author/Z/Zhang/2005_Zhang_2302.pdf:PDF},
  keywords  = {Protein Bioinformatics; Structure Comparison},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Zhang2004,
  author    = {Zhang, Yongli and Xi, Zhiqun and Hegde, Rashmi S. and Shakked, Zippora and Crothers, Donald M.},
  journal   = {Proceedings of the National Academy of Sciences of the United States of America},
  title     = {Predicting indirect readout effects in protein-DNA interactions.},
  year      = {2004},
  pages     = {8337--41},
  volume    = {101},
  abstract  = {Recognition of DNA by proteins relies on direct interactions with specific DNA-functional groups, along with indirect effects that reflect variable energetics in the response of DNA sequences to twisting and bending distortions induced by proteins. Predicting indirect readout requires knowledge of the variations in DNA curvature and flexibility in the affected region, which we have determined for a series of DNA-binding sites for the E2 regulatory protein by using the cyclization kinetics method. We examined 16 sites containing different noncontacted spacer sequences, which vary by more than three orders of magnitude in binding affinity. For 15 of these sites, the variation in affinity was predicted within a factor of 3, by using experimental curvature and flexibility values and a statistical mechanical theory. The sole exception was traced to differential magnesium ion binding.},
  file      = {:by-author/Z/Zhang/2004_Zhang_8337.pdf:PDF},
  keywords  = {DNA Protein; Readout},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Zhang2005,
  author    = {Zhang, Zhiquan and Spiering, Michelle M. and Trakselis, Michael A. and Ishmael, Faoud T. and Xi, Jun and Benkovic, Stephen J. and Hammes, Gordon G.},
  journal   = {Proceedings of the National Academy of Sciences of the United States of America},
  title     = {Assembly of the bacteriophage T4 primosome: single-molecule and ensemble studies.},
  year      = {2005},
  pages     = {3254--9},
  volume    = {102},
  abstract  = {Within replisomes for DNA replication, the primosome is responsible for unwinding double-stranded DNA and synthesizing RNA primers. Assembly of the bacteriophage T4 primosome on individual molecules of ssDNA or forked DNA (fDNA) has been studied by using FRET microscopy. On either DNA substrate, an ordered process of assembly begins with tight 1:1 binding of ssDNA-binding protein (gp32) and helicase-loading protein (gp59) to the DNA. Magnesium adenosine 5'-O-(3-thiotriphosphate) (MgATPgammaS) mediates the weak binding of helicase (gp41) to DNA coated with gp32 and gp59, whereas MgATP induces gp32 and gp59 to dissociate, leaving gp41 bound to the DNA. Finally, primase (gp61) binds to the gp41.DNA complex. Ensemble studies were used to determine protein stoichiometries and binding constants. These single-molecule studies provide an unambiguous description of the pathway for assembly of the primosome on the lagging strand of DNA at a replication fork.},
  file      = {:by-author/Z/Zhang/2005_Zhang_3254.pdf:PDF},
  keywords  = {{gp41} Helicase},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Zhao2008,
  author    = {Zhao, Hongsheng and Wu, Deqi and Yao, Jincheng and Chang, Aimin},
  journal   = {Ultramicroscopy},
  title     = {QtUCP-a program for determining unit-cell parameters in electron diffraction experiments using double-tilt and rotation-tilt holders.},
  year      = {2008},
  pages     = {1540--5},
  volume    = {108},
  abstract  = {A computer program, QtUCP, has been developed based on several well-established algorithms using GCC 4.0 and Qt 4.0 (Open Source Edition) under Debian GNU/Linux 4.0r0. It can determine the unit-cell parameters from an electron diffraction tilt series obtained from both double-tilt and rotation-tilt holders. In this approach, two or more primitive cells of the reciprocal lattice are determined from experimental data, in the meantime, the measurement errors of the tilt angles are checked and minimized. Subsequently, the derived primitive cells are converted into the reduced form and then transformed into the reduced direct primitive cell. Finally all the patterns are indexed and the least-squares refinement is employed to obtain the optimized results of the lattice parameters. Finally, two examples are given to show the application of the program, one is based on the experiment, the other is from the simulation.},
  file      = {:by-author/Z/Zhao/2008_Zhao_1540.pdf:PDF},
  keywords  = {Crystal Cell; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Manuscript{Zhao2012,
  author       = {Jun Zhao and Jose Manuel Gomez-Perez and Khalid Belhajjame and Graham Klyne and Esteban Garcia-Cuesta and Aleix Garrido and Kristina Hettne and Marco Roos and David De Roure and Carole Goble},
  title        = {Why Workflows Break - Understanding and Combating Decay in Taverna Workflows},
  year         = {2012},
  howpublished = {In 8th International Conference on eScience (IEEE eScience 2012), pages 1–9, Oct 2012.},
  keywords     = {Bit-rot; Reproducible Research},
  url          = {http://users.ox.ac.uk/~oerc0033/preprints/why-decay.pdf},
  file         = {2012_Zhao.pdf:by-author/Z/Zhao/2012_Zhao.pdf:PDF},
  groups       = {sg/Methods and tools},
  note         = {Preprint of the 8th International Conference on eScience (IEEE eScience 2012), pages 1–9, Oct 2012.},
  owner        = {saulius},
  timestamp = {2016.11.17},
  creationdate = {2016-11-17T00:00:00},
}

@Article{Zhao2007,
  author    = {Zhao, Lei and Bonocora, Richard P. and Shub, David A. and Stoddard, Barry L.},
  journal   = {The EMBO journal},
  title     = {The restriction fold turns to the dark side: a bacterial homing endonuclease with a PD-(D/E)-XK motif.},
  year      = {2007},
  pages     = {2432--42},
  volume    = {26},
  abstract  = {The homing endonuclease I-Ssp6803I causes the insertion of a group I intron into a bacterial tRNA gene-the only example of an invasive mobile intron within a bacterial genome. Using a computational fold prediction, mutagenic screen and crystal structure determination, we demonstrate that this protein is a tetrameric PD-(D/E)-XK endonuclease - a fold normally used to protect a bacterial genome from invading DNA through the action of restriction endonucleases. I-Ssp6803I uses its tetrameric assembly to promote recognition of a single long target site, whereas restriction endonuclease tetramers facilitate cooperative binding and cleavage of two short sites. The limited use of the PD-(D/E)-XK nucleases by mobile introns stands in contrast to their frequent use of LAGLIDADG and HNH endonucleases - which in turn, are rarely incorporated into restriction/modification systems.},
  file      = {:by-author/Z/Zhao/2007_Zhao_2432.pdf:PDF},
  keywords  = {Homing Endonucleases},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Zhao2014,
  author    = {Zhao, Li-Dong and Lo, Shih-Han and Zhang, Yongsheng and Sun, Hui and Tan, Gangjian and Uher, Ctirad and Wolverton, C. and Dravid, Vinayak P. and Kanatzidis, Mercouri G.},
  journal   = {Nature},
  title     = {Ultralow thermal conductivity and high thermoelectric figure of merit in SnSe crystals},
  year      = {2014},
  issn      = {0028-0836},
  pages     = {373--377},
  volume    = {508},
  abstract  = {The thermoelectric effect enables direct and reversible conversion between thermal and electrical energy, and provides a viable route for power generation from waste heat. The efficiency of thermoelectric materials is dictated by the dimensionless figure of merit, ZT (where Z is the figure of merit and T is absolute temperature), which governs the Carnot efficiency for heat conversion. Enhancements above the generally high threshold value of 2.5 have important implications for commercial deployment1, 2, especially for compounds free of Pb and Te. Here we report an unprecedented ZT of 2.6 ± 0.3 at 923 K, realized in SnSe single crystals measured along the b axis of the room-temperature orthorhombic unit cell. This material also shows a high ZT of 2.3 ± 0.3 along the c axis but a significantly reduced ZT of 0.8 ± 0.2 along the a axis. We attribute the remarkably high ZT along the b axis to the intrinsically ultralow lattice thermal conductivity in SnSe. The layered structure of SnSe derives from a distorted rock-salt structure, and features anomalously high Grüneisen parameters, which reflect the anharmonic and anisotropic bonding. We attribute the exceptionally low lattice thermal conductivity (0.23 ± 0.03 W m−1 K−1 at 973 K) in SnSe to the anharmonicity. These findings highlight alternative strategies to nanostructuring for achieving high thermoelectric performance.},
  file      = {2014_Zhao_373.pdf:by-author/Z/Zhao/2014_Zhao_373.pdf:PDF},
  owner     = {saulius},
  publisher = {Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},
  timestamp = {2015.06.09},
  creationdate = {2015-06-09T00:00:00},
  url       = {http://dx.doi.org/10.1038/nature13184},
}

@InBook{Zhao2015,
  author    = {Zhao, X. Y. and Voutila, J. and Habib, Nagy A. and Reebye, Vikash},
  chapter   = {RNA Activation},
  pages     = {241–249},
  publisher = {Springer Science + Business Media},
  title     = {Innovative Medicine},
  year      = {2015},
  isbn      = {978-4-431-55651-0},
  doi       = {10.1007/978-4-431-55651-0_20},
  file      = {2015_Zhao_241.pdf:by-author/Z/Zhao/2015_Zhao_241.pdf:PDF},
  groups    = {am/RNA activation},
  journal   = {Innovative Medicine},
  owner     = {andrius},
  timestamp = {2016.09.02},
  creationdate = {2016-09-02T00:00:00},
}

@Article{Zhao1997,
  author    = {Zhao, Y and Stuckey, J A and Lohse, D L and Dixon, J E},
  journal   = {Protein science : a publication of the Protein Society},
  title     = {Expression, characterization, and crystallization of a member of the novel phospholipase D family of phosphodiesterases.},
  year      = {1997},
  pages     = {2655--8},
  volume    = {6},
  abstract  = {A family of phospholipase D (PLD) proteins has recently been identified (Koonin, 1996; Ponting &amp; Kerr, 1996) based upon amino acid sequence identity. This family includes human and plant PLDs, proteins encoded by open reading frames in pathogenic viruses and bacteria, as well as an endonuclease. The endonuclease, known as Nuc, is encoded by the IncN plasmid, pKM101, present in Salmonella typhimurium. The recombinant Nuc protein has been expressed and purified from Escherichia coli. The amino-terminal sequencing of the purified protein indicated that the mature protein started from the 23rd residue of the predicted sequence, suggesting that the protein is proteolytically processed during export to the periplasmic space. The recombinant enzyme was able to hydrolyze both double and single-strand DNA and an artificial substrate, bis(4-nitrophenyl) phosphate, which contains a phosphodiester bond. The enzyme activity was not inhibited in the presence of EDTA and was not regulated by divalent cations. The purified protein has been crystallized by hanging drop vapor diffusion methods, and those crystals diffract to 1.9 A resolution.},
  file      = {Zhao_1997_2655-PLD_biochem_cryst.pdf:by-author/Z/Zhao/1997_Zhao_2655.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Zheleznaya2002,
  author    = {L.A. Zheleznaya and T.A. Perevyazova and E.N. Zheleznyakova and N.I. Matvienko},
  journal   = {Biochemistry (Moscow)},
  title     = {Some Properties of Site-Specific Nickase BspD6I and the Possibility of Its Use in Hybridization Analysis of DNA},
  year      = {2002},
  pages     = {498--502},
  volume    = {67},
  abstract  = {A new method for hybridization analysis of nucleic acids is proposed on the basis of the ability of site specific nick ases to cleave only one DNA strand. The method is based on the use of a labeled oligonucleotide with the recognition site of the nickase hybridized with the target (DNA or RNA) at an optimal temperature of the enzyme (55°C). The two shorter oligonucleotides formed after the cleavage with the nickase do not complex with the target. Thus, a multiple cleavage of the labeled oligonucleotide takes place on one target molecule. The cleavage of the nucleotide is recorded either by polyacrylamide gel electrophoresis (when a radioactive labeled oligonucleotide is used) or by fluorescence measurements (if the oligonu cleotide has the structure of a molecular beacon). The new method was tested on nickase BspD6I and a radioactive oligonu cleotide complementary to the polylinker region of the viral DNA strand in bacteriophage M13mp19. Unfortunately, nickase BspD6I does not cleave DNA in the RNA–DNA duplexes and therefore cannot be used for detection of RNA targets.},
  file      = {:by-author/Z/Zheleznaya/2002_Zheleznaya_498.pdf:PDF},
  keywords  = {BspD6I; Hybridization of Nucleic Acids; Molecular Beacons; Restriction Endonucleases (REases); Site Specific Nickases},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@Manuscript{Zheng2005,
  author    = {Zheng, Baihua and Xu, Jianliang and Lee, Wang-Chien and Lee, Lun},
  title     = {Grid-partition Index: A Hybrid Method for Nearest-neighbor Queries in Wireless Location-based Services},
  year      = {2005},
  abstract  = {Traditional nearest-neighbor (NN) search is based on two ba- sic indexing approaches: object-based indexing and solution-based indexing. The former is constructed based on the locations of data objects: using some distance heuristics on object locations. The latter is built on a pre-computed solution space. Thus, NN queries can be reduced to and processed as simple point queries in this solution space. Both approaches exhibit some disad- vantages, especially when employed for wireless data broadcast in mobile computing environments.},
  file      = {2005_Zheng.pdf:by-author/Z/Zheng/2005_Zheng.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Zheng2008,
  author           = {Heping Zheng and Maksymilian Chruszcz and Piotr Lasota and Lukasz Lebioda and Wladek Minor},
  journal          = {Journal of Inorganic Biochemistry},
  title            = {Data mining of metal ion environments present in protein structures},
  year             = {2008},
  issn             = {0162-0134},
  pages            = {1765 - 1776},
  volume           = {102},
  abstract         = {Analysis of metal–protein interaction distances, coordination numbers, B-factors (displacement parameters), and occupancies of metal-binding sites in protein structures determined by X-ray crystallography and deposited in the \{PDB\} shows many unusual values and unexpected correlations. By measuring the frequency of each amino acid in metal ion-binding sites, the positive or negative preferences of each residue for each type of cation were identified. Our approach may be used for fast identification of metal-binding structural motifs that cannot be identified on the basis of sequence similarity alone. The analysis compares data derived separately from high and medium-resolution structures from the \{PDB\} with those from very high-resolution small-molecule structures in the Cambridge Structural Database (CSD). For high-resolution protein structures, the distribution of metal–protein or metal–water interaction distances agrees quite well with data from CSD, but the distribution is unrealistically wide for medium (2.0–2.5&#xa0;Å) resolution data. Our analysis of cation B-factors versus average B-factors of atoms in the cation environment reveals substantial numbers of structures contain either an incorrect metal ion assignment or an unusual coordination pattern. Correlation between data resolution and completeness of the metal coordination spheres is also found.},
  creationdate     = {2014-08-15T00:00:00},
  doi              = {10.1016/j.jinorgbio.2008.05.006},
  file             = {:by-author/Z/Zheng/2008_Zheng_1765.pdf:PDF},
  keywords         = {B-factor; Crystallography; Metal Coordination; Protein Crystallography; Structural Biology; Thermal Displacement Parameters},
  modificationdate = {2024-03-14T11:25:23},
  owner            = {andrius},
  timestamp        = {2014.08.15},
}

@Article{Zheng2004a,
  author      = {Lei Zheng and Ulrich Baumann and Jean-Louis Reymond},
  journal     = {Nucleic Acids Res},
  title       = {An efficient one-step site-directed and site-saturation mutagenesis protocol.},
  year        = {2004},
  number      = {14},
  pages       = {e115},
  volume      = {32},
  abstract    = {We have developed a new primer design method based on the QuickChange site-directed mutagenesis protocol, which significantly improves the PCR amplification efficiency. This design method minimizes primer dimerization and ensures the priority of primer-template annealing over primer self-pairing during the PCR. Several different multiple mutations (up to 7 bases) were successfully performed with this partial overlapping primer design in a variety of vectors ranging from 4 to 12 kb in length. In comparison, all attempts failed when using complete-overlapping primer pairs as recommended in the standard QuickChange protocol. Our protocol was further extended to site-saturation mutagenesis by introducing randomized codons. Our data indicated no specific sequence selection during library construction, with the randomized positions resulting in average occurrence of each base in each position. This method should be useful to facilitate the preparation of high-quality site saturation libraries.},
  doi         = {10.1093/nar/gnh110},
  file        = {:by-author/Z/Zheng/2004_Zheng_e115.pdf:PDF},
  institution = {Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, CH-3012 Berne, Switzerland.},
  keywords    = {Agar Gel; DNA Primers; Directed Molecular Evolution; Electrophoresis; Gene Library; Methods; Mutagenesis; Polymerase Chain Reaction; Protein Engineering; Site-Directed},
  language    = {eng},
  medline-pst = {epublish},
  owner       = {em},
  pii         = {32/14/e115},
  pmid        = {15304544},
  timestamp = {2012.03.07},
  creationdate = {2012-03-07T00:00:00},
  url         = {http://dx.doi.org/10.1093/nar/gnh110},
}

@Article{Zheng2014,
  author    = {Zheng, Lin and Wang, Lu and Gan, Jinfeng and Zhang, Hao},
  journal   = {Cancer Letters},
  title     = {{RNA} activation: Promise as a new weapon against cancer},
  year      = {2014},
  issn      = {0304-3835},
  month     = {Dec},
  number    = {1},
  pages     = {18–24},
  volume    = {355},
  doi       = {10.1016/j.canlet.2014.09.004},
  file      = {:by-author/Z/Zheng/2014_Zheng_18.pdf:PDF},
  groups    = {am/RNA activation},
  owner     = {andrius},
  publisher = {Elsevier BV},
  timestamp = {2016.08.24},
  creationdate = {2016-08-24T00:00:00},
}

@Article{Zheng1992,
  author    = {Zheng, L. and Wang, X. and Braymer, H. D.},
  journal   = {Gene},
  title     = {Purification and N-terminal amino acid sequences of two polypeptides encoded by the mcrB gene from Escherichia coli K-12.},
  year      = {1992},
  pages     = {97--100},
  volume    = {112},
  abstract  = {This report provides a purification method for the two proteins, 51 kDa and 33 kDa, both encoded by the same mcrB gene of the McrBC restriction system in Escherichia coli K-12. The two proteins were produced in large quantity using a T7 expression system and copurified to near homogeneity by DEAE-Sepharose and Affi-Gel blue column chromatography. The N-terminal amino acid sequences of these purified McrB proteins were the same as those predicted from the mcrB DNA sequence by Ross et al. [J. Bacteriol. 171 (1989b) 1974-1981]. The 33-kDa protein totally overlaps the C-terminal part of the 51-kDa protein.},
  file      = {:by-author/Z/Zheng/1992_Zheng_97.pdf:PDF},
  keywords  = {McrBC},
  owner     = {em},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Zheng2012,
  author    = {Zheng, Shun and Kwon, Inchan},
  journal   = {Biotechnology Journal},
  title     = {Manipulation of enzyme properties by noncanonical amino acid incorporation},
  year      = {2012},
  issn      = {1860-6768},
  number    = {1},
  pages     = {47--60},
  volume    = {7},
  doi       = {10.1002/biot.201100267},
  file      = {:by-author/Z/Zheng/2012_Zheng_47.pdf:PDF},
  groups    = {am/Expanded genetic code},
  owner     = {andrius},
  publisher = {Wiley-Blackwell},
  timestamp = {2016.06.02},
  creationdate = {2016-06-02T00:00:00},
  url       = {http://dx.doi.org/10.1002/biot.201100267},
}

@Article{Zheng2004,
  author    = {Yu Zheng and Richard J. Roberts and Simon Kasif},
  journal   = {PLoS biology},
  title     = {Segmentally Variable Genes: A New Perspective on Adaptation},
  year      = {2004},
  pages     = {452--464},
  volume    = {2},
  abstract  = {Genomic sequence variation is the hallmark of life and is key to understanding diversity and adaptation among the numerous microorganisms on earth. Analysis of the sequenced microbial genomes suggests that genes are evolving at many different rates. We have attempted to derive a new classification of genes into three broad categories: lineage- specific genes that evolve rapidly and appear unique to individual species or strains; highly conserved genes that frequently perform housekeeping functions; and partially variable genes that contain highly variable regions, at least 70 amino acids long, interspersed among well-conserved regions. The latter we term segmentally variable genes (SVGs), and we suggest that they are especially interesting targets for biochemical studies. Among these genes are ones necessary to deal with the environment, including genes involved in host–pathogen interactions, defense mechanisms, and intracellular responses to internal and environmental changes. For the most part, the detailed function of these variable regions remains unknown. We propose that they are likely to perform important binding functions responsible for protein–protein, protein–nucleic acid, or protein–small molecule interactions. Discerning their function and identifying their binding partners may offer biologists new insights into the basic mechanisms of adaptation, context-dependent evolution, and the interaction between microbes and their environment.},
  file      = {:by-author/Z/Zheng/2004_Zheng_452.pdf:PDF},
  keywords  = {Evolution},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Presentation{Zhigilei2009,
  author    = {Zhigilei},
  title     = {Molecular Dynamics},
  year      = {2009},
  school    = {University of Virginia},
  file      = {:by-author/Z/Zhigilei/2009_Zhigilei_slides.pdf:PDF},
  groups    = {sg/Molecular dynamics},
  keywords  = {Hard Spheres; Molecular Dynamics (MD)},
  owner     = {saulius},
  pages     = {slides},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Zhou2005,
  author    = {Zhou},
  title     = {Optimizing Continuous Multijoin Queries over Distributed Streams},
  year      = {2005},
  pages     = {221--222},
  doi       = {10.1145/1099554.1099597},
  file      = {:by-author/Z/Zhou/2005_Zhou_221.pdf:PDF},
  keywords  = {Computer Science (CS); Continuous; Databases},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
  url       = {http://dl.acm.org/citation.cfm?doid=1099554.1099597},
}

@Article{Zhou2007,
  author    = {Zhou, Hongjun and Shatz, Whitney and Purdy, Matthew M and Fera, Nick and Dahlquist, Frederick W and Reich, Norbert O},
  journal   = {Biochemistry},
  title     = {Long-range structural and dynamical changes induced by cofactor binding in DNA methyltransferase M.HhaI.},
  year      = {2007},
  pages     = {7261--8},
  volume    = {46},
  abstract  = {The bacterial DNA cytosine methyltransferase M.HhaI sequence-specifically modifies DNA in an S-adenosylmethionine dependent reaction. The enzyme stabilizes the target cytosine (GCGC) into an extrahelical position, with a concomitant large movement of an active site loop involving residues 80-99. We used multidimensional, transverse relaxation-optimized NMR experiments to assign nearly 80% of all residues in the cofactor-bound enzyme form, providing a basis for detailed structural and dynamical characterization. We examined details of the previously unknown effects of the cofactor binding with M.HhaI in solution. Addition of the cofactor results in numerous structural changes throughout the protein, including those decorating the cofactor binding site, and distal residues more than 30 A away. The active site loop is involved in motions both on a picosecond to nanosecond time scale and on a microsecond to millisecond time scale and is not significantly affected by cofactor binding except for a few N-terminal residues. The cofactor also affects residues near the DNA binding cleft, suggesting a role for the cofactor in regulating DNA interactions. The allosteric properties we observed appear to be closely related to the significant amount of dynamics and dynamical changes in response to ligand binding detected in the protein.},
  file      = {2007_Zhou_7261.pdf:by-author/Z/Zhou/2007_Zhou_7261.pdf:PDF},
  keywords  = {HhaI},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Zhou2017,
  author    = {Pingping Zhou},
  journal   = {Zeitschrift für anorganische und allgemeine Chemie},
  title     = {Auxilary Ligand Directed Zinc({II}) Metal-Organic Frameworks with Different Topological Networks},
  year      = {2017},
  month     = {jan},
  comment   = {All of the starting materials were commercially obtained (!). Synthesis of [Zn3(HL)2(4,4Ј-bipy)3]n},
  doi       = {10.1002/zaac.201600395},
  file      = {:by-author/Z/Zhou/2017_Zhou_a.pdf:PDF;Zhou2017.pdf:by-author/Z/Zhou/2017_Zhou.pdf:PDF},
  groups    = {sg/MOF, sg/MOFs, am/MOFs},
  keywords  = {Synthesis},
  owner     = {saulius},
  publisher = {Wiley-Blackwell},
  timestamp = {2017.01.31},
  creationdate = {2017-01-31T00:00:00},
  url       = {https://doi.org/10.1002%2Fzaac.201600395},
}

@Article{Zhou2001,
  author    = {Zhou, P and Lugovskoy, A A and McCarty, J S and Li, P and Wagner, G},
  journal   = {Proceedings of the National Academy of Sciences of the United States of America},
  title     = {Solution structure of DFF40 and DFF45 N-terminal domain complex and mutual chaperone activity of DFF40 and DFF45.},
  year      = {2001},
  pages     = {6051--5},
  volume    = {98},
  abstract  = {Apoptotic DNA fragmentation is mediated by a caspase-activated DNA fragmentation factor (DFF)40. Expression and folding of DFF40 require the presence of DFF45, which also acts as a nuclease inhibitor before DFF40 activation by execution caspases. The N-terminal domains (NTDs) of both proteins are homologous, and their interaction plays a key role in the proper functioning of this two-component system. Here we report that the NTD of DFF45 alone is unstructured in solution, and its folding is induced upon binding to DFF40 NTD. Therefore, folding of both proteins regulates the formation of the DFF40/DFF45 complex. The solution structure of the heterodimeric complex between NTDs of DFF40 and DFF45 reported here shows that the mutual chaperoning includes the formation of an extensive network of intermolecular interactions that bury a hydrophobic cluster inside the interface, surrounded by intermolecular salt bridges.},
  file      = {Zhou_2001_6051-DFF_solution_structure.pdf:by-author/Z/Zhou/2001_Zhou_6051.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Zhou2010,
  author           = {Ting Zhou and Karine Lafleur and Amedeo Caflisch},
  journal          = {Journal of Molecular Graphics and Modelling},
  title            = {Complementing ultrafast shape recognition with an optical isomerism descriptor},
  year             = {2010},
  issn             = {1093-3263},
  pages            = {443 - 449},
  volume           = {29},
  abstract         = {We introduce the mixed product of three vectors spanning four molecular locations as a descriptor of optical isomerism. This descriptor is very efficient as it does not require molecular superposition, and is very robust in discriminating between a given isomer and its mirror image. In particular, conformational isomers that are mirror images of each other, as well as optical isomers have opposite sign of the descriptor value. For efficient database searches, the optical isomerism descriptor can be used to complement an available ultrafast shape recognition (USR) method based solely on distances, which is not able to distinguish enantiomers. By an extensive comparison of the USR-based similarity score with an approach based on Gaussian molecular volume overlap, the accuracy and completeness of the former are discussed.},
  creationdate     = {2015-10-14T00:00:00},
  doi              = {10.1016/j.jmgm.2010.08.007},
  file             = {Complementing ultrafast shape recognition with an optical isomerism descriptor - tzhou10.pdf:by-author/Z/Zhou/2010_Zhou_443.pdf:application/pdf},
  keywords         = {Chemical Structure Search; Chirality Descriptor; Databases; Fingreprints; Three Dimensional Structures; Ultrafast Shape Recognition},
  modificationdate = {2023-12-24T19:18:30},
  owner            = {saulius},
  timestamp        = {2015.10.14},
  url              = {http://www.sciencedirect.com/science/article/pii/S1093326310001336},
  urldate          = {2015-08-05},
}

@Article{Zhou2004,
  author      = {Xiaoyin E Zhou and Yujun Wang and Monika Reuter and Merlind Mücke and Detlev H Krüger and Edward J Meehan and Liqing Chen},
  journal     = {J Mol Biol},
  title       = {Crystal structure of type IIE restriction endonuclease EcoRII reveals an autoinhibition mechanism by a novel effector-binding fold.},
  year        = {2004},
  month       = {Jan},
  number      = {1},
  pages       = {307--319},
  volume      = {335},
  abstract    = {EcoRII is a type IIE restriction endonuclease that interacts with two copies of the DNA recognition sequence 5'CCWGG, one being the actual target of cleavage, the other serving as the allosteric effector. The mode of enzyme activation by effector binding is unknown. To investigate the molecular basis of activation and cleavage mechanisms by EcoRII, the crystal structure of EcoRII mutant R88A has been solved at 2.1A resolution. The EcoRII monomer has two domains linked through a hinge loop. The N-terminal effector-binding domain has a novel DNA recognition fold with a prominent cleft. The C-terminal catalytic domain has a restriction endonuclease-like fold. Structure-based sequence alignment identified the putative catalytic site of EcoRII that is spatially blocked by the N-terminal domain. The structure together with the earlier characterized EcoRII enzyme activity enhancement in the absence of its N-terminal domain reveal an autoinhibition/activation mechanism of enzyme activity mediated by a novel effector-binding fold. This is the first case of autoinhibition, a mechanism described for many transcription factors and signal transducing proteins, of a restriction endonuclease.},
  file        = {2004_Zhou.pdf:by-author/Z/Zhou/2004_Zhou.pdf:PDF},
  institution = {Laboratory for Structural Biology, Department of Chemistry, Graduate Programs of Biotechnology, Chemistry and Materials Science, University of Alabama in Huntsville, Huntsville, AL 35899, USA.},
  keywords    = {Allosteric Regulation; Allosteric Site; Amino Acid Sequence; Bacterial Proteins; Catalytic Domain; Chemistry; Chemistry/genetics; Crystallography; Deoxyribonucleases; Enzyme Activation; Missense; Molecular Structure; Mutation; Protein Conformation; Sequence Alignment; Type II Site-Specific; X-Ray},
  language    = {eng},
  medline-pst = {ppublish},
  owner       = {em},
  pii         = {S002228360301297X},
  pmid        = {14659759},
  timestamp = {2011.12.09},
  creationdate = {2011-12-09T00:00:00},
}

@Article{Zhou2004a,
  author    = {Xiaoyin E. Zhou and Yujun Wang and Monika Reuter and Merlind Mücke and Detlev H. Krüger and Edward J. Meehan and Liqing Chen},
  journal   = {Journal of Molecular Biology},
  title     = {Crystal Structure of Type IIE Restriction Endonuclease EcoRII Reveals an Autoinhibition Mechanism by a Novel Effector-binding Fold},
  year      = {2004},
  issn      = {0022-2836},
  pages     = {307 - 319},
  volume    = {335},
  abstract  = {EcoRII is a type IIE restriction endonuclease that interacts with two copies of the DNA recognition sequence 5′CCWGG, one being the actual target of cleavage, the other serving as the allosteric effector. The mode of enzyme activation by effector binding is unknown. To investigate the molecular basis of activation and cleavage mechanisms by EcoRII, the crystal structure of EcoRII mutant R88A has been solved at 2.1&#xa0;Å resolution. The EcoRII monomer has two domains linked through a hinge loop. The N-terminal effector-binding domain has a novel DNA recognition fold with a prominent cleft. The C-terminal catalytic domain has a restriction endonuclease-like fold. Structure-based sequence alignment identified the putative catalytic site of EcoRII that is spatially blocked by the N-terminal domain. The structure together with the earlier characterized EcoRII enzyme activity enhancement in the absence of its N-terminal domain reveal an autoinhibition/activation mechanism of enzyme activity mediated by a novel effector-binding fold. This is the first case of autoinhibition, a mechanism described for many transcription factors and signal transducing proteins, of a restriction endonuclease.},
  doi       = {10.1016/j.jmb.2003.10.030},
  file      = {Zhou_2004_307-EcoRII_structure.pdf:by-author/Z/Zhou/2004_Zhou.pdf:PDF},
  keywords  = {Allosteric Effector},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://www.sciencedirect.com/science/article/pii/S002228360301297X},
}

@Article{Zhou2008,
  author    = {Z. Hong Zhou},
  journal   = {Curr. Opin. Struct. Biol.},
  title     = {Towards atomic resolution structural determination by single-particle cryo-electron microscopy},
  year      = {2008},
  pages     = {218--228},
  volume    = {18},
  abstract  = {Recent advances in cryo-electron microscopy and single-particle reconstruction (collectively referred to as “cryoEM”) have made it possible to determine the three-dimensional (3D) structures of several macromolecular complexes at near-atomic resolution (~3.8 – 4.5 Å). These achievements were accomplished by overcoming challenges in sample handling, instrumentation, image processing, and model building. At near-atomic resolution, many detailed structural features can be resolved, such as the turns and deep grooves of helices, strand separation in β sheets, and densities for loops and bulky amino acid side chains. Such structural data of the cytoplasmic polyhedrosis virus (CPV), the Epsilon 15 bacteriophage and the GroEL complex have provided valuable constraints for atomic model building using integrative tools, thus significantly enhancing the value of the cryoEM structures. The CPV structure revealed a drastic conformational change from a helix to a β hairpin associated with RNA packaging and replication, coupling of RNA processing and release, and the long sought-after polyhedrin-binding domain. These latest advances in single-particle cryoEM provide exciting opportunities for the 3D structural determination of viruses and macromolecular complexes that are either too large or too heterogeneous to be investigated by conventional X-ray crystallography or nuclear magnetic resonance (NMR) methods.},
  doi       = {10.1016/j.sbi.2008.03.004},
  file      = {:by-author/Z/Zhou/2008_Zhou_218.pdf:PDF},
  keywords  = {CryoEM},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Zhu2012,
  author    = {Haibin Zhu and Mengchu Zhou},
  journal   = {IEEE Transactions on Systems, Man, and Cybernetics -- part A: Systems and Humans},
  title     = {Efficient Role Transfer Based on Kuhn–Munkres Algorithm},
  year      = {2012},
  pages     = {491--496},
  volume    = {42},
  abstract  = {Many-to-Many (M-M) role transfers are generalized problems that are encountered in collaboration. Exhaustive-search-based algorithms are too computationally intensive. This paper introduces the Kuhn-Munkres (or Hungarian) algorithm for the general assignment problems (GAPs) and proposes a new efficient algorithm to solve the M-M role transfer problems by converting them to the GAPs. The experiments and results validate the proposed algorithms},
  doi       = {10.1109/TSMCA.2011.2159587},
  file      = {:by-author/Z/Zhu/2012_Zhu_491.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@Article{Zhu2004,
  author    = {Mu Zhu and Arthur Y. Lu},
  journal   = {Journal of Statistics Education},
  title     = {The Counter-intuitive Non-informative Prior for the Bernoulli Family},
  year      = {2004},
  number    = {2},
  volume    = {12},
  abstract  = {In Bayesian statistics, the choice of the prior distribution is often controversial. Different rules for selecting priors have been suggested in the literature, which, sometimes, produce priors that are difficult for the students to understand intuitively. In this article, we use a simple heuristic to illustrate to the students the rather counter-intuitive fact that flat priors are not necessarily non-informative; and non-informative priors are not necessarily flat.},
  file      = {:by-author/Z/Zhu/2004_Zhu.pdf:PDF},
  groups    = {sg/Bayesian},
  keywords  = {Bayesian Statistics; Mathematics},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
  url       = {http://www.amstat.org/publications/jse/v12n2/zhu.pdf},
}

@Article{Zhu2012a,
  author    = {Zhu, Xing and Ye, Keqiong},
  journal   = {FEBS Lett.},
  title     = {Crystal structure of Cmr2 suggests a nucleotide cyclase-related enzyme in type III CRISPR-Cas systems},
  year      = {2012},
  pages     = {939–945},
  volume    = {586},
  abstract  = {CRISPR RNAs (crRNAs) mediate sequence-specific silencing of invading viruses and plasmids in pro- karyotes. The crRNA–Cmr protein complex cleaves complementary RNA. We report the crystal struc- ture of Pyrococcus furiosus Cmr2 (Cas10), a component of this Cmr complex and the signature protein in type III CRISPR systems. The structure reveals a nucleotide cyclase domain with a set of conserved catalytic residues that associates with an unexpected deviant cyclase domain like dimeric cyclases. Additionally, two helical domains resemble the thumb domain of A-family DNA polymer- ase and Cmr5, respectively. Our results suggest that Cmr2 possesses novel enzymatic activity that remains to be elucidated.},
  doi       = {10.1016/j.febslet.2012.02.036},
  file      = {:by-author/Z/Zhu/2012_Zhu_939.pdf:PDF},
  groups    = {sg/CRISPR-Cas},
  keywords  = {CRISPR; Cas10; Cmr2; Crystal Structure; Nucleotide Cyclase; Type III; X-ray Crystallography},
  owner     = {em},
  timestamp = {2013.10.01},
  creationdate = {2013-10-01T00:00:00},
}

@Manuscript{Ziff1992,
  author    = {Donald A. Ziff and Keith Waclena},
  title     = {The "Alfonzo" Language},
  year      = {1992},
  keywords  = {Programming Languages},
  file      = {:by-author/Z/Ziff/1992_Ziff.pdf:PDF;:by-author/Z/Ziff/1992_Ziff.ps:PostScript},
  owner     = {saulius},
  timestamp = {2015.02.25},
  creationdate = {2015-02-25T00:00:00},
}

@Manuscript{Ziff1992a,
  author    = {Donald A. Ziff and Keith Waclena and Stephen P. Spackman},
  title     = {CAL: Combinator Assembly Language},
  year      = {1992},
  keywords  = {Programming Languages},
  file      = {:by-author/Z/Ziff/1992_Ziff_a.pdf:PDF;:by-author/Z/Ziff/1992_Ziff_a.ps:PostScript},
  owner     = {saulius},
  timestamp = {2015.02.25},
  creationdate = {2015-02-25T00:00:00},
}

@Manuscript{Zijp2010,
  author    = {Jeroen van der Zijp},
  title     = {Fast Half Float Conversions},
  year      = {2010},
  month     = {Nov},
  abstract  = {High dynamic range imaging and signal processing require more compact floating point representations than single precision (32-bit) IEEE 754 standard allows. To meet these objectives, a 16-bit “half” float data type was introduced. Hardware support for these is now common place in Graphics Processing Units (GPU's), but unfortunately not yet in CPU's. Because of this, calculations using 16-bit half-floats must be done using regular 32-bit IEEE floats, necessitating frequent conversions from half-floats to floats and vice-versa.},
  file      = {:by-author/Z/Zijp/2010_Zijp.pdf:PDF},
  owner     = {saulius},
  timestamp = {2014.03.23},
  creationdate = {2014-03-23T00:00:00},
}

@Article{Zinkevich1992,
  author    = {Zinkevich, V. and Heslop, P. and Glover, S. W. and Weiserova, M. and Hubácek, J. and Firman, K.},
  journal   = {Journal of molecular biology},
  title     = {Mutation in the specificity polypeptide of the type I restriction endonuclease R.EcoK that affects subunit assembly.},
  year      = {1992},
  pages     = {597--601},
  volume    = {227},
  abstract  = {We describe the isolation and characterization of a temperature-sensitive mutation within the hsdS gene of the type I restriction and modification system EcoK. This mutation appears to affect the ability of the HsdR subunit to interact with the HsdS subunit when forming an active endonuclease. We discuss the possibility that this mutant, together with another mutation described previously, may define a discontinuous domain, involved in protein-protein interactions, within the HsdS polypeptide.},
  file      = {:by-author/Z/Zinkevich/1992_Zinkevich_597.pdf:PDF},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Zinkevich1997,
  author    = {Zinkevich, V. and Popova, L. and Kryukov, V. and Abadjieva, A. and Bogdarina, I. and Janscak, P. and Firman, K.},
  journal   = {Nucleic acids research},
  title     = {The HsdR subunit of R.EcoR124II: cloning and over-expression of the gene and unexpected properties of the subunit.},
  year      = {1997},
  pages     = {503--11},
  volume    = {25},
  abstract  = {Type I restriction endonucleases are composed of three subunits, HsdR, HsdM and HsdS. The HsdR subunit is absolutely required for restriction activity; while an independent methylase is composed of HsdM and HsdS subunits. DNA cleavage is associated with a powerful ATPase activity during which DNA is translocated by the enzyme prior to cleavage. The presence of a Walker type I ATP-binding site within the HsdR subunit suggested that the subunit may be capable of independent enzymatic activity. Therefore, we have, for the first time, cloned and over-expressed the hsdRgene of the type IC restriction endonuclease EcoR124II. The purified HsdR subunit was found to be a soluble monomeric protein capable of DNA- and Mg2+-dependent ATP hydrolysis. The subunit was found to have a weak nuclease activity both in vivo and in vitro, and to bind plasmid DNA; although was not capable of binding a DNA oligoduplex. We were also able to reconstitute the fully active endonuclease from purified M. EcoR124I and HsdR. This is the first clear demonstration that the HsdR subunit of a type I restriction endonuclease is capable of independent enzyme activity, and suggests a mechanism for the evolution of the endonuclease from the independent methylase.},
  file      = {:by-author/Z/Zinkevich/1997_Zinkevich_503.pdf:PDF},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@TechReport{Zlotnick1996,
  author      = {Jack Zlotnick},
  institution = {Central Intelligence Agency},
  title       = {Bayes' theorem for intelligence analysis},
  year        = {1996},
  month       = {jul},
  abstract    = {The intelligence interest in probability theory stems from the probabilistic character of customary intelligence judgment. Intelligence analysis must usually be undertaken on the basis of incomplete evidence. Intelligence conclusions are therefore characteristically hedged by such words and phrases as "very likely," "possibly," "may," "better than even chance," and other qualifiers. This manner of allowing for more than one possibility leaves intelligence open to the charge of acting the oracle whose prophecies seek to cover all contingencies. The apt reply to this charge is that intelligence would do poor service by overstating its knowledge. The very best that intelligence can do is to make the most of the evidence without making more of the evidence than it deserves. The best recourse is often to address the probabilities. The professional focus on probabilities has led to some in-house research on possible intelligence applications of Bayes' Theorem. At the time of my participation in this research, I was an analyst in the Central Intelligence Agency, which sponsored the scholarship but took no position of its own on the issues under study. My personal views on these issues, as elaborated in the following pages, have no official character.},
  file        = {:by-author/Z/Zlotnick/1996_Zlotnick.odt:OpenDocument text},
  groups      = {sg/Bayesian},
  journal     = {CIA Historical Review Program},
  keywords    = {Bayesian Statistics},
  owner       = {saulius},
  timestamp = {2012.10.03},
  creationdate = {2012-10-03T00:00:00},
  url         = {https://www.cia.gov/library/center-for-the-study-of-intelligence/kent-csi/vol16no2/html/v16i2a03p_0001.htm},
}

@Article{Zolnierkiewicz2010,
  author    = {Olga Zolnierkiewicz and Agnieszka Zylicz-Stachula and Piotr M. Skowron},
  title     = {Sinefungin - induced alterations in {TaqII} restriction specificity},
  year      = {2010},
  pages     = {poster},
  file      = {:by-author/Z/Zolnierkiewicz/2010_Zolnierkiewicz_poster.pdf:PDF},
  keywords  = {Restriction Endonucleases (REases); TspDTI; TspGWI},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Zorina2011,
  author    = {Zorina, L. V. and Simonov, S. V. and Khasanov, S. S. and Shibaeva, R. P. and Suslikova, I. Yu. and Kushch, L. A. and Yagubskii, E. B.},
  journal   = {Crystallography Reports},
  title     = {Crystal structure of the new organic conductor (TSeF)7[FeNO(CN)5]2 with unusual molecular packing of conducting layer},
  year      = {2011},
  issn      = {1562-689X},
  number    = {6},
  pages     = {1042--1046},
  volume    = {56},
  abstract  = {X-ray single crystal diffraction study of the new molecular conductor (TSeF)7[FeNO(CN)5]2 has been carried out at room temperature and 130 K. The crystal structure is composed by layers of $\pi$-electron donors TSeF, separated by anion layers along the a-direction. The conducting organic layer has unusual for molecular conductors arrangement of neutral monomeric and charged hexameric TSeF units orthogonally packed with respect to each other. Another specific feature of the structure is fully ordered state of the nitroprusside anion and deep penetrating of its functional NO-group into the adjacent organic layer.},
  doi       = {10.1134/S1063774511060307},
  file      = {2011_Zorina_1042.pdf:by-author/Z/Zorina/2011_Zorina_1042.pdf:PDF},
  keywords  = {For COD Deposition; Organic Conductors; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2016.10.03},
  creationdate = {2016-10-03T00:00:00},
  url       = {http://dx.doi.org/10.1134/S1063774511060307},
}

@TechReport{Zorn1993,
  author      = {Benjamin Zorn},
  institution = {Department of Computer Science, Campus Box No430, University of Colorado, Boulder 80309-0430},
  title       = {Memory Allocation Costs in Large C and C++ Programs},
  year        = {1993},
  month       = {August},
  file        = {:by-author/Z/Zorn/1993_Zorn.ps.Z:PostScript;:by-author/Z/Zorn/1993_Zorn.pdf:PDF},
  groups      = {sg/Garbage collectors},
  keywords    = {Computer Science (CS); Garbage Collectors},
  owner       = {saulius},
  timestamp = {2015.02.28},
  creationdate = {2015-02-28T00:00:00},
}

@TechReport{Zorn1990,
  author      = {Benjamin Zorn},
  institution = {Department of Computer Science, University of Colorado at Boulder},
  title       = {Barrier methods for garbage collection},
  year        = {1990},
  abstract    = {Garbage collection algorithms have been enhanced in recent years with two methods: generation-based collection and Baker incremental copying collection. Generation-based collection requires special actions during certain store operations to implement the 'write barrier.' Incremental collection requires special actions on certain load operations to implement the 'read barrier.' This paper evaluates the performance of different implementations of the read and write barriers and reaches several important conclusions. First, the inlining of barrier checks results in surprisingly low overheads, both for the write barrier (2-6%) and the read barrier},
  file        = {:by-author/Z/Zorn/1990_Zorn.pdf:PDF},
  groups      = {sg/Garbage collectors},
  keywords    = {Computer Science (CS); Garbage Collectors},
  owner       = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@TechReport{Zorn1988,
  author      = {Zorn, Benjamin and Hilfinger, Paul N.},
  institution = {EECS Department, University of California, Berkeley},
  title       = {A Memory Allocation Profiler for C and Lisp Programs},
  year        = {1988},
  month       = {Feb},
  number      = {UCB/CSD-88-404},
  abstract    = {This paper describes mprof, a tool used to study the memory allocation behavior of programs. mprof records the amount of memory each function allocates, breaks down allocation information by type and size, and displays a program's dynamic call graph so that functions indirectly responsible for memory allocation are easy to identify. mprof is a two-phase tool. The monitor phase is linked into executing programs and records information each time memory is allocated. The display phase reduces the data generated by the monitor and displays the information to the user in several tables. mprof has been implemented for C and Kyoto Common Lisp. Measurements of these implementations are presented.},
  file        = {1988_Zorn.pdf:by-author/Z/Zorn/1988_Zorn.pdf:PDF},
  owner       = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url         = {http://www.eecs.berkeley.edu/Pubs/TechRpts/1988/5382.html},
}

@Presentation{Zorn1997,
  author    = {Benjamin G. Zorn},
  title     = {Algol 68},
  year      = {1997},
  file      = {:by-author/Z/Zorn/1997_Zorn.ps:PostScript;:by-author/Z/Zorn/1997_Zorn.pdf:PDF},
  keywords  = {Algol; Algol 68; Computer Science (CS); Programming Languages; Static Typing},
  owner     = {saulius},
  timestamp = {2015.02.27},
  creationdate = {2015-02-27T00:00:00},
}

@Article{Zotti2013,
  author    = {Zotti, Linda A. and Leary, Edmund and Soriano, Maria and Cuevas, Juan Carlos and Palacios, Juan Jose},
  journal   = {Journal of the American Chemical Society},
  title     = {A Molecular Platinum Cluster Junction: A Single-Molecule Switch},
  year      = {2013},
  pages     = {2052--2055},
  volume    = {135},
  abstract  = {We present a theoretical study of electron transport through single-molecule junctions incorporating a Pt6 metal cluster bound within an organic framework. The insertion of this molecule between a pair of electrodes leads to a fully atomically engineered nanometallic device with high conductance at the Fermi level and two sequential high on/off switching states. The origin of this property can be traced back to the existence of a degenerate HOMO consisting of two asymmetric orbitals with energies close to the Fermi level of the metal leads. The degeneracy is broken when the molecule is contacted to the leads, giving rise to two resonances that become pinned to the Fermi level and display destructive interference.},
  doi       = {10.1021/ja3100116},
  eprint    = {http://dx.doi.org/10.1021/ja3100116},
  file      = {2013_Zotti_2052.pdf:by-author/Z/Zotti/2013_Zotti_2052.pdf:PDF},
  keywords  = {Density Functional Theory (DFT); Single Molecule Shwitches},
  owner     = {saulius},
  timestamp = {2014.10.21},
  creationdate = {2014-10-21T00:00:00},
  url       = {http://dx.doi.org/10.1021/ja3100116},
}

@Article{Zubriene2016,
  author    = {Zubrienė, Asta and Smirnov, Alexey and Dudutienė, Virginija and Timm, David D. and Matulienė, Jurgita and Michailovienė, Vilma and Zakšauskas, Audrius and Manakova, Elena and Gražulis, Saulius and Matulis, Daumantas},
  journal   = {ChemMedChem},
  title     = {Intrinsic Thermodynamics and Structures of 2,4- and 3,4-Substituted Fluorinated Benzenesulfonamides Binding to Carbonic Anhydrases},
  year      = {2016},
  issn      = {1860-7179},
  month     = {Dec},
  number    = {2},
  pages     = {161--176},
  volume    = {12},
  abstract  = {The goal of rational drug design is to understand structure– thermodynamics correlations in order to predict the chemical structure of a drug that would exhibit excellent affinity and selectivity for a target protein. In this study we explored the contribution of added functionalities of benzenesulfonamide inhibitors to the intrinsic binding affinity, enthalpy, and entropy for recombinant human carbonic anhydrases (CA) CA I, CA II, CA VII, CA IX, CA XII, and CA XIII. The binding enthalpies of compounds possessing similar chemical structures and affinities were found to be very different, spanning a range from -90 to + 10 kJ mol À1 , and are compensated by a similar opposing entropy contribution. The intrinsic parameters of binding were determined by subtracting the linked protonation reactions. The sulfonamide group pK a values of the compounds were measured spectrophotometrically, and the protonation enthalpies were measured by isothermal titration calorimetry (ITC). Herein we describe the development of meta- or ortho- substituted fluorinated benzenesulfonamides toward the highly potent compound 10 h, which exhibits an observed dissociation constant value of 43 pm and an intrinsic dissociation constant value of 1.1 pm toward CA IX, an anticancer target that is highly overexpressed in various tumors. Fluorescence thermal shift assays, ITC, and X-ray crystallography were all applied in this work.},
  doi       = {10.1002/cmdc.201600509},
  file      = {2016_Zubrienė_161.pdf:by-author/Z/Zubrienė/2016_Zubrienė_161.pdf:PDF},
  keywords  = {Intrinsic Thermodicanic Parameters; Structure-activity Relations; {hCA}},
  owner     = {saulius},
  publisher = {Wiley-Blackwell},
  timestamp = {2017.02.03},
  creationdate = {2017-02-03T00:00:00},
  url       = {http://dx.doi.org/10.1002/cmdc.201600509},
}

@Article{Zubriene2015,
  author      = {Asta Zubrienė and Joana Smirnovienė and Alexey Smirnov and Vaida Morkūnaitė and Vilma Michailovienė and Jelena Jachno and Vaida Juozapaitienė and Povilas Norvaišas and Elena Manakova and Saulius Gražulis and Daumantas Matulis},
  journal     = {Biophys Chem},
  title       = {Intrinsic thermodynamics of 4-substituted-2,3,5,6-tetrafluorobenzenesulfonamide binding to carbonic anhydrases by isothermal titration calorimetry.},
  year        = {2015},
  pages       = {51--65},
  volume      = {205},
  abstract    = {Para substituted tetrafluorobenzenesulfonamides bind to carbonic anhydrases (CAs) extremely tightly and exhibit some of the strongest known protein-small ligand interactions, reaching an intrinsic affinity of 2 pM as determined by displacement isothermal titration calorimetry (ITC). The enthalpy and entropy of binding to five CA isoforms were measured by ITC in two buffers of different protonation enthalpies. The pKa values of compound sulfonamide groups were measured potentiometrically and spectrophotometrically, and enthalpies of protonation were measured by ITC in order to evaluate the proton linkage contributions to the observed binding thermodynamics. Intrinsic means the affinity of a sulfonamide anion for the Zn bound water form of CAs. Fluorination of the benzene ring significantly enhanced the observed affinities as it increased the fraction of deprotonated ligand while having little impact on intrinsic affinities. Intrinsic enthalpy contributions to the binding affinity were dominant over entropy and were more exothermic for CA I than for other CA isoforms. Thermodynamic measurements together with the X-ray crystallographic structures of protein-ligand complexes enabled analysis of structure-activity relationships in this enzyme ligand system.},
  doi         = {10.1016/j.bpc.2015.05.009},
  file        = {2015_Zubrienė_51.pdf:by-author/Z/Zubrienė/2015_Zubrienė_51.pdf:PDF},
  groups      = {sg/inhibitors, sg/intrinsic parameters, sg/thermodynamics},
  institution = {Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Graičiūno 8, Vilnius LT-02241, Lithuania.},
  language    = {eng},
  medline-pst = {aheadofprint},
  owner       = {alexey},
  pii         = {S0301-4622(15)30002-8},
  pmid        = {26079542},
  timestamp = {2015.06.19},
  creationdate = {2015-06-19T00:00:00},
  url         = {http://dx.doi.org/10.1016/j.bpc.2015.05.009},
}

@Article{Zucker2006,
  author    = {Lynne G. Zucker and Michael R. Darby and Jonathan Furner and Robert C. Liu and Hongyan Ma},
  title     = {Minerva Unbound: Knowledge Stocks, Knowledge Flows and New Knowledge Production},
  year      = {2006},
  abstract  = {The rate of regional growth of new knowledge in the field of nanotechnology, as measured by counts of articles and patents in the open-access digital library NanoBank, is shown to be positively affected both by the size of existing regional stocks of recorded knowledge in all scientific fields, and the extent to which tacit knowledge in all fields flows between institutions of different organizational types. The level of federal funding has a large, robust impact on both publication and patenting. The data provide further support for the cumulative advantage model of knowledge production, and for ongoing efforts to institutionalize channels through which cross-organizational collaboration may be achieved.},
  file      = {:by-author/Z/Zucker/2006_Zucker.pdf:PDF},
  keywords  = {Knowledge},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Zuckerman2007,
  author    = {Zuckerman},
  title     = {Atheism: Contemporary Rates and Patterns},
  year      = {2007},
  file      = {:by-author/Z/Zuckerman/2007_Zuckerman.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@Article{Zur2013,
  author    = {Zur, Hadas and Tuller, Tamir},
  journal   = {PLoS Computational Biology},
  title     = {New Universal Rules of Eukaryotic Translation Initiation Fidelity},
  year      = {2013},
  issn      = {1553-7358},
  month     = {Jul},
  number    = {7},
  pages     = {e1003136},
  volume    = {9},
  doi       = {10.1371/journal.pcbi.1003136},
  editor    = {Chen, KevinEditor},
  file      = {2013_Zur_e1003136.pdf:by-author/Z/Zur/2013_Zur_e1003136.pdf:PDF},
  owner     = {andrius},
  publisher = {Public Library of Science (PLoS)},
  timestamp = {2017.03.02},
  creationdate = {2017-03-02T00:00:00},
  url       = {http://dx.doi.org/10.1371/journal.pcbi.1003136},
}

@Article{Zviedre2011,
  author    = {Zviedre, I. and Belyakov, S.},
  journal   = {Russian Journal of Inorganic Chemistry},
  title     = {A restudy of the crystal structure of tetraaquastrontium dicitratoborate trihydrate},
  year      = {2011},
  pages     = {375},
  volume    = {56},
  abstract  = {The crystal structure of Sr(H 2 O) 4 [(C 12 H 11 O 14 )B] · 3H 2 O ( I ) has been restudied and determined with a higher accuracy. The crystals are monoclinic, space group P 2 1 / n , a = 11.405(1) Å, b = 18.814(1) Å, c = 11.987(1) Å, β = 110.79(1)°; Z = 4. The structure was refined by full matrix least-squares calculation to R = 0.0547 on 5343 unique reflections with R int = 0.0419. The structural units of crystal I are the Sr 2+ cation, seven water molecules, and doubly charged dicitratoborate anion, which is not equivalent to the singly charged complex dicitratoborate anion identified previously in the crystal structures of complexes of boric and citric acids. The coordination polyhedron of the Sr 2+ cation is a distorted dodecahedron composed of four O atoms of coordinated water molecules and four O atoms of two complex anions. The crystal packing of I is layered. Thirteen independent O-H…O and O-H…, O′ contacts form an intricate system of hydrogen bonds.},
  file      = {:by-author/Z/Zviedre/2011_Zviedre_375.pdf:PDF},
  issue     = {3},
  keywords  = {For COD Deposition; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
  url       = {http://dx.doi.org/10.1134/S0036023611030284},
}

@Article{Zwart20XX,
  author    = {P.H. Zwart and R.W. Grosse-Kunstleve and P.D. Adams},
  title     = {Exploring Metric Symmetry},
  year      = {20XX},
  file      = {:by-author/Z/Zwart/20XX_Zwart.pdf:PDF},
  keywords  = {CCTBX; Crystallography; Group Theory; Symmetry},
  owner     = {saulius},
  timestamp = {2011.12.13},
  creationdate = {2011-12-13T00:00:00},
}

@Article{Zwart2004,
  author    = {Zwart, P. H. and Lamzin, V. S.},
  journal   = {Acta Crystallographica Section D},
  title     = {The influence of positional errors on the Debye effects},
  year      = {2004},
  pages     = {220--226},
  volume    = {60},
  doi       = {10.1107/S0907444903025526},
  file      = {dz0016.pdf:by-author/Z/Zwart/2004_Zwart_220.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444903025526},
}

@Article{Zwart2004a,
  author    = {Zwart, P. H. and Langer, G. G. and Lamzin, V. S.},
  journal   = {Acta Crystallographica Section D},
  title     = {Modelling bound ligands in protein crystal structures},
  year      = {2004},
  pages     = {2230--2239},
  volume    = {60},
  doi       = {10.1107/S0907444904012995},
  file      = {ba5069.pdf:by-author/Z/Zwart/2004_Zwart_2230.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0907444904012995},
}

@Article{Zylicz-Stachula2009a,
  author    = {Zylicz-Stachula, Agnieszka and Bujnicki, Janusz and Skowron, Piotr},
  journal   = {BMC Molecular Biology},
  title     = {Cloning and analysis of a bifunctional methyltransferase/restriction endonuclease TspGWI, the prototype of a Thermus sp. enzyme family},
  year      = {2009},
  pages     = {52},
  volume    = {10},
  abstract  = {BACKGROUND:Restriction-modification systems are a diverse class of enzymes. They are classified into four major types: I, II, III and IV. We have previously proposed the existence of a Thermus sp. enzyme family, which belongs to type II restriction endonucleases (REases), however, it features also some characteristics of types I and III. Members include related thermophilic endonucleases: TspGWI, TaqII, TspDTI, and Tth111II.RESULTS:Here we describe cloning, mutagenesis and analysis of the prototype TspGWI enzyme that recognises the 5'-ACGGA-3' site and cleaves 11/9 nt downstream. We cloned, expressed, and mutagenised the tspgwi gene and investigated the properties of its product, the bifunctional TspGWI restriction/modification enzyme. Since TspGWI does not cleave DNA completely, a cloning method was devised, based on amino acid sequencing of internal proteolytic fragments. The deduced amino acid sequence of the enzyme shares significant sequence similarity with another representative of the Thermus sp. family - TaqII. Interestingly, these enzymes recognise similar, yet different sequences in the DNA. Both enzymes cleave DNA at the same distance, but differ in their ability to cleave single sites and in the requirement of S-adenosylmethionine as an allosteric activator for cleavage. Both the restriction endonuclease (REase) and methyltransferase (MTase) activities of wild type (wt) TspGWI (either recombinant or isolated from Thermus sp.) are dependent on the presence of divalent cations.CONCLUSION:TspGWI is a bifunctional protein comprising a tandem arrangement of Type I-like domains; particularly noticeable is the central HsdM-like module comprising a helical domain and a highly conserved S-adenosylmethionine-binding/catalytic MTase domain, containing DPAVGTG and NPPY motifs. TspGWI also possesses an N-terminal PD-(D/E)XK nuclease domain related to the corresponding domains in HsdR subunits, but lacks the ATP-dependent translocase module of the HsdR subunit and the additional domains that are involved in subunit-subunit interactions in Type I systems. The MTase and REase activities of TspGWI are autonomous and can be uncoupled. Structurally and functionally, the TspGWI protomer appears to be a streamlined 'half' of a Type I enzyme.},
  doi       = {10.1186/1471-2199-10-52},
  file      = {:by-author/Z/Zylicz-Stachula/2009_Zylicz-Stachula_52.pdf:PDF},
  keywords  = {Restriction Endonucleases (REases); TspDTI; TspGWI},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
  url       = {http://www.biomedcentral.com/1471-2199/10/52},
}

@Article{Zylicz-Stachula2010,
  author    = {Agnieszka Zylicz-Stachula and Janusz M. Bujnicki and Piotr M. Skowron},
  title     = {Unusual bifunctional methyltransferase/restriction endonuclease {TspGWI}, the prototype of a {T}hermus sp. enzyme family: cloning and characterization of the enzyme},
  year      = {2010},
  pages     = {poster},
  file      = {:by-author/Z/Zylicz-Stachula/2010_Zylicz-Stachula_poster.pdf:PDF},
  keywords  = {Tsp},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Zylicz-Stachula2009,
  author    = {Agnieszka Zylicz-Stachula and Janusz M. Bujnicki and Piotr M. Skowron},
  journal   = {BMC Molecular Biology},
  title     = {Cloning and analysis of a bifunctional methyltransferase/restriction endonuclease {TspGWI}, the prototype of a {T}hermus sp. enzyme family},
  year      = {2009},
  pages     = {10:52},
  doi       = {10.1186/1471-2199-10-52},
  file      = {:by-author/Z/Zylicz-Stachula/2009_Zylicz-Stachula_10\:52.pdf:PDF},
  keywords  = {Tsp},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Zylicz-Stachula2002,
  author    = {Zylicz-Stachula, Agnieszka and Harasimowicz-Slowińska, Renata I. and Sobolewski, Ireneusz and Skowron, Piotr M.},
  journal   = {Nucleic acids research},
  title     = {TspGWI, a thermophilic class-IIS restriction endonuclease from Thermus sp., recognizes novel asymmetric sequence 5'-ACGGA(N11/9)-3'.},
  year      = {2002},
  pages     = {e33},
  volume    = {30},
  abstract  = {A novel prototype class-IIS restriction endonuclease, TspGWI, was isolated from the thermophilic bacterium Thermus sp. GW. The recognition sequence and cleavage positions have been established: TspGWI recognizes the non-palindromic 5-bp sequence 5'-ACGGA-3' and cleaves the DNA 11 and 9 nt downstream in the top and bottom strand, respectively. In addition, an accompanying endonuclease, TspGWII, an isoschizomer of Pst I, was found in Thermus sp. GW cells.},
  file      = {:by-author/Z/Zylicz-Stachula/2002_Zylicz-Stachula_e33.pdf:PDF},
  keywords  = {Restriction Endonucleases (REases); TspDTI; TspGWI},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Zylicz-Stachula2011,
  author    = {Zylicz-Stachula, Agnieszka and Zołnierkiewicz, Olga and Jeżewska-Frąckowiak, Joanna and Skowron, Piotr M.},
  journal   = {BioTechniques},
  title     = {Chemically-induced affinity star restriction specificity: a novel TspGWI/sinefungin endonuclease with theoretical 3-bp cleavage frequency.},
  year      = {2011},
  pages     = {397--406},
  volume    = {50},
  abstract  = {The type IIS/IIC restriction endonuclease TspGWI recognizes the sequence 5'-ACGGA-3', cleaving DNA 11/9 nucleotides downstream. Here we show that sinefungin, a cofactor analog of S-adenosyl methionine, induces a unique type of relaxation in DNA recognition specificity. In the presence of sinefungin, TspGWI recognizes and cleaves at least 12 degenerate variants of the original recognition sequence that vary by single base pair changes from the original 5-bp restriction site with only a single degeneracy per variant appearing to be allowed. In addition, sinefungin was found to have a stimulatory effect on cleavage at these nondegenerate TspGWI recognition sites, irrespective of their number or the DNA topology. Interestingly, no fixed &quot;core&quot; could be identified among the new recognition sequences. Theoretically, TspGWI cleaves DNA every 1024 bp, while sinefungin-induced activity cleaves every 78.8 bp, corresponding to a putative 3-bp long recognition site. Thus, the combination of sinefungin and TspGWI represents a novel frequent cutter, next only to CviJI/CviJI*, that should prove useful in DNA cloning methodologies.},
  file      = {:by-author/Z/Zylicz-Stachula/2011_Zylicz-Stachula_397-suppl.pdf:PDF},
  keywords  = {Tsp},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Zylicz2011,
  author    = {Agnieszka Żylicz-Stachula and Olga Żołnierkiewicz and Joanna Jeżewska-Frąckowiak and Piotr M. Skowron},
  journal   = {BioTechniques},
  title     = {Chemically-induced affinity star restriction specificity: a novel {TspGWI}/sinefungin endonuclease with theoretical 3-bp cleavage frequency},
  year      = {2011},
  pages     = {397--406},
  volume    = {50},
  doi       = {10.2144/000113685},
  file      = {:by-author/Z/Zylicz/2011_Zylicz_Stachula.pdf:PDF},
  keywords  = {Tsp},
  owner     = {em},
  timestamp = {2012.11.09},
  creationdate = {2012-11-09T00:00:00},
}

@Article{Вайнштейн1987,
  author    = {Б. К. Вайнштейн},
  journal   = {Успехи Физических Наук},
  title     = {Электронная Микроскопия Атомного Разрешения},
  year      = {1987},
  pages     = {75--122},
  volume    = {152},
  file      = {:by-author/В/Вайнштейн/1987_Вайнштейн_75.pdf:PDF},
  owner     = {saulius},
  timestamp = {2011.12.13},
  creationdate = {2011-12-13T00:00:00},
}

@Article{Vainshtein1966,
  author    = {Б. К. Вайнштейн},
  journal   = {Успехи Физуческих Наук},
  title     = {Рентгеноструктурный анализ глобулярных белков},
  year      = {1966},
  pages     = {527--565},
  volume    = {88},
  file      = {1966_Вайнштейн_527.pdf:by-author/В/Вайнштейн/1966_Вайнштейн_527.pdf:PDF},
  owner     = {saulius},
  timestamp = {2012.04.05},
  creationdate = {2012-04-05T00:00:00},
}

@Book{Верещагин2012,
  author    = {Н. К. Верещагин and А. Шень},
  publisher = {Издательство МЦНМО},
  title     = {Языки и исчисления},
  year      = {2012},
  file      = {2012_Верещагин.pdf:by-author/В/Верещагин/2012_Верещагин.pdf:PDF},
  keywords  = {Logics; Mathematics},
  language  = {Russian},
  location  = {Москва},
  owner     = {saulius},
  timestamp = {2016.11.04},
  creationdate = {2016-11-04T00:00:00},
  url       = {http://www.mccme.ru/free-books/shen/shen-logic-part2-2.pdf},
}

@Article{Дирак1987,
  author    = {Дирак, П. А. М.},
  journal   = {Успехи Физических наук},
  title     = {Воспоминания о Необычайной Эпохе},
  year      = {1987},
  note      = {Dirас P. A. M. Recollections of an Exciting Еrа//History of Twentieth Century Physics: Proceedings of the International [Summer] School of Physics «Enrico Fermi». Course LVII. Varenna, Lake Como, Italy, villa Monastero, July 31 — August 12, 1972.— (Rendi? conti S. I. F. — LVII).— New York: Academic Press, 1977.— P. 109—146.— Перевод H. Я. Смородинской.},
  number    = {1},
  pages     = {105--135},
  volume    = {153},
  file      = {:by-author/Д/1987_Дирак_105.pdf:PDF},
  keywords  = {History of Physics; History of Science; Non-commutativity; P Numbers; Puasson Brackets; Q-numbers; Quantum Mechanics (QM)},
  owner     = {saulius},
  timestamp = {2012.11.22},
  creationdate = {2012-11-22T00:00:00},
  url       = {http://ufn.ru/ru/articles/1987/9/c/},
}

@Article{Zorkij2000,
  author    = {П. М. Зоркий and Е. В. Соколов},
  journal   = {Вестн. Моск. Ун-та. Сер. 2. Химия},
  title     = {Компьютерное моделирование структуры жидкого бензола: построение физически содержательной стартовой модели для молекулярной динамики},
  year      = {2000},
  pages     = {169--171},
  volume    = {41},
  abstract  = {Разработан алгоритм и составлена программа для построения физически реальной модели кластеров, содержащих большое число молекул бензола. Излагаются результаты модельных расчетов. Полученные кластеры могут служить хорошим начальным приближением для метода молекулярной динамики; вместе с тем и сами по себе эти кластеры дают полезную наглядную картину строения жидкого бензола. Обсуждаются пути дальнейшего развития предложенного подхода.},
  file      = {Zorkij_2000_169-komp._modeliriv._benzola.pdf:by-author/Z/Zorkij/2000_Zorkij_169.pdf:PDF},
  groups    = {sg/applications},
  keywords  = {Molecular Dynamics (MD); Molecular Modelling},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Article{Кадомцев1994,
  author    = {Кадомцев, Б. Б.},
  journal   = {Успехи Физических Наук},
  title     = {Динамика и информация},
  year      = {1994},
  pages     = {449--530},
  volume    = {164},
  abstract  = {Статья посвящена обсуждению вопросов динамического и информационного аспектов поведения сложных физических систем. В классической физике информационная связь появляется при взаимодействии сложных нелинейных систем со стохастическим поведением, когда малое внешнее воздействие может приводить к сильному изменению траектории классической системы в фазовом пространстве. В квантовых системах информационная связь с окружением проявляется в процессах измерения, когда у квантового объекта происходит разрушение когерентности волновой функции, а во внешнем окружении появляется соответствующая информация. Такие процессы можно описать в терминах коллапсов волновых функций. В статье рассмотрены многочисленные примеры коллапсов, приводящих, в частности, к классическому поведению макротел при их информационной связи с неравновесным окружением. В статье подробно обсуждается парадокс Эйнштейна-Подольского-Розена и его возможная роль в процессах передачи информации на расстояние.},
  doi       = {10.3367/UFNr.0164.199405a.0449},
  file      = {1994_Кадомцев_449.pdf:by-author/К/Кадомцев/1994_Кадомцев_449.pdf:PDF},
  keywords  = {Entropy; Information Theory},
  owner     = {saulius},
  timestamp = {2014.08.26},
  creationdate = {2014-08-26T00:00:00},
  url       = {http://ufn.ru/ru/articles/1994/5/a/},
}

@Article{Кадомцев1996,
  author    = {Б. Б. Кадомцев and М. Б. Кадомцев},
  journal   = {Успехи физических наук},
  title     = {Коллапсы волновых функций},
  year      = {1996},
  pages     = {651--659},
  volume    = {166},
  abstract  = {В последнее время в научных публикациях по квантовой механике снова стала живо обсуждаться проблема коллапсов волновых функций. В настоящей статье описаны коллапсы волновых функций при необратимой эволюции сложных квантовых систем, включая системы, участвующие в процессах измерения.},
  doi       = {10.3367/UFNr.0166.199606d.0651},
  file      = {1996_Кадомцев_651.pdf:by-author/К/Кадомцев/1996_Кадомцев_651.pdf:PDF},
  keywords  = {Entropy; Information Theory; Quantum Mechanics (QM)},
  owner     = {saulius},
  publisher = {Успехи физических наук},
  timestamp = {2014.08.26},
  creationdate = {2014-08-26T00:00:00},
  url       = {http://ufn.ru/ru/articles/1996/6/d/},
}

@PhdThesis{Пышная2006,
  author    = {Пышная, Инна Алексеевна},
  school    = {Институт химической биологии и фундаментальной медицины СО РАН},
  title     = {«Мостиковые» олигонуклеотиды как перспективные инструменты в антисенс технологии и ДНК-диагностике},
  year      = {2006},
  file      = {2006_Пышная_phdthesis.pdf:by-author/П/Пышная/2006_Пышная_phdthesis.pdf:PDF},
  owner     = {saulius},
  timestamp = {2013.08.11},
  creationdate = {2013-08-11T00:00:00},
}

@Manuscript{Strogonov2006,
  author    = {Строгонов, Андрей Владимирович},
  title     = {Долговечность интегральных схем и методы ее прогнозирования},
  year      = {2006},
  keywords  = {Elektronika},
  file      = {:by-author/С/Строгонов/2006_Строгонов.doc:DOC},
  owner     = {saulius},
  timestamp = {2015.02.28},
  creationdate = {2015-02-28T00:00:00},
}

@Article{Шиолашвили2005,
  author    = {Л.Н. Шиолашвили},
  journal   = {Электронные библиотеки},
  title     = {Представление математических текстов в Веб},
  year      = {2005},
  number    = {6},
  volume    = {8},
  abstract  = {В статье содержится обзор известных инструментов подготовки математических текстов, а также обсуждаются различные способы представления их в Веб: TeX/LaTeX, MathML, графические форматы. Рассмотрены основные функции и возможности данных инструментов, их достоинства и недостатки. Представлен обзор инструментов для конвертирования математических данных из формата TeX/LaTeX в MathML, из MathML в TeX/LaTeX, из формата содержательной разметки MathML в формат презентационной разметки MathML.},
  file      = {:by-author/Ш/Шиолашвили/2005_Шиолашвили.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
  url       = {http://www.elbib.ru/index.phtml?page=elbib/rus/journal/2005/part6/Sh},
}

@Article{松下能孝2013,
  author           = {松下能孝},
  journal          = {Journal of Surface Analysis},
  title            = {結晶構造データベースと結晶学共通データ・フォーマット {CIF} について},
  year             = {2013},
  pages            = {177--187},
  volume           = {19},
  creationdate     = {2015-10-14T00:00:00},
  file             = {[PDF] from sasj.jp:by-author/松/unknown/2013_177.pdf:PDF},
  groups           = {sg/JAC2009, sg/NAR2012},
  keywords         = {CIF},
  modificationdate = {2023-08-07T10:23:05},
  owner            = {saulius},
  timestamp        = {2015.10.14},
  url              = {http://www.sasj.jp/JSA/CONTENTS/vol.19_3/Vol.19%20No.3/Vol19-No3-177-Matsushita.pdf},
  urldate          = {2015-08-31},
}

@Article{王晨阳2014,
  author    = {王晨阳 and 韩家广},
  journal   = {物理学报},
  title     = {L-天冬酰胺及其一水合物的太赫兹光谱研究},
  year      = {2014},
  pages     = {133203},
  volume    = {63},
  file      = {[PDF] from sinap.ac.cn:by-author/王/unknown/2014_133203.pdf:application/pdf},
  groups    = {sg/NAR2012},
  owner     = {saulius},
  timestamp = {2015.10.14},
  creationdate = {2015-10-14T00:00:00},
  url       = {http://sinapir.sinap.ac.cn/bitstream/331007/14476/2/Terahertz%20study%20of%20L-asparagine%20and%20its%20monohydrate.pdf},
  urldate   = {2015-08-31},
}

@Newsletter{CCP132003,
  editor       = {John Squire},
  number       = {11},
  file         = {:by-author/C/CCP13/2003_CCP13.pdf:PDF},
  organization = {CCP13},
  owner        = {saulius},
  timestamp = {2012.09.18},
  creationdate = {2012-09-18T00:00:00},
  title        = {CCP13 newsletter},
  year         = {2003},
}

@Presentation{BayesianStatisticsInClinicalTrials,
  author           = {Jeff},
  title            = {Bayesian statistics in clinical trials},
  year             = {2008},
  creationdate     = {2015-12-14T00:00:00},
  file             = {Bayesian Statistics in Clinical Trials.ppt:by-author/J/Jeff/2008_Jeff_1.ppt:application/vnd.ms-powerpoint},
  groups           = {sg/Clinical Trials},
  modificationdate = {2023-02-02T09:41:55},
  owner            = {saulius},
  pages            = {1--25},
  timestamp        = {2015.12.14},
  url              = {http://www.massbio.org/writable/committees/presentations/mbc_080828_v001.ppt},
  urldate          = {2015-12-12},
}

@Webpage{CertaintyMathematicsPhysics,
  retrieved        = {2008-07-28},
  title            = {Certainty In Mathematics and Physics},
  url              = {http://www.mathpages.com/home/kmath372.htm},
  creationdate     = {2015-03-02T00:00:00},
  file             = {:by-author/u/unknown/XXXX_unknown_CertaintyMathematicsPhysics.html:URL;:by-author/u/unknown/XXXX_unknown_CertaintyMathematicsPhysics.war:},
  keywords         = {Philosophy},
  modificationdate = {2023-08-17T06:50:39},
  owner            = {saulius},
  timestamp        = {2015.03.02},
}

@Manual{HelpRecoveringFile,
  title     = {Help recovering file},
  file      = {:by-author/u/unknown/XXXX_unknown.txt:Text},
  keywords  = {Computer Science (CS)},
  owner     = {saulius},
  timestamp = {2015.03.10},
  creationdate = {2015-03-10T00:00:00},
}

@Misc{HelpWhenBrokenInto,
  title     = {Help when broken into},
  file      = {:by-author/u/unknown/XXXX_unknown_a.txt:Text},
  keywords  = {Computer Science (CS)},
  owner     = {saulius},
  timestamp = {2015.03.10},
  creationdate = {2015-03-10T00:00:00},
}

@Webpage{QuantumChemistry,
  retrieved = {2008-07-28},
  title     = {Quantum Chemistry},
  url       = {http://cmm.cit.nih.gov/modeling/guide_documents/quantum_mechanics_document.html},
  file      = {:by-author/u/unknown/XXXX_unknown_a.war:},
  keywords  = {Quantum-chemistry},
  owner     = {saulius},
  timestamp = {2015.03.02},
  creationdate = {2015-03-02T00:00:00},
}

@Webpage{ResultsBayesianAnalysis,
  retrieved = {2008-07-28},
  title     = {Results for Bayesian Analysis},
  url       = {http://www.xasa.com/directorio/mozilla/Top/Science/Math/Statistics/Bayesian_Analysis/},
  file      = {:by-author/u/unknown/XXXX_unknown_b.war:},
  groups    = {sg/Bayesian},
  keywords  = {Bayesian Statistics; Mathematics},
  owner     = {saulius},
  timestamp = {2015.03.02},
  creationdate = {2015-03-02T00:00:00},
}

@Electronic{SHELXLXXXX,
  note      = {Accessed on 2013-04-18},
  title     = {User guide to crystal structure refinement with {SHELXL}},
  url       = {http://shelx.uni-ac.gwdg.de/SHELX/shelxl_user_guide.pdf},
  abstract  = {SHELXL is a program for the refinement of crystal structures from diffraction data, and is primarily intended for single crystal X-ray data of organic, inorganicand organometallic structures, though it can also be used for refinement of macromolecules against high resolution data. It is valid for all space groups in conventional settings and otherwise. Polar axis restraints and special position constraints are generated automatically. The program can handle disorder, twinning, and absolute structure determination, and provides a large variety of restraints and constraints for the control of difficult refinements. This user guide is based on the SHELX-97 manual, but has been brought up to date. See also Sheldrick (2008).},
  file      = {:by-author/u/unknown/XXXX_unknown_manual.pdf:PDF},
  owner     = {andrius},
  timestamp = {2013.04.18},
  creationdate = {2013-04-18T00:00:00},
}

@Manual{CCDC2016,
  title        = {Mogul User Guide and Tutorials. 2017 CSD Release},
  organization = {Cambridge Crystallographic Data Centre},
  year         = {2016},
  file         = {:by-author/C/CCDC/2017_CCDC_userguide.pdf:PDF},
  groups       = {sg/Crystallography, am/Crystallography},
  owner        = {andrius},
  timestamp = {2016.12.15},
  creationdate = {2016-12-15T00:00:00},
  url          = {https://www.ccdc.cam.ac.uk/support-and-resources/ccdcresources/f627c0ea4173486893f8782a62132858.pdf},
}

@Booklet{ACS2014,
  title        = {Undergraduate Professional Education in Chemistry: Guidelines and Evaluation Procedures},
  month        = {July},
  note         = {Draft},
  year         = {2014},
  file         = {:by-author/A/ACS/2014_ACS.pdf:PDF},
  lastchecked  = {2015-04-03},
  organisation = {American Chemical Society},
  owner        = {saulius},
  timestamp = {2015.04.03},
  creationdate = {2015-04-03T00:00:00},
  url          = {https://www.acs.org/content/dam/acsorg/about/governance/committees/training/acsapproved/degreeprogram/2014-acs-guidelines-for-bachelors-degree-programs-draft-10-7-2014.pdf},
}

@Manual{HOL2014,
  title     = {The HOL System TUTORIAL},
  year      = {2014},
  file      = {2014_HOL.pdf:by-author/H/HOL/2014_HOL.pdf:PDF},
  keywords  = {Correctness Proofs; Functional Programming; HOL; Higher Order Logics; Logics; Mathematics},
  owner     = {saulius},
  timestamp = {2016.11.04},
  creationdate = {2016-11-04T00:00:00},
  url       = {http://sourceforge.net/projects/hol/files/hol/kananaskis-10/kananaskis-10-tutorial.pdf?download},
}

@Article{Economist2013,
  journal   = {The Economist},
  title     = {How science goes wrong},
  year      = {2013},
  pages     = {11},
  file      = {2013_Economist_11.pdf:by-author/E/Economist/2013_Economist_11.pdf:PDF},
  owner     = {saulius},
  timestamp = {2013.10.30},
  creationdate = {2013-10-30T00:00:00},
}

@Webpage{ALUDesign2009,
  retrieved = {2009-01-31},
  title     = {Arithmetic Logic Unit (ALU) Design},
  url       = {http://library.thinkquest.org/25111/alu.shtm},
  year      = {2009},
  file      = {:by-author/u/unknown/2009_unknown.war:WAR},
  keywords  = {CPU-design; Computer Science (CS)},
  owner     = {saulius},
  timestamp = {2015.03.02},
  creationdate = {2015-03-02T00:00:00},
}

@Presentation{ClinicalTrialsAndBayesianDesign2009,
  title     = {Unit 11: Clinical Trials and Bayesian Design},
  year      = {2009},
  file      = {unit11.pdf:by-author/u/unknown/2009_unknown_a.pdf:application/pdf},
  groups    = {sg/Clinical Trials},
  owner     = {saulius},
  timestamp = {2015.12.14},
  creationdate = {2015-12-14T00:00:00},
  url       = {http://isites.harvard.edu/fs/docs/icb.topic353981.files/unit11.pdf},
  urldate   = {2015-12-12},
}

@Booklet{ACS2008,
  title        = {Undergraduate Professional Education in Chemistry},
  year         = {2008},
  file         = {:by-author/A/ACS/2008_ACS.pdf:PDF},
  lastchecked  = {2015-04-03},
  organisation = {American Chemical Society},
  owner        = {saulius},
  timestamp = {2015.04.03},
  creationdate = {2015-04-03T00:00:00},
  url          = {https://www.acs.org/content/dam/acsorg/about/governance/committees/training/acsapproved/degreeprogram/2008-acs-guidelines-for-bachelors-degree-programs.pdf},
}

@Booklet{ACA2006,
  title       = {Crystallography Education Policies for the Physical and Life Sciences: Sustaining the Science of Molecular Structure in the 21st Century},
  year        = {2006},
  abstract    = {In 2001 and 2003, the United States National Committee for Crystallography (USNC/Cr) Education Subcommittee conducted two surveys (Appendix B). The first survey aimed to determine the content and extent of coverage of crystallography in university curricula, while the second solicited the views of the broader crystallographic community on the status of crystallography education and training in the US, in both the physical and the life sciences. The results of these surveys suggested that, perhaps due to rapid technological advances in the field of modern crystallography, there appears to be a declining number of professional crystallographers, as well as a lack of sufficient education and training in crystallography for individuals who wish to understand and/or use crystallography in their hypothesis-driven research. Recognizing the opportunity to communicate to the broader scientific community the research opportunities afforded by crystallography, as well as the value of crystallographic information, the education committees of the American Crystallographic Association (ACA) and USNC/Cr organized a crystallography education summit, which took place June 1-2, 2005 at the conclusion of the ACA national meeting in Orlando, FL. A broad range of individuals known for their experience and contributions in crystallography education and training participated in this summit (Appendix A). The outcome of this process is this consensus policy statement on crystallography education and training.},
  file        = {:by-author/A/ACA/2006_ACA.pdf:PDF},
  lastchecked = {2015-04-03},
  owner       = {saulius},
  timestamp = {2015.04.03},
  creationdate = {2015-04-03T00:00:00},
  url         = {http://www.amercrystalassn.org/documents/USNCCrPolicies.pdf},
}

@InProceedings{2005,
  title     = {Basic ternary logic circuits},
  year      = {2005},
  file      = {:by-author/unknown/unknown/2005.pdf:PDF},
  owner     = {saulius},
  timestamp = {2013.08.10},
  creationdate = {2013-08-10T00:00:00},
}

@Article{2003,
  journal   = {Upgrade},
  title     = {Petition to the European Parliament on the Proposal for a Directive on the Patentability of Computer-implemented Inventions},
  year      = {2003},
  pages     = {24},
  volume    = {4},
  file      = {:by-author/U/UPGRADE/2003_UPGRADE_24.pdf:PDF},
  keywords  = {Computer Science (CS); Software Patents},
  owner     = {saulius},
  timestamp = {2012.10.21},
  creationdate = {2012-10-21T00:00:00},
}

@TechReport{ProcessorPerformance2003,
  institution = {University of Minnesota, Supercomputing Institute for Digital Simulation and Advanced Computation},
  title       = {Improving Processor Performance by Guessing and Simplifying},
  year        = {2003},
  number      = {2},
  file        = {:by-author/u/unknown/2003_unknown.war:WAR},
  journal     = {Winter 2003 Research Bulletin of the Supercomputing Institute},
  keywords    = {Computer Performance; Computer Science (CS); Program Optimisation; Supercmputing},
  owner       = {saulius},
  timestamp = {2015.03.02},
  creationdate = {2015-03-02T00:00:00},
  url         = {http://www.msi.umn.edu/general/Bulletin/Vol.19-No.2/ece.html},
  volume      = {19},
}

@Electronic{SHELX2003,
  note      = {Shelx manual?},
  title     = {High throughput phasing with SHELXC/D/E},
  url       = {http://shelx.uni-ac.gwdg.de/SHELX/fastphas.pdf},
  year      = {2003},
  abstract  = {The new program SHELXC is designed to provide a simple and fast way of setting up the files for the programs SHELXD (heavy atom location) and SHELXE (phasing and density modification) that are used for macromolecular phasing by the MAD, SAD, SIR and SIRAS methods. These three programs may be run in batch mode or called from a GUI such as hkl2map (Thomas Schneider & Thomas Pape). SHELXC is much less versatile than the Bruker Nonius XPREP program for this purpose, but if you are sure of the space group and there are no problems with the indexing or twinning and the f’ and f” parts of the scattering factors do not need to be refined, SHELXC should be adequate. SHELXC can read either HKL2000 .sca files or SHELX .hkl files (F-squared unless the -f switch is used to specify F). To transfer data from CCP4 it is advisable to generate .sca files using CCP4i. Scripts for batch mode under UNIX are described here but users are encouraged to call one or more of these programs from their own GUI-based high throughput pipelines. SHELXC, SHELXD and SHELXE are stand-alone executables that do not require environment variables or parameter files etc., so all that is needed to install them is to put them in a directory that is in the ‘path’ (e.g. /usr/local/bin under Linux).},
  file      = {:by-author/u/unknown/2003_unknown.pdf:PDF},
  owner     = {saulius},
  timestamp = {2008.07.28},
  creationdate = {2008-07-28T00:00:00},
}

@Standard{XHTML2002,
  institution  = {W3C},
  organization = {W3C},
  title        = {XHTMLTM 1.0 The Extensible HyperText Markup Language (Second Edition): A Reformulation of HTML 4 in XML 1.0},
  language     = {English},
  month        = {August},
  url          = {http://www.w3.org/TR/2002/REC-xhtml1-20020801},
  year         = {2002},
  file         = {:by-author/W/W3C/2002_W3C_XHTML1.pdf:PDF},
  keywords     = {HTML; Recommendation; Standard; W3C; WWW; Web; XHTML},
  owner        = {saulius},
  timestamp = {2015.08.07},
  creationdate = {2015-08-07T00:00:00},
}

@Manuscript{BayesianMethods2000,
  title     = {Bayesian Methods},
  year      = {2000},
  url       = {http://www.wiley.com/legacy/wileychi/eob/bct/Cab001-.pdf},
  file      = {Bayesian Methods.pdf:by-author/u/unknown/2000_unknown_a.pdf:application/pdf},
  groups    = {sg/Clinical Trials},
  owner     = {saulius},
  timestamp = {2015.12.14},
  creationdate = {2015-12-14T00:00:00},
  urldate   = {2015-12-12},
}

@Standard{HTML1999,
  institution  = {W3C},
  organization = {W3C},
  title        = {HTML 4.01 Specification},
  month        = {December},
  url          = {http://www.w3.org/TR/1999/REC-html401-19991224},
  year         = {1999},
  file         = {:by-author/W/W3C/1999_W3C_HTML40.pdf:PDF},
  keywords     = {HTML; Recommendation; Standard; W3C; WWW; Web},
  owner        = {saulius},
  timestamp = {2015.08.07},
  creationdate = {2015-08-07T00:00:00},
}

@Misc{LucentTechnologies1997,
  title       = {The Limbo Programming Language},
  year        = {1997},
  file        = {:by-author/u/unknown/1997_unknown.war:WAR},
  institution = {Lucent Technologies},
  keywords    = {Computer Science (CS); Limbo; Programming Languages},
  owner       = {saulius},
  timestamp = {2015.03.02},
  creationdate = {2015-03-02T00:00:00},
  url         = {http://www.cs.rit.edu/~ats/inferno/limbo/},
}

@Standard{ISO1996:14977,
  organization = {ISO/IEC},
  title        = {{I}nformation technology -- {S}yntactic metalanguage -- {E}xtended {BNF}},
  language     = {English},
  number       = {ISO/IEC 14977:1996(E)},
  year         = {1996},
  file         = {:by-author/I/ISO/1996_ISO_14977.pdf:PDF},
  keywords     = {BNF; Computer Languages; EBNF; Extended Backus-Naur Form; Standard},
  owner        = {saulius},
  timestamp = {2015.07.01},
  creationdate = {2015-07-01T00:00:00},
}

@Manual{PGModula1995,
  title     = {Garden Point Modula Language Reference Manual},
  year      = {1995},
  file      = {:by-author/u/unknown/1995_unknown_b.ps:PostScript;:by-author/u/unknown/1995_unknown_a.ps:PostScript;:by-author/u/unknown/1995_unknown.ps:PostScript},
  keywords  = {Computer Science (CS)},
  owner     = {saulius},
  timestamp = {2015.03.03},
  creationdate = {2015-03-03T00:00:00},
}

@Misc{UKPatentAct1988,
  title     = {UK Copyright Designs and Patents Act 1988},
  year      = {1988},
  file      = {:by-author/u/unknown/1988_unknown.PDF:},
  keywords  = {Patentai; Teise},
  owner     = {saulius},
  timestamp = {2015.03.03},
  creationdate = {2015-03-03T00:00:00},
}

@Article{Schreyer2014,
  author    = {Martin Schreyer and Liangfeng Guo and Satyanarayana Thirunahari and Feng Gao and Marc Garland},
  journal   = {Journal of Applied Crystallography},
  title     = {Simultaneous determination of several crystal structures from powder mixtures: the combination of powder X-ray diffraction, band-target entropy minimization and Rietveld methods},
  year      = {2014},
  month     = {mar},
  number    = {2},
  pages     = {659--667},
  volume    = {47},
  abstract  = {Crystal structure determination is the key to a detailed understanding of crystalline materials and their properties. This requires either single crystals or high-quality single-phase powder X-ray diffraction data. The present contribution demonstrates a novel method to reconstruct single-phase powder diffraction data from diffraction patterns of mixtures of several components and subsequently to determine the individual crystal structures. The new method does not require recourse to any database of known materials but relies purely on numerical separation of the mixture data into individual component diffractograms. The resulting diffractograms can subsequently be treated like single-phase powder diffraction data, i.e. indexing, structure solution and Rietveld refinement. This development opens up a host of new opportunities in materials science and related areas. For example, crystal structures can now be determined at much earlier stages when only impure samples or polymorphic mixtures are available.},
  date      = {2017-06-16},
  doi       = {10.1107/S1600576714003379},
  file      = {:by-author/S/Schreyer/2014_Schreyer_659a.pdf:PDF	;:by-author/S/Schreyer/2014_Schreyer_659.pdf:PDF},
  keywords  = {Band Target Entropy Minimization; COD Data Maintenancs; Mixture Analysis; Polymorphism; Powder Diffraction; Powder X-ray Diffraction; Rietveld Refinement; Structure Solution; X-ray Crystallography},
  owner     = {saulius},
  publisher = {International Union of Crystallography ({IUCr})},
  timestamp = {2017.06.16},
  creationdate = {2017-06-16T00:00:00},
  urldate   = {2017-06-16},
}

@Misc{Slonneger2006,
  author    = {Ken Slonneger},
  title     = {XML Schemas},
  year      = {2006},
  file      = {04.XMLSchemas.pdf:by-author/S/Slonneger/2006_Slonneger.pdf:PDF},
  keywords  = {XML; XML Schemas},
  owner     = {saulius},
  timestamp = {2017.03.17},
  creationdate = {2017-03-17T00:00:00},
  url       = {http://homepage.divms.uiowa.edu/~slonnegr/xml/04.XMLSchemas.pdf},
}

@InProceedings{Agier2005,
  author    = {Marie Agier and Jean-Marc Petit},
  title     = {A New and Useful Syntactic Restriction on Rule and Semantics for Tabular and Data},
  year      = {2005},
  file      = {:by-author/A/Agier/2005_Agier.pdf:PDF},
  owner     = {saulius},
  timestamp = {2017.07.14},
  creationdate = {2017-07-14T00:00:00},
  url       = {http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.96.9543&rep=rep1&type=pdf},
}

@Article{Allen1974,
  author    = {F. H. Allen and Olga Kennar and W. D. S. Motherwel and W. G. Town and D. G. Watson},
  journal   = {J. App. Cryst.},
  title     = {The Cambridge Crystallographic Data Centre. Part 3. The Unique Molecule Program},
  year      = {1974},
  issn      = {0021-8898},
  number    = {1},
  pages     = {73--78},
  volume    = {7},
  abstract  = {An extensive computer program has been developed to check the internal consistency of published, numeric, crystallographic data prior to storage in the data files of the Cambridge Crystallographic Data Centre. The coding is in Fortran IV for an IBM 3701165 with 1 megabyte store. The atomic coordinates, constitution and connectivity of the unique bonded residue(s) are determined from the published asymmetric unit coordinates. Bond lengths are calculated and compared with published values, and any discrepancies are flagged. Checks are made to ensure that the valency requirements of certain elemental types are not violated. The connectivity of the system is expressed in a compact notation. Axial projection plots may optionally be produced on the line printer. The program is likely to be generally useful to individual crystallographers at various stages of an analysis as well as for checking of published data.},
  doi       = {10.1107/S0021889874008739},
  file      = {:by-author/A/Allen/1974_Allen_73.pdf:PDF},
  keywords  = {CCDC; Crystallography; Data Management; Databases; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2017.07.26},
  creationdate = {2017-07-26T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0021889874008739},
}

@Manuscript{Hallberg2006,
  author    = {Sven Moritz Hallberg},
  title     = {About the Swedish analysis of Nazi Germany’s and crypto teleprinters},
  year      = {2006},
  url       = {https://events.ccc.de/camp/2007/Fahrplan/attachments/1305-pesco06gschreiber.pdf},
  file      = {:by-author/H/Hallberg/2006_Hallberg.pdf:PDF},
  owner     = {saulius},
  timestamp = {2017.07.26},
  creationdate = {2017-07-26T00:00:00},
}

@InBook{Майерс1982,
  author    = {Г. Майерс},
  title     = {Список вопросов для выявления ошибок при инспекции},
  year      = {1982},
  booktitle = {Искусство тестирования программ},
  file      = {:by-author/М/Майерс/1982_Майерс.pdf:PDF},
  language  = {Russian},
  owner     = {saulius},
  timestamp = {2017.07.26},
  creationdate = {2017-07-26T00:00:00},
}

@Presentation{Spek2010a,
  author    = {Ton Spek},
  title     = {Why Crystal Structure Validation?},
  year      = {2010},
  file      = {2010_Spek.pdf:by-author/S/Spek/2010_Spek.pdf:PDF},
  owner     = {saulius},
  timestamp = {2017.07.27},
  creationdate = {2017-07-27T00:00:00},
  url       = {http://xray.chem.wisc.edu/Resources/Meetings/Bruker18/06_Karlsruhe.pdf},
}

@Presentation{Raginis2017a,
  author    = {Erikas Raginis},
  title     = {Materials Data Curation System},
  year      = {2017},
  file      = {:by-author/R/Raginis/2017_Raginis.pdf:PDF},
  owner     = {erikas},
  timestamp = {2017.07.21},
  creationdate = {2017-07-21T00:00:00},
}

@Manuscript{Beeton2015,
  author    = {Barbara Beeton and Asmus Freytag and Laurențiu Iancu and Murray Sargent III},
  title     = {Proposal to Represent the Slashed Zero Variant of Empty Set},
  year      = {2015},
  url       = {http://www.unicode.org/L2/L2015/15268-slashed-zero.pdf},
  date      = {2015-10-30},
  file      = {15268-slashed-zero.pdf:by-author/B/Beeton/2015_Beeton.pdf:PDF},
  owner     = {saulius},
  timestamp = {2017.07.27},
  creationdate = {2017-07-27T00:00:00},
}

@Article{Oedegaard2017,
  author           = {Øien-Ødegaard, S. and Shearer, G. C. and Wragg, D. S. and Lillerud, K. P.},
  journal          = {Chem. Soc. Rev.},
  title            = {Pitfalls in metal–organic framework crystallography: towards more accurate crystal structures},
  year             = {2017},
  issn             = {1460-4744},
  comment          = {Cites Harlow1996.},
  creationdate     = {2017-07-26T00:00:00},
  doi              = {10.1039/c6cs00533k},
  file             = {c6cs00533k.pdf:by-author/Ø/Øien-Ødegaard/2017_Øien-Ødegaard.pdf:PDF;:by-author/Ø/Øien-Ødegaard/2017_Øien-Ødegaard_suppl/c6cs00533k2.pdf:PDF},
  keywords         = {Crystallography; Metal-Organic Frameworks (MOF); Structure Quality},
  modificationdate = {2024-08-26T13:25:08},
  owner            = {saulius},
  publisher        = {Royal Society of Chemistry (RSC)},
  rights           = {This journal is © The Royal Society of Chemistry 2017},
  timestamp        = {2017.07.26},
  url              = {http://dx.doi.org/10.1039/C6CS00533K},
}

@Manuscript{Spek2010,
  author           = {A. L. Spek},
  title            = {CIF Validation With The Program Platon (version 01-10-2010)},
  year             = {2010},
  keywords         = {CIF},
  url              = {http://www.cryst.chem.uu.nl/platon/CIF-VALIDATION.pdf},
  creationdate     = {2017-07-26T00:00:00},
  file             = {:by-author/S/Spek/2010_Spek_a.pdf:PDF},
  modificationdate = {2023-08-07T10:23:04},
  owner            = {saulius},
  timestamp        = {2017.07.26},
}

@Webpage{HarrisGeospatial2017,
  author    = {{Harris Geospatial}},
  retrieved = {2017-06-13},
  title     = {The ENVI Header Format},
  url       = {https://www.harrisgeospatial.com/docs/enviheaderfiles.html},
  year      = {2017},
  file      = {:by-author/G/Geospatial/2017_Geospatial.pdf:PDF},
  owner     = {andrius},
  publisher = {IEEE},
  timestamp = {2017.06.13},
  creationdate = {2017-06-13T00:00:00},
}

@Webpage{Larrucea2017,
  author    = {Julen Larrucea},
  retrieved = {2017-05-07},
  title     = {IR and Raman spectra calculated with Quantum Espresso},
  url       = {http://larrucea.eu/compute-ir-raman-spectra-qe/},
  year      = {2017},
  file      = {:by-author/L/Larrucea/2017_Larrucea.pdf:PDF},
  keywords  = {Quantum Espresso; Raman Spectra; Theoretical},
  owner     = {andrius},
  timestamp = {2017.05.07},
  creationdate = {2017-05-07T00:00:00},
}

@Presentation{Kahn2011,
  author    = {Richard Kahn},
  title     = {X-ray Detector Software for processing single-crystal monochromatic diffraction data recorded by the rotation method},
  year      = {2011},
  file      = {MCS2011-RK-XDS.pdf:by-author/K/Kahn/2011_Kahn.pdf:PDF},
  owner     = {saulius},
  timestamp = {2017.07.27},
  creationdate = {2017-07-27T00:00:00},
  url       = {http://www.xtal.iqfr.csic.es/MCS2011/MCS2011-RK-XDS.pdf},
}

@Manuscript{Sutter2006,
  author    = {Herb Sutter},
  title     = {A Design Rationale for C++/CLI},
  year      = {2006},
  url       = {http://www.open-std.org/jtc1/sc22/wg21/docs/papers/2006/n1956.pdf},
  file      = {n1956.pdf:by-author/S/Sutter/2006_Sutter.pdf:PDF},
  owner     = {saulius},
  timestamp = {2017.07.27},
  creationdate = {2017-07-27T00:00:00},
}

@InProceedings{Hunter2001,
  author    = {Jane Hunter and Carl and Lagoze and DSTC Pty and Ltd and Digital Library and Research Group},
  title     = {Combining RDF and XML Schemas to Enhance Interoperability Between Metadata Application Profiles},
  year      = {2001},
  publisher = {IEEE},
  abstract  = {scenarios in which interoperability between metadata descriptions The term “application profile” has recently become highly topical. is essential: Heery and Patel [1] define application profiles as metadata • To apply a single query syntax over descriptions expressed in schemas which consist of metadata elements drawn from one or multiple descriptive formats; more namespaces, combined together by implementers and • To express the relationship between multiple descriptions in optimised for a particular local application. They state that the terms of a “core” or “canonical” description; principal characteristics of an application profile are that: it may • To project community or individual specific descriptions out draw on one or more existing namespaces; does not introduce new of a single canonical description. metadata elements; it can specify permitted schemes and values; The metadata interoperability problem has been exacerbated by and it can refine standard metadata elements. Significant new the need for more complex metadata descriptions. It has become initiatives such as TV-Anytime [2], MPEG-21 [3] and the Open increasingly evident that simple standards such as Dublin Core Archives Initiative (OAI) [4] are demanding application profiles (DC) [13] cannot satisfy the requirements of communities such as which combine elements from a number of different existing TV-Anytime [2], MPEG-21 [3], BIBLINK [14] and OAI [4] who standardized metadata schemas whilst maintaining interoperability need to combine metadata standards for simple resource discovery and satisfying their own specific requirements through (DC), rights management (INDECS [15]), multimedia (MPEG-7 refinements, extensions and additions. [16]), geospatial (FGDC [17]), educational (GEM [18], IEEE So far approaches to application profiles have been based on LOM [19]) and museum (CIDOC CRM [20]) content, to satisfy either RDF Schemas [5] or XML Schemas [6,7,8]. The their application-specific requirements. SCHEMAS project [9] has adopted a purely RDF Schema In this paper we propose mechanisms for metadata interoperability approach. Justification for a pure XML Schema approach to based on both RDF Schema and XML Schema. Using examples application profiles is given in [10]. Despite high level assurances and implementations, we demonstrate how these two schema of unification from the W3C [11, 12], a purist and competitive languages can be made to work together to enable flexible, attitude has prevailed amongst implementers. This has been dynamic mapping between complex, metadata descriptions which because the demarcation of roles and the interface between these mix elements from multiple domains, i.e., application profiles. two disparate W3C Candidate Recommendations has been fuzzy; Our objective is to demonstrate how these two W3C Candidate no low level details or implementations describing interface Recommendations can be used in a complementary manner, mechanisms have been provided; and implementers have been exploiting the benefits of both. afraid of compromising interoperability. In this paper we describe In Section 2 we describe our overall web metadata architecture a hybrid collaborative approach which combines the semantic proposal and how the various components described in this paper knowledge of RDF Schemas with the explicit structural, fit together. In Section 3 we describe alternative mechanisms by cardinality and datatyping constraints provided by XML Schemas which the two schema languages can be made to work together. in a complementary manner. First we describe our view of how The first part of section 3 defines clear boundaries between the XML Schema and RDF Schema fit into the overall web metadata responsibilities of RDF Schema and XML Schema to prevent architecture. We then describe possible schema interface functional overlap which could lead to contradictory constraints or mechanisms. Finally using examples and mapping incompatibilities. The second part of section 3 examines implementations based on XSLT and a metadata ontology, we alternative mechanisms for linking complementary RDF and demonstrate how interoperability between application profiles can XML Schemas which are being used together to define a single be enhanced by using a dual schema approach. metadata element set. In Section 4 we describe MetaNet, a “super- ontology” derived by merging a number of different domain- Keywords: Metadata, Interoperability, XML, RDF, Schema, specific RDF Schemas. In Section 5 we describe how the semantic XSLT knowledge within MetaNet can be linked to XSLT to enable},
  file      = {:by-author/H/Hunter/2001_Hunter.pdf:PDF},
  owner     = {saulius},
  timestamp = {2017.07.26},
  creationdate = {2017-07-26T00:00:00},
  url       = {http://www.www10.org/cdrom/papers/pdf/p572.pdf},
}

@Article{Bruno2011,
  author           = {Bruno, I.J. and Shields, G.P. and Taylor, R.},
  journal          = {Acta Crystallographica Section B Structural Science},
  title            = {Deducing chemical structure from crystallographically determined atomic coordinates},
  year             = {2011},
  number           = {4},
  pages            = {333--349},
  volume           = {67},
  abstract         = {An improved algorithm has been developed for assigning chemical structures to incoming entries to the Cambridge Structural Database, using only the information available in the deposited CIF. Steps in the algorithm include detection of bonds, selection of polymer unit, resolution of disorder, and assignment of bond types and formal charges. The chief difficulty is posed by the large number of metallo-organic crystal structures that must be processed, given our aspiration that assigned chemical structures should accurately reflect properties such as the oxidation states of metals and redox-active ligands, metal coordination numbers and hapticities, and the aromaticity or otherwise of metal ligands. Other complications arise from disorder, especially when it is symmetry imposed or modelled with the SQUEEZE algorithm. Each assigned structure is accompanied by an estimate of reliability and, where necessary, diagnostic information indicating probable points of error. Although the algorithm was written to aid building of the Cambridge Structural Database, it has the potential to develop into a general-purpose tool for adding chemical information to newly determined crystal structures.},
  creationdate     = {2017-07-27T00:00:00},
  doi              = {10.1107/S0108768111024608},
  file             = {ps5012.pdf:by-author/B/Bruno/2011_Bruno_333.pdf:PDF},
  keywords         = {Bayesian Statistics; CIF; CSD; Catena Structure; Disorder Resolution; Structure Assignment},
  modificationdate = {2023-08-07T10:23:04},
  owner            = {saulius},
  publisher        = {International Union of Crystallography},
  rights           = {http://creativecommons.org/licenses/by/2.0/uk},
  source           = {Acta Cryst (2011). B67, 333-349 [doi:10.1107/S0108768111024608]},
  timestamp        = {2017.07.27},
  url              = {http://scripts.iucr.org/cgi-bin/paper?S0108768111024608},
}

@Reference{Vromans2006,
  author    = {Johan Vromans},
  file      = {refguide.pdf:by-author/V/Vromans/2006_Vromans.pdf:PDF},
  owner     = {saulius},
  timestamp = {2017.07.27},
  creationdate = {2017-07-27T00:00:00},
  title     = {Perl Best Practices: Reference Guide},
  url       = {https://campusvirtual.ull.es/ocw/file.php/43/perlexamples/refguide.pdf},
  year      = {2006},
}

@Article{Economist2017,
  author    = {{The Economist}},
  journal   = {The Economist},
  title     = {Breaking free; Time's up},
  year      = {2017},
  file      = {:by-author/E/Economist/2017_Economist.pdf:PDF},
  owner     = {saulius},
  timestamp = {2017.07.26},
  creationdate = {2017-07-26T00:00:00},
}

@Presentation{Blochwitz2011,
  author    = {Torsten Blochwitz and Martin Otter},
  title     = {The Functional Mockup Interface for Tool independent Exchange of Simulation Models},
  year      = {2011},
  file      = {:by-author/B/Blochwitz/2011_Blochwitz.pdf:PDF},
  owner     = {saulius},
  timestamp = {2017.07.27},
  creationdate = {2017-07-27T00:00:00},
  url       = {https://trac.fmi-standard.org/export/700/branches/public/docs/Modelica2011/The_Functional_Mockup_Interface.pdf},
}

@TechReport{Moriai2005,
  author      = {Shiho Moriai and Yiqun Lisa Yin},
  institution = {The Institute of Electronics, Information and Communication Engineers},
  title       = {Cryptanalysis of Twofish (II)},
  year        = {2005},
  file        = {:by-author/M/Moriai/2005_Moriai.pdf:PDF},
  keywords    = {AES; Cryptanalysis; Dierential Cryptanalysis; Truncated Dierential; Twosh},
  owner       = {saulius},
  timestamp = {2017.07.27},
  creationdate = {2017-07-27T00:00:00},
  url         = {https://www.schneier.com/twofish-analysis-shiho.pdf},
}

@InProceedings{Speicher2005,
  author    = {Steve Speicher and Kevin E. Kelly},
  title     = {Compound XML document profiles for rich content, Part 1: Exploring extensibility alternatives using XML Schema},
  year      = {2005},
  date      = {2005-09-13},
  file      = {:by-author/S/Speicher/2005_Speicher.pdf:PDF},
  owner     = {saulius},
  timestamp = {2017.07.26},
  creationdate = {2017-07-26T00:00:00},
  url       = {https://www.ibm.com/developerworks/library/x-cxdp1/x-cxdp1-pdf.pdf},
}

@Presentation{Diederichs2011,
  author    = {Kay Diederichs},
  title     = {Data Processing Using XDS},
  year      = {2011},
  file      = {XDS_Diederichs_ACA2011.pdf:by-author/D/Diederichs/2011_Diederichs.pdf:PDF},
  owner     = {saulius},
  timestamp = {2017.07.27},
  creationdate = {2017-07-27T00:00:00},
  url       = {http://strucbio.biologie.uni-konstanz.de/~dikay/XDS_Diederichs_ACA2011.pdf},
}

@Presentation{Costello2009,
  author    = {Roger L. Costello},
  title     = {NVDL (Namespace-based Validation Dispatching Language)},
  year      = {2009},
  file      = {:by-author/C/Costello/2009_Costello.ppt:PowerPoint},
  keywords  = {Validation; XML},
  owner     = {saulius},
  timestamp = {2017.07.27},
  creationdate = {2017-07-27T00:00:00},
  url       = {http://www.xfront.com/nvdl/nvdl.zip},
}

@Article{Bentley2008,
  author    = {David R. Bentley and Shankar Balasubramanian and Harold P. Swerdlow and Geoffrey P. Smith and John Milton and Clive G. Brown and Kevin P. Hall and Dirk J. Evers and Colin L. Barnes and Helen R. Bignell and Jonathan M. Boutell and Jason Bryant and Richard J. Carter and R. Keira Cheetham and Anthony J. Cox and Darren J. Ellis and Michael R. Flatbush and Niall A. Gormley and Sean J. Humphray and Leslie J. Irving and Mirian S. Karbelashvili and Scott M. Kirk and Heng Li and Xiaohai Liu and Klaus S. Maisinger and Lisa J. Murray and Bojan Obradovic and Tobias Ost and Michael L. Parkinson and Mark R. Pratt and Isabelle M. J. Rasolonjatovo and Mark T. Reed and Roberto Rigatti and Chiara Rodighiero and Mark T. Ross and Andrea Sabot and Subramanian V. Sankar and Aylwyn Scally and Gary P. Schroth and Mark E. Smith and Vincent P. Smith and Anastassia Spiridou and Peta E. Torrance and Svilen S. Tzonev and Eric H. Vermaas and Klaudia Walter and Xiaolin Wu and Lu Zhang and Mohammed D. Alam and Carole Anastasi and Ify C. Aniebo and David M. D. Bailey and Iain R. Bancarz and Saibal Banerjee and Selena G. Barbour and Primo A. Baybayan and Vincent A. Benoit and Kevin F. Benson and Claire Bevis and Phillip J. Black and Asha Boodhun and Joe S. Brennan and John A. Bridgham and Rob C. Brown and Andrew A. Brown and Dale H. Buermann and Abass A. Bundu and James C. Burrows and Nigel P. Carter and Nestor Castillo and Maria Chiara E. Catenazzi and Simon Chang and R. Neil Cooley and Natasha R. Crake and Olubunmi O. Dada and Konstantinos D. Diakoumakos and Belen Dominguez-Fernandez and David J. Earnshaw and Ugonna C. Egbujor and David W. Elmore and Sergey S. Etchin and Mark R. Ewan and Milan Fedurco and Louise J. Fraser and Karin V. Fuentes Fajardo and W. Scott Furey and David George and Kimberley J. Gietzen and Colin P. Goddard and George S. Golda and Philip A. Granieri and David E. Green and David L. Gustafson and Nancy F. Hansen and Kevin Harnish and Christian D. Haudenschild and Narinder I. Heyer and Matthew M. Hims and Johnny T. Ho and Adrian M. Horgan and Katya Hoschler and Steve Hurwitz and Denis V. Ivanov and Maria Q. Johnson and Terena James and T. A. Huw Jones and Gyoung-Dong Kang and Tzvetana H. Kerelska and Alan D. Kersey and Irina Khrebtukova and Alex P. Kindwall and Zoya Kingsbury and Paula I. Kokko-Gonzales and Anil Kumar and Marc A. Laurent and Cynthia T. Lawley and Sarah E. Lee and Xavier Lee and Arnold K. Liao and Jennifer A. Loch and Mitch Lok and Shujun Luo and Radhika M. Mammen and John W. Martin and Patrick G. McCauley and Paul McNitt and Parul Mehta and Keith W. Moon and Joe W. Mullens and Taksina Newington and Zemin Ning and Bee Ling Ng and Sonia M. Novo and Michael J. O'Neill and Mark A. Osborne and Andrew Osnowski and Omead Ostadan and Lambros L. Paraschos and Lea Pickering and Andrew C. Pike and Alger C. Pike and D. Chris Pinkard and Daniel P. Pliskin and Joe Podhasky and Victor J. Quijano and Come Raczy and Vicki H. Rae and Stephen R. Rawlings and Ana Chiva Rodriguez and Phyllida M. Roe and John Rogers and Maria C. Rogert Bacigalupo and Nikolai Romanov and Anthony Romieu and Rithy K. Roth and Natalie J. Rourke and Silke T. Ruediger and Eli Rusman and Raquel M. Sanches-Kuiper and Martin R. Schenker and Josefina M. Seoane and Richard J. Shaw and Mitch K. Shiver and Steven W. Short and Ning L. Sizto and Johannes P. Sluis and Melanie A. Smith and Jean Ernest Sohna Sohna and Eric J. Spence and Kim Stevens and Neil Sutton and Lukasz Szajkowski and Carolyn L. Tregidgo and Gerardo Turcatti and Stephanie vandeVondele and Yuli Verhovsky and Selene M. Virk and Suzanne Wakelin and Gregory C. Walcott and Jingwen Wang and Graham J. Worsley and Juying Yan and Ling Yau and Mike Zuerlein and Jane Rogers and James C. Mullikin and Matthew E. Hurles and Nick J. McCooke and John S. West and Frank L. Oaks and Peter L. Lundberg and David Klenerman and Richard Durbin and Anthony J. Smith},
  journal   = {Nature},
  title     = {Accurate whole human genome sequencing using reversible terminator chemistry},
  year      = {2008},
  month     = {nov},
  number    = {7218},
  pages     = {53--59},
  volume    = {456},
  doi       = {10.1038/nature07517},
  file      = {:by-author/B/Bentley/2008_Bentley_53.pdf:PDF},
  owner     = {saulius},
  publisher = {Springer Nature},
  timestamp = {2017.07.28},
  creationdate = {2017-07-28T00:00:00},
}

@Presentation{Youssef2014,
  author    = {Sharief Youssef},
  title     = {Materials Data Curation System},
  year      = {2014},
  file      = {:by-author/Y/Youssef/2014_Youssef.pptx:PowerPoint 2007+},
  keywords  = {Data Curation; Databases; Materails Data; XML},
  owner     = {saulius},
  timestamp = {2017.07.29},
  creationdate = {2017-07-29T00:00:00},
  url       = {https://www.nist.gov/document-3307},
}

@Article{Chandrasekhar1969,
  author    = {Chandrasekhar, S. and Ramaseshan, S. and Singh, A. K.},
  journal   = {Acta Crystallographica Section A},
  title     = {Experimental determination of the extinction factor by the use of polarized X-rays},
  year      = {1969},
  month     = {Jan},
  number    = {1},
  pages     = {140--142},
  volume    = {25},
  abstract  = {The problem of estimating the extinction factor by use of polarized X-rays has been re-examined in the light of the theory of X-ray diffraction in real crystals developed recently by Zachariasen. Expressions are given for deriving the extinction-free structure factors in terms of the observed integrated intensities for perpendicular and parallel polarizations. A simple attachment to a diffractometer for analysing the polarization of the diffracted beam is described. Measurements on quartz are presented; the extinction-free structure factors so obtained are in excellent agreement with Zachariasen's calculated values based on new {\it f} curves.},
  doi       = {10.1107/S0567739469000234},
  file      = {:by-author/C/Chandrasekhar/1969_Chandrasekhar_140.pdf:PDF},
  owner     = {saulius},
  timestamp = {2017.08.06},
  creationdate = {2017-08-06T00:00:00},
  url       = {https://doi.org/10.1107/S0567739469000234},
}

@Article{Frieze1988,
  author    = {A. M. Frieze},
  journal   = {Journal of algorithms},
  title     = {An Algorithm and for Finding and Hamilton Cycles and in and Random Directed and Graphs},
  year      = {1988},
  pages     = {181--204},
  volume    = {9},
  file      = {:by-author/F/Frieze/1988_Frieze_181.pdf:PDF},
  owner     = {saulius},
  timestamp = {2017.08.06},
  creationdate = {2017-08-06T00:00:00},
  url       = {http://www.math.cmu.edu/users/af1p/Texfiles/dham.pdf},
}

@Article{Alhalabi2016,
  author    = {Wadee Alhalabi and Omar Kitanneh and Amira Alharbi and Zain Balfakih and Akila Sarirete},
  journal   = {{SpringerPlus}},
  title     = {Efficient solution for finding Hamilton cycles in undirected graphs},
  year      = {2016},
  month     = {jul},
  number    = {1},
  volume    = {5},
  doi       = {10.1186/s40064-016-2746-8},
  file      = {:by-author/A/Alhalabi/2016_Alhalabi.pdf:PDF},
  owner     = {saulius},
  publisher = {Springer Nature},
  timestamp = {2017.08.06},
  creationdate = {2017-08-06T00:00:00},
}

@Article{Pyykkoe2015,
  author    = {Pekka Pyykkö},
  journal   = {The Journal of Physical Chemistry A},
  title     = {Additive Covalent Radii for Single-, Double-, and Triple-Bonded Molecules and Tetrahedrally Bonded Crystals: A Summary},
  year      = {2015},
  month     = {mar},
  number    = {11},
  pages     = {2326--2337},
  volume    = {119},
  doi       = {10.1021/jp5065819},
  file      = {:by-author/P/Pyykkö/2015_Pyykkö_2326.pdf:PDF},
  owner     = {saulius},
  publisher = {American Chemical Society ({ACS})},
  timestamp = {2017.09.26},
  creationdate = {2017-09-26T00:00:00},
}

@Article{Pezzotti2013,
  author    = {Giuseppe Pezzotti},
  journal   = {Journal of Applied Physics},
  title     = {Raman spectroscopy of piezoelectrics},
  year      = {2013},
  pages     = {211301},
  volume    = {113},
  abstract  = {Raman spectroscopy represents an insightful characterization tool in electronics, which comprehensively suits the technological needs for locally and quantitatively assessing crystal structures, domain textures, crystallographic misalignments, and residual stresses in piezoelectric materials and related devices. Recent improvements in data processing and instrumental screening of large sampling areas have provided Raman spectroscopic evaluations with rejuvenating effectiveness and presently give spin to increasingly wider and more sophisticated experimental explorations. However, the physics underlying the Raman effect represents an issue of deep complexity and its applicative development to non-cubic crystallographic structures can yet be considered in its infancy. This review paper revisits some applicative aspects of the physics governing Raman emission from crystalline matter, exploring the possibility of disentangling the convoluted dependences of the Raman spectrum on crystal orientation and mechanical stress. Attention is paid to the technologically important class of piezoelectric materials, for which working algorithms are explicitly worked out in order to quantitatively extract both structural and mechanical information from polarized Raman spectra. Systematic characterizations of piezoelectric materials and devices are successively presented as applications of the developed equations. The Raman response of complex crystal structures, described here according to a unified formalism, is interpreted as a means for assessing both crystallographic textures and stress-related issues in the three-dimensional space (thus preserving their vectorial and tensorial nature, respectively). Statistical descriptions of domain textures based on orientation distribution functions are also developed in order to provide a link between intrinsic single-crystal data and data collected on polycrystalline (partly textured) structures. This paper aims at providing rigorous spectroscopic foundations to Raman approaches dealing with the analyses of functional behavior and structural reliability of piezoelectric devices.},
  doi       = {10.1063/1.4803740},
  file      = {:by-author/P/Pezzotti/2013_Pezzotti_211301.pdf:PDF},
  owner     = {saulius},
  timestamp = {2017.09.26},
  creationdate = {2017-09-26T00:00:00},
}

@Article{Kadukova2017,
  author      = {Maria Kadukova and Sergei Grudinin},
  journal     = {Journal of Computer-Aided Molecular Design},
  title       = {Convex-{PL}: a novel knowledge-based potential for protein-ligand interactions deduced from structural databases using convex optimization},
  year        = {2017},
  issn        = {1573-4951},
  month       = {sep},
  doi         = {10.1007/s10822-017-0068-8},
  file        = {:by-author/K/Kadukova/2017_Kadukova.pdf:PDF},
  issn-online = {1573-4951},
  issn-print  = {0920-654X},
  owner       = {saulius},
  publisher   = {Springer Nature},
  timestamp = {2017.09.26},
  creationdate = {2017-09-26T00:00:00},
}

@Article{Hoffmann2017,
  author    = {Alexandre Hoffmann and Sergei Grudinin},
  journal   = {Journal of Chemical Theory and Computation},
  title     = {{NOLB}: Nonlinear Rigid Block Normal-Mode Analysis Method},
  year      = {2017},
  month     = {apr},
  number    = {5},
  pages     = {2123--2134},
  volume    = {13},
  doi       = {10.1021/acs.jctc.7b00197},
  file      = {:by-author/H/Hoffmann/2017_Hoffmann_2123.pdf:PDF},
  owner     = {saulius},
  publisher = {American Chemical Society ({ACS})},
  timestamp = {2017.09.26},
  creationdate = {2017-09-26T00:00:00},
}

@Article{Connolly1983,
  author    = {Michael L. Connolly},
  journal   = {J. Appl. Cryst.},
  title     = {Analytical Molecular Surface Calculation},
  year      = {1983},
  pages     = {548--558},
  volume    = {16},
  abstract  = {Richards,1 971R: ichmond&  Rici~ards1, 978A; lden&},
  doi       = {10.1107/S0021889883010985},
  file      = {:by-author/C/Connolly/1983_Connolly_548.pdf:PDF},
  owner     = {saulius},
  timestamp = {2017.09.26},
  creationdate = {2017-09-26T00:00:00},
}

@Article{Connolly1985a,
  author    = {M. L. Connolly},
  journal   = {Journal of Applied Crystallography},
  title     = {Molecular surface Triangulation},
  year      = {1985},
  month     = {dec},
  number    = {6},
  pages     = {499--505},
  volume    = {18},
  doi       = {10.1107/s0021889885010779},
  file      = {:by-author/C/Connolly/1985_Connolly_499.pdf:PDF},
  owner     = {saulius},
  publisher = {International Union of Crystallography ({IUCr})},
  timestamp = {2017.09.26},
  creationdate = {2017-09-26T00:00:00},
}

@Article{Terwilliger2014,
  author    = {Terwilliger, T.C. and Bricogne, G.},
  journal   = {Acta Crystallographica Section D Biological Crystallography},
  title     = {Continuous mutual improvement of macromolecular structure models in the PDB and of X-ray crystallographic software: the dual role of deposited experimental data},
  year      = {2014},
  month     = sep,
  number    = {10},
  pages     = {2533--2543},
  volume    = {70},
  abstract  = {Accurate crystal structures of macromolecules are of high importance in the biological and biomedical fields. Models of crystal structures in the Protein Data Bank (PDB) are in general of very high quality as deposited. However, methods for obtaining the best model of a macromolecular structure from a given set of experimental X-ray data continue to progress at a rapid pace, making it possible to improve most PDB entries after their deposition by re-analyzing the original deposited data with more recent software. This possibility represents a very significant departure from the situation that prevailed when the PDB was created, when it was envisioned as a cumulative repository of static contents. A radical paradigm shift for the PDB is therefore proposed, away from the static archive model towards a much more dynamic body of continuously improving results in symbiosis with continuously improving methods and software. These simultaneous improvements in methods and final results are made possible by the current deposition of processed crystallographic data (structure-factor amplitudes) and will be supported further by the deposition of raw data (diffraction images). It is argued that it is both desirable and feasible to carry out small-scale and large-scale efforts to make this paradigm shift a reality. Small-scale efforts would focus on optimizing structures that are of interest to specific investigators. Large-scale efforts would undertake a systematic re-optimization of all of the structures in the PDB, or alternatively the redetermination of groups of structures that are either related to or focused on specific questions. All of the resulting structures should be made generally available, along with the precursor entries, with various views of the structures being made available depending on the types of questions that users are interested in answering.},
  doi       = {10.1107/S1399004714017040},
  file      = {:by-author/T/Terwilliger/2014_Terwilliger_2533.pdf:PDF},
  keywords  = {Data Analysis; Model Quality; Software Development; Structure Determination; X-ray Crystallography},
  owner     = {saulius},
  publisher = {International Union of Crystallography},
  rights    = {http://creativecommons.org/licenses/by/2.0/uk},
  source    = {Acta Cryst (2014). D70, 2533-2543 [doi:10.1107/S1399004714017040]},
  timestamp = {2017.09.26},
  creationdate = {2017-09-26T00:00:00},
}

@Presentation{Bruno2011a,
  author    = {Ian Bruno},
  title     = {Accessibility vs. Sustainability: A Balancing Act},
  year      = {2011},
  file      = {:by-author/B/Bruno/2011_Bruno.pdf:PDF},
  owner     = {saulius},
  timestamp = {2017.09.26},
  creationdate = {2017-09-26T00:00:00},
  url       = {https://www.cendi.gov/presentations/11_30_11_Bruno_CCDC.pdf},
}

@Manuscript{Genin2017,
  author    = {Jean-Marie Genin and A. Christi and Y. Garcia and V. Ksenofontov and S. Mills and C. Ruby and E. Shcherbakova},
  title     = {Mössbauerite; polytypes in Tatkul Lake (Russia) marls and evidence in a Murray River reservoir (Australia)},
  year      = {2017},
  file      = {:by-author/G/Genin/2017_Genin.pdf:PDF},
  owner     = {saulius},
  timestamp = {2017.09.30},
  creationdate = {2017-09-30T00:00:00},
}

@Article{Schlichting2015,
  author    = {Ilme Schlichting},
  journal   = {{IUCrJ}},
  title     = {Serial femtosecond crystallography: the first five years},
  year      = {2015},
  month     = {feb},
  number    = {2},
  pages     = {246--255},
  volume    = {2},
  doi       = {10.1107/s205225251402702x},
  file      = {:by-author/S/Schlichting/2015_Schlichting_246.pdf:PDF},
  owner     = {saulius},
  publisher = {International Union of Crystallography ({IUCr})},
  timestamp = {2017.09.27},
  creationdate = {2017-09-27T00:00:00},
}

@Article{Johnson2017,
  author    = {Kaitlin Johnson and Scott Bailey},
  journal   = {Nature},
  title     = {Microbiology: The case of the mysterious messenger},
  year      = {2017},
  month     = {aug},
  number    = {7669},
  pages     = {527--528},
  volume    = {548},
  doi       = {10.1038/nature23532},
  file      = {:by-author/J/Johnson/2017_Johnson_527.pdf:PDF},
  owner     = {saulius},
  publisher = {Springer Nature},
  timestamp = {2017.09.30},
  creationdate = {2017-09-30T00:00:00},
}

@Article{Sheldrick2007,
  author    = {Sheldrick, G.M.},
  title     = {A short history of SHELX},
  year      = {2007},
  month     = dec,
  pages     = {112--122},
  abstract  = {An account is given of the development of the SHELX system of computer programs from SHELX-76 to the present day. In addition to identifying useful innovations that have come into general use through their implementation in SHELX, a critical analysis is presented of the less-successful features, missed opportunities and desirable improvements for future releases of the software. An attempt is made to understand how a program originally designed for photographic intensity data, punched cards and computers over 10000 times slower than an average modern personal computer has managed to survive for so long. SHELXL is the most widely used program for small-molecule refinement and SHELXS and SHELXD are often employed for structure solution despite the availability of objectively superior programs. SHELXL also finds a niche for the refinement of macromolecules against high-resolution or twinned data; SHELXPRO acts as an interface for macromolecular applications. SHELXC, SHELXD and SHELXE are proving useful for the experimental phasing of macromolecules, especially because they are fast and robust and so are often employed in pipelines for high-throughput phasing. This paper could serve as a general literature citation when one or more of the open-source SHELX programs (and the Bruker AXS version SHELXTL) are employed in the course of a crystal-structure determination.},
  doi       = {10.1107/S0108767307043930},
  file      = {:by-author/S/Sheldrick/2007_Sheldrick_112.pdf:PDF},
  keywords  = {COMPUTER PROGRAMS; CRYSTAL STRUCTURE DETERMINATION; PHASING; SHELX; STRUCTURE REFINEMENT},
  owner     = {saulius},
  publisher = {International Union of Crystallography},
  rights    = {Copyright (c) 2008 International Union of Crystallography},
  source    = {Acta Cryst (2008). A64, 112-122 [doi:10.1107/S0108767307043930]},
  timestamp = {2017.09.30},
  creationdate = {2017-09-30T00:00:00},
  url       = {http://scripts.iucr.org/cgi-bin/paper?S0108767307043930},
}

@Article{Mills2012,
  author    = {S. J. Mills and A. G. Christy and J.-M. R. G{\'{e}}nin and T. Kameda and F. Colombo},
  journal   = {Mineralogical Magazine},
  title     = {Nomenclature of the hydrotalcite supergroup: natural layered double hydroxides},
  year      = {2012},
  month     = {oct},
  number    = {5},
  pages     = {1289--1336},
  volume    = {76},
  doi       = {10.1180/minmag.2012.076.5.10},
  file      = {:by-author/M/Mills/2012_Mills_1289.pdf:PDF},
  owner     = {saulius},
  publisher = {Mineralogical Society},
  timestamp = {2017.09.30},
  creationdate = {2017-09-30T00:00:00},
}

@Article{Genin2014,
  author    = {J.-M. R. G{\'{e}}nin and S. J. Mills and A. G. Christy and O. Gu{\'{e}}rin and A. J. Herbillon and E. Kuzmann and G. Ona-Nguema and C. Ruby and C. Upadhyay},
  journal   = {Mineralogical Magazine},
  title     = {Mössbauerite, Fe 3+ 6 O 4 (OH) 8 [CO 3 ]·3H 2 O, the fully oxidized ‘green rust’ mineral from Mont Saint-Michel Bay, France},
  year      = {2014},
  month     = {apr},
  number    = {2},
  pages     = {447--465},
  volume    = {78},
  doi       = {10.1180/minmag.2014.078.2.14},
  file      = {:by-author/G/Genin/2014_Genin_447.pdf:PDF},
  owner     = {saulius},
  publisher = {Mineralogical Society},
  timestamp = {2017.09.30},
  creationdate = {2017-09-30T00:00:00},
}

@Presentation{Moore2017,
  author       = {J. Strother Moore},
  title        = {Mahines Reasoning about Mahines: A Personal Perspective},
  year         = {2017},
  organization = {Department of Computer Sciences, University of Texas at Austin},
  file         = {:by-author/M/Moore/2017_Moore.pdf:PDF;:by-author/M/Moore/2017_Moore.ps.gz:gz},
  owner        = {saulius},
  timestamp = {2017.09.30},
  creationdate = {2017-09-30T00:00:00},
  url          = {http://www.cs.utexas.edu/users/moore/publications/talks/machines.ps.gz},
}

@Manuscript{Allen2002a,
  author    = {G. Donald Allen},
  title     = {π: A brief history},
  year      = {2002},
  url       = {http://www.math.tamu.edu/~dallen/masters/alg_numtheory/pi.pdf},
  file      = {:by-author/A/Allen/2002_Allen.pdf:PDF},
  owner     = {saulius},
  timestamp = {2017.09.30},
  creationdate = {2017-09-30T00:00:00},
}

@Manuscript{Hoffmann2017a,
  author    = {Alexandre Hoffmann and Sergei Grudinin},
  title     = {NOLB: Nonlinear Rigid Block Normal Mode Analysis Method},
  year      = {2017},
  url       = {https://hal.inria.fr/hal-01505843v2},
  abstract  = {Computer Science [cs]/Modeling and Simulation, Computer Science [cs]/Bioinformatics [q-bio.QM]},
  file      = {:by-author/H/Hoffmann/2017_Hoffmann.pdf:PDF},
  owner     = {saulius},
  timestamp = {2017.09.30},
  creationdate = {2017-09-30T00:00:00},
}

@Manuscript{Pages2017,
  author    = {Guillaume Pagès and Elvira Kinzina and Sergei Grudinin},
  title     = {Analytical symmetry detection in cyclic protein assemblies},
  year      = {2017},
  file      = {:by-author/P/Pagès/2017_Pagès.pdf:PDF},
  owner     = {saulius},
  timestamp = {2017.09.30},
  creationdate = {2017-09-30T00:00:00},
}

@Article{Amitai2017,
  author    = {Gil Amitai and Rotem Sorek},
  journal   = {Science},
  title     = {Intracellular signaling in CRISPR-Cas defense},
  year      = {2017},
  month     = {aug},
  number    = {6351},
  pages     = {550--551},
  volume    = {357},
  doi       = {10.1126/science.aao2210},
  file      = {:by-author/A/Amitai/2017_Amitai_550.pdf:PDF},
  owner     = {saulius},
  publisher = {American Association for the Advancement of Science ({AAAS})},
  timestamp = {2017.09.30},
  creationdate = {2017-09-30T00:00:00},
}

@Article{Chen2012,
  author    = {Yao Chen and Vasiliki Lykourinou and Carissa Vetromile and Tran Hoang and Li-June Ming and Randy W. Larsen and Shengqian Ma},
  journal   = {Journal of the American Chemical Society},
  title     = {How Can Proteins Enter the Interior of a {MOF}? Investigation of {CytochromecTranslocation} into a {MOF} Consisting of Mesoporous Cages with Microporous Windows},
  year      = {2012},
  month     = {aug},
  number    = {32},
  pages     = {13188--13191},
  volume    = {134},
  doi       = {10.1021/ja305144x},
  file      = {:by-author/C/Chen/2012_Chen_13188.pdf:PDF},
  groups    = {sg/MOFs, am/MOFs},
  owner     = {saulius},
  publisher = {American Chemical Society ({ACS})},
  timestamp = {2017.10.03},
  creationdate = {2017-10-03T00:00:00},
}

@Article{Wolf1999,
  author    = {D. Wolf and P. Keblinski and S. R. Phillpot and J. Eggebrecht},
  journal   = {The Journal of Chemical Physics},
  title     = {Exact method for the simulation of Coulombic systems by spherically truncated, pairwise r-1 summation},
  year      = {1999},
  month     = {may},
  number    = {17},
  pages     = {8254--8282},
  volume    = {110},
  doi       = {10.1063/1.478738},
  file      = {:by-author/W/Wolf/1999_Wolf_8254.pdf:PDF},
  owner     = {saulius},
  publisher = {{AIP} Publishing},
  timestamp = {2017.10.08},
  creationdate = {2017-10-08T00:00:00},
}

@Article{Liu2004b,
  author    = {B. Liu and Y. Huang and H. Jiang and S. Qu and K.C. Hwang},
  journal   = {Computer Methods in Applied Mechanics and Engineering},
  title     = {The atomic-scale finite element method},
  year      = {2004},
  month     = {may},
  number    = {17-20},
  pages     = {1849--1864},
  volume    = {193},
  doi       = {10.1016/j.cma.2003.12.037},
  file      = {:by-author/L/Liu/2004_Liu_1849.pdf:PDF},
  groups    = {sg/MolSim},
  owner     = {saulius},
  publisher = {Elsevier {BV}},
  timestamp = {2017.10.08},
  creationdate = {2017-10-08T00:00:00},
}

@Article{Hairer2003,
  author    = {Ernst Hairer and Christian Lubich and Gerhard Wanner},
  journal   = {Acta Numerica},
  title     = {Geometric numerical integration illustrated by the {StrmerVerlet} method},
  year      = {2003},
  month     = {may},
  pages     = {399--450},
  volume    = {12},
  doi       = {10.1017/s0962492902000144},
  file      = {:by-author/H/Hairer/2003_Hairer_399.pdf:PDF},
  owner     = {saulius},
  publisher = {Cambridge University Press ({CUP})},
  timestamp = {2017.10.08},
  creationdate = {2017-10-08T00:00:00},
}

@Presentation{Zhang2002,
  author    = {Tao Zhang},
  title     = {Introduction to Prospector},
  year      = {2002},
  file      = {:by-author/Z/Zhang/2002_Zhang.pdf:PDF},
  keywords  = {Expert Systems; Knowledge Representation; Mining; PROSPECTOR},
  owner     = {saulius},
  timestamp = {2017.10.08},
  creationdate = {2017-10-08T00:00:00},
  url       = {http://web.cs.wpi.edu/~dcb/courses/CS538/documents/2002/Prospector-slides.pdf},
}

@TechReport{Hart1977,
  author      = {P. E. Hart and R. O. Duda},
  institution = {Artificial Intelligence Center, SRI International},
  title       = {PROSPECTOR -- A Computer-Based Consultation System for Mineral Exploration},
  year        = {1977},
  address     = {Menlo Park, California 94025},
  type        = {techreport},
  date        = {1977-10-20},
  file        = {:by-author/H/Hart/1977_Hart.pdf:PDF},
  keywords    = {Artificial Intelligence (AI); Mining; PROSPECTOR},
  owner       = {saulius},
  pagetotal   = {35},
  subtitle    = {Technical Note No. 155},
  timestamp = {2017.10.08},
  creationdate = {2017-10-08T00:00:00},
  url         = {https://www.sri.com/sites/default/files/uploads/publications/pdf/739.pdf},
  urldate     = {2017-10-08},
}

@Presentation{Jaidee2010,
  author    = {Ulit Jaidee},
  title     = {Expert Systems},
  year      = {2010},
  file      = {:by-author/J/Jaidee/2010_Jaidee.pdf:PDF},
  keywords  = {Bayesian Reasoning; Expert Systems},
  owner     = {saulius},
  timestamp = {2017.10.08},
  creationdate = {2017-10-08T00:00:00},
  url       = {http://www.cse.lehigh.edu/~munoz/CSE335/classes/JaideeExpertSystems.pdf},
}

@Article{Vardeman2011,
  author    = {Charles F. Vardeman and Kelsey M. Stocker and J. Daniel Gezelter},
  journal   = {Journal of Chemical Theory and Computation},
  title     = {The Langevin Hull: Constant Pressure and Temperature Dynamics for Nonperiodic Systems},
  year      = {2011},
  month     = {apr},
  number    = {4},
  pages     = {834--842},
  volume    = {7},
  doi       = {10.1021/ct100670m},
  file      = {:by-author/V/Vardeman/2011_Vardeman_834.pdf:},
  keywords  = {Molecular Dynamics (MD); Molecular Modelling},
  owner     = {saulius},
  publisher = {American Chemical Society ({ACS})},
  timestamp = {2017.10.17},
  creationdate = {2017-10-17T00:00:00},
  url       = {http://pubs.acs.org/doi/pdf/10.1021/ct100670m},
}

@Article{Fennell2005,
  author    = {Christopher J. Fennell and J. Daniel Gezelter},
  journal   = {Journal of Chemical Theory and Computation},
  title     = {Computational Free Energy Studies of a New Ice Polymorph Which Exhibits Greater Stability than Ice Ih},
  year      = {2005},
  month     = {jul},
  number    = {4},
  pages     = {662--667},
  volume    = {1},
  doi       = {10.1021/ct050005s},
  file      = {:by-author/F/Fennell/2005_Fennell_662.pdf:},
  owner     = {saulius},
  publisher = {American Chemical Society ({ACS})},
  timestamp = {2017.10.17},
  creationdate = {2017-10-17T00:00:00},
}

@Presentation{Murray-Rust2014,
  author    = {Peter Murray-Rust},
  title     = {Can machines understand the Scientific Literature?},
  year      = {2014},
  file      = {:by-author/M/Murray-Rust/2014_Murray-Rust.pptx:PowerPoint 2007+;:by-author/M/Murray-Rust/2014_Murray-Rust_email.pdf:PDF},
  owner     = {saulius},
  timestamp = {2017.10.17},
  creationdate = {2017-10-17T00:00:00},
}

@Manuscript{Georgiev2012,
  author    = {Martin Georgiev and Subodh Iyengar and Suman Jana and Rishita Anubhai and Dan Boneh and Vitaly Shmatikov},
  title     = {The Most Dangerous Code in the World: Validating SSL Certificates in Non-Browser Software},
  year      = {2012},
  keywords  = {End-to-end Encryption; HTTPS; SSL; Security Flaws},
  url       = {https://pdfs.semanticscholar.org/48fc/8f1aa0b6d1e4266b8017820ff8770fb67b6f.pdf},
  abstract  = {cations. The main purpose of SSL is to provide end-to-end security},
  file      = {:by-author/G/Georgiev/2012_Georgiev.pdf:PDF},
  owner     = {saulius},
  timestamp = {2017.10.18},
  creationdate = {2017-10-18T00:00:00},
}

@Article{OBoyle2012,
  author    = {Noel M O'Boyle},
  journal   = {Journal of Cheminformatics},
  title     = {Towards a Universal {SMILES} representation - A standard method to generate canonical {SMILES} based on the {InChI}},
  year      = {2012},
  number    = {1},
  pages     = {22},
  volume    = {4},
  doi       = {10.1186/1758-2946-4-22},
  file      = {:by-author/O/OBoyle/2012_OBoyle_22.pdf:PDF},
  owner     = {andrius},
  publisher = {Springer Nature},
  timestamp = {2017.10.19},
  creationdate = {2017-10-19T00:00:00},
}

@Article{Hennig2010,
  author    = {Christian Hennig},
  journal   = {Advances in Data Analysis and Classification},
  title     = {Methods for merging {G}aussian mixture components},
  year      = {2010},
  month     = {jan},
  number    = {1},
  pages     = {3--34},
  volume    = {4},
  doi       = {10.1007/s11634-010-0058-3},
  file      = {:by-author/H/Hennig/2010_Hennig_3.pdf:PDF},
  owner     = {andrius},
  publisher = {Springer Nature},
  timestamp = {2017.10.20},
  creationdate = {2017-10-20T00:00:00},
}

@Presentation{Streek2017,
  author    = {Jacco van de Streek},
  title     = {DFT-D and the Validation of Crystal Structures from XRPD},
  year      = {2017},
  file      = {:by-author/S/Streek/2017_Streek.pptx:PowerPoint 2007+},
  owner     = {saulius},
  timestamp = {2017.10.27},
  creationdate = {2017-10-27T00:00:00},
}

@Presentation{Moeck2017,
  author    = {Peter Moeck and Werner Kaminsky and B. Layla Mehdi and Andrew Stevens and Paul DeStefano and Nigel Browning},
  title     = {Scanning transmission electron microscopy assessment of a metal-organic framework compound},
  year      = {2017},
  file      = {:by-author/M/Moeck/2017_Moeck.ppt:PowerPoint},
  owner     = {saulius},
  timestamp = {2017.10.27},
  creationdate = {2017-10-27T00:00:00},
}

@Article{Sander2015,
  author    = {Thomas Sander and Joel Freyss and Modest von Korff and Christian Rufener},
  journal   = {Journal of Chemical Information and Modeling},
  title     = {{DataWarrior}: An Open-Source Program For Chemistry Aware Data Visualization And Analysis},
  year      = {2015},
  month     = {feb},
  number    = {2},
  pages     = {460--473},
  volume    = {55},
  doi       = {10.1021/ci500588j},
  file      = {:by-author/S/Sander/2015_Sander_460.pdf:PDF},
  keywords  = {Chemoinformatics; Using COD},
  owner     = {saulius},
  publisher = {American Chemical Society ({ACS})},
  timestamp = {2017.10.30},
  creationdate = {2017-10-30T00:00:00},
}

@Manuscript{Russell2011,
  author    = {Rosemary Russell},
  title     = {An introduction to CERIF},
  year      = {2011},
  url       = {http://www.ukoln.ac.uk/rim/documents/Introduction_to_CERIF_1.0.pdf},
  file      = {:by-author/R/Russell/2011_Russell.pdf:PDF},
  owner     = {saulius},
  timestamp = {2017.10.27},
  creationdate = {2017-10-27T00:00:00},
}

@Article{Streek2010,
  author    = {Jacco van de Streek and Marcus A. Neumann},
  journal   = {Acta Crystallographica Section B Structural Science},
  title     = {Validation of experimental molecular crystal structures with dispersion-corrected density functional theory calculations},
  year      = {2010},
  month     = {sep},
  number    = {5},
  pages     = {544--558},
  volume    = {66},
  doi       = {10.1107/s0108768110031873},
  file      = {:by-author/S/Streek/2010_Streek_544.pdf:PDF},
  keywords  = {Density Functional Theory (DFT); Structure Validation},
  owner     = {saulius},
  publisher = {International Union of Crystallography ({IUCr})},
  timestamp = {2017.10.27},
  creationdate = {2017-10-27T00:00:00},
}

@Manuscript{Bizer2009,
  author    = {Bizer, Christian and Tom Heath and Tim Berners-Lee},
  title     = {Linked Data – The story so far},
  year      = {2009},
  url       = {http://citeseerx.ist.psu.edu/viewdoc/summary;jsessionid=3CB0F3D1D510866CE11780DEFF8FFB57?doi=10.1.1.189.545&rank=10},
  abstract  = {The term Linked Data refers to a set of best practices for publishing and connecting structured data on the Web. These best practices have been adopted by an increasing number of data providers over the last three years, leading to the creation of a global data space containing billions of assertions- the Web of Data. In this article we present the concept and technical principles of Linked Data, and situate these within the broader context of related technological developments. We describe progress to date in publishing Linked Data on the Web, review applications that have been developed to exploit the Web of Data, and map out a research agenda for the Linked Data community as it moves forward.},
  file      = {Citeseer - Full Text PDF:by-author/B/Bizer/2009_Bizer.pdf:PDF},
  owner     = {saulius},
  timestamp = {2017.10.28},
  creationdate = {2017-10-28T00:00:00},
}

@Article{Authier2009,
  author    = {Andr{\'{e}} Authier},
  journal   = {Acta Crystallographica Section A Foundations of Crystallography},
  title     = {60 years of {IUCr} journals},
  year      = {2009},
  month     = {apr},
  number    = {3},
  pages     = {167--182},
  volume    = {65},
  doi       = {10.1107/s0108767309007235},
  file      = {:by-author/A/Authier/2009_Authier_167.pdf:PDF},
  owner     = {saulius},
  publisher = {International Union of Crystallography ({IUCr})},
  timestamp = {2017.10.29},
  creationdate = {2017-10-29T00:00:00},
}

@Manual{OECD2006,
  title     = {Revised Field of Science and Technology ({FOS}) Classification in the Frascati Manual},
  author    = {{Organisation for Economic Co-operation and Developmen}},
  year      = {2006},
  date      = {2007-02-26},
  file      = {:by-author/O/OECD/2006_OECD.pdf:PDF},
  keywords  = {Classification of Sciences},
  owner     = {saulius},
  timestamp = {2017.10.24},
  creationdate = {2017-10-24T00:00:00},
  url       = {https://www.oecd.org/science/inno/38235147.pdf},
}

@Article{Kamminga1989,
  author    = {H. Kamminga},
  journal   = {Acta Crystallographica Section A Foundations of Crystallography},
  title     = {The International Union of Crystallography: its formation and early development},
  year      = {1989},
  month     = {sep},
  number    = {9},
  pages     = {581--601},
  volume    = {45},
  doi       = {10.1107/s0108767389003910},
  file      = {:by-author/K/Kamminga/1989_Kamminga_581.pdf:PDF},
  owner     = {saulius},
  publisher = {International Union of Crystallography ({IUCr})},
  timestamp = {2017.10.29},
  creationdate = {2017-10-29T00:00:00},
}

@InProceedings{Chamberlin1980,
  author    = {Donald D. Chamberlin},
  booktitle = {{ICOD}},
  title     = {A Summary of user Experience with the {SQL} Data Sublanguage},
  year      = {1980},
  pages     = {181--203},
  bibsource = {dblp computer science bibliography, http://dblp.org},
  biburl    = {http://dblp.org/rec/bib/conf/icod/Chamberlin80},
  file      = {:by-author/C/Chamberlin/1980_Chamberlin_181.pdf:PDF},
  keywords  = {Databases; SQL},
  owner     = {saulius},
  timestamp = {2017.10.28},
  creationdate = {2017-10-28T00:00:00},
  url       = {http://dblp.org/rec/html/conf/icod/Chamberlin80},
}

@Article{Allen1979,
  author    = {F. H. Allen and S. Bellard and M. D. Brice and B. A. Cartwright and A. Doubleday and H. Higgs and T. Hummelink and B. G. Hummelink-Peters and O. Kennard and W. D. S. Motherwell and J. R. Rodgers and D. G. Watson},
  journal   = {Acta Crystallographica Section B Structural Crystallography and Crystal Chemistry},
  title     = {The Cambridge Crystallographic Data Centre: computer-based search, retrieval, analysis and display of information},
  year      = {1979},
  month     = {oct},
  number    = {10},
  pages     = {2331--2339},
  volume    = {35},
  doi       = {10.1107/s0567740879009249},
  file      = {:by-author/A/Allen/1979_Allen_2331.pdf:PDF},
  keywords  = {CCDC; CSD; History},
  owner     = {saulius},
  publisher = {International Union of Crystallography ({IUCr})},
  timestamp = {2017.10.29},
  creationdate = {2017-10-29T00:00:00},
}

@Article{Pauling1929,
  author    = {Linus Pauling},
  journal   = {Journal of the American Chemical Society},
  title     = {The Principles Determining the Structure of Complex Ionic Crystals},
  year      = {1929},
  month     = {apr},
  number    = {4},
  pages     = {1010--1026},
  volume    = {51},
  doi       = {10.1021/ja01379a006},
  file      = {:by-author/P/Pauling/1929_Pauling_1010.pdf:PDF},
  owner     = {saulius},
  publisher = {American Chemical Society ({ACS})},
  timestamp = {2017.10.29},
  creationdate = {2017-10-29T00:00:00},
}

@Article{Bragg1913a,
  author    = {W. L. Bragg},
  journal   = {Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences},
  title     = {The Structure of Some Crystals as Indicated by Their Diffraction of X-rays},
  year      = {1913},
  month     = {sep},
  number    = {610},
  pages     = {248--277},
  volume    = {89},
  doi       = {10.1098/rspa.1913.0083},
  file      = {:by-author/B/Bragg/1913_Bragg_248.pdf:PDF},
  keywords  = {History of Science; X-ray Crystallography},
  owner     = {saulius},
  publisher = {The Royal Society},
  timestamp = {2017.10.29},
  creationdate = {2017-10-29T00:00:00},
  url       = {http://rspa.royalsocietypublishing.org/content/royprsa/89/610/248.full.pdf},
}

@Article{Bragg1913b,
  author    = {W. H. Bragg and W. L. Bragg},
  journal   = {Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences},
  title     = {The Structure of the Diamond},
  year      = {1913},
  month     = {sep},
  number    = {610},
  pages     = {277--291},
  volume    = {89},
  doi       = {10.1098/rspa.1913.0084},
  file      = {:by-author/B/Bragg/1913_Bragg_277.pdf:PDF},
  owner     = {saulius},
  publisher = {The Royal Society},
  timestamp = {2017.10.29},
  creationdate = {2017-10-29T00:00:00},
}

@Article{Bragg1913c,
  author    = {W. H. Bragg},
  journal   = {Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences},
  title     = {The Reflection of X-rays by Crystals. ({II}.)},
  year      = {1913},
  month     = {sep},
  number    = {610},
  pages     = {246--248},
  volume    = {89},
  doi       = {10.1098/rspa.1913.0082},
  file      = {:by-author/B/Bragg/1913_Bragg_246.pdf:PDF},
  owner     = {saulius},
  publisher = {The Royal Society},
  timestamp = {2017.10.29},
  creationdate = {2017-10-29T00:00:00},
}

@Article{Friedrich1912a,
  author    = {Friedrich, Walther and Paul Knipping and Max Laue},
  journal   = {Bayerische Akademie der Wissenschaften, Mathematisch-Physikalische Klasse, Sitzungsberichte},
  title     = {{I}nterferenzerscheinungen bei {R}{\"{o}}ntgenstrahlen. {E}ine quantitative {P}r{\"{u}}fung der {T}heorie f{\"{u}}r die {I}nterferenz-{E}rscheinungen bei {R}{\"{o}}ntgenstrahlen, {II} (?)},
  year      = {1912},
  pages     = {363--373},
  owner     = {saulius},
  timestamp = {2017.10.29},
  creationdate = {2017-10-29T00:00:00},
  url       = {http://de.wikipedia.org/wiki/Paul_Knipping},
}

@Article{Friedrich1912,
  author    = {Friedrich, Walther and Paul Knipping and Max Laue},
  journal   = {Bayerische Akademie der Wissenschaften, Mathematisch-Physikalische Klasse, Sitzungsberichte},
  title     = {{I}nterferenzerscheinungen bei {R}{\"{o}}ntgenstrahlen. {E}ine quantitative {P}r{\"{u}}fung der {T}heorie f{\"{u}}r die {I}nterferenz-{E}rscheinungen bei {R}{\"{o}}ntgenstrahlen},
  year      = {1912},
  pages     = {303--322},
  owner     = {saulius},
  timestamp = {2017.10.29},
  creationdate = {2017-10-29T00:00:00},
  url       = {http://de.wikipedia.org/wiki/Paul_Knipping},
}

@Article{Blunschi2012,
  author       = {Blunschi, Lukas and Jossen, Claudio and Kossman, Donald and Mori, Magdalini and Stockinger, Kurt},
  title        = {{SODA}: Generating {SQL} for Business Users},
  pages        = {1207.0134},
  abstract     = {The purpose of data warehouses is to enable business analysts to make better decisions. Over the years the technology has matured and data warehouses have become extremely successful. As a consequence, more and more data has been added to the data warehouses and their schemas have become increasingly complex. These systems still work great in order to generate pre-canned reports. However, with their current complexity, they tend to be a poor match for non tech-savvy business analysts who need answers to ad-hoc queries that were not anticipated. This paper describes the design, implementation, and experience of the {SODA} system (Search over {DAta} Warehouse). {SODA} bridges the gap between the business needs of analysts and the technical complexity of current data warehouses. {SODA} enables a Google-like search experience for data warehouses by taking keyword queries of business users and automatically generating executable {SQL}. The key idea is to use a graph pattern matching algorithm that uses the metadata model of the data warehouse. Our results with real data from a global player in the financial services industry show that {SODA} produces queries with high precision and recall, and makes it much easier for business users to interactively explore highly-complex data warehouses.},
  date         = {2012-06-30},
  eprint       = {1207.0134},
  eprinttype   = {arxiv},
  file         = {arXiv\:1207.0134 PDF:by-author/B/Blunschi/2012_Blunschi_134.pdf:application/pdf},
  journaltitle = {{arXiv}:1207.0134 [cs]},
  keywords     = {Computer Science - Databases},
  owner        = {saulius},
  shorttitle   = {{SODA}},
  timestamp = {2017.10.28},
  creationdate = {2017-10-28T00:00:00},
  url          = {http://arxiv.org/abs/1207.0134},
  urldate      = {2017-10-28},
}

@InProceedings{Swami2000,
  author    = {A. Swami},
  booktitle = {2000 IEEE International Conference on Acoustics, Speech, and Signal Processing. Proceedings (Cat. No.00CH37100)},
  title     = {Non-{G}aussian mixture models for detection and estimation in heavy-tailed noise},
  year      = {2000},
  pages     = {3802--3805},
  volume    = {6},
  abstract  = {Scale mixtures of the Gaussian have been used to approximate the PDF
	of symmetric alpha stable processes. Such mixtures, however, cannot
	easily capture the heavy-tails. We propose to use Cauchy-Gaussian
	mixtures which are natural in this setting. Variations of standard
	EM algorithms can be used to estimate the parameters of the noise
	PDFs under various scenarios (noise-only data, weak-signal assumption,
	partially known-signal case). The fitted mixture models can be used
	for detection and estimation. In the multivariate case, we present
	several results on Gaussian mixture approximations of sub-Gaussian
	PDFs, including robust estimation of the underlying correlation matrix},
  doi       = {10.1109/ICASSP.2000.860231},
  file      = {:by-author/S/Swami/2000_Swami_3802.pdf:PDF},
  issn      = {1520-6149},
  owner     = {andrius},
  timestamp = {2017.03.28},
  creationdate = {2017-03-28T00:00:00},
}

@Article{Howlader1988,
  author    = {H. A. Howlader and G. Weiss},
  journal   = {Sankhyā: The Indian Journal of Statistics, Series B (1960-2002)},
  title     = {On {B}ayesian Estimation of the {C}auchy Parameters},
  year      = {1988},
  issn      = {05815738},
  number    = {3},
  pages     = {350--361},
  volume    = {50},
  abstract  = {In this paper we study the exact expressions due to Spiegelhalter (1985) and the approximate expressions derived by using a method due to Lindley (1980) for Bayes estimation of the location and scale parameters of a Cauchy distribution. A numerical example is given. A Monte Carlo simulation study is conducted to compare the exact and the approximate Bayes estimators. These two sets of Bayes estimators are also compared with the corresponding maximum likelihood estimators.},
  file      = {:by-author/H/Howlader/1988_Howlader_350.pdf:PDF},
  owner     = {andrius},
  publisher = {Springer},
  timestamp = {2017.10.31},
  creationdate = {2017-10-31T00:00:00},
  url       = {http://www.jstor.org/stable/25052554},
}

@Article{Cerny2017,
  author    = {Radovan Černý and Vincent Favre-Nicolin and Jan Rohl{\'{\i}}{\v{c}}ek and Michal Hu{\v{s}}{\'{a}}k},
  journal   = {Crystals},
  title     = {{FOX}, Current State and Possibilities},
  year      = {2017},
  month     = {oct},
  number    = {11},
  pages     = {322},
  volume    = {7},
  doi       = {10.3390/cryst7100322},
  file      = {:by-author/Č/Černý/2017_Černý_322.pdf:PDF},
  keywords  = {Citing COD; Computer Software; Using COD},
  owner     = {saulius},
  publisher = {{MDPI} {AG}},
  timestamp = {2017.11.01},
  creationdate = {2017-11-01T00:00:00},
}

@Presentation{Crusoe2017,
  author    = {Michael R. Crusoe},
  title     = {Common Workflow Language: Opening up complex data analysis methods with the CWL standards},
  year      = {2017},
  date      = {2017-10-23},
  file      = {:by-author/C/Crusoe/2017_Crusoe.pdf:PDF},
  keywords  = {CWL; Reproducible Research; Workflows},
  owner     = {saulius},
  timestamp = {2017.11.07},
  creationdate = {2017-11-07T00:00:00},
  url       = {https://goo.gl/55pd52},
}

@Presentation{Amstutz2015,
  author    = {Peter Amstutz},
  title     = {Common Workflow Language},
  year      = {2015},
  file      = {:by-author/A/Amstutz/2015_Amstutz.pdf:PDF},
  keywords  = {CWL; Reproducible Research; Workflows},
  owner     = {saulius},
  timestamp = {2017.11.07},
  creationdate = {2017-11-07T00:00:00},
  url       = {https://github.com/common-workflow-language/common-workflow-language/blob/master/presentations/Broad%20Institute%20CWL%20meetup%202015-11-13.pdf},
}

@Manuscript{Baxter,
  author    = {Ira D. Baxter},
  title     = {Branch Coverage for Arbitrary Languages Made Easy},
  keywords  = {Computer Languages; Language Parsing; Test Coverage},
  url       = {http://www.semdesigns.com/Company/Publications/TestCoverage.pdf},
  file      = {:by-author/B/Baxter/Baxter.pdf:PDF},
  owner     = {saulius},
  timestamp = {2017.11.02},
  creationdate = {2017-11-02T00:00:00},
}

@Article{Rodriguez2014,
  author    = {A. Rodriguez and A. Laio},
  journal   = {Science},
  title     = {Clustering by fast search and find of density peaks},
  year      = {2014},
  month     = {jun},
  number    = {6191},
  pages     = {1492--1496},
  volume    = {344},
  doi       = {10.1126/science.1242072},
  file      = {:by-author/R/Rodriguez/2014_Rodriguez_1492.pdf:PDF},
  owner     = {andrius},
  publisher = {American Association for the Advancement of Science ({AAAS})},
  timestamp = {2017.11.07},
  creationdate = {2017-11-07T00:00:00},
}

@Article{Fuentes-Montero2010,
  author    = {Luis Fuentes-Montero and Maria Elena Montero-Cabrera and Luis Fuentes-Cobas},
  journal   = {Journal of Applied Crystallography},
  title     = {The software package {ANAELU} for X-ray diffraction analysis using two-dimensional patterns},
  year      = {2010},
  month     = {dec},
  number    = {1},
  pages     = {241--246},
  volume    = {44},
  doi       = {10.1107/s0021889810048739},
  file      = {:by-author/F/Fuentes-Montero/2010_Fuentes-Montero_241.pdf:PDF;:by-author/F/Fuentes-Montero/2010_Fuentes-Montero_UserManual.pdf:PDF},
  keywords  = {ANALEU; Computer Programs; Powder Diffraction; Textures; X-ray Crystallography},
  owner     = {saulius},
  publisher = {International Union of Crystallography ({IUCr})},
  timestamp = {2017.11.14},
  creationdate = {2017-11-14T00:00:00},
}

@Article{Willighagen2017,
  author    = {Egon L. Willighagen and John W. Mayfield and Jonathan Alvarsson and Arvid Berg and Lars Carlsson and Nina Jeliazkova and Stefan Kuhn and Tomáš Pluskal and Miquel Rojas-Chertó and Ola Spjuth and Gilleain Torrance and Chris T. Evelo and Rajarshi Guha and Christoph Steinbeck},
  journal   = {Journal of Cheminformatics},
  title     = {The Chemistry Development Kit ({CDK}) v2.0: atom typing, depiction, molecular formulas, and substructure searching},
  year      = {2017},
  month     = {jun},
  number    = {1},
  volume    = {9},
  abstract  = {Journal of Cheminformatics, doi:10.1186/s13321-017-0220-4},
  doi       = {10.1186/s13321-017-0220-4},
  file      = {:by-author/W/Willighagen/2017_Willighagen.pdf:PDF},
  keywords  = {Bioinformatics; Cheminformatics; Depiction; Java; Metabolomics},
  owner     = {saulius},
  publisher = {Springer International Publishing},
  timestamp = {2017.11.09},
  creationdate = {2017-11-09T00:00:00},
}

@Manuscript{Day2009,
  author    = {Nick Day and Jim Downing and Lezan Hawizy and Nico Adams and Peter Murray-Rust},
  title     = {Towards Lensfield: data management, processing and semantic publication for vernacular e-science},
  year      = {2009},
  keywords  = {Reproducible Research; Semantic Science},
  url       = {https://www.repository.cam.ac.uk/bitstream/handle/1810/223838/ieee-lensfield.pdf;sequence=1},
  abstract  = {must surmount considerable technological barriers to},
  file      = {:by-author/D/Day/2009_Day.pdf:PDF},
  owner     = {saulius},
  timestamp = {2017.11.14},
  creationdate = {2017-11-14T00:00:00},
}

@Article{McKay2014,
  author    = {McKay, Brendan D. and Piperno, Adolfo},
  journal   = {Journal of Symbolic Computation},
  title     = {Practical graph isomorphism, {II}},
  year      = {2014},
  issn      = {0747-7171},
  month     = {Jan},
  pages     = {94--112},
  volume    = {60},
  doi       = {10.1016/j.jsc.2013.09.003},
  file      = {:by-author/M/McKay/2014_McKay_94.pdf:PDF},
  owner     = {andrius},
  publisher = {Elsevier BV},
  timestamp = {2021.03.23},
  creationdate = {2021-03-23T00:00:00},
  url       = {https://www.sciencedirect.com/science/article/pii/S0747717113001193},
}

@Article{Merkys2017,
  author      = {Andrius Merkys and Nicolas Mounet and Andrea Cepellotti and Nicola Marzari and Saulius Gražulis and Giovanni Pizzi},
  journal     = {Journal of Cheminformatics},
  title       = {A posteriori metadata from automated provenance tracking: Integration of {AiiDA} and {TCOD}},
  year        = {2017},
  number      = {1},
  pages       = {56},
  volume      = {9},
  abstract    = {In order to make results of computational scientific research findable, accessible, interoperable and re-usable, it is necessary to decorate them with standardised metadata. However, there are a number of technical and practical challenges that make this process difficult to achieve in practice. Here the implementation of a protocol is presented to tag crystal structures with their computed properties, without the need of human intervention to curate the data. This protocol leverages the capabilities of AiiDA, an open-source platform to manage and automate scientific computational workflows, and TCOD, an open-access database storing computed materials properties using a well-defined and exhaustive ontology. Based on these, the complete procedure to deposit computed data in the TCOD database is automated. All relevant metadata are extracted from the full provenance information that AiiDA tracks and stores automatically while managing the calculations. Such a protocol also enables reproducibility of scientific data in the field of computational materials science. As a proof of concept, the AiiDA-TCOD interface is used to deposit 170 theoretical structures together with their computed properties and their full provenance graphs, consisting in over 4600 AiiDA nodes.},
  date        = {2017-11-15},
  doi         = {10.1186/s13321-017-0242-y},
  eprint      = {1706.08704v3},
  eprintclass = {cond-mat.mtrl-sci},
  eprinttype  = {arXiv},
  file        = {:by-author/M/Merkys/2017_Merkys_56.pdf:PDF},
  keywords    = {cond-mat.mtrl-sci},
  owner       = {andrius},
  publisher   = {Springer Nature},
  timestamp = {2017.11.15},
  creationdate = {2017-11-15T00:00:00},
  url         = {https://jcheminf.springeropen.com/articles/10.1186/s13321-017-0242-y},
}

@Article{Kleywegt1989,
  author    = {Gerard J. Kleywegt and Hendrik-Jan Luinge and Bart-Jan P. Schuman},
  journal   = {Chemometrics and Intelligent Laboratory Systems},
  title     = {{PROLOG} for chemists. Part 2},
  year      = {1989},
  month     = {jan},
  number    = {2},
  pages     = {117--128},
  volume    = {5},
  doi       = {10.1016/0169-7439(89)80008-5},
  file      = {:by-author/K/Kleywegt/1989_Kleywegt_117.pdf:PDF},
  keywords  = {Chemoinformatics; Prolog},
  owner     = {saulius},
  publisher = {Elsevier {BV}},
  timestamp = {2017.11.24},
  creationdate = {2017-11-24T00:00:00},
}

@Article{Kleywegt1988,
  author           = {Gerard J. Kleywegt and Hendrik-Jan Luinge and Bart-Jan P. Schuman},
  journal          = {Chemometrics and Intelligent Laboratory Systems},
  title            = {{PROLOG} for chemists. Part 1},
  year             = {1988},
  month            = {oct},
  number           = {4},
  pages            = {273--297},
  volume           = {4},
  creationdate     = {2017-11-24T00:00:00},
  doi              = {10.1016/0169-7439(88)80108-4},
  file             = {:by-author/K/Kleywegt/1988_Kleywegt_273.pdf:PDF},
  keywords         = {Chemoinformatics; Prolog},
  modificationdate = {2024-08-15T18:47:35},
  owner            = {saulius},
  publisher        = {Elsevier {BV}},
  timestamp        = {2017.11.24},
}

@Article{Weininger1988,
  author    = {David Weininger},
  journal   = {Journal of Chemical Information and Modeling},
  title     = {{SMILES}, a chemical language and information system. 1. Introduction to methodology and encoding rules},
  year      = {1988},
  month     = {feb},
  number    = {1},
  pages     = {31--36},
  volume    = {28},
  doi       = {10.1021/ci00057a005},
  file      = {:by-author/W/Weininger/1988_Weininger_31.pdf:PDF},
  owner     = {andrius},
  publisher = {American Chemical Society ({ACS})},
  timestamp = {2017.11.26},
  creationdate = {2017-11-26T00:00:00},
}

@Article{Weininger1989,
  author    = {Weininger, David and Weininger, Arthur and Weininger, Joseph L.},
  journal   = {Journal of Chemical Information and Computer Sciences},
  title     = {{SMILES}. 2. Algorithm for generation of unique {SMILES} notation},
  year      = {1989},
  issn      = {0095-2338},
  month     = {May},
  number    = {2},
  pages     = {97--101},
  volume    = {29},
  doi       = {10.1021/ci00062a008},
  file      = {:by-author/W/Weininger/1989_Weininger_97.pdf:PDF},
  owner     = {andrius},
  publisher = {American Chemical Society (ACS)},
  timestamp = {2021.03.23},
  creationdate = {2021-03-23T00:00:00},
  url       = {https://pubs.acs.org/doi/10.1021/ci00062a008},
}

@Article{Fuentes1989,
  author    = {Luis Fuentes},
  journal   = {Textures and Microstructures},
  title     = {Anomalous Scattering and Null-Domain Ghost Corrections for Fibre Textures},
  year      = {1989},
  pages     = {347--360},
  volume    = {10},
  doi       = {10.1155/TSM.10.347},
  file      = {:by-author/F/Fuentes/1989_Fuentes_347.pdf:PDF},
  owner     = {saulius},
  timestamp = {2017.11.27},
  creationdate = {2017-11-27T00:00:00},
  url       = {http://blogs.cimav.edu.mx/luis.fuentes/data/files/Algunas%20publicaciones/Anomalous%20scatt%20.pdf},
}

@Article{Jenkins2012,
  author       = {Alejandro Jenkins},
  title        = {The Sun's position in the sky},
  year         = {2013},
  number       = {3},
  pages        = {633},
  volume       = {34},
  abstract     = {We express the position of the Sun in the sky as a function of time and the observer's geographic coordinates. Our method is based on applying rotation matrices to vectors describing points on the celestial sphere. We also derive direct expressions, as functions of date of the year and geographic latitude, for the duration of daylight, the maximum and minimum altitudes of the Sun, and the cardinal directions to sunrise and sunset. We discuss how to account for the eccentricity of the earth's orbit, the precessions of the equinoxes and the perihelion, the size of the solar disk, and atmospheric refraction. We illustrate these results by computing the dates of "Manhattanhenge" (when sunset aligns with the east-west streets on the main traffic grid for Manhattan, in New York City), by plotting the altitude of the Sun over representative cities as a function of time, and by showing plots ("analemmas") for the position of the Sun in the sky at a given hour of the day.},
  date         = {2012-08-05},
  doi          = {10.1088/0143-0807/34/3/633},
  eprint       = {1208.1043v3},
  eprintclass  = {physics.pop-ph},
  eprinttype   = {arXiv},
  file         = {:by-author/J/Jenkins/2013_Jenkins_633.pdf:PDF},
  journaltitle = {Eur. J. Phys.},
  keywords     = {physics.ed-ph; physics.pop-ph},
  owner        = {saulius},
  timestamp = {2017.11.27},
  creationdate = {2017-11-27T00:00:00},
  url          = {https://arxiv.org/pdf/1208.1043v3.pdf},
}

@Thesis{Veer2016,
  author           = {J. M. van der Veer},
  creationdate     = {2017-12-05T00:00:00},
  file             = {:by-author/V/Veer/2016_Veer.pdf:PDF},
  keywords         = {Algol; Algol 68; Brownian Dynamics; Code; Compiler; Molecular Dunamics},
  modificationdate = {2024-05-16T08:40:50},
  owner            = {saulius},
  timestamp        = {2017.12.05},
  title            = {On Brownian Dynamics simulations of concentrated dispersions},
  type             = {PhD thesis, re-issued by the author},
  url              = {https://jmvdveer.home.xs4all.nl/marcel-van-der-veer-thesis.pdf},
  year             = {2016},
}

@Article{Hertwich2018,
  author    = {Edgar Hertwich and Niko Heeren and Brandon Kuczenski and Guillaume Majeau-Bettez and Rupert J. Myers and Stefan Pauliuk and Konstantin Stadler and Reid Lifset},
  journal   = {Journal of Industrial Ecology},
  title     = {Nullius in Verba: Advancing Data Transparency in Industrial Ecology},
  year      = {2018},
  month     = {jan},
  doi       = {10.1111/jiec.12738},
  file      = {:by-author/H/Hertwich/2018_Hertwich_.pdf:PDF},
  owner     = {saulius},
  publisher = {Wiley-Blackwell},
  timestamp = {2018.01.30},
  creationdate = {2018-01-30T00:00:00},
}

@Article{OECD2017,
  author    = {{OECD}},
  journal   = {OECD Science, Technology and Industry Policy Papers},
  title     = {Business models for sustainable research data repositories},
  year      = {2017},
  issn      = {2307-4957},
  month     = {dec},
  doi       = {10.1787/302b12bb-en},
  file      = {:by-author/O/OECD/2017_OECD_.pdf:PDF},
  owner     = {saulius},
  publisher = {Organisation for Economic Co-Operation and Development ({OECD})},
  timestamp = {2017.12.11},
  creationdate = {2017-12-11T00:00:00},
  url       = {http://dx.doi.org/10.1787/302b12bb-en},
}

@PhdThesis{Wang2014,
  author    = {Jinnian Wang},
  title     = {A Study on Hyperspectral Remote Sensing Data Processing and Analysis applied to 3D Mineral Mapping},
  year      = {2014},
  file      = {:by-author/W/Wang/2014_Wang.pdf:PDF},
  owner     = {saulius},
  timestamp = {2018.02.14},
  creationdate = {2018-02-14T00:00:00},
}

@Article{Brembs2013,
  author    = {Björn Brembs and Katherine Button and Marcus Munaf{\`{o}}},
  journal   = {Frontiers in Human Neuroscience},
  title     = {Deep impact: unintended consequences of journal rank},
  year      = {2013},
  volume    = {7},
  doi       = {10.3389/fnhum.2013.00291},
  file      = {:by-author/B/Brembs/2013_Brembs.pdf:PDF},
  owner     = {saulius},
  publisher = {Frontiers Media {SA}},
  timestamp = {2018.01.30},
  creationdate = {2018-01-30T00:00:00},
}

@Article{Yau2008,
  author     = {Yau, Stephen S. and Yin, Yin},
  journal    = {IEEE Trans. Serv. Comput.},
  title      = {A Privacy Preserving Repository for Data Integration Across Data Sharing Services},
  year       = {2008},
  issn       = {1939-1374},
  month      = jul,
  number     = {3},
  pages      = {130--140},
  volume     = {1},
  acmid      = {1512269},
  address    = {Washington, DC, USA},
  doi        = {10.1109/TSC.2008.14},
  file       = {:by-author/Y/Yau/2008_Yau_130.pdf:PDF},
  issue_date = {July 2008},
  keywords   = {And Protection; Data Sharing; Distributed Systems; Integrity; Security},
  numpages   = {11},
  owner      = {saulius},
  publisher  = {IEEE Computer Society},
  timestamp = {2018.01.30},
  creationdate = {2018-01-30T00:00:00},
  url        = {https://doi.org/10.1109/TSC.2008.14},
}

@Article{Mounet2018,
  author    = {Mounet, Nicolas and Gibertini, Marco and Schwaller, Philippe and Campi, Davide and Merkys, Andrius and Marrazzo, Antimo and Sohier, Thibault and Castelli, Ivano Eligio and Cepellotti, Andrea and Pizzi, Giovanni and Marzari, Nicola},
  journal   = {Nature Nanotechnology},
  title     = {Two-dimensional materials from high-throughput computational exfoliation of experimentally known compounds},
  year      = {2018},
  issn      = {1748-3395},
  month     = {Feb},
  doi       = {10.1038/s41565-017-0035-5},
  file      = {:by-author/M/Mounet/2018_Mounet.pdf:PDF},
  owner     = {andrius},
  publisher = {Springer Nature},
  timestamp = {2018.02.07},
  creationdate = {2018-02-07T00:00:00},
  url       = {http://dx.doi.org/10.1038/s41565-017-0035-5},
}

@Manuscript{Dowlin2017,
  author    = {Nathan Dowlin and Ran Gilad-Bachrach and Kim Laine and Kristin Lauter and Michael Naehrig and John Wernsing},
  title     = {Manual for Using Homomorphic Encryption for Bioinformatics},
  year      = {2017},
  keywords  = {Bioinformatics; Cryptography; Homomorphic Encryption; Privacy},
  url       = {https://www.microsoft.com/en-us/research/wp-content/uploads/2015/11/ManualHE-3.pdf},
  file      = {:by-author/D/Dowlin/2017_Dowlin.pdf:PDF},
  owner     = {saulius},
  timestamp = {2018.02.08},
  creationdate = {2018-02-08T00:00:00},
}

@PhdThesis{Kuhn2001,
  author      = {Bradley M. Kuhn},
  title       = {Considerations on Porting Perl to the Java Virtual Machine},
  year        = {2001},
  date        = {2001-01-22},
  file        = {:by-author/K/Kuhn/2001_Kuhn.pdf:PDF},
  institution = {The University of Cincinnati},
  owner       = {saulius},
  timestamp = {2018.02.09},
  creationdate = {2018-02-09T00:00:00},
  url         = {http://www.ebb.org/bkuhn/articles/thesis.pdf},
}

@Article{Geilhufe2018,
  author    = {R. Matthias Geilhufe and Stanislav S. Borysov and Dmytro Kalpakchi and Alexander V. Balatsky},
  journal   = {Physical Review Materials},
  title     = {Towards novel organic high- Tc superconductors: Data mining using density of states similarity search},
  year      = {2018},
  month     = {feb},
  number    = {2},
  pages     = {024802},
  volume    = {2},
  comment   = {Citing COD},
  doi       = {10.1103/physrevmaterials.2.024802},
  file      = {:by-author/G/Geilhufe/2018_Geilhufe_24802.pdf:PDF},
  owner     = {saulius},
  publisher = {American Physical Society ({APS})},
  timestamp = {2018.02.14},
  creationdate = {2018-02-14T00:00:00},
}

@Article{Grabowskaa2017,
  author    = {Ewelina Grabowskaa and Magdalena Diak and Tomasz Klimczuk and Wojciech Lisowski and Adriana Zaleska-Medynska},
  journal   = {Molecular Catalysis},
  title     = {Novel decahedral {TiO} 2 photocatalysts modified with Ru or Rh {NPs}: Insight into the mechanism},
  year      = {2017},
  month     = {jun},
  pages     = {154--166},
  volume    = {434},
  doi       = {10.1016/j.mcat.2017.03.013},
  file      = {:by-author/G/Grabowskaa/2017_Grabowskaa_154.pdf:PDF},
  keywords  = {Ru Oxides},
  owner     = {saulius},
  publisher = {Elsevier {BV}},
  timestamp = {2018.02.14},
  creationdate = {2018-02-14T00:00:00},
}

@Article{Dixit2013,
  author    = {Purushottam D. Dixit},
  journal   = {The Journal of Chemical Physics},
  title     = {A maximum entropy thermodynamics of small systems},
  year      = {2013},
  month     = {may},
  number    = {18},
  pages     = {184111},
  volume    = {138},
  doi       = {10.1063/1.4804549},
  file      = {:by-author/D/Dixit/2013_Dixit_184111.pdf:PDF},
  owner     = {saulius},
  publisher = {{AIP} Publishing},
  timestamp = {2018.02.14},
  creationdate = {2018-02-14T00:00:00},
}

@Article{Dixit2012,
  author      = {Purushottam D. Dixit},
  title       = {A maximum entropy thermodynamics of small systems},
  pages       = {1210.3015v7},
  abstract    = {We present a maximum entropy approach to analyze the internal dynamics of a small system in contact with a large bath e.g. a solute-solvent system. For the small solute, the fluctuations around the mean values of observables are not negligible and the probability distribution P(r) of the state space depends on the intricate details of the interaction of the solute with the solvent. Here, we employ a superstatistical approach: P(r) is expressed as a marginal distribution summed over the variation in {\beta}, the inverse temperature of the solute. The joint distribution P({\beta},r) is estimated by maximizing its entropy. We also calculate the first order system-size corrections to the canonical ensemble description of the state space. We test the development on a simple harmonic oscillator interacting with two baths with very different chemical identities viz. a) Lennard-Jones particles and b) water molecules. In both cases, our method captures the state space of the oscillator sufficiently well. Future directions and connections with traditional statistical mechanics are discussed.},
  date        = {2012-10-10},
  eprint      = {1210.3015v7},
  eprintclass = {cond-mat.stat-mech},
  eprinttype  = {arXiv},
  file        = {:by-author/D/Dixit/2012_Dixit_1210.3015v7.pdf:PDF},
  keywords    = {cond-mat.stat-mech},
  owner       = {saulius},
  timestamp = {2018.02.14},
  creationdate = {2018-02-14T00:00:00},
  url         = {http://arxiv.org/pdf/1210.3015v7},
}

@Article{Chard2018,
  author    = {Chard, Kyle and Dart, Eli and Foster, Ian and Shifflett, David and Tuecke, Steven and Williams, Jason},
  journal   = {PeerJ Computer Science},
  title     = {The Modern Research Data Portal: a design pattern for networked, data-intensive science},
  year      = {2018},
  issn      = {2376-5992},
  month     = jan,
  pages     = {e144},
  volume    = {4},
  abstract  = {We describe best practices for providing convenient, high-speed, secure access to large data via research data portals. We capture these best practices in a new design pattern, the Modern Research Data Portal, that disaggregates the traditional monolithic web-based data portal to achieve orders-of-magnitude increases in data transfer performance, support new deployment architectures that decouple control logic from data storage, and reduce development and operations costs. We introduce the design pattern; explain how it leverages high-performance data enclaves and cloud-based data management services; review representative examples at research laboratories and universities, including both experimental facilities and supercomputer sites; describe how to leverage Python APIs for authentication, authorization, data transfer, and data sharing; and use coding examples to demonstrate how these APIs can be used to implement a range of research data portal capabilities. Sample code at a companion web site, https://docs.globus.org/mrdp, provides application skeletons that readers can adapt to realize their own research data portals.},
  doi       = {10.7717/peerj-cs.144},
  file      = {:by-author/C/Chard/2018_Chard_144.pdf:PDF},
  keywords  = {Data Transfer Node; Globus; High-speed Network; Portal; Science DMZ},
  owner     = {saulius},
  timestamp = {2018.02.14},
  creationdate = {2018-02-14T00:00:00},
  url       = {https://doi.org/10.7717/peerj-cs.144},
}

@Article{Pearce2012,
  author    = {J. M. Pearce},
  journal   = {Science},
  title     = {Building Research Equipment with Free, Open-Source Hardware},
  year      = {2012},
  month     = {sep},
  number    = {6100},
  pages     = {1303--1304},
  volume    = {337},
  doi       = {10.1126/science.1228183},
  file      = {:by-author/P/Pearce/2012_Pearce_1303.pdf:PDF},
  owner     = {saulius},
  publisher = {American Association for the Advancement of Science ({AAAS})},
  timestamp = {2018.02.14},
  creationdate = {2018-02-14T00:00:00},
}

@Article{Pearce2015,
  author    = {J. M. Pearce},
  journal   = {Science and Public Policy},
  title     = {Return on investment for open source scientific hardware development},
  year      = {2015},
  month     = {jun},
  number    = {2},
  pages     = {192--195},
  volume    = {43},
  doi       = {10.1093/scipol/scv034},
  file      = {:by-author/P/Pearce/2015_Pearce_192.pdf:PDF},
  owner     = {saulius},
  publisher = {Oxford University Press ({OUP})},
  timestamp = {2018.02.14},
  creationdate = {2018-02-14T00:00:00},
}

@Article{Shen2018,
  author    = {Kui Shen and Lei Zhang and Xiaodong Chen and Lingmei Liu and Daliang Zhang and Yu Han and Junying Chen and Jilan Long and Rafael Luque and Yingwei Li and Banglin Chen},
  journal   = {Science},
  title     = {Ordered macro-microporous metal-organic framework single crystals},
  year      = {2018},
  month     = {jan},
  number    = {6372},
  pages     = {206--210},
  volume    = {359},
  doi       = {10.1126/science.aao3403},
  file      = {:by-author/S/Shen/2018_Shen_206.pdf:PDF},
  groups    = {sg/MOFs, am/MOFs, sg/MOF},
  keywords  = {Metal-Organic Frameworks (MOF)},
  owner     = {saulius},
  publisher = {American Association for the Advancement of Science ({AAAS})},
  timestamp = {2018.02.15},
  creationdate = {2018-02-15T00:00:00},
}

@Article{Sicho2017,
  author    = {Martin Šícho and Christina de Bruyn Kops and Conrad Stork and Daniel Svozil and Johannes Kirchmair},
  journal   = {Journal of Chemical Information and Modeling},
  title     = {{FAME} 2: Simple and Effective Machine Learning Model of Cytochrome P450 Regioselectivity},
  year      = {2017},
  month     = {aug},
  number    = {8},
  pages     = {1832--1846},
  volume    = {57},
  doi       = {10.1021/acs.jcim.7b00250},
  file      = {:by-author/Š/Šícho/2017_Šícho_1832.pdf:PDF},
  owner     = {saulius},
  publisher = {American Chemical Society ({ACS})},
  timestamp = {2018.02.15},
  creationdate = {2018-02-15T00:00:00},
}

@Article{Moeck2018,
  author      = {Peter Moeck},
  title       = {Towards generalized noise-level dependent crystallographic symmetry classifications of more or less periodic crystal patterns},
  year        = {2018},
  abstract    = {Geometric Akaike Information Criteria (G-AICs) for generalized noise-level dependent crystallographic symmetry classifications of two-dimensional (2D) images that are more or less periodic in either two or one dimensions as well as Akaike weights for multi-model inferences and predictions are reviewed. Such novel classifications do not refer to a single crystallographic symmetry class exclusively in a qualitative and definitive way. Instead, they are quantitative, spread over a range of crystallographic symmetry classes, and provide opportunities for inferences from all classes (within the range) simultaneously. The novel classifications are based on information theory and depend only on information that has been extracted from the images themselves by means of maximal likelihood approaches so that these classifications are objective. This is in stark contrast to the common practice whereby arbitrarily set thresholds are employed to force crystallographic symmetry classifications into apparently definitive/exclusive states, while the geometric feature extraction results on which they depend are never definitive in the presence of generalized noise, i.e. in all real world applications. Thus, there is unnecessary subjectivity in the currently practiced ways of making crystallographic symmetry classifications, which can be overcome by the approach outlined in this review.},
  date        = {2018-01-03},
  eprint      = {1801.01202v1},
  eprintclass = {physics.app-ph},
  eprinttype  = {arXiv},
  file        = {:by-author/M/Moeck/2018_Moeck.pdf:PDF},
  keywords    = {cond-mat.mtrl-sci; physics.app-ph},
  owner       = {saulius},
  timestamp = {2018.02.20},
  creationdate = {2018-02-20T00:00:00},
  url         = {https://arxiv.org/abs/1801.01202},
}

@Article{Pearce2017,
  author    = {Nicholas M. Pearce and Tobias Krojer and Anthony R. Bradley and Patrick Collins and Rados{\l}aw P. Nowak and Romain Talon and Brian D. Marsden and Sebastian Kelm and Jiye Shi and Charlotte M. Deane and Frank von Delft},
  journal   = {Nature Communications},
  title     = {A multi-crystal method for extracting obscured crystallographic states from conventionally uninterpretable electron density},
  year      = {2017},
  month     = {apr},
  pages     = {15123},
  volume    = {8},
  doi       = {10.1038/ncomms15123},
  file      = {:by-author/P/Pearce/2017_Pearce_15123.pdf:PDF},
  owner     = {saulius},
  publisher = {Springer Nature},
  timestamp = {2018.03.07},
  creationdate = {2018-03-07T00:00:00},
}

@Article{Garrido1948,
  author    = {Garrido, J.},
  title     = {Observations sur la diffusion des rayons X par les cristaux de ClO3Na},
  year      = {1948},
  month     = mar,
  pages     = {3--4},
  doi       = {10.1107/S0365110X48000028},
  file      = {:by-author/G/Garrido/1948_Garrido_3.pdf:PDF},
  issue     = {1},
  owner     = {saulius},
  publisher = {International Union of Crystallography},
  source    = {Acta Cryst (1948). Q1, 3-4 [doi:10.1107/S0365110X48000028]},
  timestamp = {2018.03.13},
  creationdate = {2018-03-13T00:00:00},
}

@Article{Hanawalt1919,
  author    = {J. D. Hanawalt and H. W. Rinn and L. K. Frevel},
  journal   = {Industrial and Engineering Chemistry},
  title     = {Chemical Analysis by X-Ray Diffraction},
  year      = {1919},
  pages     = {457--512},
  file      = {:by-author/H/Hayawalt/1919_Hayawalt_457.pdf:PDF},
  owner     = {saulius},
  timestamp = {2018.03.13},
  creationdate = {2018-03-13T00:00:00},
}

@Article{Hull1919,
  author    = {A. W. Hull},
  journal   = {Journal of the American Chemical Society},
  title     = {A new method of chemical analysis},
  year      = {1919},
  month     = {aug},
  number    = {8},
  pages     = {1168--1175},
  volume    = {41},
  doi       = {10.1021/ja02229a003},
  file      = {:by-author/H/Hull/1919_Hull_1168.pdf:PDF},
  owner     = {saulius},
  publisher = {American Chemical Society ({ACS})},
  timestamp = {2018.03.13},
  creationdate = {2018-03-13T00:00:00},
}

@InBook{Meenens2006,
  author       = {Lambert Meenens},
  pages        = {289--334},
  title        = {Algorithmics: Towards programming as a mathematical activity},
  year         = {2006},
  file         = {:by-author/M/Meenens/2006_Meenens_289.pdf:PDF},
  organization = {Centre for Mathematics and Computer Science},
  owner        = {saulius},
  timestamp = {2018.03.13},
  creationdate = {2018-03-13T00:00:00},
  url          = {http://www.kestrel.edu/home/people/meertens/publications/papers/Algorithmics.pdf},
}

@Manuscript{Hestenes2007,
  author    = {David Hestenes and Jeremy Holt},
  title     = {The Crystallographic Space Groups in Geometric and Algebra},
  year      = {2007},
  url       = {http://geocalc.clas.asu.edu/pdf/CrystalGA.pdf},
  abstract  = {We present a complete formulation of the 2D and 3D crystallographic space groups in the
conformal geometric algebra of Euclidean space. This enables a simple new representation of translational
and orthogonal symmetries in a multiplicative group of versors. The generators of each group are constructed
directly from a basis of lattice vectors that define its crystal class. A new system of space group symbols
enables one to unambiguously write down all generators of a given space group directly from its symbol.},
  file      = {:by-author/H/Hestenes/2007_Hestenes.pdf:PDF},
  owner     = {saulius},
  timestamp = {2018.03.13},
  creationdate = {2018-03-13T00:00:00},
}

@Manuscript{Churkin2010,
  author       = {Valery A. Churkin},
  title        = {Crystallographic and quasicrystallographic groups},
  year         = {2010},
  organization = {Sobolev Institute of Mathematics SB RAS},
  url          = {http://www.math.nsc.ru/conference/isc/2010/ch-pres5.pdf},
  file         = {:by-author/C/Churkin/2010_Churkin.pdf:PDF},
  owner        = {saulius},
  timestamp = {2018.03.13},
  creationdate = {2018-03-13T00:00:00},
}

@Manuscript{Pool2015,
  author       = {Tõnis Pool},
  title        = {Comparison of Erlang Runtime System and Java Virtual Machine},
  year         = {2015},
  organization = {University of Tartu},
  url          = {http://ds.cs.ut.ee/courses/course-files/To303nis%20Pool%20.pdf},
  file         = {:by-author/P/Pool/2015_Pool.pdf:PDF},
  owner        = {saulius},
  timestamp = {2018.03.13},
  creationdate = {2018-03-13T00:00:00},
}

@Article{Hitzer2013,
  author    = {Eckhard Hitzer and Daisuke Ichikawa},
  journal   = {Advances in Applied Clifford Algebras},
  title     = {Representation of Crystallographic Subperiodic Groups in Clifford's Geometric Algebra},
  year      = {2013},
  month     = {jun},
  number    = {4},
  pages     = {887--906},
  volume    = {23},
  doi       = {10.1007/s00006-013-0404-6},
  file      = {:by-author/H/Hitzer/2013_Hitzer_887.pdf:PDF},
  owner     = {saulius},
  publisher = {Springer Nature},
  timestamp = {2018.03.13},
  creationdate = {2018-03-13T00:00:00},
}

@TechReport{Dijkstra1961a,
  author    = {E. W. Dijkstra},
  title     = {An {Algol} 60 translator for {X1}},
  year      = {1961},
  file      = {:by-author/D/Dijkstra/1961_Dijkstra.pdf:PDF},
  owner     = {saulius},
  timestamp = {2018.03.13},
  creationdate = {2018-03-13T00:00:00},
  url       = {http://www.cs.utexas.edu/~EWD/MCReps/MR35.PDF},
}

@InProceedings{Akerlof2009,
  author    = {Carl W. Akerlof},
  title     = {Measurement of the Muon Lifetime},
  year      = {2009},
  file      = {:by-author/A/Akerlof/2009_Akerlof.pdf:PDF},
  owner     = {saulius},
  timestamp = {2018.03.13},
  creationdate = {2018-03-13T00:00:00},
  url       = {http://instructor.physics.lsa.umich.edu/adv-labs/Muon_Lifetime/MuonLifetime.pdf},
}

@Manuscript{Anonymous2013,
  author    = {Anonymous},
  title     = {Изучение свойств слабого взаимодействия и измерение времени жизни мюона},
  year      = {2013},
  url       = {http://dep_fizika.pnzgu.ru/files/dep_fizika.pnzgu.ru/literatura/lab/yad/lab_yad_03.pdf},
  file      = {:by-author/A/Anonymous/2013_Anonymous.pdf:PDF},
  owner     = {saulius},
  timestamp = {2018.03.13},
  creationdate = {2018-03-13T00:00:00},
}

@Manuscript{MJL2001,
  author    = {MJL},
  title     = {Measurement of the Muon Lifetime},
  year      = {2001},
  url       = {http://instructor.physics.lsa.umich.edu/adv-labs/Muon_Lifetime/muon_lifetime.pdf},
  file      = {:by-author/M/MJL/2001_MJL.pdf:PDF},
  owner     = {saulius},
  timestamp = {2018.03.13},
  creationdate = {2018-03-13T00:00:00},
}

@Manuscript{Малышевский2007,
  author    = {В. С. Малышевский},
  title     = {Измерение времени жизни мюона},
  year      = {2007},
  url       = {http://sfedu.ru/www/umr_main.umr_download?p_umr_id=24468},
  file      = {:by-author/М/Малышевский/2007_Малышевский.pdf:PDF},
  owner     = {saulius},
  timestamp = {2018.03.13},
  creationdate = {2018-03-13T00:00:00},
}

@Article{Furukawa2013,
  author    = {H. Furukawa and K. E. Cordova and M. O'Keeffe and O. M. Yaghi},
  journal   = {Science},
  title     = {The Chemistry and Applications of Metal-Organic Frameworks},
  year      = {2013},
  month     = {aug},
  number    = {6149},
  pages     = {1230444--1230444},
  volume    = {341},
  doi       = {10.1126/science.1230444},
  file      = {:by-author/F/Furukawa/2013_Furukawa_1230444.pdf:PDF},
  groups    = {sg/MOFs, am/MOFs},
  owner     = {saulius},
  publisher = {American Association for the Advancement of Science ({AAAS})},
  timestamp = {2018.03.19},
  creationdate = {2018-03-19T00:00:00},
  url       = {http://yaghi.berkeley.edu/pdfPublications/13-sci-mof-rev.pdf},
}

@InBook{Simon2011,
  author    = {Ferenc Simon and Marc Monthioux},
  editor    = {Marc Monthioux},
  pages     = {273--321},
  publisher = {John Wiley \& Sons, Ltd.},
  title     = {Fullerenes inside Carbon Nanotubes: The Peapods},
  year      = {2011},
  edition   = {First Edition},
  booktitle = {Carbon Meta-Nanotubes: Synthesis, Properties and Applications},
  date      = {2012},
  file      = {:by-author/S/Simon/2011_Simon_273.pdf:PDF},
  owner     = {saulius},
  timestamp = {2018.03.24},
  creationdate = {2018-03-24T00:00:00},
  url       = {http://homepage.univie.ac.at/ferenc.simon/publications/2011/MonthiouxBookChapter.pdf},
}

@Article{Chaudhuri2017,
  author    = {Supriya K. Chaudhuri and Rajat K. Chaudhuri and Prasanta K. Mukherjee and Sudip Chattopadhyay},
  journal   = {The Journal of Chemical Physics},
  title     = {A confinement induced spectroscopic study of noble gas atoms using equation of motion architecture: Encapsulation within fullerene's voids},
  year      = {2017},
  month     = {jul},
  number    = {3},
  pages     = {034111},
  volume    = {147},
  doi       = {10.1063/1.4994569},
  file      = {:by-author/C/Chaudhuri/2017_Chaudhuri_34111.pdf:PDF},
  owner     = {saulius},
  publisher = {{AIP} Publishing},
  timestamp = {2018.03.24},
  creationdate = {2018-03-24T00:00:00},
}

@Article{Carnap1945,
  author    = {Rudolf Carnap},
  journal   = {Philosophy and Phenomenolgical Research},
  title     = {Two Concepts of Probability: The Problem of Probability},
  year      = {1945},
  number    = {4},
  pages     = {513--532},
  volume    = {5},
  date      = {June 1945},
  file      = {:by-author/C/Carnap/1945_Carnap_513.pdf:PDF},
  owner     = {saulius},
  timestamp = {2018.03.25},
  creationdate = {2018-03-25T00:00:00},
  url       = {http://people.hss.caltech.edu/~franz/Confirmation%20and%20Induction/PDFs/Rudolf%20Carnap%20-%20The%20Two%20Concepts%20of%20Probability.pdf},
}

@Article{Carnap1947,
  author    = {Rudolf Carnap},
  journal   = {Philosophy and Phenomenolgical Research},
  title     = {On the Application of Inductive Logic},
  year      = {1947},
  number    = {1},
  pages     = {133--148},
  volume    = {8},
  date      = {Sep. 1947},
  file      = {:by-author/C/Carnap/1947_Carnap_133.pdf:PDF},
  owner     = {saulius},
  timestamp = {2018.03.25},
  creationdate = {2018-03-25T00:00:00},
  url       = {http://people.hss.caltech.edu/~franz/Confirmation%20and%20Induction/PDFs/Rudolf%20Carnap%20-%20On%20the%20Application%20of%20Inductive%20Logic.pdf},
}

@Article{Lam2004,
  author    = {T. Y. Lam},
  journal   = {The American Mathematical Monthly},
  title     = {On Subgroups of Prime Index},
  year      = {2004},
  month     = {mar},
  number    = {3},
  pages     = {256},
  volume    = {111},
  doi       = {10.2307/4145135},
  file      = {:by-author/L/Lam/2004_Lam_256.ps:PostScript;:by-author/L/Lam/2004_Lam_256.pdf:PDF},
  keywords  = {Algebra; Group Theory; Normal Subgroups},
  owner     = {saulius},
  publisher = {{JSTOR}},
  timestamp = {2018.03.25},
  creationdate = {2018-03-25T00:00:00},
  url       = {http://www.jstor.org/stable/4145135},
}

@Article{Olechnovic2017,
  author    = {Kliment Olechnovič and Česlovas Venclovas},
  journal   = {Proteins: Structure, Function, and Bioinformatics},
  title     = {{VoroMQA}: Assessment of protein structure quality using interatomic contact areas},
  year      = {2017},
  month     = {mar},
  number    = {6},
  pages     = {1131--1145},
  volume    = {85},
  doi       = {10.1002/prot.25278},
  file      = {:by-author/O/Olechnovič/2017_Olechnovič_1131.pdf:;:by-author/O/Olechnovič/2017_Olechnovič_1131/prot25278-sup-0001-suppinfo1.pdf:PDF},
  keywords  = {Protein Model Quality; Quality Assessment; VoroMQA; X-ray Crystallography},
  owner     = {saulius},
  publisher = {Wiley-Blackwell},
  timestamp = {2018.03.27},
  creationdate = {2018-03-27T00:00:00},
}

@Article{Sontz2015,
  author       = {Sontz, Pamela A. and Bailey, Jake B. and Ahn, Sunhyung and Tezcan, F. Akif},
  title        = {A Metal Organic Framework with Spherical Protein Nodes: Rational Chemical Design of 3D Protein Crystals},
  issn         = {0002-7863, 1520-5126},
  number       = {36},
  pages        = {11598--11601},
  volume       = {137},
  date         = {2015-09-16},
  doi          = {10.1021/jacs.5b07463},
  file         = {:by-author/S/Sontz/2015_Sontz_11598.pdf:},
  groups       = {sg/MOFs, am/MOFs, sg/Reticular sg/Chemistry},
  journaltitle = {Journal of the American Chemical Society},
  langid       = {english},
  owner        = {saulius},
  shorttitle   = {A Metal Organic Framework with Spherical Protein Nodes},
  timestamp = {2018.03.28},
  creationdate = {2018-03-28T00:00:00},
  url          = {http://pubs.acs.org/doi/10.1021/jacs.5b07463},
  urldate      = {2018-03-28},
}

@Article{Yaghi2016,
  author       = {Yaghi, Omar M.},
  title        = {Reticular Chemistry—Construction, Properties, and Precision Reactions of Frameworks},
  issn         = {0002-7863, 1520-5126},
  number       = {48},
  pages        = {15507--15509},
  volume       = {138},
  date         = {2016-12-07},
  doi          = {10.1021/jacs.6b11821},
  file         = {:by-author/Y/Yaghi/2016_Yaghi_15507.pdf:},
  groups       = {sg/MOFs, am/MOFs, sg/Reticular sg/Chemistry},
  journaltitle = {Journal of the American Chemical Society},
  langid       = {english},
  owner        = {saulius},
  timestamp = {2018.03.28},
  creationdate = {2018-03-28T00:00:00},
  url          = {http://pubs.acs.org/doi/10.1021/jacs.6b11821},
  urldate      = {2018-03-28},
}

@Article{Tu2015,
  author       = {Tu, Binbin and Pang, Qingqing and Ning, Erlong and Yan, Wenqing and Qi, Yi and Wu, Doufeng and Li, Qiaowei},
  title        = {Heterogeneity within a Mesoporous Metal–Organic Framework with Three Distinct Metal-Containing Building Units},
  issn         = {0002-7863, 1520-5126},
  number       = {42},
  pages        = {13456--13459},
  volume       = {137},
  date         = {2015-10-28},
  doi          = {10.1021/jacs.5b07687},
  file         = {:by-author/T/Tu/2015_Tu_13456.pdf:},
  groups       = {sg/MOFs, am/MOFs, sg/Reticular sg/Chemistry},
  journaltitle = {Journal of the American Chemical Society},
  langid       = {english},
  owner        = {saulius},
  timestamp = {2018.03.28},
  creationdate = {2018-03-28T00:00:00},
  url          = {http://pubs.acs.org/doi/10.1021/jacs.5b07687},
  urldate      = {2018-03-28},
}

@Article{Qin2016,
  author       = {Qin, Jun-Sheng and Du, Dong-Ying and Li, Mian and Lian, Xi-Zhen and Dong, Long-Zhang and Bosch, Mathieu and Su, Zhong-Min and Zhang, Qiang and Li, Shun-Li and Lan, Ya-Qian and Yuan, Shuai and Zhou, Hong-Cai},
  title        = {Derivation and Decoration of Nets with Trigonal-Prismatic Nodes: A Unique Route to Reticular Synthesis of Metal–Organic Frameworks},
  issn         = {0002-7863, 1520-5126},
  number       = {16},
  pages        = {5299--5307},
  volume       = {138},
  date         = {2016-04-27},
  doi          = {10.1021/jacs.6b01093},
  file         = {:by-author/Q/Qin/2016_Qin_5299.pdf:},
  groups       = {sg/MOFs, am/MOFs, sg/Reticular sg/Chemistry},
  journaltitle = {Journal of the American Chemical Society},
  langid       = {english},
  owner        = {saulius},
  shorttitle   = {Derivation and Decoration of Nets with Trigonal-Prismatic Nodes},
  timestamp = {2018.03.28},
  creationdate = {2018-03-28T00:00:00},
  url          = {http://pubs.acs.org/doi/10.1021/jacs.6b01093},
  urldate      = {2018-03-28},
}

@Article{Inge2016,
  author       = {Inge, A. Ken and Köppen, Milan and Su, Jie and Feyand, Mark and Xu, Hongyi and Zou, Xiaodong and O’Keeffe, Michael and Stock, Norbert},
  title        = {Unprecedented Topological Complexity in a Metal–Organic Framework Constructed from Simple Building Units},
  issn         = {0002-7863, 1520-5126},
  number       = {6},
  pages        = {1970--1976},
  volume       = {138},
  date         = {2016-02-17},
  doi          = {10.1021/jacs.5b12484},
  file         = {:by-author/I/Inge/2016_Inge_1970.pdf:PDF},
  groups       = {sg/MOFs, am/MOFs, sg/Reticular sg/Chemistry},
  journaltitle = {Journal of the American Chemical Society},
  langid       = {english},
  owner        = {saulius},
  timestamp = {2018.03.28},
  creationdate = {2018-03-28T00:00:00},
  url          = {http://pubs.acs.org/doi/10.1021/jacs.5b12484},
  urldate      = {2018-03-28},
}

@Article{Alezi2016,
  author       = {Alezi, Dalal and Spanopoulos, Ioannis and Tsangarakis, Constantinos and Shkurenko, Aleksander and Adil, Karim and Belmabkhout, Youssef and O′Keeffe, Michael and Eddaoudi, Mohamed and Trikalitis, Pantelis N.},
  title        = {Reticular Chemistry at Its Best: Directed Assembly of Hexagonal Building Units into the Awaited Metal-Organic Framework with the Intricate Polybenzene Topology, pbz-{MOF}},
  issn         = {0002-7863, 1520-5126},
  number       = {39},
  pages        = {12767--12770},
  volume       = {138},
  date         = {2016-10-05},
  doi          = {10.1021/jacs.6b08176},
  file         = {:by-author/A/Alezi/2016_Alezi_12767.pdf:PDF},
  groups       = {sg/MOFs, am/MOFs, sg/Reticular sg/Chemistry},
  journaltitle = {Journal of the American Chemical Society},
  langid       = {english},
  owner        = {saulius},
  shorttitle   = {Reticular Chemistry at Its Best},
  timestamp = {2018.03.29},
  creationdate = {2018-03-29T00:00:00},
  url          = {http://pubs.acs.org/doi/10.1021/jacs.6b08176},
  urldate      = {2018-03-28},
}

@Article{Liu2015,
  author       = {Liu, Chong and Luo, Tian-Yi and Feura, Evan S. and Zhang, Chen and Rosi, Nathaniel L.},
  title        = {Orthogonal Ternary Functionalization of a Mesoporous Metal–Organic Framework via Sequential Postsynthetic Ligand Exchange},
  issn         = {0002-7863, 1520-5126},
  number       = {33},
  pages        = {10508--10511},
  volume       = {137},
  date         = {2015-08-26},
  doi          = {10.1021/jacs.5b06780},
  file         = {:by-author/L/Liu/2015_Liu_10508.pdf:},
  groups       = {sg/MOFs, am/MOFs, sg/Reticular sg/Chemistry},
  journaltitle = {Journal of the American Chemical Society},
  langid       = {english},
  owner        = {saulius},
  timestamp = {2018.03.29},
  creationdate = {2018-03-29T00:00:00},
  url          = {http://pubs.acs.org/doi/10.1021/jacs.5b06780},
  urldate      = {2018-03-28},
}

@Article{Student1908,
  author    = {Student},
  journal   = {Biometrika},
  title     = {The probable error of a mean},
  year      = {1908},
  month     = {mar},
  number    = {1},
  pages     = {1--25},
  volume    = {6},
  doi       = {10.1093/biomet/6.1.1},
  file      = {:by-author/S/Student/1908_Student_1.pdf:PDF},
  owner     = {saulius},
  publisher = {Oxford University Press ({OUP})},
  timestamp = {2018.03.30},
  creationdate = {2018-03-30T00:00:00},
}

@Article{Student1907,
  author    = {Student},
  journal   = {Biometrika},
  title     = {On the error of counting with a haemacytometer},
  year      = {1907},
  month     = {feb},
  number    = {3},
  pages     = {351--360},
  volume    = {5},
  doi       = {10.1093/biomet/5.3.351},
  file      = {:by-author/S/Student/1907_Student_351.pdf:PDF},
  owner     = {saulius},
  publisher = {Oxford University Press ({OUP})},
  timestamp = {2018.03.30},
  creationdate = {2018-03-30T00:00:00},
}

@Article{Pena1993,
  author    = {Daniel Pena and Irwin Guttman},
  journal   = {Biometrika},
  title     = {Comparing Probabilistic Methods for Outlier Detection in Linear Models},
  year      = {1993},
  month     = {sep},
  number    = {3},
  pages     = {603},
  volume    = {80},
  doi       = {10.2307/2337181},
  file      = {:by-author/P/Pena/1993_Pena_603.pdf:PDF},
  keywords  = {Bayesian Inference; Diagnostic; Outlier Detection; Posterior Distribution; Predictive Distribution},
  owner     = {saulius},
  publisher = {{JSTOR}},
  timestamp = {2018.03.30},
  creationdate = {2018-03-30T00:00:00},
}

@PhdThesis{Wang2004,
  author      = {Yusu Wang},
  title       = {Geometric and topological methods in protein structure analysis},
  year        = {2004},
  file        = {:by-author/W/Wang/2004_Wang.pdf:PDF},
  institution = {Duke University},
  owner       = {saulius},
  timestamp = {2018.04.02},
  creationdate = {2018-04-02T00:00:00},
  url         = {https://pdfs.semanticscholar.org/4ce1/ed6020dedefb8bf2ed57b2f9de49e016ddfe.pdf},
}

@Article{Edelsbrunner2005,
  author    = {Herbert Edelsbrunner and Patrice Koehl},
  journal   = {Discrete and Computational Geometry},
  title     = {The Geometry and of Biomolecular and Solvation},
  year      = {2005},
  pages     = {241--273},
  volume    = {52},
  abstract  = {Years of research in biology have established that all cellular functions are deeply connected to the shape and dynamics of their molecular actors. As a response, structural molecular biology has emerged as a new line of experimental research focused on revealing the structure of biomolecules. The analysis of these structures has led to the development of computational biology, whose aim is to predict from molecular simulation properties inaccessible to experimental probes.},
  file      = {:by-author/E/Edelsbrunner/2005_Edelsbrunner_241.pdf:PDF},
  keywords  = {Balls; Derivatives; Implicit Solvent Models; Molecular Simulations; Space-filling Diagrams; Spheres; Surface Area; Volume},
  owner     = {saulius},
  timestamp = {2018.04.02},
  creationdate = {2018-04-02T00:00:00},
  url       = {http://pub.ist.ac.at/~edels/Papers/2005-B-01-GeometryBiomolecularSolvation.pdf},
}

@Article{Altomare2013,
  author    = {Angela Altomare and Corrado Cuocci and Carmelo Giacovazzo and Anna Moliterni and Rosanna Rizzi and Nicola Corriero and Aurelia Falcicchio},
  journal   = {Journal of Applied Crystallography},
  title     = {{EXPO}2013: a kit of tools for phasing crystal structures from powder data},
  year      = {2013},
  month     = {jul},
  number    = {4},
  pages     = {1231--1235},
  volume    = {46},
  doi       = {10.1107/s0021889813013113},
  file      = {:by-author/A/Altomare/2013_Altomare_1231.pdf:PDF},
  owner     = {saulius},
  publisher = {International Union of Crystallography ({IUCr})},
  timestamp = {2018.04.08},
  creationdate = {2018-04-08T00:00:00},
}

@Article{Hill1900,
  author    = {Edwin A. Hill},
  journal   = {Journal of the American Chemical Society},
  title     = {On a system of indexing chemical literature; adopted by the classification division of the {U}. {S}. {P}atent {O}ffice},
  year      = {1900},
  month     = {aug},
  number    = {8},
  pages     = {478--494},
  volume    = {22},
  doi       = {10.1021/ja02046a005},
  file      = {:by-author/H/Hill/1900_Hill_478.pdf:PDF},
  keywords  = {Chemical Formula Standards; Chemoinformatics; Hill Notation},
  owner     = {saulius},
  publisher = {American Chemical Society ({ACS})},
  timestamp = {2018.04.08},
  creationdate = {2018-04-08T00:00:00},
}

@Article{Newberry2016,
  author    = {Robert W Newberry and Ronald T Raines},
  journal   = {Nature Chemical Biology},
  title     = {A prevalent intraresidue hydrogen bond stabilizes proteins},
  year      = {2016},
  month     = {oct},
  number    = {12},
  pages     = {1084--1088},
  volume    = {12},
  doi       = {10.1038/nchembio.2206},
  file      = {:by-author/N/Newberry/2016_Newberry_1084.pdf:PDF},
  keywords  = {Bioinformatics; For Students},
  owner     = {saulius},
  publisher = {Springer Nature},
  timestamp = {2018.04.20},
  creationdate = {2018-04-20T00:00:00},
}

@Article{Sun1996a,
  author    = {S. Sun and E. R. Bernstein},
  journal   = {The Journal of Physical Chemistry},
  title     = {Aromatic van der Waals Clusters:~ Structure and Nonrigidity},
  year      = {1996},
  month     = {jan},
  number    = {32},
  pages     = {13348--13366},
  volume    = {100},
  abstract  = {More than a dozen cases of nonrigid van der Waals clusters are presented and discussed to demonstrate that
cluster nonrigidity is a general phenomenon in all weakly bound systems. The interplay of structure and
nonrigidity complicates cluster research and mandates a dynamical approach to cluster properties in which
multiple stable configurations coexist and interconvert, and large amplitude nuclear motions are the rule
rather than the exception. Empirical potential energy surface calculations are employed to yield physical
insight into the structure and dynamics of nonrigid clusters, and molecular symmetry group theory is applied
to analyze spectroscopic manifestations of cluster nonrigidity. Empirical potentials of various forms are
successful in predicting most cluster structures, as well as estimating the potential surface barrier heights
hindering the interconversion between different local minimum-energy structures. Such calculational
approaches also emphasize the importance of large amplitude motion for one or more of the cluster vibrational
degrees of freedom. The limits of these empirical calculations are discussed, and recent attempts to derive
cluster structure and properties by ab initio techniques are reviewed. The aromatic/small molecule clusters
considered in this presentation display two types of nonrigidity: local nonrigidity in which large amplitude
motion involves the rotation of one of the molecular constituents, and global nonrigidity in which large
amplitude motion involves displacement of the centers of mass of the molecular constituents. The former
motion interchanges equivalent atoms, and the latter motion interchanges cluster conformations. The potential
surface barriers for these large amplitude motions tend to increase with constituent molecule complexity.},
  doi       = {10.1021/jp960739o},
  file      = {:by-author/S/Sun/1996_Sun_13348.pdf:PDF},
  keywords  = {Herringbone Interactions},
  owner     = {saulius},
  publisher = {American Chemical Society ({ACS})},
  timestamp = {2018.04.23},
  creationdate = {2018-04-23T00:00:00},
}

@Article{Neverov2018,
  author    = {Vladislav S. Neverov and Nikolay P. Khrapov},
  journal   = {Open Engineering},
  title     = {{\textquotedblleft}{XANSONS} for {COD}{\textquotedblright}: a new small {BOINC} project in crystallography},
  year      = {2018},
  month     = {apr},
  number    = {1},
  pages     = {102--108},
  volume    = {8},
  doi       = {10.1515/eng-2018-0014},
  file      = {:by-author/N/Neverov/2018_Neverov_102.pdf:PDF},
  keywords  = {Citing COD; Using COD},
  owner     = {saulius},
  publisher = {Walter de Gruyter {GmbH}},
  timestamp = {2018.04.26},
  creationdate = {2018-04-26T00:00:00},
}

@Article{Fuentes-Cobas2017,
  author    = {Luis E. Fuentes-Cobas and Daniel Chateigner and Mar{\'{\i}}a E. Fuentes-Montero and Giancarlo Pepponi and Saulius Grazulis},
  journal   = {Advances in Applied Ceramics},
  title     = {The representation of coupling interactions in the Material Properties Open Database ({MPOD})},
  year      = {2017},
  month     = {aug},
  number    = {8},
  pages     = {428--433},
  volume    = {116},
  doi       = {10.1080/17436753.2017.1343782},
  file      = {:by-author/F/Fuentes-Cobas/2017_Fuentes-Cobas_428.pdf:PDF},
  owner     = {saulius},
  publisher = {Informa {UK} Limited},
  timestamp = {2018.04.25},
  creationdate = {2018-04-25T00:00:00},
}

@Webpage{Sayle20XX,
  author      = {Roger Sayle},
  retrieved   = {2018-04-29},
  title       = {{PDB}: Cruft to Content (Perception of Molecular Connectivity from {3D} Coordinates)},
  url         = {http://www.daylight.com/meetings/mug01/Sayle/m4xbondage.html},
  institution = {Bioinformatics Group, Metaphorics LLC, Santa Fe, New Mexico.},
  file        = {:by-author/S/Sayle/20XX_Sayle.pdf:PDF},
  owner       = {andrius},
  timestamp = {2018.04.29},
  creationdate = {2018-04-29T00:00:00},
}

@Article{Meng1991,
  author    = {Elaine C. Meng and Richard A. Lewis},
  journal   = {Journal of Computational Chemistry},
  title     = {Determination of molecular topology and atomic hybridization states from heavy atom coordinates},
  year      = {1991},
  month     = {sep},
  number    = {7},
  pages     = {891--898},
  volume    = {12},
  doi       = {10.1002/jcc.540120716},
  file      = {:by-author/M/Meng/1991_Meng_891.pdf:PDF},
  owner     = {andrius},
  publisher = {Wiley-Blackwell},
  timestamp = {2018.04.29},
  creationdate = {2018-04-29T00:00:00},
}

@Article{Nido2016,
  author    = {Gonzalo S. Nido and Ludovica Bachschmid-Romano and Ugo Bastolla and Alberto Pascual-Garc{\'{\i}}a},
  journal   = {{PeerJ} Computer Science},
  title     = {Learning structural bioinformatics and evolution with a snake puzzle},
  year      = {2016},
  month     = {dec},
  pages     = {e100},
  volume    = {2},
  doi       = {10.7717/peerj-cs.100},
  file      = {:by-author/N/Nido/2016_Nido_100.pdf:PDF},
  keywords  = {Bioinformatics; Protein Folding; Teching},
  owner     = {saulius},
  publisher = {{PeerJ}},
  timestamp = {2018.05.10},
  creationdate = {2018-05-10T00:00:00},
}

@Article{Peng1996,
  author    = {Chunyang Peng and Philippe Y. Ayala and H. Bernhard Schlegel and Michael J. Frisch},
  journal   = {Journal of Computational Chemistry},
  title     = {Using redundant internal coordinates to optimize equilibrium geometries and transition states},
  year      = {1996},
  month     = {jan},
  number    = {1},
  pages     = {49--56},
  volume    = {17},
  doi       = {10.1002/(sici)1096-987x(19960115)17:1<49::aid-jcc5>3.0.co;2-0},
  file      = {:by-author/P/Peng/1996_Peng_49.pdf:PDF},
  keywords  = {Internal Coordinates; Optimisation; Protein Modelling},
  owner     = {saulius},
  publisher = {Wiley-Blackwell},
  timestamp = {2018.05.10},
  creationdate = {2018-05-10T00:00:00},
}

@Article{Bakken2002,
  author    = {Vebj{\o}rn Bakken and Trygve Helgaker},
  journal   = {The Journal of Chemical Physics},
  title     = {The efficient optimization of molecular geometries using redundant internal coordinates},
  year      = {2002},
  month     = {nov},
  number    = {20},
  pages     = {9160--9174},
  volume    = {117},
  doi       = {10.1063/1.1515483},
  file      = {:by-author/B/Bakken/2002_Bakken_9160.pdf:PDF},
  keywords  = {Molecule Optimisation; Redundant Internal Coordinates},
  owner     = {saulius},
  publisher = {{AIP} Publishing},
  timestamp = {2018.05.10},
  creationdate = {2018-05-10T00:00:00},
  url       = {http://folk.uio.no/helgaker/reprints/JChemPhys_117_09160_2002.pdf},
}

@Article{Pulay1992,
  author    = {P. Pulay and G. Fogarasi},
  journal   = {Journal of Chemical Physics},
  title     = {Geometry optimization in redundant internal coordinates},
  year      = {1992},
  issn      = {0021-9606},
  number    = {4},
  pages     = {2856--2860},
  volume    = {96},
  abstract  = {The gradient geometry-optimization procedure is reformulated in terms of redundant internal coordinates. By replacing the matrix inverse with the generalized inverse, the usual Newton-Raphson-type algorithms can be formulated in exactly the same way for redundant and nonredundant coordinates. Optimization in redundant coordinates is particularly useful for bridged polycyclic compounds and cage structures where it is difficult to define physically reasonable redundancy-free internal coordinates. This procedure, already used for the geometry optimization of porphine, C20N4H 14, is illustrated here at the ab initio self-consistent-field level for the four-membered ring azetidine, for bicyclo[2.2.2]octane, and for the four-ring system C16O2H22, the skeleton of taxol.},
  doi       = {10.1063/1.462844},
  file      = {:by-author/P/Pulay/1992_Pulay_2856.pdf:PDF},
  keywords  = {Molecule Optimisation; Redundant Internal Coordinates},
  language  = {English},
  owner     = {saulius},
  publisher = {American Institute of Physics Publising LLC},
  timestamp = {2018.05.10},
  creationdate = {2018-05-10T00:00:00},
}

@Article{Ayala1998,
  author    = {Philippe Y. Ayala and H. Bernhard Schlegel},
  journal   = {The Journal of Chemical Physics},
  title     = {Identification and treatment of internal rotation in normal mode vibrational analysis},
  year      = {1998},
  month     = {feb},
  number    = {6},
  pages     = {2314--2325},
  volume    = {108},
  doi       = {10.1063/1.475616},
  file      = {:by-author/A/Ayala/1998_Ayala_2314.pdf:PDF},
  owner     = {saulius},
  publisher = {{AIP} Publishing},
  timestamp = {2018.05.10},
  creationdate = {2018-05-10T00:00:00},
  url       = {http://chem.wayne.edu/schlegel/Pub_folder/200.pdf},
}

@Manuscript{Eberly2017,
  author    = {David Eberly},
  title     = {Least Squares Fitting of Data},
  year      = {2017},
  keywords  = {Fitting; Least Squares},
  url       = {https://www.geometrictools.com/Documentation/LeastSquaresFitting.pdf},
  file      = {:by-author/E/Eberly/2017_Eberly.pdf:PDF},
  owner     = {saulius},
  timestamp = {2018.05.11},
  creationdate = {2018-05-11T00:00:00},
}

@Manuscript{Muralik2000,
  author    = {B. Muralik},
  title     = {Sphere Fititng},
  year      = {2000},
  keywords  = {Algorithms; Fitting; Least Squares; Sphere Fitting},
  url       = {http://caves.org/section/commelect/DUSI/openmag/pdf/SphereFitting.pdf},
  file      = {:by-author/M/Muralik/2000_Muralik.pdf:PDF},
  owner     = {saulius},
  timestamp = {2018.05.11},
  creationdate = {2018-05-11T00:00:00},
}

@Article{Pages2018,
  author    = {Guillaume Pagès and Elvira Kinzina and Sergei Grudinin},
  journal   = {Journal of Structural Biology},
  title     = {Analytical symmetry detection in protein assemblies. I. Cyclic symmetries},
  year      = {2018},
  month     = {apr},
  doi       = {10.1016/j.jsb.2018.04.004},
  file      = {:by-author/P/Pagès/2018_Pagès_a.pdf:PDF},
  owner     = {saulius},
  publisher = {Elsevier {BV}},
  timestamp = {2018.05.11},
  creationdate = {2018-05-11T00:00:00},
}

@Manuscript{Pages2018a,
  author    = {Guillaume Pagès and Sergei Grudinin},
  title     = {Analytical symmetry detection in protein assemblies. II Dihedral and Cubic symmetries},
  year      = {2018},
  keywords  = {Continuous Optimization; Cubic Groups; Discrete Optimization; Group Theory; Point-Group Symmetry; Protein Structure},
  file      = {:by-author/P/Pagès/2018_Pagès_b.pdf:PDF},
  owner     = {saulius},
  timestamp = {2018.05.11},
  creationdate = {2018-05-11T00:00:00},
}

@TechReport{Poddebniak2017,
  author    = {Damian Poddebniak and Christian Dresen and Jens Müller and Fabian Ising and Sebastian Schinzel and Simon Friedberger and Juraj Somorovsky and Jörg Schwenk},
  title     = {Efail: Breaking S/MIME and OpenPGP Email Encryption using Exfiltration Channels (draft 0.9.0)},
  year      = {2017},
  number    = {in},
  abstract  = {End-to-end encryption. While transport security be-
tween mail servers is useful against some attacker sce-},
  file      = {:by-author/P/Poddebniak/2017_Poddebniak.pdf:PDF},
  owner     = {saulius},
  timestamp = {2018.05.15},
  creationdate = {2018-05-15T00:00:00},
  url       = {https://efail.de/efail-attack-paper.pdf},
}

@Article{Quiros2018,
  author    = {Miguel Quir{\'{o}}s and Saulius Gra{\v{z}}ulis and Saul{\.{e}} Girdzijauskait{\.{e}} and Andrius Merkys and Antanas Vaitkus},
  journal   = {Journal of Cheminformatics},
  title     = {Using {SMILES} strings for the description of chemical connectivity in the {C}rystallography {O}pen {D}atabase},
  year      = {2018},
  month     = {may},
  number    = {1},
  volume    = {10},
  doi       = {10.1186/s13321-018-0279-6},
  file      = {:by-author/Q/Quirós-Olozábal/2018_Quirós-Olozábal.pdf:PDF},
  owner     = {andrius},
  publisher = {Springer Nature},
  timestamp = {2018.05.21},
  creationdate = {2018-05-21T00:00:00},
}

@Article{Plotkin1971,
  author    = {Morris Plotkin},
  journal   = {Journal of Chemical Documentation},
  title     = {Mathematical Basis of Ring-Finding Algorithms in {CIDS}},
  year      = {1971},
  month     = {feb},
  number    = {1},
  pages     = {60--63},
  volume    = {11},
  doi       = {10.1021/c160040a013},
  file      = {:by-author/P/Plotkin/1971_Plotkin_60.pdf:PDF},
  owner     = {andrius},
  publisher = {American Chemical Society ({ACS})},
  timestamp = {2018.06.21},
  creationdate = {2018-06-21T00:00:00},
}

@Article{Rose2017,
  author    = {Frisco Rose and Cormac Toher and Eric Gossett and Corey Oses and Marco Buongiorno Nardelli and Marco Fornari and Stefano Curtarolo},
  journal   = {Computational Materials Science},
  title     = {{AFLUX}: The {LUX} materials search {API} for the {AFLOW} data repositories},
  year      = {2017},
  month     = {sep},
  pages     = {362--370},
  volume    = {137},
  doi       = {10.1016/j.commatsci.2017.04.036},
  file      = {:by-author/R/Rose/2017_Rose_362.pdf:PDF},
  keywords  = {API; Materials Modelling Databases; RESTful},
  owner     = {saulius},
  publisher = {Elsevier {BV}},
  timestamp = {2018.06.27},
  creationdate = {2018-06-27T00:00:00},
}

@Article{Podjarny1987,
  author    = {A D Podjarny and T N Bhat and M Zwick},
  journal   = {Annual Review of Biophysics and Biophysical Chemistry},
  title     = {Improving Crystallographic Macromolecular Images: The Real-Space Approach},
  year      = {1987},
  month     = {jun},
  number    = {1},
  pages     = {351--373},
  volume    = {16},
  doi       = {10.1146/annurev.bb.16.060187.002031},
  file      = {:by-author/P/Podjarny/1987_Podjarny_351.pdf:PDF},
  owner     = {saulius},
  publisher = {Annual Reviews},
  timestamp = {2018.06.27},
  creationdate = {2018-06-27T00:00:00},
}

@Manuscript{Taylor2013,
  author    = {Michael Taylor},
  title     = {Airy Operator Calculus},
  year      = {2013},
  keywords  = {Math},
  url       = {http://www.unc.edu/math/Faculty/met/airy.pdf},
  abstract  = {We study two classes of operators we call Airy operators, which arise in the construction of parametrices for boundary problems with grazing and gliding rays. In the grazing case these operators are pseudodifferential operators. In the gliding case they are of a more singular character. We analyze the latter class via a family of Airy operator identities. The derivation of such identities has some points in common with one proof of Egorov’s theorem.},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2013_Taylor.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2015y,
  author    = {Michael Taylor},
  title     = {Airy functions and Airy quotients},
  year      = {2015},
  url       = {http://www.unc.edu/math/Faculty/met/airyf.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2015_Taylor_a.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Anderson2013,
  author    = {Michael Anderson and Atsushi Katsuda and Yaroslav Kurylev and Matti Lassas and Michael Taylor},
  title     = {Boundary Regularity For the Ricci Equation, Geometric Convergence, And Gelfand’s Inverse Boundary Problem: Determining a Region By How Its Boundary Vibrates},
  year      = {2013},
  url       = {http://www.unc.edu/math/Faculty/met/aktalk.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?;Michael Anderson:uuid=49e8df3a-774e-11e7-bd9a-1b0befb8d47a,orcid=?;Atsushi Katsuda:uuid=560a438a-774e-11e7-9c4b-c7e436957013,orcid=?;Yaroslav Kurylev:uuid=641dc0be-774e-11e7-a58a-47b5a160814e,orcid=?},
  file      = {:by-author/A/Anderson/2013_Anderson.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2016f,
  author    = {Michael E. Taylor},
  title     = {Introduction to Analysis in One Variable},
  year      = {2016},
  url       = {http://www.unc.edu/math/Faculty/met/anal1v.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2016_Taylor_a.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2015d,
  author    = {Michael E. Taylor},
  title     = {Introduction to Analysis in Several Variables (Advanced Calculus)},
  year      = {2015},
  url       = {http://www.unc.edu/math/Faculty/met/analmv.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2015_Taylor_b.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2015e,
  author    = {Michael Taylor},
  title     = {A. Outline of Functional Analysis},
  year      = {2015},
  url       = {http://www.unc.edu/math/Faculty/met/appenda.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2015_Taylor_c.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2015f,
  author    = {Michael Taylor},
  title     = {C. Connections and Curvature},
  year      = {2015},
  url       = {http://www.unc.edu/math/Faculty/met/appendc.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2015_Taylor_d.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2015g,
  author    = {Michael Taylor},
  title     = {Variants of Arnold’s Stability Results for 2D Euler Equations},
  year      = {2015},
  url       = {http://www.unc.edu/math/Faculty/met/arnold.pdf},
  abstract  = {We establish variants of stability estimates in norms somewhat stronger than the H1-norm, under Arnold’s stability hypotheses on steady solutions to the Euler equa- tions for fluid flow on planar domains.},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2015_Taylor_e.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2015h,
  author    = {Michael Taylor},
  title     = {Banach Algebras – Bare Bones Basics},
  year      = {2015},
  url       = {http://www.unc.edu/math/Faculty/met/banalg.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2015_Taylor_f.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2015i,
  author    = {Michael Taylor},
  title     = {A Critical Besov Space Embedding into BMO},
  year      = {2015},
  url       = {http://www.unc.edu/math/Faculty/met/besovbmo.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2015_Taylor_g.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2015j,
  author    = {Michael Taylor},
  title     = {Bessel Functions},
  year      = {2015},
  url       = {http://www.unc.edu/math/Faculty/met/bessel.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2015_Taylor_h.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2015k,
  author    = {Michael Taylor},
  title     = {Bessel Functions and Hankel Transforms},
  year      = {2015},
  url       = {http://www.unc.edu/math/Faculty/met/bessel2.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2015_Taylor_i.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylorb,
  author    = {Michael Taylor},
  title     = {Hardy Spaces and bmo on Manifolds with Bounded Geometry},
  url       = {http://www.unc.edu/math/Faculty/met/bmom.pdf},
  abstract  = {We develop the theory of the “local” Hardy space h1(M) and John-Nirenberg space bmo(M) when M is a Riemannian manifold with bounded geometry, building on the classic work of Fefferman-Stein and subsequent material, particularly of Goldberg and Ionescu. Results include h1 − bmo duality, Lp estimates on an appropriate variant of the sharp maximal function, h1 and bmo-Sobolev spaces, and action of a natural class of pseudodifferential operators, including a natural class of functions of the Laplace operator, in a setting that unifies these results with results on Lp-Sobolev spaces. We apply results on these topics to some interpolation theorems, motivated in part by the search for dispersive estimates for wave equations.},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/XXXX_Taylor.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2015a,
  author    = {Michael E. Taylor},
  title     = {Figures for introduction to Analysis in Several Variables},
  year      = {2015},
  url       = {http://www.unc.edu/math/Faculty/met/calcfigs.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2015_Taylor_j.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2014i,
  author    = {Michael Taylor},
  title     = {Capacities},
  year      = {2014},
  url       = {http://www.unc.edu/math/Faculty/met/capac.pdf},
  abstract  = {This is a revision of a set of notes I prepared for a presentation in M. Loeve’s course in potential theory, at Berkeley, in the Fall of 1968. At the time, the notes were written longhand and mimeographed. Later, I typed them out on an old-fashioned typewriter. Eventually, I typed them in TeX.},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2014_Taylor.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2013b,
  author    = {Michael Taylor},
  title     = {Graphics on the HP LaserJet},
  year      = {2013},
  url       = {http://www.unc.edu/math/Faculty/met/cgrafx.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2013_Taylor_a.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2010g,
  author    = {Michael Taylor},
  title     = {4. Sobolev Spaces},
  year      = {2010},
  url       = {http://www.unc.edu/math/Faculty/met/chap4.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2010_Taylor_a.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2010h,
  author    = {Michael Taylor},
  title     = {7. Pseudodifferential Operators},
  year      = {2010},
  url       = {http://www.unc.edu/math/Faculty/met/chap7.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2010_Taylor_b.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2010i,
  author    = {Michael Taylor},
  title     = {8. Spectral Theory},
  year      = {2010},
  url       = {http://www.unc.edu/math/Faculty/met/chap8.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2010_Taylor_c.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2010b,
  author    = {Michael Taylor},
  title     = {Brownian Motion and Potential Theory},
  year      = {2010},
  url       = {http://www.unc.edu/math/Faculty/met/chap11.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2010_Taylor_d.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2010f,
  author    = {Michael Taylor},
  title     = {Function Space and Operator Theory for Nonlinear Analysis},
  year      = {2010},
  url       = {http://www.unc.edu/math/Faculty/met/chap13.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2010_Taylor_e.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{LeBrun2013,
  author    = {Claude LeBrun and Michael Taylor},
  title     = {The Hopf Bracket},
  year      = {2013},
  url       = {http://www.unc.edu/math/Faculty/met/claude.pdf},
  abstract  = {Given a smooth map f : M → N between smooth manifolds, we},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/L/LeBrun/2013_LeBrun.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2014ad,
  author    = {Michael Taylor},
  title     = {Figures ...},
  year      = {2014},
  url       = {http://www.unc.edu/math/Faculty/met/compfigs.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2014_Taylor_a.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2016b,
  author    = {Michael Taylor},
  title     = {Introduction to Complex Analysis},
  year      = {2016},
  url       = {http://www.unc.edu/math/Faculty/met/complex.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2016_Taylor_b.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2012i,
  author    = {Michael Taylor},
  title     = {Introduction to Complex Analysis},
  year      = {2012},
  url       = {http://www.unc.edu/math/Faculty/met/cpx.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2012_Taylor.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2012a,
  author    = {Michael Taylor},
  title     = {Variations on Complex Interpolation},
  year      = {2012},
  url       = {http://www.unc.edu/math/Faculty/met/cpxint.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2012_Taylor_a.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2012b,
  author    = {Michael Taylor},
  title     = {Jacobi’s Generalization of Cramer’s Formula},
  year      = {2012},
  url       = {http://www.unc.edu/math/Faculty/met/cramer.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2012_Taylor_b.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2013a,
  author    = {Michael Taylor},
  title     = {Wave Decay on Manifolds with Bounded Ricci},
  year      = {2013},
  url       = {http://www.unc.edu/math/Faculty/met/decay2.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2013_Taylor_b.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2010j,
  author    = {Michael Taylor},
  title     = {Waves on R2k – the Method of Descent},
  year      = {2010},
  url       = {http://www.unc.edu/math/Faculty/met/desc.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2010_Taylor_f.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2015b,
  author    = {Michael Taylor},
  title     = {Figures ...},
  year      = {2015},
  url       = {http://www.unc.edu/math/Faculty/met/dgeomfigs.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2015_Taylor_k.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2013c,
  author    = {Michael Taylor},
  title     = {Musings on the Discrete Heisenberg Group},
  year      = {2013},
  url       = {http://www.unc.edu/math/Faculty/met/dheis.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2013_Taylor_c.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2013d,
  author    = {Michael Taylor},
  title     = {Difference schemes for ODE},
  year      = {2013},
  url       = {http://www.unc.edu/math/Faculty/met/diff.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2013_Taylor_d.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor1981,
  author    = {Michael Taylor},
  title     = {Diffraction Effects in the Scattering of Waves},
  year      = {1981},
  url       = {http://www.unc.edu/math/Faculty/met/diffscat.pdf},
  abstract  = {This paper describes the use of parametrices for diffractive boundary value problems in the study of effects of grazing rays on the behavior of scattered waves. It is a TeXed version of the paper [T6], with updated references.},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/1981_Taylor.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2014j,
  author    = {Michael Taylor},
  title     = {Calculating to hundreds of digits of accuracy},
  year      = {2014},
  url       = {http://www.unc.edu/math/Faculty/met/digits.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2014_Taylor_b.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2013e,
  author    = {Michael Taylor},
  title     = {Vector Integration and Disintegration of Measures},
  year      = {2013},
  url       = {http://www.unc.edu/math/Faculty/met/disint.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2013_Taylor_e.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2016c,
  author    = {Michael Taylor},
  title     = {The Pentagon, the Dodecahedron, and the Icosahedron},
  year      = {2016},
  url       = {http://www.unc.edu/math/Faculty/met/dodec.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2016_Taylor_c.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2016a,
  author    = {Michael Taylor},
  title     = {Figures ...},
  year      = {2016},
  url       = {http://www.unc.edu/math/Faculty/met/dodfigs.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2016_Taylor_d.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2013f,
  author    = {Michael Taylor},
  title     = {The Dirichlet Problem on the Hyperbolic Ball},
  year      = {2013},
  url       = {http://www.unc.edu/math/Faculty/met/dphb.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2013_Taylor_f.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2014k,
  author    = {Michael Taylor},
  title     = {DeRham Cohomology of Compact Symmetric Spaces},
  year      = {2014},
  url       = {http://www.unc.edu/math/Faculty/met/drc.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2014_Taylor_c.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2012c,
  author    = {Michael Taylor},
  title     = {Review of “Distributions – Theory and Applications,” by J.J. Duistermaat and J.A.C. Kolk},
  year      = {2012},
  url       = {http://www.unc.edu/math/Faculty/met/duikol.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2012_Taylor_c.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2013g,
  author    = {Michael Taylor},
  title     = {Some matrix integrals related to random matrix theory},
  year      = {2013},
  url       = {http://www.unc.edu/math/Faculty/met/DYSON.pdf},
  abstract  = {We present a “naive” derivation of a formula of [BDK] for ∫ |TrM j |2 dM ,U(n) of use in random matrix theory. We also calcu∫late a more refined object, M j⊗U(n) M−j dM , which in turn yields a formula for f(M)⊗ g(M) dM.},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2013_Taylor_g.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2010k,
  author    = {Michael Taylor},
  title     = {Equivariant Isometric Embeddings of Homogeneous Spaces Into Hilbert Space},
  year      = {2010},
  url       = {http://www.unc.edu/math/Faculty/met/embed.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2010_Taylor_g.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2014l,
  author    = {Michael E. Taylor},
  title     = {Euler and Navier-Stokes Equations For Incompressible Fluids},
  year      = {2014},
  url       = {http://www.unc.edu/math/Faculty/met/eulerns.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2014_Taylor_d.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2009c,
  author    = {Michael E. Taylor},
  title     = {Finite and Infinite Dimensional Lie Groups And Evolution Equations},
  year      = {2009},
  url       = {http://www.unc.edu/math/Faculty/met/evol.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2009_Taylor_a.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2011,
  author    = {Michael Taylor},
  title     = {Singular Integrals and Elliptic Boundary Problems on Rough Domains},
  year      = {2011},
  url       = {http://www.unc.edu/math/Faculty/met/fabes.pdf},
  abstract  = {These notes discuss results on layer potential methods for elliptic boundary problems, with emphasis on the Dirichlet problem for the Laplace opera- tor. They start by reviewing results for domains with moderately smooth boundary, then for Lipschitz domains, and proceed to discuss results in [HMT], obtained with S. Hofmann and M. Mitrea, for a class of domains we call regular Semmes-Kenig- Toro (SKT) domains, often called chord-arc domains with vanishing constant, and for ε-regular SKT domains, often called chord-arc domains with small constant.},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2011_Taylor.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2014m,
  author    = {Michael E. Taylor},
  title     = {Outline of Functional Analysis},
  year      = {2014},
  url       = {http://www.unc.edu/math/Faculty/met/fctnl.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2014_Taylor_e.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2015l,
  author    = {Michael Taylor},
  title     = {Remarks on Fractional Diffusion Equations},
  year      = {2015},
  url       = {http://www.unc.edu/math/Faculty/met/fdif.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2015_Taylor_l.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2015c,
  author    = {Michael Taylor},
  title     = {Figures ...},
  year      = {2015},
  url       = {http://www.unc.edu/math/Faculty/met/fdiffigs.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2015_Taylor_m.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2013h,
  author    = {Michael E. Taylor},
  title     = {Fourier Analysis and the FFT},
  year      = {2013},
  url       = {http://www.unc.edu/math/Faculty/met/fft.pdf},
  abstract  = {These notes introduce three types of Fourier transforms, one for periodic functions of one or more real variables (also called Fourier series), one for integrable (or square-integrable) functions of one or more real variables, and one for functions defined on a set of n points, identified with the integers mod n (also called the discrete Fourier transform, or DFT). We discuss in each case the important Fourier inversion formula. We also discuss relations of these various Fourier transforms with each other. Finally, we discuss ‘fast’ algorithms for computing the DFT, when n is a power of 2.},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2013_Taylor_h.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor,
  author    = {Michael Taylor},
  title     = {Figure 4.1},
  url       = {http://www.unc.edu/math/Faculty/met/fig41.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/XXXX_Taylor_a.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylora,
  author    = {Michael Taylor},
  title     = {Figure 4.2},
  url       = {http://www.unc.edu/math/Faculty/met/fig42.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/XXXX_Taylor_b.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylorc,
  author    = {Michael Taylor},
  title     = {Figure},
  url       = {http://www.unc.edu/math/Faculty/met/fig2122.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/XXXX_Taylor_c.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2011a,
  author    = {Michael Taylor},
  title     = {Fourier Integral Operators and Harmonic Analysis On Compact Manifolds},
  year      = {2011},
  url       = {http://www.unc.edu/math/Faculty/met/FIHA.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2011_Taylor_a.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2015m,
  author    = {Michael Taylor},
  title     = {Differential Forms and Applications to Complex Analysis, Harmonic Functions, and Degree Theory},
  year      = {2015},
  url       = {http://www.unc.edu/math/Faculty/met/forms.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2015_Taylor_n.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2015n,
  author    = {Michael E. Taylor},
  title     = {Fourier Analysis, Distributions, and Constant-Coefficient Linear PDE},
  year      = {2015},
  url       = {http://www.unc.edu/math/Faculty/met/fourier.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2015_Taylor_o.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2010l,
  author    = {Michael Taylor},
  title     = {Multidimensional Analytic Fredholm Theory},
  year      = {2010},
  url       = {http://www.unc.edu/math/Faculty/met/fred.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2010_Taylor_h.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2010m,
  author    = {Michael Taylor},
  title     = {Functions of √−∆ and the Wave Equation},
  year      = {2010},
  url       = {http://www.unc.edu/math/Faculty/met/funct.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2010_Taylor_i.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2015o,
  author    = {Michael Taylor},
  title     = {The Gamma function},
  year      = {2015},
  url       = {http://www.unc.edu/math/Faculty/met/gamma.pdf},
  abstract  = {This material is excerpted from §18 of [T].},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2015_Taylor_p.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2013i,
  author    = {Michael Taylor},
  title     = {Remarks on the Gauss-Green Theorem},
  year      = {2013},
  url       = {http://www.unc.edu/math/Faculty/met/gaugr.pdf},
  abstract  = {These notes cover material related to the Gauss-Green theorem that was developed for work with S. Hofmann and M. Mitrea, which appeared in [HMT].},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2013_Taylor_i.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2010n,
  author    = {Michael E. Taylor},
  title     = {The Schrödinger equation and Gauss sums},
  year      = {2010},
  url       = {http://www.unc.edu/math/Faculty/met/gausum.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2010_Taylor_j.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2010o,
  author    = {Michael Taylor},
  title     = {Multivariate Gauss sums},
  year      = {2010},
  url       = {http://www.unc.edu/math/Faculty/met/gausum2.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2010_Taylor_k.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2013j,
  author    = {Michael Taylor},
  title     = {Variations on Gel’fand’s Inverse Boundary Problem},
  year      = {2013},
  url       = {http://www.unc.edu/math/Faculty/met/GELF.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2013_Taylor_j.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2014b,
  author    = {Michael Taylor},
  title     = {Figures ...},
  year      = {2014},
  url       = {http://www.unc.edu/math/Faculty/met/glfigs.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2014_Taylor_f.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylord,
  author    = {Richard Melrose and Michael Taylor},
  title     = {Boundary Problems for Wave Equations With Grazing and Gliding Rays},
  url       = {http://www.unc.edu/math/Faculty/met/glide.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/M/Melrose/XXXX_Melrose.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2013k,
  author    = {Michael Taylor},
  title     = {The Green Function on a Compact 2D Manifold},
  year      = {2013},
  url       = {http://www.unc.edu/math/Faculty/met/green.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2013_Taylor_k.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2013l,
  author    = {Michael Taylor},
  title     = {The Green Function for ∆−V with a Rough Potential},
  year      = {2013},
  url       = {http://www.unc.edu/math/Faculty/met/green2.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2013_Taylor_l.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2013m,
  author    = {Michael Taylor},
  title     = {Remarks on a Class of Greenian Domains},
  year      = {2013},
  url       = {http://www.unc.edu/math/Faculty/met/greeny.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2013_Taylor_m.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2014n,
  author    = {Michael E. Taylor},
  title     = {Multiple Eigenvalues of Operators with Noncommutative Symmetry Groups},
  year      = {2014},
  url       = {http://www.unc.edu/math/Faculty/met/gsym.pdf},
  abstract  = {The presence of a noncommutative finite group G of symmetries of an elliptic, self-adjoint differential operator L, with discrete spectrum, can force the existence of an infinite number of multiple eigenvalues of L. In §1 we show that such a phenomenon occurs rather generally, due to the fact that some irreducible representation ρ of G of degree > 1 must be contained in infinitely many eigenspaces of L. In §2 we show that, under mild assumptions, the relative frequency of oc- currence of each irreducible representation ρ of G in the sum of all the eigenspaces with eigenvalues ≤ R tends as R → ∞ to a limit equal to the relative frequency that ρ occurs in the regular representation of G. In §3 we study an example where the multiplicities can get arbitrarily large.},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2014_Taylor_g.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2013n,
  author    = {Michael Taylor},
  title     = {Remarks on M. Pinsky’s Derivation of the Modulus of Continuity for Brownian Paths},
  year      = {2013},
  url       = {http://www.unc.edu/math/Faculty/met/haar.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2013_Taylor_n.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2010p,
  author    = {Michael Taylor},
  title     = {Proof of the Lipschitz-Hankel integral formula},
  year      = {2010},
  url       = {http://www.unc.edu/math/Faculty/met/hankel.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2010_Taylor_l.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2014ac,
  author    = {Michael E. Taylor},
  title     = {Commutator estimates for Hölder continuous and bmo-Sobolev multipliers},
  year      = {2014},
  url       = {http://www.unc.edu/math/Faculty/met/hbcomp.pdf},
  abstract  = {We discuss conditions on a function f under which the commuta- tor [P, f ] of a pseudodifferential operator P of order m with the operation of multiplication by f is an operator of order m − r on various function spaces, namely Ho¨lder-Zygmund spaces and Lp-Sobolev spaces, given 0 < r < 1. We also establish an endpoint case involving r = 1, and we extend the scope to all r > 0 for a particularly significant case in 1 dimension.},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2014_Taylor_h.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2013o,
  author    = {Michael Taylor and Steve Hofmann and Marius Mitrea},
  title     = {The Gauss-Green Formula (And Elliptic Boundary Problems On Rough Domains)},
  year      = {2013},
  url       = {http://www.unc.edu/math/Faculty/met/hmtalk.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?;Marius Mitrea:uuid=62b9a5c8-774c-11e7-b7c8-2b92d763a8df,orcid=?;Steve Hofmann:uuid=6e3e7c02-774c-11e7-9391-935aaef3052b,orcid=?},
  file      = {:by-author/T/Taylor/2013_Taylor_o.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Hofmann2009,
  author    = {Steve Hofmann and Marius Mitrea and Michael Taylor},
  title     = {Singular integrals and elliptic boundary problems on regular Semmes-Kenig-Toro domains},
  year      = {2009},
  url       = {http://www.unc.edu/math/Faculty/met/hmtimb.pdf},
  abstract  = {We develop the theory of layer potentials and related singular integral operators as a tool to study a variety of elliptic boundary problems on a family of domains introduced by Semmes [101]–[102] and Kenig and Toro [64]–[66], which we call regular Semmes-Kenig-Toro domains. This extends the classic work of Fabes, Jodeit, and Rivière in several ways. For one, the class of domains considered contains the class of VMO 1 domains, which in turn contains the class of C 1 domains. In addition we study not only the Dirichlet and Neumann boundary problems, but also a variety of others. Furthermore, we treat not only constant coefficient operators, but also operators with variable coefficients, including operators on manifolds.},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?;Marius Mitrea:uuid=62b9a5c8-774c-11e7-b7c8-2b92d763a8df,orcid=?;Steve Hofmann:uuid=6e3e7c02-774c-11e7-9391-935aaef3052b,orcid=?},
  file      = {:by-author/H/Hofmann/2009_Hofmann.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2010u,
  author    = {Michael Taylor},
  title     = {Hypoelliptic (and Non-Hypoelliptic) Hodge Theory},
  year      = {2010},
  url       = {http://www.unc.edu/math/Faculty/met/hodge.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2010_Taylor_m.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor1985,
  author    = {Michael Taylor},
  title     = {Review of “The Analysis of Linear Partial Differential Operators, I–II,” by Lars Hörmander},
  year      = {1985},
  url       = {http://www.unc.edu/math/Faculty/met/hormrev.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/1985_Taylor.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2010q,
  author    = {Michael Taylor},
  title     = {The Heat Kernel and the Wave Kernel},
  year      = {2010},
  url       = {http://www.unc.edu/math/Faculty/met/htwave.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2010_Taylor_n.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2010r,
  author    = {Michael Taylor},
  title     = {The Inverse Function Theorem via Newton’s Method},
  year      = {2010},
  url       = {http://www.unc.edu/math/Faculty/met/invfn.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2010_Taylor_o.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2013p,
  author    = {Michael Taylor},
  title     = {Isothermal Coordinates on Bounded Planar Domains With L∞ Metric Tensor},
  year      = {2013},
  url       = {http://www.unc.edu/math/Faculty/met/isoth.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2013_Taylor_p.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2013q,
  author    = {Michael E. Taylor},
  title     = {Pseudodifferential Operators and K-Homology, II},
  year      = {2013},
  url       = {http://www.unc.edu/math/Faculty/met/KPSI.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2013_Taylor_q.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2012d,
  author    = {Michael Taylor},
  title     = {Lévy Processes},
  year      = {2012},
  url       = {http://www.unc.edu/math/Faculty/met/levy.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2012_Taylor_d.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2013r,
  author    = {Michael Taylor},
  title     = {Notes on Integration on Lie Groups},
  year      = {2013},
  url       = {http://www.unc.edu/math/Faculty/met/LIE.pdf},
  abstract  = {This is a very informal set of notes on integration on Lie groups and connections with basic representation theory. We give some constructions of the Lie group integral, show how some integrals can be computed by using simple symmetry considerations, and present some cases where more earnest efforts are required to compute integrals.},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2013_Taylor_r.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2016d,
  author    = {Michael Taylor},
  title     = {Linear Algebra},
  year      = {2016},
  url       = {http://www.unc.edu/math/Faculty/met/linalg.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2016_Taylor_e.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2013s,
  author    = {Michael Taylor},
  title     = {Lp Bounds on Functions of Generalized Laplacians On a Compact Manifold with Boundary},
  year      = {2013},
  url       = {http://www.unc.edu/math/Faculty/met/lpmb.pdf},
  abstract  = {Given a second-order, strongly elliptic, negative, self-adjoint differen- tial operator L on a compact Riema√nnian manifold M with smooth boundary, we establish conditions under which ϕ( −L) is bounded on Lp(M), for p ∈ (1,∞).},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2013_Taylor_s.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2000a,
  author    = {Michael Taylor},
  title     = {Regularity for a Class of Elliptic Operators with Dini Continuous Coefficients},
  year      = {2000},
  url       = {http://www.unc.edu/math/Faculty/met/lreg.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2000_Taylor.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2008a,
  author    = {Michael Taylor},
  title     = {Lectures on Lie Groups},
  year      = {2008},
  url       = {http://www.unc.edu/math/Faculty/met/m273.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2008_Taylor.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2014c,
  author    = {Michael Taylor},
  title     = {Figures ...},
  year      = {2014},
  url       = {http://www.unc.edu/math/Faculty/met/m273figs.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2014_Taylor_i.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2014d,
  author    = {Michael Taylor},
  title     = {Figures ...},
  year      = {2014},
  url       = {http://www.unc.edu/math/Faculty/met/m521figs.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2014_Taylor_j.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2015p,
  author    = {Michael Taylor},
  title     = {Elementary differential geometry},
  year      = {2015},
  url       = {http://www.unc.edu/math/Faculty/met/M180.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2015_Taylor_q.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2014o,
  author    = {Michael Taylor},
  title     = {Lectures on Lie Groups},
  year      = {2014},
  url       = {http://www.unc.edu/math/Faculty/met/M273.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2014_Taylor_k.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2010d,
  author    = {Irina Mitrea and Marius Mitrea and Michael Taylor},
  title     = {Multidimensional Riemann-Hilbert Problems on Domains with Uniformly Rectifiable Interfaces},
  year      = {2010},
  url       = {http://www.unc.edu/math/Faculty/met/mdrhp4.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?;Marius Mitrea:uuid=62b9a5c8-774c-11e7-b7c8-2b92d763a8df,orcid=?;Irina Mitrea:uuid=56d1820c-774d-11e7-b8a0-db9bdaf53211,orcid=?},
  file      = {:by-author/M/Mitrea/2010_Mitrea.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylore,
  author    = {Michael Taylor},
  title     = {Chapter 1: The Riemann Integral},
  url       = {http://www.unc.edu/math/Faculty/met/measch1.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/XXXX_Taylor_d.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylorf,
  author    = {Michael Taylor},
  title     = {Chapter 2: Lebesgue Measure on the Line},
  url       = {http://www.unc.edu/math/Faculty/met/measch2.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/XXXX_Taylor_e.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylorg,
  author    = {Michael Taylor},
  title     = {Chapter 3: Integration on Measure Spaces},
  url       = {http://www.unc.edu/math/Faculty/met/measch3.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/XXXX_Taylor_25.pdf:PDF},
  owner     = {saulius},
  pages     = {25--40},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylorh,
  author    = {Michael Taylor},
  title     = {Chapter 4: Lp Spaces},
  url       = {http://www.unc.edu/math/Faculty/met/measch4.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/XXXX_Taylor_f.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylori,
  author    = {Michael Taylor},
  title     = {Chapter 5: The Caratheodory Construction of Measures},
  url       = {http://www.unc.edu/math/Faculty/met/measch5.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/XXXX_Taylor_g.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylorj,
  author    = {Michael Taylor},
  title     = {Chapter 8: Signed Measures and Complex Measures},
  url       = {http://www.unc.edu/math/Faculty/met/measch8.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/XXXX_Taylor_h.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylork,
  author    = {Michael Taylor},
  title     = {Chapter 9: Lp Spaces, II},
  url       = {http://www.unc.edu/math/Faculty/met/measch9.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/XXXX_Taylor_i.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylorl,
  author    = {Michael Taylor},
  title     = {Chapter 13: Radon Measures},
  url       = {http://www.unc.edu/math/Faculty/met/measch13.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/XXXX_Taylor_j.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylorm,
  author    = {Michael Taylor},
  title     = {Chapter 14: Ergodic Theory},
  url       = {http://www.unc.edu/math/Faculty/met/measch14.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/XXXX_Taylor_k.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2014g,
  author    = {Michael Taylor},
  title     = {Appendix G: Integration of Differential Forms},
  year      = {2014},
  url       = {http://www.unc.edu/math/Faculty/met/measg.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2014_Taylor_293.pdf:PDF},
  owner     = {saulius},
  pages     = {293--301},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylorn,
  author    = {Michael Taylor},
  title     = {Appendix A: Metric Spaces, Topological Spaces, and Compactness},
  url       = {http://www.unc.edu/math/Faculty/met/metricspace.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/XXXX_Taylor_l.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Metcalfe2009,
  author    = {Jason Metcalfe and Michael Taylor},
  title     = {Nonlinear waves on 3D hyperbolic space},
  year      = {2009},
  url       = {http://www.unc.edu/math/Faculty/met/mettayms.pdf},
  abstract  = {In this article, global-in-time dispersive estimates and Strichartz estimates are explored for the wave equation on three dimensional hyperbolic space. Due to the negative curvature, extra dispersion is noted, as compared},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?;Jason Metcalfe:uuid=ee522f32-774d-11e7-a3e1-4358dc01c060,orcid=?},
  file      = {:by-author/M/Metcalfe/2009_Metcalfe.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2014ae,
  author    = {Michael Taylor},
  title     = {Toeplitz Operators on Uniformly Rectifiable Domains},
  year      = {2014},
  url       = {http://www.unc.edu/math/Faculty/met/michtalk.pdf},
  abstract  = {These notes discuss Hardy spaces of solutions to certain first-order elliptic systems of PDE on uniformly rectifiable (UR) domains, singular integral op- erators that yield projections onto the space of their boundary values, and Toeplitz operators associated with these projections. We produce results on the index of such Toeplitz operators, when they are Fredholm. This is a survey of work [MMT] with I. Mitrea and M. Mitrea, following work [HMT] with S. Hofmann and M. Mitrea.},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2014_Taylor_l.pdf:PDF},
  number    = {associated},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2013ac,
  author           = {Michael E. Taylor},
  title            = {Microlocal analysis and nonlinear {PDE}},
  year             = {2013},
  url              = {http://www.unc.edu/math/Faculty/met/micro2.pdf},
  authorid         = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  creationdate     = {2016-12-11T00:00:00},
  file             = {:by-author/T/Taylor/2013_Taylor_Microlocal Analysis and Nonlinear PDE.pdf:PDF},
  modificationdate = {2023-12-24T14:35:07},
  owner            = {saulius},
  timestamp        = {2016.12.11},
}

@Manuscript{Taylor2015x,
  author    = {Michael E. Taylor},
  title     = {Microlocal Analysis on Morrey Spaces},
  year      = {2015},
  url       = {http://www.unc.edu/math/Faculty/met/morrey.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2015_Taylor_r.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2008,
  author    = {Michael Taylor},
  title     = {Pseudodifferential operators},
  year      = {2008},
  url       = {http://www.unc.edu/math/Faculty/met/msripde.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2008_Taylor_a.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2014p,
  author    = {Michael E. Taylor},
  title     = {Manifolds, Vector Bundles, and Lie Groups},
  year      = {2014},
  url       = {http://www.unc.edu/math/Faculty/met/mvblg.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2014_Taylor_m.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2013t,
  author    = {Michael E. Taylor},
  title     = {Noncommutative Microlocal Analysis},
  year      = {2013},
  url       = {http://www.unc.edu/math/Faculty/met/NCMLMS.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2013_Taylor_t.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2008b,
  author    = {Michael E. Taylor},
  title     = {Pseudodifferential Operators And Nonlinear PDE},
  year      = {2008},
  url       = {http://www.unc.edu/math/Faculty/met/NLIN.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2008_Taylor_b.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2012e,
  author    = {Michael Taylor},
  title     = {Gibbs Phenomena and Pinsky Phenomena for Nonlinear Schrödinger Equations},
  year      = {2012},
  url       = {http://www.unc.edu/math/Faculty/met/nlsams00.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2012_Taylor_e.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2014q,
  author    = {Michael Taylor},
  title     = {Single Differential Equations},
  year      = {2014},
  url       = {http://www.unc.edu/math/Faculty/met/odech1.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2014_Taylor_n.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2014r,
  author    = {Michael Taylor},
  title     = {Linear Systems of Differential Equations},
  year      = {2014},
  url       = {http://www.unc.edu/math/Faculty/met/odech3.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2014_Taylor_o.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2014s,
  author    = {Michael Taylor},
  title     = {Nonlinear Systems of Differential Equations},
  year      = {2014},
  url       = {http://www.unc.edu/math/Faculty/met/odech4.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2014_Taylor_p.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2014t,
  author    = {Michael E. Taylor},
  title     = {Basic Theory of ODE and Vector Fields},
  year      = {2014},
  url       = {http://www.unc.edu/math/Faculty/met/odepde.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2014_Taylor_q.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2013u,
  author    = {Michael Taylor},
  title     = {The “Oscillator-Dirac” Operator, and Related Operators on Hn},
  year      = {2013},
  url       = {http://www.unc.edu/math/Faculty/met/oscdir.pdf},
  abstract  = {We have several goals: to construct an interesting first order differen- tial operator on Rn of index one, to construct a related invertible pseudodifferential operator on Rn, and to construct related differential and pseudodifferential opera- tors on the Heisenberg group Hn, including a first order operator that is hypoelliptic with loss of 1/2 derivative.},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2013_Taylor_u.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2013v,
  author    = {Michael Taylor},
  title     = {Positive Definite Zonal Functions},
  year      = {2013},
  url       = {http://www.unc.edu/math/Faculty/met/pdzf.pdf},
  abstract  = {We explore what is special about a zonal function on the sphere Sn−1},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2013_Taylor_v.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2000,
  author    = {Anna Mazzucato and Michael Taylor},
  title     = {Vanishing Viscosity Limits for a Class of Circular Pipe Flows},
  year      = {2000},
  url       = {http://www.unc.edu/math/Faculty/met/pipefl.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/M/Mazzucato/2000_Mazzucato.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2014h,
  author    = {Steve Hofmann and Marius Mitrea and Michael Taylor},
  title     = {Symbol Calculus for Operators of Layer Potential Type on},
  year      = {2014},
  url       = {http://www.unc.edu/math/Faculty/met/pscal6.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/H/Hofmann/2014_Hofmann.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2013w,
  author    = {Michael Taylor},
  title     = {Public Key Encryption Device},
  year      = {2013},
  url       = {http://www.unc.edu/math/Faculty/met/pubkey.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2013_Taylor_w.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2010a,
  author    = {Michael Taylor},
  title     = {Variations on Quantum Ergodic Theorems},
  year      = {2010},
  url       = {http://www.unc.edu/math/Faculty/met/qchaos.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2010_Taylor_p.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2014u,
  author    = {Michael Taylor},
  title     = {Discretizing the Laplacian on Radial Functions},
  year      = {2014},
  url       = {http://www.unc.edu/math/Faculty/met/radial.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2014_Taylor_r.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2013x,
  author    = {Michael Taylor},
  title     = {Averaging Rotations},
  year      = {2013},
  url       = {http://www.unc.edu/math/Faculty/met/RAVG.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2013_Taylor_x.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2013ab,
  author    = {Michael E. Taylor},
  title     = {Rayleigh Waves in Linear Elasticity as a Propagation of Singularities Phenomenon},
  year      = {2013},
  url       = {http://www.unc.edu/math/Faculty/met/rayl.pdf},
  abstract  = {We examine the propagation of surface waves known as Rayleigh waves from the perspective of microlocal analysis. This paper is a TeXed version of Taylor (1979).},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2013_Taylor_y.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2015q,
  author    = {Michael Taylor},
  title     = {Random Fields: Stationarity, Ergodicity, and Spectral Behavior},
  year      = {2015},
  url       = {http://www.unc.edu/math/Faculty/met/rndfcn.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2015_Taylor_s.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Presentation{Taylor2015r,
  author    = {Michael Taylor},
  title     = {Dirac-type Operators on a Compact Riemann Surface},
  year      = {2015},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2015_Taylor_t.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
  url       = {http://www.unc.edu/math/Faculty/met/rroch.pdf},
}

@Manuscript{Taylor2009a,
  author    = {Michael Taylor},
  title     = {Notes on Compact Riemann Surfaces},
  year      = {2009},
  url       = {http://www.unc.edu/math/Faculty/met/RSURF.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2009_Taylor_b.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2014e,
  author    = {Michael Taylor},
  title     = {Figures ...},
  year      = {2014},
  url       = {http://www.unc.edu/math/Faculty/met/rsurfigs.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2014_Taylor_s.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2015s,
  author    = {Michael Taylor},
  title     = {The Riemann zeta function},
  year      = {2015},
  url       = {http://www.unc.edu/math/Faculty/met/rzeta.pdf},
  abstract  = {This material is excerpted from Section 19 of [T].},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2015_Taylor_u.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2010s,
  author    = {Michael Taylor},
  title     = {The Schrödinger Equation on Cones},
  year      = {2010},
  url       = {http://www.unc.edu/math/Faculty/met/schcon.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2010_Taylor_q.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2014v,
  author    = {Michael Taylor},
  title     = {Higher Order Accurate Schemes for a Class of Nonlinear Evolution Equations},
  year      = {2014},
  url       = {http://www.unc.edu/math/Faculty/met/scheme.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2014_Taylor_t.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2014w,
  author    = {Michael Taylor},
  title     = {Variant of Schur’s Inequality},
  year      = {2014},
  url       = {http://www.unc.edu/math/Faculty/met/schur.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2014_Taylor_u.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Rauch2014,
  author    = {Jeffrey Rauch and Michael Taylor},
  title     = {Electrostatic screening},
  year      = {2014},
  url       = {http://www.unc.edu/math/Faculty/met/screen.pdf},
  abstract  = {Using the methods of partial differential equatiions and functional analysis, we investigate the electromagnetic field in the presence of a screen com- posed of wires of radius r, spaced at distance R, spread over a surface S. In the limit as r and R converge to zero, if (R log r)−1 → −∞ the field in the presence of the screen converges to the field with a conducting sheet spread over S. If (R log r)−1 → 0 the field converges to the field with no conductors.},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?;Jeffrey Rauch:uuid=7fdb410c-3353-11e8-b591-2b57b6801d19,orcid=?},
  file      = {:by-author/R/Rauch/2014_Rauch.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2010t,
  author    = {Michael Taylor},
  title     = {Serendipitous Fourier Inversion},
  year      = {2010},
  url       = {http://www.unc.edu/math/Faculty/met/SERENE.pdf},
  abstract  = {It is known that pointwise behavior of multidimensional spherical Fourier inversion is more complicated on the torus than on Euclidean space. Figures presented here give graphical evidence of a certain choppiness of partial sums of the Fourier series of some functions with simple singularities on the 2-torus T2. This choppiness is provably absent for the analogous partial Fourier inversion on Euclidean space R2. Curiously, this choppiness clears up for a discrete set of partial sums. We call this phenomenon serendipitous Fourier inversion. The purpose of this paper is to introduce this notion and to produce estimates that establish its existence.},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2010_Taylor_r.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2014x,
  author    = {Michael Taylor},
  title     = {Smooth Operators for Principal Series Representations Microlocal Properties},
  year      = {2014},
  url       = {http://www.unc.edu/math/Faculty/met/slsoms.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2014_Taylor_v.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2009b,
  author    = {Michael Taylor},
  title     = {Flat 2D Tori with Sparse Spectra},
  year      = {2009},
  url       = {http://www.unc.edu/math/Faculty/met/sparse.pdf},
  abstract  = {We identify a class of 2D flat tori Tω, quotients of the plane by certain lattices, on which the Laplace operator has spectrum contained in the set of integers Z, as a sparse subset, i.e., a subset of density 0.},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2009_Taylor_c.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2012f,
  author    = {Michael Taylor},
  title     = {The Spectral Theorem for Self-Adjoint and Unitary Operators},
  year      = {2012},
  url       = {http://www.unc.edu/math/Faculty/met/specthm.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2012_Taylor_f.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2014y,
  author    = {Michael Taylor},
  title     = {Curvature, Conformal Mapping, and 2D Stationary Fluid Flows},
  year      = {2014},
  url       = {http://www.unc.edu/math/Faculty/met/stream.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2014_Taylor_w.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2014f,
  author    = {Michael Taylor},
  title     = {Figures ...},
  year      = {2014},
  url       = {http://www.unc.edu/math/Faculty/met/strfigs.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2014_Taylor_x.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2014z,
  author    = {A. Bamberger and Jeffrey Rauch and Michael Taylor},
  title     = {A Model for Harmonics on Stringed Instruments},
  year      = {2014},
  url       = {http://www.unc.edu/math/Faculty/met/string.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?;Jeffrey Rauch:uuid=7fdb410c-3353-11e8-b591-2b57b6801d19,orcid=?;A. Bamberger:uuid=0ed4f300-7a0b-11e8-a72b-ab1a5c33e1d9,orcid=?},
  file      = {:by-author/B/Bamberger/2014_Bamberger.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2015t,
  author    = {Michael Taylor},
  title     = {Regularity of Szegö Projectors and Cauchy Integrals On Test Functions with Cutoffs},
  year      = {2015},
  url       = {http://www.unc.edu/math/Faculty/met/szego.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2015_Taylor_v.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Tayloro,
  author    = {Michael Taylor},
  title     = {Chapter 10: Sobolev Spaces},
  url       = {http://www.unc.edu/math/Faculty/met/taylor2-chap10.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/XXXX_Taylor_m.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylorp,
  author    = {Michael Taylor},
  title     = {Chapter 14: Ergodic Theory},
  url       = {http://www.unc.edu/math/Faculty/met/taylor2-chap14.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/XXXX_Taylor_n.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylorq,
  author    = {Michael Taylor},
  title     = {Chapter 15: Probability Spaces and Random Variables},
  url       = {http://www.unc.edu/math/Faculty/met/taylor2-chap15.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/XXXX_Taylor_o.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylorr,
  author    = {Michael Taylor},
  title     = {Chapter 16: Wiener Measure and Brownian Motion},
  url       = {http://www.unc.edu/math/Faculty/met/taylor2-chap16.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/XXXX_Taylor_p.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2010e,
  author    = {Irina Mitrea and Marius Mitrea and Michael Taylor},
  title     = {Cauchy Integrals, Calderón Projectors, and Toeplitz Operators on Uniformly Rectifiable Domains},
  year      = {2010},
  url       = {http://www.unc.edu/math/Faculty/met/toep3.pdf},
  abstract  = {We develop properties of Cauchy integrals associated to a general class of first-order elliptic systems of differential operators D on a bounded, uniformly rectifiable (UR) domain Ω in a Riemannian manifold M . We show that associated to such Cauchy integrals are analogues of Hardy spaces of functions on Ω annihilated by D, and we produce projections, of Calderón type, onto subspaces of L p (∂Ω) consisting of boundary values of elements of such Hardy spaces. We consider Toeplitz operators associated to such projections and study their index properties. Of particular interest is a “cobordism argument,” which often enables one to identify the index of a Toeplitz operator on a rough UR domain with that of one on a smoothly bounded domain.},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?;Marius Mitrea:uuid=62b9a5c8-774c-11e7-b7c8-2b92d763a8df,orcid=?;Irina Mitrea:uuid=56d1820c-774d-11e7-b8a0-db9bdaf53211,orcid=?},
  file      = {:by-author/M/Mitrea/2010_Mitrea_a.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2010c,
  author    = {Michael Taylor},
  title     = {Traveling Wave Solutions to NLS and NLKG},
  year      = {2010},
  url       = {http://www.unc.edu/math/Faculty/met/twave.pdf},
  abstract  = {We study traveling wave solutions to nonlinear Schrödinger (NLS) and nonlinear Klein-Gordon (NLKG) equations on a compact Rieman- nian manifold M , with a Killing field X, generating a group of isome- tries. The emphasis is on NLKG; then if X has length < 1 everywhere, one gets a semilinear elliptic PDE on M , to which standard variational techniques apply (for a natural class of nonlinearities), as reviewed in §1, though there remains the question of whether the associated waves are really (or just apparently) traveling, a point taken up in §2. In §§3–4 we consider sonic speed waves, in some situations that lead to subelliptic nonlinear PDE, and in §5 we consider some supersonic trav- eling waves.},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2010_Taylor_s.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2015u,
  author    = {Michael Taylor},
  title     = {Uniform Convergence of Fourier Series},
  year      = {2015},
  url       = {http://www.unc.edu/math/Faculty/met/ucfs.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2015_Taylor_w.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2012g,
  author    = {Michael Taylor},
  title     = {Uniformization of Compactly Perturbed Planes, And Related Green Function Constructions},
  year      = {2012},
  url       = {http://www.unc.edu/math/Faculty/met/ucpp.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2012_Taylor_g.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2015v,
  author    = {Michael Taylor},
  title     = {Uniformly Integrable Families of Functions},
  year      = {2015},
  url       = {http://www.unc.edu/math/Faculty/met/uint.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2015_Taylor_x.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Mazzeo2018,
  author           = {Rafe Mazzeo and Michael Taylor},
  title            = {Curvature and uniformization},
  year             = {2018},
  url              = {https://mtaylor.web.unc.edu/wp-content/uploads/sites/16915/2018/04/unif7.pdf},
  abstract         = {We approach the problem of uniformization of general Riemann surfaces through consideration of the curvature equation, and in particular the problem of constructing Poincaré metrics (i.e., complete metrics of constant negative curvature) by solving the equation ∆u−e 2u = K 0 (z) on general open surfaces. A few other topics are discussed, including boundary behavior of the conformal factor e 2u giving the Poincaré metric when the Riemann surface has smoothly bounded compact closure, and also a curvature equation proof of Koebe’s disk theorem.},
  authorid         = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?;Rafe Mazzeo:uuid=17e59a1a-7a0d-11e8-9f8f-8b7bd1f3dbd2,ircid=?},
  creationdate     = {2016-12-11T00:00:00},
  file             = {:by-author/M/Mazzeo/2018_Mazzeo_1.pdf:PDF},
  modificationdate = {2023-10-19T14:16:50},
  owner            = {saulius},
  pages            = {1--25},
  timestamp        = {2016.12.11},
}

@Manuscript{Taylor2012h,
  author    = {Michael Taylor},
  title     = {Vector Valued Integration},
  year      = {2012},
  url       = {http://www.unc.edu/math/Faculty/met/vecint.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2012_Taylor_h.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Mazzucato2000,
  author    = {Anna Mazzucato and Michael Taylor},
  title     = {Vanishing Viscosity Plane Parallel Channel Flow and Related Singular Perturbation Problems},
  year      = {2000},
  url       = {http://www.unc.edu/math/Faculty/met/vvcf03.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?;Anna Mazzucato:uuid=36831faa-774e-11e7-b3e4-7f95ce86fa2d,orcid=?},
  file      = {:by-author/M/Mazzucato/2000_Mazzucato_a.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2013y,
  author    = {Michael Taylor},
  title     = {Vanishing Viscosity Limit for Navier-Stokes Flows: No-slip Boundary Condition},
  year      = {2013},
  url       = {http://www.unc.edu/math/Faculty/met/vvtalk.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2013_Taylor_z.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2014aa,
  author    = {Michael Taylor},
  title     = {Regularity of Weakly Conformal Maps},
  year      = {2014},
  url       = {http://www.unc.edu/math/Faculty/met/wcon.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2014_Taylor_y.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2015w,
  author    = {Michael Taylor},
  title     = {Proof of the Weber integral formula},
  year      = {2015},
  url       = {http://www.unc.edu/math/Faculty/met/weber.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2015_Taylor_y.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2013z,
  author    = {Michael Taylor},
  title     = {Simple Potential Wells in R3 as a Model for the Deuteron},
  year      = {2013},
  url       = {http://www.unc.edu/math/Faculty/met/wells.pdf},
  abstract  = {We construct the wave function ψ(x) for a simple model of the deuteron. We see that, in this model, the nucleons have a greater probability of lying outside the potential well than in it, as noted in nuclear physics texts. However, our calculations yield for the ratio of these probabilities a figure closer to 1 than what these texts say. We speculate on an explanation for this discrepancy.},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2013_Taylor_aa.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2013aa,
  author    = {Michael Taylor},
  title     = {Notes on the Weyl Calculus},
  year      = {2013},
  url       = {http://www.unc.edu/math/Faculty/met/weyl.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2013_Taylor_ab.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2014ab,
  author    = {Michael Taylor},
  title     = {Alternative Formulation of the Wiener Criterion},
  year      = {2014},
  url       = {http://www.unc.edu/math/Faculty/met/wiener.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2014_Taylor_z.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2016e,
  author    = {Michael Taylor},
  title     = {Zero Sets of Random Sections of Vector Bundles},
  year      = {2016},
  url       = {http://www.unc.edu/math/Faculty/met/zerosets.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2016_Taylor_f.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Filho2004,
  author    = {M. C. Lopes Filho and A. L. Mazzucato and H. J. Nussenzveig Lopes and Michael Taylor},
  title     = {Vanishing Viscosity Limits and Boundary Layers},
  year      = {2004},
  url       = {http://www.unc.edu/math/Faculty/met/zerovjk.pdf},
  abstract  = {We continue the work of Lopes Filho, Mazzucato and Nussenzveig Lopes [10] on the vanishing viscosity limit of circularly symmetric viscous flow in a disk with rotating boundary, shown there to converge to the inviscid limit in L 2-norm as long as the prescribed angular velocity α(t) of the boundary has bounded total variation. Here we establish convergence in stronger L 2 and L p-Sobolev spaces, allow for more singular angular velocities α, and address the issue of analyzing the behavior of the boundary layer. This includes an analysis of concen- tration of vorticity in the vanishing viscosity limit. We also consider such flows on an annulus, whose two boundary components rotate independently.},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?;M. C. Lopes Filho:uuid=0791deca-7a0e-11e8-9c44-b3903ab408a3,orcid=?;Anna Mazzucato:uuid=36831faa-774e-11e7-b3e4-7f95ce86fa2d,orcid=?;H. J. Nussenzveig Lopes:uuid=395ce0c6-7a0e-11e8-8394-bf3f577971ac,orcid=?},
  file      = {:by-author/F/Filho/2004_Filho.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Manuscript{Taylor2003a,
  author    = {Michael Taylor},
  title     = {The Zeta Function and the Prime Number Theorem},
  year      = {2003},
  url       = {http://www.unc.edu/math/Faculty/met/zeta.pdf},
  authorid  = {Michael Taylor:uuid=d64b39d0-774b-11e7-a287-cba67552cf0f,orcid=?},
  file      = {:by-author/T/Taylor/2003_Taylor.pdf:PDF},
  owner     = {saulius},
  timestamp = {2016.12.11},
  creationdate = {2016-12-11T00:00:00},
}

@Article{Jamieson2018,
  author    = {E. M. G. Jamieson and F. Modicom and S. M. Goldup},
  journal   = {Chemical Society Reviews},
  title     = {Chirality in rotaxanes and catenanes},
  year      = {2018},
  number    = {14},
  pages     = {5266--5311},
  volume    = {47},
  doi       = {10.1039/c8cs00097b},
  file      = {:by-author/J/Jamieson/2018_Jamieson_5266.pdf:PDF},
  keywords  = {Catenane; Mechanically Interlocked Molecular Architecture},
  owner     = {saulius},
  publisher = {Royal Society of Chemistry ({RSC})},
  timestamp = {2018.07.22},
  creationdate = {2018-07-22T00:00:00},
}

@Article{Neal2014,
  author    = {Edward A. Neal and Stephen M. Goldup},
  journal   = {Chem. Commun.},
  title     = {Chemical consequences of mechanical bonding in catenanes and rotaxanes: isomerism, modification, catalysis and molecular machines for synthesis},
  year      = {2014},
  number    = {40},
  pages     = {5128--5142},
  volume    = {50},
  doi       = {10.1039/c3cc47842d},
  file      = {:by-author/N/Neal/2014_Neal_5128.pdf:PDF},
  keywords  = {Catenane; Mechanically Interlocked Molecular Architecture; Rotaxane},
  owner     = {saulius},
  publisher = {Royal Society of Chemistry ({RSC})},
  timestamp = {2018.07.22},
  creationdate = {2018-07-22T00:00:00},
}

@Manuscript{Edelsbrunner2013,
  author    = {Herbert Edelsbrunner and Afra Zomorodian},
  title     = {Computing Linking Numbers of a Filtration},
  year      = {2013},
  keywords  = {A Well-studied Number; Algorithms; Alpha Shapes; Combinatorial Object; Computational Geometry and Topology; Enabling the Development of Fast Algo; Filtrations; Knots; Linking Also a Filtration of the Delaunay Triangulation; Three-manifolds},
  url       = {http://pub.ist.ac.at/~edels/Papers/2003-J-03-ComputingLinkingNumbers.pdf},
  abstract  = {Catenanes and rotaxanes are examples of non-trivial structural tanglings. Our work is on detecting such interlocks.},
  file      = {:by-author/E/Edelsbrunner/2013_Edelsbrunner.pdf:PDF},
  owner     = {saulius},
  timestamp = {2018.07.23},
  creationdate = {2018-07-23T00:00:00},
}

@PhdThesis{Zomorodian2001,
  author    = {Afra Joze Zomorodian},
  school    = {University of Illinois at Urbana-Champaign},
  title     = {Computing and Comprehending Topology: Persistence and Hierarchical Morse Complexes},
  year      = {2001},
  file      = {:by-author/Z/Zomorodian/2001_Zomorodian.pdf:PDF},
  owner     = {saulius},
  publisher = {© Copyright by Afra Joze Zomorodian, 2001},
  timestamp = {2018.07.23},
  creationdate = {2018-07-23T00:00:00},
  url       = {http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.117.1070&rep=rep1&type=pdf},
}

@Presentation{Boissonnat2010,
  author       = {Jean-Daniel Boissonnat},
  title        = {Convex Hulls, Voronoi Diagrams and Delaunay Triangulations},
  year         = {2010},
  organization = {ENS-Lyon},
  school       = {Winter School on Algorithmic Geometry},
  file         = {:by-author/B/Boissonnat/2010_Boissonnat.pdf:PDF},
  keywords     = {Convex Hull; Delaunay Triangulation; Voronoi Diagrams},
  owner        = {saulius},
  timestamp = {2018.07.23},
  creationdate = {2018-07-23T00:00:00},
  url          = {http://www.ens-lyon.fr/LIP/Arenaire/ERGeoAlgo/JDB-ens-lyon-I.pdf},
}

@Manuscript{Nielsen2007,
  author    = {Frank Nielsen and Jean-Daniel Boissonnat and Richard Nock},
  title     = {Bregman Voronoi Diagrams: Properties, Algorithms and Applications},
  year      = {2007},
  url       = {https://ia801008.us.archive.org/5/items/arxiv-0709.2196/0709.2196.pdf},
  file      = {:by-author/N/Nielsen/2007_Nielsen.pdf:PDF},
  owner     = {saulius},
  timestamp = {2018.07.23},
  creationdate = {2018-07-23T00:00:00},
}

@Misc{LatticeVerilog2004,
  title     = {A Verilog HDL Test Bench Primer},
  year      = {2004},
  file      = {:by-author/L/Lattice/2004_Lattice.pdf:PDF},
  keywords  = {Electronics; HDL; Hardware Definition Languages; Hardware Design; Simulation; Verilog},
  owner     = {saulius},
  timestamp = {2018.07.27},
  creationdate = {2018-07-27T00:00:00},
  url       = {https://people.ece.cornell.edu/land/courses/ece5760/Verilog/LatticeTestbenchPrimer.pdf},
}

@TechReport{Lattice2004,
  author    = {Lattice},
  title     = {ORCA Verilog Simulation and Manual},
  year      = {2004},
  number    = {(international)},
  file      = {:by-author/L/Lattice/2004_Lattice_.pdf:PDF},
  keywords  = {Electronics; HDL; Hardware Definition Languages; Hardware Design; Simulation; Verilog},
  owner     = {saulius},
  timestamp = {2018.07.27},
  creationdate = {2018-07-27T00:00:00},
  url       = {http://www.latticesemi.com/~/media/LatticeSemi/Documents/UserManuals/MQ/ORCACadenceVerilogSimulationInterfaceManual.PDF?document_id=5116},
}

@TechReport{OVI1996,
  author    = {{Open Verilog International}},
  title     = {Verilog-A Language Reference Manual. Analog Extensions to Verilog HDL},
  year      = {1996},
  file      = {:by-author/O/OVI/1996_OVI_.pdf:PDF},
  keywords  = {Electronics; HDL; Hardware Definition Languages; Hardware Design; Simulation; Verilog},
  owner     = {saulius},
  timestamp = {2018.07.27},
  creationdate = {2018-07-27T00:00:00},
  url       = {http://www.siue.edu/~gengel/ece585WebStuff/OVI_VerilogA.pdf},
}

@Misc{Accellera2004,
  author    = {Accellera},
  title     = {SystemVerilog 3.1a Language Reference Manual},
  year      = {2004},
  abstract  = {Accellera enhancements to the IEEE 1364-2001 Verilog standard},
  file      = {:by-author/A/Accellera/2004_Accellera_.pdf:PDF},
  keywords  = {Electronics; HDL; Hardware Definition Languages; Hardware Design; Simulation; Verilog},
  owner     = {saulius},
  timestamp = {2018.07.27},
  creationdate = {2018-07-27T00:00:00},
  url       = {http://www.ece.uah.edu/~gaede/cpe526/SystemVerilog_3.1a.pdf},
}

@Misc{IEEE2013,
  author    = {{IEEE}},
  title     = {IEEE Std 1800™-2012 (Revision of IEEE Std 1800-2009) IEEE Standard for SystemVerilog—Unified Hardware Design, Specification, and Verification Language},
  year      = {2013},
  abstract  = {The definition of the language syntax and semantics for SystemVerilog, which is a unified hardware design, specification, and verification language, is provided. This standard includes support for modeling hardware at the behavioral, register transfer level (RTL), and gate-level abstraction levels, and for writing testbenches using coverage, assertions, object-oriented programming, and constrained random verification. The standard also provides application programming interfaces (APIs) to foreign programming languages.},
  file      = {:by-author/I/IEEE/2013_IEEE_.pdf:PDF},
  keywords  = {Assertions; Design Automation; Design Verification; HDL; HDVL; Hardware Description Language; IEEE 1800™; PLI; Programming Language Interface; SystemVerilog; VPI; Verilog®},
  owner     = {saulius},
  timestamp = {2018.07.27},
  creationdate = {2018-07-27T00:00:00},
  url       = {http://www.ece.uah.edu/~gaede/cpe526/2012%20System%20Verilog%20Language%20Reference%20Manual.pdf},
}

@Misc{Sutherland2001,
  author    = {Stuart Sutherland},
  title     = {Verilog-2001 Quick Reference Guide},
  year      = {2001},
  abstract  = {Verilog Hardware Description Language},
  file      = {:by-author/S/Sutherland/2001_Sutherland_.pdf:PDF},
  keywords  = {HDL; Hardware Design; Verilog},
  owner     = {saulius},
  timestamp = {2018.07.27},
  creationdate = {2018-07-27T00:00:00},
  url       = {http://sutherland-hdl.com/pdfs/verilog_2001_ref_guide.pdf},
}

@Book{Bhasker1991,
  author    = {Jayaram Bhasker},
  title     = {A VHDL Primer},
  year      = {1991},
  file      = {:by-author/B/Bhasker/1991_Bhasker_.pdf:PDF},
  keywords  = {Electronics; HDL; Hardware Definition Languages; Hardware Design; Simulation; VHDL},
  owner     = {saulius},
  timestamp = {2018.07.27},
  creationdate = {2018-07-27T00:00:00},
  url       = {https://www.edutechlearners.com/download/books/A%20VHDL%20Primer%20-%20Jayaram%20Bhasker.pdf},
}

@Manuscript{Tala2005,
  author    = {Deepak Kumar Tala},
  title     = {Verilog Tutorial},
  year      = {2005},
  url       = {http://www.ece.umd.edu/class/enee359a/verilog_tutorial.pdf},
  file      = {:by-author/T/Tala/2005_Tala_.pdf:PDF},
  owner     = {saulius},
  timestamp = {2018.07.27},
  creationdate = {2018-07-27T00:00:00},
}

@Presentation{Wolf2015,
  author    = {Clifford Wolf},
  title     = {A Free and Open Source Verilog-to-Bitstream Flow for iCE40 FPGAs},
  year      = {2015},
  file      = {:by-author/W/Wolf/2015_Wolf_.pdf:PDF},
  keywords  = {Electronics; FPGA; HDL; Hardware Definition Languages; Hardware Design; ICE40; IceStorm; Open Source; Simulation; Verilog; Yosys},
  owner     = {saulius},
  timestamp = {2018.07.28},
  creationdate = {2018-07-28T00:00:00},
  url       = {http://www.clifford.at/papers/2015/icestorm-flow/slides.pdf},
}

@TechReport{Brown2000,
  author      = {Stephen Brown and Jonathan Rose},
  institution = {Department of Electrical and Computer Engineering, University of Toronto},
  title       = {Architecture of FPGAs and CPLDs: A Tutorial},
  year        = {2000},
  file        = {:by-author/B/Brown/2000_Brown_.pdf:PDF},
  keywords    = {Altera; CPLD; FPGA; Lattice; Review; Xilinx},
  owner       = {saulius},
  timestamp = {2018.07.30},
  creationdate = {2018-07-30T00:00:00},
  url         = {http://www.eecg.toronto.edu/~jayar/pubs/brown/survey.pdf},
}

@Misc{ISO2017,
  author       = {ISO},
  howpublished = {ISO 14688-1:2017(E)},
  title        = {Geotechnical investigation and testing — Identification and classification of soil — Part 1: Identification and description},
  year         = {2017},
  file         = {:by-author/I/ISO/2017_ISO.pdf:PDF},
  owner        = {saulius},
  timestamp = {2018.07.30},
  creationdate = {2018-07-30T00:00:00},
}

@Misc{ISO2017a,
  author       = {ISO},
  howpublished = {ISO 14689:2017(E)},
  title        = {Geotechnical investigation and testing — Identification, description and classification of rock},
  year         = {2017},
  file         = {:by-author/I/ISO/2017_ISO_a.pdf:PDF},
  owner        = {saulius},
  timestamp = {2018.07.30},
  creationdate = {2018-07-30T00:00:00},
}

@Article{Imaz2008,
  author    = {Inhar Imaz and Fernando Luis and Chiara Carbonera and Daniel Ruiz-Molina and Daniel Maspoch},
  journal   = {Chemical Communications},
  title     = {Single-molecule magnet behaviour in metal{\textendash}organic nanospheres generated by simple precipitation of Mn12O12 clusters},
  year      = {2008},
  number    = {10},
  pages     = {1202},
  doi       = {10.1039/b716071b},
  file      = {:by-author/I/Imaz/2008_Imaz_1202.pdf:PDF},
  groups    = {sg/MOFs, am/MOFs, sg/MOF},
  keywords  = {Metal-Organic Frameworks (MOF); Nanoparticles},
  owner     = {saulius},
  publisher = {Royal Society of Chemistry ({RSC})},
  timestamp = {2018.08.08},
  creationdate = {2018-08-08T00:00:00},
}

@Article{Colson2013,
  author    = {Pierre Colson and Catherine Henrist and Rudi Cloots},
  journal   = {Journal of Nanomaterials},
  title     = {Nanosphere Lithography: A Powerful Method for the Controlled Manufacturing of Nanomaterials},
  year      = {2013},
  pages     = {1--19},
  volume    = {2013},
  doi       = {10.1155/2013/948510},
  file      = {:by-author/C/Colson/2013_Colson_1.pdf:PDF},
  keywords  = {Litography; Nanosphere},
  owner     = {saulius},
  publisher = {Hindawi Limited},
  timestamp = {2018.08.08},
  creationdate = {2018-08-08T00:00:00},
}

@Article{Imaz2008a,
  author    = {Inhar Imaz and Jordi Hernando and Daniel Ruiz-Molina and Daniel Maspoch},
  journal   = {Angewandte Chemie International Edition},
  title     = {Metal-Organic Spheres as Functional Systems for Guest Encapsulation},
  year      = {2008},
  month     = {dec},
  number    = {13},
  pages     = {2325--2329},
  volume    = {48},
  doi       = {10.1002/anie.200804255},
  file      = {:by-author/I/Imaz/2008_Imaz_2325.pdf:PDF},
  keywords  = {Metal-organic; Spheres},
  owner     = {saulius},
  publisher = {Wiley},
  timestamp = {2018.08.08},
  creationdate = {2018-08-08T00:00:00},
}

@Manuscript{Stoimenow2004,
  author    = {Alexander Stoimenow},
  title     = {Chord and Gauß diagrams in the Theory of Knots},
  year      = {2004},
  url       = {http://stoimenov.net/stoimeno/homepage/papers/tpl.pdf},
  file      = {:by-author/S/Stoimenow/2004_Stoimenow_.pdf:PDF},
  owner     = {saulius},
  timestamp = {2018.08.08},
  creationdate = {2018-08-08T00:00:00},
}

@Article{Grinblat2016,
  author     = {Andrey Grinblat and Viktor Lopatkin},
  title      = {On Realizability of Gauss Diagrams},
  pages      = {161001440},
  abstract   = {The problem of which Gauss diagram can be realized by knots is an old one and has been solved in several ways. In this paper, we present a direct approach to this problem. We show that the needed conditions for realizability of a Gauss diagram can be interpreted as follows "the number of exits = the number of entrances" and the sufficient condition is based on Jordan curve Theorem.},
  date       = {2016-09-21},
  eprint     = {1610.01440v2},
  eprinttype = {arXiv},
  file       = {:by-author/G/Grinblat/2016_Grinblat_161001440.pdf:PDF},
  keywords   = {Knot Theory; Topology},
  owner      = {saulius},
  timestamp = {2018.08.08},
  creationdate = {2018-08-08T00:00:00},
  url        = {https://arxiv.org/abs/1610.01440v2},
}

@Presentation{Ayers2001,
  author    = {Ayers},
  title     = {Diode-Transistor Logic (DTL)},
  year      = {2001},
  file      = {:by-author/A/Ayers/2001_Ayers_.pdf:PDF},
  keywords  = {Diode-transistor Logic; Electronics},
  owner     = {saulius},
  timestamp = {2018.08.08},
  creationdate = {2018-08-08T00:00:00},
  url       = {http://people.seas.harvard.edu/~jones/es154/lectures/lecture_7/pdfs/215ln03.pdf},
}

@InProceedings{Schocken2012,
  author    = {Shimon Schocken},
  booktitle = {Proceedings of the 43rd {ACM} technical symposium on Computer Science Education - {SIGCSE} {\textquotesingle}12},
  title     = {Taming complexity in large-scale system projects},
  year      = {2012},
  pages     = {409--414},
  publisher = {{ACM} Press},
  doi       = {10.1145/2157136.2157259},
  file      = {:by-author/S/Schocken/2012_Schocken_409.pdf:PDF},
  keywords  = {Electronics; HDL; Logic Circuits},
  owner     = {saulius},
  timestamp = {2018.08.08},
  creationdate = {2018-08-08T00:00:00},
}

@InProceedings{2011a,
  title     = {Diode transistor logic},
  year      = {2011},
  file      = {:by-author/2011__.pdf:PDF},
  keywords  = {Diode-transistor Logic},
  owner     = {saulius},
  timestamp = {2018.08.08},
  creationdate = {2018-08-08T00:00:00},
  url       = {http://www.uobabylon.edu.iq/uobColeges/ad_downloads/4_22382_163.pdf},
}

@Article{Grishanov2009,
  author    = {S. Grishanov and V. Meshkov and A. Omelchenko},
  journal   = {Textile Research Journal},
  title     = {A Topological Study of Textile Structures. Part {II}: Topological Invariants in Application to Textile Structures},
  year      = {2009},
  month     = {may},
  number    = {9},
  pages     = {822--836},
  volume    = {79},
  doi       = {10.1177/0040517508096221},
  file      = {:by-author/G/Grishanov/2009_Grishanov_822.pdf:PDF},
  groups    = {sg/MOFs, am/MOFs},
  keywords  = {Knot Theory; Metal-Organic Frameworks (MOF); Topology},
  owner     = {saulius},
  publisher = {{SAGE} Publications},
  timestamp = {2018.08.24},
  creationdate = {2018-08-24T00:00:00},
}

@Article{Grishanov2007,
  author    = {Sergei A. Grishanov and Vadim R. Meshkov and Alexander V. Omel'chenko},
  journal   = {Journal of Knot Theory and Its Ramifications},
  title     = {Kauffman-type Polynomial Invariants for Doubly Periodic Structures},
  year      = {2007},
  month     = {aug},
  number    = {06},
  pages     = {779--788},
  volume    = {16},
  doi       = {10.1142/s021821650700549x},
  file      = {:by-author/G/Grishanov/2007_Grishanov_779.pdf:PDF},
  groups    = {sg/MOFs, am/MOFs},
  keywords  = {Knot Theory; Metal-Organic Frameworks (MOF); Topology},
  owner     = {saulius},
  publisher = {World Scientific Pub Co Pte Lt},
  timestamp = {2018.08.24},
  creationdate = {2018-08-24T00:00:00},
}

@Article{Grishanov2009a,
  author    = {Sergei Grishanov and Vadim Meshkov and Alexander Omelchenko},
  journal   = {Textile Research Journal},
  title     = {A Topological Study of Textile Structures. Part I: An Introduction to Topological Methods},
  year      = {2009},
  month     = {apr},
  number    = {8},
  pages     = {702--713},
  volume    = {79},
  doi       = {10.1177/0040517508095600},
  file      = {:by-author/G/Grishanov/2009_Grishanov_702.pdf:PDF},
  groups    = {sg/MOFs, am/MOFs},
  keywords  = {Knot Theory; Metal-Organic Frameworks (MOF); Topology},
  owner     = {saulius},
  publisher = {{SAGE} Publications},
  timestamp = {2018.08.24},
  creationdate = {2018-08-24T00:00:00},
}

@Article{Mashaghi2014,
  author    = {Alireza Mashaghi and Roeland~J. van~Wijk and Sander~J. Tans},
  journal   = {Structure},
  title     = {Circuit Topology of Proteins and Nucleic Acids},
  year      = {2014},
  month     = {sep},
  number    = {9},
  pages     = {1227--1237},
  volume    = {22},
  doi       = {10.1016/j.str.2014.06.015},
  file      = {:by-author/M/Mashaghi/2014_Mashaghi_1227.pdf:PDF},
  keywords  = {Biomolecules; Topology},
  owner     = {saulius},
  publisher = {Elsevier {BV}},
  timestamp = {2018.08.27},
  creationdate = {2018-08-27T00:00:00},
}

@Presentation{OKeeffe2015,
  author    = {Michael O'Keeffe},
  title     = {Towards a Taxonomy of MOF Structures},
  year      = {2015},
  file      = {:by-author/O/OKeeffe/2015_OKeeffe.pdf:PDF},
  groups    = {sg/MOFs, am/MOFs, sg/MOF},
  keywords  = {Classification; Metal-Organic Frameworks (MOF); Topology},
  owner     = {saulius},
  timestamp = {2018.08.27},
  creationdate = {2018-08-27T00:00:00},
  url       = {http://yaghi.berkeley.edu/research-news/MOK-DeconstructingMOFs.pdf},
}

@Article{Blatov2014,
  author           = {Vladislav A. Blatov and Alexander P. Shevchenko and Davide M. Proserpio},
  journal          = {Crystal Growth {\&} Design},
  title            = {Applied Topological Analysis of Crystal Structures with the Program Package {ToposPro}},
  year             = {2014},
  month            = {jun},
  number           = {7},
  pages            = {3576--3586},
  volume           = {14},
  comment          = {Cited in Alexandrov2017 (ref. [7]).},
  creationdate     = {2018-08-27T00:00:00},
  doi              = {10.1021/cg500498k},
  file             = {:by-author/B/Blatov/2014_Blatov_3576.pdf:PDF},
  groups           = {sg/MOFs, am/MOFs, sg/MOF},
  keywords         = {Metal-Organic Frameworks (MOF); Topology},
  modificationdate = {2024-09-14T12:06:22},
  owner            = {saulius},
  publisher        = {American Chemical Society ({ACS})},
  timestamp        = {2018.08.27},
}

@Article{Alexandrov2012,
  author           = {Eugeny V. Alexandrov and Vladislav A. Blatov and Davide M. Proserpio},
  journal          = {Acta Crystallographica Section A Foundations of Crystallography},
  title            = {A topological method for the classification of entanglements in crystal {networksA} preliminary account of this work was presented at the workshop {\textasciigrave}Topological dynamics in physics and biology{\textquotesingle} held in Pisa, 12{\textendash}13 July 2011.},
  year             = {2012},
  month            = {jun},
  number           = {4},
  pages            = {484--493},
  volume           = {68},
  comment          = {Cited by Eon2016 as containing the "definition of important kinds of links in entagled nets"; cited in Alexandrov2017.},
  creationdate     = {2018-08-27T00:00:00},
  doi              = {10.1107/s0108767312019034},
  file             = {:by-author/A/Alexandrov/2012_Alexandrov_484.pdf:PDF;:by-author/A/Alexandrov/2012_Alexandrov_484_suppl/eo5016sup2.ods:OpenDocument spreadsheet;:by-author/A/Alexandrov/2012_Alexandrov_484_suppl/eo5016sup1.xls:Excel},
  groups           = {sg/MOFs, am/MOFs, sg/MOF},
  keywords         = {Metal-Organic Frameworks (MOF); Topology},
  modificationdate = {2024-09-14T12:34:33},
  owner            = {saulius},
  publisher        = {International Union of Crystallography ({IUCr})},
  timestamp        = {2018.08.27},
}

@Article{Barthel2018,
  author    = {Senja Barthel and Eugeny V. Alexandrov and Davide M. Proserpio and Berend Smit},
  journal   = {Crystal Growth {\&} Design},
  title     = {Distinguishing Metal{\textendash}Organic Frameworks},
  year      = {2018},
  month     = {jan},
  number    = {3},
  pages     = {1738--1747},
  volume    = {18},
  doi       = {10.1021/acs.cgd.7b01663},
  file      = {:by-author/B/Barthel/2018_Barthel_1738.pdf:PDF},
  groups    = {sg/MOFs, am/MOFs, sg/MOF},
  keywords  = {Metal-Organic Frameworks (MOF); Topology},
  owner     = {saulius},
  publisher = {American Chemical Society ({ACS})},
  timestamp = {2018.08.27},
  creationdate = {2018-08-27T00:00:00},
}

@Article{Blatov2004,
  author           = {V. A. Blatov and L. Carlucci and G. Ciani and D. M. Proserpio},
  journal          = {{CrystEngComm}},
  title            = {Interpenetrating metal{\textendash}organic and inorganic 3D networks: a computer-aided systematic investigation. Part I. Analysis of the Cambridge structural database},
  year             = {2004},
  number           = {65},
  pages            = {377--395},
  volume           = {6},
  comment          = {Cited in Alexandrov2017 (ref. [8]).},
  creationdate     = {2018-08-27T00:00:00},
  doi              = {10.1039/b409722j},
  file             = {:by-author/B/Blatov/2004_Blatov_377.pdf:PDF},
  groups           = {sg/MOFs, am/MOFs, sg/MOF},
  keywords         = {Metal-Organic Frameworks (MOF); Topology},
  modificationdate = {2024-09-14T12:10:09},
  owner            = {saulius},
  publisher        = {Royal Society of Chemistry ({RSC})},
  timestamp        = {2018.08.27},
}

@Article{Baburin2005,
  author    = {I.A. Baburin and V.A. Blatov and L. Carlucci and G. Ciani and D.M. Proserpio},
  journal   = {Journal of Solid State Chemistry},
  title     = {Interpenetrating metal-organic and inorganic 3D networks: a computer-aided systematic investigation. Part {II} [1]. Analysis of the Inorganic Crystal Structure Database ({ICSD})},
  year      = {2005},
  month     = {aug},
  number    = {8},
  pages     = {2452--2474},
  volume    = {178},
  doi       = {10.1016/j.jssc.2005.05.029},
  file      = {:by-author/B/Baburin/2005_Baburin_2452.pdf:PDF},
  groups    = {sg/MOFs, am/MOFs, sg/MOF},
  keywords  = {Metal-Organic Frameworks (MOF); Topology},
  owner     = {saulius},
  publisher = {Elsevier {BV}},
  timestamp = {2018.08.27},
  creationdate = {2018-08-27T00:00:00},
}

@Article{Ma2018,
  author    = {Tianqiong Ma and Eugene A. Kapustin and Shawn X. Yin and Lin Liang and Zhengyang Zhou and Jing Niu and Li-Hua Li and Yingying Wang and Jie Su and Jian Li and Xiaoge Wang and Wei David Wang and Wei Wang and Junliang Sun and Omar M. Yaghi},
  journal   = {Science},
  title     = {Single-crystal x-ray diffraction structures of covalent organic frameworks},
  year      = {2018},
  month     = {jul},
  number    = {6397},
  pages     = {48--52},
  volume    = {361},
  doi       = {10.1126/science.aat7679},
  file      = {:by-author/M/Ma/2018_Ma_48.pdf:PDF},
  groups    = {sg/MOFs, am/MOFs, sg/MOF},
  keywords  = {Covalent Frameworks; Crystal Structures; Metal-Organic Frameworks (MOF); Organic Frameworks},
  owner     = {saulius},
  publisher = {American Association for the Advancement of Science ({AAAS})},
  timestamp = {2018.08.27},
  creationdate = {2018-08-27T00:00:00},
}

@Article{Baburin2018,
  author       = {Igor A. Baburin},
  journal      = {arXiv},
  title        = {On the group-theoretical approach to the study of interpenetrating nets},
  year         = {2018},
  abstract     = {A general theoretical framework based on group-subgroup and group-supergroup relations is proposed to describe and to derive interpenetrating nets.},
  date         = {2018-05-04},
  eprint       = {1805.01773v1},
  eprintclass  = {cond-mat.mtrl-sci},
  eprinttype   = {arXiv},
  file         = {:by-author/B/Baburin/2018_Baburin_1805.01773v1.pdf:PDF},
  groups       = {sg/MOFs, am/MOFs, sg/MOF},
  journaltitle = {Acta Cryst. (2016). A72, 366-375},
  keywords     = {Metal-Organic Frameworks (MOF); Topology},
  owner        = {saulius},
  timestamp = {2018.08.27},
  creationdate = {2018-08-27T00:00:00},
  url          = {https://arxiv.org/abs/1805.01773},
}

@Article{Baburin2016,
  author           = {Igor A. Baburin},
  journal          = {Acta Crystallographica Section A Foundations and Advances},
  title            = {On the group-theoretical approach to the study of interpenetrating nets},
  year             = {2016},
  month            = {apr},
  number           = {3},
  pages            = {366--375},
  volume           = {72},
  comment          = {Cited in Alexandrov2017.},
  creationdate     = {2018-08-27T00:00:00},
  doi              = {10.1107/s2053273316002692},
  file             = {:by-author/B/Baburin/2016_Baburin_366.pdf:PDF},
  groups           = {sg/MOFs, am/MOFs, sg/MOF},
  keywords         = {Metal-Organic Frameworks (MOF); Topology},
  modificationdate = {2024-09-14T12:40:05},
  owner            = {saulius},
  publisher        = {International Union of Crystallography ({IUCr})},
  timestamp        = {2018.08.27},
}

@Article{Schoedel2016,
  author    = {Alexander Schoedel and Mian Li and Dan Li and Michael O'Keeffe and Omar M. Yaghi},
  journal   = {Chemical Reviews},
  title     = {Structures of Metal{\textendash}Organic Frameworks with Rod Secondary Building Units},
  year      = {2016},
  month     = {sep},
  number    = {19},
  pages     = {12466--12535},
  volume    = {116},
  doi       = {10.1021/acs.chemrev.6b00346},
  file      = {:by-author/S/Schoedel/2016_Schoedel_12466.pdf:PDF},
  groups    = {sg/MOFs, am/MOFs, sg/MOF},
  keywords  = {Metal-Organic Frameworks (MOF); Topology},
  owner     = {saulius},
  publisher = {American Chemical Society ({ACS})},
  timestamp = {2018.08.27},
  creationdate = {2018-08-27T00:00:00},
}

@Presentation{Gupta2014,
  author    = {Sapna Gupta},
  title     = {Dipole Moment, Resonance},
  year      = {2014},
  file      = {:by-author/G/Gupta/2014_Gupta.pdf:PDF},
  keywords  = {Dipol Moment; NO3- Ion; Resonance Structures},
  owner     = {saulius},
  timestamp = {2018.08.28},
  creationdate = {2018-08-28T00:00:00},
  url       = {http://drsapnag.manusadventures.com/chemistry/organic-chemistry/powerpoints/PP01-2DipoleResonance.pdf},
}

@Presentation{Ghedini2018,
  author           = {Emanuele Ghedini and Adham Hashibon and Jesper Friis and Gerhard Goldbeck and Georg Schmitz},
  title            = {{EMMO}: {T}he european materials modelling ontology},
  year             = {2018},
  creationdate     = {2018-08-29T00:00:00},
  file             = {:by-author/G/Ghedini/2018_Ghedini.pdf:PDF},
  modificationdate = {2022-12-14T07:33:17},
  owner            = {saulius},
  timestamp        = {2018.08.29},
  url              = {https://emmc.info/wp-content/uploads/2018/08/emmo_workshop-Ghedini-v2.pdf},
}

@Article{Blatov2000,
  author    = {V. A. Blatov and A. P. Shevchenko and V. N. Serezhkin},
  journal   = {Journal of Applied Crystallography},
  title     = {{TOPOS}3.2: a new version of the program package for multipurpose crystal-chemical analysis},
  year      = {2000},
  month     = {aug},
  number    = {4},
  pages     = {1193--1193},
  volume    = {33},
  doi       = {10.1107/s0021889800007202},
  file      = {:by-author/B/Blatov/2000_Blatov_1193.pdf:PDF},
  groups    = {sg/MOFs, am/MOFs, sg/MOF},
  keywords  = {Classification; Interpenetrating Networks; Metal-Organic Frameworks (MOF); Software; Topology},
  owner     = {saulius},
  publisher = {International Union of Crystallography ({IUCr})},
  timestamp = {2018.08.29},
  creationdate = {2018-08-29T00:00:00},
}

@Article{Wilson2014,
  author    = {Greg Wilson and D. A. Aruliah and C. Titus Brown and Neil P. Chue Hong and Matt Davis and Richard T. Guy and Steven H. D. Haddock and Kathryn D. Huff and Ian M. Mitchell and Mark D. Plumbley and Ben Waugh and Ethan P. White and Paul Wilson},
  journal   = {{PLoS} Biology},
  title     = {Best Practices for Scientific Computing},
  year      = {2014},
  month     = {jan},
  number    = {1},
  pages     = {e1001745},
  volume    = {12},
  doi       = {10.1371/journal.pbio.1001745},
  editor    = {Jonathan A. Eisen},
  file      = {:by-author/W/Wilson/2014_Wilson_1001745.pdf:PDF},
  keywords  = {Scientifc Software; Software Development},
  owner     = {saulius},
  publisher = {Public Library of Science ({PLoS})},
  timestamp = {2018.09.28},
  creationdate = {2018-09-28T00:00:00},
}

@Article{Baxter2006,
  author    = {Susan M. Baxter and Steven W. Day and Jacquelyn S. Fetrow and Stephanie J. Reisinger},
  journal   = {{PLoS} Computational Biology},
  title     = {Scientific Software Development Is Not an Oxymoron},
  year      = {2006},
  number    = {9},
  pages     = {e87},
  volume    = {2},
  doi       = {10.1371/journal.pcbi.0020087},
  file      = {:by-author/B/Baxter/2006_Baxter_87.pdf:PDF},
  keywords  = {Scientifc Software; Software Development},
  owner     = {saulius},
  publisher = {Public Library of Science ({PLoS})},
  timestamp = {2018.09.28},
  creationdate = {2018-09-28T00:00:00},
}

@InProceedings{Paz2005,
  author    = {Harel Paz and Erez Petrank and David F. Bacon and Elliot K. Kolodner and V. T. Rajan},
  booktitle = {Compiler Construction},
  title     = {An Efficient On-the-Fly Cycle Collection},
  year      = {2005},
  address   = {Berlin, Heidelberg},
  editor    = {Bodik, Rastislav},
  pages     = {156--171},
  publisher = {Springer Berlin Heidelberg},
  abstract  = {A reference-counting garbage collector cannot reclaim unreachable
cyclic structures of objects. Therefore, reference-counting collectors either use
a backup tracing collector infrequently, or employ a cycle collector to reclaim
cyclic structures. We propose a new concurrent cycle collector, i.e., one that runs
concurrently with the program threads, imposing negligible pauses (of around
1ms) on a multiprocessor.},
  doi       = {10.1007/978-3-540-31985-6_11},
  file      = {:by-author/P/Paz/2005_Paz_156.pdf:PDF},
  keywords  = {Computer Science (CS); Garbage Collector},
  owner     = {saulius},
  timestamp = {2018.09.28},
  creationdate = {2018-09-28T00:00:00},
  url       = {https://link.springer.com/content/pdf/10.1007%2F978-3-540-31985-6_11.pdf},
}

@Presentation{Paz2012,
  author    = {Harel Paz and Erez Petrank},
  title     = {An Efficient On-the-Fly Cycle Collection},
  year      = {2012},
  file      = {:by-author/P/Paz/2012_Paz.pdf:PDF},
  keywords  = {Computer Science (CS); Garbage Collector},
  owner     = {saulius},
  timestamp = {2018.09.29},
  creationdate = {2018-09-29T00:00:00},
  url       = {https://researcher.watson.ibm.com/researcher/files/us-bacon/Paz05EfficientSlides.pdf},
}

@Manuscript{Paz2005a,
  author    = {Harel Paz and David F. Bacon and Elliot K. Kolodner and Erez Petrank and V. T and Rajan},
  title     = {An Efficient On-the-Fly Cycle Collection},
  year      = {2005},
  keywords  = {Computer Science (CS); Garbage Collector},
  url       = {https://researcher.watson.ibm.com/researcher/files/us-bacon/Paz05Efficient.pdf},
  abstract  = {A reference counting garbage collector cannot reclaim unreachable
cyclic structures of objects. Therefore, reference counting collectors either use
a backup tracing collector infrequently, or employ a cycle collector to reclaim
cyclic structures. We propose a new concurrent cycle collector, i.e., one that runs
concurrently with the program threads, imposing negligible pauses (of around
1ms) on a multiprocessor.
Our new collector combines the state-of-the-art cycle collector [5] with the slid-
ing views collectors [26, 2]. The use of sliding views with cycle collection obtains
two advantages. First, it drastically reduces the number of cycle candidates, which
in turn, drastically reduces the work required to record and trace these candidates.
This yields a large improvement in cycle collection efficiency. Second, it elimi-
nates the theoretical termination problem that appeared in the previous concurrent
cycle collector. There, a rare race may delay the reclamation of an unreachable
cyclic structure forever. The proposed cycle collector guarantees reclamation of
all unreachable cyclic structures.
We have implemented the proposed collector on the Jikes RVM and we provide
measurements including a comparison between the use of backup tracing and the
use of cycle collection with reference counting. To the best of our knowledge,
such a comparison has not been reported before.},
  file      = {:by-author/P/Paz/2005_Paz.pdf:PDF},
  owner     = {saulius},
  timestamp = {2018.09.29},
  creationdate = {2018-09-29T00:00:00},
}

@TechReport{Chadwick2013,
  author      = {Gregory A. Chadwick},
  institution = {University of Cambridge, Computer Laboratory},
  title       = {Communication centric, multi-core, fine-grained processor architecture},
  year        = {2013},
  file        = {:by-author/C/Chadwick/2013_Chadwick.pdf:PDF},
  keywords    = {CPU Architecture; CPU Design; Computer Science (CS)},
  owner       = {saulius},
  timestamp = {2018.09.29},
  creationdate = {2018-09-29T00:00:00},
  url         = {https://www.cl.cam.ac.uk/techreports/UCAM-CL-TR-832.pdf},
}

@Article{Wilson2017,
  author    = {Greg Wilson and Jennifer Bryan and Karen Cranston and Justin Kitzes and Lex Nederbragt and Tracy K. Teal},
  journal   = {{PLOS} Computational Biology},
  title     = {Good enough practices in scientific computing},
  year      = {2017},
  month     = {jun},
  number    = {6},
  pages     = {e1005510},
  volume    = {13},
  doi       = {10.1371/journal.pcbi.1005510},
  editor    = {Francis Ouellette},
  file      = {:by-author/W/Wilson/2017_Wilson_1005510.pdf:PDF},
  keywords  = {Scientifc Software; Software Development},
  owner     = {saulius},
  publisher = {Public Library of Science ({PLoS})},
  timestamp = {2018.10.02},
  creationdate = {2018-10-02T00:00:00},
}

@Article{Levanoni2001,
  author    = {Yossi Levanoni and Erez Petrank},
  journal   = {OOPSLA},
  title     = {An on-the-fly reference counting garbage collector for Java},
  year      = {2001},
  issn      = {0362-1340},
  pages     = {367--380},
  volume    = {36},
  doi       = {10.1145/504311.504309},
  file      = {:by-author/L/Levanoni/2001_Levanoni_367.pdf:PDF},
  groups    = {[saulius:]},
  keywords  = {Computer Science (CS); Garbage Collector},
  owner     = {saulius},
  timestamp = {2018.10.02},
  creationdate = {2018-10-02T00:00:00},
}

@Article{Azatchi2003,
  author    = {Hezi Azatchi and Yossi Levanoni and Harel Paz and Erez Petrank},
  journal   = {OOPSLA},
  title     = {An on-the-fly mark and sweep garbage collector based on sliding views},
  year      = {2003},
  issn      = {0362-1340},
  pages     = {269},
  volume    = {38},
  doi       = {10.1145/949343.949329},
  file      = {:by-author/A/Azatchi/2003_Azatchi_269.pdf:PDF},
  groups    = {[saulius:]},
  keywords  = {Computer Science (CS); Garbage Collector},
  owner     = {saulius},
  timestamp = {2018.10.02},
  creationdate = {2018-10-02T00:00:00},
}

@Article{Levanoni2006,
  author    = {Yossi Levanoni and Erez Petrank},
  journal   = {ACM Transactions on Programming Languages and Systems},
  title     = {An on-the-fly reference-counting garbage collector for java},
  year      = {2006},
  issn      = {0164-0925},
  pages     = {1--69},
  volume    = {28},
  doi       = {10.1145/1111596.1111597},
  file      = {:by-author/L/Levanoni/2006_Levanoni_1.pdf:PDF},
  groups    = {[saulius:]},
  keywords  = {Computer Science (CS); Garbage Collector},
  owner     = {saulius},
  timestamp = {2018.10.02},
  creationdate = {2018-10-02T00:00:00},
}

@Article{Domani2001,
  author    = {Tamar Domani and Elliot K. Kolodner and Ethan Lewis and Eliot E. Salant and Katherine Barabash and Itai Lahan and Yossi Levanoni and Erez Petrank and Igor Yanorer},
  journal   = {ACM SIGPLAN Notices},
  title     = {Implementing an on-the-fly garbage collector for Java},
  year      = {2001},
  issn      = {0362-1340},
  pages     = {155--166},
  volume    = {36},
  doi       = {10.1145/362426.362484},
  file      = {:by-author/D/Domani/2001_Domani_155.pdf:PDF},
  groups    = {[saulius:]},
  keywords  = {Computer Science (CS); Garbage Collector},
  owner     = {saulius},
  timestamp = {2018.10.02},
  creationdate = {2018-10-02T00:00:00},
}

@Article{Goldreich1991,
  author           = {O. Goldreich and E. Petrank},
  journal          = {Proceedings 32nd Annual Symposium of Foundations of Computer Science},
  title            = {Quantifying knowledge complexity},
  year             = {1991},
  pages            = {59--68},
  comment          = {Cites Goldwasser1985 (ref. [GMR]). Criticises their definition.},
  creationdate     = {2018-10-02T00:00:00},
  doi              = {10.1109/sfcs.1991.185349},
  file             = {:by-author/G/Goldreich/1991_Goldreich_59.pdf:PDF},
  groups           = {[saulius:]},
  keywords         = {Criticism; Cryptography; Information Theory; NP-completness; Zero-knowledge Proofs; Zero-knowledge Protocols},
  modificationdate = {2024-10-13T09:50:35},
  owner            = {saulius},
  timestamp        = {2018.10.02},
}

@Article{OKeeffe2001,
  author    = {M. O'Keeffe and J. Pl{\'{e}}vert and Y. Teshima and Y. Watanabe and T. Ogama},
  journal   = {Acta Crystallographica Section A Foundations of Crystallography},
  title     = {The invariant cubic rod (cylinder) packings: symmetries and coordinates},
  year      = {2001},
  month     = {jan},
  number    = {1},
  pages     = {110--111},
  volume    = {57},
  doi       = {10.1107/S010876730001151X},
  file      = {:by-author/O/O'Keeffe/2001_O'Keeffe_110.pdf:PDF},
  keywords  = {Rod Groups},
  owner     = {saulius},
  publisher = {International Union of Crystallography ({IUCr})},
  timestamp = {2018.10.04},
  creationdate = {2018-10-04T00:00:00},
}

@Article{Criekinge1999,
  author    = {Wim Criekinge and Rudi Beyaert},
  journal   = {Biological Procedures Online},
  title     = {Yeast two-hybrid: State of the art},
  year      = {1999},
  month     = {oct},
  number    = {1},
  pages     = {1--38},
  volume    = {2},
  doi       = {10.1251/bpo16},
  file      = {:by-author/C/Criekinge/1999_Criekinge_1.pdf:PDF},
  keywords  = {Yest Two-hybrid},
  owner     = {saulius},
  publisher = {Springer Nature},
  timestamp = {2018.10.03},
  creationdate = {2018-10-03T00:00:00},
}

@Article{Koonin2004,
  author    = {Eugene V Koonin and Natalie D Fedorova and John D Jackson and Aviva R Jacobs and Dmitri M Krylov and Kira S Makarova and Raja Mazumder and Sergei L Mekhedov and Anastasia N Nikolskaya and B Rao and Igor B Rogozin and Sergei Smirnov and Alexander V Sorokin and Alexander V Sverdlov and Sona Vasudevan and Yuri I Wolf and Jodie J Yin and Darren A Natale},
  journal   = {Genome Biology},
  title     = {A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes},
  year      = {2004},
  number    = {2},
  pages     = {R7},
  volume    = {5},
  doi       = {10.1186/gb-2004-5-2-r7},
  file      = {:by-author/K/Koonin/2004_Koonin_7.pdf:PDF},
  keywords  = {Evolution},
  owner     = {saulius},
  publisher = {Springer Nature},
  timestamp = {2018.10.03},
  creationdate = {2018-10-03T00:00:00},
}

@Article{OKeeffe2002,
  author    = {M. O'Keeffe and J. Pl{\'{e}}vert and T. Ogawa},
  journal   = {Acta Crystallographica Section A Foundations of Crystallography},
  title     = {Homogeneous cubic cylinder packings revisited},
  year      = {2002},
  month     = {feb},
  number    = {2},
  pages     = {125--132},
  volume    = {58},
  doi       = {10.1107/s0108767301019134},
  file      = {:by-author/O/O'Keeffe/2002_O'Keeffe_125.pdf:PDF},
  keywords  = {Rod Groups},
  owner     = {saulius},
  publisher = {International Union of Crystallography ({IUCr})},
  timestamp = {2018.10.04},
  creationdate = {2018-10-04T00:00:00},
}

@Manuscript{Krishna2001,
  author    = {P. Krishna and D. Pandey},
  title     = {Close-Packed Structures},
  year      = {2001},
  keywords  = {Closed Packed Structures},
  url       = {https://www.iucr.org/__data/assets/pdf_file/0015/13254/5.pdf},
  file      = {:by-author/K/Krishna/2001_Krishna.pdf:PDF},
  owner     = {saulius},
  timestamp = {2018.10.04},
  creationdate = {2018-10-04T00:00:00},
}

@Article{Atkins1973,
  author    = {E. D. T. Atkins and I. A. Nieduszynski and W. Mackie and K. D. Parker and E. E. Smolko},
  journal   = {Biopolymers},
  title     = {Structural components of alginic acid. {II}. The crystalline structure of poly-α-L-guluronic acid. Results of X-ray diffraction and polarized infrared studies},
  year      = {1973},
  month     = {aug},
  number    = {8},
  pages     = {1879--1887},
  volume    = {12},
  doi       = {10.1002/bip.1973.360120814},
  file      = {:by-author/A/Atkins/1973_Atkins_1879.pdf:PDF},
  keywords  = {Fiber Diffraction; Polysaccharide Structures},
  owner     = {saulius},
  publisher = {Wiley},
  timestamp = {2018.10.04},
  creationdate = {2018-10-04T00:00:00},
}

@Article{Kidwell2003,
  author    = {Mark E. Kidwell and Alexander Stoimenow},
  journal   = {Michigan Math. J.},
  title     = {Examples Relating to the Crossing Number, Writhe, and Maximal Bridge Length of Knot Diagrams},
  year      = {2003},
  pages     = {3--12},
  volume    = {51},
  comment   = {Cites "The Mystery of Knots""},
  file      = {:by-author/K/Kidwell/2003_Kidwell_3.pdf:PDF},
  keywords  = {Knot Theory},
  owner     = {saulius},
  timestamp = {2018.10.07},
  creationdate = {2018-10-07T00:00:00},
  url       = {https://projecteuclid.org/download/pdf_1/euclid.mmj/1049832889},
}

@Article{Edelsbrunner1994,
  author      = {Herbert Edelsbrunner and Ernst Mücke},
  title       = {Simulation of simplicity: a technique to cope with degenerate cases in geometric algorithms},
  abstract    = {This paper describes a general-purpose programming technique, called the Simulation of Simplicity, which can be used to cope with degenerate input data for geometric algorithms. It relieves the programmer from the task to provide a consistent treatment for every single special case that can occur. The programs that use the technique tend to be considerably smaller and more robust than those that do not use it. We believe that this technique will become a standard tool in writing geometric software.},
  date        = {1994-10-12},
  eprint      = {http://arxiv.org/abs/math/9410209v1},
  eprintclass = {math.CO},
  eprinttype  = {arXiv},
  file        = {:by-author/E/Edelsbrunner/1994_Edelsbrunner_.pdf:PDF},
  keywords    = {68Q; Algorithms; Computational Geometry; Computer Science (CS); Degenerate Cases; cs.CC; math.CO},
  owner       = {saulius},
  timestamp = {2018.10.14},
  creationdate = {2018-10-14T00:00:00},
  url         = {https://arxiv.org/abs/math/9410209},
}

@InProceedings{Yap1988,
  author    = {C. K. Yap},
  booktitle = {Proceedings of the fourth annual symposium on Computational geometry - {SCG} {\textquotesingle}88},
  title     = {A geometric consistency theorem for a symbolic perturbation scheme},
  year      = {1988},
  pages     = {134--142},
  publisher = {{ACM} Press},
  doi       = {10.1145/73393.73407},
  file      = {:by-author/Y/Yap/1988_Yap_134.pdf:PDF},
  keywords  = {Algorithms; Computational Geometry; Computer Science (CS); Degenerate Cases},
  owner     = {saulius},
  timestamp = {2018.10.16},
  creationdate = {2018-10-16T00:00:00},
}

@Article{Yap1990,
  author    = {Chee-Keng Yap},
  journal   = {Journal of Symbolic Computation},
  title     = {Symbolic treatment of geometric degeneracies},
  year      = {1990},
  number    = {3-4},
  pages     = {349--370},
  volume    = {10},
  doi       = {10.1016/s0747-7171(08)80069-7},
  file      = {:by-author/Y/Yap/1990_Yap_349.pdf:PDF},
  keywords  = {Algorithms; Computational Geometry; Computer Science (CS); Degenerate Cases},
  owner     = {saulius},
  publisher = {Elsevier {BV}},
  timestamp = {2018.10.16},
  creationdate = {2018-10-16T00:00:00},
}

@Article{Hull1985,
  author    = {T. E. Hull and A. Abrham and M. S. Cohen and A. F. X. and C. B. Hall and D. A. Penny and J. T. M.},
  journal   = {{ACM} {SIGNUM} Newsletter},
  title     = {Numerical Turing},
  year      = {1985},
  month     = {jul},
  number    = {3},
  pages     = {26--34},
  volume    = {20},
  doi       = {10.1145/1057947.1057949},
  file      = {:by-author/H/Hull/1985_Hull_26.pdf:PDF},
  keywords  = {Computer Science (CS); Programming Languages},
  owner     = {saulius},
  publisher = {Association for Computing Machinery ({ACM})},
  timestamp = {2018.10.16},
  creationdate = {2018-10-16T00:00:00},
}

@Article{Jones2018,
  author    = {Christopher G. Jones and Michael W. Martynowycz and Johan Hattne and Tyler J. Fulton and Brian M. Stoltz and Jose A. Rodriguez and Hosea M. Nelson and Tamir Gonen},
  journal   = {{ACS} Central Science},
  title     = {The {CryoEM} Method {MicroED} as a Powerful Tool for Small Molecule Structure Determination},
  year      = {2018},
  month     = {nov},
  doi       = {10.1021/acscentsci.8b00760},
  file      = {:by-author/J/Jones/2018_Jones.pdf:PDF;:by-author/J/Jones/2018_Jones_suppl/oc8b00760_si_002.pdf:PDF},
  owner     = {saulius},
  publisher = {American Chemical Society ({ACS})},
  timestamp = {2018.11.04},
  creationdate = {2018-11-04T00:00:00},
}

@Article{Cruz2017,
  author    = {M Jason de la Cruz and Johan Hattne and Dan Shi and Paul Seidler and Jose Rodriguez and Francis E Reyes and Michael R Sawaya and Duilio Cascio and Simon C Weiss and Sun Kyung Kim and Cynthia S Hinck and Andrew P Hinck and Guillermo Calero and David Eisenberg and Tamir Gonen},
  journal   = {Nature Methods},
  title     = {Atomic-resolution structures from fragmented protein crystals with the {cryoEM} method {MicroED}},
  year      = {2017},
  month     = {apr},
  number    = {4},
  pages     = {399--402},
  volume    = {14},
  doi       = {10.1038/nmeth.4178},
  file      = {:by-author/C/Cruz/2017_Cruz_399.pdf:PDF},
  owner     = {saulius},
  publisher = {Springer Nature},
  timestamp = {2018.11.04},
  creationdate = {2018-11-04T00:00:00},
}

@Article{Gruene2018,
  author    = {Tim Gruene and Julian T. C. Wennmacher and Christian Zaubitzer and Julian J. Holstein and Jonas Heidler and Ariane Fecteau-Lefebvre and Sacha De Carlo and Elisabeth Müller and Kenneth N. Goldie and Irene Regeni and Teng Li and Gustavo Santiso-Quinones and Gunther Steinfeld and Stefan Handschin and Eric van Genderen and Jeroen A. van Bokhoven and Guido H. Clever and Radosav Pantelic},
  journal   = {Angewandte Chemie International Edition},
  title     = {Rapid structure determination of microcrystalline molecular compounds using electron diffraction},
  year      = {2018},
  month     = {oct},
  doi       = {10.1002/anie.201811318},
  file      = {:by-author/G/Gruene/2018_Gruene.pdf:PDF},
  owner     = {saulius},
  publisher = {Wiley},
  timestamp = {2018.11.05},
  creationdate = {2018-11-05T00:00:00},
}

@Article{Westhoff2017,
  author    = {Daniel Westhoff and Julian Feinauer and Klaus Kuchler and Tim Mitsch and Ingo Manke and Simon Hein and Arnulf Latz and Volker Schmidt},
  journal   = {Computational Materials Science},
  title     = {Parametric stochastic 3D model for the microstructure of anodes in lithium-ion power cells},
  year      = {2017},
  month     = {jan},
  pages     = {453--467},
  volume    = {126},
  doi       = {10.1016/j.commatsci.2016.09.006},
  file      = {:by-author/W/Westhoff/2017_Westhoff_453.pdf:PDF},
  keywords  = {Material Science; Microstructure; Simulations; Structure-property Relations},
  owner     = {saulius},
  publisher = {Elsevier {BV}},
  timestamp = {2018.11.06},
  creationdate = {2018-11-06T00:00:00},
}

@Article{Ding2017,
  author    = {Wenxiu Ding and Zheng Yan and Robert H. Deng},
  journal   = {Information Sciences},
  title     = {Encrypted data processing with Homomorphic Re-Encryption},
  year      = {2017},
  month     = {oct},
  pages     = {35--55},
  volume    = {409-410},
  doi       = {10.1016/j.ins.2017.05.004},
  file      = {:by-author/D/Ding/2017_Ding_35.pdf:PDF},
  keywords  = {Computer Science (CS); Cryptography; Data Processing; Homomorphic Encryption},
  owner     = {saulius},
  publisher = {Elsevier {BV}},
  timestamp = {2018.11.06},
  creationdate = {2018-11-06T00:00:00},
}

@Article{Ogburn2013,
  author    = {Monique Ogburn and Claude Turner and Pushkar Dahal},
  journal   = {Procedia Computer Science},
  title     = {Homomorphic Encryption},
  year      = {2013},
  pages     = {502--509},
  volume    = {20},
  doi       = {10.1016/j.procs.2013.09.310},
  file      = {:by-author/O/Ogburn/2013_Ogburn_502.pdf:PDF},
  keywords  = {Computer Science (CS); Cryptography; Data Processing; Homomorphic Encryption},
  owner     = {saulius},
  publisher = {Elsevier {BV}},
  timestamp = {2018.11.06},
  creationdate = {2018-11-06T00:00:00},
}

@Article{Potey2016,
  author    = {Manish M. Potey and C.A. Dhote and Deepak H. Sharma},
  journal   = {Procedia Computer Science},
  title     = {Homomorphic Encryption for Security of Cloud Data},
  year      = {2016},
  pages     = {175--181},
  volume    = {79},
  doi       = {10.1016/j.procs.2016.03.023},
  file      = {:by-author/P/Potey/2016_Potey_175.pdf:PDF},
  keywords  = {Computer Science (CS); Cryptography; Data Processing; Homomorphic Encryption},
  owner     = {saulius},
  publisher = {Elsevier {BV}},
  timestamp = {2018.11.06},
  creationdate = {2018-11-06T00:00:00},
}

@Article{Gonzalez-Serrano2017,
  author    = {Francisco-Javier Gonz{\'{a}}lez-Serrano and {\'{A}}ngel Navia-V{\'{a}}zquez and Adri{\'{a}}n Amor-Mart{\'{\i}}n},
  journal   = {Pattern Recognition},
  title     = {Training Support Vector Machines with privacy-protected data},
  year      = {2017},
  month     = {dec},
  pages     = {93--107},
  volume    = {72},
  doi       = {10.1016/j.patcog.2017.06.016},
  file      = {:by-author/G/Gonzalez-Serrano/2017_Gonzalez-Serrano_93.pdf:PDF},
  keywords  = {Computer Science (CS); Cryptography; Data Processing; Homomorphic Encryption},
  owner     = {saulius},
  publisher = {Elsevier {BV}},
  timestamp = {2018.11.06},
  creationdate = {2018-11-06T00:00:00},
}

@InCollection{Kumar2018,
  author    = {Ashutosh Kumar and Muzzammil Hussain},
  booktitle = {Advances in Intelligent Systems and Computing},
  publisher = {Springer Singapore},
  title     = {Secure Query Processing Over Encrypted Database Through {CryptDB}},
  year      = {2018},
  pages     = {307--319},
  doi       = {10.1007/978-981-10-8633-5_31},
  owner     = {saulius},
  timestamp = {2018.11.06},
  creationdate = {2018-11-06T00:00:00},
}

@PhdThesis{Gentry2009,
  author    = {Craig Gentry},
  school    = {Stanford University},
  title     = {A Fully Homomorphic Encryption Scheme},
  year      = {2009},
  file      = {:by-author/G/Gentry/2009_Gentry.pdf:PDF},
  keywords  = {Computer Science (CS); Cryptography; Data Processing; Homomorphic Encryption},
  owner     = {saulius},
  timestamp = {2018.11.06},
  creationdate = {2018-11-06T00:00:00},
  url       = {https://crypto.stanford.edu/craig/craig-thesis.pdf},
}

@PhdThesis{Kaul2013,
  author    = {Akshar Kaul},
  school    = {Indian Institute of Science},
  title     = {Query Processing in Encrypted Cloud Databases},
  year      = {2013},
  file      = {:by-author/K/Kaul/2013_Kaul.pdf:PDF},
  owner     = {saulius},
  timestamp = {2018.11.06},
  creationdate = {2018-11-06T00:00:00},
  url       = {http://dsl.cds.iisc.ac.in/publications/thesis/akshar.pdf},
}

@Article{Popa2012,
  author    = {Raluca Ada Popa and Catherine M. S. Redfield and Nickolai Zeldovich and Hari Balakrishnan},
  journal   = {Communications of the {ACM}},
  title     = {{CryptDB}: Processing Queries on an Encrypted Database},
  year      = {2012},
  month     = {sep},
  number    = {9},
  pages     = {103},
  volume    = {55},
  doi       = {10.1145/2330667.2330691},
  keywords  = {Computer Science (CS); Cryptography; Data Processing; Homomorphic Encryption},
  owner     = {saulius},
  publisher = {Association for Computing Machinery ({ACM})},
  timestamp = {2018.11.06},
  creationdate = {2018-11-06T00:00:00},
}

@Article{Baker2016,
  author    = {Monya Baker},
  journal   = {Nature},
  title     = {1,500 scientists lift the lid on reproducibility},
  year      = {2016},
  month     = {may},
  number    = {7604},
  pages     = {452--454},
  volume    = {533},
  doi       = {10.1038/533452a},
  file      = {:by-author/B/Baker/2016_Baker_452.pdf:PDF},
  groups    = {sg/Non-reproducibility},
  keywords  = {Data Quality; Reproducible Research},
  owner     = {saulius},
  publisher = {Springer Nature},
  timestamp = {2018.11.07},
  creationdate = {2018-11-07T00:00:00},
}

@Article{Casteren2017,
  author    = {Dave T. E. H. van Casteren and Johannes J. H. Paulides and Elena A. Lomonova},
  journal   = {{IEEE} Transactions on Magnetics},
  title     = {Modeling the Field of a Coil Using the Magnetic Charge Method},
  year      = {2017},
  month     = {nov},
  number    = {11},
  pages     = {1--4},
  volume    = {53},
  doi       = {10.1109/tmag.2017.2714843},
  file      = {:by-author/C/Casteren/2017_Casteren_1.pdf:PDF},
  keywords  = {Magnetic Charge Method; Magnetic Field Computation},
  owner     = {saulius},
  publisher = {Institute of Electrical and Electronics Engineers ({IEEE})},
  timestamp = {2018.11.07},
  creationdate = {2018-11-07T00:00:00},
  url       = {https://ieeexplore.ieee.org/document/7946143},
}

@Article{Li2012,
  author    = {Jiangang Li and Qingchang Tan and Yongqi Zhang and Kuo Zhang},
  journal   = {Physics Procedia},
  title     = {Study on the Calculation of Magnetic Force Based on the Equivalent Magnetic Charge Method},
  year      = {2012},
  pages     = {190--197},
  volume    = {24},
  doi       = {10.1016/j.phpro.2012.02.029},
  file      = {:by-author/L/Li/2012_Li_190.pdf:PDF},
  keywords  = {Magnetic Charge Method; Magnetic Field Computation},
  owner     = {saulius},
  publisher = {Elsevier {BV}},
  timestamp = {2018.11.07},
  creationdate = {2018-11-07T00:00:00},
}

@Article{Lukin2018,
  author    = {Stipe Lukin and Martina Tireli and Ivor Lon{\v{c}}ari{\'{c}} and Dajana Bari{\v{s}}i{\'{c}} and Primo{\v{z}} {\v{S}}ket and Domagoj Vrsaljko and Marco di Michiel and Janez Plavec and Krunoslav U{\v{z}}arevi{\'{c}} and Ivan Halasz},
  journal   = {Chemical Communications},
  title     = {Mechanochemical carbon{\textendash}carbon bond formation that proceeds via a cocrystal intermediate},
  year      = {2018},
  doi       = {10.1039/c8cc07853j},
  file      = {:by-author/L/Lukin/2018_Lukin.pdf:PDF},
  keywords  = {Crystal Engineering; Mechanochemistry; Molecular Machines},
  owner     = {saulius},
  publisher = {Royal Society of Chemistry ({RSC})},
  timestamp = {2018.11.13},
  creationdate = {2018-11-13T00:00:00},
}

@Article{Chadha2011,
  author    = {Renu Chadha and Sushma Gupta and Geeta Shukla},
  journal   = {Acta Pharmaceutica Sinica B},
  title     = {Crystal habit, characterization and pharmacological activity of various crystal forms of arteether},
  year      = {2011},
  month     = {aug},
  number    = {2},
  pages     = {129--135},
  volume    = {1},
  doi       = {10.1016/j.apsb.2011.06.010},
  file      = {:by-author/C/Chadha/2011_Chadha_129.pdf:PDF},
  keywords  = {Pharmacology; Polymorphs},
  owner     = {saulius},
  publisher = {Elsevier {BV}},
  timestamp = {2018.11.13},
  creationdate = {2018-11-13T00:00:00},
}

@Article{Lee2014,
  author    = {Eun Hee Lee},
  journal   = {Asian Journal of Pharmaceutical Sciences},
  title     = {A practical guide to pharmaceutical polymorph screening {\&} selection},
  year      = {2014},
  month     = {aug},
  number    = {4},
  pages     = {163--175},
  volume    = {9},
  doi       = {10.1016/j.ajps.2014.05.002},
  file      = {:by-author/L/Lee/2014_Lee_163.pdf:PDF},
  keywords  = {Pharmacology; Polymorphs},
  owner     = {saulius},
  publisher = {Elsevier {BV}},
  timestamp = {2018.11.13},
  creationdate = {2018-11-13T00:00:00},
}

@Article{Lambert1967,
  author    = {Karel Lambert},
  journal   = {Notre Dame Journal of Formal Logic},
  title     = {Free Logic and the Concept of Existence},
  year      = {1967},
  month     = {April},
  number    = {1 \& 2},
  pages     = {133--144},
  volume    = {8},
  file      = {:by-author/L/Lambert/1967_Lambert_133.pdf:PDF},
  keywords  = {Free Logic; Logic; Mathematics},
  owner     = {saulius},
  timestamp = {2018.11.15},
  creationdate = {2018-11-15T00:00:00},
  url       = {https://projecteuclid.org/download/pdf_1/euclid.ndjfl/1093956251},
}

@Article{Marsden2009,
  author    = {David M. Marsden and Rebecca L. Nicholson and Mark Ladlow and David R. Spring},
  journal   = {Chemical Communications},
  title     = {3D small-molecule microarrays},
  year      = {2009},
  number    = {46},
  pages     = {7107},
  doi       = {10.1039/b913665g},
  file      = {:by-author/M/Marsden/2009_Marsden_7107.pdf:PDF;:by-author/M/Marsden/2009_Marsden_7107_supplement/b913665g.pdf:PDF},
  keywords  = {Protein Derivatisation},
  owner     = {saulius},
  publisher = {Royal Society of Chemistry ({RSC})},
  timestamp = {2018.11.22},
  creationdate = {2018-11-22T00:00:00},
}

@Article{Leonard2012,
  author    = {B. P. Leonard},
  journal   = {Metrologia},
  title     = {Why the dalton should be redefined exactly in terms of the kilogram},
  year      = {2012},
  number    = {4},
  pages     = {487},
  volume    = {49},
  abstract  = {With a redefined kilogram fixing the Planck constant, h , and a redefined mole fixing the Avogadro constant, N A , as recently proposed, retaining the carbon-12-based dalton creates a fundamental incompatibility in the stoichiometric equations. To avoid this incompatibility, the dalton should be redefined, as well: exactly in terms of the fixed- h kilogram. Specifically, with the mole defined asmol = N * / N A , where N * is an exact dimensionless constant, the dalton should be redefined as Da = (1/1000 N * ) kg, exactly, so that N A /mol −1 remains exactly equal to the gram-to-dalton mass-unit ratio—as required by the fundamental compatibility condition relating the kilogram, mole and dalton. This would necessarily decouple the dalton from the carbon-12 reference mass, m a ( 12 C)/12, used for cataloguing nuclidic mass ratios to extremely high precision. Relative atomic masses, defined as A r(X) = m a (X)/Da, would then have uncertainties dominated by that of m a ( 12 C)/kg; but since this would be of order 10 −9 or less, the values of relative atomic masses, to the precision used in stoichiometry, would be totally unaffected. This is a much more straightforward and easily comprehended strategy than those using confusing inexact correction factors or the equivalent, as recommended in recent publications and implicitly endorsed by the CGPM.},
  doi       = {10.1088/0026-1394/49/4/487},
  file      = {:by-author/L/Leonard/2012_Leonard_487.pdf:PDF},
  keywords  = {SI Units},
  owner     = {saulius},
  timestamp = {2018.11.17},
  creationdate = {2018-11-17T00:00:00},
  url       = {http://stacks.iop.org/0026-1394/49/i=4/a=487},
}

@Article{Becker2013,
  author    = {Peter Becker and Detlef Schiel},
  journal   = {International Journal of Mass Spectrometry},
  title     = {The Avogadro constant and a new definition of the kilogram},
  year      = {2013},
  month     = {sep},
  pages     = {219--226},
  volume    = {349-350},
  doi       = {10.1016/j.ijms.2013.03.015},
  file      = {:by-author/B/Becker/2013_Becker_219.pdf:PDF},
  keywords  = {SI Units},
  owner     = {saulius},
  publisher = {Elsevier {BV}},
  timestamp = {2018.11.17},
  creationdate = {2018-11-17T00:00:00},
}

@Article{Mills2006,
  author    = {Ian M. Mills and Peter J. Mohr and Terry J. Quinn and Barry N. Taylor and Edwin R. Williams},
  journal   = {Metrologia},
  title     = {Redefinition of the kilogram, ampere, kelvin and mole: a proposed approach to implementing {CIPM} recommendation 1 ({CI}-2005)},
  year      = {2006},
  month     = {apr},
  number    = {3},
  pages     = {227--246},
  volume    = {43},
  doi       = {10.1088/0026-1394/43/3/006},
  file      = {:by-author/M/Mills/2006_Mills_227.pdf:PDF},
  keywords  = {Kilogram; Mole; SI Units},
  owner     = {saulius},
  publisher = {{IOP} Publishing},
  timestamp = {2018.11.17},
  creationdate = {2018-11-17T00:00:00},
}

@Article{Leonard2010,
  author    = {B. P. Leonard},
  journal   = {Metrologia},
  title     = {Comments on recent proposals for redefining the mole and kilogram},
  year      = {2010},
  month     = {apr},
  number    = {3},
  pages     = {L5--L8},
  volume    = {47},
  doi       = {10.1088/0026-1394/47/3/l01},
  file      = {:by-author/L/Leonard/2010_Leonard_5.pdf:PDF},
  keywords  = {Kilogram; Mole; SI Units},
  owner     = {saulius},
  publisher = {{IOP} Publishing},
  timestamp = {2018.11.17},
  creationdate = {2018-11-17T00:00:00},
}

@Article{Milton2009,
  author    = {M. J. T. Milton and I. M. Mills},
  journal   = {Metrologia},
  title     = {Amount of substance and the proposed redefinition of the mole},
  year      = {2009},
  month     = {may},
  number    = {3},
  pages     = {332--338},
  volume    = {46},
  doi       = {10.1088/0026-1394/46/3/022},
  file      = {:by-author/M/Milton/2009_Milton_332.pdf:PDF},
  keywords  = {Kilogram; Mole; SI Units},
  owner     = {saulius},
  publisher = {{IOP} Publishing},
  timestamp = {2018.11.17},
  creationdate = {2018-11-17T00:00:00},
}

@Article{Taylor2009d,
  author    = {Barry N Taylor},
  journal   = {Metrologia},
  title     = {Molar mass and related quantities in the New {SI}},
  year      = {2009},
  month     = {feb},
  number    = {3},
  pages     = {L16--L19},
  volume    = {46},
  doi       = {10.1088/0026-1394/46/3/l01},
  file      = {:by-author/T/Taylor/2009_Taylor_16.pdf:PDF},
  keywords  = {Kilogram; Mole; SI Units},
  owner     = {saulius},
  publisher = {{IOP} Publishing},
  timestamp = {2018.11.17},
  creationdate = {2018-11-17T00:00:00},
}

@Article{Mohr2008,
  author    = {Peter J. Mohr and Barry N. Taylor and David B. Newell},
  journal   = {Reviews of Modern Physics},
  title     = {{CODATA} recommended values of the fundamental physical constants: 2006},
  year      = {2008},
  month     = {jun},
  number    = {2},
  pages     = {633--730},
  volume    = {80},
  doi       = {10.1103/revmodphys.80.633},
  file      = {:by-author/M/Mohr/2008_Mohr_633.pdf:PDF},
  keywords  = {Kilogram; Mole; SI Units},
  owner     = {saulius},
  publisher = {American Physical Society ({APS})},
  timestamp = {2018.11.17},
  creationdate = {2018-11-17T00:00:00},
}

@Presentation{Ruf2010,
  author    = {Michael Ruf and Richard J. Staples},
  title     = {Growing and Mounting Single Crystals Your Diffractometer Will Treasure},
  year      = {2010},
  file      = {:by-author/R/Ruf/2010_Ruf.pdf:PDF},
  keywords  = {Crystal Growth; Crystallisation; Small Molecule Crystallography; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2018.11.21},
  creationdate = {2018-11-21T00:00:00},
  url       = {https://www.bruker.com/fileadmin/user_upload/8-PDF-Docs/X-rayDiffraction_ElementalAnalysis/SC-XRD/Webinars/Bruker_AXS_Growing_Mounting_Single_Crystals_Webinar_201011026.pdf},
}

@Manuscript{Staples2017,
  author    = {Richard J. Staples},
  title     = {X-Ray Crystallography Laboratory Department of Chemistry Michigan State University},
  year      = {2017},
  keywords  = {Crystal Growth; Crystallisation; Small Molecule Crystallography; X-ray Crystallography},
  url       = {https://www2.chemistry.msu.edu/facilities/crystallography/xtalgrow.pdf},
  file      = {:by-author/S/Staples/2017_Staples.pdf:PDF},
  owner     = {saulius},
  timestamp = {2018.11.21},
  creationdate = {2018-11-21T00:00:00},
}

@Article{Greenspan1977,
  author    = {Lewis Greenspan},
  journal   = {Journal of Research of the National Bureau of Standards - A. Physics and Chemistry},
  title     = {Humidity Fixed Points of Binary Saturated Aqueous Solutions},
  year      = {1977},
  month     = {January-February},
  number    = {1},
  pages     = {89--97},
  volume    = {81A},
  file      = {:by-author/G/Greenspan/1977_Greenspan_89.pdf:PDF},
  keywords  = {Chemistry; Saturated Salt Solutions; Water Vapour Pressure},
  owner     = {saulius},
  timestamp = {2018.11.21},
  creationdate = {2018-11-21T00:00:00},
  url       = {https://nvlpubs.nist.gov/nistpubs/jres/81A/jresv81An1p89_A1b.pdf},
}

@Article{Hafiz2018,
  author    = {Hasnain Hafiz and Adnan Ibne Khair and Hongchul Choi and Abdullah Mueen and Arun Bansil and Stephan Eidenbenz and John Wills and Jian-Xin Zhu and Alexander V. Balatsky and Towfiq Ahmed},
  journal   = {npj Computational Materials},
  title     = {A high-throughput data analysis and materials discovery tool for strongly correlated materials},
  year      = {2018},
  month     = {nov},
  number    = {1},
  pages     = {1--9},
  volume    = {4},
  comment   = {citing COD; using COD},
  doi       = {10.1038/s41524-018-0120-9},
  file      = {:by-author/H/Hafiz/2018_Hafiz_1.pdf:PDF},
  keywords  = {COD; Computations},
  owner     = {saulius},
  publisher = {Springer Nature America, Inc},
  timestamp = {2018.11.28},
  creationdate = {2018-11-28T00:00:00},
}

@Article{Allen2012,
  author    = {Leslie J. Allen and Adrian J. D'Alfonso and Bert Freitag and Dmitri O. Klenov},
  journal   = {{MRS} Bulletin},
  title     = {Chemical mapping at atomic resolution using energy-dispersive x-ray spectroscopy},
  year      = {2012},
  month     = {jan},
  number    = {01},
  pages     = {47--52},
  volume    = {37},
  doi       = {10.1557/mrs.2011.331},
  file      = {:by-author/A/Allen/2012_Allen_47.pdf:PDF},
  keywords  = {EDXS; Electron Microscopy; X-ray Fluorescence; XRF},
  owner     = {saulius},
  publisher = {Cambridge University Press ({CUP})},
  timestamp = {2018.11.29},
  creationdate = {2018-11-29T00:00:00},
}

@InBook{Chipman1994,
  author    = {Russell A. Chipman},
  chapter   = {22},
  editor    = {Michael Bass},
  pages     = {22 .1--22 .37},
  publisher = {McGraw-Hill},
  title     = {Polarimetry},
  year      = {1994},
  booktitle = {Handbook of Optics: Fundamentals, techniques, and design, Volume 1},
  file      = {:by-author/C/Chipman/1994_Chipman_1.pdf:PDF},
  owner     = {saulius},
  timestamp = {2018.11.29},
  creationdate = {2018-11-29T00:00:00},
  url       = {http://photonics.intec.ugent.be/education/IVPV/res_handbook/v2ch22.pdf},
}

@Article{Chyba2010,
  author    = {B. Chyba and M. Mantler and H. Ebel and R. Svagera},
  journal   = {Advances in X-ray Analysis},
  title     = {Calculation Methods of X-ray Spectra: A Comparative Study},
  year      = {2010},
  pages     = {243--247},
  file      = {:by-author/C/Chyba/2010_Chyba_243.pdf:PDF},
  keywords  = {Bremsstrahlung Model; Ebel Model; X-ray Spectra},
  owner     = {saulius},
  timestamp = {2018.11.29},
  creationdate = {2018-11-29T00:00:00},
  url       = {http://icdd.com/resources/axa/VOL53/V53_27.pdf},
}

@Article{Ioannidis2005,
  author           = {John P. A. Ioannidis},
  journal          = {{PLoS} Medicine},
  title            = {Why most published research findings are false},
  year             = {2005},
  month            = {aug},
  number           = {8},
  pages            = {e124},
  volume           = {2},
  creationdate     = {2018-12-08T00:00:00},
  doi              = {10.1371/journal.pmed.0020124},
  file             = {:by-author/I/Ioannidis/2005_Ioannidis_124.pdf:PDF},
  keywords         = {P-values; Philosophy of Science; Reproducible Research},
  modificationdate = {2022-11-13T17:58:00},
  owner            = {saulius},
  publisher        = {Public Library of Science ({PLoS})},
  timestamp        = {2018.12.08},
}

@Manuscript{Dingledine2014,
  author    = {Dingledine, Roger and Hopper, Nicholas and Kadianakis, George and Mathewson, Nick},
  title     = {One Fast Guard for Life (or 9 months)},
  year      = {2014},
  keywords  = {Anonymity; Computer Science (CS); Privacy; Tor Network},
  url       = {https://www-users.cs.umn.edu/~hoppernj/single_guard.pdf},
  file      = {:by-author/D/Dingledine/2014_Dingledine.pdf:PDF},
  owner     = {saulius},
  timestamp = {2018.12.08},
  creationdate = {2018-12-08T00:00:00},
}

@PhdThesis{Merkys2018,
  author    = {Andrius Merkys},
  school    = {Vilnius University},
  title     = {Extraction and Usage of Crystallographic Knowledge for Refinement and Validation of Molecular Models},
  year      = {2018},
  file      = {:by-author/M/Merkys/2018_Merkys_phdthesis.pdf:PDF},
  owner     = {andrius},
  timestamp = {2020.06.12},
  creationdate = {2020-06-12T00:00:00},
}

@Presentation{Merkys2018a,
  author    = {Andrius Merkys},
  title     = {Debian packaging for {COD} and other {F/LOSS}},
  year      = {2018},
  file      = {:by-author/M/Merkys/2018_Merkys.pdf:PDF},
  owner     = {andrius},
  timestamp = {2018.12.06},
  creationdate = {2018-12-06T00:00:00},
  url       = {svn+ssh://saulius-grazulis.lt/home/andrius/svn-repositories/andrius/pristatymai/2018-COD-dpkg-meeting},
}

@Article{Young2008,
  author          = {Young, Neal S. and Ioannidis, John P. A. and Al-Ubaydli, Omar},
  journal         = {PLoS medicine},
  title           = {Why current publication practices may distort science.},
  year            = {2008},
  issn            = {1549-1676},
  month           = oct,
  pages           = {e201},
  volume          = {5},
  citation-subset = {IM},
  completed       = {2009-01-05},
  country         = {United States},
  creationdate    = {2018-12-08T00:00:00},
  doi             = {10.1371/journal.pmed.0050201},
  file            = {:by-author/Y/Young/2008_Young_201.pdf:PDF},
  issn-linking    = {1549-1277},
  issue           = {10},
  keywords        = {Biomedical Research; Publication Bias; Publishing; Science; Standards},
  nlm-id          = {101231360},
  owner           = {saulius},
  pii             = {08-PLME-ES-1446},
  pmc             = {PMC2561077},
  pmid            = {18844432},
  pubmodel        = {Print},
  pubstatus       = {ppublish},
  revised         = {2018-11-13},
  timestamp       = {2018.12.08},
}

@Article{Kavvoura2007,
  author          = {Kavvoura, Fotini K and Liberopoulos, George and Ioannidis, John P A},
  journal         = {PLoS medicine},
  title           = {Selection in reported epidemiological risks: an empirical assessment.},
  year            = {2007},
  issn            = {1549-1676},
  month           = mar,
  pages           = {e79},
  volume          = {4},
  abstract        = {Epidemiological studies may be subject to selective reporting, but empirical evidence thereof is limited. We empirically evaluated the extent of selection of significant results and large effect sizes in a large sample of recent articles. We evaluated 389 articles of epidemiological studies that reported, in their respective abstracts, at least one relative risk for a continuous risk factor in contrasts based on median, tertile, quartile, or quintile categorizations. We examined the proportion and correlates of reporting statistically significant and nonsignificant results in the abstract and whether the magnitude of the relative risks presented (coined to be consistently > or =1.00) differs depending on the type of contrast used for the risk factor. In 342 articles (87.9%), > or =1 statistically significant relative risk was reported in the abstract, while only 169 articles (43.4%) reported > or =1 statistically nonsignificant relative risk in the abstract. Reporting of statistically significant results was more common with structured abstracts, and was less common in US-based studies and in cancer outcomes. Among 50 randomly selected articles in which the full text was examined, a median of nine (interquartile range 5-16) statistically significant and six (interquartile range 3-16) statistically nonsignificant relative risks were presented (p = 0.25). Paradoxically, the smallest presented relative risks were based on the contrasts of extreme quintiles; on average, the relative risk magnitude was 1.41-, 1.42-, and 1.36-fold larger in contrasts of extreme quartiles, extreme tertiles, and above-versus-below median values, respectively (p < 0.001). Published epidemiological investigations almost universally highlight significant associations between risk factors and outcomes. For continuous risk factors, investigators selectively present contrasts between more extreme groups, when relative risks are inherently lower.},
  citation-subset = {IM},
  completed       = {2007-09-07},
  country         = {United States},
  doi             = {10.1371/journal.pmed.0040079},
  file            = {:by-author/K/Kavvoura/2007_Kavvoura_79.pdf:PDF},
  issn-linking    = {1549-1277},
  issue           = {3},
  keywords        = {Bias; Epidemiologic Methods; PubMed; Publication Bias; Risk; Risk Factors},
  nlm-id          = {101231360},
  owner           = {saulius},
  pii             = {06-PLME-RA-0642R3},
  pmc             = {PMC1808481},
  pmid            = {17341129},
  pubmodel        = {Print},
  pubstatus       = {ppublish},
  revised         = {2018-11-13},
  timestamp = {2018.12.08},
  creationdate = {2018-12-08T00:00:00},
}

@Article{PLSME2006,
  author          = {{The PLoS Medicine Editors}},
  journal         = {PLoS medicine},
  title           = {The impact factor game. It is time to find a better way to assess the scientific literature.},
  year            = {2006},
  issn            = {1549-1676},
  month           = jun,
  pages           = {e291},
  volume          = {3},
  citation-subset = {IM},
  completed       = {2006-12-22},
  country         = {United States},
  doi             = {10.1371/journal.pmed.0030291},
  file            = {:by-author/P/PLSME/2006_PLSME_291.pdf:PDF},
  issn-linking    = {1549-1277},
  issue           = {6},
  keywords        = {Bibliometrics; Biomedical Research; Editorial Policies; Humans; Information Dissemination; Peer Review; Periodicals as Topic; Research},
  nlm-id          = {101231360},
  owner           = {saulius},
  pii             = {06-PLME-ED-0380},
  pmc             = {PMC1475651},
  pmid            = {16749869},
  pubmodel        = {Print},
  pubstatus       = {ppublish},
  revised         = {2008-11-20},
  timestamp = {2018.12.08},
  creationdate = {2018-12-08T00:00:00},
}

@Article{Goodman2007,
  author          = {Goodman, Steven and Greenland, Sander},
  journal         = {PLoS medicine},
  title           = {Why most published research findings are false: problems in the analysis.},
  year            = {2007},
  issn            = {1549-1676},
  month           = apr,
  pages           = {e168},
  volume          = {4},
  citation-subset = {IM},
  completed       = {2007-07-19},
  country         = {United States},
  creationdate    = {2018-12-08T00:00:00},
  doi             = {10.1371/journal.pmed.0040168},
  file            = {:by-author/G/Goodman/2007_Goodman_168.pdf:PDF},
  issn-linking    = {1549-1277},
  issue           = {4},
  keywords        = {Deception; Humans; Periodicals as Topic; Publishing; Research Design; Standards; Statistics as Topic},
  nlm-id          = {101231360},
  owner           = {saulius},
  pii             = {07-PLME-C-0162},
  pmc             = {PMC1855693},
  pmid            = {17456002},
  pubmodel        = {Print},
  pubstatus       = {ppublish},
  revised         = {2018-11-13},
  timestamp       = {2018.12.08},
}

@Article{Ioannidis2007,
  author           = {Ioannidis, John P. A.},
  journal          = {{PLoS} medicine},
  title            = {Why most published research findings are false: author's reply to {G}oodman and {G}reenland.},
  year             = {2007},
  issn             = {1549-1676},
  month            = jun,
  pages            = {e215},
  volume           = {4},
  citation-subset  = {IM},
  completed        = {2007-12-10},
  country          = {United States},
  creationdate     = {2018-12-08T00:00:00},
  doi              = {10.1371/journal.pmed.0040215},
  file             = {:by-author/I/Ioannidis/2007_Ioannidis_215.pdf:PDF},
  issn-linking     = {1549-1277},
  issue            = {6},
  keywords         = {Humans; P-values; Periodicals as Topic; Publishing; Reproducibility of Results; Research Design; Standards},
  modificationdate = {2022-11-13T17:59:12},
  nlm-id           = {101231360},
  owner            = {saulius},
  pii              = {07-PLME-C-0434},
  pmc              = {PMC1896210},
  pmid             = {17593900},
  pubmodel         = {Print},
  pubstatus        = {ppublish},
  revised          = {2018-11-13},
  timestamp        = {2018.12.08},
}

@Article{Wren2005,
  author          = {Wren, Jonathan D},
  journal         = {PLoS medicine},
  title           = {Truth, probability, and frameworks.},
  year            = {2005},
  issn            = {1549-1676},
  month           = nov,
  pages           = {e361},
  volume          = {2},
  citation-subset = {IM},
  completed       = {2006-06-13},
  country         = {United States},
  doi             = {10.1371/journal.pmed.0020361},
  file            = {:by-author/W/Wren/2005_Wren_361.pdf:PDF},
  issn-linking    = {1549-1277},
  issue           = {11},
  keywords        = {Data Interpretation; Humans; Probability; Publishing; Reproducibility of Results; Research; Research Design; Statistical; Truth Disclosure},
  nlm-id          = {101231360},
  owner           = {saulius},
  pii             = {05-PLME-C-0423},
  pmc             = {PMC1297534},
  pmid            = {16288554},
  pubmodel        = {Print-Electronic},
  pubstatus       = {ppublish},
  revised         = {2018-11-13},
  timestamp = {2018.12.08},
  creationdate = {2018-12-08T00:00:00},
}

@Article{Ioannidis2005a,
  author           = {John P. A. Ioannidis},
  journal          = {{PLoS} Medicine},
  title            = {Author's reply},
  year             = {2005},
  month            = {nov},
  number           = {11},
  pages            = {e398},
  volume           = {2},
  creationdate     = {2018-12-08T00:00:00},
  doi              = {10.1371/journal.pmed.0020398},
  file             = {:by-author/I/Ioannidis/2005_Ioannidis_398.pdf:PDF},
  keywords         = {Criticism; P-values; Reproducible Research; Statistics},
  modificationdate = {2022-11-13T17:57:47},
  owner            = {saulius},
  publisher        = {Public Library of Science ({PLoS})},
  timestamp        = {2018.12.08},
}

@Article{Pauker2005,
  author          = {Pauker, Stephen G},
  journal         = {PLoS medicine},
  title           = {The clinical interpretation of research.},
  year            = {2005},
  issn            = {1549-1676},
  month           = nov,
  pages           = {e395},
  volume          = {2},
  citation-subset = {IM},
  completed       = {2006-06-13},
  country         = {United States},
  doi             = {10.1371/journal.pmed.0020395},
  file            = {:by-author/P/Pauker/2005_Pauker_395.pdf:PDF},
  issn-linking    = {1549-1277},
  issue           = {11},
  keywords        = {Bias; Data Interpretation; Odds Ratio; Periodicals as Topic; Probability; Reproducibility of Results; Research; Research Design; Statistical; Statistics & Numerical Data},
  nlm-id          = {101231360},
  owner           = {saulius},
  pii             = {05-PLME-C-0531},
  pmc             = {PMC1297552},
  pmid            = {16288562},
  pubmodel        = {Print-Electronic},
  pubstatus       = {ppublish},
  revised         = {2018-11-13},
  timestamp = {2018.12.08},
  creationdate = {2018-12-08T00:00:00},
}

@Article{Shrier2005,
  author          = {Shrier, Ian},
  journal         = {PLoS medicine},
  title           = {Power, reliability, and heterogeneous results.},
  year            = {2005},
  issn            = {1549-1676},
  month           = nov,
  pages           = {e386; author reply e398},
  volume          = {2},
  citation-subset = {IM},
  completed       = {2006-06-13},
  country         = {United States},
  doi             = {10.1371/journal.pmed.0020386},
  file            = {:by-author/S/Shrier/2005_Shrier_386.pdf:PDF},
  issn-linking    = {1549-1277},
  issue           = {11},
  keywords        = {Data Interpretation; Periodicals as Topic; Reproducibility of Results; Research Design; Sample Size; Statistical},
  nlm-id          = {101231360},
  owner           = {saulius},
  pii             = {05-PLME-C-0515},
  pmc             = {PMC1297547},
  pmid            = {16288559},
  pubmodel        = {Print-Electronic},
  pubstatus       = {ppublish},
  revised         = {2018-11-13},
  timestamp = {2018.12.08},
  creationdate = {2018-12-08T00:00:00},
}

@Article{PLSME2005,
  author          = {{The PLoS Medicine Editors}},
  journal         = {PLoS medicine},
  title           = {Minimizing mistakes and embracing uncertainty.},
  year            = {2005},
  issn            = {1549-1676},
  month           = aug,
  pages           = {e272},
  volume          = {2},
  citation-subset = {IM},
  completed       = {2006-08-18},
  country         = {United States},
  creationdate    = {2018-12-08T00:00:00},
  doi             = {10.1371/journal.pmed.0020272},
  file            = {:by-author/P/PLSME/2005_PLSME_272.pdf:PDF},
  issn-linking    = {1549-1277},
  issue           = {8},
  keywords        = {Data Interpretation; Humans; Peer Review; Publication Bias; Reproducibility of Results; Research; Research Design; Statistical; Uncertainty},
  nlm-id          = {101231360},
  owner           = {saulius},
  pii             = {05-PLME-ED-0336},
  pmc             = {PMC1196486},
  pmid            = {16120013},
  pubmodel        = {Print-Electronic},
  pubstatus       = {ppublish},
  revised         = {2012-11-15},
  timestamp       = {2018.12.08},
}

@Article{Goodman2007a,
  author           = {Steven Goodman and Sander Greenland},
  journal          = {Johns Hopkins University, Dept. of Biostatistics Working Papers},
  title            = {Assessing the unreliability of the medical literature: a response to "why most published research findings are false"},
  year             = {2007},
  creationdate     = {2018-12-08T00:00:00},
  file             = {:by-author/G/Goodman/2007_Goodman.pdf:PDF},
  keywords         = {P-values; Polemics; Reproducible Research},
  modificationdate = {2022-11-13T17:59:37},
  owner            = {saulius},
  timestamp        = {2018.12.08},
  url              = {https://biostats.bepress.com/jhubiostat/paper135/},
}

@Article{Morey2016,
  author    = {Richard D. Morey and Jan-Willem Romeijn and Jeffrey N. Rouder},
  journal   = {Journal of Mathematical Psychology},
  title     = {The philosophy of Bayes factors and the quantification of statistical evidence},
  year      = {2016},
  month     = {jun},
  pages     = {6--18},
  volume    = {72},
  doi       = {10.1016/j.jmp.2015.11.001},
  file      = {:by-author/M/Morey/2016_Morey_6.pdf:PDF},
  keywords  = {Bayesian Statistcs; Small World Hypothesis},
  owner     = {saulius},
  publisher = {Elsevier {BV}},
  timestamp = {2018.12.08},
  creationdate = {2018-12-08T00:00:00},
}

@Article{Maskell2008,
  author    = {Simon Maskell},
  journal   = {Information Fusion},
  title     = {A Bayesian approach to fusing uncertain, imprecise and conflicting information},
  year      = {2008},
  month     = {apr},
  number    = {2},
  pages     = {259--277},
  volume    = {9},
  doi       = {10.1016/j.inffus.2007.02.003},
  file      = {:by-author/M/Maskell/2008_Maskell_259.pdf:PDF},
  keywords  = {Bayesian Statistics; Small World Hypothesis},
  owner     = {saulius},
  publisher = {Elsevier {BV}},
  timestamp = {2018.12.08},
  creationdate = {2018-12-08T00:00:00},
}

@Article{Erbas-Cakmak2015,
  author          = {Erbas-Cakmak, Sundus and Leigh, David A and McTernan, Charlie T and Nussbaumer, Alina L},
  journal         = {Chemical reviews},
  title           = {Artificial Molecular Machines},
  year            = {2015},
  issn            = {1520-6890},
  month           = sep,
  pages           = {10081--10206},
  volume          = {115},
  chemicals       = {Rotaxanes},
  citation-subset = {IM},
  completed       = {2016-03-14},
  country         = {United States},
  creationdate    = {2018-12-13T00:00:00},
  doi             = {10.1021/acs.chemrev.5b00146},
  file            = {:by-author/E/Erbas-Cakmak/2015_Erbas-Cakmak_10081.pdf:PDF},
  issn-linking    = {0009-2665},
  issue           = {18},
  keywords        = {Chemistry; Instrumentation; Methods; Molecular Biology; Molecular Machines; Nanostructures; Review; Rotaxanes},
  nlm-id          = {2985134R},
  owner           = {saulius},
  pmc             = {PMC4585175},
  pmid            = {26346838},
  pubmodel        = {Print-Electronic},
  pubstatus       = {ppublish},
  revised         = {2018-11-13},
  timestamp       = {2018.12.13},
}

@InBook{Glickman2007,
  author    = {Mark E. Glickman and David A. van Dyk},
  chapter   = {16. Basic Bayesian Methods},
  editor    = {W. T. Ambrosius},
  pages     = {319--338},
  publisher = {Humana Press Inc., Totowa, NJ},
  title     = {Methods in Molecular Biology, vol. 404: Topics in Biostatistics},
  year      = {2007},
  isbn      = {978-1-58829-531-6},
  file      = {:by-author/G/Glickman/2007_Glickman_319.pdf:PDF},
  keywords  = {Bayesian Statistics; Examples; Mathematics; Statistics},
  owner     = {saulius},
  timestamp = {2018.12.14},
  creationdate = {2018-12-14T00:00:00},
  url       = {http://www.glicko.net/research/glickman-vandyk.pdf},
}

@Presentation{Leroy2011,
  author    = {Xavier Leroy},
  title     = {Verifying a compiler: Why? How? How far?},
  year      = {2011},
  file      = {:by-author/L/Leroy/2011_Leroy.pdf:PDF},
  keywords  = {Compiler Construction; Compiler Validation; Compiler Verification; Computer Science (CS); Formal Correctness Proofs; Program Verification},
  owner     = {saulius},
  timestamp = {2018.12.16},
  creationdate = {2018-12-16T00:00:00},
  url       = {http://www.cgo.org/cgo2011/Xavier_Leroy.pdf},
}

@Manuscript{Hoare1973,
  author    = {C. A. R. Hoare},
  title     = {Hints on Programming Language Design},
  year      = {1973},
  keywords  = {Compiler Design; Computer Science (CS); Review},
  url       = {https://people.eecs.berkeley.edu/~necula/cs263_sp14/handouts/hoarehints.pdf},
  file      = {:by-author/H/Hoare/1973_Hoare.pdf:PDF},
  owner     = {saulius},
  timestamp = {2018.12.16},
  creationdate = {2018-12-16T00:00:00},
}

@Article{Hoare2003,
  author    = {Tony Hoare},
  journal   = {Journal of the {ACM}},
  title     = {The verifying compiler: A grand challenge for computing research},
  year      = {2003},
  month     = {jan},
  number    = {1},
  pages     = {63--69},
  volume    = {50},
  comment   = {Contains references to historic papers.},
  doi       = {10.1145/602382.602403},
  file      = {:by-author/H/Hoare/2003_Hoare_63.pdf:PDF},
  keywords  = {Computer Science (CS); History; References; Verifying Compiler},
  owner     = {saulius},
  publisher = {Association for Computing Machinery ({ACM})},
  timestamp = {2018.12.16},
  creationdate = {2018-12-16T00:00:00},
  url       = {https://www.cs.dartmouth.edu/~mckeeman/cs48/mxcom/doc/p63-hoare.pdf},
}

@Article{Frost2016,
  author       = {Frost, Jamie M and Harriman, Katie L M and Murugesu, Muralee},
  journal      = {Chemical science},
  title        = {The rise of 3-d single-ion magnets in molecular magnetism: towards materials from molecules?},
  year         = {2016},
  issn         = {2041-6520},
  month        = apr,
  pages        = {2470--2491},
  volume       = {7},
  abstract     = {Single-molecule magnets (SMMs) that contain one spin centre (so-called single-ion magnets) theoretically represent the smallest possible unit for spin-based electronic devices. The realisation of this and related technologies, depends on first being able to design systems with sufficiently large energy barriers to magnetisation reversal,  , and secondly, on being able to organise these molecules into addressable arrays. In recent years, significant progress has been made towards the former goal - principally as a result of efforts which have been directed towards studying complexes based on highly anisotropic lanthanide ions, such as Tb(iii) and Dy(iii). Since 2013 however, and the remarkable report by Long and co-workers of a linear Fe(i) system exhibiting   = 325 K, single-ion systems of transition metals have undergone something of a renaissance in the literature. Not only do they have important lessons to teach us about anisotropy and relaxation dynamics in the quest to enhance  , the ability to create strongly coupled spin systems potentially offers access to a whole of host of 1, 2 and 3-dimensional materials with interesting structural and physical properties. This perspective summarises recent progress in this rapidly expanding sub-genre of molecular magnetism from the viewpoint of the synthetic chemist, with a particular focus on the lessons that have so far been learned from single-ion magnets of the d-block, and, the future research directions which we feel are likely to emerge in the coming years.},
  country      = {England},
  doi          = {10.1039/c5sc03224e},
  file         = {:by-author/F/Frost/2016_Frost_2470.pdf:PDF},
  issn-linking = {2041-6520},
  issue        = {4},
  nlm-id       = {101545951},
  owner        = {saulius},
  pii          = {c5sc03224e},
  pmc          = {PMC5477015},
  pmid         = {28660017},
  pubmodel     = {Print-Electronic},
  pubstatus    = {ppublish},
  revised      = {2018-11-13},
  timestamp = {2018.12.27},
  creationdate = {2018-12-27T00:00:00},
}

@Article{Kageyama2018,
  author       = {Kageyama, Hiroshi and Hayashi, Katsuro and Maeda, Kazuhiko and Attfield, J Paul and Hiroi, Zenji and Rondinelli, James M and Poeppelmeier, Kenneth R},
  journal      = {Nature communications},
  title        = {Expanding frontiers in materials chemistry and physics with multiple anions.},
  year         = {2018},
  issn         = {2041-1723},
  month        = feb,
  pages        = {772},
  volume       = {9},
  abstract     = {During the last century, inorganic oxide compounds laid foundations for materials synthesis, characterization, and technology translation by adding new functions into devices previously dominated by main-group element semiconductor compounds. Today, compounds with multiple anions beyond the single-oxide ion, such as oxyhalides and oxyhydrides, offer a new materials platform from which superior functionality may arise. Here we review the recent progress, status, and future prospects and challenges facing the development and deployment of mixed-anion compounds, focusing mainly on oxide-derived materials. We devote attention to the crucial roles that multiple anions play during synthesis, characterization, and in the physical properties of these materials. We discuss the opportunities enabled by recent advances in synthetic approaches for design of both local and overall structure, state-of-the-art characterization techniques to distinguish unique structural and chemical states, and chemical/physical properties emerging from the synergy of multiple anions for catalysis, energy conversion, and electronic materials.},
  completed    = {2018-03-19},
  country      = {England},
  doi          = {10.1038/s41467-018-02838-4},
  file         = {:by-author/K/Kageyama/2018_Kageyama_772.pdf:PDF},
  issn-linking = {2041-1723},
  issue        = {1},
  keywords     = {Coordination Numbers; Ionic Radii},
  nlm-id       = {101528555},
  owner        = {saulius},
  pii          = {10.1038/s41467-018-02838-4},
  pmc          = {PMC5823932},
  pmid         = {29472526},
  pubmodel     = {Electronic},
  pubstatus    = {epublish},
  revised      = {2018-12-07},
  timestamp = {2018.12.27},
  creationdate = {2018-12-27T00:00:00},
}

@Article{Czapinski2017,
  author       = {Czapiński, Jakub and Kiełbus, Michał and Kałafut, Joanna and Kos, Michał and Stepulak, Andrzej and Rivero-Müller, Adolfo},
  journal      = {Frontiers in chemistry},
  title        = {How to Train a Cell-Cutting-Edge Molecular Tools.},
  year         = {2017},
  issn         = {2296-2646},
  pages        = {12},
  volume       = {5},
  abstract     = {In biological systems, the formation of molecular complexes is the currency for all cellular processes. Traditionally, functional experimentation was targeted to single molecular players in order to understand its effects in a cell or animal phenotype. In the last few years, we have been experiencing rapid progress in the development of ground-breaking molecular biology tools that affect the metabolic, structural, morphological, and (epi)genetic instructions of cells by chemical, optical (optogenetic) and mechanical inputs. Such precise dissection of cellular processes is not only essential for a better understanding of biological systems, but will also allow us to better diagnose and fix common dysfunctions. Here, we present several of these emerging and innovative techniques by providing the reader with elegant examples on how these tools have been implemented in cells, and, in some cases, organisms, to unravel molecular processes in minute detail. We also discuss their advantages and disadvantages with particular focus on their translation to multicellular organisms for   spatiotemporal regulation. We envision that further developments of these tools will not only help solve the processes of life, but will give rise to novel clinical and industrial applications.},
  country      = {Switzerland},
  doi          = {10.3389/fchem.2017.00012},
  file         = {:by-author/C/Czapiński/2017_Czapiński_12.pdf:PDF},
  issn-linking = {2296-2646},
  keywords     = {Cell Communication; Controlling Behavior; Gene Editing; Gene Expression Regulation; Optogenetics; Protein Interactions; Signaling Pathways; Synthetic Biology},
  nlm-id       = {101627988},
  owner        = {saulius},
  pmc          = {PMC5344921},
  pmid         = {28344971},
  pubmodel     = {Electronic-eCollection},
  pubstatus    = {epublish},
  revised      = {2018-11-13},
  timestamp = {2018.12.27},
  creationdate = {2018-12-27T00:00:00},
}

@Article{Johansson2016,
  author       = {Johansson, J O and Kim, J-W and Allwright, E and Rogers, D M and Robertson, N and Bigot, J-Y},
  journal      = {Chemical science},
  title        = {Directly probing spin dynamics in a molecular magnet with femtosecond time-resolution.},
  year         = {2016},
  issn         = {2041-6520},
  month        = dec,
  pages        = {7061--7067},
  volume       = {7},
  abstract     = {We show that a vanadium-chromium Prussian blue analogue, which is a room-temperature molecule-based magnet, displays a fast magnetic response on a femtosecond timescale that is attributed to the super-exchange interaction between the metal ions. These dynamics are obtained from femtosecond Faraday magneto-optical (MO) measurements, performed at 50 and 300 K. Exciting at the ligand-to-metal charge-transfer (LMCT) band results in the formation of the  E excited state on the Cr ion   intersystem crossing (ISC) from the  LMCT state in less than 250 fs. Subsequent vibrational relaxation in the  E state occurs on a 0.78 ± 0.05 ps timescale at 50 K and 1.1 ± 0.1 ps at 300 K. The MO measurements can detect the formation of the  E state on the Cr ion from the change in the super-exchange interaction taking place as a result of the corresponding spin flip associated with the formation of the  E state. These results open up a new avenue to study molecular magnets using a powerful method that is capable of directly probing spin dynamics on a sub-picosecond timescale in thin film environments.},
  country      = {England},
  doi          = {10.1039/c6sc01105e},
  file         = {:by-author/J/Johansson/2016_Johansson_7061.pdf:PDF},
  issn-linking = {2041-6520},
  issue        = {12},
  keywords     = {Molecular Magnets; Optical Switches},
  nlm-id       = {101545951},
  owner        = {saulius},
  pii          = {c6sc01105e},
  pmc          = {PMC5355827},
  pmid         = {28451141},
  pubmodel     = {Print-Electronic},
  pubstatus    = {ppublish},
  revised      = {2018-11-13},
  timestamp = {2018.12.27},
  creationdate = {2018-12-27T00:00:00},
}

@Article{Miller2011,
  author       = {Miller, Joel S},
  journal      = {Chemical Society reviews},
  title        = {Magnetically ordered molecule-based materials.},
  year         = {2011},
  issn         = {1460-4744},
  month        = jun,
  pages        = {3266--3296},
  volume       = {40},
  abstract     = {Magnets composed of molecular components that provide both electron spins and spin-coupling pathways can stabilize bulk magnetic ordering. This was first reported for the ionic, zero-dimensional (0-D) electron transfer salt [Fe(C(5)Me(5))(2)](+)[TCNE]˙(-) (TCNE = tetracyanoethylene), which orders as a ferromagnet at T(c) = 4.8 K. Later V[TCNE](x) (x ∼ 2) was characterized to order above room temperature at 400 K (127 °C). Subsequently, numerous examples of organic- and molecule-based magnets have been characterized. In this critical review, after a discussion of the important aspects of magnetism pertaining to molecule-based magnets, including the determination of the magnetic ordering temperature (T(c)) these magnetically ordered materials are reviewed from a perspective of the structural dimensionality (208 references).},
  completed    = {2011-09-09},
  country      = {England},
  doi          = {10.1039/c0cs00166j},
  file         = {:by-author/M/Miller/2011_Miller_3266.pdf:PDF},
  issn-linking = {0306-0012},
  issue        = {6},
  keywords     = {Molecular Magnets; Optical Switches},
  nlm-id       = {0335405},
  owner        = {saulius},
  pmid         = {21479292},
  pubmodel     = {Print-Electronic},
  pubstatus    = {ppublish},
  revised      = {2011-05-24},
  timestamp = {2018.12.27},
  creationdate = {2018-12-27T00:00:00},
}

@Article{Christou2000,
  author    = {George Christou and Dante Gatteschi and David N. Hendrickson and Roberta Sessoli},
  journal   = {{MRS} Bulletin},
  title     = {Single-Molecule Magnets},
  year      = {2000},
  month     = {nov},
  number    = {11},
  pages     = {66--71},
  volume    = {25},
  doi       = {10.1557/mrs2000.226},
  file      = {:by-author/C/Christou/2000_Christou_66.pdf:PDF},
  keywords  = {Single Molecule Magnets},
  owner     = {saulius},
  publisher = {Cambridge University Press ({CUP})},
  timestamp = {2018.12.27},
  creationdate = {2018-12-27T00:00:00},
}

@Article{Liu2018,
  author       = {Liu, Zheng and Dong, Bo-Wei and Meng, Hai-Bing and Xu, Mei-Xing and Wang, Tai-Shan and Wang, Bing-Wu and Wang, Chun-Ru and Jiang, Shang-Da and Gao, Song},
  journal      = {Chemical science},
  title        = {Qubit crossover in the endohedral fullerene {Sc3C2@C80}},
  year         = {2018},
  issn         = {2041-6520},
  month        = jan,
  pages        = {457--462},
  volume       = {9},
  abstract     = {The core-shell structure of endohedral fullerenes results in good protection of the encapsulated spin carriers from the environment. In this research, the quantum coherence behavior of the endohedral fullerene Sc C @C  in CS  solution is characterized from 5 K to room temperature. Below the critical temperature of around 140 K, the inner group is hindered, and the EPR spectrum consists of a single broad line. The spin carriers display a maximum phase memory time of 17.2(7) μs at 10 K. In the high temperature region, the inner group is mobile, and the EPR spectrum consists of 22 homogeneously broadened lines due to isotropic hyperfine coupling. The maximum phase memory time for each transition is around 139(1) ns at 200 K which allows arbitrary superposition state manipulations to be performed. This research demonstrates that Sc C @C  displays temperature-crossover behaviour due to weak interaction between the Sc C  core and the C  shell.},
  country      = {England},
  doi          = {10.1039/c7sc03749j},
  file         = {:by-author/L/Liu/2018_Liu_457.pdf:PDF},
  issn-linking = {2041-6520},
  issue        = {2},
  keywords     = {Single Molecule Magnets},
  nlm-id       = {101545951},
  owner        = {saulius},
  pii          = {c7sc03749j},
  pmc          = {PMC6113862},
  pmid         = {30310560},
  pubmodel     = {Electronic-eCollection},
  pubstatus    = {epublish},
  revised      = {2018-11-14},
  timestamp = {2018.12.27},
  creationdate = {2018-12-27T00:00:00},
}

@Article{Rueckerl2017,
  author       = {Rückerl, Florian and Waas, Daniel and Büchner, Bernd and Knupfer, Martin and Zahn, Dietrich R T and Haidu, Francisc and Hahn, Torsten and Kortus, Jens},
  journal      = {Beilstein journal of nanotechnology},
  title        = {Charge transfer from and to manganese phthalocyanine: bulk materials and interfaces.},
  year         = {2017},
  issn         = {2190-4286},
  pages        = {1601--1615},
  volume       = {8},
  abstract     = {Manganese phthalocyanine (MnPc) is a member of the family of transition-metal phthalocyanines, which combines interesting electronic behavior in the fields of organic and molecular electronics with local magnetic moments. MnPc is characterized by hybrid states between the Mn 3d orbitals and the π orbitals of the ligand very close to the Fermi level. This causes particular physical properties, different from those of the other phthalocyanines, such as a rather small ionization potential, a small band gap and a large electron affinity. These can be exploited to prepare particular compounds and interfaces with appropriate partners, which are characterized by a charge transfer from or to MnPc. We summarize recent spectroscopic and theoretical results that have been achieved in this regard.},
  country      = {Germany},
  doi          = {10.3762/bjnano.8.160},
  file         = {:by-author/R/Rückerl/2017_Rückerl_1601.pdf:PDF},
  issn-linking = {2190-4286},
  keywords     = {Charge Transfer; Electronic Properties; Manganese Phthalocyanine},
  nlm-id       = {101551563},
  owner        = {saulius},
  pmc          = {PMC5550819},
  pmid         = {28884064},
  pubmodel     = {Electronic-eCollection},
  pubstatus    = {epublish},
  revised      = {2018-11-13},
  timestamp = {2018.12.27},
  creationdate = {2018-12-27T00:00:00},
}

@Article{Meng2018,
  author       = {Meng, Haibing and Zhao, Chong and Nie, Mingzhe and Wang, Chunru and Wang, Taishan},
  journal      = {ACS applied materials \& interfaces},
  title        = {Optically Controlled Molecular Metallofullerene Magnetism via an Azobenzene-Functionalized Metal-Organic Framework.},
  year         = {2018},
  issn         = {1944-8252},
  month        = sep,
  pages        = {32607--32612},
  volume       = {10},
  abstract     = {Molecular magnets with optically controlled property have significant applications in data storage and quantum information processing. Herein, we report the optically controlled molecular magnetism of endohedral metallofullerenes, Sc C @C  and DySc N@C , by incarcerating them into the pores of a photoswitchable azobenzene-functionalized metal-organic framework (MOF) ( MOF). After ultraviolet (365 nm) irradiation, the isomerization of azobenzene groups in the  MOF was found to be able to modulate the spin relaxation of Sc C @C  and also improve the single-molecule magnet behavior of DySc N@C . The photoisomerization of azobenzene side groups changes the host-guest interaction between metallofullerene and  MOF pores and endows them with the potential to modulate the magnetic properties with light. These findings offer an effective method to create smart molecular magnetic materials and also promote their applications in information recording, spintronics, and sensors.},
  completed    = {2018-09-28},
  country      = {United States},
  doi          = {10.1021/acsami.8b11098},
  file         = {:by-author/M/Meng/2018_Meng_32607.pdf:PDF},
  groups       = {sg/MOF},
  issn-linking = {1944-8244},
  issue        = {38},
  keywords     = {Azobenzene Group; Light Control; Magnetic Property; Metal-Organic Frameworks (MOF); Metallofullerene},
  nlm-id       = {101504991},
  owner        = {saulius},
  pmid         = {30176722},
  pubmodel     = {Print-Electronic},
  pubstatus    = {ppublish},
  revised      = {2018-10-01},
  timestamp = {2018.12.27},
  creationdate = {2018-12-27T00:00:00},
}

@Article{Smykalla2017,
  author       = {Smykalla, Lars and Mende, Carola and Fronk, Michael and Siles, Pablo F and Hietschold, Michael and Salvan, Georgeta and Zahn, Dietrich R T and Schmidt, Oliver G and Rüffer, Tobias and Lang, Heinrich},
  journal      = {Beilstein journal of nanotechnology},
  title        = {(Metallo)porphyrins for potential materials science applications.},
  year         = {2017},
  issn         = {2190-4286},
  pages        = {1786--1800},
  volume       = {8},
  abstract     = {The bottom-up approach to replace existing devices by molecular-based systems is a subject that attracts permanently increasing interest. Molecular-based devices offer not only to miniaturize the device further, but also to benefit from advanced functionalities of deposited molecules. Furthermore, the molecules itself can be tailored to allow via their self-assembly the potential fabrication of devices with an application potential, which is still unforeseeable at this time. Herein, we review efforts to use discrete (metallo)porphyrins for the formation of (sub)monolayers by surface-confined polymerization, of monolayers formed by supramolecular recognition and of thin films formed by sublimation techniques. Selected physical properties of these systems are reported as well. The application potential of those ensembles of (metallo)porphyrins in materials science is discussed.},
  country      = {Germany},
  doi          = {10.3762/bjnano.8.180},
  file         = {:by-author/S/Smykalla/2017_Smykalla_1786.pdf:PDF},
  issn-linking = {2190-4286},
  keywords     = {Atomic Force Microscopy; Magneto-optical Kerr Effect Spectroscopy; Scanning Tunnelling Microscopy and Spectroscopy; Self-assembly; Surface-confined 2D Polymerization; Transport Properties},
  nlm-id       = {101551563},
  owner        = {saulius},
  pmc          = {PMC5588670},
  pmid         = {28904840},
  pubmodel     = {Electronic-eCollection},
  pubstatus    = {epublish},
  revised      = {2018-11-13},
  timestamp = {2018.12.27},
  creationdate = {2018-12-27T00:00:00},
}

@Article{Nguyen2016,
  author       = {Nguyen, Tu N and Wernsdorfer, Wolfgang and Shiddiq, Muhandis and Abboud, Khalil A and Hill, Stephen and Christou, George},
  journal      = {Chemical science},
  title        = {Supramolecular aggregates of single-molecule magnets: exchange-biased quantum tunneling of magnetization in a rectangular [Mn, javax.xml.bind.JAXBElement@617bed58, ], javax.xml.bind.JAXBElement@396121f6, tetramer.},
  year         = {2016},
  issn         = {2041-6520},
  month        = feb,
  pages        = {1156--1173},
  volume       = {7},
  abstract     = {The syntheses and properties of four magnetically-supramolecular oligomers of triangular Mn  units are reported: dimeric [Mn O (O CMe) (CH OH) (pdpd) ] ( ) and [Mn O (O CMe) (py) (pdpd) ](ClO )  ( ), and tetrameric [Mn O (O CR) (pdpd) ](ClO )  (R = Me ( ),   Bu ( )). They were all obtained employing 3-phenyl-1,5-di(pyridin-2-yl)pentane-1,5-dione dioxime (pdpdH ), either in direct synthesis reactions involving oxidation of Mn  salts or in metathesis reactions with the preformed complex [Mn O(O CMe) (py) ](ClO ) ( ); complex   was then obtained by carboxylate substitution on complex  . Complexes   and   contain two [MnIII2Mn (μ -O)]  and [MnIII3(μ -O)]  units, respectively, linked by two pdpd  groups. Complexes   and   contain four [MnIII3(μ -O)]  units linked by six pdpd  groups into a rectangular tetramer [MnIII3] . Solid-state dc magnetic susceptibility studies showed that the Mn  subunits in   and   have a ground-state spin of   = 3/2 and   = 2, respectively, while the Mn  subunits in   and   possess an   = 6 ground state. Complexes   and   exhibit frequency-dependent out-of-phase ( '' ) ac susceptibility signals indicating   and   to be tetramers of Mn  single-molecule magnets (SMMs). High-frequency EPR studies of a microcrystalline powder sample of  ·2CH Cl  provided precise spin Hamiltonian parameters of   = -0.33 cm , | | = 0.03 cm ,  04 = -8.0 × 10  cm , and   = 2.0. Magnetization   dc field sweeps on a single crystal of  · CH Cl  gave hysteresis loops below 1 K that exhibit exchange-biased quantum tunneling of magnetization (QTM) steps with a bias field of 0.19 T. Simulation of the loops determined that each Mn  unit is exchange-coupled to the two neighbors linked to it by the pdpd  linkers, with an antiferromagnetic inter-Mn  exchange interaction of  /  = -0.011 K (  = -2  ·  convention). The work demonstrates a rational approach to synthesizing magnetically-supramolecular aggregates of SMMs as potential multi-qubit systems for quantum computing.},
  country      = {England},
  doi          = {10.1039/c5sc02599k},
  file         = {:by-author/N/Nguyen/2016_Nguyen_1156.pdf:PDF},
  issn-linking = {2041-6520},
  issue        = {2},
  keywords     = {Quantum Entanglment; Single Molecule Magnets},
  nlm-id       = {101545951},
  owner        = {saulius},
  pii          = {c5sc02599k},
  pmc          = {PMC5952871},
  pmid         = {29896376},
  pubmodel     = {Print-Electronic},
  pubstatus    = {ppublish},
  revised      = {2018-11-14},
  timestamp = {2018.12.27},
  creationdate = {2018-12-27T00:00:00},
}

@Article{Kwon2015,
  author          = {Kwon, Sunbum and Kim, Beom Jin and Lim, Hyung-Kyu and Kang, Kyungtae and Yoo, Sung Hyun and Gong, Jintaek and Yoon, Eunyoung and Lee, Juno and Choi, Insung S and Kim, Hyungjun and Lee, Hee-Seung},
  journal         = {Nature communications},
  title           = {Magnetotactic molecular architectures from self-assembly of β-peptide foldamers.},
  year            = {2015},
  issn            = {2041-1723},
  month           = oct,
  pages           = {8747},
  volume          = {6},
  abstract        = {The design of stimuli-responsive self-assembled molecular systems capable of undergoing mechanical work is one of the most important challenges in synthetic chemistry and materials science. Here we report that foldectures, that is, self-assembled molecular architectures of β-peptide foldamers, uniformly align with respect to an applied static magnetic field, and also show instantaneous orientational motion in a dynamic magnetic field. This response is explained by the amplified anisotropy of the diamagnetic susceptibilities as a result of the well-ordered molecular packing of the foldectures. In addition, the motions of foldectures at the microscale can be translated into magnetotactic behaviour at the macroscopic scale in a way reminiscent to that of magnetosomes in magnetotactic bacteria. This study will provide significant inspiration for designing the next generation of biocompatible peptide-based molecular machines with applications in biological systems.},
  chemicals       = {Peptides},
  citation-subset = {IM},
  completed       = {2016-05-17},
  country         = {England},
  doi             = {10.1038/ncomms9747},
  file            = {:by-author/K/Kwon/2015_Kwon_8747.pdf:PDF},
  issn-linking    = {2041-1723},
  keywords        = {Chemistry; Foldamers; Magnetic Fields; Magnetosomes; Magnetotactic; Metabolism; Peptides; Protein Conformation; Protein Folding},
  nlm-id          = {101528555},
  owner           = {saulius},
  pii             = {ncomms9747},
  pmc             = {PMC4640081},
  pmid            = {26510658},
  pubmodel        = {Electronic},
  pubstatus       = {epublish},
  revised         = {2018-11-13},
  timestamp = {2018.12.27},
  creationdate = {2018-12-27T00:00:00},
}

@Article{Bagheri2016,
  author       = {Bagheri, Ali and Arandiyan, Hamidreza and Boyer, Cyrille and Lim, May},
  journal      = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
  title        = {Lanthanide-Doped Upconversion Nanoparticles: Emerging Intelligent Light-Activated Drug Delivery Systems.},
  year         = {2016},
  issn         = {2198-3844},
  month        = jul,
  pages        = {1500437},
  volume       = {3},
  abstract     = {The development of drug delivery systems (DDSs) using near infrared (NIR) light and upconversion nanoparticles (UCNPs) has generated intensive interest over the past five years. These NIR-initiated DDSs not only offer a high degree of spatial and temporal determination of therapeutic release but also provide precise control over the released dosage. Furthermore, these nanoplatforms confer several advantages over conventional light-based DDSs-NIR offers better tissue penetration depth and a reduced risk of cellular photo-damage caused by exposure to light at high-energy wavelengths (e.g., ultraviolet light, <400 nm). The development of DDSs that can be activated by low intensity NIR illumination is highly desirable to avoid exposing living tissues to excessive heat that can limit the in vivo application of these DDSs. This encompasses research in three directions: (i) enhancing the quantum yield of the UCNPs; (ii) incorporation of photo-responsive materials with red-shifted absorptions into the UCNPs; and (iii) tuning the UCNPs excitation wavelength. This review focuses on recent advances in the development of NIR-initiated DDS, with emphasis on the use of photo-responsive compounds and polymeric materials conjugated onto UCNPs. The challenges that limit UCNPs clinical applications, alongside with the aforementioned techniques that have emerged to overcome these limitations, are highlighted.},
  country      = {Germany},
  doi          = {10.1002/advs.201500437},
  file         = {:by-author/B/Bagheri/2016_Bagheri_1500437.pdf:PDF},
  issn-linking = {2198-3844},
  issue        = {7},
  keywords     = {Controllable Drug Delivery; Near‐infrared; Photocleavage; Photoswitching; Upconversion Nanoparticles},
  nlm-id       = {101664569},
  owner        = {saulius},
  pii          = {ADVS120},
  pmc          = {PMC5069703},
  pmid         = {27818904},
  pubmodel     = {Electronic-eCollection},
  pubstatus    = {epublish},
  revised      = {2018-11-13},
  timestamp = {2018.12.27},
  creationdate = {2018-12-27T00:00:00},
}

@Article{Cavallo2016,
  author          = {Cavallo, Gabriella and Metrangolo, Pierangelo and Milani, Roberto and Pilati, Tullio and Priimagi, Arri and Resnati, Giuseppe and Terraneo, Giancarlo},
  journal         = {Chemical reviews},
  title           = {The Halogen Bond.},
  year            = {2016},
  issn            = {1520-6890},
  month           = feb,
  pages           = {2478--2601},
  volume          = {116},
  abstract        = {The halogen bond occurs when there is evidence of a net attractive interaction between an electrophilic region associated with a halogen atom in a molecular entity and a nucleophilic region in another, or the same, molecular entity. In this fairly extensive review, after a brief history of the interaction, we will provide the reader with a snapshot of where the research on the halogen bond is now, and, perhaps, where it is going. The specific advantages brought up by a design based on the use of the halogen bond will be demonstrated in quite different fields spanning from material sciences to biomolecular recognition and drug design.},
  chemicals       = {Halogens, Hydrocarbons, Halogenated},
  citation-subset = {IM},
  completed       = {2016-10-27},
  country         = {United States},
  creationdate    = {2018-12-27T00:00:00},
  doi             = {10.1021/acs.chemrev.5b00484},
  file            = {:by-author/C/Cavallo/2016_Cavallo_2478.pdf:PDF},
  issn-linking    = {0009-2665},
  issue           = {4},
  keywords        = {Chemistry; Halogenated; Halogens; Hydrocarbons; Molecular Structure},
  nlm-id          = {2985134R},
  owner           = {saulius},
  pmc             = {PMC4768247},
  pmid            = {26812185},
  pubmodel        = {Print-Electronic},
  pubstatus       = {ppublish},
  revised         = {2018-11-13},
  timestamp       = {2018.12.27},
}

@Article{Deavours1973,
  author    = {C. A. Deavours},
  journal   = {The American Mathematical Monthly},
  title     = {The Quaternion Calculus},
  year      = {1973},
  month     = {nov},
  number    = {9},
  pages     = {995},
  volume    = {80},
  doi       = {10.2307/2318774},
  file      = {:by-author/D/Deavours/1973_Deavours_995.pdf:PDF},
  keywords  = {Calculus; Mathmatical Analysis; Quaternions},
  owner     = {saulius},
  publisher = {{JSTOR}},
  timestamp = {2018.12.28},
  creationdate = {2018-12-28T00:00:00},
}

@Webpage{Wikipedia2014a,
  author    = {Wikipedia},
  retrieved = {2015-04-08},
  title     = {Atlas Autocode},
  url       = {http://en.wikipedia.org/wiki/Atlas_Autocode},
  year      = {2014},
  file      = {:by-author/W/Wikipedia/2014_Wikipedia_a.odt:OpenDocument text},
  keywords  = {Atlas-autocode},
  owner     = {saulius},
  timestamp = {2019.01.01},
  creationdate = {2019-01-01T00:00:00},
}

@Webpage{Schofield2015,
  author    = {P. D. Schofield and M. R. Osborne},
  retrieved = {2015-04-08},
  title     = {Programming in {Atlas} autocode},
  url       = {http://compsoc.nuigalway.ie/~bfoley/edhist/CU-Rep-1-AA/CU-Rep-1-AA.html},
  year      = {2015},
  file      = {:by-author/S/Schofield/2015_Schofield.odt:OpenDocument text},
  keywords  = {Atlas-autocode},
  owner     = {saulius},
  timestamp = {2019.01.01},
  creationdate = {2019-01-01T00:00:00},
}

@TechReport{Schofield1965,
  author      = {P. D. Schofield and M. R. Osborne},
  institution = {University of Edinburgh, Computer Unit},
  title       = {Programming in {Atlas} autocode},
  year        = {1965},
  month       = {June},
  file        = {:by-author/S/Schofield/1965_Schofield.pdf:PDF},
  keywords    = {Atlas-autocode},
  owner       = {saulius},
  timestamp = {2019.01.01},
  creationdate = {2019-01-01T00:00:00},
  url         = {http://history.dcs.ed.ac.uk/archive/docs/CU-Rep-1-AA.pdf},
}

@Webpage{Brooker2015,
  author    = {R. A. Brooker and J. S. Rohl},
  retrieved = {2015-04-08},
  title     = {{Atlas} autocode reference manual},
  url       = {http://history.dcs.ed.ac.uk/archive/docs/atlasautocode.html},
  year      = {2015},
  file      = {:by-author/B/Brooker/2015_Brooker.odt:OpenDocument text},
  keywords  = {Atlas-autocode},
  owner     = {saulius},
  timestamp = {2019.01.01},
  creationdate = {2019-01-01T00:00:00},
}

@Manuscript{Benet2014,
  author    = {Juan Benet},
  title     = {{IPFS} - content addressed, versioned, {P2P} file system (DRAFT 3)},
  year      = {2014},
  keywords  = {Computer Science (CS); Content Adressable File Systems; Distributed File Systems},
  url       = {https://github.com/ipfs/papers/raw/master/ipfs-cap2pfs/ipfs-p2p-file-system.pdf},
  file      = {:by-author/B/Benet/2014_Benet.pdf:PDF},
  owner     = {saulius},
  timestamp = {2019.01.10},
  creationdate = {2019-01-10T00:00:00},
}

@Article{Trefz2014,
  author    = {B. Trefz and J. Siebert and P. Virnau},
  journal   = {Proceedings of the National Academy of Sciences},
  title     = {How molecular knots can pass through each other},
  year      = {2014},
  month     = {may},
  number    = {22},
  pages     = {7948--7951},
  volume    = {111},
  doi       = {10.1073/pnas.1319376111},
  file      = {:by-author/T/Trefz/2014_Trefz_7948.pdf:PDF},
  keywords  = {Molecular Knots},
  owner     = {saulius},
  publisher = {Proceedings of the National Academy of Sciences},
  timestamp = {2019.02.04},
  creationdate = {2019-02-04T00:00:00},
}

@Article{Fielden2017,
  author    = {Stephen D. P. Fielden and David A. Leigh and Steffen L. Woltering},
  journal   = {Angewandte Chemie International Edition},
  title     = {Molecular Knots},
  year      = {2017},
  month     = {aug},
  number    = {37},
  pages     = {11166--11194},
  volume    = {56},
  doi       = {10.1002/anie.201702531},
  file      = {:by-author/F/Fielden/2017_Fielden_11166.pdf:PDF},
  keywords  = {Molecular Knots},
  owner     = {saulius},
  publisher = {Wiley},
  timestamp = {2019.02.04},
  creationdate = {2019-02-04T00:00:00},
}

@Article{Fielden2017a,
  author    = {Stephen D. P. Fielden and David A. Leigh and Steffen L. Woltering},
  journal   = {Angewandte Chemie},
  title     = {Molekulare Knoten},
  year      = {2017},
  month     = {aug},
  number    = {37},
  pages     = {11318--11347},
  volume    = {129},
  doi       = {10.1002/ange.201702531},
  file      = {:by-author/F/Fielden/2017_Fielden_11318.pdf:PDF},
  keywords  = {Molecular Knots},
  language  = {German},
  owner     = {saulius},
  publisher = {Wiley},
  timestamp = {2019.02.04},
  creationdate = {2019-02-04T00:00:00},
}

@Article{Edelsbrunner1983,
  author    = {H. Edelsbrunner and D. Kirkpatrick and R. Seidel},
  journal   = {{IEEE} Transactions on Information Theory},
  title     = {On the shape of a set of points in the plane},
  year      = {1983},
  month     = {jul},
  number    = {4},
  pages     = {551--559},
  volume    = {29},
  doi       = {10.1109/tit.1983.1056714},
  file      = {:by-author/E/Edelsbrunner/1983_Edelsbrunner_551.pdf:PDF},
  keywords  = {Topological Data Analysis; Topology},
  owner     = {saulius},
  publisher = {Institute of Electrical and Electronics Engineers ({IEEE})},
  timestamp = {2019.02.08},
  creationdate = {2019-02-08T00:00:00},
}

@InCollection{Grazulis2018,
  author    = {Saulius Gražulis and Andrius Merkys and Antanas Vaitkus},
  booktitle = {Handbook of Materials Modeling},
  publisher = {Springer International Publishing},
  title     = {Crystallography {O}pen {D}atabase ({COD})},
  year      = {2018},
  pages     = {1--19},
  doi       = {10.1007/978-3-319-42913-7_66-1},
  file      = {:by-author/G/Gražulis/2018_Gražulis_1.pdf:PDF},
  keywords  = {COD; Handbooks},
  owner     = {saulius},
  timestamp = {2019.02.10},
  creationdate = {2019-02-10T00:00:00},
}

@InProceedings{Connolly1983a,
  author    = {Michael L. Connolly},
  title     = {Solvent-Accessible Surfaces of Proteins and Nucleic Acids},
  year      = {1983},
  number    = {4612},
  pages     = {709--713},
  publisher = {American Association for the Advancement of Science},
  volume    = {221},
  abstract  = {A method is presented for analytically calculating a smooth, three-dimensional contour about a molecule. The molecular surface envelope may be drawn on either color raster computer displays or real-time vector computer graphics systems. Molecular areas and volumes may be computed analytically from this surface representation. Unlike most previous computer graphics representations of molecules, which imitate wire models or space-filling plastic spheres, this surface shows only the atoms that are accessible to solvent. This analytical method extends the earlier dot surface numerical algorithm, which has been applied in enzymology, rational drug design, immunology, and understanding DNA base sequence recognition.},
  file      = {:by-author/C/Connolly/1983_Connolly_709.pdf:PDF},
  issn      = {00368075, 10959203},
  journal   = {Science},
  owner     = {saulius},
  timestamp = {2019.02.10},
  creationdate = {2019-02-10T00:00:00},
  url       = {http://www.jstor.org/stable/1691011},
}

@InCollection{Agostini2018,
  author    = {Federica Agostini and Basile F. E. Curchod and Rodolphe Vuilleumier and Ivano Tavernelli and E. K. U. Gross},
  booktitle = {Handbook of Materials Modeling},
  publisher = {Springer International Publishing},
  title     = {{TDDFT} and Quantum-Classical Dynamics: A Universal Tool Describing the Dynamics of Matter},
  year      = {2018},
  pages     = {1},
  doi       = {10.1007/978-3-319-42913-7_43-2},
  file      = {:by-author/A/Agostini/2018_Agostini_1.pdf:pdf},
  keywords  = {Density Functional Theory (DFT); Materials Modelling; Molecular Dynamics (MD)},
  owner     = {saulius},
  timestamp = {2019.02.10},
  creationdate = {2019-02-10T00:00:00},
}

@InCollection{Andrienko2018,
  author    = {Denis Andrienko},
  booktitle = {Handbook of Materials Modeling},
  publisher = {Springer International Publishing},
  title     = {Multiscale Concepts in Simulations of Organic Semiconductors},
  year      = {2018},
  pages     = {1},
  doi       = {10.1007/978-3-319-42913-7_39-1},
  file      = {:by-author/A/Andrienko/2018_Andrienko_1.pdf:pdf},
  keywords  = {Density Functional Theory (DFT); Materials Modelling; Molecular Dynamics (MD)},
  owner     = {saulius},
  timestamp = {2019.02.10},
  creationdate = {2019-02-10T00:00:00},
}

@InCollection{Bereau2018,
  author    = {Tristan Bereau},
  booktitle = {Handbook of Materials Modeling},
  publisher = {Springer International Publishing},
  title     = {Data-Driven Methods in Multiscale Modeling of Soft Matter},
  year      = {2018},
  pages     = {1},
  doi       = {10.1007/978-3-319-42913-7_40-1},
  file      = {:by-author/B/Bereau/2018_Bereau_1.pdf:pdf},
  keywords  = {Density Functional Theory (DFT); Materials Modelling; Molecular Dynamics (MD)},
  owner     = {saulius},
  timestamp = {2019.02.10},
  creationdate = {2019-02-10T00:00:00},
}

@InCollection{Blokhin2018,
  author    = {Evgeny Blokhin and Pierre Villars},
  booktitle = {Handbook of Materials Modeling},
  publisher = {Springer International Publishing},
  title     = {The {PAULING} {FILE} Project and Materials Platform for Data Science: From Big Data Toward Materials Genome},
  year      = {2018},
  pages     = {1},
  doi       = {10.1007/978-3-319-42913-7_62-1},
  file      = {:by-author/B/Blokhin/2018_Blokhin_1.pdf:pdf},
  keywords  = {Density Functional Theory (DFT); Materials Modelling; Molecular Dynamics (MD)},
  owner     = {saulius},
  timestamp = {2019.02.10},
  creationdate = {2019-02-10T00:00:00},
}

@InCollection{Bussi2018,
  author    = {Giovanni Bussi and Alessandro Laio and Pratyush Tiwary},
  booktitle = {Handbook of Materials Modeling},
  publisher = {Springer International Publishing},
  title     = {Metadynamics: A Unified Framework for Accelerating Rare Events and Sampling Thermodynamics and Kinetics},
  year      = {2018},
  pages     = {1},
  doi       = {10.1007/978-3-319-42913-7_49-1},
  file      = {:by-author/B/Bussi/2018_Bussi_1.pdf:pdf},
  keywords  = {Density Functional Theory (DFT); Materials Modelling; Molecular Dynamics (MD)},
  owner     = {saulius},
  timestamp = {2019.02.10},
  creationdate = {2019-02-10T00:00:00},
}

@InCollection{Ceriotti2018,
  author    = {Michele Ceriotti and Michael J. Willatt and G{\'{a}}bor Cs{\'{a}}nyi},
  booktitle = {Handbook of Materials Modeling},
  publisher = {Springer International Publishing},
  title     = {Machine Learning of Atomic-Scale Properties Based on Physical Principles},
  year      = {2018},
  pages     = {1},
  doi       = {10.1007/978-3-319-42913-7_68-1},
  file      = {:by-author/C/Ceriotti/2018_Ceriotti_1.pdf:pdf},
  keywords  = {Density Functional Theory (DFT); Materials Modelling; Molecular Dynamics (MD)},
  owner     = {saulius},
  timestamp = {2019.02.10},
  creationdate = {2019-02-10T00:00:00},
}

@InCollection{Chelikowsky2018,
  author    = {James R. Chelikowsky},
  booktitle = {Handbook of Materials Modeling},
  publisher = {Springer International Publishing},
  title     = {Extending the Scale with Real-Space Methods for the Electronic Structure Problem},
  year      = {2018},
  pages     = {1},
  doi       = {10.1007/978-3-319-42913-7_57-1},
  file      = {:by-author/C/Chelikowsky/2018_Chelikowsky_1.pdf:pdf},
  keywords  = {Density Functional Theory (DFT); Materials Modelling; Molecular Dynamics (MD)},
  owner     = {saulius},
  timestamp = {2019.02.10},
  creationdate = {2019-02-10T00:00:00},
}

@InCollection{Daoulas2018,
  author    = {Kostas Ch. Daoulas},
  booktitle = {Handbook of Materials Modeling},
  publisher = {Springer International Publishing},
  title     = {Top-Down Hybrid Models of Polymers},
  year      = {2018},
  pages     = {1},
  doi       = {10.1007/978-3-319-42913-7_37-1},
  file      = {:by-author/D/Daoulas/2018_Daoulas_1.pdf:pdf},
  keywords  = {Density Functional Theory (DFT); Materials Modelling; Molecular Dynamics (MD)},
  owner     = {saulius},
  timestamp = {2019.02.10},
  creationdate = {2019-02-10T00:00:00},
}

@InCollection{Duenweg2018,
  author    = {Burkhard Dünweg},
  booktitle = {Handbook of Materials Modeling},
  publisher = {Springer International Publishing},
  title     = {Polymer Solutions},
  year      = {2018},
  pages     = {1--19},
  doi       = {10.1007/978-3-319-42913-7_38-1},
  file      = {:by-author/D/Dünweg/2018_Dünweg_1.pdf:pdf},
  keywords  = {Density Functional Theory (DFT); Materials Modelling; Molecular Dynamics (MD)},
  owner     = {saulius},
  timestamp = {2019.02.10},
  creationdate = {2019-02-10T00:00:00},
}

@InCollection{Eckstein2018,
  author    = {Martin Eckstein},
  booktitle = {Handbook of Materials Modeling},
  publisher = {Springer International Publishing},
  title     = {Non-equilibrium Dynamical Mean-Field Theory},
  year      = {2018},
  pages     = {1},
  doi       = {10.1007/978-3-319-42913-7_1-1},
  file      = {:by-author/E/Eckstein/2018_Eckstein_1.pdf:pdf},
  keywords  = {Density Functional Theory (DFT); Materials Modelling; Molecular Dynamics (MD)},
  owner     = {saulius},
  timestamp = {2019.02.10},
  creationdate = {2019-02-10T00:00:00},
}

@InCollection{Germann2018,
  author    = {Timothy C. Germann},
  booktitle = {Handbook of Materials Modeling},
  publisher = {Springer International Publishing},
  title     = {Adaptive Physics Refinement at the Microstructure Scale},
  year      = {2018},
  pages     = {1},
  doi       = {10.1007/978-3-319-42913-7_83-1},
  file      = {:by-author/G/Germann/2018_Germann_1.pdf:pdf},
  keywords  = {Density Functional Theory (DFT); Materials Modelling; Molecular Dynamics (MD)},
  owner     = {saulius},
  timestamp = {2019.02.10},
  creationdate = {2019-02-10T00:00:00},
}

@InCollection{Gomez2018,
  author    = {Rafael G{\'{o}}mez-Bombarelli and Al{\'{a}}n Aspuru-Guzik},
  booktitle = {Handbook of Materials Modeling},
  publisher = {Springer International Publishing},
  title     = {Machine Learning and Big-Data in Computational Chemistry},
  year      = {2018},
  pages     = {1--24},
  doi       = {10.1007/978-3-319-42913-7_59-1},
  file      = {:by-author/G/Gomez-Bombarelli/2018_Gomez-Bombarelli_1.pdf:pdf},
  keywords  = {Density Functional Theory (DFT); Materials Modelling; Molecular Dynamics (MD)},
  owner     = {saulius},
  timestamp = {2019.02.10},
  creationdate = {2019-02-10T00:00:00},
}

@InCollection{Grueneis2018,
  author    = {Andreas Grüneis},
  booktitle = {Handbook of Materials Modeling},
  publisher = {Springer International Publishing},
  title     = {Coupled Cluster and Quantum Chemistry Schemes for Solids},
  year      = {2018},
  pages     = {1--16},
  doi       = {10.1007/978-3-319-42913-7_9-1},
  file      = {:by-author/G/Grüneis/2018_Grüneis_1.pdf:pdf},
  keywords  = {Density Functional Theory (DFT); Materials Modelling; Molecular Dynamics (MD)},
  owner     = {saulius},
  timestamp = {2019.02.10},
  creationdate = {2019-02-10T00:00:00},
}

@InCollection{Hellstroem2018,
  author    = {Matti Hellström and Jörg Behler},
  booktitle = {Handbook of Materials Modeling},
  publisher = {Springer International Publishing},
  title     = {Neural Network Potentials in Materials Modeling},
  year      = {2018},
  pages     = {1--20},
  doi       = {10.1007/978-3-319-42913-7_56-1},
  file      = {:by-author/H/Hellström/2018_Hellström_1.pdf:pdf},
  keywords  = {Density Functional Theory (DFT); Materials Modelling; Molecular Dynamics (MD)},
  owner     = {saulius},
  timestamp = {2019.02.10},
  creationdate = {2019-02-10T00:00:00},
}

@InCollection{Henkelman2018,
  author    = {Graeme Henkelman and Hannes J{\'{o}}nsson and Tony Leli{\`{e}}vre and Normand Mousseau and Arthur F. Voter},
  booktitle = {Handbook of Materials Modeling},
  publisher = {Springer International Publishing},
  title     = {Long-Timescale Simulations: Challenges, Pitfalls, Best Practices, for Development and Applications},
  year      = {2018},
  pages     = {1},
  doi       = {10.1007/978-3-319-42913-7_31-1},
  file      = {:by-author/H/Henkelman/2018_Henkelman_1.pdf:pdf},
  keywords  = {Density Functional Theory (DFT); Materials Modelling; Molecular Dynamics (MD)},
  owner     = {saulius},
  timestamp = {2019.02.10},
  creationdate = {2019-02-10T00:00:00},
}

@InCollection{Homer2018,
  author    = {Eric R. Homer and Ying Chen and Christopher A. Schuh},
  booktitle = {Handbook of Materials Modeling},
  publisher = {Springer International Publishing},
  title     = {Incorporating the Element of Stochasticity in Coarse-Grained Modeling of Materials Mechanics},
  year      = {2018},
  pages     = {1},
  doi       = {10.1007/978-3-319-42913-7_98-1},
  file      = {:by-author/H/Homer/2018_Homer_1.pdf:pdf},
  keywords  = {Density Functional Theory (DFT); Materials Modelling; Molecular Dynamics (MD)},
  owner     = {saulius},
  timestamp = {2019.02.10},
  creationdate = {2019-02-10T00:00:00},
}

@InCollection{Houcke2018,
  author    = {Kris Van Houcke and Igor S. Tupitsyn and Nikolay V. Prokof'ev},
  booktitle = {Handbook of Materials Modeling},
  publisher = {Springer International Publishing},
  title     = {Diagrammatic Monte Carlo and {GW} Approximation for Jellium and Hydrogen Chain},
  year      = {2018},
  pages     = {1},
  doi       = {10.1007/978-3-319-42913-7_3-1},
  file      = {:by-author/H/Houcke/2018_Houcke_1.pdf:pdf},
  keywords  = {Density Functional Theory (DFT); Materials Modelling; Molecular Dynamics (MD)},
  owner     = {saulius},
  timestamp = {2019.02.10},
  creationdate = {2019-02-10T00:00:00},
}

@InCollection{Hutter2018,
  author    = {Jürg Hutter and Jan Wilhelm and Vladimir V. Rybkin and Mauro Del Ben and Joost VandeVondele},
  booktitle = {Handbook of Materials Modeling},
  publisher = {Springer International Publishing},
  title     = {{MP}2- and {RPA}-Based Ab Initio Molecular Dynamics and Monte Carlo Sampling},
  year      = {2018},
  pages     = {1},
  doi       = {10.1007/978-3-319-42913-7_58-1},
  file      = {:by-author/H/Hutter/2018_Hutter_1.pdf:pdf},
  keywords  = {Density Functional Theory (DFT); Materials Modelling; Molecular Dynamics (MD)},
  owner     = {saulius},
  timestamp = {2019.02.10},
  creationdate = {2019-02-10T00:00:00},
}

@InCollection{Kalidindi2018,
  author    = {Surya R. Kalidindi and Akash Gupta and Evdokia Popova},
  booktitle = {Handbook of Materials Modeling},
  publisher = {Springer International Publishing},
  title     = {Computationally Efficient Crystal Plasticity Simulations Using Spectral Databases},
  year      = {2018},
  pages     = {1},
  doi       = {10.1007/978-3-319-42913-7_16-1},
  file      = {:by-author/K/Kalidindi/2018_Kalidindi_1.pdf:pdf},
  keywords  = {Density Functional Theory (DFT); Materials Modelling; Molecular Dynamics (MD)},
  owner     = {saulius},
  timestamp = {2019.02.10},
  creationdate = {2019-02-10T00:00:00},
}

@InCollection{Kremer2018,
  author    = {Kurt Kremer},
  booktitle = {Handbook of Materials Modeling},
  publisher = {Springer International Publishing},
  title     = {Soft Matter/Polymer Simulations and Bridging Scales: Overview},
  year      = {2018},
  pages     = {1},
  doi       = {10.1007/978-3-319-42913-7_93-1},
  file      = {:by-author/K/Kremer/2018_Kremer_1.pdf:pdf},
  keywords  = {Density Functional Theory (DFT); Materials Modelling; Molecular Dynamics (MD)},
  owner     = {saulius},
  timestamp = {2019.02.10},
  creationdate = {2019-02-10T00:00:00},
}

@InCollection{Lelievre2018,
  author    = {Tony Leli{\`{e}}vre},
  booktitle = {Handbook of Materials Modeling},
  publisher = {Springer International Publishing},
  title     = {Mathematical Foundations of Accelerated Molecular Dynamics Methods},
  year      = {2018},
  pages     = {1},
  doi       = {10.1007/978-3-319-42913-7_27-1},
  file      = {:by-author/L/Lelievre/2018_Lelievre_1.pdf:pdf},
  keywords  = {Density Functional Theory (DFT); Materials Modelling; Molecular Dynamics (MD)},
  owner     = {saulius},
  timestamp = {2019.02.10},
  creationdate = {2019-02-10T00:00:00},
}

@InCollection{Mazzola2018,
  author    = {Guglielmo Mazzola and Sandro Sorella},
  booktitle = {Handbook of Materials Modeling},
  publisher = {Springer International Publishing},
  title     = {Accelerated Molecular Dynamics for Ab Initio Electronic Simulations},
  year      = {2018},
  pages     = {1},
  doi       = {10.1007/978-3-319-42913-7_46-1},
  file      = {:by-author/M/Mazzola/2018_Mazzola_1.pdf:pdf},
  keywords  = {Density Functional Theory (DFT); Materials Modelling; Molecular Dynamics (MD)},
  owner     = {saulius},
  timestamp = {2019.02.10},
  creationdate = {2019-02-10T00:00:00},
}

@InCollection{McDowell2018,
  author    = {David L. McDowell},
  booktitle = {Handbook of Materials Modeling},
  publisher = {Springer International Publishing},
  title     = {Connecting Lower and Higher Scales in Crystal Plasticity Modeling},
  year      = {2018},
  pages     = {1},
  doi       = {10.1007/978-3-319-42913-7_17-1},
  file      = {:by-author/M/McDowell/2018_McDowell_1.pdf:pdf},
  keywords  = {Density Functional Theory (DFT); Materials Modelling; Molecular Dynamics (MD)},
  owner     = {saulius},
  timestamp = {2019.02.10},
  creationdate = {2019-02-10T00:00:00},
}

@InCollection{Paesani2018,
  author    = {Francesco Paesani},
  booktitle = {Handbook of Materials Modeling},
  publisher = {Springer International Publishing},
  title     = {Water: Many-Body Potential from First Principles (From the Gas to the Liquid Phase)},
  year      = {2018},
  pages     = {1},
  doi       = {10.1007/978-3-319-42913-7_55-1},
  file      = {:by-author/P/Paesani/2018_Paesani_1.pdf:pdf},
  keywords  = {Density Functional Theory (DFT); Materials Modelling; Molecular Dynamics (MD)},
  owner     = {saulius},
  timestamp = {2019.02.10},
  creationdate = {2019-02-10T00:00:00},
}

@InCollection{Pietrucci2018,
  author    = {Fabio Pietrucci},
  booktitle = {Handbook of Materials Modeling},
  publisher = {Springer International Publishing},
  title     = {Novel Enhanced Sampling Strategies for Transitions Between Ordered and Disordered Structures},
  year      = {2018},
  pages     = {1},
  doi       = {10.1007/978-3-319-42913-7_51-1},
  file      = {:by-author/P/Pietrucci/2018_Pietrucci_1.pdf:pdf},
  keywords  = {Density Functional Theory (DFT); Materials Modelling; Molecular Dynamics (MD)},
  owner     = {saulius},
  timestamp = {2019.02.10},
  creationdate = {2019-02-10T00:00:00},
}

@InCollection{Praprotnik2018,
  author    = {M. Praprotnik and R. Cortes-Huerto and R. Potestio and L. Delle Site},
  booktitle = {Handbook of Materials Modeling},
  publisher = {Springer International Publishing},
  title     = {Adaptive Resolution Molecular Dynamics Technique},
  year      = {2018},
  pages     = {1},
  doi       = {10.1007/978-3-319-42913-7_89-1},
  file      = {:by-author/P/Praprotnik/2018_Praprotnik_1.pdf:pdf},
  keywords  = {Density Functional Theory (DFT); Materials Modelling; Molecular Dynamics (MD)},
  owner     = {saulius},
  timestamp = {2019.02.10},
  creationdate = {2019-02-10T00:00:00},
}

@InCollection{Resta2018,
  author    = {Raffaele Resta},
  booktitle = {Handbook of Materials Modeling},
  publisher = {Springer International Publishing},
  title     = {Electrical Polarization and Orbital Magnetization: The Position Operator Tamed},
  year      = {2018},
  pages     = {1},
  doi       = {10.1007/978-3-319-42913-7_12-1},
  file      = {:by-author/R/Resta/2018_Resta_1.pdf:pdf},
  keywords  = {Density Functional Theory (DFT); Materials Modelling; Molecular Dynamics (MD)},
  owner     = {saulius},
  timestamp = {2019.02.10},
  creationdate = {2019-02-10T00:00:00},
}

@InCollection{Rubio2018,
  author    = {Angel Rubio},
  booktitle = {Handbook of Materials Modeling},
  publisher = {Springer International Publishing},
  title     = {Electronic Structure of Materials by Ab Initio Methods: Overview},
  year      = {2018},
  pages     = {1},
  doi       = {10.1007/978-3-319-42913-7_90-2},
  file      = {:by-author/R/Rubio/2018_Rubio_1.pdf:pdf},
  keywords  = {Density Functional Theory (DFT); Materials Modelling; Molecular Dynamics (MD)},
  owner     = {saulius},
  timestamp = {2019.02.10},
  creationdate = {2019-02-10T00:00:00},
}

@InCollection{Smiatek2018,
  author    = {Jens Smiatek and Christian Holm},
  booktitle = {Handbook of Materials Modeling},
  publisher = {Springer International Publishing},
  title     = {From the Atomistic to the Macromolecular Scale: Distinct Simulation Approaches for Polyelectrolyte Solutions},
  year      = {2018},
  pages     = {1},
  doi       = {10.1007/978-3-319-42913-7_33-1},
  file      = {:by-author/S/Smiatek/2018_Smiatek_1.pdf:pdf},
  keywords  = {Density Functional Theory (DFT); Materials Modelling; Molecular Dynamics (MD)},
  owner     = {saulius},
  timestamp = {2019.02.10},
  creationdate = {2019-02-10T00:00:00},
}

@InCollection{Toher2018,
  author    = {Cormac Toher and Corey Oses and David Hicks and Eric Gossett and Frisco Rose and Pinku Nath and Demet Usanmaz and Denise C. Ford and Eric Perim and Camilo E. Calderon and Jose J. Plata and Yoav Lederer and Michal Jahn{\'{a}}tek and Wahyu Setyawan and Shidong Wang and Junkai Xue and Kevin Rasch and Roman V. Chepulskii and Richard H. Taylor and Geena Gomez and Harvey Shi and Andrew R. Supka and Rabih Al Rahal Al Orabi and Priya Gopal and Frank T. Cerasoli and Laalitha Liyanage and Haihang Wang and Ilaria Siloi and Luis A. Agapito and Chandramouli Nyshadham and Gus L. W Hart and Jes{\'{u}}s Carrete and Fleur Legrain and Natalio Mingo and Eva Zurek and Olexandr Isayev and Alexander Tropsha and Stefano Sanvito and Robert M. Hanson and Ichiro Takeuchi and Michael J. Mehl and Aleksey N. Kolmogorov and Kesong Yang and Pino D'Amico and Arrigo Calzolari and Marcio Costa and Riccardo De Gennaro and Marco Buongiorno Nardelli and Marco Fornari and Ohad Levy and Stefano Curtarolo},
  booktitle = {Handbook of Materials Modeling},
  publisher = {Springer International Publishing},
  title     = {The {AFLOW} Fleet for Materials Discovery},
  year      = {2018},
  pages     = {1},
  doi       = {10.1007/978-3-319-42913-7_63-1},
  file      = {:by-author/T/Toher/2018_Toher_1.pdf:pdf},
  keywords  = {Density Functional Theory (DFT); Materials Modelling; Molecular Dynamics (MD)},
  owner     = {saulius},
  timestamp = {2019.02.10},
  creationdate = {2019-02-10T00:00:00},
}

@InCollection{Trochet2018,
  author    = {Mickaël Trochet and Normand Mousseau and Laurent Karim B{\'{e}}land and Graeme Henkelman},
  booktitle = {Handbook of Materials Modeling},
  publisher = {Springer International Publishing},
  title     = {Off-Lattice Kinetic Monte Carlo Methods},
  year      = {2018},
  pages     = {1},
  doi       = {10.1007/978-3-319-42913-7_29-1},
  file      = {:by-author/T/Trochet/2018_Trochet_1.pdf:pdf},
  keywords  = {Density Functional Theory (DFT); Materials Modelling; Molecular Dynamics (MD)},
  owner     = {saulius},
  timestamp = {2019.02.10},
  creationdate = {2019-02-10T00:00:00},
}

@InCollection{Uberuaga2018,
  author    = {Blas Pedro Uberuaga and Danny Perez},
  booktitle = {Handbook of Materials Modeling},
  publisher = {Springer International Publishing},
  title     = {Computational Methods for Long-Timescale Atomistic Simulations},
  year      = {2018},
  pages     = {1},
  doi       = {10.1007/978-3-319-42913-7_24-1},
  file      = {:by-author/U/Uberuaga/2018_Uberuaga_1.pdf:pdf},
  keywords  = {Density Functional Theory (DFT); Materials Modelling; Molecular Dynamics (MD)},
  owner     = {saulius},
  timestamp = {2019.02.10},
  creationdate = {2019-02-10T00:00:00},
}

@InCollection{Bihlmayer2018,
  author    = {Gustav Bihlmayer},
  booktitle = {Handbook of Materials Modeling},
  publisher = {Springer International Publishing},
  title     = {Density Functional Theory for Magnetism and Magnetic Anisotropy},
  year      = {2018},
  pages     = {1},
  doi       = {10.1007/978-3-319-42913-7_73-1},
  file      = {:by-author/B/Bihlmayer/2018_Bihlmayer_1.pdf:pdf},
  keywords  = {Density Functional Theory (DFT); Materials Modelling; Molecular Dynamics (MD)},
  owner     = {saulius},
  timestamp = {2019.02.10},
  creationdate = {2019-02-10T00:00:00},
}

@InCollection{Castro2018,
  author    = {Alberto Castro},
  booktitle = {Handbook of Materials Modeling},
  publisher = {Springer International Publishing},
  title     = {Optimal Control Theory for Electronic Structure Methods},
  year      = {2018},
  pages     = {1},
  doi       = {10.1007/978-3-319-42913-7_4-1},
  file      = {:by-author/C/Castro/2018_Castro_1.pdf:pdf},
  keywords  = {Density Functional Theory (DFT); Materials Modelling; Molecular Dynamics (MD)},
  owner     = {saulius},
  timestamp = {2019.02.10},
  creationdate = {2019-02-10T00:00:00},
}

@InCollection{Chen2018,
  author    = {Ying Chen},
  booktitle = {Handbook of Materials Modeling},
  publisher = {Springer International Publishing},
  title     = {Kinetic Monte Carlo Modeling of Martensitic Phase Transformation Dynamics},
  year      = {2018},
  pages     = {1},
  doi       = {10.1007/978-3-319-42913-7_100-1},
  file      = {:by-author/C/Chen/2018_Chen_1.pdf:pdf},
  keywords  = {Density Functional Theory (DFT); Materials Modelling; Molecular Dynamics (MD)},
  owner     = {saulius},
  timestamp = {2019.02.10},
  creationdate = {2019-02-10T00:00:00},
}

@InCollection{Cohen2018,
  author    = {Marvin L. Cohen},
  booktitle = {Handbook of Materials Modeling},
  publisher = {Springer International Publishing},
  title     = {Modeling Solids and Its Impact on Science and Technology},
  year      = {2018},
  pages     = {1},
  doi       = {10.1007/978-3-319-42913-7_88-1},
  file      = {:by-author/C/Cohen/2018_Cohen_1.pdf:pdf},
  keywords  = {Density Functional Theory (DFT); Materials Modelling; Molecular Dynamics (MD)},
  owner     = {saulius},
  timestamp = {2019.02.10},
  creationdate = {2019-02-10T00:00:00},
}

@InCollection{Ghosh2018,
  author    = {Somnath Ghosh},
  booktitle = {Handbook of Materials Modeling},
  publisher = {Springer International Publishing},
  title     = {Advances in Computational Mechanics to Address Challenges in Crystal Plasticity {FEM}},
  year      = {2018},
  pages     = {1},
  doi       = {10.1007/978-3-319-42913-7_14-1},
  file      = {:by-author/G/Ghosh/2018_Ghosh_1.pdf:pdf},
  keywords  = {Density Functional Theory (DFT); Materials Modelling; Molecular Dynamics (MD)},
  owner     = {saulius},
  timestamp = {2019.02.10},
  creationdate = {2019-02-10T00:00:00},
}

@InCollection{Hermann2018,
  author    = {Jan Hermann and Alexandre Tkatchenko},
  booktitle = {Handbook of Materials Modeling},
  publisher = {Springer International Publishing},
  title     = {van der Waals Interactions in Material Modelling},
  year      = {2018},
  pages     = {1},
  doi       = {10.1007/978-3-319-42913-7_6-1},
  file      = {:by-author/H/Hermann/2018_Hermann_1.pdf:pdf},
  keywords  = {Density Functional Theory (DFT); Materials Modelling; Molecular Dynamics (MD)},
  owner     = {saulius},
  timestamp = {2019.02.10},
  creationdate = {2019-02-10T00:00:00},
}

@InCollection{Huang2018,
  author    = {Bing Huang and Nadine O. Symonds and O. Anatole von Lilienfeld},
  booktitle = {Handbook of Materials Modeling},
  publisher = {Springer International Publishing},
  title     = {Quantum Machine Learning in Chemistry and Materials},
  year      = {2018},
  pages     = {1},
  doi       = {10.1007/978-3-319-42913-7_67-1},
  file      = {:by-author/H/Huang/2018_Huang_1.pdf:pdf},
  keywords  = {Density Functional Theory (DFT); Materials Modelling; Molecular Dynamics (MD)},
  owner     = {saulius},
  timestamp = {2019.02.10},
  creationdate = {2019-02-10T00:00:00},
}

@InCollection{Jain2018,
  author    = {Anubhav Jain and Joseph Montoya and Shyam Dwaraknath and Nils E. R. Zimmermann and John Dagdelen and Matthew Horton and Patrick Huck and Donny Winston and Shreyas Cholia and Shyue Ping Ong and Kristin Persson},
  booktitle = {Handbook of Materials Modeling},
  publisher = {Springer International Publishing},
  title     = {The Materials Project: Accelerating Materials Design Through Theory-Driven Data and Tools},
  year      = {2018},
  pages     = {1},
  doi       = {10.1007/978-3-319-42913-7_60-1},
  file      = {:by-author/J/Jain/2018_Jain_1.pdf:pdf},
  keywords  = {Density Functional Theory (DFT); Materials Modelling; Molecular Dynamics (MD)},
  owner     = {saulius},
  timestamp = {2019.02.10},
  creationdate = {2019-02-10T00:00:00},
}

@InCollection{Kim2018,
  author    = {Woo Kyun Kim and Ellad B. Tadmor},
  booktitle = {Handbook of Materials Modeling},
  publisher = {Springer International Publishing},
  title     = {Temporal Acceleration in Coupled Continuum-Atomistic Methods},
  year      = {2018},
  pages     = {1},
  doi       = {10.1007/978-3-319-42913-7_26-1},
  file      = {:by-author/K/Kim/2018_Kim_1.pdf:pdf},
  keywords  = {Density Functional Theory (DFT); Materials Modelling; Molecular Dynamics (MD)},
  owner     = {saulius},
  timestamp = {2019.02.10},
  creationdate = {2019-02-10T00:00:00},
}

@InCollection{Li2018,
  author    = {Li Li and Kieron Burke},
  booktitle = {Handbook of Materials Modeling},
  publisher = {Springer International Publishing},
  title     = {Recent Developments in Density Functional Approximations},
  year      = {2018},
  pages     = {1},
  doi       = {10.1007/978-3-319-42913-7_11-1},
  file      = {:by-author/L/Li/2018_Li_1.pdf:pdf},
  keywords  = {Density Functional Theory (DFT); Materials Modelling; Molecular Dynamics (MD)},
  owner     = {saulius},
  timestamp = {2019.02.10},
  creationdate = {2019-02-10T00:00:00},
}

@InCollection{Ma2018a,
  author    = {Pui-Wai Ma and S. L. Dudarev},
  booktitle = {Handbook of Materials Modeling},
  publisher = {Springer International Publishing},
  title     = {Atomistic Spin-Lattice Dynamics},
  year      = {2018},
  pages     = {1},
  doi       = {10.1007/978-3-319-42913-7_97-1},
  file      = {:by-author/M/Ma/2018_Ma_1.pdf:pdf},
  keywords  = {Density Functional Theory (DFT); Materials Modelling; Molecular Dynamics (MD)},
  owner     = {saulius},
  timestamp = {2019.02.10},
  creationdate = {2019-02-10T00:00:00},
}

@InCollection{Pizzi2018,
  author           = {Giovanni Pizzi},
  booktitle        = {Handbook of Materials Modeling},
  publisher        = {Springer International Publishing},
  title            = {Open-Science Platform for Computational Materials Science: {AiiDA} and the Materials Cloud},
  year             = {2018},
  pages            = {1},
  comment          = {Main page: https://www.materialscloud.org/.},
  creationdate     = {2019-02-10T00:00:00},
  doi              = {10.1007/978-3-319-42913-7_64-1},
  file             = {:by-author/P/Pizzi/2018_Pizzi_1.pdf:pdf},
  keywords         = {Density Functional Theory (DFT); Materials Modelling; Molecular Dynamics (MD)},
  modificationdate = {2022-12-10T17:13:48},
  owner            = {saulius},
  timestamp        = {2019.02.10},
}

@InCollection{Rizzo2018,
  author    = {Tommaso Rizzo},
  booktitle = {Handbook of Materials Modeling},
  publisher = {Springer International Publishing},
  title     = {Critical Phenomena in Glasses},
  year      = {2018},
  pages     = {1},
  doi       = {10.1007/978-3-319-42913-7_52-1},
  file      = {:by-author/R/Rizzo/2018_Rizzo_1.pdf:pdf},
  keywords  = {Density Functional Theory (DFT); Materials Modelling; Molecular Dynamics (MD)},
  owner     = {saulius},
  timestamp = {2019.02.10},
  creationdate = {2019-02-10T00:00:00},
}

@InCollection{Wagner2018,
  author    = {Lucas K. Wagner},
  booktitle = {Handbook of Materials Modeling},
  publisher = {Springer International Publishing},
  title     = {Correlations and Effective Interactions from First Principles Using Quantum Monte Carlo},
  year      = {2018},
  pages     = {1},
  doi       = {10.1007/978-3-319-42913-7_10-1},
  file      = {:by-author/W/Wagner/2018_Wagner_1.pdf:pdf},
  keywords  = {Density Functional Theory (DFT); Materials Modelling; Molecular Dynamics (MD)},
  owner     = {saulius},
  timestamp = {2019.02.10},
  creationdate = {2019-02-10T00:00:00},
}

@InCollection{Winkler2018,
  author    = {Roland G. Winkler and Gerhard Gompper},
  booktitle = {Handbook of Materials Modeling},
  publisher = {Springer International Publishing},
  title     = {Hydrodynamics in Motile Active Matter},
  year      = {2018},
  pages     = {1},
  doi       = {10.1007/978-3-319-42913-7_35-1},
  file      = {:by-author/W/Winkler/2018_Winkler_1.pdf:pdf},
  keywords  = {Density Functional Theory (DFT); Materials Modelling; Molecular Dynamics (MD)},
  owner     = {saulius},
  timestamp = {2019.02.10},
  creationdate = {2019-02-10T00:00:00},
}

@InCollection{Zamora2018,
  author    = {R. J. Zamora and D. Perez and E. Martinez and B. P. Uberuaga and A. F. Voter},
  booktitle = {Handbook of Materials Modeling},
  publisher = {Springer International Publishing},
  title     = {Accelerated Molecular Dynamics Methods in a Massively Parallel World},
  year      = {2018},
  pages     = {1},
  doi       = {10.1007/978-3-319-42913-7_25-1},
  file      = {:by-author/Z/Zamora/2018_Zamora_1.pdf:pdf},
  keywords  = {Density Functional Theory (DFT); Materials Modelling; Molecular Dynamics (MD)},
  owner     = {saulius},
  timestamp = {2019.02.10},
  creationdate = {2019-02-10T00:00:00},
}

@InCollection{Ghosh_2018,
  author    = {Somnath Ghosh and Michael A. Groeber},
  booktitle = {Handbook of Materials Modeling},
  publisher = {Springer International Publishing},
  title     = {Developing Virtual Microstructures and Statistically Equivalent Representative Volume Elements for Polycrystalline Materials},
  year      = {2018},
  pages     = {1--26},
  doi       = {10.1007/978-3-319-42913-7_13-1},
  file      = {:by-author/G/Ghosh/2018_Ghosh_1a.pdf:PDF},
  keywords  = {Density Functional Theory (DFT); Materials Modelling; Molecular Dynamics (MD)},
  owner     = {saulius},
  timestamp = {2019.02.10},
  creationdate = {2019-02-10T00:00:00},
}

@InCollection{Wagner_2018,
  author    = {Lucas K. Wagner},
  booktitle = {Handbook of Materials Modeling},
  publisher = {Springer International Publishing},
  title     = {Quantum Monte Carlo for Electronic Systems Containing d and f Electrons},
  year      = {2018},
  pages     = {1--8},
  doi       = {10.1007/978-3-319-42913-7_95-1},
  file      = {:by-author/W/Wagner/2018_Wagner_1a.pdf:PDF},
  keywords  = {Density Functional Theory (DFT); Materials Modelling; Molecular Dynamics (MD)},
  owner     = {saulius},
  timestamp = {2019.02.10},
  creationdate = {2019-02-10T00:00:00},
}

@InCollection{Zhang_2018,
  author    = {Shiwei Zhang},
  booktitle = {Handbook of Materials Modeling},
  publisher = {Springer International Publishing},
  title     = {Ab Initio Electronic Structure Calculations by Auxiliary-Field Quantum Monte Carlo},
  year      = {2018},
  pages     = {1--27},
  doi       = {10.1007/978-3-319-42913-7_47-1},
  file      = {:by-author/Z/Zhang/2018_Zhang_1.pdf:PDF},
  keywords  = {Density Functional Theory (DFT); Materials Modelling; Molecular Dynamics (MD)},
  owner     = {saulius},
  timestamp = {2019.02.10},
  creationdate = {2019-02-10T00:00:00},
}

@Article{Dabrowski-Tumanski2017,
  author    = {Pawel Dabrowski-Tumanski and Joanna I. Sulkowska},
  journal   = {Proceedings of the National Academy of Sciences},
  title     = {Topological knots and links in proteins},
  year      = {2017},
  month     = {mar},
  number    = {13},
  pages     = {3415--3420},
  volume    = {114},
  doi       = {10.1073/pnas.1615862114},
  file      = {:by-author/D/Dabrowski-Tumanski/2017_Dabrowski-Tumanski_3415.pdf:PDF},
  keywords  = {Bioinformatics; Knots; Proteins},
  owner     = {saulius},
  publisher = {Proceedings of the National Academy of Sciences},
  timestamp = {2019.02.14},
  creationdate = {2019-02-14T00:00:00},
}

@Manuscript{Stevens2017,
  author    = {Marc Stevens and Elie Bursztein and Pierre Karpman and Ange Albertini and Yarik Markov},
  title     = {The first collision for full {SHA}-1},
  year      = {2017},
  keywords  = {Collision Attack; Collision Example; Computer Science (CS); Cryptanalysis; Differential Path; Hash Function; SHA1},
  url       = {https://shattered.it/static/shattered.pdf},
  file      = {:by-author/S/Stevens/2017_Stevens.pdf:PDF},
  owner     = {saulius},
  timestamp = {2019.02.13},
  creationdate = {2019-02-13T00:00:00},
}

@InProceedings{Andersona,
  author    = {D.P. Anderson},
  booktitle = {Fifth {IEEE}/{ACM} International Workshop on Grid Computing},
  title     = {{BOINC}: A System for Public-Resource Computing and Storage},
  year      = {2004},
  month     = {November},
  pages     = {4--10},
  publisher = {{IEEE}},
  doi       = {10.1109/grid.2004.14},
  file      = {:by-author/A/Anderson/2004_Anderson_4.pdf:PDF},
  keywords  = {BOINC; Grid Compuring; Parallel Computing; Volunteer Computing},
  owner     = {saulius},
  timestamp = {2019.02.14},
  creationdate = {2019-02-14T00:00:00},
}

@Manuscript{Anderson2004,
  author    = {David P. Anderson},
  title     = {{BOINC}: A System for Public-Resource Computing and Storage},
  year      = {2004},
  keywords  = {BOINC; Grid Compuring; Parallel Computing; Volunteer Computing},
  url       = {https://boinc.berkeley.edu/grid_paper_04.pdf},
  file      = {:by-author/A/Anderson/2004_Anderson.pdf:PDF},
  owner     = {saulius},
  timestamp = {2019.02.14},
  creationdate = {2019-02-14T00:00:00},
}

@TechReport{Winograd1971,
  author      = {Terry Winograd},
  institution = {Massachussets Institute of Technology},
  title       = {Procedures as a presentation for data in a computer program for understanding natural language},
  year        = {1971},
  file        = {:by-author/W/Winograd/1971_Winograd.pdf:PDF},
  keywords    = {Artificial Intelligence (AI); ETAOIN; SHRDLU},
  owner       = {saulius},
  timestamp = {2019.02.14},
  creationdate = {2019-02-14T00:00:00},
  url         = {http://hci.stanford.edu/~winograd/shrdlu/AITR-235.pdf},
}

@Article{Yu1979,
  author    = {Victor L. Yu},
  journal   = {{JAMA}},
  title     = {Antimicrobial Selection by a Computer},
  year      = {1979},
  month     = {sep},
  number    = {12},
  pages     = {1279},
  volume    = {242},
  doi       = {10.1001/jama.1979.03300120033020},
  file      = {:by-author/Y/Yu/1979_Yu_1279.pdf:PDF},
  keywords  = {Artificial Intelligence (AI); CA; MYCIN},
  owner     = {saulius},
  publisher = {American Medical Association ({AMA})},
  timestamp = {2019.02.14},
  creationdate = {2019-02-14T00:00:00},
}

@Article{Ruch1972,
  author    = {Ernst Ruch},
  journal   = {Accounts of Chemical Research},
  title     = {Algebraic aspects of the chirality phenomenon in chemistry},
  year      = {1972},
  month     = {feb},
  number    = {2},
  pages     = {49--56},
  volume    = {5},
  doi       = {10.1021/ar50050a002},
  file      = {:by-author/R/Ruch/1972_Ruch_49.pdf:PDF},
  keywords  = {Algebra; Chemistry; Chirality; Symmetry},
  owner     = {saulius},
  publisher = {American Chemical Society ({ACS})},
  timestamp = {2019.02.17},
  creationdate = {2019-02-17T00:00:00},
}

@Article{Ruch1968,
  author    = {Ernst Ruch},
  journal   = {Theoretica Chimica Acta},
  title     = {{H}omochiralität als {K}lassifizierungsprinzip von {M}olekülen spezieller {M}olekülklassen},
  year      = {1968},
  number    = {3},
  pages     = {183--192},
  volume    = {11},
  doi       = {10.1007/bf00528337},
  file      = {:by-author/R/Ruch/1968_Ruch_183.pdf:PDF},
  keywords  = {Algebra; Chemistry; Chirality; Symmetry},
  owner     = {saulius},
  publisher = {Springer Nature America, Inc},
  timestamp = {2019.02.17},
  creationdate = {2019-02-17T00:00:00},
}

@Article{Ruch1977,
  author    = {Ernst Ruch},
  journal   = {Angewandte Chemie International Edition},
  title     = {Chiral Derivatives of Achiral Molecules: Standard Classes and the Problem of a Right-Left Classification},
  year      = {1977},
  month     = {feb},
  number    = {2},
  pages     = {65--72},
  volume    = {16},
  doi       = {10.1002/anie.197700653},
  file      = {:by-author/R/Ruch/1977_Ruch_65.pdf:PDF},
  keywords  = {Algebra; Chemistry; Chirality; Symmetry},
  owner     = {saulius},
  publisher = {Wiley},
  timestamp = {2019.02.17},
  creationdate = {2019-02-17T00:00:00},
}

@Article{King2001,
  author    = {R. B. King},
  journal   = {Chirality},
  title     = {Nonhanded chirality in octahedral metal complexes},
  year      = {2001},
  number    = {8},
  pages     = {465--473},
  volume    = {13},
  doi       = {10.1002/chir.1063},
  file      = {:by-author/K/King/2001_King_465.pdf:PDF},
  keywords  = {Algebra; Chemistry; Chirality; Symmetry},
  owner     = {saulius},
  publisher = {Wiley},
  timestamp = {2019.02.17},
  creationdate = {2019-02-17T00:00:00},
}

@Article{King2003,
  author    = {R. Bruce King},
  journal   = {Annals of the New York Academy of Sciences},
  title     = {Chirality and handedness},
  year      = {2003},
  month     = {may},
  number    = {1},
  pages     = {158--170},
  volume    = {988},
  doi       = {10.1111/j.1749-6632.2003.tb06095.x},
  file      = {:by-author/K/King/2003_King_158.pdf:PDF},
  keywords  = {Algebra; Chemistry; Chirality; Symmetry},
  owner     = {saulius},
  publisher = {Wiley},
  timestamp = {2019.02.17},
  creationdate = {2019-02-17T00:00:00},
}

@Manuscript{Waterman2011,
  author    = {Waterman, Andrew and Lee, Yunsup and Patterson, David and Asanović, Krste},
  title     = {The {RISC-V} instruction set manual. {V}olume {I}: base user-level {ISA}. {V}ersion 1.0},
  year      = {2011},
  keywords  = {Computer Architecture; Computer Science (CS); RISC},
  url       = {https://inst.eecs.berkeley.edu/~cs250/fa11/handouts/riscv-spec.pdf},
  file      = {:by-author/W/Waterman/2011_Waterman.pdf:PDF},
  owner     = {saulius},
  timestamp = {2019.02.17},
  creationdate = {2019-02-17T00:00:00},
}

@Manuscript{Jhala2009,
  author    = {Ranjit Jhala and Rupak Majumdar},
  title     = {Software model checking},
  year      = {2009},
  keywords  = {CA; Correctness Proofs; Software Model Checking},
  url       = {https://people.mpi-sws.org/~rupak/Papers/SoftwareModelChecking.pdf},
  file      = {:by-author/J/Jhala/2009_Jhala.pdf:PDF},
  owner     = {saulius},
  timestamp = {2019.02.17},
  creationdate = {2019-02-17T00:00:00},
}

@Manuscript{Hart2008,
  author    = {Hart, Thomas E. and Ku, Kelvin and Gurfinkel, Arie and Chechik, Marsha and Lie, David},
  title     = {{PtYasm}: software model checking with proof templates},
  year      = {2008},
  keywords  = {Computer Science (CS); Software Correctness Proofs},
  url       = {https://security.csl.toronto.edu/papers/hart_ase08_tool.pdf},
  file      = {:by-author/H/Hart/2008_Hart.pdf:PDF},
  owner     = {saulius},
  timestamp = {2019.02.17},
  creationdate = {2019-02-17T00:00:00},
}

@TechReport{Wing1995,
  author      = {Wing, Jeannette M. and Vaziri-Farahani, Mandana},
  institution = {Carnegie-Mellon Univ. Pittsburgh PA School of Computer Science},
  title       = {Model checking software systems: a case study},
  year        = {1995},
  file        = {:by-author/W/Wing/1995_Wing.pdf:PDF},
  keywords    = {Coherence; Computer Program Verification; Computer Programs; Computer Science (CS); Distributed Data Processing; Models; Software Engineering},
  owner       = {saulius},
  timestamp = {2019.02.17},
  creationdate = {2019-02-17T00:00:00},
  url         = {https://apps.dtic.mil/dtic/tr/fulltext/u2/a294845.pdf},
}

@InCollection{Kauffman2000,
  author    = {Luis H. Kauffman},
  booktitle = {Geometry at work},
  publisher = {Mathematical association of {A}merica},
  title     = {Three-dimensional topology and quantum physics},
  year      = {2000},
  pages     = {162--173},
  comment   = {Found the book bibliography on the Internet (Amazon), but could not verify that it is the correct one.},
  file      = {:by-author/K/Kauffman/2000_Kauffman_162.pdf:PDF},
  isbn13    = {978-0883851647},
  keywords  = {Knot Theory; Quantum Theory; Topology},
  owner     = {saulius},
  timestamp = {2019.02.27},
  creationdate = {2019-02-27T00:00:00},
  url       = {http://homepages.math.uic.edu/~kauffman/ThreeDTopologyPhysics.pdf},
}

@Article{Kauffman_2002,
  author    = {Louis H Kauffman and Samuel J Lomonaco},
  journal   = {New Journal of Physics},
  title     = {Quantum entanglement and topological entanglement},
  year      = {2002},
  month     = {oct},
  pages     = {73--73},
  volume    = {4},
  doi       = {10.1088/1367-2630/4/1/373},
  file      = {:by-author/K/Kauffman/2002_Kauffman_73.pdf:PDF},
  keywords  = {Knot Theory; Quantum Theory; Topology},
  owner     = {saulius},
  publisher = {{IOP} Publishing},
  timestamp = {2019.02.27},
  creationdate = {2019-02-27T00:00:00},
  url       = {https://pdfs.semanticscholar.org/f6a4/52b380b68c944e8375df3996153e7f6c3e6c.pdf},
}

@Presentation{Sazdanovic2012,
  author    = {Radmila Sazdanovic},
  title     = {Knots and links: software and online resources},
  year      = {2012},
  file      = {:by-author/S/Sazdanovic/2012_Sazdanovic_.pdf:PDF},
  keywords  = {Computer Programs; Knot Theory; Topology},
  owner     = {saulius},
  timestamp = {2019.02.27},
  creationdate = {2019-02-27T00:00:00},
  url       = {http://online.itp.ucsb.edu/online/knots-m12/sazdanovic2/pdf/Sazdanovic2_Knots12_KITP.pdf},
}

@Article{Bruno2018,
  author          = {Bruno, Andrew E. and Charbonneau, Patrick and Newman, Janet and Snell, Edward H. and So, David R. and Vanhoucke, Vincent and Watkins, Christopher J. and Williams, Shawn and Wilson, Julie},
  journal         = {{PloS} one},
  title           = {Classification of crystallization outcomes using deep convolutional neural networks.},
  year            = {2018},
  issn            = {1932-6203},
  pages           = {e0198883},
  volume          = {13},
  abstract        = {The Machine Recognition of Crystallization Outcomes (MARCO) initiative has assembled roughly half a million annotated images of macromolecular crystallization experiments from various sources and setups. Here, state-of-the-art machine learning algorithms are trained and tested on different parts of this data set. We find that more than 94% of the test images can be correctly labeled, irrespective of their experimental origin. Because crystal recognition is key to high-density screening and the systematic analysis of crystallization experiments, this approach opens the door to both industrial and fundamental research applications.},
  citation-subset = {IM},
  completed       = {2018-12-27},
  country         = {United States},
  doi             = {10.1371/journal.pone.0198883},
  file            = {:by-author/B/Bruno/2018_Bruno_198883.pdf:PDF},
  issn-linking    = {1932-6203},
  issue           = {6},
  keywords        = {Algorithms; Computer-Assisted; Crystallization; Crystallography; Datasets as Topic; Image Processing; Neural Networks (Computer); X-Ray},
  nlm-id          = {101285081},
  owner           = {saulius},
  pii             = {PONE-D-18-09215},
  pmc             = {PMC6010233},
  pmid            = {29924841},
  pubmodel        = {Electronic-eCollection},
  pubstatus       = {epublish},
  revised         = {2018-12-27},
  timestamp = {2019.03.04},
  creationdate = {2019-03-04T00:00:00},
}

@Article{Mills2009,
  author    = {Stuart J. Mills and Fr{\'{e}}d{\'{e}}ric Hatert and Ernest H. Nickel and Giovanni Ferraris},
  journal   = {European Journal of Mineralogy},
  title     = {The standardisation of mineral group hierarchies: application to recent nomenclature proposals},
  year      = {2009},
  month     = {oct},
  number    = {5},
  pages     = {1073--1080},
  volume    = {21},
  doi       = {10.1127/0935-1221/2009/0021-1994},
  file      = {:by-author/M/Mills/2009_Mills_1073.pdf:PDF},
  keywords  = {Mineral Classification; Strunz Classification},
  owner     = {saulius},
  publisher = {Schweizerbart},
  timestamp = {2019.03.07},
  creationdate = {2019-03-07T00:00:00},
}

@Article{Frish1961,
  author    = {H. L. Frish and E. Wasserman},
  journal   = {Journal of the {A}merical {C}hemical {S}ociety},
  title     = {Chemical topology},
  year      = {1961},
  month     = {Sep},
  number    = {18},
  pages     = {3789--3795},
  volume    = {83},
  doi       = {10.1021/ja01479a015},
  file      = {:by-author/F/Frish/1961_Frish_3789.pdf:PDF},
  keywords  = {Chemical Topology; Chemistry; Mathematics; Topology},
  owner     = {saulius},
  timestamp = {2019.03.07},
  creationdate = {2019-03-07T00:00:00},
}

@Article{Sauvage2017,
  author    = {Jean-Pierre Sauvage},
  journal   = {Angewandte Chemie International Edition},
  title     = {From chemical topology to molecular machines ({N}obel lecture)},
  year      = {2017},
  month     = {jun},
  number    = {37},
  pages     = {11080--11093},
  volume    = {56},
  doi       = {10.1002/anie.201702992},
  file      = {:by-author/S/Sauvage/2017_Sauvage_11080.pdf:PDF},
  keywords  = {Catenanes; Chemical Topology; Chemistry; Mathematics; Molecular Machines; Rotaxanes; Topology},
  owner     = {saulius},
  publisher = {Wiley},
  timestamp = {2019.03.07},
  creationdate = {2019-03-07T00:00:00},
}

@TechReport{Price2016,
  author      = {Beth A. Price and Boris Pretzel and Suzanne Quillen Lomax and Charles Davis and Haddon Dine and Janice H. Carlson},
  institution = {IRUG},
  title       = {Revised {JCAMP-DX} spectral file format for submissions to the {I}nfrared \& {R}aman {U}sers {G}roup ({IRUG}) {S}pectral {D}atabase},
  year        = {2016},
  month       = {May},
  file        = {:by-author/P/Price/2016_Price.pdf:PDF},
  keywords    = {File Format; IR Spectroscopy; JCAMP DX; Raman Spectroscopy},
  owner       = {saulius},
  timestamp = {2019.03.07},
  creationdate = {2019-03-07T00:00:00},
  url         = {http://www.irug.org/uploads/documentation/revised-jcamp-dx-spectral-file-format-white-paper-2-may-2016-version_2.pdf},
}

@Article{Sankar2017,
  author    = {Kannan Sankar and Kejue Jia and Robert L. Jernigan},
  journal   = {Proceedings of the National Academy of Sciences},
  title     = {Knowledge-based entropies improve the identification of native protein structures},
  year      = {2017},
  month     = {mar},
  number    = {11},
  pages     = {2928--2933},
  volume    = {114},
  doi       = {10.1073/pnas.1613331114},
  file      = {:by-author/S/Sankar/2017_Sankar_2928.pdf:PDF},
  keywords  = {Entropy; Molecular Dynamics (MD)},
  owner     = {saulius},
  publisher = {Proceedings of the National Academy of Sciences},
  timestamp = {2019.03.08},
  creationdate = {2019-03-08T00:00:00},
}

@Presentation{Mueller2007,
  author    = {Peter Müller},
  title     = {Refinement of disorder with {SHELXL}},
  year      = {2007},
  school    = {MIT},
  file      = {:by-author/M/Müller/2007_Müller.pdf:PDF},
  keywords  = {Chemical Crystallography; Disorder; Refinement; Restrains; Small Molecule Crystallography},
  owner     = {saulius},
  timestamp = {2019.03.17},
  creationdate = {2019-03-17T00:00:00},
  url       = {https://web.mit.edu/pmueller/www/ACA2007/WK01/Disorder.pdf},
}

@Manuscript{Fischer2003,
  author    = {Kaspar Fischer and Bernd Gärtner and Martin Kutz},
  title     = {Fast smallest-enclosing-ball computation in high dimensions},
  year      = {2003},
  keywords  = {Algorithms; Computer Science (CS); Smallest Enclosing Balls},
  url       = {https://people.inf.ethz.ch/gaertner/subdir/texts/own_work/seb.pdf},
  file      = {:by-author/F/Fischer/2003_Fischer.pdf:PDF},
  owner     = {saulius},
  timestamp = {2019.03.25},
  creationdate = {2019-03-25T00:00:00},
}

@InCollection{Fischer2003a,
  author    = {Kaspar Fischer and Bernd Gärtner and Martin Kutz},
  booktitle = {Algorithms - {ESA} 2003},
  publisher = {Springer Berlin Heidelberg},
  title     = {Fast smallest-enclosing-ball computation in high dimensions},
  year      = {2003},
  pages     = {630--641},
  doi       = {10.1007/978-3-540-39658-1_57},
  file      = {:by-author/F/Fischer/2003_Fischer_630.pdf:PDF},
  keywords  = {Algorithms; Computer Science (CS); Smallest Enclosing Balls},
  owner     = {saulius},
  timestamp = {2019.03.25},
  creationdate = {2019-03-25T00:00:00},
}

@InProceedings{Larsson2008,
  author      = {Thomas Larsson},
  booktitle   = {SIGRAD 2008. The Annual SIGRAD Conference Special Theme: Interaction; November 27-28; 2008 Stockholm; Sweden},
  title       = {Fast and tight fitting bounding spheres},
  year        = {2008},
  number      = {34},
  pages       = {27--30},
  series      = {Linköping Electronic Conference Proceedings},
  file        = {:by-author/L/Larsson/2008_Larsson_27.pdf:PDF},
  issn        = {1650-3686},
  issn-online = {1650-3740},
  keywords    = {Algorithms; Computer Science (CS); Smallest Enclosing Balls},
  owner       = {saulius},
  timestamp = {2019.03.25},
  creationdate = {2019-03-25T00:00:00},
  url         = {https://www.ep.liu.se/ecp/article.asp?issue=034&article=9},
}

@Manuscript{Badoiu2002,
  author    = {Mihai Bādoiu and Sariel Har-Peled and Piotr Indyk},
  title     = {Approximate clustering via core-sets},
  year      = {2002},
  keywords  = {Algorithms; Computer Science (CS); Smallest Enclosing Balls},
  url       = {https://www2.cs.duke.edu/courses/spring07/cps296.2/papers/badoiu02approximate.pdf},
  file      = {:by-author/B/Badoiu/2002_Badoiu.pdf:PDF},
  owner     = {saulius},
  timestamp = {2019.03.25},
  creationdate = {2019-03-25T00:00:00},
}

@InProceedings{Badoiu2002a,
  author    = {Mihai Bādoiu and Sariel Har-Peled and Piotr Indyk},
  booktitle = {Proceedings of the thiry-fourth annual {ACM} symposium on Theory of computing - {STOC} {\textquotesingle}02},
  title     = {Approximate clustering via core-sets},
  year      = {2002},
  pages     = {250--257},
  publisher = {{ACM} Press},
  doi       = {10.1145/509907.509947},
  file      = {:by-author/B/Bādoiu/2002_Bādoiu_250.pdf:PDF},
  keywords  = {Algorithms; Computer Science (CS); Smallest Enclosing Balls},
  owner     = {saulius},
  timestamp = {2019.03.25},
  creationdate = {2019-03-25T00:00:00},
}

@Article{Ramachandran1963,
  author    = {G. N. Ramachandran and C. Ramakrishnan and V. Sasisekharan},
  journal   = {Journal of Molecular Biology},
  title     = {Stereochemistry of polypeptide chain configurations},
  year      = {1963},
  month     = {jul},
  number    = {1},
  pages     = {95--99},
  volume    = {7},
  doi       = {10.1016/s0022-2836(63)80023-6},
  file      = {:by-author/R/Ramachandran/1963_Ramachandran_95.pdf:PDF},
  keywords  = {Protein Backbone Conformation; Ramachandran Plot; Seminal Paper},
  owner     = {saulius},
  publisher = {Elsevier {BV}},
  timestamp = {2019.03.31},
  creationdate = {2019-03-31T00:00:00},
}

@Lecture{Erickson2008,
  author    = {Jeff Erickson},
  title     = {Convex hulls},
  year      = {2008},
  file      = {:by-author/E/Erickson/2008_Erickson.pdf:PDF},
  keywords  = {Computational Geometry; Computer Science (CS); Convex Hull},
  owner     = {saulius},
  timestamp = {2019.04.09},
  creationdate = {2019-04-09T00:00:00},
  url       = {http://jeffe.cs.illinois.edu/teaching/compgeom/notes/01-convexhull.pdf},
}

@Article{Stout2008,
  author    = {Michael Stout and Jaume Bacardit and Jonathan D. Hirst and Natalio Krasnogor},
  journal   = {Bioinformatics},
  title     = {Prediction of recursive convex hull class assignments for protein residues},
  year      = {2008},
  month     = {feb},
  number    = {7},
  pages     = {916--923},
  volume    = {24},
  doi       = {10.1093/bioinformatics/btn050},
  file      = {:by-author/S/Stout/2008_Stout_916.pdf:PDF},
  keywords  = {Bioinformatics; Computer Science (CS); Convex Hull},
  owner     = {saulius},
  publisher = {Oxford University Press ({OUP})},
  timestamp = {2019.04.09},
  creationdate = {2019-04-09T00:00:00},
}

@Article{Guilloux2009,
  author    = {Vincent Le Guilloux and Peter Schmidtke and Pierre Tuffery},
  journal   = {{BMC} Bioinformatics},
  title     = {Fpocket: An open source platform for ligand pocket detection},
  year      = {2009},
  number    = {1},
  pages     = {168},
  volume    = {10},
  doi       = {10.1186/1471-2105-10-168},
  file      = {:by-author/G/Guilloux/2009_Guilloux_168.pdf:PDF},
  keywords  = {Bioinformatics; Computer Science (CS); Convex Hull; Docking},
  owner     = {saulius},
  publisher = {Springer Nature},
  timestamp = {2019.04.09},
  creationdate = {2019-04-09T00:00:00},
}

@Presentation{Lee2006b,
  author    = {Hyunsook Lee},
  title     = {A Convex Hull Peeling Depth Approach to Nonparametric Massive Multivariate Data Analysis with Applications},
  year      = {2006},
  file      = {:by-author/L/Lee/2006_Lee_a.pdf:PDF},
  keywords  = {Computer Science (CS); Convex Hull; Convex Hull Peeling; Data Analysis},
  owner     = {saulius},
  timestamp = {2019.04.09},
  creationdate = {2019-04-09T00:00:00},
  url       = {https://hea-www.harvard.edu/astrostat/Stat310_fMMV/hsl_20060907.pdf},
}

@Article{Zhao2018,
  author    = {Rundong Zhao and Zixuan Cang and Yiying Tong and Guo-Wei Wei},
  journal   = {Bioinformatics},
  title     = {Protein pocket detection via convex hull surface evolution and associated Reeb graph},
  year      = {2018},
  month     = {sep},
  number    = {17},
  pages     = {i830--i837},
  volume    = {34},
  doi       = {10.1093/bioinformatics/bty598},
  file      = {:by-author/Z/Zhao/2018_Zhao_830.pdf:PDF},
  keywords  = {Bioinformatics; Computer Science (CS); Convex Hull; Homology; Topology},
  owner     = {saulius},
  publisher = {Oxford University Press ({OUP})},
  timestamp = {2019.04.09},
  creationdate = {2019-04-09T00:00:00},
}

@Manuscript{Asaeedi2014,
  author    = {Saeed Asaeedi and Farzad Didehva and Ali Mohades},
  title     = {Alpha-concave hull, a generalization of convex hull},
  year      = {2014},
  keywords  = {Alpha Shape; Computer Science (CS); Concave Hull; Convex Hull},
  url       = {https://arxiv.org/pdf/1309.7829.pdf},
  file      = {:by-author/A/Asaeedi/2014_Asaeedi.pdf:PDF},
  owner     = {saulius},
  timestamp = {2019.04.09},
  creationdate = {2019-04-09T00:00:00},
}

@Article{Petrek2006,
  author    = {Martin Petřek and Michal Otyepka and Pavel Banáš and Pavlı́na Košinová and Jaroslav Koča and Jiřı́ Damborský},
  journal   = {{BMC} Bioinformatics},
  title     = {{CAVER}: a new tool to explore routes from protein clefts, pockets and cavities},
  year      = {2006},
  number    = {1},
  pages     = {316},
  volume    = {7},
  doi       = {10.1186/1471-2105-7-316},
  file      = {:by-author/P/Petřek/2006_Petřek_316.pdf:PDF},
  keywords  = {Bioinformatics; Computer Science (CS); Convex Hull; Protein Cavities},
  owner     = {saulius},
  publisher = {Springer Nature},
  timestamp = {2019.04.09},
  creationdate = {2019-04-09T00:00:00},
}

@Article{Teyra2006,
  author    = {Joan Teyra and Andreas Doms and Michael Schroeder and M. Teresa Pisabarro},
  journal   = {{BMC} Bioinformatics},
  title     = {{SCOWLP}: a web-based database for detailed characterization and visualization of protein interfaces},
  year      = {2006},
  number    = {1},
  pages     = {104},
  volume    = {7},
  doi       = {10.1186/1471-2105-7-104},
  file      = {:by-author/T/Teyra/2006_Teyra_104.pdf:PDF},
  keywords  = {Bioinformatics; Computer Science (CS); Convex Hull},
  owner     = {saulius},
  publisher = {Springer Nature},
  timestamp = {2019.04.09},
  creationdate = {2019-04-09T00:00:00},
}

@PhdThesis{Artamonova2017,
  author    = {Daria N. Artamonova},
  school    = {Skolkovo Institute of Science and Technology},
  title     = {Comparative analysis of the action of eubacterial class 1 {CRISPR}-{C}as systems},
  year      = {2017},
  file      = {:by-author/A/Artamonova/2017_Artamonova.pdf:PDF},
  keywords  = {CRISPR; Cas},
  owner     = {saulius},
  timestamp = {2019.04.09},
  creationdate = {2019-04-09T00:00:00},
  url       = {https://www.skoltech.ru/app/data/uploads/2017/09/Artamonova_THESIS_final_editedOct.pdf},
}

@Manuscript{Block2018,
  author    = {Richard Block and Carolyn Rebecca Block and Ned Levine},
  title     = {Hot spot analysis of points: {II}},
  year      = {2018},
  keywords  = {Bayesian Analysis},
  url       = {https://nij.gov/topics/technology/maps/documents/crimestat-files/CrimeStat%20IV%20Chapter%208.pdf},
  file      = {:by-author/B/Block/2018_Block.pdf:PDF},
  owner     = {saulius},
  timestamp = {2019.04.09},
  creationdate = {2019-04-09T00:00:00},
}

@Book{IOS2015,
  author    = {{International Organization for Standardization}},
  title     = {International classification for standards},
  year      = {2015},
  file      = {:by-author/I/IOS/2015_IOS.pdf:PDF},
  keywords  = {Classification; Standards},
  owner     = {saulius},
  timestamp = {2019.04.09},
  creationdate = {2019-04-09T00:00:00},
  url       = {https://www.iso.org/files/live/sites/isoorg/files/archive/pdf/en/international_classification_for_standards.pdf},
}

@Presentation{Haspel2016,
  author    = {Nurit Haspel},
  title     = {Docking},
  year      = {2016},
  file      = {:by-author/H/Haspel/2016_Haspel.pdf:PDF},
  keywords  = {Bioinformatics; Computer Science (CS); Convex Hull; Docking},
  owner     = {saulius},
  timestamp = {2019.04.09},
  creationdate = {2019-04-09T00:00:00},
  url       = {https://www.cs.umb.edu/~nurith/cs612/Docking.pdf},
}

@Article{Mikolov2013,
  author      = {Tomas Mikolov and Kai Chen and Greg Corrado and Jeffrey Dean},
  journal     = {arXiv},
  title       = {Efficient estimation of word representations in vector space},
  year        = {2013},
  abstract    = {We propose two novel model architectures for computing continuous vector representations of words from very large data sets. The quality of these representations is measured in a word similarity task, and the results are compared to the previously best performing techniques based on different types of neural networks. We observe large improvements in accuracy at much lower computational cost, i.e. it takes less than a day to learn high quality word vectors from a 1.6 billion words data set. Furthermore, we show that these vectors provide state-of-the-art performance on our test set for measuring syntactic and semantic word similarities.},
  date        = {2013-01-16},
  eprint      = {http://arxiv.org/abs/1301.3781v3},
  eprintclass = {cs.CL},
  eprinttype  = {arXiv},
  file        = {:by-author/M/Mikolov/2013_Mikolov.pdf:PDF},
  keywords    = {Artificial Neural Networks (ANN); Computer Science (CS)},
  owner       = {saulius},
  timestamp = {2019.04.09},
  creationdate = {2019-04-09T00:00:00},
  url         = {https://arxiv.org/pdf/1301.3781.pdf},
}

@Article{Zhang2016,
  author      = {Xiang Zhang and Yann LeCun},
  journal     = {arXiv},
  title       = {Text understanding from scratch},
  year        = {2016},
  abstract    = {This article demontrates that we can apply deep learning to text understanding from character-level inputs all the way up to abstract text concepts, using temporal convolutional networks (ConvNets). We apply ConvNets to various large-scale datasets, including ontology classification, sentiment analysis, and text categorization. We show that temporal ConvNets can achieve astonishing performance without the knowledge of words, phrases, sentences and any other syntactic or semantic structures with regards to a human language. Evidence shows that our models can work for both English and Chinese.},
  date        = {2015-02-05},
  eprint      = {http://arxiv.org/abs/1502.01710v5},
  eprintclass = {cs.LG},
  eprinttype  = {arXiv},
  file        = {:by-author/Z/Zhang/2016_Zhang.pdf:PDF},
  keywords    = {Artificial Neural Networks (ANN); Computer Science (CS); Neural Networks (NN); Text Undestanding},
  owner       = {saulius},
  timestamp = {2019.04.09},
  creationdate = {2019-04-09T00:00:00},
  url         = {https://arxiv.org/pdf/1502.01710.pdf},
}

@InProceedings{Kim2014,
  author    = {Yoon Kim},
  booktitle = {Proceedings of the 2014 Conference on Empirical Methods in Natural Language Processing (EMNLP)},
  title     = {Convolutional neural networks for sentence classification},
  year      = {2014},
  pages     = {1746--1751},
  file      = {:by-author/K/Kim/2014_Kim_1746.pdf:PDF},
  keywords  = {Artificail Neural Networks; Artificial Neural Networks (ANN); Computer Science (CS); Natural Language Processing; Neural Networks (NN); Text Understanding},
  owner     = {saulius},
  timestamp = {2019.04.09},
  creationdate = {2019-04-09T00:00:00},
  url       = {http://aclweb.org/anthology/D/D14/D14-1181.pdf},
}

@Manuscript{Barber1995,
  author    = {C. Bradford Barber and David P. Dobkin and Hannu Huhdanpaa},
  title     = {The {Q}uickhull algorithm for convex hulls},
  year      = {1995},
  keywords  = {Computer Science (CS); Convex Hull; Quickhull},
  language  = {English},
  month     = {jan},
  url       = {http://dpd.cs.princeton.edu/Papers/BarberDobkinHuhdanpaa.pdf},
  file      = {:by-author/B/Barber/1995_Barber.pdf:PDF},
  journal   = {Submitted to {ACM} Transactions on Mathematical Software},
  owner     = {saulius},
  timestamp = {2019.04.21},
  creationdate = {2019-04-21T00:00:00},
}

@Article{Barber1996,
  author    = {C. Bradford Barber and David P. Dobkin and Hannu Huhdanpaa},
  journal   = {{ACM} Transactions on Mathematical Software},
  title     = {The quickhull algorithm for convex hulls},
  year      = {1996},
  month     = {dec},
  number    = {4},
  pages     = {469--483},
  volume    = {22},
  doi       = {10.1145/235815.235821},
  file      = {:by-author/B/Barber/1996_Barber_469.pdf:PDF},
  keywords  = {Computer Science (CS); Convex Hull; Quickhull},
  owner     = {saulius},
  publisher = {Association for Computing Machinery ({ACM})},
  timestamp = {2019.04.21},
  creationdate = {2019-04-21T00:00:00},
  url       = {https://www.cise.ufl.edu/~ungor/courses/fall06/papers/QuickHull.pdf},
}

@Presentation{Gregorius2014,
  author    = {Dirk Gregorius},
  title     = {Implementing {Q}uickhull},
  year      = {2014},
  file      = {:by-author/G/Gregorius/2014_Gregorius.pdf:PDF},
  keywords  = {Computer Science (CS); Convex Hull; Quickhull},
  owner     = {saulius},
  timestamp = {2019.04.21},
  creationdate = {2019-04-21T00:00:00},
  url       = {http://box2d.org/files/GDC2014/DirkGregorius_ImplementingQuickHull.pdf},
}

@Webpage{Smith2019,
  author    = {Jordan Smith},
  retrieved = {2019-04-20},
  title     = {{QuickHull 3D}},
  url       = {http://algolist.manual.ru/maths/geom/convhull/qhull3d.php},
  language  = {English},
  year      = {2019},
  file      = {:by-author/S/Smith/2019_Smith.pdf:PDF},
  keywords  = {Computer Science (CS); Convex Hull; Quickhull},
  owner     = {saulius},
  timestamp = {2019.04.21},
  creationdate = {2019-04-21T00:00:00},
}

@Manuscript{Sinclair2016,
  author    = {David. A. Sinclair},
  title     = {A {3D} {S}weep {H}ull algorithm for computing convex hulls and {D}elaunay triangulation},
  year      = {2016},
  keywords  = {Computer Science (CS); Convex Hull},
  url       = {http://www.newtonapples.net/paper/NewtonWrapper.pdf},
  file      = {:by-author/S/Sinclair/2016_Sinclair.pdf:PDF},
  owner     = {saulius},
  timestamp = {2019.04.21},
  creationdate = {2019-04-21T00:00:00},
}

@Manuscript{Кантор2003,
  author    = {Кантор, Илья},
  title     = {Эффективное вычисление дискретного преобразования {Ф}урье и дискретного преобразования {Х}артли},
  year      = {2003},
  keywords  = {Computer Science (CS); FFT},
  language  = {Russian},
  month     = {may},
  site      = {algolist.manual.ru},
  siteurl   = {http://algolist.manual.ru/},
  url       = {http://algolist.manual.ru/download.php?path=/maths/fft_art.zip&pspdf=1},
  file      = {:by-author/К/Кантор/2003_Кантор.pdf:PDF},
  owner     = {saulius},
  timestamp = {2019.04.21},
  creationdate = {2019-04-21T00:00:00},
}

@Article{Halper2006,
  author    = {Sara R. Halper and Loi Do and Jay R. Stork and Seth M. Cohen},
  journal   = {Journal of the American Chemical Society},
  title     = {Topological Control in Heterometallic Metal-Organic Frameworks by Anion Templating and Metalloligand Design},
  year      = {2006},
  month     = {nov},
  number    = {47},
  pages     = {15255--15268},
  volume    = {128},
  doi       = {10.1021/ja0645483},
  file      = {:by-author/H/Halper/2006_Halper_15255.pdf:PDF},
  groups    = {sg/MOF},
  keywords  = {Metal-Organic Frameworks (MOF)},
  owner     = {saulius},
  publisher = {American Chemical Society ({ACS})},
  timestamp = {2019.06.02},
  creationdate = {2019-06-02T00:00:00},
}

@Article{Briggs1925,
  author    = {George Edward Briggs and John Burdon Sanderson Haldane},
  journal   = {Biochemical Journal},
  title     = {A Note on the Kinetics of Enzyme Action},
  year      = {1925},
  number    = {2},
  pages     = {338--339},
  volume    = {19},
  doi       = {10.1042/bj0190338},
  file      = {:by-author/B/Briggs/1925_Briggs_338.pdf:PDF},
  keywords  = {Enzyme Kinetics; Michaelis Constant},
  owner     = {saulius},
  publisher = {Portland Press Ltd.},
  timestamp = {2019.06.02},
  creationdate = {2019-06-02T00:00:00},
}

@Article{Johnson2011,
  author    = {Kenneth A. Johnson and Roger S. Goody},
  journal   = {Biochemistry},
  title     = {The Original Michaelis Constant: Translation of the 1913 Michaelis{\textendash}Menten Paper},
  year      = {2011},
  month     = {oct},
  number    = {39},
  pages     = {8264--8269},
  volume    = {50},
  doi       = {10.1021/bi201284u},
  file      = {:by-author/J/Johnson/2011_Johnson_8264.pdf:PDF;:by-author/J/Johnson/2011_Johnson_8264_suppl/bi201284u_si_001.pdf:PDF},
  keywords  = {Enzyme Kinetics; Michaelis Constant},
  owner     = {saulius},
  publisher = {American Chemical Society ({ACS})},
  timestamp = {2019.06.02},
  creationdate = {2019-06-02T00:00:00},
}

@Article{Clifford1933,
  author    = {A. H. Clifford},
  journal   = {The Annals of Mathematics},
  title     = {A System Arising from a Weakened Set of Group Postulates},
  year      = {1933},
  month     = {oct},
  number    = {4},
  pages     = {865},
  volume    = {34},
  doi       = {10.2307/1968703},
  file      = {:by-author/C/Clifford/1933_Clifford_865.pdf:PDF},
  keywords  = {Algebra; Semigroups},
  owner     = {saulius},
  publisher = {{JSTOR}},
  timestamp = {2019.06.02},
  creationdate = {2019-06-02T00:00:00},
}

@Article{Lee2009,
  author    = {C. J. Lee and Y.-M. Kang and K.-H. Cho and K. T. No},
  journal   = {Proceedings of the National Academy of Sciences},
  title     = {A robust method for searching the smallest set of smallest rings with a path-included distance matrix},
  year      = {2009},
  month     = {sep},
  number    = {41},
  pages     = {17355--17358},
  volume    = {106},
  doi       = {10.1073/pnas.0813040106},
  file      = {:by-author/L/Lee/2009_Lee_17355.pdf:PDF;:by-author/L/Lee/2009_Lee_17355/Appendix_PDF.pdf:PDF},
  keywords  = {Chemoinformatics; Computer Science (CS); Ring Perception; SSSR},
  owner     = {saulius},
  publisher = {Proceedings of the National Academy of Sciences},
  timestamp = {2019.06.09},
  creationdate = {2019-06-09T00:00:00},
}

@Article{Mendili2019,
  author    = {Yassine El Mendili and Antanas Vaitkus and Andrius Merkys and Saulius Gra{\v{z}}ulis and Daniel Chateigner and Fabrice Mathevet and St{\'{e}}phanie Gascoin and Sebastien Petit and Jean-Fran{\c{c}}ois Bardeau and Marco Zanatta and Maria Secchi and Gino Mariotto and Arun Kumar and Michele Cassetta and Luca Lutterotti and Evgeny Borovin and Beate Orberger and Patrick Simon and Bernard Hehlen and Monique Le Guen},
  journal   = {Journal of Applied Crystallography},
  title     = {{R}aman {O}pen {D}atabase: first interconnected {R}aman{\textendash}{X}-ray diffraction open-access resource for material identification},
  year      = {2019},
  month     = {may},
  number    = {3},
  pages     = {618--625},
  volume    = {52},
  doi       = {10.1107/s1600576719004229},
  file      = {:by-author/M/Mendili/2019_Mendili_618.pdf:PDF},
  keywords  = {Databases; ROD; Raman Spectroscopy},
  owner     = {saulius},
  publisher = {International Union of Crystallography ({IUCr})},
  timestamp = {2019.06.29},
  creationdate = {2019-06-29T00:00:00},
}

@PhdThesis{Laurikenas2019,
  author    = {Andrius Laurikėnas},
  school    = {Vilnius University},
  title     = {Metal-organic frameworks ({MOF}): synthesis and characterisation},
  year      = {2019},
  file      = {:by-author/L/Laurikėnas/2019_Laurikėnas.pdf:PDF},
  keywords  = {Metal-Organic Frameworks (MOF); Synthesis},
  owner     = {saulius},
  timestamp = {2019.06.29},
  creationdate = {2019-06-29T00:00:00},
}

@Article{Desai2015,
  author    = {Desai, Hardikkumar V. and Desai, Apurva A.},
  journal   = {{VNSGU} Journal of Science and Technology},
  title     = {Steganography of images using {H}ilbert curve},
  year      = {2015},
  issn      = {0975-5446},
  month     = {July},
  number    = {1},
  pages     = {8--21},
  volume    = {4},
  file      = {:by-author/D/Desai/2015_Desai_8.pdf:PDF},
  keywords  = {Hilbert Curves; Space Filling Curves; Steganography},
  owner     = {saulius},
  timestamp = {2019.06.29},
  creationdate = {2019-06-29T00:00:00},
  url       = {http://vnsgu.ac.in/dept/publication/vnsgujst41july2015/2.pdf},
}

@Article{Hussain2018,
  author    = {Mehdi Hussain and Ainuddin Wahid Abdul Wahab and Yamani Idna Bin Idris and Anthony T. S. Ho and Ki-Hyun Jung},
  journal   = {Signal Processing: Image Communication},
  title     = {Image steganography in spatial domain: a survey},
  year      = {2018},
  month     = {jul},
  pages     = {46--66},
  volume    = {65},
  doi       = {10.1016/j.image.2018.03.012},
  file      = {:by-author/H/Hussain/2018_Hussain_46.pdf:PDF},
  keywords  = {Computer Science (CS); Hilbert Curves; Image Processing; Steganography},
  owner     = {saulius},
  publisher = {Elsevier {BV}},
  timestamp = {2019.06.29},
  creationdate = {2019-06-29T00:00:00},
}

@Article{Ari2015,
  author    = {Niyazi Ari and Savaş Tuylu},
  journal   = {Donnish Journal of Educational Research and Reviews},
  title     = {Algebra of matrices and determinants with {MAXIMA} entrance},
  year      = {2015},
  month     = {January},
  number    = {1},
  pages     = {1--7},
  volume    = {2},
  file      = {:by-author/A/Ari/2015_Ari_1.pdf:PDF},
  keywords  = {Computer Algebra; Computer Science (CS); Examples; Maxyma},
  owner     = {saulius},
  timestamp = {2019.06.29},
  creationdate = {2019-06-29T00:00:00},
  url       = {http://www.donnishjournals.org/djerr/pdf/2015/january/Ari-and-Tuylu.pdf},
}

@Manuscript{Westfeld2004,
  author    = {Andreas Westfeld},
  title     = {Space filling curves in steganalysis},
  year      = {2004},
  keywords  = {Computer Science (CS); Hilbert Curves; Space Filling Curves; Steganalysis; Steganography},
  url       = {https://www2.htw-dresden.de/~westfeld/publikationen/westfeld.spie05.pdf},
  file      = {:by-author/W/Westfeld/2004_Westfeld.pdf:PDF},
  owner     = {saulius},
  timestamp = {2019.06.29},
  creationdate = {2019-06-29T00:00:00},
}

@Article{Kieu2014,
  author    = {The Duc Kieu and Andrew Rudder and Wayne Goodridge},
  journal   = {Journal of Visual Communication and Image Representation},
  title     = {A reversible steganographic scheme for {VQ} indices based on locally adaptive coding},
  year      = {2014},
  month     = {aug},
  number    = {6},
  pages     = {1378--1386},
  volume    = {25},
  doi       = {10.1016/j.jvcir.2014.06.001},
  file      = {:by-author/K/Kieu/2014_Kieu_1378.pdf:PDF},
  owner     = {saulius},
  publisher = {Elsevier {BV}},
  timestamp = {2019.06.29},
  creationdate = {2019-06-29T00:00:00},
}

@Article{Naseri2018,
  author    = {Mosayeb Naseri and Mona Abdolmaleky and Amel Laref and Fariborz Parandin and Turgay Celik and Ahmed Farouk and Masoumeh Mohamadi and Hesam Jalalian},
  journal   = {Optik},
  title     = {A new cryptography algorithm for quantum images},
  year      = {2018},
  month     = {oct},
  pages     = {947--959},
  volume    = {171},
  doi       = {10.1016/j.ijleo.2018.06.113},
  file      = {:by-author/N/Naseri/2018_Naseri_947.pdf:PDF},
  owner     = {saulius},
  publisher = {Elsevier {BV}},
  timestamp = {2019.06.29},
  creationdate = {2019-06-29T00:00:00},
  url       = {http://iranarze.ir/wp-content/uploads/2018/08/E8883-IranArze.pdf},
}

@InProceedings{Milton1979,
  author    = {D. R. Milton and L. W. Kirchhoff and B. R. Rowland},
  booktitle = {Proceedings of the 1979 {SIGPLAN} symposium on Compiler construction - {SIGPLAN} {\textquotesingle}79},
  title     = {An all(1) compiler generator},
  year      = {1979},
  pages     = {152--157},
  publisher = {{ACM} Press},
  doi       = {10.1145/800229.806965},
  file      = {:by-author/M/Milton/1979_Milton_152.pdf:PDF},
  keywords  = {Compiler Construction; Compiler Generation; Computer Languages; Computer Science (CS); Formal Specification of Semantics},
  owner     = {saulius},
  timestamp = {2019.06.29},
  creationdate = {2019-06-29T00:00:00},
}

@Article{Landin1964,
  author    = {P. J. Landin},
  journal   = {The Computer Journal},
  title     = {The mechanical evaluation of expressions},
  year      = {1964},
  month     = {jan},
  number    = {4},
  pages     = {308--320},
  volume    = {6},
  doi       = {10.1093/comjnl/6.4.308},
  file      = {:by-author/L/Landin/1964_Landin_308.pdf:PDF},
  keywords  = {Compiler Construction; Computer Science (CS); Semantics of Computer Languages},
  owner     = {saulius},
  publisher = {Oxford University Press ({OUP})},
  timestamp = {2019.06.29},
  creationdate = {2019-06-29T00:00:00},
}

@Manuscript{Wijngaarden1975,
  author    = {A. van Wijngaarden and B. J. Mailloux and J. E. L. Peck and C. H. A. Koster and M. Sintzoff and C. H. Lindsey and L. G. T. Meertens and R. G. Fisker},
  title     = {Revised report on the algorithmic language {ALGOL} 68},
  year      = {1975},
  keywords  = {Algol; Algol 68; Computer Science (CS); Programming Languages},
  url       = {http://web.eah-jena.de/~kleine/history/languages/algol68-revisedreport.pdf},
  comment   = {Publication year inferred from reading Peck1978.},
  file      = {:by-author/W/Wijngaarden/1975_Wijngaarden_.pdf:PDF},
  owner     = {saulius},
  timestamp = {2019.06.29},
  creationdate = {2019-06-29T00:00:00},
}

@Manuscript{Peck1978,
  author    = {John E. Peck},
  title     = {The {ALGOL} 68 story},
  year      = {1978},
  keywords  = {Algol; Algol 68; Computer Science (CS); History},
  url       = {http://www.softwarepreservation.org/projects/ALGOL/paper/The%20Algol%2068%20Story.pdf},
  file      = {:by-author/P/Peck/1978_Peck.pdf:PDF},
  owner     = {saulius},
  timestamp = {2019.06.29},
  creationdate = {2019-06-29T00:00:00},
}

@InProceedings{Schneider1970,
  author    = {Victor B. Schneider},
  booktitle = {Proceedings of the May 5-7, 1970, spring joint computer conference on - {AFIPS} {\textquotesingle}70 (Spring)},
  title     = {A translation grammar for {ALGOL} 68},
  year      = {1970},
  pages     = {493--505},
  publisher = {{ACM} Press},
  doi       = {10.1145/1476936.1477014},
  file      = {:by-author/S/Schneider/1970_Schneider_493.pdf:PDF},
  keywords  = {Algol; Algol 68; Compiler Construction; Computer Science (CS); Grammars},
  owner     = {saulius},
  timestamp = {2019.06.29},
  creationdate = {2019-06-29T00:00:00},
}

@Article{Knuth1968,
  author    = {Donald E. Knuth},
  journal   = {Mathematical Systems Theory},
  title     = {Semantics of context-free languages},
  year      = {1968},
  month     = {jun},
  number    = {2},
  pages     = {127--145},
  volume    = {2},
  doi       = {10.1007/bf01692511},
  file      = {:by-author/K/Knuth/1968_Knuth_127.pdf:PDF},
  keywords  = {Computer Language Semantics; Computer Science (CS)},
  owner     = {saulius},
  publisher = {Springer Science and Business Media {LLC}},
  timestamp = {2019.06.29},
  creationdate = {2019-06-29T00:00:00},
}

@Misc{Graham1989,
  author    = {Graham, Brian},
  title     = {{SECD}: design issues},
  year      = {1989},
  doi       = {10.11575/prism/31357},
  file      = {:by-author/G/Graham/1989_Graham.pdf:PDF},
  keywords  = {Chip Design; Computer Science (CS); HOL; Language Semantics; Lisp; VLSI},
  owner     = {saulius},
  publisher = {University of Calgary},
  timestamp = {2019.06.29},
  creationdate = {2019-06-29T00:00:00},
  url       = {http://hdl.handle.net/1880/46590},
}

@Lecture{Turner2012,
  author    = {D. A. Turner},
  title     = {Some history of functional programming languages},
  year      = {2012},
  lecture   = {An invited lecture given at TFP12, St Andrews University, 12 June 2012},
  file      = {:by-author/T/Turner/2012_Turner.pdf:PDF},
  keywords  = {Computer Science (CS); Functionl Languages; Language Semantics; Programming Languages},
  owner     = {saulius},
  timestamp = {2019.06.29},
  creationdate = {2019-06-29T00:00:00},
  url       = {https://www.cs.kent.ac.uk/people/staff/dat/tfp12/tfp12.pdf},
}

@Article{Landin1965,
  author    = {P. J. Landin},
  journal   = {Communications of the {ACM}},
  title     = {Correspondence between {ALGOL} 60 and {C}hurch{\textquotesingle}s {L}ambda-notation: part {I}},
  year      = {1965},
  month     = {feb},
  number    = {2},
  pages     = {89--101},
  volume    = {8},
  doi       = {10.1145/363744.363749},
  file      = {:by-author/L/Landin/1965_Landin_89.pdf:PDF},
  keywords  = {Algol; Algol 60; Computer Languages; Computer Science (CS); Lambda Calculus; Language Semantics},
  owner     = {saulius},
  publisher = {Association for Computing Machinery ({ACM})},
  timestamp = {2019.06.29},
  creationdate = {2019-06-29T00:00:00},
}

@Article{Landin1965a,
  author    = {P. J. Landin},
  journal   = {Communications of the {ACM}},
  title     = {A correspondence between {ALGOL} 60 and {C}hurch{\textquotesingle}s {L}ambda-notations: Part {II}},
  year      = {1965},
  month     = {mar},
  number    = {3},
  pages     = {158--167},
  volume    = {8},
  doi       = {10.1145/363791.363804},
  file      = {:by-author/L/Landin/1965_Landin_158.pdf:PDF},
  keywords  = {Algol; Algol 60; Computer Languages; Computer Science (CS); Lambda Calculus; Language Semantics},
  owner     = {saulius},
  publisher = {Association for Computing Machinery ({ACM})},
  timestamp = {2019.06.29},
  creationdate = {2019-06-29T00:00:00},
}

@Article{Landin_1966,
  author    = {P. J. Landin},
  journal   = {Communications of the {ACM}},
  title     = {The next 700 programming languages},
  year      = {1966},
  month     = {mar},
  number    = {3},
  pages     = {157--166},
  volume    = {9},
  doi       = {10.1145/365230.365257},
  file      = {:by-author/L/Landin/1966_Landin_157.pdf:PDF},
  keywords  = {Computer Languages; Computer Science (CS); Language Semantics},
  owner     = {saulius},
  publisher = {Association for Computing Machinery ({ACM})},
  timestamp = {2019.06.29},
  creationdate = {2019-06-29T00:00:00},
}

@Article{Landin1998,
  author    = {Peter J. Landin},
  journal   = {Higher Order Symbolic Computation},
  title     = {A Generalization of Jumps and Labels},
  year      = {1998},
  number    = {2},
  pages     = {125--143},
  volume    = {11},
  doi       = {10.1023/a:1010068630801},
  file      = {:by-author/L/Landin/1998_Landin_125.pdf:PDF},
  keywords  = {Computer Languages; Computer Science (CS); Language Semantics},
  owner     = {saulius},
  publisher = {Springer Nature},
  timestamp = {2019.06.29},
  creationdate = {2019-06-29T00:00:00},
}

@Article{Jamil1995,
  author    = {T. Jamil},
  journal   = {{IEEE} Potentials},
  title     = {{RISC} versus {CISC}},
  year      = {1995},
  number    = {3},
  pages     = {13--16},
  volume    = {14},
  doi       = {10.1109/45.464688},
  file      = {:by-author/J/Jamil/1995_Jamil_13.pdf:PDF},
  keywords  = {CISC; Computer Architecture; Computer Science (CS); RISC},
  owner     = {saulius},
  publisher = {Institute of Electrical and Electronics Engineers ({IEEE})},
  timestamp = {2019.07.17},
  creationdate = {2019-07-17T00:00:00},
}

@Article{Schuurman2008,
  author       = {Schuurman, Nadine and Leszczynski, Agnieszka},
  journal      = {Bioinformatics and biology insights},
  title        = {Ontologies for bioinformatics.},
  year         = {2008},
  issn         = {1177-9322},
  month        = mar,
  pages        = {187--200},
  volume       = {2},
  abstract     = {The past twenty years have witnessed an explosion of biological data in diverse database formats governed by heterogeneous infrastructures. Not only are semantics (attribute terms) different in meaning across databases, but their organization varies widely. Ontologies are a concept imported from computing science to describe different conceptual frameworks that guide the collection, organization and publication of biological data. An ontology is similar to a paradigm but has very strict implications for formatting and meaning in a computational context. The use of ontologies is a means of communicating and resolving semantic and organizational differences between biological databases in order to enhance their integration. The purpose of interoperability (or sharing between divergent storage and semantic protocols) is to allow scientists from around the world to share and communicate with each other. This paper describes the rapid accumulation of biological data, its various organizational structures, and the role that ontologies play in interoperability.},
  completed    = {2009-12-11},
  country      = {United States},
  doi          = {10.4137/BBI.S451},
  file         = {:by-author/S/Schuurman/2008_Schuurman_187.pdf:PDF},
  issn-linking = {1177-9322},
  keywords     = {Bioinformatics; Biological Databases; Gene Ontology; Ontologies; Semantics},
  nlm-id       = {101467187},
  owner        = {saulius},
  pmc          = {PMC2735951},
  pmid         = {19812775},
  pubmodel     = {Electronic},
  pubstatus    = {epublish},
  revised      = {2018-11-13},
  timestamp = {2019.08.22},
  creationdate = {2019-08-22T00:00:00},
}

@Presentation{ICL2017,
  author           = {{Imperial College London}},
  title            = {Citing \& referencing: {H}arvard style},
  year             = {2017},
  comment          = {Original URL: https://www.imperial.ac.uk/media/imperial-college/administration-and-support-services/library/public/Harvard-guide-2022.pdf},
  creationdate     = {2019-09-05T00:00:00},
  file             = {:by-author/I/ICL/2017_ICL_1.pdf:PDF;:by-author/I/ICL/2017_ICL.pdf:PDF},
  keywords         = {Bibliography; Citation Style; Citations; Harvard Citation Style},
  modificationdate = {2024-05-17T09:07:36},
  month            = {September},
  notes            = {accessed 2023-01-25T09:15+02:00},
  owner            = {saulius},
  timestamp        = {2019.09.05},
  url              = {https://www.imperial.ac.uk/media/imperial-college/administration-and-support-services/library/public/IMPP10649-Harvard-Guide-230822-WEB.pdf},
}

@Article{Schmidt2019,
  author    = {Schmidt, Jonathan and Marques, Mário R. G. and Botti, Silvana and Marques, Miguel A. L.},
  journal   = {npj Computational Materials},
  title     = {Recent advances and applications of machine learning in solid-state materials science},
  year      = {2019},
  issn      = {2057-3960},
  month     = {Aug},
  number    = {1},
  volume    = {5},
  comment   = {Cited by Andrius in his e-mail to grazulis@ibt.lt dated 2021-07-05 11:19},
  doi       = {10.1038/s41524-019-0221-0},
  file      = {Schmidt_2019.pdf:by-author/S/Schmidt/2019_Schmidt.pdf:PDF},
  keywords  = {Macine Learning; Material Science; Quantum Mechanics (QM)},
  owner     = {andrius},
  publisher = {Springer Science and Business Media LLC},
  timestamp = {2019.08.30},
  creationdate = {2019-08-30T00:00:00},
  url       = {http://dx.doi.org/10.1038/s41524-019-0221-0},
}

@Article{Gundersen2011,
  author    = {Sveinung Gundersen and Matúš Kalaš and Osman Abul and Arnoldo Frigessi and Eivind Hovig and Geir Sandve},
  journal   = {{BMC} Bioinformatics},
  title     = {Identifying elemental genomic track types and representing them uniformly},
  year      = {2011},
  number    = {1},
  pages     = {494},
  volume    = {12},
  doi       = {10.1186/1471-2105-12-494},
  file      = {:by-author/G/Gundersen/2011_Gundersen_494.pdf:PDF},
  keywords  = {Bioinformatics; Computer Science (CS); File Formats; Sequence Data},
  owner     = {saulius},
  publisher = {Springer Nature},
  timestamp = {2019.08.28},
  creationdate = {2019-08-28T00:00:00},
}

@Presentation{Gupta2010a,
  author    = {Dinesh Gupta},
  title     = {Sequence formats and databases in bioinformatics},
  year      = {2010},
  file      = {:by-author/G/Gupta/2010_Gupta.pdf:PDF},
  keywords  = {Bioinformatics; Computer Science (CS); File Formats; Sequences},
  owner     = {saulius},
  timestamp = {2019.08.28},
  creationdate = {2019-08-28T00:00:00},
  url       = {https://sta.uwi.edu/fst/dms/icgeb/documents/18-01-10SequenceformatsanddatabasesinbioinformaticsDGL1.pdf},
}

@Article{Brink2019,
  author    = {Alice Brink and John R. Helliwell},
  journal   = {{IUCrJ}},
  title     = {Why is interoperability between the two fields of chemical crystallography and protein crystallography so difficult?},
  year      = {2019},
  month     = {aug},
  number    = {5},
  pages     = {788--793},
  volume    = {6},
  doi       = {10.1107/s2052252519010972},
  file      = {:by-author/B/Brink/2019_Brink_788.pdf:PDF},
  keywords  = {Citing COD; Computer Science (CS); Crystallography; Data Semantics; Interoperability; Ontologies; Representation of Crystal Structures; Reproducible Research},
  owner     = {saulius},
  publisher = {International Union of Crystallography ({IUCr})},
  timestamp = {2019.09.05},
  creationdate = {2019-09-05T00:00:00},
}

@Article{Schaeffer2007,
  author    = {Satu Elisa Schaeffer},
  journal   = {Computer Science Review},
  title     = {Graph clustering},
  year      = {2007},
  month     = {aug},
  number    = {1},
  pages     = {27--64},
  volume    = {1},
  doi       = {10.1016/j.cosrev.2007.05.001},
  file      = {:by-author/S/Schaeffer/2007_Schaeffer_27.pdf:PDF},
  owner     = {saulius},
  publisher = {Elsevier {BV}},
  timestamp = {2019.09.13},
  creationdate = {2019-09-13T00:00:00},
}

@Article{Belles1958,
  author    = {Belles, F. E.},
  journal   = {Symposium (International) on Combustion},
  title     = {Detonability and chemical kinetics: prediction of limits of detonability of prediction of hydrogen},
  year      = {1958},
  number    = {1},
  pages     = {745--751},
  volume    = {7},
  doi       = {10.1016/S0082-0784(58)80115-0},
  file      = {:by-author/B/Belles/1958_Belles_745.pdf:PDF},
  keywords  = {Chemical Kinetics; Detonability; Hydrogen Detonation},
  owner     = {saulius},
  publisher = {Elsevier {BV}},
  timestamp = {2019.09.16},
  creationdate = {2019-09-16T00:00:00},
}

@InBook{Wakerly2006,
  author    = {John F. Wakerly},
  chapter   = {Transistor-Transistor-Logic Topics},
  pages     = {TTL–1--TTL–12},
  publisher = {Pearson Education, Inc.},
  title     = {Digital design principles and practices},
  year      = {2006},
  isbn      = {0-13-186389-4.},
  file      = {:by-author/W/Wakerly/2006_Wakerly_1.pdf:PDF},
  keywords  = {Electronics; TTL},
  owner     = {saulius},
  timestamp = {2019.09.16},
  creationdate = {2019-09-16T00:00:00},
  url       = {http://wakerly.org/DDPP/DDPP4student/Supplementary_sections/TTL.pdf},
}

@InCollection{Westfeld2003,
  author    = {Andreas Westfeld},
  booktitle = {Information Hiding, 5th International Workshop, IH 2002},
  publisher = {Springer},
  title     = {Detecting low embedding rates},
  year      = {2003},
  editor    = {Petitcolas, Fabien A. P.},
  pages     = {324--339},
  file      = {:by-author/W/Westfeld/2003_Westfeld_324.pdf:PDF},
  keywords  = {Computer Science (CS); MP3; Steganography},
  owner     = {saulius},
  timestamp = {2019.09.16},
  creationdate = {2019-09-16T00:00:00},
  url       = {http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.138.8578&rep=rep1&type=pdf},
}

@InProceedings{Ertl1994,
  author    = {Anton Ertl},
  booktitle = {EuroForth'94},
  title     = {Automatic scoping of local variables},
  year      = {1994},
  pages     = {31--37},
  comment   = {Original filename "10.1.1.52.9644.pdf".},
  file      = {:by-author/E/Ertl/1994_Ertl_31.pdf:PDF},
  keywords  = {Compiler Construction; Computer Science (CS); FORTH; Local Variables},
  owner     = {saulius},
  timestamp = {2019.09.16},
  creationdate = {2019-09-16T00:00:00},
}

@Article{Li2011,
  author    = {Bin Li and Junhui He and Jiwu Huang and Yun Qing Shi},
  journal   = {Journal of Information Hiding and Multimedia Signal Processing},
  title     = {A survey on image steganography and steganalysis},
  year      = {2011},
  issn      = {2073-4212},
  number    = {2},
  pages     = {142--172},
  volume    = {2},
  file      = {:by-author/L/Li/2011_Li_142.pdf:PDF},
  keywords  = {Computer Science (CS); Review; Steganography},
  owner     = {saulius},
  timestamp = {2019.09.16},
  creationdate = {2019-09-16T00:00:00},
  url       = {http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.648.4107&rep=rep1&type=pdf},
}

@Article{Kempe2005,
  author    = {Stephan Kempe},
  journal   = {Geographische Rundschau},
  title     = {Karstgebiete und {H}öhlen in {D}eutschland},
  year      = {2005},
  pages     = {44--52},
  file      = {:by-author/K/Kempe/2005_Kempe_44.pdf:PDF},
  keywords  = {Geology; Karst},
  owner     = {saulius},
  timestamp = {2019.09.16},
  creationdate = {2019-09-16T00:00:00},
  url       = {https://www.researchgate.net/publication/257542416},
}

@TechReport{Long1989,
  author      = {John P. Long and William G. Wood and David P. Wood},
  institution = {Software Engineering Institute, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213},
  title       = {Classifying software design methods},
  year        = {1989},
  file        = {:by-author/L/Long/1989_Long.pdf:PDF},
  keywords    = {Classification; Computer Programs; Embedding; Methodology; Parts; Real Time; Software Engineering; Tools},
  owner       = {saulius},
  timestamp = {2019.09.17},
  creationdate = {2019-09-17T00:00:00},
  url         = {https://resources.sei.cmu.edu/asset_files/TechnicalReport/1989_005_001_15779.pdf},
}

@Article{Gu_2019,
  author    = {Yuwei Gu and Julia Zhao and Jeremiah A. Johnson},
  journal   = {Trends in Chemistry},
  title     = {A (Macro)Molecular-Level Understanding of Polymer Network Topology},
  year      = {2019},
  month     = {jun},
  number    = {3},
  pages     = {318--334},
  volume    = {1},
  doi       = {10.1016/j.trechm.2019.02.017},
  file      = {:by-author/G/Gu/2019_Gu_318.pdf:PDF},
  owner     = {saulius},
  publisher = {Elsevier {BV}},
  timestamp = {2019.09.17},
  creationdate = {2019-09-17T00:00:00},
}

@Article{Cruickshank_1999,
  author    = {Cruickshank, D.W.J.},
  journal   = {Acta Crystallographica Section D Biological Crystallography},
  title     = {Remarks about protein structure precision},
  year      = {1999},
  month     = {mar},
  number    = {3},
  pages     = {583--601},
  volume    = {55},
  abstract  = {Full-matrix least squares is taken as the basis for an examination of protein structure precision. A two-atom protein model is used to compare the precisions of unrestrained and restrained refinements. In this model, restrained refinement determines a bond length which is the weighted mean of the unrestrained diffraction-only length and the geometric dictionary length. Data of 0.94 A resolution for the 237-residue protein concanavalin A are used in unrestrained and restrained full-matrix inversions to provide standard uncertainties [sigma](r) for positions and [sigma](l) for bond lengths. [sigma](r) is as small as 0.01 A for atoms with low Debye B values but increases strongly with B. The results emphasize the distinction between unrestrained and restrained refinements and between [sigma](r) and [sigma](l). Other full-matrix inversions are reported. Such inversions require massive calculations. Several approximate methods are examined and compared critically. These include a Fourier map formula [Cruickshank (1949). Acta Cryst. 2, 65-82], Luzzati plots [Luzzati (1952). Acta Cryst. 5, 802-810] and a new diffraction-component precision index (DPI). The DPI estimate of [sigma](r, Bavg) is given by a simple formula. It uses R or Rfree and is based on a very rough approximation to the least-squares method. Many examples show its usefulness as a precision comparator for high- and low-resolution structures. The effect of restraints as resolution varies is examined. More regular use of full-matrix inversion is urged to establish positional precision and hence the precision of non-dictionary distances in both high- and low-resolution structures. Failing this, parameter blocks for representative residues and their neighbours should be inverted to gain a general idea of [sigma](r) as a function of B. The whole discussion is subject to some caveats about the effects of disordered regions in the crystal.},
  doi       = {10.1107/S0907444998012645},
  file      = {:by-author/C/Cruickshank/1999_Cruickshank_583.pdf:PDF},
  keywords  = {FULL-MATRIX LEAST-SQUARES METHOD; PROTEIN STRUCTURE PRECISION},
  owner     = {saulius},
  publisher = {International Union of Crystallography},
  rights    = {Copyright (c) 1999 International Union of Crystallography},
  source    = {Acta Cryst (1999). D55, 583-601 [doi:10.1107/S0907444998012645]},
  timestamp = {2019.09.17},
  creationdate = {2019-09-17T00:00:00},
}

@Article{Kumar2015a,
  author    = {K. S. Dinesh Kumar and M. Gurusaran and S. N. Satheesh and P. Radha and S. Pavithra and K. P. S. Thulaa Tharshan and John R. Helliwell and K. Sekar},
  journal   = {Journal of Applied Crystallography},
  title     = {Online{\_}{DPI}: a web server to calculate the diffraction precision index for a protein structure},
  year      = {2015},
  month     = {apr},
  number    = {3},
  pages     = {939--942},
  volume    = {48},
  doi       = {10.1107/S1600576715006287},
  file      = {:by-author/K/Kumar/2015_Kumar_939.pdf:PDF},
  owner     = {saulius},
  publisher = {International Union of Crystallography ({IUCr})},
  timestamp = {2019.09.17},
  creationdate = {2019-09-17T00:00:00},
}

@Article{Faulon1998,
  author    = {Jean-Loup Faulon},
  journal   = {Journal of Chemical Information and Computer Sciences},
  title     = {Isomorphism, automorphism partitioning, and canonical labeling can be solved in polynomial-time for molecular graphs},
  year      = {1998},
  month     = {mar},
  number    = {3},
  pages     = {432--444},
  volume    = {38},
  doi       = {10.1021/ci9702914},
  file      = {:by-author/F/Faulon/1998_Faulon_432.pdf:PDF},
  keywords  = {Graph Isomorphism},
  owner     = {saulius},
  publisher = {American Chemical Society ({ACS})},
  timestamp = {2019.09.18},
  creationdate = {2019-09-18T00:00:00},
}

@Article{Blatov2010,
  author    = {V. A. Blatov and M. O'Keeffe and D. M. Proserpio},
  journal   = {{CrystEngComm}},
  title     = {Vertex-, face-, point-, {S}chläfli-, and {D}elaney-symbols in nets, polyhedra and tilings: recommended terminology},
  year      = {2010},
  number    = {1},
  pages     = {44--48},
  volume    = {12},
  doi       = {10.1039/b910671e},
  file      = {:by-author/B/Blatov/2010_Blatov_44.pdf:PDF},
  keywords  = {Crystal Polymers; Metal-Organic Frameworks (MOF); Nets},
  owner     = {saulius},
  publisher = {Royal Society of Chemistry ({RSC})},
  timestamp = {2019.09.18},
  creationdate = {2019-09-18T00:00:00},
}

@Article{Tang2019,
  author    = {Zhongjie Tang and ShaoQi Chen and Ang Chen and Bifang He and Yuwei Zhou and Guoshi Chai and FengBiao Guo and Jian Huang},
  journal   = {Database},
  title     = {{CasPDB}: an integrated and annotated database for Cas proteins from bacteria and archaea},
  year      = {2019},
  month     = {jan},
  volume    = {2019},
  doi       = {10.1093/database/baz093},
  file      = {:by-author/T/Tang/2019_Tang.pdf:PDF},
  keywords  = {CAS; CRISPR; Database},
  owner     = {saulius},
  publisher = {Oxford University Press ({OUP})},
  timestamp = {2019.09.18},
  creationdate = {2019-09-18T00:00:00},
}

@Article{Tastan_Bishop_2014,
  author    = {O. Tastan Bishop and E. F. Adebiyi and A. M. Alzohairy and D. Everett and K. Ghedira and A. Ghouila and J. Kumuthini and N. J. Mulder and S. Panji and H.-G. Patterton and},
  journal   = {Briefings in Bioinformatics},
  title     = {Bioinformatics Education--Perspectives and Challenges out of Africa},
  year      = {2014},
  month     = {jul},
  number    = {2},
  pages     = {355--364},
  volume    = {16},
  doi       = {10.1093/bib/bbu022},
  file      = {:by-author/B/Bishop/2014_Bishop_355.pdf:PDF},
  keywords  = {Africa; Bioinformatics; Education; Pedagogics; Teaching},
  owner     = {saulius},
  publisher = {Oxford University Press ({OUP})},
  timestamp = {2019.09.18},
  creationdate = {2019-09-18T00:00:00},
}

@Article{Chazal2017,
  author      = {Frédéric Chazal and Bertrand Michel},
  journal     = {ArXiv},
  title       = {An introduction to topological data analysis: fundamental and practical aspects for data scientists},
  year        = {2017},
  pages       = {171004019},
  abstract    = {Topological Data Analysis (tda) is a recent and fast growing eld providing a set of new topological and geometric tools to infer relevant features for possibly complex data. This paper is a brief introduction, through a few selected topics, to basic fundamental and practical aspects of tda for non experts. 1 Introduction and motivation Topological Data Analysis (tda) is a recent eld that emerged from various works in applied (algebraic) topology and computational geometry during the rst decade of the century. Although one can trace back geometric approaches for data analysis quite far in the past, tda really started as a eld with the pioneering works of Edelsbrunner et al. (2002) and Zomorodian and Carlsson (2005) in persistent homology and was popularized in a landmark paper in 2009 Carlsson (2009). tda is mainly motivated by the idea that topology and geometry provide a powerful approach to infer robust qualitative, and sometimes quantitative, information about the structure of data-see, e.g. Chazal (2017). tda aims at providing well-founded mathematical, statistical and algorithmic methods to infer, analyze and exploit the complex topological and geometric structures underlying data that are often represented as point clouds in Euclidean or more general metric spaces. During the last few years, a considerable eort has been made to provide robust and ecient data structures and algorithms for tda that are now implemented and available and easy to use through standard libraries such as the Gudhi library (C++ and Python) Maria et al. (2014) and its R software interface Fasy et al. (2014a). Although it is still rapidly evolving, tda now provides a set of mature and ecient tools that can be used in combination or complementary to other data sciences tools. The tdapipeline. tda has recently known developments in various directions and application elds. There now exist a large variety of methods inspired by topological and geometric approaches. Providing a complete overview of all these existing approaches is beyond the scope of this introductory survey. However, most of them rely on the following basic and standard pipeline that will serve as the backbone of this paper: 1. The input is assumed to be a nite set of points coming with a notion of distance-or similarity between them. This distance can be induced by the metric in the ambient space (e.g. the Euclidean metric when the data are embedded in R d) or come as an intrinsic metric dened by a pairwise distance matrix. The denition of the metric on the data is usually given as an input or guided by the application. It is however important to notice that the choice of the metric may be critical to reveal interesting topological and geometric features of the data.},
  date        = {2017-10-11},
  eprint      = {http://arxiv.org/abs/1710.04019v1},
  eprintclass = {math.ST},
  eprinttype  = {arXiv},
  file        = {:by-author/C/Chazal/2017_Chazal_171004019.pdf:PDF},
  keywords    = {cs.LG; math.AT; math.ST; stat.ML; stat.TH},
  owner       = {saulius},
  timestamp = {2019.09.18},
  creationdate = {2019-09-18T00:00:00},
  url         = {https://arxiv.org/abs/1710.04019},
}

@Article{Greene2015,
  author    = {Anna C. Greene and Kristine A. Giffin and Casey S. Greene and Jason H. Moore},
  journal   = {Briefings in Bioinformatics},
  title     = {Adapting bioinformatics curricula for big data},
  year      = {2015},
  month     = {mar},
  number    = {1},
  pages     = {43--50},
  volume    = {17},
  doi       = {10.1093/bib/bbv018},
  file      = {:by-author/G/Greene/2015_Greene_43.pdf:PDF},
  keywords  = {Bioinformatics; Pedagogics; Teaching},
  owner     = {saulius},
  publisher = {Oxford University Press ({OUP})},
  timestamp = {2019.09.18},
  creationdate = {2019-09-18T00:00:00},
}

@Article{Merritt2012,
  author    = {Ethan A. Merritt},
  journal   = {Acta Crystallographica Section D Biological Crystallography},
  title     = {To {B} or not to {B}: a question of resolution?},
  year      = {2012},
  month     = {mar},
  number    = {4},
  pages     = {468--477},
  volume    = {68},
  doi       = {10.1107/s0907444911028320},
  file      = {:by-author/M/Merritt/2012_Merritt_468.pdf:PDF},
  keywords  = {B-factor; Crystallography; Data Quality; Structure Representation},
  owner     = {saulius},
  publisher = {International Union of Crystallography ({IUCr})},
  timestamp = {2019.09.18},
  creationdate = {2019-09-18T00:00:00},
}

@Article{Goodman2014,
  author    = {Anya L. Goodman and Alex Dekhtyar},
  journal   = {{PLoS} Computational Biology},
  title     = {Teaching bioinformatics in concert},
  year      = {2014},
  month     = {nov},
  number    = {11},
  pages     = {e1003896},
  volume    = {10},
  doi       = {10.1371/journal.pcbi.1003896},
  editor    = {Joanne A. Fox},
  file      = {:by-author/G/Goodman/2014_Goodman_1003896.pdf:PDF;:by-author/G/Goodman/2014_Goodman_1003896_suppl/journal.pcbi.1003896.s001.PDF:PDF},
  keywords  = {Bioinformatics; Pedagogics; Teaching},
  owner     = {saulius},
  publisher = {Public Library of Science ({PLoS})},
  timestamp = {2019.09.18},
  creationdate = {2019-09-18T00:00:00},
}

@Article{Adams1978,
  author    = {Phillip M. Adams},
  journal   = {{ACM} {SIGMICRO} Newsletter},
  title     = {Microprogrammable microprocessor survey},
  year      = {1978},
  month     = {jun},
  number    = {2},
  pages     = {7--38},
  volume    = {9},
  doi       = {10.1145/1096529.1096530},
  file      = {:by-author/A/Adams/1978_Adams_7.pdf:PDF},
  keywords  = {CPU Design; Computer Science (CS); Microprogramming},
  owner     = {saulius},
  publisher = {Association for Computing Machinery ({ACM})},
  timestamp = {2019.09.18},
  creationdate = {2019-09-18T00:00:00},
}

@Article{Davies2019,
  author    = {Angela C. Davies and Diane Harris and Amanda Banks-Gatenby and Andy Brass},
  journal   = {{PLOS} Computational Biology},
  title     = {Problem-based learning in clinical bioinformatics education: Does it help to create communities of practice?},
  year      = {2019},
  month     = {jun},
  number    = {6},
  pages     = {e1006746},
  volume    = {15},
  doi       = {10.1371/journal.pcbi.1006746},
  editor    = {Francis Ouellette},
  file      = {:by-author/D/Davies/2019_Davies_1006746.pdf:PDF},
  keywords  = {Bioinformatics; Pedagogics; Teaching},
  owner     = {saulius},
  publisher = {Public Library of Science ({PLoS})},
  timestamp = {2019.09.18},
  creationdate = {2019-09-18T00:00:00},
}

@Article{Gurusaran2013,
  author    = {Manickam Gurusaran and Mani Shankar and Raju Nagarajan and John R. Helliwell and Kanagaraj Sekar},
  journal   = {{IUCrJ}},
  title     = {Do we see what we should see? {D}escribing non-covalent interactions in protein structures including precision},
  year      = {2013},
  month     = {dec},
  number    = {1},
  pages     = {74--81},
  volume    = {1},
  doi       = {10.1107/s2052252513031485},
  file      = {:by-author/G/Gurusaran/2013_Gurusaran_74.pdf:PDF},
  keywords  = {Non-covalent Interactions; Proteins; X-ray Crystallography},
  owner     = {saulius},
  publisher = {International Union of Crystallography ({IUCr})},
  timestamp = {2019.09.18},
  creationdate = {2019-09-18T00:00:00},
}

@Article{Nunes2015,
  author    = {Rhewter Nunes and Edivaldo Barbosa de Almeida J{\'{u}}nior and Ivandilson Pessoa Pinto de Menezes and Guilherme Malafaia},
  journal   = {Biochemistry and Molecular Biology Education},
  title     = {Learning nucleic acids solving by bioinformatics problems},
  year      = {2015},
  month     = {aug},
  number    = {5},
  pages     = {377--383},
  volume    = {43},
  doi       = {10.1002/bmb.20886},
  file      = {:by-author/N/Nunes/2015_Nunes_377.pdf:PDF},
  keywords  = {Bioinformatics; Pedagogics; Problem Solving; Teaching},
  owner     = {saulius},
  publisher = {Wiley},
  timestamp = {2019.09.18},
  creationdate = {2019-09-18T00:00:00},
}

@Article{Sainani2015,
  author    = {Kristin Sainani},
  journal   = {Biomedical Computation Review},
  title     = {The ever-expanding and heterogeneous landscape of bioinformatics education},
  year      = {2015},
  pages     = {12--19},
  file      = {:by-author/S/Sainani/2015_Sainani_12.pdf:PDF},
  keywords  = {Bioinformatics; Education; Pedagogics; Teaching},
  owner     = {saulius},
  timestamp = {2019.09.18},
  creationdate = {2019-09-18T00:00:00},
  url       = {http://biomedicalcomputationreview.org/sites/default/files/15fallch.6.pdf},
}

@Manuscript{Stakenas2019,
  author    = {Vilius Stakėnas},
  title     = {Kai svarbu, kas pirmas},
  year      = {2019},
  keywords  = {Bernulio Blokai; Bernulli Blocks; Probability Theory; Tikimybių Teorija},
  file      = {:by-author/S/Stakėnas/2019_Stakėnas.pdf:PDF},
  owner     = {saulius},
  timestamp = {2019.09.18},
  creationdate = {2019-09-18T00:00:00},
}

@MastersThesis{Riegler2015,
  author    = {Gregor Riegler},
  school    = {Technischen Universität Wien, Fakultät für Informatik},
  title     = {Evaluation and implementation of an optional, pluggable type system for {FORTH}},
  year      = {2015},
  file      = {:by-author/R/Riegler/2015_Riegler.pdf:PDF},
  keywords  = {Compiler Design; Computer Languages; Computer Science (CS); FORTH; Programming Languages; Static Typing; Type Systems},
  owner     = {saulius},
  timestamp = {2019.09.18},
  creationdate = {2019-09-18T00:00:00},
  url       = {http://repositum.tuwien.ac.at/obvutwhs/download/pdf/1643514?originalFilename=true},
}

@Presentation{Courtois2014,
  author    = {Nicolas T. Courtois},
  title     = {Cryptanalysis of {GOST}},
  year      = {2014},
  school    = {University College London, UK},
  file      = {:by-author/C/Courtois/2014_Courtois.pdf:PDF},
  keywords  = {Computer Science (CS); Cryptography; GOST; Russian Encryption Algorithms},
  owner     = {saulius},
  timestamp = {2019.09.18},
  creationdate = {2019-09-18T00:00:00},
  url       = {http://nicolascourtois.com/papers/GOST.pdf},
}

@TechReport{Stanley2009,
  author      = {Terry Stanley and Tyler Close and Mark S. Miller},
  institution = {Hewlett-Packard Development Company, L.P.},
  title       = {Causeway: a message-oriented distributed debugger},
  year        = {2009},
  file        = {:by-author/S/Stanley/2009_Stanley.pdf:PDF},
  owner       = {saulius},
  timestamp = {2019.09.18},
  creationdate = {2019-09-18T00:00:00},
  url         = {https://www.hpl.hp.com/techreports/2009/HPL-2009-78.pdf},
}

@Presentation{Squeeze2011,
  author    = {Schaper, F.},
  title     = {Entropy rules! {D}isorder. {S}queeze},
  year      = {2011},
  file      = {:by-author/S/Schaper/2011_Schaper.pdf:PDF},
  keywords  = {Chemical Crystallography; Disorder; Shelx; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2019.09.18},
  creationdate = {2019-09-18T00:00:00},
  url       = {https://www.chemistry.mcmaster.ca/~xman/cccw17/files/What%20to%20do%20with%20disorder.pdf},
}

@Manual{Solntsev2013,
  title     = {Tutorial: disorder refinement and using {CRYSTALS} software},
  author    = {Pavlo V. Solntsev},
  year      = {2013},
  file      = {:by-author/S/Solntsev/2013_Solntsev.pdf:PDF},
  keywords  = {Chemical Crystallography; Disorder; Refinement; X-ray Crystallography},
  owner     = {saulius},
  timestamp = {2019.09.18},
  creationdate = {2019-09-18T00:00:00},
  url       = {http://www.xtl.ox.ac.uk/wp-content/uploads/2013/04/crystals_disorder_manual-2013-04-09.pdf},
}

@Presentation{King2005,
  author    = {Philip King},
  title     = {{Cmp} {Sci} 187: {I}ntroduction to {S}oftware {D}esign},
  year      = {2005},
  file      = {:by-author/K/King/2005_King.pdf:PDF},
  keywords  = {Computer Science (CS); Software Design},
  owner     = {saulius},
  timestamp = {2019.09.18},
  creationdate = {2019-09-18T00:00:00},
  url       = {https://people.cs.umass.edu/~moss/187/lectures/lecture-b-sw-design.pdf},
}

@Misc{Tutorial,
  author    = {{Tutorials Point}},
  title     = {Software Engineering},
  year      = {2014},
  comment   = {via https://www.tutorialspoint.com/software_engineering/software_engineering_tutorial.pdf},
  file      = {:by-author/T/TutorialsPoint/2014_TutorialsPoint.pdf:PDF},
  keywords  = {Computer Science (CS); Software Design},
  owner     = {saulius},
  timestamp = {2019.09.18},
  creationdate = {2019-09-18T00:00:00},
  url       = {https://www.tutorialspoint.com/software_engineering/software_engineering_tutorial.pdf},
}

@Presentation{Telkar2010,
  author    = {Nagalaxmi Telkar},
  title     = {Software Design Techniques},
  year      = {2010},
  file      = {:by-author/T/Telkar/2010_Telkar.pdf:PDF},
  keywords  = {Computer Science (CS); Software Design},
  owner     = {saulius},
  timestamp = {2019.09.18},
  creationdate = {2019-09-18T00:00:00},
  url       = {https://www.cs.colorado.edu/~kena/classes/5828/s10/presentations/softwaredesign.pdf},
}

@Webpage{Harris2015,
  author    = {Todd Harris},
  retrieved = {2019-08-18},
  title     = {It’s time to reboot bioinformatics education},
  url       = {http://toddharris.net/blog/2015/03/23/its-time-to-reboot-bioinformatics-education/},
  month     = {March},
  year      = {2015},
  file      = {:by-author/H/Harris/2015_Harris.odt:OpenDocument text},
  keywords  = {Bioinformatics; Computer Science (CS); Necessary Education; Skills; Teaching},
  owner     = {saulius},
  timestamp = {2019.09.18},
  creationdate = {2019-09-18T00:00:00},
}

@Article{Read1977,
  author    = {Ronald C. Read and Derek G. Corneil},
  journal   = {Journal of Graph Theory},
  title     = {The graph isomorphism disease},
  year      = {1977},
  number    = {4},
  pages     = {339--363},
  volume    = {1},
  doi       = {10.1002/jgt.3190010410},
  file      = {:by-author/R/Read/1977_Read_339.pdf:PDF},
  keywords  = {Algorithms; Graph Isomorphism},
  owner     = {saulius},
  publisher = {Wiley},
  timestamp = {2019.09.18},
  creationdate = {2019-09-18T00:00:00},
}

@Article{Bauersfeld1973,
  author    = {G. Bauersfeld and Ch. Essmann and H. Löhle},
  journal   = {Computing},
  title     = {Algorithmus zur {F}eststellung der {I}somorphie von endlichen, zusammenhängenden {G}raphen},
  year      = {1973},
  month     = {jun},
  number    = {2},
  pages     = {159--168},
  volume    = {11},
  doi       = {10.1007/bf02252905},
  file      = {:by-author/B/Bauersfeld/1973_Bauersfeld_159.pdf:PDF},
  keywords  = {Algorithms; Graph Isomorphism},
  owner     = {saulius},
  publisher = {Springer Science and Business Media {LLC}},
  timestamp = {2019.09.20},
  creationdate = {2019-09-20T00:00:00},
}

@Article{Ming1971,
  author    = {Tao-Kuang Ming and Stephen J. Tauber},
  journal   = {Journal of Chemical Documentation},
  title     = {Chemical Structure and Substructure Search by Set Reduction},
  year      = {1971},
  month     = {feb},
  number    = {1},
  pages     = {47--51},
  volume    = {11},
  doi       = {10.1021/c160040a011},
  file      = {:by-author/M/Ming/1971_Ming_47.pdf:PDF},
  keywords  = {Algorithms; Graph Isomorphism},
  owner     = {saulius},
  publisher = {American Chemical Society ({ACS})},
  timestamp = {2019.09.20},
  creationdate = {2019-09-20T00:00:00},
}

@Article{Scalise2015,
  author    = {Dominic Scalise and Rebecca Schulman},
  journal   = {Natural Computing},
  title     = {Emulating cellular automata in chemical reaction{\textendash}diffusion networks},
  year      = {2015},
  month     = {jun},
  number    = {2},
  pages     = {197--214},
  volume    = {15},
  doi       = {10.1007/s11047-015-9503-8},
  file      = {:by-author/S/Scalise/2015_Scalise_197.pdf:PDF},
  keywords  = {Cellular Automata; Chemistry},
  owner     = {saulius},
  publisher = {Springer Science and Business Media {LLC}},
  timestamp = {2019.10.06},
  creationdate = {2019-10-06T00:00:00},
}

@Manuscript{Reeder2019,
  author    = {Mark Reeder},
  title     = {Notes on Group Theory},
  year      = {2019},
  url       = {https://www2.bc.edu/mark-reeder/Groups.pdf},
  file      = {:by-author/R/Reeder/2019_Reeder.pdf:PDF},
  owner     = {saulius},
  timestamp = {2019.10.11},
  creationdate = {2019-10-11T00:00:00},
}

@Manuscript{Holdener2001,
  author    = {Judy Holdener},
  title     = {Subgroups generated by subsets},
  year      = {2001},
  keywords  = {Abstract Algebra; Algorithms; Generating a Group; Mathematics; Restoring Spacegroup},
  month     = {July},
  url       = {http://personal.kenyon.edu/holdenerj/Projects/Abstract%20Algebra/Groups%20generated%20by%20subsets.pdf},
  file      = {:by-author/H/Holdener/2001_Holdener.pdf:PDF},
  owner     = {saulius},
  timestamp = {2019.10.12},
  creationdate = {2019-10-12T00:00:00},
}

@Manuscript{Hulpke2000,
  author    = {Alexander Hulpke},
  title     = {Using {GAP}},
  year      = {2000},
  keywords  = {GAP; Mathematics},
  url       = {https://www.math.colostate.edu/~hulpke/paper/gap4tut.pdf},
  file      = {:by-author/H/Hulpke/2000_Hulpke.pdf:PDF},
  owner     = {saulius},
  timestamp = {2019.10.12},
  creationdate = {2019-10-12T00:00:00},
}

@Article{Milner1978,
  author    = {Robin Milner},
  journal   = {Journal of Computer and System Sciences},
  title     = {A theory of type polymorphism in programming},
  year      = {1978},
  month     = {dec},
  number    = {3},
  pages     = {348--375},
  volume    = {17},
  doi       = {10.1016/0022-0000(78)90014-4},
  file      = {:by-author/M/Milner/1978_Milner_348.pdf:PDF},
  keywords  = {Computer Languages; Computer Science (CS); Programming Languages; Type Systems},
  owner     = {saulius},
  publisher = {Elsevier {BV}},
  timestamp = {2019.11.06},
  creationdate = {2019-11-06T00:00:00},
}

@Article{Lua2003,
  author       = {Rhonald Lua and Alexander L. Borovinskiy and Alexander Yu. Grosberg},
  journal      = {ArXiv},
  title        = {Fractal and statistical properties of large compact polymers: a computational study},
  year         = {2003},
  pages        = {305406},
  abstract     = {We propose a novel combinatorial algorithm for efficient generation of Hamiltonian walks and cycles on a cubic lattice, modeling the conformations of lattice toy proteins. Through extensive tests on small lattices (allowing complete enumeration of Hamiltonian paths), we establish that the new algorithm, although not perfect, is a significant improvement over the earlier approach by Ramakrishnan et. al., as it generates the sample of conformations with dramatically reduced statistical bias. Using this method, we examine the fractal properties of typical compact conformations. In accordance with Flory theorem celebrated in polymer physics, chain pieces are found to follow Gaussian statistics on the scale smaller than the globule size. Cross-over to this Gaussian regime is found to happen at the scales which are numerically somewhat larger than previously believed. We further used Alexander and Vassiliev degrees 2 and 3 topological invariants to identify the trivial knots among the Hamiltonian loops. We found that the probability of being knotted increases with loop length much faster than it was previously thought, and that chain pieces are consistently more compact than Gaussian if the global loop topology is that of a trivial knot.},
  date         = {2003-05-16},
  eprint       = {http://arxiv.org/abs/cond-mat/0305406v1},
  eprintclass  = {cond-mat.soft},
  eprinttype   = {arXiv},
  file         = {:by-author/L/Lua/2003_Lua_305406.pdf:PDF},
  journaltitle = {Polymer, v. 45, n. 2, p. 717-731, 2004.},
  keywords     = {Computer Simulation; Polymer Generatio; Random Knots},
  owner        = {saulius},
  timestamp = {2019.12.30},
  creationdate = {2019-12-30T00:00:00},
  url          = {https://arxiv.org/abs/cond-mat/0305406v1},
}

@Article{Lua2006,
  author          = {Lua, Rhonald C and Grosberg, Alexander Y},
  journal         = {PLoS computational biology},
  title           = {Statistics of knots, geometry of conformations, and evolution of proteins.},
  year            = {2006},
  issn            = {1553-7358},
  month           = may,
  pages           = {e45},
  volume          = {2},
  abstract        = {Like shoelaces, the backbones of proteins may get entangled and form knots. However, only a few knots in native proteins have been identified so far. To more quantitatively assess the rarity of knots in proteins, we make an explicit comparison between the knotting probabilities in native proteins and in random compact loops. We identify knots in proteins statistically, applying the mathematics of knot invariants to the loops obtained by complementing the protein backbone with an ensemble of random closures, and assigning a certain knot type to a given protein if and only if this knot dominates the closure statistics (which tells us that the knot is determined by the protein and not by a particular method of closure). We also examine the local fractal or geometrical properties of proteins via computational measurements of the end-to-end distance and the degree of interpenetration of its subchains. Although we did identify some rather complex knots, we show that native conformations of proteins have statistically fewer knots than random compact loops, and that the local geometrical properties, such as the crumpled character of the conformations at a certain range of scales, are consistent with the rarity of knots. From these, we may conclude that the known "protein universe" (set of native conformations) avoids knots. However, the precise reason for this is unknown--for instance, if knots were removed by evolution due to their unfavorable effect on protein folding or function or due to some other unidentified property of protein evolution.},
  chemicals       = {Proteins},
  citation-subset = {IM},
  completed       = {2007-05-21},
  country         = {United States},
  creationdate    = {2019-12-30T00:00:00},
  doi             = {10.1371/journal.pcbi.0020045},
  file            = {:by-author/L/Lua/2006_Lua_45.pdf:PDF},
  issn-linking    = {1553-734X},
  issue           = {5},
  keywords        = {Chemistry; Evolution; Genetics; Metabolism; Models; Molecular; Molecular Weight (MW); Probability; Protein Conformation; Protein Folding; Proteins},
  nlm-id          = {101238922},
  owner           = {saulius},
  pmc             = {PMC1463020},
  pmid            = {16710448},
  pubmodel        = {Print-Electronic},
  pubstatus       = {ppublish},
  revised         = {2018-11-13},
  timestamp       = {2019.12.30},
}

@Article{Jamroz2014,
  author    = {Michal Jamroz and Wanda Niemyska and Eric J. Rawdon and Andrzej Stasiak and Kenneth C. Millett and Piotr Su{\l}kowski and Joanna I. Sulkowska},
  journal   = {Nucleic Acids Research},
  title     = {{KnotProt}: a database of proteins with knots and slipknots},
  year      = {2014},
  month     = {oct},
  number    = {D1},
  pages     = {D306--D314},
  volume    = {43},
  doi       = {10.1093/nar/gku1059},
  file      = {:by-author/J/Jamroz/2014_Jamroz_306.pdf:PDF},
  keywords  = {Database; Knots; Proteins},
  owner     = {saulius},
  publisher = {Oxford University Press ({OUP})},
  timestamp = {2019.12.30},
  creationdate = {2019-12-30T00:00:00},
  url       = {https://academic.oup.com/nar/article/43/D1/D306/2436960},
}

@Article{Comoglio2011,
  author          = {Comoglio, Federico and Rinaldi, Maurizio},
  journal         = {{PloS} {O}ne},
  title           = {A topological framework for the computation of the {HOMFLY} polynomial and its application to proteins.},
  year            = {2011},
  issn            = {1932-6203},
  month           = apr,
  pages           = {e18693},
  volume          = {6},
  abstract        = {Polymers can be modeled as open polygonal paths and their closure generates knots. Knotted proteins detection is currently achieved via high-throughput methods based on a common framework insensitive to the handedness of knots. Here we propose a topological framework for the computation of the HOMFLY polynomial, an handedness-sensitive invariant. Our approach couples a multi-component reduction scheme with the polynomial computation. After validation on tabulated knots and links the framework was applied to the entire Protein Data Bank along with a set of selected topological checks that allowed to discard artificially entangled structures. This led to an up-to-date table of knotted proteins that also includes two newly detected right-handed trefoil knots in recently deposited protein structures. The application range of our framework is not limited to proteins and it can be extended to the topological analysis of biological and synthetic polymers and more generally to arbitrary polygonal paths.},
  chemicals       = {Proteins},
  citation-subset = {IM},
  completed       = {2011-08-30},
  country         = {United States},
  doi             = {10.1371/journal.pone.0018693},
  file            = {:by-author/C/Comoglio/2011_Comoglio_18693.pdf:PDF},
  issn-linking    = {1932-6203},
  issue           = {4},
  keywords        = {Algorithms; Chemistry; Models; Proteins; Theoretical},
  nlm-id          = {101285081},
  owner           = {saulius},
  pmc             = {PMC3076383},
  pmid            = {21533239},
  pubmodel        = {Electronic},
  pubstatus       = {epublish},
  revised         = {2019-12-10},
  timestamp = {2019.12.30},
  creationdate = {2019-12-30T00:00:00},
}

@Article{Liang1994,
  author    = {Chengzhi Liang and Kurt Mislow},
  journal   = {Journal of the American Chemical Society},
  title     = {Knots in proteins},
  year      = {1994},
  month     = {nov},
  number    = {24},
  pages     = {11189--11190},
  volume    = {116},
  doi       = {10.1021/ja00103a057},
  file      = {:by-author/L/Liang/1994_Liang_11189.pdf:PDF},
  keywords  = {Knots; Proteins},
  owner     = {saulius},
  publisher = {American Chemical Society ({ACS})},
  timestamp = {2019.12.30},
  creationdate = {2019-12-30T00:00:00},
}

@PhdThesis{Bangert2002,
  author    = {Patrick David Bangert},
  school    = {University College London},
  title     = {Algorithmic problems in the braid groups},
  year      = {2002},
  file      = {:by-author/B/Bangert/2002_Bangert.pdf:PDF},
  keywords  = {Braid Groups; Knot Theory; Mathematics},
  owner     = {saulius},
  timestamp = {2020.01.02},
  creationdate = {2020-01-02T00:00:00},
  url       = {http://212.201.48.1/pbangert/site/doc/Thesis.pdf},
}

@Article{Zaksauskas2020,
  author    = {Audrius Zakšauskas and Edita Čapkauskaitė and Linas Jezepčikas and Vaida Linkuvienė and Vaida Paketurytė and Alexey Smirnov and Janis Leitans and Andris Kazaks and Elviss Dvinskis and Elena Manakova and Saulius Gražulis and Kaspars Tars and Daumantas Matulis},
  journal   = {European Journal of Medicinal Chemistry},
  title     = {Halogenated and di-substituted benzenesulfonamides as selective inhibitors of carbonic anhydrase isoforms},
  year      = {2020},
  month     = {jan},
  pages     = {111825},
  volume    = {185},
  doi       = {10.1016/j.ejmech.2019.111825},
  file      = {:by-author/Z/Zakšauskas/2020_Zakšauskas_111825.pdf:PDF},
  keywords  = {Benzenesulphonamides; Human Carbonic Anhydrases; Inhibitors; Sulphonamides},
  owner     = {saulius},
  publisher = {Elsevier {BV}},
  timestamp = {2020.01.02},
  creationdate = {2020-01-02T00:00:00},
}

@Article{Stasyuk2020,
  author    = {Anton J. Stasyuk and Olga A. Stasyuk and Miquel Sol{\`{a}} and Alexander A. Voityuk},
  journal   = {Chemical Communications},
  title     = {Cyclo[18]carbon: the smallest all-carbon electron acceptor},
  year      = {2020},
  number    = {3},
  pages     = {352--355},
  volume    = {56},
  doi       = {10.1039/c9cc08399e},
  file      = {:by-author/S/Stasyuk/2020_Stasyuk_352.pdf:PDF},
  keywords  = {Alothropes; Carnon; QM Calculations},
  owner     = {saulius},
  publisher = {Royal Society of Chemistry ({RSC})},
  timestamp = {2020.01.02},
  creationdate = {2020-01-02T00:00:00},
}

@Article{Grabowski2019,
  author    = {Marek Grabowski and Marcin Cymborowski and Przemyslaw J. Porebski and Tomasz Osinski and Ivan G. Shabalin and David R. Cooper and Wladek Minor},
  journal   = {Structural Dynamics},
  title     = {The Integrated Resource for Reproducibility in Macromolecular Crystallography: Experiences of the first four years},
  year      = {2019},
  month     = {nov},
  number    = {6},
  pages     = {064301},
  volume    = {6},
  doi       = {10.1063/1.5128672},
  file      = {:by-author/G/Grabowski/2019_Grabowski_64301.pdf:PDF},
  keywords  = {Crystallography; Database; Image Data; Protein Crystallography},
  owner     = {saulius},
  publisher = {{AIP} Publishing},
  timestamp = {2020.01.02},
  creationdate = {2020-01-02T00:00:00},
}

@Standard{ISO2019,
  institution  = {ISO},
  organization = {ISO/IEC JTC1},
  title        = {Information technology — artificial intelligence — artificial intelligence concepts and terminology},
  author       = {{ISO}},
  url          = {https://isotc.iso.org/livelink/livelink/open/jtc1sc42},
  year         = {2019},
  file         = {:by-author/I/ISO/2019_ISO_22989.pdf:PDF},
  keywords     = {Artificial Intelligence (AI); Machine Learning (ML); Standard; Terminology},
  owner        = {saulius},
  timestamp = {2020.01.02},
  creationdate = {2020-01-02T00:00:00},
}

@PhdThesis{Saikunas2019a,
  author    = {Audrius Šaikūnas},
  school    = {Vilnius university},
  title     = {{E}arley virtualiųjų mašinų panaudojimas plečiamai programavimo kalbų sintaksinei analizei (daktaro disertacijos santrauka)},
  year      = {2019},
  file      = {:by-author/Š/Šaikūnas/2019_Šaikūnas_santrauka_v14.pdf:PDF;:by-author/Š/Šaikūnas/2019_Šaikūnas_santrauka.pdf:PDF;:by-author/Š/Šaikūnas/2019_Šaikūnas_email.pdf:PDF},
  keywords  = {Compiler Constructions; Computer Science (CS); Earley Parser; Extensible Languages; Parsing},
  owner     = {saulius},
  timestamp = {2020.01.02},
  creationdate = {2020-01-02T00:00:00},
  url       = {https://www.mii.lt/files/doc/lt/doktorantura/apgintos_disertacijos/dmsti_dis_san_2019_saikunass.pdf},
}

@PhdThesis{Saikunas2019,
  author    = {Audrius Šaikūnas},
  school    = {Vilnius university},
  title     = {Extensible parsing with {E}arley virtual machines},
  year      = {2019},
  file      = {:by-author/Š/Šaikūnas/2019_Šaikūnas_v15.pdf:PDF;:by-author/Š/Šaikūnas/2019_Šaikūnas.pdf:PDF;:by-author/Š/Šaikūnas/2019_Šaikūnas_email.pdf:PDF},
  keywords  = {Compiler Constructions; Computer Science (CS); Earley Parser; Extensible Languages; Parsing},
  owner     = {saulius},
  timestamp = {2020.01.02},
  creationdate = {2020-01-02T00:00:00},
  url       = {https://www.mii.lt/files/doc/lt/doktorantura/apgintos_disertacijos/dmsti_dis_2019_saikunass.pdf},
}

@Manuscript{Gojman2004,
  author    = {Benjamin Gojman},
  title     = {Adiabatic Logic},
  year      = {2004},
  keywords  = {CMOS; Computer Circuits; Computer Science (CS); Electronics; Logic; Quantum Computing},
  url       = {http://www.dna.caltech.edu/cbsss/finalreport/nanoscale_ind_gojman.pdf},
  file      = {:by-author/G/Gojman/2004_Gojman.pdf:PDF},
  owner     = {saulius},
  timestamp = {2020.01.02},
  creationdate = {2020-01-02T00:00:00},
}

@Article{Chen2019,
  author    = {Qiao Yi Chen and Thomas DesMarais and Max Costa},
  journal   = {Annual Review of Pharmacology and Toxicology},
  title     = {Metals and mechanisms of carcinogenesis},
  year      = {2019},
  month     = {jan},
  number    = {1},
  pages     = {537--554},
  volume    = {59},
  doi       = {10.1146/annurev-pharmtox-010818-021031},
  file      = {:by-author/C/Chen/2019_Chen_537.pdf:PDF},
  keywords  = {Biochemistry; Carcinogenesis; Metals},
  owner     = {saulius},
  publisher = {Annual Reviews},
  timestamp = {2020.01.02},
  creationdate = {2020-01-02T00:00:00},
}

@Article{Yoshikawa2019,
  author    = {Naruki Yoshikawa and Geoffrey R. Hutchison},
  journal   = {Journal of Cheminformatics},
  title     = {Fast, efficient fragment-based coordinate generation for {O}pen {B}abel},
  year      = {2019},
  month     = {aug},
  number    = {1},
  pages     = {49},
  volume    = {11},
  doi       = {10.1186/s13321-019-0372-5},
  file      = {:by-author/Y/Yoshikawa/2019_Yoshikawa_49.pdf:PDF},
  keywords  = {Chemiinformatics; Computer Science (CS); Conformer Library Generation; OpenBabel},
  owner     = {saulius},
  publisher = {Springer Science and Business Media {LLC}},
  timestamp = {2020.01.02},
  creationdate = {2020-01-02T00:00:00},
}

@Manuscript{Chakravarty2013,
  author    = {Sambuddho Chakravarty and Marco V. Barbera and Georgios Portokalidis and Michalis Polychronakis and Angelos D. Keromytis},
  title     = {On the effectiveness of traffic analysis against anonymity networks using flow records},
  year      = {2013},
  keywords  = {Anonymity; Attack; Computer Science (CS); Privacy; Timing Analysis; Tor; Traffic Analysis; Web},
  url       = {https://mice.cs.columbia.edu/getTechreport.php?techreportID=1545&format=pdf},
  file      = {:by-author/C/Chakravarty/2013_Chakravarty_1545.pdf:PDF},
  owner     = {saulius},
  timestamp = {2020.01.02},
  creationdate = {2020-01-02T00:00:00},
}

@Manuscript{Gelman2006,
  author    = {Andrew Gelman and Hal Stern},
  title     = {The difference between “significant” and “not significant” is not itself statistically significant},
  year      = {2006},
  keywords  = {Mathematics; Statistics},
  url       = {http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.65.3470},
  file      = {:by-author/G/Gelman/2006_Gelman.pdf:PDF},
  owner     = {saulius},
  timestamp = {2020.01.02},
  creationdate = {2020-01-02T00:00:00},
}

@Manuscript{Rodeheffer2008,
  author    = {Thomas L. Rodeheffer},
  title     = {Software integer division},
  year      = {2008},
  keywords  = {Algorithms; Computer Science (CS); Division},
  url       = {https://www.microsoft.com/en-us/research/wp-content/uploads/2008/08/tr-2008-141.pdf},
  file      = {:by-author/R/Rodeheffer/2008_Rodeheffer_141.pdf:PDF},
  owner     = {saulius},
  pages     = {141},
  timestamp = {2020.01.02},
  creationdate = {2020-01-02T00:00:00},
}

@Article{Fitting1994,
  author    = {Melvin Fitting},
  journal   = {Fundamenta Informaticae},
  title     = {Kleene’s three-valued logics and their children},
  year      = {1994},
  pages     = {113--131},
  volume    = {20},
  abstract  = {Abstract. Kleene’s strong three-valued logic extends naturally to a four-valued logic proposed by Belnap. We introduce a guard connective into Belnap’s logic and consider a few of its properties. Then we show that by using it four-valued analogs of Kleene’s weak three-valued logic, and the asymmetric logic of Lisp are also available. We propose an extension of these ideas to the family of distributive bilattices. Finally we show that for bilinear bilattices the extensions do not produce any new equivalences.},
  comment   = {Cited in: http://homepage.divms.uiowa.edu/~jones/ternary/biblio.shtml},
  file      = {:by-author/F/Fitting/1994_Fitting_113.pdf:PDF},
  keywords  = {Computer Science (CS); Mathematics; Three-valued Logics},
  owner     = {saulius},
  timestamp = {2020.01.02},
  creationdate = {2020-01-02T00:00:00},
  url       = {https://citeseer.ist.psu.edu/viewdoc/summary?doi=10.1.1.93.986},
}

@Article{Alexander1964,
  author    = {W. Alexander},
  journal   = {Electronics and Power},
  title     = {The ternary computer},
  year      = {1964},
  number    = {2},
  pages     = {36},
  volume    = {10},
  doi       = {10.1049/ep.1964.0037},
  file      = {:by-author/A/Alexander/1964_Alexander_36.pdf:PDF},
  keywords  = {Computer Science (CS); Logic Circuits; Ternary},
  owner     = {saulius},
  publisher = {Institution of Engineering and Technology ({IET})},
  timestamp = {2020.01.02},
  creationdate = {2020-01-02T00:00:00},
}

@Webpage{Jones2020,
  author    = {Douglas W. Jones},
  retrieved = {2020-01-02},
  title     = {Ternary bibliography},
  url       = {http://homepage.divms.uiowa.edu/~jones/ternary/biblio.shtml},
  year      = {2020},
  file      = {:by-author/J/Jones/2020_Jones_biblio.pdf:PDF;:by-author/J/Jones/2020_Jones_biblio.odt:OpenDocument text},
  keywords  = {Bibliography; Computer Science (CS); Ternary},
  owner     = {saulius},
  timestamp = {2020.01.02},
  creationdate = {2020-01-02T00:00:00},
}

@Webpage{Jones2020a,
  author    = {Douglas W. Jones},
  retrieved = {2020-01-02},
  title     = {Heptavintimal encoding of ternary values},
  url       = {http://homepage.divms.uiowa.edu/~jones/ternary/hept.shtml},
  year      = {2020},
  file      = {:by-author/J/Jones/2020_Jones_hept.pdf:PDF;:by-author/J/Jones/2020_Jones_hept.odt:OpenDocument text},
  keywords  = {Computer Science (CS); Encoding; Ternary},
  owner     = {saulius},
  timestamp = {2020.01.02},
  creationdate = {2020-01-02T00:00:00},
}

@Article{Gaikwad2012,
  author    = {V. T. Gaikwad and P. R. Deshmukh},
  journal   = {International Journal of Advanced Research in Computer Science and Software Engineering},
  title     = {Multi-valued logic applications in the design of switching circuits},
  year      = {2012},
  issn      = {2277-128X},
  number    = {5},
  pages     = {446--449},
  volume    = {2},
  file      = {:by-author/G/Gaikwad/2012_Gaikwad_446.pdf:PDF},
  keywords  = {CMOS; Circuits; Computer Science (CS); Electronics; Logic; Ternary},
  owner     = {saulius},
  timestamp = {2020.01.02},
  creationdate = {2020-01-02T00:00:00},
  url       = {https://pdfs.semanticscholar.org/c053/170536cbebc50f5e25a572f0f6568ee67725.pdf},
}

@Article{Kumericki2016,
  author      = {Kresimir Kumericki},
  title       = {Feynman Diagrams for Beginners},
  pages       = {160204182},
  abstract    = {We give a short introduction to Feynman diagrams, with many exercises. Text is targeted at students who had little or no prior exposure to quantum field theory. We present condensed description of single-particle Dirac equation, free quantum fields and construction of Feynman amplitude using Feynman diagrams. As an example, we give a detailed calculation of cross-section for annihilation of electron and positron into a muon pair. We also show how such calculations are done with the aid of computer.},
  date        = {2016-02-08},
  eprint      = {http://arxiv.org/abs/1602.04182v1},
  eprintclass = {physics.ed-ph},
  eprinttype  = {arXiv},
  file        = {:by-author/K/Kumericki/2016_Kumericki_160204182.pdf:PDF},
  keywords    = {Feynman Diagrams; Physics},
  owner       = {saulius},
  timestamp = {2020.01.06},
  creationdate = {2020-01-06T00:00:00},
  url         = {https://arxiv.org/abs/1602.04182},
}

@Article{Burton2012,
  author      = {Benjamin A. Burton},
  title       = {Computational topology with {R}egina: algorithms, heuristics and implementations},
  pages       = {12082504},
  abstract    = {Regina is a software package for studying 3-manifold triangulations and normal surfaces. It includes a graphical user interface and Python bindings, and also supports angle structures, census enumeration, combinatorial recognition of triangulations, and high-level functions such as 3-sphere recognition, unknot recognition and connected sum decomposition. This paper brings 3-manifold topologists up-to-date with Regina as it appears today, and documents for the first time in the literature some of the key algorithms, heuristics and implementations that are central to Regina's performance. These include the all-important simplification heuristics, key choices of data structures and algorithms to alleviate bottlenecks in normal surface enumeration, modern implementations of 3-sphere recognition and connected sum decomposition, and more. We also give some historical background for the project, including the key role played by Rubinstein in its genesis 15 years ago, and discuss current directions for future development.},
  date        = {2012-08-13},
  eprint      = {http://arxiv.org/abs/1208.2504v2},
  eprintclass = {math.GT},
  eprinttype  = {arXiv},
  file        = {:by-author/B/Burton/2012_Burton_12082504.pdf:PDF},
  keywords    = {Manifolds; Mathematics; Regina; Software; Topology; Triangulation},
  owner       = {saulius},
  timestamp = {2020.01.08},
  creationdate = {2020-01-08T00:00:00},
  url         = {https://arxiv.org/abs/1208.2504},
}

@Article{Bernstein2020,
  author    = {Herbert J. Bernstein and Lawrence C. Andrews and Jorge A. Diaz and Jean Jakoncic and Thu Nguyen and Nicholas K. Sauter and Alexei S. Soares and Justin Y. Wei and Maciej R. Wlodek and Mario A. Xerri},
  journal   = {Structural Dynamics},
  title     = {Best practices for high data-rate macromolecular crystallography ({HDRMX})},
  year      = {2020},
  month     = {jan},
  number    = {1},
  pages     = {014302},
  volume    = {7},
  doi       = {10.1063/1.5128498},
  file      = {:by-author/B/Bernstein/2020_Bernstein_14302.pdf:PDF},
  keywords  = {Crystallography; Data Management; Macromolecular},
  owner     = {saulius},
  publisher = {{AIP} Publishing},
  timestamp = {2020.01.20},
  creationdate = {2020-01-20T00:00:00},
}

@Article{Bernstein2020a,
  author           = {Bernstein, Herbert J. and Förster, Andreas and Bhowmick, Asmit and Brewster, Aaron S. and Brockhauser, Sandor and Gelisio, Luca and Hall, David R. and Leonarski, Filip and Mariani, Valerio and Santoni, Gianluca and Vonrhein, Clements and Winter, Graeme},
  journal          = {IUCrJ},
  title            = {Gold Standard for macromolecular crystallography diffraction data},
  year             = {2020},
  issn             = {2052-2525},
  month            = {Jul},
  number           = {5},
  pages            = {784--792},
  volume           = {7},
  creationdate     = {2021-09-09T00:00:00},
  doi              = {10.1107/s2052252520008672},
  file             = {:by-author/B/Bernstein/2020_Bernstein_784.pdf:PDF},
  keywords         = {Data Management; Data Reuse; Macromolecular Crystallography; Raw Data; X-ray Data; X-ray Diffraction Images},
  modificationdate = {2024-05-17T15:19:17},
  publisher        = {International Union of Crystallography (IUCr)},
  timestamp        = {2021.09.09},
  url              = {https://doi.org/10.1107/S2052252520008672},
}

@Manuscript{Weiss2008,
  author    = {William A. R. Weiss},
  title     = {An introduction to set theory},
  year      = {2008},
  keywords  = {Mathematics; Set Theory},
  url       = {http://www.math.toronto.edu/weiss/set_theory.pdf},
  file      = {:by-author/W/Weiss/2008_Weiss.pdf:PDF},
  owner     = {saulius},
  timestamp = {2020.01.20},
  creationdate = {2020-01-20T00:00:00},
}

@Manuscript{Schwichtenberg2003,
  author    = {Helmut Schwichtenberg},
  title     = {Mathematical logic},
  year      = {2003},
  keywords  = {Mathematical Logics; Mathematics},
  url       = {https://www.mathematik.uni-muenchen.de/~schwicht/lectures/logic/ws03/ml.pdf},
  file      = {:by-author/S/Schwichtenberg/2003_Schwichtenberg.pdf:PDF},
  owner     = {saulius},
  timestamp = {2020.01.20},
  creationdate = {2020-01-20T00:00:00},
}

@Article{Canepa2010,
  author    = {Pieremanuele Canepa and Robert M. Hanson and Piero Ugliengo and Maria Alfredsson},
  journal   = {Journal of Applied Crystallography},
  title     = {J-{ICE}: a new {Jmol} interface for handling and visualizing crystallographic and electronic properties},
  year      = {2010},
  month     = {dec},
  number    = {1},
  pages     = {225--229},
  volume    = {44},
  doi       = {10.1107/s0021889810049411},
  file      = {:by-author/C/Canepa/2010_Canepa_225.pdf:PDF},
  keywords  = {Computer Graphics; Computer Science (CS); Crystallography; Jmol; Molecular Graphics},
  owner     = {saulius},
  publisher = {International Union of Crystallography ({IUCr})},
  timestamp = {2020.02.03},
  creationdate = {2020-02-03T00:00:00},
}

@Manuscript{Khan2012,
  author    = {M. A. Khan and M. Chiu and M. A. Herbordt},
  title     = {{FPGA}-accelerated molecular dynamics},
  year      = {2012},
  keywords  = {Computer Science (CS); FPGA; Molecular Dynamics (MD)},
  url       = {http://www.bu.edu/caadlab/Khan13.pdf},
  file      = {:by-author/K/Khan/2012_Khan.pdf:PDF},
  owner     = {saulius},
  timestamp = {2020.02.07},
  creationdate = {2020-02-07T00:00:00},
}

@Presentation{Chiu2010,
  author    = {Matt Chiu and Martin Herbordt},
  title     = {Towards production {FPGA}‐accelerated molecular dynamics: progress and challenge},
  year      = {2010},
  file      = {:by-author/C/Chiu/2010_Chiu.pdf:PDF},
  keywords  = {Computer Science (CS); FPGA; Molecular Dynamics (MD)},
  owner     = {saulius},
  timestamp = {2020.02.07},
  creationdate = {2020-02-07T00:00:00},
  url       = {http://www.ncsa.illinois.edu/Conferences/HPRCTA10/presentations/chiu.pdf},
}

@Article{Schaffner2018,
  author      = {Michael Schaffner and Luca Benini},
  journal     = {ArXiv},
  title       = {On the feasibility of {FPGA} acceleration of molecular dynamics simulations},
  year        = {2018},
  pages       = {180804201},
  abstract    = {Classical molecular dynamics (MD) simulations are important tools in life and material sciences since they allow studying chemical and biological processes in detail. However, the inherent scalability problem of particle-particle interactions and the sequential dependency of subsequent time steps render MD computationally intensive and difficult to scale. To this end, specialized FPGA-based accelerators have been repeatedly proposed to ameliorate this problem. However, to date none of the leading MD simulation packages fully support FPGA acceleration and a direct comparison of GPU versus FPGA accelerated codes has remained elusive so far. With this report, we aim at clarifying this issue by comparing measured application performance on GPU-dense compute nodes with performance and cost estimates of a FPGA-based single- node system. Our results show that an FPGA-based system can indeed outperform a similarly configured GPU-based system, but the overall application-level speedup remains in the order of 2x due to software overheads on the host. Considering the price for GPU and FPGA solutions, we observe that GPU-based solutions provide the better cost/performance tradeoff, and hence pure FPGA-based solutions are likely not going to be commercially viable. However, we also note that scaled multi-node systems could potentially benefit from a hybrid composition, where GPUs are used for compute intensive parts and FPGAs for latency and communication sensitive tasks.},
  date        = {2018-08-08},
  eprint      = {http://arxiv.org/abs/1808.04201v1},
  eprintclass = {cs.DC},
  eprinttype  = {arXiv},
  file        = {:by-author/S/Schaffner/2018_Schaffner_180804201.pdf:PDF},
  keywords    = {Computer Science (CS); FPGA; Molecular Dynamics (MD)},
  owner       = {saulius},
  timestamp = {2020.02.07},
  creationdate = {2020-02-07T00:00:00},
  url         = {https://arxiv.org/pdf/1808.04201.pdf},
}

@Presentation{Yang2019,
  author    = {Chen Yang and Tong Geng and Tianqi Wang and Charles Lin and Jiayi Sheng and Vipin Sachdeva and Woody Sherman and Martin Herbordt},
  title     = {Molecular dynamics range-limited force evaluation optimized for {FPGA}},
  year      = {2019},
  file      = {:by-author/Y/Yang/2019_Yang.pdf:PDF},
  keywords  = {Computer Science (CS); FPGA; Molecular Dynamics (MD)},
  owner     = {saulius},
  timestamp = {2020.02.07},
  creationdate = {2020-02-07T00:00:00},
  url       = {https://asap2019.csl.cornell.edu/presentations/48_Yang.pdf},
}

@Manuscript{Yang2019a,
  author    = {Chen Yang and Tong Geng and Tianqi Wang and Charles Lin and Jiayi Sheng and Vipin Sachdeva and Woody Sherman and Martin Herbordt},
  title     = {Molecular dynamics range-limited force evaluation optimized for {FPGA}s},
  year      = {2019},
  keywords  = {Computer Science (CS); FPGA; Molecular Dynamics (MD)},
  url       = {http://www.bu.edu/caadlab/ASAP19b.pdf},
  file      = {:by-author/Y/Yang/2019_Yang_a.pdf:PDF},
  owner     = {saulius},
  timestamp = {2020.02.07},
  creationdate = {2020-02-07T00:00:00},
}

@Article{Yang2019b,
  author      = {Chen Yang and Tong Geng and Tianqi Wang and Rushi Patel and Qingqing Xiong and Ahmed Sanaullah and Jiayi Sheng and Charles Lin and Vipin Sachdeva and Woody Sherman and Martin C. Herbordt},
  journal     = {ArXiv},
  title       = {Fully integrated on-{FPGA} molecular dynamics simulations},
  year        = {2019},
  pages       = {190505359},
  abstract    = {The implementation of Molecular Dynamics (MD) on FPGAs has received substantial attention. Previous work, however, has consisted of either proof-of-concept implementations of components, usually the range-limited force; full systems, but with much of the work shared by the host CPU; or prototype demonstrations, e.g., using OpenCL, that neither implement a whole system nor have competitive performance. In this paper, we present what we believe to be the first full-scale FPGA-based simulation engine, and show that its performance is competitive with a GPU (running Amber in an industrial production environment). The system features on-chip particle data storage and management, short- and long-range force evaluation, as well as bonded forces, motion update, and particle migration. Other contributions of this work include exploring numerous architectural trade-offs and analysis on various mappings schemes among particles/cells and the various on-chip compute units. The potential impact is that this system promises to be the basis for long timescale Molecular Dynamics with a commodity cluster.},
  date        = {2019-05-14},
  eprint      = {http://arxiv.org/abs/1905.05359v1},
  eprintclass = {cs.DC},
  eprinttype  = {arXiv},
  file        = {:by-author/Y/Yang/2019_Yang_190505359.pdf:PDF},
  keywords    = {Computer Science (CS); FPGA; Molecular Dynamics (MD)},
  owner       = {saulius},
  timestamp = {2020.02.07},
  creationdate = {2020-02-07T00:00:00},
  url         = {https://arxiv.org/pdf/1905.05359.pdf},
}

@InProceedings{Waidyasooriya2016,
  author    = {Hasitha Muthumala Waidyasooriya and Masanori Hariyama and Kota Kasahara},
  booktitle = {2016 {IEEE}/{ACIS} 15th International Conference on Computer and Information Science ({ICIS})},
  title     = {Architecture of an {FPGA} accelerator for molecular dynamics simulation using {OpenCL}},
  year      = {2016},
  month     = {jun},
  pages     = {7550743},
  publisher = {{IEEE}},
  doi       = {10.1109/icis.2016.7550743},
  file      = {:by-author/W/Waidyasooriya/2016_Waidyasooriya_7550743.pdf:PDF},
  keywords  = {Computer Science (CS); FPGA; Molecular Dynamics (MD)},
  owner     = {saulius},
  timestamp = {2020.02.07},
  creationdate = {2020-02-07T00:00:00},
}

@TechReport{Collins2018,
  author      = {Sandra Collins and Françoise Genova and Natalie Harrower and Simon Hodson and Sarah Jones and Leif Laaksonen and Daniel Mietchen and Rūta Petrauskaitė and Peter Wittenburg},
  institution = {European Commission Expert Group on FAIR Data},
  title       = {Turning {FAIR} into reality},
  year        = {2018},
  doi         = {10.2777/1524},
  file        = {:by-author/C/Collins/2018_Collins.pdf:PDF},
  keywords    = {Data Management; Data Sharing; European Commission; FAIR},
  owner       = {saulius},
  timestamp = {2020.02.07},
  creationdate = {2020-02-07T00:00:00},
  url         = {https://www.eoscsecretariat.eu/sites/default/files/ki0618206enn.en_.pdf},
}

@TechReport{Witt2015,
  author      = {Michael Witt},
  institution = {Research Data Alliance},
  title       = {23 things: libraries for research data},
  year        = {2015},
  file        = {:by-author/W/Witt/2015_Witt.pdf:PDF},
  keywords    = {Data Management; Data Sharing; FAIR},
  owner       = {saulius},
  timestamp = {2020.02.07},
  creationdate = {2020-02-07T00:00:00},
  url         = {https://rd-alliance.org/system/files/documents/23Things_Libraries_For_Data_Management.pdf},
}

@MastersThesis{Torvalds1997,
  author    = {Linus Torvalds},
  school    = {University of Helsinki, Department of Computer Science},
  title     = {Linux: a portable operating system},
  year      = {1997},
  file      = {:by-author/T/Torvalds/1997_Torvalds.pdf:PDF},
  keywords  = {Computer Science (CS); Linux; OS Architecture; Operating Systems},
  owner     = {saulius},
  timestamp = {2020.02.12},
  creationdate = {2020-02-12T00:00:00},
  url       = {https://www.cs.helsinki.fi/u/kutvonen/index_files/linus.pdf},
}

@Manuscript{Mood2016,
  author    = {Benjamin Mood and Debayan Gupta and Henry Carter and Kevin R. B. Butler and Patrick Traynor},
  title     = {Frigate: a validated, extensible, and efficient compiler and interpreterfor secure computation},
  year      = {2016},
  keywords  = {Compiler Construction; Computer Science (CS); Program Verification},
  url       = {https://www.cise.ufl.edu/~butler/pubs/eurosp16.pdf},
  file      = {:by-author/M/Mood/2016_Mood.pdf:PDF},
  owner     = {saulius},
  timestamp = {2020.03.03},
  creationdate = {2020-03-03T00:00:00},
}

@Article{Kang2018,
  author    = {Jeehoon Kang and Chung-Kil Hur and Kwangkeun Yi and Yoonseung Kim and Youngju Song and Juneyoung Lee and Sanghoon Park and Mark Dongyeon Shin and Yonghyun Kim and Sungkeun Cho and Joonwon Choi},
  journal   = {{ACM} {SIGPLAN} Notices},
  title     = {Crellvm: verified credible compilation for {LLVM}},
  year      = {2018},
  month     = {jun},
  number    = {4},
  pages     = {631--645},
  volume    = {53},
  doi       = {10.1145/3296979.3192377},
  file      = {:by-author/K/Kang/2018_Kang_631.pdf:PDF},
  keywords  = {Compiler Construction; Computer Science (CS); Program Verification},
  owner     = {saulius},
  publisher = {Association for Computing Machinery ({ACM})},
  timestamp = {2020.03.03},
  creationdate = {2020-03-03T00:00:00},
}

@Manual{SGSTHOMSONMicroelectronics1995,
  title        = {{Occam} 2.1 reference manual},
  author       = {{SGS-THOMSONMicroelectronics}},
  month        = {May},
  organization = {SGS-THOMSON Microelectronics Limited},
  year         = {1995},
  file         = {:by-author/S/SGSTHOMSONMicroelectronics/1995_SGSTHOMSONMicroelectronics.pdf:PDF},
  keywords     = {Computer Languages; Computer Science (CS); Occam; Programming Languages},
  owner        = {saulius},
  timestamp = {2020.03.03},
  creationdate = {2020-03-03T00:00:00},
  url          = {http://www.wotug.org/occam/documentation/oc21refman.pdf},
}

@Standard{ISO/IEC2002,
  institution  = {ISO},
  organization = {ISO/IEC},
  title        = {Information technology — {Z} formal specification notation — syntax, type system and semantics},
  author       = {ISO/IEC},
  number       = {ISO/IEC 13568:2002},
  url          = {https://standards.iso.org/ittf/PubliclyAvailableStandards/c021573_ISO_IEC_13568_2002(E).zip},
  year         = {2002},
  file         = {:by-author/I/ISO/IEC/2002_ISO_IEC.pdf:PDF},
  keywords     = {Computer Languages; Computer Science (CS); Standards; Z-notation},
  owner        = {saulius},
  timestamp = {2020.03.03},
  creationdate = {2020-03-03T00:00:00},
}

@Presentation{Hoogeboom2011,
  author    = {Hendrik Jan Hoogeboom},
  title     = {Formal methods in software engineering},
  year      = {2011},
  file      = {:by-author/H/Hoogeboom/2011_Hoogeboom.pdf:PDF},
  keywords  = {Computer Science (CS); Formal Methods; Program Verification; Proof Theory},
  owner     = {saulius},
  timestamp = {2020.03.03},
  creationdate = {2020-03-03T00:00:00},
  url       = {http://liacs.leidenuniv.nl/~hoogeboomhj/praatjes/formalmethods/formalmethods.pdf},
}

@TechReport{Christopher1997,
  author      = {Thomas W. Christopher},
  institution = {Illinois Institute of Technology},
  title       = {{EULER}. {A}n experiment in language definition},
  year        = {1997},
  file        = {:by-author/C/Christopher/1997_Christopher.pdf:PDF},
  keywords    = {Computer Languages; Computer Science (CS); Euler; Programming Languages},
  owner       = {saulius},
  timestamp = {2020.03.03},
  creationdate = {2020-03-03T00:00:00},
  url         = {https://web.archive.org/web/20060901063907/http://www.iit.edu/~tc/euler.pdf},
}

@Article{Milner-White2008,
  author    = {E. James Milner-White},
  journal   = {Protein Science},
  title     = {The partial charge of the nitrogen atom in peptide bonds},
  year      = {2008},
  month     = {dec},
  number    = {11},
  pages     = {2477--2482},
  volume    = {6},
  doi       = {10.1002/pro.5560061125},
  file      = {:by-author/M/Milner-White/2008_Milner-White_2477.pdf:PDF},
  keywords  = {Biochemistry; Bioinformatics; Peptide Bond},
  owner     = {saulius},
  publisher = {Wiley},
  timestamp = {2020.03.06},
  creationdate = {2020-03-06T00:00:00},
}

@Article{Bergstra2019,
  author      = {Jan A. Bergstra and Alban Ponse},
  journal     = {ArXiv},
  title       = {Division by zero in common meadows (v3)},
  year        = {2019},
  pages       = {14066878},
  abstract    = {Common meadows are fields expanded with a total inverse function. Division by zero produces an additional value denoted with "a" that propagates through all operations of the meadow signature (this additional value can be interpreted as an error element). We provide a basis theorem for so-called common cancellation meadows of characteristic zero, that is, common meadows of characteristic zero that admit a certain cancellation law.},
  date        = {2014-06-26},
  eprint      = {http://arxiv.org/abs/1406.6878v3},
  eprintclass = {math.RA},
  eprinttype  = {arXiv},
  file        = {:by-author/B/Bergstra/2019_Bergstra_14066878.pdf:PDF},
  keywords    = {Abstract Algebra; Algebra; Common Meadows; Divison by 0; Mathematics; Meadows},
  owner       = {saulius},
  timestamp = {2020.03.06},
  creationdate = {2020-03-06T00:00:00},
  url         = {http://arxiv.org/abs/1406.6878v3},
}

@Manual{MEL1962,
  title     = {Norbit sub-assemblies {YL.} 6000 series},
  author    = {{Mullard Equipment Limited}},
  month     = {Feb},
  year      = {1962},
  file      = {:by-author/M/MEL/1962_MEL.pdf:PDF},
  keywords  = {Binary Logic; Computer Science (CS); History of Computing; History of Electronics; Logic Gates; RTL; Resistor-transistor Logic; Transistor Gates; Transistor-resistor Logic},
  owner     = {saulius},
  timestamp = {2020.03.08},
  creationdate = {2020-03-08T00:00:00},
  url       = {http://electrojumble.org/DATA/Norbits.pdf},
}

@Article{Spirtes1991,
  author    = {Peter Spirtes and Clark Glymour},
  journal   = {Social Science Computer Review},
  title     = {An algorithm for fast recovery of sparse causal graphs},
  year      = {1991},
  month     = {apr},
  number    = {1},
  pages     = {62--72},
  volume    = {9},
  doi       = {10.1177/089443939100900106},
  file      = {:by-author/S/Spirtes/1991_Spirtes_62.pdf:PDF},
  keywords  = {Algorithms; Causality; Computer Science (CS)},
  owner     = {saulius},
  publisher = {{SAGE} Publications},
  timestamp = {2020.03.08},
  creationdate = {2020-03-08T00:00:00},
}

@InCollection{Helliwell2020,
  author    = {John R. Helliwell},
  booktitle = {Methods in Enzymology},
  publisher = {Elsevier},
  title     = {Fundamentals of neutron crystallography in structural biology},
  year      = {2020},
  pages     = {1--19},
  doi       = {10.1016/bs.mie.2020.01.006},
  file      = {:by-author/H/Helliwell/2020_Helliwell_1.pdf:PDF},
  keywords  = {Crystallography; Neutron},
  owner     = {saulius},
  timestamp = {2020.03.08},
  creationdate = {2020-03-08T00:00:00},
}

@Article{Bergstra2015,
  author    = {Jan A. Bergstra and Inge Bethke and Alban Ponse},
  journal   = {Journal of Applied Logic},
  title     = {Equations for formally real meadows},
  year      = {2015},
  month     = {jun},
  number    = {2},
  pages     = {1--23},
  volume    = {13},
  doi       = {10.1016/j.jal.2015.01.004},
  file      = {:by-author/B/Bergstra/2015_Bergstra_1.pdf:PDF},
  keywords  = {Computer Science (CS); Division by 0; Mathematics; Meadows},
  owner     = {saulius},
  publisher = {Elsevier {BV}},
  timestamp = {2020.03.08},
  creationdate = {2020-03-08T00:00:00},
}

@Manuscript{Raesch2019,
  author    = {Thoralf Räsch},
  title     = {Lineare {A}lgebra},
  year      = {2019},
  keywords  = {Lectures; Linear Algebra; Mathematics},
  month     = {oct},
  url       = {https://www.math.uni-bonn.de/people/raesch/Papers_and_Notes/ThR_LA_Skript.pdf},
  file      = {:by-author/R/Räsch/2019_Räsch.pdf:PDF},
  owner     = {saulius},
  timestamp = {2020.03.08},
  creationdate = {2020-03-08T00:00:00},
  version   = {3.2},
}

@Article{Bergstra2020,
  author    = {Jan A. Bergstra and Alban Ponse},
  journal   = {Acta Informatica},
  title     = {Arithmetical datatypes with true fractions},
  year      = {2020},
  month     = {jan},
  abstract  = {We consider several novel congruences on the signature of meadows with the aim to survey different notions of fractions. In particular we suggest a notion of “true fraction”.},
  doi       = {10.1007/s00236-019-00352-8},
  file      = {:by-author/B/Bergstra/2020_Bergstra.pdf:PDF},
  keywords  = {Computer Science (CS); Division by 0; Mathematics; Meadows},
  owner     = {saulius},
  publisher = {Springer Science and Business Media {LLC}},
  timestamp = {2020.03.08},
  creationdate = {2020-03-08T00:00:00},
}

@Article{Bethke2010,
  author    = {Inge Bethke and Piet Rodenburg},
  journal   = {The Journal of Symbolic Logic},
  title     = {The initial meadows},
  year      = {2010},
  month     = {sep},
  number    = {3},
  pages     = {888--895},
  volume    = {75},
  doi       = {10.2178/jsl/1278682205},
  file      = {:by-author/B/Bethke/2010_Bethke_888.pdf:PDF},
  keywords  = {Computer Science (CS); Division by 0; Mathematics; Meadows},
  owner     = {saulius},
  publisher = {Cambridge University Press ({CUP})},
  timestamp = {2020.03.08},
  creationdate = {2020-03-08T00:00:00},
}

@Article{Bethke2008,
  author      = {Inge Bethke and Piet Rodenburg},
  journal     = {ArXiv},
  title       = {The initial meadows},
  year        = {2008},
  abstract    = {A \emph{meadow} is a commutative ring with an inverse operator satisfying $0^{-1}=0$. We determine the initial algebra of the meadows of characteristic 0 and show that its word problem is decidable.},
  date        = {2008-06-13},
  eprint      = {http://arxiv.org/abs/0806.2256v1},
  eprintclass = {math.RA},
  eprinttype  = {arXiv},
  file        = {:by-author/B/Bethke/2010_Bethke_888.pdf:PDF},
  keywords    = {Computer Science (CS); Division by 0; Mathematics; Meadows; math.RA},
  owner       = {saulius},
  timestamp = {2020.03.08},
  creationdate = {2020-03-08T00:00:00},
}

@Article{Larsen2010,
  author           = {Larsen, Peder Olesen and von Ins, Markus},
  journal          = {Scientometrics},
  title            = {The rate of growth in scientific publication and the decline in coverage provided by {S}cience {C}itation {I}ndex},
  year             = {2010},
  issn             = {0138-9130},
  month            = sep,
  pages            = {575--603},
  volume           = {84},
  abstract         = {The growth rate of scientific publication has been studied from 1907 to 2007 using available data from a number of literature databases, including Science Citation Index (SCI) and Social Sciences Citation Index (SSCI). Traditional scientific publishing, that is publication in peer-reviewed journals, is still increasing although there are big differences between fields. There are no indications that the growth rate has decreased in the last 50 years. At the same time publication using new channels, for example conference proceedings, open archives and home pages, is growing fast. The growth rate for SCI up to 2007 is smaller than for comparable databases. This means that SCI was covering a decreasing part of the traditional scientific literature. There are also clear indications that the coverage by SCI is especially low in some of the scientific areas with the highest growth rate, including computer science and engineering sciences. The role of conference proceedings, open access archives and publications published on the net is increasing, especially in scientific fields with high growth rates, but this has only partially been reflected in the databases. The new publication channels challenge the use of the big databases in measurements of scientific productivity or output and of the growth rate of science. Because of the declining coverage and this challenge it is problematic that SCI has been used and is used as the dominant source for science indicators based on publication and citation numbers. The limited data available for social sciences show that the growth rate in SSCI was remarkably low and indicate that the coverage by SSCI was declining over time. National Science Indicators from Thomson Reuters is based solely on SCI, SSCI and Arts and Humanities Citation Index (AHCI). Therefore the declining coverage of the citation databases problematizes the use of this source.},
  country          = {Netherlands},
  creationdate     = {2020-03-08T00:00:00},
  doi              = {10.1007/s11192-010-0202-z},
  file             = {:by-author/L/Larsen/2010_Larsen_575.pdf:PDF},
  issn-linking     = {0138-9130},
  issue            = {3},
  keywords         = {Bibliometry; Dissemination of Science; Publication Metrics},
  modificationdate = {2023-02-16T15:55:56},
  nlm-id           = {7901197},
  owner            = {saulius},
  pmc              = {PMC2909426},
  pmid             = {20700371},
  pubmodel         = {Print-Electronic},
  pubstatus        = {ppublish},
  revised          = {2019-11-20},
  timestamp        = {2020.03.08},
}

@Article{Samwald2011,
  author    = {Matthias Samwald and Anja Jentzsch and Christopher Bouton and Claus Stie Kallesøe and Egon Willighagen and Janos Hajagos and M. Scott Marshall and Eric Prudhommeaux and Oktie Hassanzadeh and Elgar Pichler and Susie Stephens},
  journal   = {Journal of Cheminformatics},
  title     = {Linked open drug data for pharmaceutical research and development},
  year      = {2011},
  month     = {may},
  number    = {1},
  volume    = {3},
  doi       = {10.1186/1758-2946-3-19},
  file      = {:by-author/S/Samwald/2011_Samwald.pdf:PDF},
  keywords  = {Chemiinformatics; LOD},
  owner     = {saulius},
  publisher = {Springer Science and Business Media {LLC}},
  timestamp = {2020.03.08},
  creationdate = {2020-03-08T00:00:00},
}

@InProceedings{Floyd1967,
  author    = {Floyd, Robert W.},
  booktitle = {Mathematical Aspects of Computer Science},
  title     = {Assigning meanings to programs},
  year      = {1967},
  editor    = {Schwartz, J. T.},
  pages     = {19--32},
  publisher = {American Mathematical Society},
  series    = {Proceedings of Symposium on Applied Mathematics},
  volume    = {19},
  file      = {:by-author/F/Floyd/1967_Floyd_19.pdf:PDF},
  keywords  = {Computer Science (CS); Programming Languages; Semantics},
  owner     = {saulius},
  timestamp = {2020.03.08},
  creationdate = {2020-03-08T00:00:00},
  url       = {https://www.cs.tau.ac.il/~nachumd/term/FloydMeaning.pdf},
}

@InCollection{Parker2015,
  author    = {Matt Parker},
  booktitle = {Things to make and do in the fourth dimension},
  publisher = {Farrar, Straus and Giroux},
  title     = {Schläfli symbols},
  year      = {2015},
  isbn      = {978-0-374-53563-6},
  pages     = {217--219},
  file      = {:by-author/P/Parker/2015_Parker_217.pdf:PDF},
  keywords  = {Mathematics; Polyhedra; Topology},
  owner     = {saulius},
  timestamp = {2020.03.09},
  creationdate = {2020-03-09T00:00:00},
  url       = {http://makeanddo4d.com/},
}

@Article{Yaghi2009,
  author    = {Omar M. Yaghi and Qiaowei Li},
  journal   = {{MRS} Bulletin},
  title     = {Reticular chemistry and metal-organic frameworks for clean energy},
  year      = {2009},
  pages     = {682--690},
  volume    = {34},
  file      = {:by-author/Y/Yaghi/2009_Yaghi_682.pdf:PDF},
  keywords  = {Crystallography; Metal-Organic Frameworks (MOF); Polymers; Reticular Chemistry},
  owner     = {saulius},
  timestamp = {2020.03.09},
  creationdate = {2020-03-09T00:00:00},
  url       = {http://yaghi.berkeley.edu/pdfPublications/09cleanEnergy.pdf},
}

@Article{Nguyen2020,
  author       = {Ha L. Nguyen and Cornelius Gropp and Omar M. Yaghi},
  journal      = {Journal of the American Chemical Society},
  title        = {Reticulating 1D Ribbons into 2D Covalent Organic Frameworks by Imine and Imide Linkages},
  year         = {2020},
  month        = {jan},
  number       = {6},
  pages        = {2771--2776},
  volume       = {142},
  doi          = {10.1021/jacs.9b13971},
  file         = {:by-author/N/Nguyen/2020_Nguyen_2771.pdf:PDF},
  journaltitle = {JACS},
  keywords     = {Metal-Organic Frameworks (MOF)},
  owner        = {saulius},
  publisher    = {American Chemical Society ({ACS})},
  timestamp = {2020.03.09},
  creationdate = {2020-03-09T00:00:00},
  url          = {http://yaghi.berkeley.edu/pdfPublications/20RibbonCOF.pdf},
}

@Article{Bareiss1968,
  author    = {Erwin H. Bareiss},
  journal   = {Mathematics of Computation},
  title     = {Sylvester's identity and multistep integer-preserving gaussian elimination},
  year      = {1968},
  month     = {jul},
  number    = {103},
  pages     = {565},
  volume    = {22},
  doi       = {10.2307/2004533},
  file      = {:by-author/B/Bareiss/1968_Bareiss_565.pdf:PDF},
  groups    = {sg/Linear Algebra},
  keywords  = {Algorithms; Computer Science (CS); Exact Computations; Gaussian Elimination; Mathematics; Rational Arithmetic},
  owner     = {saulius},
  publisher = {{JSTOR}},
  timestamp = {2020.03.29},
  creationdate = {2020-03-29T00:00:00},
}

@Article{Magagnoli2020,
  author    = {Joseph Magagnoli and Siddharth Narendran and Felipe Pereira and Tammy Cummings and James W. Hardin and S. Scott Sutton and Jayakrishna Ambati},
  title     = {Outcomes of hydroxychloroquine usage in {U}nited {S}tates veterans hospitalized with {C}ovid-19},
  year      = {2020},
  month     = {apr},
  doi       = {10.1101/2020.04.16.20065920},
  file      = {:by-author/M/Magagnoli/2020_Magagnoli.pdf:PDF},
  owner     = {saulius},
  publisher = {Cold Spring Harbor Laboratory},
  timestamp = {2020.05.14},
  creationdate = {2020-05-14T00:00:00},
}

@Article{Kaagstroem1980,
  author    = {Bo Kågström and Axel Ruhe},
  journal   = {{ACM} Transactions on Mathematical Software ({TOMS})},
  title     = {An Algorithm for Numerical Computation of the Jordan Normal Form of a Complex Matrix},
  year      = {1980},
  month     = {sep},
  number    = {3},
  pages     = {398--419},
  volume    = {6},
  doi       = {10.1145/355900.355912},
  file      = {:by-author/K/Kågström/1980_Kågström_398.pdf:PDF},
  groups    = {sg/Linear Algebra},
  owner     = {saulius},
  publisher = {Association for Computing Machinery ({ACM})},
  timestamp = {2020.05.14},
  creationdate = {2020-05-14T00:00:00},
  url       = {https://doi.org/10.1145/355900.355912},
}

@Article{Kabsch1984,
  author    = {W. Kabsch and C. Sander},
  journal   = {Proceedings of the National Academy of Sciences},
  title     = {On the use of sequence homologies to predict protein structure: identical pentapeptides can have completely different conformations.},
  year      = {1984},
  month     = {feb},
  number    = {4},
  pages     = {1075--1078},
  volume    = {81},
  doi       = {10.1073/pnas.81.4.1075},
  file      = {:by-author/K/Kabsch/1984_Kabsch_1075.pdf:PDF},
  owner     = {saulius},
  publisher = {Proceedings of the National Academy of Sciences},
  timestamp = {2020.05.14},
  creationdate = {2020-05-14T00:00:00},
}

@Article{Hung1998,
  author    = {Li-Wei Hung and Masanori Kohmura and Yasuo Ariyoshi and Sung-Hou Kim},
  title     = {Structure of an enantiomeric protein, {D}-{M}onellin at 1.8~{Å} resolution},
  year      = {1998},
  month     = {jul},
  number    = {4},
  pages     = {494--500},
  volume    = {54},
  comment   = {"Mirrored" protein from D-amino acids.},
  doi       = {10.1107/s0907444997012225},
  file      = {:by-author/H/Hung/1998_Hung_494.pdf:PDF},
  keywords  = {Assymmetry of Life; Mirrored Protein; Protein From D-amino Acids},
  owner     = {saulius},
  publisher = {International Union of Crystallography ({IUCr})},
  timestamp = {2020.05.14},
  creationdate = {2020-05-14T00:00:00},
}

@Presentation{Black2011,
  author    = {Andrew P. Black},
  title     = {Object - oriented programming: challenges for the next fifty years},
  year      = {2011},
  file      = {:by-author/B/Black/2011_Black.pdf:PDF},
  keywords  = {Computer Science (CS); OO Programming; Programming Languages; Simula67},
  owner     = {saulius},
  timestamp = {2020.05.14},
  creationdate = {2020-05-14T00:00:00},
  url       = {http://simula67.at.ifi.uio.no/Archive/AP-Black-talk-2011.pdf},
}

@Article{Sun2018,
  author    = {Qi Sun and Briana Aguila and Shengqian Ma},
  journal   = {Chem},
  title     = {Metalloenzyme mimicry at the nodes of metal-organic frameworks},
  year      = {2018},
  month     = {dec},
  number    = {12},
  pages     = {2736--2738},
  volume    = {4},
  doi       = {10.1016/j.chempr.2018.11.017},
  file      = {:by-author/S/Sun/2018_Sun_2736.pdf:PDF},
  owner     = {saulius},
  publisher = {Elsevier {BV}},
  timestamp = {2020.05.19},
  creationdate = {2020-05-19T00:00:00},
}

@Article{Villadsen2018,
  author    = {J{\o}rgen Villadsen and Andreas Halkj{\ae}r From and Anders Schlichtkrull},
  journal   = {Electronic Proceedings in Theoretical Computer Science},
  title     = {Natural deduction and the {I}sabelle proof assistant},
  year      = {2018},
  month     = {mar},
  pages     = {140--155},
  volume    = {267},
  doi       = {10.4204/eptcs.267.9},
  file      = {:by-author/V/Villadsen/2018_Villadsen_140.pdf:PDF},
  keywords  = {Formal Proofs; Mathematics; Proff Assistants},
  owner     = {saulius},
  publisher = {Open Publishing Association},
  timestamp = {2020.05.19},
  creationdate = {2020-05-19T00:00:00},
}

@Article{Lamprecht2019,
  author    = {Lamprecht, Anna-Lena and Garcia, Leyla and Kuzak, Mateusz and Martinez, Carlos and Arcila, Ricardo and Martin Del Pico, Eva and Dominguez Del Angel, Victoria and van de Sandt, Stephanie and Ison, Jon and Martinez, Paula Andrea and McQuilton, Peter and Valencia, Alfonso and Harrow, Jennifer and Psomopoulos, Fotis and Gelpi, Josep Ll. and Chue Hong, Neil and Goble, Carole and Capella-Gutierrez, Salvador},
  journal   = {Data Science},
  title     = {Towards {FAIR} principles for research software},
  year      = {2019},
  issn      = {2451-8492},
  number    = {Preprint},
  pages     = {1--23},
  volume    = {Preprint},
  abstract  = {The FAIR Guiding Principles, published in 2016, aim to improve the findability, accessibility, interoperability and reusability of digital research objects for both humans and machines. Until now the FAIR principles have been mostly applied to research data. The ideas behind these principles are, however, also directly relevant to research software. Hence there is a distinct need to explore how the FAIR principles can be applied to software. In this work, we aim to summarize the current status of the debate around FAIR and software, as basis for the development of community-agreed principles for FAIR research software in the future. We discuss what makes software different from data with regard to the application of the FAIR principles, and which desired characteristics of research software go beyond FAIR. Then we present an analysis of where the existing principles can directly be applied to software, where they need to be adapted or reinterpreted, and where the definition of additional principles is required. Here interoperability has proven to be the most challenging principle, calling for particular attention in future discussions. Finally, we outline next steps on the way towards definite FAIR principles for research software.},
  doi       = {10.3233/DS-190026},
  file      = {:by-author/L/Lamprecht/2019_Lamprecht_1.pdf:PDF},
  keywords  = {FAIR; Reproducible Research; Research Software; Software Sustainability},
  owner     = {saulius},
  publisher = {IOS Press},
  timestamp = {2020.05.19},
  creationdate = {2020-05-19T00:00:00},
}

@Article{Kan2015,
  author    = {Tetsuo Kan and Akihiro Isozaki and Natsuki Kanda and Natsuki Nemoto and Kuniaki Konishi and Hidetoshi Takahashi and Makoto Kuwata-Gonokami and Kiyoshi Matsumoto and Isao Shimoyama},
  journal   = {Nature Communications},
  title     = {Enantiomeric switching of chiral metamaterial for terahertz polarization modulation employing vertically deformable {MEMS} spirals},
  year      = {2015},
  month     = {oct},
  number    = {1},
  volume    = {6},
  doi       = {10.1038/ncomms9422},
  file      = {:by-author/K/Kan/2015_Kan_.pdf:PDF},
  owner     = {saulius},
  publisher = {Springer Science and Business Media {LLC}},
  timestamp = {2020.05.19},
  creationdate = {2020-05-19T00:00:00},
}

@Article{Mendenhall2020,
  author    = {Jeffrey Mendenhall and Benjamin Brown and Sandeepkumar Kothiwale and Jens Meiler},
  title     = {{BCL::Conf} – improved open-source knowledge-based conformation sampling using the {C}rystallographic {O}pen {D}atabase},
  year      = {2020},
  month     = {apr},
  doi       = {10.26434/chemrxiv.12085521.v1},
  file      = {:by-author/M/Mendenhall/2020_Mendenhall.pdf:PDF},
  owner     = {saulius},
  publisher = {American Chemical Society ({ACS})},
  timestamp = {2020.05.19},
  creationdate = {2020-05-19T00:00:00},
}

@Article{Gingeras1978,
  author    = {Gingeras, T. R. and Milazzo, J. P. and Roberts, R. J.},
  journal   = {Nucleic Acids Research},
  title     = {A computer assisted method for the determination of restriction enzyme recognition sites},
  year      = {1978},
  number    = {11},
  pages     = {4105--4128},
  volume    = {5},
  doi       = {10.1093/nar/5.11.4105},
  file      = {:by-author/G/Gingeras/1978_Gingeras_4105.pdf:PDF},
  keywords  = {Algorithms; Bioinformatics; DNA Sequence Processing; Restriction Endonucleases (REases)},
  owner     = {saulius},
  publisher = {Oxford University Press ({OUP})},
  timestamp = {2020.05.30},
  creationdate = {2020-05-30T00:00:00},
}

@Article{Zheng2008a,
  author    = {Yu Zheng and Janos Posfai and Richard D. Morgan and Tamas Vincze and Richard J. Roberts},
  journal   = {Nucleic Acids Research},
  title     = {Using shotgun sequence data to find active restriction enzyme genes},
  year      = {2008},
  month     = {nov},
  number    = {1},
  pages     = {e1--e1},
  volume    = {37},
  doi       = {10.1093/nar/gkn883},
  file      = {:by-author/Z/Zheng/2008_Zheng_1.pdf:PDF},
  keywords  = {Raw Data; Restriction Endonucleases (REases)},
  owner     = {saulius},
  publisher = {Oxford University Press ({OUP})},
  timestamp = {2020.05.30},
  creationdate = {2020-05-30T00:00:00},
}

@Article{Berman2020,
  author    = {Helen M. Berman and Brinda Vallat and Catherine L. Lawson},
  journal   = {{IUCrJ}},
  title     = {The data universe of structural biology},
  year      = {2020},
  month     = {may},
  number    = {4},
  volume    = {7},
  doi       = {10.1107/s205225252000562x},
  file      = {:by-author/B/Berman/2020_Berman.pdf:PDF},
  keywords  = {Data Management; PDB; Scientific Databases; Structural Biology},
  owner     = {saulius},
  publisher = {International Union of Crystallography ({IUCr})},
  timestamp = {2020.05.30},
  creationdate = {2020-05-30T00:00:00},
}

@Article{Li2008,
  author    = {Chuan-Yun Li and Xizeng Mao and Liping Wei},
  journal   = {{PLoS} Computational Biology},
  title     = {Genes and (common) pathways underlying drug addiction},
  year      = {2008},
  month     = {jan},
  number    = {1},
  pages     = {e2},
  volume    = {4},
  doi       = {10.1371/journal.pcbi.0040002},
  editor    = {Peter D Karp},
  file      = {:by-author/L/Li/2008_Li_2.pdf:PDF},
  owner     = {saulius},
  publisher = {Public Library of Science ({PLoS})},
  timestamp = {2020.05.30},
  creationdate = {2020-05-30T00:00:00},
}

@Webpage{BernersLee1998,
  author    = {Tim Berners-Lee},
  retrieved = {2020-05-31},
  title     = {Cool {URI}s don't change},
  url       = {https://www.w3.org/Provider/Style/URI.html},
  year      = {1998},
  abstract  = {What makes a cool URI?
A cool URI is one which does not change.
What sorts of URI change?
URIs don't change: people change them.
There are no reasons at all in theory for people to change URIs (or stop maintaining documents), but millions of reasons in practice.},
  file      = {:by-author/B/Berners-Lee/1998_Berners-Lee.pdf:PDF},
  keywords  = {Identifiers; Web Archietcture},
  owner     = {saulius},
  timestamp = {2020.05.31},
  creationdate = {2020-05-31T00:00:00},
}

@Article{Wilkinson2016,
  author           = {Mark D. Wilkinson and Michel Dumontier and IJsbrand Jan Aalbersberg and Gabrielle Appleton and Myles Axton and Arie Baak and Niklas Blomberg and Jan-Willem Boiten and Luiz Bonino da Silva Santos and Philip E. Bourne and Jildau Bouwman and Anthony J. Brookes and Tim Clark and Merc{\`{e}} Crosas and Ingrid Dillo and Olivier Dumon and Scott Edmunds and Chris T. Evelo and Richard Finkers and Alejandra Gonzalez-Beltran and Alasdair J.G. Gray and Paul Groth and Carole Goble and Jeffrey S. Grethe and Jaap Heringa and Peter A.C 't Hoen and Rob Hooft and Tobias Kuhn and Ruben Kok and Joost Kok and Scott J. Lusher and Maryann E. Martone and Albert Mons and Abel L. Packer and Bengt Persson and Philippe Rocca-Serra and Marco Roos and Rene van Schaik and Susanna-Assunta Sansone and Erik Schultes and Thierry Sengstag and Ted Slater and George Strawn and Morris A. Swertz and Mark Thompson and Johan van der Lei and Erik van Mulligen and Jan Velterop and Andra Waagmeester and Peter Wittenburg and Katherine Wolstencroft and Jun Zhao and Barend Mons},
  journal          = {Scientific Data},
  title            = {The {FAIR} guiding principles for scientific data management and stewardship},
  year             = {2016},
  month            = {mar},
  number           = {1},
  volume           = {3},
  creationdate     = {2020-05-31T00:00:00},
  doi              = {10.1038/sdata.2016.18},
  file             = {:by-author/W/Wilkinson/2016_Wilkinson.pdf:PDF},
  keywords         = {Data Management; FAIR; Reproducible Research},
  modificationdate = {2023-01-03T09:26:50},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media {LLC}},
  timestamp        = {2020.05.31},
}

@Manuscript{McIlroy2011,
  author    = {M. Douglas McIlroy},
  title     = {A research {UNIX} reader: annotated excerpts from the programmer’s manual,1971-1986},
  year      = {2011},
  keywords  = {Computer Science (CS); Programming; Unix},
  url       = {https://pic.plover.com/UnixReader/reader.pdf},
  file      = {:by-author/M/McIlroy/2011_McIlroy.pdf:PDF},
  owner     = {saulius},
  timestamp = {2020.06.18},
  creationdate = {2020-06-18T00:00:00},
}

@TechReport{Hucka2010,
  author    = {Hucka, Michael and Bergmann, Frank and Hoops, Stefan and Keating, Sarah M and Sahle, Sven and Wilkinson, Darren J},
  title     = {Systems {Biology} {Markup} {Language} ({SBML}) {Level} {3Core}},
  year      = {2010},
  file      = {:by-author/H/Hucka/2010_Hucka_167.pdf:PDF},
  keywords  = {Ontologies; XML; XML Schema},
  language  = {en},
  owner     = {saulius},
  pages     = {167},
  timestamp = {2020.07.03},
  creationdate = {2020-07-03T00:00:00},
  url       = {http://sbml.org/Special/specifications/sbml-level-3/version-1/core/sbml-level-3-version-1-core.pdf},
}

@InProceedings{Dasgupta2019,
  author    = {Sandeep Dasgupta and Daejun Park and Theodoros Kasampalis and Vikram S. Adve and Grigore Roşu},
  booktitle = {Proceedings of the 40th {ACM} {SIGPLAN} Conference on Programming Language Design and Implementation - {PLDI} 2019},
  title     = {A complete formal semantics of x86-64 user-level instruction set architecture},
  year      = {2019},
  pages     = {1133--1148},
  publisher = {{ACM} Press},
  doi       = {10.1145/3314221.3314601},
  file      = {:by-author/D/Dasgupta/2019_Dasgupta_1133.pdf:PDF},
  keywords  = {Computer Architecture; Computer Science (CS); Formal Semantics; ISA; Instruction Set; X86_64},
  owner     = {saulius},
  timestamp = {2020.07.25},
  creationdate = {2020-07-25T00:00:00},
}

@Misc{Dasgupta2019a,
  author    = {Dasgupta, Sandeep and Daejun Park},
  title     = {sdasgup3/PLDI19-ArtifactEvaluation: X86-64-semantics},
  year      = {2019},
  copyright = {Open Access},
  doi       = {10.5281/ZENODO.2646617},
  keywords  = {Computer Architecture; Computer Science (CS); Formal Semantics; ISA; Instruction Set; X86_64},
  owner     = {saulius},
  publisher = {Zenodo},
  timestamp = {2020.07.25},
  creationdate = {2020-07-25T00:00:00},
}

@TechReport{Hubicka2003,
  author      = {Jan Hubička and Andreas Jaeger and Mark Mitchell},
  institution = {AMD},
  title       = {System {V} Application Binary Interface: {AMD64} Architecture Processor Supplement},
  year        = {2003},
  file        = {:by-author/H/Hubička/2003_Hubička_.pdf:PDF},
  owner       = {saulius},
  timestamp = {2020.07.25},
  creationdate = {2020-07-25T00:00:00},
  url         = {https://people.freebsd.org/~obrien/amd64-elf-abi.pdf},
}

@Article{Glasser2020,
  author           = {Leslie Glasser},
  journal          = {Journal of Applied Crystallography},
  title            = {From atoms to bonds, angles and torsions: molecular metrics from crystal space, and two {E}xcel implementations},
  year             = {2020},
  month            = {jul},
  number           = {4},
  pages            = {1--7},
  volume           = {53},
  comment          = {See 'by-author/G/Glasser/2020_Glasser_1_discussion/' for e-mails and files exchanged during a discussion. Clarifies formulae (6) and (2a).},
  creationdate     = {2020-07-26T00:00:00},
  doi              = {10.1107/s1600576720007311},
  file             = {:by-author/G/Glasser/2020_Glasser_1.pdf:PDF;:by-author/G/Glasser/2020_Glasser_1_suppl/gj5247sup3.pdf:PDF;:by-author/G/Glasser/2020_Glasser_1_suppl/gj5247sup1.xls:Excel;:by-author/G/Glasser/2020_Glasser_1_suppl/gj5247sup2.xlsx:Excel 2007+;:by-author/G/Glasser/2020_Glasser_1_discussion/2020-07-26_06_10_Leslie_Glasser_L.Glasser_at_exchange.curtin.edu.au.pdf:PDF},
  keywords         = {Algorithm; Bond Angles; Crystallographic Computing; Crystallography; Dihedral Angles; Teaching; Torsion Angles},
  modificationdate = {2024-04-04T09:28:57},
  owner            = {saulius},
  publisher        = {International Union of Crystallography ({IUCr})},
  timestamp        = {2020.07.26},
}

@InProceedings{ARM1998,
  author    = {{ARM}},
  title     = {Application Note 53 Configuring ARM Caches},
  year      = {1998},
  pages     = {1--11},
  comment   = {Original file name: "DAI0053B_cache_config.pdf".},
  file      = {:by-author/A/ARM/1998_ARM_1.pdf:PDF},
  keywords  = {ARM; Computer Architecture; Computer Science (CS); Memory Cache; RISC},
  owner     = {saulius},
  timestamp = {2020.07.26},
  creationdate = {2020-07-26T00:00:00},
  url       = {https://documentation-service.arm.com/static/5f19525920b7cf4bc524c651},
}

@Article{Bergstra2014,
  author      = {Jan A. Bergstra and Alban Ponse},
  journal     = {ArXiv},
  title       = {Division by zero in common meadows (v2)},
  year        = {2014},
  pages       = {140668782},
  abstract    = {Common meadows are fields expanded with a total inverse function. Division by zero produces an additional value denoted with "a" that propagates through all operations of the meadow signature (this additional value can be interpreted as an error element). We provide a basis theorem for so-called common cancellation meadows of characteristic zero, that is, common meadows of characteristic zero that admit a certain cancellation law.},
  date        = {2014-06-26},
  eprint      = {1406.6878v2},
  eprintclass = {math.RA},
  eprinttype  = {arXiv},
  file        = {:by-author/B/Bergstra/2014_Bergstra_140668782.pdf:PDF},
  keywords    = {Abstract Algebra; Algebra; Common Meadows; Divison by 0; Mathematics; Meadows},
  owner       = {saulius},
  timestamp = {2020.07.26},
  creationdate = {2020-07-26T00:00:00},
  url         = {https://arxiv.org/abs/1406.6878v2},
}

@TechReport{AMD2020,
  author      = {{AMD}},
  institution = {{AMD}},
  title       = {Software optimization guide for {AMD} family 17h models 30h and greater processors},
  year        = {2020},
  month       = mar,
  type        = {techreport},
  eprint      = {https://www.amd.com/en/support/tech-docs/software-optimization-guide-for-amd-family-17h-models-30h-and-greater-processors},
  file        = {:by-author/A/AMD/2020_AMD_1.pdf:PDF;:by-author/A/AMD/2020_AMD_1_suppl/Family 17h Models 30h and Greater Instruction Latencies version_1.00.xlsx:Excel 2007+},
  owner       = {saulius},
  pages       = {1--45},
  timestamp = {2020.07.26},
  creationdate = {2020-07-26T00:00:00},
  url         = {https://www.amd.com/system/files/TechDocs/56305.zip},
}

@Manuscript{Sinha2002,
  author    = {Steve Sinha and Satrajit Chatterjee and Kaushik Ravindran},
  title     = {{BOOST}: {B}erkeley’s out-of-order stack thingy},
  year      = {2002},
  keywords  = {Computer Architecture; Computer Science (CS); Out-of-order Execution; Stack Machines},
  url       = {https://www.researchgate.net/publication/228556746},
  eprint    = {https://www.semanticscholar.org/paper/BOOST%3A-Berkeley%E2%80%99s-Out-of-Order-Stack-Thingy-Sinha-Chatterjee/0366820530b662bd1c3a912720ce23795862d1ba},
  file      = {:by-author/S/Sinha/2002_Sinha_1.pdf:PDF},
  owner     = {saulius},
  pages     = {1--11},
  timestamp = {2020.07.26},
  creationdate = {2020-07-26T00:00:00},
}

@TechReport{Celio2015,
  author      = {Christopher Celio and David A. Patterson and Krste Asanović},
  institution = {The Engineering and Computer Sciences, University of {C}alifornia at {B}erkeley},
  title       = {{B}erkeley out-of-order machine ({BOOM}): an industry-competitive, synthesizable, parameterized {RISC-V} processor},
  year        = {2015},
  number      = {Technical Report No. UCB/EECS-2015-167},
  file        = {:by-author/C/Celio/2015_Celio_1.pdf:PDF},
  keywords    = {Computer Architecture; Computer Science (CS); Out-of-order Execution; RISC; RISC-V},
  owner       = {saulius},
  pages       = {1--5},
  timestamp = {2020.07.26},
  creationdate = {2020-07-26T00:00:00},
  url         = {https://www2.eecs.berkeley.edu/Pubs/TechRpts/2015/EECS-2015-167.pdf},
}

@Article{Slinger2005,
  author    = {Chris Slinger and Colin Cameron and Maurice Stanley},
  journal   = {Computer},
  title     = {Computer-generated holography as a generic displaytechnology},
  year      = {2005},
  pages     = {46--53},
  file      = {:by-author/S/Slinger/2005_Slinger_46.pdf:PDF},
  keywords  = {Computer Science (CS); Displays; Holography},
  owner     = {saulius},
  timestamp = {2020.07.26},
  creationdate = {2020-07-26T00:00:00},
  url       = {http://www.macs.hw.ac.uk/modules/F24VS2/Resources/Holography.pdf},
}

@Standard{ISO2020,
  institution  = {ISO/IEC JTC 1/SC 37},
  organization = {ISO/IEC},
  title        = {Biometric data interchange formats -- part 14: {DNA} data},
  author       = {ISO},
  language     = {en},
  month        = may,
  url          = {https://isotc.iso.org/livelink/livelink/open/jtc1sc37},
  year         = {2020},
  file         = {:by-author/I/ISO/2020_ISO_1.pdf:PDF},
  keywords     = {Bioinformatics; Biometrics; DNA Data; Data Exchange; Standards},
  owner        = {saulius},
  pages        = {1--148},
  timestamp = {2020.07.26},
  creationdate = {2020-07-26T00:00:00},
}

@Manuscript{Kohno2005,
  author    = {Tadayoshi Kohno and Andre Broido and K. C. Claffy},
  title     = {Remote physical device fingerprinting},
  year      = {2005},
  keywords  = {Computer Science (CS); Computer Security; Device Fingerprinting; Privacy; Remote Fingerprinting},
  url       = {https://web.archive.org/web/20090816024911/http://www.cs.washington.edu/homes/yoshi/papers/PDF/KoBrCl05PDF-lowres.pdf},
  file      = {:by-author/K/Kohno/2005_Kohno_1.pdf:PDF},
  owner     = {saulius},
  pages     = {1--15},
  timestamp = {2020.07.26},
  creationdate = {2020-07-26T00:00:00},
}

@Manuscript{Kohno2005a,
  author    = {Tadayoshi Kohno and Andre Broido and K. C. Claffy},
  title     = {Remote physical device fingerprinting (full version)},
  year      = {2005},
  keywords  = {Computer Science (CS); Computer Security; Device Fingerprinting; Privacy; Remote Fingerprinting},
  url       = {https://web.archive.org/web/20090824022902/http://www.cs.washington.edu/homes/yoshi/papers/PDF/KoBrCl2005PDF-Extended-lowres.pdf},
  file      = {:by-author/K/Kohno/2005_Kohno_1a.pdf:PDF},
  owner     = {saulius},
  pages     = {1--29},
  timestamp = {2020.07.26},
  creationdate = {2020-07-26T00:00:00},
}

@Article{Wang2020,
  author    = {Pei Wang and Junan Lu and Yanyu Jin and Mengfan Zhu and Lingling Wang and Shunjie Chen},
  journal   = {MedRxiv},
  title     = {Epidemiological characteristics of 1212 {COVID}-19 patients in Henan, China},
  year      = {2020},
  month     = {feb},
  pages     = {1--12},
  doi       = {10.1101/2020.02.21.20026112},
  file      = {:by-author/W/Wang/2020_Wang_1.pdf:PDF},
  keywords  = {COVID-19; Dataset; Epidemiology; Medicine},
  owner     = {saulius},
  publisher = {Cold Spring Harbor Laboratory},
  timestamp = {2020.07.26},
  creationdate = {2020-07-26T00:00:00},
}

@Manuscript{Soltani2009,
  author    = {Ashkan Soltani and Shannon Canty and Quentin Mayo and Lauren Thomas and Chris Jay Hoofnagle},
  title     = {Flash cookies and privacy},
  year      = {2009},
  doi       = {10.2139/ssrn.1446862},
  url       = {https://ssrn.com/abstract=1446862},
  file      = {:by-author/S/Soltani/2009_Soltani_1.pdf:PDF},
  journal   = {{SSRN} Electronic Journal},
  owner     = {saulius},
  pages     = {1--8},
  publisher = {Elsevier {BV}},
  timestamp = {2020.07.26},
  creationdate = {2020-07-26T00:00:00},
}

@Article{Gustafson1968,
  author    = {Karl Gustafson},
  journal   = {Bulletin of the American Mathematical Society},
  title     = {The angle of an operator and positive operator products},
  year      = {1968},
  month     = {may},
  number    = {3},
  pages     = {488--493},
  volume    = {74},
  doi       = {10.1090/s0002-9904-1968-11974-3},
  file      = {:by-author/G/Gustafson/1968_Gustafson_488.pdf:PDF},
  keywords  = {Abstract Algebra; Algebra; Mathematics; Operator Products; Operators},
  owner     = {saulius},
  publisher = {American Mathematical Society ({AMS})},
  timestamp = {2020.07.26},
  creationdate = {2020-07-26T00:00:00},
}

@TechReport{Dahl1970,
  author      = {Ole-Johan Dahl and Bjørn Myhrhaug and Kristen Nygaard},
  institution = {University of Oslo},
  title       = {{SIMULA} information. {C}ommon base language},
  year        = {1970},
  file        = {:by-author/D/Dahl/1970_Dahl_1.pdf:PDF},
  keywords    = {Computer Science (CS); Object-oriented Programming; Programming Languages; Simula},
  owner       = {saulius},
  pages       = {1--151},
  timestamp = {2020.07.26},
  creationdate = {2020-07-26T00:00:00},
  url         = {http://simula67.at.ifi.uio.no/Standard-70/Simula-1970-NR-22.pdf},
}

@TechReport{Dahl1967,
  author      = {Ole-Johan Dahl and Kristen Nygaard},
  institution = {University of Oslo},
  title       = {Simula 67. {C}ommon base definition},
  year        = {1967},
  file        = {:by-author/D/Dahl/1967_Dahl_1.pdf:PDF},
  keywords    = {Computer Science (CS); Object-oriented Programming; Programming Languages; Simula},
  owner       = {saulius},
  pages       = {1--34},
  timestamp = {2020.07.26},
  creationdate = {2020-07-26T00:00:00},
  url         = {http://simula67.at.ifi.uio.no/Archive/commonbasedefinition1967.pdf},
}

@Manuscript{Stinnett2001,
  author    = {Mickey Stinnett},
  title     = {{XML} schema versioning},
  year      = {2001},
  keywords  = {Computer Science (CS); Design Guidlines; Schema Versioning; XML; XML Schema},
  url       = {http://www.xfront.com/Versioning.pdf},
  file      = {:by-author/S/Stinnett/2001_Stinnett_1.pdf:PDF},
  owner     = {saulius},
  pages     = {1--5},
  timestamp = {2020.07.26},
  creationdate = {2020-07-26T00:00:00},
}

@TechReport{Farrell2004,
  author      = {Joel Farrell and Scott Hinkelman and Valerie Smothers and Darin McBeath},
  institution = {MedBiquitous},
  title       = {{XML} Schema Design Guidelines},
  year        = {2004},
  month       = oct,
  file        = {:by-author/F/Farrell/2004_Farrell_1.pdf:PDF},
  keywords    = {Bioinformatics; Computer Science (CS); Design Guidlines; Medical Informatics; XML; XML Schema},
  owner       = {saulius},
  pages       = {1--18},
  timestamp = {2020.07.26},
  creationdate = {2020-07-26T00:00:00},
  url         = {https://www.medbiq.org/std_specs/techguidelines/xmldesignguidelines.pdf},
}

@Standard{ECMA2017,
  institution      = {ECMA},
  organization     = {ECMA},
  title            = {The {JSON} data interchange syntax},
  author           = {ECMA},
  url              = {https://www.ecma-international.org/publications/files/ECMA-ST/ECMA-404.pdf},
  year             = {2017},
  creationdate     = {2020-07-27T00:00:00},
  file             = {:by-author/E/ECMA/2017_ECMA_1.pdf:PDF},
  keywords         = {Computer Science (CS); Data Formats; File Formats; JSON; Standard},
  modificationdate = {2022-11-10T12:49:39},
  owner            = {saulius},
  pages            = {1--16},
  timestamp        = {2020.07.27},
}

@Article{Vollmar2006,
  author    = {Kenneth Vollmar and Pete Sanderson},
  journal   = {{ACM} {SIGCSE} Bulletin},
  title     = {{MARS}, an education-oriented {MIPS} assembly language simulator},
  year      = {2006},
  month     = {mar},
  number    = {1},
  pages     = {239},
  volume    = {38},
  doi       = {10.1145/1124706.1121415},
  file      = {:by-author/V/Vollmar/2006_Vollmar_239.pdf:PDF},
  keywords  = {Computer Science (CS); Education; MIPS; Simulator},
  owner     = {saulius},
  publisher = {Association for Computing Machinery ({ACM})},
  timestamp = {2020.07.29},
  creationdate = {2020-07-29T00:00:00},
}

@Article{Schwartz1978,
  author    = {Jules L. Schwartz},
  journal   = {ACM SIGPLAN Notices},
  title     = {The development of {Jovial}},
  year      = {1978},
  month     = aug,
  number    = {8},
  pages     = {203--214},
  volume    = {13},
  file      = {:by-author/S/Schwartz/1978_Schwartz_203.pdf:PDF},
  keywords  = {Computer Science (CS); Jovial; Programming Languages},
  timestamp = {2020.08.01},
  creationdate = {2020-08-01T00:00:00},
  url       = {http://jovial.com/documents/p203-schwartz-jovial.pdf},
}

@Standard{DoD1984,
  institution  = {DoD},
  organization = {United States Department of Defense},
  title        = {{MIL-STD-1589C}, Military Standard: {JOVIAL} ({J}73)},
  author       = {{DoD}},
  language     = {English},
  month        = jul,
  url          = {http://everyspec.com/MIL-STD/MIL-STD-1500-1599/download.php?spec=MIL-STD-1589C.014577.pdf},
  year         = {1984},
  file         = {:by-author/D/DoD/1984_DoD_1.pdf:PDF},
  keywords     = {Computer Languages; Computer Science (CS); Jovial; Millitary Applications; Programming Languages},
  pages        = {1--168},
  timestamp = {2020.08.01},
  creationdate = {2020-08-01T00:00:00},
}

@Article{Ocaya2016,
  author    = {R. O. Ocaya},
  journal   = {{IET} Science, Measurement {\&} Technology},
  title     = {Versatile {CCD}-based spectrometer with field programmable gate array controller core},
  year      = {2016},
  month     = {oct},
  number    = {7},
  pages     = {719--727},
  volume    = {10},
  doi       = {10.1049/iet-smt.2016.0063},
  file      = {:by-author/O/Ocaya/2016_Ocaya_719.pdf:PDF},
  keywords  = {Computer Science (CS); FPGA; Scientifc Instruments; Spectrometers},
  publisher = {Institution of Engineering and Technology ({IET})},
  timestamp = {2020.08.01},
  creationdate = {2020-08-01T00:00:00},
}

@Article{Kornerup1983,
  author    = {Kornerup and Matula},
  journal   = {{IEEE} Transactions on Computers},
  title     = {Finite precision rational arithmetic: an arithmetic unit},
  year      = {1983},
  month     = {apr},
  number    = {4},
  pages     = {378--388},
  volume    = {C-32},
  doi       = {10.1109/TC.1983.1676239},
  file      = {:by-author/K/Kornerup/1983_Kornerup_378.pdf:PDF},
  keywords  = {ALU; Arithmetic; Computer Science (CS); Floating Slash},
  owner     = {saulius},
  publisher = {Institute of Electrical and Electronics Engineers ({IEEE})},
  timestamp = {2020.08.04},
  creationdate = {2020-08-04T00:00:00},
  url       = {https://www.researchgate.net/publication/3048224},
}

@Manuscript{Kahan1989,
  author    = {W. Kahan},
  title     = {How {I}ntel 80x87 stack over/undeflow should have been handled},
  year      = {1989},
  keywords  = {80387; 80x87; Computer Science (CS); Coprocessor; FPU; Floating Point; Intel},
  url       = {https://web.archive.org/web/20130612040231/http://www.cims.nyu.edu/~dbindel/class/cs279/stack87.pdf},
  file      = {:by-author/K/Kahan/1989_Kahan_1.pdf:PDF},
  pages     = {1--7},
  timestamp = {2020.08.04},
  creationdate = {2020-08-04T00:00:00},
}

@Article{Clark2017,
  author    = {Clark, Michael and Hoult, Bruce},
  title     = {{rv8}: a high performance {RISC-V} to x86 binary translator},
  year      = {2017},
  pages     = {1--7},
  doi       = {10.13140/RG.2.2.30957.69601},
  file      = {:by-author/C/Clark/2017_Clark_1.pdf:PDF},
  owner     = {saulius},
  publisher = {ResearchGate},
  timestamp = {2020.08.05},
  creationdate = {2020-08-05T00:00:00},
}

@TechReport{RISCVTeam2019,
  author      = {{RISCV Team}},
  institution = {RISC-V Project},
  title       = {{RISC-V} "{V}" vector extension, version 0.8},
  year        = {2019},
  address     = {https://github.com/riscv},
  file        = {:by-author/R/RISCVTeam/2019_RISCVTeam_1.pdf:PDF},
  keywords    = {Computer Architecture; Computer Science (CS); RISC-V; Vector Architecture},
  owner       = {saulius},
  pages       = {1--103},
  timestamp = {2020.08.05},
  creationdate = {2020-08-05T00:00:00},
  url         = {https://github.com/riscv/riscv-v-spec/releases/download/0.8/riscv-v-spec-0.8.pdf},
}

@Article{Sun2015,
  author    = {Chen Sun and Mark T. Wade and Yunsup Lee and Jason S. Orcutt and Luca Alloatti and Michael S. Georgas and Andrew S. Waterman and Jeffrey M. Shainline and Rimas R. Avizienis and Sen Lin and Benjamin R. Moss and Rajesh Kumar and Fabio Pavanello and Amir H. Atabaki and Henry M. Cook and Albert J. Ou and Jonathan C. Leu and Yu-Hsin Chen and Krste Asanovi{\'{c}} and Rajeev J. Ram and Milo{\v{s}} A. Popovi{\'{c}} and Vladimir M. Stojanovi{\'{c}}},
  journal   = {Nature},
  title     = {Single-chip microprocessor that communicates directly using light},
  year      = {2015},
  month     = {dec},
  number    = {7583},
  pages     = {534--538},
  volume    = {528},
  doi       = {10.1038/nature16454},
  file      = {:by-author/S/Sun/2015_Sun_534.pdf:PDF},
  keywords  = {CPU; Computer Architecture; Computer Science (CS); Optical Computing; Optical Link},
  owner     = {saulius},
  publisher = {Springer Science and Business Media {LLC}},
  timestamp = {2020.08.05},
  creationdate = {2020-08-05T00:00:00},
}

@Article{Gustafson2017,
  author    = {John L. Gustafson and Isaac Yonemoto},
  journal   = {Supercomputing Frontiers and Innovations},
  title     = {Beating Floating Point at its Own Game: Posit Arithmetic},
  year      = {2017},
  month     = {jun},
  number    = {2},
  pages     = {71--86},
  volume    = {4},
  doi       = {10.14529/jsfi170206},
  file      = {:by-author/G/Gustafson/2017_Gustafson_71.pdf:PDF},
  keywords  = {Computer Arithmetic; Computer Science (CS); Floating Point; Rounding Errors; Unums},
  owner     = {saulius},
  publisher = {{FSAEIHE} South Ural State University (National Research University)},
  timestamp = {2020.08.06},
  creationdate = {2020-08-06T00:00:00},
  url       = {http://superfri.org/superfri/article/download/137/232},
}

@Article{Tichy2016,
  author    = {Walter Tichy},
  journal   = {Ubiquity},
  title     = {The End of (Numeric) Error},
  year      = {2016},
  month     = {apr},
  number    = {April},
  pages     = {1--14},
  volume    = {2016},
  doi       = {10.1145/2913029},
  file      = {:by-author/T/Tichy/2016_Tichy_1.PDF:PDF},
  keywords  = {Computer Arithmetic; Computer Science (CS); Floating Point; Rounding Errors; Unums},
  owner     = {saulius},
  publisher = {Association for Computing Machinery ({ACM})},
  timestamp = {2020.08.06},
  creationdate = {2020-08-06T00:00:00},
}

@Manuscript{Gustafson2017a,
  author    = {John L. Gustafson},
  title     = {Posit arithmetic},
  year      = {2017},
  keywords  = {Computer Science (CS); Floating Point; Posits; Unums},
  language  = {English},
  month     = oct,
  url       = {https://posithub.org/docs/Posits4.pdf},
  file      = {:by-author/G/Gustafson/2017_Gustafson_1.pdf:PDF},
  owner     = {saulius},
  pages     = {1--137},
  timestamp = {2020.08.06},
  creationdate = {2020-08-06T00:00:00},
}

@Article{Kulisch1986,
  author    = {U. W. Kulisch and W. L. Miranker},
  journal   = {{SIAM} Review},
  title     = {The Arithmetic of the Digital Computer: A New Approach},
  year      = {1986},
  month     = {mar},
  number    = {1},
  pages     = {1--40},
  volume    = {28},
  doi       = {10.1137/1028001},
  file      = {:by-author/K/Kulisch/1986_Kulisch_1.pdf:PDF},
  keywords  = {Computer Arithmetic; Computer Science (CS); Floating Point},
  owner     = {saulius},
  publisher = {Society for Industrial {\&} Applied Mathematics ({SIAM})},
  timestamp = {2020.08.06},
  creationdate = {2020-08-06T00:00:00},
}

@Manuscript{Chaurasiya2018,
  author    = {Chaurasiya, Rohit and Gustafson, John and Shrestha, Rahul and Neudorfer, Jonathan and Nambiar, Sangeeth and Niyogi, Kaustav and Merchant, Farhad and Leupers, Rainer},
  title     = {Parameterized {P}osit arithmetic hardware generator},
  year      = {2018},
  keywords  = {Computer Science (CS); Floating Point; Posits; Unums},
  url       = {https://posithub.org/docs/iccd_submission_v1.pdf},
  file      = {:by-author/C/Chaurasiya/2018_Chaurasiya_1.pdf:PDF},
  owner     = {saulius},
  pages     = {1--9},
  timestamp = {2020.08.06},
  creationdate = {2020-08-06T00:00:00},
}

@Manuscript{Kahan2016,
  author    = {Kahan, William M.},
  title     = {Prof. {W.} {K}ahan's commentary on "{THE END of ERROR} — {U}num {C}omputing" by {J}ohn {L.} {G}ustafson},
  year      = {2016},
  keywords  = {Computer Science (CS); Floating Point; Posits; Unums},
  url       = {https://people.eecs.berkeley.edu/~wkahan/EndErErs.pdf},
  file      = {:by-author/K/Kahan/2016_Kahan_1.pdf:PDF},
  owner     = {saulius},
  pages     = {1--39},
  timestamp = {2020.08.06},
  creationdate = {2020-08-06T00:00:00},
}

@Presentation{Kahan2016a,
  author    = {W. Kahan},
  title     = {A Critique of {J}ohn {L.} {G}ustafson’s {THE END of ERROR — Unum Computation} and his "{A Radical Approach to Computation with Real Numbers}"},
  year      = {2016},
  file      = {:by-author/K/Kahan/2016_Kahan_1a.pdf:PDF},
  keywords  = {Computer Science (CS); Floating Point; Unums},
  owner     = {saulius},
  pages     = {1--26},
  timestamp = {2020.08.06},
  creationdate = {2020-08-06T00:00:00},
  url       = {http://people.eecs.berkeley.edu/~wkahan/UnumSORN.pdf},
}

@Presentation{Gustafson2016,
  author    = {John L. Gustafson},
  title     = {“{T}he {G}reat {D}ebate”: {U}num arithmetic position statement},
  year      = {2016},
  file      = {:by-author/G/Gustafson/2016_Gustafson_1.pdf:PDF},
  keywords  = {Computer Science (CS); Floating Point; Unums},
  owner     = {saulius},
  pages     = {1--94},
  timestamp = {2020.08.06},
  creationdate = {2020-08-06T00:00:00},
  url       = {https://groups.google.com/group/unum-computing/attach/b9d9a10a1e53e/PositionSlides-builds.pdf?part=0.1},
}

@TechReport{Miller2018,
  author      = {Erin Miller},
  institution = {MarkLogic},
  title       = {Understanding system resources},
  year        = {2018},
  file        = {:by-author/M/Miller/2018_Miller_1.pdf:PDF},
  keywords    = {Benchmarks; Computer Science (CS); I/O; Performance},
  owner       = {saulius},
  pages       = {1--43},
  timestamp = {2020.08.07},
  creationdate = {2020-08-07T00:00:00},
  url         = {https://cdn1.marklogic.com/wp-content/uploads/2018/10/Understanding-System-Resources.pdf},
}

@Presentation{Doolittle2011,
  author    = {Alan Doolittle},
  title     = {{MOSFET} basics (understanding with math)},
  year      = {2011},
  lecture   = {25},
  school    = {Georgia Tech},
  file      = {:by-author/D/Doolittle/2011_Doolittle_25.pdf:PDF},
  keywords  = {Computer Science (CS); Electronics; FET; Field-effected Transistors; MOSFET; Quantitative Transistor Analysis; Transistors},
  pages     = {1--28},
  timestamp = {2020.08.09},
  creationdate = {2020-08-09T00:00:00},
  url       = {http://alan.ece.gatech.edu/ECE3040/Lectures/Lecture25-MOSTransQuantitativeId-Vd-Vg.pdf},
}

@PhdThesis{Fulcher2001,
  author    = {J. R. Fulcher},
  school    = {CLRC},
  title     = {Radiation effects in electronics for the {CMC} tracking detector},
  year      = {2001},
  file      = {:by-author/F/Fulcher/2001_Fulcher_1.pdf:PDF},
  keywords  = {CMOS; Electronics; MOSFET; MOSFET SEM Image; MOSFET Scanning Electrom Microscopy},
  owner     = {saulius},
  pages     = {1--156},
  timestamp = {2020.08.09},
  creationdate = {2020-08-09T00:00:00},
  url       = {http://cds.cern.ch/record/559026/files/CM-P00040988.pdf},
}

@InProceedings{Guo2015a,
  author    = {Ning Guo and Yipeng Huang and Tao Mai and Sharvil Patil and Chi Cao and Mingoo Seok and Simha Sethumadhavan and Yannis Tsividis},
  booktitle = {{ESSCIRC} Conference 2015 - 41st European Solid-State Circuits Conference ({ESSCIRC})},
  title     = {Continuous-time hybrid computation with programmable nonlinearities},
  year      = {2015},
  month     = {sep},
  pages     = {279--282},
  publisher = {{IEEE}},
  doi       = {10.1109/esscirc.2015.7313881},
  file      = {:by-author/G/Guo/2015_Guo_279.pdf:PDF},
  keywords  = {Amalogue Computers; Computer Science (CS); Continuous Time Integration; Hybrid Computers},
  owner     = {saulius},
  timestamp = {2020.08.13},
  creationdate = {2020-08-13T00:00:00},
}

@TechReport{TexasInstruments2019,
  author      = {{Texas Instruments}},
  institution = {Texas Instruments},
  title       = {Integrator circuit},
  year        = {2019},
  file        = {:by-author/T/TexasInstruments/2019_TexasInstruments_1.pdf:PDF},
  keywords    = {Computer Science (CS); Electronics; Integrator Circuit},
  owner       = {saulius},
  pages       = {1--6},
  timestamp = {2020.08.13},
  creationdate = {2020-08-13T00:00:00},
  url         = {https://www.ti.com/lit/an/sboa275a/sboa275a.pdf},
}

@TechReport{Connelly2008,
  author      = {Jeff Connelly},
  institution = {California Polytechnic State University of San Luis Obispo, Computer Engineering Department},
  title       = {Ternary computing testbed. 3-trit computer architecture},
  year        = {2008},
  month       = aug,
  comment     = {Referenced in: http://homepage.divms.uiowa.edu/~jones/ternary/biblio.shtml},
  file        = {:by-author/C/Connelly/2008_Connelly_1.pdf:PDF},
  keywords    = {CPU; Computer; Computer Science (CS); Ternary},
  owner       = {saulius},
  pages       = {1--192},
  timestamp = {2020.08.26},
  creationdate = {2020-08-26T00:00:00},
  url         = {http://xyzzy.freeshell.org/trinary/CPE Report - Ternary Computing Testbed - RC6a.pdf},
}

@InProceedings{Doostaregan2010,
  author    = {Akbar Doostaregan and Mohammad Hossein Moaiyeri and Keivan Navi and Omid Hashemipour},
  booktitle = {2010 15th {CSI} International Symposium on Computer Architecture and Digital Systems},
  title     = {On the design of new low-power {CMOS} standard ternary logic gates},
  year      = {2010},
  month     = {sep},
  publisher = {{IEEE}},
  doi       = {10.1109/cads.2010.5623544},
  file      = {:by-author/D/Doostaregan/2010_Doostaregan_.pdf:PDF},
  keywords  = {CMOS; Circuits; Computer; Computer Science (CS); Implementation; Ternary},
  owner     = {saulius},
  timestamp = {2020.08.26},
  creationdate = {2020-08-26T00:00:00},
}

@TechReport{Gorde2010,
  author      = {Kanchan S. Gorde},
  institution = {Electronics Engg., TEC},
  title       = {Design and simulation of ternary logic based arithmetic circuits},
  year        = {2010},
  file        = {:by-author/G/Gorde/2010_Gorde_1.pdf:PDF},
  keywords    = {CMOS; Circuits; Computer Science (CS); Implementation; Ternary},
  owner       = {saulius},
  pages       = {1--7},
  timestamp = {2020.08.26},
  creationdate = {2020-08-26T00:00:00},
  url         = {http://web.archive.org/web/20150208102912/http://www.terna.org/enewsletter/Apr-Jun%202010/VLSI.pdf},
}

@Article{Massalin1987,
  author    = {Henry Massalin},
  journal   = {{ACM} {SIGOPS} Operating Systems Review},
  title     = {Superoptimizer: a look at the smallest program},
  year      = {1987},
  month     = {oct},
  number    = {4},
  pages     = {122--126},
  volume    = {21},
  doi       = {10.1145/36204.36194},
  file      = {:by-author/M/Massalin/1987_Massalin_122.pdf:PDF},
  keywords  = {Code Generation; Compilers; Computer Architecture; Computer Science (CS); Optimisers},
  owner     = {saulius},
  publisher = {Association for Computing Machinery ({ACM})},
  timestamp = {2020.08.26},
  creationdate = {2020-08-26T00:00:00},
}

@Article{Muskens1999,
  author    = {Reinhard Muskens},
  journal   = {Notre Dame Journal of Formal Logic},
  title     = {On partial and paraconsistent logics},
  year      = {1999},
  pages     = {352--374},
  comment   = {Cited in: http://homepage.divms.uiowa.edu/~jones/ternary/biblio.shtml},
  file      = {:by-author/M/Muskens/1999_Muskens_352.pdf:PDF},
  keywords  = {Computer Science (CS); Multi-valued Logics; Paraconsisten Logics},
  owner     = {saulius},
  timestamp = {2020.08.26},
  creationdate = {2020-08-26T00:00:00},
  url       = {https://semanticsarchive.net/Archive/2QwOTY4M/parpar.pdf},
}

@Lecture{GutierrezOsuna2000,
  author    = {Ricardo Gutierrez-Osuna},
  title     = {Lecture 2: {MC68000} architecture},
  year      = {2000},
  course    = {Microprocessor-based System Design},
  file      = {:by-author/G/Gutierrez-Osuna/2000_Gutierrez-Osuna_l2.pdf:PDF},
  keywords  = {CISC; Computer Architecture; Computer Science (CS); MC68000},
  owner     = {saulius},
  pages     = {1--20},
  timestamp = {2020.08.31},
  creationdate = {2020-08-31T00:00:00},
  url       = {http://courses.cs.tamu.edu/rgutier/ceg411_f01/l2.pdf},
}

@Manual{Motorolla1993,
  title     = {{M680008}-/16-/32-bit microprocessors user’s manual},
  author    = {{Motorola}},
  year      = {1993},
  file      = {:by-author/M/Motorola/1993_Motorola_1.pdf:PDF},
  keywords  = {CISC; Computer Architecture; Computer Science (CS); ISA; MC68000},
  owner     = {saulius},
  pages     = {1--189},
  timestamp = {2020.08.31},
  creationdate = {2020-08-31T00:00:00},
  url       = {https://www.nxp.com/docs/en/reference-manual/MC68000UM.pdf},
}

@Lecture{GutierrezOsuna2001,
  author    = {Ricardo Gutierrez-Osuna},
  title     = {Lecture 1: {C}ourse introduction},
  year      = {2001},
  course    = {Microprocessor-based System Design},
  file      = {:by-author/G/Gutierrez-Osuna/2001_Gutierrez-Osuna_l1.pdf:PDF},
  keywords  = {CISC; Computer Architecture; Computer Science (CS); MC68000},
  owner     = {saulius},
  pages     = {1--15},
  timestamp = {2020.08.31},
  creationdate = {2020-08-31T00:00:00},
  url       = {http://courses.cs.tamu.edu/rgutier/ceg411_f01/l1.pdf},
}

@Article{Vopson2019,
  author    = {Melvin M. Vopson},
  journal   = {{AIP} Advances},
  title     = {The mass-energy-information equivalence principle},
  year      = {2019},
  month     = {sep},
  number    = {9},
  pages     = {095206},
  volume    = {9},
  doi       = {10.1063/1.5123794},
  file      = {:by-author/V/Vopson/2019_Vopson_95206.pdf:PDF},
  owner     = {saulius},
  publisher = {{AIP} Publishing},
  timestamp = {2020.08.31},
  creationdate = {2020-08-31T00:00:00},
}

@Article{Vopson2020,
  author    = {Melvin M. Vopson},
  journal   = {{AIP} Advances},
  title     = {The information catastrophe},
  year      = {2020},
  month     = {aug},
  number    = {8},
  pages     = {085014},
  volume    = {10},
  doi       = {10.1063/5.0019941},
  file      = {:by-author/V/Vopson/2020_Vopson_85014.pdf:PDF},
  owner     = {saulius},
  publisher = {{AIP} Publishing},
  timestamp = {2020.08.31},
  creationdate = {2020-08-31T00:00:00},
}

@Manual{Motorola2006,
  title     = {{MC68000} and {MC68EC000} instruction set summary},
  author    = {{Motorola}},
  year      = {2006},
  file      = {:by-author/M/Motorola/2006_Motorola_1.pdf:PDF},
  keywords  = {CISC; Computer Architecture; Computer Science (CS); ISA; MC68000},
  owner     = {saulius},
  pages     = {1--101},
  timestamp = {2020.08.31},
  creationdate = {2020-08-31T00:00:00},
  url       = {https://web.njit.edu/~rosensta/classes/architecture/252software/code.pdf},
}

@Manual{Motorolla1992,
  title     = {Motorola {M68000} family programmer’s reference manual (includes {CPU32} instructions)},
  author    = {{Motorola}},
  year      = {1992},
  file      = {:by-author/M/Motorola/1992_Motorola_1.pdf:PDF},
  keywords  = {CISC; Computer Architecture; Computer Science (CS); ISA; MC68000},
  owner     = {saulius},
  pages     = {1--646},
  timestamp = {2020.08.31},
  creationdate = {2020-08-31T00:00:00},
  url       = {https://www.nxp.com/docs/en/reference-manual/M68000PRM.pdf},
}

@Lecture{Gutierrez-Osuna2001,
  author    = {Ricardo Gutierrez-Osuna},
  title     = {{CEG} 411/611: {M}icroprocessor-based system design},
  year      = {2001},
  course    = {Microprocessor-based System Design, Fall 2001},
  file      = {:by-author/G/Gutierrez-Osuna/2001_Gutierrez-Osuna_syllabus.pdf:PDF},
  keywords  = {CISC; Computer Architecture; Computer Science (CS); MC68000},
  owner     = {saulius},
  pages     = {1a--4},
  timestamp = {2020.08.31},
  creationdate = {2020-08-31T00:00:00},
  url       = {http://courses.cs.tamu.edu/rgutier/ceg411_f01/ceg411_fa01_syllabus.pdf},
}

@Lecture{GutierrezOsuna2001a,
  author    = {Ricardo Gutierrez-Osuna},
  title     = {Lecture 10: PI/T timer},
  year      = {2001},
  course    = {Microprocessor-based System Design},
  file      = {:by-author/G/Gutierrez-Osuna/2001_Gutierrez-Osuna_l10.pdf:PDF},
  keywords  = {CISC; Computer Architecture; Computer Science (CS); MC68000},
  owner     = {saulius},
  pages     = {1--1},
  timestamp = {2020.08.31},
  creationdate = {2020-08-31T00:00:00},
  url       = {http://courses.cs.tamu.edu/rgutier/ceg411_f01/l10.pdf},
}

@Lecture{GutierrezOsuna2001b,
  author    = {Ricardo Gutierrez-Osuna},
  title     = {Lecture 11: {PI/T} parallel {I/O}, part {I}},
  year      = {2001},
  course    = {Microprocessor-based System Design},
  file      = {:by-author/G/Gutierrez-Osuna/2001_Gutierrez-Osuna_l11.pdf:},
  keywords  = {CISC; Computer Architecture; Computer Science (CS); MC68000},
  owner     = {saulius},
  pages     = {1--1},
  timestamp = {2020.08.31},
  creationdate = {2020-08-31T00:00:00},
  url       = {http://courses.cs.tamu.edu/rgutier/ceg411_f01/l11.pdf},
}

@Lecture{GutierrezOsuna2001c,
  author    = {Ricardo Gutierrez-Osuna},
  title     = {Lecture 12: {PI/T} parallel {I/O}, part {II}},
  year      = {2001},
  course    = {Microprocessor-based System Design},
  file      = {:by-author/G/Gutierrez-Osuna/2001_Gutierrez-Osuna_l12.pdf:},
  keywords  = {CISC; Computer Architecture; Computer Science (CS); MC68000},
  owner     = {saulius},
  pages     = {1--1},
  timestamp = {2020.08.31},
  creationdate = {2020-08-31T00:00:00},
  url       = {http://courses.cs.tamu.edu/rgutier/ceg411_f01/l12.pdf},
}

@Lecture{GutierrezOsuna2001d,
  author    = {Ricardo Gutierrez-Osuna},
  title     = {Lecture 13: {DUART} serial {I/O}, part {I}},
  year      = {2001},
  course    = {Microprocessor-based System Design},
  file      = {:by-author/G/Gutierrez-Osuna/2001_Gutierrez-Osuna_l13.pdf:},
  keywords  = {CISC; Computer Architecture; Computer Science (CS); MC68000},
  owner     = {saulius},
  pages     = {1--1},
  timestamp = {2020.08.31},
  creationdate = {2020-08-31T00:00:00},
  url       = {http://courses.cs.tamu.edu/rgutier/ceg411_f01/l13.pdf},
}

@Lecture{GutierrezOsuna2001e,
  author    = {Ricardo Gutierrez-Osuna},
  title     = {Lecture 14: {DUART} serial {I/O} part {II}},
  year      = {2001},
  course    = {Microprocessor-based System Design},
  file      = {:by-author/G/Gutierrez-Osuna/2001_Gutierrez-Osuna_l14.pdf:},
  keywords  = {CISC; Computer Architecture; Computer Science (CS); MC68000},
  owner     = {saulius},
  pages     = {1--1},
  timestamp = {2020.08.31},
  creationdate = {2020-08-31T00:00:00},
  url       = {http://courses.cs.tamu.edu/rgutier/ceg411_f01/l14.pdf},
}

@Lecture{GutierrezOsuna2001f,
  author    = {Ricardo Gutierrez-Osuna},
  title     = {Lecture 15: {M}emory and {I/O} interface},
  year      = {2001},
  course    = {Microprocessor-based System Design},
  file      = {:by-author/G/Gutierrez-Osuna/2001_Gutierrez-Osuna_l15.pdf:},
  keywords  = {CISC; Computer Architecture; Computer Science (CS); MC68000},
  owner     = {saulius},
  pages     = {1--1},
  timestamp = {2020.08.31},
  creationdate = {2020-08-31T00:00:00},
  url       = {http://courses.cs.tamu.edu/rgutier/ceg411_f01/l15.pdf},
}

@Lecture{GutierrezOsuna2001g,
  author    = {Ricardo Gutierrez-Osuna},
  title     = {Lecture 16: {A}ddress decoding},
  year      = {2001},
  course    = {Microprocessor-based System Design},
  file      = {:by-author/G/Gutierrez-Osuna/2001_Gutierrez-Osuna_l16.pdf:},
  keywords  = {CISC; Computer Architecture; Computer Science (CS); MC68000},
  owner     = {saulius},
  pages     = {1--1},
  timestamp = {2020.08.31},
  creationdate = {2020-08-31T00:00:00},
  url       = {http://courses.cs.tamu.edu/rgutier/ceg411_f01/l16.pdf},
}

@Lecture{GutierrezOsuna2001h,
  author    = {Ricardo Gutierrez-Osuna},
  title     = {Lecture 3: {MC68000} instruction set},
  year      = {2001},
  course    = {Microprocessor-based System Design},
  file      = {:by-author/G/Gutierrez-Osuna/2001_Gutierrez-Osuna_l3.pdf:},
  keywords  = {CISC; Computer Architecture; Computer Science (CS); MC68000},
  owner     = {saulius},
  pages     = {1--1},
  timestamp = {2020.08.31},
  creationdate = {2020-08-31T00:00:00},
  url       = {http://courses.cs.tamu.edu/rgutier/ceg411_f01/l3.pdf},
}

@Lecture{GutierrezOsuna2001i,
  author    = {Ricardo Gutierrez-Osuna},
  title     = {Lecture 4: {A}ddressing modes},
  year      = {2001},
  course    = {Microprocessor-based System Design},
  file      = {:by-author/G/Gutierrez-Osuna/2001_Gutierrez-Osuna_l4.pdf:},
  keywords  = {CISC; Computer Architecture; Computer Science (CS); MC68000},
  owner     = {saulius},
  pages     = {1--1},
  timestamp = {2020.08.31},
  creationdate = {2020-08-31T00:00:00},
  url       = {http://courses.cs.tamu.edu/rgutier/ceg411_f01/l4.pdf},
}

@Lecture{GutierrezOsuna2001j,
  author    = {Ricardo Gutierrez-Osuna},
  title     = {Lecture 5: {P}rogram control},
  year      = {2001},
  course    = {Microprocessor-based System Design},
  file      = {:by-author/G/Gutierrez-Osuna/2001_Gutierrez-Osuna_l5.pdf:},
  keywords  = {CISC; Computer Architecture; Computer Science (CS); MC68000},
  owner     = {saulius},
  pages     = {1--1},
  timestamp = {2020.08.31},
  creationdate = {2020-08-31T00:00:00},
  url       = {http://courses.cs.tamu.edu/rgutier/ceg411_f01/l5.pdf},
}

@Lecture{GutierrezOsuna2001k,
  author    = {Ricardo Gutierrez-Osuna},
  title     = {Lecture 6: {S}ubroutines {I}},
  year      = {2001},
  course    = {Microprocessor-based System Design},
  file      = {:by-author/G/Gutierrez-Osuna/2001_Gutierrez-Osuna_l6.pdf:},
  keywords  = {CISC; Computer Architecture; Computer Science (CS); MC68000},
  owner     = {saulius},
  pages     = {1--1},
  timestamp = {2020.08.31},
  creationdate = {2020-08-31T00:00:00},
  url       = {http://courses.cs.tamu.edu/rgutier/ceg411_f01/l6.pdf},
}

@Lecture{GutierrezOsuna2001l,
  author    = {Ricardo Gutierrez-Osuna},
  title     = {Lecture 7: {S}ubroutines and stack frames},
  year      = {2001},
  course    = {Microprocessor-based System Design},
  file      = {:by-author/G/Gutierrez-Osuna/2001_Gutierrez-Osuna_l7.pdf:},
  keywords  = {CISC; Computer Architecture; Computer Science (CS); MC68000},
  owner     = {saulius},
  pages     = {1--1},
  timestamp = {2020.08.31},
  creationdate = {2020-08-31T00:00:00},
  url       = {http://courses.cs.tamu.edu/rgutier/ceg411_f01/l7.pdf},
}

@Lecture{GutierrezOsuna2001m,
  author    = {Ricardo Gutierrez-Osuna},
  title     = {Lecture 8: {C} language},
  year      = {2001},
  course    = {Microprocessor-based System Design},
  file      = {:by-author/G/Gutierrez-Osuna/2001_Gutierrez-Osuna_l8.pdf:},
  keywords  = {CISC; Computer Architecture; Computer Science (CS); MC68000},
  owner     = {saulius},
  pages     = {1--1},
  timestamp = {2020.08.31},
  creationdate = {2020-08-31T00:00:00},
  url       = {http://courses.cs.tamu.edu/rgutier/ceg411_f01/l8.pdf},
}

@Lecture{GutierrezOsuna2001n,
  author    = {Ricardo Gutierrez-Osuna},
  title     = {Lecture 9: {E}xception processing},
  year      = {2001},
  course    = {Microprocessor-based System Design},
  file      = {:by-author/G/Gutierrez-Osuna/2001_Gutierrez-Osuna_l9.pdf:},
  keywords  = {CISC; Computer Architecture; Computer Science (CS); MC68000},
  owner     = {saulius},
  pages     = {1--1},
  timestamp = {2020.08.31},
  creationdate = {2020-08-31T00:00:00},
  url       = {http://courses.cs.tamu.edu/rgutier/ceg411_f01/l9.pdf},
}

@Lecture{GutierrezOsuna2001o,
  author    = {Ricardo Gutierrez-Osuna},
  title     = {Midterm sample},
  year      = {2001},
  course    = {Microprocessor-based System Design},
  file      = {:by-author/G/Gutierrez-Osuna/2001_Gutierrez-Osuna_midterm_sample.pdf:},
  keywords  = {CISC; Computer Architecture; Computer Science (CS); MC68000},
  owner     = {saulius},
  pages     = {1--1},
  timestamp = {2020.08.31},
  creationdate = {2020-08-31T00:00:00},
  url       = {http://courses.cs.tamu.edu/rgutier/ceg411_f01/midterm_sample.pdf},
}

@InCollection{Nuernberg2004,
  author    = {Peter J. Nürnberg and Uffe K. Wiil and David L. Hicks},
  booktitle = {Metainformatics},
  publisher = {Springer Berlin Heidelberg},
  title     = {A grand unified theory for structural computing},
  year      = {2004},
  pages     = {1--16},
  doi       = {10.1007/978-3-540-24647-3_1},
  file      = {:by-author/N/Nürnberg/2004_Nürnberg_1.pdf:PDF},
  keywords  = {Computer Architecture; Computer Science (CS); OISC; SISC; Single Instruction Set Computer},
  owner     = {saulius},
  timestamp = {2020.09.05},
  creationdate = {2020-09-05T00:00:00},
}

@Article{Mazonka2010,
  author    = {Oleg Mazonka and},
  journal   = {Complex Systems},
  title     = {Bit copying: the ultimate computational simplicity},
  year      = {2010},
  month     = {oct},
  number    = {3},
  pages     = {263--286},
  volume    = {19},
  doi       = {10.25088/complexsystems.19.3.263},
  file      = {:by-author/M/Mazonka/2010_Mazonka_263.pdf:PDF},
  keywords  = {Computer Architecture; Computer Science (CS); OISC; SISC; Single Instruction Set Computer},
  owner     = {saulius},
  publisher = {Wolfram Research, Inc.},
  timestamp = {2020.09.05},
  creationdate = {2020-09-05T00:00:00},
  url       = {https://wpmedia.wolfram.com/uploads/sites/13/2019/03/19-3-5.pdf},
}

@Article{Jeong2019,
  author    = {Jae Won Jeong and Young-Eun Choi and Woo-Seok Kim and Jee-Ho Park and Sunmean Kim and Sunhae Shin and Kyuho Lee and Jiwon Chang and Seong-Jin Kim and Kyung Rok Kim},
  journal   = {Nature Electronics},
  title     = {Tunnelling-based ternary metal{\textendash}oxide{\textendash}semiconductor technology},
  year      = {2019},
  month     = {jul},
  number    = {7},
  pages     = {307--312},
  volume    = {2},
  doi       = {10.1038/s41928-019-0272-8},
  file      = {:by-author/J/Jeong/2019_Jeong_307.pdf:PDF},
  keywords  = {CMOS; Circuits; Computer Science (CS); Ternary Logic; Tunnelling},
  owner     = {saulius},
  publisher = {Springer Science and Business Media {LLC}},
  timestamp = {2020.09.23},
  creationdate = {2020-09-23T00:00:00},
}

@Article{Srivastava2000,
  author    = {A. Srivastava},
  journal   = {Microelectronics Reliability},
  title     = {Back gate bias method of threshold voltage control for the design of low voltage {CMOS} ternary logic circuits},
  year      = {2000},
  month     = {dec},
  number    = {12},
  pages     = {2107--2110},
  volume    = {40},
  doi       = {10.1016/s0026-2714(00)00013-5},
  file      = {:by-author/S/Srivastava/2000_Srivastava_2107.pdf:PDF},
  keywords  = {CMOS; Circuits; Computer Science (CS); Ternary Logic},
  owner     = {saulius},
  publisher = {Elsevier {BV}},
  timestamp = {2020.09.23},
  creationdate = {2020-09-23T00:00:00},
}

@Article{Ferrara2020,
  author    = {Pietro Ferrara and Agostino Cortesi and Fausto Spoto},
  journal   = {Science of Computer Programming},
  title     = {From {CIL} to {J}ava bytecode: {S}emantics-based translation for static analysis leveraging},
  year      = {2020},
  month     = {jun},
  pages     = {102392},
  volume    = {191},
  doi       = {10.1016/j.scico.2020.102392},
  file      = {:by-author/F/Ferrara/2020_Ferrara_102392.pdf:PDF},
  keywords  = {.NET; Bytecode; CIL; Compilers; Computer Science (CS); Dot Net; Java; Static Analysis},
  owner     = {saulius},
  publisher = {Elsevier {BV}},
  timestamp = {2020.09.27},
  creationdate = {2020-09-27T00:00:00},
}

@Article{Cao2020,
  author    = {Yue Cao and Thomas Andrew Geddes and Jean Yee Hwa Yang and Pengyi Yang},
  journal   = {Nature Machine Intelligence},
  title     = {Ensemble deep learning in bioinformatics},
  year      = {2020},
  month     = {aug},
  number    = {9},
  pages     = {500--508},
  volume    = {2},
  doi       = {10.1038/s42256-020-0217-y},
  file      = {:by-author/C/Cao/2020_Cao_500.pdf:PDF},
  owner     = {saulius},
  publisher = {Springer Science and Business Media {LLC}},
  timestamp = {2020.10.22},
  creationdate = {2020-10-22T00:00:00},
}

@Article{Roche2015,
  author    = {Dominique G. Roche and Loeske E. B. Kruuk and Robert Lanfear and Sandra A. Binning},
  journal   = {{PLOS} {B}iology},
  title     = {Public data archiving in ecology and evolution: how well are we doing?},
  year      = {2015},
  month     = {nov},
  number    = {11},
  pages     = {e1002295},
  volume    = {13},
  doi       = {10.1371/journal.pbio.1002295},
  file      = {:by-author/R/Roche/2015_Roche_1002295.pdf:PDF},
  keywords  = {Bioinformatics; Ecologu; FAIR; Reusable Data},
  owner     = {saulius},
  publisher = {Public Library of Science ({PLoS})},
  timestamp = {2020.10.20},
  creationdate = {2020-10-20T00:00:00},
}

@Article{Culina2020,
  author    = {Antica Culina and Ilona van den Berg and Simon Evans and Alfredo S{\'{a}}nchez-T{\'{o}}jar},
  journal   = {{PLOS} Biology},
  title     = {Low availability of code in ecology: A~call for urgent action},
  year      = {2020},
  month     = {jul},
  number    = {7},
  pages     = {e3000763},
  volume    = {18},
  doi       = {10.1371/journal.pbio.3000763},
  file      = {:by-author/C/Culina/2020_Culina_3000763.pdf:PDF},
  keywords  = {Bioinformatics; Ecology; FAIR; Reusable Data},
  owner     = {saulius},
  publisher = {Public Library of Science ({PLoS})},
  timestamp = {2020.10.20},
  creationdate = {2020-10-20T00:00:00},
}

@Article{Hall1981,
  author    = {S. R. Hall},
  journal   = {Acta Crystallographica Section A},
  title     = {Space-group notation with an explicit origin},
  year      = {1981},
  month     = {jul},
  number    = {4},
  pages     = {517--525},
  volume    = {37},
  doi       = {10.1107/s0567739481001228},
  file      = {:by-author/H/Hall/1981_Hall_517.pdf:PDF},
  keywords  = {Algorithms; Crystallography; Space Group Reconstruction; Space Group Symbols; Space Groups},
  owner     = {saulius},
  publisher = {International Union of Crystallography ({IUCr})},
  timestamp = {2020.11.01},
  creationdate = {2020-11-01T00:00:00},
}

@Article{Helliwell2019,
  author    = {John R. Helliwell},
  journal   = {Structural Dynamics},
  title     = {{FACT} and {FAIR} with {B}ig {D}ata allows objectivity in science: {T}he view of crystallography},
  year      = {2019},
  month     = {sep},
  number    = {5},
  pages     = {054306},
  volume    = {6},
  doi       = {10.1063/1.5124439},
  file      = {:by-author/H/Helliwell/2019_Helliwell_54306.pdf:PDF},
  keywords  = {FACT; FAIR; Reproducible Research; X-ray Crystallography},
  owner     = {saulius},
  publisher = {{AIP} Publishing},
  timestamp = {2020.11.04},
  creationdate = {2020-11-04T00:00:00},
}

@Article{Jessop2011,
  author    = {David M. Jessop and Sam E. Adams and Egon L. Willighagen and Lezan Hawizy and Peter Murray-Rust},
  journal   = {Journal of Cheminformatics},
  title     = {{OSCAR}4: a flexible architecture for chemical text-mining},
  year      = {2011},
  month     = {oct},
  number    = {1},
  pages     = {41},
  volume    = {3},
  doi       = {10.1186/1758-2946-3-41},
  file      = {:by-author/J/Jessop/2011_Jessop_41.pdf:PDF},
  owner     = {saulius},
  publisher = {Springer Science and Business Media {LLC}},
  timestamp = {2020.11.03},
  creationdate = {2020-11-03T00:00:00},
}

@Article{Paulson2000,
  author       = {Lawrence C. Paulson},
  title        = {Natural deduction as higher-order resolution},
  year         = {2000},
  pages        = {9301104},
  abstract     = {An interactive theorem prover, Isabelle, is under development. In LCF, each inference rule is represented by one function for forwards proof and another (a tactic) for backwards proof. In Isabelle, each inference rule is represented by a Horn clause. Resolution gives both forwards and backwards proof, supporting a large class of logics. Isabelle has been used to prove theorems in Martin-L\"of's Constructive Type Theory. Quantifiers pose several difficulties: substitution, bound variables, Skolemization. Isabelle's representation of logical syntax is the typed lambda-calculus, requiring higher- order unification. It may have potential for logic programming. Depth-first subgoaling along inference rules constitutes a higher-order Prolog.},
  date         = {2000-10-31},
  eprint       = {cs/9301104v1},
  eprintclass  = {cs.LO},
  eprinttype   = {arXiv},
  file         = {:by-author/P/Paulson/2000_Paulson_9301104.pdf:PDF},
  journaltitle = {Journal of Logic Programming 3 (1986), 237-258},
  keywords     = {Computer Science (CS); Higher Order Logic; Isabelle; Proof Assistants},
  owner        = {saulius},
  timestamp = {2020.11.12},
  creationdate = {2020-11-12T00:00:00},
}

@Article{Paulson2000a,
  author       = {Lawrence C. Paulson},
  title        = {The foundation of a generic theorem prover},
  year         = {2000},
  pages        = {9301105},
  abstract     = {Isabelle is an interactive theorem prover that supports a variety of logics. It represents rules as propositions (not as functions) and builds proofs by combining rules. These operations constitute a meta-logic (or `logical framework') in which the object-logics are formalized. Isabelle is now based on higher-order logic -- a precise and well-understood foundation. Examples illustrate use of this meta-logic to formalize logics and proofs. Axioms for first-order logic are shown sound and complete. Backwards proof is formalized by meta-reasoning about object-level entailment. Higher-order logic has several practical advantages over other meta-logics. Many proof techniques are known, such as Huet's higher-order unification procedure.},
  date         = {2000-10-31},
  eprint       = {cs/9301105v1},
  eprintclass  = {cs.LO},
  eprinttype   = {arXiv},
  file         = {:by-author/P/Paulson/2000_Paulson_9301105.pdf:PDF},
  journaltitle = {Journal of Automated Reasoning 5 (1989), 363-397},
  keywords     = {Computer Science (CS); Higher Order Logic; Isabelle; Proof Assistants},
  owner        = {saulius},
  timestamp = {2020.11.12},
  creationdate = {2020-11-12T00:00:00},
}

@Article{Paulson1986,
  author    = {Lawrence C. Paulson},
  journal   = {The Journal of Logic Programming},
  title     = {Natural deduction as higher-order resolution},
  year      = {1986},
  month     = {oct},
  number    = {3},
  pages     = {237--258},
  volume    = {3},
  doi       = {10.1016/0743-1066(86)90015-4},
  file      = {:by-author/P/Paulson/1986_Paulson_237.pdf:PDF},
  keywords  = {Computer Science (CS); Higher Order Logic; Isabelle; Proof Assistants},
  owner     = {saulius},
  publisher = {Elsevier {BV}},
  timestamp = {2020.11.12},
  creationdate = {2020-11-12T00:00:00},
}

@InProceedings{Narayanan2008,
  author    = {Arvind Narayanan and Vitaly Shmatikov},
  booktitle = {2008 {IEEE} Symposium on Security and Privacy (sp 2008)},
  title     = {Robust de-anonymization of large sparse datasets},
  year      = {2008},
  month     = {may},
  pages     = {1},
  publisher = {{IEEE}},
  doi       = {10.1109/sp.2008.33},
  file      = {:by-author/N/Narayanan/2008_Narayanan_1.pdf:PDF},
  keywords  = {Computer Science (CS); Data Surveilance; Privacy},
  owner     = {saulius},
  timestamp = {2020.11.14},
  creationdate = {2020-11-14T00:00:00},
  url       = {https://www.cs.cornell.edu/~shmat/shmat_oak08netflix.pdf},
}

@Manuscript{Narayanan2019,
  author    = {Arvind Narayanan and Vitaly Shmatikov},
  title     = {Robust de-anonymization of large sparse datasets: a decade later},
  year      = {2019},
  keywords  = {Computer Science (CS); Data Surveilance; Privacy},
  language  = {English},
  month     = {may},
  url       = {https://www.cs.princeton.edu/~arvindn/publications/de-anonymization-retrospective.pdf},
  file      = {:by-author/N/Narayanan/2019_Narayanan_1.pdf:PDF},
  owner     = {saulius},
  pages     = {1},
  timestamp = {2020.11.14},
  creationdate = {2020-11-14T00:00:00},
}

@Presentation{Jancoriene2020,
  author     = {Ligita Jančorienė},
  title      = {Pirmoji patirtis diagnozuojant ir gydant {COVID} infekciją {V}ilniaus universiteto ligoninės {S}antaros klinikų {I}nfekcinių ligų centre},
  year       = {2020},
  conference = {Mokslo naujienos Lietuvos mokytojams},
  file       = {:by-author/J/Jančorienė/2020_Jančorienė_1.pdf:PDF},
  keywords   = {COVID},
  owner      = {saulius},
  pages      = {1},
  timestamp = {2020.11.15},
  creationdate = {2020-11-15T00:00:00},
}

@Article{Rubtsov2002a,
  author    = {Denis V. Rubtsov and Sergei V. Butakov},
  journal   = {Computer Standards {\&} Interfaces},
  title     = {Application of {XML} for neural network exchange},
  year      = {2002},
  month     = {sep},
  number    = {4},
  pages     = {311--322},
  volume    = {24},
  doi       = {10.1016/S0920-5489(02)00034-X},
  file      = {:by-author/R/Rubtsov/2002_Rubtsov_311.pdf:PDF},
  keywords  = {Artificial Neural Networks (ANN); Computer Science (CS); Machine Learning (ML); Neural Networks (NN); XML},
  owner     = {saulius},
  publisher = {Elsevier {BV}},
  timestamp = {2020.11.17},
  creationdate = {2020-11-17T00:00:00},
}

@InProceedings{Rubtsov2002,
  author    = {Denis V. Rubtsov and Sergei V. Butakov},
  booktitle = {FLAIRS-02 Proceedings},
  title     = {A new {XML}-based language for neural solution interchange},
  year      = {2002},
  pages     = {385--389},
  file      = {:by-author/R/Rubtsov/2002_Rubtsov_385.pdf:PDF},
  keywords  = {Artificial Neural Networks (ANN); Computer Science (CS); Machine Learning (ML); Neural Networks (NN); XML},
  owner     = {saulius},
  timestamp = {2020.11.17},
  creationdate = {2020-11-17T00:00:00},
  url       = {https://www.aaai.org/Papers/FLAIRS/2002/FLAIRS02-076.pdf},
}

@Article{Denning2005,
  author    = {Peter J. Denning},
  journal   = {Communications of the {ACM}},
  title     = {Is computer science science?},
  year      = {2005},
  month     = {apr},
  number    = {4},
  pages     = {27--31},
  volume    = {48},
  doi       = {10.1145/1053291.1053309},
  file      = {:by-author/D/Denning/2005_Denning_27.pdf:PDF},
  keywords  = {ACM; Computer Science (CS); Mission Statement},
  owner     = {saulius},
  publisher = {Association for Computing Machinery ({ACM})},
  timestamp = {2020.11.22},
  creationdate = {2020-11-22T00:00:00},
}

@Article{Austing1979,
  author    = {Richard H. Austing and Bruce H. Barnes and Della T. Bonnette and Gerald L. Engel and Gordon Stokes},
  journal   = {Communications of the {ACM}},
  title     = {Curriculum {\textquotesingle}78: recommendations for the undergraduate program in computer science{\textemdash} a report of the {ACM} curriculum committee on computer science},
  year      = {1979},
  month     = {mar},
  number    = {3},
  pages     = {147--166},
  volume    = {22},
  doi       = {10.1145/359080.359083},
  file      = {:by-author/A/Austing/1979_Austing_147.pdf:PDF},
  keywords  = {ACM; Computer Science (CS); Curriculum; Teaching},
  owner     = {saulius},
  publisher = {Association for Computing Machinery ({ACM})},
  timestamp = {2020.11.22},
  creationdate = {2020-11-22T00:00:00},
}

@Article{Tucker1991,
  journal   = {Communications of the {ACM}},
  title     = {Computing Curricula 1991},
  year      = {1991},
  month     = {jun},
  number    = {6},
  pages     = {68--84},
  volume    = {34},
  doi       = {10.1145/103701.103710},
  editor    = {Allen B. Tucker},
  file      = {:by-author/T/Tucker/1991_Tucker_68.pdf:PDF},
  keywords  = {ACM; Computer Science (CS); Curriculum; Teaching},
  owner     = {saulius},
  publisher = {Association for Computing Machinery ({ACM})},
  timestamp = {2020.11.22},
  creationdate = {2020-11-22T00:00:00},
}

@Article{Turner1985,
  journal   = {Communications of the {ACM}},
  title     = {Computer science in secondary schools: curriculum and teacher certification},
  year      = {1985},
  month     = {mar},
  number    = {3},
  pages     = {269--279},
  volume    = {28},
  doi       = {10.1145/3166.3168},
  editor    = {A. J. Turner},
  file      = {:by-author/T/Turner/1985_Turner_269.pdf:PDF},
  keywords  = {ACM; Computer Science (CS); Curriculum; Teaching},
  owner     = {saulius},
  publisher = {Association for Computing Machinery ({ACM})},
  timestamp = {2020.11.22},
  creationdate = {2020-11-22T00:00:00},
}

@Book{ACMCCTF2013,
  author    = {{ACM Computing Curricula Task Force}},
  editor    = {{ACM Computing Curricula Task Force}},
  publisher = {{ACM}, Inc.},
  title     = {Computer science curricula 2013: curriculum guidelines for undergraduate degree programs in computer science},
  year      = {2013},
  month     = {jan},
  doi       = {10.1145/2534860},
  file      = {:by-author/A/ACMCCTF/2013_ACMCCTF_1.pdf:PDF},
  keywords  = {ACM; Computer Science (CS); Curriculum; Teaching},
  owner     = {saulius},
  pages     = {1--514},
  timestamp = {2020.11.22},
  creationdate = {2020-11-22T00:00:00},
  url       = {https://www.acm.org/binaries/content/assets/education/cs2013_web_final.pdf},
}

@Book{JTFCCIEEECSACM2001,
  author    = {{The Joint Task Force on Computing Curricula IEEE Computer Society Association for Computing Machinery}},
  title     = {Computing Curricula 2001 {C}omputer {S}cience. Final Report},
  year      = {2001},
  file      = {:by-author/J/JTFCCIEEECSACM/2001_JTFCCIEEECSACM_1.pdf:PDF},
  keywords  = {ACM; Computer Science (CS); Curriculum; Teaching},
  owner     = {saulius},
  pages     = {1--236},
  timestamp = {2020.11.22},
  creationdate = {2020-11-22T00:00:00},
}

@Book{TGITC2017,
  author    = {{Task Group on Information Technology Curricula}},
  publisher = {Association for Computing Machinery},
  title     = {Information Technology Curricula 2017: Curriculum Guidelines for Baccalaureate Degree Programs in Information Technology},
  year      = {2017},
  month     = {dec},
  doi       = {10.1145/3173161},
  file      = {:by-author/T/TGITC/2017_TGITC_1.pdf:PDF},
  keywords  = {ACM; Computer Science (CS); Curriculum; Teaching},
  owner     = {saulius},
  pages     = {1--163},
  timestamp = {2020.11.22},
  creationdate = {2020-11-22T00:00:00},
  url       = {https://www.acm.org/binaries/content/assets/education/curricula-recommendations/it2017.pdf},
}

@Book{JTFCE2017,
  author    = {{Joint Task Force on Cybersecurity Education}},
  publisher = {Association for Computing Machinery},
  title     = {Curriculum Guidelines for Post-Secondary Degree Programs in Cybersecurity},
  year      = {2017},
  isbn      = {9781450352789},
  file      = {:by-author/J/JTFCE/2017_JTFCE_1.pdf:PDF},
  keywords  = {ACM; Computer Science (CS); Curriculum; Teaching},
  owner     = {saulius},
  pages     = {1--121},
  timestamp = {2020.11.22},
  creationdate = {2020-11-22T00:00:00},
  url       = {https://www.acm.org/binaries/content/assets/education/curricula-recommendations/csec2017.pdf},
}

@Book{JTFCC2015,
  author    = {{Joint Task Force on Computing Curricula}},
  title     = {{S}oftware {E}ngineering 2014: {C}urriculum guidelines for undergraduate degree programs in {S}oftware {E}ngineering},
  year      = {2015},
  file      = {:by-author/J/JTFCC/2015_JTFCC_1.pdf:PDF},
  keywords  = {ACM; Computer Science (CS); Curriculum; Teaching},
  owner     = {saulius},
  pages     = {1--133},
  timestamp = {2020.11.22},
  creationdate = {2020-11-22T00:00:00},
  url       = {https://www.acm.org/binaries/content/assets/education/se2014.pdf},
}

@Article{Walker1996,
  author    = {Henry M. Walker and G. Michael Schneider},
  journal   = {Communications of the {ACM}},
  title     = {A revised model curriculum for a liberal arts degree in computer science},
  year      = {1996},
  month     = {dec},
  number    = {12},
  pages     = {85--95},
  volume    = {39},
  doi       = {10.1145/240483.240502},
  file      = {:by-author/W/Walker/1996_Walker_85.pdf:PDF},
  keywords  = {ACM; Computer Science (CS); Curriculum; Teaching},
  owner     = {saulius},
  publisher = {Association for Computing Machinery ({ACM})},
  timestamp = {2020.11.22},
  creationdate = {2020-11-22T00:00:00},
}

@Webpage{ACM,
  author    = {{ACM}},
  retrieved = {2020-11-22},
  title     = {Curricula Recommendations},
  url       = {https://www.acm.org/education/curricula-recommendations},
  year      = {2020},
  file      = {:by-author/A/ACM/2020_ACM_1.odt:OpenDocument text;:by-author/A/ACM/2020_ACM_1.pdf:PDF},
  keywords  = {ACM; Computer Science (CS); Curriculum; Teaching},
  owner     = {saulius},
  pages     = {1--2},
  timestamp = {2020.11.22},
  creationdate = {2020-11-22T00:00:00},
}

@Presentation{Bettati2017,
  author    = {Riccardo Bettati},
  title     = {Memory management},
  year      = {2017},
  course    = {CPSC 410/611 : Operating Systems},
  file      = {:by-author/B/Bettati/2017_Bettati_1.pdf:PDF},
  keywords  = {Computer Architecture; Computer Science (CS); Paging; Virtual Memory},
  owner     = {saulius},
  pages     = {1--12},
  timestamp = {2020.11.29},
  creationdate = {2020-11-29T00:00:00},
  url       = {https://people.engr.tamu.edu/bettati/Courses/410/2017A/Slides/memory.pdf},
}

@InProceedings{Coleman2001,
  author    = {J. N. Coleman and C. I. Softley and J. Kadlec and R. Matousek and M. Licko and Z. Pohl and A. Hermanek},
  booktitle = {Conference Record of Thirty-Fifth Asilomar Conference on Signals, Systems and Computers (Cat.No.01CH37256)},
  title     = {The {E}uropean {L}ogarithmic {M}icroprocessor - a {QR} {RLS} application},
  year      = {2001},
  pages     = {155--159},
  publisher = {{IEEE}},
  doi       = {10.1109/acssc.2001.986897},
  file      = {:by-author/C/Coleman/2001_Coleman_155.pdf:PDF},
  keywords  = {CPU Design; Computer Science (CS); Logarithmic Microprocessor; Real Number Arithmetic},
  owner     = {saulius},
  timestamp = {2020.11.29},
  creationdate = {2020-11-29T00:00:00},
}

@Article{Coleman2008,
  author    = {John N. Coleman and Christopher I. Softley and Jiri Kadlec and Rudolf Matousek and Milan Tichy and Z. Pohl and Antonin Hermanek and Nico F. Benschop},
  journal   = {{IEEE} Transactions on Computers},
  title     = {The {E}uropean {L}ogarithmic {M}icroprocesor},
  year      = {2008},
  number    = {4},
  pages     = {532--546},
  volume    = {57},
  doi       = {10.1109/tc.2007.70791},
  file      = {:by-author/C/Coleman/2008_Coleman_532.pdf:PDF},
  keywords  = {CPU Design; Computer Science (CS); Logarithmic Microprocessor; Real Number Arithmetic},
  owner     = {saulius},
  publisher = {Institute of Electrical and Electronics Engineers ({IEEE})},
  timestamp = {2020.11.29},
  creationdate = {2020-11-29T00:00:00},
}

@InProceedings{Ismail2011,
  author    = {R. Che Ismail and J. N. Coleman},
  booktitle = {2011 {IEEE} 20th Symposium on Computer Arithmetic},
  title     = {{ROM}-less {LNS}},
  year      = {2011},
  month     = {jul},
  pages     = {43--51},
  publisher = {{IEEE}},
  doi       = {10.1109/arith.2011.15},
  file      = {:by-author/I/Ismail/2011_Ismail_43.pdf:PDF},
  keywords  = {CPU Design; Computer Science (CS); Logarithmic Number System; Real Number Arithmetic},
  owner     = {saulius},
  timestamp = {2020.11.29},
  creationdate = {2020-11-29T00:00:00},
}

@Presentation{Corden2008,
  author    = {Martyn Corden},
  title     = {Consistency of floating point results, or {W}hy doesn’t my application always give the same answer?},
  year      = {2008},
  file      = {:by-author/C/Corden/2008_Corden_1.pdf:PDF},
  keywords  = {Compilers; Computer Science (CS); Floating Point; Intel; Optimisation},
  owner     = {saulius},
  pages     = {1--32},
  timestamp = {2020.11.29},
  creationdate = {2020-11-29T00:00:00},
  url       = {https://www.nccs.nasa.gov/images/FloatingPoint_consistency.pdf},
}

@Presentation{Engelen2008,
  author    = {Robert van Engelen},
  title     = {Floating point operations and {SIMD} extensions},
  year      = {2008},
  file      = {:by-author/E/Engelen/2008_Engelen_1.pdf:PDF},
  keywords  = {CPU; Computer Science (CS); Floating Point; Intel},
  owner     = {saulius},
  pages     = {1--34},
  timestamp = {2020.11.29},
  creationdate = {2020-11-29T00:00:00},
  url       = {http://www.cs.fsu.edu/~engelen/courses/HPC-adv-2008/FP.pdf},
}

@Manuscript{Kahan1983,
  author    = {W. Kahan},
  title     = {Mathematics written in sand - the hp-15{C}, {I}ntel 8087, etc.},
  year      = {1983},
  keywords  = {Computer Science (CS); Floating Point},
  url       = {https://people.eecs.berkeley.edu/~wkahan/MathSand.pdf},
  file      = {:by-author/K/Kahan/1983_Kahan_1.pdf:PDF},
  owner     = {saulius},
  pages     = {1--49},
  timestamp = {2020.11.29},
  creationdate = {2020-11-29T00:00:00},
}

@InProceedings{Adams2018,
  author    = {Ulf Adams},
  booktitle = {Proceedings of the 39th {ACM} {SIGPLAN} Conference on Programming Language Design and Implementation - {PLDI} 2018},
  title     = {Ry{\={u}}: fast float-to-string conversion},
  year      = {2018},
  pages     = {270--282},
  publisher = {{ACM} Press},
  doi       = {10.1145/3192366.3192369},
  file      = {:by-author/A/Adams/2018_Adams_270.pdf:PDF},
  keywords  = {Computer Science (CS); Conversion; Floating Point},
  owner     = {saulius},
  timestamp = {2020.11.30},
  creationdate = {2020-11-30T00:00:00},
}

@Article{Zwart2020,
  author      = {Simon Portegies Zwart},
  title       = {The Ecological Impact of High-performance Computing in Astrophysics},
  pages       = {1--10},
  abstract    = {The importance of computing in astronomy continues to increase, and so is its impact on the environment. When analyzing data or performing simulations, most researchers raise concerns about the time to reach a solution rather than its impact on the environment. Luckily, a reduced time-to-solution due to faster hardware or optimizations in the software generally also leads to a smaller carbon footprint. This is not the case when the reduced wall-clock time is achieved by overclocking the processor, or when using supercomputers. The increase in the popularity of interpreted scripting languages, and the general availability of high-performance workstations form a considerable threat to the environment. A similar concern can be raised about the trend of running single-core instead of adopting efficient many-core programming paradigms. In astronomy, computing is among the top producers of green-house gasses, surpassing telescope operations. Here I hope to raise the awareness of the environmental impact of running non-optimized code on overpowered computer hardware.},
  date        = {2020-09-23},
  doi         = {10.1038/s41550-020-1208-y},
  eprint      = {2009.11295v1},
  eprintclass = {astro-ph.IM},
  eprinttype  = {arXiv},
  file        = {:http\://arxiv.org/pdf/2009.11295v1:PDF;:by-author/Z/Zwart/2020_Zwart_1.pdf:PDF},
  keywords    = {astro-ph.IM; physics.comp-ph; physics.ins-det},
  owner       = {saulius},
  timestamp = {2020.11.30},
  creationdate = {2020-11-30T00:00:00},
}

@Standard{IEEE1985,
  institution  = {{IEEE}},
  organization = {{IEEE}},
  title        = {{IEEE} standard for binary floating-point arithmetic},
  author       = {{IEEE}},
  url          = {http://kfe.fjfi.cvut.cz/~klimo/nm/ieee754.pdf},
  year         = {1985},
  file         = {:by-author/I/IEEE/1985_IEEE_1.pdf:PDF},
  keywords     = {Computer Science (CS); Floating Point; Standard},
  owner        = {saulius},
  pages        = {1--23},
  timestamp = {2020.11.30},
  creationdate = {2020-11-30T00:00:00},
}

@Article{Cody1981,
  author    = {W. J. Cody},
  journal   = {Computer},
  title     = {Analysis of proposals for the floating-point standard},
  year      = {1981},
  month     = {mar},
  number    = {3},
  pages     = {63--68},
  volume    = {14},
  doi       = {10.1109/c-m.1981.220379},
  file      = {:by-author/C/Cody/1981_Cody_63.pdf:PDF},
  keywords  = {Computer Science (CS); Floating Point; Standard},
  owner     = {saulius},
  publisher = {Institute of Electrical and Electronics Engineers ({IEEE})},
  timestamp = {2020.11.30},
  creationdate = {2020-11-30T00:00:00},
}

@Presentation{Meskauskas2020,
  author    = {Tadas Meškauskas},
  title     = {Defektuotų biologinių membranų kompiuterinis modeliavimas},
  year      = {2020},
  file      = {:by-author/M/Meškauskas/2020_Meškauskas_1.pdf:PDF},
  keywords  = {Biofizika; Computer Science (CS); Skaitiniai Modeliai},
  owner     = {saulius},
  pages     = {1--23},
  timestamp = {2020.12.01},
  creationdate = {2020-12-01T00:00:00},
  url       = {https://klevas.mif.vu.lt/~meska/Meskauskas_Skaidres.pdf},
}

@Article{Nagaraju2014,
  author    = {Punnam Nagaraju and Neerati Vishnuvardhan},
  journal   = {International Journal of Science and Research},
  title     = {Ternary logic gates and ternary {SRAM} cell implementation in {VLSI}},
  year      = {2014},
  pages     = {1920--1924},
  file      = {:by-author/N/Nagaraju/2014_Nagaraju_1920.pdf:PDF},
  keywords  = {CMOS; Computer Science (CS); Logic Gates; Ternary Logic},
  owner     = {saulius},
  timestamp = {2020.12.01},
  creationdate = {2020-12-01T00:00:00},
  url       = {https://pdfs.semanticscholar.org/e540/a0b745c45b03e7d1e2f3326f7dc9751910c6.pdf},
}

@Presentation{Beleites2015,
  author    = {Claudia Beleites},
  title     = {Import and export of spectra files. {V}ignette for the {R} package {hyperSpec}},
  year      = {2015},
  file      = {:by-author/B/Beleites/2015_Beleites_1.pdf:PDF},
  keywords  = {Databases; Spectra},
  owner     = {saulius},
  pages     = {1--28},
  timestamp = {2020.12.03},
  creationdate = {2020-12-03T00:00:00},
  url       = {http://hyperspec.r-forge.r-project.org/blob/fileio.pdf},
}

@TechReport{Waterman2014,
  author      = {Andrew Waterman and Yunsup Lee and David A. Patterson and Krste Asanovic},
  institution = {Electrical Engineering and Computer Sciences, University of California at Berkeley},
  title       = {The {RISC-V} instruction set manual, volume {I}: user-level {ISA}, version 2.0},
  year        = {2014},
  number      = {UCB/EECS-2014-54},
  file        = {:by-author/W/Waterman/2014_Waterman_1.pdf:PDF},
  keywords    = {CPU Design; Computer Architecture; Computer Science (CS); RISC; RISC-V},
  owner       = {saulius},
  pages       = {1--102},
  timestamp = {2020.12.06},
  creationdate = {2020-12-06T00:00:00},
  url         = {https://www2.eecs.berkeley.edu/Pubs/TechRpts/2014/EECS-2014-54.pdf},
}

@TechReport{Waterman2015,
  author      = {Andrew Waterman and Yunsup Lee and David A. Patterson and Krste Asanović},
  institution = {Electrical Engineering and Computer Sciences, University of California at Berkeley},
  title       = {The {RISC-V} compressed instruction set manual, version 1.9},
  year        = {2015},
  month       = nov,
  number      = {UCB/EECS-2015-209},
  type        = {techreport},
  file        = {:by-author/W/Waterman/2015_Waterman_1.pdf:PDF},
  keywords    = {CPU Design; Computer Architecture; Computer Science (CS); RISC; RISC-V},
  owner       = {saulius},
  pages       = {1--23},
  timestamp = {2020.12.06},
  creationdate = {2020-12-06T00:00:00},
  url         = {https://www2.eecs.berkeley.edu/Pubs/TechRpts/2015/EECS-2015-209.pdf},
}

@TechReport{Asanovic2014,
  author      = {Krste Asanović and David A. Patterson},
  institution = {Electrical Engineering and Computer Sciences, University of California at Berkeley},
  title       = {Instruction sets should be free: the case for {RISC-V}},
  year        = {2014},
  file        = {:by-author/A/Asanović/2014_Asanović_1.pdf:PDF},
  keywords    = {CPU Design; Computer Architecture; Computer Science (CS); RISC; RISC-V},
  owner       = {saulius},
  pages       = {1--7},
  timestamp = {2020.12.06},
  creationdate = {2020-12-06T00:00:00},
  url         = {https://www2.eecs.berkeley.edu/Pubs/TechRpts/2014/EECS-2014-146.pdf},
}

@TechReport{Waterman2015a,
  author      = {Waterman, Andrew and Lee, Yunsup and Patterson, David A. and Asanović, Krste},
  institution = {EECS Department, University of California, Berkeley},
  title       = {The {RISC-V} compressed instruction set manual, version 1.7},
  year        = {2015},
  month       = {May},
  number      = {UCB/EECS-2015-157},
  abstract    = {This is a draft specification version 1.7 of the RISC-V Compressed ISA extension. This draft specification will change before being accepted as standard, so implementations made to this draft specification will likely not conform to the future standard.},
  file        = {:by-author/W/Waterman/2015_Waterman_1a.pdf:PDF},
  keywords    = {CPU Design; Computer Architecture; Computer Science (CS); RISC; RISC-V},
  owner       = {saulius},
  timestamp = {2020.12.06},
  creationdate = {2020-12-06T00:00:00},
  url         = {http://www2.eecs.berkeley.edu/Pubs/TechRpts/2015/EECS-2015-157.html},
}

@TechReport{Waterman2015b,
  author      = {Waterman, Andrew and Lee, Yunsup and Avizienis, Rimas and Patterson, David A. and Asanović, Krste},
  institution = {EECS Department, University of California, Berkeley},
  title       = {The {RISC-V} instruction set manual volume {II}: privileged architecture version 1.7},
  year        = {2015},
  month       = {May},
  number      = {UCB/EECS-2015-49},
  abstract    = {This is a draft specification version 1.7 of the RISC-V Privileged Architecture.  This draft specification will change before being accepted as standard, so implementations made to this draft specification will likely not
conform to the future standard.},
  file        = {:by-author/W/Waterman/2015_Waterman_1b.pdf:PDF},
  keywords    = {CPU Design; Computer Architecture; Computer Science (CS); RISC; RISC-V},
  owner       = {saulius},
  timestamp = {2020.12.06},
  creationdate = {2020-12-06T00:00:00},
  url         = {http://www2.eecs.berkeley.edu/Pubs/TechRpts/2015/EECS-2015-49.html},
}

@TechReport{Waterman2016,
  author      = {Waterman, Andrew and Lee, Yunsup and Avizienis, Rimas and Patterson, David A. and Asanović, Krste},
  institution = {EECS Department, University of California, Berkeley},
  title       = {The {RISC-V} instruction set manual volume {II}: privileged architecture version 1.9.1},
  year        = {2016},
  month       = {Nov},
  number      = {UCB/EECS-2016-161},
  file        = {:by-author/W/Waterman/2016_Waterman_1.pdf:PDF},
  keywords    = {CPU Design; Computer Architecture; Computer Science (CS); RISC; RISC-V},
  owner       = {saulius},
  pages       = {1--89},
  timestamp = {2020.12.06},
  creationdate = {2020-12-06T00:00:00},
  url         = {http://www2.eecs.berkeley.edu/Pubs/TechRpts/2016/EECS-2016-161.html},
}

@TechReport{Celio2016,
  author      = {Celio, Christopher and Dabbelt, Daniel and Patterson, David A. and Asanović, Krste},
  institution = {EECS Department, University of California, Berkeley},
  title       = {The renewed case for the reduced instruction set computer: avoiding {ISA} bloat with macro-op fusion for {RISC-V}},
  year        = {2016},
  month       = {Jul},
  number      = {UCB/EECS-2016-130},
  abstract    = {This report makes the case that a well-designed Reduced Instruction Set Computer (RISC) can match, and even exceed, the performance and code density of existing commercial Complex Instruction Set Computers (CISC) while maintaining the simplicity and cost-effectiveness that underpins the original RISC goals.

We begin by comparing the dynamic instruction counts and dynamic instruction bytes fetched for the popular proprietary ARMv7, ARMv8, IA-32, and x86-64 Instruction Set Architectures (ISAs) against the free and open RISC-V RV64G and RV64GC ISAs when running the SPEC CINT2006 benchmark suite. RISC-V was designed as a very small ISA to support a wide range of implementations, and has a less mature compiler toolchain. However, we observe that on SPEC CINT2006 RV64G executes on average 16% more instructions than x86-64, 3% more instructions than IA-32, 9% more instructions than ARMv8, but 4% fewer instructions than ARMv7.

CISC x86 implementations break up complex instructions into smaller internal RISC-like micro-ops, and the RV64G instruction count is within 2% of the x86-64 retired micro-op count. RV64GC, the compressed variant of RV64G, is the densest ISA studied, fetching 8% fewer dynamic instruction bytes than x86-64. We observed that much of the increased RISC-V instruction count is due to a small set of common multi-instruction idioms.

Exploiting this fact, the RV64G and RV64GC effective instruction count can be reduced by 5.4% on average by leveraging macro-op fusion. Combining the compressed RISC-V ISA extension with macro-op fusion provides both the densest ISA and the fewest dynamic operations retired per program, reducing the motivation to add more instructions to the ISA. This approach retains a single simple ISA suitable for both low-end and high-end implementations, where high-end implementations can boost performance through microarchitectural techniques.},
  file        = {:by-author/C/Celio/2016_Celio_1.pdf:PDF},
  keywords    = {CPU Design; Computer Architecture; Computer Science (CS); RISC; RISC-V},
  owner       = {saulius},
  pages       = {1--18},
  timestamp = {2020.12.06},
  creationdate = {2020-12-06T00:00:00},
  url         = {http://www2.eecs.berkeley.edu/Pubs/TechRpts/2016/EECS-2016-130.html},
}

@TechReport{Waterman2016a,
  author      = {Waterman, Andrew and Lee, Yunsup and Avizienis, Rimas and Patterson, David A. and Asanović, Krste},
  institution = {EECS Department, University of California, Berkeley},
  title       = {The {RISC-V} instruction set manual volume {II}: privileged architecture version 1.9.1},
  year        = {2016},
  month       = {Nov},
  number      = {UCB/EECS-2016-161},
  file        = {:by-author/W/Waterman/2016_Waterman_1a.pdf:PDF},
  keywords    = {CPU Design; Computer Architecture; Computer Science (CS); RISC; RISC-V},
  owner       = {saulius},
  pages       = {1--89},
  timestamp = {2020.12.06},
  creationdate = {2020-12-06T00:00:00},
  url         = {http://www2.eecs.berkeley.edu/Pubs/TechRpts/2016/EECS-2016-161.html},
}

@TechReport{Waterman2016b,
  author      = {Waterman, Andrew and Lee, Yunsup and Patterson, David A. and Asanović, Krste},
  institution = {EECS Department, University of California, Berkeley},
  title       = {The {RISC-V} instruction set manual, volume {I}: user-level {ISA}, version 2.1},
  year        = {2016},
  month       = {May},
  number      = {UCB/EECS-2016-118},
  file        = {:by-author/W/Waterman/2016_Waterman_1b.pdf:PDF},
  keywords    = {CPU Design; Computer Architecture; Computer Science (CS); RISC; RISC-V},
  owner       = {saulius},
  pages       = {1--133},
  timestamp = {2020.12.06},
  creationdate = {2020-12-06T00:00:00},
  url         = {http://www2.eecs.berkeley.edu/Pubs/TechRpts/2016/EECS-2016-118.html},
}

@PhdThesis{Waterman2016c,
  author      = {Waterman, Andrew},
  school      = {EECS Department, University of California, Berkeley},
  title       = {Design of the {RISC-V} instruction set architecture},
  year        = {2016},
  month       = {Jan},
  abstract    = {The hardware-software interface, embodied in the instruction set architecture (ISA), is arguably the most important interface in a computer system. Yet, in contrast to nearly all other interfaces in a modern computer system, all commercially popular ISAs are proprietary. A free and open ISA standard has the potential to increase innovation in microprocessor design, reduce computer system cost, and, as Moore’s law wanes, ease the transition to more specialized computational devices.

In this dissertation, I present the RISC-V instruction set architecture. RISC-V is a free and open ISA that, with three decades of hindsight, builds and improves upon the original Reduced Instruction Set Computer (RISC) architectures. It is structured as a small base ISA with a variety of optional extensions. The base ISA is very simple, making RISC-V suitable for research and education, but complete enough to be a suitable ISA for inexpensive, low- power embedded devices. The optional extensions form a more powerful ISA for general- purpose and high-performance computing. I also present and evaluate a new RISC-V ISA extension for reduced code size, which makes RISC-V more compact than all popular 64-bit ISAs.},
  file        = {:by-author/W/Waterman/2016_Waterman_1c.pdf:PDF},
  institution = {Electrical Engineering and Computer Sciences, University of California at Berkeley},
  keywords    = {CPU Design; Computer Architecture; Computer Science (CS); RISC; RISC-V},
  number      = {UCB/EECS-2016-1},
  owner       = {saulius},
  pages       = {1--117},
  timestamp = {2020.12.06},
  creationdate = {2020-12-06T00:00:00},
  url         = {http://www2.eecs.berkeley.edu/Pubs/TechRpts/2016/EECS-2016-1.html},
}

@TechReport{Chen2016,
  author      = {Chen, Tony and Patterson, David A.},
  institution = {EECS Department, University of California, Berkeley},
  title       = {{RISC-V} geneology},
  year        = {2016},
  month       = jan,
  number      = {UCB/EECS-2016-6},
  type        = {techreport},
  file        = {:by-author/C/Chen/2016_Chen_1.pdf:PDF},
  keywords    = {CPU Design; Computer Architecture; Computer Science (CS); RISC; RISC-V},
  owner       = {saulius},
  pages       = {1--8},
  timestamp = {2020.12.06},
  creationdate = {2020-12-06T00:00:00},
  url         = {https://www2.eecs.berkeley.edu/Pubs/TechRpts/2016/EECS-2016-6.pdf},
}

@TechReport{Celio2017,
  author      = {Celio, Christopher and Chiu, Pi-Feng and Nikolic, Borivoje and Patterson, David A. and Asanović, Krste},
  institution = {EECS Department, University of California, Berkeley},
  title       = {{BOOM} v2: an open-source out-of-order {RISC-V} core},
  year        = {2017},
  month       = {Sep},
  number      = {UCB/EECS-2017-157},
  abstract    = {This paper presents BOOM version 2, an updated version of the Berkeley Out-of-Order Machine. The design exploration was performed through synthesis, place and route using the foundry-provided standard-cell library and the memory compiler in the TSMC 28 nm HPM process (high performance mobile).

BOOM is an open-source processor that implements the RV64G RISC-V Instruction Set Architecture (ISA). Like most contemporary high-performance cores, BOOM is superscalar (able to execute multiple instructions per cycle) and out-of-order (able to execute instructions as their dependencies are resolved and not restricted to their program order).  BOOM is implemented as a parameterizable generator written using the Chisel hardware construction language that can used to generate synthesizable implementations targeting both FPGAs and ASICs.

BOOMv2 is an update in which the design effort has been informed by analysis of synthesized, placed and routed data provided by a contemporary industrial tool flow. We also had access to standard single- and dual-ported memory compilers provided by the foundry, allowing us to explore design trade-offs using different SRAM memories and comparing against synthesized flip-flop arrays. The main distinguishing features of BOOMv2 include an updated 3-stage front-end design with a bigger set-associative Branch Target Buffer (BTB); a pipelined register rename stage; split floating point and integer register files; a dedicated floating point pipeline; separate issue windows for floating point, integer, and memory micro-operations; and separate stages for issue-select and register read.  

Managing the complexity of the register file was the largest obstacle to improving BOOM's clock frequency. We spent considerable effort on placing-and-routing a semi-custom 9-port register file to explore the potential improvements over a fully synthesized design, in conjunction with microarchitectural techniques to reduce the size and port count of the register file. BOOMv2 has a 37 fanout-of-four (FO4) inverter delay after synthesis and 50 FO4 after place-and-route, a 24% reduction from BOOMv1's 65 FO4 after place-and-route. Unfortunately, instruction per cycle (IPC) performance drops up to 20%, mostly due to the extra latency between load instructions and dependent instructions. However, the new BOOMv2 physical design paves the way for IPC recovery later.},
  file        = {:by-author/C/Celio/2017_Celio_1.pdf:PDF},
  keywords    = {CPU Design; Computer Architecture; Computer Science (CS); RISC; RISC-V},
  owner       = {saulius},
  pages       = {1--8},
  timestamp = {2020.12.06},
  creationdate = {2020-12-06T00:00:00},
  url         = {http://www2.eecs.berkeley.edu/Pubs/TechRpts/2017/EECS-2017-157.html},
}

@MastersThesis{Li2019,
  author    = {Li, Peijie},
  school    = {EECS Department, University of California, Berkeley},
  title     = {Reduce static code size and improve {RISC-V} compression},
  year      = {2019},
  month     = {Jun},
  file      = {:by-author/L/Li/2019_Li_1.pdf:PDF},
  keywords  = {CPU Design; Computer Architecture; Computer Science (CS); RISC; RISC-V},
  number    = {UCB/EECS-2019-107},
  owner     = {saulius},
  pages     = {1--39},
  timestamp = {2020.12.06},
  creationdate = {2020-12-06T00:00:00},
  url       = {http://www2.eecs.berkeley.edu/Pubs/TechRpts/2019/EECS-2019-107.html},
}

@MastersThesis{Amid2019,
  author    = {Amid, Alon},
  school    = {EECS Department, University of California, Berkeley},
  title     = {Nested-parallelism {PageRank} on {RISC-V} vector multi-processors},
  year      = {2019},
  month     = {Apr},
  abstract  = {Graph processing kernels and sparse-representation linear algebra workloads such as PageRank are increasingly used in machine learning and graph analytics contexts. While data-parallel processing and chip-multiprocessors have both been used in recent years as complementary mitigations to the slowing rate of single-thread performance improvements, they have been used together most efficiently on dense data-structure representations as opposed to sparse representations. This work presents nested-parallelism implementations of PageRank for RISC-V multi-processor Rocket chip SoCs with vector architecture accelerators. These software implementations are used for hardware and software design-space exploration using FPGA-accelerated simulation with multiple silicon-proven multi-processor SoC configurations. The design space includes a variety of scalar cores, vector accelerator cores, and cache parameters, as well as multiple software implementations with tunable parallelism parameters. This report shows the benefits of the loop-raking vectorizing technique
compared to an alternative vectoring technique, and presents up to a 14x run-time speedup relative to a parallel-scalar implementation running on the same SoC configuration. A 25x speedup is demonstrated in a dual-tile SoC with dual-lanes-per-tile vector accelerators, compared to a minimal scalar implementation, demonstrating the scalability of the proposed nested-parallelism techniques.},
  editor    = {Nikolic, Borivoje and Asanović, Krste},
  file      = {:by-author/A/Amid/2019_Amid_1.pdf:PDF},
  keywords  = {CPU Design; Computer Architecture; Computer Science (CS); RISC; RISC-V},
  number    = {UCB/EECS-2019-6},
  owner     = {saulius},
  pages     = {1--64},
  timestamp = {2020.12.06},
  creationdate = {2020-12-06T00:00:00},
  url       = {http://www2.eecs.berkeley.edu/Pubs/TechRpts/2019/EECS-2019-6.html},
}

@Manuscript{Underwood2019,
  author    = {Alex Underwood and Tuan Nguyen and James E. Stine},
  title     = {{IEEE} floating-point extension for containing error in the {RISC-V} architecture},
  year      = {2019},
  keywords  = {CPU Design; Computer Architecture; Computer Science (CS); Floating Point; RISC; RISC-V},
  url       = {https://carrv.github.io/2019/papers/carrv2019_paper_11.pdf},
  comment   = {DOI is broken...},
  file      = {:by-author/U/Underwood/2019_Underwood_1.pdf:PDF},
  owner     = {saulius},
  pages     = {1--6},
  timestamp = {2020.12.06},
  creationdate = {2020-12-06T00:00:00},
}

@Manuscript{Amid2019a,
  author    = {Amid, Alon and Asanovic, Krste and Baum, Allen and Bradbury, Alex and Brewer, Tony and Celio, Chris and AliakseiChapyzhenka and Chiricescu, Silviu and Dockser, Ken and Dreyer, Bob and Espasa, Roger and Halle, Sean and Hauser, John and Horner, David and Hoult, Bruce and Huffman, Bill and Korikov, Constantine and Korpan, Ben and Kruppe, Robin and Lee, Yunsup and Lemieux, Guy and Moc, Filip and RichNewell and Ou, Albert and Patterson, David and Schmidt, Colin and Solomatnikov, Alex and Wallach, Steve and Waterman, Andrew and Wilson, Jim},
  title     = {{RISC-V} "{V}" vector extension},
  year      = {2019},
  keywords  = {CPU Design; Computer Architecture; Computer Science (CS); RISC; RISC-V; Vector Architectures},
  url       = {https://riscv.github.io/documents/riscv-v-spec/riscv-v-spec.pdf},
  file      = {:by-author/A/Amid/2019_Amid_1a.pdf:PDF},
  owner     = {saulius},
  timestamp = {2020.12.06},
  creationdate = {2020-12-06T00:00:00},
}

@Manuscript{Porter2018,
  author    = {Porter, III, Harry H.},
  title     = {{RISC-V}: an overview of the instruction set architecture},
  year      = {2018},
  keywords  = {CPU Design; Computer Architecture; Computer Science (CS); RISC; RISC-V},
  url       = {https://web.cecs.pdx.edu/~harry/riscv/RISCV-Summary.pdf},
  file      = {:by-author/P/Porter/2018_Porter_1.pdf:PDF},
  owner     = {saulius},
  pages     = {1--323},
  timestamp = {2020.12.06},
  creationdate = {2020-12-06T00:00:00},
}

@TechReport{Long2017b,
  author    = {Long, Jiang},
  title     = {Reasoning about high-level constructs in hardware/software formal verification},
  year      = {2017},
  month     = {Aug},
  number    = {UCB/EECS-2017-150},
  abstract  = {The ever shrinking feature size of modern electronic chips leads to more designs being done as well as more complex chips being designed. These in turn lead to greater use of high-level specifications and to more sophisticated optimizations applied at the word -level. These steps make it more difficult to verify that the final design is faithful to the initial specification. We tackle two steps in this process and their formal equivalence checking to help verify the correctness of the steps.
First, we present LEC, a combinational equivalence checking tool that is learning driven. It focuses on data-path equivalence checking with the goal of transforming the two logics under comparison to be more similar in order to reduce the complexity of a final Boolean (bit-level) solving. LEC does equivalence checking of combinational logic between two RTL (word-level) designs, one the original and one an optimized RTL version. LEC features an open architecture such that users and developers can learn with the system as new designs and optimizations are met, and then it can be modularly extended with new proof procedures as they are discovered.

To address the use of higher level specifications, we build a simple trusted C to Verilog trans- lation procedure based on the LLVM compiler infrastructure. The translator was designed to implement an almost vertatim translation of the C language operators and control structures into the Verilog always ff and always comb blocks through traversing LLVM Bytecode pro- grams. The procedure reliably bridges the language barrier between software and hardware and allows hardware synthesis and verification techniques to be applied readily.
In combination, these two procedures allow for equivalence checking between a software-like specification and an optimized word-level RTL implementation.},
  file      = {:by-author/L/Long/2017_Long_1.pdf:PDF},
  owner     = {saulius},
  pages     = {1--117},
  school    = {EECS Department, University of California, Berkeley},
  timestamp = {2020.12.06},
  creationdate = {2020-12-06T00:00:00},
  url       = {http://www2.eecs.berkeley.edu/Pubs/TechRpts/2017/EECS-2017-150.html},
}

@InProceedings{Wu1990a,
  author    = {Chung-Yu Wu and Hong-Yi Huang},
  booktitle = {{IEEE} International Symposium on Circuits and Systems},
  title     = {A new two-phase pipelined dynamic {CMOS} ternary logic},
  year      = {1990},
  pages     = {582--586},
  publisher = {{IEEE}},
  doi       = {10.1109/iscas.1990.112127},
  file      = {:by-author/W/Wu/1990_Wu_582.pdf:PDF},
  owner     = {saulius},
  timestamp = {2020.12.06},
  creationdate = {2020-12-06T00:00:00},
}

@Standard{IEEE1985a,
  organization = {IEEE},
  title        = {{IEEE} standard for binary floating-point arithmetic},
  author       = {{IEEE}},
  month        = oct,
  year         = {1985},
  doi          = {10.1109/ieeestd.1985.82928},
  file         = {:by-author/I/IEEE/1985_IEEE_1a.pdf:PDF},
  keywords     = {Computer Science (CS); Floating Point; IEEE; Standard},
  owner        = {saulius},
  pages        = {1--20},
  publisher    = {{IEEE}},
  timestamp = {2020.12.06},
  creationdate = {2020-12-06T00:00:00},
}

@Standard{IEEE2008,
  institution = {IEEE},
  title       = {{IEEE} standard for floating-point arithmetic},
  author      = {{IEEE}},
  year        = {2008},
  doi         = {10.1109/ieeestd.2008.4610935},
  file        = {:by-author/I/IEEE/2008_IEEE_1.pdf:PDF},
  keywords    = {Computer Science (CS); Floating Point; IEEE; Standard},
  owner       = {saulius},
  pages       = {1--70},
  publisher   = {{IEEE}},
  timestamp = {2020.12.06},
  creationdate = {2020-12-06T00:00:00},
}

@Standard{IEEE2019,
  organization = {IEEE},
  title        = {{IEEE} standard for floating-point arithmetic},
  author       = {{IEEE}},
  year         = {2019},
  doi          = {10.1109/ieeestd.2019.8766229},
  file         = {:by-author/I/IEEE/2019_IEEE_1.pdf:PDF},
  keywords     = {Computer Science (CS); Floating Point; IEEE; Standard},
  owner        = {saulius},
  pages        = {1--84},
  publisher    = {{IEEE}},
  timestamp = {2020.12.06},
  creationdate = {2020-12-06T00:00:00},
}

@Manuscript{Michal2012,
  author    = {Vratislav Michal},
  title     = {On the low-power design, stability improvement and frequency estimation of the {CMOS} ring oscillator},
  year      = {2012},
  keywords  = {CMOS; Circuit Design; Computer Science (CS); Electronics; Ring Oscillator},
  url       = {http://www.postreh.com/vmichal/papers/Stability-CMOS-ring-oscillator.pdf},
  file      = {:by-author/M/Michal/2012_Michal_1.pdf:PDF},
  owner     = {saulius},
  pages     = {1--4},
  timestamp = {2020.12.07},
  creationdate = {2020-12-07T00:00:00},
}

@Manuscript{Hanson2004,
  author    = {Donald F. Hanson},
  title     = {A {VHDL} conversion tool for logic equations with embedded {D} latches},
  year      = {2004},
  keywords  = {6502; Circuit Design; Computer Architecture; Computer Science (CS); VHDL},
  url       = {https://projects.ncsu.edu/wcae/WCAE1/hanson.pdf},
  file      = {:by-author/H/Hanson/2004_Hanson_1.pdf:PDF},
  owner     = {saulius},
  pages     = {1--8},
  timestamp = {2020.12.08},
  creationdate = {2020-12-08T00:00:00},
}

@Presentation{Naidu2017,
  author           = {Prathik Naidu and Adam Pahlavan},
  title            = {Fun with {B}eamer: {A}n epic quest to create the perfect presentation},
  year             = {2017},
  creationdate     = {2020-12-13T00:00:00},
  file             = {:by-author/N/Naidu/2017_Naidu_1.pdf:PDF},
  keywords         = {Beamer; Communication of Science; LaTeX; PDF; Presentation},
  modificationdate = {2023-02-15T09:30:43},
  owner            = {saulius},
  pages            = {1--58},
  timestamp        = {2020.12.13},
  url              = {http://web.mit.edu/rsi/www/pdfs/beamer-tutorial.pdf},
}

@Article{Tshitoyan2019,
  author    = {Vahe Tshitoyan and John Dagdelen and Leigh Weston and Alexander Dunn and Ziqin Rong and Olga Kononova and Kristin A. Persson and Gerbrand Ceder and Anubhav Jain},
  journal   = {Nature},
  title     = {Unsupervised word embeddings capture latent knowledge from materials science literature},
  year      = {2019},
  month     = {jul},
  number    = {7763},
  pages     = {95--98},
  volume    = {571},
  doi       = {10.1038/s41586-019-1335-8},
  file      = {:by-author/T/Tshitoyan/2019_Tshitoyan_95.pdf:PDF},
  keywords  = {Computer Science (CS); Knowledge Extraction; Machine Learning (ML); Scientific Publication},
  owner     = {saulius},
  publisher = {Springer Science and Business Media {LLC}},
  timestamp = {2020.12.13},
  creationdate = {2020-12-13T00:00:00},
}

@InProceedings{Breitinger2017,
  author    = {Breitinger, Corinna and Gipp, Bela},
  booktitle = {{P}roceedings of the 15th {I}nternational {S}ymposium of {I}nformation {S}cience},
  title     = {{V}irtual{P}atent - enabling the traceability of ideas shared online using decentralized trusted timestamping},
  year      = {2017},
  pages     = {1--7},
  file      = {:by-author/B/Breitinger/2017_Breitinger_1.pdf:PDF},
  keywords  = {Blockchain; Computer Science (CS); Timestamping},
  location  = {Berlin},
  owner     = {saulius},
  timestamp = {2020.12.13},
  creationdate = {2020-12-13T00:00:00},
  url       = {https://www.gipp.com/wp-content/papercite-data/pdf/breitinger2017.pdf},
}

@Presentation{Henning2010,
  author           = {Stephan Henning},
  title            = {Advanced {B}eamer techniques},
  year             = {2010},
  creationdate     = {2020-12-13T00:00:00},
  file             = {:by-author/H/Henning/2010_Henning_1.pdf:PDF},
  keywords         = {Beamer; Communication of Science; LaTeX; PDF; Presentation},
  modificationdate = {2023-02-15T09:30:48},
  owner            = {saulius},
  pages            = {1--30},
  timestamp        = {2020.12.13},
  url              = {http://www.eng.auburn.edu/~sjreeves/Classes/ELEC6970-latex/Advanced_Beamer/Advanced_Beamer.pdf},
}

@Article{Alexander1975,
  author    = {W. C. Alexander and D. B. Wortman},
  journal   = {Computer},
  title     = {Static and Dynamic characteristics of {XPL} programs},
  year      = {1975},
  month     = nov,
  number    = {11},
  pages     = {41--46},
  volume    = {8},
  comment   = {Form Patterson2003: "measurements of a particular IBM 360 compiler found that 10 instructions accounted for 80% of all instructions executed, 16 for 90%, 21 for 95%, and 30 for 99% [Alexander75](p. 3)"},
  doi       = {10.1109/c-m.1975.218804},
  file      = {:by-author/A/Alexander/1975_Alexander_41.pdf:PDF},
  keywords  = {Computer Science (CS); Efficiency; ISA; Instruction Set},
  owner     = {saulius},
  timestamp = {2020.12.13},
  creationdate = {2020-12-13T00:00:00},
}

@Article{Foster1971,
  author    = {C. C. Foster and R. H. Gonter and E. M. Riseman},
  journal   = {{IEEE} Transactions on Computers},
  title     = {Measures of op-code utilization},
  year      = {1971},
  month     = may,
  pages     = {582--584},
  doi       = {10.1109/t-c.1971.223296},
  file      = {:by-author/F/Foster/1971_Foster_582.pdf:PDF},
  keywords  = {Computer Science (CS); Efficiency; ISA; Instruction Set},
  owner     = {saulius},
  timestamp = {2020.12.13},
  creationdate = {2020-12-13T00:00:00},
}

@Article{Wiecek1982,
  author    = {Cheryl A. Wiecek},
  journal   = {{ACM} {SIGPLAN} Notices},
  title     = {A case study of {VAX}-11 instruction set usage for compiler execution},
  year      = {1982},
  month     = {apr},
  number    = {4},
  pages     = {177--184},
  volume    = {17},
  doi       = {10.1145/960120.801841},
  file      = {:by-author/W/Wiecek/1982_Wiecek_177.pdf:PDF},
  keywords  = {Computer Science (CS); DEC; Efficiency; ISA; Instruction Set; VAX},
  owner     = {saulius},
  publisher = {Association for Computing Machinery ({ACM})},
  timestamp = {2020.12.13},
  creationdate = {2020-12-13T00:00:00},
}

@InProceedings{Peuto1977,
  author    = {B. L. Peuto and L. J. Shustek},
  booktitle = {Fourth Annual Symposium on Computer Architecture},
  title     = {An instruction timing model of {CPU} performance},
  year      = {1977},
  month     = mar,
  pages     = {165--178},
  doi       = {10.1145/800255.810667},
  file      = {:by-author/P/Peuto/1977_Peuto_165.pdf:PDF},
  keywords  = {Computer Science (CS); Efficiency; ISA; Instruction Set},
  owner     = {saulius},
  timestamp = {2020.12.13},
  creationdate = {2020-12-13T00:00:00},
}

@TechReport{Waterman2015c,
  author      = {Andrew Waterman and Yunsup Lee and David A. Patterson and Krste Asanović},
  institution = {Electrical Engineering and Computer Sciences, University of California at Berkeley},
  title       = {The {RISC-V} compressed instruction set manual, version 1.9},
  year        = {2015},
  month       = nov,
  file        = {:by-author/W/Waterman/2015_Waterman_1c.pdf:PDF},
  keywords    = {CPU Design; Computer Architecture; Computer Science (CS); RISC; RISC-V},
  owner       = {saulius},
  pages       = {1--23},
  timestamp = {2020.12.13},
  creationdate = {2020-12-13T00:00:00},
  url         = {https://www2.eecs.berkeley.edu/Pubs/TechRpts/2015/EECS-2015-209.pdf},
}

@Article{Hegde2020,
  author      = {Vinay I. Hegde and Christopher K. H. Borg and Zachary del Rosario and Yoolhee Kim and Maxwell Hutchinson and Erin Antono and Julia Ling and Paul Saxe and James E. Saal and Bryce Meredig},
  journal     = {arXiv},
  title       = {Reproducibility in high-throughput density functional theory: a comparison of {AFLOW}, {M}aterials {P}roject, and {OQMD}},
  year        = {2020},
  pages       = {1--32},
  abstract    = {A central challenge in high throughput density functional theory (HT-DFT) calculations is selecting a combination of input parameters and post-processing techniques that can be used across all materials classes, while also managing accuracy-cost tradeoffs. To investigate the effects of these parameter choices, we consolidate three large HT-DFT databases: Automatic-FLOW (AFLOW), the Materials Project (MP), and the Open Quantum Materials Database (OQMD), and compare reported properties across each pair of databases for materials calculated using the same initial crystal structure. We find that HT-DFT formation energies and volumes are generally more reproducible than band gaps and total magnetizations; for instance, a notable fraction of records disagree on whether a material is metallic (up to 7%) or magnetic (up to 15%). The variance between calculated properties is as high as 0.105 eV/atom (median relative absolute difference, or MRAD, of 6%) for formation energy, 0.65 {\AA}$^3$/atom (MRAD of 4%) for volume, 0.21 eV (MRAD of 9%) for band gap, and 0.15 $\mu_{\rm B}$/formula unit (MRAD of 8%) for total magnetization, comparable to the differences between DFT and experiment. We trace some of the larger discrepancies to choices involving pseudopotentials, the DFT+U formalism, and elemental reference states, and argue that further standardization of HT-DFT would be beneficial to reproducibility.},
  date        = {2020-07-04},
  eprint      = {2007.01988},
  eprintclass = {cond-mat.mtrl-sci},
  eprinttype  = {arXiv},
  file        = {:by-author/H/Hegde/2020_Hegde_1.pdf:PDF},
  keywords    = {Computational Material Science; Density Functional Theory (DFT)},
  owner       = {saulius},
  timestamp = {2020.12.17},
  creationdate = {2020-12-17T00:00:00},
}

@Manuscript{Roussel2005,
  author    = {Marc R. Roussel},
  title     = {Reaction-diffusion equations},
  year      = {2005},
  keywords  = {Diffusion-reaction Equation; PDE},
  month     = nov,
  url       = {http://people.uleth.ca/~roussel/nld/Turing.pdf},
  file      = {:by-author/R/Roussel/2005_Roussel_1.pdf:PDF},
  owner     = {saulius},
  pages     = {1--13},
  timestamp = {2020.12.17},
  creationdate = {2020-12-17T00:00:00},
}

@Misc{Asmi2017,
  author       = {Asmi, Ari and Cordewener, Bas and Goble, Carole and Castelli, Donatella and Kühn, Eileen and Pasian, Fabio and Niccolucci, Franco and Glaves, Helen and Jeffery, Keith and Assante, Massimiliano and Dovey, Matthew and Manola, Natalia and Juty, Nick and Juty, Nick and Jimenez, Rafael and Jimenez, Rafael},
  howpublished = {Web PDF},
  month        = dec,
  title        = {{EOSC} datasets minimum information. {D}6.3: 1st report on data interoperability: findability and interoperability},
  year         = {2017},
  comment      = {Via https://fairsharing.org/bsg-s001135/ .},
  file         = {:by-author/A/Asmi/2017_Asmi_1.pdf:PDF},
  keywords     = {Data Sharing; EOSC; FAIR; Metadata},
  owner        = {saulius},
  pages        = {1--64},
  timestamp = {2020.12.19},
  creationdate = {2020-12-19T00:00:00},
  url          = {https://eoscpilot.eu/sites/default/files/eoscpilot-d6.3.pdf},
}

@Article{Wu1993,
  author    = {Chung-Yu Wu and Hong-Yi Huang},
  journal   = {{IEEE} Journal of Solid-State Circuits},
  title     = {Design and application of pipelined dynamic {CMOS} ternary logic and simple ternary differential logic},
  year      = {1993},
  month     = aug,
  number    = {8},
  pages     = {895--906},
  volume    = {28},
  doi       = {10.1109/4.231326},
  file      = {:by-author/W/Wu/1993_Wu_895.pdf:PDF},
  keywords  = {CMOS; Computer Science (CS); Dynamic Logic; Ternary Circuits},
  owner     = {saulius},
  timestamp = {2020.12.20},
  creationdate = {2020-12-20T00:00:00},
  url       = {https://ir.nctu.edu.tw/bitstream/11536/2920/1/A1993LR12600003.pdf},
}

@InProceedings{Groves1995,
  author    = {Groves, R.},
  booktitle = {18th {CERN} School of Computing},
  title     = {Brief history of computer architecture evolution and future trends},
  year      = {1995},
  pages     = {147--159},
  publisher = {CERN},
  doi       = {10.5170/CERN-1995-005.147},
  file      = {:by-author/G/Groves/1995_Groves_147.pdf:PDF;:by-author/G/Groves/1995_Groves_147a.pdf:PDF},
  keywords  = {Computer Architecture; Computer Science (CS)},
  language  = {en},
  owner     = {saulius},
  timestamp = {2020.12.30},
  creationdate = {2020-12-30T00:00:00},
  url       = {https://cds.cern.ch/record/399391/files/p147.pdf},
}

@Article{Shou2006,
  author    = {Xiaoqiang Shou and Nader Kalantari and Michael M. Green},
  journal   = {{IEEE} Transactions on Circuits and Systems I: Regular Papers},
  title     = {Design of {CMOS} ternary latches},
  year      = {2006},
  month     = {dec},
  number    = {12},
  pages     = {2588--2594},
  volume    = {53},
  doi       = {10.1109/TCSI.2006.885697},
  file      = {:by-author/S/Shou/2006_Shou_2588.pdf:PDF},
  keywords  = {Computer Science (CS); Ternary Logic; Tristable Circuits},
  owner     = {saulius},
  publisher = {Institute of Electrical and Electronics Engineers ({IEEE})},
  timestamp = {2020.12.30},
  creationdate = {2020-12-30T00:00:00},
}

@TechReport{Lepkowski2001,
  author      = {Jim Lepkowski and Mike Hoogstra and Christopher Young},
  institution = {{ON} {S}emiconductor},
  title       = {{NL27WZ04} dual gate inverter oscillator increases the brightness of {LED}s while reducing power consumption},
  year        = {2001},
  comment     = {"/.../ the human eye functions as both a peak detector and an integrator; therefore, the eye perceives a pulsed LED’s brightness somewhere between the peak and the average brightness [4]."},
  file        = {:by-author/L/Lepkowski/2001_Lepkowski_1.pdf:PDF},
  keywords    = {CMOS; Computer Science (CS); Electronics; Eye Physiology; Eye as Peak Detector; LED; Oscillator},
  owner       = {saulius},
  pages       = {1--8},
  timestamp = {2020.12.30},
  creationdate = {2020-12-30T00:00:00},
  url         = {https://www.onsemi.com/pub/Collateral/AND8067-D.PDF},
}

@Standard{CENCENELEC2020,
  institution  = {CEN},
  organization = {CENELEC},
  title        = {Road map on {A}rtificial {I}ntelligence ({AI}) (draft)},
  author       = {{CEN-CENELEC}},
  language     = {eng},
  number       = {BT N 12195},
  year         = {2020},
  file         = {:by-author/C/CENCENELEC/2020_CENCENELEC_1.pdf:PDF},
  keywords     = {Artificial Intelligence (AI); Computer Science (CS); Machine Learning (ML)},
  owner        = {saulius},
  pages        = {1--39},
  timestamp = {2020.12.30},
  creationdate = {2020-12-30T00:00:00},
}

@Manuscript{Hill1999,
  author    = {Mark D. Hill and Norman P. Jouppi and Gurindar S. Sohi},
  title     = {Readings in Computer Architecture},
  year      = {1999},
  keywords  = {Bibliography; Computer Architecture; Computer Science (CS)},
  file      = {:by-author/H/Hill/1999_Hill_1.pdf:PDF},
  owner     = {saulius},
  pages     = {1--5},
  timestamp = {2020.12.30},
  creationdate = {2020-12-30T00:00:00},
}

@Manuscript{Schoeberl2011,
  author    = {Martin Schoeberl},
  title     = {Leros: a tiny microcontroller for {FPGA}s},
  year      = {2011},
  keywords  = {Computer Architecture; Computer Science (CS); FPGA; Microcontrollers; RISC; SoC},
  url       = {https://www.jopdesign.com/doc/leros.pdf},
  comment   = {Found via the Ripes GitHub repo (S.G.).},
  file      = {:by-author/S/Schoeberl/2011_Schoeberl_1.pdf:PDF},
  owner     = {saulius},
  pages     = {1--5},
  timestamp = {2020.12.30},
  creationdate = {2020-12-30T00:00:00},
}

@InProceedings{Caska2011,
  author    = {James Caska and Martin Schoeberl},
  booktitle = {Proceedings of the 9th International Workshop on Java Technologies for Real-Time and Embedded Systems - {JTRES} {\textquotesingle}11},
  title     = {Java dust: how small can embedded {J}ava be?},
  year      = {2011},
  pages     = {1--5},
  publisher = {{ACM} Press},
  doi       = {10.1145/2043910.2043931},
  file      = {:by-author/C/Caska/2011_Caska_1.pdf:PDF},
  keywords  = {Computer Architecture; Computer Science (CS); FPGA; Microcontrollers; RISC; SoC},
  owner     = {saulius},
  timestamp = {2020.12.30},
  creationdate = {2020-12-30T00:00:00},
  url       = {https://www.jopdesign.com/doc/lerosjvm.pdf},
}

@Article{Soueidy2009,
  author    = {Ch. P. El Soueidy and A. Younes and P. Ackerer},
  journal   = {International Journal for Numerical Methods in Engineering},
  title     = {Solving the advection-diffusion equation on unstructured meshes with discontinuous/mixed finite elements and a local time stepping procedure},
  year      = {2009},
  month     = {apr},
  number    = {9},
  pages     = {1068--1093},
  volume    = {79},
  doi       = {10.1002/nme.2609},
  file      = {:by-author/S/Soueidy/2009_Soueidy_1068.pdf:PDF},
  keywords  = {Diffusion Equation; Diffusion Reaction Equations; PDE},
  owner     = {saulius},
  publisher = {Wiley},
  timestamp = {2020.12.30},
  creationdate = {2020-12-30T00:00:00},
  url       = {https://hal.archives-ouvertes.fr/hal-01007312/file/CPES.pdf},
}

@Article{Diehl2020,
  author      = {Nicolau M. L. Diehl and Rafayel Teymurazyan},
  journal     = {arXiV},
  title       = {Reaction-diffusion equations for the infinity {L}aplacian},
  year        = {2020},
  pages       = {1--15},
  abstract    = {We derive sharp regularity for viscosity solutions of an inhomogeneous infinity Laplace equation across the free boundary, when the right hand side does not change sign and satisfies a certain growth condition. We prove geometric regularity estimates for solutions and conclude that once the source term is comparable to a homogeneous function, then the free boundary is a porous set and hence, has zero Lebesgue measure. Additionally, we derive a Liouville type theorem. When near the origin the right hand side grows not faster than third degree homogeneous function, we show that if a non-negative viscosity solution vanishes at a point, then it has to vanish everywhere.},
  date        = {2020-05-04},
  eprint      = {2005.01551},
  eprintclass = {math.AP},
  eprinttype  = {arXiv},
  file        = {:by-author/D/Diehl/2020_Diehl_111956.pdf:PDF},
  keywords    = {Diffusion Equation; Diffusion-reaction; PDE},
  owner       = {saulius},
  timestamp = {2020.12.30},
  creationdate = {2020-12-30T00:00:00},
}

@Article{Diehl2020a,
  author    = {Nicolau M.L. Diehl and Rafayel Teymurazyan},
  journal   = {Nonlinear Analysis},
  title     = {Reaction{\textendash}diffusion equations for the infinity Laplacian},
  year      = {2020},
  month     = {oct},
  pages     = {111956},
  volume    = {199},
  doi       = {10.1016/j.na.2020.111956},
  file      = {:by-author/D/Diehl/2020_Diehl_111956.pdf:PDF},
  keywords  = {Diffusion Equation; Diffusion-reaction; PDE},
  owner     = {saulius},
  publisher = {Elsevier {BV}},
  timestamp = {2020.12.30},
  creationdate = {2020-12-30T00:00:00},
}

@Presentation{CushmanRoisin2010,
  author    = {Benoit Cushman-Roisin},
  title     = {Diffusion – part 2: other initial & boundary conditions},
  year      = {2010},
  file      = {:by-author/C/Cushman-Roisin/2010_Cushman-Roisin_1.pdf:PDF},
  keywords  = {Diffusion Equation; PDE},
  owner     = {saulius},
  pages     = {1--8},
  timestamp = {2020.12.30},
  creationdate = {2020-12-30T00:00:00},
  url       = {http://www.dartmouth.edu/~cushman/courses/engs43/Diffusion-variations.pdf},
}

@Manuscript{Oklobdzija2000,
  author    = {Vojin G. Oklobdzija and Kazuo Yano},
  title     = {Dynamic {CMOS} circuits},
  year      = {2000},
  keywords  = {CMOS; Computer Science (CS); Dynamic Logic},
  url       = {https://www.ece.ucdavis.edu/~vojin/CLASSES/EEC280/protected/Book/Chpt-4a-dyn&domin.pdf},
  file      = {:by-author/O/Oklobdzija/2000_Oklobdzija_1.pdf:PDF},
  owner     = {saulius},
  pages     = {1--7},
  timestamp = {2020.12.30},
  creationdate = {2020-12-30T00:00:00},
}

@Article{Mandal2010,
  author    = {M. K. Mandal and B. C. Sarkar},
  journal   = {Indian Journal of Pure & Applied Physics},
  title     = {Ring oscillators: characteristics and applications},
  year      = {2010},
  month     = feb,
  pages     = {136--145},
  volume    = {48},
  file      = {:by-author/M/Mandal/2010_Mandal_136.pdf:PDF},
  keywords  = {Computer Science (CS); Electronics; Ring Oscillator},
  owner     = {saulius},
  timestamp = {2020.12.30},
  creationdate = {2020-12-30T00:00:00},
  url       = {http://nopr.niscair.res.in/bitstream/123456789/7244/1/IJPAP 48(2) 136-145.pdf},
}

@Manuscript{Jun1999,
  author       = {Benjamin Jun and Paul Kocher},
  title        = {The {I}ntel random number generator},
  year         = {1999},
  keywords     = {Cryptography; Electronics; Random Naumbers},
  month        = apr,
  organization = {Intel},
  url          = {https://www.rambus.com/wp-content/uploads/2015/08/IntelRNG.pdf},
  file         = {:by-author/J/Jun/1999_Jun_1.pdf:PDF},
  owner        = {saulius},
  pages        = {1--8},
  timestamp = {2020.12.30},
  creationdate = {2020-12-30T00:00:00},
}

@Presentation{Johnson2012,
  author    = {John M. Johnson},
  title     = {Propagation delay, circuittiming & adder design},
  year      = {2012},
  file      = {:by-author/J/Johnson/2012_Johnson_1.pdf:PDF},
  keywords  = {Circuit Design; Computer Science (CS); Digital Circuits; Electronics; Propagation Delay},
  owner     = {saulius},
  pages     = {1--57},
  timestamp = {2020.12.30},
  creationdate = {2020-12-30T00:00:00},
  url       = {https://web.ece.ucsb.edu/Faculty/Johnson/ECE152A/L4 - Propagation Delay, Circuit Timing & Adder Design.pdf},
}

@Manual{USDoD1991,
  title     = {Encoders: shaft angle to digital},
  author    = {{US DoD}},
  month     = sep,
  year      = {1991},
  comment   = {Found via: https://en.wikipedia.org/wiki/Two-out-of-five_code},
  file      = {:by-author/U/USDoD/1991_USDoD_1.pdf:PDF},
  keywords  = {Computer I/O; Computer Science (CS); Electronics; Encoders},
  owner     = {saulius},
  pages     = {1--342},
  timestamp = {2020.12.30},
  creationdate = {2020-12-30T00:00:00},
  url       = {http://everyspec.com/MIL-HDBK/MIL-HDBK-0200-0299/download.php?spec=MIL_HDBK_231A.1809.pdf},
}

@Newsletter{Tokieda2014,
  editor    = {Tadashi Tokieda},
  number    = {120},
  file      = {:by-author/T/Tokieda/2014_Tokieda_265.pdf:PDF},
  keywords  = {Mathematics; Popular Mathematics},
  owner     = {saulius},
  pages     = {265--282},
  timestamp = {2020.12.30},
  creationdate = {2020-12-30T00:00:00},
  title     = {Roll Models},
  url       = {https://www.maa.org/sites/default/files/pdf/upload_library/2/Tokieda-Monthly-2014.pdf},
  year      = {2014},
}

@Book{Milne2006,
  author    = {J. S. Milne},
  publisher = {J. S. Milne},
  title     = {Algebraic groups and arithmetic groups},
  year      = {2006},
  file      = {:by-author/M/Milne/2006_Milne_1.pdf:PDF},
  keywords  = {Algebra; Group Theory; Mathematics},
  owner     = {saulius},
  pages     = {1--219},
  timestamp = {2020.12.30},
  creationdate = {2020-12-30T00:00:00},
  url       = {https://www.jmilne.org/math/CourseNotes/aag.pdf},
  version   = {1.01},
}

@Manuscript{Strang2006,
  author    = {Gilbert Strang},
  title     = {The Heat Equation and Convection-Diffusion},
  year      = {2006},
  keywords  = {Diffusion Equation; Heat Equation; Mathematics; PDE},
  url       = {https://ocw.mit.edu/courses/mathematics/18-086-mathematical-methods-for-engineers-ii-spring-2006/readings/am54.pdf},
  file      = {:by-author/S/Strang/2006_Strang_1.pdf:PDF},
  owner     = {saulius},
  pages     = {1--10},
  timestamp = {2020.12.30},
  creationdate = {2020-12-30T00:00:00},
}

@Manuscript{Hulpke2010,
  author    = {Alexander Hulpke},
  title     = {Notes on computational group theory},
  year      = {2010},
  keywords  = {Algebra; Computational Group Theory; GAP; Groups; Mathematics},
  url       = {https://www.math.colostate.edu/~hulpke/CGT/cgtnotes.pdf},
  file      = {:by-author/H/Hulpke/2010_Hulpke_1.pdf:PDF},
  owner     = {saulius},
  pages     = {1--152},
  timestamp = {2020.12.30},
  creationdate = {2020-12-30T00:00:00},
}

@Lecture{Fulling2015,
  author    = {Stephen A. Fulling},
  title     = {Delta “functions”},
  year      = {2015},
  file      = {:by-author/F/Fulling/2015_Fulling_1.pdf:PDF},
  keywords  = {Delta Function; Green Function; Mathematics; PDE},
  owner     = {saulius},
  pages     = {1--37},
  timestamp = {2020.12.30},
  creationdate = {2020-12-30T00:00:00},
  url       = {https://calclab.math.tamu.edu/~fulling/m412/f15/deltagr.pdf},
}

@InBook{Belinfante2005,
  author    = {Axel Belinfante and Lars Frantzen and Christian Schallhart},
  editor    = {M. Broy et al.},
  pages     = {391--438},
  publisher = {Springer-Verlag},
  title     = {Tools for test case generation},
  year      = {2005},
  isbn      = {9783540262787},
  booktitle = {Model-Based Testing of Reactive Systems},
  file      = {:by-author/B/Belinfante/2005_Belinfante_391.pdf:PDF},
  keywords  = {Computer Science (CS); Software Development; Software Testing},
  owner     = {saulius},
  timestamp = {2020.12.30},
  creationdate = {2020-12-30T00:00:00},
  url       = {https://link.springer.com/chapter/10.1007%2F978-3-319-29643-2_13},
}

@Manuscript{Dawson2007,
  author    = {Jeremy Dawson},
  title     = {{I}sabelle theories for machine words},
  year      = {2007},
  keywords  = {Computer Science (CS); Isabelle; Machine Words; Mechanised Reasoning; Proof Assistants; Twos-complement},
  url       = {http://users.cecs.anu.edu.au/~jeremy/pubs/l4/avocs/word.pdf},
  file      = {:by-author/D/Dawson/2007_Dawson_1.pdf:PDF},
  owner     = {saulius},
  pages     = {1--15},
  timestamp = {2020.12.30},
  creationdate = {2020-12-30T00:00:00},
}

@Manuscript{Shuman2003,
  author    = {Derek Shuman},
  title     = {The diffusion equation},
  year      = {2003},
  keywords  = {Diffusion Equation; Mathematics; PDE},
  url       = {http://www-eng.lbl.gov/~shuman/NEXT/MATERIALS&COMPONENTS/Xe_damage/diffusion_eq.pdf},
  file      = {:by-author/S/Shuman/2003_Shuman_23.pdf:PDF},
  owner     = {saulius},
  pages     = {23--44},
  timestamp = {2020.12.30},
  creationdate = {2020-12-30T00:00:00},
}

@Manuscript{Ursell2016,
  author    = {Tristan S. Ursell},
  title     = {The diffusion equation: a multi-dimensional tutorial},
  year      = {2016},
  keywords  = {Diffusion Equation; Mathematics; PDE},
  url       = {https://www.dropbox.com/s/s0470m594llwcc7/diffusion.pdf?raw=1},
  file      = {:by-author/U/Ursell/2016_Ursell_1.pdf:PDF},
  owner     = {saulius},
  pages     = {1--25},
  timestamp = {2020.12.30},
  creationdate = {2020-12-30T00:00:00},
}

@Manuscript{Langtangen2015,
  author    = {Hans Petter Langtangen},
  title     = {The {1D} diffusion equation},
  year      = {2015},
  url       = {https://hplgit.github.io/num-methods-for-PDEs/doc/pub/diffu/sphinx/._main_diffu001.html},
  file      = {:by-author/L/Langtangen/2015_Langtangen_1.pdf:PDF},
  owner     = {saulius},
  pages     = {1--28},
  timestamp = {2020.12.30},
  creationdate = {2020-12-30T00:00:00},
}

@Article{Merz2002,
  author    = {Stephan Merz},
  journal   = {Synthese},
  title     = {Model checking techniqes for the analysis of reactive systems},
  year      = {2002},
  pages     = {173--201},
  volume    = {133},
  doi       = {10.1023/a:1020887910943},
  file      = {:by-author/M/Merz/2002_Merz_173.pdf:PDF},
  keywords  = {Computer Science (CS); Correctness Proofs; Model Checking},
  owner     = {saulius},
  timestamp = {2020.12.30},
  creationdate = {2020-12-30T00:00:00},
}

@Manuscript{Ballarin2006,
  author    = {Clemens Ballarin},
  title     = {Interpretation of locales in {I}sabelle: theories and proof contexts},
  year      = {2006},
  doi       = {10.1007/11812289_4},
  keywords  = {Computer Science (CS); HOL; Isabelle; Proof Assistants},
  url       = {http://isabelle.in.tum.de/~ballarin/publications/mkm2006.pdf},
  file      = {:by-author/B/Ballarin/2006_Ballarin_1.pdf:PDF},
  owner     = {saulius},
  pages     = {1--13},
  timestamp = {2020.12.30},
  creationdate = {2020-12-30T00:00:00},
}

@Presentation{Marzuki2011,
  author    = {A. Marzuki},
  title     = {Dynamic logic circuits},
  year      = {2011},
  file      = {:by-author/M/Marzuki/2011_Marzuki_1.pdf:PDF},
  keywords  = {Computer Science (CS); Dynamic Logic; Logic Circuits; MOS},
  owner     = {saulius},
  pages     = {1--25},
  timestamp = {2020.12.30},
  creationdate = {2020-12-30T00:00:00},
  url       = {https://ee.eng.usm.my/eeacad/arjuna/dynamlogicircuitII.pdf},
}

@Article{Herrfeld1994,
  author    = {A. Herrfeld and S. Hentschke},
  journal   = {Electronic Letters},
  title     = {{CMOS} ternary dynamic differential logic},
  year      = {1994},
  month     = may,
  number    = {10},
  pages     = {762--763},
  volume    = {30},
  doi       = {10.1049/el:19940542},
  file      = {:by-author/H/Herrfeld/1994_Herrfeld_762.pdf:PDF},
  keywords  = {CMOS; Computer Science (CS); Dynamic Logic; Electronic; Ternary},
  owner     = {saulius},
  timestamp = {2020.12.30},
  creationdate = {2020-12-30T00:00:00},
}

@Presentation{Allen2007,
  author    = {Samuel M. Allen},
  title     = {Solutions to the diffusion equation},
  year      = {2007},
  lecture   = {3},
  school    = {MIT},
  file      = {:by-author/A/Allen/2007_Allen_1.pdf:PDF},
  keywords  = {Diffusion Equation; Fick's Law; Mathematics; PDE},
  owner     = {saulius},
  pages     = {1--18},
  timestamp = {2020.12.30},
  creationdate = {2020-12-30T00:00:00},
  url       = {https://ocw.mit.edu/courses/materials-science-and-engineering/3-205-thermodynamics-and-kinetics-of-materials-fall-2006/lecture-notes/lecture03_slides.pdf},
}

@Presentation{Tullsen2005,
  author    = {Dean Tullsen},
  title     = {Pipeline hazards},
  year      = {2005},
  file      = {:by-author/T/Tullsen/2005_Tullsen_1.pdf:PDF},
  keywords  = {CPU Design; Computer Science (CS); Hardware; Pipeline Hazards; Pipelines},
  owner     = {saulius},
  pages     = {1--28},
  timestamp = {2020.12.30},
  creationdate = {2020-12-30T00:00:00},
  url       = {http://cseweb.ucsd.edu/classes/wi05/cse240a/pipe2.pdf},
}

@TechReport{TexasInstruments1997,
  author      = {{Texas Instruments, Incorporated}},
  institution = {Texas Instruments},
  title       = {{CMOS} power consumptionand ${C}_{pd}$ calculation},
  year        = {1997},
  month       = jun,
  number      = {SCAA035B},
  type        = {techreport},
  file        = {:by-author/T/TexasInstruments/1997_TexasInstruments_1.pdf:PDF},
  keywords    = {CMOS; Electronics; Power Dissipation},
  owner       = {saulius},
  pages       = {1--16},
  timestamp = {2020.12.30},
  creationdate = {2020-12-30T00:00:00},
  url         = {https://www.ti.com/lit/an/scaa035b/scaa035b.pdf},
}

@TechReport{Haque2004,
  author      = {Moshiul Haque and Ernest Cox},
  institution = {Texas Instruments},
  title       = {Use of the {CMOS} unbuffered inverter in oscillator circuits},
  year        = {2004},
  month       = jan,
  number      = {SZZA043},
  type        = {techreport},
  file        = {:by-author/H/Haque/2004_Haque_1.pdf:PDF},
  keywords    = {Computer Science (CS); Electronics; Inverter; Oscillators},
  owner       = {saulius},
  pages       = {1--25},
  timestamp = {2020.12.30},
  creationdate = {2020-12-30T00:00:00},
  url         = {https://www.ti.com/lit/an/szza043/szza043.pdf?ts=1604803262519},
}

@TechReport{Ada2020,
  author      = {Lady Ada},
  institution = {Adafruit},
  title       = {Micro:bit with {A}rduino},
  year        = {2020},
  file        = {:by-author/A/Ada/2020_Ada_1.pdf:PDF},
  keywords    = {Arduino; Electronics; Micro:bit; Open Source Electroniccs},
  owner       = {saulius},
  pages       = {1--42},
  timestamp = {2020.12.30},
  creationdate = {2020-12-30T00:00:00},
  url         = {https://cdn-learn.adafruit.com/downloads/pdf/use-micro-bit-with-arduino.pdf},
}

@TechReport{Drepper2013,
  author    = {Ulrich Drepper},
  title     = {{ELF} handling for thread-local storage},
  year      = {2013},
  month     = aug,
  type      = {techreport},
  file      = {:by-author/D/Drepper/2013_Drepper_1.pdf:PDF},
  owner     = {saulius},
  pages     = {1--81},
  timestamp = {2020.12.30},
  creationdate = {2020-12-30T00:00:00},
  url       = {https://uclibc.org/docs/tls.pdf},
}

@Article{Patterson1985,
  author    = {David A. Patterson},
  journal   = {Communications of the {ACM}},
  title     = {Reduced instruction set computers},
  year      = {1985},
  month     = {jan},
  number    = {1},
  pages     = {8--21},
  volume    = {28},
  doi       = {10.1145/2465.214917},
  file      = {:by-author/P/Patterson/1985_Patterson_8.pdf:PDF},
  keywords  = {Computer Architecture; Computer Science (CS); RISC},
  owner     = {saulius},
  publisher = {Association for Computing Machinery ({ACM})},
  timestamp = {2020.12.30},
  creationdate = {2020-12-30T00:00:00},
}

@Article{Patterson1980,
  author    = {David A. Patterson and David R. Ditzel},
  journal   = {{ACM} {SIGARCH} Computer Architecture News},
  title     = {The case for the reduced instruction set computer},
  year      = {1980},
  month     = {oct},
  number    = {6},
  pages     = {25--33},
  volume    = {8},
  doi       = {10.1145/641914.641917},
  file      = {:by-author/P/Patterson/1980_Patterson_25.pdf:PDF},
  keywords  = {Computer Architercure; Computer Science (CS); RISC},
  owner     = {saulius},
  publisher = {Association for Computing Machinery ({ACM})},
  timestamp = {2020.12.30},
  creationdate = {2020-12-30T00:00:00},
}

@Presentation{Nasirifar2015,
  author    = {Mohammad Nasirifar},
  title     = {Introduction to cellular automata},
  year      = {2015},
  file      = {:by-author/N/Nasirifar/2015_Nasirifar_1.pdf:PDF},
  keywords  = {Cellular Automata; Computer Science (CS); Life; Von Neumann},
  owner     = {saulius},
  pages     = {1--58},
  timestamp = {2021.01.02},
  creationdate = {2021-01-02T00:00:00},
  url       = {http://www.cs.toronto.edu/~farnasirim/blob/cellular.pdf},
}

@InCollection{Povalej2005,
  author    = {Petra Povalej and Peter Kokol and Tatjana Welzer Družovec and Bruno Stiglic},
  booktitle = {Lecture Notes in Computer Science},
  publisher = {Springer Berlin Heidelberg},
  title     = {Machine-learning with cellular automata},
  year      = {2005},
  pages     = {305--315},
  doi       = {10.1007/11552253_28},
  file      = {:by-author/P/Povalej/2005_Povalej_305.pdf:PDF},
  keywords  = {Cellular Automata; Classifiers; Computer Science (CS); Machine Learning (ML)},
  owner     = {saulius},
  timestamp = {2021.01.02},
  creationdate = {2021-01-02T00:00:00},
  url       = {https://www.researchgate.net/publication/221460875_Machine-Learning_with_Cellular_Automata},
}

@Article{Langton1987,
  author    = {Chris Langton},
  journal   = {Complex Systems},
  title     = {Virtual state machines in cellular automata},
  year      = {1987},
  pages     = {257--271},
  volume    = {1},
  file      = {:by-author/L/Langton/1987_Langton_257.pdf:PDF},
  owner     = {saulius},
  timestamp = {2021.01.02},
  creationdate = {2021-01-02T00:00:00},
  url       = {http://wpmedia.wolfram.com/uploads/sites/13/2018/02/01-2-3.pdf},
}

@InCollection{Backus1978,
  author    = {John Backus},
  booktitle = {Communications of the {ACM}},
  publisher = {Association of Computing Machinery},
  title     = {Can programming be liberated from the von {N}eumann style?: a functional style and its algebra of programs},
  year      = {1978},
  number    = {8},
  pages     = {613--641},
  volume    = {21},
  file      = {:by-author/B/Backus/1978_Backus_613.pdf:PDF},
  keywords  = {Computer Science (CS); Functional Programming; Von Neumann Architecture},
  owner     = {saulius},
  timestamp = {2021.01.02},
  creationdate = {2021-01-02T00:00:00},
  url       = {https://dl.acm.org/doi/10.1145/1283920.1283933},
}

@Article{Chiang2011,
  author    = {Ann-Shyn Chiang and Chih-Yung Lin and Chao-Chun Chuang and Hsiu-Ming Chang and Chang-Huain Hsieh and Chang-Wei Yeh and Chi-Tin Shih and Jian-Jheng Wu and Guo-Tzau Wang and Yung-Chang Chen and Cheng-Chi Wu and Guan-Yu Chen and Yu-Tai Ching and Ping-Chang Lee and Chih-Yang Lin and Hui-Hao Lin and Chia-Chou Wu and Hao-Wei Hsu and Yun-Ann Huang and Jing-Yi Chen and Hsin-Jung Chiang and Chun-Fang Lu and Ru-Fen Ni and Chao-Yuan Yeh and Jenn-Kang Hwang},
  journal   = {Current Biology},
  title     = {Three-dimensional reconstruction of brain-wide wiring networks in {D}rosophila at single-cell resolution},
  year      = {2011},
  month     = {jan},
  number    = {1},
  pages     = {1--11},
  volume    = {21},
  doi       = {10.1016/j.cub.2010.11.056},
  file      = {:by-author/C/Chiang/2011_Chiang_1.pdf:PDF},
  keywords  = {Brain; Brain Wireing; Connectome; Drosofilla; Natural Neural Networks},
  owner     = {saulius},
  publisher = {Elsevier {BV}},
  timestamp = {2021.01.02},
  creationdate = {2021-01-02T00:00:00},
}

@TechReport{Kleene1951,
  author      = {S. C. Kleene},
  institution = {The {RAND} Corporation},
  title       = {Representation of events in nerve nets and finite automata},
  year        = {1951},
  month       = dec,
  number      = {RM-704},
  file        = {:by-author/K/Kleene/1951_Kleene_1.pdf:PDF},
  keywords    = {Brain Function; Computer Science (CS); Natural Neural Networks; Neurons; Neurophysiology},
  owner       = {saulius},
  pages       = {1--101},
  timestamp = {2021.01.03},
  creationdate = {2021-01-03T00:00:00},
  url         = {https://www.rand.org/content/dam/rand/pubs/research_memoranda/2008/RM704.pdf},
}

@Article{McCulloch1943,
  author    = {Warren S. McCulloch and Walter Pitts},
  journal   = {The Bulletin of Mathematical Biophysics},
  title     = {A logical calculus of the ideas immanent in nervous activity},
  year      = {1943},
  month     = {dec},
  number    = {4},
  pages     = {115--133},
  volume    = {5},
  doi       = {10.1007/bf02478259},
  file      = {:by-author/M/McCulloch/1943_McCulloch_115.pdf:PDF},
  keywords  = {Brain Function; Computer Science (CS); Natural Neural Networks; Neurons; Neurophysiology},
  owner     = {saulius},
  publisher = {Springer Science and Business Media {LLC}},
  timestamp = {2021.01.03},
  creationdate = {2021-01-03T00:00:00},
  url       = {https://www.cs.cmu.edu/~./epxing/Class/10715/reading/McCulloch.and.Pitts.pdf},
}

@Article{Lettvin1968,
  author    = {J. Y. Lettvin and H. R. Maturana and W. S. Mcculloch and W. H. Pitts},
  journal   = {The Mind: Biological Approaches to its Functions},
  title     = {What the frog's eye tells the frog's brain},
  year      = {1968},
  pages     = {233--258},
  file      = {:by-author/L/Lettvin/1968_Lettvin_233.pdf:PDF},
  keywords  = {Brain Function; Computer Science (CS); Natural Neural Networks; Neurons; Neurophysiology},
  owner     = {saulius},
  timestamp = {2021.01.03},
  creationdate = {2021-01-03T00:00:00},
  url       = {https://web.archive.org/web/20110928024235/http://jerome.lettvin.info/lettvin/Jerome/WhatTheFrogsEyeTellsTheFrogsBrain.pdf},
}

@Article{Alom2018,
  author      = {Md Zahangir Alom and Tarek M. Taha and Christopher Yakopcic and Stefan Westberg and Mahmudul Hasan and Brian C Van Esesn and Abdul A S. Awwal and Vijayan K. Asari},
  journal     = {arXiv},
  title       = {The history began from {AlexNet}: a comprehensive survey on deep learning approaches},
  year        = {2018},
  pages       = {1--39},
  abstract    = {Deep learning has demonstrated tremendous success in variety of application domains in the past few years. This new field of machine learning has been growing rapidly and applied in most of the application domains with some new modalities of applications, which helps to open new opportunity. There are different methods have been proposed on different category of learning approaches, which includes supervised, semi-supervised and un-supervised learning. The experimental results show state-of-the-art performance of deep learning over traditional machine learning approaches in the field of Image Processing, Computer Vision, Speech Recognition, Machine Translation, Art, Medical imaging, Medical information processing, Robotics and control, Bio-informatics, Natural Language Processing (NLP), Cyber security, and many more. This report presents a brief survey on development of DL approaches, including Deep Neural Network (DNN), Convolutional Neural Network (CNN), Recurrent Neural Network (RNN) including Long Short Term Memory (LSTM) and Gated Recurrent Units (GRU), Auto-Encoder (AE), Deep Belief Network (DBN), Generative Adversarial Network (GAN), and Deep Reinforcement Learning (DRL). In addition, we have included recent development of proposed advanced variant DL techniques based on the mentioned DL approaches. Furthermore, DL approaches have explored and evaluated in different application domains are also included in this survey. We have also comprised recently developed frameworks, SDKs, and benchmark datasets that are used for implementing and evaluating deep learning approaches. There are some surveys have published on Deep Learning in Neural Networks [1, 38] and a survey on RL [234]. However, those papers have not discussed the individual advanced techniques for training large scale deep learning models and the recently developed method of generative models [1].},
  date        = {2018-03-03},
  eprint      = {1803.01164},
  eprintclass = {cs.CV},
  eprinttype  = {arXiv},
  file        = {:by-author/A/Alom/2018_Alom_1.pdf:PDF},
  keywords    = {Artificial Neural Networks (ANN); Computer Science (CS)},
  owner       = {saulius},
  timestamp = {2021.01.03},
  creationdate = {2021-01-03T00:00:00},
  url         = {https://arxiv.org/abs/1803.01164v1},
}

@TechReport{Rosenblatt1957,
  author      = {Frank Rosenblatt},
  institution = {Cornaell Aeronautical Laboratory, Inc.},
  title       = {The {P}erceptron: a perceiving and recognising automaton},
  year        = {1957},
  file        = {:by-author/R/Rosenblatt/1957_Rosenblatt_1.pdf:PDF},
  keywords    = {Artificial Neural Networks (ANN); Computer Science (CS); Perceptron},
  owner       = {saulius},
  pages       = {1--33},
  timestamp = {2021.01.03},
  creationdate = {2021-01-03T00:00:00},
  url         = {https://blogs.umass.edu/brain-wars/files/2016/03/rosenblatt-1957.pdf},
}

@Article{Press2020,
  author    = {William H. Press and John A. Hawkins and Stephen K. Jones and Jeffrey M. Schaub and Ilya J. Finkelstein},
  journal   = {Proceedings of the National Academy of Sciences},
  title     = {{HEDGES} error-correcting code for {DNA} storage corrects indels and allows sequence constraints},
  year      = {2020},
  month     = {jul},
  number    = {31},
  pages     = {18489--18496},
  volume    = {117},
  doi       = {10.1073/pnas.2004821117},
  file      = {:by-author/P/Press/2020_Press_18489.pdf:PDF},
  keywords  = {Biochemistry; Computer Memory; Computer Science (CS); Computer Storage; DNA; Error-correcting Codes; Indels},
  owner     = {saulius},
  publisher = {Proceedings of the National Academy of Sciences},
  timestamp = {2021.01.04},
  creationdate = {2021-01-04T00:00:00},
}

@Article{Church2012,
  author    = {G. M. Church and Y. Gao and S. Kosuri},
  journal   = {Science},
  title     = {Next-Generation Digital Information Storage in {DNA}},
  year      = {2012},
  month     = {aug},
  number    = {6102},
  pages     = {1628--1628},
  volume    = {337},
  doi       = {10.1126/science.1226355},
  file      = {:by-author/C/Church/2012_Church_1628.pdf:PDF;:by-author/C/Church/2012_Church_1628_suppl/Church.SM.pdf:PDF},
  keywords  = {Biochemistry; Computer Memory; Computer Science (CS); Computer Storage; DNA; Error-correcting Codes},
  owner     = {saulius},
  publisher = {American Association for the Advancement of Science ({AAAS})},
  timestamp = {2021.01.04},
  creationdate = {2021-01-04T00:00:00},
  url       = {http://nook.cs.ucdavis.edu/~koehl/Teaching/ECS129/Reprints/Church_DNAStorage_12.pdf},
}

@Article{Gibson2010,
  author    = {D. G. Gibson and J. I. Glass and C. Lartigue and V. N. Noskov and R.-Y. Chuang and M. A. Algire and G. A. Benders and M. G. Montague and L. Ma and M. M. Moodie and C. Merryman and S. Vashee and R. Krishnakumar and N. Assad-Garcia and C. Andrews-Pfannkoch and E. A. Denisova and L. Young and Z.-Q. Qi and T. H. Segall-Shapiro and C. H. Calvey and P. P. Parmar and C. A. Hutchison and H. O. Smith and J. C. Venter},
  journal   = {Science},
  title     = {Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome},
  year      = {2010},
  month     = {may},
  number    = {5987},
  pages     = {52--56},
  volume    = {329},
  doi       = {10.1126/science.1190719},
  file      = {:by-author/G/Gibson/2010_Gibson_52.pdf:PDF},
  keywords  = {Synthetic Bacteria; Synthetic Genome},
  owner     = {saulius},
  publisher = {American Association for the Advancement of Science ({AAAS})},
  timestamp = {2021.01.04},
  creationdate = {2021-01-04T00:00:00},
}

@Article{Mirzianov2017,
  author    = {Oleg Mirzianov and Antanas Mitasiunas and Leonids Novickis and Saulius Ragaisis},
  journal   = {Procedia Computer Science},
  title     = {Development and validation of learning process assessment model},
  year      = {2017},
  pages     = {258--265},
  volume    = {104},
  doi       = {10.1016/j.procs.2017.01.133},
  file      = {:by-author/M/Mirzianov/2017_Mirzianov_258.pdf:PDF},
  keywords  = {Assesments; Computer Science (CS); Pedagogy; Teaching},
  owner     = {saulius},
  publisher = {Elsevier {BV}},
  timestamp = {2021.01.07},
  creationdate = {2021-01-07T00:00:00},
}

@Presentation{Methni2014,
  author    = {Amira Methni and Matthieu Lemerre and Serge Haddad},
  title     = {{C2TLA+}: a translator from {C} to {TLA+}},
  year      = {2014},
  comment   = {Rekomendavo Karolis Petrauskas savo 2021-01-07 22:56 el. laiške į saulius.grazulis@bti.vu.lt .},
  file      = {:by-author/M/Methni/2014_Methni_1.pdf:PDF},
  keywords  = {C Compilers; CIL; Computer Science (CS); TLA},
  owner     = {saulius},
  pages     = {1--54},
  timestamp = {2021.01.08},
  creationdate = {2021-01-08T00:00:00},
  url       = {https://tla2014.loria.fr/slides/methni.pdf},
}

@Article{Senior2020,
  author    = {Andrew W. Senior and Richard Evans and John Jumper and James Kirkpatrick and Laurent Sifre and Tim Green and Chongli Qin and Augustin {\v{Z}}{\'{\i}}dek and Alexander W. R. Nelson and Alex Bridgland and Hugo Penedones and Stig Petersen and Karen Simonyan and Steve Crossan and Pushmeet Kohli and David T. Jones and David Silver and Koray Kavukcuoglu and Demis Hassabis},
  journal   = {Nature},
  title     = {Improved protein structure prediction using potentials from deep learning},
  year      = {2020},
  month     = {jan},
  number    = {7792},
  pages     = {706--710},
  volume    = {577},
  doi       = {10.1038/s41586-019-1923-7},
  file      = {:by-author/S/Senior/2020_Senior_706.pdf:PDF},
  keywords  = {AlphaFold; Artificial Neural Networks (ANN); Bioinformatics; Computer Science (CS); Machine Learning (ML); Protein Folding},
  owner     = {saulius},
  publisher = {Springer Science and Business Media {LLC}},
  timestamp = {2021.01.08},
  creationdate = {2021-01-08T00:00:00},
}

@Presentation{Jumper2020,
  author    = {John Jumper and others},
  title     = {{AlphaFold} 2},
  year      = {2020},
  file      = {:by-author/J/Jumper/2020_Jumper_1.pdf:PDF},
  keywords  = {AlphaFold; Artificial Neural Networks (ANN); Bioinformatics; Computer Science (CS); Machine Learning (ML); Protein Folding},
  owner     = {saulius},
  pages     = {1--42},
  timestamp = {2021.01.08},
  creationdate = {2021-01-08T00:00:00},
  url       = {https://predictioncenter.org/casp14/doc/presentations/2020_12_01_TS_predictor_AlphaFold2.pdf},
}

@Webpage{AlQuraishi2020,
  author    = {Mohammed AlQuraishi},
  retrieved = {2021-01-08 18:58},
  title     = {{AlphaFold2} @ {CASP14}: “{I}t feels like one’s child has left home.”},
  url       = {https://moalquraishi.wordpress.com/2020/12/08/alphafold2-casp14-it-feels-like-ones-child-has-left-home},
  language  = {English},
  month     = dec,
  year      = {2020},
  file      = {:by-author/A/AlQuraishi/2020_AlQuraishi_1.pdf:PDF;:by-author/A/AlQuraishi/2020_AlQuraishi_1.odt:OpenDocument text},
  keywords  = {AlphaFold; Artificial Neural Networks (ANN); Bioinformatics; Computer Science (CS); Machine Learning (ML); Protein Folding},
  owner     = {saulius},
  pages     = {1--25},
  timestamp = {2021.01.08},
  creationdate = {2021-01-08T00:00:00},
}

@Webpage{Wikipedia2020,
  author    = {{Wikipedia}},
  retrieved = {2021-01-08 19:10},
  title     = {AlphaFold},
  url       = {https://en.wikipedia.org/wiki/AlphaFold},
  site      = {Wikipedia},
  siteurl   = {https://en.wikipedia.org},
  year      = {2020},
  file      = {:by-author/W/Wikipedia/2020_Wikipedia_AlphaFold.pdf:PDF},
  keywords  = {AlphaFold; Artificial Neural Networks (ANN); Bioinformatics; Computer Science (CS); Machine Learning (ML); Protein Folding},
  owner     = {saulius},
  timestamp = {2021.01.08},
  creationdate = {2021-01-08T00:00:00},
}

@Article{Pitts1947,
  author    = {Walter Pitts and Warren S. McCulloch},
  journal   = {The Bulletin of Mathematical Biophysics},
  title     = {How we know universals the perception of auditory and visual forms},
  year      = {1947},
  month     = {sep},
  number    = {3},
  pages     = {127--147},
  volume    = {9},
  doi       = {10.1007/bf02478291},
  file      = {:by-author/P/Pitts/1947_Pitts_127.pdf:PDF},
  owner     = {saulius},
  publisher = {Springer Science and Business Media {LLC}},
  timestamp = {2021.01.09},
  creationdate = {2021-01-09T00:00:00},
}

@Article{Rosenblatt1958,
  author    = {F. Rosenblatt},
  journal   = {Psychological Review},
  title     = {The perceptron: A probabilistic model for information storage and organization in the brain.},
  year      = {1958},
  number    = {6},
  pages     = {386--408},
  volume    = {65},
  doi       = {10.1037/h0042519},
  file      = {:by-author/R/Rosenblatt/1958_Rosenblatt_386.pdf:PDF},
  keywords  = {Artificial Intelligences; Brain Function; Computer Science (CS); Machine Learning (ML); Perceptrons},
  owner     = {saulius},
  publisher = {American Psychological Association ({APA})},
  timestamp = {2021.01.09},
  creationdate = {2021-01-09T00:00:00},
  url       = {https://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.588.3775},
}

@Article{Chalk2016,
  author    = {Stuart J. Chalk},
  journal   = {Journal of Cheminformatics},
  title     = {{SciData}: a data model and ontology for semantic representation of scientific data},
  year      = {2016},
  month     = {oct},
  number    = {1},
  pages     = {8:54},
  volume    = {8},
  doi       = {10.1186/s13321-016-0168-9},
  file      = {:by-author/C/Chalk/2016_Chalk_8.pdf:PDF},
  keywords  = {Crystallography; Ontologies},
  owner     = {saulius},
  publisher = {Springer Science and Business Media {LLC}},
  timestamp = {2021.01.11},
  creationdate = {2021-01-11T00:00:00},
}

@Article{Ruelle2000,
  author    = {Paul Ruelle},
  journal   = {Chemosphere},
  title     = {The n-octanol and n-hexane/water partition coefficient of environmentally relevant chemicals predicted from the mobile order and disorder ({MOD}) thermodynamics},
  year      = {2000},
  month     = {mar},
  number    = {5},
  pages     = {457--512},
  volume    = {40},
  doi       = {10.1016/s0045-6535(99)00268-4},
  file      = {:by-author/R/Ruelle/2000_Ruelle_457.pdf:PDF},
  owner     = {saulius},
  publisher = {Elsevier {BV}},
  timestamp = {2021.01.20},
  creationdate = {2021-01-20T00:00:00},
}

@Article{Laibinis2021,
  author    = {Linas Laibinis and Alexei Iliasov and Alexander Romanovsky},
  journal   = {{IEEE} Transactions on Reliability},
  title     = {Mutation testing for rule-based verification of railway signaling data},
  year      = {2021},
  pages     = {1--16},
  doi       = {10.1109/tr.2020.3047462},
  file      = {:by-author/L/Laibinis/2021_Laibinis_1.pdf:PDF},
  keywords  = {Computer Science (CS); Formal Verification; Railway Safety},
  owner     = {saulius},
  publisher = {Institute of Electrical and Electronics Engineers ({IEEE})},
  timestamp = {2021.01.21},
  creationdate = {2021-01-21T00:00:00},
}

@Manuscript{Shaitan2006,
  author    = {K. V. Shaitan and Ye. V. Tourleigh and A. K. Shaytan and K. B. Tereshkina and O. V. Levtsova and M. P. Kirpichnikov},
  title     = {Application of molecular dynamics simulations to study of membrane related structures},
  year      = {2006},
  keywords  = {Membranes; Molecular Dynamics (MD); Simulations},
  url       = {http://molsim.org/sites/default/files/IEEE-membranes.doc},
  file      = {:by-author/S/Shaitan/2006_Shaitan_1.doc:Word},
  owner     = {saulius},
  pages     = {1--10},
  timestamp = {2021.01.26},
  creationdate = {2021-01-26T00:00:00},
}

@Presentation{Kriviene2017,
  author    = {Irena Krivienė and Žibutė Petrauskienė},
  title     = {{MIDAS}: galimybės įgyvendinti atvirojo mokslo idėjas},
  year      = {2017},
  file      = {:by-author/K/Krivienė/2017_Krivienė_1.pdf:PDF},
  keywords  = {Computer Science (CS); DropBox; MIDAS; Scientific Archives; Scientific Databases},
  owner     = {saulius},
  pages     = {1--22},
  timestamp = {2021.01.26},
  creationdate = {2021-01-26T00:00:00},
  url       = {https://biblioteka.ktu.edu/wp-content/uploads/sites/38/2017/06/Petrauskiene_Kriviene.pdf},
}

@InProceedings{Beyers1981,
  author    = {J. Beyers and L. Dohse and J. Fucetola and R. Kochis and C. Lob and G. Taylor and E. Zeller},
  booktitle = {1981 {IEEE} International Solid-State Circuits Conference. Digest of Technical Papers},
  title     = {A 32b {VLSI} {CPU} chip},
  year      = {1981},
  pages     = {104--105},
  publisher = {{IEEE}},
  doi       = {10.1109/isscc.1981.1156198},
  file      = {:by-author/B/Beyers/1981_Beyers_104.pdf:PDF},
  keywords  = {Chips; Computer Architecture; Computer Science (CS); Microprocessors; VLSI},
  owner     = {saulius},
  timestamp = {2021.01.29},
  creationdate = {2021-01-29T00:00:00},
}

@InProceedings{Mikkelson1981,
  author    = {J. Mikkelson and L. Hall and A. Malhotra and S. Seccombe and M. Wilson},
  booktitle = {1981 {IEEE} International Solid-State Circuits Conference. Digest of Technical Papers},
  title     = {An {NMOS} {VLSI} process for fabrication of a 32b {CPU} chip},
  year      = {1981},
  pages     = {106--107},
  publisher = {{IEEE}},
  doi       = {10.1109/isscc.1981.1156188},
  file      = {:by-author/M/Mikkelson/1981_Mikkelson_106.pdf:PDF},
  keywords  = {Chips; Computer Architecture; Computer Science (CS); Microprocessors; VLSI},
  owner     = {saulius},
  timestamp = {2021.01.29},
  creationdate = {2021-01-29T00:00:00},
}

@InProceedings{Olsen1981,
  author    = {R. Olsen and D. Dobberpuhl},
  booktitle = {1981 {IEEE} International Solid-State Circuits Conference. Digest of Technical Papers},
  title     = {A 13,000 transistor {NMOS} microprocessor},
  year      = {1981},
  pages     = {108--109,260},
  publisher = {{IEEE}},
  doi       = {10.1109/isscc.1981.1156187},
  file      = {:by-author/O/Olsen/1981_Olsen_108.pdf:PDF},
  keywords  = {Chips; Computer Architecture; Computer Science (CS); DEC; ISA; Microprocessors; PDP-11; T-11; VLSI},
  owner     = {saulius},
  timestamp = {2021.01.29},
  creationdate = {2021-01-29T00:00:00},
}

@InProceedings{Lattin1981,
  author    = {W. Lattin and J. Bayliss and D. Budde and S. Colley and G. Cox and A. Goodman and J. Rattner and W. Richardson and R. Swanson},
  booktitle = {1981 {IEEE} International Solid-State Circuits Conference. Digest of Technical Papers},
  title     = {A 32b {VLSI} micromainframe computer system},
  year      = {1981},
  pages     = {110--111},
  publisher = {{IEEE}},
  doi       = {10.1109/isscc.1981.1156189},
  file      = {:by-author/L/Lattin/1981_Lattin_110.pdf:PDF},
  keywords  = {Chips; Computer Architecture; Computer Science (CS); Microprocessors; VLSI},
  owner     = {saulius},
  timestamp = {2021.01.29},
  creationdate = {2021-01-29T00:00:00},
}

@InProceedings{Budde1981,
  author    = {D. Budde and S. Colley and A. Goodman and J. Howard and S. Domenik},
  booktitle = {1981 {IEEE} International Solid-State Circuits Conference. Digest of Technical Papers},
  title     = {The 32b computer execution unit},
  year      = {1981},
  pages     = {112--113,261},
  publisher = {{IEEE}},
  doi       = {10.1109/isscc.1981.1156186},
  file      = {:by-author/B/Budde/1981_Budde_112.pdf:PDF},
  keywords  = {Chips; Computer Architecture; Computer Science (CS); Microprocessors; VLSI},
  owner     = {saulius},
  timestamp = {2021.01.29},
  creationdate = {2021-01-29T00:00:00},
}

@InProceedings{Richardson1981,
  author    = {W. Richardson and J. Bayliss and S. Colley and R. Kravitz and G. McCormick and D. Wilde and L. Wittmer},
  booktitle = {1981 {IEEE} International Solid-State Circuits Conference. Digest of Technical Papers},
  title     = {The 32b computer instruction decoding unit},
  year      = {1981},
  pages     = {114--115,262},
  publisher = {{IEEE}},
  doi       = {10.1109/isscc.1981.1156185},
  file      = {:by-author/R/Richardson/1981_Richardson_114.pdf:PDF},
  keywords  = {Chips; Computer Architecture; Computer Science (CS); Microprocessors; VLSI},
  owner     = {saulius},
  timestamp = {2021.01.29},
  creationdate = {2021-01-29T00:00:00},
}

@InProceedings{Bayliss1981,
  author    = {J. Bayliss and S. Colley and G. Cox and J. Deetz and Chun-Kit Ng and C. Peterson and D. Wilde},
  booktitle = {1981 {IEEE} International Solid-State Circuits Conference. Digest of Technical Papers},
  title     = {The interface processor for the 32b computer},
  year      = {1981},
  pages     = {116--117,263},
  publisher = {{IEEE}},
  doi       = {10.1109/isscc.1981.1156182},
  file      = {:by-author/B/Bayliss/1981_Bayliss_116.pdf:PDF},
  keywords  = {Chips; Computer Architecture; Computer Science (CS); Microprocessors; VLSI},
  owner     = {saulius},
  timestamp = {2021.01.29},
  creationdate = {2021-01-29T00:00:00},
}

@InProceedings{Dean2020,
  author    = {Jeffrey Dean},
  booktitle = {2020 {IEEE} International Solid- State Circuits Conference - ({ISSCC})},
  title     = {1.1 The Deep Learning Revolution and Its Implications for Computer Architecture and Chip Design},
  year      = {2020},
  month     = {feb},
  pages     = {8--14},
  publisher = {{IEEE}},
  doi       = {10.1109/isscc19947.2020.9063049},
  file      = {:by-author/D/Dean/2020_Dean_8.pdf:PDF},
  keywords  = {Chips; Computer Architecture; Computer Science (CS); Deep Learning (DL); Machine Learning (ML); Microprocessors; VLSI},
  owner     = {saulius},
  timestamp = {2021.01.29},
  creationdate = {2021-01-29T00:00:00},
}

@InProceedings{Loh2020,
  author    = {Kou-Hung Lawrence Loh},
  booktitle = {2020 {IEEE} International Solid- State Circuits Conference - ({ISSCC})},
  title     = {1.2 Fertilizing {AIoT} from Roots to Leaves},
  year      = {2020},
  month     = {feb},
  pages     = {15--21},
  publisher = {{IEEE}},
  doi       = {10.1109/isscc19947.2020.9062950},
  file      = {:by-author/L/Loh/2020_Loh_15.pdf:PDF},
  keywords  = {Artificial Intelligence (AI); Chips; Computer Architecture; Computer Science (CS); IoT; Machine Learning (ML); Microprocessors; VLSI},
  owner     = {saulius},
  timestamp = {2021.01.29},
  creationdate = {2021-01-29T00:00:00},
}

@InProceedings{Collaert2020,
  author    = {Nadine Collaert},
  booktitle = {2020 {IEEE} International Solid- State Circuits Conference - ({ISSCC})},
  title     = {1.3 Future Scaling: Where Systems and Technology Meet},
  year      = {2020},
  month     = {feb},
  pages     = {25--29},
  publisher = {{IEEE}},
  doi       = {10.1109/isscc19947.2020.9063033},
  file      = {:by-author/C/Collaert/2020_Collaert_25.pdf:PDF},
  keywords  = {Chips; Computer Architecture; Computer Science (CS); Microprocessors; VLSI},
  owner     = {saulius},
  timestamp = {2021.01.29},
  creationdate = {2021-01-29T00:00:00},
}

@InProceedings{Gil2020,
  author    = {Dario Gil and William M. J. Green},
  booktitle = {2020 {IEEE} International Solid- State Circuits Conference - ({ISSCC})},
  title     = {1.4 The Future of Computing: Bits $\mathplus$ Neurons $\mathplus$ Qubits},
  year      = {2020},
  month     = {feb},
  pages     = {30--39},
  publisher = {{IEEE}},
  doi       = {10.1109/isscc19947.2020.9062918},
  file      = {:by-author/G/Gil/2020_Gil_30.pdf:PDF},
  keywords  = {Chips; Computer Architecture; Computer Science (CS); Microprocessors; VLSI},
  owner     = {saulius},
  timestamp = {2021.01.29},
  creationdate = {2021-01-29T00:00:00},
}

@InProceedings{DASS2020,
  author    = {{Digital Architectures and Systems Subcommittee}},
  booktitle = {2020 IEEE International Solid- State Circuits Conference - (ISSCC)},
  title     = {Session 2 Overview: Processors: Digital Architectures and Systems Subcommittee},
  year      = {2020},
  month     = {Feb},
  pages     = {40--41},
  abstract  = {Start of the above-titled section of the conference proceedings record.},
  doi       = {10.1109/ISSCC19947.2020.9063152},
  file      = {:by-author/D/DASS/2020_DASS_40.pdf:PDF},
  issn      = {2376-8606},
  keywords  = {Chips; Computer Architecture; Computer Science (CS); Microprocessors; VLSI},
  owner     = {saulius},
  timestamp = {2021.01.29},
  creationdate = {2021-01-29T00:00:00},
}

@InProceedings{9063113,
  author    = {T. {Singh} and S. {Rangarajan} and D. {John} and R. {Schreiber} and S. {Oliver} and R. {Seahra} and A. {Schaefer}},
  booktitle = {2020 IEEE International Solid- State Circuits Conference - (ISSCC)},
  title     = {2.1 Zen 2: The AMD 7nm Energy-Efficient High-Performance x86-64 Microprocessor Core},
  year      = {2020},
  month     = {Feb},
  pages     = {42--44},
  abstract  = {Codenamed “Zen 2”, the AMD next-generation, high-efficiency core is an x86-64 design, fabricated in an energy-efficient TSMC 7nm FinFET process. Similar to AMD's prior-generation core, codenamed “Zen” [1], the Core Complex Unit (CCX) with 4 cores in this version (Fig. 2.1.1) is used across a wide array of client, semi-custom, embedded, and server market segments. A 475M-transistor core slice is 7.83mm2 with a 0.5MB L2 cache and 4MB of shared L3 cache. The design uses new custom circuits and memory design techniques to achieve the specified performance and power.},
  doi       = {10.1109/ISSCC19947.2020.9063113},
  file      = {:by-author/S/Singh/2020_Singh_42.pdf:PDF},
  issn      = {2376-8606},
  keywords  = {475M-transistor Core Slice; AMD; AMD 7nm Energy-efficient High-performance X86-64 Microprocessor Core; AMD's Prior-generation Core; CCX; Cache Storage; Chips; Clocks; Codenamed Zen 2; Computer Architecture; Computer Science (CS); Core Complex Unit; Custom Circuits; Energy-efficient TSMC 7nm FinFET Process; High-efficiency Core; L2 Cache; Latches; Logic Gates; MOSFET; Memory Design Techniques; Metals; Microprocessor Chips; Microprocessors; Multiprocessing Systems; Shared L3 Cache; Timing; VLSI; X86-64 Design},
  owner     = {saulius},
  timestamp = {2021.01.29},
  creationdate = {2021-01-29T00:00:00},
}

@InProceedings{9063103,
  author    = {S. {Naffziger} and K. {Lepak} and M. {Paraschou} and M. {Subramony}},
  booktitle = {2020 IEEE International Solid- State Circuits Conference - (ISSCC)},
  title     = {2.2 AMD Chiplet Architecture for High-Performance Server and Desktop Products},
  year      = {2020},
  month     = {Feb},
  pages     = {44--45},
  abstract  = {AMO's “Rome” and “Matisse” are second-generation AMD Infinity Fabric-based SoCs using 3 unique hybrid process technology chiplets to achieve leading performance, performance/$ and performance/W, targeting server and client markets, respectively (Fig. 2.2.1). The chiplet architecture enables leading edge 7nm [1] CPUs for multiple markets, while retaining backward compatibility to complex 10 and memory subsystems in a scalable design with high reuse for improved time-to-market. A key benefit is the heterogeneous technology deployed between the CPUs and the 10/mixed-signaIP. It is well known that shrink factors in advanced nodes are much lower for analog circuitry than for digital logic and SRAM. By keeping the memory interfaces and SerOes in mature 12nm technology, costs are mitigated since those circuits see a very small shrink factor to 7nm and very little performance or power gain from advanced nodes. A low-cost 12nm 10 die (IOD) with the high-yielding 8 “Zen2” core, 74mm2 7nm CPU compute die (CCD) combine to provide very cost-effective performance.},
  doi       = {10.1109/ISSCC19947.2020.9063103},
  file      = {:by-author/N/Naffziger/2020_Naffziger_44.pdf:PDF},
  issn      = {2376-8606},
  keywords  = {AMD; AMD Chiplet Architecture; Advanced Nodes; Backward Compatibility; Bandwidth; CPU Compute Die Combine; Charge Coupled Devices; Chips; Client Markets; Clocks; Computer Architecture; Computer Science (CS); Desktop Products; Fabrics; Heterogeneous Technology; High-performance Server; Hybrid Process Technology Chiplets; Improved Time-to-market; Leading Performance; Memory Interfaces; Memory Subsystems; Microprocessor Chips; Microprocessors; Network Synthesis; Routing; Scalable Design; Second-generation AMD Infinity Fabric-based SoCs; Servers; Shrink Factor; System-on-chip; Time to Market; VLSI; size 12.0 nm; size 7.0 nm},
  owner     = {saulius},
  timestamp = {2021.01.29},
  creationdate = {2021-01-29T00:00:00},
}

@InProceedings{9062927,
  author    = {P. {Vivet} and E. {Guthmuller} and Y. {Thonnart} and G. {Pillonnet} and G. {Moritz} and I. {Miro-Panadès} and C. {Fuguet} and J. {Durupt} and C. {Bernard} and D. {Varreau} and J. {Pontes} and S. {Thuries} and D. {Coriat} and M. {Harrand} and D. {Dutoit} and D. {Lattard} and L. {Arnaud} and J. {Charbonnier} and P. {Coudrain} and A. {Garnier} and F. {Berger} and A. {Gueugnot} and A. {Greiner} and Q. {Meunier} and A. {Farcy} and A. {Arriordaz} and S. {Cheramy} and F. {Clermidy}},
  booktitle = {2020 IEEE International Solid- State Circuits Conference - (ISSCC)},
  title     = {2.3 A 220GOPS 96-Core Processor with 6 Chiplets 3D-Stacked on an Active Interposer Offering 0.6ns/mm Latency, 3Tb/s/mm2 Inter-Chiplet Interconnects and 156mW/mm2@ 82%-Peak-Efficiency DC-DC Converters},
  year      = {2020},
  month     = {Feb},
  pages     = {46--48},
  abstract  = {In the context of high-performance computing and big-data applications, the quest for performance requires modular, scalable, energy-efficient, low-cost manycore systems. Partitioning the system into multiple chiplets 3D-stacked onto large-scale interposers - organic substrate [1], 2.5D passive interposer [2] or silicon bridge [3] -leads to large modular architectures and cost reductions in advanced technologies by the Known Good Die (KGD) strategy and yield management. However, these approaches lack flexible efficient long-distance communications, smooth integration of heterogeneous chiplets, and easy integration of less-scalable analog functions, such as power management [4] and system IOs. To tackle these issues, this paper presents an active interposer integrating: i) a Switched Capacitor Voltage Regulator (SCVR) for on-chip power management; ii) flexible system interconnect topologies between all chiplets for scalable cache coherency support; iii) energy-efficient 3D-plugs for dense inter-layer communication; iv) a memory-IO controller and PHY for socket communication. The chip (Fig. 2.3.7) integrates 96 cores in 6 chiplets in 28nm FDSOI CMOS, 30-stacked in a face-to-face configuration using 20μm-pitch micro-bumps (μ-bumps) onto a 200 mm2 active interposer with 40μm-pitch Through Silicon Via (TSV) middle in a 65nm technology node. Even though complex functions are integrated, active-interposer yield is high thanks to the mature 65nm node and a reduced complexity (0.08transistors/μm2), with 30% of interposer area devoted to a SCVR variability-tolerant capacitors scheme.},
  doi       = {10.1109/ISSCC19947.2020.9062927},
  file      = {:by-author/V/Vivet/2020_Vivet_46.pdf:PDF},
  issn      = {2376-8606},
  keywords  = {2.5D passive interposer; 220GOPS 96-core Processor; Active Interposer Integrating; Active-interposer Yield; Bandwidth; Big-data Applications; CMOS Integrated Circuits; Capacitors; Chips; Clocks; Computer Architecture; Computer Science (CS); Cost Reductions; DC-DC Converters; DC-DC Power Convertors; Dense Interlayer Communication; Energy Conservation; Energy-efficient 3D-plugs; FDSOI CMOS; Heterogeneous Chiplets; High-performance Computing; Integrated Circuit Interconnections; Interchiplet Interconnects; KGD Strategy; Known Good Die Strategy; Large-scale Interposers; Less-scalable Analog Functions; Long-distance Communications; Low-power Electronics; Memory-IO Controller; Microbumps; Microprocessor Chips; Microprocessors; Modular Architectures; On-chip Power Management; Organic Substrate; Power Integrated Circuits; Power Management; Regulators; SCVR Variability-tolerant Capacitors Scheme; Scalable Cache Coherency Support; Silicon Bridge; Silicon-on-insulator; Size 20 Mum; Size 40 Mum; Socket Communication; Switched Capacitor Networks; Switched Capacitor Voltage Regulator; TSV; Three-dimensional Displays; Three-dimensional Integrated Circuits; Through Silicon Via; VLSI; Voltage Control; Voltage Regulators; Yield Management; size 28.0 nm; size 65.0 nm},
  owner     = {saulius},
  timestamp = {2021.01.29},
  creationdate = {2021-01-29T00:00:00},
}

@InProceedings{9062907,
  author       = {Y. {Duk Kim} and W. {Jeong} and L. {Jung} and D. {Shin} and J. G. {Song} and J. {Song} and H. {Kwon} and J. {Lee} and J. {Jung} and M. {Kang} and J. {Jeong} and Y. {Kwon} and N. H. {Seong}},
  booktitle    = {2020 IEEE International Solid- State Circuits Conference - (ISSCC)},
  title        = {2.4 A 7nm High-Performance and Energy-Efficient Mobile Application Processor with Tri-Cluster CPUs and a Sparsity-Aware NPU},
  year         = {2020},
  month        = {Feb},
  pages        = {48--50},
  abstract     = {Mobile application processors (APs) must be extremely power efficient, while providing high performance for improved user experiences, higher graphic-rendering performance, fancy camera operations, faster data communication, as well as longer battery life [1]-[3]. In this paper, we introduce a power-efficient high-performance 7nm Exynos™ AP processor with tri-cluster CPUs, a sparsity-aware NPU, and a HW auto-clock gating (HWACG) feature.},
  creationdate = {2021-01-29T00:00:00},
  doi          = {10.1109/ISSCC19947.2020.9062907},
  file         = {:by-author/D/Duk Kim/2020_Duk Kim_48.pdf:PDF},
  issn         = {2376-8606},
  keywords     = {Central Processing Unit; Chips; Clocks; Computer Architecture; Computer Science (CS); Data Communication; Energy-efficient Mobile Application Processor; Fancy Camera Operations; Graphic-rendering Performance; HW Auto-clock Gating Feature; HWACG; IP Networks; Longer Battery Life; Microprocessor Chips; Microprocessors; Mobile Applications; Mobile Computing; Neural Chips; Power Aware Computing; Power Demand; Power-efficient High-performance 7nm Exynos™ AP Processor; Program Processors; Rendering (computer Graphics); Sparsity-aware NPU; Tri-cluster CPUs; VLSI},
  owner        = {saulius},
  timestamp    = {2021.01.29},
}

@InProceedings{9062897,
  author       = {H. {Mair} and E. {Wang} and A. {Nayak} and R. {Lagerquist} and L. {Chou} and G. {Gammie} and H. {Chen} and L. {Yong} and M. {Rahman} and J. {Wiedemeier} and R. {Madhavaram} and A. {Chiou} and B. {Li} and V. {Lin} and R. {Huang} and M. {Yanq} and A. {Thippana} and O. {Su} and S. {Huang}},
  booktitle    = {2020 IEEE International Solid- State Circuits Conference - (ISSCC)},
  title        = {2.5 A 7nm FinFET 2.5GHz/2.0GHz Dual-Gear Octa-Core CPU Subsystem with Power/Performance Enhancements for a Fully Integrated 5G Smartphone SoC},
  year         = {2020},
  month        = {Feb},
  pages        = {50--52},
  abstract     = {This paper introduces the heterogenous CPU complex of a fully integrated 5G mobile Smartphone SoC, implemented in 7nm FinFET technology. Circuit techniques developed to achieve competitive CPU PPA are detailed, and associated silicon results are presented.},
  creationdate = {2021-01-29T00:00:00},
  doi          = {10.1109/ISSCC19947.2020.9062897},
  file         = {:by-author/M/Mair/2020_Mair_50.pdf:PDF},
  issn         = {2376-8606},
  keywords     = {5G Mobile Communication; Chips; Clocks; Competitive CPU PPA; Computer Architecture; Computer Science (CS); Delays; Dual-gear Octa-core CPU Subsystem; Elemental Semiconductors; FinFET Technology; Frequency Locked Loops; Heterogenous CPU Complex; Integrated 5G Mobile Smartphone SoC; MOSFET; Microprocessor Chips; Microprocessors; Oscillators; Si; Silicon; Smart Phones; Software; System-on-chip; VLSI; frequency 2.0 GHz; frequency 2.5 GHz; size 7.0 nm},
  owner        = {saulius},
  timestamp    = {2021.01.29},
}

@InProceedings{9062915,
  author    = {R. {Venkatasubramanian} and D. {Steiss} and G. {Shurtz} and T. {Anderson} and K. {Chirca} and R. {Santhanagopal} and N. {Nandan} and A. {Reghunath} and H. {Sanghvi} and D. {Wu} and A. {Chachad} and B. {Karguth} and D. {Beaudoin} and C. {Fuoco} and L. {Nardini} and C. {Hu} and S. {Visalli} and A. {Mundra} and D. {Varadarajan} and F. {Cano} and S. {Stelmach} and M. {Mody} and A. {Redfern} and H. {Bilhan} and M. {Sarraj} and A. {Siddiki} and A. {Lell} and E. {Falik} and A. {Hill} and A. {Armstrong} and T. {Beck} and V. {Kanumuri} and S. {Mullinnix} and D. {Moore} and J. {Jones} and M. {Koul} and S. {Agarwala}},
  booktitle = {2020 IEEE International Solid- State Circuits Conference - (ISSCC)},
  title     = {2.6 A 16nm 3.5B+ Transistor >14TOPS 2-to-10W Multicore SoC Platform for Automotive and Embedded Applications with Integrated Safety MCU, 512b Vector VLIW DSP, Embedded Vision and Imaging Acceleration},
  year      = {2020},
  month     = {Feb},
  pages     = {52--54},
  abstract  = {The 7th generation Jacinto™ SoC platform is an evolution of prior architectures [1], [2] and integrates new capabilities to support a wide set of applications, including automotive, industrial, and broad market. This drives a diverse set of requirements which need IP innovation and new techniques across the entire SoC stack including: high-reliability techniques for automotive, including circuit analysis and screening; new IP development including new DSP, signal processing and data movement architectures; embedded vision, machine learning, and imaging and video acceleration; new security and safety innovations, including an integrated safety MCU; dedicated security controller, and hardware features to enable ASIL-D support. This SoC platform and first implementation also integrates techniques for simplified power-supply management and support for cost-sensitive systems through on-die micro-architecture solutions.},
  doi       = {10.1109/ISSCC19947.2020.9062915},
  file      = {:by-author/V/Venkatasubramanian/2020_Venkatasubramanian_52.pdf:PDF},
  issn      = {2376-8606},
  keywords  = {ASIL-D Support; Acceleration; Automotive Electronics; Automotive Embedded Applications; Automotive Engineering; Automotive Market; Broad Market; Chips; Circuit Analysis; Clocks; Computer Architecture; Computer Science (CS); Data Movement Architectures; Dedicated Security Controller; Digital Signal Processing Chips; Electronic Data Interchange; Embedded Vision; Engines; Entire SoC Stack Including; High-reliability Techniques; IP Development; IP Innovation; Imaging Acceleration; Integrated Circuit Design; Integrated Safety MCU; Microarchitecture Solutions; Microprocessors; Multicore Processing; Multicore SoC Platform; Multiprocessing Systems; Prior Architectures; Safety; Safety Innovations; Signal Processing; System-on-chip; Thermal Sensors; VLSI; Vector VLIW DSP; Video Acceleration; power 10.0 W; size 16.0 nm},
  owner     = {saulius},
  timestamp = {2021.01.29},
  creationdate = {2021-01-29T00:00:00},
}

@InProceedings{9063030,
  author    = {C. {Berry} and B. {Bell} and A. {Jatkowski} and J. {Surprise} and J. {Isakson} and O. {Geva} and B. {Deskin} and M. {Cichanowski} and D. {Hamid} and C. {Cavitt} and G. {Fredeman} and A. {Saporito} and A. {Mishra} and A. {Buyuktosunoglu} and T. {Webel} and P. {Lobo} and P. {Parashurama} and R. {Bertran} and D. {Chidambarrao} and D. {Wolpert} and B. {Bruen}},
  booktitle = {2020 IEEE International Solid- State Circuits Conference - (ISSCC)},
  title     = {2.7 IBM z15: A 12-Core 5.2GHz Microprocessor},
  year      = {2020},
  month     = {Feb},
  pages     = {54--56},
  abstract  = {The latest IBM Z microprocessor in the z15 system has been redesigned to have improved performance, system capacity and security over the previous z14 system [1]. These achievements are made while maintaining the central processor (CP) and system controller (SC) chip die sizes at 696mm2 in the GlobalFoundries 14nm high performance (14HP) SOI FinFET technology and 17 layers of copper interconnect [2], both design points of the z14 system. The system contains up to 20 CP and 5 SC chips. Each CP, shown in die photo A (Fig. 2.7.7), operates at 5.2GHz and is comprised of 12 cores, 3 PCle Gen4 interfaces, 256MB of L3 embedded DRAM (eDRAM) cache, two X-BUS interfaces connecting to one other CP chip and one SC chip, and a redundant array of independent memory (RAIM) interface. Each core on the CP chip has 8MB of L2 eDRAM cache as well as 256KB of L1 SRAM cache, both caches split evenly between data and instruction. Each SC, shown in die photo B, operates at half the frequency of the CP, or 2.6GHz, has 960MB of L4 eDRAM cache, X-BUS interfaces connecting to half of the CP chips in the drawer and four A-BUS interfaces connecting to the SC chips on the other drawers in the system. The CP contains 9.2B transistors and the SC contains 12.2B transistors. The total 10 bandwidth of the CP and SC are 2.3Tb/s and 5.6Tb/s, respectively.},
  doi       = {10.1109/ISSCC19947.2020.9063030},
  file      = {:by-author/B/Berry/2020_Berry_54.pdf:PDF},
  issn      = {2376-8606},
  keywords  = {12-core Microprocessor; A-BUS Interfaces; CP Chip; Cache Storage; Central Processor; Chips; Computer Architecture; Computer Science (CS); Copper Interconnect; DRAM Chips; Design Points; GlobalFoundries High Performance SOI FinFET Technology; Hardware; IBM Z Microprocessor; IBM Z15; Integrated Circuit Design; L1 SRAM Cache; L2 EDRAM Cache; L3 Embedded DRAM Cache; Low-power Electronics; MOSFET Circuits; Microprocessors; Out of Order; PCle Gen4 Interfaces; Peripheral Interfaces; Redundant Array of Independent Memory Interface; SC Chip; SRAM Chips; Sensors; Silicon-on-insulator; Storage Capacity 256 Kbit; Storage Capacity 8 Mbit; Storage Capacity 960 Mbit; System Capacity; System Controller Chip; Topology; VLSI; X-BUS Interfaces; Z15 System; bit rate 2.3 Tbit/s; bit rate 5.6 Tbit/s; frequency 2.6 GHz; frequency 5.2 GHz; size 14.0 nm},
  owner     = {saulius},
  timestamp = {2021.01.29},
  creationdate = {2021-01-29T00:00:00},
}

@Article{Benzmueller2012,
  author    = {Christoph Benzmüller and Jens Otten and Thomas Raths},
  journal   = {Frontiers in Artificial Intelligence and Applications},
  title     = {Implementing and Evaluating Provers for First-order Modal Logics},
  year      = {2012},
  issn      = {0922-6389},
  pages     = {163--168},
  volume    = {242},
  doi       = {10.3233/978-1-61499-098-7-163},
  file      = {:by-author/B/Benzmüller/2012_Benzmüller_163a.pdf:PDF;:by-author/B/Benzmüller/2012_Benzmüller_163.pdf:PDF},
  keywords  = {Computer Science (CS); First Order Modal Logics; HOL; Modal Logics; Theorem Proovers},
  owner     = {saulius},
  publisher = {IOS Press},
  timestamp = {2021.02.04},
  creationdate = {2021-02-04T00:00:00},
}

@Article{Solomon1991,
  author    = {E. Solomon and J. Borrow and A. Goddard},
  journal   = {Science},
  title     = {Chromosome aberrations and cancer},
  year      = {1991},
  month     = {nov},
  number    = {5035},
  pages     = {1153--1160},
  volume    = {254},
  doi       = {10.1126/science.1957167},
  file      = {:by-author/S/Solomon/1991_Solomon_1153.pdf:PDF},
  keywords  = {Cancer; Chromosom Aberrations; Genetics; Molecular Biology},
  owner     = {saulius},
  publisher = {American Association for the Advancement of Science ({AAAS})},
  timestamp = {2021.02.06},
  creationdate = {2021-02-06T00:00:00},
}

@Article{Froehling2008,
  author    = {Stefan Fröhling and Hartmut Döhner},
  journal   = {New England Journal of Medicine},
  title     = {Chromosomal abnormalities in cancer},
  year      = {2008},
  month     = {aug},
  number    = {7},
  pages     = {722--734},
  volume    = {359},
  doi       = {10.1056/nejmra0803109},
  file      = {:by-author/F/Fröhling/2008_Fröhling_722.pdf:PDF},
  keywords  = {Cancer; Chromosom Aberrations; Genetics; Molecular Biology},
  owner     = {saulius},
  publisher = {Massachusetts Medical Society},
  timestamp = {2021.02.06},
  creationdate = {2021-02-06T00:00:00},
}

@Article{Ozery_Flato_2011,
  author    = {Michal Ozery-Flato and Chaim Linhart and Luba Trakhtenbrot and Shai Izraeli and Ron Shamir},
  journal   = {Genome Biology},
  title     = {Large-scale analysis of chromosomal aberrations in cancer karyotypes reveals two distinct paths to aneuploidy},
  year      = {2011},
  number    = {6},
  pages     = {R61},
  volume    = {12},
  abstract  = {Chromosomal aneuploidy, that is to say the gain or loss of chromosomes, is the most common abnormality in cancer. While certain aberrations, most commonly translocations, are known to be strongly associated with specific cancers and contribute to their formation, most aberrations appear to be non-specific and arbitrary, and do not have a clear effect. The understanding of chromosomal aneuploidy and its role in tumorigenesis is a fundamental open problem in cancer biology.},
  doi       = {10.1186/gb-2011-12-6-r61},
  file      = {:by-author/O/Ozery-Flato/2011_Ozery-Flato_61.pdf:PDF},
  keywords  = {Cancer; Chromosom Aberrations; Genetics; Molecular Biology},
  owner     = {saulius},
  publisher = {Springer Science and Business Media {LLC}},
  timestamp = {2021.02.06},
  creationdate = {2021-02-06T00:00:00},
  url       = {http://genomebiology.com/2011/12/6/R61},
}

@Article{Boffetta2006,
  author    = {P. Boffetta and O. van der Hel and H. Norppa and E. Fabianova and A. Fucic and S. Gundy and J. Lazutka and A. Cebulska-Wasilewska and D. Puskailerova and A. Znaor and Z. Kelecsenyi and J. Kurtinaitis and J. Rachtan and A. Forni and R. Vermeulen and S. Bonassi},
  journal   = {American Journal of Epidemiology},
  title     = {Chromosomal aberrations and cancer risk: results of a cohort study from central europe},
  year      = {2006},
  month     = {oct},
  number    = {1},
  pages     = {36--43},
  volume    = {165},
  doi       = {10.1093/aje/kwj367},
  file      = {:by-author/B/Boffetta/2006_Boffetta_36.pdf:PDF},
  keywords  = {Biostatistics; Cancer; Chromosom Aberrations; Genetics; Molecular Biology},
  owner     = {saulius},
  publisher = {Oxford University Press ({OUP})},
  timestamp = {2021.02.06},
  creationdate = {2021-02-06T00:00:00},
}

@Webpage{DFCI2018,
  author      = {{Dana-Farber Cancer Institute}},
  retrieved   = {2021-02-06 12:17:31 EET},
  title       = {How do chromosome abnormalities result in cancer?},
  url         = {https://blog.dana-farber.org/insight/2018/02/chromosome-abnormalities-result-cancer/},
  institution = {Dana-Farber Cancer Institute},
  siteurl     = {https://blog.dana-farber.org/},
  year        = {2018},
  comment     = {Published: February 5, 2018
Updated: February 7, 2018},
  file        = {:by-author/D/DFCI/2018_DFCI_.odt:OpenDocument text},
  keywords    = {Cancer; Chromosom Aberrations; Genetics; Molecular Biology},
  owner       = {saulius},
  timestamp = {2021.02.06},
  creationdate = {2021-02-06T00:00:00},
}

@InCollection{Brosgol2010,
  author    = {Benjamin M. Brosgol},
  booktitle = {Reliable Software Technologiey {\textendash} Ada-Europe 2010},
  publisher = {Springer Berlin Heidelberg},
  title     = {A comparison of generic template support: {Ada}, {C++}, {C}{\#}, and {JavaTM}},
  year      = {2010},
  pages     = {222--237},
  doi       = {10.1007/978-3-642-13550-7_16},
  file      = {:by-author/B/Brosgol/2010_Brosgol_222.pdf:PDF},
  keywords  = {Ada; Code Generation; Compilers; Computer Science (CS); Generics},
  owner     = {saulius},
  timestamp = {2021.02.06},
  creationdate = {2021-02-06T00:00:00},
}

@InProceedings{Karnaukhov2002,
  author    = {Karnaukhov, A. V.},
  booktitle = {Exo-Astrobiology},
  title     = {The role of biosphere in the formation of planetary climate: Greenhouse catastrophe},
  year      = {2002},
  editor    = {{Lacoste}, Huguette},
  month     = nov,
  pages     = {417--420},
  series    = {ESA Special Publication},
  volume    = {518},
  abstract  = {If take into consideration the role of planet atmospheres in a climate         formation, the habitable zone around a star system would be more         wide than it is supposed now. Reflection of the incident         radiation (reflectance) and greenhouse effect is significantly         changing the planet temperature. As a result of slow         accumulation of greenhouse gases in the atmosphere the planet         global temperature will increase from minimum values to hundred         degrees Celsius. Thus on a certain stage of evolution the         planetary environments of the planets placed at a wide range         distances from the central star may be fit to origin of life.         Originating at the time of the favorable climatic conditions,         the photosynthetic life stabilizes later the global temperature         of the planet absorbing atmospheric CO$_{2}$ in to the         nonequilibrium lithospheric buffer. Civilization may disturb the         biospheric stabilization mechanisms of the atmospheric and         lithospheric nonequilibrium state, that will cause irreversible         transition of climate system in a equilibrium state which is         accompanied by the significant increase of the planet surface         temperature and concentration of the atmospheric greenhouse         gases. This irreversible transition, which able to eliminate         life on the planet, is named ``Greenhouse catastrophe''.},
  file      = {:by-author/K/Karnaukhov/2002_Karnaukhov_417.pdf:PDF},
  keywords  = {Earth Climate; Extrasolar Planets: Habitable Zones; Greenhouse Catastrophe; Mathematical Models},
  owner     = {saulius},
  timestamp = {2021.02.07},
  creationdate = {2021-02-07T00:00:00},
  url       = {https://ui.adsabs.harvard.edu/abs/2002ESASP.518..417K},
}

@InProceedings{Karnaukhov2002a,
  author    = {Karnaukhov, A. V.},
  booktitle = {The Evolving Sun and its Influence on Planetary Environments},
  title     = {The {Earth} climate change model with regard to the thermal inertia of the world ocean and aerosol pollution of high layers of the atmosphere},
  year      = {2002},
  editor    = {{Montesinos}, Benjamin and {Gimenez}, Alvaro and {Guinan}, Edward F.},
  month     = jan,
  pages     = {331--336},
  series    = {Astronomical Society of the Pacific Conference Series},
  volume    = {269},
  file      = {:by-author/K/Karnaukhov/2002_Karnaukhov_331.pdf:PDF},
  keywords  = {Earth Climate; Greenhouse Catastrophe; Mathematical Models},
  owner     = {saulius},
  timestamp = {2021.02.07},
  creationdate = {2021-02-07T00:00:00},
  url       = {https://ui.adsabs.harvard.edu/abs/2002ASPC..269..331K},
}

@Article{Wulf1973,
  author    = {W. Wulf and Mary Shaw},
  journal   = {{ACM} {SIGPLAN} Notices},
  title     = {Global variable considered harmful},
  year      = {1973},
  month     = {feb},
  number    = {2},
  pages     = {28--34},
  volume    = {8},
  doi       = {10.1145/953353.953355},
  file      = {:by-author/W/Wulf/1973_Wulf_28.pdf:PDF},
  keywords  = {Computer Science (CS); Global Variables; Programming Languages; Programming Style; Software Project Management},
  owner     = {saulius},
  publisher = {Association for Computing Machinery ({ACM})},
  timestamp = {2021.02.07},
  creationdate = {2021-02-07T00:00:00},
}

@Article{Patterson2019,
  author    = {Daniel Patterson and Amal Ahmed},
  journal   = {Proceedings of the {ACM} on Programming Languages},
  title     = {The next 700 compiler correctness theorems (functional pearl)},
  year      = {2019},
  month     = {jul},
  number    = {{ICFP}},
  pages     = {1--29},
  volume    = {3},
  doi       = {10.1145/3341689},
  file      = {:by-author/P/Patterson/2019_Patterson_1.pdf:PDF},
  keywords  = {Compiler Construction; Compiler Verification; Computer Science (CS)},
  owner     = {saulius},
  publisher = {Association for Computing Machinery ({ACM})},
  timestamp = {2021.02.10},
  creationdate = {2021-02-10T00:00:00},
}

@Article{Chisnall2018,
  author    = {David Chisnall},
  journal   = {Communications of the {ACM}},
  title     = {{C} is not a low-level language},
  year      = {2018},
  month     = {jun},
  number    = {7},
  pages     = {44--48},
  volume    = {61},
  doi       = {10.1145/3209212},
  file      = {:by-author/C/Chisnall/2018_Chisnall_44.pdf:PDF},
  keywords  = {C Language; Compiler Construction; Compilers; Computer Architectures; Computer Science (CS); High Level Languages; Parallel Computations},
  owner     = {saulius},
  publisher = {Association for Computing Machinery ({ACM})},
  timestamp = {2021.02.17},
  creationdate = {2021-02-17T00:00:00},
}

@TechReport{Watson2014,
  author      = {Robert N. M. Watson and Peter G. Neumann and Jonathan Woodruff and Jonathan Anderson and David Chisnall and Brooks Davis and Ben Laurie and Simon W. Moore and Steven J. Murdoch and Michael Roe},
  institution = {University of Cambridge},
  title       = {Capability hardware enhanced {RISC} instructions: {CHERI} instruction-set architecture},
  year        = {2014},
  note        = {Cited by 2015_Chisnall_117.pdf},
  number      = {UCAM-CL-TR-864},
  type        = {techreport},
  file        = {:by-author/W/Watson/2014_Watson_1.pdf:PDF},
  issn        = {1476-2986},
  keywords    = {CHERI; Capability Architecture; Computer Architecture; Computer Science (CS); Computer Security; RISC},
  owner       = {saulius},
  pages       = {1--142},
  timestamp = {2021.02.18},
  creationdate = {2021-02-18T00:00:00},
  url         = {https://www.cl.cam.ac.uk/techreports/UCAM-CL-TR-864.pdf},
}

@InProceedings{Jorgensen1992,
  author    = {Jesper Jørgensen},
  booktitle = {Proceedings of the 19th {ACM} {SIGPLAN}-{SIGACT} symposium on Principles of programming languages - {POPL} {\textquotesingle}92},
  title     = {Generating a compiler for a lazy language by partial evaluation},
  year      = {1992},
  pages     = {258--268},
  publisher = {{ACM} Press},
  doi       = {10.1145/143165.143220},
  file      = {:by-author/J/Jørgensen/1992_Jørgensen_258.pdf:PDF},
  owner     = {saulius},
  timestamp = {2021.02.18},
  creationdate = {2021-02-18T00:00:00},
}

@Article{Chlipala2010,
  author    = {Adam Chlipala},
  journal   = {{ACM} {SIGPLAN} Notices},
  title     = {A verified compiler for an impure functional language},
  year      = {2010},
  month     = {jan},
  number    = {1},
  pages     = {93--106},
  volume    = {45},
  doi       = {10.1145/1707801.1706312},
  file      = {:by-author/C/Chlipala/2010_Chlipala_93.pdf:PDF},
  keywords  = {Compiler Construction; Compiler Verification; Computer Science (CS); Functional Languages; Program Verification},
  owner     = {saulius},
  publisher = {Association for Computing Machinery ({ACM})},
  timestamp = {2021.02.18},
  creationdate = {2021-02-18T00:00:00},
}

@Article{Wagner2001,
  author    = {Jens Wagner and Rainer Leupers},
  journal   = {{ACM} {SIGPLAN} Notices},
  title     = {C Compiler Design for an Industrial Network Processor},
  year      = {2001},
  month     = {aug},
  number    = {8},
  pages     = {155--164},
  volume    = {36},
  doi       = {10.1145/384196.384218},
  file      = {:by-author/W/Wagner/2001_Wagner_155.pdf:PDF},
  keywords  = {C Language; Compiler Construction; Computer Science (CS)},
  owner     = {saulius},
  publisher = {Association for Computing Machinery ({ACM})},
  timestamp = {2021.02.18},
  creationdate = {2021-02-18T00:00:00},
}

@Article{Gisselquist1986,
  author    = {Richard Gisselquist},
  journal   = {{ACM} {SIGPLAN} Notices},
  title     = {An experimental {C} compiler for the {Cray} 2 computer},
  year      = {1986},
  month     = {sep},
  number    = {9},
  pages     = {32--41},
  volume    = {21},
  doi       = {10.1145/885694.885699},
  file      = {:by-author/G/Gisselquist/1986_Gisselquist_32.pdf:PDF},
  keywords  = {C Language; Compiler Design; Computer Science (CS)},
  owner     = {saulius},
  publisher = {Association for Computing Machinery ({ACM})},
  timestamp = {2021.02.18},
  creationdate = {2021-02-18T00:00:00},
}

@InProceedings{Dakkak2020,
  author    = {Abdul Dakkak and Tom Wickham-Jones and Wen-mei Hwu},
  booktitle = {Proceedings of the 18th {ACM}/{IEEE} International Symposium on Code Generation and Optimization},
  title     = {The design and implementation of the {W}olfram language compiler},
  year      = {2020},
  month     = {feb},
  pages     = {212--228},
  publisher = {{ACM}},
  doi       = {10.1145/3368826.3377913},
  file      = {:by-author/D/Dakkak/2020_Dakkak_212.pdf:PDF},
  keywords  = {Compiler Construction; Computer Science (CS)},
  owner     = {saulius},
  timestamp = {2021.02.18},
  creationdate = {2021-02-18T00:00:00},
}

@InProceedings{Ball2019,
  author    = {Thomas Ball and Peli de Halleux and Michał Moskal},
  booktitle = {Proceedings of the 16th {ACM} {SIGPLAN} International Conference on Managed Programming Languages and Runtimes - {MPLR} 2019},
  title     = {Static {TypeScript}: an implementation of a static compiler for the {TypeScript} language},
  year      = {2019},
  pages     = {105--116},
  publisher = {{ACM} Press},
  doi       = {10.1145/3357390.3361032},
  file      = {:by-author/B/Ball/2019_Ball_105.pdf:PDF},
  keywords  = {Compiler Construction; Computer Science (CS); Static Typing; TypeScript},
  owner     = {saulius},
  timestamp = {2021.02.18},
  creationdate = {2021-02-18T00:00:00},
}

@InProceedings{Carlson2019,
  author    = {Travis Carlson and Eric Van Wyk},
  booktitle = {Proceedings of the 24th Symposium on Principles and Practice of Parallel Programming},
  title     = {Building parallel programming language constructs in the {AbleC} extensible {C} compiler framework},
  year      = {2019},
  month     = {feb},
  pages     = {443--446},
  publisher = {{ACM}},
  doi       = {10.1145/3293883.3302574},
  file      = {:by-author/C/Carlson/2019_Carlson_443.pdf:PDF},
  keywords  = {C Language; Compiler Construction; Computer Science (CS)},
  owner     = {saulius},
  timestamp = {2021.02.18},
  creationdate = {2021-02-18T00:00:00},
}

@InProceedings{Ginsbach2018,
  author    = {Philip Ginsbach and Lewis Crawford and Michael F. P. O{\textquotesingle}Boyle},
  booktitle = {Proceedings of the 27th International Conference on Compiler Construction},
  title     = {{CAnDL}: a domain specific language for compiler analysis},
  year      = {2018},
  month     = {feb},
  pages     = {151--162},
  publisher = {{ACM}},
  doi       = {10.1145/3178372.3179515},
  file      = {:by-author/G/Ginsbach/2018_Ginsbach_151.pdf:PDF},
  keywords  = {Compiler Constrcution; Compiler Verification; Computer Science (CS)},
  owner     = {saulius},
  timestamp = {2021.02.18},
  creationdate = {2021-02-18T00:00:00},
}

@InProceedings{Chen2017,
  author    = {Hanfeng Chen and Wai-Mee Ching and Laurie Hendren},
  booktitle = {Proceedings of the 4th {ACM} {SIGPLAN} International Workshop on Libraries, Languages, and Compilers for Array Programming},
  title     = {An {ELI}-to-{C} compiler: design, implementation, and performance},
  year      = {2017},
  month     = {jun},
  pages     = {9--16},
  publisher = {{ACM}},
  doi       = {10.1145/3091966.3091969},
  file      = {:by-author/C/Chen/2017_Chen_9.pdf:PDF},
  keywords  = {C Language; Compipler Construction; Computer Science (CS); Transpilers},
  owner     = {saulius},
  timestamp = {2021.02.18},
  creationdate = {2021-02-18T00:00:00},
}

@InProceedings{Truong2016,
  author    = {Leonard Truong and Rajkishore Barik and Ehsan Totoni and Hai Liu and Chick Markley and Armando Fox and Tatiana Shpeisman},
  booktitle = {Proceedings of the 37th {ACM} {SIGPLAN} Conference on Programming Language Design and Implementation},
  title     = {Latte: a language, compiler, and runtime for elegant and efficient deep neural networks},
  year      = {2016},
  month     = {jun},
  pages     = {209--223},
  publisher = {{ACM}},
  doi       = {10.1145/2908080.2908105},
  file      = {:by-author/T/Truong/2016_Truong_209.pdf:PDF},
  keywords  = {Compiler Construction; Computer Science (CS); Neural Networks (NN)},
  owner     = {saulius},
  timestamp = {2021.02.18},
  creationdate = {2021-02-18T00:00:00},
}

@InProceedings{Garg2015,
  author    = {Rahul Garg and Sameer Jagdale and Laurie Hendren},
  booktitle = {Proceedings of the 2nd {ACM} {SIGPLAN} International Workshop on Libraries, Languages, and Compilers for Array Programming},
  title     = {{V}elociraptor: a compiler toolkit for array-based languages targeting {CPUs} and {GPUs}},
  year      = {2015},
  month     = {jun},
  pages     = {19--24},
  publisher = {{ACM}},
  doi       = {10.1145/2774959.2774967},
  file      = {:by-author/G/Garg/2015_Garg_19.pdf:PDF},
  keywords  = {Array-based Languages; CPU; Compiler Constrcution; Computer Science (CS); GPU},
  owner     = {saulius},
  timestamp = {2021.02.18},
  creationdate = {2021-02-18T00:00:00},
}

@InProceedings{Wang2014a,
  author    = {Peng Wang and Santiago Cuellar and Adam Chlipala},
  booktitle = {Proceedings of the 2014 {ACM} International Conference on Object Oriented Programming Systems Languages {\&} Applications},
  title     = {Compiler verification meets cross-language linking via data abstraction},
  year      = {2014},
  month     = {oct},
  pages     = {675--690},
  publisher = {{ACM}},
  doi       = {10.1145/2660193.2660201},
  file      = {:by-author/W/Wang/2014_Wang_675.pdf:PDF},
  keywords  = {Compiler Construction; Compiler Verification; Computer Science (CS)},
  owner     = {saulius},
  timestamp = {2021.02.18},
  creationdate = {2021-02-18T00:00:00},
}

@Presentation{She2020,
  author    = {Adrian She},
  title     = {The {Cook-Levin} theorem},
  year      = {2020},
  file      = {:by-author/S/She/2020_She_1.pdf:PDF},
  keywords  = {Computer Science (CS); Cook-Levin Theorem; NP-completenes; Proof Theory},
  owner     = {saulius},
  pages     = {1--19},
  timestamp = {2021.02.18},
  creationdate = {2021-02-18T00:00:00},
  url       = {http://www.cs.toronto.edu/~ashe/cook-levin-handout.pdf},
}

@Webpage{Kong2007,
  author    = {Shijin Kong and David Malec},
  retrieved = {2021-02-18},
  title     = {{Cook-Levin} Theorem},
  url       = {http://pages.cs.wisc.edu/~shuchi/courses/787-F07/scribe-notes/lecture09.pdf},
  language  = {eng},
  site      = {http://pages.cs.wisc.edu/},
  siteurl   = {http://pages.cs.wisc.edu/~shuchi/},
  year      = {2007},
  file      = {:by-author/K/Kong/2007_Kong_1.pdf:PDF},
  keywords  = {Computer Science (CS); Cook-Levin Theorem; NP-completenes; Proof Theory},
  owner     = {saulius},
  pages     = {1--7},
  timestamp = {2021.02.18},
  creationdate = {2021-02-18T00:00:00},
}

@Article{Yandell2002,
  author    = {Mark D. Yandell and William H. Majoros},
  journal   = {Nature Reviews Genetics},
  title     = {Genomics and natural language processing},
  year      = {2002},
  month     = {aug},
  number    = {8},
  pages     = {601--610},
  volume    = {3},
  doi       = {10.1038/nrg861},
  file      = {:by-author/Y/Yandell/2002_Yandell_601.pdf:PDF},
  owner     = {saulius},
  publisher = {Springer Science and Business Media {LLC}},
  timestamp = {2021.03.01},
  creationdate = {2021-03-01T00:00:00},
}

@Article{Bagherian2020,
  author    = {Maryam Bagherian and Elyas Sabeti and Kai Wang and Maureen A. Sartor and Zaneta Nikolovska-Coleska and Kayvan Najarian},
  journal   = {Briefings in Bioinformatics},
  title     = {Machine learning approaches and databases for prediction of drug{\textendash}target interaction: a survey paper},
  year      = {2020},
  month     = {jan},
  number    = {1},
  pages     = {247--269},
  volume    = {22},
  doi       = {10.1093/bib/bbz157},
  file      = {:by-author/B/Bagherian/2020_Bagherian_247.pdf:PDF},
  keywords  = {Chemical Property Prediction; Chemoinformatics; Computer Science (CS); Machine Learning (ML)},
  owner     = {saulius},
  publisher = {Oxford University Press ({OUP})},
  timestamp = {2021.03.03},
  creationdate = {2021-03-03T00:00:00},
}

@Article{Jiang2021,
  author    = {Dejun Jiang and Zhenxing Wu and Chang-Yu Hsieh and Guangyong Chen and Ben Liao and Zhe Wang and Chao Shen and Dongsheng Cao and Jian Wu and Tingjun Hou},
  journal   = {Journal of Cheminformatics},
  title     = {Could graph neural networks learn better molecular representation for drug discovery? A comparison study of descriptor-based and graph-based models},
  year      = {2021},
  month     = {feb},
  number    = {1},
  pages     = {1--23},
  volume    = {13},
  doi       = {10.1186/s13321-020-00479-8},
  file      = {:by-author/J/Jiang/2021_Jiang_1.pdf:PDF},
  keywords  = {Chemical Property Prediction; Chemoinformatics; Computer Science (CS); Machine Learning (ML)},
  owner     = {saulius},
  publisher = {Springer Science and Business Media {LLC}},
  timestamp = {2021.03.03},
  creationdate = {2021-03-03T00:00:00},
}

@Article{Nasser2020,
  author    = {Maged Nasser and Naomie Salim and Hentabli Hamza and Faisal Saeed and Idris Rabiu},
  journal   = {Molecules},
  title     = {Improved Deep Learning Based Method for Molecular Similarity Searching Using Stack of Deep Belief Networks},
  year      = {2020},
  month     = {dec},
  number    = {1},
  pages     = {128},
  volume    = {26},
  doi       = {10.3390/molecules26010128},
  file      = {:by-author/N/Nasser/2020_Nasser_128.pdf:PDF},
  keywords  = {Chemical Property Prediction; Chemoinformatics; Computer Science (CS); Machine Learning (ML)},
  owner     = {saulius},
  publisher = {{MDPI} {AG}},
  timestamp = {2021.03.03},
  creationdate = {2021-03-03T00:00:00},
}

@Article{Mouchlis2021,
  author    = {Varnavas D. Mouchlis and Antreas Afantitis and Angela Serra and Michele Fratello and Anastasios G. Papadiamantis and Vassilis Aidinis and Iseult Lynch and Dario Greco and Georgia Melagraki},
  journal   = {International Journal of Molecular Sciences},
  title     = {Advances in De Novo Drug Design: From Conventional to Machine Learning Methods},
  year      = {2021},
  month     = {feb},
  number    = {4},
  pages     = {1676},
  volume    = {22},
  doi       = {10.3390/ijms22041676},
  file      = {:by-author/M/Mouchlis/2021_Mouchlis_1676.pdf:PDF},
  keywords  = {Chemical Property Prediction; Chemoinformatics; Computer Science (CS); Machine Learning (ML)},
  owner     = {saulius},
  publisher = {{MDPI} {AG}},
  timestamp = {2021.03.03},
  creationdate = {2021-03-03T00:00:00},
}

@Article{Bort2021,
  author    = {William Bort and Igor I. Baskin and Timur Gimadiev and Artem Mukanov and Ramil Nugmanov and Pavel Sidorov and Gilles Marcou and Dragos Horvath and Olga Klimchuk and Timur Madzhidov and Alexandre Varnek},
  journal   = {Scientific Reports},
  title     = {Discovery of novel chemical reactions by deep generative recurrent neural network},
  year      = {2021},
  month     = feb,
  number    = {1},
  pages     = {3178},
  volume    = {11},
  doi       = {10.1038/s41598-021-81889-y},
  file      = {:by-author/B/Bort/2021_Bort_3178.pdf:PDF},
  keywords  = {Chemical Property Prediction; Chemical Reaction Predicion; Chemoinformatics; Computer Science (CS); Machine Learning (ML)},
  owner     = {saulius},
  publisher = {Springer Science and Business Media {LLC}},
  timestamp = {2021.03.03},
  creationdate = {2021-03-03T00:00:00},
}

@Article{Krassowski2020,
  author    = {Michal Krassowski and Vivek Das and Sangram K. Sahu and Biswapriya B. Misra},
  journal   = {Frontiers in Genetics},
  title     = {State of the Field in Multi-Omics Research: From Computational Needs to Data Mining and Sharing},
  year      = {2020},
  month     = {dec},
  pages     = {610798},
  volume    = {11},
  doi       = {10.3389/fgene.2020.610798},
  file      = {:by-author/K/Krassowski/2020_Krassowski_610798.pdf:PDF},
  keywords  = {Bioinformatics; Data Management; Data Science},
  owner     = {saulius},
  publisher = {Frontiers Media {SA}},
  timestamp = {2021.03.03},
  creationdate = {2021-03-03T00:00:00},
}

@Article{Chiu2019,
  author    = {Yu-Chiao Chiu and Hung-I Harry Chen and Aparna Gorthi and Milad Mostavi and Siyuan Zheng and Yufei Huang and Yidong Chen},
  journal   = {Briefings in Bioinformatics},
  title     = {Deep learning of pharmacogenomics resources: moving towards precision oncology},
  year      = {2019},
  month     = {dec},
  number    = {6},
  pages     = {2066--2083},
  volume    = {21},
  doi       = {10.1093/bib/bbz144},
  file      = {:by-author/C/Chiu/2019_Chiu_2066.pdf:PDF},
  keywords  = {Bioinformatics; Data Management; Data Science},
  owner     = {saulius},
  publisher = {Oxford University Press ({OUP})},
  timestamp = {2021.03.03},
  creationdate = {2021-03-03T00:00:00},
}

@Article{MedinaFranco2020,
  author          = {Medina-Franco, José L. and Saldívar-González, Fernanda I.},
  journal         = {Biomolecules},
  title           = {Cheminformatics to Characterize Pharmacologically Active Natural Products.},
  year            = {2020},
  issn            = {2218-273X},
  month           = nov,
  pages           = {1566},
  volume          = {10},
  abstract        = {Natural products have a significant role in drug discovery. Natural products have distinctive chemical structures that have contributed to identifying and developing drugs for different therapeutic areas. Moreover, natural products are significant sources of inspiration or starting points to develop new therapeutic agents. Natural products such as peptides and macrocycles, and other compounds with unique features represent attractive sources to address complex diseases. Computational approaches that use chemoinformatics and molecular modeling methods contribute to speed up natural product-based drug discovery. Several research groups have recently used computational methodologies to organize data, interpret results, generate and test hypotheses, filter large chemical databases before the experimental screening, and design experiments. This review discusses a broad range of chemoinformatics applications to support natural product-based drug discovery. We emphasize profiling natural product data sets in terms of diversity; complexity; acid/base; absorption, distribution, metabolism, excretion, and toxicity (ADME/Tox) properties; and fragment analysis. Novel techniques for the visual representation of the chemical space are also discussed.},
  citation-subset = {IM},
  country         = {Switzerland},
  doi             = {10.3390/biom10111566},
  file            = {:by-author/M/Medina-Franco/2020_Medina-Franco_1566.pdf:PDF},
  issn-linking    = {2218-273X},
  issue           = {11},
  keywords        = {ADME/Tox; Bioinformatics; Chemical Space; Chemoinformatics; Data Management; Data Science; Databases; Drug Discovery; Molecular Modelling; Natural Products; Toxicity; Web Servers},
  nlm-id          = {101596414},
  owner           = {saulius},
  pii             = {E1566},
  pmc             = {PMC7698493},
  pmid            = {33213003},
  pubmodel        = {Electronic},
  pubstate        = {epublish},
  revised         = {2021-02-05},
  timestamp = {2021.03.03},
  creationdate = {2021-03-03T00:00:00},
}

@Article{Balcells2020,
  author          = {Balcells, David and Skjelstad, Bastian Bjerkem},
  journal         = {Journal of chemical information and modeling},
  title           = {tmQM Dataset-Quantum Geometries and Properties of 86k Transition Metal Complexes.},
  year            = {2020},
  issn            = {1549-960X},
  month           = dec,
  pages           = {6135--6146},
  volume          = {60},
  abstract        = {We report the transition metal quantum mechanics (tmQM) data set, which contains the geometries and properties of a large transition metal-organic compound space. tmQM comprises 86,665 mononuclear complexes extracted from the Cambridge Structural Database, including Werner, bioinorganic, and organometallic complexes based on a large variety of organic ligands and 30 transition metals (the 3d, 4d, and 5d from groups 3 to 12). All complexes are closed-shell, with a formal charge in the range {+1, 0, -1} . The tmQM data set provides the Cartesian coordinates of all metal complexes optimized at the GFN2-xTB level, and their molecular size, stoichiometry, and metal node degree. The quantum properties were computed at the DFT(TPSSh-D3BJ/def2-SVP) level and include the electronic and dispersion energies, highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies, HOMO/LUMO gap, dipole moment, and natural charge of the metal center; GFN2-xTB polarizabilities are also provided. Pairwise representations showed the low correlation between these properties, providing nearly continuous maps with unusual regions of the chemical space, for example, complexes combining large polarizabilities with wide HOMO/LUMO gaps and complexes combining low-energy HOMO orbitals with electron-rich metal centers. The tmQM data set can be exploited in the data-driven discovery of new metal complexes, including predictive models based on machine learning. These models may have a strong impact on the fields in which transition metal chemistry plays a key role, for example, catalysis, organic synthesis, and materials science. tmQM is an open data set that can be downloaded free of charge from https://github.com/bbskjelstad/tmqm.},
  citation-subset = {IM},
  country         = {United States},
  doi             = {10.1021/acs.jcim.0c01041},
  file            = {:by-author/B/Balcells/2020_Balcells_6135.pdf:PDF},
  issn-linking    = {1549-9596},
  issue           = {12},
  keywords        = {CSD; Chemiinformatics; Crystallographic Databases; QM Computations},
  nlm-id          = {101230060},
  owner           = {saulius},
  pmc             = {PMC7768608},
  pmid            = {33166143},
  pubmodel        = {Print-Electronic},
  pubstate        = {ppublish},
  revised         = {2021-01-10},
  timestamp = {2021.03.03},
  creationdate = {2021-03-03T00:00:00},
}

@Article{Rajan2020,
  author       = {Rajan, Kohulan and Zielesny, Achim and Steinbeck, Christoph},
  journal      = {Journal of cheminformatics},
  title        = {DECIMER: towards deep learning for chemical image recognition.},
  year         = {2020},
  issn         = {1758-2946},
  month        = oct,
  pages        = {65},
  volume       = {12},
  abstract     = {The automatic recognition of chemical structure diagrams from the literature is an indispensable component of workflows to re-discover information about chemicals and to make it available in open-access databases. Here we report preliminary findings in our development of Deep lEarning for Chemical ImagE Recognition (DECIMER), a deep learning method based on existing show-and-tell deep neural networks, which makes very few assumptions about the structure of the underlying problem. It translates a bitmap image of a molecule, as found in publications, into a SMILES. The training state reported here does not yet rival the performance of existing traditional approaches, but we present evidence that our method will reach a comparable detection power with sufficient training time. Training success of DECIMER depends on the input data representation: DeepSMILES are superior over SMILES and we have a preliminary indication that the recently reported SELFIES outperform DeepSMILES. An extrapolation of our results towards larger training data sizes suggests that we might be able to achieve near-accurate prediction with 50 to 100 million training structures. This work is entirely based on open-source software and open data and is available to the general public for any purpose.},
  country      = {England},
  doi          = {10.1186/s13321-020-00469-w},
  file         = {:by-author/R/Rajan/2020_Rajan_65.pdf:PDF},
  issn-linking = {1758-2946},
  issue        = {1},
  keywords     = {Artificial Neural Networks (ANN); Autoencoder/decoder; Chemical Structure; Deep Learning (DL); Deep Neural Networks; Machine Learning (ML); Neural Networks (NN); Optical Chemical Entity Recognition},
  nlm-id       = {101516718},
  owner        = {saulius},
  pii          = {10.1186/s13321-020-00469-w},
  pmc          = {PMC7590713},
  pmid         = {33372621},
  pubmodel     = {Electronic},
  pubstate     = {epublish},
  revised      = {2021-01-01},
  timestamp = {2021.03.03},
  creationdate = {2021-03-03T00:00:00},
}

@Article{Tsou2020,
  author          = {Tsou, Lun K. and Yeh, Shiu-Hwa and Ueng, Shau-Hua and Chang, Chun-Ping and Song, Jen-Shin and Wu, Mine-Hsine and Chang, Hsiao-Fu and Chen, Sheng-Ren and Shih, Chuan and Chen, Chiung-Tong and Ke, Yi-Yu},
  journal         = {Scientific reports},
  title           = {Comparative study between deep learning and QSAR classifications for TNBC inhibitors and novel GPCR agonist discovery.},
  year            = {2020},
  issn            = {2045-2322},
  month           = oct,
  pages           = {16771},
  volume          = {10},
  abstract        = {Machine learning is a well-known approach for virtual screening. Recently, deep learning, a machine learning algorithm in artificial neural networks, has been applied to the advancement of precision medicine and drug discovery. In this study, we performed comparative studies between deep neural networks (DNN) and other ligand-based virtual screening (LBVS) methods to demonstrate that DNN and random forest (RF) were superior in hit prediction efficiency. By using DNN, several triple-negative breast cancer (TNBC) inhibitors were identified as potent hits from a screening of an in-house database of 165,000 compounds. In broadening the application of this method, we harnessed the predictive properties of trained model in the discovery of G protein-coupled receptor (GPCR) agonist, by which computational structure-based design of molecules could be greatly hindered by lack of structural information. Notably, a potent (~ 500 nM) mu-opioid receptor (MOR) agonist was identified as a hit from a small-size training set of 63 compounds. Our results show that DNN could be an efficient module in hit prediction and provide experimental evidence that machine learning could identify potent hits in silico from a limited training set.},
  chemicals       = {Antineoplastic Agents, Receptors, G-Protein-Coupled},
  citation-subset = {IM},
  completed       = {2020-12-07},
  country         = {England},
  doi             = {10.1038/s41598-020-73681-1},
  file            = {:by-author/T/Tsou/2020_Tsou_16771.pdf:PDF},
  issn-linking    = {2045-2322},
  issue           = {1},
  keywords        = {Agonists; Algorithms; Antineoplastic Agents; Computer; Deep Learning (DL); Drug Discovery; Drug Therapy; G-Protein-Coupled; Humans; Methods; Neural Networks (NN); Receptors; Therapeutic Use; Triple Negative Breast Neoplasms},
  nlm-id          = {101563288},
  owner           = {saulius},
  pii             = {10.1038/s41598-020-73681-1},
  pmc             = {PMC7545175},
  pmid            = {33033310},
  pubmodel        = {Electronic},
  pubstate        = {epublish},
  revised         = {2020-12-14},
  timestamp = {2021.03.03},
  creationdate = {2021-03-03T00:00:00},
}

@Article{Merwin2020,
  author          = {Merwin, Nishanth J. and Mousa, Walaa K. and Dejong, Chris A. and Skinnider, Michael A. and Cannon, Michael J. and Li, Haoxin and Dial, Keshav and Gunabalasingam, Mathusan and Johnston, Chad and Magarvey, Nathan A.},
  journal         = {Proceedings of the National Academy of Sciences of the United States of America},
  title           = {DeepRiPP integrates multiomics data to automate discovery of novel ribosomally synthesized natural products.},
  year            = {2020},
  issn            = {1091-6490},
  month           = jan,
  pages           = {371--380},
  volume          = {117},
  abstract        = {Microbial natural products represent a rich resource of evolved chemistry that forms the basis for the majority of pharmacotherapeutics. Ribosomally synthesized and posttranslationally modified peptides (RiPPs) are a particularly interesting class of natural products noted for their unique mode of biosynthesis and biological activities. Analyses of sequenced microbial genomes have revealed an enormous number of biosynthetic loci encoding RiPPs but whose products remain cryptic. In parallel, analyses of bacterial metabolomes typically assign chemical structures to only a minority of detected metabolites. Aligning these 2 disparate sources of data could provide a comprehensive strategy for natural product discovery. Here we present DeepRiPP, an integrated genomic and metabolomic platform that employs machine learning to automate the selective discovery and isolation of novel RiPPs. DeepRiPP includes 3 modules. The first, NLPPrecursor, identifies RiPPs independent of genomic context and neighboring biosynthetic genes. The second module, BARLEY, prioritizes loci that encode novel compounds, while the third, CLAMS, automates the isolation of their corresponding products from complex bacterial extracts. DeepRiPP pinpoints target metabolites using large-scale comparative metabolomics analysis across a database of 10,498 extracts generated from 463 strains. We apply the DeepRiPP platform to expand the landscape of novel RiPPs encoded within sequenced genomes and to discover 3 novel RiPPs, whose structures are exactly as predicted by our platform. By building on advances in machine learning technologies, DeepRiPP integrates genomic and metabolomic data to guide the isolation of novel RiPPs in an automated manner.},
  chemicals       = {Bacterial Proteins, Biological Products, Peptides},
  citation-subset = {IM},
  completed       = {2020-05-11},
  country         = {United States},
  creationdate    = {2021-03-03T00:00:00},
  doi             = {10.1073/pnas.1901493116},
  file            = {:by-author/M/Merwin/2020_Merwin_371.pdf:PDF},
  issn-linking    = {0027-8424},
  issue           = {1},
  keywords        = {Bacteria; Bacterial Proteins; Biological Products; Biosynthesis; Drug Discovery; Genetics; Genome Mining; Genomics; Isolation & Purification; Machine Learning (ML); Metabolism; Metabolomics; Methods; Natural Products; Peptide Biosynthesis; Peptides; Post-Translational; Protein Processing; RiPPs; Ribosomes; Software},
  nlm-id          = {7505876},
  owner           = {saulius},
  pii             = {1901493116},
  pmc             = {PMC6955231},
  pmid            = {31871149},
  pubmodel        = {Print-Electronic},
  pubstate        = {ppublish},
  revised         = {2020-06-23},
  timestamp       = {2021.03.03},
}

@Article{Cova2019,
  author       = {Cova, Tânia F. G. G. and Pais, Alberto A. C. C.},
  journal      = {Frontiers in chemistry},
  title        = {Deep Learning for Deep Chemistry: Optimizing the Prediction of Chemical Patterns.},
  year         = {2019},
  issn         = {2296-2646},
  pages        = {809},
  volume       = {7},
  abstract     = {Computational Chemistry is currently a synergistic assembly between   calculations, simulation, machine learning (ML) and optimization strategies for describing, solving and predicting chemical data and related phenomena. These include accelerated literature searches, analysis and prediction of physical and quantum chemical properties, transition states, chemical structures, chemical reactions, and also new catalysts and drug candidates. The generalization of scalability to larger chemical problems, rather than specialization, is now the main principle for transforming chemical tasks in multiple fronts, for which systematic and cost-effective solutions have benefited from ML approaches, including those based on deep learning (e.g. quantum chemistry, molecular screening, synthetic route design, catalysis, drug discovery). The latter class of ML algorithms is capable of combining raw input into layers of intermediate features, enabling bench-to-bytes designs with the potential to transform several chemical domains. In this review, the most exciting developments concerning the use of ML in a range of different chemical scenarios are described. A range of different chemical problems and respective rationalization, that have hitherto been inaccessible due to the lack of suitable analysis tools, is thus detailed, evidencing the breadth of potential applications of these emerging multidimensional approaches. Focus is given to the models, algorithms and methods proposed to facilitate research on compound design and synthesis, materials design, prediction of binding, molecular activity, and soft matter behavior. The information produced by pairing Chemistry and ML, through data-driven analyses, neural network predictions and monitoring of chemical systems, allows (i) prompting the ability to understand the complexity of chemical data, (ii) streamlining and designing experiments, (ii) discovering new molecular targets and materials, and also (iv) planning or rethinking forthcoming chemical challenges. In fact, optimization engulfs all these tasks directly.},
  country      = {Switzerland},
  doi          = {10.3389/fchem.2019.00809},
  file         = {:by-author/C/Cova/2019_Cova_809.pdf:PDF},
  issn-linking = {2296-2646},
  keywords     = {Chemistry; Deep-learning; Machine-learning; Models; Molecular Simulation; Optimization},
  nlm-id       = {101627988},
  owner        = {saulius},
  pmc          = {PMC6988795},
  pmid         = {32039134},
  pubmodel     = {Electronic-eCollection},
  pubstate     = {epublish},
  revised      = {2020-09-28},
  timestamp = {2021.03.03},
  creationdate = {2021-03-03T00:00:00},
}

@Article{Polykovskiy2020,
  author    = {Daniil Polykovskiy and Alexander Zhebrak and Benjamin Sanchez-Lengeling and Sergey Golovanov and Oktai Tatanov and Stanislav Belyaev and Rauf Kurbanov and Aleksey Artamonov and Vladimir Aladinskiy and Mark Veselov and Artur Kadurin and Simon Johansson and Hongming Chen and Sergey Nikolenko and Al{\'{a}}n Aspuru-Guzik and Alex Zhavoronkov},
  journal   = {Frontiers in Pharmacology},
  title     = {Molecular Sets ({MOSES}): A Benchmarking Platform for Molecular Generation Models},
  year      = {2020},
  month     = {dec},
  pages     = {1--10},
  volume    = {11},
  doi       = {10.3389/fphar.2020.565644},
  file      = {:by-author/P/Polykovskiy/2020_Polykovskiy_1.pdf:PDF},
  keywords  = {Chemiinformatics; Molecular Geometry},
  owner     = {saulius},
  publisher = {Frontiers Media {SA}},
  timestamp = {2021.03.03},
  creationdate = {2021-03-03T00:00:00},
}

@Article{Kim2020,
  author           = {Kim, Hyunho and Kim, Eunyoung and Lee, Ingoo and Bae, Bongsung and Park, Minsu and Nam, Hojung},
  journal          = {Biotechnology and bioprocess engineering : BBE},
  title            = {Artificial intelligence in drug discovery: a comprehensive review of data-driven and machine learning approaches},
  year             = {2020},
  issn             = {1226-8372},
  pages            = {895--930},
  volume           = {25},
  abstract         = {As expenditure on drug development increases exponentially, the overall drug discovery process requires a sustainable revolution. Since artificial intelligence (AI) is leading the fourth industrial revolution, AI can be considered as a viable solution for unstable drug research and development. Generally, AI is applied to fields with sufficient data such as computer vision and natural language processing, but there are many efforts to revolutionize the existing drug discovery process by applying AI. This review provides a comprehensive, organized summary of the recent research trends in AI-guided drug discovery process including target identification, hit identification, ADMET prediction, lead optimization, and drug repositioning. The main data sources in each field are also summarized in this review. In addition, an in-depth analysis of the remaining challenges and limitations will be provided, and proposals for promising future directions in each of the aforementioned areas.},
  country          = {Korea (South)},
  creationdate     = {2021-03-03T00:00:00},
  doi              = {10.1007/s12257-020-0049-y},
  file             = {:by-author/K/Kim/2020_Kim_895.pdf:PDF},
  issn-linking     = {1226-8372},
  issue            = {6},
  keywords         = {Artificial Intelligence (AI); Data-driven; Drug Discovery; Machine Learning (ML)},
  modificationdate = {2024-01-08T15:47:34},
  nlm-id           = {101263166},
  owner            = {saulius},
  pii              = {49},
  pmc              = {PMC7790479},
  pmid             = {33437151},
  pubmodel         = {Print-Electronic},
  pubstate         = {ppublish},
  revised          = {2021-01-14},
  timestamp        = {2021.03.03},
}

@Article{Fjodorova2020,
  author       = {Fjodorova, Natalja and Novič, Marjana and Venko, Katja and Rasulev, Bakhtiyor},
  journal      = {Nanomaterials (Basel, Switzerland)},
  title        = {A Comprehensive Cheminformatics Analysis of Structural Features Affecting the Binding Activity of Fullerene Derivatives.},
  year         = {2020},
  issn         = {2079-4991},
  month        = jan,
  pages        = {10010090},
  volume       = {10},
  abstract     = {Nanostructures like fullerene derivatives (FDs) belong to a new family of nano-sized organic compounds. Fullerenes have found a widespread application in material science, pharmaceutical, biomedical, and medical fields. This fact caused the importance of the study of pharmacological as well as toxicological properties of this relatively new family of chemicals. In this work, a large set of 169 FDs and their binding activity to 1117 proteins was investigated. The structure-based descriptors widely used in drug design (so-called drug-like descriptors) were applied to understand cheminformatics characteristics related to the binding activity of fullerene nanostructures. Investigation of applied descriptors demonstrated that polarizability, topological diameter, and rotatable bonds play the most significant role in the binding activity of FDs. Various cheminformatics methods, including the counter propagation artificial neural network (CPANN) and Kohonen network as visualization tool, were applied. The results of this study can be applied to compose the priority list for testing in risk assessment related to the toxicological properties of FDs. The pharmacologist can filter the data from the heat map to view all possible side effects for selected FDs.},
  country      = {Switzerland},
  doi          = {10.3390/nano10010090},
  file         = {:by-author/F/Fjodorova/2020_Fjodorova_10010090.pdf:PDF},
  issn-linking = {2079-4991},
  issue        = {1},
  keywords     = {Binding Activity; Cheminformatics; Drug-like Descriptors; Fullerene Derivatives; Hydrogenation; Neural Networks Modelling; Pharmacology; Toxicology},
  nlm-id       = {101610216},
  owner        = {saulius},
  pii          = {E90},
  pmc          = {PMC7023229},
  pmid         = {31906497},
  pubmodel     = {Electronic},
  pubstate     = {epublish},
  revised      = {2020-09-28},
  timestamp = {2021.03.03},
  creationdate = {2021-03-03T00:00:00},
}

@Article{Robinson2020,
  author          = {Robinson, Matthew C. and Glen, Robert C. and Lee, Alpha A.},
  journal         = {Journal of computer-aided molecular design},
  title           = {Validating the validation: reanalyzing a large-scale comparison of deep learning and machine learning models for bioactivity prediction.},
  year            = {2020},
  issn            = {1573-4951},
  month           = jul,
  pages           = {717--730},
  volume          = {34},
  abstract        = {Machine learning methods may have the potential to significantly accelerate drug discovery. However, the increasing rate of new methodological approaches being published in the literature raises the fundamental question of how models should be benchmarked and validated. We reanalyze the data generated by a recently published large-scale comparison of machine learning models for bioactivity prediction and arrive at a somewhat different conclusion. We show that the performance of support vector machines is competitive with that of deep learning methods. Additionally, using a series of numerical experiments, we question the relevance of area under the receiver operating characteristic curve as a metric in virtual screening. We further suggest that area under the precision-recall curve should be used in conjunction with the receiver operating characteristic curve. Our numerical experiments also highlight challenges in estimating the uncertainty in model performance via scaffold-split nested cross validation.},
  citation-subset = {IM},
  country         = {Netherlands},
  doi             = {10.1007/s10822-019-00274-0},
  file            = {:by-author/R/Robinson/2020_Robinson_717.pdf:PDF},
  issn-linking    = {0920-654X},
  issue           = {7},
  keywords        = {Chemiinformatics; Machine Learning (ML); Validation},
  nlm-id          = {8710425},
  owner           = {saulius},
  pii             = {10.1007/s10822-019-00274-0},
  pmc             = {PMC7292817},
  pmid            = {31960253},
  pubmodel        = {Print-Electronic},
  pubstate        = {ppublish},
  revised         = {2021-01-11},
  timestamp = {2021.03.03},
  creationdate = {2021-03-03T00:00:00},
}

@Article{Mouchlis2020,
  author          = {Mouchlis, Varnavas D. and Melagraki, Georgia and Zacharia, Lefteris C. and Afantitis, Antreas},
  journal         = {International journal of molecular sciences},
  title           = {Computer-Aided Drug Design of β-Secretase, γ-Secretase and Anti-Tau Inhibitors for the Discovery of Novel Alzheimer's Therapeutics.},
  year            = {2020},
  issn            = {1422-0067},
  month           = jan,
  pages           = {703},
  volume          = {21},
  abstract        = {Aging-associated neurodegenerative diseases, which are characterized by progressive neuronal death and synapses loss in human brain, are rapidly growing affecting millions of people globally. Alzheimer's is the most common neurodegenerative disease and it can be caused by genetic and environmental risk factors. This review describes the amyloid-β and Tau hypotheses leading to amyloid plaques and neurofibrillary tangles, respectively which are the predominant pathways for the development of anti-Alzheimer's small molecule inhibitors. The function and structure of the druggable targets of these two pathways including β-secretase, γ-secretase, and Tau are discussed in this review article. Computer-Aided Drug Design including computational structure-based design and ligand-based design have been employed successfully to develop inhibitors for biomolecular targets involved in Alzheimer's. The application of computational molecular modeling for the discovery of small molecule inhibitors and modulators for β-secretase and γ-secretase is summarized. Examples of computational approaches employed for the development of anti-amyloid aggregation and anti-Tau phosphorylation, proteolysis and aggregation inhibitors are also reported.},
  chemicals       = {Ligands, tau Proteins, Amyloid Precursor Protein Secretases, Aspartic Acid Endopeptidases, BACE1 protein, human},
  citation-subset = {IM},
  completed       = {2020-11-12},
  country         = {Switzerland},
  creationdate    = {2021-03-03T00:00:00},
  doi             = {10.3390/ijms21030703},
  file            = {:by-author/M/Mouchlis/2020_Mouchlis_703.pdf:PDF},
  issn-linking    = {1422-0067},
  issue           = {3},
  keywords        = {Alzheimer Disease; Alzheimer’s Disease; Amyloid; Amyloid Precursor Protein Secretases; Animals; Aspartic Acid Endopeptidases; Brain; Cheminformatics; Chemistry; Computational Ligand-based Design; Computational Structure-based Design; Computer-aided Drug Design; Drug Design; Drug Effects; Drug Therapy; Humans; Ligands; Metabolism; Molecular Docking; Molecular Docking Simulation; Molecular Dynamics (MD); Molecular Dynamics Simulation; Neurodegenerative Diseases; Neurofibrillary Tangles; Phosphorylation; Plaque; Protein Conformation; Quantitative Structure-activity Relationship (QSAR); Tau; Tau Proteins; β-secretase; γ-secretase},
  nlm-id          = {101092791},
  owner           = {saulius},
  pii             = {E703},
  pmc             = {PMC7038192},
  pmid            = {31973122},
  pubmodel        = {Electronic},
  pubstate        = {epublish},
  revised         = {2020-11-12},
  timestamp       = {2021.03.03},
}

@Article{Parks2020,
  author          = {Parks, Conor D. and Gaieb, Zied and Chiu, Michael and Yang, Huanwang and Shao, Chenghua and Walters, W. Patrick and Jansen, Johanna M. and McGaughey, Georgia and Lewis, Richard A. and Bembenek, Scott D. and Ameriks, Michael K. and Mirzadegan, Tara and Burley, Stephen K. and Amaro, Rommie E. and Gilson, Michael K.},
  journal         = {Journal of computer-aided molecular design},
  title           = {D3R grand challenge 4: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies.},
  year            = {2020},
  issn            = {1573-4951},
  month           = feb,
  pages           = {99--119},
  volume          = {34},
  abstract        = {The Drug Design Data Resource (D3R) aims to identify best practice methods for computer aided drug design through blinded ligand pose prediction and affinity challenges. Herein, we report on the results of Grand Challenge 4 (GC4). GC4 focused on proteins beta secretase 1 and Cathepsin S, and was run in an analogous manner to prior challenges. In Stage 1, participant ability to predict the pose and affinity of BACE1 ligands were assessed. Following the completion of Stage 1, all BACE1 co-crystal structures were released, and Stage 2 tested affinity rankings with co-crystal structures. We provide an analysis of the results and discuss insights into determined best practice methods.},
  citation-subset = {IM},
  country         = {Netherlands},
  doi             = {10.1007/s10822-020-00289-y},
  file            = {:by-author/P/Parks/2020_Parks_99.pdf:PDF},
  issn-linking    = {0920-654X},
  issue           = {2},
  keywords        = {Blinded Prediction Challenge; D3R; Docking; Free-energy; Ligand Ranking; Scoring},
  mid             = {NIHMS1551505},
  nlm-id          = {8710425},
  owner           = {saulius},
  pii             = {10.1007/s10822-020-00289-y},
  pmc             = {PMC7261493},
  pmid            = {31974851},
  pubmodel        = {Print-Electronic},
  pubstate        = {ppublish},
  revised         = {2021-02-01},
  timestamp = {2021.03.03},
  creationdate = {2021-03-03T00:00:00},
}

@Article{Zhang2020,
  author          = {Zhang, Xiayin and Zhang, Kai and Lin, Duoru and Zhu, Yi and Chen, Chuan and He, Lin and Guo, Xusen and Chen, Kexin and Wang, Ruixin and Liu, Zhenzhen and Wu, Xiaohang and Long, Erping and Huang, Kai and He, Zhiqiang and Liu, Xiyang and Lin, Haotian},
  journal         = {GigaScience},
  title           = {Artificial intelligence deciphers codes for color and odor perceptions based on large-scale chemoinformatic data.},
  year            = {2020},
  issn            = {2047-217X},
  month           = feb,
  pages           = {1--9},
  volume          = {9},
  abstract        = {Color vision is the ability to detect, distinguish, and analyze the wavelength distributions of light independent of the total intensity. It mediates the interaction between an organism and its environment from multiple important aspects. However, the physicochemical basis of color coding has not been explored completely, and how color perception is integrated with other sensory input, typically odor, is unclear. Here, we developed an artificial intelligence platform to train algorithms for distinguishing color and odor based on the large-scale physicochemical features of 1,267 and 598 structurally diverse molecules, respectively. The predictive accuracies achieved using the random forest and deep belief network for the prediction of color were 100% and 95.23% ± 0.40% (mean ± SD), respectively. The predictive accuracies achieved using the random forest and deep belief network for the prediction of odor were 93.40% ± 0.31% and 94.75% ± 0.44% (mean ± SD), respectively. Twenty-four physicochemical features were sufficient for the accurate prediction of color, while 39 physicochemical features were sufficient for the accurate prediction of odor. A positive correlation between the color-coding and odor-coding properties of the molecules was predicted. A group of descriptors was found to interlink prominently in color and odor perceptions. Our random forest model and deep belief network accurately predicted the colors and odors of structurally diverse molecules. These findings extend our understanding of the molecular and structural basis of color vision and reveal the interrelationship between color and odor perceptions in nature.},
  citation-subset = {IM},
  completed       = {2021-01-27},
  country         = {United States},
  doi             = {10.1093/gigascience/giaa011},
  file            = {:by-author/Z/Zhang/2020_Zhang_1.pdf:PDF},
  issn-linking    = {2047-217X},
  issue           = {2},
  keywords        = {Artificial Intelligence (AI); Cheminformatics; Color; Color Perception; Deep Belief Network; Methods; Odor Perception; Odorants; Physicochemical Features; Random Forest; Software},
  nlm-id          = {101596872},
  owner           = {saulius},
  pii             = {giaa011},
  pmc             = {PMC7043059},
  pmid            = {32101298},
  pubmodel        = {Print},
  pubstate        = {ppublish},
  revised         = {2021-01-27},
  timestamp = {2021.03.03},
  creationdate = {2021-03-03T00:00:00},
}

@Article{Playe2020,
  author       = {Playe, Benoit and Stoven, Veronique},
  journal      = {Journal of cheminformatics},
  title        = {Evaluation of deep and shallow learning methods in chemogenomics for the prediction of drugs specificity.},
  year         = {2020},
  issn         = {1758-2946},
  month        = feb,
  pages        = {11},
  volume       = {12},
  abstract     = {Chemogenomics, also called proteochemometrics, covers a range of computational methods that can be used to predict protein-ligand interactions at large scales in the protein and chemical spaces. They differ from more classical ligand-based methods (also called QSAR) that predict ligands for a given protein receptor. In the context of drug discovery process, chemogenomics allows to tackle the question of predicting off-target proteins for drug candidates, one of the main causes of undesirable side-effects and failure within drugs development processes. The present study compares shallow and deep machine-learning approaches for chemogenomics, and explores data augmentation techniques for deep learning algorithms in chemogenomics. Shallow machine-learning algorithms rely on expert-based chemical and protein descriptors, while recent developments in deep learning algorithms enable to learn abstract numerical representations of molecular graphs and protein sequences, in order to optimise the performance of the prediction task. We first propose a formulation of chemogenomics with deep learning, called the chemogenomic neural network (CN), as a feed-forward neural network taking as input the combination of molecule and protein representations learnt by molecular graph and protein sequence encoders. We show that, on large datasets, the deep learning CN model outperforms state-of-the-art shallow methods, and competes with deep methods with expert-based descriptors. However, on small datasets, shallow methods present better prediction performance than deep learning methods. Then, we evaluate data augmentation techniques, namely multi-view and transfer learning, to improve the prediction performance of the chemogenomic neural network. We conclude that a promising research direction is to integrate heterogeneous sources of data such as auxiliary tasks for which large datasets are available, or independently, multiple molecule and protein attribute views.},
  country      = {England},
  doi          = {10.1186/s13321-020-0413-0},
  file         = {:by-author/P/Playe/2020_Playe_11.pdf:PDF},
  issn-linking = {1758-2946},
  issue        = {1},
  keywords     = {Chemogenomics; Deep Learning (DL); Drug Virtual Screening; Graph Neural Networks (GNN)},
  nlm-id       = {101516718},
  owner        = {saulius},
  pii          = {10.1186/s13321-020-0413-0},
  pmc          = {PMC7011501},
  pmid         = {33431042},
  pubmodel     = {Electronic},
  pubstate     = {epublish},
  revised      = {2021-01-15},
  timestamp = {2021.03.03},
  creationdate = {2021-03-03T00:00:00},
}

@Article{Baltruschat2020,
  author          = {Baltruschat, Marcel and Czodrowski, Paul},
  journal         = {{F1000Research}},
  title           = {Machine learning meets {pK}},
  year            = {2020},
  issn            = {2046-1402},
  pages           = {113},
  volume          = {9},
  abstract        = {We present a small molecule pK   prediction tool entirely written in Python. It predicts the macroscopic pK   value and is trained on a literature compilation of monoprotic compounds. Different machine learning models were tested and random forest performed best given a five-fold cross-validation (mean absolute error=0.682, root mean squared error=1.032, correlation coefficient r   =0.82). We test our model on two external validation sets, where our model performs comparable to Marvin and is better than a recently published open source model. Our Python tool and all data is freely available at https://github.com/czodrowskilab/Machine-learning-meets-pKa.},
  citation-subset = {IM},
  completed       = {2020-07-27},
  country         = {England},
  doi             = {10.12688/f1000research.22090.2},
  file            = {:by-author/B/Baltruschat/2020_Baltruschat_113.pdf:PDF},
  issn-linking    = {2046-1402},
  keywords        = {Chemical; Dissociation; Kinetics; Machine Learning (ML); Models; PKa Value; Protonation; Software},
  nlm-id          = {101594320},
  owner           = {saulius},
  pii             = {Chem Inf Sci-113},
  pmc             = {PMC7096188},
  pmid            = {32226607},
  pubmodel        = {Electronic-eCollection},
  pubstate        = {epublish},
  revised         = {2021-01-10},
  timestamp = {2021.03.03},
  creationdate = {2021-03-03T00:00:00},
}

@Article{Rayhan2020,
  author       = {Rayhan, Farshid and Ahmed, Sajid and Mousavian, Zaynab and Farid, Dewan Md and Shatabda, Swakkhar},
  journal      = {Heliyon},
  title        = {FRnet-DTI: Deep convolutional neural network for drug-target interaction prediction.},
  year         = {2020},
  issn         = {2405-8440},
  month        = mar,
  pages        = {e03444},
  volume       = {6},
  abstract     = {The task of drug-target interaction prediction holds significant importance in pharmacology and therapeutic drug design. In this paper, we present FRnet-DTI, an auto-encoder based feature manipulation and a convolutional neural network based classifier for drug target interaction prediction. Two convolutional neural networks are proposed: FRnet-Encode and FRnet-Predict. Here, one model is used for feature manipulation and the other one for classification. Using the first method FRnet-Encode, we generate 4096 features for each of the instances in each of the datasets and use the second method, FRnet-Predict, to identify interaction probability employing those features. We have tested our method on four gold standard datasets extensively used by other researchers. Experimental results shows that our method significantly improves over the state-of-the-art method on three out of four drug-target interaction gold standard datasets on both area under curve for Receiver Operating Characteristic (auROC) and area under Precision Recall curve (auPR) metric. We also introduce twenty new potential drug-target pairs for interaction based on high prediction scores. The source codes and implementation details of our methods are available from https://github.com/farshidrayhanuiu/FRnet-DTI/ and also readily available to use as an web application from http://farshidrayhan.pythonanywhere.com/FRnet-DTI/.},
  country      = {England},
  doi          = {10.1016/j.heliyon.2020.e03444},
  file         = {:by-author/R/Rayhan/2020_Rayhan_3444.pdf:PDF},
  issn-linking = {2405-8440},
  issue        = {3},
  keywords     = {Bioinformatics; Class Imbalance; Classification; Computer Science (CS); Drug-Target; Ensemble Classifier; Feature Engineering},
  nlm-id       = {101672560},
  owner        = {saulius},
  pii          = {e03444},
  pmc          = {PMC7052404},
  pmid         = {32154410},
  pubmodel     = {Electronic-eCollection},
  pubstate     = {epublish},
  revised      = {2020-09-28},
  timestamp = {2021.03.03},
  creationdate = {2021-03-03T00:00:00},
}

@Article{Karlov2020,
  author       = {Karlov, Dmitry S. and Sosnin, Sergey and Fedorov, Maxim V. and Popov, Petr},
  journal      = {ACS omega},
  title        = {graphDelta: MPNN Scoring Function for the Affinity Prediction of Protein-Ligand Complexes.},
  year         = {2020},
  issn         = {2470-1343},
  month        = mar,
  pages        = {5150--5159},
  volume       = {5},
  abstract     = {In this work, we present graph-convolutional neural networks for the prediction of binding constants of protein-ligand complexes. We derived the model using multi task learning, where the target variables are the dissociation constant ( ), inhibition constant ( ), and half maximal inhibitory concentration (IC ). Being rigorously trained on the PDBbind dataset, the model achieves the Pearson correlation coefficient of 0.87 and the RMSE value of 1.05 in pK units, outperforming recently developed 3D convolutional neural network model  .},
  country      = {United States},
  doi          = {10.1021/acsomega.9b04162},
  file         = {:by-author/K/Karlov/2020_Karlov_5150.pdf:PDF},
  issn-linking = {2470-1343},
  issue        = {10},
  nlm-id       = {101691658},
  owner        = {saulius},
  pmc          = {PMC7081425},
  pmid         = {32201802},
  pubmodel     = {Electronic-eCollection},
  pubstate     = {epublish},
  revised      = {2020-09-28},
  timestamp = {2021.03.03},
  creationdate = {2021-03-03T00:00:00},
}

@Article{Lin2020,
  author          = {Lin, Xiaoqian and Li, Xiu and Lin, Xubo},
  journal         = {Molecules (Basel, Switzerland)},
  title           = {A Review on Applications of Computational Methods in Drug Screening and Design.},
  year            = {2020},
  issn            = {1420-3049},
  month           = mar,
  pages           = {1375},
  volume          = {25},
  abstract        = {Drug development is one of the most significant processes in the pharmaceutical industry. Various computational methods have dramatically reduced the time and cost of drug discovery. In this review, we firstly discussed roles of multiscale biomolecular simulations in identifying drug binding sites on the target macromolecule and elucidating drug action mechanisms. Then, virtual screening methods (e.g., molecular docking, pharmacophore modeling, and QSAR) as well as structure- and ligand-based classical/de novo drug design were introduced and discussed. Last, we explored the development of machine learning methods and their applications in aforementioned computational methods to speed up the drug discovery process. Also, several application examples of combining various methods was discussed. A combination of different methods to jointly solve the tough problem at different scales and dimensions will be an inevitable trend in drug screening and design.},
  citation-subset = {IM},
  completed       = {2020-12-16},
  country         = {Switzerland},
  doi             = {10.3390/molecules25061375},
  file            = {:by-author/L/Lin/2020_Lin_1375.pdf:PDF},
  issn-linking    = {1420-3049},
  issue           = {6},
  keywords        = {De Novo Design; Drug Design; Drug Discovery; Machine Learning (ML); Molecular Docking Simulation; Molecular Dynamics Simulation; Multiscale Models; Virtual Screening},
  nlm-id          = {100964009},
  owner           = {saulius},
  pii             = {E1375},
  pmc             = {PMC7144386},
  pmid            = {32197324},
  pubmodel        = {Electronic},
  pubstate        = {epublish},
  revised         = {2020-12-16},
  timestamp = {2021.03.03},
  creationdate = {2021-03-03T00:00:00},
}

@Article{Karpov2020,
  author       = {Karpov, Pavel and Godin, Guillaume and Tetko, Igor V.},
  journal      = {Journal of cheminformatics},
  title        = {Transformer-CNN: Swiss knife for QSAR modeling and interpretation.},
  year         = {2020},
  issn         = {1758-2946},
  month        = mar,
  pages        = {17},
  volume       = {12},
  abstract     = {We present SMILES-embeddings derived from the internal encoder state of a Transformer [1] model trained to canonize SMILES as a Seq2Seq problem. Using a CharNN [2] architecture upon the embeddings results in higher quality interpretable QSAR/QSPR models on diverse benchmark datasets including regression and classification tasks. The proposed Transformer-CNN method uses SMILES augmentation for training and inference, and thus the prognosis is based on an internal consensus. That both the augmentation and transfer learning are based on embeddings allows the method to provide good results for small datasets. We discuss the reasons for such effectiveness and draft future directions for the development of the method. The source code and the embeddings needed to train a QSAR model are available on https://github.com/bigchem/transformer-cnn. The repository also has a standalone program for QSAR prognosis which calculates individual atoms contributions, thus interpreting the model's result. OCHEM [3] environment (https://ochem.eu) hosts the on-line implementation of the method proposed.},
  country      = {England},
  doi          = {10.1186/s13321-020-00423-w},
  file         = {:by-author/K/Karpov/2020_Karpov_17.pdf:PDF},
  issn-linking = {1758-2946},
  issue        = {1},
  keywords     = {Augmentation; Character-based Models; Cheminformatics; Classification; Convolutional Neural Neural Networks; Embeddings; Quantitative Structure-activity Relationship (QSAR); Regression; SMILES; Transformer Model},
  nlm-id       = {101516718},
  owner        = {saulius},
  pii          = {10.1186/s13321-020-00423-w},
  pmc          = {PMC7079452},
  pmid         = {33431004},
  pubmodel     = {Electronic},
  pubstate     = {epublish},
  revised      = {2021-01-15},
  timestamp = {2021.03.03},
  creationdate = {2021-03-03T00:00:00},
}

@InCollection{Miftahutdinov2020,
  author    = {Zulfat Miftahutdinov and Ilseyar Alimova and Elena Tutubalina},
  booktitle = {Lecture Notes in Computer Science},
  publisher = {Springer International Publishing},
  title     = {On Biomedical Named Entity Recognition: Experiments in Interlingual Transfer for Clinical and Social Media Texts},
  year      = {2020},
  pages     = {281--288},
  doi       = {10.1007/978-3-030-45442-5_35},
  file      = {:by-author/M/Miftahutdinov/2020_Miftahutdinov_281.pdf:PDF},
  keywords  = {Artificial Neural Networks (ANN); Chemiinformatics; Machine Learning (ML); NLP; Natural Language Processing; Term Recognition; Text Processing},
  owner     = {saulius},
  timestamp = {2021.03.03},
  creationdate = {2021-03-03T00:00:00},
}

@Article{Harada2020,
  author          = {Harada, Shonosuke and Akita, Hirotaka and Tsubaki, Masashi and Baba, Yukino and Takigawa, Ichigaku and Yamanishi, Yoshihiro and Kashima, Hisashi},
  journal         = {BMC bioinformatics},
  title           = {Dual graph convolutional neural network for predicting chemical networks.},
  year            = {2020},
  issn            = {1471-2105},
  month           = apr,
  pages           = {94},
  volume          = {21},
  abstract        = {Predicting of chemical compounds is one of the fundamental tasks in bioinformatics and chemoinformatics, because it contributes to various applications in metabolic engineering and drug discovery. The recent rapid growth of the amount of available data has enabled applications of computational approaches such as statistical modeling and machine learning method. Both a set of chemical interactions and chemical compound structures are represented as graphs, and various graph-based approaches including graph convolutional neural networks have been successfully applied to chemical network prediction. However, there was no efficient method that can consider the two different types of graphs in an end-to-end manner. We give a new formulation of the chemical network prediction problem as a link prediction problem in a graph of graphs (GoG) which can represent the hierarchical structure consisting of compound graphs and an inter-compound graph. We propose a new graph convolutional neural network architecture called dual graph convolutional network that learns compound representations from both the compound graphs and the inter-compound network in an end-to-end manner. Experiments using four chemical networks with different sparsity levels and degree distributions shows that our dual graph convolution approach achieves high prediction performance in relatively dense networks, while the performance becomes inferior on extremely-sparse networks.},
  citation-subset = {IM},
  completed       = {2020-04-29},
  country         = {England},
  doi             = {10.1186/s12859-020-3378-0},
  file            = {:by-author/H/Harada/2020_Harada_94.pdf:PDF},
  issn-linking    = {1471-2105},
  issue           = {Suppl 3},
  keywords        = {Chemical; Chemical Network Prediction; Computational Biology; Computer; Computer Graphics; Drug Discovery; Graph Convolutional Neural Network; Graph of Graphs; Methods; Models; Neural Networks (NN)},
  nlm-id          = {100965194},
  owner           = {saulius},
  pii             = {10.1186/s12859-020-3378-0},
  pmc             = {PMC7178944},
  pmid            = {32321421},
  pubmodel        = {Electronic},
  pubstate        = {epublish},
  revised         = {2020-04-29},
  timestamp = {2021.03.03},
  creationdate = {2021-03-03T00:00:00},
}

@Article{RodriguezPerez2020,
  author          = {Rodríguez-Pérez, Raquel and Bajorath, Jürgen},
  journal         = {Journal of computer-aided molecular design},
  title           = {Interpretation of machine learning models using shapley values: application to compound potency and multi-target activity predictions.},
  year            = {2020},
  issn            = {1573-4951},
  month           = oct,
  pages           = {1013--1026},
  volume          = {34},
  abstract        = {Difficulties in interpreting machine learning (ML) models and their predictions limit the practical applicability of and confidence in ML in pharmaceutical research. There is a need for agnostic approaches aiding in the interpretation of ML models regardless of their complexity that is also applicable to deep neural network (DNN) architectures and model ensembles. To these ends, the SHapley Additive exPlanations (SHAP) methodology has recently been introduced. The SHAP approach enables the identification and prioritization of features that determine compound classification and activity prediction using any ML model. Herein, we further extend the evaluation of the SHAP methodology by investigating a variant for exact calculation of Shapley values for decision tree methods and systematically compare this variant in compound activity and potency value predictions with the model-independent SHAP method. Moreover, new applications of the SHAP analysis approach are presented including interpretation of DNN models for the generation of multi-target activity profiles and ensemble regression models for potency prediction.},
  citation-subset = {IM},
  country         = {Netherlands},
  doi             = {10.1007/s10822-020-00314-0},
  file            = {:by-author/R/Rodríguez-Pérez/2020_Rodríguez-Pérez_1013.pdf:PDF},
  issn-linking    = {0920-654X},
  issue           = {10},
  keywords        = {Black Box Character; Compound Activity; Compound Potency Prediction; Feature Importance; Machine Learning (ML); Model Interpretation; Multi-target Modeling; Shapley Values; Structure-activity Relationships},
  nlm-id          = {8710425},
  owner           = {saulius},
  pii             = {10.1007/s10822-020-00314-0},
  pmc             = {PMC7449951},
  pmid            = {32361862},
  pubmodel        = {Print-Electronic},
  pubstate        = {ppublish},
  revised         = {2021-02-10},
  timestamp = {2021.03.03},
  creationdate = {2021-03-03T00:00:00},
}

@Article{JimenezLuna2020,
  author          = {Jiménez-Luna, José and Cuzzolin, Alberto and Bolcato, Giovanni and Sturlese, Mattia and Moro, Stefano},
  journal         = {Molecules (Basel, Switzerland)},
  title           = {A Deep-Learning Approach toward Rational Molecular Docking Protocol Selection.},
  year            = {2020},
  issn            = {1420-3049},
  month           = may,
  pages           = {2487},
  volume          = {25},
  abstract        = {While a plethora of different protein-ligand docking protocols have been developed over the past twenty years, their performances greatly depend on the provided input protein-ligand pair. In this study, we developed a machine-learning model that uses a combination of convolutional and fully connected neural networks for the task of predicting the performance of several popular docking protocols given a protein structure and a small compound. We also rigorously evaluated the performance of our model using a widely available database of protein-ligand complexes and different types of data splits. We further open-source all code related to this study so that potential users can make informed selections on which protocol is best suited for their particular protein-ligand pair.},
  citation-subset = {IM},
  completed       = {2021-03-01},
  country         = {Switzerland},
  doi             = {10.3390/molecules25112487},
  file            = {:by-author/J/Jiménez-Luna/2020_Jiménez-Luna_2487.pdf:PDF},
  issn-linking    = {1420-3049},
  issue           = {11},
  keywords        = {Cheminformatics; Chemoinformatics; Databases; Deep Learning (DL); Machine Learning (ML); Molecular Docking; Molecular Docking Simulation; Protein; Structural Biology},
  nlm-id          = {100964009},
  owner           = {saulius},
  pii             = {E2487},
  pmc             = {PMC7321124},
  pmid            = {32471211},
  pubmodel        = {Electronic},
  pubstate        = {epublish},
  revised         = {2021-03-01},
  timestamp = {2021.03.03},
  creationdate = {2021-03-03T00:00:00},
}

@Article{Terayama2020,
  author       = {Terayama, Kei and Sumita, Masato and Tamura, Ryo and Payne, Daniel T. and Chahal, Mandeep K. and Ishihara, Shinsuke and Tsuda, Koji},
  journal      = {Chemical science},
  title        = {Pushing property limits in materials discovery , javax.xml.bind.JAXBElement@116e1f08, boundless objective-free exploration.},
  year         = {2020},
  issn         = {2041-6520},
  month        = jun,
  pages        = {5959--5968},
  volume       = {11},
  abstract     = {Materials chemists develop chemical compounds to meet often conflicting demands of industrial applications. This process may not be properly modeled by black-box optimization because the target property is not well defined in some cases. Herein, we propose a new algorithm for automated materials discovery called BoundLess Objective-free eXploration (BLOX) that uses a novel criterion based on kernel-based Stein discrepancy in the property space. Unlike other objective-free exploration methods, a boundary for the materials properties is not needed; hence, BLOX is suitable for open-ended scientific endeavors. We demonstrate the effectiveness of BLOX by finding light-absorbing molecules from a drug database. Our goal is to minimize the number of density functional theory calculations required to discover out-of-trend compounds in the intensity-wavelength property space. Using absorption spectroscopy, we experimentally verified that eight compounds identified as outstanding exhibit the expected optical properties. Our results show that BLOX is useful for chemical repurposing, and we expect this search method to have numerous applications in various scientific disciplines.},
  country      = {England},
  doi          = {10.1039/d0sc00982b},
  file         = {:by-author/T/Terayama/2020_Terayama_5959_suppl.pdf:PDF;:by-author/T/Terayama/2020_Terayama_5959.pdf:PDF},
  issn-linking = {2041-6520},
  issue        = {23},
  nlm-id       = {101545951},
  owner        = {saulius},
  pii          = {d0sc00982b},
  pmc          = {PMC7409358},
  pmid         = {32832058},
  pubmodel     = {Electronic-eCollection},
  pubstate     = {epublish},
  revised      = {2020-09-28},
  timestamp = {2021.03.03},
  creationdate = {2021-03-03T00:00:00},
}

@Article{Lin2020a,
  author          = {Lin, Eugene and Lin, Chieh-Hsin and Lane, Hsien-Yuan},
  journal         = {Molecules (Basel, Switzerland)},
  title           = {Relevant Applications of Generative Adversarial Networks in Drug Design and Discovery: Molecular Design, Dimensionality Reduction, and Peptide and Protein Design.},
  year            = {2020},
  issn            = {1420-3049},
  month           = jul,
  pages           = {3250},
  volume          = {25},
  abstract        = {A growing body of evidence now suggests that artificial intelligence and machine learning techniques can serve as an indispensable foundation for the process of drug design and discovery. In light of latest advancements in computing technologies, deep learning algorithms are being created during the development of clinically useful drugs for treatment of a number of diseases. In this review, we focus on the latest developments for three particular arenas in drug design and discovery research using deep learning approaches, such as generative adversarial network (GAN) frameworks. Firstly, we review drug design and discovery studies that leverage various GAN techniques to assess one main application such as molecular   design in drug design and discovery. In addition, we describe various GAN models to fulfill the dimension reduction task of single-cell data in the preclinical stage of the drug development pipeline. Furthermore, we depict several studies in   peptide and protein design using GAN frameworks. Moreover, we outline the limitations in regard to the previous drug design and discovery studies using GAN models. Finally, we present a discussion of directions and challenges for future research.},
  chemicals       = {Peptides, Proteins},
  citation-subset = {IM},
  completed       = {2021-02-26},
  country         = {Switzerland},
  creationdate    = {2021-03-03T00:00:00},
  doi             = {10.3390/molecules25143250},
  file            = {:by-author/L/Lin/2020_Lin_3250.pdf:PDF},
  issn-linking    = {1420-3049},
  issue           = {14},
  keywords        = {Algorithms; Artificial Intelligence (AI); Chemical Synthesis; Chemistry; Computer; De Novo Peptide and Protein Design; Deep Learning (DL); Dimension Reduction; Drug Design; Drug Discovery; Generative Adversarial Networks (GAN); Humans; Machine Learning (ML); Molecular de Novo Design; Neural Networks (NN); Peptides; Proteins; Single-cell RNA Sequencing; Therapeutic Use},
  nlm-id          = {100964009},
  owner           = {saulius},
  pii             = {E3250},
  pmc             = {PMC7397124},
  pmid            = {32708785},
  pubmodel        = {Electronic},
  pubstate        = {epublish},
  revised         = {2021-02-26},
  timestamp       = {2021.03.03},
}

@Article{Bai2020,
  author          = {Bai, Qifeng and Tan, Shuoyan and Xu, Tingyang and Liu, Huanxiang and Huang, Junzhou and Yao, Xiaojun},
  journal         = {Briefings in bioinformatics},
  title           = {MolAICal: a soft tool for 3D drug design of protein targets by artificial intelligence and classical algorithm.},
  year            = {2020},
  issn            = {1477-4054},
  month           = aug,
  pages           = {1--12},
  abstract        = {Deep learning is an important branch of artificial intelligence that has been successfully applied into medicine and two-dimensional ligand design. The three-dimensional (3D) ligand generation in the 3D pocket of protein target is an interesting and challenging issue for drug design by deep learning. Here, the MolAICal software is introduced to supply a way for generating 3D drugs in the 3D pocket of protein targets by combining with merits of deep learning model and classical algorithm. The MolAICal software mainly contains two modules for 3D drug design. In the first module of MolAICal, it employs the genetic algorithm, deep learning model trained by FDA-approved drug fragments and Vinardo score fitting on the basis of PDBbind database for drug design. In the second module, it uses deep learning generative model trained by drug-like molecules of ZINC database and molecular docking invoked by Autodock Vina automatically. Besides, the Lipinski's rule of five, Pan-assay interference compounds (PAINS), synthetic accessibility (SA) and other user-defined rules are introduced for filtering out unwanted ligands in MolAICal. To show the drug design modules of MolAICal, the membrane protein glucagon receptor and non-membrane protein SARS-CoV-2 main protease are chosen as the investigative drug targets. The results show MolAICal can generate the various and novel ligands with good binding scores and appropriate XLOGP values. We believe that MolAICal can use the advantages of deep learning model and classical programming for designing 3D drugs in protein pocket. MolAICal is freely for any nonprofit purpose and accessible at https://molaical.github.io.},
  citation-subset = {IM},
  country         = {England},
  doi             = {10.1093/bib/bbaa161},
  file            = {:by-author/B/Bai/2020_Bai_1.pdf:PDF},
  issn-linking    = {1467-5463},
  keywords        = {Artificial Intelligence (AI); De Novo Drug Design; Drug Design; GCGR; SARS-CoV-2 Main Protease; Virtual Screening},
  nlm-id          = {100912837},
  owner           = {saulius},
  pii             = {bbaa161},
  pmc             = {PMC7454275},
  pmid            = {32778891},
  pubmodel        = {Print-Electronic},
  pubstate        = {aheadofprint},
  revised         = {2020-09-01},
  timestamp = {2021.03.03},
  creationdate = {2021-03-03T00:00:00},
}

@Article{Snow2020,
  author          = {Snow, Oliver and Lallous, Nada and Ester, Martin and Cherkasov, Artem},
  journal         = {International journal of molecular sciences},
  title           = {Deep Learning Modeling of Androgen Receptor Responses to Prostate Cancer Therapies.},
  year            = {2020},
  issn            = {1422-0067},
  month           = aug,
  pages           = {5847},
  volume          = {21},
  abstract        = {Gain-of-function mutations in human androgen receptor (AR) are among the major causes of drug resistance in prostate cancer (PCa). Identifying mutations that cause resistant phenotype is of critical importance for guiding treatment protocols, as well as for designing drugs that do not elicit adverse responses. However, experimental characterization of these mutations is time consuming and costly; thus, predictive models are needed to anticipate resistant mutations and to guide the drug discovery process. In this work, we leverage experimental data collected on 68 AR mutants, either observed in the clinic or described in the literature, to train a deep neural network (DNN) that predicts the response of these mutants to currently used and experimental anti-androgens and testosterone. We demonstrate that the use of this DNN, with general 2D descriptors, provides a more accurate prediction of the biological outcome (inhibition, activation, no-response, mixed-response) in AR mutant-drug pairs compared to other machine learning approaches. Finally, the developed approach was used to make predictions of AR mutant response to the latest AR inhibitor darolutamide, which were then validated by in-vitro experiments.},
  chemicals       = {Androgen Receptor Antagonists, Receptors, Androgen},
  citation-subset = {IM},
  completed       = {2021-02-18},
  country         = {Switzerland},
  creationdate    = {2021-03-03T00:00:00},
  doi             = {10.3390/ijms21165847},
  file            = {:by-author/S/Snow/2020_Snow_5847.pdf:PDF},
  issn-linking    = {1422-0067},
  issue           = {16},
  keywords        = {Androgen; Androgen Receptor; Androgen Receptor Antagonists; Cell Line; Chemistry; Computer; Deep Learning (DL); Drug Effects; Drug Therapy; Genetic; Genetics; Humans; Male; Metabolism; Mutation; Neural Networks (NN); Pharmacology; Prostate Cancer; Prostatic Neoplasms; Proteochemometrics; ROC Curve; Receptors; Transcription; Tumor},
  nlm-id          = {101092791},
  owner           = {saulius},
  pii             = {E5847},
  pmc             = {PMC7461580},
  pmid            = {32823970},
  pubmodel        = {Electronic},
  pubstate        = {epublish},
  revised         = {2021-02-18},
  timestamp       = {2021.03.03},
}

@Article{Chen2020,
  author          = {Chen, Ya and Kirchmair, Johannes},
  journal         = {Molecular informatics},
  title           = {Cheminformatics in Natural Product-based Drug Discovery.},
  year            = {2020},
  issn            = {1868-1751},
  month           = dec,
  pages           = {e2000171},
  volume          = {39},
  abstract        = {This review seeks to provide a timely survey of the scope and limitations of cheminformatics methods in natural product-based drug discovery. Following an overview of data resources of chemical, biological and structural information on natural products, we discuss, among other aspects, in silico methods for (i) data curation and natural products dereplication, (ii) analysis, visualization, navigation and comparison of the chemical space, (iii) quantification of natural product-likeness, (iv) prediction of the bioactivities (virtual screening, target prediction), ADME and safety profiles (toxicity) of natural products, (v) natural products-inspired de novo design and (vi) prediction of natural products prone to cause interference with biological assays. Among the many methods discussed are rule-based, similarity-based, shape-based, pharmacophore-based and network-based approaches, docking and machine learning methods.},
  citation-subset = {IM},
  country         = {Germany},
  doi             = {10.1002/minf.202000171},
  file            = {:by-author/C/Chen/2020_Chen_2000171.pdf:PDF},
  issn-linking    = {1868-1743},
  issue           = {12},
  keywords        = {Cheminformatics; Databases; Drug Discovery; In Silico Methods; Natural Products},
  nlm-id          = {101529315},
  owner           = {saulius},
  pmc             = {PMC7757247},
  pmid            = {32725781},
  pubmodel        = {Print-Electronic},
  pubstate        = {ppublish},
  revised         = {2021-01-08},
  timestamp = {2021.03.03},
  creationdate = {2021-03-03T00:00:00},
}

@Article{Mendolia2020,
  author          = {Mendolia, Isabella and Contino, Salvatore and Perricone, Ugo and Ardizzone, Edoardo and Pirrone, Roberto},
  journal         = {BMC bioinformatics},
  title           = {Convolutional architectures for virtual screening.},
  year            = {2020},
  issn            = {1471-2105},
  month           = sep,
  pages           = {310},
  volume          = {21},
  abstract        = {A Virtual Screening algorithm has to adapt to the different stages of this process. Early screening needs to ensure that all bioactive compounds are ranked in the first positions despite of the number of false positives, while a second screening round is aimed at increasing the prediction accuracy. A novel CNN architecture is presented to this aim, which predicts bioactivity of candidate compounds on CDK1 using a combination of molecular fingerprints as their vector representation, and has been trained suitably to achieve good results as regards both enrichment factor and accuracy in different screening modes (98.55% accuracy in active-only selection, and 98.88% in high precision discrimination). The proposed architecture outperforms state-of-the-art ML approaches, and some interesting insights on molecular fingerprints are devised.},
  citation-subset = {IM},
  completed       = {2020-10-21},
  country         = {England},
  doi             = {10.1186/s12859-020-03645-9},
  file            = {:by-author/M/Mendolia/2020_Mendolia_310.pdf:PDF},
  issn-linking    = {1471-2105},
  issue           = {Suppl 8},
  keywords        = {Algorithms; Bioactivity Prediction; Deep Learning (DL); Drug Design; Molecular Fingerprints; User-Computer Interface; Virtual Screening},
  nlm-id          = {100965194},
  owner           = {saulius},
  pii             = {10.1186/s12859-020-03645-9},
  pmc             = {PMC7493874},
  pmid            = {32938359},
  pubmodel        = {Electronic},
  pubstate        = {epublish},
  revised         = {2020-10-21},
  timestamp = {2021.03.03},
  creationdate = {2021-03-03T00:00:00},
}

@Article{Gasteiger2020,
  author          = {Gasteiger, Johann},
  journal         = {Chemphyschem : a European journal of chemical physics and physical chemistry},
  title           = {Chemistry in Times of Artificial Intelligence.},
  year            = {2020},
  issn            = {1439-7641},
  month           = oct,
  pages           = {2233--2242},
  volume          = {21},
  abstract        = {Chemists have to a large extent gained their knowledge by doing experiments and thus gather data. By putting various data together and then analyzing them, chemists have fostered their understanding of chemistry. Since the 1960s, computer methods have been developed to perform this process from data to information to knowledge. Simultaneously, methods were developed for assisting chemists in solving their fundamental questions such as the prediction of chemical, physical, or biological properties, the design of organic syntheses, and the elucidation of the structure of molecules. This eventually led to a discipline of its own: chemoinformatics. Chemoinformatics has found important applications in the fields of drug discovery, analytical chemistry, organic chemistry, agrichemical research, food science, regulatory science, material science, and process control. From its inception, chemoinformatics has utilized methods from artificial intelligence, an approach that has recently gained more momentum.},
  citation-subset = {IM},
  completed       = {2020-12-15},
  country         = {Germany},
  doi             = {10.1002/cphc.202000518},
  file            = {:by-author/G/Gasteiger/2020_Gasteiger_2233.pdf:PDF},
  issn-linking    = {1439-4235},
  issue           = {20},
  keywords        = {Artificial Neural Networks (ANN); Chemoinformatics; Chemometrics; Drug Design; Prediction of Data},
  nlm-id          = {100954211},
  owner           = {saulius},
  pmc             = {PMC7702165},
  pmid            = {32808729},
  pubmodel        = {Print-Electronic},
  pubstate        = {ppublish},
  revised         = {2020-12-15},
  timestamp = {2021.03.03},
  creationdate = {2021-03-03T00:00:00},
}

@Article{Brewer2012,
  author    = {Eric Brewer},
  journal   = {Computer},
  title     = {{CAP} twelve years later: How the "rules" have changed},
  year      = {2012},
  month     = {feb},
  number    = {2},
  pages     = {23--29},
  volume    = {45},
  doi       = {10.1109/mc.2012.37},
  file      = {:by-author/B/Brewer/2012_Brewer_23.pdf:PDF},
  owner     = {saulius},
  publisher = {Institute of Electrical and Electronics Engineers ({IEEE})},
  timestamp = {2021.03.06},
  creationdate = {2021-03-06T00:00:00},
}

@Article{Gao2020,
  author    = {Hao Gao and Junjie Wang and Zhaopeng Guo and Jian Sun},
  journal   = {npj Computational Materials},
  title     = {Determining dimensionalities and multiplicities of crystal nets},
  year      = {2020},
  month     = {sep},
  number    = {1},
  pages     = {1--9},
  volume    = {6},
  doi       = {10.1038/s41524-020-00409-0},
  file      = {:by-author/G/Gao/2020_Gao_1.pdf:PDF},
  keywords  = {Citing COD; Multidimensional Networks},
  owner     = {saulius},
  publisher = {Springer Science and Business Media {LLC}},
  timestamp = {2021.03.08},
  creationdate = {2021-03-08T00:00:00},
}

@Presentation{Chow1999,
  author    = {C. Edward Chow},
  title     = {Why study computer architecture?},
  year      = {1999},
  file      = {:by-author/C/Chow/1999_Chow_1.ppt:PowerPoint},
  groups    = {sg/Computer Architecture (teaching)},
  keywords  = {Computer Architecture; Computer Science (CS); Teaching},
  owner     = {saulius},
  pages     = {1--59},
  timestamp = {2021.03.13},
  creationdate = {2021-03-13T00:00:00},
  url       = {http://cs.uccs.edu/~cs520/S99ch1.ppt},
}

@Presentation{Chow1999a,
  author    = {C. Edward Chow},
  title     = {Classifying instruction set architectures},
  year      = {1999},
  file      = {:by-author/C/Chow/1999_Chow_2.pdf:PDF},
  groups    = {sg/Computer Architecture (teaching)},
  keywords  = {Computer Architecture; Computer Science (CS); Teaching},
  owner     = {saulius},
  pages     = {1--48},
  timestamp = {2021.03.14},
  creationdate = {2021-03-14T00:00:00},
  url       = {http://cs.uccs.edu/~cs520/S99ch2.PDF},
}

@Article{Golovin2009,
  author    = {Adel Golovin and Kim Henrick},
  journal   = {Journal of Chemical Information and Modeling},
  title     = {Chemical substructure search in {SQL}},
  year      = {2009},
  month     = {jan},
  number    = {1},
  pages     = {22--27},
  volume    = {49},
  doi       = {10.1021/ci8003013},
  file      = {:by-author/G/Golovin/2009_Golovin_22.pdf:PDF},
  owner     = {saulius},
  publisher = {American Chemical Society ({ACS})},
  timestamp = {2021.03.27},
  creationdate = {2021-03-27T00:00:00},
}

@InProceedings{Dice2019,
  author    = {Bradley Dice and Vyas Ramasubramani and Eric Harper and Matthew Spellings and Joshua Anderson and Sharon Glotzer},
  booktitle = {Proceedings of the 18th {P}ython in science conference},
  title     = {Analyzing particle systems for machine learning and data visualization with freud},
  year      = {2019},
  pages     = {27--33},
  publisher = {{SciPy}},
  doi       = {10.25080/Majora-7ddc1dd1-004},
  file      = {:by-author/D/Dice/2019_Dice_27.pdf:PDF},
  owner     = {saulius},
  timestamp = {2021.03.27},
  creationdate = {2021-03-27T00:00:00},
}

@Article{Hendlich2003,
  author    = {Manfred Hendlich and Andreas Bergner and Judith Günther and Gerhard Klebe},
  journal   = {Journal of Molecular Biology},
  title     = {{R}elibase: design and development of a database for comprehensive analysis of protein–ligand interactions},
  year      = {2003},
  month     = {feb},
  number    = {2},
  pages     = {607--620},
  volume    = {326},
  comment   = {Cited in Golovin2009.},
  doi       = {10.1016/s0022-2836(02)01408-0},
  file      = {:by-author/H/Hendlich/2003_Hendlich_607.pdf:PDF},
  owner     = {saulius},
  publisher = {Elsevier {BV}},
  timestamp = {2021.03.27},
  creationdate = {2021-03-27T00:00:00},
}

@Article{Klekota2006,
  author    = {J. Klekota and F. P. Roth and S. L. Schreiber},
  journal   = {Bioinformatics},
  title     = {Query Chem: a Google-powered web search combining text and chemical structures},
  year      = {2006},
  month     = {may},
  number    = {13},
  pages     = {1670--1673},
  volume    = {22},
  comment   = {Cited in Golovin2009.},
  doi       = {10.1093/bioinformatics/btl155},
  file      = {:by-author/K/Klekota/2006_Klekota_1670.pdf:PDF},
  owner     = {saulius},
  publisher = {Oxford University Press ({OUP})},
  timestamp = {2021.03.27},
  creationdate = {2021-03-27T00:00:00},
}

@InProceedings{Zhang1991,
  author    = {Ying Zhang and A. K. Mackworth},
  booktitle = {Proceedings of the Third {IEEE} Symposium on Parallel and Distributed Processing},
  title     = {Parallel and distributed algorithms for finite constraint satisfaction problems},
  year      = {1991},
  pages     = {394--391},
  publisher = {{IEEE} Comput. Soc. Press},
  comment   = {Cited in Golovin2009.},
  doi       = {10.1109/spdp.1991.218214},
  file      = {:by-author/Z/Zhang/1991_Zhang_391.pdf:PDF},
  owner     = {saulius},
  timestamp = {2021.03.27},
  creationdate = {2021-03-27T00:00:00},
}

@Article{Li2010,
  author    = {Li, Xingjian and Epstein, Susan},
  journal   = {AAAI Workshop - Technical Report},
  title     = {Visualization for structured constraint satisfaction problems},
  year      = {2010},
  month     = {01},
  pages     = {1--9},
  file      = {:by-author/L/Li/2010_Li_1.pdf:PDF},
  owner     = {saulius},
  timestamp = {2021.03.27},
  creationdate = {2021-03-27T00:00:00},
  url       = {https://www.researchgate.net/publication/228943946_Visualization_for_structured_constraint_satisfaction_problems},
}

@Article{Gyssens1994,
  author    = {Marc Gyssens and Peter G. Jeavons and David A. Cohen},
  journal   = {Artificial Intelligence},
  title     = {Decomposing constraint satisfaction problems using database techniques},
  year      = {1994},
  month     = {mar},
  number    = {1},
  pages     = {57--89},
  volume    = {66},
  comment   = {Cited in Golovin2009.},
  doi       = {10.1016/0004-3702(94)90003-5},
  file      = {:by-author/G/Gyssens/1994_Gyssens_57.pdf:PDF},
  owner     = {saulius},
  publisher = {Elsevier {BV}},
  timestamp = {2021.03.27},
  creationdate = {2021-03-27T00:00:00},
}

@Article{Contreras2007,
  author    = {M. L. Contreras and J. Alvarez and D. Guajardo and R. Rozas},
  journal   = {Journal of Computational Chemistry},
  title     = {Understanding topological symmetry: A heuristic approach to its determination},
  year      = {2007},
  month     = {aug},
  number    = {4},
  pages     = {588--600},
  volume    = {29},
  comment   = {Cited in Golovin2009.},
  doi       = {10.1002/jcc.20816},
  file      = {:by-author/C/Contreras/2007_Contreras_588.pdf:PDF},
  owner     = {saulius},
  publisher = {Wiley},
  timestamp = {2021.03.27},
  creationdate = {2021-03-27T00:00:00},
}

@Article{Aloul2010,
  author    = {Fadi A. Aloul},
  journal   = {Symmetry},
  title     = {Symmetry in Boolean Satisfiability},
  year      = {2010},
  month     = {jun},
  number    = {2},
  pages     = {1121--1134},
  volume    = {2},
  doi       = {10.3390/sym2021121},
  file      = {:by-author/A/Aloul/2010_Aloul_1121.pdf:PDF},
  owner     = {saulius},
  publisher = {{MDPI} {AG}},
  timestamp = {2021.03.27},
  creationdate = {2021-03-27T00:00:00},
}

@InCollection{Katebi2010,
  author    = {Hadi Katebi and Karem A. Sakallah and Igor L. Markov},
  booktitle = {Theory and Applications of Satisfiability Testing {\textendash} {SAT} 2010},
  publisher = {Springer Berlin Heidelberg},
  title     = {Symmetry and Satisfiability: An Update},
  year      = {2010},
  pages     = {113--127},
  doi       = {10.1007/978-3-642-14186-7_11},
  file      = {:by-author/K/Katebi/2010_Katebi_113.pdf:PDF},
  owner     = {saulius},
  timestamp = {2021.03.27},
  creationdate = {2021-03-27T00:00:00},
}

@Article{Crawford1992,
  author    = {James M. Crawford},
  title     = {A theoretical analysis of reasoning by symmetry in first-order logic (extended abstract)},
  year      = {1992},
  pages     = {17--22},
  booktitle = {In AAAI Workshop on Tractable Reasoning},
  file      = {:by-author/C/Crawford/1992_Crawford_17.pdf:PDF},
  owner     = {saulius},
  timestamp = {2021.03.27},
  creationdate = {2021-03-27T00:00:00},
  url       = {http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.51.4039},
}

@Article{Kong2020,
  author    = {Xiangjie Kong and Jun Zhang and Da Zhang and Yi Bu and Ying Ding and Feng Xia},
  journal   = {{ACM} Transactions on Knowledge Discovery from Data},
  title     = {The gene of scientific success},
  year      = {2020},
  month     = {jul},
  number    = {4},
  pages     = {41},
  volume    = {14},
  doi       = {10.1145/3385530},
  file      = {:by-author/K/Kong/2020_Kong_41.pdf:PDF},
  owner     = {saulius},
  publisher = {Association for Computing Machinery ({ACM})},
  timestamp = {2021.03.27},
  creationdate = {2021-03-27T00:00:00},
}

@Article{Chakraborty_2017,
  author    = {Tanmoy Chakraborty and Subrata Nandi},
  journal   = {Knowledge and Information Systems},
  title     = {Universal trajectories of scientific success},
  year      = {2017},
  month     = {jul},
  number    = {2},
  pages     = {487--509},
  volume    = {54},
  doi       = {10.1007/s10115-017-1080-y},
  file      = {:by-author/C/Chakraborty/2017_Chakraborty_487.pdf:PDF},
  owner     = {saulius},
  publisher = {Springer Science and Business Media {LLC}},
  timestamp = {2021.03.27},
  creationdate = {2021-03-27T00:00:00},
}

@InProceedings{Rudolf1998,
  author    = {Michael Rudolf},
  booktitle = {6th International Workshop on Theory an Application of Graph Transformations ({TAGT})},
  title     = {Utilizing constraint satisfaction techniques for efficient graph pattern matching},
  year      = {1998},
  pages     = {238--251},
  publisher = {Springer},
  comment   = {Possibly the citation (11) in Golovin2009.},
  doi       = {10.1007/978-3-540-46464-8_17},
  file      = {:by-author/R/Rudolf/1998_Rudolf_238.pdf:PDF},
  owner     = {saulius},
  timestamp = {2021.03.29},
  creationdate = {2021-03-29T00:00:00},
  url       = {http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.37.8764},
}

@Article{Thomassen1984,
  author    = {Carsten Thomassen},
  journal   = {Journal of Combinatorial Theory, Series B},
  title     = {A refinement of {K}uratowski's theorem},
  year      = {1984},
  pages     = {245--253},
  volume    = {37},
  doi       = {10.1016/0095-8956(84)90057-1},
  file      = {:by-author/T/Thomassen/1984_Thomassen_245.pdf:PDF},
  owner     = {saulius},
  timestamp = {2021.03.29},
  creationdate = {2021-03-29T00:00:00},
  url       = {https://core.ac.uk/download/pdf/82439408.pdf},
}

@Article{Thomassen1981,
  author    = {Carsten Thomassen},
  journal   = {Journal of Graph Theory},
  title     = {{K}uratowski's theorem},
  year      = {1981},
  number    = {3},
  pages     = {225--241},
  volume    = {5},
  comment   = {Cited in Golovin2009.},
  doi       = {10.1002/jgt.3190050304},
  file      = {:by-author/T/Thomassen/1981_Thomassen_225.pdf:PDF},
  owner     = {saulius},
  timestamp = {2021.03.29},
  creationdate = {2021-03-29T00:00:00},
}

@Article{RagueSchleyer2001,
  author    = {Paul von Ragué Schleyer},
  journal   = {Chemical Reviews},
  title     = {Introduction: Aromaticity},
  year      = {2001},
  month     = {may},
  number    = {5},
  pages     = {1115--1118},
  volume    = {101},
  comment   = {Cited in Golovin2009.},
  doi       = {10.1021/cr0103221},
  file      = {:by-author/S/Schleyer/2001_Schleyer_1115.pdf:PDF},
  owner     = {saulius},
  publisher = {American Chemical Society ({ACS})},
  timestamp = {2021.03.29},
  creationdate = {2021-03-29T00:00:00},
}

@Article{Balaban2005,
  author    = {Alexandru T. Balaban and Paul v. R. Schleyer and Henry S. Rzepa},
  journal   = {Chemical Reviews},
  title     = {Crocker, Not Armit and Robinson, Begat the Six Aromatic Electrons},
  year      = {2005},
  month     = {oct},
  number    = {10},
  pages     = {3436--3447},
  volume    = {105},
  comment   = {Cited in Golovin2009.},
  doi       = {10.1021/cr0300946},
  file      = {:by-author/B/Balaban/2005_Balaban_3436.pdf:PDF},
  owner     = {saulius},
  publisher = {American Chemical Society ({ACS})},
  timestamp = {2021.03.29},
  creationdate = {2021-03-29T00:00:00},
}

@Article{Brauner2020,
  author    = {Jan M. Brauner and Sören Mindermann and Mrinank Sharma and David Johnston and John Salvatier and Tom{\'{a}}{\v{s}} Gaven{\v{c}}iak and Anna B. Stephenson and Gavin Leech and George Altman and Vladimir Mikulik and Alexander John Norman and Joshua Teperowski Monrad and Tamay Besiroglu and Hong Ge and Meghan A. Hartwick and Yee Whye Teh and Leonid Chindelevitch and Yarin Gal and Jan Kulveit},
  journal   = {Science},
  title     = {Inferring the effectiveness of government interventions against {COVID}-19},
  year      = {2020},
  month     = {dec},
  number    = {6531},
  pages     = {eabd9338},
  volume    = {371},
  doi       = {10.1126/science.abd9338},
  file      = {:by-author/B/Brauner/2020_Brauner_9338.pdf:PDF},
  owner     = {saulius},
  publisher = {American Association for the Advancement of Science ({AAAS})},
  timestamp = {2021.03.29},
  creationdate = {2021-03-29T00:00:00},
}

@Presentation{Chow1999b,
  author    = {C. Edward Chow},
  title     = {Pipelining},
  year      = {1999},
  lecture   = {3},
  file      = {:by-author/C/Chow/1999_Chow_3.pdf:PDF},
  owner     = {saulius},
  pages     = {1--70},
  timestamp = {2021.04.04},
  creationdate = {2021-04-04T00:00:00},
  url       = {http://cs.uccs.edu/~cs520/S99ch3.PDF},
}

@Presentation{Chow1999c,
  author    = {C. Edward Chow},
  title     = {Instruction-level parallelism ({ILP})},
  year      = {1999},
  file      = {:by-author/C/Chow/1999_Chow_4.pdf:PDF},
  owner     = {saulius},
  pages     = {1--17},
  timestamp = {2021.04.04},
  creationdate = {2021-04-04T00:00:00},
  url       = {http://cs.uccs.edu/~cs520/S99ch4.PDF},
}

@Presentation{Chow1999d,
  author    = {C. Edward Chow},
  title     = {Memory hierarchy design},
  year      = {1999},
  file      = {:by-author/C/Chow/1999_Chow_5.pdf:PDF;:by-author/C/Chow/1999_Chow_5.ppt:PowerPoint},
  owner     = {saulius},
  pages     = {1--76},
  timestamp = {2021.04.04},
  creationdate = {2021-04-04T00:00:00},
  url       = {http://cs.uccs.edu/~cs520/S99ch5.PDF},
}

@Presentation{Chow1999e,
  author    = {C. Edward Chow},
  title     = {Typical interface of {I/O} devices},
  year      = {1999},
  file      = {:by-author/C/Chow/1999_Chow_6.pdf:PDF},
  owner     = {saulius},
  pages     = {1--48},
  timestamp = {2021.04.04},
  creationdate = {2021-04-04T00:00:00},
  url       = {http://cs.uccs.edu/~cs520/S99ch6.PDF},
}

@Presentation{Chow1999f,
  author    = {C. Edward Chow},
  title     = {Basic integer arithmetic building block},
  year      = {1999},
  file      = {:by-author/C/Chow/1999_Chow_a.ppt:PowerPoint},
  owner     = {saulius},
  pages     = {1--41},
  timestamp = {2021.04.04},
  creationdate = {2021-04-04T00:00:00},
  url       = {http://cs.uccs.edu/~cs520/S99cha.ppt},
}

@Manuscript{Dolan2013,
  author    = {Stephen Dolan},
  title     = {{\texttt{mov}} is {T}uring-complete},
  year      = {2013},
  keywords  = {Computer Science (CS); SISC; Single Instruction Set Computer; Turing-complete},
  url       = {https://drwho.virtadpt.net/files/mov.pdf},
  file      = {:by-author/D/Dolan/2013_Dolan_1.pdf:PDF},
  owner     = {saulius},
  pages     = {1--4},
  timestamp = {2021.04.07},
  creationdate = {2021-04-07T00:00:00},
}

@Article{Kuratowski1930,
  author    = {Casimir Kuratowski},
  journal   = {Fundamenta Mathematicae},
  title     = {Sur le problème des courbes gauches en topologie},
  year      = {1930},
  pages     = {271--283},
  volume    = {15},
  doi       = {10.4064/fm-15-1-271-283},
  file      = {:by-author/K/Kuratowski/1930_Kuratowski_271.pdf:PDF},
  keywords  = {Graph Theory; Mathematics},
  language  = {French},
  owner     = {saulius},
  publisher = {Institute of Mathematics, Polish Academy of Sciences},
  timestamp = {2021.04.08},
  creationdate = {2021-04-08T00:00:00},
  url       = {http://matwbn.icm.edu.pl/ksiazki/fm/fm15/fm15126.pdf},
}

@Article{Holden1993,
  author    = {James R. Holden and Zuyue Du and Herman L. Ammon},
  journal   = {Journal of Computational Chemistry},
  title     = {Prediction of possible crystal structures for {C}-, {H}-, {N}-, {O}-, and {F}-containing organic compounds},
  year      = {1993},
  month     = {apr},
  number    = {4},
  pages     = {422--437},
  volume    = {14},
  comment   = {Describes MOLPAK program.},
  doi       = {10.1002/jcc.540140406},
  file      = {:by-author/H/Holden/1993_Holden_422.pdf:PDF},
  keywords  = {Crystal Structure Prediction (CSP); Crystallographic Software; MOLPAK},
  owner     = {saulius},
  publisher = {Wiley},
  timestamp = {2021.04.14},
  creationdate = {2021-04-14T00:00:00},
}

@Manuscript{Domas2017,
  author    = {Christopher Domas},
  title     = {Breaking the x86 {ISA}},
  year      = {2017},
  url       = {https://github.com/xoreaxeaxeax/sandsifter/blob/master/references/domas_breaking_the_x86_isa_wp.pdf},
  file      = {:by-author/D/Domas/2017_Domas_1.pdf:PDF},
  owner     = {saulius},
  pages     = {1--6},
  timestamp = {2021.04.10},
  creationdate = {2021-04-10T00:00:00},
}

@Article{Luo2019,
  author    = {Hongyuan Luo and Xuan Hao and Yanqing Gong and Jiahai Zhou and Xiao He and Jinjin Li},
  journal   = {Crystal Growth {\&} Design},
  title     = {Rational Crystal Polymorph Design of Olanzapine},
  year      = {2019},
  month     = {feb},
  number    = {4},
  pages     = {2388--2395},
  volume    = {19},
  doi       = {10.1021/acs.cgd.9b00068},
  file      = {:by-author/L/Luo/2019_Luo_2388.pdf:PDF},
  owner     = {saulius},
  publisher = {American Chemical Society ({ACS})},
  timestamp = {2021.04.14},
  creationdate = {2021-04-14T00:00:00},
}

@Article{Li2013b,
  author    = {Jinjin Li and Olaseni Sode and Gregory A. Voth and So Hirata},
  journal   = {Nature Communications},
  title     = {A solid{\textendash}solid phase transition in carbon dioxide at high pressures and intermediate temperatures},
  year      = {2013},
  month     = {oct},
  number    = {1},
  volume    = {4},
  doi       = {10.1038/ncomms3647},
  file      = {:by-author/L/Li/2013_Li_3647.pdf:PDF},
  owner     = {saulius},
  publisher = {Springer Science and Business Media {LLC}},
  timestamp = {2021.04.14},
  creationdate = {2021-04-14T00:00:00},
}

@Article{Liu2017,
  author    = {Liu, Jinfeng and Qi, Lian-Wen and Zhang, John Z. H. and He, Xiao},
  journal   = {J. Chem. Theory Comput.},
  title     = {Fragment Quantum Mechanical Method for Large-Sized Ion-Water Clusters},
  year      = {2017},
  issn      = {1549-9618},
  month     = may,
  number    = {5},
  pages     = {2021--2034},
  volume    = {13},
  abstract  = {Fragmentation methods have been widely studied for computing quantum mechanical (QM) energy of medium-sized water clusters, but less attention has been paid to large-sized ion-water clusters, in which many-body QM interaction is more significant, because of the charge-transfer effect between ions and water molecules. In this study, we utilized electrostatically embedded generalized molecular fractionation (EE-GMF) method for full QM calculation of the large-sized ion-water clusters (up to 15 Na+ and 15 Cl- ions solvated with 119 water molecules). Through systematic validation using different fragment sizes, we show that, by using distance thresholds of 6 Å for both the two-body and three-body QM interactions, the EE-GMF method is capable of providing accurate ground-state energies of large-sized ion-water clusters at different ab initio levels (including HF, B3LYP, M06-2X, and MP2) with significantly reduced computational cost. The deviations of EE-GMF from full system calculations are within a few kcal/mol. The result clearly shows that the calculated energies of the ion-water clusters using EE-GMF are close to converge after the distance thresholds are larger than 6 Å for both the two-body and three-body QM interactions. This study underscores the importance of the three-body interactions in ion-water clusters. The EE-GMF method can also accurately reproduce the relative energy profiles of the ion-water clusters.},
  comment   = {doi: 10.1021/acs.jctc.7b00149},
  doi       = {10.1021/acs.jctc.7b00149},
  file      = {:by-author/L/Liu/2017_Liu_2021.pdf:PDF},
  owner     = {saulius},
  publisher = {American Chemical Society},
  timestamp = {2021.04.14},
  creationdate = {2021-04-14T00:00:00},
  url       = {https://doi.org/10.1021/acs.jctc.7b00149},
}

@Article{He2014,
  author    = {Xiao He and Tong Zhu and Xianwei Wang and Jinfeng Liu and John Z. H. Zhang},
  journal   = {Accounts of Chemical Research},
  title     = {Fragment Quantum Mechanical Calculation of Proteins and Its Applications},
  year      = {2014},
  month     = {may},
  number    = {9},
  pages     = {2748--2757},
  volume    = {47},
  doi       = {10.1021/ar500077t},
  file      = {:by-author/H/He/2014_He_2748.pdf:PDF},
  owner     = {saulius},
  publisher = {American Chemical Society ({ACS})},
  timestamp = {2021.04.14},
  creationdate = {2021-04-14T00:00:00},
}

@Article{Baias2013,
  author    = {Maria Baias and Jean-Nicolas Dumez and Per H. Svensson and Staffan Schantz and Graeme M. Day and Lyndon Emsley},
  journal   = {Journal of the American Chemical Society},
  title     = {{\textit{De novo}} determination of the crystal structure of a large drug molecule by crystal structure prediction-based powder {NMR} crystallography},
  year      = {2013},
  month     = {nov},
  number    = {46},
  pages     = {17501--17507},
  volume    = {135},
  doi       = {10.1021/ja4088874},
  file      = {:by-author/B/Baias/2013_Baias_17501.pdf:PDF},
  owner     = {saulius},
  publisher = {American Chemical Society ({ACS})},
  timestamp = {2021.04.14},
  creationdate = {2021-04-14T00:00:00},
}

@Article{Han2019,
  author    = {Yanqiang Han and Jinfeng Liu and Lei Huang and Xiao He and Jinjin Li},
  journal   = {npj Quantum Materials},
  title     = {Predicting the phase diagram of solid carbon dioxide at high pressure from first principles},
  year      = {2019},
  month     = {mar},
  number    = {1},
  pages     = {10},
  volume    = {4},
  doi       = {10.1038/s41535-019-0149-0},
  file      = {:by-author/H/Han/2019_Han_10.pdf:PDF},
  owner     = {saulius},
  publisher = {Springer Science and Business Media {LLC}},
  timestamp = {2021.04.14},
  creationdate = {2021-04-14T00:00:00},
}

@Article{Sode2012,
  author    = {Olaseni Sode and So Hirata},
  journal   = {Physical Chemistry Chemical Physics},
  title     = {Second-order many-body perturbation study of solid hydrogen fluoride under pressure},
  year      = {2012},
  number    = {21},
  pages     = {7765},
  volume    = {14},
  doi       = {10.1039/c2cp40236j},
  file      = {:by-author/S/Sode/2012_Sode_7765.pdf:PDF},
  owner     = {saulius},
  publisher = {Royal Society of Chemistry ({RSC})},
  timestamp = {2021.04.14},
  creationdate = {2021-04-14T00:00:00},
}

@Article{Tennant2017,
  author    = {Jonathan P. Tennant and Jonathan M. Dugan and Daniel Graziotin and Damien C. Jacques and Fran{\c{c}}ois Waldner and Daniel Mietchen and Yehia Elkhatib and Lauren B. Collister and Christina K. Pikas and Tom Crick and Paola Masuzzo and Anthony Caravaggi and Devin R. Berg and Kyle E. Niemeyer and Tony Ross-Hellauer and Sara Mannheimer and Lillian Rigling and Daniel S. Katz and Bastian Greshake Tzovaras and Josmel Pacheco-Mendoza and Nazeefa Fatima and Marta Poblet and Marios Isaakidis and Dasapta Erwin Irawan and S{\'{e}}bastien Renaut and Christopher R. Madan and Lisa Matthias and Jesper N{\o}rgaard Kj{\ae}r and Daniel Paul O{\textquotesingle}Donnell and Cameron Neylon and Sarah Kearns and Manojkumar Selvaraju and Julien Colomb},
  journal   = {F1000Research},
  title     = {A multi-disciplinary perspective on emergent and future innovations in peer review},
  year      = {2017},
  month     = {nov},
  pages     = {1151},
  volume    = {6},
  doi       = {10.12688/f1000research.12037.3},
  file      = {:by-author/T/Tennant/2017_Tennant_1151.pdf:PDF},
  owner     = {saulius},
  publisher = {F1000 Research Ltd},
  timestamp = {2021.04.14},
  creationdate = {2021-04-14T00:00:00},
}

@Article{Brinckman2019,
  author    = {Adam Brinckman and Kyle Chard and Niall Gaffney and Mihael Hategan and Matthew B. Jones and Kacper Kowalik and Sivakumar Kulasekaran and Bertram Ludäscher and Bryce D. Mecum and Jarek Nabrzyski and Victoria Stodden and Ian J. Taylor and Matthew J. Turk and Kandace Turner},
  journal   = {Future Generation Computer Systems},
  title     = {Computing environments for reproducibility: Capturing the {\textquotedblleft}Whole Tale{\textquotedblright}},
  year      = {2019},
  month     = {may},
  pages     = {854--867},
  volume    = {94},
  doi       = {10.1016/j.future.2017.12.029},
  file      = {:by-author/B/Brinckman/2019_Brinckman_854.pdf:PDF},
  owner     = {saulius},
  publisher = {Elsevier {BV}},
  timestamp = {2021.04.14},
  creationdate = {2021-04-14T00:00:00},
}

@Article{Pourret2020,
  author    = {Olivier Pourret and Dasapta Irawan and Jonathan Tennant},
  journal   = {Sustainability},
  title     = {On the Potential of Preprints in Geochemistry: The Good, the Bad, and the Ugly},
  year      = {2020},
  month     = {apr},
  number    = {8},
  pages     = {3360},
  volume    = {12},
  doi       = {10.3390/su12083360},
  file      = {:by-author/P/Pourret/2020_Pourret_3360.pdf:PDF},
  owner     = {saulius},
  publisher = {{MDPI} {AG}},
  timestamp = {2021.04.14},
  creationdate = {2021-04-14T00:00:00},
}

@Article{Hasselbring2020,
  author    = {Wilhelm Hasselbring and Leslie Carr and Simon Hettrick and Heather Packer and Thanassis Tiropanis},
  journal   = {it - Information Technology},
  title     = {From {FAIR} research data toward {FAIR} and open research software},
  year      = {2020},
  month     = {feb},
  number    = {1},
  pages     = {39--47},
  volume    = {62},
  doi       = {10.1515/itit-2019-0040},
  file      = {:by-author/H/Hasselbring/2020_Hasselbring_39.pdf:PDF},
  owner     = {saulius},
  publisher = {Walter de Gruyter {GmbH}},
  timestamp = {2021.04.14},
  creationdate = {2021-04-14T00:00:00},
}

@Article{Wofford2020,
  author    = {Morgan F. Wofford and Bernadette M. Boscoe and Christine L. Borgman and Irene V. Pasquetto and Milena S. Golshan},
  journal   = {Computing in Science {\&} Engineering},
  title     = {Jupyter Notebooks as Discovery Mechanisms for Open Science: Citation Practices in the Astronomy Community},
  year      = {2020},
  month     = {jan},
  number    = {1},
  pages     = {5--15},
  volume    = {22},
  doi       = {10.1109/mcse.2019.2932067},
  file      = {:by-author/W/Wofford/2020_Wofford_5.pdf:PDF},
  owner     = {saulius},
  publisher = {Institute of Electrical and Electronics Engineers ({IEEE})},
  timestamp = {2021.04.14},
  creationdate = {2021-04-14T00:00:00},
}

@Article{Horsch2019,
  author    = {Martin Thomas Horsch and Christoph Niethammer and Gianluca Boccardo and Paola Carbone and Silvia Chiacchiera and Mara Chiricotto and Joshua D. Elliott and Vladimir Lobaskin and Philipp Neumann and Peter Schiffels and Michael A. Seaton and Ilian T. Todorov and Jadran Vrabec and Welchy Leite Cavalcanti},
  journal   = {Journal of Chemical {\&} Engineering Data},
  title     = {Semantic Interoperability and Characterization of Data Provenance in Computational Molecular Engineering},
  year      = {2019},
  month     = {dec},
  number    = {3},
  pages     = {1313--1329},
  volume    = {65},
  doi       = {10.1021/acs.jced.9b00739},
  file      = {:by-author/H/Horsch/2019_Horsch_1313.pdf:PDF},
  owner     = {saulius},
  publisher = {American Chemical Society ({ACS})},
  timestamp = {2021.04.14},
  creationdate = {2021-04-14T00:00:00},
}

@Article{Katz2021,
  author           = {Daniel S. Katz and Neil P. Chue Hong and Tim Clark and August Muench and Shelley Stall and Daina Bouquin and Matthew Cannon and Scott Edmunds and Telli Faez and Patricia Feeney and Martin Fenner and Michael Friedman and Gerry Grenier and Melissa Harrison and Joerg Heber and Adam Leary and Catriona MacCallum and Hollydawn Murray and Erika Pastrana and Katherine Perry and Douglas Schuster and Martina Stockhause and Jake Yeston},
  journal          = {F1000Research},
  title            = {Recognizing the value of software: a software citation guide},
  year             = {2021},
  month            = {jan},
  pages            = {1257},
  volume           = {9},
  creationdate     = {2021-04-14T00:00:00},
  doi              = {10.12688/f1000research.26932.2},
  file             = {:by-author/K/Katz/2021_Katz_1257.pdf:PDF},
  keywords         = {Attribution; Software Citation; Software Credit},
  modificationdate = {2024-02-06T10:45:38},
  owner            = {saulius},
  publisher        = {F1000 Research Ltd},
  timestamp        = {2021.04.14},
}

@Article{Bouquin2020,
  author           = {Daina R. Bouquin and Daniel A. Chivvis and Edwin Henneken and Kelly Lockhart and August Muench and Jennifer Koch},
  journal          = {The Astrophysical Journal Supplement Series},
  title            = {Credit Lost: Two Decades of Software Citation in Astronomy},
  year             = {2020},
  month            = {jun},
  number           = {1},
  pages            = {8},
  volume           = {249},
  creationdate     = {2021-04-14T00:00:00},
  doi              = {10.3847/1538-4365/ab7be6},
  file             = {:by-author/B/Bouquin/2020_Bouquin_8.pdf:PDF},
  keywords         = {Attribution; Software Citation; Software Credit},
  modificationdate = {2023-12-22T14:06:50},
  owner            = {saulius},
  publisher        = {American Astronomical Society},
  timestamp        = {2021.04.14},
}

@Article{Jimenez2017,
  author    = {Rafael C. Jim{\'{e}}nez and Mateusz Kuzak and Monther Alhamdoosh and Michelle Barker and B{\'{e}}r{\'{e}}nice Batut and Mikael Borg and Salvador Capella-Gutierrez and Neil Chue Hong and Martin Cook and Manuel Corpas and Madison Flannery and Leyla Garcia and Josep Ll. Gelp{\'{\i}} and Simon Gladman and Carole Goble and Montserrat Gonz{\'{a}}lez Ferreiro and Alejandra Gonzalez-Beltran and Philippa C. Griffin and Björn Grüning and Jonas Hagberg and Petr Holub and Rob Hooft and Jon Ison and Daniel S. Katz and Brane Lesko{\v{s}}ek and Federico L{\'{o}}pez G{\'{o}}mez and Luis J. Oliveira and David Mellor and Rowland Mosbergen and Nicola Mulder and Yasset Perez-Riverol and Robert Pergl and Horst Pichler and Bernard Pope and Ferran Sanz and Maria V. Schneider and Victoria Stodden and Rados{\l}aw Suchecki and Radka Svobodov{\'{a}} Va{\v{r}}ekov{\'{a}} and Harry-Anton Talvik and Ilian Todorov and Andrew Treloar and Sonika Tyagi and Maarten van Gompel and Daniel Vaughan and Allegra Via and Xiaochuan Wang and Nathan S. Watson-Haigh and Steve Crouch},
  journal   = {F1000Research},
  title     = {Four simple recommendations to encourage best practices in research software},
  year      = {2017},
  month     = {jun},
  pages     = {876},
  volume    = {6},
  doi       = {10.12688/f1000research.11407.1},
  file      = {:by-author/J/Jiménez/2017_Jiménez_876.pdf:PDF},
  owner     = {saulius},
  publisher = {F1000 Research Ltd},
  timestamp = {2021.04.14},
  creationdate = {2021-04-14T00:00:00},
}

@Article{Radio2017,
  author    = {Erik Radio and Fernando Rios and Jeffrey C. Oliver and Benjamin Hickson and Niamh Wallace},
  journal   = {Journal of Library Metadata},
  title     = {Manifestations of Metadata Structures in Research Datasets and Their Ontic Implications},
  year      = {2017},
  month     = {oct},
  number    = {3-4},
  pages     = {161--182},
  volume    = {17},
  doi       = {10.1080/19386389.2018.1439278},
  file      = {:by-author/R/Radio/2017_Radio_161.pdf:PDF},
  owner     = {saulius},
  publisher = {Informa {UK} Limited},
  timestamp = {2021.04.14},
  creationdate = {2021-04-14T00:00:00},
}

@Article{Heinle2017,
  author    = {Albert Heinle and Wolfram Koepf and Wolfram Sperber},
  journal   = {{ACM} Communications in Computer Algebra},
  title     = {Some steps to improve software information},
  year      = {2017},
  month     = {may},
  number    = {1},
  pages     = {1--11},
  volume    = {51},
  doi       = {10.1145/3096730.3096731},
  file      = {:by-author/H/Heinle/2017_Heinle_1.pdf:PDF},
  owner     = {saulius},
  publisher = {Association for Computing Machinery ({ACM})},
  timestamp = {2021.04.14},
  creationdate = {2021-04-14T00:00:00},
}

@Article{Willighagen2019,
  author    = {Lars G. Willighagen},
  journal   = {{PeerJ} Computer Science},
  title     = {Citation.js: a format-independent, modular bibliography tool for the browser and command line},
  year      = {2019},
  month     = {aug},
  pages     = {e214},
  volume    = {5},
  doi       = {10.7717/peerj-cs.214},
  file      = {:by-author/W/Willighagen/2019_Willighagen_214.pdf:PDF},
  owner     = {saulius},
  publisher = {{PeerJ}},
  timestamp = {2021.04.14},
  creationdate = {2021-04-14T00:00:00},
}

@Article{Jay2020,
  author    = {Caroline Jay and Robert Haines and Daniel S. Katz and Jeffrey C. Carver and Sandra Gesing and Steven R. Brandt and James Howison and Anshu Dubey and James C. Phillips and Hui Wan and Matthew J. Turk},
  journal   = {F1000Research},
  title     = {The challenges of theory-software translation},
  year      = {2020},
  month     = {oct},
  pages     = {1192},
  volume    = {9},
  doi       = {10.12688/f1000research.25561.1},
  file      = {:by-author/J/Jay/2020_Jay_1192.pdf:PDF},
  owner     = {saulius},
  publisher = {F1000 Research Ltd},
  timestamp = {2021.04.14},
  creationdate = {2021-04-14T00:00:00},
}

@Article{Finkel2020,
  author    = {M. Finkel and A. Baur and T.K.D. Weber and K. Osenbrück and H. Rügner and C. Leven and M. Schwientek and J. Schlögl and U. Hahn and T. Streck and O.A. Cirpka and T. Walter and P. Grathwohl},
  journal   = {Earth Science Informatics},
  title     = {Managing collaborative research data for integrated, interdisciplinary environmental research},
  year      = {2020},
  month     = {jan},
  number    = {3},
  pages     = {641--654},
  volume    = {13},
  doi       = {10.1007/s12145-020-00441-0},
  file      = {:by-author/F/Finkel/2020_Finkel_641.pdf:PDF},
  owner     = {saulius},
  publisher = {Springer Science and Business Media {LLC}},
  timestamp = {2021.04.14},
  creationdate = {2021-04-14T00:00:00},
}

@Article{Janssen2020,
  author    = {Marco A. Janssen and Calvin Pritchard and Allen Lee},
  journal   = {Environmental Modelling {\&} Software},
  title     = {On code sharing and model documentation of published individual and agent-based models},
  year      = {2020},
  month     = {dec},
  pages     = {104873},
  volume    = {134},
  doi       = {10.1016/j.envsoft.2020.104873},
  file      = {:by-author/J/Janssen/2020_Janssen_104873.pdf:PDF},
  owner     = {saulius},
  publisher = {Elsevier {BV}},
  timestamp = {2021.04.14},
  creationdate = {2021-04-14T00:00:00},
}

@InCollection{Cosmo2020,
  author    = {Roberto Di Cosmo},
  booktitle = {Lecture Notes in Computer Science},
  publisher = {Springer International Publishing},
  title     = {Archiving and Referencing Source Code with Software Heritage},
  year      = {2020},
  pages     = {362--373},
  doi       = {10.1007/978-3-030-52200-1_36},
  file      = {:by-author/C/Cosmo/2020_Cosmo_362.pdf:PDF},
  owner     = {saulius},
  timestamp = {2021.04.14},
  creationdate = {2021-04-14T00:00:00},
}

@Presentation{Petrauskas2021,
  author    = {Karolis Petrauskas},
  title     = {Software engineering models and methods: {TLA$^{+}$} lecture 1/3: specification language, basics},
  year      = {2021},
  comment   = {Original file name: MSC_SEMM_TLA-01-Basics.pdf
You need to be logged in into MS Teams to follow the Teams URL link.},
  file      = {:by-author/P/Petrauskas/2021_Petrauskas_1.pdf:PDF},
  owner     = {saulius},
  pages     = {1--54},
  timestamp = {2021.04.15},
  creationdate = {2021-04-15T00:00:00},
  url       = {https://teams.microsoft.com/l/file/C0A3BD4B-E8AD-40D9-A924-C3ECB1F3740E?tenantId=82c51a82-548d-43ca-bcf9-bf4b7eb1d012&fileType=pdf&objectUrl=https://vult.sharepoint.com/sites/Formalistai/Shared Documents/General/TLA Lectures 2021/MSC_SEMM_TLA-01-Basics.pdf&baseUrl=https://vult.sharepoint.com/sites/Formalistai&serviceName=teams&threadId=19:fdd19a50fb364312873fedfcc61058eb@thread.tacv2&groupId=47d21ac7-f5b8-42e0-894d-71e7846be09e},
}

@Presentation{Petrauskas2021a,
  author    = {Karolis Petrauskas},
  title     = {Software engineering models and methods: {TLA$^{+}$} lecture 2/3: abstractions and refinements},
  year      = {2021},
  comment   = {Original file name: MSC_SEMM_TLA-02-AbsRef.pdf
You need to be logged in into MS Teams to follow the Teams URL link.},
  file      = {:by-author/P/Petrauskas/2021_Petrauskas_1a.pdf:PDF},
  owner     = {saulius},
  pages     = {1--51},
  timestamp = {2021.04.15},
  creationdate = {2021-04-15T00:00:00},
  url       = {https://teams.microsoft.com/l/file/89E0DBCF-1FE3-4282-9E07-6C1FC01A0ABA?tenantId=82c51a82-548d-43ca-bcf9-bf4b7eb1d012&fileType=pdf&objectUrl=https://vult.sharepoint.com/sites/Formalistai/Shared Documents/General/TLA Lectures 2021/MSC_SEMM_TLA-02-AbsRef.pdf&baseUrl=https://vult.sharepoint.com/sites/Formalistai&serviceName=teams&threadId=19:fdd19a50fb364312873fedfcc61058eb@thread.tacv2&groupId=47d21ac7-f5b8-42e0-894d-71e7846be09e},
}

@Presentation{Petrauskas2021b,
  author    = {Karolis Petrauskas},
  title     = {Software engineering models and methods: {TLA$^{+}$} lecture 3/3: proofs},
  year      = {2021},
  comment   = {Original file name: MSC_SEMM_TLA-03-Proofs.pdf
You need to be logged in into MS Teams to follow the Teams URL link.},
  file      = {:by-author/P/Petrauskas/2021_Petrauskas_1b.pdf:PDF},
  owner     = {saulius},
  pages     = {1--49},
  timestamp = {2021.04.15},
  creationdate = {2021-04-15T00:00:00},
  url       = {https://teams.microsoft.com/l/file/7006D767-5676-4C6A-AEC8-16CC7F751930?tenantId=82c51a82-548d-43ca-bcf9-bf4b7eb1d012&fileType=pdf&objectUrl=https://vult.sharepoint.com/sites/Formalistai/Shared Documents/General/TLA Lectures 2021/MSC_SEMM_TLA-03-Proofs.pdf&baseUrl=https://vult.sharepoint.com/sites/Formalistai&serviceName=teams&threadId=19:fdd19a50fb364312873fedfcc61058eb@thread.tacv2&groupId=47d21ac7-f5b8-42e0-894d-71e7846be09e},
}

@Webpage{DCIS2001,
  author    = {{Daylight Chemical Information Systems Inc.}},
  retrieved = {2021-04-16},
  title     = {Reaction {SMILES} and {SMIRKS}},
  url       = {https://www.daylight.com/meetings/summerschool01/course/basics/smirks.html},
  siteurl   = {https://www.daylight.com},
  year      = {2001},
  file      = {:by-author/D/DCIS/2001_DCIS_1.pdf:PDF;:by-author/D/DCIS/2001_DCIS_1.odt:OpenDocument text},
  keywords  = {Chemiinformatics; Reaction SMILES; SMILES; SMIRKS},
  owner     = {saulius},
  pages     = {1--4},
  timestamp = {2021.04.16},
  creationdate = {2021-04-16T00:00:00},
}

@Article{McDonald1994,
  author          = {McDonald, I. K. and Thornton, J. M.},
  journal         = {Journal of molecular biology},
  title           = {Satisfying hydrogen bonding potential in proteins.},
  year            = {1994},
  issn            = {0022-2836},
  month           = may,
  pages           = {777--793},
  volume          = {238},
  abstract        = {We have analysed the frequency with which potential hydrogen bond donors and acceptors are satisfied in protein molecules. There are a small percentage of nitrogen or oxygen atoms that do not form hydrogen bonds with either solvent or protein atoms, when standard criteria are used. For high resolution structures 9.5% and 5.1% of buried main-chain nitrogen and oxygen atoms, respectively, fail to hydrogen bond under our standard criteria, representing 5.8% and 2.1% of all main-chain nitrogen and oxygen atoms. We find that as the resolution of the data improves, the percentages fall. If the hydrogen bond criteria are relaxed many of these unsatisfied atoms form weak hydrogen bonds. However, there remain some buried atoms (1.3% NH and 1.8% CO) that fail to hydrogen bond without any immediately obvious compensating interactions.},
  chemicals       = {Amino Acids, Proteins, Hydrogen, Nitrogen, Oxygen},
  citation-subset = {IM},
  completed       = {1994-06-16},
  country         = {England},
  creationdate    = {2021-04-19T00:00:00},
  doi             = {10.1006/jmbi.1994.1334},
  file            = {:by-author/M/McDonald/1994_McDonald_777.pdf:PDF},
  issn-linking    = {0022-2836},
  issue           = {5},
  keywords        = {Algorithms; Amino Acids; Chemistry; Hydrogen; Hydrogen Bonding; Nitrogen; Oxygen; Protein Structure; Proteins; Secondary},
  nlm-id          = {2985088R},
  owner           = {saulius},
  pii             = {S0022-2836(84)71334-9},
  pmid            = {8182748},
  pubmodel        = {Print},
  pubstate        = {ppublish},
  revised         = {2013-11-21},
  timestamp       = {2021.04.19},
}

@Article{Torshin2002a,
  author    = {Ivan Y. Torshin and Irene T. Weber and Robert W. Harrison},
  journal   = {Protein Engineering, Design and Selection},
  title     = {Geometric criteria of hydrogen bonds in proteins and identification of {\textasciigrave}bifurcated{\textquotesingle} hydrogen bonds},
  year      = {2002},
  month     = {may},
  number    = {5},
  pages     = {359--363},
  volume    = {15},
  doi       = {10.1093/protein/15.5.359},
  file      = {:by-author/T/Torshin/2002_Torshin_359.pdf:PDF},
  keywords  = {Bioinformatics; H-bond Donor and Acceptor Criteria; Hydrogen Bonds},
  owner     = {saulius},
  publisher = {Oxford University Press ({OUP})},
  timestamp = {2021.04.19},
  creationdate = {2021-04-19T00:00:00},
}

@InBook{DaPoian2020,
  author    = {Da Poian, Andrea T. and Castanho, Miguel A. R. B.},
  chapter   = {3},
  pages     = {89--185},
  publisher = {Springer},
  title     = {The families of biological molecules},
  year      = {2020},
  month     = {May},
  abstract  = {Diversity is essential to the sustainability of living systems. This is true for species in ecosystems as it is for molecules in cells, tissues, and organisms. Yet, the same way different species are linked by common ancestors and may be grouped in taxonomic classes according to common characteristics they share, molecules may be grouped in classes and classified according to common chemical and physical characteristics. One of such characteristics is solubility in water (in other words: how polar atoms are distributed in the 3D structure of molecules). One class of biological molecules, the lipids, includes only low water solubility (“hydrophobic”) molecules, this being the characteristic that defines this class. Other classes include molecules that are mostly moderately or highly soluble in water and can be recognized for the dominant presence of specific chemical groups: OH in saccharides (also referred to as “carbohydrates”) and a combination of amino and carboxyl groups in amino acids. Lipids, saccharides, and amino acids may combine with molecules of its own class to form either polymers (molecules formed by successively covalently attaching smaller molecules), such as polysaccharides and proteins, or supramolecular assemblies (organized arrangements of molecules that are in contact but are not covalently attached), such as the lipid bilayer of cell membranes. It is common to find molecules and supramolecular assemblies that combine elements from different classes, such as nucleotides, which contain saccharides. Proteins are extremely versatile in this regard because proteins’ interactions with saccharides, lipids, and nucleic acids (nucleotide polymers) are ubiquitous in virtually all cells. Figure 3.1 depicts the basic principles that support the organization of biological molecules in different classes.},
  doi       = {10.1007/978-3-030-48740-9_3},
  file      = {:by-author/D/DaPoian/2020_DaPoian_89.pdf:PDF},
  journal   = {Integrative Human BiochemistryA Textbook for Medical Biochemistry},
  keywords  = {Biochemistry; Bioinformatics; Biological Molecules; Chirality; For Teaching; Overview},
  owner     = {saulius},
  timestamp = {2021.04.19},
  creationdate = {2021-04-19T00:00:00},
  url       = {https://europepmc.org/articles/PMC7980830},
}

@Article{Chung1984,
  author    = {Chung, S. J. and Hahn, Th. and Klee, W. E.},
  journal   = {Acta Crystallographica Section A},
  title     = {Nomenclature and generation of three-periodic nets: the vector method},
  year      = {1984},
  month     = {Jan},
  number    = {1},
  pages     = {42--50},
  volume    = {40},
  abstract  = {Three-periodic nets are connected graphs which permit embeddings having a threefold periodicity. To many crystal structures such nets can be meaningfully assigned and used to express the topology of the structures. It is shown that such a net can be fully characterized by a finite graph in which the edges are labelled in a suitable way. The reversal of the process of assigning a labelled finite graph to a given net can be used to generate nets of real and hypothetical crystal structures in a systematic fashion.},
  comment   = {Cited by Eon2016: "The combinatorial topology of a crystal structure, being defined by the _underlying net_  (Alexandrov2011), can be encoded in a labelled quotient graph (Chung1984)."},
  doi       = {10.1107/S0108767384000088},
  file      = {:by-author/C/Chung/1984_Chung_42.pdf:PDF},
  owner     = {saulius},
  timestamp = {2021.04.20},
  creationdate = {2021-04-20T00:00:00},
  url       = {https://doi.org/10.1107/S0108767384000088},
}

@Presentation{Arafah2018a,
  author       = {Mohammed Amer Arafah},
  title        = {8086/8088 hardware specifications},
  year         = {2018},
  course       = {CEN433},
  organization = {King Saud University},
  file         = {:by-author/A/Arafah/2018_Arafah_1a.pdf:PDF},
  keywords     = {Computer Architecture; Computer Science (CS)},
  owner        = {saulius},
  pages        = {1--67},
  timestamp = {2021.04.20},
  creationdate = {2021-04-20T00:00:00},
  url          = {https://fac.ksu.edu.sa/sites/default/files/part1_8088.pdf},
}

@Manual{Patterson2015,
  title     = {Free and open {RISC-V} reference card},
  author    = {David Patterson},
  year      = {2015},
  file      = {:by-author/P/Patterson/2015_Patterson_1.pdf:PDF},
  keywords  = {Computer Science (CS); Documentation; RISC-V},
  owner     = {saulius},
  pages     = {1--2},
  timestamp = {2021.04.20},
  creationdate = {2021-04-20T00:00:00},
  url       = {https://ascslab.org/research/briscv/simulator/manual.html},
}

@Article{Baez2017,
  author        = {John C. Baez},
  journal       = {London Math. Soc. Newsletter 476 (2018), 18-23},
  title         = {From the Icosahedron to E8},
  year          = {2017},
  month         = dec,
  pages         = {1--9},
  abstract      = {The regular icosahedron is connected to many exceptional objects in mathematics. Here we describe two constructions of the $\mathrm{E}_8$ lattice from the icosahedron. One uses a subring of the quaternions called the "icosians", while the other uses du Val's work on the resolution of Kleinian singularities. Together they link the golden ratio, the quaternions, the quintic equation, the 600-cell, and the Poincare homology 3-sphere. We leave it as a challenge to the reader to find the connection between these two constructions.},
  archiveprefix = {arXiv},
  eprint        = {1712.06436},
  file          = {:by-author/B/Baez/2017_Baez_1.pdf:PDF},
  keywords      = {Icosahedron; Mathematics; Quaternions; Symmetry},
  owner         = {saulius},
  primaryclass  = {math.HO},
  timestamp = {2021.04.21},
  creationdate = {2021-04-21T00:00:00},
}

@Article{Curry1934,
  author    = {H. B. Curry},
  journal   = {Proceedings of the National Academy of Sciences},
  title     = {Functionality in combinatory logic},
  year      = {1934},
  month     = {nov},
  number    = {11},
  pages     = {584--590},
  volume    = {20},
  doi       = {10.1073/pnas.20.11.584},
  file      = {:by-author/C/Curry/1934_Curry_584.pdf:PDF},
  keywords  = {Computer Science (CS); Curry-Howard Correspondence; Logic; Program Correctness Proofs; Semantics},
  owner     = {saulius},
  publisher = {Proceedings of the National Academy of Sciences},
  timestamp = {2021.04.21},
  creationdate = {2021-04-21T00:00:00},
}

@Manuscript{Smolka2008,
  author    = {Gert Smolka and Jan Schwinghammer},
  title     = {Lecture notes for semantics ({WS} 07/08)},
  year      = {2008},
  keywords  = {Computer Science (CS); Curry-Howard Correspondence; Logic; Program Correctness Proofs; Semantics},
  url       = {https://www.ps.uni-saarland.de/courses/sem-ws07/notes/0.pdf},
  file      = {:by-author/S/Smolka/2008_Smolka_1.pdf:PDF},
  owner     = {saulius},
  pages     = {1--96},
  timestamp = {2021.04.21},
  creationdate = {2021-04-21T00:00:00},
}

@Manuscript{Goldblatt2011,
  author    = {Robert Goldblatt},
  title     = {Mathematical modal logic: a view of its evolution},
  year      = {2011},
  keywords  = {Computer Science (CS); Mathematics; Modal Logic; Proof Theory},
  url       = {https://homepages.ecs.vuw.ac.nz/~rob/papers/modalhist.pdf},
  comment   = {Probably published as: Handbook of the History of Logic.  Volume 7 Dov M. Gabbay and John Woods (Editors) ©2006 Elsevier BV.},
  file      = {:by-author/G/Goldblatt/2011_Goldblatt_1.pdf:PDF},
  owner     = {saulius},
  pages     = {1--98},
  timestamp = {2021.04.21},
  creationdate = {2021-04-21T00:00:00},
}

@Manuscript{Kocher2018,
  author    = {Paul Kocher and Jann Horn and Anders Fogh and Daniel Genkin and Daniel Gruss and Werner Haas and Mike Hamburg and Moritz Lipp and Stefan Mangard and Thomas Prescher and Michael Schwarz and Yuval Yarom},
  title     = {Spectre attacks: exploiting speculative execution},
  year      = {2018},
  keywords  = {Computer Science (CS); Computer Security; Spectre; Speculative Execution},
  url       = {https://spectreattack.com/spectre.pdf},
  file      = {:by-author/K/Kocher/2018_Kocher_1.pdf:PDF},
  owner     = {saulius},
  pages     = {1--19},
  timestamp = {2021.04.22},
  creationdate = {2021-04-22T00:00:00},
}

@InProceedings{Kocher2019,
  author    = {Paul Kocher and Jann Horn and Anders Fogh and Daniel Genkin and Daniel Gruss and Werner Haas and Mike Hamburg and Moritz Lipp and Stefan Mangard and Thomas Prescher and Michael Schwarz and Yuval Yarom},
  booktitle = {2019 {IEEE} Symposium on Security and Privacy ({SP})},
  title     = {Spectre Attacks: Exploiting Speculative Execution},
  year      = {2019},
  month     = {may},
  pages     = {1--19},
  publisher = {{IEEE}},
  doi       = {10.1109/sp.2019.00002},
  file      = {:by-author/K/Kocher/2019_Kocher_1.pdf:PDF},
  keywords  = {Computer Science (CS); Computer Security; Spectre; Speculative Execution},
  owner     = {saulius},
  timestamp = {2021.04.22},
  creationdate = {2021-04-22T00:00:00},
}

@Article{Porter2006,
  author    = {M. F. Porter},
  journal   = {Program},
  title     = {An algorithm for suffix stripping},
  year      = {2006},
  month     = {jul},
  number    = {3},
  pages     = {211--218},
  volume    = {40},
  doi       = {10.1108/00330330610681286},
  file      = {:by-author/P/Porter/2006_Porter_211.pdf:PDF},
  keywords  = {NLP; Natural Language Processing},
  owner     = {saulius},
  publisher = {Emerald},
  timestamp = {2021.04.23},
  creationdate = {2021-04-23T00:00:00},
  url       = {https://www.emerald.com/insight/content/doi/10.1108/eb046814/full/html},
}

@InCollection{WardeFarley2016,
  author       = {David Warde-Farley and Ian Goodfellow},
  booktitle    = {Perturbations, Optimization, and Statistics},
  publisher    = {The {MIT} Press},
  title        = {Adversarial perturbations of deep neural networks},
  year         = {2016},
  pages        = {311--342},
  creationdate = {2021-04-23T13:21:09},
  doi          = {10-7551/mitpress/10761-003.0012},
  file         = {:by-author/W/Warde-Farley/2016_Warde-Farley_311.pdf:PDF},
  keywords     = {Adversarial Neural Networks; Artificial Neural Networks (ANN); Computer Science (CS)},
  owner        = {saulius},
  timestamp = {2021.04.23},
}

@InCollection{Miller2019,
  author    = {Arthur I. Miller},
  booktitle = {The Artist in the Machine},
  publisher = {The {MIT} Press},
  title     = {{I}an {G}oodfellow's {G}enerative {A}dversarial {N}etworks: {AI} learns to imagine},
  year      = {2019},
  pages     = {87--98},
  doi       = {10.7551/mitpress/11585.003.0015},
  file      = {:by-author/M/Miller/2019_Miller_87.pdf:PDF},
  owner     = {saulius},
  timestamp = {2021.04.23},
  creationdate = {2021-04-23T00:00:00},
}

@InCollection{Louridas2020,
  author    = {Panos Louridas},
  booktitle = {Algorithms},
  publisher = {The {MIT} Press},
  title     = {{PageRank}},
  year      = {2020},
  pages     = {143--180},
  doi       = {10.7551/mitpress/11884.003.0008},
  file      = {:by-author/L/Louridas/2020_Louridas_143.pdf:PDF},
  keywords  = {Algorithms; Computer Science (CS); PageRank},
  owner     = {saulius},
  timestamp = {2021.04.23},
  creationdate = {2021-04-23T00:00:00},
}

@InCollection{Louridas2020a,
  author    = {Panos Louridas},
  booktitle = {Algorithms},
  publisher = {The {MIT} Press},
  title     = {Deep learning},
  year      = {2020},
  pages     = {181--230},
  doi       = {10.7551/mitpress/11884.003.0009},
  file      = {:by-author/L/Louridas/2020_Louridas_181.pdf:PDF},
  keywords  = {Algorithms; Artificial Neural Networks (ANN); Computer Science (CS); Deep Learning (DL)},
  owner     = {saulius},
  timestamp = {2021.04.23},
  creationdate = {2021-04-23T00:00:00},
}

@InCollection{Louridas2020b,
  author    = {Panos Louridas},
  booktitle = {Algorithms},
  publisher = {The {MIT} Press},
  title     = {Graphs},
  year      = {2020},
  pages     = {43--78},
  doi       = {10.7551/mitpress/11884.003.0005},
  file      = {:by-author/L/Louridas/2020_Louridas_43.pdf:PDF},
  keywords  = {Algorithms; Computer Science (CS); Graphs},
  owner     = {saulius},
  timestamp = {2021.04.23},
  creationdate = {2021-04-23T00:00:00},
}

@InCollection{Louridas2020c,
  author    = {Panos Louridas},
  booktitle = {Algorithms},
  publisher = {The {MIT} Press},
  title     = {Searching},
  year      = {2020},
  pages     = {79--104},
  doi       = {10.7551/mitpress/11884.003.0006},
  file      = {:by-author/L/Louridas/2020_Louridas_79.pdf:PDF},
  owner     = {saulius},
  timestamp = {2021.04.23},
  creationdate = {2021-04-23T00:00:00},
}

@InProceedings{Lipp2020,
  author    = {Moritz Lipp and Vedad Hažić and Michael Schwarz and Arthur Perais and Clémentine Maurice and Daniel Gruss},
  booktitle = {Proceedings of the 15th {ACM} Asia Conference on Computer and Communications Security},
  title     = {Take a way: exploring the security implications of {AMD}{\textquotesingle}s cache way predictors},
  year      = {2020},
  month     = {oct},
  pages     = {1--14},
  publisher = {{ACM}},
  doi       = {10.1145/3320269.3384746},
  file      = {:by-author/L/Lipp/2020_Lipp_1.pdf:PDF},
  keywords  = {AMD; CPU Vulnerability; Cache; Computer Science (CS); Computer Security},
  owner     = {saulius},
  timestamp = {2021.04.23},
  creationdate = {2021-04-23T00:00:00},
}

@Manuscript{Lipp2020a,
  author    = {Moritz Lipp and Vedad Hažić and Michael Schwarz and Arthur Perais and Clémentine Maurice and Daniel Gruss},
  title     = {Take a way: exploring the security implications of {AMD}{\textquotesingle}s cache way predictors},
  year      = {2020},
  keywords  = {AMD; CPU Vulnerability; Cache; Computer Science (CS); Computer Security},
  url       = {https://mlq.me/download/takeaway.pdf},
  file      = {:by-author/L/Lipp/2020_Lipp_1a.pdf:PDF},
  owner     = {saulius},
  pages     = {1--13},
  timestamp = {2021.04.23},
  creationdate = {2021-04-23T00:00:00},
}

@Manuscript{Rizzo1999,
  author    = {C. J. Rizzo},
  title     = {Fischer projection},
  year      = {1999},
  keywords  = {Chemistry; Fisher Projections; Stereochemistry},
  url       = {https://www.vanderbilt.edu/AnS/Chemistry/Rizzo/Chem220b/Fischer.pdf},
  comment   = {Describes also Haworth Projections.},
  file      = {:by-author/R/Rizzo/1999_Rizzo_1.pdf:PDF},
  owner     = {saulius},
  pages     = {1--4},
  timestamp = {2021.04.27},
  creationdate = {2021-04-27T00:00:00},
}

@Manuscript{Barbaro2007,
  author    = {John Barbaro},
  title     = {Drawing sugar structures: {F}ischer projections, {H}aworth structures and chair conformers},
  year      = {2007},
  keywords  = {Chemistry; Fisher Projections; Stereochemistry},
  url       = {http://www.chtf.stuba.sk/~szolcsanyi/education/files/Chemia heterocyklickych zlucenin/Prednaska 6/Odporucane studijne materialy/Drawing sugar structures.pdf},
  file      = {:by-author/B/Barbaro/2007_Barbaro_1.pdf:PDF},
  owner     = {saulius},
  pages     = {1--7},
  timestamp = {2021.04.27},
  creationdate = {2021-04-27T00:00:00},
}

@Manuscript{Holmes2010,
  author           = {Randall R. Holmes and Tin-Yau Tam},
  title            = {Group representations},
  year             = {2010},
  keywords         = {Group Representations; Group Theory; Mathematics; Representation Theory},
  url              = {https://web.auburn.edu/holmerr/papers/group%20representations%20-%20crc.pdf},
  creationdate     = {2021-04-29T00:00:00},
  file             = {:by-author/H/Holmes/2010_Holmes_1.pdf:PDF},
  modificationdate = {2023-11-08T15:05:51},
  owner            = {saulius},
  pages            = {1--19},
  timestamp        = {2021.04.29},
}

@MastersThesis{Arenas2005,
  author           = {Ruben Arenas},
  school           = {Claremont Colleges, Harvey Mudd College},
  title            = {Constructing a matrix representation of the {L}ie group {G2}},
  year             = {2005},
  creationdate     = {2021-04-29T00:00:00},
  file             = {:by-author/A/Arenas/2005_Arenas_1.pdf:PDF},
  keywords         = {Group Representations; Group Theory; Mathematics},
  modificationdate = {2023-11-08T15:06:04},
  owner            = {saulius},
  pages            = {1--101},
  timestamp        = {2021.04.29},
  url              = {https://scholarship.claremont.edu/cgi/viewcontent.cgi?article=1169&context=hmc_theses},
}

@MastersThesis{Saikia2015,
  author           = {Manjil P. Saikia},
  school           = {The Abdus Salam International Centre for Theoretical Physics},
  title            = {Representations of the symmetric group},
  year             = {2015},
  creationdate     = {2021-04-29T00:00:00},
  file             = {:by-author/S/Saikia/2015_Saikia_1.pdf:PDF},
  keywords         = {Group Representations; Group Theory; Mathematics; Representation Theory},
  modificationdate = {2023-11-08T15:07:30},
  owner            = {saulius},
  pages            = {1--44},
  timestamp        = {2021.04.29},
  url              = {https://homepage.univie.ac.at/manjil.saikia/thesis/saikia-diploma-thesis.pdf},
}

@Manuscript{Kreher2020,
  author    = {Donald L. Kreher},
  title     = {Group theory notes},
  year      = {2020},
  keywords  = {Group Theory; Mathematics},
  url       = {https://pages.mtu.edu/~kreher/ABOUTME/syllabus/GTN.pdf},
  file      = {:by-author/K/Kreher/2020_Kreher_1.pdf:PDF},
  owner     = {saulius},
  pages     = {1--135},
  timestamp = {2021.04.29},
  creationdate = {2021-04-29T00:00:00},
}

@Presentation{Suslick2014,
  author           = {Ken Suslick},
  title            = {Origin of character tables},
  year             = {2014},
  creationdate     = {2021-04-29T00:00:00},
  file             = {:by-author/S/Suslick/2014_Suslick_1.pdf:PDF},
  keywords         = {Group Characters; Group Representations; Group Theory; Mathematics; Representation Theory},
  modificationdate = {2023-11-08T15:07:57},
  owner            = {saulius},
  pages            = {1--19},
  timestamp        = {2021.04.29},
  url              = {http://xuv.scs.illinois.edu/516/lectures/chem516.02.pdf},
}

@Webpage{Vallance2020,
  author    = {Claire Vallance},
  retrieved = {2021-04-29 19:25:34 EEST},
  title     = {Matrix representations of groups},
  url       = {https://chem.libretexts.org/@go/page/9361},
  year      = {2020},
  file      = {:by-author/V/Vallance/2020_Vallance_1.pdf:PDF},
  keywords  = {Chemistry; Group Theory; Mathematics; Molecule Symmetry},
  owner     = {saulius},
  pages     = {1--3},
  refid     = {temp_id_6836975899854971},
  timestamp = {2021.04.29},
  creationdate = {2021-04-29T00:00:00},
}

@Book{Vallance2020a,
  author    = {Claire Vallance},
  title     = {Symmetry},
  year      = {2020},
  file      = {:by-author/V/Vallance/2020_Vallance_1a.pdf:PDF},
  keywords  = {Chemistry; Group Theory; Mathematics; Molecule Symmetry},
  owner     = {saulius},
  pages     = {1--83},
  refid     = {temp_id_8607640493518055},
  timestamp = {2021.04.29},
  creationdate = {2021-04-29T00:00:00},
  url       = {https://chem.libretexts.org/@go/page/1883},
}

@Presentation{Berg2012,
  author    = {Benno van den Berg},
  title     = {Slides for a course on model theory},
  year      = {2012},
  file      = {:by-author/B/Berg/2012_Berg_1.pdf:PDF},
  keywords  = {Computer Science (CS); History of Logic; Logic; Mathematics; Model Theory},
  owner     = {saulius},
  pages     = {1--22},
  timestamp = {2021.05.03},
  creationdate = {2021-05-03T00:00:00},
  url       = {https://staff.fnwi.uva.nl/b.vandenberg3/Onderwijs/Modeltheory_2012/slides_modeltheorie_lecture1.pdf},
}

@TechReport{Kent2006,
  author    = {K. Kent and M. P. Souppaya},
  title     = {Guide to computer security log management},
  year      = {2006},
  comment   = {Other URL with different contents (reached from resolving the DOI): https://nvlpubs.nist.gov/nistpubs/Legacy/SP/nistspecialpublication800-92.pdf .},
  doi       = {10.6028/nist.sp.800-92},
  file      = {:by-author/K/Kent/2006_Kent_1.pdf:PDF;:by-author/K/Kent/2006_Kent_1a.pdf:PDF},
  keywords  = {Computer Science (CS); Computer Security},
  owner     = {saulius},
  pages     = {1--72},
  publisher = {National Institute of Standards and Technology},
  timestamp = {2021.05.08},
  creationdate = {2021-05-08T00:00:00},
  url       = {https://www.govinfo.gov/content/pkg/GOVPUB-C13-52c3b5520393598b18782a7b55fde7e6/pdf/GOVPUB-C13-52c3b5520393598b18782a7b55fde7e6.pdf},
}

@Presentation{Gudeliene2020,
  author    = {Danutė Gudelienė and Antanas Apynis},
  title     = {Matematikos mokymosi turinys},
  year      = {2020},
  comment   = {Mini terminus: „transformacijos, posūkis, postūmis, atspindys“.},
  file      = {:by-author/G/Gudelienė/2020_Gudelienė_1.pdf:PDF},
  keywords  = {Matematika; Matematikos Terminai; Mathematics; Terminology},
  owner     = {saulius},
  pages     = {1--24},
  timestamp = {2021.05.12},
  creationdate = {2021-05-12T00:00:00},
  url       = {https://www.emokykla.lt/upload/EMOKYKLA/Nuotolinis/renginiu_medziaga/matematinis/Matematikos mokymosi turinys. Danutė Gudelienė, Antanas Apynis, 2020-09-04.pdf},
}

@Manuscript{Chen2014a,
  author    = {Daming D. Chen and Gail-Joon Ahn},
  title     = {Security analysis of {x86} processor microcode},
  year      = {2014},
  keywords  = {Computer Science (CS); Microcode; Security; X86},
  url       = {https://www.dcddcc.com/docs/2014_paper_microcode.pdf},
  file      = {:by-author/C/Chen/2014_Chen_1.pdf:PDF},
  owner     = {saulius},
  pages     = {1--23},
  timestamp = {2021.05.18},
  creationdate = {2021-05-18T00:00:00},
}

@Manuscript{Koppe2017,
  author    = {Philipp Koppe and Benjamin Kollenda and Marc Fyrbiak and Christian Kison and Robert Gawlik and Christof Paar and Thorsten Holz},
  title     = {Reverse engineering {x86} processor microcode},
  year      = {2017},
  keywords  = {Computer Science (CS); Microcode; Security; X86},
  url       = {https://www.usenix.org/system/files/conference/usenixsecurity17/sec17-koppe.pdf},
  file      = {:by-author/K/Koppe/2017_Koppe_1.pdf:PDF},
  owner     = {saulius},
  pages     = {1--19},
  timestamp = {2021.05.18},
  creationdate = {2021-05-18T00:00:00},
}

@Manuscript{Alliet2004,
  author           = {Brian Alliet and Adam Megacz},
  title            = {Complete translation of unsafe native code to safe bytecode},
  year             = {2004},
  keywords         = {C; C-to-Java Compiler; C/C++; Compiler; Compiler Construction; Computer Science (CS); JVM; Java; MIPS; R2000; Safe Execution},
  url              = {http://www.megacz.com/berkeley/research/papers/nestedvm.ivme04.pdf},
  creationdate     = {2021-05-20T00:00:00},
  file             = {:by-author/A/Alliet/2004_Alliet_1.pdf:PDF},
  modificationdate = {2024-05-06T17:54:30},
  owner            = {saulius},
  pages            = {1--10},
  timestamp        = {2021.05.20},
}

@InCollection{Gilreath2003,
  author    = {William F. Gilreath and Phillip A. Laplante},
  booktitle = {Computer Architecture: A Minimalist Perspective},
  publisher = {Springer {US}},
  title     = {Types of computer architectures},
  year      = {2003},
  pages     = {15--21},
  doi       = {10.1007/978-1-4615-0237-1_3},
  file      = {:by-author/G/Gilreath/2003_Gilreath_15.pdf:PDF},
  keywords  = {Computer Architecture; Computer Science (CS)},
  owner     = {saulius},
  timestamp = {2021.05.23},
  creationdate = {2021-05-23T00:00:00},
}

@Presentation{Arvind2006c,
  author    = {Arvind and Krste Asanovic},
  title     = {Instruction set evolutionin the sixties: {GPR}, stack, and load-store architectures},
  year      = {2006},
  course    = {Computer System Architecture},
  lecture   = {3},
  school    = {MIT},
  file      = {:by-author/A/Arvind/2006_Arvind_1c.pdf:PDF},
  keywords  = {Computer Architecture; Computer Science (CS); Instruction Set Architecture},
  owner     = {saulius},
  pages     = {1--32},
  timestamp = {2021.05.27},
  creationdate = {2021-05-27T00:00:00},
  url       = {https://ocw.mit.edu/courses/electrical-engineering-and-computer-science/6-823-computer-system-architecture-fall-2005/lecture-notes/l03_sixties.pdf},
}

@Manuscript{Atkins2006,
  author    = {P. W. Atkins and M. S. Child and C. S. G. Phillips},
  title     = {Tables for group theory},
  year      = {2006},
  keywords  = {Group Multiplication Tables; Group Theory},
  url       = {https://www.ifi.unicamp.br/~cabrera/teaching/tabela.pdf},
  file      = {:by-author/A/Atkins/2006_Atkins_1.pdf:PDF},
  owner     = {saulius},
  pages     = {1--39},
  timestamp = {2021.05.27},
  creationdate = {2021-05-27T00:00:00},
}

@Lecture{Hughbanks2017,
  author    = {Timothy Hughbanks},
  title     = {Molecules and symmetry groups},
  year      = {2017},
  file      = {:by-author/H/Hughbanks/2017_Hughbanks_1.pdf:PDF},
  keywords  = {Chemistry; Group Theory},
  owner     = {saulius},
  pages     = {1--10},
  timestamp = {2021.05.27},
  creationdate = {2021-05-27T00:00:00},
  url       = {https://www.chem.tamu.edu/rgroup/hughbanks/courses/673/lecturenotes/notes-2.pdf},
}

@Presentation{Arvind2006a,
  author    = {Arvind and Krste Asanovic},
  title     = {Early developments: from {D}ifference {E}ngine to {IBM} 701},
  year      = {2006},
  course    = {Computer System Architecture},
  lecture   = {1},
  school    = {MIT},
  file      = {:by-author/A/Arvind/2006_Arvind_1a.pdf:PDF},
  keywords  = {Computer Architecture; Computer History; Computer Science (CS); Instruction Set Architecture},
  owner     = {saulius},
  pages     = {1--24},
  timestamp = {2021.05.27},
  creationdate = {2021-05-27T00:00:00},
  url       = {https://ocw.mit.edu/courses/electrical-engineering-and-computer-science/6-823-computer-system-architecture-fall-2005/lecture-notes/l01_earlydev.pdf},
}

@Presentation{Arvind2006b,
  author    = {Arvind and Krste Asanovic},
  title     = {Influence of technology and software on instruction sets: up to the dawn of {IBM} 360},
  year      = {2006},
  course    = {Computer System Architecture},
  lecture   = {2},
  school    = {MIT},
  file      = {:by-author/A/Arvind/2006_Arvind_1b.pdf:PDF},
  keywords  = {Computer Architecture; Computer History; Computer Science (CS); Instruction Set Architecture},
  owner     = {saulius},
  pages     = {1--30},
  timestamp = {2021.05.27},
  creationdate = {2021-05-27T00:00:00},
  url       = {https://ocw.mit.edu/courses/electrical-engineering-and-computer-science/6-823-computer-system-architecture-fall-2005/lecture-notes/l02_fifties.pdf},
}

@Presentation{Arvind2006d,
  author    = {Arvind and Krste Asanovic},
  title     = {Microprogramming},
  year      = {2006},
  course    = {Computer System Architecture},
  lecture   = {4},
  school    = {MIT},
  file      = {:by-author/A/Arvind/2006_Arvind_1d.pdf:PDF},
  keywords  = {Computer Architecture; Computer History; Computer Science (CS); Instruction Set Architecture; MIPS; RISC},
  owner     = {saulius},
  pages     = {1--38},
  timestamp = {2021.05.27},
  creationdate = {2021-05-27T00:00:00},
  url       = {https://ocw.mit.edu/courses/electrical-engineering-and-computer-science/6-823-computer-system-architecture-fall-2005/lecture-notes/l04_microprog.pdf},
}

@Presentation{Arvind2006e,
  author    = {Arvind and Krste Asanovic},
  title     = {Single-cycle processors: datapath & control},
  year      = {2006},
  course    = {Computer System Architecture},
  lecture   = {5},
  school    = {MIT},
  file      = {:by-author/A/Arvind/2006_Arvind_1e.pdf:PDF},
  keywords  = {Computer Architecture; Computer Science (CS); Instruction Set Architecture; MIPS; RISC},
  owner     = {saulius},
  pages     = {1--34},
  timestamp = {2021.05.27},
  creationdate = {2021-05-27T00:00:00},
  url       = {https://ocw.mit.edu/courses/electrical-engineering-and-computer-science/6-823-computer-system-architecture-fall-2005/lecture-notes/l05_singlecycle.pdf},
}

@Presentation{Arvind2006f,
  author    = {Arvind and Krste Asanovic},
  title     = {Pipeline hazards},
  year      = {2006},
  course    = {Computer System Architecture},
  lecture   = {6},
  school    = {MIT},
  file      = {:by-author/A/Arvind/2006_Arvind_1f.pdf:PDF},
  keywords  = {Computer Architecture; Computer Science (CS); Instruction Set Architecture; MIPS; RISC},
  owner     = {saulius},
  pages     = {1--38},
  timestamp = {2021.05.27},
  creationdate = {2021-05-27T00:00:00},
  url       = {https://ocw.mit.edu/courses/electrical-engineering-and-computer-science/6-823-computer-system-architecture-fall-2005/lecture-notes/l06_pipeline.pdf},
}

@Presentation{Emer2006a,
  author    = {Joel Emer and Krste Asanovic and Arvind},
  title     = {Multilevel memories},
  year      = {2006},
  course    = {Computer System Architecture},
  lecture   = {7},
  school    = {MIT},
  file      = {:by-author/E/Emer/2006_Emer_1a.pdf:PDF},
  keywords  = {Computer Architecture; Computer Science (CS); Instruction Set Architecture; MIPS; Memory Cache; RISC},
  owner     = {saulius},
  pages     = {1--35},
  timestamp = {2021.05.27},
  creationdate = {2021-05-27T00:00:00},
  url       = {https://ocw.mit.edu/courses/electrical-engineering-and-computer-science/6-823-computer-system-architecture-fall-2005/lecture-notes/l07_caches.pdf},
}

@Presentation{Emer2006b,
  author    = {Joel Emer and Krste Asanovic and Arvind},
  title     = {Cache optimizations},
  year      = {2006},
  course    = {Computer System Architecture},
  lecture   = {8},
  school    = {MIT},
  file      = {:by-author/E/Emer/2006_Emer_1b.pdf:PDF},
  keywords  = {Computer Architecture; Computer Science (CS); Instruction Set Architecture; MIPS; Memory Cache; RISC},
  owner     = {saulius},
  pages     = {1--39},
  timestamp = {2021.05.27},
  creationdate = {2021-05-27T00:00:00},
  url       = {https://ocw.mit.edu/courses/electrical-engineering-and-computer-science/6-823-computer-system-architecture-fall-2005/lecture-notes/l08_caches_2.pdf},
}

@Presentation{Emer2006c,
  author    = {Joel Emer and Krste Asanovic and Arvind},
  title     = {Memory management: from absolute addresses to demand paging},
  year      = {2006},
  course    = {Computer System Architecture},
  lecture   = {9},
  school    = {MIT},
  file      = {:by-author/E/Emer/2006_Emer_1c.pdf:PDF},
  keywords  = {Computer Architecture; Computer Science (CS); Instruction Set Architecture; MIPS; Memory Cache; RISC; Virtual Memory},
  owner     = {saulius},
  pages     = {1--33},
  timestamp = {2021.05.27},
  creationdate = {2021-05-27T00:00:00},
  url       = {https://ocw.mit.edu/courses/electrical-engineering-and-computer-science/6-823-computer-system-architecture-fall-2005/lecture-notes/l09_add_trans.pdf},
}

@Presentation{Arvind2006g,
  author    = {Arvind and Krste Asanovic},
  title     = {Modern virtual memory systems},
  year      = {2006},
  course    = {Computer System Architecture},
  lecture   = {10},
  school    = {MIT},
  file      = {:by-author/A/Arvind/2006_Arvind_1g.pdf:PDF},
  keywords  = {Computer Architecture; Computer Science (CS); Instruction Set Architecture; MIPS; Memory Cache; RISC; Virtual Memory},
  owner     = {saulius},
  pages     = {1--34},
  timestamp = {2021.05.27},
  creationdate = {2021-05-27T00:00:00},
  url       = {https://ocw.mit.edu/courses/electrical-engineering-and-computer-science/6-823-computer-system-architecture-fall-2005/lecture-notes/l10_vrtl_mem.pdf},
}

@Presentation{Arvind2006h,
  author    = {Arvind and Krste Asanovic},
  title     = {Complex pipelining},
  year      = {2006},
  course    = {Computer System Architecture},
  lecture   = {11},
  school    = {MIT},
  file      = {:by-author/A/Arvind/2006_Arvind_1h.pdf:PDF},
  keywords  = {Computer Architecture; Computer Science (CS); Floating Point Unit; Instruction Set Architecture; MIPS; Memory Cache; RISC},
  owner     = {saulius},
  pages     = {1--30},
  timestamp = {2021.05.27},
  creationdate = {2021-05-27T00:00:00},
  url       = {https://ocw.mit.edu/courses/electrical-engineering-and-computer-science/6-823-computer-system-architecture-fall-2005/lecture-notes/l11_cmplx_pipes.pdf},
}

@Presentation{Arvind2006i,
  author    = {Arvind and Krste Asanovic},
  title     = {Complex pipelining: out-of-order execution & register renaming},
  year      = {2006},
  course    = {Computer System Architecture},
  lecture   = {12},
  school    = {MIT},
  file      = {:by-author/A/Arvind/2006_Arvind_1i.pdf:PDF},
  keywords  = {Computer Architecture; Computer Science (CS); Floating Point Unit; Instruction Set Architecture; MIPS; Memory Cache; RISC},
  owner     = {saulius},
  pages     = {1--28},
  timestamp = {2021.05.27},
  creationdate = {2021-05-27T00:00:00},
  url       = {https://ocw.mit.edu/courses/electrical-engineering-and-computer-science/6-823-computer-system-architecture-fall-2005/lecture-notes/l12_ooo_pipes.pdf},
}

@Presentation{Arvind2006j,
  author    = {Arvind and Krste Asanovic},
  title     = {Branch prediction and speculative execution},
  year      = {2006},
  course    = {Computer System Architecture},
  lecture   = {13},
  school    = {MIT},
  file      = {:by-author/A/Arvind/2006_Arvind_1j.pdf:PDF},
  keywords  = {Computer Architecture; Computer Science (CS); Instruction Set Architecture; MIPS; RISC},
  owner     = {saulius},
  pages     = {1--38},
  timestamp = {2021.05.27},
  creationdate = {2021-05-27T00:00:00},
  url       = {https://ocw.mit.edu/courses/electrical-engineering-and-computer-science/6-823-computer-system-architecture-fall-2005/lecture-notes/l13_brnchpred.pdf},
}

@Presentation{Emer2006d,
  author    = {Joel Emer and Krste Asanovic and Arvind},
  title     = {Advanced superscalar microprocessors},
  year      = {2006},
  course    = {Computer System Architecture},
  lecture   = {14},
  school    = {MIT},
  file      = {:by-author/E/Emer/2006_Emer_1d.pdf:PDF},
  keywords  = {Computer Architecture; Computer Science (CS); Instruction Set Architecture; MIPS; RISC},
  owner     = {saulius},
  pages     = {1--41},
  timestamp = {2021.05.27},
  creationdate = {2021-05-27T00:00:00},
  url       = {https://ocw.mit.edu/courses/electrical-engineering-and-computer-science/6-823-computer-system-architecture-fall-2005/lecture-notes/l14_superscalar.pdf},
}

@Presentation{Emer2006e,
  author    = {Joel Emer and Krste Asanovic and Arvind},
  title     = {Microprocessor evolution: 4004 to {P}entium-4},
  year      = {2006},
  course    = {Computer System Architecture},
  lecture   = {15},
  file      = {:by-author/E/Emer/2006_Emer_1e.pdf:PDF},
  keywords  = {Computer Architecture; Computer Science (CS); Instruction Set Architecture; MIPS; Pentium; RISC},
  owner     = {saulius},
  pages     = {1--34},
  timestamp = {2021.05.27},
  creationdate = {2021-05-27T00:00:00},
  url       = {https://ocw.mit.edu/courses/electrical-engineering-and-computer-science/6-823-computer-system-architecture-fall-2005/lecture-notes/l15_micro_evlutn.pdf},
}

@Presentation{Mason2007,
  author    = {A. Mason},
  title     = {Review: {CMOS} logic gates},
  year      = {2007},
  file      = {:by-author/M/Mason/2007_Mason_1.pdf:PDF},
  keywords  = {CMOS; Computer Science (CS); Electronics; Fabrication},
  owner     = {saulius},
  pages     = {1--69},
  timestamp = {2021.05.28},
  creationdate = {2021-05-28T00:00:00},
  url       = {https://www.egr.msu.edu/classes/ece410/mason/files/Ch3-5.pdf},
}

@Presentation{Terman2005c,
  author    = {Chris Terman and Krste Asanovic and Arvind},
  title     = {{CMOS} technology and logic gates},
  year      = {2005},
  comment   = {Mentions that NMOS are to be used for pull-down networks (PDNs), and PMOS should be used for pull-up networks (PUNs).},
  file      = {:by-author/C/Christopher/2005_Terman_1c.pdf:PDF},
  keywords  = {CMOS; Computer Science (CS); Electronics; Fabrication},
  owner     = {saulius},
  pages     = {1--37},
  timestamp = {2021.05.28},
  creationdate = {2021-05-28T00:00:00},
  url       = {https://ocw.mit.edu/courses/electrical-engineering-and-computer-science/6-884-complex-digital-systems-spring-2005/lecture-notes/l03_cmos_gates.pdf},
}

@Article{Beals1999,
  author    = {Robert Beals},
  journal   = {Journal of Computer and System Sciences},
  title     = {Algorithms for matrix groups and the {T}its alternative},
  year      = {1999},
  month     = {apr},
  number    = {2},
  pages     = {260--279},
  volume    = {58},
  doi       = {10.1006/jcss.1998.1614},
  file      = {:by-author/B/Beals/1999_Beals_260.pdf:PDF},
  keywords  = {Algebra; Algorithms; Computer Science (CS); Group Theory},
  owner     = {saulius},
  publisher = {Elsevier {BV}},
  timestamp = {2021.05.28},
  creationdate = {2021-05-28T00:00:00},
  url       = {https://www.math.ucla.edu/~pak/papers/Beals.pdf},
}

@Article{Plesken1977,
  author    = {Wilhelm Plesken and Michael Pohs},
  journal   = {Mathematics of computation},
  title     = {On maximal finite irreducible subgroups of {GL(n, Z)}. {I}. {T}he five and seven dimensional cases},
  year      = {1977},
  month     = apr,
  number    = {138},
  pages     = {536--551},
  volume    = {31},
  doi       = {10.2307/2006436},
  file      = {:by-author/P/Plesken/1977_Plesken_536.pdf:PDF},
  keywords  = {Algorithms; Group Theory; Mathematics},
  owner     = {saulius},
  timestamp = {2021.05.28},
  creationdate = {2021-05-28T00:00:00},
  url       = {https://www.ams.org/journals/mcom/1977-31-138/S0025-5718-1977-0444789-X/S0025-5718-1977-0444789-X.pdf},
}

@Article{Eick2002,
  author    = {Bettina Eick and Charles R. B. Wright},
  journal   = {Journal of Symbolic Computation},
  title     = {Computing subgroups by exhibition in finite solvable groups},
  year      = {2002},
  month     = {feb},
  number    = {2},
  pages     = {129--143},
  volume    = {33},
  doi       = {10.1006/jsco.2000.0503},
  file      = {:by-author/E/Eick/2002_Eick_129.pdf:PDF},
  keywords  = {Algorithms; Group Theory; Mathematics},
  owner     = {saulius},
  publisher = {Elsevier {BV}},
  timestamp = {2021.05.28},
  creationdate = {2021-05-28T00:00:00},
  url       = {https://core.ac.uk/download/pdf/82819473.pdf},
}

@Article{Baumslag1991,
  author    = {Gilbert Baumslag and Frank B. Cannonito and Derek J. S. Robinson and Dan Segal},
  journal   = {Journal of Algebra},
  title     = {The algorithmic theory of polycyclic-by-finite groups},
  year      = {1991},
  month     = {sep},
  number    = {1},
  pages     = {118--149},
  volume    = {142},
  doi       = {10.1016/0021-8693(91)90221-s},
  file      = {:by-author/B/Baumslag/1991_Baumslag_118.pdf:PDF},
  keywords  = {Algorithms; Group Theory; Mathematics},
  owner     = {saulius},
  publisher = {Elsevier {BV}},
  timestamp = {2021.05.28},
  creationdate = {2021-05-28T00:00:00},
  url       = {https://core.ac.uk/download/pdf/82601224.pdf},
}

@Article{Leymann2020,
  author    = {Frank Leymann and Johanna Barzen},
  journal   = {Quantum Science and Technology},
  title     = {The bitter truth about gate-based quantum algorithms in the {NISQ} era},
  year      = {2020},
  month     = {sep},
  number    = {4},
  pages     = {044007},
  volume    = {5},
  doi       = {10.1088/2058-9565/abae7d},
  file      = {:by-author/L/Leymann/2020_Leymann_44007.pdf:PDF},
  keywords  = {Computer Science (CS); Error Correcting Codes; Quantum Computing},
  owner     = {saulius},
  publisher = {{IOP} Publishing},
  timestamp = {2021.05.30},
  creationdate = {2021-05-30T00:00:00},
  url       = {https://iopscience.iop.org/article/10.1088/2058-9565/abae7d/pdf},
}

@Article{Nam2018,
  author    = {Yunseong Nam and Neil J. Ross and Yuan Su and Andrew M. Childs and Dmitri Maslov},
  journal   = {npj Quantum Information},
  title     = {Automated optimization of large quantum circuits with continuous parameters},
  year      = {2018},
  month     = {may},
  number    = {1},
  pages     = {1--12},
  volume    = {4},
  doi       = {10.1038/s41534-018-0072-4},
  file      = {:by-author/N/Nam/2018_Nam_1.pdf:PDF},
  keywords  = {Computer Science (CS); Quantum Computers},
  owner     = {saulius},
  publisher = {Springer Science and Business Media {LLC}},
  timestamp = {2021.05.30},
  creationdate = {2021-05-30T00:00:00},
  url       = {https://www.nature.com/articles/s41534-018-0072-4},
}

@MastersThesis{Karlsson2018,
  author    = {Vera Blomkvist Karlsson and Philip Strömberg},
  title     = {4-qubit {G}rover's algorithm implemented for the ibmqx5 architecture},
  year      = {2018},
  file      = {:by-author/K/Karlsson/2018_Karlsson_1.pdf:PDF},
  keywords  = {Computer Science (CS); Quantum Computers},
  owner     = {saulius},
  pages     = {1--46},
  timestamp = {2021.05.30},
  creationdate = {2021-05-30T00:00:00},
  url       = {http://www.diva-portal.org/smash/get/diva2:1214481/FULLTEXT01.pdf},
}

@InCollection{Otten2014,
  author    = {Jens Otten},
  booktitle = {Automated Reasoning},
  publisher = {Springer International Publishing},
  title     = {{MleanCoP}: a connection prover for first-order modal logic},
  year      = {2014},
  pages     = {269--276},
  doi       = {10.1007/978-3-319-08587-6_20},
  file      = {:by-author/O/Otten/2014_Otten_269.pdf:PDF},
  keywords  = {Automated Reasoning; Computer Science (CS); Mathematical Logic; MleanCoP; Proof Assistants},
  owner     = {saulius},
  timestamp = {2021.06.04},
  creationdate = {2021-06-04T00:00:00},
}

@InCollection{Otten2016,
  author    = {Jens Otten},
  booktitle = {Automated Reasoning},
  publisher = {Springer International Publishing},
  title     = {{nanoCoP}: a non-clausal connection prover},
  year      = {2016},
  pages     = {302--312},
  doi       = {10.1007/978-3-319-40229-1_21},
  file      = {:by-author/O/Otten/2016_Otten_302.pdf:PDF},
  keywords  = {Automated Reasoning; Computer Science (CS); Mathematical Logic; MleanCoP; Proof Assistants},
  owner     = {saulius},
  timestamp = {2021.06.04},
  creationdate = {2021-06-04T00:00:00},
}

@Article{Venturelli2019,
  author    = {Davide Venturelli and Minh Do and Bryan O'Gorman and Jeremy Frank and Eleanor Rieffel and Kyle E. C. Booth and Thanh Nguyen and Parvathi Narayan and Sasha Nanda},
  journal   = {ICAPS 2019 Workshop SPARK},
  title     = {Quantum circuit compilation: an emerging application for automated reasoning},
  year      = {2019},
  pages     = {1--9},
  comment   = {PDF UR: https://openreview.net/pdf?id=S1eEBO3nFE},
  file      = {:by-author/V/Venturelli/2019_Venturelli_1.pdf:PDF},
  keywords  = {Artificial Intelligence Planning; Automated Reasoning; Computer Science (CS); Constraint Programming; NISQ; Quantum Circuit Compilation},
  owner     = {saulius},
  timestamp = {2021.06.05},
  creationdate = {2021-06-05T00:00:00},
  url       = {https://openreview.net/forum?id=S1eEBO3nFE},
}

@Article{Preskill2018,
  author    = {John Preskill},
  journal   = {Quantum},
  title     = {Quantum computing in the {NISQ} era and beyond},
  year      = {2018},
  month     = {aug},
  pages     = {79},
  volume    = {2},
  doi       = {10.22331/q-2018-08-06-79},
  file      = {:by-author/P/Preskill/2018_Preskill_79.pdf:PDF},
  keywords  = {Computer Science (CS); NISQ; Quantum Circuit Compilation; Quantum Computing},
  owner     = {saulius},
  publisher = {Verein zur Forderung des Open Access Publizierens in den Quantenwissenschaften},
  timestamp = {2021.06.05},
  creationdate = {2021-06-05T00:00:00},
  url       = {https://quantum-journal.org/papers/q-2018-08-06-79/pdf/},
}

@InProceedings{Kumar2019,
  author    = {Srijan Kumar and Xikun Zhang and Jure Leskovec},
  booktitle = {Proceedings of the 25th {ACM} {SIGKDD} International Conference on Knowledge Discovery {\&} Data Mining},
  title     = {Predicting dynamic embedding trajectory in temporal interaction networks},
  year      = {2019},
  month     = {jul},
  pages     = {1--10},
  publisher = {{ACM}},
  doi       = {10.1145/3292500.3330895},
  file      = {:by-author/K/Kumar/2019_Kumar_1.pdf:PDF},
  keywords  = {Computer Science (CS); JODIE; Prediction Systems},
  owner     = {saulius},
  timestamp = {2021.06.05},
  creationdate = {2021-06-05T00:00:00},
  url       = {https://cs.stanford.edu/~srijan/pubs/jodie-kdd2019.pdf},
}

@Article{Rajan2020a,
  author       = {Kohulan Rajan and Henning Otto Brinkhaus and Achim Zielesny and Christoph Steinbeck},
  journal      = {Journal of Cheminformatics},
  title        = {A review of optical chemical structure recognition tools},
  year         = {2020},
  issn         = {1758-2946},
  month        = {oct},
  number       = {1},
  pages        = {60},
  volume       = {12},
  abstract     = {Structural information about chemical compounds is typically conveyed as 2D images of molecular structures in scientific documents. Unfortunately, these depictions are not a machine-readable representation of the molecules. With a backlog of decades of chemical literature in printed form not properly represented in open-access databases, there is a high demand for the translation of graphical molecular depictions into machine-readable formats. This translation process is known as Optical Chemical Structure Recognition (OCSR). Today, we are looking back on nearly three decades of development in this demanding research field. Most OCSR methods follow a rule-based approach where the key step of vectorization of the depiction is followed by the interpretation of vectors and nodes as bonds and atoms. Opposed to that, some of the latest approaches are based on deep neural networks (DNN). This review provides an overview of all methods and tools that have been published in the field of OCSR. Additionally, a small benchmark study was performed with the available open-source OCSR tools in order to examine their performance.},
  country      = {England},
  doi          = {10.1186/s13321-020-00465-0},
  file         = {:by-author/R/Rajan/2020_Rajan_60.pdf:PDF},
  issn-linking = {1758-2946},
  issue        = {1},
  keywords     = {Chemical Data Extraction; Chemical Structure; Data Mining; Machine Learning (ML); Named Entity Recognition; Open Data; Optical Chemical Structure Recognition},
  nlm-id       = {101516718},
  owner        = {saulius},
  pii          = {10.1186/s13321-020-00465-0},
  pmc          = {PMC7541205},
  pmid         = {33372625},
  publisher    = {Springer Science and Business Media {LLC}},
  pubmodel     = {Electronic},
  pubstate     = {epublish},
  revised      = {2021-01-01},
  timestamp = {2021.03.03},
  creationdate = {2021-03-03T00:00:00},
}

@Presentation{Blanco2007f,
  author    = {Christian Blanco and Brandon Eltiste},
  title     = {Theorem environments},
  year      = {2007},
  course    = {LaTeX for Math and Science},
  file      = {:by-author/B/Blanco/2007_Blanco_1f.pdf:PDF},
  keywords  = {LaTeX; Math Typesetting},
  owner     = {saulius},
  pages     = {1--14},
  timestamp = {2021.06.25},
  creationdate = {2021-06-25T00:00:00},
  url       = {https://www.ocf.berkeley.edu/~latex/files/theorems_lecture6.pdf},
}

@Manuscript{Vektaris2001,
  author    = {G. Vektaris},
  title     = {Kristalo gardelė},
  year      = {2001},
  keywords  = {Crystallography; Solid State Physics},
  url       = {http://www.itpa.lt/~vektaris/lectures/Gardele.pdf},
  comment   = {Pavyzdys, kaip naudojami lietuviški kristalografiniai terminai: „elementarusis narvelis“, „gardelė“, „paprastoji/primityvioji gardelė“, „Bravės gardelė“, „taškinės simetrijos“, „mikroskopinės simetrijos (pvz. sraigtinės ašys), „erdvinės grupės“.},
  file      = {:by-author/V/Vektaris/2001_Vektaris_1.pdf:PDF},
  owner     = {saulius},
  pages     = {1--4},
  timestamp = {2021.07.02T09:39 EEST},
  creationdate = {2021-07-02T09:39 EESTT00:00:00},
  urldate   = {2021-07-02},
}

@Article{Rigden2020,
  author    = {Daniel J Rigden and Xosé M Fernández},
  journal   = {Nucleic Acids Research},
  title     = {The 2021 {Nucleic Acids Research} database issue and the online molecular biology database collection},
  year      = {2020},
  month     = {dec},
  number    = {D1},
  pages     = {D1--D9},
  volume    = {49},
  doi       = {10.1093/nar/gkaa1216},
  file      = {:by-author/R/Rigden/2020_Rigden_1.pdf:PDF},
  keywords  = {Biological Databases; Databases},
  owner     = {saulius},
  publisher = {Oxford University Press ({OUP})},
  timestamp = {2021.07.02},
  creationdate = {2021-07-02T00:00:00},
}

@Article{Spjuth2013,
  author    = {Ola Spjuth and Arvid Berg and Samuel Adams and Egon L. Willighagen},
  journal   = {Journal of Cheminformatics},
  title     = {Applications of the {InChI} in cheminformatics with the {CDK} and {B}ioclipse},
  year      = {2013},
  month     = {mar},
  number    = {1},
  volume    = {5},
  doi       = {10.1186/1758-2946-5-14},
  file      = {:by-author/S/Spjuth/2013_Spjuth_14.pdf:PDF},
  keywords  = {CDK; Chemistry; Chemoinformatics},
  owner     = {saulius},
  publisher = {Springer Science and Business Media {LLC}},
  timestamp = {2021.07.02},
  creationdate = {2021-07-02T00:00:00},
}

@Article{Heller2015,
  author    = {Stephen R. Heller and Alan McNaught and Igor Pletnev and Stephen Stein and Dmitrii Tchekhovskoi},
  journal   = {Journal of Cheminformatics},
  title     = {{InChI}, the {IUPAC} {I}nternational {C}hemical {I}dentifier},
  year      = {2015},
  month     = {may},
  number    = {1},
  pages     = {23},
  volume    = {7},
  doi       = {10.1186/s13321-015-0068-4},
  file      = {:by-author/H/Heller/2015_Heller_23.pdf:PDF},
  keywords  = {Chemoinformatics; InChI},
  owner     = {saulius},
  publisher = {Springer Science and Business Media {LLC}},
  timestamp = {2021.07.04},
  creationdate = {2021-07-04T00:00:00},
}

@Article{Drefahl2011,
  author    = {Axel Drefahl},
  journal   = {Journal of Cheminformatics},
  title     = {{CurlySMILES}: a chemical language to customize and annotate encodings of molecular and nanodevice structures},
  year      = {2011},
  month     = {jan},
  number    = {1},
  pages     = {1},
  volume    = {3},
  comment   = {Cited by Clark2011.},
  doi       = {10.1186/1758-2946-3-1},
  file      = {:by-author/D/Drefahl/2011_Drefahl_1.pdf:PDF},
  keywords  = {Chemoinformatics; CurlySMILES; SMILES; Zero-order Bond Representation},
  owner     = {saulius},
  publisher = {Springer Science and Business Media {LLC}},
  timestamp = {2021.07.04},
  creationdate = {2021-07-04T00:00:00},
}

@InCollection{Reynolds1974,
  author    = {John C. Reynolds},
  booktitle = {Lecture Notes in Computer Science},
  publisher = {Springer Berlin Heidelberg},
  title     = {Towards a theory of type structure},
  year      = {1974},
  pages     = {408--425},
  doi       = {10.1007/3-540-06859-7_148},
  file      = {:by-author/R/Reynolds/1974_Reynolds_408.pdf:PDF},
  keywords  = {Compiler Construction; Computer Science (CS); Programming Languages; Type Systems},
  owner     = {saulius},
  timestamp = {2021.07.07},
  creationdate = {2021-07-07T00:00:00},
  url       = {https://kilthub.cmu.edu/articles/journal_contribution/Towards_a_Theory_of_Type_Structure/6611015/files/12103187.pdf},
}

@TechReport{Detlefs1998,
  author      = {David L. Detlefs and K. Rustan M. Leino and Greg Nelson and James B. Saxe},
  institution = {Compaq Systems Research Center},
  title       = {Extended static checking},
  year        = {1998},
  file        = {:by-author/D/Detlefs/1998_Detlefs_1.pdf:PDF},
  keywords    = {Computer Science (CS); Correctness Proofs; Program Verification; Programming Languages; Type Systems},
  owner       = {saulius},
  pages       = {1--50},
  timestamp = {2021.07.05},
  creationdate = {2021-07-05T00:00:00},
  url         = {https://www.hpl.hp.com/techreports/Compaq-DEC/SRC-RR-159.pdf},
}

@Article{Gries1977,
  author    = {David Gries and Narain Gehani},
  journal   = {Communications of the {ACM}},
  title     = {Some ideas on data types in high-level languages},
  year      = {1977},
  month     = {jun},
  number    = {6},
  pages     = {414--420},
  volume    = {20},
  doi       = {10.1145/359605.359624},
  file      = {:by-author/G/Gries/1977_Gries_414.ps:PostScript;:by-author/G/Gries/1977_Gries_414.pdf:PDF},
  keywords  = {Compiler Construction; Computer Science (CS); Programming Languages; Type Systems},
  owner     = {saulius},
  publisher = {Association for Computing Machinery ({ACM})},
  timestamp = {2021.07.07},
  creationdate = {2021-07-07T00:00:00},
  url       = {https://ecommons.cornell.edu/xmlui/bitstream/handle/1813/6563/75-244.ps?sequence=2},
}

@InProceedings{Mikkonen2008,
  author    = {Tommi Mikkonen and Antero Taivalsaari},
  booktitle = {2008 Sixth International Conference on Software Engineering Research, Management and Applications},
  title     = {Web applications: spaghetti code for the 21st century},
  year      = {2008},
  pages     = {166},
  publisher = {{IEEE}},
  doi       = {10.1109/sera.2008.16},
  file      = {:by-author/M/Mikkonen/2008_Mikkonen_166.pdf:PDF},
  keywords  = {Computer Science (CS); Programming Languages; Type Systems},
  owner     = {saulius},
  timestamp = {2021.07.07},
  creationdate = {2021-07-07T00:00:00},
  url       = {https://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.93.8586&rep=rep1&type=pdf},
}

@Article{Hewitt1973,
  author    = {Hewitt, Carl and Bishop, Peter and Steiger, Richard},
  title     = {A universal modular {ACTOR} formalism for artificial intelligence},
  year      = {1973},
  pages     = {235–245},
  abstract  = {This paper proposes a modular ACTOR architecture and definitional method for artificial intelligence that is conceptually based on a single kind of object: actors [or, if you will, virtual processors, activation frames, or streams]. The formalism makes no presuppositions about the representation of primitive data structures and control structures. Such structures can be programmed, micro-coded, or hard wired in a uniform modular fashion. In fact it is impossible to determine whether a given object is "really" represented as a list, a vector, a hash table, a function, or a process. The architecture will efficiently run the coming generation of PLANNER-like artificial intelligence languages including those requiring a high degree of parallelism. The efficiency is gained without loss of programming generality because it only makes certain actors more efficient; it does not change their behavioral characteristics. The architecture is general with respect to control structure and does not have or need goto, interrupt, or semaphore primitives. The formalism achieves the goals that the disallowed constructs are intended to achieve by other more structured methods.},
  address   = {San Francisco, CA, USA},
  booktitle = {Proceedings of the 3rd International Joint Conference on Artificial Intelligence},
  doi       = {10.5555/1624775.1624804},
  file      = {:by-author/H/Hewitt/1973_Hewitt_235.pdf:PDF},
  location  = {Stanford, USA},
  numpages  = {11},
  owner     = {saulius},
  publisher = {Morgan Kaufmann Publishers Inc.},
  series    = {IJCAI'73},
  timestamp = {2021.07.07},
  creationdate = {2021-07-07T00:00:00},
  url       = {http://www.eighty-twenty.org/files/Hewitt, Bishop, Steiger - 1973 - A universal modular ACTOR formalism for artificial intelligence.pdf},
}

@Article{Shaffer1946,
  author    = {P. A. Shaffer and Verner Schomaker and Linus Pauling},
  journal   = {The Journal of Chemical Physics},
  title     = {The use of punched cards in molecular structure determinations {I}. Crystal structure calculations},
  year      = {1946},
  month     = {nov},
  number    = {11},
  pages     = {648--658},
  volume    = {14},
  doi       = {10.1063/1.1724081},
  file      = {:by-author/S/Shaffer/1946_Shaffer_648.pdf:PDF},
  keywords  = {Crystallographic Computing; Early Use of Computers in Crystallography},
  owner     = {saulius},
  publisher = {{AIP} Publishing},
  timestamp = {2021.07.08},
  creationdate = {2021-07-08T00:00:00},
  url       = {https://authors.library.caltech.edu/45530/1/SCHjcp46a.pdf},
}

@Article{Shaffer1946a,
  author    = {P. A. Shaffer and Verner Schomaker and Linus Pauling},
  journal   = {The Journal of Chemical Physics},
  title     = {The use of punched cards in molecular structure determinations {II}. Electron diffraction calculations},
  year      = {1946},
  month     = {nov},
  number    = {11},
  pages     = {659--664},
  volume    = {14},
  doi       = {10.1063/1.1724082},
  file      = {:by-author/S/Shaffer/1946_Shaffer_659.pdf:PDF},
  keywords  = {Crystallographic Computing; Early Use of Computers in Crystallography},
  owner     = {saulius},
  publisher = {{AIP} Publishing},
  timestamp = {2021.07.08},
  creationdate = {2021-07-08T00:00:00},
  url       = {https://authors.library.caltech.edu/45531/1/SCHjcp46b.pdf},
}

@Article{Jones1951,
  author    = {Morton E. Jones and Verner Schomaker},
  journal   = {The Journal of Chemical Physics},
  title     = {The use of punched cards in molecular structure determinations. {IV}. Approximations to the temperature factor},
  year      = {1951},
  month     = {apr},
  number    = {4},
  pages     = {511--512},
  volume    = {19},
  doi       = {10.1063/1.1748272},
  file      = {:by-author/J/Jones/1951_Jones_511.pdf:PDF},
  keywords  = {Crystallographic Computing; Early Use of Computers in Crystallography},
  owner     = {saulius},
  publisher = {{AIP} Publishing},
  timestamp = {2021.07.08},
  creationdate = {2021-07-08T00:00:00},
  url       = {https://authors.library.caltech.edu/71157/1/1.1748272.pdf},
}

@Article{Marlow2004,
  author    = {Simon Marlow and Simon Peyton Jones},
  journal   = {{ACM} {SIGPLAN} Notices},
  title     = {Making a fast curry},
  year      = {2004},
  month     = {sep},
  number    = {9},
  pages     = {4--15},
  volume    = {39},
  doi       = {10.1145/1016848.1016856},
  file      = {:by-author/M/Marlow/2004_Marlow_4.pdf:PDF},
  keywords  = {Boxed Integers; Computer Science (CS); Functional Languages; Implementation},
  owner     = {saulius},
  publisher = {Association for Computing Machinery ({ACM})},
  timestamp = {2021.07.08},
  creationdate = {2021-07-08T00:00:00},
  url       = {http://simonmar.github.io/bib/papers/evalapplyjfp06.pdf},
}

@Article{Rupp2015,
  author    = {Matthias Rupp and Raghunathan Ramakrishnan and O. Anatole von Lilienfeld},
  journal   = {The Journal of Physical Chemistry Letters},
  title     = {Machine learning for quantum mechanical properties of atoms in molecules},
  year      = {2015},
  month     = {aug},
  number    = {16},
  pages     = {3309--3313},
  volume    = {6},
  comment   = {Cited by Andrius in his e-mail to grazulis@ibt.lt dated 2021-07-05 11:19},
  doi       = {10.1021/acs.jpclett.5b01456},
  file      = {:by-author/R/Rupp/2015_Rupp_3309.pdf:PDF},
  keywords  = {Chemical Comprehension; Machine Learning (ML)},
  owner     = {saulius},
  publisher = {American Chemical Society ({ACS})},
  timestamp = {2021.07.10},
  creationdate = {2021-07-10T00:00:00},
}

@PhdThesis{Thimm2008,
  author    = {Georg Thimm},
  title     = {Graph theoretical approach to the analysis, comparison, and enumeration of crystal structures},
  year      = {2008},
  comment   = {Cited by Gao2020.},
  file      = {:by-author/T/Thimm/2008_Thimm_1.pdf:PDF},
  keywords  = {Algorithms; COD; Crystal Nets; Crystal Structure Prediction (CSP); QG; Quotien Graph; Topology},
  owner     = {saulius},
  pages     = {1--131},
  timestamp = {2021.08.04},
  creationdate = {2021-08-04T00:00:00},
  url       = {https://d-nb.info/1001825144/34},
}

@Article{Huang2009a,
  author    = {Y. Huang and S. Wuchty and M. T. Ferdig and T. M. Przytycka},
  journal   = {Bioinformatics},
  title     = {Graph theoretical approach to study {eQTL}: a case study of Plasmodium falciparum},
  year      = {2009},
  month     = {may},
  number    = {12},
  pages     = {i15--i20},
  volume    = {25},
  doi       = {10.1093/bioinformatics/btp189},
  file      = {:by-author/H/Huang/2009_Huang_15.pdf:PDF},
  keywords  = {Bioinformatics; Topology},
  owner     = {saulius},
  publisher = {Oxford University Press ({OUP})},
  timestamp = {2021.08.04},
  creationdate = {2021-08-04T00:00:00},
}

@Article{Eon2016,
  author    = {Eon, J. G.},
  journal   = {Acta Cryst. A},
  title     = {Topological features in crystal structures: a quotient graph assisted analysis of underlying nets and their embeddings},
  year      = {2016},
  pages     = {268--293},
  volume    = {72},
  comment   = {Cited by Gao2020.},
  doi       = {10.1107/S2053273315022950},
  file      = {:by-author/E/Eon/2016_Eon_268.pdf:PDF},
  keywords  = {Crystal Nets; Crystallography; Quotient Graph; Topology},
  owner     = {saulius},
  refid     = {Eon2016},
  timestamp = {2021.08.04},
  creationdate = {2021-08-04T00:00:00},
  url       = {https://doi.org/10.1107/S2053273315022950},
}

@Article{DelgadoFriedrichs2016,
  author    = {Olaf Delgado-Friedrichs and Stephen T. Hyde and Michael O'Keeffe and Omar M. Yaghi},
  journal   = {Structural Chemistry},
  title     = {Crystal structures as periodic graphs: the topological genome and graph databases},
  year      = {2016},
  month     = {sep},
  number    = {1},
  pages     = {39--44},
  volume    = {28},
  doi       = {10.1007/s11224-016-0853-3},
  file      = {:by-author/D/Delgado-Friedrichs/2016_Delgado-Friedrichs_39.pdf:PDF},
  keywords  = {Crystal Nets; Crystallography; Topology},
  owner     = {saulius},
  publisher = {Springer Science and Business Media {LLC}},
  timestamp = {2021.08.04},
  creationdate = {2021-08-04T00:00:00},
}

@Article{Yan2011,
  author    = {Yan Yan and Shenggui Zhang and Fang-Xiang Wu},
  journal   = {Proteome Science},
  title     = {Applications of graph theory in protein structure identification},
  year      = {2011},
  number    = {Suppl 1},
  pages     = {S17},
  volume    = {9},
  doi       = {10.1186/1477-5956-9-s1-s17},
  file      = {:by-author/Y/Yan/2011_Yan_17.pdf:PDF},
  keywords  = {Bioinformatics; Topology},
  owner     = {saulius},
  publisher = {Springer Science and Business Media {LLC}},
  timestamp = {2021.08.04},
  creationdate = {2021-08-04T00:00:00},
}

@Article{Hughes2017,
  author    = {David S. Hughes and Amit Delori and Abida Rehman and William Jones},
  journal   = {Chemistry Central Journal},
  title     = {Using crystallography, topology and graph set analysis for the description of the hydrogen bond network of triamterene: a rational approach to solid form selection},
  year      = {2017},
  month     = {jul},
  number    = {1},
  volume    = {11},
  doi       = {10.1186/s13065-017-0293-1},
  file      = {:by-author/H/Hughes/2017_Hughes_.pdf:PDF},
  keywords  = {Crystal Nets; Crystallography; Topology},
  owner     = {saulius},
  publisher = {Springer Science and Business Media {LLC}},
  timestamp = {2021.08.04},
  creationdate = {2021-08-04T00:00:00},
}

@InBook{Blatov2011,
  author    = {Vladislav A. Blatov and Davide M. Proserpio},
  chapter   = {1},
  editor    = {Artem R. Oganov},
  pages     = {1--28},
  publisher = {Springer},
  title     = {Periodic-graph approaches in crystal structure prediction},
  year      = {2011},
  booktitle = {Modern Methods of Crystal Structure Prediction},
  file      = {:by-author/B/Blatov/2011_Blatov_1.pdf:PDF},
  keywords  = {Crystal Nets; Crystal Structure Prediction (CSP); Topology},
  owner     = {saulius},
  timestamp = {2021.08.04},
  creationdate = {2021-08-04T00:00:00},
  url       = {https://application.wiley-vch.de/books/sample/3527409394_c01.pdf},
}

@Article{Hawthorne2012,
  author    = {Frank C. Hawthorne},
  journal   = {Physics and Chemistry of Minerals},
  title     = {A bond-topological approach to theoretical mineralogy: crystal structure, chemical composition and chemical reactions},
  year      = {2012},
  month     = {sep},
  number    = {10},
  pages     = {841--874},
  volume    = {39},
  comment   = {Cited in Eon2016: "The corresponding metric topology is the combinatorial or bond topology and is thus given by the crystal graph, or network, representing the structure (see also Blatov, 2011; Hawthorne, 2012; O’Keeffe & Yaghi, 2012).".},
  doi       = {10.1007/s00269-012-0538-4},
  file      = {:by-author/H/Hawthorne/2012_Hawthorne_841.pdf:PDF},
  keywords  = {Crystal Nets; Crystallography; Topology},
  owner     = {saulius},
  publisher = {Springer Science and Business Media {LLC}},
  timestamp = {2021.08.04},
  creationdate = {2021-08-04T00:00:00},
}

@Presentation{DelgadoFriedrichs2019,
  author    = {Olaf Delgado-Friedrichs},
  title     = {When is a crystal graph not crystallographic?},
  year      = {2019},
  comment   = {Provided as a link in http://gavrog.org/, which is itself cited in Gao2020.},
  file      = {:by-author/D/Delgado-Friedrichs/2019_Delgado-Friedrichs_1.pdf:PDF},
  keywords  = {Chemistry; Crystallographic Nets; Crystallography; Graph Theory; Reticular Chemistry},
  owner     = {saulius},
  pages     = {1--27},
  timestamp = {2021.08.05},
  creationdate = {2021-08-05T00:00:00},
  url       = {http://gavrog.org/order-order.pdf},
}

@Presentation{DelgadoFriedrichs2008a,
  author    = {Olaf Delgado-Friedrichs},
  title     = {Analyzing periodic nets via the barycentre construction},
  year      = {2008},
  file      = {:by-author/D/Delgado-Friedrichs/2008_Delgado-Friedrichs_1a.pdf:PDF},
  keywords  = {Chemistry; Crystallographic Nets; Crystallography; Graph Theory; Reticular Chemistry},
  owner     = {saulius},
  pages     = {1--80},
  timestamp = {2021.08.05},
  creationdate = {2021-08-05T00:00:00},
  url       = {http://gavrog.org/systre-lecture.pdf},
}

@Presentation{DelgadoFriedrichs2008b,
  author    = {Olaf Delgado-Friedrichs},
  title     = {Some elementary tiling theory},
  year      = {2008},
  file      = {:by-author/D/Delgado-Friedrichs/2008_Delgado-Friedrichs_1b.pdf:PDF},
  keywords  = {Chemistry; Crystallographic Nets; Crystallography; Graph Theory; Reticular Chemistry},
  owner     = {saulius},
  pages     = {1--99},
  timestamp = {2021.08.05},
  creationdate = {2021-08-05T00:00:00},
  url       = {http://gavrog.org/tiling-lecture-I.pdf},
}

@Manuscript{DelgadoFriedrichs2004,
  author    = {Olaf Delgado-Friedrichs},
  title     = {Data structures and algorithms for tilings {I}},
  year      = {2004},
  keywords  = {Algorithms; Chemistry; Crystallographic Nets; Crystallography; Data Structures; Graph Theory; Reticular Chemistry},
  url       = {http://gavrog.org/TCS.pdf},
  file      = {:by-author/D/Delgado-Friedrichs/2004_Delgado-Friedrichs_1.pdf:PDF},
  owner     = {saulius},
  pages     = {1--13},
  timestamp = {2021.08.05},
  creationdate = {2021-08-05T00:00:00},
}

@Article{DelgadoFriedrichs2003,
  author    = {Olaf Delgado-Friedrichs},
  journal   = {Theoretical Computer Science},
  title     = {Data structures and algorithms for tilings {I}},
  year      = {2003},
  month     = {jul},
  number    = {2-3},
  pages     = {431--445},
  volume    = {303},
  doi       = {10.1016/s0304-3975(02)00500-5},
  file      = {:by-author/D/Delgado-Friedrichs/2003_Delgado-Friedrichs_431.pdf:PDF},
  keywords  = {Algorithms; Chemistry; Crystallographic Nets; Crystallography; Graph Theory; Reticular Chemistry},
  owner     = {saulius},
  publisher = {Elsevier {BV}},
  timestamp = {2021.08.05},
  creationdate = {2021-08-05T00:00:00},
}

@Presentation{DelgadoFriedrichs2004a,
  author    = {Olaf Delgado-Friedrichs},
  title     = {Crystal topologies and discrete mathematics},
  year      = {2004},
  file      = {:by-author/D/Delgado-Friedrichs/2004_Delgado-Friedrichs_1a.pdf:PDF},
  keywords  = {Chemistry; Crystallographic Nets; Crystallography; Graph Theory; Reticular Chemistry},
  owner     = {saulius},
  pages     = {1--54},
  timestamp = {2021.08.05},
  creationdate = {2021-08-05T00:00:00},
  url       = {http://gavrog.org/leipzig.pdf},
}

@Presentation{DelgadoFriedrichs2004b,
  author    = {Olaf Delgado-Friedrichs},
  title     = {Periodische graphen und ein resultat von tutte},
  year      = {2004},
  file      = {:by-author/D/Delgado-Friedrichs/2004_Delgado-Friedrichs_1b.pdf:PDF},
  keywords  = {Chemistry; Crystallographic Nets; Crystallography; Graph Theory; Reticular Chemistry},
  owner     = {saulius},
  pages     = {1--88},
  timestamp = {2021.08.05},
  creationdate = {2021-08-05T00:00:00},
  url       = {http://gavrog.org/heidelberg.pdf},
}

@Webpage{DelgadoFriedrichs2019a,
  author           = {Olaf Delgado-Friedrichs},
  retrieved        = {2021-08-05 12:44:17 EEST},
  title            = {The {Gavrog} {Project}. http://gavrog.org/.},
  url              = {http://gavrog.org/},
  year             = {2019},
  creationdate     = {2021-08-05T00:00:00},
  file             = {:by-author/D/Delgado-Friedrichs/2019_Delgado-Friedrichs_1a.odt:OpenDocument text;:by-author/D/Delgado-Friedrichs/2019_Delgado-Friedrichs_1a.pdf:PDF},
  keywords         = {Computer Science (CS); Crystallographic Nets; Java Library; Reticular Nets; Software Library},
  modificationdate = {2022-11-30T18:55:28},
  owner            = {saulius},
  pages            = {1--4},
  refid            = {ref21},
  timestamp        = {2021.08.05},
}

@Article{Larsen2019,
  author    = {Peter Mahler Larsen and Mohnish Pandey and Mikkel Strange and Karsten Wedel Jacobsen},
  journal   = {Physical Review Materials},
  title     = {Definition of a scoring parameter to identify low-dimensional materials components},
  year      = {2019},
  month     = {mar},
  number    = {3},
  pages     = {034003},
  volume    = {3},
  comment   = {Cited by Gao2020.},
  doi       = {10.1103/physrevmaterials.3.034003},
  file      = {:by-author/L/Larsen/2019_Larsen_34003.pdf:PDF},
  keywords  = {Crystallography; Molecular Nets; Reticular Chemistry; Topology},
  owner     = {saulius},
  publisher = {American Physical Society ({APS})},
  timestamp = {2021.08.07},
  creationdate = {2021-08-07T00:00:00},
}

@Presentation{Cini2017,
  author    = {Michele Cini},
  title     = {Crystallographic space groups},
  year      = {2017},
  file      = {:by-author/C/Cini/2017_Cini_1.pdf:PDF},
  owner     = {saulius},
  pages     = {1--33},
  timestamp = {2021.08.26},
  creationdate = {2021-08-26T00:00:00},
  url       = {http://people.roma2.infn.it/~cini/ts2017/ts2017-6.pdf},
}

@Manuscript{1999b,
  author    = {anonymous},
  title     = {{A}rtur {S}choenflies (1853-1928): {I}n {M}emoriam},
  year      = {1999},
  keywords  = {History; Original Papers; Sapce Groups},
  url       = {https://www.iucr.org/__data/assets/pdf_file/0012/750/schoenfl.pdf},
  file      = {:by-author/a/anonymous/1999_anonymous_351.pdf:PDF},
  owner     = {saulius},
  pages     = {351--353},
  timestamp = {2021.08.26},
  creationdate = {2021-08-26T00:00:00},
}

@Article{Downward2015,
  author    = {Michael Downward},
  journal   = {Foundations of Chemistry},
  title     = {Symmetry and representation in a three dimensional space},
  year      = {2015},
  month     = {apr},
  number    = {3},
  pages     = {275--287},
  volume    = {17},
  doi       = {10.1007/s10698-015-9227-y},
  file      = {:by-author/D/Downward/2015_Downward_275.pdf:PDF},
  keywords  = {Crystallography; Space Groups},
  owner     = {saulius},
  publisher = {Springer Science and Business Media {LLC}},
  timestamp = {2021.08.26},
  creationdate = {2021-08-26T00:00:00},
}

@Article{Mulliken1955,
  author    = {Robert S. Mulliken},
  journal   = {The Journal of Chemical Physics},
  title     = {Report on Notation for the Spectra of Polyatomic Molecules},
  year      = {1955},
  month     = {nov},
  number    = {11},
  pages     = {1997--2011},
  volume    = {23},
  comment   = {Cited by Downward2015.},
  doi       = {10.1063/1.1740655},
  file      = {:by-author/M/Mulliken/1955_Mulliken_1997.pdf:PDF},
  keywords  = {Molecular Symmetry; Molecules; Notation; Spectroscopy; Symmetry},
  owner     = {saulius},
  publisher = {{AIP} Publishing},
  timestamp = {2021.08.26},
  creationdate = {2021-08-26T00:00:00},
}

@Article{Henn2016,
  author    = {Julian Henn},
  journal   = {Acta Crystallographica Section A Foundations and Advances},
  title     = {An alternative to the goodness of fit},
  year      = {2016},
  month     = {oct},
  number    = {6},
  pages     = {696--703},
  volume    = {72},
  doi       = {10.1107/s2053273316013206},
  file      = {:by-author/H/Henn/2016_Henn_696.pdf:PDF;:by-author/H/Henn/2016_Henn_696_suppl/ae5018sup1.pdf:PDF;:by-author/H/Henn/2016_Henn_696_suppl/ae5018sup2.pdf:PDF;:by-author/H/Henn/2016_Henn_696_suppl/ae5018sup3.pdf:PDF},
  keywords  = {Crystallographic Data; Data Curation; Data Quality; Systematic Errors},
  owner     = {saulius},
  publisher = {International Union of Crystallography ({IUCr})},
  timestamp = {2021.08.26},
  creationdate = {2021-08-26T00:00:00},
}

@Article{Downward2010,
  author    = {Michael James Downward},
  journal   = {Zeitschrift für Kristallographie},
  title     = {Crystallographic point groups in five dimensions},
  year      = {2010},
  month     = {nov},
  number    = {1},
  pages     = {32--39},
  volume    = {226},
  comment   = {Cited by Downward2015.},
  doi       = {10.1524/zkri.2011.1260},
  file      = {:by-author/D/Downward/2010_Downward_32.pdf:PDF},
  keywords  = {Crystallography; Higher Dimensions; Space Groups},
  owner     = {saulius},
  publisher = {Walter de Gruyter {GmbH}},
  timestamp = {2021.08.26},
  creationdate = {2021-08-26T00:00:00},
}

@Article{Wolcott1988,
  author    = {P. Wolcott and S. E. Goodman},
  journal   = {Computer},
  title     = {High-speed computers of the {S}oviet {U}nion},
  year      = {1988},
  month     = {sep},
  number    = {9},
  pages     = {32--41},
  volume    = {21},
  doi       = {10.1109/2.14345},
  file      = {:by-author/W/Wolcott/1988_Wolcott_32.pdf:PDF},
  keywords  = {Computer Architecture; Computer Science (CS); Computing History},
  owner     = {saulius},
  publisher = {Institute of Electrical and Electronics Engineers ({IEEE})},
  timestamp = {2021.09.01},
  creationdate = {2021-09-01T00:00:00},
}

@Article{Henn2014,
  author    = {Julian Henn and Kathrin Meindl},
  journal   = {Acta Crystallographica Section A Foundations and Advances},
  title     = {More about systematic errors in charge-density studies},
  year      = {2014},
  month     = {aug},
  number    = {5},
  pages     = {499--513},
  volume    = {70},
  doi       = {10.1107/s2053273314012984},
  file      = {:by-author/H/Henn/2014_Henn_499.pdf:PDF},
  keywords  = {Bayesian Statistics; Crystallography; Data Quality; Error Measures; Systematic Errors},
  owner     = {saulius},
  publisher = {International Union of Crystallography ({IUCr})},
  timestamp = {2021.09.14},
  creationdate = {2021-09-14T00:00:00},
}

@Article{Henn2013,
  author    = {Julian Henn and Andreas Schönleber},
  journal   = {Acta Crystallographica Section A Foundations of Crystallography},
  title     = {More about residual values},
  year      = {2013},
  month     = {oct},
  number    = {6},
  pages     = {549--558},
  volume    = {69},
  doi       = {10.1107/s0108767313022514},
  file      = {:by-author/H/Henn/2013_Henn_549.pdf:PDF},
  keywords  = {Bayesian Statistics; Crystallography; Data Quality; Error Measures; Systematic Errors},
  owner     = {saulius},
  publisher = {International Union of Crystallography ({IUCr})},
  timestamp = {2021.09.14},
  creationdate = {2021-09-14T00:00:00},
}

@Article{Henn2014a,
  author    = {Julian Henn and Kathrin Meindl},
  journal   = {Acta Crystallographica Section A Foundations and Advances},
  title     = {About systematic errors in charge-density studies},
  year      = {2014},
  month     = {mar},
  number    = {3},
  pages     = {248--256},
  volume    = {70},
  doi       = {10.1107/s2053273314000898},
  file      = {:by-author/H/Henn/2014_Henn_248.pdf:PDF},
  keywords  = {Bayesian Statistics; Crystallography; Data Quality; Error Measures; Systematic Errors},
  owner     = {saulius},
  publisher = {International Union of Crystallography ({IUCr})},
  timestamp = {2021.09.14},
  creationdate = {2021-09-14T00:00:00},
}

@Article{Winter2018,
  author          = {Winter, Graeme and Waterman, David G. and Parkhurst, James M. and Brewster, Aaron S. and Gildea, Richard J. and Gerstel, Markus and Fuentes-Montero, Luis and Vollmar, Melanie and Michels-Clark, Tara and Young, Iris D. and Sauter, Nicholas K. and Evans, Gwyndaf},
  journal         = {Acta crystallographica. Section D, Structural biology},
  title           = {DIALS: implementation and evaluation of a new integration package.},
  year            = {2018},
  issn            = {2059-7983},
  month           = feb,
  pages           = {85--97},
  volume          = {74},
  abstract        = {The DIALS project is a collaboration between Diamond Light Source, Lawrence Berkeley National Laboratory and CCP4 to develop a new software suite for the analysis of crystallographic X-ray diffraction data, initially encompassing spot finding, indexing, refinement and integration. The design, core algorithms and structure of the software are introduced, alongside results from the analysis of data from biological and chemical crystallography experiments.},
  chemicals       = {Bacterial Proteins, Repressor Proteins, Thermolysin},
  citation-subset = {IM},
  completed       = {2019-01-14},
  country         = {United States},
  creationdate    = {2021-09-15T00:00:00},
  doi             = {10.1107/S2059798317017235},
  file            = {:by-author/W/Winter/2018_Winter_85.pdf:PDF},
  issn-linking    = {2059-7983},
  issue           = {Pt 2},
  keywords        = {Algorithms; Bacterial Proteins; Chemistry; Computer-Assisted; Crystallography; DIALS; Data Processing; Electronic Data Processing; Methods; Methods Development; Radiographic Image Interpretation; Repressor Proteins; Software; Thermolysin; X-Ray; X-ray Diffraction},
  nlm-id          = {101676043},
  owner           = {saulius},
  pii             = {S2059798317017235},
  pmc             = {PMC5947772},
  pmid            = {29533234},
  pubmodel        = {Print-Electronic},
  pubstate        = {ppublish},
  revised         = {2021-01-09},
  timestamp       = {2021.09.15},
}

@Article{Heidrich2017,
  author    = {Nadja Heidrich and Saskia Bauriedl and Lars Barquist and Lei Li and Christoph Schoen and Jörg Vogel},
  journal   = {Nucleic Acids Research},
  title     = {The primary transcriptome of {N}eisseria meningitidis and its interaction with the {RNA} chaperone {Hfq}},
  year      = {2017},
  month     = {mar},
  number    = {10},
  pages     = {6147--6167},
  volume    = {45},
  doi       = {10.1093/nar/gkx168},
  file      = {:by-author/H/Heidrich/2017_Heidrich_6147.pdf:PDF;:by-author/H/Heidrich/2017_Heidrich_6147_suppl/gkx168_Supp.zip:zip},
  keywords  = {NGS; New Generation Sequenceing; RNA Sequenceing},
  owner     = {saulius},
  publisher = {Oxford University Press ({OUP})},
  timestamp = {2021.09.16},
  creationdate = {2021-09-16T00:00:00},
}

@TechReport{Rushby2003,
  author      = {John Rushby},
  institution = {NASA},
  title       = {A comparison of bus architectures for safety-critical embedded systems},
  year        = {2003},
  number      = {NASA/CR-2003-2 12 16 1},
  file        = {:by-author/R/Rushby/2003_Rushby_1.pdf:PDF},
  keywords    = {Bus Architecture; Computer Architecture; Computer Science (CS); Embeded Systems; Safety Critical Systems; Software Reliability},
  owner       = {saulius},
  pages       = {1--59},
  timestamp = {2021.09.17},
  creationdate = {2021-09-17T00:00:00},
  url         = {https://ntrs.nasa.gov/api/citations/20030032956/downloads/20030032956.pdf},
}

@Article{Wang2021,
  author        = {Zhi Wang and Chaoge Liu and Xiang Cui},
  title         = {EvilModel: Hiding Malware Inside of Neural Network Models},
  year          = {2021},
  month         = jul,
  pages         = {1--7},
  abstract      = {Delivering malware covertly and evasively is critical to advanced malware campaigns. In this paper, we present a new method to covertly and evasively deliver malware through a neural network model. Neural network models are poorly explainable and have a good generalization ability. By embedding malware in neurons, the malware can be delivered covertly, with minor or no impact on the performance of neural network. Meanwhile, because the structure of the neural network model remains unchanged, it can pass the security scan of antivirus engines. Experiments show that 36.9MB of malware can be embedded in a 178MB-AlexNet model within 1% accuracy loss, and no suspicion is raised by anti-virus engines in VirusTotal, which verifies the feasibility of this method. With the widespread application of artificial intelligence, utilizing neural networks for attacks becomes a forwarding trend. We hope this work can provide a reference scenario for the defense on neural network-assisted attacks.},
  archiveprefix = {arXiv},
  eprint        = {2107.08590},
  file          = {:by-author/W/Wang/2021_Wang_1.pdf:PDF},
  keywords      = {cs.AI; cs.CR},
  owner         = {saulius},
  primaryclass  = {cs.CR},
  timestamp = {2021.09.17},
  creationdate = {2021-09-17T00:00:00},
}

@InProceedings{Alglave2008,
  author    = {Jade Alglave and Anthony Fox and Samin Ishtiaq and Magnus O. Myreen and Susmit Sarkar and Peter Sewell and Francesco Zappa Nardelli},
  booktitle = {Proceedings of the 4th workshop on Declarative aspects of multicore programming - {DAMP} {\textquotesingle}09},
  title     = {The semantics of power and {ARM} multiprocessor machine code},
  year      = {2008},
  pages     = {13–24},
  publisher = {{ACM} Press},
  doi       = {10.1145/1481839.1481842},
  file      = {:by-author/A/Alglave/2008_Alglave_13.pdf:PDF},
  keywords  = {ARM; Computer Science (CS); Formal Verification; Machine Code; PowerPC; RISC; Semantics},
  owner     = {saulius},
  timestamp = {2021.09.17},
  creationdate = {2021-09-17T00:00:00},
}

@Article{Batcher1982,
  author    = {Batcher},
  journal   = {{IEEE} Transactions on Computers},
  title     = {Bit-serial parallel processing systems},
  year      = {1982},
  month     = {may},
  number    = {5},
  pages     = {377--384},
  volume    = {C-31},
  doi       = {10.1109/tc.1982.1676015},
  file      = {:by-author/B/Batcher/1982_Batcher_377.pdf:PDF},
  keywords  = {Bit-serial Systems; Computer Architecture; Computer Science (CS); Hardware; STARAN; VLSI},
  owner     = {saulius},
  publisher = {Institute of Electrical and Electronics Engineers ({IEEE})},
  timestamp = {2021.09.17},
  creationdate = {2021-09-17T00:00:00},
}

@Presentation{Hagersten2004,
  author    = {Erik Hagersten},
  title     = {{CPU} design options},
  year      = {2004},
  file      = {:by-author/H/Hagersten/2004_Hagersten_1.pdf:PDF},
  keywords  = {CPU Design; CPU Pipelines; Cache Memory; Computer Architecture; Computer Science (CS); Superscalar Architecture; VLIW},
  owner     = {saulius},
  pages     = {1--43},
  timestamp = {2021.09.17},
  creationdate = {2021-09-17T00:00:00},
  url       = {https://www.it.uu.se/edu/course/homepage/dark2/ht04/slides/CPUs-4.pdf},
}

@Article{AMS1953,
  author    = {{AMS}},
  journal   = {Mathematics of Computation},
  title     = {Automatic computing machinery. The {C}ircle computer},
  year      = {1953},
  number    = {44},
  pages     = {249--268},
  volume    = {7},
  doi       = {10.1090/S0025-5718-53-99352-1},
  file      = {:by-author/A/AMS/1953_AMS_249.pdf:PDF},
  keywords  = {Computer Architecture; Computer History; Computer Science (CS); First Computers; The Circle Computer},
  owner     = {saulius},
  publisher = {American Mathematical Society ({AMS})},
  timestamp = {2021.09.17},
  creationdate = {2021-09-17T00:00:00},
  url       = {https://www.ams.org/journals/mcom/1953-07-044/S0025-5718-53-99352-1/S0025-5718-53-99352-1.pdf},
}

@Article{Pagiamtzis2006,
  author    = {K. Pagiamtzis and A. Sheikholeslami},
  journal   = {{IEEE} Journal of Solid-State Circuits},
  title     = {Content-addressable memory ({CAM}) circuits and architectures: a tutorial and survey},
  year      = {2006},
  month     = {mar},
  number    = {3},
  pages     = {712--727},
  volume    = {41},
  doi       = {10.1109/jssc.2005.864128},
  file      = {:by-author/P/Pagiamtzis/2006_Pagiamtzis_712.pdf:PDF},
  keywords  = {Computer Science (CS); Content Addressible Memory; Hardware},
  owner     = {saulius},
  publisher = {Institute of Electrical and Electronics Engineers ({IEEE})},
  timestamp = {2021.09.17},
  creationdate = {2021-09-17T00:00:00},
  url       = {https://www.eecg.utoronto.ca/~ali/papers/jssc2006-03.pdf},
}

@Misc{Floether2020,
  author    = {Frederik Flöther and Christopher Moose and Ivano Tavernelli},
  title     = {Exploring quantum computing use cases for life sciences},
  year      = {2020},
  file      = {:by-author/F/Flöther/2020_Flöther_1.pdf:PDF},
  keywords  = {Computer Architecture; Computer Science (CS); Quantum Computers},
  owner     = {saulius},
  pages     = {1--12},
  timestamp = {2021.09.17},
  creationdate = {2021-09-17T00:00:00},
  url       = {https://www.ibm.com/downloads/cas/EVBKAZGJ},
}

@InProceedings{Mahasinghe2019,
  author    = {Anuradha Mahasinghe and Richard Hua and Michael J. Dinneen and Rajni Goyal},
  booktitle = {Proceedings of the Australasian Computer Science Week Multiconference},
  title     = {Solving the {H}amiltonian cycle problem using a quantum computer},
  year      = {2019},
  month     = {jan},
  pages     = {1--9},
  publisher = {{ACM}},
  doi       = {10.1145/3290688.3290703},
  file      = {:by-author/M/Mahasinghe/2019_Mahasinghe_1.pdf:PDF},
  keywords  = {Applications; Computer Science (CS); Hamiltinian Cycle; NP-complete Problems; Quantum Computers},
  owner     = {saulius},
  timestamp = {2021.09.17},
  creationdate = {2021-09-17T00:00:00},
}

@InProceedings{Koh2021,
  author    = {John S. Koh and Jason Nieh and Steven M. Bellovin},
  booktitle = {Proceedings of the 19th Annual International Conference on Mobile Systems, Applications, and Services},
  title     = {Encrypted cloud photo storage using {G}oogle photos},
  year      = {2021},
  month     = {jun},
  pages     = {136--149},
  publisher = {{ACM}},
  doi       = {10.1145/3458864.3468220},
  file      = {:by-author/K/Koh/2021_Koh_136.pdf:PDF},
  keywords  = {Computer Science (CS); Encryption; Photos; Privacy},
  owner     = {saulius},
  timestamp = {2021.09.17},
  creationdate = {2021-09-17T00:00:00},
}

@Lecture{Niroula2016,
  author    = {Abhishek Niroula},
  title     = {Sequence comparison},
  year      = {2016},
  file      = {:by-author/N/Niroula/2016_Niroula_1.pdf:PDF},
  keywords  = {Bioinformatics; Sequence Alignment; Sequence Comparison},
  owner     = {saulius},
  pages     = {1--30},
  timestamp = {2021.09.17},
  creationdate = {2021-09-17T00:00:00},
  url       = {https://moodle.med.lu.se/pluginfile.php/61141/mod_resource/content/1/sequence_comparison_2016.pdf},
}

@InProceedings{Andraka1996,
  author    = {Raymond J. Andraka},
  booktitle = {On-Chip System Design Conference},
  title     = {Building a high performance bit serial processor in an {FPGA}},
  year      = {1996},
  pages     = {1--22},
  file      = {:by-author/A/Andraka/1996_Andraka_1.pdf:PDF},
  keywords  = {Bit-serial CPU; Computer Architecture; Computer Science (CS); FPGA},
  owner     = {saulius},
  timestamp = {2021.09.17},
  creationdate = {2021-09-17T00:00:00},
  url       = {http://www.fpga-guru.com/files/supercn.pdf},
}

@Article{Rand2019,
  author        = {Robert Rand},
  title         = {Verification Logics for Quantum Programs},
  year          = {2019},
  month         = apr,
  pages         = {1--42},
  abstract      = {We survey the landscape of Hoare logics for quantum programs. We review three papers: "Reasoning about imperative quantum programs" by Chadha, Mateus and Sernadas; "A logic for formal verification of quantum programs" by Yoshihiko Kakutani; and "Floyd-hoare logic for quantum programs" by Mingsheng Ying. We compare the mathematical foundations of the logics, their underlying languages, and the expressivity of their assertions. We also use the languages to verify the Deutsch-Jozsa Algorithm, and discuss their relative usability in practice.},
  archiveprefix = {arXiv},
  eprint        = {1904.04304},
  file          = {:by-author/R/Rand/2019_Rand_1.pdf:PDF;:http\://arxiv.org/pdf/1904.04304v1:PDF},
  keywords      = {cs.ET; cs.LO; cs.PL},
  owner         = {saulius},
  primaryclass  = {cs.LO},
  timestamp = {2021.09.17},
  creationdate = {2021-09-17T00:00:00},
}

@Article{Feng2020,
  author        = {Yuan Feng and Mingsheng Ying},
  title         = {Quantum {H}oare logic with classical variables},
  year          = {2020},
  month         = aug,
  pages         = {1--44},
  abstract      = {Hoare logic provides a syntax-oriented method to reason about program correctness and has been proven effective in the verification of classical and probabilistic programs. Existing proposals for quantum Hoare logic either lack completeness or support only quantum variables, thus limiting their capability in practical use. In this paper, we propose a quantum Hoare logic for a simple while language which involves both classical and quantum variables. Its soundness and relative completeness are proven for both partial and total correctness of quantum programs written in the language. Remarkably, with novel definitions of classical-quantum states and corresponding assertions, the logic system is quite simple and similar to the traditional Hoare logic for classical programs. Furthermore, to simplify reasoning in real applications, auxiliary proof rules are provided which support standard logical operation in the classical part of assertions, and of super-operator application in the quantum part. Finally, a series of practical quantum algorithms, in particular the whole algorithm of Shor's factorisation, are formally verified to show the effectiveness of the logic.},
  archiveprefix = {arXiv},
  eprint        = {2008.06812},
  file          = {:by-author/F/Feng/2020_Feng_1.pdf:PDF;:http\://arxiv.org/pdf/2008.06812v2:PDF},
  keywords      = {Quant-ph; cs.LO},
  owner         = {saulius},
  primaryclass  = {cs.LO},
  timestamp = {2021.09.17},
  creationdate = {2021-09-17T00:00:00},
}

@Article{Kugelgen2021,
  author    = {Stephen von Kugelgen and Matthew D. Krzyaniak and Mingqiang Gu and Danilo Puggioni and James M. Rondinelli and Michael R. Wasielewski and Danna E. Freedman},
  journal   = {Journal of the American Chemical Society},
  title     = {Spectral Addressability in a Modular Two Qubit System},
  year      = {2021},
  month     = {may},
  number    = {21},
  pages     = {8069--8077},
  volume    = {143},
  doi       = {10.1021/jacs.1c02417},
  file      = {:by-author/K/Kugelgen/2021_Kugelgen_8069.pdf:PDF},
  keywords  = {Computer Science (CS); Molecular Computers; QC; QC Chips; Quantum Computers},
  owner     = {saulius},
  publisher = {American Chemical Society ({ACS})},
  timestamp = {2021.09.17},
  creationdate = {2021-09-17T00:00:00},
}

@Article{Correa2020,
  author        = {J. C. Correa and H. Laverde-Rojas and F. Marmolejo-Ramos and J. Tejada and Š. Bahník},
  title         = {The {S}ci-hub effect: {S}ci-hub downloads lead to more article citations},
  year          = {2020},
  month         = jun,
  pages         = {1--19},
  abstract      = {Citations are often used as a metric of the impact of scientific publications. Here, we examine how the number of downloads from Sci-hub as well as various characteristics of publications and their authors predicts future citations. Using data from 12 leading journals in economics, consumer research, neuroscience, and multidisciplinary research, we found that articles downloaded from Sci-hub were cited 1.72 times more than papers not downloaded from Sci-hub and that the number of downloads from Sci-hub was a robust predictor of future citations. Among other characteristics of publications, the number of figures in a manuscript consistently predicts its future citations. The results suggest that limited access to publications may limit some scientific research from achieving its full impact.},
  archiveprefix = {arXiv},
  eprint        = {2006.14979},
  file          = {:by-author/C/Correa/2020_Correa_1.pdf:PDF},
  keywords      = {Bibliometry; Open-access; Sci-hub; Shadow Libraries; cs.DL; cs.IR; stat.AP},
  owner         = {saulius},
  primaryclass  = {cs.DL},
  timestamp = {2021.09.17},
  creationdate = {2021-09-17T00:00:00},
}

@Article{Terry1979,
  author    = {S. C. Terry and J. H. Jerman and J. B. Angell},
  journal   = {{IEEE} Transactions on Electron Devices},
  title     = {A gas chromatographic air analyzer fabricated on a silicon wafer},
  year      = {1979},
  month     = {dec},
  number    = {12},
  pages     = {1880--1886},
  volume    = {26},
  doi       = {10.1109/t-ed.1979.19791},
  file      = {:by-author/T/Terry/1979_Terry_1880.pdf:PDF},
  keywords  = {Integrated Circuits},
  owner     = {saulius},
  publisher = {Institute of Electrical and Electronics Engineers ({IEEE})},
  timestamp = {2021.09.17},
  creationdate = {2021-09-17T00:00:00},
}

@Article{Gaitan2008,
  author        = {Frank Gaitan and Franco Nori},
  journal       = {Phys. Rev. B vol. 79, 205117 (2009)},
  title         = {Density functional theory and quantum computation},
  year          = {2008},
  month         = sep,
  pages         = {1--17},
  abstract      = {This paper establishes the applicability of density functional theory methods to quantum computing systems. We show that ground-state and time-dependent density functional theory can be applied to quantum computing systems by proving the Hohenberg-Kohn and Runge-Gross theorems for a fermionic representation of an N qubit system. As a first demonstration of this approach, time-dependent density functional theory is used to determine the minimum energy gap Delta(N) arising when the quantum adiabatic evolution algorithm is used to solve instances of the NP-Complete problem MAXCUT. It is known that the computational efficiency of this algorithm is largely determined by the large-N scaling behavior of Delta(N), and so determining this behavior is of fundamental significance. As density functional theory has been used to study quantum systems with N ~ 1000 interacting degrees of freedom, the approach introduced in this paper raises the realistic prospect of evaluating the gap Delta(N) for systems with N ~ 1000 qubits. Although the calculation of Delta(N) serves to illustrate how density functional theory methods can be applied to problems in quantum computing, the approach has a much broader range and shows promise as a means for determining the properties of very large quantum computing systems.},
  archiveprefix = {arXiv},
  doi           = {10.1103/PhysRevB.79.205117},
  eprint        = {0809.1170},
  file          = {:http\://arxiv.org/pdf/0809.1170v3:PDF;:by-author/G/Gaitan/2008_Gaitan_1.pdf:PDF},
  keywords      = {Quant-ph; cond-mat.other},
  owner         = {saulius},
  primaryclass  = {quant-ph},
  timestamp = {2021.09.17},
  creationdate = {2021-09-17T00:00:00},
}

@Presentation{Young2015,
  author    = {Young, Rupert and Birch, Phil and Chatwin, Chris},
  title     = {Implementation of quantum {F}ourier transform},
  year      = {2015},
  file      = {:by-author/Y/Young/2015_Young_1.pdf:PDF},
  keywords  = {Computer Science (CS); Density Functional Theory (DFT); FFT; Quantum Computers},
  month     = {7},
  owner     = {saulius},
  pages     = {1--27},
  timestamp = {2021.09.17},
  creationdate = {2021-09-17T00:00:00},
  url       = {https://www.researchgate.net/publication/280041653_Implementation_of_quantum_Fourier_transform_-_Presentation},
}

@Manuscript{Coles2018,
  author    = {Coles, Patrick and Eidenbenz, Stephan and Pakin, Scott and Adedoyin, Adetokunbo and Ambrosiano, John and Anisimov, Petr and Casper, William and Chennupati, Gopinath and Coffrin, Carleton and Djidjev, Hristo and Gunter, David and Karra, Satish and Lemons, Nathan and Lin, Shizeng and Lokhov, Andrey and Malyzhenkov, Alexander and Mascarenas, David and Mniszewski, Susan and Nadiga, Balasubramanya and Zhu, Wei},
  title     = {Quantum algorithm implementations for beginners},
  year      = {2018},
  keywords  = {Computer Science (CS); Quantum Computers},
  month     = {04},
  url       = {https://www.researchgate.net/publication/324472130_Quantum_Algorithm_Implementations_for_Beginners},
  file      = {:by-author/C/Coles/2018_Coles_1.pdf:PDF},
  owner     = {saulius},
  pages     = {1},
  timestamp = {2021.09.17},
  creationdate = {2021-09-17T00:00:00},
}

@MastersThesis{Dam1996,
  author    = {Wim van Dam},
  school    = {University of Nijmegen, The Netherlands},
  title     = {Quantum cellular automata},
  year      = {1996},
  file      = {:by-author/D/Dam/1996_Dam_1.pdf:PDF},
  keywords  = {Cellular Automata; Computer Science (CS); Quantum Cellular Automata; Quantum Computer Architecture; Quantum Computers},
  owner     = {saulius},
  pages     = {1--73},
  timestamp = {2021.09.19},
  creationdate = {2021-09-19T00:00:00},
  url       = {https://sites.cs.ucsb.edu/~vandam/qca.pdf},
}

@Article{PerezDelgado2007,
  author        = {Carlos A. Perez-Delgado and Donny Cheung},
  journal       = {Phys. Rev. A 76, 032320, 2007},
  title         = {Local Unitary Quantum Cellular Automata},
  year          = {2007},
  month         = aug,
  pages         = {1--16},
  abstract      = {In this paper we present a quantization of Cellular Automata. Our formalism is based on a lattice of qudits, and an update rule consisting of local unitary operators that commute with their own lattice translations. One purpose of this model is to act as a theoretical model of quantum computation, similar to the quantum circuit model. It is also shown to be an appropriate abstraction for space-homogeneous quantum phenomena, such as quantum lattice gases, spin chains and others. Some results that show the benefits of basing the model on local unitary operators are shown: universality, strong connections to the circuit model, simple implementation on quantum hardware, and a wealth of applications.},
  archiveprefix = {arXiv},
  doi           = {10.1103/PhysRevA.76.032320},
  eprint        = {0709.0006},
  file          = {:by-author/P/Perez-Delgado/2007_Perez-Delgado_1.pdf:PDF;:http\://arxiv.org/pdf/0709.0006v1:PDF},
  keywords      = {Cellular Automata; Computer Science (CS); Quant-ph; Quantum Cellular Automata; Quantum Computer Arcitecture; Quantum Computers},
  owner         = {saulius},
  primaryclass  = {quant-ph},
  timestamp = {2021.09.19},
  creationdate = {2021-09-19T00:00:00},
}

@InProceedings{Watrous1995,
  author    = {J. Watrous},
  booktitle = {Proceedings of {IEEE} 36th Annual Foundations of Computer Science},
  title     = {On one-dimensional quantum cellular automata},
  year      = {1995},
  pages     = {528--537},
  publisher = {{IEEE} Comput. Soc. Press},
  doi       = {10.1109/sfcs.1995.492583},
  file      = {:by-author/W/Watrous/1995_Watrous_528.pdf:PDF},
  keywords  = {Cellular Automata; Computer Science (CS); Quantum Cellular Automata; Quantum Computer Architecture; Quantum Computers},
  owner     = {saulius},
  timestamp = {2021.09.19},
  creationdate = {2021-09-19T00:00:00},
}

@Article{Arrighi2007,
  author        = {Pablo Arrighi and Renan Fargetton and Zizhu Wang},
  journal       = {Fudam. Informaticae},
  title         = {Intrinsically universal one-dimensional quantum cellular automata in two flavours},
  year          = {2007},
  month         = apr,
  pages         = {1--27},
  abstract      = {We give a one-dimensional quantum cellular automaton (QCA) capable of simulating all others. By this we mean that the initial configuration and the local transition rule of any one-dimensional QCA can be encoded within the initial configuration of the universal QCA. Several steps of the universal QCA will then correspond to one step of the simulated QCA. The simulation preserves the topology in the sense that each cell of the simulated QCA is encoded as a group of adjacent cells in the universal QCA. The encoding is linear and hence does not carry any of the cost of the computation. We do this in two flavours: a weak one which requires an infinite but periodic initial configuration and a strong one which needs only a finite initial configuration. KEYWORDS: Quantum cellular automata, Intrinsic universality, Quantum computation.},
  archiveprefix = {arXiv},
  eprint        = {0704.3961},
  file          = {:by-author/A/Arrighi/2007_Arrighi_1.pdf:PDF;:http\://arxiv.org/pdf/0704.3961v3:PDF},
  keywords      = {Cellular Automata; Computer Science (CS); Quant-ph; Quantum Cellular Automata; Quantum Computer Architecture; Quantum Computers},
  owner         = {saulius},
  primaryclass  = {quant-ph},
  timestamp = {2021.09.19},
  creationdate = {2021-09-19T00:00:00},
}

@Article{Weber2010,
  author    = {J. R. Weber and W. F. Koehl and J. B. Varley and A. Janotti and B. B. Buckley and C. G. Van de Walle and D. D. Awschalom},
  journal   = {Proceedings of the National Academy of Sciences},
  title     = {Quantum computing with defects},
  year      = {2010},
  month     = {apr},
  number    = {19},
  pages     = {8513--8518},
  volume    = {107},
  doi       = {10.1073/pnas.1003052107},
  file      = {:by-author/W/Weber/2010_Weber_8513.pdf:PDF;:by-author/W/Weber/2010_Weber_8513_arXiv.pdf:PDF},
  keywords  = {Computer Science (CS); Controlled Crystals; Quantum Computer Architecture; Quantum Computers},
  owner     = {saulius},
  publisher = {Proceedings of the National Academy of Sciences},
  timestamp = {2021.09.19},
  creationdate = {2021-09-19T00:00:00},
  url       = {https://www.pnas.org/content/pnas/107/19/8513.full.pdf},
}

@Article{Kanamori2020,
  author    = {Kanamori, Yoshito and Yoo, Seong-Moo},
  journal   = {Journal of International Technology and Information Management},
  title     = {Quantum computing: principles and applications},
  year      = {2020},
  number    = {2},
  pages     = {3},
  volume    = {29},
  articleno = {3},
  file      = {:by-author/K/Kanamori/2020_Kanamori_3.pdf:PDF},
  owner     = {saulius},
  timestamp = {2021.09.19},
  creationdate = {2021-09-19T00:00:00},
  url       = {https://scholarworks.lib.csusb.edu/cgi/viewcontent.cgi?article=1410&context=jitim},
}

@Article{Cai2020,
  author    = {Xiaoxia Cai and Wei-Hai Fang and Heng Fan and Zhendong Li},
  journal   = {Physical Review Research},
  title     = {Quantum computation of molecular response properties},
  year      = {2020},
  month     = {aug},
  number    = {3},
  pages     = {033324},
  volume    = {2},
  doi       = {10.1103/physrevresearch.2.033324},
  file      = {:by-author/C/Cai/2020_Cai_33324.pdf:PDF},
  keywords  = {Computation of Molecular Properties; Computer Science (CS); Qauntum Computers; Quantum Computer Architecture},
  owner     = {saulius},
  publisher = {American Physical Society ({APS})},
  timestamp = {2021.09.19},
  creationdate = {2021-09-19T00:00:00},
  url       = {https://journals.aps.org/prresearch/pdf/10.1103/PhysRevResearch.2.033324},
}

@Webpage{Clavin2020,
  author    = {Whitney Clavin},
  retrieved = {2021-09-19 10:46:57 EEST},
  title     = {A molecular approach to quantum computing},
  url       = {https://www.technology.org/2020/09/02/a-molecular-approach-to-quantum-computing/},
  month     = sep,
  site      = {https://www.technology.org},
  siteurl   = {https://www.technology.org/tag/quantum-computing/},
  year      = {2020},
  file      = {:by-author/C/Clavin/2020_Clavin_1.pdf:PDF},
  keywords  = {Computer Science (CS); Controlable Crystals; Molecular Computations; Quantum Computers},
  owner     = {saulius},
  pages     = {1--8},
  timestamp = {2021.09.19},
  creationdate = {2021-09-19T00:00:00},
}

@Article{Ganzhorn2019,
  author    = {M. Ganzhorn and D. J. Egger and P. Barkoutsos and P. Ollitrault and G. Salis and N. Moll and M. Roth and A. Fuhrer and P. Mueller and S. Woerner and I. Tavernelli and S. Filipp},
  journal   = {Physical Review Applied},
  title     = {Gate-efficient simulation of molecular eigenstates on a quantum computer},
  year      = {2019},
  month     = {apr},
  number    = {4},
  pages     = {044092},
  volume    = {11},
  doi       = {10.1103/physrevapplied.11.044092},
  file      = {:by-author/G/Ganzhorn/2019_Ganzhorn_44092.pdf:PDF},
  keywords  = {Coherence Time; Computer Science (CS); Molecular Simulations; Quantum Circuits; Quantum Computers},
  owner     = {saulius},
  publisher = {American Physical Society ({APS})},
  timestamp = {2021.09.19},
  creationdate = {2021-09-19T00:00:00},
}

@Webpage{Ganzhorn2019a,
  author    = {Marc Ganzhorn and Daniel Egger and Stefan Filipp},
  retrieved = {2021-09-19 11:41:14 EEST},
  title     = {Cracking the molecular code with the right type of quantum hardware},
  url       = {https://www.ibm.com/blogs/research/2019/06/molecular-quantum-hardware/},
  month     = jul,
  year      = {2019},
  file      = {:by-author/G/Ganzhorn/2019_Ganzhorn_1.pdf:PDF},
  keywords  = {Coherence Time; Computer Science (CS); Molecular Simulations; Quantum Circuits; Quantum Computers},
  owner     = {saulius},
  pages     = {1--7},
  timestamp = {2021.09.19},
  creationdate = {2021-09-19T00:00:00},
}

@Article{AspuruGuzik2005,
  author    = {A. Aspuru-Guzik},
  journal   = {Science},
  title     = {Simulated Quantum Computation of Molecular Energies},
  year      = {2005},
  month     = {sep},
  number    = {5741},
  pages     = {1704--1707},
  volume    = {309},
  doi       = {10.1126/science.1113479},
  file      = {:by-author/A/Aspuru-Guzik/2005_Aspuru-Guzik_1704_preprint.pdf:PDF},
  keywords  = {Computer Science (CS); Molecular Simulations; Quantum Computers},
  owner     = {saulius},
  publisher = {American Association for the Advancement of Science ({AAAS})},
  timestamp = {2021.09.19},
  creationdate = {2021-09-19T00:00:00},
  url       = {https://dash.harvard.edu/bitstream/handle/1/29405815/Simulated Quantum Computation of Molecular Engergies.pdf?sequence=1},
}

@Webpage{IRES,
  author      = {{IBM Research Editorial Staff}},
  retrieved   = {2021-09-19 11:50:39 EEST},
  title       = {How to measure a molecule’s energy using a quantum computer},
  url         = {https://www.ibm.com/blogs/research/2017/09/quantum-molecule/},
  institution = {IBM},
  language    = {English},
  month       = sep,
  site        = {https://www.ibm.com/},
  siteurl     = {https://www.ibm.com/blogs/},
  year        = {2017},
  file        = {:by-author/I/IRES/2017_IRES_1.pdf:PDF},
  keywords    = {Computer Science (CS); Molecular Simulations; Quantum Computers},
  owner       = {saulius},
  pages       = {1-11},
  timestamp = {2021.09.19},
  creationdate = {2021-09-19T00:00:00},
}

@Article{Kandala2017,
  author    = {Abhinav Kandala and Antonio Mezzacapo and Kristan Temme and Maika Takita and Markus Brink and Jerry M. Chow and Jay M. Gambetta},
  journal   = {Nature},
  title     = {Hardware-efficient variational quantum eigensolver for small molecules and quantum magnets},
  year      = {2017},
  month     = {sep},
  number    = {7671},
  pages     = {242--246},
  volume    = {549},
  doi       = {10.1038/nature23879},
  file      = {:by-author/K/Kandala/2017_Kandala_242_preprint.pdf:PDF},
  keywords  = {Computer Science (CS); Molecular Simulations; Quantum Computers},
  owner     = {saulius},
  publisher = {Springer Science and Business Media {LLC}},
  timestamp = {2021.09.19},
  creationdate = {2021-09-19T00:00:00},
}

@Article{Outeiral2020,
  author    = {Carlos Outeiral and Martin Strahm and Jiye Shi and Garrett M. Morris and Simon C. Benjamin and Charlotte M. Deane},
  journal   = {{WIREs} Computational Molecular Science},
  title     = {The prospects of quantum computing in computational molecular biology},
  year      = {2020},
  month     = {may},
  number    = {1},
  volume    = {11},
  doi       = {10.1002/wcms.1481},
  file      = {:by-author/O/Outeiral/2020_Outeiral_1481.pdf:PDF},
  keywords  = {Computer Science (CS); Molecular Simulations; Quantum Computers; Quantum Computers for Molecular Biology},
  owner     = {saulius},
  publisher = {Wiley},
  timestamp = {2021.09.19},
  creationdate = {2021-09-19T00:00:00},
}

@Article{Karle1998,
  author    = {J. Karle and L. Huang and L. Massa},
  journal   = {Pure and Applied Chemistry},
  title     = {Quantum crystallography, a technique for extending the concept of structure},
  year      = {1998},
  month     = {feb},
  number    = {2},
  pages     = {319--324},
  volume    = {70},
  doi       = {10.1351/pac199870020319},
  file      = {:by-author/K/Karle/1998_Karle_319.pdf:PDF},
  keywords  = {Crystallography; Quantum Crystallography; Quantum Mechanics (QM)},
  owner     = {saulius},
  publisher = {Walter de Gruyter {GmbH}},
  timestamp = {2021.09.19},
  creationdate = {2021-09-19T00:00:00},
  url       = {http://publications.iupac.org/pac-2007/1998/pdf/7002x0319.pdf},
}

@Article{Grabowsky2017,
  author    = {Simon Grabowsky and Alessandro Genoni and Hans-Beat Bürgi},
  journal   = {Chemical Science},
  title     = {Quantum crystallography},
  year      = {2017},
  number    = {6},
  pages     = {4159--4176},
  volume    = {8},
  doi       = {10.1039/c6sc05504d},
  file      = {:by-author/G/Grabowsky/2017_Grabowsky_4159.pdf:PDF},
  keywords  = {Crystallography; Quantum Crystallography; Quantum Mechanics (QM)},
  owner     = {saulius},
  publisher = {Royal Society of Chemistry ({RSC})},
  timestamp = {2021.09.19},
  creationdate = {2021-09-19T00:00:00},
  url       = {https://pubs.rsc.org/en/content/articlehtml/2017/sc/c6sc05504d},
}

@Article{Agbaje2019,
  author    = {Agbaje, Michael and Akanbi, Olumide},
  journal   = {Caribbean Journal of Science},
  title     = {A review of quantum computing and its architecture},
  year      = {2019},
  month     = {04},
  number    = {1},
  pages     = {314-329},
  volume    = {53},
  file      = {:by-author/A/Agbaje/2019_Agbaje_314.pdf:PDF},
  keywords  = {Computer Science (CS); Quantum Computer Architecture; Quantum Computers},
  owner     = {saulius},
  timestamp = {2021.09.19},
  creationdate = {2021-09-19T00:00:00},
  url       = {https://www.researchgate.net/publication/332329302_A_review_of_quantum_computing_and_its_architecture},
}

@Article{Bombin2021,
  author        = {Hector Bombin and Isaac H. Kim and Daniel Litinski and Naomi Nickerson and Mihir Pant and Fernando Pastawski and Sam Roberts and Terry Rudolph},
  title         = {Interleaving: Modular architectures for fault-tolerant photonic quantum computing},
  year          = {2021},
  month         = mar,
  pages         = {1--22},
  abstract      = {Useful fault-tolerant quantum computers require very large numbers of physical qubits. Quantum computers are often designed as arrays of static qubits executing gates and measurements. Photonic qubits require a different approach. In photonic fusion-based quantum computing (FBQC), the main hardware components are resource-state generators (RSGs) and fusion devices connected via waveguides and switches. RSGs produce small entangled states of a few photonic qubits, whereas fusion devices perform entangling measurements between different resource states, thereby executing computations. In addition, low-loss photonic delays such as optical fiber can be used as fixed-time quantum memories simultaneously storing thousands of photonic qubits. Here, we present a modular architecture for FBQC in which these components are combined to form "interleaving modules" consisting of one RSG with its associated fusion devices and a few fiber delays. Exploiting the multiplicative power of delays, each module can add thousands of physical qubits to the computational Hilbert space. Networks of modules are universal fault-tolerant quantum computers, which we demonstrate using surface codes and lattice surgery as a guiding example. Our numerical analysis shows that in a network of modules containing 1-km-long fiber delays, each RSG can generate four logical distance-35 surface-code qubits while tolerating photon loss rates above 2% in addition to the fiber-delay loss. We illustrate how the combination of interleaving with further uses of non-local fiber connections can reduce the cost of logical operations and facilitate the implementation of unconventional geometries such as periodic boundaries or stellated surface codes. Interleaving applies beyond purely optical architectures, and can also turn many small disconnected matter-qubit devices with transduction to photons into a large-scale quantum computer.},
  archiveprefix = {arXiv},
  eprint        = {2103.08612},
  file          = {:by-author/B/Bombin/2021_Bombin_1.pdf:PDF;:http\://arxiv.org/pdf/2103.08612v1:PDF},
  keywords      = {Computer Science (CS); Quant-ph; Quantum Computer Architecture; Quantum Computers},
  owner         = {saulius},
  primaryclass  = {quant-ph},
  timestamp = {2021.09.19},
  creationdate = {2021-09-19T00:00:00},
  url           = {https://arxiv.org/pdf/2103.08612.pdf},
}

@Article{Linke2017,
  author    = {Norbert M. Linke and Dmitri Maslov and Martin Roetteler and Shantanu Debnath and Caroline Figgatt and Kevin A. Landsman and Kenneth Wright and Christopher Monroe},
  journal   = {Proceedings of the National Academy of Sciences},
  title     = {Experimental comparison of two quantum computing architectures},
  year      = {2017},
  month     = {mar},
  number    = {13},
  pages     = {3305--3310},
  volume    = {114},
  doi       = {10.1073/pnas.1618020114},
  file      = {:by-author/L/Linke/2017_Linke_3305.pdf:PDF},
  keywords  = {Computer Science (CS); Quantum Computer Architecture; Quantum Computers},
  owner     = {saulius},
  publisher = {Proceedings of the National Academy of Sciences},
  timestamp = {2021.09.19},
  creationdate = {2021-09-19T00:00:00},
  url       = {https://www.pnas.org/content/pnas/114/13/3305.full.pdf},
}

@Manuscript{Bolhasani2019,
  author    = {Hamidreza Bolhasani and Amir Masoud Rahmani},
  title     = {An introduction to quantum computers architecture},
  year      = {2019},
  keywords  = {Computer Science (CS); Quantum Computer Architecture; Quantum Computers},
  month     = {01},
  url       = {https://www.researchgate.net/publication/337144719_An_Introduction_to_Quantum_Computers_Architecture},
  comment   = {Gives a reference to and lists values of decoherence times of for several different QC architectures.},
  file      = {:by-author/B/Bolhasani/2019_Bolhasani_1.pdf:PDF},
  owner     = {saulius},
  pages     = {1--12},
  timestamp = {2021.09.19},
  creationdate = {2021-09-19T00:00:00},
  uthor     = {Bolhasani, Hamidreza and Rahmani, Amir},
}

@Article{Lindgren2020,
  author    = {Jussi Lindgren and Jukka Liukkonen},
  journal   = {Symmetry},
  title     = {The Heisenberg Uncertainty Principle as an Endogenous Equilibrium Property of Stochastic Optimal Control Systems in Quantum Mechanics},
  year      = {2020},
  month     = {sep},
  number    = {9},
  pages     = {1533},
  volume    = {12},
  doi       = {10.3390/sym12091533},
  file      = {:by-author/L/Lindgren/2020_Lindgren_1533.pdf:PDF},
  keywords  = {Computer Science (CS); Interpretation of Quantm Mechanics; Qauntum Mechanics; Quantum Computers; Schroedinger's Cat},
  owner     = {saulius},
  publisher = {{MDPI} {AG}},
  timestamp = {2021.09.19},
  creationdate = {2021-09-19T00:00:00},
}

@Webpage{UniAalto2020,
  author    = {{Aalto University}},
  retrieved = {2021-09-19 13:44:26 EEST},
  title     = {Reality does not depend on the measurer according to new interpretation of quantum mechanics},
  url       = {https://scitechdaily.com/reality-does-not-depend-on-the-measurer-according-to-new-interpretation-of-quantum-mechanics/},
  month     = oct,
  year      = {2020},
  file      = {:by-author/U/UniAalto/2020_UniAalto_1.pdf:PDF},
  owner     = {saulius},
  pages     = {1--24},
  timestamp = {2021.09.19},
  creationdate = {2021-09-19T00:00:00},
}

@Webpage{Haller2021,
  author      = {Joachim Haller},
  retrieved   = {2021-09-19 13:50:34 EEST},
  title       = {An introduction to quantum computing architecture},
  url         = {https://www.redhat.com/architect/quantum-computing},
  institution = {Red Hat},
  language    = {English},
  month       = feb,
  site        = {https://www.redhat.com},
  siteurl     = {https://www.redhat.com/architect},
  year        = {2021},
  file        = {:by-author/H/Haller/2021_Haller_1.pdf:PDF},
  keywords    = {Computer Science (CS); Quantum Computer Architecture; Quantum Computers},
  owner       = {saulius},
  pages       = {1--4},
  timestamp = {2021.09.19},
  creationdate = {2021-09-19T00:00:00},
}

@Article{Meter2013,
  author    = {Rodney Van Meter and Clare Horsman},
  journal   = {Communications of the {ACM}},
  title     = {A blueprint for building a quantum computer},
  year      = {2013},
  month     = {oct},
  number    = {10},
  pages     = {84--93},
  volume    = {56},
  doi       = {10.1145/2494568},
  file      = {:by-author/M/Meter/2013_Meter_84.pdf:PDF},
  keywords  = {Computer Science (CS); Quantum Computer Architecture; Quantum Computers},
  owner     = {saulius},
  publisher = {Association for Computing Machinery ({ACM})},
  timestamp = {2021.09.19},
  creationdate = {2021-09-19T00:00:00},
  url       = {https://cacm.acm.org/magazines/2013/10/168172-a-blueprint-for-building-a-quantum-computer/fulltext},
}

@Manuscript{Perkowski2011,
  author    = {Marek Andrzej Perkowski},
  title     = {Quantum computing basics and concepts},
  year      = {2011},
  keywords  = {Computer Science (CS); Quantum Computer Architecture; Quantum Computers},
  url       = {http://web.cecs.pdx.edu/~mperkows/CLASS_FUTURE/NEW_MATERIALS_2011/lukac_perkowski_book_introduction_and_quantum_mechanics.pdf},
  file      = {:by-author/P/Perkowski/2011_Perkowski_1.pdf:PDF},
  owner     = {saulius},
  pages     = {1--104},
  timestamp = {2021.09.19},
  creationdate = {2021-09-19T00:00:00},
}

@Article{Bartolucci2021,
  author        = {Sara Bartolucci and Patrick Birchall and Hector Bombin and Hugo Cable and Chris Dawson and Mercedes Gimeno-Segovia and Eric Johnston and Konrad Kieling and Naomi Nickerson and Mihir Pant and Fernando Pastawski and Terry Rudolph and Chris Sparrow},
  title         = {Fusion-based quantum computation},
  year          = {2021},
  month         = jan,
  pages         = {1--25},
  abstract      = {We introduce fusion-based quantum computing (FBQC) - a model of universal quantum computation in which entangling measurements, called fusions, are performed on the qubits of small constant-sized entangled resource states. We introduce a stabilizer formalism for analyzing fault tolerance and computation in these schemes. This framework naturally captures the error structure that arises in certain physical systems for quantum computing, such as photonics. FBQC can offer significant architectural simplifications, enabling hardware made up of many identical modules, requiring an extremely low depth of operations on each physical qubit and reducing classical processing requirements. We present two pedagogical examples of fault-tolerant schemes constructed in this framework and numerically evaluate their threshold under a hardware agnostic fusion error model including both erasure and Pauli error. We also study an error model of linear optical quantum computing with probabilistic fusion and photon loss. In FBQC the non-determinism of fusion is directly dealt with by the quantum error correction protocol, along with other errors. We find that tailoring the fault-tolerance framework to the physical system allows the scheme to have a higher threshold than schemes reported in literature. We present a ballistic scheme which can tolerate a 10.4% probability of suffering photon loss in each fusion.},
  archiveprefix = {arXiv},
  eprint        = {2101.09310},
  file          = {:by-author/B/Bartolucci/2021_Bartolucci_1.pdf:PDF;:http\://arxiv.org/pdf/2101.09310v1:PDF},
  keywords      = {Computer Science (CS); Photonic Quantum Computers; Quant-ph; Quantum Computer Architectures; Quantum Computers},
  owner         = {saulius},
  primaryclass  = {quant-ph},
  timestamp = {2021.09.19},
  creationdate = {2021-09-19T00:00:00},
}

@Article{Cao2018,
  author    = {Y. Cao and J. Romero and A. Aspuru-Guzik},
  journal   = {{IBM} Journal of Research and Development},
  title     = {Potential of quantum computing for drug discovery},
  year      = {2018},
  month     = {nov},
  number    = {6},
  pages     = {6:1--6:20},
  volume    = {62},
  doi       = {10.1147/jrd.2018.2888987},
  file      = {:by-author/C/Cao/2018_Cao_1.pdf:PDF},
  keywords  = {Computer Science (CS); Drug Discovery; Quantum Computers},
  owner     = {saulius},
  publisher = {{IBM}},
  timestamp = {2021.09.19},
  creationdate = {2021-09-19T00:00:00},
}

@Article{Gircha2021,
  author        = {A. I. Gircha and A. S. Boev and K. Avchaciov and P. O. Fedichev and A. K. Fedorov},
  title         = {Training a discrete variational autoencoder for generative chemistry and drug design on a quantum annealer},
  year          = {2021},
  month         = aug,
  pages         = {1--7},
  abstract      = {Deep generative chemistry models emerge as powerful tools to expedite drug discovery. However, the immense size and complexity of the structural space of all possible drug-like molecules pose significant obstacles, which could be overcome with hybrid architectures combining quantum computers with deep classical networks. We built a compact discrete variational autoencoder (DVAE) with a Restricted Boltzmann Machine (RBM) of reduced size in its latent layer. The size of the proposed model was small enough to fit on a state-of-the-art D-Wave quantum annealer and allowed training on a subset of the ChEMBL dataset of biologically active compounds. Finally, we generated $4290$ novel chemical structures with medicinal chemistry and synthetic accessibility properties in the ranges typical for molecules from ChEMBL. The experimental results point towards the feasibility of using already existing quantum annealing devices for drug discovery problems, which opens the way to building quantum generative models for practically relevant applications.},
  archiveprefix = {arXiv},
  eprint        = {2108.11644},
  file          = {:by-author/G/Gircha/2021_Gircha_1.pdf:PDF;:http\://arxiv.org/pdf/2108.11644v1:PDF},
  keywords      = {Artificial Intelligence (AI); Artificial Neural Networks (ANN); Cheminformatics; Computer Science (CS); Drug Discovery; Generative Adversarial Networks (GAN); Molecule Structure Encoding; Quant-ph; Quantum Computers; cs.LG; q-bio.BM; q-bio.QM},
  owner         = {saulius},
  primaryclass  = {quant-ph},
  timestamp = {2021.09.19},
  creationdate = {2021-09-19T00:00:00},
}

@Article{Kaiser2021,
  author        = {Jan Kaiser and Supriyo Datta},
  title         = {Perspective: Probabilistic computing with p-bits},
  year          = {2021},
  month         = aug,
  pages         = {1--8},
  abstract      = {Digital computers store information in the form of $bits$ that can take on one of two values $0$ and $1$, while quantum computers are based on $qubits$ that are described by a complex wavefunction whose squared magnitude gives the probability of measuring either a $0$ or a $1$. Here we make the case for a probabilistic computer based on \textit{p-bits} which take on values $0$ and $1$ with controlled probabilities and can be implemented with specialized compact energy-efficient hardware. We propose a generic architecture for such \textit{p-computers} and show that they can significantly accelerate randomized algorithms used in a wide variety of applications including but not limited to Bayesian networks, optimization, Ising models and quantum Monte Carlo.},
  archiveprefix = {arXiv},
  eprint        = {2108.09836},
  file          = {:by-author/K/Kaiser/2021_Kaiser_1.pdf:PDF;:http\://arxiv.org/pdf/2108.09836v1:PDF},
  keywords      = {Computer Architecture; Linear Feedback Register; Probabilitic Computers; QS; Quant-ph; Quantum Computers; RNG; cond-mat.dis-nn; cs.ET},
  owner         = {saulius},
  primaryclass  = {cs.ET},
  timestamp = {2021.09.19},
  creationdate = {2021-09-19T00:00:00},
}

@Article{Potempa2021,
  author        = {Rafal Potempa and Sebastian Porebski},
  journal       = {In: Choras M., Choras R.S., Kurzynski M., Trajdos P., Pejas J., Hyla T. (eds) Progress in Image Processing, Pattern Recognition and Communication Systems. CORES 2021, IP&C 2021, ACS 2021. LNNS, 255. Springer, Cham},
  title         = {Comparing concepts of quantum and classical neural network models for image classification task},
  year          = {2021},
  month         = aug,
  pages         = {1--11},
  abstract      = {While quantum architectures are still under development, when available, they will only be able to process quantum data when machine learning algorithms can only process numerical data. Therefore, in the issues of classification or regression, it is necessary to simulate and study quantum systems that will transfer the numerical input data to a quantum form and enable quantum computers to use the available methods of machine learning. This material includes the results of experiments on training and performance of a hybrid quantum-classical neural network developed for the problem of classification of handwritten digits from the MNIST data set. The comparative results of two models: classical and quantum neural networks of a similar number of training parameters, indicate that the quantum network, although its simulation is time-consuming, overcomes the classical network (it has better convergence and achieves higher training and testing accuracy).},
  archiveprefix = {arXiv},
  doi           = {10.1007/978-3-030-81523-3_6},
  eprint        = {2108.08875},
  file          = {:by-author/P/Potempa/2021_Potempa_1.pdf:PDF;:http\://arxiv.org/pdf/2108.08875v2:PDF},
  keywords      = {Artificial Intelligence (AI); Artificial Neural Networks (ANN); Computer Architecture; Computer Science (CS); Quantum Computer Architecture; Quantum Computers; cs.LG},
  owner         = {saulius},
  primaryclass  = {cs.LG},
  timestamp = {2021.09.19},
  creationdate = {2021-09-19T00:00:00},
}

@Article{Shor1999,
  author    = {Peter W. Shor},
  journal   = {{SIAM} Review},
  title     = {Polynomial-time algorithms for prime factorization and discrete logarithms on a quantum computer},
  year      = {1999},
  month     = {jan},
  number    = {2},
  pages     = {303--332},
  volume    = {41},
  doi       = {10.1137/s0036144598347011},
  file      = {:by-author/S/Shor/1999_Shor_303.pdf:PDF},
  keywords  = {Computer Science (CS); Integer Factorisation; Quantum Advantage; Quanum Computers; Shor's Algorithm},
  owner     = {saulius},
  publisher = {Society for Industrial {\&} Applied Mathematics ({SIAM})},
  timestamp = {2021.09.19},
  creationdate = {2021-09-19T00:00:00},
}

@Article{Shor1995,
  author        = {Peter W. Shor},
  journal       = {arXiv},
  title         = {Polynomial-time algorithms for prime factorization and discrete logarithms on a quantum computer},
  year          = {1995},
  month         = aug,
  pages         = {1--28},
  abstract      = {A digital computer is generally believed to be an efficient universal computing device; that is, it is believed able to simulate any physical computing device with an increase in computation time of at most a polynomial factor. This may not be true when quantum mechanics is taken into consideration. This paper considers factoring integers and finding discrete logarithms, two problems which are generally thought to be hard on a classical computer and have been used as the basis of several proposed cryptosystems. Efficient randomized algorithms are given for these two problems on a hypothetical quantum computer. These algorithms take a number of steps polynomial in the input size, e.g., the number of digits of the integer to be factored.},
  archiveprefix = {arXiv},
  eprint        = {quant-ph/9508027},
  file          = {:by-author/S/Shor/1995_Shor_1.pdf:PDF;:http\://arxiv.org/pdf/quant-ph/9508027v2:PDF},
  keywords      = {Computer Science (CS); Integer Factorisation; Quant-ph; Quantum Advantage; Quanum Computers; Shor's Algorithm},
  owner         = {saulius},
  primaryclass  = {quant-ph},
  timestamp = {2021.09.19},
  creationdate = {2021-09-19T00:00:00},
  url           = {https://arxiv.org/abs/quant-ph/9508027v2},
}

@Article{Egger2020,
  author    = {Daniel J. Egger and Claudio Gambella and Jakub Marecek and Scott McFaddin and Martin Mevissen and Rudy Raymond and Andrea Simonetto and Stefan Woerner and Elena Yndurain},
  journal   = {{IEEE} Transactions on Quantum Engineering},
  title     = {Quantum computing for finance: state-of-the-art and future prospects},
  year      = {2020},
  pages     = {1--24},
  volume    = {1},
  doi       = {10.1109/tqe.2020.3030314},
  file      = {:by-author/E/Egger/2020_Egger_3101724.pdf:PDF},
  keywords  = {Computer Science (CS); Finances; Quantum Advantage; Quantum Computer Applications; Quanum Computers},
  owner     = {saulius},
  publisher = {Institute of Electrical and Electronics Engineers ({IEEE})},
  timestamp = {2021.09.19},
  creationdate = {2021-09-19T00:00:00},
}

@InProceedings{Shaikh2016,
  author    = {Tawseef Ayoub Shaikh and Rashid Ali},
  booktitle = {2016 {IEEE} International Conference on Computer and Information Technology ({CIT})},
  title     = {Quantum computing in big data analytics: a survey},
  year      = {2016},
  month     = {dec},
  pages     = {112--115},
  publisher = {{IEEE}},
  doi       = {10.1109/cit.2016.79},
  file      = {:by-author/S/Shaikh/2016_Shaikh_112.pdf:PDF},
  keywords  = {Big Data; Computer Science (CS); Data Analytics; Data Science; Quantum Advantage; Quantum Computer Applications; Quanum Computers},
  owner     = {saulius},
  timestamp = {2021.09.19},
  creationdate = {2021-09-19T00:00:00},
}

@Article{Grangier1986,
  author    = {P. Grangier and G. Roger and A. Aspect},
  journal   = {Europhysics Letters ({EPL})},
  title     = {Experimental evidence for a photon anticorrelation effect on a beam splitter: a new light on single-photon interferences},
  year      = {1986},
  month     = {feb},
  number    = {4},
  pages     = {173--179},
  volume    = {1},
  doi       = {10.1209/0295-5075/1/4/004},
  file      = {:by-author/G/Grangier/1986_Grangier_173.pdf:PDF},
  keywords  = {Photon States; Physics; Qauntum Mechanics},
  owner     = {saulius},
  publisher = {{IOP} Publishing},
  timestamp = {2021.09.21},
  creationdate = {2021-09-21T00:00:00},
  url       = {https://courses.physics.illinois.edu/phys513/sp2016/reading/week1/GrangierSinglePhoton1986.pdf},
}

@Article{Ma2013,
  author       = {Ma, Xiao-Song and Kofler, Johannes and Qarry, Angie and Tetik, Nuray and Scheidl, Thomas and Ursin, Rupert and Ramelow, Sven and Herbst, Thomas and Ratschbacher, Lothar and Fedrizzi, Alessandro and Jennewein, Thomas and Zeilinger, Anton},
  journal      = {Proceedings of the National Academy of Sciences of the United States of America},
  title        = {Quantum erasure with causally disconnected choice.},
  year         = {2013},
  issn         = {1091-6490},
  month        = jan,
  pages        = {1221--1226},
  volume       = {110},
  abstract     = {The counterintuitive features of quantum physics challenge many common-sense assumptions. In an interferometric quantum eraser experiment, one can actively choose whether or not to erase which-path information (a particle feature) of one quantum system and thus observe its wave feature via interference or not by performing a suitable measurement on a distant quantum system entangled with it. In all experiments performed to date, this choice took place either in the past or, in some delayed-choice arrangements, in the future of the interference. Thus, in principle, physical communications between choice and interference were not excluded. Here, we report a quantum eraser experiment in which, by enforcing Einstein locality, no such communication is possible. This is achieved by independent active choices, which are space-like separated from the interference. Our setup employs hybrid path-polarization entangled photon pairs, which are distributed over an optical fiber link of 55 m in one experiment, or over a free-space link of 144 km in another. No naive realistic picture is compatible with our results because whether a quantum could be seen as showing particle- or wave-like behavior would depend on a causally disconnected choice. It is therefore suggestive to abandon such pictures altogether.},
  completed    = {2013-03-21},
  country      = {United States},
  doi          = {10.1073/pnas.1213201110},
  file         = {:by-author/M/Ma/2013_Ma_1221.pdf:PDF},
  issn-linking = {0027-8424},
  issue        = {4},
  keywords     = {Photon States; Physics; Qauntum Mechanics; Quantum Erasure},
  nlm-id       = {7505876},
  owner        = {saulius},
  pii          = {1213201110},
  pmc          = {PMC3557028},
  pmid         = {23288900},
  pubmodel     = {Print-Electronic},
  pubstate     = {ppublish},
  revised      = {2018-11-13},
  timestamp = {2021.09.21},
  creationdate = {2021-09-21T00:00:00},
  url          = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3557028/pdf/pnas.201213201.pdf},
}

@Article{Hellmuth1987,
  author       = {T. Hellmuth and H. Walther and A. Zajonc and W. Schleich},
  journal      = {Physical review. A, General physics},
  title        = {Delayed-choice experiments in quantum interference.},
  year         = {1987},
  issn         = {0556-2791},
  month        = mar,
  pages        = {2532--2541},
  volume       = {35},
  country      = {United States},
  doi          = {10.1103/physreva.35.2532},
  file         = {:by-author/H/Hellmuth/1987_Hellmuth_2532.pdf:PDF},
  issn-linking = {0556-2791},
  issue        = {6},
  keywords     = {Photon States; Physics; Qauntum Mechanics; Quantum Erasure},
  nlm-id       = {0250142},
  owner        = {saulius},
  pmid         = {9898442},
  pubmodel     = {Print},
  pubstate     = {ppublish},
  revised      = {2019-11-20},
  timestamp = {2021.09.21},
  creationdate = {2021-09-21T00:00:00},
  url          = {https://cs.uwaterloo.ca/~ijdavis/qic890/PR1987_delayed.pdf},
}

@Presentation{Dzemyda2015,
  author    = {Gintautas Dzemyda},
  title     = {Nacionalinis atviros prieigos mokslo informacijos duomenų archyvas {MIDAS}},
  year      = {2015},
  comment   = {Cituoja 15 mln. litų finansavimą, skirtą MIDAS.},
  file      = {:by-author/D/Dzemyda/2015_Dzemyda_1.pdf:PDF},
  keywords  = {MIDAS; Mokslo Duomenys; Mokslo Duomenų Archyvas},
  owner     = {saulius},
  pages     = {1--35},
  timestamp = {2021.09.23},
  creationdate = {2021-09-23T00:00:00},
  url       = {https://biblioteka.ktu.edu/wp-content/uploads/sites/38/2017/05/MIDAS_7_Kaunas-G.Dzemyda1.pdf},
}

@TechReport{EuropeanCommission2021,
  author      = {{European Commission}},
  institution = {{European Commission}},
  title       = {Regional innovation scoreboard 2021},
  year        = {2021},
  comment     = {Gauta iš Eugenijaus Butkaus <eugenijus.butkus@chf.vu.lt> 2021-09-25 10:24 el. laiške, po GMC strateginio plano aptarimo.},
  doi         = {10.2873/674111},
  file        = {:by-author/E/EuropeanCommission/2021_EuropeanCommission_1.pdf:PDF},
  keywords    = {EU Financing; EU Policy; Innovations},
  owner       = {saulius},
  pages       = {1--108},
  timestamp = {2021.09.25},
  creationdate = {2021-09-25T00:00:00},
}

@Article{Ritchie2016,
  author    = {David W. Ritchie and Sergei Grudinin},
  journal   = {Journal of Applied Crystallography},
  title     = {Spherical polar {F}ourier assembly of protein complexes with arbitrary point group symmetry},
  year      = {2016},
  month     = {feb},
  number    = {1},
  pages     = {158--167},
  volume    = {49},
  doi       = {10.1107/s1600576715022931},
  file      = {:by-author/R/Ritchie/2016_Ritchie_158.pdf:PDF},
  keywords  = {Bioinformatics; Crystallography; Protein Structure Prediction},
  owner     = {saulius},
  publisher = {International Union of Crystallography ({IUCr})},
  timestamp = {2021.09.25},
  creationdate = {2021-09-25T00:00:00},
  url       = {https://hal.inria.fr/hal-01261402/document},
}

@Article{Wren2008,
  author    = {J. D. Wren and A. Bateman},
  journal   = {Bioinformatics},
  title     = {Databases, data tombs and dust in the wind},
  year      = {2008},
  month     = {sep},
  number    = {19},
  pages     = {2127--2128},
  volume    = {24},
  doi       = {10.1093/bioinformatics/btn464},
  file      = {:by-author/W/Wren/2008_Wren_2127.pdf:PDF},
  keywords  = {Bioinformatics; Data Curation; Data Preservation; Data Tombs; Databases},
  owner     = {saulius},
  publisher = {Oxford University Press ({OUP})},
  timestamp = {2021.09.26},
  creationdate = {2021-09-26T00:00:00},
}

@Article{Hao1987,
  author    = {Q. Hao and Y.-w. Liu and H.-f. Fan},
  journal   = {Acta Crystallographica Section A Foundations of Crystallography},
  title     = {Direct methods in superspace. I. Preliminary theory and test on the determination of incommensurate modulated structures},
  year      = {1987},
  month     = {nov},
  number    = {6},
  pages     = {820--824},
  volume    = {43},
  doi       = {10.1107/s0108767387098465},
  file      = {:by-author/H/Hao/1987_Hao_820.pdf:PDF},
  keywords  = {Aperiodic Structures; Crystallography; Direct Methods; Modulated Structures; Superspace},
  owner     = {saulius},
  publisher = {International Union of Crystallography ({IUCr})},
  timestamp = {2021.09.26},
  creationdate = {2021-09-26T00:00:00},
}

@Article{Galperin2006,
  author    = {M. Y. Galperin},
  journal   = {Nucleic Acids Research},
  title     = {The molecular biology database collection: 2006 update},
  year      = {2006},
  month     = {jan},
  number    = {90001},
  pages     = {D3--D5},
  volume    = {34},
  comment   = {Cited by Wren2008.},
  doi       = {10.1093/nar/gkj162},
  file      = {:by-author/G/Galperin/2006_Galperin_3.pdf:PDF},
  keywords  = {Bioinformatics; Data Curation; Data Preservation; Data Tombs; Databases},
  owner     = {saulius},
  publisher = {Oxford University Press ({OUP})},
  timestamp = {2021.09.26},
  creationdate = {2021-09-26T00:00:00},
}

@Article{Wren2008a,
  author    = {J. D. Wren},
  journal   = {Bioinformatics},
  title     = {{URL} decay in {MEDLINE}--a 4-year follow-up study},
  year      = {2008},
  month     = {apr},
  number    = {11},
  pages     = {1381--1385},
  volume    = {24},
  doi       = {10.1093/bioinformatics/btn127},
  file      = {:by-author/W/Wren/2008_Wren_1381.pdf:PDF},
  keywords  = {Bioinformatics; Cool URIs do Not Change; Data Persistence},
  owner     = {saulius},
  publisher = {Oxford University Press ({OUP})},
  timestamp = {2021.09.26},
  creationdate = {2021-09-26T00:00:00},
}

@Article{Wren2004,
  author    = {J. D. Wren},
  journal   = {Bioinformatics},
  title     = {404 not found: the stability and persistence of {URLs} published in {MEDLINE}},
  year      = {2004},
  month     = {jan},
  number    = {5},
  pages     = {668--672},
  volume    = {20},
  doi       = {10.1093/bioinformatics/btg465},
  file      = {:by-author/W/Wren/2004_Wren_668.pdf:PDF},
  keywords  = {Bioinformatics; Cool URIs do Not Change; Data Persistence},
  owner     = {saulius},
  publisher = {Oxford University Press ({OUP})},
  timestamp = {2021.09.26},
  creationdate = {2021-09-26T00:00:00},
}

@Article{Benet2014a,
  author        = {Juan Benet},
  journal       = {arXiv},
  title         = {{IPFS} - content addressed, versioned, {P2P} file system},
  year          = {2014},
  month         = jul,
  pages         = {1--11},
  abstract      = {The InterPlanetary File System (IPFS) is a peer-to-peer distributed file system that seeks to connect all computing devices with the same system of files. In some ways, IPFS is similar to the Web, but IPFS could be seen as a single BitTorrent swarm, exchanging objects within one Git repository. In other words, IPFS provides a high throughput content-addressed block storage model, with content-addressed hyper links. This forms a generalized Merkle DAG, a data structure upon which one can build versioned file systems, blockchains, and even a Permanent Web. IPFS combines a distributed hashtable, an incentivized block exchange, and a self-certifying namespace. IPFS has no single point of failure, and nodes do not need to trust each other.},
  archiveprefix = {arXiv},
  eprint        = {1407.3561},
  file          = {:by-author/B/Benet/2014_Benet_1.pdf:PDF;:http\://arxiv.org/pdf/1407.3561v1:PDF},
  keywords      = {Distributed File System; Distributed Storage; IPFS; cs.DC; cs.NI},
  owner         = {saulius},
  primaryclass  = {cs.NI},
  timestamp = {2021.09.28},
  creationdate = {2021-09-28T00:00:00},
  url           = {https://arxiv.org/abs/1407.3561},
}

@Presentation{Sessions2014,
  author    = {Richard B. Sessions},
  title     = {{BUDE}: a general purpose molecular docking program using {OpenCL}},
  year      = {2014},
  file      = {:by-author/S/Sessions/2014_Sessions_1.pdf:PDF},
  keywords  = {Algorithms; GPU; Gibbs Free Energy; Molecular Docking; OpenCL; Pseudocode},
  owner     = {saulius},
  pages     = {1--33},
  timestamp = {2021.09.28},
  creationdate = {2021-09-28T00:00:00},
  url       = {https://on-demand.gputechconf.com/gtc/2014/presentations/S4604-bude-molecular-docking-drug-discovery.pdf},
}

@Article{Irwin2005,
  author          = {Irwin, John J. and Shoichet, Brian K.},
  journal         = {Journal of chemical information and modeling},
  title           = {{ZINC} -- a free database of commercially available compounds for virtual screening},
  year            = {2005},
  issn            = {1549-9596},
  pages           = {177--182},
  volume          = {45},
  abstract        = {A critical barrier to entry into structure-based virtual screening is the lack of a suitable, easy to access database of purchasable compounds. We have therefore prepared a library of 727,842 molecules, each with 3D structure, using catalogs of compounds from vendors (the size of this library continues to grow). The molecules have been assigned biologically relevant protonation states and are annotated with properties such as molecular weight, calculated LogP, and number of rotatable bonds. Each molecule in the library contains vendor and purchasing information and is ready for docking using a number of popular docking programs. Within certain limits, the molecules are prepared in multiple protonation states and multiple tautomeric forms. In one format, multiple conformations are available for the molecules. This database is available for free download (http://zinc.docking.org) in several common file formats including SMILES, mol2, 3D SDF, and DOCK flexibase format. A Web-based query tool incorporating a molecular drawing interface enables the database to be searched and browsed and subsets to be created. Users can process their own molecules by uploading them to a server. Our hope is that this database will bring virtual screening libraries to a wide community of structural biologists and medicinal chemists.},
  citation-subset = {IM},
  completed       = {2005-02-25},
  country         = {United States},
  doi             = {10.1021/ci049714+},
  file            = {:by-author/I/Irwin/2005_Irwin_177.pdf:PDF},
  issn-linking    = {1549-9596},
  issue           = {1},
  keywords        = {Databases; Digital; Drug Design; Economics; Factual; Libraries; Molecular Conformation; Molecular Structure; ZINC},
  mid             = {NIHMS2574},
  nlm-id          = {101230060},
  owner           = {saulius},
  pmc             = {PMC1360656},
  pmid            = {15667143},
  pubmodel        = {Print},
  pubstate        = {ppublish},
  revised         = {2018-11-13},
  timestamp = {2021.09.28},
  creationdate = {2021-09-28T00:00:00},
}

@Article{Batemen2007,
  author    = {A. Batemen},
  journal   = {Nucleic Acids Research},
  title     = {{EDITORIAL}},
  year      = {2007},
  month     = {jan},
  number    = {Database},
  pages     = {D1--D2},
  volume    = {35},
  comment   = {Cited in Wren2008.},
  doi       = {10.1093/nar/gkl1051},
  file      = {:by-author/B/Batemen/2007_Batemen_1.pdf:PDF},
  keywords  = {Bioinformatics; Database Quality Criteria; Databases},
  owner     = {saulius},
  publisher = {Oxford University Press ({OUP})},
  timestamp = {2021.09.28},
  creationdate = {2021-09-28T00:00:00},
}

@Article{Altona1972,
  author    = {C. Altona and M. Sundaralingam},
  journal   = {Journal of the American Chemical Society},
  title     = {Conformational analysis of the sugar ring in nucleosides and nucleotides. New description using the concept of pseudorotation},
  year      = {1972},
  month     = {nov},
  number    = {23},
  pages     = {8205--8212},
  volume    = {94},
  doi       = {10.1021/ja00778a043},
  file      = {:by-author/A/Altona/1972_Altona_8205.pdf:PDF},
  keywords  = {Bioinformatics; DNA; DNA Conformation; Pseudorotation},
  owner     = {saulius},
  publisher = {American Chemical Society ({ACS})},
  timestamp = {2021.09.29},
  creationdate = {2021-09-29T00:00:00},
}

@Presentation{Olson2009a,
  author    = {Wilma K. Olson},
  title     = {Nucleic acid structural principles},
  year      = {2009},
  lecture   = {5},
  file      = {:by-author/O/Olson/2009_Olson_1e.pdf:PDF},
  owner     = {saulius},
  pages     = {1--75},
  timestamp = {2021.09.29},
  creationdate = {2021-09-29T00:00:00},
  url       = {https://casegroup.rutgers.edu/lnotes/BioPhysChem_week5.pdf},
}

@Article{Borman2007,
  author    = {Stu Borman},
  journal   = {Chemical {\&} Engineering News Archive},
  title     = {Structure quality},
  year      = {2007},
  month     = {aug},
  number    = {34},
  pages     = {11},
  volume    = {85},
  doi       = {10.1021/cen-v085n034.p011},
  file      = {:by-author/B/Borman/2007_Borman_11.pdf:PDF},
  keywords  = {"glamure" Journals; Crystallography; Journal Impac Factor; Structure Quality},
  owner     = {saulius},
  publisher = {American Chemical Society ({ACS})},
  timestamp = {2021.10.03},
  creationdate = {2021-10-03T00:00:00},
}

@PhdThesis{Radul2009,
  author    = {Radul, Alexey},
  school    = {MIT},
  title     = {Propagation networks: a flexible and expressive substrate for computation},
  year      = {2009},
  file      = {:by-author/R/Radul/2009_Radul_1.pdf:PDF},
  keywords  = {Computation Medium; Computer Science (CS)},
  owner     = {saulius},
  pages     = {1--174},
  timestamp = {2021.10.06},
  creationdate = {2021-10-06T00:00:00},
  url       = {https://dspace.mit.edu/handle/1721.1/54635},
}

@Article{DeKeer2021,
  author    = {De Keer, Lies and Kilic, Karsu I. and Van Steenberge, Paul H. M. and Daelemans, Lode and Kodura, Daniel and Frisch, Hendrik and De Clerck, Karen and Reyniers, Marie-Françoise and Barner-Kowollik, Christopher and Dauskardt, Reinhold H. and D’hooge, Dagmar R.},
  journal   = {Nature Materials},
  title     = {Computational prediction of the molecular configuration of three-dimensional network polymers},
  year      = {2021},
  issn      = {1476-4660},
  number    = {10},
  pages     = {1422--1430},
  volume    = {20},
  abstract  = {The three-dimensional arrangement of natural and synthetic network materials determines their application range. Control over the real-time incorporation of each building block and functional group is desired to regulate the macroscopic properties of the material from the molecular level onwards. Here we report an approach combining kinetic Monte Carlo and molecular dynamics simulations that chemically and physically predicts the interactions between building blocks in time and in space for the entire formation process of three-dimensional networks. This framework takes into account variations in inter- and intramolecular chemical reactivity, diffusivity, segmental compositions, branch/network point locations and defects. From the kinetic and three-dimensional structural information gathered, we construct structure-property relationships based on molecular descriptors such as pore size or dangling chain distribution and differentiate ideal from non-ideal structural elements. We validate such relationships by synthesizing organosilica, epoxy-amine and Diels-Alder networks with tailored properties and functions, further demonstrating the broad applicability of the platform.},
  doi       = {10.1038/s41563-021-01040-0},
  file      = {:by-author/D/De_Keer/2021_De_Keer_1422.pdf:PDF},
  owner     = {saulius},
  refid     = {De Keer2021},
  timestamp = {2021.10.06},
  creationdate = {2021-10-06T00:00:00},
  url       = {https://doi.org/10.1038/s41563-021-01040-0},
}

@Article{Booch2020,
  author        = {Grady Booch and Francesco Fabiano and Lior Horesh and Kiran Kate and Jon Lenchner and Nick Linck and Andrea Loreggia and Keerthiram Murugesan and Nicholas Mattei and Francesca Rossi and Biplav Srivastava},
  journal       = {arXiv},
  title         = {Thinking fast and slow in {AI}},
  year          = {2020},
  month         = oct,
  pages         = {1--5},
  abstract      = {This paper proposes a research direction to advance AI which draws inspiration from cognitive theories of human decision making. The premise is that if we gain insights about the causes of some human capabilities that are still lacking in AI (for instance, adaptability, generalizability, common sense, and causal reasoning), we may obtain similar capabilities in an AI system by embedding these causal components. We hope that the high-level description of our vision included in this paper, as well as the several research questions that we propose to consider, can stimulate the AI research community to define, try and evaluate new methodologies, frameworks, and evaluation metrics, in the spirit of achieving a better understanding of both human and machine intelligence.},
  archiveprefix = {arXiv},
  comment       = {Discussed in the Zoom session of the OMDI2021 (Ontologies for Material Science) workshop.},
  eprint        = {2010.06002},
  file          = {:http\://arxiv.org/pdf/2010.06002v2:PDF;:by-author/B/Booch/2020_Booch_1.pdf:PDF},
  keywords      = {cs.AI},
  owner         = {saulius},
  primaryclass  = {cs.AI},
  timestamp = {2021.10.09},
  creationdate = {2021-10-09T00:00:00},
}

@Article{Alexandrov2011,
  author           = {E. V. Alexandrov and V. A. Blatov and A. V. Kochetkov and D. M. Proserpio},
  journal          = {{CrystEngComm}},
  title            = {Underlying nets in three-periodic coordination polymers: topology, taxonomy and prediction from a computer-aided analysis of the {C}ambridge {S}tructural {D}atabase},
  year             = {2011},
  number           = {12},
  pages            = {3947--3958},
  volume           = {13},
  comment          = {Cited by Eon2016 as containing the definition of the "underlying net". Cited in Alexandrov2017.},
  creationdate     = {2021-10-09T00:00:00},
  doi              = {10.1039/c0ce00636j},
  file             = {:by-author/A/Alexandrov/2011_Alexandrov_3947_suppl.pdf:PDF;:by-author/A/Alexandrov/2011_Alexandrov_3947.pdf:PDF},
  keywords         = {Crystal Nets; Crystallography; Polymers; Polymers in Crystals; Topology},
  modificationdate = {2024-09-14T12:42:34},
  owner            = {saulius},
  publisher        = {Royal Society of Chemistry ({RSC})},
  timestamp        = {2021.10.09},
}

@Article{Eon2011,
  author    = {Jean-Guillaume Eon},
  journal   = {Acta Crystallographica Section A Foundations of Crystallography},
  title     = {Euclidian embeddings of periodic nets: definition of a topologically induced complete set of geometric descriptors for crystal structures},
  year      = {2011},
  month     = {dec},
  number    = {1},
  pages     = {68--86},
  volume    = {67},
  comment   = {Cited in Eon2016.},
  doi       = {10.1107/s0108767310042832},
  file      = {:by-author/E/Eon/2011_Eon_68.pdf:PDF},
  keywords  = {Periodic Nets; Polymers; Polymers in Crystals},
  owner     = {saulius},
  publisher = {International Union of Crystallography ({IUCr})},
  timestamp = {2021.10.09},
  creationdate = {2021-10-09T00:00:00},
}

@Article{Eon2013,
  author       = {Eon, Jean Guillaume},
  journal      = {Acta crystallographica. Section A, Foundations of crystallography},
  title        = {Topological density of lattice nets.},
  year         = {2013},
  issn         = {1600-5724},
  month        = jan,
  pages        = {119--121},
  volume       = {69},
  abstract     = {It was shown in a previous paper [Eon (2004). Acta Cryst. A60, 7-18] that the topological density of a periodic net can be calculated directly from its cycles figure, a polytope constructed from those cycles of the quotient graph of the net that are associated with its geodesic lines. It may happen that these lines generate a grid pattern forming a supercell, a phenomenon that was not considered in the former derivation of the formula but is common for lattice nets. An adjustment of the expression is proposed to this effect and applied to the square and hexagonal lattice nets as well as to the 13 families of cubic lattice nets.},
  completed    = {2013-06-17},
  country      = {United States},
  doi          = {10.1107/S0108767312042298},
  file         = {:by-author/E/Eon/2013_Eon_119.pdf:PDF},
  issn-linking = {0108-7673},
  issue        = {Pt 1},
  nlm-id       = {8305825},
  owner        = {saulius},
  pii          = {S0108767312042298},
  pmid         = {23250068},
  pubmodel     = {Print-Electronic},
  pubstate     = {ppublish},
  revised      = {2012-12-19},
  timestamp = {2021.10.09},
  creationdate = {2021-10-09T00:00:00},
}

@Article{Nespolo2007,
  author    = {Massimo Nespolo},
  journal   = {Acta Crystallographica Section A Foundations of Crystallography},
  title     = {Does mathematical crystallography still have a role in the {XXI} century?},
  year      = {2007},
  month     = {dec},
  number    = {1},
  pages     = {96--111},
  volume    = {64},
  doi       = {10.1107/s0108767307044625},
  file      = {:by-author/N/Nespolo/2007_Nespolo_96.pdf:PDF},
  owner     = {saulius},
  publisher = {International Union of Crystallography ({IUCr})},
  timestamp = {2021.10.09},
  creationdate = {2021-10-09T00:00:00},
}

@Article{Eon2007,
  author          = {Eon, Jean Guillaume},
  journal         = {Acta crystallographica. Section A, Foundations of crystallography},
  title           = {Infinite geodesic paths and fibers, new topological invariants in periodic graphs.},
  year            = {2007},
  issn            = {0108-7673},
  month           = jan,
  pages           = {53--65},
  volume          = {63},
  abstract        = {Rings are well known invariants of nets. In this work, a generalization of the concepts of cycles and rings is introduced. Infinite paths in periodic graphs are defined as connected, acyclic, regular subgraphs of degree two; geodesics are defined as infinite paths such that the unique path between any pair of vertices is a geodesic path in the whole graph. An infinite path can be thought of as an infinite cycle and a geodesic as an infinite ring. In a further step, a geodesic fiber is defined as a minimal 1-periodic subgraph that contains all geodesic paths between any pair of its vertices. Geodesic fibers are topological invariants of periodic graphs whose labeled quotient graphs are subgraphs of the labeled quotient graph of the whole graph; the paper describes applications of geodesic fibers to the analysis of the automorphisms of minimal nets, crystallographic and non-crystallographic nets.},
  citation-subset = {IM},
  comment         = {Cited in Eon2016.},
  completed       = {2007-02-26},
  country         = {United States},
  doi             = {10.1107/S0108767306047702},
  file            = {:by-author/E/Eon/2007_Eon_53.pdf:PDF},
  issn-linking    = {0108-7673},
  issue           = {Pt 1},
  keywords        = {Crystallography; Methods; X-Ray},
  nlm-id          = {8305825},
  owner           = {saulius},
  pii             = {S0108767306047702},
  pmid            = {17179607},
  pubmodel        = {Print-Electronic},
  pubstate        = {ppublish},
  revised         = {2006-12-20},
  timestamp = {2021.10.09},
  creationdate = {2021-10-09T00:00:00},
}

@Article{Eon2005,
  author    = {Jean-Guillaume Eon},
  journal   = {Acta Crystallographica Section A Foundations of Crystallography},
  title     = {Graph-theoretical characterization of periodicity in crystallographic nets and other infinite graphs},
  year      = {2005},
  month     = {aug},
  number    = {5},
  pages     = {501--511},
  volume    = {61},
  comment   = {Cited in Eon2016.},
  doi       = {10.1107/s0108767305019963},
  file      = {:by-author/E/Eon/2005_Eon_501.pdf:PDF},
  owner     = {saulius},
  publisher = {International Union of Crystallography ({IUCr})},
  timestamp = {2021.10.09},
  creationdate = {2021-10-09T00:00:00},
}

@Article{Bonneau2004,
  author    = {Charlotte Bonneau and Olaf Delgado-Friedrichs and Michael O{\textquotesingle}Keeffe and Omar M. Yaghi},
  journal   = {Acta Crystallographica Section A Foundations of Crystallography},
  title     = {Three-periodic nets and tilings: minimal nets},
  year      = {2004},
  month     = {oct},
  number    = {6},
  pages     = {517--520},
  volume    = {60},
  doi       = {10.1107/s0108767304015442},
  file      = {:by-author/B/Bonneau/2004_Bonneau_517.pdf:PDF},
  keywords  = {Crystal Nets; Periodic Nets; Polymers; Polymers in Crystals},
  owner     = {saulius},
  publisher = {International Union of Crystallography ({IUCr})},
  timestamp = {2021.10.10},
  creationdate = {2021-10-10T00:00:00},
}

@Article{DelgadoFriedrichs2003a,
  author    = {Olaf Delgado-Friedrichs and Michael O{\textquotesingle}Keeffe},
  journal   = {Acta Crystallographica Section A Foundations of Crystallography},
  title     = {Identification of and symmetry computation for crystal nets},
  year      = {2003},
  month     = {jun},
  number    = {4},
  pages     = {351--360},
  volume    = {59},
  comment   = {Cited by Eon2016: "the embedding topology of most crystal structures is the same as that of the barycentric representation of the underlying net, as also given by the SYSTRE program".},
  doi       = {10.1107/s0108767303012017},
  file      = {:by-author/D/Delgado-Friedrichs/2003_Delgado-Friedrichs_351.pdf:PDF},
  keywords  = {Crystal Nets; Periodic Nets; Polymers; Polymers in Crystals},
  owner     = {saulius},
  publisher = {International Union of Crystallography ({IUCr})},
  timestamp = {2021.10.10},
  creationdate = {2021-10-10T00:00:00},
}

@Article{Taylor1939,
  author    = {W. H. Taylor},
  journal   = {Reports on Progress in Physics},
  title     = {{X} rays and crystal: {II}. The structures of silicates},
  year      = {1939},
  month     = {jan},
  number    = {1},
  pages     = {351--360},
  volume    = {6},
  doi       = {10.1088/0034-4885/6/1/320},
  file      = {:by-author/T/Taylor/1939_Taylor_351.pdf:PDF},
  keywords  = {Crystallography; First Structures; History},
  owner     = {saulius},
  publisher = {{IOP} Publishing},
  timestamp = {2021.10.10},
  creationdate = {2021-10-10T00:00:00},
  url       = {https://doi.org/10.1088/0034-4885/6/1/320},
}

@Article{Bragg1930,
  author    = {W. L. Bragg},
  journal   = {Zeitschrift für Kristallographie - Crystalline Materials},
  title     = {{XXV}. The Structure of Silicates},
  year      = {1930},
  month     = {dec},
  number    = {1-6},
  pages     = {237--305},
  volume    = {74},
  comment   = {Cited by Eon2016: "the classification of crystal structures has been based on the geometrical and topological properties of chemical linkages".},
  doi       = {10.1524/zkri.1930.74.1.237},
  file      = {:by-author/B/Bragg/1930_Bragg_237.pdf:PDF},
  keywords  = {Crystallography; First Structures; History},
  owner     = {saulius},
  publisher = {Walter de Gruyter {GmbH}},
  timestamp = {2021.10.10},
  creationdate = {2021-10-10T00:00:00},
}

@Article{Blatov2009,
  author    = {Vladislav A. Blatov and Davide M. Proserpio},
  journal   = {Acta Crystallographica Section A Foundations of Crystallography},
  title     = {Topological relations between three-periodic nets. {II}. Binodal nets},
  year      = {2009},
  month     = {apr},
  number    = {3},
  pages     = {202--212},
  volume    = {65},
  doi       = {10.1107/s0108767309006096},
  file      = {:by-author/B/Blatov/2009_Blatov_202.pdf:PDF},
  keywords  = {Crystal Nets; Crystallography; Periodic Nets},
  owner     = {saulius},
  publisher = {International Union of Crystallography ({IUCr})},
  timestamp = {2021.10.10},
  creationdate = {2021-10-10T00:00:00},
}

@Article{OKeefe1980,
  author    = {M. O'Keefe and B. G. Hyde},
  journal   = {Philosophical Transactions of the Royal Society of London. Series A, Mathematical and Physical Sciences},
  title     = {Plane nets in crystal chemistry},
  year      = {1980},
  month     = {feb},
  number    = {1417},
  pages     = {553--618},
  volume    = {295},
  comment   = {Cited in Eon2016: "Much effort has been spent to unravel and describe what is called the bond topology of crystal structures, or crystal nets, as initiated in the works of Wells (1977) and later O’Keeffe & Hyde (1980).".},
  doi       = {10.1098/rsta.1980.0150},
  file      = {:by-author/O/OKeefe/1980_OKeefe_553.pdf:PDF},
  keywords  = {Crystal Nets; Crystallography; Periodic Nets},
  owner     = {saulius},
  publisher = {The Royal Society},
  timestamp = {2021.10.10},
  creationdate = {2021-10-10T00:00:00},
}

@Article{Coxeter1978,
  author    = {H. S. M. Coxeter},
  journal   = {Bulletin of the American Mathematical Society},
  title     = {Three-dimensional nets and polyhedra, by {A. F. Wells, Wiley, New York}, 1977,xii + 268 pp., $29.95},
  year      = {1978},
  month     = may,
  number    = {3},
  pages     = {466--470},
  volume    = {84},
  comment   = {This is a book review for a book (Wells1977) cited in Eon2016: "Much effort has been spent to unravel and describe what is called the bond topology of crystal structures, or crystal nets, as initiated in the works of Wells (1977) and later O’Keeffe & Hyde (1980).". The book itself can not be found that easily, but the review contains some important notation examples and tables.},
  file      = {:by-author/C/Coxeter/1978_Coxeter_466.pdf:PDF},
  keywords  = {Crystal Nets; Crystallography; Periodic Nets},
  owner     = {saulius},
  timestamp = {2021.10.10},
  creationdate = {2021-10-10T00:00:00},
  url       = {https://projecteuclid.org/download/pdf_1/euclid.bams/1183540634},
}

@Book{Harary2018,
  author    = {Frank Harary},
  publisher = {CRC Press},
  title     = {Graph theory},
  year      = {2018},
  comment   = {Cited in Eon2016: "The distance between two atoms in a crystal structure may be defined as the minimum number of bonds that separate them in a path stepping from one to another bonded atom. This is the current definition of distances in a graph (Harary, 1972)."},
  file      = {:by-author/H/Harary/2018_Harary_1.pdf:PDF},
  keywords  = {Graph Theory; Mathematics},
  owner     = {saulius},
  pages     = {1--285},
  timestamp = {2021.10.10},
  creationdate = {2021-10-10T00:00:00},
  url       = {https://isbnsearch.org/isbn/9780201410334},
}

@Article{OKeeffe2012,
  author    = {Michael O'Keeffe and Omar M. Yaghi},
  journal   = {Chemical Reviews},
  title     = {Deconstructing the crystal structures of metal{\textendash}organic frameworks and related materials into their underlying nets},
  year      = {2012},
  month     = {sep},
  number    = {2},
  pages     = {675--702},
  volume    = {112},
  comment   = {Cited in Eon2016: "The corresponding metric topology is the combinatorial or bond topology and is thus given by the crystal graph, or network, representing the structure (see also Blatov, 2011; Hawthorne, 2012; O’Keeffe & Yaghi, 2012).".},
  doi       = {10.1021/cr200205j},
  file      = {:by-author/O/O'Keeffe/2012_O'Keeffe_675.pdf:PDF},
  keywords  = {Crystal Nets; Crystallography; Periodic Nets},
  owner     = {saulius},
  publisher = {American Chemical Society ({ACS})},
  timestamp = {2021.10.10},
  creationdate = {2021-10-10T00:00:00},
  url       = {http://yaghi.berkeley.edu/pdfPublications/11-deconstructing.pdf},
}

@Article{OKeeffe2008,
  author           = {Michael O'Keeffe and Maxim A. Peskov and Stuart J. Ramsden and Omar M. Yaghi},
  journal          = {Accounts of Chemical Research},
  title            = {The Reticular Chemistry Structure Resource ({RCSR}) Database of, and Symbols for, Crystal Nets},
  year             = {2008},
  month            = {oct},
  number           = {12},
  pages            = {1782--1789},
  volume           = {41},
  comment          = {Cited in Eon2016: "we will adopt the three-letter symbols from the RCSR (Reticular Chemistry Structure esource) used to designate combinatorial (net) topologies (O’Keeffe et al., 2008).". Cited in Alexandrov2017.},
  creationdate     = {2021-10-10T00:00:00},
  doi              = {10.1021/ar800124u},
  file             = {:by-author/O/O'Keeffe/2008_O'Keeffe_1782.pdf:PDF},
  keywords         = {Chemical Databases; Crystal Nets; Crystallographic Databases; Crystallography; Databases; Periodic Nets},
  modificationdate = {2024-09-14T12:47:59},
  owner            = {saulius},
  publisher        = {American Chemical Society ({ACS})},
  timestamp        = {2021.10.10},
  url              = {http://yaghi.berkeley.edu/pdfPublications/09RCSRaccChem.pdf},
}

@Article{Shevchenko2021,
  author    = {Alexander P. Shevchenko and Vladislav A. Blatov},
  journal   = {Structural Chemistry},
  title     = {Simplify to understand: how to elucidate crystal structures?},
  year      = {2021},
  month     = {jan},
  number    = {2},
  pages     = {507--519},
  volume    = {32},
  doi       = {10.1007/s11224-020-01724-4},
  file      = {:by-author/S/Shevchenko/2021_Shevchenko_507.pdf:PDF},
  keywords  = {Crystal Nets; Crystallography; Periodic Nets},
  owner     = {saulius},
  publisher = {Springer Science and Business Media {LLC}},
  timestamp = {2021.10.10},
  creationdate = {2021-10-10T00:00:00},
}

@Article{Blatov2006,
  author    = {Vladislav A. Blatov},
  journal   = {Acta Crystallographica Section A Foundations of Crystallography},
  title     = {A method for hierarchical comparative analysis of crystal structures},
  year      = {2006},
  month     = {aug},
  number    = {5},
  pages     = {356--364},
  volume    = {62},
  comment   = {Cited by Eon2016: " An automatic search for finite building units and their hierarchical organization in a given 3-periodic net was introduced by Blatov (2006).".},
  doi       = {10.1107/s0108767306025591},
  file      = {:by-author/B/Blatov/2006_Blatov_356.pdf:PDF},
  keywords  = {Building Blocks; Crystal Nets; Crystallography; Periodic Nets},
  owner     = {saulius},
  publisher = {International Union of Crystallography ({IUCr})},
  timestamp = {2021.10.10},
  creationdate = {2021-10-10T00:00:00},
}

@Article{Batten2012,
  author    = {Stuart R. Batten and Neil R. Champness and Xiao-Ming Chen and Javier Garcia-Martinez and Susumu Kitagawa and Lars Öhrström and Michael O{\textquotesingle}Keeffe and Myunghyun Paik Suh and Jan Reedijk},
  journal   = {{CrystEngComm}},
  title     = {Coordination polymers, metal{\textendash}organic frameworks and the need for terminology guidelines},
  year      = {2012},
  number    = {9},
  pages     = {3001},
  volume    = {14},
  doi       = {10.1039/c2ce06488j},
  file      = {:by-author/B/Batten/2012_Batten_3001.pdf:PDF},
  keywords  = {Crystal Nets; Metal-Organic Frameworks (MOF); Periodic Nets; Terminology},
  owner     = {saulius},
  publisher = {Royal Society of Chemistry ({RSC})},
  timestamp = {2021.10.10},
  creationdate = {2021-10-10T00:00:00},
}

@Article{Batten2013,
  author           = {Stuart R. Batten and Neil R. Champness and Xiao-Ming Chen and Javier Garcia-Martinez and Susumu Kitagawa and Lars Öhrström and Michael O'Keeffe and Myunghyun Paik Suh and Jan Reedijk},
  journal          = {Pure and Applied Chemistry},
  title            = {Terminology of metal{\textendash}organic frameworks and coordination polymers ({IUPAC} Recommendations 2013)},
  year             = {2013},
  month            = {jul},
  number           = {8},
  pages            = {1715--1724},
  volume           = {85},
  comment          = {Cited in Eon2016, Alexandrov2017(ref. [2]): the IUPAC recommendation for the terminology of coordination polymers.},
  creationdate     = {2021-10-10T00:00:00},
  doi              = {10.1351/pac-rec-12-11-20},
  file             = {:by-author/B/Batten/2013_Batten_1715.pdf:PDF},
  keywords         = {Crystal Nets; Metal-Organic Frameworks (MOF); Periodic Nets; Terminology},
  modificationdate = {2024-09-13T16:37:55},
  owner            = {saulius},
  publisher        = {Walter de Gruyter {GmbH}},
  timestamp        = {2021.10.10},
}

@Article{Klee2004,
  author    = {W. E. Klee},
  journal   = {Crystal Research and Technology},
  title     = {Crystallographic nets and their quotient graphs},
  year      = {2004},
  month     = {nov},
  number    = {11},
  pages     = {959--968},
  volume    = {39},
  comment   = {Cited by Eon2016: a net is a simple, 3-connected, locally finite graph. Gives definition of a quotient graph for a crystallographic net.},
  doi       = {10.1002/crat.200410281},
  file      = {:by-author/K/Klee/2004_Klee_959.pdf:PDF},
  keywords  = {Crystal Nets; Crystallographic Nets; Metal-Organic Frameworks (MOF); Periodic Nets; Quotient Graphs},
  owner     = {saulius},
  publisher = {Wiley},
  timestamp = {2021.10.10},
  creationdate = {2021-10-10T00:00:00},
}

@Manuscript{Gentleman2010,
  author    = {Robert Gentleman and Ross Ihaka},
  title     = {Lexical scope and statistical computing},
  year      = {2010},
  keywords  = {Compiler Design; Computer Languages; Computer Science (CS); Lexical Scoping},
  url       = {https://www.stat.auckland.ac.nz/~ihaka/downloads/lexical.pdf},
  file      = {:by-author/G/Gentleman/2010_Gentleman_1.pdf:PDF},
  owner     = {saulius},
  pages     = {1--19},
  timestamp = {2021.10.12},
  creationdate = {2021-10-12T00:00:00},
}

@TechReport{Woodman2007,
  author      = {Oliver J. Woodman},
  institution = {University of Cambridge Computer Laboratory},
  title       = {An introduction to inertial navigation},
  year        = {2007},
  file        = {:by-author/W/Woodman/2007_Woodman_1.pdf:PDF},
  keywords    = {Computer Architecture; Inertial Navigation; Integrators},
  owner       = {saulius},
  pages       = {1--37},
  timestamp = {2021.10.11},
  creationdate = {2021-10-11T00:00:00},
  url         = {https://www.cl.cam.ac.uk/techreports/UCAM-CL-TR-696.pdf},
}

@Article{Henn2016a,
  author    = {Julian Henn},
  journal   = {International Journal of Materials Chemistry and Physics},
  title     = {An application of negative powers of {P}oisson numbers in crystallography},
  year      = {2016},
  number    = {2},
  pages     = {50--53},
  volume    = {2},
  comment   = {Bibliograhy obtained from https://www.dataqintelligence.com/publications/.},
  eprint    = {http://www.aiscience.org/journal/paperInfo/ijmcp?paperId=2132},
  file      = {:by-author/H/Henn/2016_Henn_50.pdf:PDF},
  keywords  = {Crystallography; Data Quality; Statistics},
  owner     = {saulius},
  timestamp = {2021.10.12},
  creationdate = {2021-10-12T00:00:00},
  url       = {http://files.aiscience.org/journal/article/pdf/70130079.pdf},
}

@Article{Henn2015,
  author    = {Julian Henn and Kathrin Meindl},
  journal   = {International Journal of Materials Chemistry and Physics},
  title     = {Two common sources of systematic errors in charge density studies},
  year      = {2015},
  number    = {3},
  pages     = {417--430},
  volume    = {1},
  comment   = {Bibliograhy obtained from https://www.dataqintelligence.com/publications/.},
  eprint    = {http://www.aiscience.org/journal/paperInfo/ijmcp?paperId=2152},
  file      = {:by-author/H/Henn/2015_Henn_417.pdf:PDF},
  keywords  = {Crystallography; Data Quality; Statistics},
  owner     = {saulius},
  timestamp = {2021.10.12},
  creationdate = {2021-10-12T00:00:00},
  url       = {http://files.aiscience.org/journal/article/pdf/70130081.pdf},
}

@Article{Henn2019,
  author    = {Henn, Julian},
  journal   = {Crystallography Reviews},
  title     = {Metrics for crystallographic diffraction- and fit-data: a review of existing ones and the need for new ones},
  year      = {2019},
  issn      = {1476-3508},
  month     = {Apr},
  number    = {2},
  pages     = {83--156},
  volume    = {25},
  comment   = {Bibliograhy obtained from https://www.dataqintelligence.com/publications/.},
  doi       = {10.1080/0889311x.2019.1607845},
  file      = {:by-author/H/Henn/2019_Henn_83.pdf:PDF;:by-author/H/Henn/2019_Henn_83_suppl/2019_Henn_83_suppl.pdf:PDF},
  keywords  = {Crystallography; Data Quality; Statistics},
  owner     = {saulius},
  publisher = {Informa UK Limited},
  timestamp = {2021.10.12},
  creationdate = {2021-10-12T00:00:00},
  url       = {http://dx.doi.org/10.1080/0889311X.2019.1607845},
}

@Article{Henn2018,
  author    = {Henn, Julian},
  journal   = {Zeitschrift für Kristallographie - Crystalline Materials},
  title     = {On predicted {R} factors for dynamic structure crystallography},
  year      = {2018},
  issn      = {2194-4946},
  month     = {Jun},
  number    = {9-10},
  pages     = {689--694},
  volume    = {233},
  comment   = {Bibliograhy obtained from https://www.dataqintelligence.com/publications/.},
  doi       = {10.1515/zkri-2018-2078},
  file      = {:by-author/H/Henn/2018_Henn_689.pdf:PDF},
  keywords  = {Crystallography; Data Quality; Statistics},
  owner     = {saulius},
  publisher = {Walter de Gruyter GmbH},
  timestamp = {2021.10.12},
  creationdate = {2021-10-12T00:00:00},
  url       = {http://dx.doi.org/10.1515/zkri-2018-2078},
}

@Article{Henn2012,
  author    = {Henn, Julian and Meindl, Kathrin},
  journal   = {Acta Crystallographica Section A Foundations of Crystallography},
  title     = {Response to "{O}n the significance of {B}ragg reflections" by {J}ørgensenet al.},
  year      = {2012},
  issn      = {0108-7673},
  month     = {Feb},
  number    = {2},
  pages     = {304--304},
  volume    = {68},
  comment   = {Bibliograhy obtained from https://www.dataqintelligence.com/publications/.},
  doi       = {10.1107/s010876731200325x},
  file      = {:by-author/H/Henn/2012_Henn_304.pdf:PDF},
  keywords  = {Crystallography; Data Quality; Statistics},
  owner     = {saulius},
  publisher = {International Union of Crystallography (IUCr)},
  timestamp = {2021.10.12},
  creationdate = {2021-10-12T00:00:00},
  url       = {http://dx.doi.org/10.1107/S010876731200325X},
}

@Article{Henn2010,
  author    = {Henn, Julian and Meindl, Kathrin},
  journal   = {Acta Crystallographica Section A Foundations of Crystallography},
  title     = {Is there a fundamental upper limit for the significance {I}/σ({I}) of observations from {X}-ray and neutron diffraction experiments?},
  year      = {2010},
  issn      = {0108-7673},
  month     = {Oct},
  number    = {6},
  pages     = {676--684},
  volume    = {66},
  comment   = {Bibliograhy obtained from https://www.dataqintelligence.com/publications/.},
  doi       = {10.1107/s0108767310038808},
  file      = {:by-author/H/Henn/2010_Henn_676.pdf:PDF},
  keywords  = {Crystallography; Data Quality; Statistics},
  owner     = {saulius},
  publisher = {International Union of Crystallography (IUCr)},
  timestamp = {2021.10.12},
  creationdate = {2021-10-12T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0108767310038808},
}

@Article{Meindl2008,
  author    = {Meindl, Kathrin and Henn, Julian},
  journal   = {Acta Crystallographica Section A Foundations of Crystallography},
  title     = {Foundations of residual-density analysis},
  year      = {2008},
  issn      = {0108-7673},
  month     = {Apr},
  number    = {3},
  pages     = {404--418},
  volume    = {64},
  comment   = {Bibliograhy obtained from https://www.dataqintelligence.com/publications/.},
  doi       = {10.1107/s0108767308006879},
  file      = {:by-author/M/Meindl/2008_Meindl_404.pdf:PDF},
  keywords  = {Crystallography; Data Quality; Statistics},
  owner     = {saulius},
  publisher = {International Union of Crystallography (IUCr)},
  timestamp = {2021.10.12},
  creationdate = {2021-10-12T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0108767308006879},
}

@Article{Joergensen2012,
  author    = {Mads Ry Vogel Jørgensen and Helle Svendsen and Mette Stokkebro Schmøkel and Jacob Overgaard and Bo Brummerstedt Iversen},
  journal   = {Acta Crystallographica Section A Foundations of Crystallography},
  title     = {On the significance of {B}ragg reflections},
  year      = {2012},
  month     = {feb},
  number    = {2},
  pages     = {301--303},
  volume    = {68},
  doi       = {10.1107/s0108767312003066},
  file      = {:by-author/J/Jørgensen/2012_Jørgensen_301.pdf:PDF},
  keywords  = {Crystallography; Data Quality; Statistics},
  owner     = {saulius},
  publisher = {International Union of Crystallography ({IUCr})},
  timestamp = {2021.10.12},
  creationdate = {2021-10-12T00:00:00},
}

@Article{Beukemann1992,
  author    = {A. Beukemann and W. E. Klee},
  journal   = {Zeitschrift für Kristallographie - Crystalline Materials},
  title     = {Minimal nets},
  year      = {1992},
  month     = {nov},
  number    = {1-4},
  pages     = {37--53},
  volume    = {201},
  comment   = {Cited in Eon2016: "Minimal nets were introduced by Beukemann & Klee (1992) as p-periodic nets of genus p".},
  doi       = {10.1524/zkri.1992.201.14.37},
  file      = {:by-author/B/Beukemann/1992_Beukemann_37.pdf:PDF},
  keywords  = {Crystal Nets; Crystallography; Periodic Nets},
  owner     = {saulius},
  publisher = {Walter de Gruyter {GmbH}},
  timestamp = {2021.10.12},
  creationdate = {2021-10-12T00:00:00},
}

@Article{Blatov2007a,
  author    = {Vladislav A. Blatov and Olaf Delgado-Friedrichs and Michael O{\textquotesingle}Keeffe and Davide M. Proserpio},
  journal   = {Acta Crystallographica Section A Foundations of Crystallography},
  title     = {Three-periodic nets and tilings: natural tilings for nets},
  year      = {2007},
  month     = {aug},
  number    = {5},
  pages     = {418--425},
  volume    = {63},
  doi       = {10.1107/s0108767307038287},
  file      = {:by-author/B/Blatov/2007_Blatov_418.pdf:PDF},
  keywords  = {Crystal Nets; Crystallography; Essential Rings; Periodic Nets; Strong Rings},
  owner     = {saulius},
  publisher = {International Union of Crystallography ({IUCr})},
  timestamp = {2021.10.12},
  creationdate = {2021-10-12T00:00:00},
}

@Article{DelgadoFriedrichs2003b,
  author    = {Olaf Delgado-Friedrichs and Michael O'Keeffe and Omar M. Yaghi},
  journal   = {Acta Crystallographica Section A Foundations of Crystallography},
  title     = {Three-periodic nets and tilings: semiregular nets},
  year      = {2003},
  month     = {oct},
  number    = {6},
  pages     = {515--525},
  volume    = {59},
  doi       = {10.1107/s0108767303017100},
  file      = {:by-author/D/Delgado-Friedrichs/2003_Delgado-Friedrichs_515.pdf:PDF},
  keywords  = {Crystal Nets; Crystallography; Periodic Nets; Tilings},
  owner     = {saulius},
  publisher = {International Union of Crystallography ({IUCr})},
  timestamp = {2021.10.12},
  creationdate = {2021-10-12T00:00:00},
}

@Article{OKeeffe1991,
  author    = {M. O'Keeffe},
  journal   = {Zeitschrift für Kristallographie - Crystalline Materials},
  title     = {Dense and rare four-connected nets},
  year      = {1991},
  month     = {jan},
  number    = {1-4},
  pages     = {21--37},
  volume    = {196},
  doi       = {10.1524/zkri.1991.196.14.21},
  file      = {:by-author/O/O'Keeffe/1991_O'Keeffe_21.pdf:PDF},
  keywords  = {Crystal Nets; Crystallography; Periodic Nets},
  owner     = {saulius},
  publisher = {Walter de Gruyter {GmbH}},
  timestamp = {2021.10.12},
  creationdate = {2021-10-12T00:00:00},
}

@Article{Yaghi2003,
  author    = {Omar M. Yaghi and Michael O'Keeffe and Nathan W. Ockwig and Hee K. Chae and Mohamed Eddaoudi and Jaheon Kim},
  journal   = {Nature},
  title     = {Reticular synthesis and the design of new materials},
  year      = {2003},
  month     = {jun},
  number    = {6941},
  pages     = {705--714},
  volume    = {423},
  comment   = {Cited in Eon2016.},
  doi       = {10.1038/nature01650},
  file      = {:by-author/Y/Yaghi/2003_Yaghi_705.pdf:PDF},
  owner     = {saulius},
  publisher = {Springer Science and Business Media {LLC}},
  timestamp = {2021.10.12},
  creationdate = {2021-10-12T00:00:00},
}

@Article{Jagodzinski1991,
  author    = {H. Jagodzinski},
  journal   = {Zeitschrift für Kristallographie - Crystalline Materials},
  title     = {Diffraction from the {F}ibonacci chain},
  year      = {1991},
  month     = {jan},
  number    = {1-4},
  pages     = {1--20},
  volume    = {196},
  doi       = {10.1524/zkri.1991.196.14.1},
  file      = {:by-author/J/Jagodzinski/1991_Jagodzinski_1.pdf:PDF},
  keywords  = {Crystallography; Quasicrystals},
  owner     = {saulius},
  publisher = {Walter de Gruyter {GmbH}},
  timestamp = {2021.10.12},
  creationdate = {2021-10-12T00:00:00},
}

@Manuscript{Rutanen2007,
  author    = {Kalle Rutanen},
  title     = {The {F}ourier transform of a gaussian function},
  year      = {2007},
  keywords  = {Fourier Transform; Gausian Function; Mathematics; Normal Distribution},
  url       = {https://kaba.hilvi.org/homepage/cg/texts/gaussianfourier.pdf},
  file      = {:by-author/R/Rutanen/2007_Rutanen_1.pdf:PDF},
  owner     = {saulius},
  pages     = {1--5},
  timestamp = {2021.10.13},
  creationdate = {2021-10-13T00:00:00},
}

@Manuscript{Gubner2013,
  author    = {John A. Gubner},
  title     = {Derivation of the {F}ourier inversion formula, {B}ochner’s theorem, and {H}erglotz’s theorem},
  year      = {2013},
  keywords  = {Crystallography; Fourier Transform; Inverse Fourier Transform; Mathematics; Physics; Signal Processing},
  url       = {https://gubner.ece.wisc.edu/notes/FTintro.pdf},
  comment   = {Derives Inverse Fourier Transform formula.},
  file      = {:by-author/G/Gubner/2013_Gubner_1.pdf:PDF},
  owner     = {saulius},
  pages     = {1--15},
  timestamp = {2021.10.13},
  creationdate = {2021-10-13T00:00:00},
}

@Article{Friese2013,
  author    = {Friese, K. and Grzechnik, A. and Posse, J. M. and Petricek, V.},
  journal   = {High Pressure Research},
  title     = {Refinement of high pressure single-crystal diffraction data using {J}ana2006},
  year      = {2013},
  issn      = {1477-2299},
  month     = {Mar},
  number    = {1},
  pages     = {196--201},
  volume    = {33},
  comment   = {Cited by Henn2015.},
  doi       = {10.1080/08957959.2012.758723},
  file      = {:by-author/F/Friese/2013_Friese_196.pdf:PDF},
  keywords  = {Crystallography; Data Quality},
  owner     = {saulius},
  publisher = {Informa UK Limited},
  timestamp = {2021.10.13},
  creationdate = {2021-10-13T00:00:00},
  url       = {http://dx.doi.org/10.1080/08957959.2012.758723},
}

@Article{Hooft2009,
  author    = {Hooft, Rob W. W. and Straver, Leo H. and Spek, Anthony L.},
  journal   = {Acta Crystallographica Section A Foundations of Crystallography},
  title     = {Probability plots based on {S}tudent’s t-distribution},
  year      = {2009},
  issn      = {0108-7673},
  month     = {May},
  number    = {4},
  pages     = {319--321},
  volume    = {65},
  comment   = {Cited by Henn2015.},
  doi       = {10.1107/s0108767309009908},
  file      = {:by-author/H/Hooft/2009_Hooft_319.pdf:PDF},
  keywords  = {Crystallography; Data Quality; Statistics},
  owner     = {saulius},
  publisher = {International Union of Crystallography (IUCr)},
  timestamp = {2021.10.13},
  creationdate = {2021-10-13T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0108767309009908},
}

@Article{Mondal2012,
  author    = {Mondal, Swastik and Prathapa, Siriyara Jagannatha and van Smaalen, Sander},
  journal   = {Acta Crystallographica Section A Foundations of Crystallography},
  title     = {Experimental dynamic electron densities of multipole models at different temperatures},
  year      = {2012},
  issn      = {1600-5724},
  month     = {Aug},
  number    = {5},
  pages     = {568--581},
  volume    = {68},
  comment   = {Cited by Henn2015.},
  doi       = {10.1107/s0108767312029005},
  file      = {:by-author/M/Mondal/2012_Mondal_568.pdf:PDF},
  keywords  = {Crystallography; Data Quality},
  owner     = {saulius},
  publisher = {International Union of Crystallography (IUCr)},
  timestamp = {2021.10.13},
  creationdate = {2021-10-13T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0108767312029005},
}

@Article{Henn2012a,
  author    = {Henn, Julian},
  journal   = {Acta Crystallographica Section A Foundations of Crystallography},
  title     = {Expectation values for integer powers of a {P}oisson-distributed random number},
  year      = {2012},
  issn      = {1600-5724},
  month     = {Sep},
  number    = {6},
  pages     = {703--704},
  volume    = {68},
  doi       = {10.1107/s010876731203200x},
  file      = {:by-author/H/Henn/2012_Henn_703.pdf:PDF},
  keywords  = {Crystallography; Data Quality; Statistics},
  owner     = {saulius},
  publisher = {International Union of Crystallography (IUCr)},
  timestamp = {2021.10.13},
  creationdate = {2021-10-13T00:00:00},
  url       = {http://dx.doi.org/10.1107/S010876731203200X},
}

@Article{Abrahams1971,
  author    = {Abrahams, S. C. and Keve, E. T.},
  journal   = {Acta Crystallographica Section A},
  title     = {Normal probability plot analysis of error in measured and derived quantities and standard deviations},
  year      = {1971},
  issn      = {0567-7394},
  month     = {Mar},
  number    = {2},
  pages     = {157--165},
  volume    = {27},
  comment   = {Cited by Henn2015.},
  doi       = {10.1107/s0567739471000305},
  file      = {:by-author/A/Abrahams/1971_Abrahams_157.pdf:PDF},
  keywords  = {Crystallography; Data Quality; Normal Plot Analysis; Statistics},
  owner     = {saulius},
  publisher = {International Union of Crystallography (IUCr)},
  timestamp = {2021.10.13},
  creationdate = {2021-10-13T00:00:00},
  url       = {http://dx.doi.org/10.1107/S0567739471000305},
}

@Article{Henn2015a,
  author    = {Henn, Julian and Meindl, Kathrin},
  journal   = {Acta Crystallographica Section A Foundations and Advances},
  title     = {Statistical tests against systematic errors in data sets based on the equality of residual means and variances from control samples: theory and applications},
  year      = {2015},
  issn      = {2053-2733},
  month     = {Jan},
  number    = {2},
  pages     = {203--211},
  volume    = {71},
  doi       = {10.1107/s2053273314027363},
  file      = {:by-author/H/Henn/2015_Henn_203.pdf:PDF;:by-author/H/Henn/2015_Henn_203_suppl/pc5048sup1.pdf:PDF},
  keywords  = {Crystallography; Data Quality; Statistics},
  owner     = {saulius},
  publisher = {International Union of Crystallography (IUCr)},
  timestamp = {2021.10.13},
  creationdate = {2021-10-13T00:00:00},
  url       = {http://dx.doi.org/10.1107/S2053273314027363},
}

@Article{Abrahams1969,
  author    = {S. C. Abrahams},
  journal   = {Acta Crystallographica Section A: Crystal Physics, Diffraction, Theoretical and General Crystallography},
  title     = {Indicators of accuracy in structure factor measurement},
  year      = {1969},
  month     = {jan},
  number    = {1},
  pages     = {165--173},
  volume    = {25},
  comment   = {Cited by Julian Henn.},
  doi       = {10.1107/s0567739469000283},
  file      = {:by-author/A/Abrahams/1969_Abrahams_165.pdf:PDF},
  keywords  = {Crystallography; Data Quality},
  owner     = {saulius},
  publisher = {International Union of Crystallography ({IUCr})},
  timestamp = {2021.10.13},
  creationdate = {2021-10-13T00:00:00},
}

@Article{Thompson2019,
  author    = {Amber L. Thompson},
  journal   = {Crystallography Reviews},
  title     = {Chemical crystallography: when are `bad data' `good data'?},
  year      = {2019},
  month     = {jan},
  number    = {1},
  pages     = {3--53},
  volume    = {25},
  doi       = {10.1080/0889311x.2019.1569643},
  file      = {:by-author/T/Thompson/2019_Thompson_3.pdf:PDF},
  keywords  = {Crystallography; Data Quality; Statistics},
  owner     = {saulius},
  publisher = {Informa {UK} Limited},
  timestamp = {2021.10.13},
  creationdate = {2021-10-13T00:00:00},
}

@Presentation{Evans2006a,
  author    = {Brian L. Evans and Niranjan Damera-Venkata and Magesh Valliappan},
  title     = {Introduction to digital signalprocessors ({DSP}s)},
  year      = {2006},
  file      = {:by-author/E/Evans/2006_Evans_1a.pdf:PDF},
  keywords  = {Accumulator Architecture; Computer Architecture; Computer Science (CS); DSP; Load-store Architecture; Memory-register Architecture; Register Architecture},
  owner     = {saulius},
  pages     = {1--30},
  timestamp = {2021.10.17},
  creationdate = {2021-10-17T00:00:00},
  url       = {http://signal.ece.utexas.edu/~arslan/courses/realtime/lectures/01_Architecture/lecture1.pdf},
}

@Presentation{Heller2019,
  author    = {William T. Heller},
  title     = {An introduction to small-angle scattering},
  year      = {2019},
  file      = {:by-author/H/Heller/2019_Heller_1.pdf:PDF},
  keywords  = {SANS; SAXS; Scattering Theory; Small Angle Scattering; Structural Biology},
  owner     = {saulius},
  pages     = {1--30},
  timestamp = {2021.10.19},
  creationdate = {2021-10-19T00:00:00},
  url       = {https://neutrons.ornl.gov/sites/default/files/heller_NXSchool_2019.pdf},
}

@Article{Weyl1919,
  author    = {H. Weyl},
  title     = {Ausbreitung elektromagnetischer {W}ellen über einem ebenen {L}eiter},
  year      = {1919},
  number    = {21},
  pages     = {481--500},
  volume    = {365},
  comment   = {Found via https://mathoverflow.net/questions/149692/fourier-transform-of-the-unit-sphere.},
  doi       = {10.1002/andp.19193652104},
  file      = {:by-author/W/Weyl/1919_Weyl_481.pdf:PDF},
  keywords  = {Crystallography; Electromagnetic Fields; Fourier Transform; Fourier Transform of a Solid Sphere},
  owner     = {saulius},
  publisher = {Wiley},
  timestamp = {2021.10.20},
  creationdate = {2021-10-20T00:00:00},
}

@Article{Vembu1961,
  author    = {S. Vembu},
  title     = {{F}ourier transformation of the n-dimensional radial delta function},
  year      = {1961},
  number    = {1},
  pages     = {165--168},
  volume    = {12},
  doi       = {10.1093/qmath/12.1.165},
  file      = {:by-author/V/Vembu/1961_Vembu_165.pdf:PDF},
  keywords  = {Crystallography; Delta Function; Fourier Transform},
  owner     = {saulius},
  publisher = {Oxford University Press ({OUP})},
  timestamp = {2021.10.20},
  creationdate = {2021-10-20T00:00:00},
}

@Manuscript{Hammouda2009,
  author    = {Boualem Hammouda},
  title     = {Single particle form factors},
  year      = {2009},
  keywords  = {Crystallography; Fourier Transform; Fourier Transform of a Solid Sphere; Scattering; Unit Sphere},
  url       = {https://www.ncnr.nist.gov/staff/hammouda/distance_learning/chapter_27.pdf},
  file      = {:by-author/H/Hammouda/2009_Hammouda_1pdf:PDF},
  owner     = {saulius},
  pages     = {1--13},
  timestamp = {2021-10-20},
  creationdate = {2021-10-20T00:00:00},
}

@Manuscript{anonymous2010,
  author    = {{anonymous}},
  title     = {Scattering geometries},
  year      = {2010},
  keywords  = {Crystallography; Dynamic Theory; Scattering; Structure Factors},
  url       = {https://www2.physics.ox.ac.uk/sites/default/files/CrystalStructure_fullnotes6.pdf},
  file      = {:by-author/a/anonymous/2010_anonymous_1.pdf:PDF},
  owner     = {saulius},
  pages     = {1--42},
  timestamp = {2021-10-20},
  creationdate = {2021-10-20T00:00:00},
}

@Presentation{Khan2018,
  author    = {Nagma Khan},
  title     = {Deconvoluting graph convolutional networks},
  year      = {2018},
  file      = {:by-author/K/Khan/2018_Khan_1.pdf:PDF},
  keywords  = {Artificial Neural Networks (ANN); Computer Science (CS); Graph Neural Networks (GNN); Graphs; Neural Networks (NN)},
  owner     = {saulius},
  pages     = {1--35},
  timestamp = {2021.10.20},
  creationdate = {2021-10-20T00:00:00},
  url       = {https://www.ee.iitb.ac.in/~eestudentrg/presentations/Deconvoluting_Graph_Convolutional_Networks.pdf},
}

@Book{Wagner2008,
  author    = {Alexander J. Wagner},
  publisher = {Alexander J. Wagner},
  title     = {A practical introduction to the lattice {B}oltzmann method},
  year      = {2008},
  file      = {:by-author/W/Wagner/2008_Wagner_1.pdf:PDF},
  keywords  = {Computer Science (CS); Lattice Boltzmann Equation; Statistical Physics; Thermodynamics},
  owner     = {saulius},
  pages     = {1--46},
  timestamp = {2021.10.20},
  creationdate = {2021-10-20T00:00:00},
  url       = {https://www.ndsu.edu/fileadmin/physics.ndsu.edu/Wagner/LBbook.pdf},
}

@Presentation{Rana2009,
  author    = {Farhan Rana},
  title     = {The reciprocal lattice},
  year      = {2009},
  file      = {:by-author/R/Rana/2009_Rana_1.pdf:PDF},
  keywords  = {Crystallography; Delta Function; Fourier Transform; Infinite Sum of Imaginary Exponents; Lattice Fourier Transform; Reciprocal Lattice},
  owner     = {saulius},
  pages     = {1--16},
  timestamp = {2021.10.20},
  creationdate = {2021-10-20T00:00:00},
  url       = {https://courses.cit.cornell.edu/mse5470/handout5.pdf},
}

@Manuscript{Nepf2003b,
  author    = {Heidi Nepf},
  title     = {Propagation of uncertainty through mathematical operations},
  year      = {2003},
  keywords  = {Physics; Propagation of Uncertainties},
  url       = {http://web.mit.edu/fluids-modules/www/exper_techniques/2.Propagation_of_Uncertaint.pdf},
  file      = {:by-author/N/Nepf/2003_Nepf_1b.pdf:PDF},
  owner     = {saulius},
  pages     = {1--7},
  timestamp = {2021.10.22},
  creationdate = {2021-10-22T00:00:00},
}

@Article{Stall2020,
  author    = {Shelley Stall and Leah McEwen and Lesley Wyborn and Nancy Hoebelheinrich and Ian Bruno},
  journal   = {Data Intelligence},
  title     = {Growing the {FAIR} community at the intersection of the geosciences and pure and applied chemistry},
  year      = {2020},
  month     = {jan},
  number    = {1-2},
  pages     = {139--150},
  volume    = {2},
  doi       = {10.1162/dint_a_00036},
  file      = {:by-author/S/Stall/2020_Stall_139.pdf:PDF},
  keywords  = {Data Management; Data Quality; Data Sharing; FAIR},
  owner     = {saulius},
  publisher = {{MIT} Press - Journals},
  timestamp = {2021.10.22},
  creationdate = {2021-10-22T00:00:00},
}

@Article{Holler2017,
  author    = {Mirko Holler and Manuel Guizar-Sicairos and Esther H. R. Tsai and Roberto Dinapoli and Elisabeth Müller and Oliver Bunk and Jörg Raabe and Gabriel Aeppli},
  journal   = {Nature},
  title     = {High-resolution non-destructive three-dimensional imaging of integrated circuits},
  year      = {2017},
  month     = {mar},
  number    = {7645},
  pages     = {402--406},
  volume    = {543},
  doi       = {10.1038/nature21698},
  file      = {:by-author/H/Holler/2017_Holler_402.pdf:PDF},
  keywords  = {Computer Science (CS); Harware; Ptychography; Reverse Engineeering},
  owner     = {saulius},
  publisher = {Springer Science and Business Media {LLC}},
  timestamp = {2021.10.26},
  creationdate = {2021-10-26T00:00:00},
}

@Presentation{Brown2019,
  author    = {Harvey Brown},
  title     = {The evolution of {B}ell’s thinking about the {B}ell theorem in quantum mechanics},
  year      = {2019},
  file      = {:by-author/B/Brown/2019_Brown_1.pdf:PDF},
  keywords  = {Bell's Inequalities; Measurement Problem; Physics; Quantum Mechanics (QM)},
  owner     = {saulius},
  pages     = {1--15},
  timestamp = {2021.10.27},
  creationdate = {2021-10-27T00:00:00},
  url       = {https://drive.google.com/file/d/1lqOrJhLqNQoMyRSsOlSuGnpI0b2qE0IR/view},
}

@Presentation{Richards2004,
  author    = {Paul G. Richards},
  title     = {On {F}ourier transforms and delta functions},
  year      = {2004},
  file      = {:by-author/R/Richards/2004_Richards_1.pdf:PDF},
  keywords  = {Crystallography; Deltta Function; Fourier Transform},
  owner     = {saulius},
  pages     = {1--15},
  timestamp = {2021.10.27},
  creationdate = {2021-10-27T00:00:00},
  url       = {https://www.ldeo.columbia.edu/~richards/webpage_rev_Jan06/Ch3_FourTrans&DeltaFns.pdf},
}

@Article{Garfield1972,
  author    = {Eugene Garfield},
  journal   = {Science},
  title     = {Citation analysis as a tool in journal evaluation},
  year      = {1972},
  month     = {nov},
  number    = {4060},
  pages     = {471--479},
  volume    = {178},
  doi       = {10.1126/science.178.4060.471},
  file      = {:by-author/G/Garfield/1972_Garfield_471.pdf:PDF},
  keywords  = {Bibliometry; Citation Factors; Impact Factor (IF)},
  owner     = {saulius},
  publisher = {American Association for the Advancement of Science ({AAAS})},
  timestamp = {2021.10.31},
  creationdate = {2021-10-31T00:00:00},
}

@Article{Landhuis2016,
  author    = {Esther Landhuis},
  journal   = {Nature},
  title     = {Scientific literature: Information overload},
  year      = {2016},
  month     = {jul},
  number    = {7612},
  pages     = {457--458},
  volume    = {535},
  doi       = {10.1038/nj7612-457a},
  file      = {:by-author/L/Landhuis/2016_Landhuis_457.pdf:PDF},
  keywords  = {Article Counts; One Publication Per Minute; Publication Numbers; Scientific Publishing},
  owner     = {saulius},
  publisher = {Springer Science and Business Media {LLC}},
  timestamp = {2021.10.31},
  creationdate = {2021-10-31T00:00:00},
}

@Article{Wieder2021,
  author    = {Oliver Wieder and Mélaine Kuenemann and Marcus Wieder and Thomas Seidel and Christophe Meyer and Thierry Langer},
  journal   = {Preprints},
  title     = {Improved lipophilicity and aqueous solubility prediction with composite graph neural networks},
  year      = {2021},
  month     = {aug},
  pages     = {1--43},
  doi       = {10.20944/preprints202108.0548.v1},
  file      = {:by-author/W/Wieder/2021_Wieder_1.pdf:PDF},
  keywords  = {Artificial Neural Networks (ANN); Computer Science (CS); Crystal Property Prediction; Crystallography; Graph Neural Networks (GNN); Machine Learning (ML); Neural Networks (NN)},
  owner     = {saulius},
  publisher = {{MDPI} {AG}},
  timestamp = {2021.11.02},
  creationdate = {2021-11-02T00:00:00},
}

@Article{Wieder2021a,
  author    = {Oliver Wieder and Mélaine Kuenemann and Marcus Wieder and Thomas Seidel and Christophe Meyer and Sharon D. Bryant and Thierry Langer},
  journal   = {Molecules},
  title     = {Improved lipophilicity and aqueous solubility prediction with composite graph neural networks},
  year      = {2021},
  month     = {oct},
  number    = {20},
  pages     = {6185},
  volume    = {26},
  doi       = {10.3390/molecules26206185},
  file      = {:by-author/W/Wieder/2021_Wieder_6185.pdf:PDF},
  keywords  = {Artificial Neural Networks (ANN); Computer Science (CS); Crystal Property Prediction; Crystallography; Graph Neural Networks (GNN); Machine Learning (ML); Neural Networks (NN)},
  owner     = {saulius},
  publisher = {{MDPI} {AG}},
  timestamp = {2021.11.02},
  creationdate = {2021-11-02T00:00:00},
}

@TechReport{Thomson2018,
  author      = {Stuart Thomson},
  institution = {Edinburgh Instruments},
  title       = {Observing phase transitions in a halide perovskite using temperature dependent photoluminescence spectroscopy},
  year        = {2018},
  number      = {AN_P45;},
  type        = {Application Note},
  file        = {:by-author/T/Thomson/2018_Thomson_1.pdf:PDF},
  keywords    = {Crystallography; Cubic; Material Science; Perovskites; Phase Transition; Photoluminescence Spectroscopy; Tetragocal},
  owner       = {saulius},
  pages       = {1--4},
  timestamp = {2021.11.02},
  creationdate = {2021-11-02T00:00:00},
  url         = {https://www.edinst.com/wp-content/uploads/2018/05/AN45_Phase-Transitions_Halide-Perovskites.pdf},
}

@Article{Saidi2016,
  author       = {Saidi, Wissam A. and Choi, Joshua J.},
  journal      = {The Journal of chemical physics},
  title        = {Nature of the cubic to tetragonal phase transition in methylammonium lead iodide perovskite.},
  year         = {2016},
  issn         = {1089-7690},
  month        = oct,
  pages        = {144702},
  volume       = {145},
  abstract     = {Hybrid organic-inorganic perovskites, as well as the perovskites in general, are known for their phase complexity evidenced by the stabilization of different polymorphs, and thus an understanding of their regions of stability and transitions can be important for their photovoltaic and optoelectronic technologies. Here we use a multiscale approach based on first-principles calculations with van der Waals corrections and classical force-field molecular dynamics to determine the finite-temperature properties of the tetragonal and cubic phases of CH NH PbI . Temperature effects are implicitly included using the quasi-harmonic approximation that can describe anharmonic behavior due to thermal expansion through the dependence of the harmonic frequencies on structural parameters. Our finite-temperature free-energy surfaces predict the lattice and elastic moduli evolution with temperature, and show in particular that the calculated lattice parameters of the cubic and tetragonal phases are to within 1% of experimental values. Further, our results show that the phonons are the major contributing factor for stabilizing the cubic phase at high temperatures mainly due to the low-energy phonon modes that are associated with the inorganic lattice. On the other hand, the configurational entropy due to CH NH  rotational degrees of freedom is slightly more favored in the cubic phase and amounts to less than 0.2% of the T = 0 K free-energy difference between the two phases.},
  completed    = {2017-02-17},
  country      = {United States},
  doi          = {10.1063/1.4964094},
  file         = {:by-author/S/Saidi/2016_Saidi_144702.pdf:PDF},
  issn-linking = {0021-9606},
  issue        = {14},
  keywords     = {Crystallography; Cubic; Material Science; Perovskites; Phase Transition; Photoluminescence Spectroscopy; Tetragocal},
  nlm-id       = {0375360},
  owner        = {saulius},
  pmid         = {27782531},
  pubmodel     = {Print},
  pubstate     = {ppublish},
  revised      = {2017-02-17},
  timestamp = {2021.11.02},
  creationdate = {2021-11-02T00:00:00},
}

@Article{Micheli2009,
  author       = {Micheli, Alessio},
  journal      = {{IEEE} transactions on neural networks},
  title        = {Neural network for graphs: a contextual constructive approach.},
  year         = {2009},
  issn         = {1941-0093},
  month        = mar,
  pages        = {498--511},
  volume       = {20},
  abstract     = {This paper presents a new approach for learning in structured domains (SDs) using a constructive neural network for graphs (NN4G). The new model allows the extension of the input domain for supervised neural networks to a general class of graphs including both acyclic/cyclic, directed/undirected labeled graphs. In particular, the model can realize adaptive contextual transductions, learning the mapping from graphs for both classification and regression tasks. In contrast to previous neural networks for structures that had a recursive dynamics, NN4G is based on a constructive feedforward architecture with state variables that uses neurons with no feedback connections. The neurons are applied to the input graphs by a general traversal process that relaxes the constraints of previous approaches derived by the causality assumption over hierarchical input data. Moreover, the incremental approach eliminates the need to introduce cyclic dependencies in the definition of the system state variables. In the traversal process, the NN4G units exploit (local) contextual information of the graphs vertices. In spite of the simplicity of the approach, we show that, through the compositionality of the contextual information developed by the learning, the model can deal with contextual information that is incrementally extended according to the graphs topology. The effectiveness and the generality of the new approach are investigated by analyzing its theoretical properties and providing experimental results.},
  comment      = {Cited in Wieder2021{,a}.},
  completed    = {2009-05-18},
  country      = {United States},
  doi          = {10.1109/TNN.2008.2010350},
  file         = {:by-author/M/Micheli/2009_Micheli_498.pdf:PDF},
  issn-linking = {1045-9227},
  issue        = {3},
  keywords     = {Artificial Neural Networks (ANN); Computer Science (CS); Crystal Property Prediction; Crystallography; Graph Neural Networks (GNN); Machine Learning (ML); Neural Networks (NN)},
  nlm-id       = {101211035},
  owner        = {saulius},
  pmid         = {19193509},
  pubmodel     = {Print-Electronic},
  pubstate     = {ppublish},
  revised      = {2016-10-20},
  timestamp = {2021.11.02},
  creationdate = {2021-11-02T00:00:00},
}

@Article{Hu2019,
  author        = {Weihua Hu and Bowen Liu and Joseph Gomes and Marinka Zitnik and Percy Liang and Vijay Pande and Jure Leskovec},
  journal       = {arXiv},
  title         = {Strategies for pre-training graph neural networks},
  year          = {2019},
  month         = may,
  pages         = {1--22},
  abstract      = {Many applications of machine learning require a model to make accurate pre-dictions on test examples that are distributionally different from training ones, while task-specific labels are scarce during training. An effective approach to this challenge is to pre-train a model on related tasks where data is abundant, and then fine-tune it on a downstream task of interest. While pre-training has been effective in many language and vision domains, it remains an open question how to effectively use pre-training on graph datasets. In this paper, we develop a new strategy and self-supervised methods for pre-training Graph Neural Networks (GNNs). The key to the success of our strategy is to pre-train an expressive GNN at the level of individual nodes as well as entire graphs so that the GNN can learn useful local and global representations simultaneously. We systematically study pre-training on multiple graph classification datasets. We find that naive strategies, which pre-train GNNs at the level of either entire graphs or individual nodes, give limited improvement and can even lead to negative transfer on many downstream tasks. In contrast, our strategy avoids negative transfer and improves generalization significantly across downstream tasks, leading up to 9.4% absolute improvements in ROC-AUC over non-pre-trained models and achieving state-of-the-art performance for molecular property prediction and protein function prediction.},
  archiveprefix = {arXiv},
  comment       = {Cited in Wieder2021{,a}.},
  eprint        = {1905.12265},
  file          = {:by-author/H/Hu/2019_Hu_1.pdf:PDF},
  keywords      = {cs.LG; stat.ML},
  owner         = {saulius},
  primaryclass  = {cs.LG},
  timestamp = {2021.11.02},
  creationdate = {2021-11-02T00:00:00},
  url           = {https://arxiv.org/abs/1905.12265},
}

@Article{Wieder2020,
  author    = {Oliver Wieder and Stefan Kohlbacher and M{\'{e}}laine Kuenemann and Arthur Garon and Pierre Ducrot and Thomas Seidel and Thierry Langer},
  journal   = {Drug Discovery Today: Technologies},
  title     = {A compact review of molecular property prediction with graph neural networks},
  year      = {2020},
  month     = {dec},
  pages     = {1--12},
  comment   = {Cited in Wieder2021{,a}.},
  doi       = {10.1016/j.ddtec.2020.11.009},
  file      = {:by-author/W/Wieder/2020_Wieder_1.pdf:PDF},
  keywords  = {Artificial Neural Networks (ANN); Computer Science (CS); Crystal Property Prediction; Crystallography; Graph Neural Networks (GNN); Machine Learning (ML); Neural Networks (NN)},
  owner     = {saulius},
  publisher = {Elsevier {BV}},
  timestamp = {2021.11.02},
  creationdate = {2021-11-02T00:00:00},
}

@Article{Hu2020,
  author    = {Jianjun Hu and Wenhui Yang and Edirisuriya M. Dilanga Siriwardane},
  title     = {Distance matrix-based crystal structure prediction using evolutionary algorithms},
  year      = {2020},
  month     = {dec},
  number    = {51},
  pages     = {10909--10919},
  volume    = {124},
  doi       = {10.1021/acs.jpca.0c08775},
  file      = {:by-author/H/Hu/2020_Hu_10909.pdf:PDF},
  owner     = {saulius},
  publisher = {American Chemical Society ({ACS})},
  timestamp = {2021.11.03},
  creationdate = {2021-11-03T00:00:00},
}

@Article{Krause2015,
  author    = {Lennard Krause and Regine Herbst-Irmer and Dietmar Stalke},
  journal   = {J. Appl. Crystallogr.},
  title     = {An empirical correction for the influence of low-energy contamination},
  year      = {2015},
  month     = {nov},
  number    = {6},
  pages     = {1907--1913},
  volume    = {48},
  comment   = {Cited in Henn2019 (2019_Henn_83).},
  doi       = {10.1107/s1600576715020440},
  file      = {:by-author/K/Krause/2015_Krause_1907.pdf:PDF},
  keywords  = {Crystallography; Data Qualiy},
  owner     = {saulius},
  publisher = {International Union of Crystallography ({IUCr})},
  timestamp = {2021.11.09},
  creationdate = {2021-11-09T00:00:00},
}

@Manuscript{Bai2019,
  author    = {Yunsheng Bai and Hao Ding and Yang Qiao and Agustin Marinovic and Ken Gu and Ting Chen and Yizhou Sun and Wei Wang},
  title     = {Unsupervised inductive whole-graph embedding by preserving graph proximity},
  year      = {2019},
  keywords  = {Computer Science (CS); Graph Neural Networks (GNN)},
  url       = {https://deep-learning-graphs.bitbucket.io/dlg-kdd19/accepted_papers/DLG_2019_paper_15.pdf},
  comment   = {Cited in Hu2019.},
  file      = {:by-author/B/Bai/2019_Bai_1.pdf:PDF},
  owner     = {saulius},
  pages     = {1--14},
  timestamp = {2021.11.11},
  creationdate = {2021-11-11T00:00:00},
}

@Article{Thomas2018,
  author        = {Nathaniel Thomas and Tess Smidt and Steven Kearnes and Lusann Yang and Li Li and Kai Kohlhoff and Patrick Riley},
  journal       = {arXiv},
  title         = {Tensor field networks: rotation- and translation-equivariant neural networks for 3{D} point clouds},
  year          = {2018},
  month         = feb,
  pages         = {1--19},
  abstract      = {We introduce tensor field neural networks, which are locally equivariant to 3D rotations, translations, and permutations of points at every layer. 3D rotation equivariance removes the need for data augmentation to identify features in arbitrary orientations. Our network uses filters built from spherical harmonics; due to the mathematical consequences of this filter choice, each layer accepts as input (and guarantees as output) scalars, vectors, and higher-order tensors, in the geometric sense of these terms. We demonstrate the capabilities of tensor field networks with tasks in geometry, physics, and chemistry.},
  archiveprefix = {arXiv},
  comment       = {Recommended by S. Grudinin.},
  eprint        = {1802.08219},
  file          = {:by-author/T/Thomas/2018_Thomas_1.pdf:PDF},
  keywords      = {Artificial Neural Networks (ANN); Computer Science (CS); Machine Learning (ML); Neural Networks (NN); cs.AI; cs.CV; cs.LG; cs.NE},
  owner         = {saulius},
  primaryclass  = {cs.LG},
  timestamp = {2021.11.11},
  creationdate = {2021-11-11T00:00:00},
}

@Article{Klicpera2020,
  author        = {Johannes Klicpera and Shankari Giri and Johannes T. Margraf and Stephan Günnemann},
  journal       = {arXiv},
  title         = {Fast and uncertainty-aware directional message passing for non-equilibrium molecules},
  year          = {2020},
  month         = nov,
  pages         = {1--6},
  abstract      = {Many important tasks in chemistry revolve around molecules during reactions. This requires predictions far from the equilibrium, while most recent work in machine learning for molecules has been focused on equilibrium or near-equilibrium states. In this paper we aim to extend this scope in three ways. First, we propose the DimeNet++ model, which is 8x faster and 10% more accurate than the original DimeNet on the QM9 benchmark of equilibrium molecules. Second, we validate DimeNet++ on highly reactive molecules by developing the challenging COLL dataset, which contains distorted configurations of small molecules during collisions. Finally, we investigate ensembling and mean-variance estimation for uncertainty quantification with the goal of accelerating the exploration of the vast space of non-equilibrium structures. Our DimeNet++ implementation as well as the COLL dataset are available online.},
  archiveprefix = {arXiv},
  eprint        = {2011.14115},
  file          = {:by-author/K/Klicpera/2020_Klicpera_1.pdf:PDF},
  keywords      = {Artificial Neural Networks (ANN); Chemiinformatics; Chemoinformatics; Computer Science (CS); Machine Learning (ML); Neural Networks (NN); cs.LG; physics.chem-ph; physics.comp-ph},
  owner         = {saulius},
  primaryclass  = {cs.LG},
  timestamp = {2021.11.11},
  creationdate = {2021-11-11T00:00:00},
}

@Article{Klicpera2020a,
  author        = {Johannes Klicpera and Janek Groß and Stephan Günnemann},
  journal       = {arXiv},
  title         = {Directional message passing for molecular graphs},
  year          = {2020},
  month         = mar,
  pages         = {1--13},
  abstract      = {Graph neural networks have recently achieved great successes in predicting quantum mechanical properties of molecules. These models represent a molecule as a graph using only the distance between atoms (nodes). They do not, however, consider the spatial direction from one atom to another, despite directional information playing a central role in empirical potentials for molecules, e.g. in angular potentials. To alleviate this limitation we propose directional message passing, in which we embed the messages passed between atoms instead of the atoms themselves. Each message is associated with a direction in coordinate space. These directional message embeddings are rotationally equivariant since the associated directions rotate with the molecule. We propose a message passing scheme analogous to belief propagation, which uses the directional information by transforming messages based on the angle between them. Additionally, we use spherical Bessel functions and spherical harmonics to construct theoretically well-founded, orthogonal representations that achieve better performance than the currently prevalent Gaussian radial basis representations while using fewer than 1/4 of the parameters. We leverage these innovations to construct the directional message passing neural network (DimeNet). DimeNet outperforms previous GNNs on average by 76% on MD17 and by 31% on QM9. Our implementation is available online.},
  archiveprefix = {arXiv},
  eprint        = {2003.03123},
  file          = {:by-author/K/Klicpera/2020_Klicpera_1a.pdf:PDF},
  keywords      = {Artificial Neural Networks (ANN); Chemiinformatics; Chemoinformatics; Computer Science (CS); Machine Learning (ML); Neural Networks (NN); cs.LG; physics.comp-ph; stat.ML},
  owner         = {saulius},
  primaryclass  = {cs.LG},
  timestamp = {2021.11.11},
  creationdate = {2021-11-11T00:00:00},
}

@Article{Schuett2017,
  author    = {Kristof T. Schütt and Farhad Arbabzadah and Stefan Chmiela and Klaus R. Müller and Alexandre Tkatchenko},
  title     = {Quantum-chemical insights from deep tensor neural networks},
  year      = {2017},
  month     = {jan},
  number    = {1},
  pages     = {1--8},
  volume    = {8},
  comment   = {Cited by Thomas2018.},
  doi       = {10.1038/ncomms13890},
  file      = {:by-author/S/Schütt/2017_Schütt_1.pdf:PDF;:by-author/S/Schütt/2017_Schütt_1_arXiv.pdf:PDF},
  keywords  = {Artificial Neural Networks (ANN); Cheminformatics; Computer Science (CS); Neural Networks (NN)},
  owner     = {saulius},
  publisher = {Springer Science and Business Media {LLC}},
  timestamp = {2021.11.11},
  creationdate = {2021-11-11T00:00:00},
  url       = {https://www.nature.com/articles/ncomms13890.pdf},
}

@Article{Marcos2016,
  author        = {Diego Marcos and Michele Volpi and Nikos Komodakis and Devis Tuia},
  journal       = {arXiv},
  title         = {Rotation equivariant vector field networks},
  year          = {2016},
  month         = dec,
  pages         = {1--10},
  abstract      = {In many computer vision tasks, we expect a particular behavior of the output with respect to rotations of the input image. If this relationship is explicitly encoded, instead of treated as any other variation, the complexity of the problem is decreased, leading to a reduction in the size of the required model. In this paper, we propose the Rotation Equivariant Vector Field Networks (RotEqNet), a Convolutional Neural Network (CNN) architecture encoding rotation equivariance, invariance and covariance. Each convolutional filter is applied at multiple orientations and returns a vector field representing magnitude and angle of the highest scoring orientation at every spatial location. We develop a modified convolution operator relying on this representation to obtain deep architectures. We test RotEqNet on several problems requiring different responses with respect to the inputs' rotation: image classification, biomedical image segmentation, orientation estimation and patch matching. In all cases, we show that RotEqNet offers extremely compact models in terms of number of parameters and provides results in line to those of networks orders of magnitude larger.},
  archiveprefix = {arXiv},
  comment       = {Cited by Thomas2018.},
  doi           = {10.1109/ICCV.2017.540},
  eprint        = {1612.09346},
  file          = {:by-author/M/Marcos/2016_Marcos_1.pdf:PDF},
  keywords      = {Artificial Neural Networks (ANN); Neural Networks (NN); cs.CV},
  owner         = {saulius},
  primaryclass  = {cs.CV},
  timestamp = {2021.11.11},
  creationdate = {2021-11-11T00:00:00},
}

@Presentation{Lipson2011,
  author    = {Hod Lipson},
  title     = {First order logic},
  year      = {2011},
  file      = {:by-author/L/Lipson/2011_Lipson_1.pdf:PDF},
  keywords  = {Computer Science (CS); First Order Logic; Modus Ponens; Prolig; Proof Theory; Resolution Method},
  owner     = {saulius},
  pages     = {1--79},
  timestamp = {2021.11.12},
  creationdate = {2021-11-12T00:00:00},
  url       = {https://www.cs.cornell.edu/courses/cs4700/2011fa/lectures/16_FirstOrderLogic.pdf},
}

@Manuscript{Weiss2019,
  author    = {Michael Weiss},
  title     = {Basics of first-order logic},
  year      = {2019},
  keywords  = {Computer Science (CS); First Order Logics; Logics; Proof Theory},
  url       = {https://michaelcweiss.files.wordpress.com/2020/10/logic.pdf},
  file      = {:by-author/W/Weiss/2019_Weiss_1.pdf:PDF},
  owner     = {saulius},
  pages     = {1--102},
  timestamp = {2021.11.12},
  creationdate = {2021-11-12T00:00:00},
}

@Webpage{GraphMLTeam2002,
  author    = {{GraphML Team}},
  retrieved = {2021-11-16},
  title     = {The {GraphML} schema documentation},
  url       = {http://graphml.graphdrawing.org/specification/schema_element.xsd.htm},
  year      = {2002},
  file      = {:by-author/G/GraphMLTeam/2002_GraphMLTeam_1.pdf:PDF;:by-author/G/GraphMLTeam/2002_GraphMLTeam_1.odt:OpenDocument text},
  keywords  = {Computer Science (CS); Formats; Graph Theory; Graphs; XML},
  owner     = {saulius},
  pages     = {1--3},
  timestamp = {2021.11.16},
  creationdate = {2021-11-16T00:00:00},
}

@Article{Garrabrant2016,
  author           = {Scott Garrabrant and Tsvi Benson-Tilsen and Andrew Critch and Nate Soares and Jessica Taylor},
  journal          = {arXiv},
  title            = {Logical induction},
  year             = {2016},
  month            = sep,
  pages            = {1--131},
  abstract         = {We present a computable algorithm that assigns probabilities to every logical statement in a given formal language, and refines those probabilities over time. For instance, if the language is Peano arithmetic, it assigns probabilities to all arithmetical statements, including claims about the twin prime conjecture, the outputs of long-running computations, and its own probabilities. We show that our algorithm, an instance of what we call a logical inductor, satisfies a number of intuitive desiderata, including: (1) it learns to predict patterns of truth and falsehood in logical statements, often long before having the resources to evaluate the statements, so long as the patterns can be written down in polynomial time; (2) it learns to use appropriate statistical summaries to predict sequences of statements whose truth values appear pseudorandom; and (3) it learns to have accurate beliefs about its own current beliefs, in a manner that avoids the standard paradoxes of self-reference. For example, if a given computer program only ever produces outputs in a certain range, a logical inductor learns this fact in a timely manner; and if late digits in the decimal expansion of $\pi$ are difficult to predict, then a logical inductor learns to assign $\approx 10\%$ probability to "the $n$th digit of $\pi$ is a 7" for large $n$. Logical inductors also learn to trust their future beliefs more than their current beliefs, and their beliefs are coherent in the limit (whenever $\phi \implies \psi$, $\mathbb{P}_\infty(\phi) \le \mathbb{P}_\infty(\psi)$, and so on); and logical inductors strictly dominate the universal semimeasure in the limit. These properties and many others all follow from a single logical induction criterion, which is motivated by a series of stock trading analogies. Roughly speaking, each logical sentence $\phi$ is associated with a stock that is worth \$1 per share if [...]},
  archiveprefix    = {arXiv},
  creationdate     = {2021-10-22T00:00:00},
  eprint           = {1609.03543},
  file             = {:by-author/G/Garrabrant/2016_Garrabrant_1.pdf:PDF},
  keywords         = {Bayesian Inference; Bayesian Statistics; Foundations of Mathematics; Logic; Mathematical Proofs; Proof Theory; cs.AI; cs.LO; math.LO; math.PR},
  modificationdate = {2023-02-18T14:31:58},
  owner            = {saulius},
  primaryclass     = {cs.AI},
  timestamp        = {2021.10.22},
}

@Article{Andersen2021,
  author    = {Casper W. Andersen and Rickard Armiento and Evgeny Blokhin and Gareth J. Conduit and Shyam Dwaraknath and Matthew L. Evans and {\'{A}}d{\'{a}}m Fekete and Abhijith Gopakumar and Saulius Gra{\v{z}}ulis and Andrius Merkys and Fawzi Mohamed and Corey Oses and Giovanni Pizzi and Gian-Marco Rignanese and Markus Scheidgen and Leopold Talirz and Cormac Toher and Donald Winston and Rossella Aversa and Kamal Choudhary and Pauline Colinet and Stefano Curtarolo and Davide Di Stefano and Claudia Draxl and Suleyman Er and Marco Esters and Marco Fornari and Matteo Giantomassi and Marco Govoni and Geoffroy Hautier and Vinay Hegde and Matthew K. Horton and Patrick Huck and Georg Huhs and Jens Hummelsh{\o}j and Ankit Kariryaa and Boris Kozinsky and Snehal Kumbhar and Mohan Liu and Nicola Marzari and Andrew J. Morris and Arash A. Mostofi and Kristin A. Persson and Guido Petretto and Thomas Purcell and Francesco Ricci and Frisco Rose and Matthias Scheffler and Daniel Speckhard and Martin Uhrin and Antanas Vaitkus and Pierre Villars and David Waroquiers and Chris Wolverton and Michael Wu and Xiaoyu Yang},
  journal   = {Scientific Data},
  title     = {{OPTIMADE}, an {API} for exchanging materials data},
  year      = {2021},
  month     = {aug},
  number    = {1},
  pages     = {1--10},
  volume    = {8},
  doi       = {10.1038/s41597-021-00974-z},
  file      = {:by-author/A/Andersen/2021_Andersen_1.pdf:PDF},
  keywords  = {API; Computer Science (CS); Databases; Materials Science; OPTIMADE; REST},
  owner     = {saulius},
  publisher = {Springer Science and Business Media {LLC}},
  timestamp = {2021.11.21},
  creationdate = {2021-11-21T00:00:00},
}

@Article{Curkovic2018,
  author    = {Marko Ćurković and Andro Košec},
  journal   = {{BMC} Medical Research Methodology},
  title     = {Bubble effect: including internet search engines in systematic reviews introduces selection bias and impedes scientific reproducibility},
  year      = {2018},
  month     = {nov},
  number    = {1},
  pages     = {130},
  volume    = {18},
  doi       = {10.1186/s12874-018-0599-2},
  file      = {:by-author/C/Ćurković/2018_Ćurković_130.pdf:PDF},
  keywords  = {"search Bubble"; Computer Science (CS); Reproducible Research; Search Engines},
  owner     = {saulius},
  publisher = {Springer Science and Business Media {LLC}},
  timestamp = {2021.11.21},
  creationdate = {2021-11-21T00:00:00},
  url       = {https://www.researchgate.net/publication/328921618_Bubble_effect_Including_internet_search_engines_in_systematic_reviews_introduces_selection_bias_and_impedes_scientific_reproducibility/link/5fc24b31299bf104cf888cec/download},
}

@Article{Righelli2021,
  author          = {Righelli, Dario and Angelini, Claudia},
  journal         = {PloS one},
  title           = {Easyreporting simplifies the implementation of {Reproducible} {Research} layers in {R} software.},
  year            = {2021},
  issn            = {1932-6203},
  pages           = {e0244122},
  volume          = {16},
  abstract        = {During last years "irreproducibility" became a general problem in omics data analysis due to the use of sophisticated and poorly described computational procedures. For avoiding misleading results, it is necessary to inspect and reproduce the entire data analysis as a unified product. Reproducible Research (RR) provides general guidelines for public access to the analytic data and related analysis code combined with natural language documentation, allowing third-parties to reproduce the findings. We developed easyreporting, a novel R/Bioconductor package, to facilitate the implementation of an RR layer inside reports/tools. We describe the main functionalities and illustrate the organization of an analysis report using a typical case study concerning the analysis of RNA-seq data. Then, we show how to use easyreporting in other projects to trace R functions automatically. This latter feature helps developers to implement procedures that automatically keep track of the analysis steps. Easyreporting can be useful in supporting the reproducibility of any data analysis project and shows great advantages for the implementation of R packages and GUIs. It turns out to be very helpful in bioinformatics, where the complexity of the analyses makes it extremely difficult to trace all the steps and parameters used in the study.},
  citation-subset = {IM},
  completed       = {2021-10-05},
  country         = {United States},
  doi             = {10.1371/journal.pone.0244122},
  file            = {:by-author/R/Righelli/2021_Righelli_244122.pdf:PDF},
  issn-linking    = {1932-6203},
  issue           = {5},
  keywords        = {R; Reproducibility of Results; Reproducible Research; Software; User-Computer Interface},
  nlm-id          = {101285081},
  owner           = {saulius},
  pii             = {PONE-D-20-37776},
  pmc             = {PMC8109797},
  pmid            = {33970927},
  pubmodel        = {Electronic-eCollection},
  pubstate        = {epublish},
  revised         = {2021-10-05},
  timestamp = {2021.11.21},
  creationdate = {2021-11-21T00:00:00},
  url             = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8109797/},
}

@Article{Mariano2017,
  author        = {Diego C. B. Mariano and Carmelina Leite and Lucianna H. S. Santos and Rafael E. O. Rocha and Raquel C. de Melo-Minardi},
  title         = {A guide to performing systematic literature reviews in bioinformatics},
  year          = {2017},
  month         = jul,
  pages         = {5813},
  abstract      = {Bioinformatics research depends on high-quality databases to provide accurate results. In silico experiments, correctly performed, may prospect novel discoveries and elucidates pathways for biological experiments through data analysis in large scale. However, most biological databases have presented mistakes, such as data incorrectly classified or incomplete information. Also, sometimes, data mining algorithms cannot treat these errors, leading to serious problems for the in silico analysis. Manual curation of data extracted from literature is a possible solution for this problem. Systematic Literature Review (SLR), or Systematic Review, is a method to identify, evaluate and summarize the state-of-the-art of a specific theme. Moreover, SLR allows the collection from databases restrictively, which allows an analysis with lower bias than traditional reviews. The SRL approaches have been widely used for decision-making in medical and environmental studies. However, other research areas, such as bioinformatics, do not have a specific step-by-step to guide researchers undertaking the procedures of an SLR. In this study, we propose a guideline, called BiSRL, to perform SLR in bioinformatics. Our procedures cover the most traditional guides to produce SLRs adapted to bioinformatics. To evaluate our method, we propose a case study to detect and summarize SLRs developed for bioinformatics data. We used two databases: PubMed and ScienceDirect. A total of 207 papers were screened in four steps: title, abstract, diagonal and full-text reading. Four evaluators performed the SLR independently to reduce bias risk. A total of 8 papers was included in the SLR case study. The case study demonstrates how to implement the methods of BiSLR to procedure SLR for bioinformatics. BiSLR may guide bioinformaticians to perform systematic reviews reproducible to collect accurate data for higher quality analysis.},
  archiveprefix = {arXiv},
  eprint        = {1707.05813},
  file          = {:by-author/M/Mariano/2017_Mariano_5813.pdf:PDF},
  keywords      = {Systematic Reviews},
  owner         = {saulius},
  primaryclass  = {q-bio.QM},
  timestamp = {2021.11.21},
  creationdate = {2021-11-21T00:00:00},
}

@Article{Mammoliti2021,
  author    = {Anthony Mammoliti and Petr Smirnov and Minoru Nakano and Zhaleh Safikhani and Christopher Eeles and Heewon Seo and Sisira Kadambat Nair and Arvind S. Mer and Ian Smith and Chantal Ho and Gangesh Beri and Rebecca Kusko and Thakkar Shraddha and Susanna-Assunta Sansone and Weida Tong and Russ D. Wolfinger and Christopher E. Mason and Wendell Jones and Joaquin Dopazo and Cesare Furlanello and Eva Lin and Yihong Yu and Scott Martin and Marc Hafner and Benjamin Haibe-Kains},
  journal   = {Nature Communications},
  title     = {Orchestrating and sharing large multimodal data for transparent and reproducible research},
  year      = {2021},
  month     = {oct},
  number    = {1},
  pages     = {1--10},
  volume    = {12},
  doi       = {10.1038/s41467-021-25974-w},
  file      = {:by-author/M/Mammoliti/2021_Mammoliti_1.pdf:PDF},
  keywords  = {Computer Science (CS); Reproducible Research},
  owner     = {saulius},
  publisher = {Springer Science and Business Media {LLC}},
  timestamp = {2021.11.21},
  creationdate = {2021-11-21T00:00:00},
}

@Article{Archmiller2020,
  author           = {Althea A. Archmiller and Andrew D. Johnson and Jane Nolan and Margaret Edwards and Lisa H. Elliott and Jake M. Ferguson and Fabiola Iannarilli and Juliana V{\'{e}}lez and Kelsey Vitense and Douglas H. Johnson and John Fieberg},
  journal          = {The Journal of Wildlife Management},
  title            = {Computational reproducibility in the wildlife society{\textquotesingle}s flagship journals},
  year             = {2020},
  month            = {mar},
  number           = {5},
  pages            = {1012--1017},
  volume           = {84},
  comment          = {Supplementary data downloaded from https://wildlife.onlinelibrary.wiley.com/action/downloadSupplement?doi=10.1002%2Fjwmg.21855&file=jwmg21855-sup-0001-Supplemental_Table_S1.docx on 2023-01-02T18:18+02:00.},
  creationdate     = {2021-11-21T00:00:00},
  doi              = {10.1002/jwmg.21855},
  file             = {:by-author/A/Archmiller/2020_Archmiller_1012.pdf:PDF;:by-author/A/Archmiller/2020_Archmiller_1012_Supplemental_Table_S1.docx:Word 2007+},
  keywords         = {Reproducible Research},
  modificationdate = {2023-01-02T18:19:29},
  owner            = {saulius},
  publisher        = {Wiley},
  timestamp        = {2021.11.21},
}

@Article{Boernigen2015,
  author           = {Börnigen, Daniela and Moon, Yo Sup and Rahnavard, Gholamali and Waldron, Levi and McIver, Lauren and Shafquat, Afrah and Franzosa, Eric A. and Miropolsky, Larissa and Sweeney, Christopher and Morgan, Xochitl C. and Garrett, Wendy S. and Huttenhower, Curtis},
  journal          = {PeerJ},
  title            = {A reproducible approach to high-throughput biological data acquisition and integration.},
  year             = {2015},
  issn             = {2167-8359},
  pages            = {e791},
  volume           = {3},
  abstract         = {Modern biological research requires rapid, complex, and reproducible integration of multiple experimental results generated both internally and externally (e.g., from public repositories). Although large systematic meta-analyses are among the most effective approaches both for clinical biomarker discovery and for computational inference of biomolecular mechanisms, identifying, acquiring, and integrating relevant experimental results from multiple sources for a given study can be time-consuming and error-prone. To enable efficient and reproducible integration of diverse experimental results, we developed a novel approach for standardized acquisition and analysis of high-throughput and heterogeneous biological data. This allowed, first, novel biomolecular network reconstruction in human prostate cancer, which correctly recovered and extended the NFκB signaling pathway. Next, we investigated host-microbiome interactions. In less than an hour of analysis time, the system retrieved data and integrated six germ-free murine intestinal gene expression datasets to identify the genes most influenced by the gut microbiota, which comprised a set of immune-response and carbohydrate metabolism processes. Finally, we constructed integrated functional interaction networks to compare connectivity of peptide secretion pathways in the model organisms Escherichia coli, Bacillus subtilis, and Pseudomonas aeruginosa.},
  completed        = {2015-07-09},
  country          = {United States},
  creationdate     = {2021-11-21T00:00:00},
  doi              = {10.7717/peerj.791},
  file             = {:by-author/B/Börnigen/2015_Börnigen_791.pdf:PDF},
  issn-linking     = {2167-8359},
  keywords         = {ARepA; Data Acquisition; Data Integration; Heterogeneous Data; High-throughput Data; Meta-analysis; Reproducibility; Reproducible Research; Work Flows; Workflow Management},
  modificationdate = {2023-01-02T18:40:31},
  nlm-id           = {101603425},
  owner            = {saulius},
  pii              = {791},
  pmc              = {PMC4493686},
  pmid             = {26157642},
  pubmodel         = {Electronic-eCollection},
  pubstate         = {epublish},
  revised          = {2020-10-01},
  timestamp        = {2021.11.21},
}

@Article{Sobolev2014,
  author    = {Andrey Sobolev and Adrian Stoewer and Michael Pereira and Christian J. Kellner and Christian Garbers and Philipp L. Rautenberg and Thomas Wachtler},
  journal   = {Frontiers in Neuroinformatics},
  title     = {Data management routines for reproducible research using the {G-Node} {P}ython client library},
  year      = {2014},
  month     = {mar},
  volume    = {8},
  doi       = {10.3389/fninf.2014.00015},
  file      = {:by-author/S/Sobolev/2014_Sobolev_1.pdf:PDF},
  keywords  = {Reproducible Research},
  owner     = {saulius},
  papers    = {1--8},
  publisher = {Frontiers Media {SA}},
  timestamp = {2021.11.21},
  creationdate = {2021-11-21T00:00:00},
}

@InProceedings{Freire2012,
  author    = {Juliana Freire and Philippe Bonnet and Dennis Shasha},
  booktitle = {Proceedings of the 2012 international conference on Management of Data - {SIGMOD} {\textquotesingle}12},
  title     = {Computational reproducibility},
  year      = {2012},
  pages     = {1--6},
  publisher = {{ACM} Press},
  doi       = {10.1145/2213836.2213908},
  file      = {:by-author/F/Freire/2012_Freire_1.pdf:PDF},
  keywords  = {Computer Science (CS); Reproducible Computations; Reproducible Research},
  owner     = {saulius},
  timestamp = {2021.11.21},
  creationdate = {2021-11-21T00:00:00},
}

@Article{Maj2021,
  author           = {Maj, Petr and Siek, Konrad and Kovalenko, Alexander and Vitek, Jan},
  title            = {{CodeDJ}: reproducible queries over large-scale software repositories (artifact)},
  year             = {2021},
  pages            = {1--4},
  copyright        = {Creative Commons Attribution 4.0 International license},
  creationdate     = {2021-11-21T00:00:00},
  doi              = {10.4230/DARTS.7.2.13},
  file             = {:by-author/M/Maj/2021_Maj_1.pdf:PDF},
  keywords         = {Mining Code Repositories; Reproducible Queries; Reproducible Research; Software; Software and Its Engineering → Ultra-large-scale Systems; Source Code Analysis},
  language         = {en},
  modificationdate = {2022-11-13T14:28:09},
  owner            = {saulius},
  publisher        = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
  timestamp        = {2021.11.21},
  url              = {https://drops.dagstuhl.de/opus/volltexte/2021/14037/},
}

@Manuscript{Hrynaszkiewicz2013,
  author    = {Iain Hrynaszkiewicz and Peter Li and Scott Edmunds},
  title     = {Open science and the role of publishers in reproducible research},
  year      = {2013},
  keywords  = {Reproducible Research},
  url       = {https://osf.io/35s9d},
  file      = {:by-author/H/Hrynaszkiewicz/2013_Hrynaszkiewicz_1.pdf:PDF},
  owner     = {saulius},
  pages     = {1--27},
  timestamp = {2021.11.21},
  creationdate = {2021-11-21T00:00:00},
}

@Manuscript{Davison2013,
  author    = {Andrew P. Davison and Michele Mattioni and Dmitry Samarkanov and Bartosz Teleńczuk},
  title     = {Sumatra: a toolkit for reproducible research},
  year      = {2013},
  keywords  = {Reproducible Research},
  url       = {https://osf.io/rc5jf},
  file      = {:by-author/D/Davison/2013_Davison_1.pdf:PDF},
  owner     = {saulius},
  pages     = {1--19},
  timestamp = {2021.11.21},
  creationdate = {2021-11-21T00:00:00},
}

@Article{Markley2016,
  author    = {John L. Markley and Ad Bax and Yoji Arata and C. W. Hilbers and Robert Kaptein and Brian D. Sykes and Peter E. Wright and Kurt Wüthrich},
  journal   = {Journal of Biomolecular {NMR}},
  title     = {Recommendations for the presentation of {NMR} structures of proteins and nucleic acids},
  year      = {2016},
  month     = {feb},
  pages     = {1--23},
  volume    = {12},
  doi       = {10.1515/iupac.70.0001},
  file      = {:by-author/M/Markley/2016_Markley_1.pdf:PDF},
  keywords  = {Data Management; NMR; Structural Biology},
  owner     = {saulius},
  publisher = {De Gruyter},
  timestamp = {2021.11.23},
  creationdate = {2021-11-23T00:00:00},
  url       = {https://spin.niddk.nih.gov/bax/lit/spdf/268.pdf},
}

@Article{Deng2018,
  author       = {Deng, Haiyou and Jia, Ya and Zhang, Yang},
  journal      = {International journal of modern physics. B},
  title        = {Protein structure prediction.},
  year         = {2018},
  issn         = {0217-9792},
  month        = jul,
  pages        = {1--18},
  volume       = {32},
  abstract     = {Predicting 3D structure of protein from its amino acid sequence is one of the most important unsolved problems in biophysics and computational biology. This paper attempts to give a comprehensive introduction of the most recent effort and progress on protein structure prediction. Following the general flowchart of structure prediction, related concepts and methods are presented and discussed. Moreover, brief introductions are made to several widely-used prediction methods and the community-wide critical assessment of protein structure prediction (CASP) experiments.},
  country      = {Singapore},
  doi          = {10.1142/S021797921840009X},
  file         = {:by-author/D/Deng/2018_Deng_1.pdf:PDF},
  issn-linking = {0217-9792},
  issue        = {18},
  keywords     = {Ab Initio Prediction; Bioinformatics; CASP; Homology Modeling; Protein Structure Prediction; Structure Refinement},
  mid          = {NIHMS1014961},
  nlm-id       = {101608568},
  owner        = {saulius},
  pii          = {1840009},
  pmc          = {PMC6407873},
  pmid         = {30853739},
  pubmodel     = {Print-Electronic},
  pubstate     = {ppublish},
  revised      = {2020-10-01},
  timestamp = {2021.11.23},
  creationdate = {2021-11-23T00:00:00},
  url          = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6407873/pdf/nihms-1014961.pdf},
}

@Article{Ryan2018,
  author    = {Kevin Ryan and Jeff Lengyel and Michael Shatruk},
  journal   = {Journal of the American Chemical Society},
  title     = {Crystal structure prediction via deep learning},
  year      = {2018},
  month     = {jun},
  number    = {32},
  pages     = {10158--10168},
  volume    = {140},
  doi       = {10.1021/jacs.8b03913},
  file      = {:by-author/R/Ryan/2018_Ryan_10158.pdf:PDF},
  keywords  = {Artificial Intelligence (AI); Artificial Neural Networks (ANN); Chemical Fingerprints; Crystal Structure Prediction (CSP); Crystallography; Deep Learning (DL)},
  owner     = {saulius},
  publisher = {American Chemical Society ({ACS})},
  timestamp = {2021.11.23},
  creationdate = {2021-11-23T00:00:00},
}

@Article{Behler2016,
  author    = {Jörg Behler},
  journal   = {The Journal of Chemical Physics},
  title     = {Perspective: Machine learning potentials for atomistic simulations},
  year      = {2016},
  month     = {nov},
  number    = {17},
  pages     = {170901},
  volume    = {145},
  doi       = {10.1063/1.4966192},
  file      = {:by-author/B/Behler/2016_Behler_170901.pdf:PDF},
  keywords  = {Atomistic Simulations; Chemiinformatics; Machine Learning (ML)},
  owner     = {saulius},
  publisher = {{AIP} Publishing},
  timestamp = {2021.11.23},
  creationdate = {2021-11-23T00:00:00},
}

@Article{Valle2010,
  author    = {Mario Valle and Artem R. Oganov},
  journal   = {Acta Crystallographica Section A Foundations of Crystallography},
  title     = {Crystal fingerprint space {\textendash} a novel paradigm for studying crystal-structure sets},
  year      = {2010},
  month     = {aug},
  number    = {5},
  pages     = {507--517},
  volume    = {66},
  comment   = {Cited by Ryan2018.},
  doi       = {10.1107/s0108767310026395},
  file      = {:by-author/V/Valle/2010_Valle_507.pdf:PDF},
  keywords  = {Chemical Fingerprints; Crystal Nets},
  owner     = {saulius},
  publisher = {International Union of Crystallography ({IUCr})},
  timestamp = {2021.11.23},
  creationdate = {2021-11-23T00:00:00},
}

@TechReport{Kester2009,
  author      = {Walt Kester},
  institution = {Analog Devices},
  title       = {Analog switches and multiplexers basics},
  year        = {2009},
  number      = {MT-088},
  type        = {Tutorial},
  file        = {:by-author/K/Kester/2009_Kester_1.pdf:PDF},
  keywords    = {Analogue Switches; CMOS; Computer Science (CS); Electronics},
  owner       = {saulius},
  pages       = {1--23},
  timestamp = {2021.11.24},
  creationdate = {2021-11-24T00:00:00},
  url         = {https://www.analog.com/media/en/training-seminars/tutorials/MT-088.pdf},
}

@TechReport{Goualard2014,
  author      = {Frédéric Goualard},
  institution = {Universiré de Nantes},
  title       = {How do you compute the midpoint of an interval?},
  year        = {2014},
  file        = {:by-author/G/Goualard/2014_Goualard_1.pdf:PDF},
  keywords    = {Computer Science (CS); Floating Point},
  owner       = {saulius},
  pages       = {1-29},
  timestamp = {2021.11.29},
  creationdate = {2021-11-29T00:00:00},
  url         = {https://hal.archives-ouvertes.fr/file/index/docid/576641/filename/computing-midpoint.pdf},
}

@TechReport{Gudeman1993,
  author      = {David Gudeman},
  institution = {The University of Arizona},
  title       = {Representing type information in dynamically typed languages},
  year        = {1993},
  number      = {TR 93-27},
  type        = {Techreport},
  file        = {:by-author/G/Gudeman/1993_Gudeman_1.pdf:PDF},
  keywords    = {Boxed Values; Computer Science (CS); Dynamically Typed Languages; Type Representation},
  owner       = {saulius},
  pages       = {1--40},
  timestamp = {2021.11.29},
  creationdate = {2021-11-29T00:00:00},
  url         = {http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.39.4394&rep=rep1&type=pdf},
}

@Article{Dittrich2018,
  author    = {B. Dittrich and F. P. A. Fabbiani and J. Henn and M. U. Schmidt and P. Macchi and K. Meindl and M. A. Spackman},
  journal   = {Acta Crystallographica Section B Structural Science, Crystal Engineering and Materials},
  title     = {Azulene revisited: solid-state structure, invariom modeling and lattice-energy minimization of a classical example of disorder},
  year      = {2018},
  month     = {aug},
  number    = {5},
  pages     = {416--426},
  volume    = {74},
  comment   = {Sent by Julian Henn <JulianHenn@web.de>.},
  doi       = {10.1107/s2052520618010120},
  file      = {:by-author/D/Dittrich/2018_Dittrich_416.pdf:PDF},
  keywords  = {Azulene; Crystallography; Disorder},
  owner     = {saulius},
  publisher = {International Union of Crystallography ({IUCr})},
  timestamp = {2021.11.30},
  creationdate = {2021-11-30T00:00:00},
}

@Article{Hoeffel1998,
  author    = {C. Hoeffel},
  journal   = {Allergy},
  title     = {Journal impact factors},
  year      = {1998},
  month     = {dec},
  number    = {12},
  pages     = {1225--1225},
  volume    = {53},
  comment   = {Cited by Colquhoun2007{,a}.},
  doi       = {10.1111/j.1398-9995.1998.tb03848.x},
  file      = {:by-author/H/Hoeffel/1998_Hoeffel_1225.pdf:PDF},
  keywords  = {Bibliometrics; Impact Factor (IF); Impact Factors; Research Quality},
  owner     = {saulius},
  publisher = {Wiley},
  timestamp = {2021.12.01},
  creationdate = {2021-12-01T00:00:00},
}

@Article{Seglen1997,
  author    = {P. O. Seglen},
  journal   = {Allergy},
  title     = {Citations and journal impact factors: questionable indicators of research quality},
  year      = {1997},
  month     = {nov},
  number    = {11},
  pages     = {1050--1056},
  volume    = {52},
  doi       = {10.1111/j.1398-9995.1997.tb00175.x},
  file      = {:by-author/S/Seglen/1997_Seglen_1050.pdf:PDF},
  keywords  = {Bibliometrics; Impact Factor (IF); Impact Factors; Research Quality},
  owner     = {saulius},
  publisher = {Wiley},
  timestamp = {2021.12.01},
  creationdate = {2021-12-01T00:00:00},
}

@Article{Garfield1955,
  author    = {Eugene Garfield},
  journal   = {Science},
  title     = {Citation Indexes for Science},
  year      = {1955},
  month     = {jul},
  number    = {3159},
  pages     = {108--111},
  volume    = {122},
  doi       = {10.1126/science.122.3159.108},
  file      = {:by-author/G/Garfield/1955_Garfield_108.pdf:PDF},
  keywords  = {Bibliometrics; Impact Factor (IF); Impact Factors; Research Quality},
  owner     = {saulius},
  publisher = {American Association for the Advancement of Science ({AAAS})},
  timestamp = {2021.12.01},
  creationdate = {2021-12-01T00:00:00},
  url       = {http://garfield.library.upenn.edu/essays/v6p468y1983.pdf},
}

@Article{Garfield1999,
  author          = {Eugene Garfield},
  journal         = {Canadian Medical Association Journal},
  title           = {Journal impact factor: a brief review},
  year            = {1999},
  number          = {8},
  pages           = {979--980},
  volume          = {161},
  citation-subset = {AIM, IM, N},
  completed       = {1999-11-23},
  country         = {Canada},
  file            = {:by-author/G/Garfield/1999_Garfield_979.pdf:PDF},
  issn-linking    = {0820-3946},
  keywords        = {Abstracting and Indexing; Bibliometrics; Impact Factor (IF); Impact Factors; Periodicals as Topic; Research Quality; Standards},
  nlm-id          = {9711805},
  owner           = {saulius},
  pmc             = {PMC1230709},
  pmid            = {10551195},
  pubmodel        = {Print},
  pubstate        = {ppublish},
  revised         = {2019-12-10},
  timestamp = {2021.12.01},
  creationdate = {2021-12-01T00:00:00},
  url             = {http://www.garfield.library.upenn.edu/papers/journalimpactCMAJ1999.pdf},
}

@Article{Joseph1999,
  author          = {Joseph, K. S. and Hoey, J.},
  journal         = {CMAJ : Canadian Medical Association journal = journal de l'Association medicale canadienne},
  title           = {CMAJ's impact factor: room for recalculation.},
  year            = {1999},
  issn            = {0820-3946},
  month           = oct,
  pages           = {977--978},
  volume          = {161},
  citation-subset = {AIM, IM, N},
  comment         = {This is a comment on "Journal impact factor: a brief review." CMAJ. 1999 Oct 19;161(8):979-80.},
  completed       = {1999-11-23},
  country         = {Canada},
  file            = {:by-author/J/Joseph/1999_Joseph_977.pdf:PDF},
  issn-linking    = {0820-3946},
  issue           = {8},
  keywords        = {Abstracting and Indexing; Bibliometrics; Impact Factor (IF); Impact Factors; Periodicals as Topic; Research Quality; Standards},
  nlm-id          = {9711805},
  owner           = {saulius},
  pmc             = {PMC1230708},
  pmid            = {10551194},
  pubmodel        = {Print},
  pubstate        = {ppublish},
  revised         = {2019-12-10},
  timestamp = {2021.12.01},
  creationdate = {2021-12-01T00:00:00},
  url             = {https://europepmc.org/article/MED/10551194},
}

@Article{Newcombe2015,
  author    = {Chris Newcombe and Tim Rath and Fan Zhang and Bogdan Munteanu and Marc Brooker and Michael Deardeuff},
  journal   = {Communications of the {ACM}},
  title     = {How {A}mazon web services uses formal methods},
  year      = {2015},
  month     = {mar},
  number    = {4},
  pages     = {66--73},
  volume    = {58},
  doi       = {10.1145/2699417},
  file      = {:by-author/N/Newcombe/2015_Newcombe_66.pdf:PDF},
  keywords  = {Computer Science (CS); Formal Methods; Program Correctnes Proofs; TLA; TLA+},
  owner     = {saulius},
  publisher = {Association for Computing Machinery ({ACM})},
  timestamp = {2021.12.16},
  creationdate = {2021-12-16T00:00:00},
}

@Presentation{Matulis2021,
  author    = {Daumantas Matulis},
  title     = {Kaip vertinti mokslinius tyrimus, keletas minčių},
  year      = {2021},
  file      = {:by-author/M/Matulis/2021_Matulis_1.pptx:PowerPoint 2007+},
  keywords  = {Impact Factor (IF); Mokslo Vertinimas; Mokslometrija},
  owner     = {saulius},
  pages     = {1--10},
  timestamp = {2021.12.21},
  creationdate = {2021-12-21T00:00:00},
}

@Presentation{Sheldrick2015,
  author     = {George M. Sheldrick},
  title      = {Determining symmetry from phases},
  year       = {2015},
  conference = {ECM29 Computing School, Rovinj},
  file       = {:by-author/S/Sheldrick/2015_Sheldrick_1.pdf:PDF},
  keywords   = {Centric Reflections; Crystal Symmetry; Crystallography; Friedel's Law; Phases; Symmetry},
  owner      = {saulius},
  pages      = {1--5},
  timestamp = {2021.12.22},
  creationdate = {2021-12-22T00:00:00},
  url        = {http://www.cryst.chem.uu.nl/lutz/ecacomsig/pdfs-rovinj/Symmetry_from_phases_p-george.sheldrick.pdf},
}

@Article{SanchezLengeling2021,
  author    = {Sanchez-Lengeling, Benjamin and Reif, Emily and Pearce, Adam and Wiltschko, Alexander B.},
  journal   = {Distill},
  title     = {A gentle introduction to graph neural networks},
  year      = {2021},
  doi       = {10.23915/distill.00033},
  file      = {:by-author/S/Sanchez-Lengeling/2021_Sanchez-Lengeling.html:URL},
  keywords  = {Graph Neural Networks (GNN); Molecular Recognition; Neural Networks (NN)},
  owner     = {saulius},
  timestamp = {2021.12.22},
  creationdate = {2021-12-22T00:00:00},
  url       = {https://distill.pub/2021/gnn-intro},
}

@Presentation{Leskovec2018a,
  author    = {Jure Leskovec and William L. Hamilton and Rex Ying and Rok Sosic},
  title     = {Representation learning on networks},
  year      = {2018},
  school    = {Stanford University},
  file      = {:by-author/L/Leskovec/2018_Leskovec_1a.pdf:PDF},
  keywords  = {Artificial Neural Networks (ANN); Graph Neural Networks (GNN); Machine Learning (ML)},
  owner     = {saulius},
  pages     = {1--17},
  timestamp = {2021.12.24},
  creationdate = {2021-12-24T00:00:00},
  url       = {http://snap.stanford.edu/proj/embeddings-www/files/nrltutorial-part0-intro.pdf},
}

@Presentation{Leskovec2018d,
  author    = {Jure Leskovec and William L. Hamilton and Rex Ying and Rok Sosic},
  title     = {Representation learning on networks. Applications},
  year      = {2018},
  file      = {:by-author/L/Leskovec/2018_Leskovec_1d.pdf:PDF},
  keywords  = {Artificial Neural Networks (ANN); Graph Neural Networks (GNN); Machine Learning (ML)},
  owner     = {saulius},
  pages     = {1--43},
  timestamp = {2021.12.24},
  creationdate = {2021-12-24T00:00:00},
  url       = {http://snap.stanford.edu/proj/embeddings-www/files/nrltutorial-part3-applications.pdf},
}

@Presentation{Leskovec2018c,
  author    = {Jure Leskovec and William L. Hamilton and Rex Ying and Rok Sosic},
  title     = {Representation learning on networks. Graph neural networks},
  year      = {2018},
  file      = {:by-author/L/Leskovec/2018_Leskovec_1c.pdf:PDF},
  keywords  = {Artificial Neural Networks (ANN); Graph Neural Networks (GNN); Machine Learning (ML)},
  owner     = {saulius},
  pages     = {1--66},
  timestamp = {2021.12.24},
  creationdate = {2021-12-24T00:00:00},
  url       = {http://snap.stanford.edu/proj/embeddings-www/files/nrltutorial-part2-gnns.pdf},
}

@Presentation{Leskovec2018b,
  author    = {Jure Leskovec and William L. Hamilton and Rex Ying and Rok Sosic},
  title     = {Representation learning on networks. Node embeddings},
  year      = {2018},
  file      = {:by-author/L/Leskovec/2018_Leskovec_1b.pdf:PDF},
  keywords  = {Artificial Neural Networks (ANN); Graph Neural Networks (GNN); Machine Learning (ML)},
  owner     = {saulius},
  pages     = {1--59},
  timestamp = {2021.12.24},
  creationdate = {2021-12-24T00:00:00},
  url       = {http://snap.stanford.edu/proj/embeddings-www/files/nrltutorial-part1-embeddings.pdf},
}

@TechReport{Mwiti2021,
  author      = {Derrick Mwiti},
  institution = {cnvrg.io},
  title       = {The essential guide to {GNN} ({G}raph {N}eural {N}etworks)},
  year        = {2021},
  file        = {:by-author/M/Mwiti/2021_Mwiti_1.pdf:PDF},
  keywords    = {Artificial Neural Networks (ANN); Graph Neural Networks (GNN); Machine Learning (ML)},
  owner       = {saulius},
  pages       = {1--24},
  timestamp = {2021.12.24},
  creationdate = {2021-12-24T00:00:00},
  url         = {https://cnvrg.io/graph-neural-networks/},
}

@Article{Newton1986a,
  author           = {Newton, T. D.},
  title            = {An implementation of {A}da generics},
  year             = {1986},
  creationdate     = {2021-12-25T00:00:00},
  keywords         = {Ada; Compiler Design; Computer Science (CS); Generic Types; Type Systems},
  modificationdate = {2022-12-08T10:19:59},
  owner            = {saulius},
  timestamp        = {2021.12.25},
  url              = {https://searchworks.stanford.edu/catalog?q="Carnegie Mellon University. Computer Science Department CMU-CS-86-125."&search_field=search_author},
}

@Manuscript{Johnston1995,
  author    = {Simon Johnston},
  title     = {{A}da-95: a guide for {C} and {C}++ programmers},
  year      = {1995},
  keywords  = {Ada; Compiler Design; Computer Science (CS); Generic Types; Programming Languages; Type Systems},
  url       = {http://www.cs.uni.edu/~mccormic/4740/guide-c2ada.pdf},
  file      = {:by-author/J/Johnston/1995_Johnston_1.pdf:PDF},
  owner     = {saulius},
  pages     = {1--68},
  timestamp = {2021.12.25},
  creationdate = {2021-12-25T00:00:00},
}

@Manuscript{Beall2015,
  author    = {Jeffrey Beall},
  title     = {Criteria for determining predatory open-access publishers},
  year      = {2015},
  keywords  = {Open-access; Predatory Journals; Publication Quality; Scientific Ethics; Scientific Publishing},
  url       = {https://beallslist.net/wp-content/uploads/2019/12/criteria-2015.pdf},
  file      = {:by-author/B/Beall/2015_Beall_1.pdf:PDF},
  owner     = {saulius},
  pages     = {1--6},
  timestamp = {2021.12.31},
  creationdate = {2021-12-31T00:00:00},
}

@Article{Beall2009,
  author    = {Jeffrey Beall},
  journal   = {Science},
  title     = {Cataloguing names the old-fashioned way},
  year      = {2009},
  month     = {jun},
  number    = {5934},
  pages     = {1514--1515},
  volume    = {324},
  doi       = {10.1126/science.324.5934.1514-b},
  editor    = {Jennifer Sills},
  file      = {:by-author/B/Beall/2009_Beall_1514.pdf:PDF},
  keywords  = {Author Names; Authorship; Disambiguation; Scientific Publishinh},
  owner     = {saulius},
  publisher = {American Association for the Advancement of Science ({AAAS})},
  timestamp = {2021.12.31},
  creationdate = {2021-12-31T00:00:00},
}

@Article{Enserink2009,
  author    = {Martin Enserink},
  journal   = {Science},
  title     = {Are You Ready to Become a Number?},
  year      = {2009},
  month     = {mar},
  number    = {5922},
  pages     = {1662--1664},
  volume    = {323},
  doi       = {10.1126/science.323.5922.1662},
  file      = {:by-author/E/Enserink/2009_Enserink_1662.pdf:PDF},
  keywords  = {Author Names; Authorship; Disambiguation; Researcher Identifiers; Scientific Publishinh},
  owner     = {saulius},
  publisher = {American Association for the Advancement of Science ({AAAS})},
  timestamp = {2021.12.31},
  creationdate = {2021-12-31T00:00:00},
}

@InCollection{Dross2020,
  author    = {Claire Dross and Johannes Kanig},
  booktitle = {Computer Aided Verification},
  publisher = {Springer International Publishing},
  title     = {Recursive data structures in {SPARK}},
  year      = {2020},
  pages     = {178--189},
  doi       = {10.1007/978-3-030-53291-8_11},
  file      = {:by-author/D/Dross/2020_Dross_178.pdf:PDF},
  keywords  = {Ada; Computer Science (CS); Formal Verification; SPARK},
  owner     = {saulius},
  timestamp = {2021.12.31},
  creationdate = {2021-12-31T00:00:00},
  url       = {https://www.researchgate.net/publication/342967187_Recursive_Data_Structures_in_SPARK},
}

@Article{Astrauskas2019,
  author    = {Vytautas Astrauskas and Peter Müller and Federico Poli and Alexander J. Summers},
  journal   = {Proceedings of the {ACM} on Programming Languages},
  title     = {Leveraging {Rust} types for modular specification and verification},
  year      = {2019},
  month     = {oct},
  number    = {{OOPSLA}},
  pages     = {1--30},
  volume    = {3},
  abstract  = {Cited by Dross2020.},
  comment   = {Cited in Dross2020.},
  doi       = {10.1145/3360573},
  file      = {:by-author/A/Astrauskas/2019_Astrauskas_1.pdf:PDF},
  keywords  = {Computer Science (CS); Data Types; Program Verification; Programming Languages; Rust},
  owner     = {saulius},
  publisher = {Association for Computing Machinery ({ACM})},
  timestamp = {2022.01.01},
  creationdate = {2022-01-01T00:00:00},
  url       = {https://dl.acm.org/doi/pdf/10.1145/3360573},
}

@Presentation{Boyland2004,
  author    = {John Boyland and James Noble and William Retert},
  title     = {Capabilities for sharing: a generalisation of uniqueness and read-only},
  year      = {2004},
  comment   = {Cited in Astrauskas2019.},
  file      = {:by-author/B/Boyland/2004_Boyland_1.pdf:PDF},
  keywords  = {Computer Science (CS); Data Types; Program Verification; Programming Languages; Rust},
  owner     = {saulius},
  pages     = {1--28},
  timestamp = {2022.01.01},
  creationdate = {2022-01-01T00:00:00},
  url       = {https://www.researchgate.net/publication/225821296_Capabilities_for_Sharing},
  volume    = {2072},
}

@InBook{Boyland2001,
  author    = {John Boyland and James Noble and William Retert},
  pages     = {2--27},
  publisher = {Springer},
  title     = {Capabilities for sharing: a generalisation of uniqueness and read-only},
  year      = {2001},
  volume    = {2072},
  abstract  = {Many languages and language extensions include annotations on pointer variables suchas “read-only,” “unique,” and “borrowed”; many more annotations have been proposed but not implemented. Unfortunately, all these annotations are described individually and formalised independently — assuming they are formalised at all. In this paper, we show how these annotations can be subsumed into a general capability system for pointers. This system separates mechanism (defining the semantics of sharing and exclusion) from policy (defining the invariants that are intended to be preserved). The capability system has a welldefined semantics which can be used as a reference for the correctness of various extended type systems using annotations. Furthermore, it supports researchin new less-restrictive type systems that permit a wider range of idioms to be statically checked.},
  booktitle = {In European Conference on Object-Oriented Programming (ECOOP) (Lecture Notes in Computer Science), Jùrgen Lindskov Knudsen (Ed.)},
  comment   = {Cited in Astrauskas2019.},
  doi       = {10.1007/3-540-45337-7_2},
  keywords  = {Computer Science (CS); Data Types; Program Verification; Programming Languages; Rust},
  owner     = {saulius},
  timestamp = {2022.01.01},
  creationdate = {2022-01-01T00:00:00},
  url       = {https://www.researchgate.net/publication/225821296_Capabilities_for_Sharing},
}

@Manuscript{Bihani2017,
  author    = {Ankita Bihani and Anupriya Gagneja},
  title     = {Graph processing library in {Rust}},
  year      = {2017},
  keywords  = {Computer Science (CS); Data Types; Program Verification; Programming Languages; Recursive Data Structures; Rust; Static Typing; Type Systems},
  url       = {https://stanford-cs242.github.io/f17/assets/projects/2017/ankitab-anupriya.pdf},
  file      = {:by-author/B/Bihani/2017_Bihani_1.pdf:PDF},
  owner     = {saulius},
  pages     = {1--10},
  timestamp = {2022.01.02},
  creationdate = {2022-01-02T00:00:00},
}

@InProceedings{Matsakis2014,
  author    = {Matsakis, Nicholas D. and Klock, II, Felix S.},
  booktitle = {Proceedings of the 2014 {ACM} {SIGAda} annual conference on High integrity language technology - {HILT} {\textquotesingle}14},
  title     = {The rust language},
  year      = {2014},
  pages     = {103--104},
  publisher = {{ACM} Press},
  volume    = {34},
  comment   = {Cited in Bihani2017.},
  doi       = {10.1145/2663171.2663188},
  file      = {:by-author/M/Matsakis/2014_Matsakis_103.pdf:PDF},
  journal   = {ACM SIGAda Ada Letters},
  keywords  = {Computer Science (CS); Programming Languages; Rust},
  owner     = {saulius},
  timestamp = {2022.01.02},
  creationdate = {2022-01-02T00:00:00},
}

@TechReport{Kolecki2002,
  author      = {Joseph C. Kolecki},
  institution = {NASA},
  title       = {An introduction to tensors for students of physics and engineering},
  year        = {2002},
  file        = {:by-author/K/Kolecki/2002_Kolecki_1.pdf:PDF},
  keywords    = {Mathematics; Physics; Tensor Calculus},
  owner       = {saulius},
  pages       = {1--29},
  timestamp = {2022.01.02},
  creationdate = {2022-01-02T00:00:00},
  url         = {https://www.grc.nasa.gov/www/k-12/Numbers/Math/documents/Tensors_TM2002211716.pdf},
}

@Article{Haloi2014,
  author    = {Rupam Haloi},
  journal   = {Gonit Sora},
  title     = {A brief introduction to tensor},
  year      = {2014},
  pages     = {1--13},
  file      = {:by-author/H/Haloi/2014_Haloi_1.pdf:PDF},
  keywords  = {Mathematics; Physics; Tensor Calculus},
  owner     = {saulius},
  timestamp = {2022.01.02},
  creationdate = {2022-01-02T00:00:00},
  url       = {https://gonitsora.com/wp-content/uploads/2014/06/Rupam_Haloi2_Gonit_Sora.pdf},
}

@Article{Shannon1969,
  author    = {R. D. Shannon and C. T. Prewitt},
  journal   = {Acta Crystallographica Section B Structural Crystallography and Crystal Chemistry},
  title     = {Effective ionic radii in oxides and fluorides},
  year      = {1969},
  month     = {may},
  number    = {5},
  pages     = {925--946},
  volume    = {25},
  doi       = {10.1107/s0567740869003220},
  file      = {:by-author/S/Shannon/1969_Shannon_925.pdf:PDF},
  keywords  = {Atomic Radii; Crystallography; Ionic Radii},
  owner     = {saulius},
  publisher = {International Union of Crystallography ({IUCr})},
  timestamp = {2022.01.03},
  creationdate = {2022-01-03T00:00:00},
}

@Article{Waroquiers2017,
  author    = {David Waroquiers and Xavier Gonze and Gian-Marco Rignanese and Cathrin Welker-Nieuwoudt and Frank Rosowski and Michael Göbel and Stephan Schenk and Peter Degelmann and Rute Andr{\'{e}} and Robert Glaum and Geoffroy Hautier},
  journal   = {Chemistry of Materials},
  title     = {Statistical Analysis of Coordination Environments in Oxides},
  year      = {2017},
  month     = {sep},
  number    = {19},
  pages     = {8346--8360},
  volume    = {29},
  doi       = {10.1021/acs.chemmater.7b02766},
  file      = {:by-author/W/Waroquiers/2017_Waroquiers_8346.pdf:PDF;:by-author/W/Waroquiers/2017_Waroquiers_8346_supp/cm7b02766_si_001.xls:Excel;:by-author/W/Waroquiers/2017_Waroquiers_8346_supp/cm7b02766_si_002.txt:Text;:by-author/W/Waroquiers/2017_Waroquiers_8346_supp/cm7b02766_si_003.zip:zip;:by-author/W/Waroquiers/2017_Waroquiers_8346_supp/cm7b02766_si_004.pdf:PDF},
  keywords  = {Atomic Radii; Coordination Environments; Crystallography; Ionic Radii},
  owner     = {saulius},
  publisher = {American Chemical Society ({ACS})},
  timestamp = {2022.01.03},
  creationdate = {2022-01-03T00:00:00},
}

@Article{Waroquiers2020,
  author    = {David Waroquiers and Janine George and Matthew Horton and Stephan Schenk and Kristin A. Persson and Gian-Marco Rignanese and Xavier Gonze and Geoffroy Hautier},
  journal   = {Acta Crystallographica Section B Structural Science, Crystal Engineering and Materials},
  title     = {{ChemEnv}: a fast and robust coordination environment identification tool},
  year      = {2020},
  month     = {jul},
  number    = {4},
  pages     = {683--695},
  volume    = {76},
  doi       = {10.1107/s2052520620007994},
  file      = {:by-author/W/Waroquiers/2020_Waroquiers_683.pdf:PDF},
  keywords  = {Atomic Radii; Coordination Environments; Crystallography; Ionic Radii},
  owner     = {saulius},
  publisher = {International Union of Crystallography ({IUCr})},
  timestamp = {2022.01.03},
  creationdate = {2022-01-03T00:00:00},
  url       = {https://journals.iucr.org/b/issues/2020/04/00/lo5066/lo5066.pdf},
}

@Article{Shannon1976,
  author    = {R. D. Shannon},
  journal   = {Acta Crystallographica Section A},
  title     = {Revised effective ionic radii and systematic studies of interatomic distances in halides and chalcogenides},
  year      = {1976},
  month     = {sep},
  number    = {5},
  pages     = {751--767},
  volume    = {32},
  doi       = {10.1107/s0567739476001551},
  file      = {:by-author/S/Shannon/1976_Shannon_751.pdf:PDF},
  keywords  = {Atomic Radii; Crystallography; Ionic Radii},
  owner     = {saulius},
  publisher = {International Union of Crystallography ({IUCr})},
  timestamp = {2022.01.03},
  creationdate = {2022-01-03T00:00:00},
}

@Article{Gagne2016,
  author    = {Olivier Charles Gagn{\'{e}} and Frank Christopher Hawthorne},
  journal   = {Acta Crystallographica Section B Structural Science, Crystal Engineering and Materials},
  title     = {Bond-length distributions for ions bonded to oxygen: alkali and alkaline-earth metals},
  year      = {2016},
  month     = {aug},
  number    = {4},
  pages     = {602--625},
  volume    = {72},
  doi       = {10.1107/s2052520616008507},
  file      = {:by-author/G/Gagné/2016_Gagné_602.pdf:PDF},
  keywords  = {Atomic Radii; Bond Length Distributions; Crystallography; Ionic Radii},
  owner     = {saulius},
  publisher = {International Union of Crystallography ({IUCr})},
  timestamp = {2022.01.03},
  creationdate = {2022-01-03T00:00:00},
}

@Article{Gagne2020,
  author    = {Olivier Charles Gagn{\'{e}} and Frank Christopher Hawthorne},
  journal   = {{IUCrJ}},
  title     = {Bond-length distributions for ions bonded to oxygen: results for the transition metals and quantification of the factors underlying bond-length variation in inorganic solids},
  year      = {2020},
  month     = {jun},
  number    = {4},
  pages     = {581--629},
  volume    = {7},
  doi       = {10.1107/s2052252520005928},
  file      = {:by-author/G/Gagné/2020_Gagné_581.pdf:PDF},
  keywords  = {Atomic Radii; Bond Length Distributions; Crystallography; Ionic Radii},
  owner     = {saulius},
  publisher = {International Union of Crystallography ({IUCr})},
  timestamp = {2022.01.03},
  creationdate = {2022-01-03T00:00:00},
}

@Article{Gagne2015,
  author    = {Olivier Charles Gagn{\'{e}} and Frank Christopher Hawthorne},
  journal   = {Acta Crystallographica Section B Structural Science, Crystal Engineering and Materials},
  title     = {Comprehensive derivation of bond-valence parameters for ion pairs involving oxygen},
  year      = {2015},
  month     = {sep},
  number    = {5},
  pages     = {562--578},
  volume    = {71},
  doi       = {10.1107/s2052520615016297},
  file      = {:by-author/G/Gagné/2015_Gagné_562.pdf:PDF},
  keywords  = {Atomic Radii; Bond Length Distributions; Crystallography; Ionic Radii},
  owner     = {saulius},
  publisher = {International Union of Crystallography ({IUCr})},
  timestamp = {2022.01.03},
  creationdate = {2022-01-03T00:00:00},
}

@Article{Pauling1927,
  author    = {Linus Pauling},
  journal   = {Journal of the American Chemical Society},
  title     = {The sizes of ions and the structure of ionic crystals},
  year      = {1927},
  month     = {mar},
  number    = {3},
  pages     = {765--790},
  volume    = {49},
  doi       = {10.1021/ja01402a019},
  file      = {:by-author/P/Pauling/1927_Pauling_765.pdf:PDF},
  keywords  = {Crystallography; Ionic Radii},
  owner     = {saulius},
  publisher = {American Chemical Society ({ACS})},
  timestamp = {2022.01.04},
  creationdate = {2022-01-04T00:00:00},
}

@Presentation{Pyykkoe2009b,
  author       = {Pekka Pyykkö},
  title        = {Covalent radii},
  year         = {2009},
  conference   = {Winter School in Theoretical Chemistry, Helsinki},
  organization = {University of Helsinki},
  school       = {Department of Chemistry},
  file         = {:by-author/P/Pyykkö/2009_Pyykkö_1.pdf:PDF},
  keywords     = {Chemistry; Covalent Radii; Crystallography; Ionic Radii; Theoretical Chemistry},
  owner        = {saulius},
  pages        = {1--35},
  timestamp = {2022.01.04},
  creationdate = {2022-01-04T00:00:00},
  url          = {http://www.chem.helsinki.fi/~sundholm/winterschool/lecture_notes_2009/Pyykko_radii.pdf},
}

@Article{Zimmermann2020,
  author    = {Nils E. R. Zimmermann and Anubhav Jain},
  journal   = {{RSC} Advances},
  title     = {Local structure order parameters and site fingerprints for quantification of coordination environment and crystal structure similarity},
  year      = {2020},
  number    = {10},
  pages     = {6063--6081},
  volume    = {10},
  doi       = {10.1039/c9ra07755c},
  file      = {:by-author/Z/Zimmermann/2020_Zimmermann_6063.pdf:PDF;:by-author/Z/Zimmermann/2020_Zimmermann_6063_supp.pdf:PDF},
  keywords  = {Atomic Radii; Citing COD; Crystallography; Ionic Radii; Local Environments},
  owner     = {saulius},
  publisher = {Royal Society of Chemistry ({RSC})},
  timestamp = {2022.01.04},
  creationdate = {2022-01-04T00:00:00},
}

@Article{Ganose2019,
  author    = {Alex M. Ganose and Anubhav Jain},
  journal   = {{MRS} Communications},
  title     = {Robocrystallographer: automated crystal structure text descriptions and analysis},
  year      = {2019},
  month     = {sep},
  number    = {3},
  pages     = {874--881},
  volume    = {9},
  doi       = {10.1557/mrc.2019.94},
  file      = {:by-author/G/Ganose/2019_Ganose_874.pdf:PDF},
  keywords  = {Artificial Intelligence (AI); Crystal Structure Prediction (CSP); Crystallography; Local Environments; Machine Learning (ML)},
  owner     = {saulius},
  publisher = {Springer Science and Business Media {LLC}},
  timestamp = {2022.01.04},
  creationdate = {2022-01-04T00:00:00},
}

@Article{Bragg1927,
  author    = {William Lawrence Bragg and J. West},
  journal   = {Proceedings of the Royal Society of London. Series A, Containing Papers of a Mathematical and Physical Character},
  title     = {The structure of certain silicates},
  year      = {1927},
  month     = {apr},
  number    = {768},
  pages     = {450--473},
  volume    = {114},
  doi       = {10.1098/rspa.1927.0052},
  file      = {:by-author/B/Bragg/1927_Bragg_450.pdf:PDF},
  keywords  = {Atomic Radii; Crystallography},
  owner     = {saulius},
  publisher = {The Royal Society},
  timestamp = {2022.01.04},
  creationdate = {2022-01-04T00:00:00},
}

@Article{Tosi1964,
  author    = {M. P. Tosi and F. G. Fumi},
  journal   = {Journal of Physics and Chemistry of Solids},
  title     = {Ionic sizes and born repulsive parameters in the {NaCl}-type alkali halides{\textemdash}{II}},
  year      = {1964},
  month     = {jan},
  number    = {1},
  pages     = {45--52},
  volume    = {25},
  doi       = {10.1016/0022-3697(64)90160-x},
  file      = {:by-author/T/Tosi/1964_Tosi_45.pdf:PDF},
  keywords  = {Crystal Radii; Crystallography; Ionic Radii},
  owner     = {saulius},
  publisher = {Elsevier {BV}},
  timestamp = {2022.01.04},
  creationdate = {2022-01-04T00:00:00},
}

@Article{Fumi1964,
  author    = {F.G. Fumi and M.P. Tosi},
  journal   = {Journal of Physics and Chemistry of Solids},
  title     = {Ionic sizes and born repulsive parameters in the {NaCl}-type alkali halides{\textemdash}I},
  year      = {1964},
  month     = {jan},
  number    = {1},
  pages     = {31--43},
  volume    = {25},
  doi       = {10.1016/0022-3697(64)90159-3},
  file      = {:by-author/F/Fumi/1964_Fumi_31.pdf:PDF},
  keywords  = {Crystal Radii; Crystallography; Ionic Radii},
  owner     = {saulius},
  publisher = {Elsevier {BV}},
  timestamp = {2022.01.04},
  creationdate = {2022-01-04T00:00:00},
}

@InCollection{Tosi1964a,
  author    = {Mario P. Tosi},
  booktitle = {Solid State Physics},
  publisher = {Elsevier},
  title     = {Cohesion of Ionic Solids in the Born Model},
  year      = {1964},
  pages     = {1--120},
  doi       = {10.1016/s0081-1947(08)60515-9},
  file      = {:by-author/T/Tosi/1964_Tosi_1.pdf:PDF},
  keywords  = {Born Mode; Crystallography; Ionic Crystals; Ionic Radii; Madelung Energy},
  owner     = {saulius},
  timestamp = {2022.01.04},
  creationdate = {2022-01-04T00:00:00},
}

@Article{Bragg1920,
  author    = {W. Lawrence Bragg},
  journal   = {The London, Edinburgh, and Dublin Philosophical Magazine and Journal of Science},
  title     = {{XVIII}. The arrangement of atoms in crystals},
  year      = {1920},
  month     = {aug},
  number    = {236},
  pages     = {169--189},
  volume    = {40},
  doi       = {10.1080/14786440808636111},
  file      = {:by-author/B/Bragg/1920_Bragg_169.pdf:PDF},
  keywords  = {Crystal Radii; Crystallography; Ionic Radii},
  owner     = {saulius},
  publisher = {Informa {UK} Limited},
  timestamp = {2022.01.04},
  creationdate = {2022-01-04T00:00:00},
}

@Presentation{Becker2017,
  author       = {Martin Becker},
  title        = {Introduction to {SPARK} 2014: how to develop ultra-low defect software},
  year         = {2017},
  organization = {Technical University of Munich},
  file         = {:by-author/B/Becker/2017_Becker_1.pdf:PDF},
  keywords     = {Ada; Computer Science (CS); High Reliability Systems; SPARK; Software Verification},
  owner        = {saulius},
  pages        = {1--89},
  timestamp = {2022.01.07},
  creationdate = {2022-01-07T00:00:00},
  url          = {https://www.ei.tum.de/fileadmin/tueifei/rcs/becker/spark2014-intro.pdf},
}

@InProceedings{Comar1995,
  author    = {Cyrille Comar and Gary Dismukes and Franco Gasperoni},
  booktitle = {Proceedings of the conference on {TRI}-Ada {\textquotesingle}95 Ada{\textquotesingle}s role in global markets: solutions for a changing complex world - {TRI}-Ada {\textquotesingle}95},
  title     = {The {GNAT} implementation of controlled types},
  year      = {1995},
  pages     = {467--473},
  publisher = {{ACM} Press},
  doi       = {10.1145/376503.376724},
  file      = {:by-author/C/Comar/1995_Comar_467.pdf:PDF},
  keywords  = {Ada; Computer Science (CS); Controlled Types; OO Programming},
  owner     = {saulius},
  timestamp = {2022.01.07},
  creationdate = {2022-01-07T00:00:00},
  url       = {https://www.adacore.com/uploads/techPapers/The_GNAT_Implementation_of_Controlled_Types.pdf},
}

@InProceedings{Cho1988,
  author    = {Y. H. Cho and H. T. Mouftah},
  booktitle = {[1988] Proceedings. The Eighteenth International Symposium on Multiple-Valued Logic},
  title     = {A {CMOS} ternary {ROM} chip},
  year      = {1988},
  pages     = {358--363},
  publisher = {{IEEE} Comput. Soc. Press},
  doi       = {10.1109/ismvl.1988.5195},
  file      = {:by-author/C/Cho/1988_Cho_358.pdf:PDF},
  keywords  = {Computer Science (CS); Ternary Computers; Ternary Logic; Ternary Number System},
  owner     = {saulius},
  timestamp = {2022.01.07},
  creationdate = {2022-01-07T00:00:00},
  url       = {https://wwwee.ee.bgu.ac.il/~kushnero/ternary/Using CMOS gates/A CMOS ternary ROM chip.pdf},
}

@Article{Srivastava1996,
  author    = {A. Srivastava and K. Venkatapathy},
  journal   = {{VLSI} Design},
  title     = {Design and implementation of a low power ternary full adder},
  year      = {1996},
  month     = {jan},
  number    = {1},
  pages     = {75--81},
  volume    = {4},
  doi       = {10.1155/1996/94696},
  file      = {:by-author/S/Srivastava/1996_Srivastava_75.pdf:PDF},
  keywords  = {Computer Science (CS); Ternary Computers; Ternary Logic; Ternary Number System},
  owner     = {saulius},
  publisher = {Hindawi Limited},
  timestamp = {2022.01.07},
  creationdate = {2022-01-07T00:00:00},
  url       = {https://downloads.hindawi.com/journals/vlsi/1996/094696.pdf},
}

@Manuscript{Moy2021,
  author    = {Yannick Moy},
  title     = {How the analyzer can help the user help the analyzer},
  year      = {2021},
  keywords  = {Ada; Computer Science (CS); High Reliability Systems; SPARK; Software Verification},
  url       = {https://www.adacore.com/uploads/techPapers/fide_2021.pdf},
  file      = {:by-author/M/Moy/2021_Moy_1.pdf:PDF},
  owner     = {saulius},
  pages     = {1--8},
  timestamp = {2022.01.08},
  creationdate = {2022-01-08T00:00:00},
}

@Manuscript{Guitton2011,
  author    = {Jérôme Guitton and Johannes Kanig and Yannick Moy},
  title     = {Why {Hi}-{Lite} {Ada}?},
  year      = {2011},
  keywords  = {Ada; Computer Science (CS); High Reliability Systems; SPARK; Software Verification},
  url       = {https://www.open-do.org/wp-content/uploads/2011/06/Why_Hi_Lite_Ada.pdf},
  file      = {:by-author/G/Guitton/2011_Guitton_1.pdf:PDF},
  owner     = {saulius},
  pages     = {1--13},
  timestamp = {2022.01.09},
  creationdate = {2022-01-09T00:00:00},
}

@Article{Kumura2002,
  author    = {T. Kumura and M. Ikekawa and M. Yosbida and I. Kuroda},
  journal   = {{IEEE} Signal Processing Magazine},
  title     = {{VLIW} {DSP} for mobile applications},
  year      = {2002},
  month     = {jul},
  number    = {4},
  pages     = {10--21},
  volume    = {19},
  doi       = {10.1109/msp.2002.1012346},
  file      = {:by-author/K/Kumura/2002_Kumura_10.pdf:PDF},
  keywords  = {CPU Design; Computer Architecture; Computer Science (CS); DSP; VLIW},
  owner     = {saulius},
  publisher = {Institute of Electrical and Electronics Engineers ({IEEE})},
  timestamp = {2022.01.10},
  creationdate = {2022-01-10T00:00:00},
}

@Book{Bronstein2021,
  author        = {Michael M. Bronstein and Joan Bruna and Taco Cohen and Petar Veličković},
  title         = {Geometric deep learning: grids, groups, graphs, geodesics, and gauges},
  year          = {2021},
  month         = apr,
  abstract      = {The last decade has witnessed an experimental revolution in data science and machine learning, epitomised by deep learning methods. Indeed, many high-dimensional learning tasks previously thought to be beyond reach -- such as computer vision, playing Go, or protein folding -- are in fact feasible with appropriate computational scale. Remarkably, the essence of deep learning is built from two simple algorithmic principles: first, the notion of representation or feature learning, whereby adapted, often hierarchical, features capture the appropriate notion of regularity for each task, and second, learning by local gradient-descent type methods, typically implemented as backpropagation. While learning generic functions in high dimensions is a cursed estimation problem, most tasks of interest are not generic, and come with essential pre-defined regularities arising from the underlying low-dimensionality and structure of the physical world. This text is concerned with exposing these regularities through unified geometric principles that can be applied throughout a wide spectrum of applications. Such a 'geometric unification' endeavour, in the spirit of Felix Klein's Erlangen Program, serves a dual purpose: on one hand, it provides a common mathematical framework to study the most successful neural network architectures, such as CNNs, RNNs, GNNs, and Transformers. On the other hand, it gives a constructive procedure to incorporate prior physical knowledge into neural architectures and provide principled way to build future architectures yet to be invented.},
  archiveprefix = {arXiv},
  eprint        = {2104.13478},
  file          = {:by-author/B/Bronstein/2021_Bronstein_1.pdf:PDF},
  keywords      = {Abstract Algebra; Artificial Intelligence (AI); Atificial Intelligence; Computer Science (CS); Deep Learning (DL); Graph Neural Networks (GNN); Machine Learning (ML); Relativity; Rieman Geometry},
  owner         = {saulius},
  primaryclass  = {cs.LG},
  timestamp = {2022.01.13},
  creationdate = {2022-01-13T00:00:00},
  url           = {https://arxiv.org/abs/2104.13478},
}

@Article{Zhang2020a,
  author    = {Ziwei Zhang and Peng Cui and Wenwu Zhu},
  journal   = {{IEEE} Transactions on Knowledge and Data Engineering},
  title     = {Deep learning on graphs: a survey},
  year      = {2020},
  pages     = {1--24},
  doi       = {10.1109/tkde.2020.2981333},
  file      = {:by-author/Z/Zhang/2020_Zhang_1a.pdf:PDF},
  keywords  = {Artificial Intelligence (AI); Atificial Intelligence; Computer Science (CS); Deep Learning (DL); Graph Neural Networks (GNN); Machine Learning (ML)},
  owner     = {saulius},
  publisher = {Institute of Electrical and Electronics Engineers ({IEEE})},
  timestamp = {2022.01.13},
  creationdate = {2022-01-13T00:00:00},
  url       = {https://arxiv.org/abs/1812.04202},
}

@Article{Xie2018,
  author    = {Tian Xie and Jeffrey C. Grossman},
  journal   = {Physical Review Letters},
  title     = {Crystal Graph Convolutional Neural Networks for an Accurate and Interpretable Prediction of Material Properties},
  year      = {2018},
  month     = {apr},
  number    = {14},
  pages     = {145301},
  volume    = {120},
  comment   = {Cited more than 600 times, according to Sergei Grudinin.},
  doi       = {10.1103/physrevlett.120.145301},
  file      = {:by-author/X/Xie/2018_Xie_145301.pdf:PDF;:by-author/X/Xie/2018_Xie_145301_suppl/SM.pdf:PDF},
  keywords  = {Artificial Intelligence (AI); Atificial Intelligence; Computer Science (CS); Deep Learning (DL); Graph Neural Networks (GNN); Machine Learning (ML)},
  owner     = {saulius},
  publisher = {American Physical Society ({APS})},
  timestamp = {2022.01.13},
  creationdate = {2022-01-13T00:00:00},
  url       = {https://arxiv.org/abs/1710.10324},
}

@Article{Chen2019a,
  author    = {Chi Chen and Weike Ye and Yunxing Zuo and Chen Zheng and Shyue Ping Ong},
  journal   = {Chemistry of Materials},
  title     = {Graph Networks as a Universal Machine Learning Framework for Molecules and Crystals},
  year      = {2019},
  month     = {apr},
  number    = {9},
  pages     = {3564--3572},
  volume    = {31},
  doi       = {10.1021/acs.chemmater.9b01294},
  file      = {:by-author/C/Chen/2019_Chen_3564.pdf:PDF},
  keywords  = {Artificial Intelligence (AI); Atificial Intelligence; Computer Science (CS); Deep Learning (DL); Graph Neural Networks (GNN); Machine Learning (ML)},
  owner     = {saulius},
  publisher = {American Chemical Society ({ACS})},
  timestamp = {2022.01.13},
  creationdate = {2022-01-13T00:00:00},
  url       = {https://arxiv.org/abs/1812.05055},
}

@Article{Mater2019,
  author    = {Adam C. Mater and Michelle L. Coote},
  journal   = {Journal of Chemical Information and Modeling},
  title     = {Deep Learning in Chemistry},
  year      = {2019},
  month     = {jun},
  number    = {6},
  pages     = {2545--2559},
  volume    = {59},
  doi       = {10.1021/acs.jcim.9b00266},
  file      = {:by-author/M/Mater/2019_Mater_2545.pdf:PDF},
  keywords  = {Artificial Intelligence (AI); Atificial Intelligence; Chemistry; Computer Science (CS); Deep Learning (DL); Graph Neural Networks (GNN); Machine Learning (ML)},
  owner     = {saulius},
  publisher = {American Chemical Society ({ACS})},
  timestamp = {2022.01.13},
  creationdate = {2022-01-13T00:00:00},
}

@Article{Zhuo2018,
  author    = {Ya Zhuo and Aria Mansouri Tehrani and Jakoah Brgoch},
  journal   = {The Journal of Physical Chemistry Letters},
  title     = {Predicting the Band Gaps of Inorganic Solids by Machine Learning},
  year      = {2018},
  month     = {mar},
  number    = {7},
  pages     = {1668--1673},
  volume    = {9},
  doi       = {10.1021/acs.jpclett.8b00124},
  file      = {:by-author/Z/Zhuo/2018_Zhuo_1668.pdf:PDF},
  keywords  = {Artificial Intelligence (AI); Atificial Intelligence; Computer Science (CS); Deep Learning (DL); Graph Neural Networks (GNN); Machine Learning (ML); Materials Science},
  owner     = {saulius},
  publisher = {American Chemical Society ({ACS})},
  timestamp = {2022.01.13},
  creationdate = {2022-01-13T00:00:00},
}

@Article{Schleder_2019,
  author    = {Gabriel R Schleder and Antonio C M Padilha and Carlos Mera Acosta and Marcio Costa and Adalberto Fazzio},
  journal   = {Journal of Physics: Materials},
  title     = {From {DFT} to machine learning: recent approaches to materials science{\textendash}a review},
  year      = {2019},
  month     = {may},
  number    = {3},
  pages     = {032001},
  volume    = {2},
  abstract  = {Recent advances in experimental and computational methods are increasing the quantity and complexity of generated data. This massive amount of raw data needs to be stored and interpreted in order to advance the materials science field. Identifying correlations and patterns from large amounts of complex data is being performed by machine learning algorithms for decades. Recently, the materials science community started to invest in these methodologies to extract knowledge and insights from the accumulated data. This review follows a logical sequence starting from density functional theory as the representative instance of electronic structure methods, to the subsequent high-throughput approach, used to generate large amounts of data. Ultimately, data-driven strategies which include data mining, screening, and machine learning techniques, employ the data generated. We show how these approaches to modern computational materials science are being used to uncover complexities and design novel materials with enhanced properties. Finally, we point to the present research problems, challenges, and potential future perspectives of this new exciting field.},
  doi       = {10.1088/2515-7639/ab084b},
  file      = {:by-author/S/Schleder/2019_Schleder_32001.pdf:PDF},
  keywords  = {Artificial Intelligence (AI); Atificial Intelligence; Computer Science (CS); Deep Learning (DL); Graph Neural Networks (GNN); Machine Learning (ML); Materials Science},
  owner     = {saulius},
  publisher = {{IOP} Publishing},
  timestamp = {2022.01.13},
  creationdate = {2022-01-13T00:00:00},
  url       = {https://iopscience.iop.org/article/10.1088/2515-7639/ab084b/pdf},
}

@Article{Ying2019,
  author       = {Ying, Rex and Bourgeois, Dylan and You, Jiaxuan and Zitnik, Marinka and Leskovec, Jure},
  journal      = {Advances in neural information processing systems},
  title        = {GNNExplainer: Generating Explanations for Graph Neural Networks.},
  year         = {2019},
  issn         = {1049-5258},
  month        = dec,
  pages        = {9240--9251},
  volume       = {32},
  abstract     = {Graph Neural Networks (GNNs) are a powerful tool for machine learning on graphs. GNNs combine node feature information with the graph structure by recursively passing neural messages along edges of the input graph. However, incorporating both graph structure and feature information leads to complex models and explaining predictions made by GNNs remains unsolved. Here we propose GnnExplainer, the first general, model-agnostic approach for providing interpretable explanations for predictions of any GNN-based model on any graph-based machine learning task. Given an instance, GnnExplainer identifies a compact subgraph structure and a small subset of node features that have a crucial role in GNN's prediction. Further, GnnExplainer can generate consistent and concise explanations for an entire class of instances. We formulate GnnExplainer as an optimization task that maximizes the mutual information between a GNN's prediction and distribution of possible subgraph structures. Experiments on synthetic and real-world graphs show that our approach can identify important graph structures as well as node features, and outperforms alternative baseline approaches by up to 43.0% in explanation accuracy. GnnExplainer provides a variety of benefits, from the ability to visualize semantically relevant structures to interpretability, to giving insights into errors of faulty GNNs.},
  country      = {United States},
  file         = {:by-author/Y/Ying/2019_Ying_9240.pdf:PDF},
  issn-linking = {1049-5258},
  keywords     = {Artificial Intelligence (AI); Atificial Intelligence; Computer Science (CS); Deep Learning (DL); Graph Neural Networks (GNN); Machine Learning (ML); Materials Science},
  mid          = {NIHMS1062398},
  nlm-id       = {9607483},
  owner        = {saulius},
  pmc          = {PMC7138248},
  pmid         = {32265580},
  pubmodel     = {Print},
  pubstate     = {ppublish},
  revised      = {2020-04-11},
  timestamp = {2022.01.13},
  creationdate = {2022-01-13T00:00:00},
  url          = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7138248/pdf/nihms-1062398.pdf},
}

@Article{Himanen2020,
  author    = {Lauri Himanen and Marc O.J. Jäger and Eiaki V. Morooka and Filippo Federici Canova and Yashasvi S. Ranawat and David Z. Gao and Patrick Rinke and Adam S. Foster},
  journal   = {Computer Physics Communications},
  title     = {{DScribe}: Library of descriptors for machine learning in materials science},
  year      = {2020},
  month     = {feb},
  pages     = {106949},
  volume    = {247},
  doi       = {10.1016/j.cpc.2019.106949},
  file      = {:by-author/H/Himanen/2020_Himanen_106949.pdf:PDF;:by-author/H/Himanen/2020_Himanen_106949_arXiv.pdf:PDF},
  keywords  = {Artificial Intelligence (AI); Atificial Intelligence; Computer Science (CS); Deep Learning (DL); Graph Neural Networks (GNN); Machine Learning (ML); Materials Science},
  owner     = {saulius},
  publisher = {Elsevier {BV}},
  timestamp = {2022.01.13},
  creationdate = {2022-01-13T00:00:00},
}

@InProceedings{Townsend2009,
  author    = {Joseph A. Townsend and Jim Downing and Peter Murray-Rust},
  booktitle = {2009 Fifth {IEEE} International Conference on e-Science},
  title     = {{CHIC} - converting hamburgers into cows},
  year      = {2009},
  month     = {dec},
  pages     = {337--343},
  publisher = {{IEEE}},
  doi       = {10.1109/e-science.2009.54},
  file      = {:by-author/T/Townsend/2009_Townsend_337.pdf:PDF},
  keywords  = {Computer Science (CS); Text Mining},
  owner     = {saulius},
  timestamp = {2022.01.13},
  creationdate = {2022-01-13T00:00:00},
}

@Article{Joosten2014,
  author    = {Robbie P. Joosten and Fei Long and Garib N. Murshudov and Anastassis Perrakis},
  journal   = {{IUCrJ}},
  title     = {{The PDB}{\_}{REDO} server for macromolecular structure model optimization},
  year      = {2014},
  month     = {may},
  number    = {4},
  pages     = {213--220},
  volume    = {1},
  doi       = {10.1107/s2052252514009324},
  file      = {:by-author/J/Joosten/2014_Joosten_213.pdf:PDF},
  keywords  = {Crystallography; Data Quality; Macromolecular Crystallography; PDB_REDO; Structure Re-refinement},
  owner     = {saulius},
  publisher = {International Union of Crystallography ({IUCr})},
  timestamp = {2022.01.15},
  creationdate = {2022-01-15T00:00:00},
}

@Article{Joosten2012,
  author    = {Robbie P. Joosten and Krista Joosten and Garib N. Murshudov and Anastassis Perrakis},
  journal   = {Acta Crystallographica Section D Biological Crystallography},
  title     = {{PDB}{\_}{REDO}: constructive validation, more than just looking for errors},
  year      = {2012},
  month     = {mar},
  number    = {4},
  pages     = {484--496},
  volume    = {68},
  doi       = {10.1107/s0907444911054515},
  file      = {:by-author/J/Joosten/2012_Joosten_484.pdf:PDF},
  keywords  = {Crystallography; Data Quality; Macromolecular Crystallography; PDB_REDO; Structure Re-refinement},
  owner     = {saulius},
  publisher = {International Union of Crystallography ({IUCr})},
  timestamp = {2022.01.15},
  creationdate = {2022-01-15T00:00:00},
}

@Article{Joosten2011,
  author    = {R. P. Joosten and K. Joosten and S. X. Cohen and G. Vriend and A. Perrakis},
  journal   = {Bioinformatics},
  title     = {Automatic rebuilding and optimization of crystallographic structures in the Protein Data Bank},
  year      = {2011},
  month     = {oct},
  number    = {24},
  pages     = {3392--3398},
  volume    = {27},
  doi       = {10.1093/bioinformatics/btr590},
  file      = {:by-author/J/Joosten/2011_Joosten_3392.pdf:PDF},
  keywords  = {Crystallography; Data Quality; Macromolecular Crystallography; PDB_REDO; Structure Re-refinement},
  owner     = {saulius},
  publisher = {Oxford University Press ({OUP})},
  timestamp = {2022.01.15},
  creationdate = {2022-01-15T00:00:00},
}

@Article{Joosten2010,
  author    = {R. P. Joosten and T. A. H. te Beek and E. Krieger and M. L. Hekkelman and R. W. W. Hooft and R. Schneider and C. Sander and G. Vriend},
  journal   = {Nucleic Acids Research},
  title     = {A series of {PDB} related databases for everyday needs},
  year      = {2010},
  month     = {nov},
  number    = {Database},
  pages     = {D411--D419},
  volume    = {39},
  doi       = {10.1093/nar/gkq1105},
  file      = {:by-author/J/Joosten/2010_Joosten_411.pdf:PDF},
  keywords  = {Crystallography; Data Quality; Macromolecular Crystallography; PDB_REDO; Structure Re-refinement},
  owner     = {saulius},
  publisher = {Oxford University Press ({OUP})},
  timestamp = {2022.01.15},
  creationdate = {2022-01-15T00:00:00},
}

@Article{Joosten2007,
  author    = {Robbie P. Joosten and Gert Vriend},
  journal   = {Science},
  title     = {{PDB} improvement starts with data deposition},
  year      = {2007},
  pages     = {195--196},
  volume    = {317},
  doi       = {10.1126/science.317.5835.195},
  file      = {:by-author/J/Joosten/2007_Joosten_195.pdf:PDF},
  keywords  = {Crystallography; Data Deposition; Data Quality; Macromolecular Crystallography; PDB_REDO; Structure Re-refinement},
  owner     = {saulius},
  timestamp = {2022.01.15},
  creationdate = {2022-01-15T00:00:00},
  url       = {https://pdb-redo.eu/publications/science.pdf},
}

@Article{Joosten2009a,
  author    = {Robbie P. Joosten and Thomas Womack and Gert Vriend and Gérard Bricogne},
  journal   = {Acta Crystallographica Section D Biological Crystallography},
  title     = {Re-refinement from deposited {X}-ray data can deliver improved models for most {PDB} entries},
  year      = {2009},
  month     = {jan},
  number    = {2},
  pages     = {176--185},
  volume    = {65},
  doi       = {10.1107/s0907444908037591},
  file      = {:by-author/J/Joosten/2009_Joosten_176.pdf:PDF},
  keywords  = {Crystallography; Data Quality; Macromolecular Crystallography; PDB_REDO; Structure Re-refinement},
  owner     = {saulius},
  publisher = {International Union of Crystallography ({IUCr})},
  timestamp = {2022.01.15},
  creationdate = {2022-01-15T00:00:00},
}

@Article{Beusekom2017,
  author    = {Bart van Beusekom and Wouter G. Touw and Mahidhar Tatineni and Sandeep Somani and Gunaretnam Rajagopal and Jinquan Luo and Gary L. Gilliland and Anastassis Perrakis and Robbie P. Joosten},
  journal   = {Protein Science},
  title     = {Homology-based hydrogen bond information improves crystallographic structures in the {PDB}},
  year      = {2017},
  month     = {dec},
  number    = {3},
  pages     = {798--808},
  volume    = {27},
  doi       = {10.1002/pro.3353},
  file      = {:by-author/B/Beusekom/2017_Beusekom_798.pdf:PDF},
  keywords  = {Crystallography; Data Quality; Macromolecular Crystallography; PDB_REDO; Structure Re-refinement},
  owner     = {saulius},
  publisher = {Wiley},
  timestamp = {2022.01.15},
  creationdate = {2022-01-15T00:00:00},
  url       = {https://pdb-redo.eu/publications/Beusekom_et_al-2018-Protein_Science.pdf},
}

@TechReport{Rossebo2006,
  author      = {Bryan Rossebo and Paul Oman and Jim Alves-Foss and Ryan Blue and Paul Jaszkowiak},
  institution = {University of Idaho, Center for Secure and Dependable Systems},
  title       = {Using {SPARK}-{A}da to model and verify a {MILS} message router},
  year        = {2006},
  file        = {:by-author/R/Rossebo/2006_Rossebo_1.pdf:PDF},
  keywords    = {Ada; Computer Science (CS); Correctness Proofs; SPARK; Software Verification},
  owner       = {saulius},
  pages       = {1--9},
  timestamp = {2022.01.16},
  creationdate = {2022-01-16T00:00:00},
  url         = {https://www.uidaho.edu/~/media/UIdaho-Responsive/Files/engr/research/csds/publications/2006/Using%20SPARK-Ada%20to%20Model%20and%20Verify%20a%20MILS%20Message%20Router%202006.ashx},
}

@TechReport{Berghofer2011,
  author           = {Stefan Berghofer},
  institution      = {Security Networks AG},
  title            = {Verification of dependable software using {SPARK} and {I}sabelle},
  year             = {2011},
  comment          = {Another source URL: https://drops.dagstuhl.de/opus/volltexte/2012/3587/pdf/3.pdf},
  creationdate     = {2022-01-16T00:00:00},
  eprint           = {https://drops.dagstuhl.de/opus/volltexte/2012/3587/pdf/3.pdf},
  file             = {:by-author/B/Berghofer/2011_Berghofer_1.pdf:PDF;:by-author/B/Berghofer/2011_Berghofer_1a.pdf:PDF},
  keywords         = {Ada; Computer Science (CS); Correctness Proofs; HOL; SPARK; Software Verification},
  modificationdate = {2023-02-13T08:04:31},
  owner            = {saulius},
  pages            = {1--18},
  timestamp        = {2022.01.16},
  url              = {https://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.261.1877},
}

@InCollection{Dross2017,
  author    = {Claire Dross and Yannick Moy},
  booktitle = {Lecture Notes in Computer Science},
  publisher = {Springer International Publishing},
  title     = {Auto-active proof of red-black trees in {SPARK}},
  year      = {2017},
  pages     = {68--83},
  doi       = {10.1007/978-3-319-57288-8_5},
  file      = {:by-author/D/Dross/2017_Dross_68.pdf:PDF},
  keywords  = {Ada; Computer Science (CS); Correctness Proofs; SPARK; Software Verification},
  owner     = {saulius},
  timestamp = {2022.01.16},
  creationdate = {2022-01-16T00:00:00},
  url       = {https://blog.adacore.com/uploads/Auto-Active-Proof-of-Red-Black-Trees-in-SPARK.pdf},
}

@Article{Jia2011,
  author    = {Yue Jia and Mark Harman},
  journal   = {{IEEE} Transactions on Software Engineering},
  title     = {An analysis and survey of the development of mutation testing},
  year      = {2011},
  month     = {sep},
  number    = {5},
  pages     = {649--678},
  volume    = {37},
  doi       = {10.1109/tse.2010.62},
  file      = {:by-author/J/Jia/2011_Jia_649.pdf:PDF},
  keywords  = {Computer Science (CS); Mutation Testing; Software Testing},
  owner     = {saulius},
  publisher = {Institute of Electrical and Electronics Engineers ({IEEE})},
  timestamp = {2022.01.19},
  creationdate = {2022-01-19T00:00:00},
}

@InProceedings{Khan2015,
  author    = {Rijwan Khan and Mohd. Amjad},
  booktitle = {2015 {IEEE} {UP} Section Conference on Electrical Computer and Electronics ({UPCON})},
  title     = {Automatic test case generation for unit software testing using genetic algorithm and mutation analysis},
  year      = {2015},
  month     = {dec},
  pages     = {1--5},
  publisher = {{IEEE}},
  doi       = {10.1109/upcon.2015.7456734},
  file      = {:by-author/K/Khan/2015_Khan_1.pdf:PDF},
  keywords  = {Computer Science (CS); Genetic Algorithms; Mutation Testing; Software Testing},
  owner     = {saulius},
  timestamp = {2022.01.19},
  creationdate = {2022-01-19T00:00:00},
}

@Article{Back1997,
  author    = {Ralph Back and Jim Grundy and Joakim von Wright},
  journal   = {Formal Aspects of Computing},
  title     = {Structured calculational proof},
  year      = {1997},
  month     = {sep},
  number    = {5-6},
  pages     = {469--483},
  volume    = {9},
  doi       = {10.1007/bf01211456},
  file      = {:by-author/B/Back/1997_Back_469.pdf:PDF},
  keywords  = {Computer Science (CS); Notation; Proof Theory},
  owner     = {saulius},
  publisher = {Association for Computing Machinery ({ACM})},
  timestamp = {2022.01.22},
  creationdate = {2022-01-22T00:00:00},
}

@InProceedings{Lau2007,
  author    = {Kung-Kiu Lau and Zheng Wang},
  booktitle = {Proceedings of the 2007 {ACM} international conference on {SIGAda} annual international conference - {SIGAda} {\textquotesingle}07},
  title     = {Verified component-based software in {SPARK}},
  year      = {2007},
  pages     = {51--56},
  publisher = {{ACM} Press},
  doi       = {10.1145/1315580.1315594},
  file      = {:by-author/L/Lau/2007_Lau_51.pdf:PDF},
  keywords  = {Ada; Computer Science (CS); Correctness Proofs; SPARK; Software Verification},
  owner     = {saulius},
  timestamp = {2022.01.22},
  creationdate = {2022-01-22T00:00:00},
}

@InProceedings{Taft2013,
  author    = {S. Tucker Taft},
  booktitle = {Proceedings of the 2013 {ACM} {SIGAda} annual conference on High integrity language technology - {HILT} {\textquotesingle}13},
  title     = {Bringing safe, dynamic parallel programming to the spark verifiable subset of ada},
  year      = {2013},
  pages     = {37--39},
  publisher = {{ACM} Press},
  doi       = {10.1145/2527269.2527279},
  file      = {:by-author/T/Taft/2013_Taft_37.pdf:PDF},
  keywords  = {Ada; Computer Science (CS); Correctness Proofs; SPARK; Software Verification},
  owner     = {saulius},
  timestamp = {2022.01.22},
  creationdate = {2022-01-22T00:00:00},
}

@InProceedings{Tokar2011,
  author    = {Joyce L. Tokar and F. David Jones and Paul E. Black and Chris E. Dupilka},
  booktitle = {Proceedings of the 2011 {ACM} annual international conference on Special interest group on the ada programming language - {SIGAda} {\textquotesingle}11},
  title     = {Software vulnerabilities precluded by spark},
  year      = {2011},
  pages     = {39--46},
  publisher = {{ACM} Press},
  doi       = {10.1145/2070337.2070356},
  file      = {:by-author/T/Tokar/2011_Tokar_39.pdf:PDF},
  keywords  = {Ada; Computer Science (CS); Correctness Proofs; SPARK; Software Verification},
  owner     = {saulius},
  timestamp = {2022.01.22},
  creationdate = {2022-01-22T00:00:00},
}

@InProceedings{Loseby2009,
  author    = {Chad Loseby and Peter Chapin and Carl Brandon},
  booktitle = {Proceedings of the {ACM} {SIGAda} annual international conference on Ada and related technologies - {SIGAda} {\textquotesingle}09},
  title     = {Use of {SPARK} in a resource constrained embedded system},
  year      = {2009},
  pages     = {87--90},
  publisher = {{ACM} Press},
  doi       = {10.1145/1647420.1647441},
  file      = {:by-author/L/Loseby/2009_Loseby_87.pdf:PDF},
  keywords  = {Ada; Computer Science (CS); Correctness Proofs; SPARK; Software Verification},
  owner     = {saulius},
  timestamp = {2022.01.22},
  creationdate = {2022-01-22T00:00:00},
}

@Article{Dillon1997,
  author    = {Laura K. Dillon},
  journal   = {{ACM} Transactions on Software Engineering and Methodology},
  title     = {Task dependence and termination in Ada},
  year      = {1997},
  month     = {jan},
  number    = {1},
  pages     = {80--110},
  volume    = {6},
  doi       = {10.1145/237432.237459},
  file      = {:by-author/D/Dillon/1997_Dillon_80.pdf:PDF},
  keywords  = {Ada; Computer Science (CS); Correctness Proofs; SPARK; Software Verification},
  owner     = {saulius},
  publisher = {Association for Computing Machinery ({ACM})},
  timestamp = {2022.01.22},
  creationdate = {2022-01-22T00:00:00},
}

@Article{Tubella2018,
  author    = {Andrea Aler Tubella and Alessio Guglielmi},
  journal   = {{ACM} Transactions on Computational Logic},
  title     = {Subatomic Proof Systems},
  year      = {2018},
  month     = {jan},
  number    = {1},
  pages     = {1--33},
  volume    = {19},
  doi       = {10.1145/3173544},
  file      = {:by-author/T/Tubella/2018_Tubella_1.pdf:PDF},
  keywords  = {Computer Science (CS); Correctness Proofs; Formal Proofs; Proof Systems},
  owner     = {saulius},
  publisher = {Association for Computing Machinery ({ACM})},
  timestamp = {2022.01.22},
  creationdate = {2022-01-22T00:00:00},
}

@InCollection{Maalej2018,
  author    = {Maroua Maalej and Tucker Taft and Yannick Moy},
  booktitle = {Reliable Software Technologies {\textendash} Ada-Europe 2018},
  publisher = {Springer International Publishing},
  title     = {Safe dynamic memory management in {A}da and {SPARK}},
  year      = {2018},
  pages     = {37--52},
  doi       = {10.1007/978-3-319-92432-8_3},
  file      = {:by-author/M/Maalej/2018_Maalej_37.pdf:PDF},
  keywords  = {Ada; Computer Science (CS); Correctness Proofs; Dynamic Allocation; Memory Allocation; SPARK; Software Verification},
  owner     = {saulius},
  timestamp = {2022.01.22},
  creationdate = {2022-01-22T00:00:00},
  url       = {https://www.adacore.com/uploads/techPapers/Safe-Dynamic-Memory-Management-in-Ada-and-SPARK.pdf},
}

@InProceedings{Johnson2017a,
  author    = {Clifford D. Johnson and Michael E. Miller and Christina F. Rusnock and David R. Jacques},
  booktitle = {2017 {IEEE} International Conference on Systems, Man, and Cybernetics ({SMC})},
  title     = {A framework for understanding automation in terms of levels of human control abstraction},
  year      = {2017},
  month     = {oct},
  pages     = {1145--1150},
  publisher = {{IEEE}},
  doi       = {10.1109/smc.2017.8122766},
  file      = {:by-author/J/Johnson/2017_Johnson_1145.pdf:PDF},
  keywords  = {Computer Science (CS); Huma-machine Interaction},
  owner     = {saulius},
  timestamp = {2022.01.22},
  creationdate = {2022-01-22T00:00:00},
}

@Article{Brandt2022,
  author    = {Nico Brandt and Nikolay T. Garabedian and Ephraim Schoof and Paul J. Schreiber and Philipp Zschumme and Christian Greiner and Michael Selzer},
  journal   = {Data},
  title     = {Managing {FAIR} Tribological Data Using Kadi4Mat},
  year      = {2022},
  month     = {jan},
  number    = {2},
  pages     = {15},
  volume    = {7},
  doi       = {10.3390/data7020015},
  file      = {:by-author/B/Brandt/2022_Brandt_15.pdf:PDF},
  keywords  = {Data Management; Data Science; FAIR Data; Tribology},
  owner     = {saulius},
  publisher = {{MDPI} {AG}},
  timestamp = {2022.01.26},
  creationdate = {2022-01-26T00:00:00},
}

@InBook{Shneiderman1998,
  author    = {Shneiderman, Ben},
  chapter   = {3.3},
  pages     = {99--103},
  publisher = {Addison Wesley Longman,},
  title     = {Designing the user interface: strategies for effective human-computer-interaction /},
  year      = {1998},
  address   = {Reading, Mass :},
  edition   = {3rd ed.},
  file      = {:by-author/S/Shneiderman/1998_Shneiderman_99.pdf:PDF},
  keywords  = {Computer Science (CS); Design; Human-machine Interaction; User Interface},
  owner     = {saulius},
  timestamp = {2022.01.27},
  creationdate = {2022-01-27T00:00:00},
}

@Article{Bucci1993,
  author    = {A. Bucci and P. Inverardi and S. Martini},
  journal   = {Formal Aspects of Computing},
  title     = {An "executable" impredicative semantics for the {A}da configuration},
  year      = {1993},
  month     = {mar},
  number    = {2},
  pages     = {91--120},
  volume    = {5},
  doi       = {10.1007/bf01211301},
  file      = {:by-author/B/Bucci/1993_Bucci_91.pdf:PDF},
  keywords  = {Ada; Computer Science (CS); Lambda Calculus; Program Verification; Semantics},
  owner     = {saulius},
  publisher = {Association for Computing Machinery ({ACM})},
  timestamp = {2022.01.27},
  creationdate = {2022-01-27T00:00:00},
  url       = {https://dl.acm.org/doi/pdf/10.1007/BF01211301},
}

@Article{Burns2007,
  author    = {A. Burns and T. -M. Lin},
  journal   = {Formal Aspects of Computing},
  title     = {An engineering process for the verification of real-time systems},
  year      = {2007},
  month     = {mar},
  number    = {1},
  pages     = {111--136},
  volume    = {19},
  doi       = {10.1007/s00165-006-0021-4},
  file      = {:by-author/B/Burns/2007_Burns_111.pdf:PDF},
  keywords  = {Ada; Computer Science (CS); Program Verification; SPARK; Semantics},
  owner     = {saulius},
  publisher = {Association for Computing Machinery ({ACM})},
  timestamp = {2022.01.27},
  creationdate = {2022-01-27T00:00:00},
  url       = {https://dl.acm.org/doi/pdf/10.1007/s00165-006-0021-4},
}

@Article{Wellings2000,
  author    = {A. J. Wellings and B. Johnson and B. Sanden and J. Kienzle and T. Wolf and S. Michell},
  journal   = {{ACM} Transactions on Programming Languages and Systems},
  title     = {Integrating object-oriented programming and protected objects in Ada 95},
  year      = {2000},
  month     = {may},
  number    = {3},
  pages     = {506--539},
  volume    = {22},
  doi       = {10.1145/353926.353938},
  file      = {:by-author/W/Wellings/2000_Wellings_506.pdf:PDF},
  keywords  = {Ada; Computer Science (CS); Object-oriented Programming; Program Verification; Semantics},
  owner     = {saulius},
  publisher = {Association for Computing Machinery ({ACM})},
  timestamp = {2022.01.27},
  creationdate = {2022-01-27T00:00:00},
  url       = {https://dl.acm.org/doi/pdf/10.1145/353926.353938},
}

@Article{Duri1994,
  author    = {S. Duri and U. Buy and R. Devarapalli and S. M. Shatz},
  journal   = {{ACM} Transactions on Software Engineering and Methodology},
  title     = {Application and experimental evaluation of state space reduction methods for deadlock analysis in Ada},
  year      = {1994},
  month     = {oct},
  number    = {4},
  pages     = {340--380},
  volume    = {3},
  doi       = {10.1145/201024.201038},
  file      = {:by-author/D/Duri/1994_Duri_340.pdf:PDF},
  keywords  = {Ada; Computer Science (CS); Deadlock; Petri Nets; Program Verification; Semantics},
  owner     = {saulius},
  publisher = {Association for Computing Machinery ({ACM})},
  timestamp = {2022.01.27},
  creationdate = {2022-01-27T00:00:00},
  url       = {https://dl.acm.org/doi/pdf/10.1145/201024.201038},
}

@Article{Young1995a,
  author    = {Michal Young and Richard N. Taylor and David L. Levine and Kari A. Nies and Debra Brodbeck},
  journal   = {{ACM} Transactions on Software Engineering and Methodology},
  title     = {A concurrency analysis tool suite for Ada programs},
  year      = {1995},
  month     = {jan},
  number    = {1},
  pages     = {65--106},
  volume    = {4},
  doi       = {10.1145/201055.201080},
  file      = {:by-author/Y/Young/1995_Young_65.pdf:PDF},
  keywords  = {Ada; Computer Science (CS); Program Verification; Semantics},
  owner     = {saulius},
  publisher = {Association for Computing Machinery ({ACM})},
  timestamp = {2022.01.27},
  creationdate = {2022-01-27T00:00:00},
  url       = {https://dl.acm.org/doi/pdf/10.1145/201055.201080},
}

@Article{Luckham1980,
  author    = {David C. Luckham and W. Polak},
  journal   = {{ACM} Transactions on Programming Languages and Systems},
  title     = {Ada exception handling: an axiomatic approach},
  year      = {1980},
  month     = {apr},
  number    = {2},
  pages     = {225--233},
  volume    = {2},
  doi       = {10.1145/357094.357100},
  file      = {:by-author/L/Luckham/1980_Luckham_225.pdf:PDF},
  keywords  = {Ada; Computer Science (CS); Exception Handling; Program Verification; Semantics},
  owner     = {saulius},
  publisher = {Association for Computing Machinery ({ACM})},
  timestamp = {2022.01.27},
  creationdate = {2022-01-27T00:00:00},
  url       = {https://dl.acm.org/doi/pdf/10.1145/357094.357100},
}

@Article{Hallerstede2011,
  author    = {Stefan Hallerstede},
  journal   = {Formal Aspects of Computing},
  title     = {On the purpose of Event-B proof obligations},
  year      = {2011},
  month     = {jan},
  number    = {1},
  pages     = {133--150},
  volume    = {23},
  doi       = {10.1007/s00165-009-0138-3},
  file      = {:by-author/H/Hallerstede/2011_Hallerstede_133.pdf:PDF},
  keywords  = {Computer Science (CS); Event-B; Formal Proof; Program Correctness; Proof Obligations},
  owner     = {saulius},
  publisher = {Association for Computing Machinery ({ACM})},
  timestamp = {2022.01.27},
  creationdate = {2022-01-27T00:00:00},
  url       = {https://dl.acm.org/doi/pdf/10.1007/s00165-009-0138-3},
}

@Article{Xing2007,
  author     = {Xing, Cong-Cong},
  journal    = {J. Comput. Sci. Coll.},
  title      = {Proof diagrams: a graphical tool for assisting set proofs},
  year       = {2007},
  issn       = {1937-4771},
  month      = {may},
  number     = {5},
  pages      = {70--77},
  volume     = {22},
  abstract   = {The traditional way of carrying out a set proof is to write it in English combined with set notations. This linearform description of logical reasoning can cause many difficulties in the process of learning set proofs for students with insufficient mathematics and English background. Furthermore, teaching these students to write set proofs in such a style can be a frustrating task. Toward solving this learning-teaching problem, a graphical approach for constructing set proofs is presented in this paper. We first identify some common learning difficulties of students when dealing with set proofs written in the tradition style. Then, we introduce the notion of proof diagrams and provide two examples to illustrate how a set proof can be constructed using proof diagrams. Finally, we compare our new graphical approach with the traditional one to summarize its contributions.},
  address    = {Evansville, IN, USA},
  file       = {:by-author/X/Xing/2007_Xing_70.pdf:PDF},
  issue_date = {May 2007},
  numpages   = {8},
  owner      = {saulius},
  publisher  = {Consortium for Computing Sciences in Colleges},
  timestamp = {2022.01.27},
  creationdate = {2022-01-27T00:00:00},
  url        = {https://dl.acm.org/doi/pdf/10.5555/1229688.1229699},
}

@Article{Hesselink1993,
  author    = {Wim H. Hesselink},
  journal   = {Formal Aspects of Computing},
  title     = {Proof rules for recursive procedures},
  year      = {1993},
  month     = {nov},
  number    = {6},
  pages     = {554--570},
  volume    = {5},
  doi       = {10.1007/bf01211249},
  file      = {:by-author/H/Hesselink/1993_Hesselink_554.pdf:PDF},
  keywords  = {Computer Science (CS); Formal Proofs; Proof Rule; Recursive Procedure; Software Verification; Specification; Weakest Precondition; Well-founded Relation},
  owner     = {saulius},
  publisher = {Association for Computing Machinery ({ACM})},
  timestamp = {2022.01.27},
  creationdate = {2022-01-27T00:00:00},
  url       = {https://dl.acm.org/doi/pdf/10.1007/BF01211249},
}

@Article{Riesco2018,
  author    = {Adri{\'{a}}n Riesco and Kazuhiro Ogata},
  journal   = {{ACM} Transactions on Software Engineering and Methodology},
  title     = {Prove it! Inferring Formal Proof Scripts from {CafeOBJ} Proof Scores},
  year      = {2018},
  month     = {apr},
  number    = {2},
  pages     = {1--32},
  volume    = {27},
  doi       = {10.1145/3208951},
  file      = {:by-author/R/Riesco/2018_Riesco_1.pdf:PDF},
  keywords  = {Computer Science (CS); Formal Proofs; Software Verification},
  owner     = {saulius},
  publisher = {Association for Computing Machinery ({ACM})},
  timestamp = {2022.01.27},
  creationdate = {2022-01-27T00:00:00},
  url       = {https://dl.acm.org/doi/pdf/10.1145/3208951},
}

@Article{First2020,
  author       = {Emily First and Yuriy Brun and Arjun Guha},
  journal      = {Proceedings of the {ACM} on Programming Languages},
  title        = {{TacTok}: semantics-aware proof synthesis},
  year         = {2020},
  month        = {nov},
  number       = {{OOPSLA}},
  pages        = {1--31},
  volume       = {4},
  creationdate = {2022-01-27T00:00:00},
  doi          = {10.1145/3428299},
  file         = {:by-author/F/First/2020_First_1.pdf:PDF},
  keywords     = {Automated Proofscript Synthesis; Computer Science (CS); Coq; Formal Software Verification; Proof Script Synthesis},
  owner        = {saulius},
  publisher    = {Association for Computing Machinery ({ACM})},
  timestamp    = {2022.01.27},
  url          = {https://dl.acm.org/doi/pdf/10.1145/3428299},
}

@Article{Petiot2018,
  author    = {Guillaume Petiot and Nikolai Kosmatov and Bernard Botella and Alain Giorgetti and Jacques Julliand},
  journal   = {Formal Aspects of Computing},
  title     = {How testing helps to diagnose proof failures},
  year      = {2018},
  month     = {nov},
  number    = {6},
  pages     = {629--657},
  volume    = {30},
  doi       = {10.1007/s00165-018-0456-4},
  file      = {:by-author/P/Petiot/2018_Petiot_629.pdf:PDF},
  keywords  = {Computer Science (CS); Deductive Verification; Formal Verification; Frama-C; Proof Debugging; Software Correctness Proffs; Specification; Test Generation},
  owner     = {saulius},
  publisher = {Association for Computing Machinery ({ACM})},
  timestamp = {2022.01.27},
  creationdate = {2022-01-27T00:00:00},
  url       = {https://dl.acm.org/doi/pdf/10.1007/s00165-018-0456-4},
}

@Article{WeberWulff1993,
  author    = {Debora Weber-Wulff},
  journal   = {Formal Aspects of Computing},
  title     = {Proof movie {\textemdash} a proof with the {B}oyer-{M}oore prover},
  year      = {1993},
  month     = {mar},
  number    = {2},
  pages     = {121--151},
  volume    = {5},
  doi       = {10.1007/bf01211302},
  file      = {:by-author/W/Weber-Wulff/1993_Weber-Wulff_121.pdf:PDF},
  keywords  = {Automatic Theorem Proving; Compiler Verification; Computer Science (CS); Correctness Proofs; Formal Verification; Software Verification},
  owner     = {saulius},
  publisher = {Association for Computing Machinery ({ACM})},
  timestamp = {2022.01.27},
  creationdate = {2022-01-27T00:00:00},
  url       = {https://dl.acm.org/doi/pdf/10.1007/BF01211302},
}

@Article{Hoare1971,
  author    = {C. A. R. Hoare},
  journal   = {Communications of the {ACM}},
  title     = {Proof of a program},
  year      = {1971},
  month     = {jan},
  number    = {1},
  pages     = {39--45},
  volume    = {14},
  doi       = {10.1145/362452.362489},
  file      = {:by-author/H/Hoare/1971_Hoare_39.pdf:PDF},
  keywords  = {Computer Science (CS); Correctness Proofs; Formal Verification; Program Correctness; Program Documentation; Programming Methodology; Proofs of Programs; Theory of Programming},
  owner     = {saulius},
  publisher = {Association for Computing Machinery ({ACM})},
  timestamp = {2022.01.27},
  creationdate = {2022-01-27T00:00:00},
  url       = {https://dl.acm.org/doi/pdf/10.1145/362452.362489},
}

@Article{London1970,
  author    = {Ralph L. London},
  journal   = {Communications of the {ACM}},
  title     = {Certification of algorithm 245 [M1]:treesort 3:proof of algorithms{\textemdash}a new kind of certification},
  year      = {1970},
  month     = {jun},
  number    = {6},
  pages     = {371--373},
  volume    = {13},
  doi       = {10.1145/362384.362507},
  file      = {:by-author/L/London/1970_London_371.pdf:PDF},
  keywords  = {Computer Science (CS); Correctness Proofs; Formal Verification; Program Correctness; Program Documentation; Programming Methodology; Proofs of Programs; Theory of Programming},
  owner     = {saulius},
  publisher = {Association for Computing Machinery ({ACM})},
  timestamp = {2022.01.27},
  creationdate = {2022-01-27T00:00:00},
  url       = {https://dl.acm.org/doi/pdf/10.1145/362384.362507},
}

@Article{Lamport1979,
  author    = {Leslie Lamport},
  journal   = {Communications of the {ACM}},
  title     = {On the proof of correctness of a calendar program},
  year      = {1979},
  month     = {oct},
  number    = {10},
  pages     = {554--556},
  volume    = {22},
  doi       = {10.1145/359156.359160},
  file      = {:by-author/L/Lamport/1979_Lamport_554.pdf:PDF},
  keywords  = {Computer Science (CS); Correctness Proofs; Formal Verification},
  owner     = {saulius},
  publisher = {Association for Computing Machinery ({ACM})},
  timestamp = {2022.01.27},
  creationdate = {2022-01-27T00:00:00},
  url       = {https://dl.acm.org/doi/pdf/10.1145/359156.359160},
}

@Webpage{Dross2014,
  author    = {Claire Dross},
  retrieved = {2022-01-27},
  title     = {Manual proof with ghost code in {SPARK} 2014},
  url       = {https://blog.adacore.com/manual-proof-in-spark-2014},
  year      = {2014},
  file      = {:by-author/D/Dross/2014_Dross_1.pdf:PDF;:2014_Dross_1.odt:OpenDocument text},
  keywords  = {Ada; Computer Science (CS); Correctness Proofs; Formal Verification; SPARK},
  owner     = {saulius},
  pages     = {1--7},
  timestamp = {2022.01.27},
  creationdate = {2022-01-27T00:00:00},
}

@Article{Fidge1997,
  author    = {C. J. Fidge and A. J. Wellings},
  journal   = {Formal Aspects of Computing},
  title     = {An action-based formal model for concurrent real-time systems},
  year      = {1997},
  month     = {mar},
  number    = {2},
  pages     = {175--207},
  volume    = {9},
  doi       = {10.1007/bf01211618},
  file      = {:by-author/F/Fidge/1997_Fidge_175.pdf:PDF},
  keywords  = {Action Systems; Ada 95; Computer Science (CS); Concurrency; Correctness Proofs; Formal Verification; Real-time; Z},
  owner     = {saulius},
  publisher = {Association for Computing Machinery ({ACM})},
  timestamp = {2022.01.27},
  creationdate = {2022-01-27T00:00:00},
  url       = {https://dl.acm.org/doi/pdf/10.1007/BF01211618},
}

@Article{Sitaraman2011,
  author    = {Murali Sitaraman and Bruce Adcock and Jeremy Avigad and Derek Bronish and Paolo Bucci and David Frazier and Harvey M. Friedman and Heather Harton and Wayne Heym and Jason Kirschenbaum and Joan Krone and Hampton Smith and Bruce W. Weide},
  journal   = {Formal Aspects of Computing},
  title     = {Building a push-button {RESOLVE} verifier: Progress and challenges},
  year      = {2011},
  month     = {sep},
  number    = {5},
  pages     = {607--626},
  volume    = {23},
  doi       = {10.1007/s00165-010-0154-3},
  file      = {:by-author/S/Sitaraman/2011_Sitaraman_607.pdf:PDF},
  keywords  = {Computer Science (CS); Correctness Proofs; Formal Verification},
  owner     = {saulius},
  publisher = {Association for Computing Machinery ({ACM})},
  timestamp = {2022.01.27},
  creationdate = {2022-01-27T00:00:00},
  url       = {https://dl.acm.org/doi/pdf/10.1007/s00165-010-0154-3},
}

@Article{Cavalcanti2011,
  author    = {Ana Cavalcanti and Phil Clayton and Colin O'Halloran},
  journal   = {Formal Aspects of Computing},
  title     = {From control law diagrams to Ada via Circus},
  year      = {2011},
  month     = {jul},
  number    = {4},
  pages     = {465--512},
  volume    = {23},
  doi       = {10.1007/s00165-010-0170-3},
  file      = {:by-author/C/Cavalcanti/2011_Cavalcanti_465.pdf:PDF},
  keywords  = {Computer Science (CS); Correctness Proofs; Crystal Structure Prediction (CSP); Formal Verification; Refinement; Simulink; Z},
  owner     = {saulius},
  publisher = {Association for Computing Machinery ({ACM})},
  timestamp = {2022.01.27},
  creationdate = {2022-01-27T00:00:00},
  url       = {https://dl.acm.org/doi/pdf/10.1007/s00165-010-0170-3},
}

@Article{Woodcock2009,
  author    = {Jim Woodcock and Peter Gorm Larsen and Juan Bicarregui and John Fitzgerald},
  journal   = {{ACM} Computing Surveys},
  title     = {Formal methods},
  year      = {2009},
  month     = {oct},
  number    = {4},
  pages     = {1--36},
  volume    = {41},
  doi       = {10.1145/1592434.1592436},
  file      = {:by-author/W/Woodcock/2009_Woodcock_1.pdf:PDF},
  keywords  = {Computer Science (CS); Formal Methods; Software Project Management; Software Verification},
  owner     = {saulius},
  publisher = {Association for Computing Machinery ({ACM})},
  timestamp = {2022.01.27},
  creationdate = {2022-01-27T00:00:00},
  url       = {https://dl.acm.org/doi/pdf/10.1145/1592434.1592436},
}

@Article{Clarke1996,
  author    = {Edmund M. Clarke and Jeannette M. Wing},
  journal   = {{ACM} Computing Surveys},
  title     = {Formal methods},
  year      = {1996},
  month     = {dec},
  number    = {4},
  pages     = {626--643},
  volume    = {28},
  doi       = {10.1145/242223.242257},
  file      = {:by-author/C/Clarke/1996_Clarke_626.pdf:PDF},
  keywords  = {Computer Science (CS); Formal Methods; Software Project Management; Software Verification},
  owner     = {saulius},
  publisher = {Association for Computing Machinery ({ACM})},
  timestamp = {2022.01.27},
  creationdate = {2022-01-27T00:00:00},
  url       = {https://dl.acm.org/doi/pdf/10.1145/242223.242257},
}

@Article{Chalin2007,
  author    = {Patrice Chalin},
  journal   = {Formal Aspects of Computing},
  title     = {Are the Logical Foundations of Verifying Compiler Prototypes Matching user Expectations?},
  year      = {2007},
  month     = {jun},
  number    = {2},
  pages     = {139--158},
  volume    = {19},
  doi       = {10.1007/s00165-006-0016-1},
  file      = {:by-author/C/Chalin/2007_Chalin_139.pdf:PDF},
  keywords  = {Computer Science (CS); Criticism; Formal Methods; Software Verification},
  owner     = {saulius},
  publisher = {Association for Computing Machinery ({ACM})},
  timestamp = {2022.01.27},
  creationdate = {2022-01-27T00:00:00},
  url       = {https://dl.acm.org/doi/pdf/10.1007/s00165-006-0016-1},
}

@Article{Kirchner2015,
  author    = {Florent Kirchner and Nikolai Kosmatov and Virgile Prevosto and Julien Signoles and Boris Yakobowski},
  journal   = {Formal Aspects of Computing},
  title     = {Frama-C: A software analysis perspective},
  year      = {2015},
  month     = {may},
  number    = {3},
  pages     = {573--609},
  volume    = {27},
  doi       = {10.1007/s00165-014-0326-7},
  file      = {:by-author/K/Kirchner/2015_Kirchner_573.pdf:PDF},
  keywords  = {C; Computer Science (CS); Formal Methods; Frama-C; Software Verification},
  owner     = {saulius},
  publisher = {Association for Computing Machinery ({ACM})},
  timestamp = {2022.01.27},
  creationdate = {2022-01-27T00:00:00},
  url       = {https://dl.acm.org/doi/pdf/10.1007/s00165-014-0326-7},
}

@Article{Krueger1992,
  author    = {Charles W. Krueger},
  journal   = {{ACM} Computing Surveys},
  title     = {Software reuse},
  year      = {1992},
  month     = {jun},
  number    = {2},
  pages     = {131--183},
  volume    = {24},
  doi       = {10.1145/130844.130856},
  file      = {:by-author/K/Krueger/1992_Krueger_131.pdf:PDF},
  keywords  = {Computer Science (CS); Software Engineering; Software Reuse},
  owner     = {saulius},
  publisher = {Association for Computing Machinery ({ACM})},
  timestamp = {2022.01.27},
  creationdate = {2022-01-27T00:00:00},
  url       = {https://dl.acm.org/doi/pdf/10.1145/130844.130856},
}

@Article{Hierons2009,
  author    = {Robert M. Hierons and Kirill Bogdanov and Jonathan P. Bowen and Rance Cleaveland and John Derrick and Jeremy Dick and Marian Gheorghe and Mark Harman and Kalpesh Kapoor and Paul Krause and Gerald Lüttgen and Anthony J. H. Simons and Sergiy Vilkomir and Martin R. Woodward and Hussein Zedan},
  journal   = {{ACM} Computing Surveys},
  title     = {Using formal specifications to support testing},
  year      = {2009},
  month     = {feb},
  number    = {2},
  pages     = {1--76},
  volume    = {41},
  doi       = {10.1145/1459352.1459354},
  file      = {:by-author/H/Hierons/2009_Hierons_1.pdf:PDF},
  keywords  = {Computer Science (CS); Correctness Proofs; Formal Methods; Software Testing; Software Verification},
  owner     = {saulius},
  publisher = {Association for Computing Machinery ({ACM})},
  timestamp = {2022.01.27},
  creationdate = {2022-01-27T00:00:00},
  url       = {https://dl.acm.org/doi/pdf/10.1145/1459352.1459354},
}

@Article{Clinger2020,
  author    = {William D. Clinger and Mitchell Wand},
  journal   = {Proceedings of the {ACM} on Programming Languages},
  title     = {Hygienic macro technology},
  year      = {2020},
  month     = {jun},
  number    = {{HOPL}},
  pages     = {1--110},
  volume    = {4},
  doi       = {10.1145/3386330},
  file      = {:by-author/C/Clinger/2020_Clinger_1.pdf:PDF},
  keywords  = {Computer Science (CS); List; Programming Languages; Software Correctness; Software Engineering; Software Reuse},
  owner     = {saulius},
  publisher = {Association for Computing Machinery ({ACM})},
  timestamp = {2022.01.27},
  creationdate = {2022-01-27T00:00:00},
  url       = {https://dl.acm.org/doi/pdf/10.1145/3386330},
}

@Article{Syme2020,
  author    = {Don Syme},
  journal   = {Proceedings of the {ACM} on Programming Languages},
  title     = {The early history of F{\#}},
  year      = {2020},
  month     = {jun},
  number    = {{HOPL}},
  pages     = {1--58},
  volume    = {4},
  doi       = {10.1145/3386325},
  file      = {:by-author/S/Syme/2020_Syme_1.pdf:PDF},
  keywords  = {Computer Science (CS); F#; Generic Types; Programming Languages; Strong Typing},
  owner     = {saulius},
  publisher = {Association for Computing Machinery ({ACM})},
  timestamp = {2022.01.27},
  creationdate = {2022-01-27T00:00:00},
  url       = {https://dl.acm.org/doi/pdf/10.1145/3386325},
}

@Article{Geisler2020,
  author    = {Dietrich Geisler and Irene Yoon and Aditi Kabra and Horace He and Yinnon Sanders and Adrian Sampson},
  journal   = {Proceedings of the {ACM} on Programming Languages},
  title     = {Geometry types for graphics programming},
  year      = {2020},
  month     = {nov},
  number    = {{OOPSLA}},
  pages     = {1--25},
  volume    = {4},
  doi       = {10.1145/3428241},
  file      = {:by-author/G/Geisler/2020_Geisler_1.pdf:PDF},
  keywords  = {Computer Geometry; Computer Graphics; Computer Science (CS); Programming Languages; Static Typing},
  owner     = {saulius},
  publisher = {Association for Computing Machinery ({ACM})},
  timestamp = {2022.01.27},
  creationdate = {2022-01-27T00:00:00},
  url       = {https://dl.acm.org/doi/pdf/10.1145/3428241},
}

@Article{Nguyen2014,
  author    = {Thanhvu Nguyen and Deepak Kapur and Westley Weimer and Stephanie Forrest},
  journal   = {{ACM} Transactions on Software Engineering and Methodology},
  title     = {{DIG}: a dynamic invariant generator for polynomial and array invariants},
  year      = {2014},
  month     = {sep},
  number    = {4},
  pages     = {1--30},
  volume    = {23},
  doi       = {10.1145/2556782},
  file      = {:by-author/N/Nguyen/2014_Nguyen_1.pdf:PDF},
  keywords  = {Array Invariants; Computer Science (CS); Correctness Proofs; Dynamic Analysis; Geometric Invariant Inference; Invariant Generation; Non-linear Invariants; Program Analysis; Software Verification; Theorem Proving},
  owner     = {saulius},
  publisher = {Association for Computing Machinery ({ACM})},
  timestamp = {2022.01.27},
  creationdate = {2022-01-27T00:00:00},
  url       = {https://dl.acm.org/doi/pdf/10.1145/2556782},
}

@TechReport{EEBWFA2020,
  author      = {{EOSC Executive Board WG FAIR and Architecture}},
  institution = {European Commission},
  title       = {A persistent identifier ({PID}) policy for the {E}uropean {O}pen {S}cience {C}loud},
  year        = {2020},
  month       = oct,
  doi         = {10.2777/926037},
  file        = {:by-author/E/EEBWFA/2020_EEBWFA_1.pdf:PDF},
  isbn        = {978-92-76-22780-9},
  keywords    = {Data Management; EOSC; Persistent Identifiers},
  owner       = {saulius},
  pages       = {1--20},
  timestamp = {2022.02.04},
  creationdate = {2022-02-04T00:00:00},
  url         = {https://op.europa.eu/en/publication-detail/-/publication/35c5ca10-1417-11eb-b57e-01aa75ed71a1/language-en},
}

@Webpage{Bernardeschi2017,
  author    = {Cinzia Bernardeschi},
  retrieved = {2022-02-06T09:43:32 EET},
  title     = {Redundancy in fault tolerant computing},
  url       = {http://www.iet.unipi.it/c.bernardeschi/didattica/Anno-2017-18/Redundancyv2.pdf},
  year      = {2017},
  file      = {:by-author/B/Bernardeschi/2017_Bernardeschi_1.pdf:PDF},
  keywords  = {Computer Science (CS); Dual Redundancy; Fault Tolerant Systems; Harware Redundancy; Multi-version Software; Software Redundancy; Triple Redundancy},
  owner     = {saulius},
  pages     = {1--40},
  timestamp = {2022.02.06},
  creationdate = {2022-02-06T00:00:00},
}

@Manuscript{Williams2003,
  author    = {T. J. Williams and E. J. Schaffer and T. J. Williams and A. Rohr},
  title     = {Redundant and voting systems},
  year      = {2003},
  keywords  = {Computer Science (CS); Fault-tolerant Systems; Redundancy},
  url       = {https://kishorekaruppaswamy.files.wordpress.com/2011/10/redundant-and-voting-systems.pdf},
  file      = {:by-author/W/Williams/2003_Williams_126.pdf:PDF},
  owner     = {saulius},
  pages     = {126--135},
  timestamp = {2022.02.06},
  creationdate = {2022-02-06T00:00:00},
}

@Presentation{Das2017,
  author       = {Arun Das and Steven Waslander},
  title        = {Rotations and transformations},
  year         = {2017},
  course       = {Geometry; SLAM},
  lecture      = {2},
  organization = {University of Waterloo},
  file         = {:by-author/D/Das/2017_Das_1b.pdf:PDF},
  keywords     = {Computer Science (CS); Geometry; Quaternions; Rotations},
  owner        = {saulius},
  pages        = {1--78},
  timestamp = {2022.02.11},
  creationdate = {2022-02-11T00:00:00},
  url          = {http://wavelab.uwaterloo.ca/slam/2017-SLAM/Lecture2-Geometry_part1/Session2-Geometry_part1_SLW.pdf},
}

@Article{Faber2015,
  author    = {Faber, Felix and Lindmaa, Alexander and von Lilienfeld, O. Anatole and Armiento, Rickard},
  journal   = {International Journal of Quantum Chemistry},
  title     = {Crystal structure representations for machine learning models of formation energies},
  year      = {2015},
  issn      = {1097-461X},
  month     = {Apr},
  number    = {16},
  pages     = {1094--1101},
  volume    = {115},
  comment   = {Cited in 2018_Xie_145301.},
  doi       = {10.1002/qua.24917},
  file      = {:by-author/F/Faber/2015_Faber_1094.pdf:PDF;:by-author/F/Faber/2015_Faber_1094a.pdf:PDF},
  owner     = {saulius},
  publisher = {Wiley},
  timestamp = {2022.02.13},
  creationdate = {2022-02-13T00:00:00},
  url       = {https://arxiv.org/abs/1503.07406},
}

@Article{Isayev2015,
  author    = {Isayev, Olexandr and Fourches, Denis and Muratov, Eugene N. and Oses, Corey and Rasch, Kevin and Tropsha, Alexander and Curtarolo, Stefano},
  journal   = {Chemistry of Materials},
  title     = {Materials Cartography: Representing and Mining Materials Space Using Structural and Electronic Fingerprints},
  year      = {2015},
  issn      = {1520-5002},
  month     = {Jan},
  number    = {3},
  pages     = {735--743},
  volume    = {27},
  comment   = {Cited in 2018_Xie_145301.},
  doi       = {10.1021/cm503507h},
  file      = {:by-author/I/Isayev/2015_Isayev_735.pdf:PDF},
  owner     = {saulius},
  publisher = {American Chemical Society (ACS)},
  timestamp = {2022.02.13},
  creationdate = {2022-02-13T00:00:00},
  url       = {http://dx.doi.org/10.1021/cm503507h},
}

@Article{Schuett2014,
  author    = {Schütt, K. T. and Glawe, H. and Brockherde, F. and Sanna, A. and Müller, K. R. and Gross, E. K. U.},
  journal   = {Physical Review B},
  title     = {How to represent crystal structures for machine learning: Towards fast prediction of electronic properties},
  year      = {2014},
  issn      = {1550-235X},
  month     = {May},
  number    = {20},
  pages     = {205118},
  volume    = {89},
  comment   = {Cited in 2018_Xie_145301.},
  doi       = {10.1103/physrevb.89.205118},
  file      = {:by-author/S/Schütt/2014_Schütt_205118.pdf:PDF},
  owner     = {saulius},
  publisher = {American Physical Society (APS)},
  timestamp = {2022.02.13},
  creationdate = {2022-02-13T00:00:00},
  url       = {http://dx.doi.org/10.1103/PhysRevB.89.205118},
}

@Article{Seko2017,
  author    = {Seko, Atsuto and Hayashi, Hiroyuki and Nakayama, Keita and Takahashi, Akira and Tanaka, Isao},
  journal   = {Physical Review B},
  title     = {Representation of compounds for machine-learning prediction of physical properties},
  year      = {2017},
  issn      = {2469-9969},
  month     = {Apr},
  number    = {14},
  pages     = {144110},
  volume    = {95},
  comment   = {Cited in 2018_Xie_145301.},
  doi       = {10.1103/physrevb.95.144110},
  file      = {:by-author/S/Seko/2017_Seko_144110.pdf:PDF},
  owner     = {saulius},
  publisher = {American Physical Society (APS)},
  timestamp = {2022.02.13},
  creationdate = {2022-02-13T00:00:00},
  url       = {http://dx.doi.org/10.1103/PhysRevB.95.144110},
}

@Manuscript{Liao2003,
  author    = {Sen-Ben Liao},
  title     = {Chapter 11: {I}nductance and magnetic energy},
  year      = {2003},
  keywords  = {Electodynamics; Physics; Teaching},
  url       = {http://web.mit.edu/viz/EM/visualizations/coursenotes/modules/guide11.pdf},
  file      = {:by-author/L/Liao/2003_Liao_1k.pdf:PDF},
  owner     = {saulius},
  pages     = {1--53},
  timestamp = {2022.02.13},
  creationdate = {2022-02-13T00:00:00},
}

@Article{Bento2020,
  author    = {A. Patrı́cia Bento and Anne Hersey and Eloy Félix and Greg Landrum and Anna Gaulton and Francis Atkinson and Louisa J. Bellis and Marleen De Veij and Andrew R. Leach},
  journal   = {Journal of Cheminformatics},
  title     = {An open source chemical structure curation pipeline using {RDKit}},
  year      = {2020},
  month     = {sep},
  number    = {1},
  pages     = {1--16},
  volume    = {12},
  doi       = {10.1186/s13321-020-00456-1},
  file      = {:by-author/B/Bento/2020_Bento_1.pdf:PDF},
  keywords  = {Cheminformatics; Data Curation; RDKit},
  owner     = {saulius},
  publisher = {Springer Science and Business Media {LLC}},
  timestamp = {2022.02.14},
  creationdate = {2022-02-14T00:00:00},
}

@Article{Durinx2017,
  author    = {Christine Durinx and Jo McEntyre and Ron Appel and Rolf Apweiler and Mary Barlow and Niklas Blomberg and Chuck Cook and Elisabeth Gasteiger and Jee-Hyub Kim and Rodrigo Lopez and Nicole Redaschi and Heinz Stockinger and Daniel Teixeira and Alfonso Valencia},
  journal   = {F1000Research},
  title     = {Identifying {ELIXIR} {C}ore {D}ata {R}esources [version 2; peer review: 2 approved]},
  year      = {2017},
  month     = {mar},
  pages     = {2422},
  volume    = {5},
  doi       = {10.12688/f1000research.9656.2},
  file      = {:by-author/D/Durinx/2017_Durinx_2422.pdf:PDF},
  keywords  = {Bioinformatics; Databases},
  owner     = {saulius},
  publisher = {F1000 Research Ltd},
  timestamp = {2022.02.15},
  creationdate = {2022-02-15T00:00:00},
}

@Article{Drysdale2018,
  author    = {Drysdale, Rachel and Repo, Susanna and Garcia, Pablo Roman and McEntyre, Jo and Durinx, Christine and Blomberg, Niklas},
  journal   = {F1000Research},
  title     = {Implementing a process for the selection of {C}ore {D}ata {R}esources [version 1; not peer reviewed]},
  year      = {2018},
  pages     = {1--9},
  doi       = {10.7490/F1000RESEARCH.1116247.1},
  file      = {:by-author/D/Drysdale/2018_Drysdale_1.pdf:PDF},
  keywords  = {Bioinformatics; Databases},
  owner     = {saulius},
  publisher = {F1000 Research Limited},
  timestamp = {2022.02.15},
  creationdate = {2022-02-15T00:00:00},
}

@Article{Chandonia2021,
  author    = {John-Marc Chandonia and Lindsey Guan and Shiangyi Lin and Changhua Yu and Naomi~K Fox and Steven~E Brenner},
  journal   = {Nucleic Acids Research},
  title     = {{SCOPe}: improvements to the structural classification of proteins {\textendash} extended database to facilitate variant interpretation and machine learning},
  year      = {2021},
  month     = {dec},
  number    = {D1},
  pages     = {D553--D559},
  volume    = {50},
  comment   = {Web site URL: https://scop.berkeley.edu/},
  doi       = {10.1093/nar/gkab1054},
  file      = {:by-author/C/Chandonia/2021_Chandonia_553.pdf:PDF},
  keywords  = {Bioinformatics; Protein Classification},
  owner     = {saulius},
  publisher = {Oxford University Press ({OUP})},
  timestamp = {2022.02.15},
  creationdate = {2022-02-15T00:00:00},
}

@Article{Sillitoe2021,
  author          = {Sillitoe, Ian and Bordin, Nicola and Dawson, Natalie and Waman, Vaishali P. and Ashford, Paul and Scholes, Harry M. and Pang, Camilla S. M. and Woodridge, Laurel and Rauer, Clemens and Sen, Neeladri and Abbasian, Mahnaz and Le Cornu, Sean and Lam, Su Datt and Berka, Karel and Varekova, Ivana Hutařová and Svobodova, Radka and Lees, Jon and Orengo, Christine A.},
  journal         = {Nucleic acids research},
  title           = {{CATH}: increased structural coverage of functional space.},
  year            = {2021},
  issn            = {1362-4962},
  month           = jan,
  pages           = {D266--D273},
  volume          = {49},
  abstract        = {CATH (https://www.cathdb.info) identifies domains in protein structures from wwPDB and classifies these into evolutionary superfamilies, thereby providing structural and functional annotations. There are two levels: CATH-B, a daily snapshot of the latest domain structures and superfamily assignments, and CATH+, with additional derived data, such as predicted sequence domains, and functionally coherent sequence subsets (Functional Families or FunFams). The latest CATH+ release, version 4.3, significantly increases coverage of structural and sequence data, with an addition of 65,351 fully-classified domains structures (+15%), providing 500 238 structural domains, and 151 million predicted sequence domains (+59%) assigned to 5481 superfamilies. The FunFam generation pipeline has been re-engineered to cope with the increased influx of data. Three times more sequences are captured in FunFams, with a concomitant increase in functional purity, information content and structural coverage. FunFam expansion increases the structural annotations provided for experimental GO terms (+59%). We also present CATH-FunVar web-pages displaying variations in protein sequences and their proximity to known or predicted functional sites. We present two case studies (1) putative cancer drivers and (2) SARS-CoV-2 proteins. Finally, we have improved links to and from CATH including SCOP, InterPro, Aquaria and 2DProt.},
  chemicals       = {Proteins, Viral Proteins},
  citation-subset = {IM},
  comment         = {Web site URL: https://www.cathdb.info/},
  completed       = {2021-01-25},
  country         = {England},
  doi             = {10.1093/nar/gkaa1079},
  file            = {:by-author/S/Sillitoe/2021_Sillitoe_266.pdf:PDF},
  issn-linking    = {0305-1048},
  issue           = {D1},
  keywords        = {Bioinformatics; Protein Classification},
  nlm-id          = {0411011},
  owner           = {saulius},
  pii             = {6006195},
  pmc             = {PMC7778904},
  pmid            = {33237325},
  pubmodel        = {Print},
  pubstate        = {ppublish},
  revised         = {2021-01-25},
  timestamp = {2022.02.15},
  creationdate = {2022-02-15T00:00:00},
}

@Article{Lewis2018,
  author       = {Lewis, Tony E. and Sillitoe, Ian and Dawson, Natalie and Lam, Su Datt and Clarke, Tristan and Lee, David and Orengo, Christine and Lees, Jonathan},
  journal      = {Nucleic acids research},
  title        = {{Gene3D}: Extensive prediction of globular domains in proteins (erratum).},
  year         = {2018},
  issn         = {1362-4962},
  month        = jan,
  pages        = {D1282},
  volume       = {46},
  country      = {England},
  doi          = {10.1093/nar/gkx1187},
  file         = {:by-author/L/Lewis/2018_Lewis_1282.pdf:PDF},
  issn-linking = {0305-1048},
  issue        = {D1},
  keywords     = {Bioinformatics; Protein Classification},
  nlm-id       = {0411011},
  owner        = {saulius},
  pii          = {4670953},
  pmc          = {PMC5753360},
  pmid         = {29194501},
  pubmodel     = {Print},
  pubstate     = {ppublish},
  revised      = {2020-05-11},
  timestamp = {2022.02.15},
  creationdate = {2022-02-15T00:00:00},
}

@Article{Lewis2018a,
  author       = {Lewis, Tony E. and Sillitoe, Ian and Dawson, Natalie and Lam, Su Datt and Clarke, Tristan and Lee, David and Orengo, Christine and Lees, Jonathan},
  journal      = {Nucleic acids research},
  title        = {{Gene3D}: Extensive prediction of globular domains in proteins.},
  year         = {2018},
  issn         = {1362-4962},
  month        = jan,
  pages        = {D435--D439},
  volume       = {46},
  abstract     = {Gene3D (http://gene3d.biochem.ucl.ac.uk) is a database of globular domain annotations for millions of available protein sequences. Gene3D has previously featured in the Database issue of NAR and here we report a significant update to the Gene3D database. The current release, Gene3D v16, has significantly expanded its domain coverage over the previous version and now contains over 95 million domain assignments. We also report a new method for dealing with complex domain architectures that exist in Gene3D, arising from discontinuous domains. Amongst other updates, we have added visualization tools for exploring domain annotations in the context of other sequence features and in gene families. We also provide web-pages to visualize other domain families that co-occur with a given query domain family.},
  chemicals    = {Proteins},
  completed    = {2019-08-07},
  country      = {England},
  doi          = {10.1093/nar/gkx1069},
  file         = {:by-author/L/Lewis/2018_Lewis_435.pdf:PDF},
  issn-linking = {0305-1048},
  issue        = {D1},
  keywords     = {Bioinformatics; Protein Classification},
  nlm-id       = {0411011},
  owner        = {saulius},
  pii          = {4588111},
  pmc          = {PMC5753370},
  pmid         = {29112716},
  pubmodel     = {Print},
  pubstate     = {ppublish},
  revised      = {2019-08-07},
  timestamp = {2022.02.15},
  creationdate = {2022-02-15T00:00:00},
}

@Article{Holm1997,
  author    = {L. Holm and C. Sander},
  journal   = {Nucleic Acids Research},
  title     = {{D}ali/{FSSP} classification of three-dimensional protein folds},
  year      = {1997},
  month     = {jan},
  number    = {1},
  pages     = {231--234},
  volume    = {25},
  doi       = {10.1093/nar/25.1.231},
  file      = {:by-author/H/Holm/1997_Holm_231.pdf:PDF},
  keywords  = {Bioinformatics; Protein Classification},
  owner     = {saulius},
  publisher = {Oxford University Press ({OUP})},
  timestamp = {2022.02.15},
  creationdate = {2022-02-15T00:00:00},
}

@Article{Holm1998a,
  author          = {Holm, L. and Sander, C.},
  journal         = {Nucleic acids research},
  title           = {Touring protein fold space with Dali/FSSP.},
  year            = {1998},
  issn            = {0305-1048},
  month           = jan,
  pages           = {316--319},
  volume          = {26},
  abstract        = {The FSSP database and its new supplement, the Dali Domain Dictionary, present a continuously updated classification of all known 3D protein structures. The classification is derived using an automatic structure alignment program (Dali) for the all-against-all comparison of structures in the Protein Data Bank. From the resulting enumeration of structural neighbours (which form a surprisingly continuous distribution in fold space) we derive a discrete fold classification in three steps: (i) sequence-related families are covered by a representative set of protein chains; (ii) protein chains are decomposed into structural domains based on the recurrence of structural motifs; (iii) folds are defined as tight clusters of domains in fold space. The fold classification, domain definitions and test sets for sequence-structure alignment (threading) are accessible on the web at www.embl-ebi.ac.uk/dali . The web interface provides a rich network of links between neighbours in fold space, between domains and proteins, and between structures and sequences leading, for example, to a database of explicit multiple alignments of protein families in the twilight zone of sequence similarity. The Dali/FSSP organization of protein structures provides a map of the currently known regions of the protein universe that is useful for the analysis of folding principles, for the evolutionary unification of protein families and for maximizing the information return from experimental structure determination.},
  chemicals       = {Proteins},
  citation-subset = {IM},
  completed       = {1998-02-18},
  country         = {England},
  doi             = {10.1093/nar/26.1.316},
  file            = {:by-author/H/Holm/1998_Holm_316.pdf:PDF},
  issn-linking    = {0305-1048},
  issue           = {1},
  keywords        = {Bioinformatics; Protein Classification},
  nlm-id          = {0411011},
  owner           = {saulius},
  pii             = {gkb088},
  pmc             = {PMC147193},
  pmid            = {9399863},
  pubmodel        = {Print},
  pubstate        = {ppublish},
  revised         = {2019-05-01},
  timestamp = {2022.02.15},
  creationdate = {2022-02-15T00:00:00},
}

@Article{Zemke2012,
  author    = {Fred Zemke},
  journal   = {{ACM} {SIGMOD} Record},
  title     = {What's new in {SQL}:2011},
  year      = {2012},
  month     = {apr},
  number    = {1},
  pages     = {67--73},
  volume    = {41},
  doi       = {10.1145/2206869.2206883},
  file      = {:by-author/Z/Zemke/2012_Zemke_67.pdf:PDF},
  keywords  = {Computer Science (CS); Databases; Relational Data Model; Relational Databases; SQL; Standard},
  owner     = {saulius},
  publisher = {Association for Computing Machinery ({ACM})},
  timestamp = {2022.02.17},
  creationdate = {2022-02-17T00:00:00},
}

@Presentation{Grinis2022,
  author    = {Irus Grinis},
  title     = {Catlab.jl},
  year      = {2022},
  file      = {:by-author/G/Grinis/2022_Grinis_1.pdf:PDF;:by-author/G/Grinis/2022_Grinis_1.odp:OpenDocument presentation},
  keywords  = {Category Theory; Computer Science (CS); Julia Programming Language; Mathematics},
  owner     = {saulius},
  pages     = {1--43},
  timestamp = {2022.02.18},
  creationdate = {2022-02-18T00:00:00},
  url       = {https://docs.google.com/presentation/d/1v4lu29wsz1-zmn9ihBAHw7UKhaEB_b4aayutP92hGzU/edit#slide=id.p},
}

@Book{ECDGRI2021,
  author    = {{European Commission and Directorate-General for Research and Innovation}},
  publisher = {Publications Office},
  title     = {Towards a reform of the research assessment system : scoping report},
  year      = {2021},
  doi       = {10.2777/707440},
  file      = {:by-author/E/ECDGRI/2021_ECDGRI_1.pdf:PDF},
  keywords  = {Criticism; Impact Factor (IF); Impact Factors; Publication Quality; Science Assesement},
  owner     = {saulius},
  pages     = {1--25},
  timestamp = {2022.02.20},
  creationdate = {2022-02-20T00:00:00},
}

@InProceedings{Ioannidis1988,
  author       = {Yannis E. Ioannidis and Raghu Ramakrishnan},
  booktitle    = {Proceedings of the 14th VLDB Conference},
  title        = {Efficient transitive closure algorithms},
  year         = {1988},
  address      = {Los Angeles, California},
  organization = {Computer Sciences Department, University of Wisconsin},
  pages        = {382--394},
  file         = {:by-author/I/Ioannidis/1988_Ioannidis_382.pdf:PDF},
  keywords     = {Algorithm; Computer Science (CS); Transitive Closure},
  owner        = {saulius},
  timestamp = {2022.02.21},
  creationdate = {2022-02-21T00:00:00},
  url          = {https://www.vldb.org/conf/1988/P382.PDF},
}

@Article{Han2022,
  author    = {Xueting Han and Ruixia Xie and Xutao Li and Junyi Li},
  journal   = {Life},
  title     = {{SmileGNN}: drug–drug interaction prediction based on the {SMILES} and {G}raph {N}eural {N}etwork},
  year      = {2022},
  month     = {feb},
  number    = {2},
  pages     = {319},
  volume    = {12},
  doi       = {10.3390/life12020319},
  file      = {:by-author/H/Han/2022_Han_319.pdf:PDF},
  keywords  = {Artificial Neural Networks (ANN); Chemical Property Prediction; Computer Science (CS); Graph Neural Networks (GNN); Machine Learning (ML); SMILES},
  owner     = {saulius},
  publisher = {{MDPI} {AG}},
  timestamp = {2022.02.22},
  creationdate = {2022-02-22T00:00:00},
}

@Article{Chen2019b,
  author           = {Chen, Kathleen M. and Cofer, Evan M. and Zhou, Jian and Troyanskaya, Olga G.},
  journal          = {Nature methods},
  title            = {Selene: a {PyTorch}-based deep learning library for sequence data.},
  year             = {2019},
  issn             = {1548-7105},
  month            = apr,
  number           = {4},
  pages            = {315--318},
  volume           = {16},
  abstract         = {To enable the application of deep learning in biology, we present Selene (https://selene.flatironinstitute.org/), a PyTorch-based deep learning library for fast and easy development, training, and application of deep learning model architectures for any biological sequence data. We demonstrate on DNA sequences how Selene allows researchers to easily train a published architecture on new data, develop and evaluate a new architecture, and use a trained model to answer biological questions of interest.},
  citation-subset  = {IM},
  completed        = {2019-05-29},
  country          = {United States},
  creationdate     = {2022-02-24T14:32:25},
  doi              = {10.1038/s41592-019-0360-8},
  file             = {:by-author/C/Chen/2019_Chen_315.pdf:PDF},
  issn-linking     = {1548-7091},
  issue            = {4},
  keywords         = {Algorithms; Alzheimer Disease; Area Under Curve; Computational Biology; Computer; DNA; Deep Learning (DL); Gene Library; Genomics; Humans; Metabolism; Methods; Models; Mutagenesis; Mutation; Neural Networks (NN); Normal Distribution; Programming Languages; Sequence Analysis; Software; Statistical},
  mid              = {NIHMS1522285},
  modificationdate = {2022-02-24T14:46:55},
  nlm-id           = {101215604},
  owner            = {saulius},
  pii              = {10.1038/s41592-019-0360-8},
  pmc              = {PMC7148117},
  pmid             = {30923381},
  publisher        = {Springer Science and Business Media {LLC}},
  pubmodel         = {Print-Electronic},
  pubstate         = {ppublish},
  revised          = {2020-04-14},
}

@Article{LeCun2015,
  author           = {LeCun, Yann and Bengio, Yoshua and Hinton, Geoffrey},
  journal          = {Nature},
  title            = {Deep learning.},
  year             = {2015},
  issn             = {1476-4687},
  month            = may,
  pages            = {436--444},
  volume           = {521},
  abstract         = {Deep learning allows computational models that are composed of multiple processing layers to learn representations of data with multiple levels of abstraction. These methods have dramatically improved the state-of-the-art in speech recognition, visual object recognition, object detection and many other domains such as drug discovery and genomics. Deep learning discovers intricate structure in large data sets by using the backpropagation algorithm to indicate how a machine should change its internal parameters that are used to compute the representation in each layer from the representation in the previous layer. Deep convolutional nets have brought about breakthroughs in processing images, video, speech and audio, whereas recurrent nets have shone light on sequential data such as text and speech.},
  citation-subset  = {IM},
  completed        = {2015-06-29},
  country          = {England},
  creationdate     = {2022-02-24T14:36:55},
  doi              = {10.1038/nature14539},
  file             = {:by-author/L/LeCun/2015_LeCun_436.pdf:PDF},
  issn-linking     = {0028-0836},
  issue            = {7553},
  keywords         = {Algorithms; Artificial Intelligence (AI); Computer; Computers; Language; Neural Networks (NN); Trends},
  modificationdate = {2022-02-24T14:42:36},
  nlm-id           = {0410462},
  owner            = {saulius},
  pii              = {nature14539},
  pmid             = {26017442},
  pubmodel         = {Print},
  pubstate         = {ppublish},
  revised          = {2019-12-10},
}

@Presentation{Schaper2011,
  author           = {F. Schaper},
  title            = {The {CIF} file, refinement details and validation of the structure},
  year             = {2011},
  creationdate     = {2022-03-01T00:00:00},
  file             = {:by-author/S/Schaper/2011_Schaper_1.pdf:PDF},
  keywords         = {CIF; Crystallography; Data Quality; Structure Validation},
  modificationdate = {2023-08-07T10:23:04},
  owner            = {saulius},
  pages            = {1--35},
  timestamp        = {2022.03.01},
  url              = {https://www.chemistry.mcmaster.ca/~xman/cccw17/files/CIF-file%20and%20validation.pdf},
}

@Article{Steipe2002a,
  author    = {Boris Steipe},
  journal   = {Acta Crystallographica Section A Foundations of Crystallography},
  title     = {Metric properties of the root-mean-square deviation of vector sets. Erratum},
  year      = {2002},
  month     = {aug},
  number    = {5},
  pages     = {507--507},
  volume    = {58},
  doi       = {10.1107/s0108767302012047},
  file      = {:by-author/S/Steipe/2002_Steipe_507.pdf:PDF},
  keywords  = {Algorithms; Proof; RMSD; Structure Superposition},
  owner     = {saulius},
  publisher = {International Union of Crystallography ({IUCr})},
  timestamp = {2022.03.01},
  creationdate = {2022-03-01T00:00:00},
}

@Manuscript{Liu2012c,
  author    = {Jennifer Liu},
  title     = {An extension of {Z}eeman’s "{A}n introduction to topology"},
  year      = {2012},
  keywords  = {Mathematics; Proof; Surface Triangulation; Surfaces},
  url       = {http://ccs.math.ucsb.edu/senior-thesis/JenniferLiu.pdf},
  comment   = {Įrodoma teorema, kad kiekvienas pavišius gali būti trianguliuotas. R. Krasauskas: „Įrodymas labai specifinis“.},
  file      = {:by-author/L/Liu/2012_Liu_1.pdf:PDF},
  owner     = {saulius},
  pages     = {1--22},
  timestamp = {2022.03.03},
  creationdate = {2022-03-03T00:00:00},
}

@Article{Broer2008,
  author    = {Henk W. Broer and Tasso J. Kaper and Martin Krupa},
  title     = {Geometric desingularization of a cusp singularity in slow-fast systems with applications to {Z}eeman's examples},
  year      = {2008},
  pages     = {1--47},
  doi       = {10.1007/s10884-01309322-5},
  file      = {:by-author/B/Broer/2008_Broer_1.pdf:PDF},
  keywords  = {Computational Biology; Mathematics},
  owner     = {saulius},
  timestamp = {2022.03.03},
  creationdate = {2022-03-03T00:00:00},
  url       = {https://www.researchgate.net/publication/259482299},
}

@Manuscript{Ranicki2014,
  author    = {Andrew Ranicki},
  title     = {An Introduction to Topology: The Classification theorem for Surfaces By {E}. {C}. {Z}eeman},
  year      = {2014},
  keywords  = {Mathematics; Surfaces; Topology},
  url       = {https://www.maths.ed.ac.uk/~v1ranick/surgery/zeeman.pdf},
  file      = {:by-author/R/Ranicki/2014_Ranicki_1.pdf:PDF},
  owner     = {saulius},
  pages     = {1--27},
  timestamp = {2022.03.03},
  creationdate = {2022-03-03T00:00:00},
}

@Manuscript{Putman2014,
  author    = {Andrew Putman},
  title     = {A quick proof of the classification of surfaces},
  year      = {2014},
  keywords  = {Mathematics; Proof; Surface Triangulation; Surfaces},
  url       = {https://www.math.csi.cuny.edu/abhijit/70800/surfaces/zeeman-classification.pdf},
  comment   = {This note contains a very short and elegant proof of the classification of surfaces that is due to Zeeman.},
  file      = {:by-author/P/Putman/2014_Putman_1.pdf:PDF},
  owner     = {saulius},
  pages     = {1--2},
  timestamp = {2022.03.03},
  creationdate = {2022-03-03T00:00:00},
}

@Article{Hatcher2013,
  author        = {Allen Hatcher},
  title         = {The Kirby torus trick for surfaces},
  year          = {2013},
  month         = dec,
  pages         = {1--9},
  abstract      = {This is an expository paper giving a proof of the existence and uniqueness of smooth structures (hence also PL structures) on topological surfaces. Most published proofs rely on the topological Schoenflies theorem, but here we use instead the Kirby torus trick. This has the advantage of reducing the point-set topology in the proof to practically nothing, replacing it by a few basic facts about smooth surfaces. Uniqueness of smooth structures is proved in the strong form that every homeomorphism between smooth surfaces is isotopic to a diffeomorphism.},
  archiveprefix = {arXiv},
  comment       = {Cited in Putman2014.},
  eprint        = {1312.3518},
  file          = {:by-author/H/Hatcher/2013_Hatcher_1.pdf:PDF},
  keywords      = {math.GT},
  owner         = {saulius},
  primaryclass  = {math.GT},
  timestamp = {2022.03.03},
  creationdate = {2022-03-03T00:00:00},
}

@Article{Moriwaki2018,
  author    = {Hirotomo Moriwaki and Yu-Shi Tian and Norihito Kawashita and Tatsuya Takagi},
  journal   = {Journal of Cheminformatics},
  title     = {Mordred: a molecular descriptor calculator},
  year      = {2018},
  month     = {feb},
  number    = {1},
  pages     = {4},
  volume    = {10},
  doi       = {10.1186/s13321-018-0258-y},
  file      = {:by-author/M/Moriwaki/2018_Moriwaki_4.pdf:PDF},
  keywords  = {Cheminformatics; Molecular Descriptors},
  owner     = {saulius},
  publisher = {Springer Science and Business Media {LLC}},
  timestamp = {2022.03.15},
  creationdate = {2022-03-15T00:00:00},
}

@Article{Nespolo2021,
  author    = {Nespolo, Massimo and Benahsene, Amani Hind},
  journal   = {Journal of Applied Crystallography},
  title     = {Symmetry and chirality in crystals},
  year      = {2021},
  month     = {Dec},
  number    = {6},
  pages     = {1594-1599},
  volume    = {54},
  doi       = {10.1107/S1600576721009109},
  file      = {:by-author/N/Nespolo/2021_Nespolo_1594.pdf:PDF},
  keywords  = {Chirality; Crystallography; Mathematical Crystallography; Optical Isomers; Stereoisomers},
  owner     = {saulius},
  timestamp = {2022.03.16},
  creationdate = {2022-03-16T00:00:00},
  url       = {https://doi.org/10.1107/S1600576721009109},
}

@Article{McMahon1996,
  author           = {McMahon, Brian},
  journal          = {Journal of research of the National Institute of Standards and Technology},
  title            = {The Role of Journals in Maintaining Data Integrity: Checking of Crystal Structure Data in Acta Crystallographica.},
  year             = {1996},
  issn             = {1044-677X},
  pages            = {347--355},
  volume           = {101},
  abstract         = {Quality control of the papers in its journals is a major concern of the International Union of Crystallography. Recent technological developments, not least the emergence of a standard data interchange file format, have facilitated the checking of numerical data in a paper, and its error-free transference to the printed page. Consequently, database holdings derived from IUCr journals will be of greater accuracy. Other publishers of crystallographic data may benefit from these innovations.},
  country          = {United States},
  creationdate     = {2015-10-01T00:00:00},
  doi              = {10.6028/jres.101.036},
  file             = {:by-author/M/McMahon/1996_McMahon_347.pdf:PDF},
  issn-linking     = {1044-677X},
  issue            = {3},
  keywords         = {CIF; Crystallographic Information File (CIF); Data Checking; Publishing; Quality Control},
  modificationdate = {2023-08-07T10:23:05},
  nlm-id           = {8912688},
  owner            = {antanas},
  pii              = {j3mcma},
  pmc              = {PMC4894614},
  pmid             = {27805171},
  pubmodel         = {Print},
  pubstate         = {ppublish},
  revised          = {2019-11-20},
  timestamp        = {2015.10.01},
}

@Article{Yamawaki1982,
  author    = {Michio Yamawaki and Mutsumi Hirai and Masaru Yasumoto and Masayoshi Kanno},
  journal   = {Journal of Nuclear Science and Technology},
  title     = {Mass spectrometric study of vaporization of lithium fluoride},
  year      = {1982},
  month     = {jul},
  number    = {7},
  pages     = {563--570},
  volume    = {19},
  doi       = {10.1080/18811248.1982.9734183},
  file      = {:by-author/Y/Yamawaki/1982_Yamawaki_563.pdf:PDF},
  keywords  = {Chemistry; LiF; Valence Bond Theory; Vapour Structure of Ionic Compounds},
  owner     = {saulius},
  publisher = {Informa {UK} Limited},
  timestamp = {2022.03.23},
  creationdate = {2022-03-23T00:00:00},
}

@Article{Snelson1969,
  author    = {Alan Snelson},
  journal   = {The Journal of Physical Chemistry},
  title     = {Heats of vaporization of the lithium fluoride vapor species by the matrix isolation technique},
  year      = {1969},
  month     = {jun},
  number    = {6},
  pages     = {1919--1928},
  volume    = {73},
  doi       = {10.1021/j100726a046},
  file      = {:by-author/S/Snelson/1969_Snelson_1919.pdf:PDF},
  keywords  = {Chemistry; LiF; Valence Bond Theory; Vapour Structure of Ionic Compounds},
  owner     = {saulius},
  publisher = {American Chemical Society ({ACS})},
  timestamp = {2022.03.23},
  creationdate = {2022-03-23T00:00:00},
}

@Article{Mountain2010,
  author    = {Raymond D. Mountain},
  journal   = {The Journal of Physical Chemistry B},
  title     = {Microstructure and Hydrogen Bonding in Water-Acetonitrile Mixtures},
  year      = {2010},
  month     = {dec},
  number    = {49},
  pages     = {16460--16464},
  volume    = {114},
  doi       = {10.1021/jp105272q},
  file      = {:by-author/M/Mountain/2010_Mountain_16460.pdf:PDF},
  keywords  = {Chemistry; Hydrogen Bonds; Molecular Dynamics (MD)},
  owner     = {saulius},
  publisher = {American Chemical Society ({ACS})},
  timestamp = {2022.03.29},
  creationdate = {2022-03-29T00:00:00},
}

@Article{Linkuviene2018,
  author    = {Vaida Linkuvien{\.{e}} and Asta Zubrien{\.{e}} and Elena Manakova and Vytautas Petrauskas and Lina Baranauskien{\.{e}} and Audrius Zak{\v{s}}auskas and Alexey Smirnov and Saulius Gra{\v{z}}ulis and John E. Ladbury and Daumantas Matulis},
  journal   = {Quarterly Reviews of Biophysics},
  title     = {Thermodynamic, kinetic, and structural parameterization of human carbonic anhydrase interactions toward enhanced inhibitor design},
  year      = {2018},
  pages     = {1--48},
  volume    = {51},
  doi       = {10.1017/s0033583518000082},
  file      = {:by-author/L/Linkuvienė/2018_Linkuvienė_1.pdf:PDF},
  keywords  = {Binding Parameters; Carbonic Anhydrases; Thermodinamics},
  owner     = {saulius},
  publisher = {Cambridge University Press ({CUP})},
  timestamp = {2022.03.31},
  creationdate = {2022-03-31T00:00:00},
}

@Article{Peng2022,
  author    = {Ge Peng and Carlo Lacagnina and Robert R. Downs and Anette Ganske and Hampapuram K. Ramapriyan and Ivana Iv{\'{a}}nov{\'{a}} and Lesley Wyborn and Dave Jones and Lucy Bastin and Chung-lin Shie and David F. Moroni},
  journal   = {Data Science Journal},
  title     = {Global community guidelines for documenting, sharing, and reusing quality information of individual digital datasets},
  year      = {2022},
  pages     = {8:1--20},
  volume    = {21},
  doi       = {10.5334/dsj-2022-008},
  file      = {:by-author/P/Peng/2022_Peng_8.pdf:PDF},
  keywords  = {Data Management; Data Sharing; FAIR},
  owner     = {saulius},
  publisher = {Ubiquity Press, Ltd.},
  timestamp = {2022.04.01},
  creationdate = {2022-04-01T00:00:00},
}

@Webpage{Admin2021,
  author           = {{Admin}},
  retrieved        = {2022-04-06T09:02+03:00},
  title            = {Creating overlays in {B}eamer},
  url              = {https://latex-beamer.com/tutorials/overlays/},
  language         = {English},
  month            = jul,
  siteurl          = {https://latex-beamer.com/},
  year             = {2021},
  comment          = {11. Overlay area environment
#
When we talk about changing dynamically elements of the frame, we mean that in a given area different elements may be shown in every slide. For example, you can dynamically change text using the \only command like this:
#
	% Changing text dynamically
	\only<1>{This text is shown on the first slide.}
	\only<2>{And replaced by this one on the second.}
	\only<3->{And finally set to this text for the rest of the slides.}
#
The problem with this approach is that the height of the lines may not be consistent from slide to slide, making undesired and distracting moving effects. When the text is multiple lines long, the effect becomes much more severe.
#
Beamer has a couple of environments that prevent this undesired effect. Here is an example:
#
	% Overlay area environment
	\begin{overlayarea}{area width}{area height}
	% Your content here
	\end{overlayarea}
#
Everything inside this environment will be placed in a rectangular area of the specified size, which will remain the same along all the slides of the frame, regardless of the contents it contains.},
  creationdate     = {2022-04-06T00:00:00},
  date             = {2021-07-26},
  file             = {:by-author/A/Admin/2021_Admin_overlays/Creating Overlays in Beamer - LaTeX Beamer.html:URL;:by-author/A/Admin/2021_Admin_overlays/Creating Overlays in Beamer - Page 2 of 3 - LaTeX Beamer.html:URL;:by-author/A/Admin/2021_Admin_overlays/Creating Overlays in Beamer - Page 3 of 3 - LaTeX Beamer.html:URL},
  keywords         = {Beamer; Communication of Science; LaTeX; PDF; Presentation},
  modificationdate = {2023-05-22T10:33:36},
  owner            = {saulius},
  timestamp        = {2022.04.06},
}

@Presentation{French2012,
  author           = {Benjamin French},
  title            = {An introduction to {B}eamer},
  year             = {2012},
  course           = {Biostatistics Computing Seminar},
  school           = {Department of Biostatistics and EpidemiologyUniversity of Pennsylvania School of Medicinedbe.med.upenn.edu/biostat-research/bcfrench},
  creationdate     = {2022-04-13T00:00:00},
  file             = {:by-author/F/French/2012_French_1.pdf:PDF},
  keywords         = {Beamer; Communication of Science; LaTeX; Presentation},
  modificationdate = {2023-02-15T09:30:13},
  owner            = {saulius},
  pages            = {1--27},
  timestamp        = {2022.04.13},
  url              = {https://dbe.med.upenn.edu/biostat-research/sites/files/seminar/Beamer.pdf},
}

@Article{Hanwell2017,
  author           = {Marcus D. Hanwell and Wibe A. de Jong and Christopher J. Harris},
  journal          = {Journal of Cheminformatics},
  title            = {Open chemistry: {RESTful} web {APIs}, {JSON}, {NWChem} and the modern web application},
  year             = {2017},
  month            = {oct},
  number           = {1},
  pages            = {55},
  volume           = {9},
  creationdate     = {2022-04-13T00:00:00},
  doi              = {10.1186/s13321-017-0241-z},
  file             = {:by-author/H/Hanwell/2017_Hanwell_55.pdf:PDF},
  keywords         = {API; Chemistry; File Formats; JSON; NWChem; REST},
  modificationdate = {2022-11-10T12:49:19},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media {LLC}},
  timestamp        = {2022.04.13},
}

@Article{Theisen2019,
  author    = {Kevin J. Theisen},
  journal   = {Journal of Cheminformatics},
  title     = {Programming languages in chemistry: a review of {HTML}5/{JavaScript}},
  year      = {2019},
  month     = {feb},
  number    = {1},
  pages     = {11},
  volume    = {11},
  doi       = {10.1186/s13321-019-0331-1},
  file      = {:by-author/T/Theisen/2019_Theisen_11.pdf:PDF},
  keywords  = {Chemistry; JavaScript; Programming Languages},
  owner     = {saulius},
  publisher = {Springer Science and Business Media {LLC}},
  timestamp = {2022.04.13},
  creationdate = {2022-04-13T00:00:00},
}

@Article{Dickerson1989,
  author       = {Richard E. Dickerson},
  journal      = {Journal of Biomolecular Structure and Dynamics},
  title        = {Definitions and nomenclature of nucleic acid structure parameters},
  year         = {1989},
  month        = {feb},
  number       = {4},
  pages        = {627--634},
  volume       = {6},
  comment      = {The same information was repeatedly published in EMBO J. and JMB?},
  creationdate = {2022-04-16T00:00:00},
  doi          = {10.1080/07391102.1989.10507726},
  file         = {:by-author/D/Dickerson/1989_Dickerson_627.pdf:PDF},
  keywords     = {Biochemistry; DNA Geometry; Definitions; Nucleic Acids; RNA Geometry; Roll; Structural Biology; Twist},
  owner        = {saulius},
  publisher    = {Informa {UK} Limited},
  timestamp    = {2022.04.16},
}

@Article{Gabb1996,
  author       = {H.A. Gabb and S.R. Sanghani and C.H. Robert and C. Pr{\'{e}}vost},
  journal      = {Journal of Molecular Graphics},
  title        = {Finding and visualizing nucleic acid base stacking},
  year         = {1996},
  month        = {feb},
  number       = {1},
  pages        = {6--11},
  volume       = {14},
  creationdate = {2022-04-16T00:00:00},
  doi          = {10.1016/0263-7855(95)00086-0},
  file         = {:by-author/G/Gabb/1996_Gabb_6.pdf:PDF},
  keywords     = {Biochemistry; DNA Geometry; Definitions; Nucleic Acids; RNA Geometry; Roll; Structural Biology; Twist},
  owner        = {saulius},
  publisher    = {Elsevier {BV}},
  timestamp    = {2022.04.16},
}

@Article{McLachlan1979,
  author       = {A.D. McLachlan},
  journal      = {Journal of Molecular Biology},
  title        = {Gene duplications in the structural evolution of chymotrypsin},
  year         = {1979},
  month        = {feb},
  number       = {1},
  pages        = {49--79},
  volume       = {128},
  comment      = {Cited by 1989_Lavrey_655.},
  creationdate = {2022-04-16T00:00:00},
  doi          = {10.1016/0022-2836(79)90308-5},
  file         = {:by-author/M/McLachlan/1979_McLachlan_49.pdf:PDF},
  keywords     = {Base Planes; Biochemistry; DNA Geometry; Definitions; Nucleic Acids; RNA Geometry; Roll; Structural Biology; Twist},
  owner        = {saulius},
  publisher    = {Elsevier {BV}},
  timestamp    = {2022.04.16},
}

@Article{1989a,
  journal      = {The {EMBO} Journal},
  title        = {Definitions and nomenclature of nucleic acid structure parameters.},
  year         = {1989},
  month        = {jan},
  number       = {1},
  pages        = {1--4},
  volume       = {8},
  comment      = {Same information as in Dickerson1989 ???},
  creationdate = {2022-04-16T00:00:00},
  doi          = {10.1002/j.1460-2075.1989.tb03339.x},
  file         = {:by-author/u/unknown/1989__1.pdf:PDF},
  keywords     = {Biochemistry; DNA Geometry; Definitions; Nucleic Acids; RNA Geometry; Roll; Structural Biology; Twist},
  owner        = {saulius},
  publisher    = {Wiley},
  timestamp    = {2022.04.16},
  url          = {https://www.embopress.org/doi/pdf/10.1002/j.1460-2075.1989.tb03339.x},
}

@Article{Matsumoto2002,
  author    = {Atsushi Matsumoto and Wilma K. Olson},
  journal   = {Biophysical Journal},
  title     = {Sequence-dependent motions of {DNA}: a normal mode analysis at the base-pair level},
  year      = {2002},
  month     = {jul},
  number    = {1},
  pages     = {22--41},
  volume    = {83},
  doi       = {10.1016/s0006-3495(02)75147-3},
  file      = {:by-author/M/Matsumoto/2002_Matsumoto_22.pdf:PDF},
  keywords  = {Biochemistry; Biophysics; DNA Structure; Normal Modes; RNA Structure; Software},
  owner     = {saulius},
  publisher = {Elsevier {BV}},
  timestamp = {2022.04.17},
  creationdate = {2022-04-17T00:00:00},
}

@Article{Diekmann1989,
  author       = {Stephan Diekmann},
  journal      = {Journal of Molecular Biology},
  title        = {Definitions and nomenclature of nucleic acid structure parameters},
  year         = {1989},
  month        = {feb},
  number       = {4},
  pages        = {787--791},
  volume       = {205},
  comment      = {Same information as in Dickerson1989 ???},
  creationdate = {2022-04-17T00:00:00},
  doi          = {10.1016/0022-2836(89)90324-0},
  file         = {:by-author/D/Diekmann/1989_Diekmann_787.pdf:PDF},
  keywords     = {Biochemistry; DNA Geometry; Definitions; Nucleic Acids; RNA Geometry; Roll; Structural Biology; Twist},
  owner        = {saulius},
  publisher    = {Elsevier {BV}},
  timestamp    = {2022.04.17},
}

@Article{Markley1998,
  author    = {John L Markley and Ad Bax and Yoji Arata and C.W Hilbers and Robert Kaptein and Brian D Sykes and Peter E Wright and Kurt Wüthrich},
  journal   = {Journal of Molecular Biology},
  title     = {Recommendations for the presentation of {NMR} structures of proteins and nucleic acids},
  year      = {1998},
  month     = {jul},
  number    = {5},
  pages     = {933--952},
  volume    = {280},
  doi       = {10.1006/jmbi.1998.1852},
  file      = {:by-author/M/Markley/1998_Markley_933.pdf:PDF},
  keywords  = {Amino Acids; DNA; Nomenclature; Nucleotides; Protteins; RNA},
  owner     = {saulius},
  publisher = {Elsevier {BV}},
  timestamp = {2022.04.17},
  creationdate = {2022-04-17T00:00:00},
}

@Article{Doreleijers1998,
  author    = {Jurgen F. Doreleijers and Johan A. C. Rullmann and Robert Kaptein},
  journal   = {Journal of Molecular Biology},
  title     = {Quality assessment of {NMR} structures: a statistical survey},
  year      = {1998},
  issn      = {0022-2836},
  number    = {1},
  pages     = {149-164},
  volume    = {281},
  abstract  = {A statistical analysis is reported of experimental data and coordinates of a set of 97 NMR structures deposited in the PDB. The aim is to assess the quality of these structures in relation to the amount of experimental information. Experimental restraints were analysed using the program AQUA. Many nomenclature inconsistencies between deposited restraint and coordinate files were observed. The experimental restraint files were found to contain a high proportion of redundant restraints. Procedures for analysing and correcting the inconsistencies and restraint counts are described. The analysis of NOE restraint violations (using AQUA) and of a wide variety of geometrical quality indicators (using PROCHECK-NMR and WHAT IF) provides a reference for other NMR structure determinations. The extent of NOE violations is anti-correlated with the quality of the Ramachandran map. The precision as measured by the circular variance of backbone dihedral angles, does increase with the amount of experimental data, as expected, but is sometimes overestimated. Bond lengths, bond angles and planarity of groups can deviate considerably from ideal values. Outliers appear to cluster per laboratory, indicating that the results depend on particulars of refinement protocols and/or software. We have identified a problem of atom overlap in a number of refined structures. We recommend adhering to the standard nomenclature as put forward by an IUPAC Task Group, to ensure consistency between restraints and coordinates, and to omit redundant restraints from the deposition. The results obtained from this analysis and the AQUA program are available through the World Wide Web.},
  doi       = {https://doi.org/10.1006/jmbi.1998.1808},
  file      = {:by-author/D/Doreleijers/1998_Doreleijers_149.pdf:PDF},
  keywords  = {Geometry; NMR; NOE Restraints; Protein Structures; Quality Assessment},
  owner     = {saulius},
  timestamp = {2022.04.17},
  creationdate = {2022-04-17T00:00:00},
  url       = {https://www.sciencedirect.com/science/article/pii/S0022283698918083},
}

@Article{Lu1997,
  author          = {Lu, X. J. and El Hassan, M. A. and Hunter, C. A.},
  journal         = {Journal of molecular biology},
  title           = {Structure and conformation of helical nucleic acids: analysis program ({SCHNAaP}).},
  year            = {1997},
  issn            = {0022-2836},
  month           = oct,
  pages           = {668--680},
  volume          = {273},
  abstract        = {We present a new versatile program, SCHNAaP, for the analysis of double-helical nucleic acid structures. The program uses mathematically rigorous and fully reversible procedures for calculating the structural parameters: the Cambridge University Engineering Department Helix computation Scheme (CEHS) is used to determine the local helical parameters and an analogous procedure is used to determine the global helical parameters. These parameters form a complete set that conforms to the "Cambridge Accord" on definitions and nomenclature of nucleic acid structure parameters. In addition to the two standard Watson-Crick base-pairs, the program handles mismatched base-pairs and chemically modified bases. An analysis of the sugar-phosphate backbone conformation is included. Standardized base-stacking diagrams of each dinucleotide step with reference to the mid-step triad are generated. Structures are classified as one of the four polymorphic families, A/B, Z, W or R, although W- and R-DNA (two types of hypothetical structure) have yet to be observed experimentally.},
  chemicals       = {DNA},
  citation-subset = {IM},
  comment         = {Cited by Lu2003 (2003_Lu_5108.pdf, "3DNA ...").},
  completed       = {1998-01-20},
  country         = {England},
  doi             = {10.1006/jmbi.1997.1346},
  file            = {:by-author/L/Lu/1997_Lu_668.pdf:PDF},
  issn-linking    = {0022-2836},
  issue           = {3},
  keywords        = {Base Composition; Chemistry; Classification; DNA; Mathematical Computing; Molecular Structure; Nucleic Acid Conformation; Software},
  nlm-id          = {2985088R},
  owner           = {saulius},
  pii             = {S0022-2836(97)91346-2},
  pmid            = {9356255},
  pubmodel        = {Print},
  pubstate        = {ppublish},
  revised         = {2006-11-15},
  timestamp = {2022.04.17},
  creationdate = {2022-04-17T00:00:00},
}

@Article{Hassan1995,
  author          = {el Hassan, M. A. and Calladine, C. R.},
  journal         = {Journal of molecular biology},
  title           = {The assessment of the geometry of dinucleotide steps in double-helical {DNA}; a new local calculation scheme.},
  year            = {1995},
  issn            = {0022-2836},
  month           = sep,
  pages           = {648--664},
  volume          = {251},
  abstract        = {In this paper, we develop a new local Euler-angle-based scheme for assessing the internal kinematics or geometry of a general dinucleotide step in double-helical DNA. The geometry of a dinucleotide step is completely defined by: (1) the base-pair parameters that describe the relative position and orientation of one base with respect to the other in a standard Watson-Crick base-pair, and (2) the step parameters that describe the relative position and orientation of the two base-pairs. The key feature of our scheme is that it makes use of the concept of a mid-step reference frame. In addition to ensuring that identical values of step parameters are obtained irrespective of the direction of reckoning of a dinucleotide step (in the 5'-->3' direction along either strand), this mid-step-triad concept leads to local definitions of the step parameters that render them independent of the overall global conformation of the oligomer in question. In addition to presenting our own calculation scheme we also examine critically the most widely used package for the calculation of some of the step and base-pair parameters, viz, the NEWHELIX suite of programmes by R.E. Dickerson. Finally, a dodecamer, a decamer and an octamer are arbitrarily selected from a public data-base (N.D.B at Rutgers), and their step parameters are calculated by using both NEWHELIX and the proposed scheme. A comparison of the results is given whereby it is shown that for the step parameters: Helical Twist and Slide, and the base-pair parameters Propeller and Buckle, NEWHELIX and our proposed scheme give rather similar values. Substantial differences are seen, however, in the case of Rise. Two alternative definitions are given by NEWHELIX for the calculation of Roll and Tilt. Whereas one definition agrees well with our proposed scheme, the other is substantially different.},
  chemicals       = {Oligodeoxyribonucleotides, DNA},
  citation-subset = {IM},
  comment         = {Cited by Lu1997 (1997_Lu_668.pdf, "... (SCHNAaP)").},
  completed       = {1995-10-06},
  country         = {England},
  creationdate    = {2022-04-17T00:00:00},
  doi             = {10.1006/jmbi.1995.0462},
  file            = {:by-author/H/Hassan/1995_Hassan_648.pdf:PDF},
  issn-linking    = {0022-2836},
  issue           = {5},
  keywords        = {Base Composition; Base Sequence; Chemistry; DNA; Mathematics; Molecular Sequence Data; Nucleic Acid Conformation; Oligodeoxyribonucleotides; Software},
  nlm-id          = {2985088R},
  owner           = {saulius},
  pii             = {S0022-2836(85)70462-7},
  pmid            = {7666417},
  pubmodel        = {Print},
  pubstate        = {ppublish},
  revised         = {2006-11-15},
  timestamp       = {2022.04.17},
}

@Article{Meng2020,
  author          = {Meng, Zhenyu and Anand, D. Vijay and Lu, Yunpeng and Wu, Jie and Xia, Kelin},
  journal         = {Scientific reports},
  title           = {Weighted persistent homology for biomolecular data analysis.},
  year            = {2020},
  issn            = {2045-2322},
  month           = feb,
  pages           = {2079},
  volume          = {10},
  abstract        = {In this paper, we systematically review weighted persistent homology (WPH) models and their applications in biomolecular data analysis. Essentially, the weight value, which reflects physical, chemical and biological properties, can be assigned to vertices (atom centers), edges (bonds), or higher order simplexes (cluster of atoms), depending on the biomolecular structure, function, and dynamics properties. Further, we propose the first localized weighted persistent homology (LWPH). Inspired by the great success of element specific persistent homology (ESPH), we do not treat biomolecules as an inseparable system like all previous weighted models, instead we decompose them into a series of local domains, which may be overlapped with each other. The general persistent homology or weighted persistent homology analysis is then applied on each of these local domains. In this way, functional properties, that are embedded in local structures, can be revealed. Our model has been applied to systematically study DNA structures. It has been found that our LWPH based features can be used to successfully discriminate the A-, B-, and Z-types of DNA. More importantly, our LWPH based principal component analysis (PCA) model can identify two configurational states of DNA structures in ion liquid environment, which can be revealed only by the complicated helical coordinate system. The great consistence with the helical-coordinate model demonstrates that our model captures local structure variations so well that it is comparable with geometric models. Moreover, geometric measurements are usually defined in local regions. For instance, the helical-coordinate system is limited to one or two basepairs. However, our LWPH can quantitatively characterize structure information in regions or domains with arbitrary sizes and shapes, where traditional geometrical measurements fail.},
  citation-subset = {IM},
  completed       = {2020-07-22},
  country         = {England},
  doi             = {10.1038/s41598-019-55660-3},
  file            = {:by-author/M/Meng/2020_Meng_2079.pdf:PDF},
  issn-linking    = {2045-2322},
  issue           = {1},
  keywords        = {Biochemistry; DNA; Persistent Homology; Structural Biology},
  nlm-id          = {101563288},
  owner           = {saulius},
  pii             = {10.1038/s41598-019-55660-3},
  pmc             = {PMC7005716},
  pmid            = {32034168},
  pubmodel        = {Electronic},
  pubstate        = {epublish},
  revised         = {2021-02-06},
  timestamp = {2022.04.17},
  creationdate = {2022-04-17T00:00:00},
}

@Article{Lu1999,
  author    = {Xiang-Jun Lu and Maria S. Babcock and Wilma K. Olson},
  journal   = {Journal of Biomolecular Structure and Dynamics},
  title     = {Overview of Nucleic Acid Analysis Programs},
  year      = {1999},
  month     = {feb},
  number    = {4},
  pages     = {833--843},
  volume    = {16},
  doi       = {10.1080/07391102.1999.10508296},
  file      = {:by-author/L/Lu/1999_Lu_833.pdf:PDF},
  keywords  = {Base Composition; Chemistry; Classification; DNA; Mathematical Computing; Molecular Structure; Nucleic Acid Conformation; Software},
  owner     = {saulius},
  publisher = {Informa {UK} Limited},
  timestamp = {2022.04.17},
  creationdate = {2022-04-17T00:00:00},
}

@Article{Peckham2011,
  author          = {Peckham, Heather E. and Olson, Wilma K.},
  journal         = {Biopolymers},
  title           = {Nucleic-acid structural deformability deduced from anisotropic displacement parameters.},
  year            = {2011},
  issn            = {0006-3525},
  month           = apr,
  pages           = {254--269},
  volume          = {95},
  abstract        = {The growing numbers of very well resolved nucleic-acid crystal structures with anisotropic displacement parameters provide an unprecedented opportunity to learn about the natural motions of DNA and RNA. Here we report a new Monte-Carlo approach that takes direct account of this information to extract the distortions of covalent structure, base pairing, and dinucleotide geometry intrinsic to regularly organized double-helical molecules. We present new methods to test the validity of the anisotropic parameters and examine the apparent deformability of a variety of structures, including several A, B, and Z DNA duplexes, an AB helical intermediate, an RNA, a ligand-DNA complex, and an enzyme-bound DNA. The rigid-body parameters characterizing the positions of the bases in the structures mirror the mean parameters found when atomic motion is taken into account. The base-pair fluctuations intrinsic to a single structure, however, differ from those extracted from collections of nucleic-acid structures, although selected base-pair steps undergo conformational excursions along routes suggested by the ensembles. The computations reveal surprising new molecular insights, such as the stiffening of DNA and concomitant separation of motions of contacted nucleotides on opposite strands by the binding of Escherichia coli endonuclease VIII, which suggest how the protein may direct enzymatic action.},
  chemicals       = {DNA, A-Form, DNA, Z-Form, DNA-Binding Proteins, Nucleotides, RNA, DNA},
  citation-subset = {IM},
  completed       = {2011-05-12},
  country         = {United States},
  creationdate    = {2022-04-17T00:00:00},
  doi             = {10.1002/bip.21570},
  file            = {:by-author/P/Peckham/2011_Peckham_254.pdf:PDF},
  issn-linking    = {0006-3525},
  issue           = {4},
  keywords        = {A-Form; Anisotropy; Base Pairing; Chemistry; Computer Simulation; DNA; DNA-Binding Proteins; Models; Molecular; Motion; Nucleic Acid Conformation; Nucleotides; Protein Binding; RNA; Z-Form},
  mid             = {NIHMS254759},
  nlm-id          = {0372525},
  owner           = {saulius},
  pmc             = {PMC4163913},
  pmid            = {21280021},
  pubmodel        = {Print-Electronic},
  pubstate        = {ppublish},
  revised         = {2021-10-20},
  timestamp       = {2022.04.17},
}

@Article{Drew1981,
  author          = {Drew, H. R. and Wing, R. M. and Takano, T. and Broka, C. and Tanaka, S. and Itakura, K. and Dickerson, R. E.},
  journal         = {Proceedings of the National Academy of Sciences of the United States of America},
  title           = {Structure of a B-DNA dodecamer: conformation and dynamics.},
  year            = {1981},
  issn            = {0027-8424},
  month           = apr,
  pages           = {2179--2183},
  volume          = {78},
  abstract        = {The crystal structure of the synthetic DNA dodecamer d(CpGpCpGpApApTpTpCpGpCpG) has been refined to a residual error of R = 17.8% at 1.9-A resolution (two-sigma data). The molecule forms slightly more than one complete turn of right-handed double-stranded B helix. The two ends of the helix overlap and interlock minor grooves with neighboring molecules up and down a 2(1) screw axis, producing a 19 degrees bend in helix axis over the 11-base-pair steps of the dodecamer. In the center of the molecule, where perturbation is least, the helix has a mean rotation of 36.9 degrees per step, or 9.8 base pairs per turn. The mean propeller twist (total dihedral angle between base planes) between A . T base pairs in the center of the molecule is 17.3 degrees, and that between C . G pairs on the two ends averages 11.5 degrees. Individual deoxyribose ring conformations as measured by the C5'-C4'-C3'-O3' torsion angle delta, exhibit an approximately Gaussian distribution centered around the C1'-exo position with delta avg = 123 degrees and a range of 79 degrees to 157 degrees. Purine sugars cluster at high delta values, and pyrimidine sugars cluster at lower delta. A tendency toward 2-fold symmetry in sugar conformation about the center of the molecule is detectable in spite of the destruction of ideal 2-fold symmetry by the molecular bending. More strikingly, sugar conformations of paired based appear to follow a "principle of anticorrelation," with delta values lying approximately the same distance to either side of the center value, delta = 123 degrees. This same anticorrelation is also observed in other DNA and DNA . RNA structures.},
  chemicals       = {Oligodeoxyribonucleotides, Oligonucleotides, Deoxyribose},
  citation-subset = {IM},
  completed       = {1981-08-20},
  country         = {United States},
  doi             = {10.1073/pnas.78.4.2179},
  file            = {:by-author/D/Drew/1981_Drew_2179.pdf:PDF},
  issn-linking    = {0027-8424},
  issue           = {4},
  keywords        = {Crystal Structure; Deoxyribose; Models; Molecular; Motion; Nucleic Acid Conformation; Oligodeoxyribonucleotides; Oligonucleotides; X-ray Crystallography},
  nlm-id          = {7505876},
  owner           = {saulius},
  pmc             = {PMC319307},
  pmid            = {6941276},
  pubmodel        = {Print},
  pubstate        = {ppublish},
  revised         = {2019-05-01},
  timestamp = {2022.04.17},
  creationdate = {2022-04-17T00:00:00},
}

@Article{Srinivasan1990,
  author          = {Srinivasan, J. and Withka, J. M. and Beveridge, D. L.},
  journal         = {Biophysical journal},
  title           = {Molecular dynamics of an in vacuo model of duplex d({CGCGAATTCGCG}) in the {B}-form based on the amber 3.0 force field.},
  year            = {1990},
  issn            = {0006-3495},
  month           = aug,
  pages           = {533--547},
  volume          = {58},
  abstract        = {The characteristics of 100 ps of molecular dynamics (MD) on the DNA dodecamer d(CGCGAATTCGCG) at 300 K are described and investigated. The simulation is based on an in vacuo model of the oligomer and the AMBER 3.0 force field configured in the manner of Singh, U. C., S. J. Weiner, and P. A. Kollman, (1985, Proc. Natl. Acad. Sci. USA. 82:755-759). The analysis of the results was carried out using the "curves, dials, and windows" procedure (Ravishanker, G., S. Swaminathan, D. L. Beveridge, R. Lavery, and H. Sklenar. 1989. J. Biomol. Struct. Dyn. 6:669-699). The results indicate this dynamical model to be a provisionally stable double helix which lies at approximately 3.2 A rms deviation from the canonical B-form. There is, however, a persistent nonplanarity in the base pair orientations which resemble that observed in canonical A-DNA. The major groove width is seen to narrow during the course of the simulation and the minor groove expands, contravariant to the alterations in groove width seen in the crystal structure of the native dodecamer (Drew, H. R., R. M. Wing, T. Takano, C. Broka, S. Tanaka, I. Itakura, and R. E. Dickerson, 1981. Proc. Natl. Acad. Sci. USA. 78:2179-2183). The propeller twist in the bases, the sequence dependence of the base pair roll and aspects of bending in the helix axis are in some degree of agreement with the crystal structure. The patterns in DNA bending are observed to follow Zhurkin theory (Zhurkin, V. B. 1985. J. Biomol. Struct. Dyn. 2:785-804.). The relationship between the dynamical model and structure in solution is discussed.},
  chemicals       = {Oligodeoxyribonucleotides, DNA},
  citation-subset = {IM},
  completed       = {1990-10-31},
  country         = {United States},
  doi             = {10.1016/S0006-3495(90)82397-3},
  file            = {:by-author/S/Srinivasan/1990_Srinivasan_533.pdf:PDF},
  issn-linking    = {0006-3495},
  issue           = {2},
  keywords        = {Base Composition; Base Sequence; DNA; Hydrogen Bonding; Models; Molecular; Molecular Sequence Data; Nucleic Acid Conformation; Oligodeoxyribonucleotides},
  nlm-id          = {0370626},
  owner           = {saulius},
  pii             = {S0006-3495(90)82397-3},
  pmc             = {PMC1280992},
  pmid            = {2207251},
  pubmodel        = {Print},
  pubstate        = {ppublish},
  revised         = {2018-11-13},
  timestamp = {2022.04.17},
  creationdate = {2022-04-17T00:00:00},
}

@Article{Zhurkin1985,
  author          = {Zhurkin, V. B.},
  journal         = {Journal of biomolecular structure & dynamics},
  title           = {Sequence-dependent bending of {DNA} and phasing of nucleosomes.},
  year            = {1985},
  issn            = {0739-1102},
  month           = feb,
  pages           = {785--804},
  volume          = {2},
  abstract        = {Conformational analysis has revealed anisotropic flexibility of the B-DNA double helix: it bends most easily into the grooves, being the most rigid when bent in a perpendicular direction. This result implies that DNA in a nucleosome is curved by means of relatively sharp bends ("mini-kinks") which are directed into the major and minor grooves alternatively and separated by 5-6 base pairs. The "mini-kink" model proved to be in keeping with the x-ray structure of the B-DNA dodecamer resolved later, which exhibits two "annealed kinks", also directed into the grooves. The anisotropy of B DNA is sequence-dependent: the pyrimidine-purine dimers (YR) favor bending into the minor groove, and the purine-pyrimidine dinucleotides (RY), into the minor one. The RR and YY dimers appear to be the most rigid dinucleotides. Thus, a DNA fragment consisting of the interchanging oligopurine and oligopyrimidine blocks 5-6 base pairs long should manifest a spectacular curvature in solution. Similarly, a nucleotide sequence containing the RY and YR dimers separated by a half-pitch of the double helix is the most suitable for wrapping around the nucleosomal core. Analysis of the numerous examples demonstrating the specific alignment of nucleosomes on DNA confirms this concept. So, the sequence-dependent "mechanical" properties of the double helix influence the spatial arrangement of DNA in chromatin.},
  chemicals       = {Heat-Shock Proteins, Nucleosomes, DNA},
  citation-subset = {IM},
  comment         = {Cited in Srinivasan1990.},
  completed       = {1990-03-20},
  country         = {England},
  creationdate    = {2022-04-17T00:00:00},
  doi             = {10.1080/07391102.1985.10506324},
  file            = {:by-author/Z/Zhurkin/1985_Zhurkin_785.pdf:PDF},
  issn-linking    = {0739-1102},
  issue           = {4},
  keywords        = {Animals; Base Sequence; DNA; Drosophila; Genetics; Heat-Shock Proteins; Models; Molecular; Nucleic Acid Conformation; Nucleosomes},
  nlm-id          = {8404176},
  owner           = {saulius},
  pmid            = {3917119},
  pubmodel        = {Print},
  pubstate        = {ppublish},
  revised         = {2003-11-14},
  timestamp       = {2022.04.17},
}

@Article{Babcock1994,
  author          = {Babcock, M. S. and Olson, W. K.},
  journal         = {Journal of molecular biology},
  title           = {The effect of mathematics and coordinate system on comparability and "dependencies" of nucleic acid structure parameters.},
  year            = {1994},
  issn            = {0022-2836},
  month           = mar,
  pages           = {98--124},
  volume          = {237},
  abstract        = {This paper critically examines the methodologies used to analyze nucleic acid three-dimensional structure based on guidelines set at a 1988 EMBO workshop. The implications of these analyses cannot be fully understood without a thorough knowledge of how the numbers are calculated. This paper addresses one aspect of the calculations, namely the observed correlations between various parameters. These correlations are addressed in the mathematics by explicitly incorporating the concept of a pivot point, which is the point about which a base rotates as it buckles, propeller twists and opens. Pivot points enable one to model the physical motion of bases more accurately. As a result, they greatly reduce and/or eliminate the statistical correlations between rotational and translational parameters found in other approaches. The correlations that are reduced or eliminated are actually artifacts of the mathematics employed and do not reflect true structural properties of nucleic acids. The mathematics we have developed, including the mathematics of pivot points, are presented in the companion paper. Here, we explain how some of the observed correlations occur as a by-product of the method of calculation, while others are truly structural, and we show how optimum pivot points can be determined to minimize artifactual correlations. The observation that experimental bases often rotate about the long axis in a "propeller" motion as well as rotate about the Z-axis of each base, "opening" into the major groove, is evident in the location of the optimum region for the pivot point as determined in this study. We consider locating a pivot point as a calibration step to increase the agreement between physical intuition and the mathematics of our program.},
  chemicals       = {DNA},
  citation-subset = {IM},
  comment         = {Critically cited by Hassan1995. Cited in Lu1997 (1997_Lu_668.pdf, "... (SCHNAaP)").},
  completed       = {1994-04-18},
  country         = {England},
  doi             = {10.1006/jmbi.1994.1212},
  file            = {:by-author/B/Babcock/1994_Babcock_98.pdf:PDF},
  issn-linking    = {0022-2836},
  issue           = {1},
  keywords        = {Base Sequence; Chemical; Chemistry; DNA; Mathematical Computing; Mathematics; Models; Molecular Sequence Data; Nucleic Acid Conformation; Rotation; Software},
  nlm-id          = {2985088R},
  owner           = {saulius},
  pii             = {S0022-2836(84)71212-5},
  pmid            = {8133524},
  pubmodel        = {Print},
  pubstate        = {ppublish},
  revised         = {2007-11-14},
  timestamp = {2022.04.17},
  creationdate = {2022-04-17T00:00:00},
}

@Article{Babcock1994a,
  author          = {Babcock, M. S. and Pednault, E. P. and Olson, W. K.},
  journal         = {Journal of molecular biology},
  title           = {Nucleic acid structure analysis. Mathematics for local Cartesian and helical structure parameters that are truly comparable between structures.},
  year            = {1994},
  issn            = {0022-2836},
  month           = mar,
  pages           = {125--156},
  volume          = {237},
  abstract        = {Analyzing nucleic acid structures in a comparable manner has become increasingly important as the number of solved structures has increased. This paper presents the concepts, mathematics, theorems, and proofs that form the basis of a new program to analyze three-dimensional DNA and RNA structures. The approach taken here provides numerical data in accordance with guidelines set at a 1988 EMBO workshop. Mathematical definitions are provided for all local structural parameters described in the guidelines. The definitions satisfy the guideline requirements while preserving the original physical intuition of the parameters. In particular, the rotational parameters are true rotations based on a simple physical model (net rotation at constant angular velocity), not Euler angles or angles between vectors and planes as is the case with other approaches. As a result, the mathematical definitions are symmetrical with the property that a 5 degrees tilt is the same as a 5 degrees roll and a 5 degrees twist, except that the rotations take place about different axes. In other approaches, a 5 degrees tilt can mean a different amount of net rotation than a 5 degrees roll or a 5 degrees twist. A second unique feature of the mathematics is that it explicitly incorporates the concept of a pivot point, which is the point about which a base in a base-pair rotates as it buckles, propeller twists, and opens. Pivot points enable one to model the physical motion of bases more accurately. As a result, they greatly reduce and/or eliminate the statistical correlations between rotational and translational parameters that arise as mathematically induced artifacts in other approaches. This paper, together with the statistical analysis in the companion paper for determining the locations of the pivot points, provides everything needed to understand the output of the program as it relates to individual structures.},
  chemicals       = {DNA},
  citation-subset = {IM},
  comment         = {Critically cited by Hassan1995. Cited in Lu1997 (1997_Lu_668.pdf, "... (SCHNAaP)").},
  completed       = {1994-04-18},
  country         = {England},
  creationdate    = {2022-04-17T00:00:00},
  doi             = {10.1006/jmbi.1994.1213},
  file            = {:by-author/B/Babcock/1994_Babcock_125.pdf:PDF},
  issn-linking    = {0022-2836},
  issue           = {1},
  keywords        = {Base Composition; Base Sequence; Chemical; Chemistry; DNA; Mathematics; Models; Molecular; Molecular Sequence Data; Nucleic Acid Conformation; Rotation},
  nlm-id          = {2985088R},
  owner           = {saulius},
  pii             = {S0022-2836(84)71213-7},
  pmid            = {8133513},
  pubmodel        = {Print},
  pubstate        = {ppublish},
  revised         = {2007-11-14},
  timestamp       = {2022.04.17},
}

@Article{Mazur1995,
  author          = {Mazur, J. and Jernigan, R. L.},
  journal         = {Biophysical journal},
  title           = {Comparison of rotation models for describing DNA conformations: application to static and polymorphic forms.},
  year            = {1995},
  issn            = {0006-3495},
  month           = apr,
  pages           = {1472--1489},
  volume          = {68},
  abstract        = {A new method, based on a space-fixed rotation axis, or local helix axis, is proposed for the calculation of the relative orientation variables for a sequence of base pairs. With this method, orientation variables are determined through the rotation of a base pair about this axis. These variables uniquely determine a set of helical variables, similar to the roll, tilt, and twist, commonly used for a description of spatial orientations of internally rigid base pairs. The proposed identification of roll and tilt with the direction cosines of the space-fixed rotation axis agrees well with their customary definitions as the openings of the angles between adjoining base pairs toward the minor groove and toward the ascending (5' to 3') backbone strand, respectively. These new variables permit a more direct physical comprehension of DNA conformations and also the behavior of self-complementary sequences. These direction cosines, together with the rotation angle about the space-fixed axis, form a set of three independent orientation variables of the bases that afford some advantages over the variously defined twist, roll, and tilt angles, either for static or average forms. An example for the static form of these variables is shown through their use to interpret crystal coordinates. An example for the average of orientation variables is based on statistical calculations. In this example, the orientation variables, together with the translational variables that describe the relative displacements of a pair of adjacent base pairs, form a canonically distributed ensemble in phase space spanned by these variables. Two sets of conformational variables are generated by using two different methods for performing rotation operations on the sequences of base pairs. The first method is based on the new single rotation about a space-fixed axis of rotation. This space-fixed axis of rotation is, in fact, the local helical axis as constructed previously by others. The second method is based on three consecutive rotations by Euler angles. Because of large flexibilities and anisotropies along various conformational variables of DNA base pairs, the two sets of generated conformational variables, based on these two different methods of performing rotation operations, lead to slightly different sets of structurally different, but energetically equivalent, spatial arrangements of the base pairs.},
  chemicals       = {DNA},
  citation-subset = {IM},
  comment         = {Cited in Lu1997 (1997_Lu_668.pdf, "... (SCHNAaP)").},
  completed       = {1995-07-24},
  country         = {United States},
  creationdate    = {2022-04-17T00:00:00},
  doi             = {10.1016/S0006-3495(95)80320-6},
  file            = {:by-author/M/Mazur/1995_Mazur_1472.pdf:PDF},
  issn-linking    = {0006-3495},
  issue           = {4},
  keywords        = {Base Composition; Base Sequence; Biophysical Phenomena; Biophysics; Chemical; Chemistry; DNA; Mathematics; Models; Molecular; Molecular Sequence Data; Nucleic Acid Conformation; Rotation; Thermodynamics},
  nlm-id          = {0370626},
  owner           = {saulius},
  pii             = {S0006-3495(95)80320-6},
  pmc             = {PMC1282042},
  pmid            = {7787033},
  pubmodel        = {Print},
  pubstate        = {ppublish},
  revised         = {2018-11-13},
  timestamp       = {2022.04.17},
}

@Article{Bansal1995,
  author          = {Bansal, M. and Bhattacharyya, D. and Ravi, B.},
  journal         = {Computer applications in the biosciences : CABIOS},
  title           = {{NUPARM} and {NUCGEN}: software for analysis and generation of sequence dependent nucleic acid structures.},
  year            = {1995},
  issn            = {0266-7061},
  month           = jun,
  pages           = {281--287},
  volume          = {11},
  abstract        = {Software packages NUPARM and NUCGEN, are described, which can be used to understand sequence directed structural variations in nucleic acids, by analysis and generation of non-uniform structures. A set of local inter basepair parameters (viz. tilt, roll, twist, shift, slide and rise) have been defined, which use geometry and coordinates of two successive basepairs only and can be used to generate polymeric structures with varying geometries for each of the 16 possible dinucleotide steps. Intra basepair parameters, propeller, buckle, opening and the C6...C8 distance can also be varied, if required, while the sugar phosphate backbone atoms are fixed in some standard conformation in each of the nucleotides. NUPARM can be used to analyse both DNA and RNA structures, with single as well as double stranded helices. The NUCGEN software generates double helical models with the backbone fixed in B-form DNA, but with appropriate modifications in the input data, it can also generate A-form DNA and RNA duplex structures.},
  chemicals       = {RNA, DNA},
  citation-subset = {IM},
  comment         = {Cited in Lu1997 (1997_Lu_668.pdf, "... (SCHNAaP)").},
  completed       = {1995-12-15},
  country         = {England},
  creationdate    = {2022-04-17T00:00:00},
  doi             = {10.1093/bioinformatics/11.3.281},
  file            = {:by-author/B/Bansal/1995_Bansal_281.pdf:PDF},
  issn-linking    = {0266-7061},
  issue           = {3},
  keywords        = {Base Composition; Base Sequence; Chemistry; DNA; Genetics; Models; Molecular; Molecular Sequence Data; Molecular Structure; Nucleic Acid Conformation; RNA; Software},
  nlm-id          = {8511758},
  owner           = {saulius},
  pmid            = {7583696},
  pubmodel        = {Print},
  pubstate        = {ppublish},
  revised         = {2019-10-23},
  timestamp       = {2022.04.17},
}

@Article{Jursa1994,
  author          = {Jursa, J.},
  journal         = {Computer applications in the biosciences : CABIOS},
  title           = {DNA modeller: an interactive program for modelling stacks of DNA base pairs on a microcomputer.},
  year            = {1994},
  issn            = {0266-7061},
  month           = feb,
  pages           = {61--65},
  volume          = {10},
  abstract        = {DNA Modeller is a microcomputer program for interactively manipulating up to 20 bp in a DNA double helical arrangement. It calculates the van der Waals and electrostatic energies of base-base interactions using the AMBER potential, minimizes the energy with respect to the pair (buckle, propeller, opening, shear, stretch, stagger) and step (tilt, roll, twist, shift, slide, rise) parameters, calculates lengths of the canonical hydrogen bonds between the complementary bases, and calculates interatomic distances between the successive base pairs. Input/output files are simple lists of the step and pair parameters or lists of the atom specifications (N1, C2, etc.) and their Cartesian coordinates (compatible with the Desktop Molecular Modeller*.mol files). The program is supplied with a readbrk utility which transforms PDB/NDB to the *.mol format readable by DNA Modeller. The DNA crystal structures deposited in the PDB or NDB databases can thus be analyzed, and their bases visualized and interactively manipulated. In addition, DNA Modeller can calculate the base pair and step geometrical parameters and interaction energies. A plotter utility creates wire mono or stereo pictures of the bases. This program is designed for IBM-compatible computers working under DOS or can run as a DOS application under MS Windows 3.x or Merge (SCO Unix DOS emulator).},
  chemicals       = {DNA},
  citation-subset = {IM},
  comment         = {Cited in Lu1997 (1997_Lu_668.pdf, "... (SCHNAaP)").},
  completed       = {1994-06-30},
  country         = {England},
  doi             = {10.1093/bioinformatics/10.1.61},
  file            = {:by-author/J/Jursa/1994_Jursa_61.pdf:PDF},
  issn-linking    = {0266-7061},
  issue           = {1},
  keywords        = {Base Composition; Chemistry; DNA; Evaluation Studies as Topic; Genetics; Models; Molecular; Molecular Structure; Nucleic Acid Conformation; Software},
  nlm-id          = {8511758},
  owner           = {saulius},
  pmid            = {8193957},
  pubmodel        = {Print},
  pubstate        = {ppublish},
  revised         = {2019-10-23},
  timestamp = {2022.04.17},
  creationdate = {2022-04-17T00:00:00},
}

@Article{Prive1991,
  author          = {Privé, G. G. and Yanagi, K. and Dickerson, R. E.},
  journal         = {Journal of molecular biology},
  title           = {Structure of the B-DNA decamer C-C-A-A-C-G-T-T-G-G and comparison with isomorphous decamers C-C-A-A-G-A-T-T-G-G and C-C-A-G-G-C-C-T-G-G.},
  year            = {1991},
  issn            = {0022-2836},
  month           = jan,
  pages           = {177--199},
  volume          = {217},
  abstract        = {The crystal structure of the DNA decamer C-C-A-A-C-G-T-T-G-G has been solved to a resolution of 1.4 A, and is compared with the 1.3 A structure of C-C-A-A-G-A-T-T-G-G and the 1.6 A structure of C-C-A-G-G-C-C-T-G-G. All three decamers crystallize isomorphously in space group C2 with five base-pairs per asymmetric unit, and with decamer double helices stacked atop one another along the c axis in a manner that closely approximates a continuous B helix. This efficient stacking probably accounts for the high resolution of the crystal data. Comparison of the three decamers reveals the following. (1) Minor groove width is more variable than heretofore realized. Regions of A.T base-pairs tend to be narrower than average, although two successive A.T base-pairs alone may not be sufficient to produce narrowing. The minor groove is wider in regions where BII phosphate conformations are opposed diagonally across the groove. (2) Narrow regions of minor groove exhibit a zig-zag spine of hydration, as was first seen in C-G-C-G-A-A-T-T-C-G-C-G, whereas wide regions show two ribbons of water molecules down the walls, connecting base edge N or O with sugar O-4' atoms. Regions of intermediate groove width may accommodate neither pattern of hydration well, and may exhibit a less regular pattern of hydration. (3) Base-pair stacking is virtually identical at equivalent positions in the three decamers. The unconnected step from the top of one decamer helix to the bottom of the next helix is a normal helix step in all respects, except for the absence of connecting phosphate groups. (4) BII phosphate conformation require the unstacking of the two bases linked by the phosphate, but do not necessarily follow as an inevitable consequence of unstacking. They have an influence on minor groove width as noted in point (1) above. (5) Sugar ring pseudorotation P and main-chain torsion angle delta show an excellent correlation as given by the equation: delta = 40 degrees cos (P + 144 degrees) + 120 degrees. Although centered around C-2'-endo, the conformations in these B-DNA helices are distributed broadly from C-3'-exo to O-4'-endo, unlike the tighter clustering around C-3'-endo observed in A-DNA oligomer structures.},
  chemicals       = {Oligodeoxyribonucleotides, DNA},
  citation-subset = {IM},
  comment         = {Cited in Jursa1994 (1994_Jursa_61.pdf, "DNA modeller: ...").},
  completed       = {1991-02-27},
  country         = {England},
  creationdate    = {2022-04-17T00:00:00},
  doi             = {10.1016/0022-2836(91)90619-h},
  file            = {:by-author/P/Privé/1991_Privé_177.pdf:PDF},
  issn-linking    = {0022-2836},
  issue           = {1},
  keywords        = {Base Composition; Base Sequence; Chemistry; DNA; Genetics; Models; Molecular; Molecular Sequence Data; NEWHEL90; NEWHELIX; Nucleic Acid; Nucleic Acid Conformation; Oligodeoxyribonucleotides; Sequence Homology; X-Ray Diffraction},
  nlm-id          = {2985088R},
  owner           = {saulius},
  pii             = {0022-2836(91)90619-H},
  pmid            = {1988677},
  pubmodel        = {Print},
  pubstate        = {ppublish},
  revised         = {2019-07-10},
  timestamp       = {2022.04.17},
}

@Article{Tung1994,
  author          = {Tung, C. S. and Soumpasis, D. M. and Hummer, G.},
  journal         = {Journal of biomolecular structure & dynamics},
  title           = {An extension of the rigorous base-unit oriented description of nucleic acid structures.},
  year            = {1994},
  issn            = {0739-1102},
  month           = jun,
  pages           = {1327--1344},
  volume          = {11},
  abstract        = {Our proposed description for DNA base/base-pair structures (1), though rigorous, does not satisfy some of the requirements as established at the Cambridge Workshop (2). Here, we propose a revised description for base/base-unit structures of nucleic acids. This new description is as rigorous and satisfies all the requirements (2). Following the original approach, the moment-of-inertia frame is still the choice of the internal coordinate system for a base/base-unit. The revised description has the minimum number of parameters (i.e., six parameters per rigid body) in the set. Besides regular Watson-Crick type of helices (e.g., A-DNA, A-RNA, B-DNA, Z-DNA, etc.), the revised description also works for non-Watson-Crick, multiple stranded molecules (e.g., triplex, quadruplex, etc.) as well as parallel stranded molecules.},
  chemicals       = {Polydeoxyribonucleotides, triplex DNA, DNA},
  citation-subset = {IM},
  comment         = {Cited in Lu1997 (1997_Lu_668.pdf, "... (SCHNAaP)").
Suggests to use moments of inertia to define local base axes.},
  completed       = {1994-12-22},
  country         = {England},
  creationdate    = {2022-04-17T00:00:00},
  doi             = {10.1080/07391102.1994.10508071},
  file            = {:by-author/T/Tung/1994_Tung_1327.pdf:PDF},
  issn-linking    = {0739-1102},
  issue           = {6},
  keywords        = {Base Composition; Base Sequence; Chemistry; Computer Simulation; DNA; Models; Molecular; Molecular Sequence Data; Nucleic Acid Conformation; Polydeoxyribonucleotides},
  nlm-id          = {8404176},
  owner           = {saulius},
  pmid            = {7946077},
  pubmodel        = {Print},
  pubstate        = {ppublish},
  revised         = {2006-11-15},
  timestamp       = {2022.04.17},
}

@Article{Soumpasis1988,
  author          = {Soumpasis, D. M. and Tung, C. S.},
  journal         = {Journal of biomolecular structure & dynamics},
  title           = {A rigorous basepair oriented description of DNA structures.},
  year            = {1988},
  issn            = {0739-1102},
  month           = dec,
  pages           = {397--420},
  volume          = {6},
  abstract        = {We propose new, rigorous definitions for (i) basepair fixed coordinate systems and (ii) the twist, tilt, and roll angles (called tau, t, rho) describing the relative orientation of adjacent basepairs and bases in a pair, in arbitrary DNA structures obtained from x-ray diffraction, 2D NMR, or energy calculations. In contrast to the corresponding angular parameters (tg, theta T, theta R) and coordinate systems introduced by Dickerson and co-workers and currently in use, our angular parameters and coordinate systems, together with a set of three displacement parameters, dx, dy, dz, provide a mathematically correct and general description of DNA conformations at the basepairs and/or base level. For instance, our description is applicable when the DNA structure considered is inherently curved, irregular, and/or does not possess dyad (or pseudodyad) axes. We develop a computationally convenient algorithm for rigorous DNA conformational analysis and apply it to some of the known crystal structures. We establish the connection to the currently used parameters and test the consistency and efficiency of our methodology by reconstructing the Dickerson B dodecamer using only the sequence and the set of parameters obtained from the atomic coordinates. The six parameter (tau, t, rho, dx, dy, dz) basepair level reconstruction is good but not perfect. Perfect reconstruction is obtained when one also considers each base in a basepair (consideration of propeller twist alone is not sufficient). The variation of the rigorous parameters proposed along the sequence is much larger, but their average values agree with fiber and solution data much better than in the case of the currently used set. The results of our analysis do not support Trifonov's AA.TT wedge model for DNA curvature but provide some evidence in favor of the Crothers junction-bend model. We point out some of the limitations of basepair level approaches when applied to DNA structure prediction and quantitative understanding of sequence-dependent variations in structure.},
  chemicals       = {DNA},
  citation-subset = {IM},
  comment         = {Cited in Tung1994 (1994_Tung_1327.pdf); uses settings different from the "Cambridge Workshop" definitions (Diekmann1989, Dickerson1989).},
  completed       = {1990-03-21},
  country         = {England},
  doi             = {10.1080/07391102.1988.10506497},
  file            = {:by-author/S/Soumpasis/1988_Soumpasis_397.pdf:PDF},
  issn-linking    = {0739-1102},
  issue           = {3},
  keywords        = {Base Composition; Computer Simulation; DNA; Models; Molecular; Nucleic Acid Conformation},
  nlm-id          = {8404176},
  owner           = {saulius},
  pmid            = {3271529},
  pubmodel        = {Print},
  pubstate        = {ppublish},
  revised         = {2007-11-14},
  timestamp = {2022.04.17},
  creationdate = {2022-04-17T00:00:00},
}

@Article{Dickerson1992,
  author          = {Dickerson, R. E.},
  journal         = {Methods in enzymology},
  title           = {DNA structure from A to Z.},
  year            = {1992},
  issn            = {0076-6879},
  pages           = {67--111},
  volume          = {211},
  chemicals       = {DNA},
  citation-subset = {IM},
  completed       = {1992-10-29},
  country         = {United States},
  doi             = {10.1016/0076-6879(92)11007-6},
  file            = {:by-author/D/Dickerson/1992_Dickerson_67.pdf:PDF},
  issn-linking    = {0076-6879},
  keywords        = {Base Sequence; Chemistry; DNA; Molecular Sequence Data; Nucleic Acid Conformation; X-Ray Diffraction},
  nlm-id          = {0212271},
  owner           = {saulius},
  pmid            = {1406328},
  pubmodel        = {Print},
  pubstate        = {ppublish},
  references      = {115},
  revised         = {2019-07-11},
  timestamp = {2022.04.17},
  creationdate = {2022-04-17T00:00:00},
}

@Article{Pauling1953,
  author       = {Pauling, L. and Corey, R. B.},
  journal      = {Proceedings of the National Academy of Sciences of the United States of America},
  title        = {A Proposed Structure For The Nucleic Acids.},
  year         = {1953},
  issn         = {0027-8424},
  month        = feb,
  pages        = {84--97},
  volume       = {39},
  completed    = {2006-06-01},
  country      = {United States},
  doi          = {10.1073/pnas.39.2.84},
  file         = {:by-author/P/Pauling/1953_Pauling_84.pdf:PDF},
  issn-linking = {0027-8424},
  issue        = {2},
  keywords     = {DNA Structure; History of Science; Incorrect Model},
  nlm-id       = {7505876},
  owner        = {saulius},
  pmc          = {PMC1063734},
  pmid         = {16578429},
  pubmodel     = {Print},
  pubstate     = {ppublish},
  revised      = {2019-05-01},
  timestamp = {2022.04.17},
  creationdate = {2022-04-17T00:00:00},
}

@Article{Allemand1998,
  author          = {Allemand, J. F. and Bensimon, D. and Lavery, R. and Croquette, V.},
  journal         = {Proceedings of the National Academy of Sciences of the United States of America},
  title           = {Stretched and overwound DNA forms a Pauling-like structure with exposed bases.},
  year            = {1998},
  issn            = {0027-8424},
  month           = nov,
  pages           = {14152--14157},
  volume          = {95},
  abstract        = {We investigate structural transitions within a single stretched and supercoiled DNA molecule. With negative supercoiling, for a stretching force >0.3 pN, we observe the coexistence of B-DNA and denatured DNA from sigma approximately -0.015 down to sigma = -1. Surprisingly, for positively supercoiled DNA (sigma > +0.037) stretched by 3 pN, we observe a similar coexistence of B-DNA and a new, highly twisted structure. Experimental data and molecular modeling suggest that this structure has approximately 2.62 bases per turn and an extension 75% larger than B-DNA. This structure has tightly interwound phosphate backbones and exposed bases in common with Pauling's early DNA structure [Pauling, L. & Corey, R. B. (1953), Proc. Natl. Acad. Sci. USA 39, 84-97] and an unusual structure proposed for the Pf1 bacteriophage [Liu, D. J. & Day, L. A. (1994) Science 265, 671-674].},
  chemicals       = {Antibodies, Glyoxal, Biotin, DNA, Digoxigenin},
  citation-subset = {IM},
  completed       = {1998-12-28},
  country         = {United States},
  creationdate    = {2022-04-17T00:00:00},
  doi             = {10.1073/pnas.95.24.14152},
  file            = {:by-author/A/Allemand/1998_Allemand_14152.pdf:PDF},
  issn-linking    = {0027-8424},
  issue           = {24},
  keywords        = {Antibodies; Biotin; Biotinylation; Chemical; Chemistry; DNA; Digoxigenin; Glass; Glyoxal; Immunology; Kinetics; Mechanical; Models; Molecular; Nucleic Acid Conformation; Nucleic Acid Denaturation; Stress},
  nlm-id          = {7505876},
  owner           = {saulius},
  pmc             = {PMC24342},
  pmid            = {9826669},
  pubmodel        = {Print},
  pubstate        = {ppublish},
  revised         = {2019-05-01},
  timestamp       = {2022.04.17},
}

@Article{Kuratowski1921,
  author    = {Casimir Kuratowski},
  journal   = {Fundamenta Mathematicae},
  title     = {Sur la notion de l'ordre dans la théorie des ensembles},
  year      = {1921},
  pages     = {161--171},
  volume    = {2},
  comment   = {Contains Kuraowski's ordered pair definition: (a,b) = \{\{a\},\{a,b\}\} (the original article?). Found via https://wikimili.com/en/Ordered_pair .},
  doi       = {10.4064/fm-2-1-161-171},
  file      = {:by-author/K/Kuratowski/1921_Kuratowski_161.pdf:PDF},
  keywords  = {Foundations of Mathematics; Mathematics; Set Theory},
  owner     = {saulius},
  publisher = {Institute of Mathematics, Polish Academy of Sciences},
  timestamp = {2022.04.27},
  creationdate = {2022-04-27T00:00:00},
}

@Book{DuBois2005,
  author    = {DuBois, Paul},
  publisher = {Sams Publishing},
  title     = {{MySQL}},
  year      = {2005},
  address   = {Indianapolis, IN},
  edition   = {3},
  isbn      = {0672326736},
  month     = mar,
  series    = {Developer's library},
  isbn-13   = {978-0672326738},
  keywords  = {Computer Science (CS); Databases; MySQL; Relational Databases},
  language  = {en},
  owner     = {saulius},
  timestamp = {2022.04.28},
  creationdate = {2022-04-28T00:00:00},
  url       = {https://www.amazon.com/Mysql-definitive-guide-programming-administering/dp/0672326736},
}

@Book{Dubois2013,
  author    = {Dubois, Paul},
  publisher = {Addison-Wesley Educational},
  title     = {{MySQL}},
  year      = {2013},
  address   = {Boston, MA},
  edition   = {5},
  isbn      = {9780321833877},
  month     = apr,
  isbn-13   = {978-9332523852},
  keywords  = {Computer Science (CS); Databases; MySQL; Relational Databases},
  language  = {en},
  owner     = {saulius},
  timestamp = {2022.04.28},
  creationdate = {2022-04-28T00:00:00},
  url       = {https://www.amazon.com/MySQL-Developers-Library-Paul-DuBois-dp-0321833872/dp/0321833872},
}

@Electronic{PGDG2022,
  author           = {{PostgreSQL Global Development Group}},
  note             = {Accessed 2022-04-28T07:45:16 EEST},
  title            = {PostgreSQL 14.2 Documentation},
  url              = {https://www.postgresql.org/files/documentation/pdf/14/postgresql-14-A4.pdf},
  year             = {2022},
  creationdate     = {2022-04-28T00:00:00},
  file             = {:by-author/P/PGDG/2022_PGDG_1.pdf:PDF},
  keywords         = {Computer Science (CS); Databases; JSON; PostgreSQL; Relational Databases},
  modificationdate = {2022-11-10T12:47:24},
  owner            = {saulius},
  pages            = {1--2836},
  timestamp        = {2022.04.28},
  urldate          = {2022-04-28T07:45+03:00},
}

@Book{Allen2010,
  author    = {Allen, Grant and Owens, Mike},
  publisher = {APress},
  title     = {The definitive guide to {SQLite}},
  year      = {2010},
  address   = {Berlin, Germany},
  edition   = {2},
  isbn      = {1430232250},
  month     = nov,
  isbn-13   = {978-1430232254},
  keywords  = {Computer Science (CS); Databases; Relational Databases; SQLite3},
  language  = {en},
  owner     = {saulius},
  timestamp = {2022.04.28},
  creationdate = {2022-04-28T00:00:00},
}

@Book{Kreibich2010,
  author    = {Kreibich, Jay A.},
  publisher = {O'Reilly Media},
  title     = {Using {SQLite}},
  year      = {2010},
  address   = {Sebastopol, CA},
  month     = aug,
  keywords  = {Computer Science (CS); Databases; Relational Databases; SQLite3},
  language  = {en},
  owner     = {saulius},
  timestamp = {2022.04.28},
  creationdate = {2022-04-28T00:00:00},
  url       = {https://www.oreilly.com/library/view/using-sqlite/9781449394592/},
}

@Article{Bimler2022,
  author    = {David Bimler},
  title     = {Better living through coordination chemistry: a descriptive study of a prolific papermill that combines crystallography and medicine},
  year      = {2022},
  month     = {apr},
  pages     = {1--21},
  comment   = {Describes a list of 800 fake crystallograpy paperson MOFs... This is a manuscript whicbh is still under review.},
  doi       = {10.21203/rs.3.rs-1537438/v1},
  file      = {:by-author/B/Bimler/2022_Bimler_1.pdf:PDF},
  keywords  = {Crystallography; Fake Structures; Research Integrity; Scientific Fraud},
  owner     = {saulius},
  publisher = {Research Square Platform {LLC}},
  timestamp = {2022.04.29},
  creationdate = {2022-04-29T00:00:00},
}

@Article{Scheffler2022,
  author    = {Scheffler, Matthias and Aeschlimann, Martin and Albrecht, Martin and Bereau, Tristan and Bungartz, Hans-Joachim and Felser, Claudia and Greiner, Mark and Groß, Axel and Koch, Christoph T. and Kremer, Kurt and Nagel, Wolfgang E. and Scheidgen, Markus and Wöll, Christof and Draxl, Claudia},
  journal   = {Nature},
  title     = {{FAIR} data enabling new horizons for materials research},
  year      = {2022},
  issn      = {1476-4687},
  number    = {7907},
  pages     = {635--642},
  volume    = {604},
  abstract  = {The prosperity and lifestyle of our society are very much governed by achievements in condensed matter physics, chemistry and materials science, because new products for sectors such as energy, the environment, health, mobility and information technology (IT) rely largely on improved or even new materials. Examples include solid-state lighting, touchscreens, batteries, implants, drug delivery and many more. The enormous amount of research data produced every day in these fields represents a gold mine of the twenty-first century. This gold mine is, however, of little value if these data are not comprehensively characterized and made available. How can we refine this feedstock; that is, turn data into knowledge and value? For this, a FAIR (findable, accessible, interoperable and reusable) data infrastructure is a must. Only then can data be readily shared and explored using data analytics and artificial intelligence (AI) methods. Making data 'findable and AI ready' (a forward-looking interpretation of the acronym) will change the way in which science is carried out today. In this Perspective, we discuss how we can prepare to make this happen for the field of materials science.},
  doi       = {10.1038/s41586-022-04501-x},
  file      = {:by-author/S/Scheffler/2022_Scheffler_635.pdf:PDF},
  owner     = {saulius},
  refid     = {Scheffler2022},
  timestamp = {2022.04.30},
  creationdate = {2022-04-30T00:00:00},
  url       = {https://doi.org/10.1038/s41586-022-04501-x},
}

@Article{Wiedijk2009,
  author    = {Freek Wiedijk},
  journal   = {Sadhana},
  title     = {Formalizing {A}rrow's theorem},
  year      = {2009},
  month     = {feb},
  number    = {1},
  pages     = {193--220},
  volume    = {34},
  comment   = {Found via Wikipedia [1]. The Wikipedia article cites this source as the evidence that "In 2009 the Mizar Mathematical Library was the largest coherent body of strictly formalized mathematics in existence."

Ref:

[1] https://en.wikipedia.org/wiki/Mizar_system [accessed 2022-04-30T10:34+03:00, permalink: https://en.wikipedia.org/w/index.php?title=Mizar_system&oldid=1073792605]},
  doi       = {10.1007/s12046-009-0005-1},
  file      = {:by-author/W/Wiedijk/2009_Wiedijk_193preprint.pdf:PDF;:by-author/W/Wiedijk/2009_Wiedijk_193.pdf:PDF},
  keywords  = {Coq; Formalised Proofs; Isabelle; Mathematics; Metamathematics; Mizar System; Proof Assistants},
  owner     = {saulius},
  publisher = {Springer Science and Business Media {LLC}},
  timestamp = {2022.04.30},
  creationdate = {2022-04-30T00:00:00},
  url       = {https://repository.ubn.ru.nl/handle/2066/75428},
}

@Article{OviedoGarcia2021,
  author    = {M. Ángeles Oviedo-Garcı́a},
  journal   = {Research Evaluation},
  title     = {Journal citation reports and the definition of a predatory journal: The case of the {M}ultidisciplinary {D}igital {P}ublishing {I}nstitute ({MDPI})},
  year      = {2021},
  month     = {jul},
  number    = {3},
  pages     = {405--419},
  volume    = {30},
  doi       = {10.1093/reseval/rvab020},
  file      = {:by-author/O/Oviedo-Garcı́a/2021_Oviedo-Garcı́a_405.pdf:PDF},
  keywords  = {Bibliometry; Crticism; MDPI; Predatory Journals; Quality of Research; Research Assessment},
  owner     = {saulius},
  publisher = {Oxford University Press ({OUP})},
  timestamp = {2022.05.02},
  creationdate = {2022-05-02T00:00:00},
}

@TechReport{Leach2005,
  author      = {P. Leach and M. Mealling and R. Salz},
  institution = {IETF},
  title       = {A universally unique {IDentifier} ({UUID}) {URN} namespace},
  year        = {2005},
  month       = {jul},
  doi         = {10.17487/rfc4122},
  file        = {:by-author/L/Leach/2005_Leach_1.pdf:PDF},
  keywords    = {Internet; RFC; UUID; Unique Identifiers},
  owner       = {saulius},
  pages       = {1--32},
  publisher   = {{RFC} Editor},
  timestamp = {2022.05.05},
  creationdate = {2022-05-05T00:00:00},
}

@Article{Pahari2019,
  author    = {Swagata Pahari and Lexuan Sun and Emil Alexov},
  journal   = {Database},
  title     = {{PKAD}: a database of experimentally measured {pKa} values of ionizable groups in proteins},
  year      = {2019},
  month     = {jan},
  pages     = {1--7},
  volume    = {2019},
  doi       = {10.1093/database/baz024},
  file      = {:by-author/P/Pahari/2019_Pahari_1.pdf:PDF},
  keywords  = {Average PKa Values; Biophysics; Databases},
  owner     = {saulius},
  publisher = {Oxford University Press ({OUP})},
  timestamp = {2022.05.05},
  creationdate = {2022-05-05T00:00:00},
}

@Article{Grimsley2009,
  author          = {Grimsley, Gerald R. and Scholtz, J. Martin and Pace, C. Nick},
  journal         = {Protein science : a publication of the Protein Society},
  title           = {A summary of the measured pK values of the ionizable groups in folded proteins.},
  year            = {2009},
  issn            = {1469-896X},
  month           = jan,
  pages           = {247--251},
  volume          = {18},
  abstract        = {We tabulated 541 measured pK values reported in the literature for the Asp, Glu, His, Cys, Tyr, and Lys side chains, and the C and N termini of 78 folded proteins. The majority of these values are for the Asp, Glu, and His side chains. The average pK values are Asp 3.5 +/- 1.2 (139); Glu 4.2 +/- 0.9 (153); His 6.6 +/- 1.0 (131); Cys 6.8 +/- 2.7 (25); Tyr 10.3 +/- 1.2 (20); Lys 10.5 +/- 1.1 (35); C-terminus 3.3 +/- 0.8 (22) and N-terminus 7.7 +/- 0.5 (16). We compare these results with the measured pK values of these groups in alanine pentapeptides, and comment on our overall findings.},
  chemicals       = {Amino Acids, Proteins, Aspartic Acid, Glutamic Acid, Histidine},
  citation-subset = {IM},
  completed       = {2009-08-07},
  country         = {United States},
  creationdate    = {2022-05-05T00:00:00},
  doi             = {10.1002/pro.19},
  file            = {:by-author/G/Grimsley/2009_Grimsley_247.pdf:PDF},
  issn-linking    = {0961-8368},
  issue           = {1},
  keywords        = {Amino Acid Sequence; Amino Acids; Aspartic Acid; Average PKa Values; Biomolecular; Biophysics; Chemistry; Databases; Glutamic Acid; Histidine; Hydrogen-Ion Concentration; Isoelectric Point; Nuclear Magnetic Resonance; Physiology; Protein Folding; Protein Structure; Proteins; Tertiary; Titrimetry},
  nlm-id          = {9211750},
  owner           = {saulius},
  pmc             = {PMC2708032},
  pmid            = {19177368},
  pubmodel        = {Print},
  pubstate        = {ppublish},
  revised         = {2021-10-20},
  timestamp       = {2022.05.05},
}

@Article{Toure2013,
  author    = {O. Toure and C.-G. Dussap and A. Lebert},
  journal   = {Oil \& Gas Science and Technology -- Revue d'{IFP} Energies nouvelles},
  title     = {Comparison of predicted {pK} values for some amino-acids, dipeptides and tripeptides, using {COSMO-RS}, {ChemAxon} and {ACD/Labs} methods},
  year      = {2013},
  month     = {mar},
  number    = {2},
  pages     = {281--297},
  volume    = {68},
  doi       = {10.2516/ogst/2012094},
  file      = {:by-author/T/Toure/2013_Toure_281.pdf:PDF},
  keywords  = {Average PKa Values; Biophysics; Databases},
  owner     = {saulius},
  publisher = {{EDP} Sciences},
  timestamp = {2022.05.05},
  creationdate = {2022-05-05T00:00:00},
  url       = {https://hal.archives-ouvertes.fr/hal-01936096/document},
}

@MastersThesis{Wagner2020,
  author    = {Wagner, Matt},
  school    = {Rochester Institute of Technology},
  title     = {Posits: an alternative to floating point calculations},
  year      = {2020},
  file      = {:by-author/W/Wagner/2020_Wagner_1.pdf:PDF},
  keywords  = {Computer Science (CS); Criticism; Floating Point; Posit; Unum},
  owner     = {saulius},
  pages     = {1--205},
  timestamp = {2022.05.07},
  creationdate = {2022-05-07T00:00:00},
  url       = {https://scholarworks.rit.edu/cgi/viewcontent.cgi?article=11516&context=theses},
}

@Article{Azurmendi2002,
  author    = {Hugo F. Azurmendi and C. Allen Bush},
  journal   = {Journal of the American Chemical Society},
  title     = {Tracking Alignment from the Moment of Inertia Tensor ({TRAMITE}) of Biomolecules in Neutral Dilute Liquid Crystal Solutions},
  year      = {2002},
  month     = {feb},
  number    = {11},
  pages     = {2426--2427},
  volume    = {124},
  doi       = {10.1021/ja017524z},
  file      = {:by-author/A/Azurmendi/2002_Azurmendi_2426.pdf:PDF},
  keywords  = {Bioinformatics; Biophysics; Inertia Tensor; Liquid Crystals; Molecule Alignment; PDB},
  owner     = {saulius},
  publisher = {American Chemical Society ({ACS})},
  timestamp = {2022.05.10},
  creationdate = {2022-05-10T00:00:00},
  url       = {https://userpages.umbc.edu/~bush/glycogroup/papers/Hugo/jacs124_2426.pdf},
}

@TechReport{ITUT2012,
  author      = {{ITU-T}},
  institution = {{ITU-T}},
  title       = {Information technology – procedures for theoperation of object identifier registration authorities: generation of universally uniqueidentifiers and their use in object identifiers},
  year        = {2012},
  month       = oct,
  number      = {X.667},
  file        = {:by-author/I/ITUT/2012_ITUT_1.pdf:PDF},
  keywords    = {Computer Science (CS); Standard; Telecommunications; UUID; Unique Identifiers},
  owner       = {saulius},
  pages       = {1--34},
  timestamp = {2022.05.12},
  creationdate = {2022-05-12T00:00:00},
  url         = {https://www.itu.int/rec/T-REC-X.667-201210-I/en},
}

@TechReport{Shafranovich2005,
  author       = {Yakov Shafranovich},
  institution  = {IETF},
  title        = {Common format and {MIME} type for {C}omma-separated values ({CSV}) files},
  year         = {2005},
  month        = oct,
  number       = {4180},
  abstract     = {This RFC documents the format used for {C}omma-Separated Values (CSV) files and registers the associated MIME type "text/csv". This memo provides information for the Internet community.},
  comment      = {Other URLs: https://datatracker.ietf.org/doc/html/rfc4180},
  doi          = {10.17487/RFC4180},
  file         = {:by-author/S/Shafranovich/2005_Shafranovich_1.pdf:PDF},
  howpublished = {RFC 4180},
  keywords     = {CSV; Computer Science (CS); RFC},
  owner        = {saulius},
  pages        = {1--8},
  pagetotal    = {8},
  publisher    = {RFC Editor},
  series       = {Request for Comments},
  timestamp = {2022.05.12},
  creationdate = {2022-05-12T00:00:00},
  url          = {https://www.rfc-editor.org/info/rfc4180},
}

@TechReport{Hausenblas2014,
  author       = {Michael Hausenblas and Erik Wilde and Jeni Tennison},
  institution  = {IETF},
  title        = {{URI} fragment identifiers for the text/csv media type},
  year         = {2014},
  month        = jan,
  number       = {7111},
  abstract     = {This memo defines URI fragment identifiers for text/csv MIME entities. These fragment identifiers make it possible to refer to parts of a text/csv MIME entity identified by row, column, or cell. Fragment identification can use single items or ranges.},
  doi          = {10.17487/RFC7111},
  file         = {:by-author/H/Hausenblas/2014_Hausenblas_1.pdf:PDF},
  howpublished = {RFC 7111},
  keywords     = {CSV; Computer Science (CS); RFC},
  owner        = {saulius},
  pages        = {1--13},
  pagetotal    = {13},
  publisher    = {RFC Editor},
  series       = {Request for Comments},
  timestamp = {2022.05.12},
  creationdate = {2022-05-12T00:00:00},
  url          = {https://www.rfc-editor.org/info/rfc7111},
}

@Webpage{LOC2021,
  author    = {{Library of Congress}},
  retrieved = {2022-05-12T14:28+03:00},
  title     = {{CSV}, {C}omma separated values ({RFC} 4180)},
  url       = {https://www.loc.gov/preservation/digital/formats/fdd/fdd000323.shtml},
  month     = feb,
  year      = {2021},
  date      = {2020-02-11},
  file      = {:by-author/L/LibraryCongress/2021_CSV.pdf:PDF;:by-author/L/LibraryCongress/2021_CSV.odt:OpenDocument text},
  keywords  = {CSV; Computer Science (CS); Data Formats},
  owner     = {saulius},
  pages     = {1--8},
  pagetotal = {8},
  timestamp = {2022.05.12},
  creationdate = {2022-05-12T00:00:00},
}

@Webpage{LOC2021a,
  author    = {{Library of Congress}},
  retrieved = {2022-05-12T14:39+03:00},
  title     = {{TSV}, {TAB}-separated values},
  url       = {https://www.loc.gov/preservation/digital/formats/fdd/fdd000533.shtml},
  month     = feb,
  year      = {2021},
  date      = {2021-02-11},
  file      = {:by-author/L/LibraryCongress/2021_TSV.pdf:PDF;:by-author/L/LibraryCongress/2021_TSV.odt:OpenDocument text},
  keywords  = {Computer Science (CS); Data Formats; TSV},
  owner     = {saulius},
  pages     = {1--6},
  pagetotal = {6},
  timestamp = {2022.05.12},
  creationdate = {2022-05-12T00:00:00},
}

@Article{Kolluru2022,
  author           = {Kolluru, Adeesh and Shoghi, Nima and Shuaibi, Muhammed and Goyal, Siddharth and Das, Abhishek and Zitnick, C. Lawrence and Ulissi, Zachary},
  journal          = {The Journal of chemical physics},
  title            = {Transfer learning using attentions across atomic systems with graph neural networks ({TAAG}).},
  year             = {2022},
  issn             = {1089-7690},
  month            = may,
  pages            = {184702},
  volume           = {156},
  abstract         = {Recent advances in Graph Neural Networks (GNNs) have transformed the space of molecular and catalyst discovery. Despite the fact that the underlying physics across these domains remain the same, most prior work has focused on building domain-specific models either in small molecules or in materials. However, building large datasets across all domains is computationally expensive; therefore, the use of transfer learning (TL) to generalize to different domains is a promising but under-explored approach to this problem. To evaluate this hypothesis, we use a model that is pretrained on the Open Catalyst Dataset (OC20), and we study the model's behavior when fine-tuned for a set of different datasets and tasks. This includes MD17, the *CO adsorbate dataset, and OC20 across different tasks. Through extensive TL experiments, we demonstrate that the initial layers of GNNs learn a more basic representation that is consistent across domains, whereas the final layers learn more task-specific features. Moreover, these well-known strategies show significant improvement over the non-pretrained models for in-domain tasks with improvements of 53% and 17% for the *CO dataset and across the Open Catalyst Project (OCP) task, respectively. TL approaches result in up to 4× speedup in model training depending on the target data and task. However, these do not perform well for the MD17 dataset, resulting in worse performance than the non-pretrained model for few molecules. Based on these observations, we propose transfer learning using attentions across atomic systems with graph Neural Networks (TAAG), an attention-based approach that adapts to prioritize and transfer important features from the interaction layers of GNNs. The proposed method outperforms the best TL approach for out-of-domain datasets, such as MD17, and gives a mean improvement of 6% over a model trained from scratch.},
  citation-subset  = {IM},
  country          = {United States},
  creationdate     = {2022-05-16T18:17:25},
  doi              = {10.1063/5.0088019},
  file             = {:by-author/K/Kolluru/2022_Kolluru_184702.pdf:PDF},
  issn-linking     = {0021-9606},
  issue            = {18},
  keywords         = {Artificial Neural Networks (ANN); Computer Science (CS); Graph Neural Networks (GNN); Molecular Recognition},
  modificationdate = {2023-01-30T09:55:15},
  nlm-id           = {0375360},
  owner            = {saulius},
  pmid             = {35568535},
  pubmodel         = {Print},
  pubstate         = {ppublish},
  revised          = {2022-05-14},
}

@Article{Pal2002,
  author    = {Debnath Pal and Pinak Chakrabarti},
  journal   = {Biopolymers},
  title     = {On residues in the disallowed region of the {R}amachandran map},
  year      = {2002},
  month     = {jan},
  number    = {3},
  pages     = {195--206},
  volume    = {63},
  doi       = {10.1002/bip.10051},
  file      = {:by-author/P/Pal/2002_Pal_195.pdf:PDF},
  keywords  = {Bioinformatics; Chi1 Angle; Outliers; Phi/psi Angles; Ramachandran Plor},
  owner     = {saulius},
  publisher = {Wiley},
  timestamp = {2022.05.18},
  creationdate = {2022-05-18T00:00:00},
}

@Article{IUPACIUB1970,
  author          = {{IUPAC-IUB}},
  journal         = {Biochemistry},
  title           = {{IUPAC-IUB} Commission on Biochemical Nomenclature. Abbreviations and symbols for the description of the conformation of polypeptide chains. Tentative rules (1969).},
  year            = {1970},
  issn            = {0006-2960},
  month           = sep,
  pages           = {3471--3479},
  volume          = {9},
  chemicals       = {Peptides},
  citation-subset = {IM},
  completed       = {1971-06-02},
  country         = {United States},
  doi             = {10.1021/bi00820a001},
  file            = {:by-author/I/IUPAC-IUB/1970_IUPAC-IUB_3471.pdf:PDF},
  issn-linking    = {0006-2960},
  issue           = {18},
  keywords        = {Biochemistry; Bioinformatics; Classification; Peptides; Terminology as Topic},
  nlm-id          = {0370623},
  owner           = {saulius},
  pmid            = {5509841},
  pubmodel        = {Print},
  pubstate        = {ppublish},
  revised         = {2019-06-13},
  timestamp = {2022.05.18},
  creationdate = {2022-05-18T00:00:00},
}

@Article{Zhang2007a,
  author    = {Yang Zhang and Jeffrey Skolnick},
  journal   = {Proteins: Structure, Function, and Bioinformatics},
  title     = {Scoring function for automated assessment of protein structure template quality. Erratum},
  year      = {2007},
  month     = {jun},
  number    = {4},
  pages     = {1020--1020},
  volume    = {68},
  doi       = {10.1002/prot.21643},
  file      = {:by-author/Z/Zhang/2007_Zhang_1020.pdf:PDF},
  keywords  = {Bioinformatics; Protein Modelling; Scoring Function},
  owner     = {saulius},
  publisher = {Wiley},
  timestamp = {2022.05.24},
  creationdate = {2022-05-24T00:00:00},
}

@Article{Zhang2004b,
  author           = {Zhang, Yang and Skolnick, Jeffrey},
  journal          = {Proteins: Structure, Function, and Bioinformatics},
  title            = {Scoring function for automated assessment of protein structure template quality},
  year             = {2004},
  issn             = {1097-0134},
  number           = {4},
  pages            = {702--710},
  volume           = {57},
  creationdate     = {2022-05-24T00:00:00},
  doi              = {10.1002/prot.20264},
  file             = {:by-author/Z/Zhang/2004_Zhang_702.pdf:PDF},
  keywords         = {Bioinformatics; Scoring Function},
  modificationdate = {2022-12-08T10:20:04},
  owner            = {saulius},
  publisher        = {Wiley},
  timestamp        = {2022.05.24},
  url              = {http://dx.doi.org/10.1002/prot.20264},
}

@Article{Jones1995,
  author    = {Capers Jones},
  journal   = {Computer},
  title     = {Backfiring: converting lines of code to function points},
  year      = {1995},
  number    = {11},
  pages     = {87--88},
  volume    = {28},
  comment   = {Cited in: National Research Council (1997) "Ada and Beyond: Software Policies for the
Department of Defense". Washington, DC: The National Academies Press.
https://doi.org/10.17226/5463},
  doi       = {10.1109/2.471193},
  file      = {:by-author/J/Jones/1995_Jones_87.pdf:PDF},
  keywords  = {Computer Science (CS); Function Points; SLOC; Software Metrics; Software Productivity Research},
  owner     = {saulius},
  publisher = {Institute of Electrical and Electronics Engineers ({IEEE})},
  timestamp = {2022.05.27},
  creationdate = {2022-05-27T00:00:00},
}

@Book{NRC1997,
  author           = {{National Research Council}},
  publisher        = {National Academies Press},
  title            = {Ada and beyond},
  year             = {1997},
  month            = {jan},
  comment          = {The PDF of this book is large and is not commited to this repository; it is openly available on the Web (follow the DOI link) and also committed to our 'books' repo.
"Projects will use the highest-level language that meets quality, cost, and schedule constraints for each
software component" (p. 55).
"Standardized and non-proprietary languages are preferred" (p. 55).},
  creationdate     = {2022-05-27T00:00:00},
  doi              = {10.17226/5463},
  keywords         = {Ada; Assesment; CA; Criticism},
  modificationdate = {2023-02-21T09:45:39},
  owner            = {saulius},
  timestamp        = {2022.05.27},
}

@Article{Mohr2014,
  author    = {Peter J. Mohr and William D. Phillips},
  journal   = {Metrologia},
  title     = {Dimensionless units in the {SI}},
  year      = {2014},
  month     = {dec},
  number    = {1},
  pages     = {40--47},
  volume    = {52},
  doi       = {10.1088/0026-1394/52/1/40},
  file      = {:by-author/M/Mohr/2014_Mohr_40.pdf:PDF},
  keywords  = {Physics; SI; Units},
  owner     = {saulius},
  publisher = {{IOP} Publishing},
  timestamp = {2022.06.01},
  creationdate = {2022-06-01T00:00:00},
}

@TechReport{Bradner1997,
  author       = {Scott O. Bradner},
  title        = {Key words for use in {RFC}s to indicate requirement levels},
  year         = {1997},
  month        = mar,
  number       = {2119},
  abstract     = {In many standards track documents several words are used to signify the requirements in the specification. These words are often capitalized. This document defines these words as they should be interpreted in IETF documents. This document specifies an Internet Best Current Practices for the Internet Community, and requests discussion and suggestions for improvements.},
  doi          = {10.17487/RFC2119},
  file         = {:by-author/B/Bradner/1997_Bradner_rfc2119.pdf:PDF},
  howpublished = {RFC 2119},
  keywords     = {Best Practices; IETF; Internet Standards; RFC; Software Specification},
  owner        = {saulius},
  pagetotal    = {3},
  publisher    = {RFC Editor},
  retrieved    = {2022-06-05T11:00+03:00},
  series       = {Request for Comments},
  timestamp = {2022.06.05},
  creationdate = {2022-06-05T00:00:00},
  url          = {https://www.rfc-editor.org/info/rfc2119},
}

@InCollection{Miller1992,
  author    = {Miller, III, Charles F.},
  booktitle = {Mathematical Sciences Research Institute Publications},
  publisher = {Springer New York},
  title     = {Decision problems for groups - survey and reflections},
  year      = {1992},
  pages     = {1--59},
  comment   = {Found via https://en.wikipedia.org/wiki/Group_isomorphism_problem [accessed 2022-06-10T12:13+03:00].},
  doi       = {10.1007/978-1-4613-9730-4_1},
  file      = {:by-author/M/Miller/1992_Miller_1.pdf:PDF},
  keywords  = {Abstract Algebra; Algebra; Algorithms; Goupr Isomorphism; Group Theory; Mathematics},
  owner     = {saulius},
  timestamp = {2022.06.10},
  creationdate = {2022-06-10T00:00:00},
  url       = {https://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.135.2827},
}

@Article{Grochow2017,
  author    = {Joshua A. Grochow and Youming Qiao},
  journal   = {{SIAM} Journal on Computing},
  title     = {Algorithms for group isomorphism via group extensions and cohomology},
  year      = {2017},
  month     = {jan},
  number    = {4},
  pages     = {1153--1216},
  volume    = {46},
  doi       = {10.1137/15m1009767},
  file      = {:by-author/G/Grochow/2017_Grochow_1153.pdf:PDF},
  keywords  = {Abstract Algebra; Algebra; Algorithms; Goupr Isomorphism; Group Theory; Mathematics},
  owner     = {saulius},
  publisher = {Society for Industrial {\&} Applied Mathematics ({SIAM})},
  timestamp = {2022.06.10},
  creationdate = {2022-06-10T00:00:00},
}

@Article{Shmueli1984,
  author    = {U. Shmueli},
  journal   = {Acta Crystallographica Section A Foundations of Crystallography},
  title     = {Space-group algorithms. I. The space group and its symmetry elements},
  year      = {1984},
  month     = {sep},
  number    = {5},
  pages     = {559--567},
  volume    = {40},
  doi       = {10.1107/s0108767384001161},
  file      = {:by-author/S/Shmueli/1984_Shmueli_559.pdf:PDF},
  keywords  = {Algorithms; Crystallography; Space Groups},
  owner     = {saulius},
  publisher = {International Union of Crystallography ({IUCr})},
  timestamp = {2022.06.10},
  creationdate = {2022-06-10T00:00:00},
}

@Article{Hall1981a,
  author    = {S. R. Hall},
  journal   = {Acta Crystallographica Section A},
  title     = {Space-group notation with an explicit origin; erratum},
  year      = {1981},
  month     = {nov},
  number    = {6},
  pages     = {921--921},
  volume    = {37},
  doi       = {10.1107/s0567739481001976},
  file      = {:by-author/H/Hall/1981_Hall_921.pdf:PDF},
  keywords  = {Algorithms; Crystallography; Errata; Space Group Reconstruction; Space Group Symbols; Space Groups},
  owner     = {saulius},
  publisher = {International Union of Crystallography ({IUCr})},
  timestamp = {2022.06.10},
  creationdate = {2022-06-10T00:00:00},
}

@Article{Petrauskas2022,
  author    = {Karolis Petrauskas and Andrius Merkys and Antanas Vaitkus and Linas Laibinis and Saulius Gra{\v{z}}ulis},
  journal   = {Journal of Applied Crystallography},
  title     = {Proving the correctness of the algorithm for building a crystallographic space group},
  year      = {2022},
  month     = {may},
  number    = {3},
  pages     = {515--525},
  volume    = {55},
  doi       = {10.1107/s1600576722003107},
  file      = {:by-author/P/Petrauskas/2022_Petrauskas_515.pdf:PDF},
  keywords  = {Algebra; Algortithm; Computer Science (CS); Correctness Proofs; Crystallography; Formal Verification; Software Development; Space-group Builder; Symmetry; Symmetry Groups},
  owner     = {saulius},
  publisher = {International Union of Crystallography ({IUCr})},
  timestamp = {2022.06.13},
  creationdate = {2022-06-13T00:00:00},
}

@Presentation{Taft2021,
  author    = {S. Tucker Taft},
  title     = {A sampling of {Ada} 2022},
  year      = {2021},
  comment   = {Keynote lecture.},
  file      = {:by-author/T/Taft/2021_Taft_1.pdf:PDF},
  keywords  = {Ada; Computer Science (CS); Parallel Programming; Programming Languages; Reliable Programming},
  owner     = {saulius},
  pages     = {1--58},
  timestamp = {2022.06.17},
  creationdate = {2022-06-17T00:00:00},
  url       = {https://bit.ly/taftkeynote2021},
}

@Article{Zwart2007,
  author    = {Peter H. Zwart and Ralf W. Grosse-Kunstleve and Andrey A. Lebedev and Garib N. Murshudov and Paul D. Adams},
  journal   = {Acta Crystallographica Section D Biological Crystallography},
  title     = {Surprises and pitfalls arising from (pseudo)symmetry},
  year      = {2007},
  month     = {dec},
  number    = {1},
  pages     = {99--107},
  volume    = {64},
  doi       = {10.1107/s090744490705531x},
  file      = {:by-author/Z/Zwart/2007_Zwart_99.pdf:PDF},
  keywords  = {Crystallography; Hermann-Mauguin Symbols; Symmetry Operators},
  owner     = {saulius},
  publisher = {International Union of Crystallography ({IUCr})},
  timestamp = {2022.06.27},
  creationdate = {2022-06-27T00:00:00},
}

@Manuscript{Shaik2004a,
  author    = {Sason Shaik and Philippe C. Hiberty},
  title     = {Valence bond theory, its history, fundamentals, and applications: a primer},
  year      = {2004},
  doi       = {10.1002/0471678856.ch1},
  keywords  = {Chemical Bond; Chemistry; Molecular Orbital Theory; Valence Bond Theory},
  month     = {aug},
  url       = {http://pagesperso.lcp.u-psud.fr/hiberty/Cours/VBTheory.pdf},
  booktitle = {Reviews in Computational Chemistry},
  file      = {:by-author/S/Shaik/2004_Shaik_1a.pdf:PDF},
  owner     = {saulius},
  pages     = {1--100},
  publisher = {John Wiley {\&} Sons, Inc.},
  timestamp = {2022.07.02},
  creationdate = {2022-07-02T00:00:00},
}

@InCollection{Shaik2004,
  author    = {Sason Shaik and Philippe C. Hiberty},
  booktitle = {Reviews in Computational Chemistry},
  publisher = {John Wiley {\&} Sons, Inc.},
  title     = {Valence bond theory, its history, fundamentals, and applications: a primer},
  year      = {2004},
  month     = {aug},
  pages     = {1--100},
  doi       = {10.1002/0471678856.ch1},
  file      = {:by-author/S/Shaik/2004_Shaik_1.pdf:PDF},
  keywords  = {Chemical Bond; Chemistry; Molecular Orbital Theory; Valence Bond Theory},
  owner     = {saulius},
  timestamp = {2022.07.02},
  creationdate = {2022-07-02T00:00:00},
  url       = {http://pagesperso.lcp.u-psud.fr/hiberty/Cours/VBTheory.pdf},
}

@Article{Gerratt1997,
  author    = {J. Gerratt and D. L. Cooper and P. B. Karadakov and M. Raimondi},
  journal   = {Chemical Society Reviews},
  title     = {Modern valence bond theory},
  year      = {1997},
  number    = {2},
  pages     = {87},
  volume    = {26},
  doi       = {10.1039/cs9972600087},
  file      = {:by-author/G/Gerratt/1997_Gerratt_87.pdf:PDF},
  keywords  = {Chemical Bond; Chemistry; Molecular Orbital Theory; Valence Bond Theory},
  owner     = {saulius},
  publisher = {Royal Society of Chemistry ({RSC})},
  timestamp = {2022.07.02},
  creationdate = {2022-07-02T00:00:00},
  url       = {http://molphys.org/files/articulo_2.pdf},
}

@Manuscript{Preuss2012,
  author    = {Kathryn Preuss},
  title     = {Valence bond ({VB}) theory},
  year      = {2012},
  keywords  = {Chemical Bond; Chemistry; Molecular Orbital Theory; Valence Bond Theory},
  url       = {http://www.chemistry.uoguelph.ca/educmat/chm364_preuss/4_1 VB Theory.pdf},
  file      = {:by-author/P/Preuss/2012_Preuss_1.pdf:PDF},
  owner     = {saulius},
  pages     = {1--7},
  timestamp = {2022.07.02},
  creationdate = {2022-07-02T00:00:00},
}

@Lecture{Corn2009,
  author    = {Robert Corn},
  title     = {Valence bond theory},
  year      = {2009},
  lecture   = {LectureB5},
  file      = {:by-author/C/Corn/2009_Corn_1.pdf:PDF},
  keywords  = {Chemical Bond; Chemistry; Molecular Orbital Theory; Valence Bond Theory},
  owner     = {saulius},
  pages     = {1--41},
  timestamp = {2022.07.02},
  creationdate = {2022-07-02T00:00:00},
  url       = {https://www.chem.uci.edu/~unicorn/old/H2A/handouts/PDFs/LectureB5.pdf},
}

@Article{Shaik2019,
  author    = {Sason Shaik and David Danovich and John Morrison Galbraith and Beno{\^{\i}}t Braïda and Wei Wu and Philippe C. Hiberty},
  journal   = {Angewandte Chemie International Edition},
  title     = {Charge-Shift Bonding: A New and Unique Form of Bonding},
  year      = {2019},
  month     = {nov},
  number    = {3},
  pages     = {984--1001},
  volume    = {59},
  doi       = {10.1002/anie.201910085},
  file      = {:by-author/S/Shaik/2019_Shaik_984.pdf:PDF},
  keywords  = {Chemical Bond; Chemistry; Molecular Orbital Theory; Valence Bond Theory},
  owner     = {saulius},
  publisher = {Wiley},
  timestamp = {2022.07.02},
  creationdate = {2022-07-02T00:00:00},
}

@Booklet{BIPM2019,
  title     = {The internationalsystem of units ({SI}), 9th edition},
  author    = {{Bureau Internationaldes Poids et Mesures}},
  year      = {2019},
  file      = {:by-author/B/BIPM/2019_BIPM_1.pdf:PDF},
  keywords  = {International System; Kilogram; Measurement Units; SI},
  language  = {fr,en},
  owner     = {saulius},
  pages     = {1--218},
  timestamp = {2022.07.02},
  creationdate = {2022-07-02T00:00:00},
  url       = {https://www.bipm.org/documents/20126/41483022/SI-Brochure-9.pdf/fcf090b2-04e6-88cc-1149-c3e029ad8232?version=1.18&t=1645193776058&download=true},
}

@Presentation{Vyboishchikov2020,
  author    = {Sergei Vyboishchikov},
  title     = {Valence-bond method: an overview},
  year      = {2020},
  file      = {:by-author/V/Vyboishchikov/2020_Vyboishchikov_1.pdf:PDF},
  keywords  = {Chemical Bond; Chemistry; Hybridisation of Orbitals; Molecular Orbital Theory; Valence Bond Theory},
  owner     = {saulius},
  pages     = {1--13},
  timestamp = {2022.07.02},
  creationdate = {2022-07-02T00:00:00},
  url       = {http://iqc.udg.edu/~vybo/DOCENCIA/NEW_TOOLS/VB.pdf},
}

@Article{Jensen2006,
  author    = {William B. Jensen},
  journal   = {Journal of Chemical Education},
  title     = {More on the nature of resonance},
  year      = {2006},
  month     = {sep},
  number    = {9},
  pages     = {1290},
  volume    = {83},
  comment   = {Cited in the blog https://depth-first.com/articles/2021/06/17/delocalization-induced-molecular-equality/ [accessed 2022-07-05T16:45+03:00].},
  doi       = {10.1021/ed083p1290.3},
  file      = {:by-author/J/Jensen/2006_Jensen_1290.pdf:PDF},
  keywords  = {Chemical Bond; Chemistry; Molecular Orbital Theory; Molecular Resonance; Valence Bond Theory},
  owner     = {saulius},
  publisher = {American Chemical Society ({ACS})},
  timestamp = {2022.07.05},
  creationdate = {2022-07-05T00:00:00},
}

@Article{Ghiringhelli2017,
  author    = {Luca M. Ghiringhelli and Christian Carbogno and Sergey Levchenko and Fawzi Mohamed and Georg Huhs and Martin Lüders and Micael Oliveira and Matthias Scheffler},
  journal   = {npj Computational Materials},
  title     = {Towards efficient data exchange and sharing for big-data driven materials science: metadata and data formats},
  year      = {2017},
  month     = {nov},
  number    = {1},
  pages     = {1--9},
  volume    = {3},
  comment   = {"In order to enable interoperability and reusability of energies computed with different electronic-structure methods, it is
necessary to define a “general energy zero”. An analysis of this problem and some clues on how to tackle it were already
discussed by some of us in a previous work (Ghiringhelli2017)".},
  doi       = {10.1038/s41524-017-0048-5},
  file      = {:by-author/G/Ghiringhelli/2017_Ghiringhelli_1.pdf:PDF},
  keywords  = {Computational Material Science; Data Science; Ontologies},
  owner     = {saulius},
  publisher = {Springer Science and Business Media {LLC}},
  timestamp = {2022.07.14},
  creationdate = {2022-07-14T00:00:00},
}

@Article{Leitherer2021,
  author    = {Andreas Leitherer and Angelo Ziletti and Luca M. Ghiringhelli},
  journal   = {Nature Communications},
  title     = {Robust recognition and exploratory analysis of crystal structures via {B}ayesian deep learning},
  year      = {2021},
  month     = {oct},
  number    = {1},
  pages     = {1--13},
  volume    = {12},
  doi       = {10.1038/s41467-021-26511-5},
  file      = {:by-author/L/Leitherer/2021_Leitherer_1.pdf:PDF},
  keywords  = {Chemoinformatics; Crystallography; Machine Learning (ML)},
  owner     = {saulius},
  publisher = {Springer Science and Business Media {LLC}},
  timestamp = {2022.07.14},
  creationdate = {2022-07-14T00:00:00},
}

@InCollection{Westbrook2006,
  author           = {J. D. Westbrook and H. Yang and Z. Feng and H. M. Berman},
  booktitle        = {International Tables for Crystallography},
  publisher        = {International Union of Crystallography},
  title            = {The use of {mmCIF} architecture for {PDB} data management},
  year             = {2006},
  month            = {oct},
  pages            = {539--543},
  creationdate     = {2022-07-14T00:00:00},
  doi              = {10.1107/97809553602060000755},
  file             = {:by-author/W/Westbrook/2006_Westbrook_539.pdf:PDF},
  keywords         = {CIF; Crystallography; Data Exchange; Data Standards; Metadata; PDB; Structural Biology; {mmCIF}},
  modificationdate = {2023-08-07T10:23:04},
  owner            = {saulius},
  timestamp        = {2022.07.14},
  url              = {https://it.iucr.org/Ga/ch5o5v0001/ch5o5.pdf},
}

@TechReport{BernersLee1994,
  author    = {T. Berners-Lee},
  title     = {{U}niversal {R}esource {I}dentifiers in {WWW}: {A} unifying syntax for the expression of names and addresses of objects on the network as used in the world-wide web},
  year      = {1994},
  month     = {jun},
  doi       = {10.17487/rfc1630},
  file      = {:by-author/B/Berners-Lee/1994_Berners-Lee_1.pdf:PDF},
  keywords  = {RFC; URI; URL; WWW; Web Documentation},
  owner     = {saulius},
  pages     = {1--28},
  publisher = {{RFC} Editor},
  timestamp = {2022.07.14},
  creationdate = {2022-07-14T00:00:00},
}

@Webpage{Wikipedia2022URI,
  author    = {Wikipedia},
  retrieved = {2022-07-14T18:41+03:00},
  title     = {Uniform Resource Identifier},
  url       = {https://en.wikipedia.org/wiki/Uniform_Resource_Identifier},
  year      = {2022},
  file      = {:by-author/W/Wikipedia/2022_Wikipedia_URI.pdf:PDF},
  keywords  = {Data Management; Identifiers; PID; Permanent Identifier; URI; URL; URN; WWW},
  owner     = {saulius},
  pages     = {1--6},
  permalink = {https://en.wikipedia.org/w/index.php?title=Uniform_Resource_Identifier&oldid=1097106884},
  timestamp = {2022.07.14},
  creationdate = {2022-07-14T00:00:00},
}

@Article{Kim2015,
  author    = {Yeonjoon Kim and Woo Youn Kim},
  journal   = {Bulletin of the Korean Chemical Society},
  title     = {Universal structure conversion method for organic molecules: from atomic connectivity to three-dimensional geometry},
  year      = {2015},
  month     = {jun},
  number    = {7},
  pages     = {1769--1777},
  volume    = {36},
  comment   = {Cited in https://github.com/jensengroup/xyz2mol (commit f512673).},
  doi       = {10.1002/bkcs.10334},
  file      = {:by-author/K/Kim/2015_Kim_1769.pdf:PDF},
  keywords  = {Chemical Representations; Chemoinformatics; Metal-organic Compounds; Organometallic Compounds; Valence Bond Theory},
  owner     = {saulius},
  publisher = {Wiley},
  timestamp = {2022.07.28},
  creationdate = {2022-07-28T00:00:00},
}

@Article{Bannwarth2020,
  author    = {Christoph Bannwarth and Eike Caldeweyher and Sebastian Ehlert and Andreas Hansen and Philipp Pracht and Jakob Seibert and Sebastian Spicher and Stefan Grimme},
  journal   = {{WIREs} Computational Molecular Science},
  title     = {Extended tight-binding quantum chemistry methods},
  year      = {2020},
  month     = {aug},
  number    = {2},
  pages     = {1493},
  volume    = {11},
  comment   = {Recommended by Wiley next to the (Kim2015) paper.},
  doi       = {10.1002/wcms.1493},
  file      = {:by-author/B/Bannwarth/2020_Bannwarth_1493.pdf:PDF},
  keywords  = {Chemoinformatics; Quantum Chemistry},
  owner     = {saulius},
  publisher = {Wiley},
  timestamp = {2022.07.28},
  creationdate = {2022-07-28T00:00:00},
}

@Article{Wigh2022,
  author    = {Daniel S. Wigh and Jonathan M. Goodman and Alexei A. Lapkin},
  journal   = {{WIREs} Computational Molecular Science},
  title     = {A review of molecular representation in the age of machine learning},
  year      = {2022},
  month     = {feb},
  pages     = {1603},
  comment   = {Recommended by Wiley next to the (Kim2015) paper.},
  doi       = {10.1002/wcms.1603},
  file      = {:by-author/W/Wigh/2022_Wigh_1603.pdf:PDF},
  keywords  = {Chemoinformatics; Machine Learning (ML)},
  owner     = {saulius},
  publisher = {Wiley},
  timestamp = {2022.07.28},
  creationdate = {2022-07-28T00:00:00},
}

@Presentation{Jensen2020,
  author       = {Jan H. Jensen},
  title        = {Dealing with organometallic molecules in {RDKit}(?)},
  year         = {2020},
  organization = {Department of Chemistry, University of Copenhagen},
  comment      = {Talk available at: https://www.youtube.com/watch?v=HD6IpXMVKeo (accessed 2022-07-28T10:12+03:00).
Cites Quiros2018.},
  file         = {:by-author/J/Jensen/2020_Jensen_1.pdf:PDF},
  keywords     = {Chemical Representations; Chemoinformatics; Dative Bonds; Metal-organic Compounds; Organometallic Compounds; RDKit},
  owner        = {saulius},
  pages        = {1--20},
  timestamp = {2022.07.28},
  creationdate = {2022-07-28T00:00:00},
  url          = {https://raw.githubusercontent.com/rdkit/UGM_2020/master/Presentations/JanJensen.pdf},
}

@Misc{Strasser2022,
  author    = {Strasser, Carly and Hertweck, Kate and Greenberg, Josh and Taraborelli, Dario and Vu, Elizabeth},
  title     = {10 simple rules for funding scientific {O}pen {S}ource {S}oftware},
  year      = {2022},
  comment   = {Announced by the jklump <Jens Klump> via Software Source Code IG <software-source-code-ig@rda-groups.org> on the 2022-08-10 10:24.
Dr Jens Klump 
Group Leader Exploration Through Cover  |  CSIRO 
jens.klump@csiro.au   |  +61 8 6436 8828},
  copyright = {Creative Commons Attribution 4.0 International},
  doi       = {10.5281/ZENODO.6611500},
  file      = {:by-author/S/Strasser/2022_Strasser_1.pdf:PDF},
  keywords  = {Funding; Open Source},
  owner     = {saulius},
  pages     = {1--13},
  publisher = {Zenodo},
  timestamp = {2022.08.12},
  creationdate = {2022-08-12T00:00:00},
}

@Article{Sugahara2022,
  author    = {Tomohiro Sugahara and Daisuke Hashizume and Norihiro Tokitoh and Hiroshi Matsui and Ryohei Kishi and Masayoshi Nakano and Takahiro Sasamori},
  journal   = {Physical Chemistry Chemical Physics},
  title     = {Characterization of resonance structures in aromatic rings of benzene and its heavier-element analogues},
  year      = {2022},
  comment   = {Structures cod/7245380 and cod/7245381 deposited to the COD.},
  doi       = {10.1039/d2cp03068c},
  file      = {:by-author/S/Sugahara/2022_Sugahara.pdf:PDF;:by-author/S/Sugahara/2022_Sugahara_suppl.pdf:PDF},
  keywords  = {Chemistry; Resonance},
  owner     = {saulius},
  publisher = {Royal Society of Chemistry ({RSC})},
  timestamp = {2022.08.26},
  creationdate = {2022-08-26T00:00:00},
}

@Article{Gale2021,
  author    = {Julian D. Gale and Luc M. LeBlanc and Peter R. Spackman and Alessandro Silvestri and Paolo Raiteri},
  journal   = {Journal of Chemical Theory and Computation},
  title     = {A universal force field for materials, periodic {GFN}-{FF}: implementation and examination},
  year      = {2021},
  month     = {nov},
  number    = {12},
  pages     = {7827--7849},
  volume    = {17},
  doi       = {10.1021/acs.jctc.1c00832},
  file      = {:by-author/G/Gale/2021_Gale_7827.pdf:PDF},
  keywords  = {COD; Computer Science (CS); Force Fields; Material Science; Quantum Chemistry; Quantum Mechanics (QM)},
  owner     = {saulius},
  publisher = {American Chemical Society ({ACS})},
  timestamp = {2022.09.17},
  creationdate = {2022-09-17T00:00:00},
}

@Presentation{Petrauskas2022a,
  author    = {Karolis Petrauskas},
  title     = {Finite model for a randomized binary agreement: model checking safety and liveness properties in {TLA+}},
  year      = {2022},
  comment   = {K.P.: „Prašyčiau neplatinti, nes čia dar nepublikuoti rezultatai“.},
  file      = {:by-author/P/Petrauskas/2022_Petrauskas_1.pdf:PDF;:by-author/P/Petrauskas/2022_Petrauskas_1_supplement/2022-09-18_09-19_Karolis-Petrauskas_karolis.petrauskas-at-mif.vu.lt.pdf:PDF},
  keywords  = {CSl TLA; Distributed Systems; Formal Proofs},
  owner     = {saulius},
  pages     = {1--42},
  timestamp = {2022.09.19},
  creationdate = {2022-09-19T00:00:00},
}

@Article{Gog2021,
  author    = {Heleen van Gog},
  journal   = {Applied Surface Science},
  title     = {First-principles study of dehydration interfaces between diaspore and corundum, gibbsite and boehmite, and boehmite and $\upgamma$-{Al2O3}: Energetic stability, interface charge effects, and dehydration defects},
  year      = {2021},
  month     = {mar},
  pages     = {148501},
  volume    = {541},
  comment   = {"or the present DFT calculations of large interface systems, however, a γ-Al 2 O 3 bulk phase simulation unit cell with less than 160 atoms was to be preferred".
"With a unit cell of 40 atoms, for the present study, this model is a good compromise between structural reliability and computational costs."},
  doi       = {10.1016/j.apsusc.2020.148501},
  file      = {:by-author/G/Gog/2021_Gog_148501.pdf:PDF},
  keywords  = {Density Functional Theory (DFT); First Principles; Material Science; Simulations},
  owner     = {saulius},
  publisher = {Elsevier {BV}},
  timestamp = {2022.09.29},
  creationdate = {2022-09-29T00:00:00},
}

@Article{Spicher2020,
  author    = {Sebastian Spicher and Stefan Grimme},
  journal   = {Angewandte Chemie International Edition},
  title     = {Robust Atomistic Modeling of Materials, Organometallic, and Biochemical Systems},
  year      = {2020},
  month     = {may},
  number    = {36},
  pages     = {15665--15673},
  volume    = {59},
  comment   = {Cited in Gale2021.},
  doi       = {10.1002/anie.202004239},
  file      = {:by-author/S/Spicher/2020_Spicher_15665.pdf:PDF},
  keywords  = {COD; Computer Science (CS); Force Fields; Material Science; Quantum Chemistry; Quantum Mechanics (QM)},
  owner     = {saulius},
  publisher = {Wiley},
  timestamp = {2022.09.29},
  creationdate = {2022-09-29T00:00:00},
}

@Article{Karthikeyan2016,
  author    = {Muthukumarasamy Karthikeyan and Renu Vyas},
  journal   = {Journal of Cheminformatics},
  title     = {{ChemEngine}: harvesting {3D} chemical structures of supplementary data from {PDF} files},
  year      = {2016},
  month     = {dec},
  number    = {1},
  pages     = {8:73},
  volume    = {8},
  doi       = {10.1186/s13321-016-0175-x},
  file      = {:by-author/K/Karthikeyan/2016_Karthikeyan_73.pdf:PDF},
  keywords  = {Chemoinformatics; Computer Science (CS); Data Harvesting},
  owner     = {saulius},
  publisher = {Springer Science and Business Media {LLC}},
  timestamp = {2022.09.29},
  creationdate = {2022-09-29T00:00:00},
}

@Article{Papapanagiotu2000,
  author    = {Evangelos G. Papapanagiotu and John N. Hatzopoulos},
  journal   = {International Archives of Photogrammetry and Remote Sensing},
  title     = {Automatic extraction of {3D} model coordinates using digital stereo images},
  year      = {2000},
  number    = {B4},
  pages     = {805--812},
  volume    = {33},
  file      = {:by-author/P/Papapanagiotu/2000_Papapanagiotu_805.pdf:PDF},
  keywords  = {Algorithms; Computer Science (CS); Image Processing; Stereo Images},
  owner     = {saulius},
  timestamp = {2022.09.29},
  creationdate = {2022-09-29T00:00:00},
  url       = {https://www.isprs.org/proceedings/XXXIII/congress/part4/805_XXXIII-part4.pdf},
}

@Article{Wilton2019,
  author          = {Wilton, Richard and Wheelan, Sarah J. and Szalay, Alexander S. and Salzberg, Steven L.},
  journal         = {Bioinformatics (Oxford, England)},
  title           = {The {T}erabase {S}earch {E}ngine: a large-scale relational database of short-read sequences.},
  year            = {2019},
  issn            = {1367-4811},
  month           = feb,
  pages           = {665--670},
  volume          = {35},
  abstract        = {DNA sequencing archives have grown to enormous scales in recent years, and thousands of human genomes have already been sequenced. The size of these data sets has made searching the raw read data infeasible without high-performance data-query technology. Additionally, it is challenging to search a repository of short-read data using relational logic and to apply that logic across samples from multiple whole-genome sequencing samples. We have built a compact, efficiently-indexed database that contains the raw read data for over 250 human genomes, encompassing trillions of bases of DNA, and that allows users to search these data in real-time. The Terabase Search Engine enables retrieval from this database of all the reads for any genomic location in a matter of seconds. Users can search using a range of positions or a specific sequence that is aligned to the genome on the fly. Public access to the Terabase Search Engine database is available at http://tse.idies.jhu.edu. Supplementary data are available at Bioinformatics online.},
  citation-subset = {IM},
  completed       = {2019-11-04},
  country         = {England},
  doi             = {10.1093/bioinformatics/bty657},
  file            = {:by-author/W/Wilton/2019_Wilton_665.pdf:PDF},
  issn-linking    = {1367-4803},
  issue           = {4},
  keywords        = {DNA; Databases; Genetic; Genome; Genomics; Human; Humans; Search Engine; Sequence Analysis; Software},
  nlm-id          = {9808944},
  owner           = {saulius},
  pii             = {5057158},
  pmc             = {PMC6379032},
  pmid            = {30052772},
  pubmodel        = {Print},
  pubstate        = {ppublish},
  revised         = {2020-03-09},
  timestamp = {2022.09.29},
  creationdate = {2022-09-29T00:00:00},
}

@Article{Katsura2017,
  author    = {Yukari Katsura and Masaya Kumagai and Sakiko Gunji and Yoji Imai and Kaoru Kimura},
  journal   = {Journal of the Japan Society of Powder and Powder Metallurgy},
  title     = {Development of {\textquotedblleft}{Starry data}{\textquotedblright} web system for data curation of published experimental thermoelectric properties},
  year      = {2017},
  number    = {8},
  pages     = {467--470},
  volume    = {64},
  doi       = {10.2497/jjspm.64.467},
  file      = {:by-author/K/Katsura/2017_Katsura_467.pdf:PDF},
  keywords  = {Data Curation; Data Extraction; Material Science; Scientific Database},
  owner     = {saulius},
  publisher = {Japan Society of Powder and Powder Metallurgy},
  timestamp = {2022.09.29},
  creationdate = {2022-09-29T00:00:00},
}

@Article{Katsura2019,
  author    = {Yukari Katsura and Masaya Kumagai and Takushi Kodani and Mitsunori Kaneshige and Yuki Ando and Sakiko Gunji and Yoji Imai and Hideyasu Ouchi and Kazuki Tobita and Kaoru Kimura and Koji Tsuda},
  journal   = {Science and Technology of Advanced Materials},
  title     = {Data-driven analysis of electron relaxation times in {PbTe}-type thermoelectric materials},
  year      = {2019},
  month     = {jun},
  number    = {1},
  pages     = {511--520},
  volume    = {20},
  doi       = {10.1080/14686996.2019.1603885},
  file      = {:by-author/K/Katsura/2019_Katsura_511.pdf:PDF},
  keywords  = {Data Curation; Data Extraction; Material Science; Scientific Database},
  owner     = {saulius},
  publisher = {Informa {UK} Limited},
  timestamp = {2022.09.29},
  creationdate = {2022-09-29T00:00:00},
}

@Article{Kratzer2019,
  author    = {Peter Kratzer and Jörg Neugebauer},
  journal   = {Frontiers in Chemistry},
  title     = {The basics of electronic structure theory for periodic systems},
  year      = {2019},
  month     = {mar},
  pages     = {106},
  volume    = {7},
  comment   = {"With the increase of computer power, computational physicists and materials scientists started to work on more and more complex systems comprising hundreds of atoms in one unit cell." This allows to justify 500--1000 atom limit.},
  doi       = {10.3389/fchem.2019.00106},
  file      = {:by-author/K/Kratzer/2019_Kratzer_106.pdf:PDF},
  keywords  = {Atom Number Limits; Computational Chemistry; Computational Material Science; Material Science; Quantum Mechanics (QM)},
  owner     = {saulius},
  publisher = {Frontiers Media {SA}},
  timestamp = {2022.09.30},
  creationdate = {2022-09-30T00:00:00},
}

@Article{Kuban2022,
  author        = {Martin Kuban and Santiago Rigamonti and Markus Scheidgen and Claudia Draxl},
  title         = {Density-of-states similarity descriptor for unsupervised learning from materials data},
  abstract      = {We develop a materials descriptor based on the electronic density of states and investigate the similarity of materials based on it. As an application example, we study the Computational 2D Materials Database that hosts thousands of two-dimensional materials with their properties calculated by density-functional theory. Combining our descriptor with a clustering algorithm, we identify groups of materials with similar electronic structure. We characterize these clusters in terms of their crystal structure, their atomic composition, and the respective electronic configurations to rationalize the found (dis)similarities.},
  archiveprefix = {arXiv},
  comment       = {Referenced in CECAM workshop "AI methods and scalability" talk: 2022-10-12	3	Martin Kuban	"Data analysis and quality assessment by fingerprinting"},
  date          = {2022-01-06},
  eprint        = {arxiv:2201.02187},
  eprintclass   = {cond-mat.mtrl-sci},
  eprinttype    = {arXiv},
  file          = {:by-author/K/Kuban/2022_Kuban_1.pdf:PDF},
  keywords      = {cond-mat.mtrl-sci},
  owner         = {saulius},
  timestamp = {2022.10.12},
  creationdate = {2022-10-12T00:00:00},
  url           = {https://doi.org/10.48550/arxiv.2201.02187},
}

@Article{Choudhary2022,
  author        = {Kamal Choudhary and Mathew L. Kelley},
  title         = {{ChemNLP}: a natural language processing based library for materials chemistry text data},
  abstract      = {Natural language processing (NLP) has an immense potential to aid materials design processes. While there have been several advancements in this field, a complete and integrated framework with well-curated dataset and tools to apply NLP is still needed. In this work, we present the ChemNLP library and an accompanying web-app that can be used to analyze important materials chemistry information. We use the publicly available arXiv dataset that has been collected over 34 years and contains ~1.8 million articles. First, we analyze the article publication trend, categorizations, and common phrases in the arXiv dataset. Then, we develop a user-friendly, interactive web-app to retrieve articles for a given chemical compound. Furthermore, we demonstrate the effectiveness of the proposed framework to accelerate the identification of superconducting materials. We determine the overlap between density functional theory and text-based databases for superconductors. Finally, we perform machine learning based clustering and classification tasks to quickly categorize scholarly articles given article title information with accuracy up to 81.2 %. ChemNLP is available at the websites: https://github.com/usnistgov/chemnlp and https://jarvis.nist.gov/jarvischemnlp.},
  archiveprefix = {arXiv},
  comment       = {Referenced in CECAM workshop "AI methods and scalability" talk: 2022-10-11	A	Kamal Choudhary	"NIST-JARVIS infrastructure for Improved Materials Design"},
  date          = {2022-09-17},
  eprint        = {2209.08203},
  eprintclass   = {cond-mat.mtrl-sci},
  eprinttype    = {arXiv},
  file          = {:by-author/C/Choudhary/2022_Choudhary_1.pdf:PDF},
  keywords      = {cond-mat.mtrl-sci; physics.chem-ph},
  owner         = {saulius},
  timestamp = {2022.10.12},
  creationdate = {2022-10-12T00:00:00},
  url           = {https://arxiv.org/abs/2209.08203},
}

@Article{Zhou2022,
  author        = {Yuxing Zhou and Wei Zhang and En Ma and Volker L. Deringer},
  title         = {Unlocking device-scale atomistic modelling of phase-change memory materials},
  abstract      = {Quantum-accurate computer simulations play a central role in understanding phase-change materials (PCMs) for advanced memory technologies. However, direct quantum-mechanical simulations are necessarily limited to simplified models, containing no more than a few hundred or a thousand atoms. Machine learning (ML) based potential models that are "trained" on quantum-mechanical data are an emerging alternative approach, currently evolving from highly specialised to more widely applied simulation tools. Here we show that a universal, compositionally flexible ML model can describe a wide range of flagship Ge-Sb-Te PCMs under real device conditions, including non-isothermal heating and chemical disorder which are relevant for memory applications. The speed of the ML model enables atomistic simulations of multiple thermal cycles and delicate operations for neuro-inspired computing, namely, cumulative SET and iterative RESET. A device-scale capability demonstration (40 x 20 x 20 nm3) shows that the new ML potential can directly describe technologically relevant processes in PCM-based memory products. In a wider context, our work demonstrates how ML-driven materials simulations are now entering a stage where they can guide architecture design for high-performance electronic devices.},
  archiveprefix = {arXiv},
  comment       = {Referenced in CECAM workshop "AI methods and scalability" talk: 2022-10-11	3	Gabor Csanyi	"First principles force fields"},
  date          = {2022-07-28},
  eprint        = {2207.14228},
  eprintclass   = {cond-mat.mtrl-sci},
  eprinttype    = {arXiv},
  file          = {:by-author/Z/Zhou/2022_Zhou_1.pdf:PDF},
  keywords      = {cond-mat.mtrl-sci},
  owner         = {saulius},
  timestamp = {2022.10.12},
  creationdate = {2022-10-12T00:00:00},
  url           = {https://arxiv.org/abs/2207.14228},
}

@Article{Gurunathan2022,
  author        = {Ramya Gurunathan and Kamal Choudhary and Francesca Tavazza},
  title         = {Rapid prediction of phonon structure and properties using an {A}tomistic {L}ine {G}raph {N}eural {N}etwork ({ALIGNN})},
  pages         = {1--22},
  abstract      = {The phonon density-of-states (DOS) summarizes the lattice vibrational modes supported by a structure, and gives access to rich information about the material's stability, thermodynamic constants, and thermal transport coefficients. Here, we present an atomistic line graph neural network (ALIGNN) model for the prediction of the phonon density of states and the derived thermal and thermodynamic properties. The model is trained on a database of over 14,000 phonon spectra included in the JARVIS-DFT (Joint Automated Repository for Various Integrated Simulations: Density Functional Theory) database. The model predictions are shown to capture the spectral features of the phonon density-of-states, effectively categorize dynamical stability, and lead to accurate predictions of DOS-derived thermal and thermodynamic properties, including heat capacity $C_{\mathrm{V}}$, vibrational entropy $S_{\mathrm{vib}}$, and the isotopic phonon scattering rate $\tau^{-1}_{\mathrm{i}}$. The DOS-mediated ALIGNN model provides superior predictions when compared to a direct deep-learning prediction of these material properties as well as predictions based on analytic simplifications of the phonon DOS, including the Debye or Born-von Karman models. Finally, the ALIGNN model is used to predict the phonon spectra and properties for about 40,000 additional materials listed in the JARVIS-DFT database, which are validated as far as possible against other open-sourced high-throughput DFT phonon databases.},
  archiveprefix = {arXiv},
  comment       = {Referenced in CECAM workshop "AI methods and scalability" talk: 2022-10-11	A	Kamal Choudhary	"NIST-JARVIS infrastructure for Improved Materials Design"},
  date          = {2022-07-25},
  eprint        = {2207.12510},
  eprintclass   = {cond-mat.mtrl-sci},
  eprinttype    = {arXiv},
  file          = {:by-author/G/Gurunathan/2022_Gurunathan_1.pdf:PDF},
  keywords      = {cond-mat.mtrl-sci},
  owner         = {saulius},
  timestamp = {2022.10.12},
  creationdate = {2022-10-12T00:00:00},
  url           = {https://arxiv.org/abs/2207.12510},
}

@Article{Lyngby2022,
  author        = {Peder Lyngby and Kristian Sommer Thygesen},
  title         = {Data-driven discovery of novel {2D} materials by deep generative models},
  abstract      = {Efficient algorithms to generate candidate crystal structures with good stability properties can play a key role in data-driven materials discovery. Here we show that a crystal diffusion variational autoencoder (CDVAE) is capable of generating two-dimensional (2D) materials of high chemical and structural diversity and formation energies mirroring the training structures. Specifically, we train the CDVAE on 2615 2D materials with energy above the convex hull $\Delta H_{\mathrm{hull}}< 0.3$ eV/atom, and generate 5003 materials that we relax using density functional theory (DFT). We also generate 14192 new crystals by systematic element substitution of the training structures. We find that the generative model and lattice decoration approach are complementary and yield materials with similar stability properties but very different crystal structures and chemical compositions. In total we find 11630 predicted new 2D materials, where 8599 of these have $\Delta H_{\mathrm{hull}}< 0.3$ eV/atom as the seed structures, while 2004 are within 50 meV of the convex hull and could potentially be synthesized. The relaxed atomic structures of all the materials are available in the open Computational 2D Materials Database (C2DB). Our work establishes the CDVAE as an efficient and reliable crystal generation machine, and significantly expands the space of 2D materials.},
  archiveprefix = {arXiv},
  comment       = {Referenced in CECAM workshop "AI methods and scalability" talk: 2022-10-12	2	Kristian Thygesen	"Accelerating materials discovery using deep generative models and electronic descriptors"},
  date          = {2022-06-24},
  eprint        = {2206.12159},
  eprintclass   = {cond-mat.mtrl-sci},
  eprinttype    = {arXiv},
  file          = {:by-author/L/Lyngby/2022_Lyngby_1.pdf:PDF},
  keywords      = {cond-mat.mtrl-sci; cs.LG; physics.comp-ph},
  owner         = {saulius},
  timestamp = {2022.10.12},
  creationdate = {2022-10-12T00:00:00},
  url           = {https://arxiv.org/abs/2206.12159},
}

@Article{Batatia2022,
  author        = {Ilyes Batatia and Dávid Péter Kovács and Gregor N. C. Simm and Christoph Ortner and Gábor Csányi},
  title         = {{MACE}: higher order equivariant message passing neural networks for fast and accurate force fields},
  abstract      = {Creating fast and accurate force fields is a long-standing challenge in computational chemistry and materials science. Recently, several equivariant message passing neural networks (MPNNs) have been shown to outperform models built using other approaches in terms of accuracy. However, most MPNNs suffer from high computational cost and poor scalability. We propose that these limitations arise because MPNNs only pass two-body messages leading to a direct relationship between the number of layers and the expressivity of the network. In this work, we introduce MACE, a new equivariant MPNN model that uses higher body order messages. In particular, we show that using four-body messages reduces the required number of message passing iterations to just \emph{two}, resulting in a fast and highly parallelizable model, reaching or exceeding state-of-the-art accuracy on the rMD17, 3BPA, and AcAc benchmark tasks. We also demonstrate that using higher order messages leads to an improved steepness of the learning curves.},
  archiveprefix = {arXiv},
  comment       = {Referenced in CECAM workshop "AI methods and scalability" talk: 2022-10-11	4	James Darby	"Tensor-reduced atomic density representations"},
  date          = {2022-06-15},
  eprint        = {2206.07697},
  eprintclass   = {stat.ML},
  eprinttype    = {arXiv},
  file          = {:by-author/B/Batatia/2022_Batatia_1.pdf:PDF},
  keywords      = {cond-mat.mtrl-sci; cs.LG; physics.chem-ph; stat.ML},
  owner         = {saulius},
  timestamp = {2022.10.12},
  creationdate = {2022-10-12T00:00:00},
  url           = {https://arxiv.org/abs/2206.07697},
}

@Article{Choudhary2022a,
  author        = {Kamal Choudhary and Bobby G. Sumpter},
  title         = {A deep-learning model for fast prediction of vacancy formation in diverse materials},
  abstract      = {The presence of point defects such as vacancies plays an important role in material design. Here, we demonstrate that a graph neural network (GNN) model trained only on perfect materials can also be used to predict vacancy formation energies ($E_{vac}$) of defect structures without the need for additional training data. Such GNN-based predictions are considerably faster than density functional theory (DFT) calculations with reasonable accuracy and show the potential that GNNs are able to capture a functional form for energy predictions. To test this strategy, we developed a DFT dataset of 508 $E_{vac}$ consisting of 3D elemental solids, alloys, oxides, nitrides, and 2D monolayer materials. We analyzed and discussed the applicability of such direct and fast predictions. We applied the model to predict 192494 $E_{vac}$ for 55723 materials in the JARVIS-DFT database.},
  archiveprefix = {arXiv},
  comment       = {Referenced in CECAM workshop "AI methods and scalability" talk: 2022-10-11	A	Kamal Choudhary	"NIST-JARVIS infrastructure for Improved Materials Design"},
  date          = {2022-05-17},
  eprint        = {2205.08366},
  eprintclass   = {cond-mat.mtrl-sci},
  eprinttype    = {arXiv},
  file          = {:by-author/C/Choudhary/2022_Choudhary_1a.pdf:PDF},
  keywords      = {cond-mat.mtrl-sci},
  owner         = {saulius},
  timestamp = {2022.10.12},
  creationdate = {2022-10-12T00:00:00},
  url           = {https://arxiv.org/abs/2205.08366},
}

@Article{Choudhary2022b,
  author        = {Kamal Choudhary and Kevin Garrity},
  title         = {Designing high-{Tc} superconductors with {BCS}-inspired screening, density functional theory and deep-learning},
  abstract      = {Recent advances in first principles calculations and machine learning techniques allow for a systematic search for phonon-mediated superconductors. We develop a multi-step workflow for the discovery of conventional superconductors, starting with a Bardeen-Cooper-Schrieffer inspired pre-screening of 1736 materials with high Debye temperature and electronic density of states at the Fermi-level. Next, we perform electron-phonon coupling calculations for 988 of them to establish a large and systematic database of BCS superconducting properties. Using the McMillan-Allen-Dynes formula, we identify 112 dynamically stable materials with transition temperatures, Tc > 5 K. In addition, we analyze trends in our dataset and individual materials including MoN, VC, VTe, KB6, Ru3NbC, V3Pt, ScN, LaN2, RuO2, and TaC. Finally, we demonstrate that deep-learning models can predict superconductor properties, including the Eliashberg function, thousands of times faster than direct first principles computations. We apply the trained model on the crystallographic open database and pre-screen 8293 candidates for further DFT calculations.},
  archiveprefix = {arXiv},
  comment       = {Referenced in CECAM workshop "AI methods and scalability" talk: 2022-10-11	A	Kamal Choudhary	"NIST-JARVIS infrastructure for Improved Materials Design"},
  date          = {2022-04-29},
  eprint        = {2205.00060},
  eprintclass   = {cond-mat.supr-con},
  eprinttype    = {arXiv},
  file          = {:by-author/C/Choudhary/2022_Choudhary_1b.pdf:PDF},
  keywords      = {cond-mat.supr-con},
  owner         = {saulius},
  timestamp = {2022.10.12},
  creationdate = {2022-10-12T00:00:00},
  url           = {https://arxiv.org/abs/2205.00060},
}

@Article{Wang2022,
  author        = {Wujie Wang and Minkai Xu and Chen Cai and Benjamin Kurt Miller and Tess Smidt and Yusu Wang and Jian Tang and Rafael Gómez-Bombarelli},
  title         = {Generative coarse-graining of molecular conformations},
  abstract      = {Coarse-graining (CG) of molecular simulations simplifies the particle representation by grouping selected atoms into pseudo-beads and drastically accelerates simulation. However, such CG procedure induces information losses, which makes accurate backmapping, i.e., restoring fine-grained (FG) coordinates from CG coordinates, a long-standing challenge. Inspired by the recent progress in generative models and equivariant networks, we propose a novel model that rigorously embeds the vital probabilistic nature and geometric consistency requirements of the backmapping transformation. Our model encodes the FG uncertainties into an invariant latent space and decodes them back to FG geometries via equivariant convolutions. To standardize the evaluation of this domain, we provide three comprehensive benchmarks based on molecular dynamics trajectories. Experiments show that our approach always recovers more realistic structures and outperforms existing data-driven methods with a significant margin.},
  archiveprefix = {arXiv},
  comment       = {Referenced in CECAM workshop "AI methods and scalability" talk: 2022-10-11	6	Tess Smidt	"A Quick Tour of Applications, Symmetry, and Symmetry-Breaking of Euclidean Neural Networks"},
  date          = {2022-01-28},
  eprint        = {2201.12176},
  eprintclass   = {cs.LG},
  eprinttype    = {arXiv},
  file          = {:by-author/W/Wang/2022_Wang_1.pdf:PDF},
  journaltitle  = {International Conference on Machine Learning (ICML), 2022},
  keywords      = {cs.LG; physics.chem-ph; physics.comp-ph},
  owner         = {saulius},
  timestamp = {2022.10.12},
  creationdate = {2022-10-12T00:00:00},
  url           = {https://arxiv.org/abs/2201.12176},
}

@Article{Pozdnyakov2022,
  author        = {Sergey N. Pozdnyakov and Michele Ceriotti},
  title         = {Incompleteness of graph convolutional neural networks for points clouds in three dimensions},
  abstract      = {Graph neural networks (GNN) are very popular methods in machine learning and have been applied very successfully to the prediction of the properties of molecules and materials. First-order GNNs are well known to be incomplete, i.e., there exist graphs that are distinct but appear identical when seen through the lens of the GNN. More complicated schemes have thus been designed to increase their resolving power. Applications to molecules (and more generally, point clouds), however, add a geometric dimension to the problem. The most straightforward and prevalent approach to construct graph representation for molecules regards atoms as vertices in a graph and draws a bond between each pair of atoms within a chosen cutoff. Bonds can be decorated with the distance between atoms, and the resulting "distance graph NNs" (dGNN) have empirically demonstrated excellent resolving power and are widely used in chemical ML, with all known indistinguishable graphs being resolved in the fully-connected limit. Here we show that even for the restricted case of fully-connected graphs induced by 3D atom clouds dGNNs are not complete. We construct pairs of distinct point clouds that generate graphs that, for any cutoff radius, are equivalent based on a first-order Weisfeiler-Lehman test. This class of degenerate structures includes chemically-plausible configurations, setting an ultimate limit to the expressive power of some of the well-established GNN architectures for atomistic machine learning. Models that explicitly use angular or directional information in the description of atomic environments can resolve these degeneracies.},
  archiveprefix = {arXiv},
  comment       = {Referenced in CECAM workshop "AI methods and scalability" talk: 2022-10-10	1	Michele Ceriotti	"Atom-density representations for machine learning"},
  date          = {2022-01-18},
  eprint        = {2201.07136},
  eprintclass   = {stat.ML},
  eprinttype    = {arXiv},
  file          = {:by-author/P/Pozdnyakov/2022_Pozdnyakov_1.pdf:PDF},
  keywords      = {cs.LG; physics.chem-ph; stat.ML},
  owner         = {saulius},
  timestamp = {2022.10.12},
  creationdate = {2022-10-12T00:00:00},
  url           = {https://arxiv.org/abs/2201.07136},
}

@Article{Rackers2022,
  author        = {Joshua A. Rackers and Lucas Tecot and Mario Geiger and Tess E. Smidt},
  title         = {Cracking the quantum scaling limit with machine learned electron densities},
  abstract      = {A long-standing goal of science is to accurately solve the Schr\"odinger equation for large molecular systems. The poor scaling of current quantum chemistry algorithms on classical computers imposes an effective limit of about a few dozen atoms for which we can calculate molecular electronic structure. We present a machine learning (ML) method to break through this scaling limit and make quantum chemistry calculations of very large systems possible. We show that Euclidean Neural Networks can be trained to predict the electron density with high fidelity from limited data. Learning the electron density allows us to train a machine learning model on small systems and make accurate predictions on large ones. We show that this ML electron density model can break through the quantum scaling limit and calculate the electron density of systems of thousands of atoms with quantum accuracy.},
  archiveprefix = {arXiv},
  comment       = {Referenced in CECAM workshop "AI methods and scalability" talk: 2022-10-11	6	Tess Smidt	"A Quick Tour of Applications, Symmetry, and Symmetry-Breaking of Euclidean Neural Networks"},
  date          = {2022-01-11},
  eprint        = {2201.03726},
  eprintclass   = {physics.chem-ph},
  eprinttype    = {arXiv},
  file          = {:by-author/R/Rackers/2022_Rackers_1.pdf:PDF},
  keywords      = {cond-mat.soft; physics.bio-ph; physics.chem-ph},
  owner         = {saulius},
  timestamp = {2022.10.12},
  creationdate = {2022-10-12T00:00:00},
  url           = {https://arxiv.org/abs/2201.03726},
}

@Article{Garrity2021,
  author        = {Kevin F. Garrity and Kamal Choudhary},
  title         = {Fast and accurate prediction of material properties with three-body tight-binding model for the periodic table},
  abstract      = {Parameterized tight-binding models fit to first principles calculations can provide an efficient and accurate quantum mechanical method for predicting properties of molecules and solids. However, well-tested parameter sets are generally only available for a limited number of atom combinations, making routine use of this method difficult. Furthermore, most previous models consider only simple two-body interactions, which limits accuracy. To tackle these challenges, we develop a density functional theory database of nearly one million materials, which we use to fit a universal set of tight-binding parameters for 65 elements and their binary combinations. We include both two-body and three-body effective interaction terms in our model, plus self-consistent charge transfer, enabling our model to work for metallic, covalent, and ionic bonds with the same parameter set. To ensure predictive power, we adopt a learning framework where we repeatedly test the model on new low energy crystal structures and then add them to the fitting dataset, iterating until predictions improve. We distribute the materials database and tools developed in this work publicly.},
  archiveprefix = {arXiv},
  comment       = {Referenced in CECAM workshop "AI methods and scalability" talk: 2022-10-11	A	Kamal Choudhary	"NIST-JARVIS infrastructure for Improved Materials Design"},
  date          = {2021-12-22},
  eprint        = {2112.11585},
  eprintclass   = {cond-mat.mtrl-sci},
  eprinttype    = {arXiv},
  file          = {:by-author/G/Garrity/2021_Garrity_1.pdf:PDF},
  keywords      = {cond-mat.mtrl-sci},
  owner         = {saulius},
  timestamp = {2022.10.12},
  creationdate = {2022-10-12T00:00:00},
  url           = {https://arxiv.org/abs/2112.11585},
}

@Article{Sato2020,
  author        = {Ryoma Sato},
  title         = {A survey on the expressive power of graph neural networks},
  abstract      = {Graph neural networks (GNNs) are effective machine learning models for various graph learning problems. Despite their empirical successes, the theoretical limitations of GNNs have been revealed recently. Consequently, many GNN models have been proposed to overcome these limitations. In this survey, we provide a comprehensive overview of the expressive power of GNNs and provably powerful variants of GNNs.},
  archiveprefix = {arXiv},
  comment       = {Referenced in CECAM workshop "AI methods and scalability" talk: 2022-10-10	1	Michele Ceriotti	"Atom-density representations for machine learning"},
  date          = {2020-03-09},
  eprint        = {2003.04078},
  eprintclass   = {cs.LG},
  eprinttype    = {arXiv},
  file          = {:by-author/S/Sato/2020_Sato_1.pdf:PDF},
  keywords      = {cs.LG; stat.ML},
  owner         = {saulius},
  timestamp = {2022.10.12},
  creationdate = {2022-10-12T00:00:00},
  url           = {https://arxiv.org/abs/2003.04078},
}

@Article{Gold2019,
  author        = {Jacob M. Gold and Jeremy L. England},
  title         = {Self-organized novelty detection in driven spin glasses},
  abstract      = {We consider a glassy system of interacting spins driven by continual switching amongst a finite set of nonuniform external fields. We find that the system evolves over time towards configurations that minimize the work absorbed from this external drive. The configurations which achieve this are specific to the details of the external fields used to drive the system, and therefore act effectively as a self-organized novelty-detector that embodies accurate predictions about the typical future of its external environment.},
  archiveprefix = {arXiv},
  comment       = {Referenced in CECAM workshop "AI methods and scalability" talk: 2022-10-10	2	Nicole Yunger Halpern	"Learning about learning by many-body systems"},
  date          = {2019-11-17},
  eprint        = {1911.07216},
  eprintclass   = {nlin.AO},
  eprinttype    = {arXiv},
  file          = {:by-author/G/Gold/2019_Gold_1.pdf:PDF},
  keywords      = {cond-mat.stat-mech; nlin.AO},
  owner         = {saulius},
  timestamp = {2022.10.12},
  creationdate = {2022-10-12T00:00:00},
  url           = {https://arxiv.org/abs/1911.07216},
}

@Article{Dusson2019,
  author        = {Genevieve Dusson and Markus Bachmayr and Gabor Csanyi and Ralf Drautz and Simon Etter and Cas van der Oord and Christoph Ortner},
  title         = {{A}tomic {C}luster {E}xpansion: completeness, efficiency and stability},
  abstract      = {The Atomic Cluster Expansion (Drautz, Phys. Rev. B 99, 2019) provides a framework to systematically derive polynomial basis functions for approximating isometry and permutation invariant functions, particularly with an eye to modelling properties of atomistic systems. Our presentation extends the derivation by proposing a precomputation algorithm that yields immediate guarantees that a complete basis is obtained. We provide a fast recursive algorithm for efficient evaluation and illustrate its performance in numerical tests. Finally, we discuss generalisations and open challenges, particularly from a numerical stability perspective, around basis optimisation and parameter estimation, paving the way towards a comprehensive analysis of the convergence to a high-fidelity reference model.},
  archiveprefix = {arXiv},
  comment       = {Referenced in CECAM workshop "AI methods and scalability" talk: 2022-10-11	4	James Darby	"Tensor-reduced atomic density representations"},
  date          = {2019-11-08},
  eprint        = {1911.03550},
  eprintclass   = {math.NA},
  eprinttype    = {arXiv},
  file          = {:by-author/D/Dusson/2019_Dusson_1.pdf:PDF},
  keywords      = {cs.NA; math.NA},
  owner         = {saulius},
  timestamp = {2022.10.12},
  creationdate = {2022-10-12T00:00:00},
  url           = {https://arxiv.org/abs/1911.03550},
}

@Article{Lambrix2019,
  author        = {Patrick Lambrix},
  title         = {Completing and debugging ontologies: state of the art and challenges},
  abstract      = {As semantically-enabled applications require high-quality ontologies, developing and maintaining ontologies that are as correct and complete as possible is an important although difficult task in ontology engineering. A key step is ontology debugging and completion. In general, there are two steps: detecting defects and repairing defects. In this paper we discuss the state of the art regarding the repairing step. We do this by formalizing the repairing step as an abduction problem and situating the state of the art with respect to this framework. We show that there are still many open research problems and show opportunities for further work and advancing the field.},
  archiveprefix = {arXiv},
  comment       = {Referenced in CECAM workshop "AI methods and scalability" talk: 2022-10-11	9	Rickard Armiento	"Charting the space of crystalline materials by symmetry"},
  date          = {2019-08-08},
  eprint        = {1908.03171},
  eprintclass   = {cs.AI},
  eprinttype    = {arXiv},
  file          = {:by-author/L/Lambrix/2019_Lambrix_1.pdf:PDF},
  keywords      = {cs.AI; cs.LO},
  owner         = {saulius},
  timestamp = {2022.10.12},
  creationdate = {2022-10-12T00:00:00},
  url           = {https://arxiv.org/abs/1908.03171},
}

@Article{Togo2018,
  author           = {Atsushi Togo and Isao Tanaka},
  title            = {$\texttt{Spglib}$: a software library for crystal symmetry search},
  abstract         = {A computer algorithm to search crystal symmetries of crystal structures has been implemented in software $\texttt{spglib}$. An iterative algorithm is employed to find a set of space group operations that belongs to any one of space group types by accepting certain amount of distortion for input unit cell structures. The source code is distributed under the BSD 3-Clause License that is a permissive free software licence. Although $\texttt{spglib}$ is a small code, the iteration loops made the source code complicated. The aim of this text is to provide the algorithm details to those people who are interested in inside-$\texttt{spglib}$. This text is written for $\texttt{spglib}$ v1.10.4.},
  archiveprefix    = {arXiv},
  comment          = {Referenced in CECAM workshop "AI methods and scalability" talk: 2022-10-12	5	Andreas Leitherer	"Exploring materials space by combining supervised structure recognition and unsupervised machine learning"},
  creationdate     = {2022-10-12T00:00:00},
  date             = {2018-08-05},
  eprint           = {1808.01590},
  eprintclass      = {cond-mat.mtrl-sci},
  eprinttype       = {arXiv},
  file             = {:by-author/T/Togo/2018_Togo_1.pdf:PDF},
  keywords         = {Algorithms; C Library; Crystallography; Materials Science (cond-mat.mtrl-sci), FOS: Physical sciences, FOS: Physical sciences; Spacegroup Determination; Spacegroups; Spglib; Symmetry Determination; cond-mat.mtrl-sci},
  modificationdate = {2024-06-02T17:50:45},
  owner            = {saulius},
  timestamp        = {2022.10.12},
  url              = {https://arxiv.org/abs/1808.01590},
}

@Article{Alemi2018,
  author        = {Alexander A. Alemi and Ian Fischer},
  title         = {{TherML}: thermodynamics of machine learning},
  abstract      = {In this work we offer a framework for reasoning about a wide class of existing objectives in machine learning. We develop a formal correspondence between this work and thermodynamics and discuss its implications.},
  archiveprefix = {arXiv},
  comment       = {Referenced in CECAM workshop "AI methods and scalability" talk: 2022-10-10	2	Nicole Yunger Halpern	"Learning about learning by many-body systems"},
  date          = {2018-07-11},
  eprint        = {1807.04162},
  eprintclass   = {cs.LG},
  eprinttype    = {arXiv},
  file          = {:by-author/A/Alemi/2018_Alemi_1.pdf:PDF},
  keywords      = {cond-mat.stat-mech; cs.LG; stat.ML},
  owner         = {saulius},
  timestamp = {2022.10.12},
  creationdate = {2022-10-12T00:00:00},
  url           = {https://arxiv.org/abs/1807.04162},
}

@Article{Willatt2018,
  author        = {Michael J. Willatt and Félix Musil and Michele Ceriotti},
  title         = {Feature optimization for atomistic machine learning yields a data-driven construction of the periodic table of the elements},
  abstract      = {Machine-learning of atomic-scale properties amounts to extracting correlations between structure, composition and the quantity that one wants to predict. Representing the input structure in a way that best reflects such correlations makes it possible to improve the accuracy of the model for a given amount of reference data. When using a description of the structures that is transparent and well-principled, optimizing the representation might reveal insights into the chemistry of the data set. Here we show how one can generalize the SOAP kernel to introduce a distance-dependent weight that accounts for the multi-scale nature of the interactions, and a description of correlations between chemical species. We show that this improves substantially the performance of ML models of molecular and materials stability, while making it easier to work with complex, multi-component systems and to extend SOAP to coarse-grained intermolecular potentials. The element correlations that give the best performing model show striking similarities with the conventional periodic table of the elements, providing an inspiring example of how machine learning can rediscover, and generalize, intuitive concepts that constitute the foundations of chemistry.},
  archiveprefix = {arXiv},
  comment       = {Referenced in CECAM workshop "AI methods and scalability" talk: 2022-10-10	1	Michele Ceriotti	"Atom-density representations for machine learning"},
  date          = {2018-06-30},
  doi           = {10.1039/C8CP05921G},
  eprint        = {1807.00236},
  eprintclass   = {physics.chem-ph},
  eprinttype    = {arXiv},
  file          = {:by-author/W/Willatt/2018_Willatt_1.pdf:PDF;:by-author/W/Willatt/2018_Willatt_1_suppl.pdf:PDF},
  journaltitle  = {Physical Chemistry Chemical Physics, 20, 29661 (2018)},
  keywords      = {physics.chem-ph; physics.comp-ph; stat.ML},
  owner         = {saulius},
  timestamp = {2022.10.12},
  creationdate = {2022-10-12T00:00:00},
  url           = {https://arxiv.org/abs/1807.00236},
}

@Article{McInnes2018,
  author        = {Leland McInnes and John Healy and James Melville},
  title         = {{UMAP}: {U}niform {M}anifold {A}pproximation and {P}rojection for dimension reduction},
  abstract      = {UMAP (Uniform Manifold Approximation and Projection) is a novel manifold learning technique for dimension reduction. UMAP is constructed from a theoretical framework based in Riemannian geometry and algebraic topology. The result is a practical scalable algorithm that applies to real world data. The UMAP algorithm is competitive with t-SNE for visualization quality, and arguably preserves more of the global structure with superior run time performance. Furthermore, UMAP has no computational restrictions on embedding dimension, making it viable as a general purpose dimension reduction technique for machine learning.},
  archiveprefix = {arXiv},
  comment       = {Referenced in CECAM workshop "AI methods and scalability" talk: 2022-10-12	5	Andreas Leitherer	"Exploring materials space by combining supervised structure recognition and unsupervised machine learning"},
  date          = {2018-02-09},
  eprint        = {1802.03426},
  eprintclass   = {stat.ML},
  eprinttype    = {arXiv},
  file          = {:by-author/M/McInnes/2018_McInnes_1.pdf:PDF},
  keywords      = {cs.CG; cs.LG; stat.ML},
  owner         = {saulius},
  timestamp = {2022.10.12},
  creationdate = {2022-10-12T00:00:00},
  url           = {https://arxiv.org/abs/1802.03426},
}

@Article{Kingma2013,
  author           = {Diederik P. Kingma and Max Welling},
  title            = {Auto-encoding {V}ariational {B}ayes},
  abstract         = {How can we perform efficient inference and learning in directed probabilistic models, in the presence of continuous latent variables with intractable posterior distributions, and large datasets? We introduce a stochastic variational inference and learning algorithm that scales to large datasets and, under some mild differentiability conditions, even works in the intractable case. Our contributions is two-fold. First, we show that a reparameterization of the variational lower bound yields a lower bound estimator that can be straightforwardly optimized using standard stochastic gradient methods. Second, we show that for i.i.d. datasets with continuous latent variables per datapoint, posterior inference can be made especially efficient by fitting an approximate inference model (also called a recognition model) to the intractable posterior using the proposed lower bound estimator. Theoretical advantages are reflected in experimental results.},
  archiveprefix    = {arXiv},
  comment          = {Referenced in CECAM workshop "AI methods and scalability" talk: 2022-10-10	2	Nicole Yunger Halpern	"Learning about learning by many-body systems"},
  creationdate     = {2022-10-12T00:00:00},
  date             = {2013-12-20},
  eprint           = {1312.6114},
  eprintclass      = {stat.ML},
  eprinttype       = {arXiv},
  file             = {:by-author/K/Kingma/2013_Kingma_1.pdf:PDF},
  keywords         = {cs.LG; stat.ML},
  modificationdate = {2023-06-18T10:04:09},
  owner            = {saulius},
  timestamp        = {2022.10.12},
  url              = {https://arxiv.org/abs/1312.6114},
}

@Article{Bengio2012,
  author        = {Yoshua Bengio and Aaron Courville and Pascal Vincent},
  title         = {{R}epresentation {L}earning: a review and new perspectives},
  abstract      = {The success of machine learning algorithms generally depends on data representation, and we hypothesize that this is because different representations can entangle and hide more or less the different explanatory factors of variation behind the data. Although specific domain knowledge can be used to help design representations, learning with generic priors can also be used, and the quest for AI is motivating the design of more powerful representation-learning algorithms implementing such priors. This paper reviews recent work in the area of unsupervised feature learning and deep learning, covering advances in probabilistic models, auto-encoders, manifold learning, and deep networks. This motivates longer-term unanswered questions about the appropriate objectives for learning good representations, for computing representations (i.e., inference), and the geometrical connections between representation learning, density estimation and manifold learning.},
  archiveprefix = {arXiv},
  comment       = {Referenced in CECAM workshop "AI methods and scalability" talk: 2022-10-10	2	Nicole Yunger Halpern	"Learning about learning by many-body systems"},
  date          = {2012-06-24},
  eprint        = {1206.5538},
  eprintclass   = {cs.LG},
  eprinttype    = {arXiv},
  file          = {:by-author/B/Bengio/2012_Bengio_1.pdf:PDF},
  keywords      = {cs.LG},
  owner         = {saulius},
  timestamp = {2022.10.12},
  creationdate = {2022-10-12T00:00:00},
  url           = {https://arxiv.org/abs/1206.5538},
}

@Book{Berghofer2021,
  author    = {Stefan Berghofer},
  publisher = {secunet Security Networks AG},
  title     = {The {HOL}-{SPARK} program verification environment},
  year      = {2021},
  file      = {:by-author/B/Berghofer/2021_Berghofer_1.pdf:PDF},
  keywords  = {Ada; Computer Science (CS); Correctness Proofs; HOL; SPARK; Software Verification},
  owner     = {saulius},
  pages     = {1--30},
  timestamp = {2022.10.13},
  creationdate = {2022-10-13T00:00:00},
  url       = {https://isabelle.in.tum.de/library/HOL/HOL-SPARK-Manual/document.pdf},
}

@Article{Dailler2018,
  author    = {Sylvain Dailler and Claude March{\'{e}} and Yannick Moy},
  journal   = {Electronic Proceedings in Theoretical Computer Science},
  title     = {Lightweight Interactive Proving inside an Automatic Program Verifier},
  year      = {2018},
  month     = {nov},
  pages     = {1--15},
  volume    = {284},
  doi       = {10.4204/eptcs.284.1},
  file      = {:by-author/D/Dailler/2018_Dailler_1.pdf:PDF},
  keywords  = {Ada; Computer Science (CS); Coq; Correctness Proofs; HOL; SPARK; Software Verification},
  owner     = {saulius},
  publisher = {Open Publishing Association},
  timestamp = {2022.10.13},
  creationdate = {2022-10-13T00:00:00},
}

@Manuscript{Dailler2018a,
  author    = {Sylvain Dailler and Claude March{\'{e}} and Yannick Moy},
  title     = {Lightweight Interactive Proving inside an Automatic Program Verifier},
  year      = {2018},
  keywords  = {Ada; Computer Science (CS); Coq; Correctness Proofs; HOL; SPARK; Software Verification},
  month     = {nov},
  url       = {https://www.adacore.com/uploads/techPapers/f-ide.pdf},
  file      = {:by-author/D/Dailler/2018_Dailler_1a.pdf:PDF},
  journal   = {Electronic Proceedings in Theoretical Computer Science},
  owner     = {saulius},
  pages     = {1--15},
  publisher = {Open Publishing Association},
  timestamp = {2022.10.13},
  creationdate = {2022-10-13T00:00:00},
  volume    = {284},
}

@InProceedings{Gori2005,
  author    = {M. Gori and G. Monfardini and F. Scarselli},
  booktitle = {Proceedings. 2005 {IEEE} International Joint Conference on Neural Networks, 2005.},
  title     = {A new model for learning in graph domains},
  year      = {2005},
  pages     = {729--734},
  publisher = {{IEEE}},
  comment   = {Cited by Sato2020 (https://arxiv.org/abs/2003.04078).},
  doi       = {10.1109/ijcnn.2005.1555942},
  file      = {:by-author/G/Gori/2005_Gori_729.pdf:PDF},
  keywords  = {Artificial Neural Networks (ANN); Computer Science (CS); Graph Neural Networks (GNN); Machine Learning (ML); Neural Networks (NN)},
  owner     = {saulius},
  timestamp = {2022.10.21},
  creationdate = {2022-10-21T00:00:00},
}

@Article{Scarselli2009,
  author    = {F. Scarselli and M. Gori and Ah Chung Tsoi and M. Hagenbuchner and G. Monfardini},
  journal   = {{IEEE} Transactions on Neural Networks},
  title     = {The graph neural network model},
  year      = {2009},
  month     = {jan},
  number    = {1},
  pages     = {61--80},
  volume    = {20},
  comment   = {Cited by Sato2020 (https://arxiv.org/abs/2003.04078).},
  doi       = {10.1109/tnn.2008.2005605},
  file      = {:by-author/S/Scarselli/2009_Scarselli_61.pdf:PDF},
  keywords  = {Artificial Neural Networks (ANN); Computer Science (CS); Graph Neural Networks (GNN); Machine Learning (ML); Neural Networks (NN)},
  owner     = {saulius},
  publisher = {Institute of Electrical and Electronics Engineers ({IEEE})},
  timestamp = {2022.10.21},
  creationdate = {2022-10-21T00:00:00},
}

@Article{Sperduti1997,
  author           = {Sperduti, A. and Starita, A.},
  journal          = {IEEE transactions on neural networks},
  title            = {Supervised neural networks for the classification of structures.},
  year             = {1997},
  issn             = {1045-9227},
  pages            = {714--735},
  volume           = {8},
  abstract         = {Standard neural networks and statistical methods are usually believed to be inadequate when dealing with complex structures because of their feature-based approach. In fact, feature-based approaches usually fail to give satisfactory solutions because of the sensitivity of the approach to the a priori selection of the features, and the incapacity to represent any specific information on the relationships among the components of the structures. However, we show that neural networks can, in fact, represent and classify structured patterns. The key idea underpinning our approach is the use of the so called "generalized recursive neuron", which is essentially a generalization to structures of a recurrent neuron. By using generalized recursive neurons, all the supervised networks developed for the classification of sequences, such as backpropagation through time networks, real-time recurrent networks, simple recurrent networks, recurrent cascade correlation networks, and neural trees can, on the whole, be generalized to structures. The results obtained by some of the above networks (with generalized recursive neurons) on the classification of logic terms are presented.},
  comment          = {Cited by Sato2020 (https://arxiv.org/abs/2003.04078) and Gori2005.},
  completed        = {2012-10-02},
  country          = {United States},
  creationdate     = {2022-10-21T00:00:00},
  doi              = {10.1109/72.572108},
  file             = {:by-author/S/Sperduti/1997_Sperduti_714.pdf:PDF},
  issn-linking     = {1045-9227},
  issue            = {3},
  keywords         = {Artificial Neural Networks (ANN); Computer Science (CS); Graph Neural Networks (GNN); Machine Learning (ML); Neural Networks (NN)},
  modificationdate = {2023-06-25T10:01:43},
  nlm-id           = {101211035},
  owner            = {saulius},
  pmid             = {18255672},
  pubmodel         = {Print},
  pubstate         = {ppublish},
  revised          = {2016-10-20},
  timestamp        = {2022.10.21},
}

@Article{Baskin1997,
  author           = {Igor I. Baskin and Vladimir A. Palyulin and Nikolai S. Zefirov},
  journal          = {Journal of Chemical Information and Computer Sciences},
  title            = {A neural device for searching direct correlations between structures and properties of chemical compounds},
  year             = {1997},
  month            = {jul},
  number           = {4},
  pages            = {715--721},
  volume           = {37},
  comment          = {Cited by Sato2020 (https://arxiv.org/abs/2003.04078).},
  creationdate     = {2022-10-21T00:00:00},
  doi              = {10.1021/ci940128y},
  file             = {:by-author/B/Baskin/1997_Baskin_715.pdf:PDF},
  keywords         = {Artificial Neural Networks (ANN); Computer Science (CS); Graph Neural Networks (GNN); Machine Learning (ML); Neural Networks (NN)},
  modificationdate = {2022-10-25T09:30:55},
  owner            = {saulius},
  publisher        = {American Chemical Society ({ACS})},
  timestamp        = {2022.10.21},
}

@Article{Gilmer2017,
  author        = {Justin Gilmer and Samuel S. Schoenholz and Patrick F. Riley and Oriol Vinyals and George E. Dahl},
  title         = {Neural message passing for quantum chemistry},
  year          = {2017},
  month         = apr,
  abstract      = {Supervised learning on molecules has incredible potential to be useful in chemistry, drug discovery, and materials science. Luckily, several promising and closely related neural network models invariant to molecular symmetries have already been described in the literature. These models learn a message passing algorithm and aggregation procedure to compute a function of their entire input graph. At this point, the next step is to find a particularly effective variant of this general approach and apply it to chemical prediction benchmarks until we either solve them or reach the limits of the approach. In this paper, we reformulate existing models into a single common framework we call Message Passing Neural Networks (MPNNs) and explore additional novel variations within this framework. Using MPNNs we demonstrate state of the art results on an important molecular property prediction benchmark; these results are strong enough that we believe future work should focus on datasets with larger molecules or more accurate ground truth labels.},
  archiveprefix = {arXiv},
  comment       = {Cited by Sato2020 (https://arxiv.org/abs/2003.04078).},
  eprint        = {1704.01212},
  file          = {:by-author/G/Gilmer/2017_Gilmer_1.pdf:PDF},
  keywords      = {Artificial Neural Networks (ANN); Computer Science (CS); Graph Neural Networks (GNN); I.2.6; Machine Learning (ML); Neural Networks (NN); cs.LG},
  owner         = {saulius},
  primaryclass  = {cs.LG},
  timestamp = {2022.10.21},
  creationdate = {2022-10-21T00:00:00},
}

@Article{Zhang2018,
  author           = {Muhan Zhang and Zhicheng Cui and Marion Neumann and Yixin Chen},
  journal          = {Proceedings of the {AAAI} Conference on Artificial Intelligence},
  title            = {An end-to-end deep learning architecture for graph classification},
  year             = {2018},
  month            = {apr},
  number           = {1},
  pages            = {4438--4445},
  volume           = {32},
  comment          = {Cited by Sato2020 (https://arxiv.org/abs/2003.04078).},
  creationdate     = {2022-10-21T00:00:00},
  doi              = {10.1609/aaai.v32i1.11782},
  file             = {:by-author/Z/Zhang/2018_Zhang_4438.pdf:PDF},
  keywords         = {Artificial Neural Networks (ANN); Computer Science (CS); Graph Neural Networks (GNN); Machine Learning (ML); Neural Networks (NN)},
  modificationdate = {2022-10-25T09:30:27},
  owner            = {saulius},
  publisher        = {Association for the Advancement of Artificial Intelligence ({AAAI})},
  timestamp        = {2022.10.21},
}

@Article{Xu2018,
  author        = {Keyulu Xu and Weihua Hu and Jure Leskovec and Stefanie Jegelka},
  title         = {How powerful are {G}raph {N}eural {N}etworks?},
  year          = {2018},
  month         = oct,
  abstract      = {Graph Neural Networks (GNNs) are an effective framework for representation learning of graphs. GNNs follow a neighborhood aggregation scheme, where the representation vector of a node is computed by recursively aggregating and transforming representation vectors of its neighboring nodes. Many GNN variants have been proposed and have achieved state-of-the-art results on both node and graph classification tasks. However, despite GNNs revolutionizing graph representation learning, there is limited understanding of their representational properties and limitations. Here, we present a theoretical framework for analyzing the expressive power of GNNs to capture different graph structures. Our results characterize the discriminative power of popular GNN variants, such as Graph Convolutional Networks and GraphSAGE, and show that they cannot learn to distinguish certain simple graph structures. We then develop a simple architecture that is provably the most expressive among the class of GNNs and is as powerful as the Weisfeiler-Lehman graph isomorphism test. We empirically validate our theoretical findings on a number of graph classification benchmarks, and demonstrate that our model achieves state-of-the-art performance.},
  archiveprefix = {arXiv},
  comment       = {Cited by Sato2020 (https://arxiv.org/abs/2003.04078): "demonstrated that GNNs cannot distinguish some pairs of graphs"},
  eprint        = {1810.00826},
  file          = {:by-author/X/Xu/2018_Xu_1.pdf:PDF},
  keywords      = {Artificial Neural Networks (ANN); Computer Science (CS); Graph Neural Networks (GNN); Limitations of GNNs; Machine Learning (ML); Neural Networks (NN); cs.CV; cs.LG; stat.ML},
  owner         = {saulius},
  primaryclass  = {cs.LG},
  timestamp = {2022.10.21},
  creationdate = {2022-10-21T00:00:00},
}

@Article{Morris2018,
  author        = {Christopher Morris and Martin Ritzert and Matthias Fey and William L. Hamilton and Jan Eric Lenssen and Gaurav Rattan and Martin Grohe},
  title         = {{W}eisfeiler and {L}eman go neural: higher-order {G}raph {N}eural {N}etworks},
  year          = {2018},
  month         = oct,
  abstract      = {In recent years, graph neural networks (GNNs) have emerged as a powerful neural architecture to learn vector representations of nodes and graphs in a supervised, end-to-end fashion. Up to now, GNNs have only been evaluated empirically -- showing promising results. The following work investigates GNNs from a theoretical point of view and relates them to the $1$-dimensional Weisfeiler-Leman graph isomorphism heuristic ($1$-WL). We show that GNNs have the same expressiveness as the $1$-WL in terms of distinguishing non-isomorphic (sub-)graphs. Hence, both algorithms also have the same shortcomings. Based on this, we propose a generalization of GNNs, so-called $k$-dimensional GNNs ($k$-GNNs), which can take higher-order graph structures at multiple scales into account. These higher-order structures play an essential role in the characterization of social networks and molecule graphs. Our experimental evaluation confirms our theoretical findings as well as confirms that higher-order information is useful in the task of graph classification and regression.},
  archiveprefix = {arXiv},
  comment       = {Cited by Sato2020 (https://arxiv.org/abs/2003.04078): "demonstrated that GNNs cannot distinguish some pairs of graphs"},
  eprint        = {1810.02244},
  file          = {:by-author/M/Morris/2018_Morris_1.pdf:PDF},
  keywords      = {Artificial Neural Networks (ANN); Computer Science (CS); Graph Neural Networks (GNN); Limitations of GNNs; Machine Learning (ML); Neural Networks (NN); cs.AI; cs.CV; cs.LG; cs.NE; stat.ML},
  owner         = {saulius},
  primaryclass  = {cs.LG},
  timestamp = {2022.10.21},
  creationdate = {2022-10-21T00:00:00},
}

@Article{Cybenko1989,
  author    = {G. Cybenko},
  journal   = {Mathematics of Control, Signals, and Systems},
  title     = {Approximation by superpositions of a sigmoidal function},
  year      = {1989},
  month     = {dec},
  number    = {4},
  pages     = {303--314},
  volume    = {2},
  comment   = {Cited by Sato2020 (https://arxiv.org/abs/2003.04078): "(describes) the universal approximation power of multi layer perceptrons"},
  doi       = {10.1007/bf02551274},
  file      = {:by-author/C/Cybenko/1989_Cybenko_303.pdf:PDF},
  keywords  = {Artificial Neural Networks (ANN); Graph Neural Networks (GNN); Limitations of GNNs; Machine Learning (ML); Multi-layer Perceptrons; Neural Networks (NN)},
  owner     = {saulius},
  publisher = {Springer Science and Business Media {LLC}},
  timestamp = {2022.10.21},
  creationdate = {2022-10-21T00:00:00},
}

@Article{Hornik1989,
  author    = {Kurt Hornik and Maxwell Stinchcombe and Halbert White},
  journal   = {Neural Networks},
  title     = {Multilayer feedforward networks are universal approximators},
  year      = {1989},
  month     = {jan},
  number    = {5},
  pages     = {359--366},
  volume    = {2},
  comment   = {Cited by Sato2020 (https://arxiv.org/abs/2003.04078): "(describes) the universal approximation power of multi layer perceptrons"},
  doi       = {10.1016/0893-6080(89)90020-8},
  file      = {:by-author/H/Hornik/1989_Hornik_359.pdf:PDF},
  keywords  = {Artificial Neural Networks (ANN); Graph Neural Networks (GNN); Limitations of GNNs; Machine Learning (ML); Multi-layer Perceptrons; Neural Networks (NN)},
  owner     = {saulius},
  publisher = {Elsevier {BV}},
  timestamp = {2022.10.21},
  creationdate = {2022-10-21T00:00:00},
}

@Article{Hornik1991,
  author    = {Kurt Hornik},
  journal   = {Neural Networks},
  title     = {Approximation capabilities of multilayer feedforward networks},
  year      = {1991},
  number    = {2},
  pages     = {251--257},
  volume    = {4},
  comment   = {Cited by Sato2020 (https://arxiv.org/abs/2003.04078): "(describes) the universal approximation power of multi layer perceptrons"},
  doi       = {10.1016/0893-6080(91)90009-t},
  file      = {:by-author/H/Hornik/1991_Hornik_251.pdf:PDF},
  keywords  = {Artificial Neural Networks (ANN); Graph Neural Networks (GNN); Limitations of GNNs; Machine Learning (ML); Multi-layer Perceptrons; Neural Networks (NN)},
  owner     = {saulius},
  publisher = {Elsevier {BV}},
  timestamp = {2022.10.21},
  creationdate = {2022-10-21T00:00:00},
}

@Article{Sato2019,
  author        = {Ryoma Sato and Makoto Yamada and Hisashi Kashima},
  title         = {Approximation ratios of {G}raph {N}eural {N}etworks for combinatorial problems},
  year          = {2019},
  month         = may,
  abstract      = {In this paper, from a theoretical perspective, we study how powerful graph neural networks (GNNs) can be for learning approximation algorithms for combinatorial problems. To this end, we first establish a new class of GNNs that can solve a strictly wider variety of problems than existing GNNs. Then, we bridge the gap between GNN theory and the theory of distributed local algorithms. We theoretically demonstrate that the most powerful GNN can learn approximation algorithms for the minimum dominating set problem and the minimum vertex cover problem with some approximation ratios with the aid of the theory of distributed local algorithms. We also show that most of the existing GNNs such as GIN, GAT, GCN, and GraphSAGE cannot perform better than with these ratios. This paper is the first to elucidate approximation ratios of GNNs for combinatorial problems. Furthermore, we prove that adding coloring or weak-coloring to each node feature improves these approximation ratios. This indicates that preprocessing and feature engineering theoretically strengthen model capabilities.},
  archiveprefix = {arXiv},
  comment       = {Cited by Sato2020 (https://arxiv.org/abs/2003.04078): "showed that GNNs are at most as powerful as distributed local algorithms"},
  eprint        = {1905.10261},
  file          = {:by-author/S/Sato/2019_Sato_1.pdf:PDF},
  keywords      = {Artificial Neural Networks (ANN); Graph Neural Networks (GNN); Machine Learning (ML); Neural Networks (NN); cs.LG; stat.ML},
  owner         = {saulius},
  primaryclass  = {cs.LG},
  timestamp = {2022.10.21},
  creationdate = {2022-10-21T00:00:00},
}

@InProceedings{Angluin1980,
  author    = {Dana Angluin},
  booktitle = {Proceedings of the twelfth annual {ACM} symposium on Theory of computing - {STOC} {\textquotesingle}80},
  title     = {Local and global properties in networks of processors (Extended Abstract)},
  year      = {1980},
  pages     = {82--93},
  publisher = {{ACM} Press},
  comment   = {Cited by Sato2020 (https://arxiv.org/abs/2003.04078): "showed that GNNs are at most as powerful as distributed local algorithms"},
  doi       = {10.1145/800141.804655},
  file      = {:by-author/A/Angluin/1980_Angluin_82.pdf:PDF},
  keywords  = {Artificial Neural Networks (ANN); Graph Neural Networks (GNN); Machine Learning (ML); Neural Networks (NN)},
  owner     = {saulius},
  timestamp = {2022.10.21},
  creationdate = {2022-10-21T00:00:00},
}

@Article{Suomela2013,
  author    = {Jukka Suomela},
  journal   = {{ACM} Computing Surveys},
  title     = {Survey of local algorithms},
  year      = {2013},
  month     = {feb},
  number    = {2},
  pages     = {1--40},
  volume    = {45},
  comment   = {Cited by Sato2020 (https://arxiv.org/abs/2003.04078): "showed that GNNs are at most as powerful as distributed local algorithms"},
  doi       = {10.1145/2431211.2431223},
  file      = {:by-author/S/Suomela/2013_Suomela_1.pdf:PDF},
  keywords  = {Artificial Neural Networks (ANN); Graph Neural Networks (GNN); Machine Learning (ML); Neural Networks (NN)},
  owner     = {saulius},
  publisher = {Association for Computing Machinery ({ACM})},
  timestamp = {2022.10.21},
  creationdate = {2022-10-21T00:00:00},
}

@Article{Hamilton2017,
  author        = {William L. Hamilton and Rex Ying and Jure Leskovec},
  title         = {Representation learning on graphs: methods and applications},
  year          = {2017},
  month         = sep,
  abstract      = {Machine learning on graphs is an important and ubiquitous task with applications ranging from drug design to friendship recommendation in social networks. The primary challenge in this domain is finding a way to represent, or encode, graph structure so that it can be easily exploited by machine learning models. Traditionally, machine learning approaches relied on user-defined heuristics to extract features encoding structural information about a graph (e.g., degree statistics or kernel functions). However, recent years have seen a surge in approaches that automatically learn to encode graph structure into low-dimensional embeddings, using techniques based on deep learning and nonlinear dimensionality reduction. Here we provide a conceptual review of key advancements in this area of representation learning on graphs, including matrix factorization-based methods, random-walk based algorithms, and graph convolutional networks. We review methods to embed individual nodes as well as approaches to embed entire (sub)graphs. In doing so, we develop a unified framework to describe these recent approaches, and we highlight a number of important applications and directions for future work.},
  archiveprefix = {arXiv},
  comment       = {Cited by Sato2020 (https://arxiv.org/abs/2003.04078): "Comprehensive surveys on GNNs were provided (in this paper)"},
  eprint        = {1709.05584},
  file          = {:by-author/H/Hamilton/2017_Hamilton_1.pdf:PDF},
  keywords      = {Artificial Neural Networks (ANN); Graph Neural Networks (GNN); Machine Learning (ML); Neural Networks (NN); Review; cs.LG; cs.SI},
  owner         = {saulius},
  primaryclass  = {cs.SI},
  timestamp = {2022.10.21},
  creationdate = {2022-10-21T00:00:00},
}

@Article{Zhou2018,
  author        = {Jie Zhou and Ganqu Cui and Shengding Hu and Zhengyan Zhang and Cheng Yang and Zhiyuan Liu and Lifeng Wang and Changcheng Li and Maosong Sun},
  title         = {{G}raph {N}eural {N}etworks: a review of methods and applications},
  year          = {2018},
  month         = dec,
  abstract      = {Lots of learning tasks require dealing with graph data which contains rich relation information among elements. Modeling physics systems, learning molecular fingerprints, predicting protein interface, and classifying diseases demand a model to learn from graph inputs. In other domains such as learning from non-structural data like texts and images, reasoning on extracted structures (like the dependency trees of sentences and the scene graphs of images) is an important research topic which also needs graph reasoning models. Graph neural networks (GNNs) are neural models that capture the dependence of graphs via message passing between the nodes of graphs. In recent years, variants of GNNs such as graph convolutional network (GCN), graph attention network (GAT), graph recurrent network (GRN) have demonstrated ground-breaking performances on many deep learning tasks. In this survey, we propose a general design pipeline for GNN models and discuss the variants of each component, systematically categorize the applications, and propose four open problems for future research.},
  archiveprefix = {arXiv},
  comment       = {Cited by Sato2020 (https://arxiv.org/abs/2003.04078): "Comprehensive surveys on GNNs were provided (in this paper)"},
  eprint        = {1812.08434},
  file          = {:by-author/Z/Zhou/2018_Zhou_1.pdf:PDF},
  keywords      = {Artificial Neural Networks (ANN); Graph Neural Networks (GNN); Machine Learning (ML); Neural Networks (NN); Review; cs.AI; cs.LG; stat.ML},
  owner         = {saulius},
  primaryclass  = {cs.LG},
  timestamp = {2022.10.21},
  creationdate = {2022-10-21T00:00:00},
}

@Article{Wu2021,
  author          = {Wu, Zonghan and Pan, Shirui and Chen, Fengwen and Long, Guodong and Zhang, Chengqi and Yu, Philip S.},
  journal         = {{IEEE} transactions on neural networks and learning systems},
  title           = {A comprehensive survey on {G}raph {N}eural {N}etworks.},
  year            = {2021},
  issn            = {2162-2388},
  month           = jan,
  pages           = {4--24},
  volume          = {32},
  abstract        = {Deep learning has revolutionized many machine learning tasks in recent years, ranging from image classification and video processing to speech recognition and natural language understanding. The data in these tasks are typically represented in the Euclidean space. However, there is an increasing number of applications, where data are generated from non-Euclidean domains and are represented as graphs with complex relationships and interdependency between objects. The complexity of graph data has imposed significant challenges on the existing machine learning algorithms. Recently, many studies on extending deep learning approaches for graph data have emerged. In this article, we provide a comprehensive overview of graph neural networks (GNNs) in data mining and machine learning fields. We propose a new taxonomy to divide the state-of-the-art GNNs into four categories, namely, recurrent GNNs, convolutional GNNs, graph autoencoders, and spatial-temporal GNNs. We further discuss the applications of GNNs across various domains and summarize the open-source codes, benchmark data sets, and model evaluation of GNNs. Finally, we propose potential research directions in this rapidly growing field.},
  citation-subset = {IM},
  comment         = {Cited by Sato2020 (https://arxiv.org/abs/2003.04078): "Comprehensive surveys on GNNs were provided (in this paper)"},
  completed       = {2022-01-28},
  country         = {United States},
  doi             = {10.1109/TNNLS.2020.2978386},
  file            = {:by-author/W/Wu/2021_Wu_4.pdf:PDF},
  issn-linking    = {2162-237X},
  issue           = {1},
  keywords        = {Algorithms; Artificial Neural Networks (ANN); Computer; Data Mining; Graph Neural Networks (GNN); Humans; Machine Learning (ML); Neural Networks (NN); Review; Surveys and Questionnaires},
  nlm-id          = {101616214},
  owner           = {saulius},
  pmid            = {32217482},
  pubmodel        = {Print-Electronic},
  pubstate        = {ppublish},
  revised         = {2022-01-28},
  timestamp = {2022.10.21},
  creationdate = {2022-10-21T00:00:00},
}

@Article{Devlin2018,
  author        = {Jacob Devlin and Ming-Wei Chang and Kenton Lee and Kristina Toutanova},
  title         = {{BERT}: pre-training of {D}eep {B}idirectional {T}ransformers for language understanding},
  year          = {2018},
  month         = oct,
  abstract      = {We introduce a new language representation model called BERT, which stands for Bidirectional Encoder Representations from Transformers. Unlike recent language representation models, BERT is designed to pre-train deep bidirectional representations from unlabeled text by jointly conditioning on both left and right context in all layers. As a result, the pre-trained BERT model can be fine-tuned with just one additional output layer to create state-of-the-art models for a wide range of tasks, such as question answering and language inference, without substantial task-specific architecture modifications. BERT is conceptually simple and empirically powerful. It obtains new state-of-the-art results on eleven natural language processing tasks, including pushing the GLUE score to 80.5% (7.7% point absolute improvement), MultiNLI accuracy to 86.7% (4.6% absolute improvement), SQuAD v1.1 question answering Test F1 to 93.2 (1.5 point absolute improvement) and SQuAD v2.0 Test F1 to 83.1 (5.1 point absolute improvement).},
  archiveprefix = {arXiv},
  eprint        = {1810.04805},
  file          = {:by-author/D/Devlin/2018_Devlin_1.pdf:PDF},
  keywords      = {cs.CL},
  owner         = {saulius},
  primaryclass  = {cs.CL},
  timestamp = {2022.10.21},
  creationdate = {2022-10-21T00:00:00},
}

@Article{Jakse2022,
  author        = {Noel Jakse and Johannes Sandberg and Leon F. Granz and Anthony Saliou and Philippe Jarry and Emilie Devijver and Thomas Voigtmann and Jürgen Horbach and Andreas Meyer},
  title         = {Interatomic machine learning potentials for aluminium: application to solidification phenomena},
  year          = {2022},
  month         = jan,
  abstract      = {In studying solidification process by simulations on the atomic scale, the modeling of crystal nucleation or amorphisation requires the construction of interatomic interactions that are able to reproduce the properties of both the solid and the liquid states. Taking into account rare nucleation events or structural relaxation under deep undercooling conditions requires much larger length scales and longer time scales than those achievable by \textit{ab initio} molecular dynamics (AIMD). This problem is addressed by means of classical MD simulations using a well established high dimensional neural network potential trained on a relevant set of configurations generated by AIMD. Our dataset contains various crystalline structures and liquid states at different pressures, including their time fluctuations in a wide range of temperatures considering only their energy labels. Applied to elemental aluminium, the resulting potential is shown to be efficient to reproduce the basic structural, dynamics and thermodynamic quantities in the liquid and undercooled states without the need to include neither explicitly the forces nor all kind of configurations in the training procedure. The early stage of crystallization is further investigated on a much larger scale with one million atoms, allowing us to unravel features of the homogeneous nucleation mechanisms in the fcc phase at ambient pressure as well as in the bcc phase at high pressure with unprecedented accuracy close to the \textit{ab initio} one. In both case, a single step nucleation process is observed.},
  archiveprefix = {arXiv},
  comment       = {Discussed at the OPTIMADE meeting (2022-10-21) as an example of a trajectory containing a "liquid" reference frame.},
  eprint        = {2201.01370},
  file          = {:by-author/J/Jakse/2022_Jakse_1.pdf:PDF},
  keywords      = {For OPTIMADE; Machine Learning (ML); Molecular Dynamics (MD); cond-mat.dis-nn; cond-mat.mtrl-sci; physics.comp-ph},
  owner         = {saulius},
  primaryclass  = {cond-mat.mtrl-sci},
  timestamp = {2022.10.21},
  creationdate = {2022-10-21T00:00:00},
}

@InProceedings{Zuegner2018,
  author           = {Daniel Zügner and Amir Akbarnejad and Stephan Günnemann},
  booktitle        = {Proceedings of the 24th {ACM} {SIGKDD} International Conference on Knowledge Discovery {\&}amp$\mathsemicolon$ Data Mining},
  title            = {Adversarial attacks on neural networks for graph data},
  year             = {2018},
  month            = {jul},
  pages            = {2847--2856},
  publisher        = {{ACM}},
  comment          = {Cited in Zhou2022.},
  creationdate     = {2022-10-23T00:00:00},
  doi              = {10.1145/3219819.3220078},
  file             = {:by-author/Z/Zügner/2018_Zügner_2847.pdf:PDF},
  keywords         = {Adversarial; Artificial Neural Networks (ANN); Computer Science (CS); Machine Learning (ML); Neural Networks (NN)},
  modificationdate = {2022-10-25T09:28:26},
  owner            = {saulius},
  timestamp        = {2022.10.23},
}

@Article{Eisen2022,
  author           = {Michael B. Eisen and Anna Akhmanova and Timothy E. Behrens and Jörn Diedrichsen and Diane M. Harper and Mihaela D. Iordanova and Detlef Weigel and Mone Zaidi},
  journal          = {{eLife}},
  title            = {Peer review without gatekeeping},
  year             = {2022},
  month            = {oct},
  volume           = {11},
  creationdate     = {2022-10-23T00:00:00},
  doi              = {10.7554/elife.83889},
  file             = {:by-author/E/Eisen/2022_Eisen_1.pdf:PDF},
  keywords         = {Open Access; Open Peer Review; Peer Review; Publication Quality; Research Assessment},
  modificationdate = {2022-10-25T09:29:30},
  owner            = {saulius},
  publisher        = {{eLife} Sciences Publications, Ltd},
  timestamp        = {2022.10.23},
}

@Article{Baker1996,
  author           = {Baker, B. M. and Murphy, K. P.},
  journal          = {Biophysical Journal},
  title            = {Evaluation of linked protonation effects in protein binding reactions using isothermal titration calorimetry},
  year             = {1996},
  issn             = {0006-3495},
  month            = oct,
  number           = {4},
  pages            = {2049--2055},
  volume           = {71},
  abstract         = {A theoretical development in the evaluation of proton linkage in protein binding reactions by isothermal titration calorimetry (ITC) is presented. For a system in which binding is linked to protonation of an ionizable group on a protein, we show that by performing experiments as a function of pH in buffers with varying ionization enthalpy, one can determine the pK(a)'s of the group responsible for the proton linkage in the free and the liganded states, the protonation enthalpy for this group in these states, as well as the intrinsic energetics for ligand binding (delta H(o), delta S(o), and delta C(p)). Determination of intrinsic energetics in this fashion allows for comparison with energetics calculated empirically from structural information. It is shown that in addition to variation of the ligand binding constant with pH, the observed binding enthalpy and heat capacity change can undergo extreme deviations from their intrinsic values, depending upon pH and buffer conditions.},
  creationdate     = {2022-11-03T11:42:55},
  doi              = {10.1016/S0006-3495(96)79403-1},
  file             = {:by-author/B/Baker/1996_Baker_2049.pdf:PDF},
  modificationdate = {2022-11-03T11:46:07},
  owner            = {saulius},
}

@Article{Reilly2016,
  author           = {Reilly, Anthony M. and Cooper, Richard I. and Adjiman, Claire S. and Bhattacharya, Saswata and Boese, A. Daniel and Brandenburg, Jan Gerit and Bygrave, Peter J. and Bylsma, Rita and Campbell, Josh E. and Car, Roberto and Case, David H. and Chadha, Renu and Cole, Jason C. and Cosburn, Katherine and Cuppen, Herma M. and Curtis, Farren and Day, Graeme M. and DiStasio, Robert A. and Dzyabchenko, Alexander and van Eijck, Bouke P. and Elking, Dennis M. and van den Ende, Joost A. and Facelli, Julio C. and Ferraro, Marta B. and Fusti-Molnar, Laszlo and Gatsiou, Christina Anna and Gee, Thomas S. and de Gelder, René and Ghiringhelli, Luca M. and Goto, Hitoshi and Grimme, Stefan and Guo, Rui and Hofmann, Detlef W. M. and Hoja, Johannes and Hylton, Rebecca K. and Iuzzolino, Luca and Jankiewicz, Wojciech and de Jong, Daniël T. and Kendrick, John and de Klerk, Niek J. J. and Ko, Hsin Yu and Kuleshova, Liudmila N. and Li, Xiayue and Lohani, Sanjaya and Leusen, Frank J. J. and Lund, Albert M. and Lv, Jian and Ma, Yanming and Marom, Noa and Masunov, Artëm E. and McCabe, Patrick and McMahon, David P. and Meekes, Hugo and Metz, Michael P. and Misquitta, Alston J. and Mohamed, Sharmarke and Monserrat, Bartomeu and Needs, Richard J. and Neumann, Marcus A. and Nyman, Jonas and Obata, Shigeaki and Oberhofer, Harald and Oganov, Artem R. and Orendt, Anita M. and Pagola, Gabriel I. and Pantelides, Constantinos C. and Pickard, Chris J. and Podeszwa, Rafal and Price, Louise S. and Price, Sarah L. and Pulido, Angeles and Read, Murray G. and Reuter, Karsten and Schneider, Elia and Schober, Christoph and Shields, Gregory P. and Singh, Pawanpreet and Sugden, Isaac J. and Szalewicz, Krzysztof and Taylor, Christopher R. and Tkatchenko, Alexandre and Tuckerman, Mark E. and Vacarro, Francesca and Vasileiadis, Manolis and Vazquez-Mayagoitia, Alvaro and Vogt, Leslie and Wang, Yanchao and Watson, Rona E. and de Wijs, Gilles A. and Yang, Jack and Zhu, Qiang and Groom, Colin R.},
  journal          = {Acta crystallographica Section B, Structural science, crystal engineering and materials},
  title            = {Report on the sixth blind test of organic crystal structure prediction methods},
  year             = {2016},
  issn             = {2052-5206},
  month            = aug,
  pages            = {439--459},
  volume           = {72},
  abstract         = {The sixth blind test of organic crystal structure prediction (CSP) methods has been held, with five target systems: a small nearly rigid molecule, a polymorphic former drug candidate, a chloride salt hydrate, a co-crystal and a bulky flexible molecule. This blind test has seen substantial growth in the number of participants, with the broad range of prediction methods giving a unique insight into the state of the art in the field. Significant progress has been seen in treating flexible molecules, usage of hierarchical approaches to ranking structures, the application of density-functional approximations, and the establishment of new workflows and `best practices' for performing CSP calculations. All of the targets, apart from a single potentially disordered Z' = 2 polymorph of the drug candidate, were predicted by at least one submission. Despite many remaining challenges, it is clear that CSP methods are becoming more applicable to a wider range of real systems, including salts, hydrates and larger flexible molecules. The results also highlight the potential for CSP calculations to complement and augment experimental studies of organic solid forms.},
  comment          = {Cited in Bowskill2021.},
  completed        = {2017-06-08},
  country          = {England},
  creationdate     = {2022-11-08T11:49:08},
  doi              = {10.1107/S2052520616007447},
  file             = {:by-author/R/Reilly/2016_Reilly_439.pdf:PDF},
  issn-linking     = {2052-5192},
  issue            = {Pt 4},
  keywords         = {CSD; Crystal Structure Prediction (CSP); Lattice Energies; Polymorphism},
  modificationdate = {2022-11-22T07:54:32},
  nlm-id           = {101609037},
  owner            = {saulius},
  pii              = {S2052520616007447},
  pmc              = {PMC4971545},
  pmid             = {27484368},
  pubmodel         = {Print-Electronic},
  pubstate         = {ppublish},
  revised          = {2019-01-12},
}

@Article{Braga2022,
  author           = {Braga, Dario and Casali, Lucia and Grepioni, Fabrizia},
  journal          = {International journal of molecular sciences},
  title            = {The Relevance of Crystal Forms in the Pharmaceutical Field: Sword of Damocles or Innovation Tools?},
  year             = {2022},
  issn             = {1422-0067},
  month            = aug,
  pages            = {23169013},
  volume           = {23},
  abstract         = {This review is aimed to provide to an "educated but non-expert" readership and an overview of the scientific, commercial, and ethical importance of investigating the crystalline forms (polymorphs, hydrates, and co-crystals) of active pharmaceutical ingredients (API). The existence of multiple crystal forms of an API is relevant not only for the selection of the best solid material to carry through the various stages of drug development, including the choice of dosage and of excipients suitable for drug development and marketing, but also in terms of intellectual property protection and/or extension. This is because the physico-chemical properties, such as solubility, dissolution rate, thermal stability, processability, etc., of the solid API may depend, sometimes dramatically, on the crystal form, with important implications on the drug's ultimate efficacy. This review will recount how the scientific community and the pharmaceutical industry learned from the catastrophic consequences of the appearance of new, more stable, and unsuspected crystal forms. The relevant aspects of hydrates, the most common pharmaceutical solid solvates, and of co-crystals, the association of two or more solid components in the same crystalline materials, will also be discussed. Examples will be provided of how to tackle multiple crystal forms with screening protocols and theoretical approaches, and ultimately how to turn into discovery and innovation the purposed preparation of new crystalline forms of an API.},
  chemicals        = {Excipients, Pharmaceutical Preparations},
  citation-subset  = {IM},
  completed        = {2022-08-29},
  country          = {Switzerland},
  creationdate     = {2022-11-08T11:54:09},
  doi              = {10.3390/ijms23169013},
  file             = {:by-author/B/Braga/2022_Braga_23169013.pdf:PDF},
  issn-linking     = {1422-0067},
  issue            = {16},
  keywords         = {Co-crystals of Active Pharmaceuticals; Crystal Polymorphism; Crystallization; Excipients; Hydrates; Pharmaceutical Preparations; Solubility},
  modificationdate = {2022-11-08T11:59:02},
  nlm-id           = {101092791},
  owner            = {saulius},
  pii              = {9013},
  pmc              = {PMC9408954},
  pmid             = {36012275},
  pubmodel         = {Electronic},
  pubstate         = {epublish},
  revised          = {2022-08-30},
}

@Article{Kim2020a,
  author           = {Kim, Sungwon and Noh, Juhwan and Gu, Geun Ho and Aspuru-Guzik, Alan and Jung, Yousung},
  journal          = {ACS central science},
  title            = {Generative adversarial networks for crystal structure prediction},
  year             = {2020},
  issn             = {2374-7943},
  month            = aug,
  pages            = {1412--1420},
  volume           = {6},
  abstract         = {The constant demand for novel functional materials calls for efficient strategies to accelerate the materials discovery, and crystal structure prediction is one of the most fundamental tasks along that direction. In addressing this challenge, generative models can offer new opportunities since they allow for the continuous navigation of chemical space via latent spaces. In this work, we employ a crystal representation that is inversion-free based on unit cell and fractional atomic coordinates and build a generative adversarial network for crystal structures. The proposed model is applied to generate the Mg-Mn-O ternary materials with the theoretical evaluation of their photoanode properties for high-throughput virtual screening (HTVS). The proposed generative HTVS framework predicts 23 new crystal structures with reasonable calculated stability and band gap. These findings suggest that the generative model can be an effective way to explore hidden portions of the chemical space, an area that is usually unreachable when conventional substitution-based discovery is employed.},
  country          = {United States},
  creationdate     = {2022-11-08T12:01:15},
  doi              = {10.1021/acscentsci.0c00426},
  file             = {:by-author/K/Kim/2020_Kim_1412.pdf:PDF},
  issn-linking     = {2374-7943},
  issue            = {8},
  keywords         = {Artificial Neural Networks (ANN); Crystal Structure Prediction (CSP); Generative Adversarial Networks (GAN); Machine Learning (ML)},
  modificationdate = {2022-11-08T12:11:04},
  nlm-id           = {101660035},
  owner            = {saulius},
  pmc              = {PMC7453563},
  pmid             = {32875082},
  pubmodel         = {Print-Electronic},
  pubstate         = {ppublish},
  revised          = {2022-03-31},
}

@Article{Kim2022,
  author           = {Kim, Sungwon and Noh, Juhwan and Gu, Geun Ho and Aspuru-Guzik, Alan and Jung, Yousung},
  journal          = {ACS central science},
  title            = {Correction to "{G}enerative adversarial networks for crystal structure prediction"},
  year             = {2022},
  issn             = {2374-7943},
  month            = mar,
  pages            = {402},
  volume           = {8},
  abstract         = {[This corrects the article DOI: 10.1021/acscentsci.0c00426.].},
  country          = {United States},
  creationdate     = {2022-11-08T12:04:30},
  doi              = {10.1021/acscentsci.2c00218},
  file             = {:by-author/K/Kim/2022_Kim_402.pdf:PDF},
  issn-linking     = {2374-7943},
  issue            = {3},
  keywords         = {Artificial Neural Networks (ANN); Correction; Crystal Structure Prediction (CSP); Generative Adversarial Networks (GAN); Machine Learning (ML)},
  modificationdate = {2022-11-08T12:11:01},
  nlm-id           = {101660035},
  owner            = {saulius},
  pmc              = {PMC8949623},
  pmid             = {35355815},
  pubmodel         = {Print-Electronic},
  pubstate         = {ppublish},
  revised          = {2022-03-31},
}

@Article{Liu2022,
  author           = {Liu, Yan and An, Chongwei and Liu, Ning and Wang, Minchang and Ye, Baoyun and Liao, Dongjie},
  journal          = {Molecules (Basel, Switzerland)},
  title            = {Noncovalent Interactions and Crystal Structure Prediction of Energetic Materials},
  year             = {2022},
  issn             = {1420-3049},
  month            = jun,
  pages            = {27123755},
  volume           = {27},
  abstract         = {The crystal and molecular structures, intermolecular interactions, and energy of CL-20, HATO, and FOX-7 were comparatively predicted based on molecular dynamic (MD) simulations. By comparison, the 2D fingerprint plot, Hirshfeld surface, reduced density gradient isosurface, and electrostatic potential surface were studied to detect the intermolecular interactions. Meanwhile, the effects of vacuum and different solvents on the crystal habit of CL-20, HATO, and FOX-7 were studied by AE and MAE model, respectively. The energy calculation was also analysed based on the equilibrium structures of these crystal models by MD simulations. Our results would provide fundamental insights for the crystal engineering of energetic materials.},
  chemicals        = {Solvents},
  citation-subset  = {IM},
  completed        = {2022-06-27},
  country          = {Switzerland},
  creationdate     = {2022-11-08T12:08:03},
  doi              = {10.3390/molecules27123755},
  file             = {:by-author/L/Liu/2022_Liu_27123755.pdf:PDF},
  issn-linking     = {1420-3049},
  issue            = {12},
  keywords         = {Crystal; Crystal Structure Prediction (CSP); Crystallography, X-Ray; Energetic Material; Energy; Intermolecular Interaction; Molecular Dynamics (MD); Molecular Dynamics Simulation; Molecular Structure; Solvents, Chemistry; Static Electricity},
  modificationdate = {2024-04-04T10:21:36},
  nlm-id           = {100964009},
  owner            = {saulius},
  pii              = {3755},
  pmc              = {PMC9229783},
  pmid             = {35744882},
  pubmodel         = {Electronic},
  pubstate         = {epublish},
  revised          = {2022-07-16},
}

@Article{Xiao2022,
  author           = {Xiao, Fu and Cheng, Yinxiang and Wang, Jian-Rong and Wang, Dingyan and Zhang, Yuanyuan and Chen, Kaixian and Mei, Xuefeng and Luo, Xiaomin},
  journal          = {Pharmaceutics},
  title            = {Cocrystal Prediction of Bexarotene by Graph Convolution Network and Bioavailability Improvement.},
  year             = {2022},
  issn             = {1999-4923},
  month            = oct,
  pages            = {14102198},
  volume           = {14},
  abstract         = {Bexarotene (BEX) was approved by the FDA in 1999 for the treatment of cutaneous T-cell lymphoma (CTCL). The poor aqueous solubility causes the low bioavailability of the drug and thereby limits the clinical application. In this study, we developed a GCN-based deep learning model (CocrystalGCN) for in-silico screening of the cocrystals of BEX. The results show that our model obtained high performance relative to baseline models. The top 30 of 109 coformer candidates were scored by CocrystalGCN and then validated experimentally. Finally, cocrystals of BEX-pyrazine, BEX-2,5-dimethylpyrazine, BEX-methyl isonicotinate, and BEX-ethyl isonicotinate were successfully obtained. The crystal structures were determined by single-crystal X-ray diffraction. Powder X-ray diffraction, differential scanning calorimetry, and thermogravimetric analysis were utilized to characterize these multi-component forms. All cocrystals present superior solubility and dissolution over the parent drug. The pharmacokinetic studies show that the plasma exposures (AUC ) of BEX-pyrazine and BEX-2,5-dimethylpyrazine are 1.7 and 1.8 times that of the commercially available BEX powder, respectively. This work sets a good example for integrating virtual prediction and experimental screening to discover the new cocrystals of water-insoluble drugs.},
  country          = {Switzerland},
  creationdate     = {2022-11-08T12:12:33},
  doi              = {10.3390/pharmaceutics14102198},
  file             = {:by-author/X/Xiao/2022_Xiao_14102198.pdf:PDF},
  issn-linking     = {1999-4923},
  issue            = {10},
  keywords         = {Artificial Neural Networks (ANN); Bexarotene; Bioavailability; Cocrystal Prediction; Crystal Structure Prediction (CSP); GCN; Graph Neural Networks (GNN); Machine Learning (ML)},
  modificationdate = {2022-11-08T12:24:23},
  nlm-id           = {101534003},
  owner            = {saulius},
  pii              = {2198},
  pmc              = {PMC9611166},
  pmid             = {36297633},
  pubmodel         = {Electronic},
  pubstate         = {epublish},
  revised          = {2022-10-30},
}

@Article{Krenn2022,
  author           = {Krenn, Mario and Ai, Qianxiang and Barthel, Senja and Carson, Nessa and Frei, Angelo and Frey, Nathan C. and Friederich, Pascal and Gaudin, Théophile and Gayle, Alberto Alexander and Jablonka, Kevin Maik and Lameiro, Rafael F. and Lemm, Dominik and Lo, Alston and Moosavi, Seyed Mohamad and Nápoles-Duarte, José Manuel and Nigam, AkshatKumar and Pollice, Robert and Rajan, Kohulan and Schatzschneider, Ulrich and Schwaller, Philippe and Skreta, Marta and Smit, Berend and Strieth-Kalthoff, Felix and Sun, Chong and Tom, Gary and Falk von Rudorff, Guido and Wang, Andrew and White, Andrew D. and Young, Adamo and Yu, Rose and Aspuru-Guzik, Alán},
  journal          = {Patterns (New York, N.Y.)},
  title            = {{SELFIES} and the future of molecular string representations.},
  year             = {2022},
  issn             = {2666-3899},
  month            = oct,
  pages            = {100588},
  volume           = {3},
  abstract         = {Artificial intelligence (AI) and machine learning (ML) are expanding in popularity for broad applications to challenging tasks in chemistry and materials science. Examples include the prediction of properties, the discovery of new reaction pathways, or the design of new molecules. The machine needs to read and write fluently in a chemical language for each of these tasks. Strings are a common tool to represent molecular graphs, and the most popular molecular string representation, Smiles, has powered cheminformatics since the late 1980s. However, in the context of AI and ML in chemistry, Smiles has several shortcomings-most pertinently, most combinations of symbols lead to invalid results with no valid chemical interpretation. To overcome this issue, a new language for molecules was introduced in 2020 that guarantees 100% robustness: SELF-referencing embedded string (Selfies). Selfies has since simplified and enabled numerous new applications in chemistry. In this perspective, we look to the future and discuss molecular string representations, along with their respective opportunities and challenges. We propose 16 concrete future projects for robust molecular representations. These involve the extension toward new chemical domains, exciting questions at the interface of AI and robust languages, and interpretability for both humans and machines. We hope that these proposals will inspire several follow-up works exploiting the full potential of molecular string representations for the future of AI in chemistry and materials science.},
  country          = {United States},
  creationdate     = {2022-11-08T12:23:15},
  doi              = {10.1016/j.patter.2022.100588},
  file             = {:by-author/K/Krenn/2022_Krenn_100588.pdf:PDF},
  issn-linking     = {2666-3899},
  issue            = {10},
  keywords         = {Artificial Neural Networks (ANN); Crystal Structure Prediction (CSP); Machine Learning (ML); SELFIES},
  modificationdate = {2022-11-08T12:24:20},
  nlm-id           = {101767765},
  owner            = {saulius},
  pii              = {S2666-3899(22)00206-9},
  pmc              = {PMC9583042},
  pmid             = {36277819},
  pubmodel         = {Electronic-eCollection},
  pubstate         = {epublish},
  revised          = {2022-10-25},
}

@Presentation{Petrauskas2022b,
  author           = {Karolis Petrauskas},
  title            = {Distributed systems. 6: {C}ommunication abstractions, reliable broadcast (2/2) et al.},
  year             = {2022},
  creationdate     = {2022-11-08T13:56:27},
  file             = {:by-author/P/Petrauskas/2022_Petrauskas_1b.pdf:PDF},
  keywords         = {Algorithms; Bracha Algorithm; Broadcast; Communication Abstractions; Distributed Systems; Reliable Broadcast},
  modificationdate = {2022-11-08T14:01:32},
  owner            = {saulius},
  pages            = {1--48},
}

@Article{Bracha1987,
  author           = {Gabriel Bracha},
  journal          = {Information and Computation},
  title            = {Asynchronous {B}yzantine agreement protocols},
  year             = {1987},
  month            = {nov},
  number           = {2},
  pages            = {130--143},
  volume           = {75},
  creationdate     = {2022-11-08T14:03:20},
  doi              = {10.1016/0890-5401(87)90054-x},
  file             = {:by-author/B/Bracha/1987_Bracha_130.pdf:PDF},
  keywords         = {Algorithms; Bracha Algorithm; Broadcast; Byzantine Protocols; Communication Abstractions; Distributed Systems; Reliable Broadcast},
  modificationdate = {2022-11-08T14:05:28},
  owner            = {saulius},
  publisher        = {Elsevier {BV}},
}

@InProceedings{Greenan2010,
  author           = {Greenan, Kevin M. and Plank, James S. and Wylie, Jay J.},
  booktitle        = {Proceedings of the 2nd USENIX Conference on Hot Topics in Storage and File Systems},
  title            = {Mean time to meaningless: {MTTDL}, {M}arkov models, and storage system reliability},
  year             = {2010},
  address          = {USA},
  pages            = {5},
  publisher        = {USENIX Association},
  series           = {HotStorage'10},
  abstract         = {Mean Time To Data Loss (MTTDL) has been the standard reliability metric in storage systems for more than 20 years. MTTDL represents a simple formula that can be used to compare the reliability of small disk arrays and to perform comparative trending analyses. The MTTDL metric is often misused, with egregious examples relying on the MTTDL to generate reliability estimates that span centuries or millennia. Moving forward, the storage community needs to replace MTTDL with a metric that can be used to accurately compare the reliability of systems in a way that reflects the impact of data loss in the real world.},
  creationdate     = {2022-11-08T16:14:02},
  eprint           = {https://dl.acm.org/doi/10.5555/1863122.1863127},
  file             = {:by-author/G/Greenan/2010_Greenan_5.pdf:PDF},
  keywords         = {Computer Science (CS); Reliability Theory; Storage Reliability},
  location         = {Boston, MA},
  modificationdate = {2022-11-08T16:25:11},
  numpages         = {1},
  owner            = {saulius},
  url              = {https://www.usenix.org/legacy/events/hotstorage10/tech/full_papers/Greenan.pdf},
}

@Article{Mroz2022,
  author           = {Austin M. Mroz and Victor Posligua and Andrew Tarzia and Emma H. Wolpert and Kim E. Jelfs},
  journal          = {Journal of the American Chemical Society},
  title            = {Into the unknown: how computation can help explore uncharted material space},
  year             = {2022},
  month            = {oct},
  number           = {41},
  pages            = {18730--18743},
  volume           = {144},
  creationdate     = {2022-11-08T16:32:16},
  doi              = {10.1021/jacs.2c06833},
  file             = {:by-author/M/Mroz/2022_Mroz_18730.pdf:PDF},
  keywords         = {Chemoinformatics; Crystal Structure Prediction (CSP); Crystallography},
  modificationdate = {2022-11-08T16:33:55},
  owner            = {saulius},
  publisher        = {American Chemical Society ({ACS})},
  url              = {https://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC9585593&blobtype=pdf},
}

@Article{Nussinov2022,
  author           = {Nussinov, Ruth and Zhang, Mingzhen and Liu, Yonglan and Jang, Hyunbum},
  journal          = {The journal of physical chemistry. B},
  title            = {{AlphaFold}, artificial intelligence ({AI}), and allostery},
  year             = {2022},
  issn             = {1520-5207},
  month            = sep,
  pages            = {6372--6383},
  volume           = {126},
  abstract         = {AlphaFold has burst into our lives. A powerful algorithm that underscores the strength of biological sequence data and artificial intelligence (AI). AlphaFold has appended projects and research directions. The database it has been creating promises an untold number of applications with vast potential impacts that are still difficult to surmise. AI approaches can revolutionize personalized treatments and usher in better-informed clinical trials. They promise to make giant leaps toward reshaping and revamping drug discovery strategies, selecting and prioritizing combinations of drug targets. Here, we briefly overview AI in structural biology, including in molecular dynamics simulations and prediction of microbiota-human protein-protein interactions. We highlight the advancements accomplished by the deep-learning-powered AlphaFold in protein structure prediction and their powerful impact on the life sciences. At the same time, AlphaFold does not resolve the decades-long protein folding challenge, nor does it identify the folding pathways. The models that AlphaFold provides do not capture conformational mechanisms like frustration and allostery, which are rooted in ensembles, and controlled by their dynamic distributions. Allostery and signaling are properties of populations. AlphaFold also does not generate ensembles of intrinsically disordered proteins and regions, instead describing them by their low structural probabilities. Since AlphaFold generates single ranked structures, rather than conformational ensembles, it cannot elucidate the mechanisms of allosteric activating driver hotspot mutations nor of allosteric drug resistance. However, by capturing key features, deep learning techniques can use the single predicted conformation as the basis for generating a diverse ensemble.},
  chemicals        = {Intrinsically Disordered Proteins},
  citation-subset  = {IM},
  completed        = {2022-09-08},
  country          = {United States},
  creationdate     = {2022-11-08T16:39:21},
  doi              = {10.1021/acs.jpcb.2c04346},
  file             = {:by-author/N/Nussinov/2022_Nussinov_6372.pdf:PDF},
  issn-linking     = {1520-5207},
  issue            = {34},
  keywords         = {Allosteric Regulation; Artificial Intelligence (AI); Humans; Intrinsically Disordered Proteins, Chemistry; Molecular Dynamics Simulation; Protein Conformation; Protein Folding},
  modificationdate = {2024-09-06T08:36:28},
  nlm-id           = {101157530},
  owner            = {saulius},
  pmc              = {PMC9442638},
  pmid             = {35976160},
  pubmodel         = {Print-Electronic},
  pubstate         = {ppublish},
  revised          = {2022-09-26},
  url              = {https://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC9442638&blobtype=pdf},
}

@Article{Levine2002,
  author           = {Timothy R. Levine and Craig R. Hullett},
  journal          = {Human Communication Research},
  title            = {Eta squared, partial eta squared, and misreporting of effect size in communication research},
  year             = {2002},
  month            = {oct},
  number           = {4},
  pages            = {612--625},
  volume           = {28},
  creationdate     = {2022-11-09T15:30:05},
  doi              = {10.1111/j.1468-2958.2002.tb00828.x},
  file             = {:by-author/L/Levine/2002_Levine_612.pdf:PDF},
  keywords         = {ANOVA; Criticism; Effect Size; Eta Squared; Mathematics; Statistics},
  modificationdate = {2022-11-09T15:37:09},
  owner            = {saulius},
  publisher        = {Oxford University Press ({OUP})},
}

@Article{Okada2013,
  author           = {Kensuke Okada},
  journal          = {Behaviormetrika},
  title            = {Is omega squared less biased? A comparison of three major effect size indices in one-way anova},
  year             = {2013},
  month            = {jul},
  number           = {2},
  pages            = {129--147},
  volume           = {40},
  creationdate     = {2022-11-09T15:38:47},
  doi              = {10.2333/bhmk.40.129},
  file             = {:by-author/O/Okada/2013_Okada_129.pdf:PDF},
  keywords         = {ANOVA; Criticism; Effect Size; Eta Squared; Mathematics; Omega Squared; Statistics},
  modificationdate = {2022-11-09T15:39:53},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media {LLC}},
}

@Article{Cohen1973,
  author           = {Jacob Cohen},
  journal          = {Educational and Psychological Measurement},
  title            = {Eta-squared and partial eta-squared in fixed factor {ANOVA} designs},
  year             = {1973},
  month            = {apr},
  number           = {1},
  pages            = {107--112},
  volume           = {33},
  creationdate     = {2022-11-09T16:42:51},
  doi              = {10.1177/001316447303300111},
  file             = {:by-author/C/Cohen/1973_Cohen_107.pdf:PDF},
  keywords         = {ANOVA; Effect Size; Eta Squared; Mathematics; Statistics},
  modificationdate = {2022-11-09T16:48:14},
  owner            = {saulius},
  publisher        = {{SAGE} Publications},
}

@Article{Kennedy1970,
  author           = {John J. Kennedy},
  journal          = {Educational and Psychological Measurement},
  title            = {The eta coefficient in complex {ANOVA} designs},
  year             = {1970},
  month            = {dec},
  number           = {4},
  pages            = {885--889},
  volume           = {30},
  creationdate     = {2022-11-09T16:49:53},
  doi              = {10.1177/001316447003000409},
  file             = {:by-author/K/Kennedy/1970_Kennedy_885.pdf:PDF},
  keywords         = {ANOVA; Effect Size; Eta Squared; Mathematics; Statistics},
  modificationdate = {2022-11-09T16:51:55},
  owner            = {saulius},
  publisher        = {{SAGE} Publications},
}

@InProceedings{Pezoa2016,
  author           = {Pezoa, Felipe and Reutter, Juan L. and Suarez, Fernando and Ugarte, Martı́n and Vrgoč, Domagoj},
  booktitle        = {Proceedings of the 25th International Conference on World Wide Web},
  title            = {Foundations of {JSON} schema},
  year             = {2016},
  organization     = {International World Wide Web Conferences Steering Committee},
  pages            = {263--273},
  creationdate     = {2022-11-10T11:57:03},
  doi              = {10.1145/2872427.2883029},
  file             = {:by-author/P/Pezoa/2016_Pezoa_263.pdf:PDF},
  keywords         = {Computer Science (CS); Data Management; JSON; JSON Schema},
  modificationdate = {2022-11-10T12:25:57},
  owner            = {saulius},
}

@Electronic{Katz2022,
  author           = {Yehuda Katz and Dan Gebhardt and Gabe Sullice and Jeldrik Hanschke and Tyler Kellen and Steve Klabnik and Ethan Resnick},
  note             = {Accessed: 2022-11-10T12:32+02:00},
  title            = {{JSON:API} version 1.1},
  url              = {https://jsonapi.org/format/1.1/},
  year             = {2022},
  creationdate     = {2022-11-10T12:27:42},
  keywords         = {Computer Science (CS); JSON; JSON API; REST},
  modificationdate = {2022-11-10T12:33:14},
  owner            = {saulius},
}

@Article{Bowskill2021,
  author           = {Bowskill, David H. and Sugden, Isaac J. and Konstantinopoulos, Stefanos and Adjiman, Claire S. and Pantelides, Constantinos C.},
  journal          = {Annual review of chemical and biomolecular engineering},
  title            = {Crystal structure prediction methods for organic molecules: state of the art.},
  year             = {2021},
  issn             = {1947-5446},
  month            = jun,
  pages            = {593--623},
  volume           = {12},
  abstract         = {The prediction of the crystal structures that a given organic molecule is likely to form is an important theoretical problem of significant interest for the pharmaceutical and agrochemical industries, among others. As evidenced by a series of six blind tests organized over the past 2 decades, methodologies for crystal structure prediction (CSP) have witnessed substantial progress and have now reached a stage of development where they can begin to be applied to systems of practical significance. This article reviews the state of the art in general-purpose methodologies for CSP, placing them within a common framework that highlights both their similarities and their differences. The review discusses specific areas that constitute the main focus of current research efforts toward improving the reliability and widening applicability of these methodologies, and offers some perspectives for the evolution of this technology over the next decade.},
  chemicals        = {Pharmaceutical Preparations},
  citation-subset  = {IM},
  completed        = {2021-10-25},
  country          = {United States},
  creationdate     = {2022-11-13T15:25:12},
  doi              = {10.1146/annurev-chembioeng-060718-030256},
  file             = {:by-author/B/Bowskill/2021_Bowskill_593.pdf:PDF},
  issn-linking     = {1947-5438},
  keywords         = {Crystal Structure Prediction (CSP); Crystallography, X-Ray; Free Energy of Crystals; Lattice Energy; Models, Molecular; Pharmaceutical Preparations; Polymorphs; Reproducibility of Results},
  modificationdate = {2023-01-30T09:55:12},
  nlm-id           = {101574034},
  owner            = {saulius},
  pmid             = {33770462},
  pubmodel         = {Print-Electronic},
  pubstate         = {ppublish},
  revised          = {2021-10-25},
}

@Manual{RCT2020,
  title            = {{R}: a language and environment for statistical computing},
  address          = {Vienna, Austria},
  author           = {{R Core Team}},
  organization     = {R Foundation for Statistical Computing},
  year             = {2020},
  creationdate     = {2022-11-13T18:46:47},
  keywords         = {R; Statistical Computing; Statistics; The R Programming Language},
  modificationdate = {2022-11-13T18:47:54},
  owner            = {saulius},
  url              = {https://www.R-project.org},
}

@Article{Buttliere2021,
  author           = {Brett Buttliere},
  journal          = {Methodological Innovations},
  title            = {Adopting standard variable labels solves many of the problems with sharing and reusing data},
  year             = {2021},
  month            = {may},
  number           = {2},
  pages            = {205979912110266},
  volume           = {14},
  comment          = {A paper cited by Brett Buttliere <brettbuttliere@gmail.com> in a collaboration offer on CHIST-ERA grant.},
  creationdate     = {2022-11-14T10:46:52},
  doi              = {10.1177/20597991211026616},
  file             = {:by-author/B/Buttliere/2021_Buttliere_205979912110266.pdf:PDF;:by-author/B/Buttliere/2021_Buttliere_205979912110266.epub:ePUB},
  keywords         = {Computer Science (CS); Data Labels; Data Management; FAIR; Metadata; Standards; Statistics},
  modificationdate = {2022-11-14T10:51:26},
  owner            = {saulius},
  publisher        = {{SAGE} Publications},
}

@Article{Egorova2020,
  author           = {Olga Egorova and Roohollah Hafizi and David C. Woods and Graeme Day},
  title            = {Multi-fidelity statistical machine learning for molecular crystal structure prediction},
  year             = {2020},
  month            = {jun},
  pages            = {1--13},
  comment          = {Cited in the Bowskill2021 review.},
  creationdate     = {2022-11-15T11:27:13},
  doi              = {10.26434/chemrxiv.12407831.v1},
  file             = {:by-author/E/Egorova/2020_Egorova_1.pdf:PDF},
  keywords         = {Crystal Structure Prediction (CSP); Crystallography, X-Ray; Machine Learning (ML)},
  modificationdate = {2022-11-15T11:29:25},
  owner            = {saulius},
  publisher        = {American Chemical Society ({ACS})},
  timestamp        = {2022.11.15},
}

@Article{Lenstra1982,
  author           = {A. K. Lenstra and H. W. Lenstra and L. Lovász},
  journal          = {Mathematische Annalen},
  title            = {Factoring polynomials with rational coefficients},
  year             = {1982},
  month            = {dec},
  number           = {4},
  pages            = {515--534},
  volume           = {261},
  comment          = {Found via: https://en.wikipedia.org/wiki/Lattice_reduction},
  creationdate     = {2022-11-16T10:49:15},
  doi              = {10.1007/bf01457454},
  file             = {:by-author/L/Lenstra/1982_Lenstra_515.pdf:PDF},
  keywords         = {Algorithms; Computer Science (CS); Crystallography; Lattice Reduction},
  modificationdate = {2022-11-16T10:50:46},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media {LLC}},
  url              = {https://link.springer.com/content/pdf/10.1007/BF01457454.pdf},
}

@Article{Chen2022,
  author           = {Chi Chen and Shyue Ping Ong},
  journal          = {arXiv},
  title            = {A universal graph deep learning interatomic potential for the periodic table},
  year             = {2022},
  month            = feb,
  pages            = {1--58},
  abstract         = {Interatomic potentials (IAPs), which describe the potential energy surface of atoms, are a fundamental input for atomistic simulations. However, existing IAPs are either fitted to narrow chemistries or too inaccurate for general applications. Here, we report a universal IAP for materials based on graph neural networks with three-body interactions (M3GNet). The M3GNet IAP was trained on the massive database of structural relaxations performed by the Materials Project over the past 10 years and has broad applications in structural relaxation, dynamic simulations and property prediction of materials across diverse chemical spaces. About 1.8 million materials were identified from a screening of 31 million hypothetical crystal structures to be potentially stable against existing Materials Project crystals based on M3GNet energies. Of the top 2000 materials with the lowest energies above hull, 1578 were verified to be stable using DFT calculations. These results demonstrate a machine learning-accelerated pathway to the discovery of synthesizable materials with exceptional properties.},
  archiveprefix    = {arXiv},
  creationdate     = {2022-11-16T18:15:58},
  eprint           = {2202.02450},
  file             = {:by-author/C/Chen/2022_Chen_1.pdf:PDF},
  keywords         = {Crystallography; Graph Neural Networks (GNN); Phonon Spectra; cond-mat.mtrl-sci; physics.chem-ph},
  modificationdate = {2024-05-23T14:45:38},
  owner            = {saulius},
  primaryclass     = {cond-mat.mtrl-sci},
  url              = {https://arxiv.org/abs/2202.02450},
}

@Article{Wang2002a,
  author           = {Wang, Lichun and Riethoven, Jean-Jack and Robinson, Alan},
  journal          = {Bioinformatics (Oxford, England)},
  title            = {{XEMBL}: distributing {EMBL} data in {XML} format.},
  year             = {2002},
  issn             = {1367-4803},
  month            = aug,
  pages            = {1147--1148},
  volume           = {18},
  abstract         = {Data in the EMBL Nucleotide Sequence Database is traditionally available in a flat file format that has a number of known shortcomings. With XML rapidly emerging as a standard data exchange format that can address some problems of flat file formats by defining data structure and syntax, there is now a demand to distribute EMBL data in an XML format. XEMBL is a service tool that employs CORBA servers to access EMBL data, and distributes the data in XML format via a number of mechanisms. Use of the XEMBL service is free of charge at http://www.ebi.ac.uk/xembl/, and can be accessed via web forms, CGI, and a SOAP-enabled service. Information on the EMBL Nucleotide Sequence Database is available at http://www.ebi.ac.uk/embl/. The EMBL Object Model is available at http://corba.ebi.ac.uk/models/. Information on the EMBL CORBA servers is at http://corba.ebi.ac.uk/},
  citation-subset  = {IM},
  comment          = {Unfortunately, most of the mentioned URLs are not reachable as of 2022-11-17T10:47+02:00 :(.},
  completed        = {2002-10-17},
  country          = {England},
  creationdate     = {2022-11-17T09:51:56},
  doi              = {10.1093/bioinformatics/18.8.1147},
  file             = {:by-author/W/Wang/2002_Wang_1147a.pdf:PDF},
  issn-linking     = {1367-4803},
  issue            = {8},
  keywords         = {Computer Communication Networks; Computer Science (CS); Computing Methodologies; Database Management Systems; Databases, Nucleic Acid; Information Storage and Retrieval, Methods; Internet; Programming Languages; Sequence Analysis, Methods},
  modificationdate = {2023-01-30T09:55:07},
  nlm-id           = {9808944},
  owner            = {saulius},
  pmid             = {12176844},
  pubmodel         = {Print},
  pubstate         = {ppublish},
  revised          = {2019-05-13},
}

@Article{Liang2020,
  author           = {Haotong Liang and Valentin Stanev and A. Gilad Kusne and Ichiro Takeuchi},
  journal          = {Physical Review Materials},
  title            = {{CRYSPNet}: Crystal structure predictions via neural networks},
  year             = {2020},
  month            = {dec},
  number           = {12},
  pages            = {123802},
  volume           = {4},
  creationdate     = {2022-11-17T17:56:01},
  doi              = {10.1103/physrevmaterials.4.123802},
  file             = {:by-author/L/Liang/2020_Liang_123802.pdf:PDF},
  keywords         = {Artificial Neural Networks (ANN); Computer Science (CS); CryspNet; Crystal Structure Prediction (CSP); Neural Networks (NN)},
  modificationdate = {2022-11-17T17:56:40},
  owner            = {saulius},
  publisher        = {American Physical Society ({APS})},
}

@TechReport{Zwart2006,
  author           = {P. H. Zwart and R. W. Grosse-Kunstleve and P. D. Adams},
  title            = {Exploring metric symmetry},
  year             = {2006},
  month            = {jul},
  creationdate     = {2022-11-18T14:53:29},
  doi              = {10.2172/926901},
  file             = {:by-author/Z/Zwart/2006_Zwart_1.pdf:PDF},
  keywords         = {Crystal Structure; Detection; Exploration; Freezing; Halides; Heavy Metals; Metrics; Space Groups; Symmetry; Transformations; Twinning},
  modificationdate = {2022-11-18T14:53:29},
  owner            = {saulius},
  pages            = {1--6},
  publisher        = {Office of Scientific and Technical Information ({OSTI})},
  school           = {U.S. Department of Energy},
}

@Article{Venkatraman2022,
  author           = {Vishwesh Venkatraman and Patricia Almeida Carvalho},
  journal          = {Acta Materialia},
  title            = {On the value of popular crystallographic databases for machine learning prediction of space groups},
  year             = {2022},
  month            = {nov},
  pages            = {118353},
  volume           = {240},
  creationdate     = {2022-11-22T16:18:56},
  doi              = {10.1016/j.actamat.2022.118353},
  file             = {:by-author/V/Venkatraman/2022_Venkatraman_118353.pdf:PDF},
  keywords         = {Artificial Neural Networks (ANN); COD; Crystal Structure Prediction (CSP); Databases; Machine Learning (ML)},
  modificationdate = {2022-11-22T16:23:03},
  owner            = {saulius},
  publisher        = {Elsevier {BV}},
}

@Article{Hu2021,
  author           = {Jianjun Hu and Yong Zhao and Yuqi Song and Rongzhi Dong and Wenhui Yang and Yuxin Li and Edirisuriya M. D. Siriwardane},
  title            = {{AlphaCrystal}: Contact map based crystal structure prediction using deep learning},
  year             = {2021},
  month            = feb,
  pages            = {1--15},
  abstract         = {Crystal structure prediction is one of the major unsolved problems in materials science. Traditionally, this problem is formulated as a global optimization problem for which global search algorithms are combined with first principle free energy calculations to predict the ground-state crystal structure given only a material composition or a chemical system. These ab initio algorithms usually cannot exploit a large amount of implicit physicochemical rules or geometric constraints (deep knowledge) of atom configurations embodied in a large number of known crystal structures. Inspired by the deep learning enabled breakthrough in protein structure prediction, herein we propose AlphaCrystal, a crystal structure prediction algorithm that combines a deep residual neural network model that learns deep knowledge to guide predicting the atomic contact map of a target crystal material followed by reconstructing its 3D crystal structure using genetic algorithms. Based on the experiments of a selected set of benchmark crystal materials, we show that our AlphaCrystal algorithm can predict structures close to the ground truth structures. It can also speed up the crystal structure prediction process by predicting and exploiting the predicted contact map so that it has the potential to handle relatively large systems. We believe that our deep learning based ab initio crystal structure prediction method that learns from existing material structures can be used to scale up current crystal structure prediction practice. To our knowledge, AlphaCrystal is the first neural network based algorithm for crystal structure contact map prediction and the first method for directly reconstructing crystal structures from materials composition, which can be further optimized by DFT calculations.},
  archiveprefix    = {arXiv},
  creationdate     = {2022-11-22T16:25:23},
  eprint           = {2102.01620},
  file             = {:by-author/H/Hu/2021_Hu_1.pdf:PDF},
  keywords         = {Artificial Neural Networks (ANN); Crystal Structure Prediction (CSP); Databases; Machine Learning (ML); cond-mat.mtrl-sci},
  modificationdate = {2022-11-22T16:27:03},
  owner            = {saulius},
  primaryclass     = {cond-mat.mtrl-sci},
}

@Article{Epstein1974,
  author           = {George Epstein and Gideon Frieder and David C. Rine},
  journal          = {Computer},
  title            = {The development of multiple-valued logic as related to computer science},
  year             = {1974},
  month            = {sep},
  number           = {9},
  pages            = {20--32},
  volume           = {7},
  creationdate     = {2022-11-24T21:32:49},
  doi              = {10.1109/mc.1974.6323304},
  file             = {:by-author/E/Epstein/1974_Epstein_20.pdf:PDF},
  keywords         = {Computer Science (CS); Ternary Logic},
  modificationdate = {2022-11-24T21:34:23},
  owner            = {saulius},
  publisher        = {Institute of Electrical and Electronics Engineers ({IEEE})},
}

@Article{Gomes2022,
  author           = {Dylan G. E. Gomes and Patrice Pottier and Robert Crystal-Ornelas and Emma J. Hudgins and Vivienne Foroughirad and Luna L. S{\'{a}}nchez-Reyes and Rachel Turba and Paula Andrea Martinez and David Moreau and Michael G. Bertram and Cooper A. Smout and Kaitlyn M. Gaynor},
  journal          = {Proceedings of the Royal Society B: Biological Sciences},
  title            = {Why don't we share data and code? Perceived barriers and benefits to public archiving practices},
  year             = {2022},
  month            = {nov},
  number           = {1987},
  pages            = {20221113},
  volume           = {289},
  comment          = {Recommended by John R. Helliwell (e-mail to Discussion on Data <commdat@iucr.org> on 2022-11-26 12:51).},
  creationdate     = {2022-11-26T16:17:59},
  doi              = {10.1098/rspb.2022.1113},
  file             = {:by-author/G/Gomes/2022_Gomes_20221113.pdf:PDF},
  keywords         = {Data Publishing; Data Sharing; Open Data; Open Science; Publishing},
  modificationdate = {2022-11-26T17:01:47},
  owner            = {saulius},
  publisher        = {The Royal Society},
}

@Article{Flack1983,
  author           = {H. D. Flack},
  journal          = {Acta Crystallographica Section A Foundations of Crystallography},
  title            = {On enantiomorph-polarity estimation},
  year             = {1983},
  month            = {nov},
  number           = {6},
  pages            = {876--881},
  volume           = {39},
  comment          = {Found via https://en.wikipedia.org/wiki/Flack_parameter.},
  creationdate     = {2022-11-30T18:27:21},
  doi              = {10.1107/s0108767383001762},
  file             = {:by-author/F/Flack/1983_Flack_876.pdf:PDF},
  keywords         = {Anomalous Scattering; Crystallography; Enantiomorphs; Flack Paramater; X-ray Crystallography},
  modificationdate = {2022-12-03T15:15:27},
  owner            = {saulius},
  publisher        = {International Union of Crystallography ({IUCr})},
}

@Article{Matuliene2022,
  author           = {Jurgita Matulienė and Gediminas Žvinys and Vytautas Petrauskas and Agnė Kvietkauskaitė and Audrius Zakšauskas and Kirill Shubin and Asta Zubrienė and Lina Baranauskienė and Lina Kačenauskaitė and Sergei Kopanchuk and Santa Veiksina and Vaida Paketurytė-Latvė and Joana Smirnovienė and Vaida Juozapaitienė and Aurelija Mickevičiūtė and Vilma Michailovienė and Jelena Jachno and Dovilė Stravinskienė and Aistė Sližienė and Agnė Petrošiūtė and Holger M. Becker and Justina Kazokaitė-Adomaitienė and Ala Yaromina and Edita Čapkauskaitė and Ago Rinken and Virginija Dudutienė and Ludwig J. Dubois and Daumantas Matulis},
  journal          = {Scientific Reports},
  title            = {Picomolar fluorescent probes for compound affinity determination to carbonic anhydrase {IX} expressed in live cancer cells},
  year             = {2022},
  month            = {oct},
  number           = {1},
  pages            = {1--25},
  volume           = {12},
  creationdate     = {2022-12-01T17:07:07},
  doi              = {10.1038/s41598-022-22436-1},
  file             = {:by-author/M/Matulienė/2022_Matulienė_1.pdf:PDF},
  keywords         = {Anti Cancer Drugs; Cancer; Carbonic Anhydrases; Fluorescence Microscopy},
  modificationdate = {2022-12-01T17:10:14},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media {LLC}},
}

@Presentation{Shubin2022,
  author           = {Kirill Shubin},
  title            = {Imaging of carbonic anhydrases \emph{in vivo}: new probes},
  year             = {2022},
  comment          = {Presented at the CA Workshop on Dec. 1st, 2022 (Taiwan-Lithuania project of Daumantas). Sent by Kirill in his 2022-12-02 18:27 e-mail to grazulis@ibt.lt.},
  creationdate     = {2022-12-03T11:16:39},
  file             = {:by-author/S/Shubin/2022_Shubin_1.pptx:PowerPoint 2007+},
  keywords         = {Biochemistry; Carbonic Anhydrases; Dyes; Imaging; PET Scans; Radioactive Probes},
  modificationdate = {2022-12-03T11:31:48},
  owner            = {saulius},
  pages            = {1--16},
}

@Presentation{Alkauskas2022,
  author           = {Giedrius Alkauskas},
  title            = {New problems in geometric combinatorics: cycles, extremal polygons, integer sequences},
  year             = {2022},
  comment          = {Presented at the seminat of the II (MIF). Sent on 2022-11-18 10:21 to ii@mif.vu.lt.},
  creationdate     = {2022-12-03T11:30:59},
  file             = {:by-author/A/Alkauskas/2022_Alkauskas_1.pdf:PDF},
  keywords         = {Chessboard; Computer Science (CS); Geometry; Graph Theory; Mathematics; Number Sequences},
  modificationdate = {2022-12-03T11:38:15},
  owner            = {saulius},
  pages            = {1--27},
}

@Manuscript{Alkauskas2022a,
  author           = {Giedrius Alkauskas},
  title            = {$n^2$-gons supported on a subset $1 \le x,y, \le n$ of an integer lattice},
  year             = {2022},
  keywords         = {Chessboard; Computer Science (CS); Geometry; Graph Theory; Mathematics; Number Sequences},
  comment          = {Presented at the seminat of the II (MIF). Sent on 2022-11-18 10:21 to ii@mif.vu.lt.},
  creationdate     = {2022-12-03T11:33:10},
  file             = {:by-author/A/Alkauskas/2022_Alkauskas_1a.pdf:PDF},
  modificationdate = {2022-12-03T11:38:08},
  owner            = {saulius},
  pages            = {1--3},
}

@Article{Price2018,
  author           = {Sarah L. Price},
  journal          = {Faraday Discussions},
  title            = {Is zeroth order crystal structure prediction ({CSP}{\_}0) coming to maturity? What should we aim for in an ideal crystal structure prediction code?},
  year             = {2018},
  pages            = {9--30},
  volume           = {211},
  comment          = {Cited in Bowskill2021.},
  creationdate     = {2022-12-03T14:04:20},
  doi              = {10.1039/c8fd00121a},
  file             = {:by-author/P/Price/2018_Price_9.pdf:PDF},
  keywords         = {Chemoinformatics; Crystal Structure Prediction (CSP)},
  modificationdate = {2022-12-03T14:06:08},
  owner            = {saulius},
  publisher        = {Royal Society of Chemistry ({RSC})},
}

@Article{Nyman2018,
  author           = {Jonas Nyman and Susan M. Reutzel-Edens},
  journal          = {Faraday Discussions},
  title            = {Crystal structure prediction is changing from basic science to applied technology},
  year             = {2018},
  pages            = {459--476},
  volume           = {211},
  comment          = {Cited in Bowskill2021.},
  creationdate     = {2022-12-03T14:11:33},
  doi              = {10.1039/c8fd00033f},
  file             = {:by-author/N/Nyman/2018_Nyman_459.pdf:PDF},
  keywords         = {Chemoinformatics; Crystal Structure Prediction (CSP)},
  modificationdate = {2022-12-03T14:15:24},
  owner            = {saulius},
  publisher        = {Royal Society of Chemistry ({RSC})},
}

@Article{Axilrod1943,
  author           = {B. M. Axilrod and E. Teller},
  journal          = {The Journal of Chemical Physics},
  title            = {Interaction of the van der {W}aals type between three atoms},
  year             = {1943},
  month            = {jun},
  number           = {6},
  pages            = {299--300},
  volume           = {11},
  comment          = {Cited in Bowskill2021.},
  creationdate     = {2022-12-03T16:00:38},
  doi              = {10.1063/1.1723844},
  file             = {:by-author/A/Axilrod/1943_Axilrod_299.pdf:PDF},
  keywords         = {Chemoinformatics; Crystal Structure Prediction (CSP)},
  modificationdate = {2022-12-03T16:05:29},
  owner            = {saulius},
  publisher        = {{AIP} Publishing},
}

@Article{Nyman2019,
  author           = {Jonas Nyman and Lian Yu and Susan M. Reutzel-Edens},
  journal          = {{CrystEngComm}},
  title            = {Accuracy and reproducibility in crystal structure prediction: the curious case of {ROY}},
  year             = {2019},
  number           = {13},
  pages            = {2080--2088},
  volume           = {21},
  comment          = {Cited in Bowskill2021.},
  creationdate     = {2022-12-03T16:37:44},
  doi              = {10.1039/c8ce01902a},
  file             = {:by-author/N/Nyman/2019_Nyman_2080.pdf:PDF},
  keywords         = {Chemoinformatics; Crystal Structure Prediction (CSP); Multiple Polymorphs; ROY},
  modificationdate = {2022-12-03T16:51:27},
  owner            = {saulius},
  publisher        = {Royal Society of Chemistry ({RSC})},
}

@Article{Perdew1996,
  author           = {Perdew, J. P. and Burke, K. and Ernzerhof, M.},
  journal          = {Physical review letters},
  title            = {Generalized gradient approximation made simple.},
  year             = {1996},
  issn             = {1079-7114},
  month            = oct,
  pages            = {3865--3868},
  volume           = {77},
  comment          = {Cited in Bowskill2021.},
  country          = {United States},
  creationdate     = {2022-12-03T16:43:42},
  doi              = {10.1103/PhysRevLett.77.3865},
  file             = {:by-author/P/Perdew/1996_Perdew_3865.pdf:PDF},
  issn-linking     = {0031-9007},
  issue            = {18},
  keywords         = {Chemoinformatics; Crystal Structure Prediction (CSP); Density Functional Theory (DFT); GGA; Quantum Mechanics (QM)},
  modificationdate = {2022-12-10T14:20:00},
  nlm-id           = {0401141},
  owner            = {saulius},
  pmid             = {10062328},
  pubmodel         = {Print},
  pubstate         = {ppublish},
  revised          = {2022-03-11},
}

@Article{Tan2018,
  author           = {Melissa Tan and Alexander G. Shtukenberg and Shengcai Zhu and Wenqian Xu and Eric Dooryhee and Shane~M. Nichols and Michael D. Ward and Bart Kahr and Qiang Zhu},
  journal          = {Faraday Discussions},
  title            = {{ROY} revisited, again: the eighth solved structure},
  year             = {2018},
  pages            = {477--491},
  volume           = {211},
  comment          = {Cited in Bowskill2021.},
  creationdate     = {2022-12-03T16:51:17},
  doi              = {10.1039/c8fd00039e},
  file             = {:by-author/T/Tan/2018_Tan_477.pdf:PDF},
  keywords         = {Chemoinformatics; Crystal Structure Prediction (CSP); Multiple Polymorphs; ROY},
  modificationdate = {2022-12-03T16:54:01},
  owner            = {saulius},
  publisher        = {Royal Society of Chemistry ({RSC})},
}

@Article{Walsh2022,
  author           = {Walsh, Mark P. and Barclay, James A. and Begg, Callum S. and Xuan, Jinyi and Johnson, Natalie T. and Cole, Jason C. and Kitching, Matthew O.},
  journal          = {JACS Au},
  title            = {Identifying a Hidden Conglomerate Chiral Pool in the CSD},
  year             = {2022},
  issn             = {2691-3704},
  month            = {October},
  number           = {10},
  pages            = {2235--2250},
  volume           = {2},
  abstract         = {Conglomerate crystallization is the spontaneous generation of individually enantioenriched crystals from a nonenantioenriched material. This behavior is responsible for spontaneous resolution and the discovery of molecular chirality by Pasteur. The phenomenon of conglomerate crystallization of chiral organic molecules has been left largely undocumented, with no actively curated list available in the literature. While other crystallographic behaviors can be interrogated by automated searching, conglomerate crystallizations are not identified within the Cambridge Structural Database (CSD) and are therefore not accessible by conventional automated searching. By conducting a manual search of the CSD and literature, a list of over 1800 chiral species capable of conglomerate crystallization was curated by inspection of the racemic synthetic routes described in each publication. The majority of chiral conglomerate crystals are produced and published by synthetic chemists who seldom note and rarely exploit the implications this phenomenon can have on the enantiopurity of their crystalline materials. With their structures revealed, we propose that this list of compounds represents a new chiral pool which is not tied to biological sources of chirality.},
  creationdate     = {2022-12-04T13:28:15},
  doi              = {10.1021/jacsau.2c00394},
  file             = {:by-author/W/Walsh/2022_Walsh_2235.pdf:PDF},
  keywords         = {CSD; Chirality; Database},
  modificationdate = {2022-12-04T13:29:09},
  owner            = {saulius},
  url              = {https://europepmc.org/articles/PMC9597607},
}

@Article{Zhang2019,
  author           = {Zhang, Yao and Yang, Ben and Ghafoor, Atif and Zhang, Yang and Zhang, Yu-Fan and Wang, Rui-Pu and Yang, Jin-Long and Luo, Yi and Dong, Zhen-Chao and Hou, J. G.},
  journal          = {National science review},
  title            = {Visually constructing the chemical structure of a single molecule by scanning {R}aman picoscopy},
  year             = {2019},
  issn             = {2095-5138},
  month            = {November},
  number           = {6},
  pages            = {1169--1175},
  volume           = {6},
  abstract         = {The strong spatial confinement of a nanocavity plasmonic field has made it possible to visualize the inner structure of a single molecule and even to distinguish its vibrational modes in real space. With such ever-improved spatial resolution, it is anticipated that full vibrational imaging of a molecule could be achieved to reveal molecular structural details. Here we demonstrate full Raman images of individual vibrational modes at the ångström level for a single Mg-porphine molecule, revealing distinct characteristics of each vibrational mode in real space. Furthermore, by exploiting the underlying interference effect and Raman fingerprint database, we propose a new methodology for structural determination, which we have called 'scanning Raman picoscopy', to show how such ultrahigh-resolution spectromicroscopic vibrational images can be used to visually assemble the chemical structure of a single molecule through a simple Lego-like building process.},
  comment          = {ArXiv preprint exists.},
  creationdate     = {2022-12-04T13:35:12},
  doi              = {10.1093/nsr/nwz180},
  file             = {:by-author/Z/Zhang/2019_Zhang_1169.pdf:PDF},
  keywords         = {Molecular Modelling; Scanning Raman Picoscopy; Single Molecule Imaging},
  modificationdate = {2022-12-04T13:37:19},
  owner            = {saulius},
  url              = {https://europepmc.org/articles/PMC8291412},
}

@Article{Petretto2018,
  author           = {Guido Petretto and Shyam Dwaraknath and Henrique P. C. Miranda and Donald Winston and Matteo Giantomassi and Michiel J. van Setten and Xavier Gonze and Kristin A. Persson and Geoffroy Hautier and Gian-Marco Rignanese},
  journal          = {Scientific Data},
  title            = {High-throughput density-functional perturbation theory phonons for inorganic materials},
  year             = {2018},
  month            = {may},
  number           = {1},
  pages            = {1--12},
  volume           = {5},
  creationdate     = {2022-12-06T09:13:42},
  doi              = {10.1038/sdata.2018.65},
  file             = {:by-author/P/Petretto/2018_Petretto_1.pdf:PDF},
  keywords         = {Phonon Calculation; Raman Spectroscopy; Theoretical Raman Spectra},
  modificationdate = {2022-12-06T09:15:10},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media {LLC}},
}

@Article{FiilFlynn2022,
  author           = {Sean M. Fiil-Flynn and Brandon Butler and Michael Carroll and Or Cohen-Sasson and Carys Craig and Lucie Guibault and Peter Jaszi and Bernd Justin Jütte and Ariel Katz and João Pedro Quintais and Thomas Margoni and Allan Rocha de Souza and Matthew Sag and Rachael Samberg and Luca Schirru and Martin Senftleben and Ofer Tur-Sinai and Jorge L. Contreras},
  journal          = {Science},
  title            = {Legal reform to enhance global text and data mining research},
  year             = {2022},
  month            = {dec},
  number           = {6623},
  pages            = {951--953},
  volume           = {378},
  creationdate     = {2022-12-06T09:26:03},
  doi              = {10.1126/science.add6124},
  file             = {:by-author/F/Fiil-Flynn/2022_Fiil-Flynn_951.pdf:PDF},
  keywords         = {Copyright; Data Sharing; Open Data; Scientific Publishing; Text Mining},
  modificationdate = {2022-12-06T09:27:20},
  owner            = {saulius},
  publisher        = {American Association for the Advancement of Science ({AAAS})},
}

@Manuscript{Choudhary2022c,
  author           = {Kamal Choudhary and Brian DeCost and Lily Major and Keith Butler and Jeyan Thiyagalingam and Francesca Tavazza},
  title            = {Unified graph neural network force-field for the periodic table},
  year             = {2022},
  keywords         = {Density Functional Theory (DFT); Machine Learning (ML); Phonon Spectra; Rama Spectra; cond-mat.mtrl-sci},
  month            = sep,
  url              = {http://arxiv.org/pdf/2209.05554v2},
  abstract         = {Classical force fields (FF) based on machine learning (ML) methods show great potential for large scale simulations of materials. MLFFs have hitherto largely been designed and fitted for specific systems and are not usually transferable to chemistries beyond the specific training set. We develop a unified atomisitic line graph neural network-based FF (ALIGNN-FF) that can model both structurally and chemically diverse materials with any combination of 89 elements from the periodic table. To train the ALIGNN-FF model, we use the JARVIS-DFT dataset which contains around 75000 materials and 4 million energy-force entries, out of which 307113 are used in the training. We demonstrate the applicability of this method for fast optimization of atomic structures in the crystallography open database and by predicting accurate crystal structures using genetic algorithm for alloys.},
  archiveprefix    = {arXiv},
  creationdate     = {2022-12-06T09:30:57},
  eprint           = {2209.05554},
  file             = {:by-author/C/Choudhary/2022_Choudhary_1c.pdf:PDF},
  modificationdate = {2023-05-18T07:52:47},
  owner            = {saulius},
  primaryclass     = {cond-mat.mtrl-sci},
}

@Article{Gonze2002,
  author           = {X. Gonze and J.-M. Beuken and R. Caracas and F. Detraux and M. Fuchs and G.-M. Rignanese and L. Sindic and M. Verstraete and G. Zerah and F. Jollet and M. Torrent and A. Roy and M. Mikami and Ph. Ghosez and J.-Y. Raty and D.C. Allan},
  journal          = {Computational Materials Science},
  title            = {First-principles computation of material properties: the {ABINIT} software project},
  year             = {2002},
  month            = {nov},
  number           = {3},
  pages            = {478--492},
  volume           = {25},
  creationdate     = {2022-12-10T16:46:05},
  doi              = {10.1016/s0927-0256(02)00325-7},
  file             = {:by-author/G/Gonze/2002_Gonze_478.pdf:PDF},
  keywords         = {ABINIT; ABINIT v3.0; Computational Material Science; Density Functional Theory (DFT); Quantum Mechanics (QM); Quantum Mechanics Codes},
  modificationdate = {2022-12-10T16:50:18},
  owner            = {saulius},
  publisher        = {Elsevier {BV}},
}

@Article{Schuett2017a,
  author           = {Kristof T. Schütt and Pieter-Jan Kindermans and Huziel E. Sauceda and Stefan Chmiela and Alexandre Tkatchenko and Klaus-Robert Müller},
  journal          = {Advances in Neural Information Processing Systems 30 (2017), pp. 992-1002},
  title            = {{SchNet}: A continuous-filter convolutional neural network for modeling quantum interactions},
  year             = {2017},
  month            = jun,
  pages            = {992--1002},
  abstract         = {Deep learning has the potential to revolutionize quantum chemistry as it is ideally suited to learn representations for structured data and speed up the exploration of chemical space. While convolutional neural networks have proven to be the first choice for images, audio and video data, the atoms in molecules are not restricted to a grid. Instead, their precise locations contain essential physical information, that would get lost if discretized. Thus, we propose to use continuous-filter convolutional layers to be able to model local correlations without requiring the data to lie on a grid. We apply those layers in SchNet: a novel deep learning architecture modeling quantum interactions in molecules. We obtain a joint model for the total energy and interatomic forces that follows fundamental quantum-chemical principles. This includes rotationally invariant energy predictions and a smooth, differentiable potential energy surface. Our architecture achieves state-of-the-art performance for benchmarks of equilibrium molecules and molecular dynamics trajectories. Finally, we introduce a more challenging benchmark with chemical and structural variations that suggests the path for further work.},
  archiveprefix    = {arXiv},
  creationdate     = {2022-12-11T16:55:15},
  eprint           = {1706.08566},
  file             = {:by-author/S/Schütt/2017_Schütt_992.pdf:PDF},
  keywords         = {Machine Learning (ML); physics.chem-ph; stat.ML},
  modificationdate = {2022-12-11T16:57:41},
  owner            = {saulius},
  primaryclass     = {stat.ML},
}

@WWW{Downs2022,
  author           = {Gordon Downs},
  creationdate     = {2022-12-11T17:03:49},
  keywords         = {Machine Learning (ML); Raman Spectra; Raman Spectra Prediction},
  modificationdate = {2022-12-11T17:03:49},
  owner            = {saulius},
  retrieved        = {2022-12-11T17:01+02:00},
  title            = {A graph machine learning approach to synthesizing {R}aman spectra},
  url              = {https://medium.com/stanford-cs224w/a-graph-machine-learning-approach-to-synthesizing-raman-spectra-eaab620b34bb},
  year             = {2022},
}

@Article{Alsaui2022,
  author           = {Abdulmohsen Alsaui and Saad M. Alqahtani and Faisal Mumtaz and Alsayoud G. Ibrahim and Alghadeer Mohammed and Ali H. Muqaibel and Sergey N. Rashkeev and Ahmer A. B. Baloch and Fahhad H. Alharbi},
  journal          = {Scientific Reports},
  title            = {Highly accurate machine learning prediction of crystal point groups for ternary materials from chemical formula},
  year             = {2022},
  month            = {jan},
  number           = {1},
  pages            = {1--10},
  volume           = {12},
  creationdate     = {2022-12-11T17:06:45},
  doi              = {10.1038/s41598-022-05642-9},
  file             = {:by-author/A/Alsaui/2022_Alsaui_1.pdf:PDF},
  keywords         = {Crystal Structure Prediction (CSP); Machine Learning (ML)},
  modificationdate = {2022-12-11T17:08:19},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media {LLC}},
}

@Article{Kusaba2022,
  author           = {Minoru Kusaba and Chang Liu and Ryo Yoshida},
  journal          = {Computational Materials Science},
  title            = {Crystal structure prediction with machine learning-based element substitution},
  year             = {2022},
  month            = {aug},
  pages            = {111496},
  volume           = {211},
  creationdate     = {2022-12-11T17:10:05},
  doi              = {10.1016/j.commatsci.2022.111496},
  file             = {:by-author/K/Kusaba/2022_Kusaba_111496.pdf:PDF;:by-author/K/Kusaba/2022_Kusaba_111496preprint.pdf:PDF},
  keywords         = {Crystal Structure Prediction (CSP); Machine Learning (ML)},
  modificationdate = {2022-12-11T17:11:50},
  owner            = {saulius},
  publisher        = {Elsevier {BV}},
}

@Article{Yamashita2021,
  author           = {Tomoki Yamashita and Shinichi Kanehira and Nobuya Sato and Hiori Kino and Kei Terayama and Hikaru Sawahata and Takumi Sato and Futoshi Utsuno and Koji Tsuda and Takashi Miyake and Tamio Oguchi},
  journal          = {Science and Technology of Advanced Materials: Methods},
  title            = {{CrySPY}: a crystal structure prediction tool accelerated by machine learning},
  year             = {2021},
  month            = {jan},
  number           = {1},
  pages            = {87--97},
  volume           = {1},
  creationdate     = {2022-12-11T17:22:45},
  doi              = {10.1080/27660400.2021.1943171},
  file             = {:by-author/Y/Yamashita/2021_Yamashita_87.pdf:PDF;:by-author/Y/Yamashita/2021_Yamashita_87.epub:ePUB},
  keywords         = {Crystal Structure Prediction (CSP); Crystallography; Machine Learning (ML)},
  modificationdate = {2022-12-11T17:25:05},
  owner            = {saulius},
  publisher        = {Informa {UK} Limited},
}

@Article{Han2021,
  author           = {Yanqiang Han and Imran Ali and Zhilong Wang and Junfei Cai and Sicheng Wu and Jiequn Tang and Lin Zhang and Jiahao Ren and Rui Xiao and Qianqian Lu and Lei Hang and Hongyuan Luo and Jinjin Li},
  journal          = {Physics Reports},
  title            = {Machine learning accelerates quantum mechanics predictions of molecular crystals},
  year             = {2021},
  month            = {nov},
  pages            = {1--71},
  volume           = {934},
  creationdate     = {2022-12-11T17:30:53},
  doi              = {10.1016/j.physrep.2021.08.002},
  file             = {:by-author/H/Han/2021_Han_1.pdf:PDF},
  keywords         = {Crystallography; Machine Learning (ML); Quantum Mechanics (QM)},
  modificationdate = {2022-12-11T17:32:26},
  owner            = {saulius},
  publisher        = {Elsevier {BV}},
}

@Article{Wengert2021,
  author           = {Simon Wengert and G{\'{a}}bor Cs{\'{a}}nyi and Karsten Reuter and Johannes T. Margraf},
  journal          = {Chemical Science},
  title            = {Data-efficient machine learning for molecular crystal structure prediction},
  year             = {2021},
  number           = {12},
  pages            = {4536--4546},
  volume           = {12},
  creationdate     = {2022-12-11T17:34:01},
  doi              = {10.1039/d0sc05765g},
  file             = {:by-author/W/Wengert/2021_Wengert_4536.pdf:PDF},
  keywords         = {Crystal Structure Prediction (CSP); Crystallography; Machine Learning (ML)},
  modificationdate = {2022-12-11T17:34:19},
  owner            = {saulius},
  publisher        = {Royal Society of Chemistry ({RSC})},
}

@Article{Podryabinkin2019,
  author           = {Evgeny V. Podryabinkin and Evgeny V. Tikhonov and Alexander V. Shapeev and Artem R. Oganov},
  journal          = {Physical Review B},
  title            = {Accelerating crystal structure prediction by machine-learning interatomic potentials with active learning},
  year             = {2019},
  month            = {feb},
  number           = {6},
  pages            = {064114},
  volume           = {99},
  creationdate     = {2022-12-11T17:59:55},
  doi              = {10.1103/physrevb.99.064114},
  file             = {:by-author/P/Podryabinkin/2019_Podryabinkin_64114.pdf:PDF;:by-author/P/Podryabinkin/2019_Podryabinkin_64114manuscript.pdf:PDF},
  keywords         = {Crystal Structure Prediction (CSP); Machine Learning (ML)},
  modificationdate = {2022-12-11T18:02:55},
  owner            = {saulius},
  publisher        = {American Physical Society ({APS})},
}

@Article{Wei2021,
  author           = {Zhiyong Wei and Tianhang Qi and Weiyu Chen and Yunfei Chen},
  journal          = {Chinese Physics B},
  title            = {Phonon dispersion relations of crystalline solids based on {LAMMPS} package},
  year             = {2021},
  month            = {nov},
  number           = {11},
  pages            = {114301},
  volume           = {30},
  creationdate     = {2022-12-12T07:25:45},
  doi              = {10.1088/1674-1056/abf4c0},
  file             = {:by-author/W/Wei/2021_Wei_114301.pdf:PDF},
  keywords         = {Dispersion Relations; Force Fields; LAMMPS; MM; Molecular Dynamics (MD); Molecular Mechanics; Phonon Spectra},
  modificationdate = {2022-12-12T07:29:54},
  owner            = {saulius},
  publisher        = {{IOP} Publishing},
}

@Article{Gale2003,
  author           = {Julian D. Gale and Andrew L. Rohl},
  journal          = {Molecular Simulation},
  title            = {The {G}eneral {U}tility {L}attice {P}rogram ({GULP})},
  year             = {2003},
  month            = {may},
  number           = {5},
  pages            = {291--341},
  volume           = {29},
  creationdate     = {2022-12-12T07:33:30},
  doi              = {10.1080/0892702031000104887},
  file             = {:by-author/G/Gale/2003_Gale_291.pdf:PDF},
  keywords         = {MM; Molecular Dynamics (MD); Molecular Mechanics; Phon Spectra},
  modificationdate = {2022-12-12T07:37:00},
  owner            = {saulius},
  publisher        = {Informa {UK} Limited},
}

@Article{Togo2015b,
  author           = {Atsushi Togo and Isao Tanaka},
  journal          = {Scripta Materialia},
  title            = {First principles phonon calculations in materials science},
  year             = {2015},
  month            = {nov},
  pages            = {1--5},
  volume           = {108},
  creationdate     = {2022-12-12T07:39:09},
  doi              = {10.1016/j.scriptamat.2015.07.021},
  file             = {:by-author/T/Togo/2015_Togo_1.pdf:PDF},
  keywords         = {Phonon Spectra; Phonopy},
  modificationdate = {2022-12-12T07:41:30},
  owner            = {saulius},
  publisher        = {Elsevier {BV}},
}

@Webpage{PrestonWerner2022,
  author           = {Tom Preston-Werner},
  retrieved        = {2022-12-13T23:05+02:00},
  title            = {Semantic versioning 2.0.0},
  url              = {https://semver.org/},
  year             = {2022},
  creationdate     = {2022-12-13T23:03:20},
  file             = {:by-author/P/Preston-Werner/2022_Preston-Werner_1.pdf:PDF;:by-author/P/Preston-Werner/2022_Preston-Werner_1.odt:OpenDocument text},
  keywords         = {Semantic Versioning; Software Development; Software Interfaces},
  modificationdate = {2022-12-13T23:16:19},
  owner            = {saulius},
  pages            = {1--6},
}

@Webpage{Rsync2008,
  title            = {Rsync},
  url              = {http://samba.anu.edu.au/rsync/},
  year             = {2022},
  creationdate     = {2022-12-13T23:33:08},
  key              = {Rsync},
  modificationdate = {2022-12-13T23:34:29},
  owner            = {saulius},
}

@Article{Hu2022,
  author           = {Xiaojuan Hu and Maja-Olivia Lenz-Himmer and Carsten Baldauf},
  journal          = {Scientific Data},
  title            = {Better force fields start with better data: A data set of cation dipeptide interactions},
  year             = {2022},
  month            = {jun},
  number           = {1},
  pages            = {1--14},
  volume           = {9},
  comment          = {Uses EMMO.},
  creationdate     = {2022-12-14T07:34:24},
  doi              = {10.1038/s41597-022-01297-3},
  file             = {:by-author/H/Hu/2022_Hu_1.pdf:PDF},
  keywords         = {Density Functional Theory (DFT); EMMO; Force Fields; NOMAD; Ontologies},
  modificationdate = {2022-12-14T07:49:12},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media {LLC}},
}

@Preprint{Zeb2022,
  author           = {Akhtar Zeb and Teemu Mätäsniemi},
  comment          = {Uses EMMO.},
  creationdate     = {2022-12-14T07:40:36},
  doi              = {10.21203/rs.3.rs-1807190/v1},
  file             = {:by-author/Z/Zeb/2022_Zeb_1.pdf:PDF},
  keywords         = {EMMO; Machine Learning (ML); Ontologies},
  modificationdate = {2022-12-14T07:42:24},
  month            = {jul},
  owner            = {saulius},
  pages            = {1--22},
  publisher        = {Research Square Platform {LLC}},
  title            = {Ontological modelling of creep void analysis data to automate machine learning training process},
  year             = {2022},
}

@Article{Himanen2019,
  author           = {Lauri Himanen and Amber Geurts and Adam Stuart Foster and Patrick Rinke},
  journal          = {Advanced Science},
  title            = {Data-driven materials science: status, challenges, and perspectives},
  year             = {2019},
  month            = {sep},
  number           = {21},
  pages            = {1900808},
  volume           = {6},
  comment          = {Cites EMMO.},
  creationdate     = {2022-12-14T07:44:50},
  doi              = {10.1002/advs.201900808},
  file             = {:by-author/H/Himanen/2019_Himanen_1900808.pdf:PDF;:by-author/H/Himanen/2019_Himanen_1900808_arXiv_preprint.pdf:PDF},
  keywords         = {EMMO; Ontologies; Open Science},
  modificationdate = {2022-12-14T07:47:00},
  owner            = {saulius},
  publisher        = {Wiley},
}

@Article{Giannozzi2017,
  author           = {P Giannozzi and O Andreussi and T Brumme and O Bunau and M Buongiorno Nardelli and M Calandra and R Car and C Cavazzoni and D Ceresoli and M Cococcioni and N Colonna and I Carnimeo and A Dal Corso and S de Gironcoli and P Delugas and R A DiStasio and A Ferretti and A Floris and G Fratesi and G Fugallo and R Gebauer and U Gerstmann and F Giustino and T Gorni and J Jia and M Kawamura and H-Y Ko and A Kokalj and E Kü{\c{c}}ükbenli and M Lazzeri and M Marsili and N Marzari and F Mauri and N L Nguyen and H-V Nguyen and A Otero-de-la-Roza and L Paulatto and S Ponc{\'{e}} and D Rocca and R Sabatini and B Santra and M Schlipf and A P Seitsonen and A Smogunov and I Timrov and T Thonhauser and P Umari and N Vast and X Wu and S Baroni},
  journal          = {Journal of Physics: Condensed Matter},
  title            = {Advanced capabilities for materials modelling with Quantum {ESPRESSO}},
  year             = {2017},
  month            = {oct},
  number           = {46},
  pages            = {465901},
  volume           = {29},
  creationdate     = {2022-12-14T12:00:34},
  doi              = {10.1088/1361-648x/aa8f79},
  file             = {:by-author/G/Giannozzi/2017_Giannozzi_465901.pdf:PDF;:by-author/G/Giannozzi/2017_Giannozzi_465901manuscript.pdf:PDF},
  keywords         = {Computatinal Materials Science; Density Functional Theory (DFT); Quantum Espresso; Quantum Mechanics (QM)},
  modificationdate = {2022-12-14T12:03:15},
  owner            = {saulius},
  publisher        = {{IOP} Publishing},
}

@Article{Carter1994,
  author           = {Jeffrey R. Carter and Bo I. Sanden},
  journal          = {{ACM} {SIGAda} Ada Letters},
  title            = {Ada design of a neural network},
  year             = {1994},
  month            = {may},
  number           = {3},
  pages            = {61--73},
  volume           = {{XIV}},
  creationdate     = {2022-12-15T18:21:04},
  doi              = {10.1145/181468.181471},
  file             = {:by-author/C/Carter/1994_Carter_61.pdf:PDF},
  keywords         = {Ada; Artificial Neural Networks (ANN); Computer Science (CS); Machine Learning (ML)},
  modificationdate = {2022-12-15T18:22:36},
  owner            = {saulius},
  publisher        = {Association for Computing Machinery ({ACM})},
}

@Article{Sommer2022,
  author           = {Timo Sommer and Roland Willa and Jörg Schmalian and Pascal Friederich},
  journal          = {arXiv},
  title            = {{3DSC} - a new dataset of superconductors including crystal structures},
  year             = {2022},
  month            = dec,
  pages            = {1--25},
  abstract         = {Data-driven methods, in particular machine learning, can help to speed up the discovery of new materials by finding hidden patterns in existing data and using them to identify promising candidate materials. In the case of superconductors, which are a highly interesting but also a complex class of materials with many relevant applications, the use of data science tools is to date slowed down by a lack of accessible data. In this work, we present a new and publicly available superconductivity dataset ('3DSC'), featuring the critical temperature $T_\mathrm{c}$ of superconducting materials additionally to tested non-superconductors. In contrast to existing databases such as the SuperCon database which contains information on the chemical composition, the 3DSC is augmented by the approximate three-dimensional crystal structure of each material. We perform a statistical analysis and machine learning experiments to show that access to this structural information improves the prediction of the critical temperature $T_\mathrm{c}$ of materials. Furthermore, we see the 3DSC not as a finished dataset, but we provide ideas and directions for further research to improve the 3DSC in multiple ways. We are confident that this database will be useful in applying state-of-the-art machine learning methods to eventually find new superconductors.},
  archiveprefix    = {arXiv},
  comment          = {Recommended by Daniel Chateigner. Code and crystal structures in the GitHub repository https://github.com/aimat-lab/3DSC.},
  creationdate     = {2022-12-16T08:50:19},
  eprint           = {2212.06071},
  file             = {:by-author/S/Sommer/2022_Sommer_1.pdf:PDF},
  keywords         = {Crystal Structures; Databases; Machine Learning (ML); Scientific Databases; Superconductivity; Tc; cond-mat.supr-con, cond-mat.mtrl-sci},
  modificationdate = {2022-12-16T08:53:45},
  owner            = {saulius},
  primaryclass     = {cond-mat.supr-con},
}

@Article{Shrestha2022,
  author           = {Shrestha, Utsab R. and Mamontov, Eugene and O'Neill, Hugh M. and Zhang, Qiu and Kolesnikov, Alexander I. and Chu, Xiangqiang},
  journal          = {Innovation (Cambridge (Mass.))},
  title            = {Experimental mapping of short-wavelength phonons in proteins.},
  year             = {2022},
  issn             = {2666-6758},
  month            = jan,
  pages            = {100199},
  volume           = {3},
  abstract         = {Phonons are quasi-particles, observed as lattice vibrations in periodic materials, that often dampen in the presence of structural perturbations. Nevertheless, phonon-like collective excitations exist in highly complex systems, such as proteins, although the origin of such collective motions has remained elusive. Here we present a picture of temperature and hydration dependence of collective excitations in green fluorescent protein (GFP) obtained by inelastic neutron scattering. Our results provide evidence that such excitations can be used as a measure of flexibility/softness and are possibly associated with the protein's activity. Moreover, we show that the hydration water in GFP interferes with the phonon propagation pathway, enhancing the structural rigidity and stability of GFP.},
  country          = {United States},
  creationdate     = {2022-12-16T15:12:47},
  doi              = {10.1016/j.xinn.2021.100199},
  file             = {:by-author/S/Shrestha/2022_Shrestha_100199.pdf:PDF},
  issn-linking     = {2666-6758},
  issue            = {1},
  keywords         = {Collective Excitations; Inelastic Neutron Scattering; Phonons; Protein Activity; Protein Dynamics; Proteins},
  modificationdate = {2023-01-30T09:54:17},
  nlm-id           = {101771342},
  owner            = {saulius},
  pii              = {100199},
  pmc              = {PMC8760453},
  pmid             = {35059681},
  pubmodel         = {Electronic-eCollection},
  pubstate         = {epublish},
  revised          = {2022-07-16},
}

@Article{Lawrence1987,
  author           = {Lawrence, A. F. and McDaniel, J. C. and Chang, D. B. and Birge, R. R.},
  journal          = {Biophysical journal},
  title            = {The nature of phonons and solitary waves in alpha-helical proteins.},
  year             = {1987},
  issn             = {0006-3495},
  month            = may,
  pages            = {785--793},
  volume           = {51},
  abstract         = {A parametric study of the Davydov model of energy transduction in alpha-helical proteins is described. Previous investigations have shown that the Davydov model predicts that nonlinear interactions between phonons and amide-I excitations can stabilize the latter and produce a long-lived combined excitation (the so-called Davydov soliton), which propagates along the helix. The dynamics of this solitary wave are approximately those of solitons described using the nonlinear Schrödinger equation. The present study extends these previous investigations by analyzing the effect of helix length and nonlinear coupling efficiency on the phonon spectrum in short and medium length alpha-helical segments. The phonon energy accompanying amide-I excitation shows periodic variation in time with fluctuations that follow three different time scales. The phonon spectrum is highly dependent upon chain length but a majority of the energy remains localized in normal mode vibrations even in the long chain alpha-helices. Variation of the phonon-exciton coupling coefficient changes the amplitudes but not the frequencies of the phonon spectrum. The computed spectra contain frequencies ranging from 200 GHz to 6 THz, and as the chain length is increased, the long period oscillations increase in amplitude. The most important prediction of this study, however, is that the dynamics predicted by the numerical calculations have more in common with dynamics described by using the Frohlich polaron model than by using the Davydov soliton. Accordingly, the relevance of the Davydov soliton model was applied to energy transduction in alpha-helical proteins is questionable. We conclude that the Raman lines that have been assigned to solitons in E. coli are either associated with low frequency normal modes or are instrumental- or fluorescence-induced artifacts.},
  chemicals        = {Proteins},
  citation-subset  = {IM},
  completed        = {1987-08-10},
  country          = {United States},
  creationdate     = {2022-12-16T15:16:28},
  doi              = {10.1016/S0006-3495(87)83405-7},
  file             = {:by-author/L/Lawrence/1987_Lawrence_785.pdf:PDF},
  issn-linking     = {0006-3495},
  issue            = {5},
  keywords         = {Mathematics; Models, Biological; Phonons; Probability; Protein Conformation; Proteins},
  modificationdate = {2023-01-30T09:54:12},
  nlm-id           = {0370626},
  owner            = {saulius},
  pii              = {S0006-3495(87)83405-7},
  pmc              = {PMC1329966},
  pmid             = {3593874},
  pubmodel         = {Print},
  pubstate         = {ppublish},
  revised          = {2018-11-13},
}

@InProceedings{Acbas2013,
  author           = {Gheorghe Acbas and Katherine A. Niessen and Deepu K. George and Edward Snell and A. G. Markelz},
  booktitle        = {{SPIE} Proceedings},
  title            = {Measuring phonons in protein crystals},
  year             = {2013},
  editor           = {Markus Betz and Abdulhakem Y. Elezzabi and Jin-Joo Song and Kong-Thon Tsen},
  month            = {mar},
  pages            = {1--5},
  publisher        = {{SPIE}},
  creationdate     = {2022-12-16T15:18:55},
  doi              = {10.1117/12.2006275},
  file             = {:by-author/A/Acbas/2013_Acbas_1.pdf:PDF},
  keywords         = {Crystals; Mathematics; Models, Biological; Phonons; Probability; Protein Conformation; Protein Crystallography; Proteins},
  modificationdate = {2022-12-16T15:20:51},
  owner            = {saulius},
}

@Article{Choi2022,
  author           = {Won Jin Choi and Keiichi Yano and Minjeong Cha and Felippe M. Colombari and Ji-Young Kim and Yichun Wang and Sang Hyun Lee and Kai Sun and John M. Kruger and Andr{\'{e}} F. de Moura and Nicholas A. Kotov},
  journal          = {Nature Photonics},
  title            = {Chiral phonons in microcrystals and nanofibrils of biomolecules},
  year             = {2022},
  month            = {mar},
  number           = {5},
  pages            = {366--373},
  volume           = {16},
  creationdate     = {2022-12-16T15:22:45},
  doi              = {10.1038/s41566-022-00969-1},
  file             = {:by-author/C/Choi/2022_Choi_366.pdf:PDF},
  keywords         = {Crystals; Mathematics; Models, Biological; Phonons; Probability; Protein Conformation; Protein Crystallography; Proteins},
  modificationdate = {2022-12-16T15:23:00},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media {LLC}},
}

@Article{Liu2022a,
  author           = {Liwang Liu and Marina Simon and Giovanna Muggiolu and Florent Vilotte and Mikael Antoine and Jer{\^{o}}me Caron and Guy Kantor and Philippe Barberet and Herv{\'{e}} Seznec and Bertrand Audoin},
  journal          = {Photoacoustics},
  title            = {Changes in intra-nuclear mechanics in response to {DNA} damaging agents revealed by time-domain Brillouin micro-spectroscopy},
  year             = {2022},
  month            = {sep},
  pages            = {100385},
  volume           = {27},
  creationdate     = {2022-12-16T15:25:38},
  doi              = {10.1016/j.pacs.2022.100385},
  file             = {:by-author/L/Liu/2022_Liu_100385.pdf:PDF},
  keywords         = {Crystals; DNA; Mathematics; Models, Biological; Phonons; Probability; Protein Conformation; Protein Crystallography; Proteins},
  modificationdate = {2022-12-16T15:26:33},
  owner            = {saulius},
  publisher        = {Elsevier {BV}},
}

@Article{Nganfo2022,
  author           = {W.A. Nganfo and C. Kenfack-Sadem and A.J. Fotu{\'{e}} and M.C. Ekosso and S.N. Wopunghwo and L.C. Fai},
  journal          = {Heliyon},
  title            = {Dynamics of exciton polaron in microtubule},
  year             = {2022},
  month            = {feb},
  number           = {2},
  pages            = {e08897},
  volume           = {8},
  creationdate     = {2022-12-16T15:28:36},
  doi              = {10.1016/j.heliyon.2022.e08897},
  file             = {:by-author/N/Nganfo/2022_Nganfo_8897.pdf:PDF},
  keywords         = {Mathematics; Models, Biological; Phonons; Probability; Protein Conformation; Proteins},
  modificationdate = {2022-12-16T15:29:22},
  owner            = {saulius},
  publisher        = {Elsevier {BV}},
}

@Article{Kojima2022,
  author           = {Seiji Kojima},
  journal          = {Materials},
  title            = {100th Anniversary of Brillouin Scattering: Impact on Materials Science},
  year             = {2022},
  month            = {may},
  number           = {10},
  pages            = {3518},
  volume           = {15},
  creationdate     = {2022-12-16T15:30:22},
  doi              = {10.3390/ma15103518},
  file             = {:by-author/K/Kojima/2022_Kojima_3518.pdf:PDF},
  keywords         = {Brillouin Scattering; Inelastic Light Scattering},
  modificationdate = {2022-12-16T15:31:55},
  owner            = {saulius},
  publisher        = {{MDPI} {AG}},
}

@Article{Faraji2021,
  author           = {Elham Faraji and Roberto Franzosi and Stefano Mancini and Marco Pettini},
  journal          = {Scientific Reports},
  title            = {Energy transfer to the phonons of a macromolecule through light pumping},
  year             = {2021},
  month            = {mar},
  number           = {1},
  pages            = {6591},
  volume           = {11},
  creationdate     = {2022-12-16T15:33:41},
  doi              = {10.1038/s41598-021-85856-5},
  file             = {:by-author/F/Faraji/2021_Faraji_6591.pdf:PDF},
  keywords         = {Macromolecules; Phonons},
  modificationdate = {2022-12-16T15:36:22},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media {LLC}},
}

@Article{Merzel2007,
  author           = {F. Merzel and F. Fontaine-Vive and M. R. Johnson and G. J. Kearley},
  journal          = {Physical Review E},
  title            = {Atomistic model of {DNA}: Phonons and base-pair opening},
  year             = {2007},
  month            = {sep},
  number           = {3},
  pages            = {031917},
  volume           = {76},
  creationdate     = {2022-12-16T15:37:36},
  doi              = {10.1103/physreve.76.031917},
  file             = {:by-author/M/Merzel/2007_Merzel_31917.pdf:PDF},
  keywords         = {DNA; Phonons},
  modificationdate = {2022-12-16T15:37:53},
  owner            = {saulius},
  publisher        = {American Physical Society ({APS})},
}

@Article{Kwon2022,
  author           = {Junyoung Kwon and Won Jin Choi and Uichang Jeong and Wookjin Jung and Inkook Hwang and Ki Hyun Park and Seowoo Genevieve Ko and Sung Min Park and Nicholas A. Kotov and Jihyeon Yeom},
  journal          = {Nano Convergence},
  title            = {Recent advances in chiral nanomaterials with unique electric and magnetic properties},
  year             = {2022},
  month            = {jul},
  number           = {1},
  pages            = {32},
  volume           = {9},
  creationdate     = {2022-12-16T15:39:01},
  doi              = {10.1186/s40580-022-00322-w},
  file             = {:by-author/K/Kwon/2022_Kwon_32.pdf:PDF},
  keywords         = {Chiral Materials; DNA; Phonons},
  modificationdate = {2022-12-16T15:40:32},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media {LLC}},
}

@Article{Baydin2022,
  author           = {Andrey Baydin and Fuyang Tay and Jichao Fan and Manukumara Manjappa and Weilu Gao and Junichiro Kono},
  journal          = {Materials},
  title            = {Carbon Nanotube Devices for Quantum Technology},
  year             = {2022},
  month            = {feb},
  number           = {4},
  pages            = {1535},
  volume           = {15},
  creationdate     = {2022-12-16T15:43:20},
  doi              = {10.3390/ma15041535},
  file             = {:by-author/B/Baydin/2022_Baydin_1535.pdf:PDF},
  keywords         = {Carbon Nanotubes; Phonons; Quantum Computing},
  modificationdate = {2022-12-16T15:44:25},
  owner            = {saulius},
  publisher        = {{MDPI} {AG}},
}

@Article{Luo2022,
  author           = {Yuhui Luo and Chunhua Zeng and Baowen Li},
  journal          = {Physical Review E},
  title            = {Negative rectification and anomalous diffusion in nonlinear substrate potentials: Dynamical relaxation and information entropy},
  year             = {2022},
  month            = {feb},
  number           = {2},
  pages            = {024204},
  volume           = {105},
  creationdate     = {2022-12-16T15:45:17},
  doi              = {10.1103/physreve.105.024204},
  file             = {:by-author/L/Luo/2022_Luo_24204.pdf:PDF},
  keywords         = {Entropy; Information Theory; Phonons},
  modificationdate = {2022-12-16T15:46:08},
  owner            = {saulius},
  publisher        = {American Physical Society ({APS})},
}

@Article{Zhang2022,
  author           = {Zhichao Zhang and Yeageun Lee and Md Farhadul Haque and Juyoung Leem and Ezekiel Y. Hsieh and SungWoo Nam},
  journal          = {Nano Convergence},
  title            = {Plasmonic sensors based on graphene and graphene hybrid materials},
  year             = {2022},
  month            = {jun},
  number           = {1},
  pages            = {28},
  volume           = {9},
  creationdate     = {2022-12-16T15:47:00},
  doi              = {10.1186/s40580-022-00319-5},
  file             = {:by-author/Z/Zhang/2022_Zhang_28.pdf:PDF},
  keywords         = {2D Materials; Graphene; Phonons; Plasmons},
  modificationdate = {2022-12-16T15:47:44},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media {LLC}},
}

@Article{Hanson2022,
  author           = {Robert M. Hanson and Damien Jeannerat and Mark Archibald and Ian J. Bruno and Stuart J. Chalk and Antony N. Davies and Robert J. Lancashire and Jeffrey Lang and Henry S. Rzepa},
  journal          = {Pure and Applied Chemistry},
  title            = {{IUPAC} specification for the {FAIR} management of spectroscopic data in chemistry ({IUPAC} {FAIRSpec})~{\textendash} guiding principles},
  year             = {2022},
  month            = {apr},
  number           = {6},
  pages            = {623--636},
  volume           = {94},
  creationdate     = {2022-12-20T08:57:28},
  doi              = {10.1515/pac-2021-2009},
  file             = {:by-author/H/Hanson/2022_Hanson_623.pdf:PDF},
  keywords         = {Chemistry; Data Management; FAIR Data; IUPAC; Standards},
  modificationdate = {2022-12-28T11:52:53},
  owner            = {saulius},
  publisher        = {Walter de Gruyter {GmbH}},
  url              = {https://chemrxiv.org/engage/chemrxiv/article-details/626671c388636c48051e91dd},
}

@Article{Hanson2016,
  author           = {Robert M. Hanson},
  journal          = {Journal of Cheminformatics},
  title            = {{J}mol {SMILES} and {J}mol {SMARTS}: specifications and applications},
  year             = {2016},
  month            = {sep},
  number           = {1},
  pages            = {50},
  volume           = {8},
  creationdate     = {2022-12-20T11:03:01},
  doi              = {10.1186/s13321-016-0160-4},
  file             = {:by-author/H/Hanson/2016_Hanson_50.pdf:PDF},
  keywords         = {Jmol; SMILES},
  modificationdate = {2022-12-21T15:26:12},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media {LLC}},
}

@Misc{Linge2022,
  author           = {Lingė, Darius and Gedgaudas, Marius and Merkys, Andrius and Petrauskas, Vytautas and Vaitkus, Antanas and Grybauskas, Algirdas and Paketurytė, Vaida and Zubrienė, Asta and Zakšauskas, Audrius and Mickevičiūtė, Aurelija and Smirnovienė, Joana and Baranauskienė, Lina and Čapkauskaitė, Edita and Dudutienė, Virginija and Urniežius, Ernestas and Konovalovas, Aleksandras and Kazlauskas, Egidijus and Gražulis, Saulius and Matulis, Daumantas},
  title            = {PLBD (Protein Ligand Binding Database) table description XML file},
  year             = {2022},
  copyright        = {Creative Commons Attribution 4.0 International},
  creationdate     = {2022-12-25T16:50:58},
  doi              = {10.5281/ZENODO.7482008},
  keywords         = {Database Description; Database Semantics; Protein-Ligand Binding; SQL; Thermodynamics; XML},
  language         = {en},
  modificationdate = {2022-12-25T16:50:59},
  owner            = {saulius},
  publisher        = {Zenodo},
}

@Misc{Vaitkus2022,
  author           = {Vaitkus, Antanas and Merkys, Andrius and Grybauskas, Algirdas and Gražulis, Saulius},
  title            = {solsa-database-scripts},
  year             = {2022},
  copyright        = {GNU General Public License v3.0 only},
  creationdate     = {2022-12-25T16:53:23},
  doi              = {10.5281/ZENODO.7468052},
  keywords         = {Database Schema Generation; REST; Relational Database; RestfulDB; SQL},
  language         = {en},
  modificationdate = {2022-12-25T16:53:24},
  owner            = {saulius},
  publisher        = {Zenodo},
}

@Misc{Merkys2022,
  author           = {Merkys, Andrius and Grybauskas, Algirdas and Gražulis, Saulius and Konovalovas, Aleksandras and Vaitkus, Antanas},
  title            = {restfuldb},
  year             = {2022},
  copyright        = {GNU General Public License v2.0 only},
  creationdate     = {2022-12-25T16:54:00},
  doi              = {10.5281/ZENODO.7468801},
  keywords         = {Database Web GUI; REST; RESTful API; Relational Database; RestfulDB; SQL},
  modificationdate = {2022-12-25T16:54:00},
  owner            = {saulius},
  publisher        = {Zenodo},
}

@Misc{Linge2022a,
  author           = {Lingė, Darius and Gedgaudas, Marius and Merkys, Andrius and Petrauskas, Vytautas and Vaitkus, Antanas and Grybauskas, Algirdas and Paketurytė, Vaida and Zubrienė, Asta and Zakšauskas, Audrius and Smirnovienė, Joana and Baranauskienė, Lina and Čapkauskaitė, Edita and Dudutienė, Virginija and Urniežius, Ernestas and Konovalovas, Aleksandras and Kazlauskas, Egidijus and Gražulis, Saulius and Matulis, Daumantas},
  title            = {Data snapshot from the Protein Ligand Binding Database (PLBD)},
  year             = {2022},
  copyright        = {Creative Commons Attribution 4.0 International},
  creationdate     = {2022-12-25T17:11:45},
  doi              = {10.5281/ZENODO.7482058},
  keywords         = {Intrinsic Binding Constants; Protein-Ligan Binding; Protein-Ligand Binding Database; Thermodynamics},
  language         = {en},
  modificationdate = {2022-12-25T17:11:45},
  owner            = {saulius},
  publisher        = {Zenodo},
}

@Article{Merkys2023,
  author           = {Merkys, Andrius and Vaitkus, Antanas and Grybauskas, Algirdas and Konovalovas, Aleksandras and Quirós, Miguel and Gražulis, Saulius},
  journal          = {Journal of Cheminformatics},
  title            = {Graph isomorphism-based algorithm for cross-checking chemical and crystallographic descriptions},
  year             = {2023},
  issn             = {1758-2946},
  month            = {feb},
  number           = {1},
  volume           = {15},
  creationdate     = {2023-03-31T11:02:30+0300},
  doi              = {10.1186/s13321-023-00692-1},
  file             = {:by-author/M/Merkys/2023_Merkys_25.pdf:PDF},
  modificationdate = {2023-04-23T10:05:10},
  owner            = {andrius},
  publisher        = {Springer Science and Business Media LLC},
  url              = {https://jcheminf.biomedcentral.com/articles/10.1186/s13321-023-00692-1},
}

@Article{Moeller2018,
  author           = {Morten Hylander M{\o}ller and John P. A. Ioannidis and Michael Darmon},
  journal          = {Intensive Care Medicine},
  title            = {Are systematic reviews and meta-analyses still useful research? We are not sure},
  year             = {2018},
  month            = {apr},
  number           = {4},
  pages            = {518--520},
  volume           = {44},
  creationdate     = {2023-01-02T17:30:45},
  doi              = {10.1007/s00134-017-5039-y},
  file             = {:by-author/M/Møller/2018_Møller_518.pdf:PDF},
  keywords         = {Computer Science (CS); Meta-analysis; Reproducible Research},
  modificationdate = {2023-01-02T17:31:58},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media {LLC}},
}

@Article{Adams2016,
  author           = {Jean Adams and Frances C. Hillier-Brown and Helen J. Moore and Amelia A. Lake and Vera Araujo-Soares and Martin White and Carolyn Summerbell},
  journal          = {Systematic Reviews},
  title            = {Searching and synthesising `grey literature' and `grey information' in public health: critical reflections on three case studies},
  year             = {2016},
  month            = {sep},
  number           = {1},
  pages            = {164},
  volume           = {5},
  creationdate     = {2023-01-02T17:33:17},
  doi              = {10.1186/s13643-016-0337-y},
  file             = {:by-author/A/Adams/2016_Adams_164.pdf:PDF},
  keywords         = {Computer Science (CS); Reproducible Research; Review},
  modificationdate = {2023-01-02T17:33:59},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media {LLC}},
}

@Article{Moher2009,
  author           = {Moher, David and Liberati, Alessandro and Tetzlaff, Jennifer and Altman, Douglas G. and {the PRISMA Group}},
  journal          = {PLoS medicine},
  title            = {Preferred reporting items for systematic reviews and meta-analyses: the PRISMA statement.},
  year             = {2009},
  issn             = {1549-1676},
  month            = jul,
  pages            = {e1000097},
  volume           = {6},
  citation-subset  = {IM},
  completed        = {2009-09-23},
  country          = {United States},
  creationdate     = {2023-01-02T17:47:17},
  doi              = {10.1371/journal.pmed.1000097},
  file             = {:by-author/M/Moher/2009_Moher_1000097.pdf:PDF},
  investigator     = {Altman, Doug and Antes, Gerd and Atkins, David and Barbour, Virginia and Barrowman, Nick and Berlin, Jesse A and Clark, Jocalyn and Clarke, Mike and Cook, Deborah and D'Amico, Roberto and Deeks, Jonathan and Devereaux, P J and Dickersin, Kay and Egger, Matthias and Ernst, Edzard and Gøtzsche, Peter C and Grimshaw, Jeremy and Guyatt, Gordon and Higgins, Julian and Ioannidis, John P A and Kleijnen, Jos and Lang, Tom and Liberati, Alessandro and Magrini, Nicola and McNamee, David and Moja, Lorenzo and Moher, David and Mulrow, Cynthia and Napoli, Maryann and Oxman, Andy and Pham, Ba' and Rennie, Drummond and Sampson, Margaret and Schulz, Kenneth F and Shekelle, Paul G and Tetzlaff, Jennifer and Tovey, David and Tugwell, Peter},
  issn-linking     = {1549-1277},
  issue            = {7},
  keywords         = {Evidence-Based Practice, Standards; Humans; Meta-Analysis as Topic; Periodicals as Topic, Standards; Publication Bias; Publishing, Standards; Quality Control; Reproducible Research; Review Literature as Topic; Terminology as Topic},
  modificationdate = {2023-01-02T17:49:36},
  nlm-id           = {101231360},
  owner            = {saulius},
  pii              = {e1000097},
  pmc              = {PMC2707599},
  pmid             = {19621072},
  pubmodel         = {Print-Electronic},
  pubstate         = {ppublish},
  revised          = {2022-11-29},
}

@Article{Kanehisa2016,
  author           = {Kanehisa, Minoru and Sato, Yoko and Kawashima, Masayuki and Furumichi, Miho and Tanabe, Mao},
  journal          = {Nucleic acids research},
  title            = {{KEGG} as a reference resource for gene and protein annotation.},
  year             = {2016},
  issn             = {1362-4962},
  month            = jan,
  pages            = {D457--D462},
  volume           = {44},
  abstract         = {KEGG (http://www.kegg.jp/ or http://www.genome.jp/kegg/) is an integrated database resource for biological interpretation of genome sequences and other high-throughput data. Molecular functions of genes and proteins are associated with ortholog groups and stored in the KEGG Orthology (KO) database. The KEGG pathway maps, BRITE hierarchies and KEGG modules are developed as networks of KO nodes, representing high-level functions of the cell and the organism. Currently, more than 4000 complete genomes are annotated with KOs in the KEGG GENES database, which can be used as a reference data set for KO assignment and subsequent reconstruction of KEGG pathways and other molecular networks. As an annotation resource, the following improvements have been made. First, each KO record is re-examined and associated with protein sequence data used in experiments of functional characterization. Second, the GENES database now includes viruses, plasmids, and the addendum category for functionally characterized proteins that are not represented in complete genomes. Third, new automatic annotation servers, BlastKOALA and GhostKOALA, are made available utilizing the non-redundant pangenome data set generated from the GENES database. As a resource for translational bioinformatics, various data sets are created for antimicrobial resistance and drug interaction networks.},
  chemicals        = {Proteins},
  citation-subset  = {IM},
  completed        = {2016-07-13},
  country          = {England},
  creationdate     = {2023-01-02T17:54:01},
  doi              = {10.1093/nar/gkv1070},
  file             = {:by-author/K/Kanehisa/2016_Kanehisa_457.pdf:PDF},
  issn-linking     = {0305-1048},
  issue            = {D1},
  keywords         = {Amino Acid Sequence; Databases; Databases, Genetic; Drug Resistance, Microbial; Genes; Genome; Metabolic Networks and Pathways; Molecular Sequence Annotation; Plasmids, Genetics; Proteins, Genetics; Reproducible Research; Scientific Databases; Viruses, Genetics},
  modificationdate = {2023-01-30T09:54:06},
  nlm-id           = {0411011},
  owner            = {saulius},
  pii              = {gkv1070},
  pmc              = {PMC4702792},
  pmid             = {26476454},
  pubmodel         = {Print-Electronic},
  pubstate         = {ppublish},
  revised          = {2022-04-09},
}

@Article{Hull2006,
  author           = {D. Hull and K. Wolstencroft and R. Stevens and C. Goble and M. R. Pocock and P. Li and T. Oinn},
  journal          = {Nucleic Acids Research},
  title            = {Taverna: a tool for building and running workflows of services},
  year             = {2006},
  month            = {jul},
  number           = {Web Server},
  pages            = {W729--W732},
  volume           = {34},
  creationdate     = {2023-01-02T18:32:50},
  doi              = {10.1093/nar/gkl320},
  file             = {:by-author/H/Hull/2006_Hull_729.pdf:PDF},
  keywords         = {Computer Science (CS); Reproducible Research; Taverna; Work Flows; Workflow Management},
  modificationdate = {2023-01-02T18:34:33},
  owner            = {saulius},
  publisher        = {Oxford University Press ({OUP})},
}

@Article{Alston2021,
  author           = {Jesse M. Alston and Jessica A. Rick},
  journal          = {The Bulletin of the Ecological Society of America},
  title            = {A beginner{\textquotesingle}s guide to conducting reproducible research},
  year             = {2021},
  month            = {jan},
  number           = {2},
  pages            = {e01801},
  volume           = {102},
  creationdate     = {2023-01-02T19:43:39},
  doi              = {10.1002/bes2.1801},
  file             = {:by-author/A/Alston/2021_Alston_1801.pdf:PDF},
  keywords         = {Reproducible Research},
  modificationdate = {2023-01-02T19:45:37},
  owner            = {saulius},
  publisher        = {Wiley},
}

@Article{OtextquotesingleDea2021,
  author           = {Rose E. O'Dea and Malgorzata Lagisz and Michael D. Jennions and Julia Koricheva and Daniel W. A. Noble and Timothy H. Parker and Jessica Gurevitch and Matthew J. Page and Gavin Stewart and David Moher and Shinichi Nakagawa},
  journal          = {Biological Reviews},
  title            = {Preferred reporting items for systematic reviews and meta-analyses in ecology and evolutionary biology: a {PRISMA} extension},
  year             = {2021},
  month            = {may},
  number           = {5},
  pages            = {1695--1722},
  volume           = {96},
  creationdate     = {2023-01-02T19:47:18},
  doi              = {10.1111/brv.12721},
  file             = {:by-author/O/O'Dea/2021_O'Dea_1695.pdf:PDF},
  keywords         = {PRISM; Reproducible Research},
  modificationdate = {2023-01-02T19:49:34},
  owner            = {saulius},
  publisher        = {Wiley},
}

@Article{Bada1985,
  author           = {Jeffrey L. Bada},
  journal          = {Annual Review of Earth and Planetary Sciences},
  title            = {Amino acid racemization dating of fossil bones},
  year             = {1985},
  month            = {may},
  number           = {1},
  pages            = {241--268},
  volume           = {13},
  creationdate     = {2023-01-04T11:01:52},
  doi              = {10.1146/annurev.ea.13.050185.001325},
  file             = {:by-author/B/Bada/1985_Bada_241.pdf:PDF},
  keywords         = {Dating; Fossile Dating; Paleobiology; Racemisation; Racemistion Rates; Thermodynamics},
  modificationdate = {2023-01-04T11:03:42},
  owner            = {saulius},
  publisher        = {Annual Reviews},
}

@Article{Kabayama1958,
  author           = {M. A. Kabayama and D. Patterson and L. Piche},
  journal          = {Canadian Journal of Chemistry},
  title            = {The thermodynamics of mutarotation of some sugars: {I}. measurement of the heat of mutarotation by microcalorimetry},
  year             = {1958},
  month            = {mar},
  number           = {3},
  pages            = {557--562},
  volume           = {36},
  creationdate     = {2023-01-04T12:03:29},
  doi              = {10.1139/v58-078},
  file             = {:by-author/K/Kabayama/1958_Kabayama_557.pdf:PDF},
  keywords         = {Calorimetry; Entropy; Mutarotation; Optical Isomers; Thermodynamics},
  modificationdate = {2023-01-04T12:05:33},
  owner            = {saulius},
  publisher        = {Canadian Science Publishing},
}

@Article{Kabayama1958a,
  author           = {M. A. Kabayama and D. Patterson},
  journal          = {Canadian Journal of Chemistry},
  title            = {The thermodynamics of mutarotation of some sugars: {II}. Theoretical considerations},
  year             = {1958},
  month            = {mar},
  number           = {3},
  pages            = {563--573},
  volume           = {36},
  creationdate     = {2023-01-04T12:08:13},
  doi              = {10.1139/v58-079},
  file             = {:by-author/K/Kabayama/1958_Kabayama_563.pdf:PDF},
  keywords         = {Calorimetry; Entropy; Mutarotation; Optical Isomers; Thermodynamics},
  modificationdate = {2023-01-04T12:10:07},
  owner            = {saulius},
  publisher        = {Canadian Science Publishing},
}

@InCollection{Demarchi2014,
  author           = {Beatrice Demarchi and Matthew Collins},
  booktitle        = {Encyclopedia of Scientific Dating Methods},
  publisher        = {Springer Netherlands},
  title            = {Amino acid racemization dating},
  year             = {2014},
  pages            = {1--22},
  creationdate     = {2023-01-04T13:30:57},
  doi              = {10.1007/978-94-007-6326-5_73-1},
  file             = {:by-author/D/Demarchi/2014_Demarchi_1.pdf:PDF},
  keywords         = {Dating; Fossile Dating; Paleobiology; Racemisation; Racemistion Rates; Review; Thermodynamics},
  modificationdate = {2023-01-04T13:35:53},
  owner            = {saulius},
}

@Electronic{Tautkeviciene2022,
  author           = {Gintarė Tautkevičienė and Aušra Gribauskienė and Fausta Kepalienė and Julija Kiršienė and Limas Kupčinskas and Gintė Medzvieckaitė and Rūta Petrauskaitė and Julija Umbrasaitė},
  title            = {Atvirosios prieigos prie mokslo publikacijų ir duomenų gairių taikymo praktikos ir pasiektos pažangos įvertinimas},
  url              = {https://www.lmt.lt/lt/doclib/wakj1omienmt1ct479xhqn5by9ht26dy},
  year             = {2022},
  comment          = {accessed: 2023-01-04T14:21+02:00.},
  creationdate     = {2023-01-04T14:15:00},
  file             = {:by-author/T/Tautkevičienė/2022_Tautkevičienė_1.pdf:PDF},
  isbn             = {978-609-462-220-5},
  keywords         = {Atviras Mokslas; Atviri Duomenys; Data Sharing; LMT; Open Data; Open Science; Policy; Research Council of Lithuania},
  modificationdate = {2023-01-04T14:21:59},
  owner            = {saulius},
  pages            = {1--82},
}

@Article{Burley2022,
  author           = {Burley, Stephen K. and Bhikadiya, Charmi and Bi, Chunxiao and Bittrich, Sebastian and Chao, Henry and Chen, Li and Craig, Paul A. and Crichlow, Gregg V. and Dalenberg, Kenneth and Duarte, Jose M. and Dutta, Shuchismita and Fayazi, Maryam and Feng, Zukang and Flatt, Justin W. and Ganesan, Sai J. and Ghosh, Sutapa and Goodsell, David S. and Green, Rachel Kramer and Guranovic, Vladimir and Henry, Jeremy and Hudson, Brian P. and Khokhriakov, Igor and Lawson, Catherine L. and Liang, Yuhe and Lowe, Robert and Peisach, Ezra and Persikova, Irina and Piehl, Dennis W. and Rose, Yana and Sali, Andrej and Segura, Joan and Sekharan, Monica and Shao, Chenghua and Vallat, Brinda and Voigt, Maria and Webb, Benjamin and Westbrook, John D. and Whetstone, Shamara and Young, Jasmine Y. and Zalevsky, Arthur and Zardecki, Christine},
  journal          = {Protein science: a publication of the Protein Society},
  title            = {{RCSB} {P}rotein {D}ata bank: tools for visualizing and understanding biological macromolecules in {3D}},
  year             = {2022},
  issn             = {1469-896X},
  month            = dec,
  pages            = {e4482},
  volume           = {31},
  abstract         = {Now in its 52nd year of continuous operations, the Protein Data Bank (PDB) is the premiere open-access global archive housing three-dimensional (3D) biomolecular structure data. It is jointly managed by the Worldwide Protein Data Bank (wwPDB) partnership. The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is funded by the National Science Foundation, National Institutes of Health, and US Department of Energy and serves as the US data center for the wwPDB. RCSB PDB is also responsible for the security of PDB data in its role as wwPDB-designated Archive Keeper. Every year, RCSB PDB serves tens of thousands of depositors of 3D macromolecular structure data (coming from macromolecular crystallography, nuclear magnetic resonance spectroscopy, electron microscopy, and micro-electron diffraction). The RCSB PDB research-focused web portal (RCSB.org) makes PDB data available at no charge and without usage restrictions to many millions of PDB data consumers around the world. The RCSB PDB training, outreach, and education web portal (PDB101.RCSB.org) serves nearly 700 K educators, students, and members of the public worldwide. This invited Tools Issue contribution describes how RCSB PDB (i) is organized; (ii) works with wwPDB partners to process new depositions; (iii) serves as the wwPDB-designated Archive Keeper; (iv) enables exploration and 3D visualization of PDB data via RCSB.org; and (v) supports training, outreach, and education via PDB101.RCSB.org. New tools and features at RCSB.org are presented using examples drawn from high-resolution structural studies of proteins relevant to treatment of human cancers by targeting immune checkpoints.},
  chemicals        = {Proteins, Macromolecular Substances},
  citation-subset  = {IM},
  completed        = {2022-12-01},
  country          = {United States},
  creationdate     = {2023-01-05T14:11:49},
  doi              = {10.1002/pro.4482},
  file             = {:by-author/B/Burley/2022_Burley_4482.pdf:PDF},
  issn-linking     = {0961-8368},
  issue            = {12},
  keywords         = {Computational Biology, Methods; Databases, Protein; Electron Microscopy; Humans; Macromolecular Crystallography; Macromolecular Substances, Chemistry; Micro-electron Diffraction; Mol*; Nuclear Magnetic Resonance Spectroscopy; Open Access; PDB; Protein Conformation; Protein Data Bank; Proteins, Chemistry; RCSB Protein Data Bank; Validation; Worldwide Protein Data Bank},
  modificationdate = {2024-04-27T11:15:27},
  nlm-id           = {9211750},
  owner            = {saulius},
  pii              = {e4482},
  pmc              = {PMC9667899},
  pmid             = {36281733},
  pubmodel         = {Print},
  pubstate         = {ppublish},
  revised          = {2022-12-12},
}

@InCollection{Smirnov2011,
  author           = {V. I. Smirnov},
  booktitle        = {{IFIP} Advances in Information and Communication Technology},
  publisher        = {Springer Berlin Heidelberg},
  title            = {Some hardware aspects of the {BESM}-6 design},
  year             = {2011},
  pages            = {20--25},
  creationdate     = {2023-01-07T12:08:27},
  doi              = {10.1007/978-3-642-22816-2_3},
  file             = {:by-author/S/Smirnov/2011_Smirnov_20.pdf:PDF},
  keywords         = {BESM-6; Computer Architecture; Computer Science (CS); Historic Computers},
  modificationdate = {2023-01-07T12:10:08},
  owner            = {saulius},
}

@InProceedings{Jackson2009,
  author           = {Paul B. Jackson and Grant Olney Passmore},
  title            = {Proving {SPARK} verification conditions with {SMT} solvers},
  year             = {2009},
  pages            = {1--38},
  comment          = {Cited by Berghofer2011.},
  creationdate     = {2023-01-20T16:29:40},
  eprint           = {https://www.semanticscholar.org/paper/Proving-SPARK-Verification-Conditions-with-SMT-Jackson-Passmore/29f24ec1aa2e6100fae27f3da165f26d28abdde1},
  file             = {:by-author/J/Jackson/2009_Jackson_1.pdf:PDF},
  keywords         = {Ada; Computer Science (CS); Formal Methods; Formal Verification; SPARK; Software Development},
  modificationdate = {2023-01-20T17:00:05},
  owner            = {saulius},
  url              = {https://homepages.inf.ed.ac.uk/pbj/papers/vct-dec09-draft.pdf},
}

@InProceedings{Brito2012,
  author           = {Eduardo Brito},
  title            = {Developing a program logic for the {SPARK} programming language},
  year             = {2012},
  pages            = {1--12},
  creationdate     = {2023-01-20T16:44:50},
  eprint           = {https://www.semanticscholar.org/paper/Developing-a-Program-Logic-for-the-SPARK-Language-Brito/34fce10b3562dba4af24f3ae9890475cf4ed8b11},
  file             = {:by-author/B/Brito/2012_Brito_1.pdf:PDF},
  keywords         = {Ada; Computer Science (CS); Formal Methods; Formal Verification; SPARK; Software Development},
  modificationdate = {2023-01-20T17:00:12},
  owner            = {saulius},
  url              = {https://paginas.fe.up.pt/~prodei/dsie12/papers/paper_36.pdf},
}

@Article{Woodcock2021VerificationIT,
  author           = {Jim Woodcock and Janet Barnes and Roderick Chapman and Simon Foster and Thomas Santen},
  journal          = {Theories of Programming},
  title            = {Verification in the Grand Challenge},
  year             = {2021},
  pages            = {661--668},
  creationdate     = {2023-01-20T16:51:45},
  doi              = {10.1145/3477355.3477363},
  eprint           = {https://www.semanticscholar.org/paper/Verification-in-the-Grand-Challenge-Woodcock-Barnes/88b5a41550e2e85dadf6ce92512a306730240b48},
  file             = {:by-author/W/Woodcock/2021_Woodcock_661.pdf:PDF},
  keywords         = {Computer Science (CS); Formal Methods; Formal Verification; Software Development},
  modificationdate = {2023-01-20T16:59:50},
  owner            = {saulius},
  url              = {https://www.jucs.org/jucs_13_5/the_verification_grand_challenge/jucs_13_5_0661_0668_woodcock.pdf},
}

@Article{Cordeiro2009,
  author           = {Lucas C. Cordeiro and Bernd Fischer and Joao Marques-Silva},
  journal          = {IEEE Transactions on Software Engineering},
  title            = {{SMT}-based bounded model checking for embedded {ANSI}-{C} software},
  year             = {2009},
  pages            = {957-974},
  volume           = {38},
  creationdate     = {2023-01-20T16:56:39},
  doi              = {10.1109/ase.2009.63},
  eprint           = {https://www.semanticscholar.org/paper/SMT-Based-Bounded-Model-Checking-for-Embedded-Cordeiro-Fischer/da5b1ce3df7b600ec7c42c19c2713e52a7dec4bb},
  file             = {:by-author/C/Cordeiro/2009_Cordeiro_957.pdf:PDF},
  keywords         = {Computer Science (CS); Formal Methods; Formal Verification; Software Development},
  modificationdate = {2023-01-20T16:59:38},
  owner            = {saulius},
  url              = {https://eprints.soton.ac.uk/272291/1/ieee_tse.pdf},
}

@Article{Stokes2010,
  author           = {Harold T. Stokes and Branton J. Campbell and Sander van Smaalen},
  journal          = {Acta Crystallographica Section A Foundations of Crystallography},
  title            = {Generation of (3+d)-dimensional superspace groups for describing the symmetry of modulated crystalline structures},
  year             = {2010},
  month            = {nov},
  number           = {1},
  pages            = {45--55},
  volume           = {67},
  creationdate     = {2023-01-27T09:30:19},
  doi              = {10.1107/s0108767310042297},
  file             = {:by-author/S/Stokes/2010_Stokes_45.pdf:PDF},
  keywords         = {Crystallography; Modulated Structures; Spacegroup Generation; Superspacegroups},
  modificationdate = {2023-01-27T09:32:16},
  owner            = {saulius},
  publisher        = {International Union of Crystallography ({IUCr})},
  url              = {https://iso.byu.edu/iso/2011 Stokes.pdf},
}

@Article{Wolff1974,
  author           = {P. M. de Wolff},
  journal          = {Acta Crystallographica Section A},
  title            = {The Pseudo-Symmetry of Modulated Crystal Structures},
  year             = {1974},
  month            = {nov},
  number           = {6},
  pages            = {777--785},
  volume           = {30},
  comment          = {Cited by Stokes2010.},
  creationdate     = {2023-01-27T09:40:25},
  doi              = {10.1107/s0567739474010710},
  file             = {:by-author/W/Wolff/1974_Wolff_777.pdf:PDF},
  keywords         = {Crystallography; Modulated Structures; Spacegroup Generation; Superspacegroups},
  modificationdate = {2023-01-27T09:59:55},
  owner            = {saulius},
  publisher        = {International Union of Crystallography ({IUCr})},
}

@Article{Zhou2016,
  author           = {Zhengyang Zhou and Lukáš Palatinus and Junliang Sun},
  journal          = {Inorganic Chemistry Frontiers},
  title            = {Structure determination of modulated structures by powder {X}-ray diffraction and electron diffraction},
  year             = {2016},
  number           = {11},
  pages            = {1351--1362},
  volume           = {3},
  creationdate     = {2023-01-27T10:01:20},
  doi              = {10.1039/c6qi00219f},
  file             = {:by-author/Z/Zhou/2016_Zhou_1351.pdf:PDF},
  keywords         = {Crystallography; Modulated Structures; Structure Determination; Superspacegroups},
  modificationdate = {2023-01-27T10:02:18},
  owner            = {saulius},
  publisher        = {Royal Society of Chemistry ({RSC})},
}

@InProceedings{Wodak1998,
  author           = {Shoshana J. Wodak and A. A. Vaguine and Jean Richelle},
  title            = {Procedures for assessing the quality of {X}–ray structures of macromolecules},
  year             = {1998},
  pages            = {1--12},
  creationdate     = {2023-01-27T15:08:30},
  file             = {:by-author/W/Wodak/1998_Wodak_1.pdf:PDF},
  keywords         = {Crystallography; Data Quality; Macromolecular Crystallography; Voronoi Diagram},
  modificationdate = {2023-01-27T15:11:43},
  owner            = {saulius},
  url              = {https://www.iucr.org/__data/assets/pdf_file/0018/8028/sw.pdf},
}

@Article{Westrip2010,
  author           = {Simon P. Westrip},
  journal          = {Journal of Applied Crystallography},
  title            = {{publCIF}: software for editing, validating and formatting crystallographic information files},
  year             = {2010},
  month            = {jun},
  number           = {4},
  pages            = {920--925},
  volume           = {43},
  creationdate     = {2023-01-27T15:13:47},
  doi              = {10.1107/s0021889810022120},
  file             = {:by-author/W/Westrip/2010_Westrip_920.pdf:PDF},
  keywords         = {CIF; Crystallography; Data Quality; Data Validation; Structure Validation},
  modificationdate = {2023-08-07T10:23:04},
  owner            = {saulius},
  publisher        = {International Union of Crystallography ({IUCr})},
}

@Electronic{IUCr2023,
  author           = {{IUCr}},
  language         = {English},
  organization     = {IUCr},
  title            = {Data requirements for structures},
  url              = {https://journals.iucr.org/c/services/cif/reqdata.html},
  year             = {2023},
  comment          = {Accessed 2023-01-27T15:20+02:00.},
  creationdate     = {2023-01-27T15:19:14},
  file             = {:by-author/I/IUCr/2023_IUCr_data_requirements.html:URL},
  keywords         = {Crystallography; Data Quality; Data Validation; Structure Validation},
  modificationdate = {2023-01-27T15:22:02},
  owner            = {saulius},
}

@Article{Puchala2023,
  author           = {Brian Puchala and John C. Thomas and Anirudh Raju Natarajan and Jon Gabriel Goiri and Sesha Sai Behara and Jonas L. Kaufman and Anton Van der Ven},
  journal          = {Computational Materials Science},
  title            = {{CASM} {\textemdash} A software package for first-principles based study of multicomponent crystalline solids},
  year             = {2023},
  month            = {jan},
  pages            = {111897},
  volume           = {217},
  creationdate     = {2023-01-27T18:40:33},
  doi              = {10.1016/j.commatsci.2022.111897},
  file             = {:by-author/P/Puchala/2023_Puchala_111897.pdf:PDF},
  keywords         = {Ab Initio; CASM; Cluster Expansion; Computational Materials Science; Computer Science (CS); Crystal Sructure; Crystal Structure Enumeration; Crystallography; First Principles; Kinetic Monte Carlo; Material Science; Materials Modelling; Monte Carlo; Open Source; Software; Software Package; Symmetry; Thermodynamics},
  modificationdate = {2023-01-30T09:51:20},
  owner            = {saulius},
  publisher        = {Elsevier {BV}},
}

@TechReport{STMicroelectronics2016,
  author           = {{STMicroelectronics}},
  institution      = {STMicroelectronics},
  title            = {Floating point unit demonstration on {STM32} microcontrollers},
  year             = {2016},
  month            = may,
  number           = {AN4044},
  type             = {Application note},
  comment          = {Contains discussion of the IEEE 754 Floating Point and peculiarities of the STM32 implementation.},
  creationdate     = {2023-01-29T12:38:40},
  file             = {:by-author/S/STMicroelectronics/2016_STMicroelectronics_1.pdf:PDF},
  keywords         = {Computer Architecture; Computer Arithmetics; Computer Science (CS); Floating Point; STM32},
  modificationdate = {2023-01-29T12:44:43},
  owner            = {saulius},
  pages            = {1--31},
  url              = {https://www.st.com/resource/en/application_note/dm00047230-floating-point-unit-demonstration-on-stm32-microcontrollers-stmicroelectronics.pdf},
}

@TechReport{STMicroelectronics2020,
  author           = {{STMicroelectronics}},
  institution      = {STMicroelectronics},
  title            = {{STM32} Cortex$^{®}$-{M}4 {MCU}s and {MPU}s programming manual},
  year             = {2020},
  creationdate     = {2023-01-29T12:47:21},
  file             = {:by-author/S/STMicroelectronics/2020_STMicroelectronics_1.pdf:PDF},
  keywords         = {Assembler Programming; Computer Architecture; Computer Arithmetics; Computer Science (CS); Floating Point; ISA; Machine Language; STM32},
  modificationdate = {2023-01-29T12:50:56},
  owner            = {saulius},
  pages            = {1--262},
  url              = {https://www.st.com/resource/en/programming_manual/pm0214-stm32-cortexm4-mcus-and-mpus-programming-manual-stmicroelectronics.pdf},
}

@Article{Ahmed2010,
  author           = {Alauddin Ahmed and Richard J. Sadus},
  journal          = {The Journal of Chemical Physics},
  title            = {Effect of potential truncations and shifts on the solid-liquid phase coexistence of Lennard-Jones fluids},
  year             = {2010},
  month            = {sep},
  number           = {12},
  pages            = {124515},
  volume           = {133},
  comment          = {Discussed and cited in https://computecanada.github.io/molmodsim-md-theory-lesson-novice/07-thermostats/index.html and https://computecanada.github.io/molmodsim-md-theory-lesson-novice/reference.html.},
  creationdate     = {2023-01-29T13:06:46},
  doi              = {10.1063/1.3481102},
  file             = {:by-author/A/Ahmed/2010_Ahmed_124515.pdf:PDF},
  keywords         = {Molecular Dynamics (MD); Physics; Thermostat},
  modificationdate = {2023-01-29T13:09:27},
  owner            = {saulius},
  publisher        = {{AIP} Publishing},
}

@Article{Basconi2013,
  author           = {Joseph E. Basconi and Michael R. Shirts},
  journal          = {Journal of Chemical Theory and Computation},
  title            = {Effects of Temperature Control Algorithms on Transport Properties and Kinetics in Molecular Dynamics Simulations},
  year             = {2013},
  month            = {jun},
  number           = {7},
  pages            = {2887--2899},
  volume           = {9},
  comment          = {Discussed and cited in https://computecanada.github.io/molmodsim-md-theory-lesson-novice/07-thermostats/index.html and https://computecanada.github.io/molmodsim-md-theory-lesson-novice/reference.html.},
  creationdate     = {2023-01-29T13:16:23},
  doi              = {10.1021/ct400109a},
  file             = {:by-author/B/Basconi/2013_Basconi_2887.pdf:PDF},
  keywords         = {Molecular Dynamics (MD); Physics; Thermostat},
  modificationdate = {2023-01-29T13:17:02},
  owner            = {saulius},
  publisher        = {American Chemical Society ({ACS})},
}

@Article{Bernetti2020,
  author           = {Mattia Bernetti and Giovanni Bussi},
  journal          = {The Journal of Chemical Physics},
  title            = {Pressure control using stochastic cell rescaling},
  year             = {2020},
  month            = {sep},
  number           = {11},
  pages            = {114107},
  volume           = {153},
  comment          = {Discussed and cited in https://computecanada.github.io/molmodsim-md-theory-lesson-novice/07-thermostats/index.html and https://computecanada.github.io/molmodsim-md-theory-lesson-novice/reference.html.},
  creationdate     = {2023-01-29T13:25:12},
  doi              = {10.1063/5.0020514},
  file             = {:by-author/B/Bernetti/2020_Bernetti_114107.pdf:PDF},
  keywords         = {Molecular Dynamics (MD); Physics; Thermostat},
  modificationdate = {2023-01-29T13:25:54},
  owner            = {saulius},
  publisher        = {{AIP} Publishing},
}

@Article{Verlet1967,
  author           = {Loup Verlet},
  journal          = {Physical Review},
  title            = {Computer "Experiments" on Classical Fluids. I. Thermodynamical Properties of Lennard-Jones Molecules},
  year             = {1967},
  month            = {jul},
  number           = {1},
  pages            = {98--103},
  volume           = {159},
  comment          = {Discussed and cited in https://computecanada.github.io/molmodsim-md-theory-lesson-novice/07-thermostats/index.html and https://computecanada.github.io/molmodsim-md-theory-lesson-novice/reference.html.},
  creationdate     = {2023-01-29T13:48:45},
  doi              = {10.1103/physrev.159.98},
  file             = {:by-author/V/Verlet/1967_Verlet_98.pdf:PDF},
  keywords         = {Molecular Dynamics (MD); Physics},
  modificationdate = {2023-01-29T13:49:44},
  owner            = {saulius},
  publisher        = {American Physical Society ({APS})},
}

@Article{Alder1960,
  author           = {B. J. Alder and T. E. Wainwright},
  journal          = {The Journal of Chemical Physics},
  title            = {Studies in molecular dynamics. {II}. Behavior of a small number of elastic spheres},
  year             = {1960},
  month            = {nov},
  number           = {5},
  pages            = {1439--1451},
  volume           = {33},
  comment          = {Cited in Verlet1967.},
  creationdate     = {2023-01-29T14:05:39},
  doi              = {10.1063/1.1731425},
  file             = {:by-author/A/Alder/1960_Alder_1439.pdf:PDF},
  keywords         = {Molecular Dynamics (MD); Physics},
  modificationdate = {2023-01-29T15:36:26},
  owner            = {saulius},
  publisher        = {{AIP} Publishing},
}

@Article{Alder1959,
  author           = {B. J. Alder and T. E. Wainwright},
  journal          = {The Journal of Chemical Physics},
  title            = {Studies in molecular dynamics. {I}. General method},
  year             = {1959},
  month            = {aug},
  number           = {2},
  pages            = {459--466},
  volume           = {31},
  comment          = {The first part of the Alder1960 that was cited in Verlet1967.},
  creationdate     = {2023-01-29T14:09:24},
  doi              = {10.1063/1.1730376},
  file             = {:by-author/A/Alder/1959_Alder_459.pdf:PDF},
  keywords         = {Molecular Dynamics (MD); Physics},
  modificationdate = {2023-01-29T15:37:15},
  owner            = {saulius},
  publisher        = {{AIP} Publishing},
}

@Article{Braun2019,
  author           = {Efrem Braun and Justin Gilmer and Heather B. Mayes and David L. Mobley and Jacob I. Monroe and Samarjeet Prasad and Daniel M. Zuckerman},
  journal          = {Living Journal of Computational Molecular Science},
  title            = {Best practices for foundations in molecular simulations [article v1.0]},
  year             = {2019},
  number           = {1},
  pages            = {5957},
  volume           = {1},
  comment          = {Discussed and cited in https://computecanada.github.io/molmodsim-md-theory-lesson-novice/07-thermostats/index.html and https://computecanada.github.io/molmodsim-md-theory-lesson-novice/reference.html.},
  creationdate     = {2023-01-29T15:31:44},
  doi              = {10.33011/livecoms.1.1.5957},
  file             = {:by-author/B/Braun/2019_Braun_5957.pdf:PDF},
  keywords         = {Molecular Dynamics (MD); Physics},
  modificationdate = {2023-01-29T15:33:08},
  owner            = {saulius},
  publisher        = {University of Colorado at Boulder},
}

@Article{DauberOsguthorpe2018,
  author           = {Pnina Dauber-Osguthorpe and A. T. Hagler},
  journal          = {Journal of Computer-Aided Molecular Design},
  title            = {Biomolecular force fields: where have we been, where are we now, where do we need to go and how do we get there?},
  year             = {2018},
  month            = {nov},
  number           = {2},
  pages            = {133--203},
  volume           = {33},
  comment          = {Discussed and cited in https://computecanada.github.io/molmodsim-md-theory-lesson-novice/07-thermostats/index.html and https://computecanada.github.io/molmodsim-md-theory-lesson-novice/reference.html.},
  creationdate     = {2023-01-29T15:42:32},
  doi              = {10.1007/s10822-018-0111-4},
  file             = {:by-author/D/Dauber-Osguthorpe/2018_Dauber-Osguthorpe_133.pdf:PDF},
  keywords         = {Biomolecules; FF; Force Fields; Molecular Dynamics (MD); Physics; Structural Biology},
  modificationdate = {2023-01-29T15:43:46},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media {LLC}},
}

@Article{Bussi2007,
  author           = {Giovanni Bussi and Davide Donadio and Michele Parrinello},
  journal          = {The Journal of Chemical Physics},
  title            = {Canonical sampling through velocity rescaling},
  year             = {2007},
  month            = {jan},
  number           = {1},
  pages            = {014101},
  volume           = {126},
  comment          = {Discussed and cited in https://computecanada.github.io/molmodsim-md-theory-lesson-novice/07-thermostats/index.html and https://computecanada.github.io/molmodsim-md-theory-lesson-novice/reference.html.},
  creationdate     = {2023-01-29T15:45:30},
  doi              = {10.1063/1.2408420},
  file             = {:by-author/B/Bussi/2007_Bussi_14101.pdf:PDF},
  keywords         = {Molecular Dynamics (MD); Physics},
  modificationdate = {2023-01-29T15:46:13},
  owner            = {saulius},
  publisher        = {{AIP} Publishing},
}

@Article{Grosfils2009,
  author           = {Patrick Grosfils and James F. Lutsko},
  journal          = {The Journal of Chemical Physics},
  title            = {Dependence of the liquid-vapor surface tension on the range of interaction: A test of the law of corresponding states},
  year             = {2009},
  month            = {feb},
  number           = {5},
  pages            = {054703},
  volume           = {130},
  comment          = {Discussed and cited in https://computecanada.github.io/molmodsim-md-theory-lesson-novice/07-thermostats/index.html and https://computecanada.github.io/molmodsim-md-theory-lesson-novice/reference.html.},
  creationdate     = {2023-01-29T15:47:56},
  doi              = {10.1063/1.3072156},
  file             = {:by-author/G/Grosfils/2009_Grosfils_54703.pdf:PDF},
  keywords         = {Molecular Dynamics (MD); Physics},
  modificationdate = {2023-01-29T15:48:51},
  owner            = {saulius},
  publisher        = {{AIP} Publishing},
}

@Article{Grossfield2019,
  author           = {Alan Grossfield and Paul N. Patrone and Daniel R. Roe and Andrew J. Schultz and Daniel Siderius and Daniel M. Zuckerman},
  journal          = {Living Journal of Computational Molecular Science},
  title            = {Best practices for quantification of uncertainty and sampling quality in molecular simulations [article v1.0]},
  year             = {2019},
  number           = {1},
  pages            = {5067},
  volume           = {1},
  comment          = {Discussed and cited in https://computecanada.github.io/molmodsim-md-theory-lesson-novice/07-thermostats/index.html and https://computecanada.github.io/molmodsim-md-theory-lesson-novice/reference.html.},
  creationdate     = {2023-01-29T15:49:40},
  doi              = {10.33011/livecoms.1.1.5067},
  file             = {:by-author/G/Grossfield/2019_Grossfield_5067.pdf:PDF},
  keywords         = {Molecular Dynamics (MD); Physics},
  modificationdate = {2023-01-29T15:51:05},
  owner            = {saulius},
  publisher        = {University of Colorado at Boulder},
}

@Article{Hagler2018,
  author           = {A. T. Hagler},
  journal          = {Journal of Computer-Aided Molecular Design},
  title            = {Force field development phase {II}: Relaxation of physics-based criteria{\ldots} or inclusion of more rigorous physics into the representation of molecular energetics},
  year             = {2018},
  month            = {nov},
  number           = {2},
  pages            = {205--264},
  volume           = {33},
  comment          = {Discussed and cited in https://computecanada.github.io/molmodsim-md-theory-lesson-novice/07-thermostats/index.html and https://computecanada.github.io/molmodsim-md-theory-lesson-novice/reference.html.},
  creationdate     = {2023-01-29T15:54:10},
  doi              = {10.1007/s10822-018-0134-x},
  file             = {:by-author/H/Hagler/2018_Hagler_205.pdf:PDF},
  keywords         = {FF; Force Fields; Molecular Dynamics (MD); Physics},
  modificationdate = {2023-01-29T15:55:07},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media {LLC}},
}

@Article{Kriz2023,
  author           = {Kříž, Kristian and Schmidt, Lisa and Andersson, Alfred T. and Walz, Marie-Madeleine and van der Spoel, David},
  journal          = {Journal of chemical information and modeling},
  title            = {An Imbalance in the Force: The Need for Standardized Benchmarks for Molecular Simulation.},
  year             = {2023},
  issn             = {1549-960X},
  month            = jan,
  pages            = {412--431},
  volume           = {63},
  abstract         = {Force fields (FFs) for molecular simulation have been under development for more than half a century. As with any predictive model, rigorous testing and comparisons of models critically depends on the availability of standardized data sets and benchmarks. While such benchmarks are rather common in the fields of quantum chemistry, this is not the case for empirical FFs. That is, few benchmarks are reused to evaluate FFs, and development teams rather use their own training and test sets. Here we present an overview of currently available tests and benchmarks for computational chemistry, focusing on organic compounds, including halogens and common ions, as FFs for these are the most common ones. We argue that many of the benchmark data sets from quantum chemistry can in fact be reused for evaluating FFs, but new gas phase data is still needed for compounds containing phosphorus and sulfur in different valence states. In addition, more nonequilibrium interaction energies and forces, as well as molecular properties such as electrostatic potentials around compounds, would be beneficial. For the condensed phases there is a large body of experimental data available, and tools to utilize these data in an automated fashion are under development. If FF developers, as well as researchers in artificial intelligence, would adopt a number of these data sets, it would become easier to compare the relative strengths and weaknesses of different models and to, eventually, restore the balance in the force.},
  chemicals        = {Ions},
  citation-subset  = {IM},
  completed        = {2023-01-24},
  country          = {United States},
  creationdate     = {2023-01-29T16:05:53},
  doi              = {10.1021/acs.jcim.2c01127},
  file             = {:by-author/K/Kříž/2023_Kříž_412.pdf:PDF},
  issn-linking     = {1549-9596},
  issue            = {2},
  keywords         = {Artificial Intelligence (AI); Benchmarking; Computer Simulation; FF; Force Fields; Ions; Molecular Dynamics (MD); Physics},
  modificationdate = {2023-01-29T16:07:02},
  nlm-id           = {101230060},
  owner            = {saulius},
  pmc              = {PMC9875315},
  pmid             = {36630710},
  pubmodel         = {Print-Electronic},
  pubstate         = {ppublish},
  revised          = {2023-01-27},
  url              = {https://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC9875315&blobtype=pdf},
}

@Article{Tadmor2011,
  author           = {E. B. Tadmor and R. S. Elliott and J. P. Sethna and R. E. Miller and C. A. Becker},
  journal          = {{JOM}},
  title            = {The potential of atomistic simulations and the knowledgebase of interatomic models},
  year             = {2011},
  month            = {jul},
  number           = {7},
  pages            = {17--17},
  volume           = {63},
  creationdate     = {2023-01-29T16:21:06},
  doi              = {10.1007/s11837-011-0102-6},
  file             = {:by-author/T/Tadmor/2011_Tadmor_17.pdf:PDF},
  keywords         = {FF; Force Fields; MF; Molecular Dynamics (MD); OpenKIM},
  modificationdate = {2023-01-29T16:21:42},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media {LLC}},
}

@Article{Tadmor2013,
  author           = {Ellad B. Tadmor and Ryan S. Elliott and Simon R. Phillpot and Susan B. Sinnott},
  journal          = {Current Opinion in Solid State and Materials Science},
  title            = {{NSF} cyberinfrastructures: A new paradigm for advancing materials simulation},
  year             = {2013},
  month            = {dec},
  number           = {6},
  pages            = {298--304},
  volume           = {17},
  creationdate     = {2023-01-29T16:30:15},
  doi              = {10.1016/j.cossms.2013.10.004},
  file             = {:by-author/T/Tadmor/2013_Tadmor_298.pdf:PDF},
  keywords         = {FF; Force Fields; MF; Molecular Dynamics (MD); OpenKIM},
  modificationdate = {2023-01-29T16:31:18},
  owner            = {saulius},
  publisher        = {Elsevier {BV}},
}

@Article{Hagler1974,
  author           = {A. T. Hagler and E. Huler and S. Lifson},
  journal          = {Journal of the American Chemical Society},
  title            = {Energy functions for peptides and proteins. I. Derivation of a consistent force field including the hydrogen bond from amide crystals},
  year             = {1974},
  month            = {aug},
  number           = {17},
  pages            = {5319--5327},
  volume           = {96},
  creationdate     = {2023-01-29T17:49:24},
  doi              = {10.1021/ja00824a004},
  file             = {:by-author/H/Hagler/1974_Hagler_5319.pdf:PDF},
  keywords         = {Amides; FF; Force Fields; Hydrogen Bonds; MF; Molecular Dynamics (MD); Peptide Bonds},
  modificationdate = {2023-01-29T17:50:22},
  owner            = {saulius},
  publisher        = {American Chemical Society ({ACS})},
}

@Article{Hagler1979,
  author           = {A. T. Hagler and S. Lifson and P. Dauber},
  journal          = {Journal of the American Chemical Society},
  title            = {Consistent force field studies of intermolecular forces in hydrogen-bonded crystals. 2. A benchmark for the objective comparison of alternative force fields},
  year             = {1979},
  month            = {aug},
  number           = {18},
  pages            = {5122--5130},
  volume           = {101},
  creationdate     = {2023-01-29T17:53:53},
  doi              = {10.1021/ja00512a002},
  file             = {:by-author/H/Hagler/1979_Hagler_5122.pdf:PDF},
  keywords         = {FF; Force Fields; Hydrogen Bonds; MF; Molecular Dynamics (MD)},
  modificationdate = {2023-01-29T17:58:05},
  owner            = {saulius},
  publisher        = {American Chemical Society ({ACS})},
}

@Article{Lifson1979,
  author           = {S. Lifson and A. T. Hagler and P. Dauber},
  journal          = {Journal of the American Chemical Society},
  title            = {Consistent force field studies of intermolecular forces in hydrogen-bonded crystals. 1. Carboxylic acids, amides, and the C:O.cntdot..cntdot..cntdot.H- hydrogen bonds},
  year             = {1979},
  month            = {aug},
  number           = {18},
  pages            = {5111--5121},
  volume           = {101},
  creationdate     = {2023-01-29T17:58:51},
  doi              = {10.1021/ja00512a001},
  file             = {:by-author/L/Lifson/1979_Lifson_5111.pdf:PDF},
  keywords         = {FF; Force Fields; Hydrogen Bonds; MF; Molecular Dynamics (MD)},
  modificationdate = {2023-01-29T17:59:18},
  owner            = {saulius},
  publisher        = {American Chemical Society ({ACS})},
}

@Article{Hagler1979a,
  author           = {A. T. Hagler and P. Dauber and S. Lifson},
  journal          = {Journal of the American Chemical Society},
  title            = {Consistent force field studies of intermolecular forces in hydrogen-bonded crystals. 3. The C:O.cntdot..cntdot..cntdot.H-O hydrogen bond and the analysis of the energetics and packing of carboxylic acids},
  year             = {1979},
  month            = {aug},
  number           = {18},
  pages            = {5131--5141},
  volume           = {101},
  creationdate     = {2023-01-29T18:00:58},
  doi              = {10.1021/ja00512a003},
  file             = {:by-author/H/Hagler/1979_Hagler_5131.pdf:PDF},
  keywords         = {FF; Force Fields; Hydrogen Bonds; MF; Molecular Dynamics (MD)},
  modificationdate = {2023-01-29T18:01:24},
  owner            = {saulius},
  publisher        = {American Chemical Society ({ACS})},
}

@Article{Dauber1980,
  author           = {Pnina Dauber and Arnold T. Hagler},
  journal          = {Accounts of Chemical Research},
  title            = {Crystal packing, hydrogen bonding, and the effect of crystal forces on molecular conformation},
  year             = {1980},
  month            = {apr},
  number           = {4},
  pages            = {105--112},
  volume           = {13},
  creationdate     = {2023-01-29T18:03:38},
  doi              = {10.1021/ar50148a002},
  file             = {:by-author/D/Dauber/1980_Dauber_105.pdf:PDF},
  keywords         = {FF; Force Fields; Hydrogen Bonds; MF; Molecular Dynamics (MD)},
  modificationdate = {2023-01-29T18:03:57},
  owner            = {saulius},
  publisher        = {American Chemical Society ({ACS})},
}

@Article{Huang2014a,
  author           = {Kun Huang and Angel E. Garc{\'{\i}}a},
  journal          = {The Journal of Chemical Physics},
  title            = {Effects of truncating van der Waals interactions in lipid bilayer simulations},
  year             = {2014},
  month            = {sep},
  number           = {10},
  pages            = {105101},
  volume           = {141},
  comment          = {Discussed and cited in https://computecanada.github.io/molmodsim-md-theory-lesson-novice/07-thermostats/index.html and https://computecanada.github.io/molmodsim-md-theory-lesson-novice/reference.html.},
  creationdate     = {2023-01-29T18:17:43},
  doi              = {10.1063/1.4893965},
  file             = {:by-author/H/Huang/2014_Huang_105101.pdf:PDF},
  keywords         = {FF; Force Fields; Molecular Dynamics (MD); Physics},
  modificationdate = {2023-01-29T18:18:31},
  owner            = {saulius},
  publisher        = {{AIP} Publishing},
}

@Article{Koopman2006,
  author           = {E. A. Koopman and C. P. Lowe},
  journal          = {The Journal of Chemical Physics},
  title            = {Advantages of a Lowe-Andersen thermostat in molecular dynamics simulations},
  year             = {2006},
  month            = {may},
  number           = {20},
  pages            = {204103},
  volume           = {124},
  comment          = {Discussed and cited in https://computecanada.github.io/molmodsim-md-theory-lesson-novice/07-thermostats/index.html and https://computecanada.github.io/molmodsim-md-theory-lesson-novice/reference.html.},
  creationdate     = {2023-01-29T18:21:07},
  doi              = {10.1063/1.2198824},
  file             = {:by-author/K/Koopman/2006_Koopman_204103.pdf:PDF},
  keywords         = {Molecular Dynamics (MD); Physics; Thermostats},
  modificationdate = {2023-01-29T18:22:06},
  owner            = {saulius},
  publisher        = {{AIP} Publishing},
}

@Article{Larsson2011,
  author           = {Per Larsson and Berk Hess and Erik Lindahl},
  journal          = {{WIREs} Computational Molecular Science},
  title            = {Algorithm improvements for molecular dynamics simulations},
  year             = {2011},
  month            = {jan},
  number           = {1},
  pages            = {93--108},
  volume           = {1},
  comment          = {Discussed and cited in https://computecanada.github.io/molmodsim-md-theory-lesson-novice/07-thermostats/index.html and https://computecanada.github.io/molmodsim-md-theory-lesson-novice/reference.html.},
  creationdate     = {2023-01-29T18:26:51},
  doi              = {10.1002/wcms.3},
  file             = {:by-author/L/Larsson/2011_Larsson_93.pdf:PDF},
  keywords         = {Molecular Dynamics (MD); Physics; Thermostats},
  modificationdate = {2023-01-29T18:35:45},
  owner            = {saulius},
  publisher        = {Wiley},
}

@Article{Lemkul2019,
  author           = {Justin Lemkul},
  journal          = {Living Journal of Computational Molecular Science},
  title            = {From Proteins to Perturbed Hamiltonians: A Suite of Tutorials for the {GROMACS}-2018 Molecular Simulation Package [Article v1.0]},
  year             = {2019},
  number           = {1},
  pages            = {5068},
  volume           = {1},
  comment          = {Discussed and cited in https://computecanada.github.io/molmodsim-md-theory-lesson-novice/07-thermostats/index.html and https://computecanada.github.io/molmodsim-md-theory-lesson-novice/reference.html.},
  creationdate     = {2023-01-29T18:27:24},
  doi              = {10.33011/livecoms.1.1.5068},
  file             = {:by-author/L/Lemkul/2019_Lemkul_5068.pdf:PDF},
  keywords         = {GROMACS; Molecular Dynamics (MD); Physics; Thermostats},
  modificationdate = {2023-01-29T18:28:45},
  owner            = {saulius},
  publisher        = {University of Colorado at Boulder},
}

@Article{Lifson1968,
  author           = {S. Lifson and A. Warshel},
  journal          = {The Journal of Chemical Physics},
  title            = {Consistent Force Field for Calculations of Conformations, Vibrational Spectra, and Enthalpies of Cycloalkane and$\less$i$\greater$n$\less$/i$\greater$-Alkane Molecules},
  year             = {1968},
  month            = {dec},
  number           = {11},
  pages            = {5116--5129},
  volume           = {49},
  comment          = {Discussed and cited in https://computecanada.github.io/molmodsim-md-theory-lesson-novice/07-thermostats/index.html and https://computecanada.github.io/molmodsim-md-theory-lesson-novice/reference.html.},
  creationdate     = {2023-01-29T18:33:53},
  doi              = {10.1063/1.1670007},
  file             = {:by-author/L/Lifson/1968_Lifson_5116.pdf:PDF},
  keywords         = {Molecular Dynamics (MD); Physics; Thermostats},
  modificationdate = {2023-01-29T18:35:28},
  owner            = {saulius},
  publisher        = {{AIP} Publishing},
}

@Article{Maginn2020,
  author           = {Edward J. Maginn and Richard A. Messerly and Daniel J. Carlson and Daniel R. Roe and J. Richard Elliot},
  journal          = {Living Journal of Computational Molecular Science},
  title            = {Best Practices for Computing Transport Properties 1. Self-Diffusivity and Viscosity from Equilibrium Molecular Dynamics [Article v1.0]},
  year             = {2020},
  number           = {1},
  pages            = {6324},
  volume           = {2},
  comment          = {Discussed and cited in https://computecanada.github.io/molmodsim-md-theory-lesson-novice/07-thermostats/index.html and https://computecanada.github.io/molmodsim-md-theory-lesson-novice/reference.html.},
  creationdate     = {2023-01-29T18:46:47},
  doi              = {10.33011/livecoms.1.1.6324},
  file             = {:by-author/M/Maginn/2020_Maginn_6324.pdf:PDF},
  keywords         = {Molecular Dynamics (MD); Physics; Thermostats},
  modificationdate = {2023-01-29T18:48:06},
  owner            = {saulius},
  publisher        = {University of Colorado at Boulder},
}

@Article{Markthaler2019,
  author           = {Daniel Markthaler and Sven Jakobtorweihen and Niels Hansen},
  journal          = {Living Journal of Computational Molecular Science},
  title            = {Lessons Learned from the Calculation of One-Dimensional Potentials of Mean Force [Article v1.0]},
  year             = {2019},
  number           = {1},
  pages            = {11073},
  volume           = {1},
  comment          = {Discussed and cited in https://computecanada.github.io/molmodsim-md-theory-lesson-novice/07-thermostats/index.html and https://computecanada.github.io/molmodsim-md-theory-lesson-novice/reference.html.},
  creationdate     = {2023-01-29T18:48:39},
  doi              = {10.33011/livecoms.1.2.11073},
  file             = {:by-author/M/Markthaler/2019_Markthaler_11073.pdf:PDF},
  keywords         = {Molecular Dynamics (MD); Physics; Thermostats},
  modificationdate = {2023-01-29T18:49:45},
  owner            = {saulius},
  publisher        = {University of Colorado at Boulder},
}

@Article{Martyna1992,
  author           = {Glenn J. Martyna and Michael L. Klein and Mark Tuckerman},
  journal          = {The Journal of Chemical Physics},
  title            = {Nos{\'{e}}{\textendash}Hoover chains: The canonical ensemble via continuous dynamics},
  year             = {1992},
  month            = {aug},
  number           = {4},
  pages            = {2635--2643},
  volume           = {97},
  comment          = {Discussed and cited in https://computecanada.github.io/molmodsim-md-theory-lesson-novice/07-thermostats/index.html and https://computecanada.github.io/molmodsim-md-theory-lesson-novice/reference.html.},
  creationdate     = {2023-01-29T18:51:17},
  doi              = {10.1063/1.463940},
  file             = {:by-author/M/Martyna/1992_Martyna_2635.pdf:PDF},
  keywords         = {Molecular Dynamics (MD); Physics; Thermostats},
  modificationdate = {2023-01-29T18:51:59},
  owner            = {saulius},
  publisher        = {{AIP} Publishing},
}

@Article{Nose1984a,
  author           = {Sh{\={u}}ichi Nos{\'{e}}},
  journal          = {Molecular Physics},
  title            = {A molecular dynamics method for simulations in the canonical ensemble},
  year             = {1984},
  month            = {jun},
  number           = {2},
  pages            = {255--268},
  volume           = {52},
  comment          = {Discussed and cited in https://computecanada.github.io/molmodsim-md-theory-lesson-novice/07-thermostats/index.html and https://computecanada.github.io/molmodsim-md-theory-lesson-novice/reference.html.},
  creationdate     = {2023-01-29T18:53:06},
  doi              = {10.1080/00268978400101201},
  file             = {:by-author/N/Nosé/1984_Nosé_255.pdf:PDF},
  keywords         = {Molecular Dynamics (MD); Physics; Thermostats},
  modificationdate = {2023-01-29T18:56:00},
  owner            = {saulius},
  publisher        = {Informa {UK} Limited},
}

@Article{Parrinello1980,
  author           = {M. Parrinello and A. Rahman},
  journal          = {Physical Review Letters},
  title            = {Crystal Structure and Pair Potentials: A Molecular-Dynamics Study},
  year             = {1980},
  month            = {oct},
  number           = {14},
  pages            = {1196--1199},
  volume           = {45},
  comment          = {Discussed and cited in https://computecanada.github.io/molmodsim-md-theory-lesson-novice/07-thermostats/index.html and https://computecanada.github.io/molmodsim-md-theory-lesson-novice/reference.html.},
  creationdate     = {2023-01-29T18:58:10},
  doi              = {10.1103/physrevlett.45.1196},
  file             = {:by-author/P/Parrinello/1980_Parrinello_1196.pdf:PDF},
  keywords         = {Crystal Structure; Molecular Dynamics (MD); Physics; Thermostats},
  modificationdate = {2023-01-29T19:01:23},
  owner            = {saulius},
  publisher        = {American Physical Society ({APS})},
}

@Article{Parrinello1981,
  author           = {M. Parrinello and A. Rahman},
  journal          = {Journal of Applied Physics},
  title            = {Polymorphic transitions in single crystals: A new molecular dynamics method},
  year             = {1981},
  month            = {dec},
  number           = {12},
  pages            = {7182--7190},
  volume           = {52},
  comment          = {Discussed and cited in https://computecanada.github.io/molmodsim-md-theory-lesson-novice/07-thermostats/index.html and https://computecanada.github.io/molmodsim-md-theory-lesson-novice/reference.html.},
  creationdate     = {2023-01-29T19:02:53},
  doi              = {10.1063/1.328693},
  file             = {:by-author/P/Parrinello/1981_Parrinello_7182.pdf:PDF},
  keywords         = {Crystal Structure; Molecular Dynamics (MD); Physics; Thermostats},
  modificationdate = {2023-01-29T19:03:49},
  owner            = {saulius},
  publisher        = {{AIP} Publishing},
}

@Article{Piana2012,
  author           = {Stefano Piana and Kresten Lindorff-Larsen and Robert M. Dirks and John K. Salmon and Ron O. Dror and David E. Shaw},
  journal          = {{PLoS} {ONE}},
  title            = {Evaluating the Effects of Cutoffs and Treatment of Long-range Electrostatics in Protein Folding Simulations},
  year             = {2012},
  month            = {jun},
  number           = {6},
  pages            = {e39918},
  volume           = {7},
  comment          = {Discussed and cited in https://computecanada.github.io/molmodsim-md-theory-lesson-novice/07-thermostats/index.html and https://computecanada.github.io/molmodsim-md-theory-lesson-novice/reference.html.},
  creationdate     = {2023-01-29T19:05:25},
  doi              = {10.1371/journal.pone.0039918},
  editor           = {Chandra Verma},
  file             = {:by-author/P/Piana/2012_Piana_39918.pdf:PDF},
  keywords         = {Electrostatics; Long-range Interactions; Molecular Dynamics (MD); Physics; Protein Structure; Structural Biology; Thermostats},
  modificationdate = {2023-01-29T19:06:35},
  owner            = {saulius},
  publisher        = {Public Library of Science ({PLoS})},
}

@Article{Rogge2015,
  author           = {S.M.J. Rogge and L. Vanduyfhuys and A. Ghysels and M. Waroquier and T. Verstraelen and G. Maurin and V. Van Speybroeck},
  journal          = {Journal of Chemical Theory and Computation},
  title            = {A Comparison of Barostats for the Mechanical Characterization of Metal{\textendash}Organic Frameworks},
  year             = {2015},
  month            = {nov},
  number           = {12},
  pages            = {5583--5597},
  volume           = {11},
  comment          = {Discussed and cited in https://computecanada.github.io/molmodsim-md-theory-lesson-novice/07-thermostats/index.html and https://computecanada.github.io/molmodsim-md-theory-lesson-novice/reference.html.},
  creationdate     = {2023-01-29T19:07:13},
  doi              = {10.1021/acs.jctc.5b00748},
  file             = {:by-author/R/Rogge/2015_Rogge_5583.pdf:PDF;:by-author/R/Rogge/2015_Rogge_5583preprint.pdf:PDF},
  keywords         = {Barostats; Molecular Dynamics (MD); Physics; Thermostats},
  modificationdate = {2023-01-29T19:11:12},
  owner            = {saulius},
  publisher        = {American Chemical Society ({ACS})},
}

@Article{Shirts2013,
  author           = {Michael R. Shirts},
  journal          = {Journal of Chemical Theory and Computation},
  title            = {Simple Quantitative Tests to Validate Sampling from Thermodynamic Ensembles},
  year             = {2013},
  month            = {jan},
  number           = {2},
  pages            = {909--926},
  volume           = {9},
  comment          = {Discussed and cited in https://computecanada.github.io/molmodsim-md-theory-lesson-novice/07-thermostats/index.html and https://computecanada.github.io/molmodsim-md-theory-lesson-novice/reference.html.},
  creationdate     = {2023-01-29T19:08:45},
  doi              = {10.1021/ct300688p},
  file             = {:by-author/S/Shirts/2013_Shirts_909.pdf:PDF;:by-author/S/Shirts/2013_Shirts_909arXiv.pdf:PDF},
  keywords         = {Molecular Dynamics (MD); Physics; Quality Evaluation},
  modificationdate = {2023-01-29T19:14:43},
  owner            = {saulius},
  publisher        = {American Chemical Society ({ACS})},
}

@Article{Winger2009,
  author           = {Moritz Winger and Daniel Trzesniak and Riccardo Baron and Wilfred F. van Gunsteren},
  journal          = {Physical Chemistry Chemical Physics},
  title            = {On using a too large integration time step in molecular dynamics simulations of coarse-grained molecular models},
  year             = {2009},
  pages            = {1934--1941},
  comment          = {Discussed and cited in https://computecanada.github.io/molmodsim-md-theory-lesson-novice/07-thermostats/index.html and https://computecanada.github.io/molmodsim-md-theory-lesson-novice/reference.html.},
  creationdate     = {2023-01-29T19:16:14},
  doi              = {10.1039/b818713d},
  file             = {:by-author/W/Winger/2009_Winger_1934.pdf:PDF},
  keywords         = {Molecular Dynamics (MD); Physics; Quality Evaluation},
  modificationdate = {2023-01-29T19:46:22},
  owner            = {saulius},
  publisher        = {Royal Society of Chemistry ({RSC})},
}

@Article{Smith2019a,
  author           = {David J. Smith and Jeffrey B. Klauda and Alexander J. Sodt},
  journal          = {Living Journal of Computational Molecular Science},
  title            = {Simulation Best Practices for Lipid Membranes [Article v1.0]},
  year             = {2019},
  number           = {1},
  pages            = {5966},
  volume           = {1},
  comment          = {Discussed and cited in https://computecanada.github.io/molmodsim-md-theory-lesson-novice/07-thermostats/index.html and https://computecanada.github.io/molmodsim-md-theory-lesson-novice/reference.html.},
  creationdate     = {2023-01-29T19:32:50},
  doi              = {10.33011/livecoms.1.1.5966},
  file             = {:by-author/S/Smith/2019_Smith_5966.pdf:PDF},
  keywords         = {Best Practices; Molecular Dynamics (MD); Physics; Quality Evaluation},
  modificationdate = {2023-01-29T19:34:37},
  owner            = {saulius},
  publisher        = {University of Colorado at Boulder},
}

@Article{Yonetani2006,
  author           = {Yoshiteru Yonetani},
  journal          = {The Journal of Chemical Physics},
  title            = {Liquid water simulation: A critical examination of cutoff length},
  year             = {2006},
  month            = {may},
  number           = {20},
  pages            = {204501},
  volume           = {124},
  comment          = {Discussed and cited in https://computecanada.github.io/molmodsim-md-theory-lesson-novice/07-thermostats/index.html and https://computecanada.github.io/molmodsim-md-theory-lesson-novice/reference.html.},
  creationdate     = {2023-01-29T19:38:28},
  doi              = {10.1063/1.2198208},
  file             = {:by-author/Y/Yonetani/2006_Yonetani_204501.pdf:PDF},
  keywords         = {Best Practices; Coulomb Interactions; Electrostatics; Molecular Dynamics (MD); Physics; Quality Evaluation},
  modificationdate = {2023-01-29T19:40:37},
  owner            = {saulius},
  publisher        = {{AIP} Publishing},
}

@Article{Wongekkabut2016,
  author           = {Jirasak Wong-Ekkabut and Mikko Karttunen},
  journal          = {Biochimica et Biophysica Acta ({BBA}) - Biomembranes},
  title            = {The good, the bad and the user in soft matter simulations},
  year             = {2016},
  month            = {oct},
  number           = {10},
  pages            = {2529--2538},
  volume           = {1858},
  comment          = {Discussed and cited in https://computecanada.github.io/molmodsim-md-theory-lesson-novice/07-thermostats/index.html and https://computecanada.github.io/molmodsim-md-theory-lesson-novice/reference.html.},
  creationdate     = {2023-01-29T19:42:44},
  doi              = {10.1016/j.bbamem.2016.02.004},
  file             = {:by-author/W/Wong-Ekkabut/2016_Wong-Ekkabut_2529.pdf:PDF},
  keywords         = {Best Practices; Molecular Dynamics (MD); Physics; Quality Evaluation},
  modificationdate = {2023-01-29T19:44:45},
  owner            = {saulius},
  publisher        = {Elsevier {BV}},
}

@Article{Broek2018,
  author           = {van den Broek, Karina and Daniel, Mirco and Epple, Matthias and Kuhn, Hubert and Schaub, Jonas and Zielesny, Achim},
  journal          = {Journal of cheminformatics},
  title            = {SPICES: a particle-based molecular structure line notation and support library for mesoscopic simulation.},
  year             = {2018},
  issn             = {1758-2946},
  month            = aug,
  pages            = {35},
  volume           = {10},
  abstract         = {Simplified Particle Input ConnEction Specification (SPICES) is a particle-based molecular structure representation derived from straightforward simplifications of the atom-based SMILES line notation. It aims at supporting tedious and error-prone molecular structure definitions for particle-based mesoscopic simulation techniques like Dissipative Particle Dynamics by allowing for an interplay of different molecular encoding levels that range from topological line notations and corresponding particle-graph visualizations to 3D structures with support of their spatial mapping into a simulation box. An open Java library for SPICES structure handling and mesoscopic simulation support in combination with an open Java Graphical User Interface viewer application for visual topological inspection of SPICES definitions are provided.},
  country          = {England},
  creationdate     = {2023-01-29T20:04:06},
  doi              = {10.1186/s13321-018-0294-7},
  file             = {:by-author/B/Broek/2018_Broek_35.pdf:PDF},
  issn-linking     = {1758-2946},
  issue            = {1},
  keywords         = {DPD; Dissipative Particle Dynamics; Line Notation; Mesoscopic Simulation; Molecular Structure Representation},
  modificationdate = {2023-01-30T09:53:54},
  nlm-id           = {101516718},
  owner            = {saulius},
  pii              = {35},
  pmc              = {PMC6085218},
  pmid             = {30094683},
  pubmodel         = {Electronic},
  pubstate         = {epublish},
  revised          = {2020-09-30},
}

@Article{Shaw2008,
  author           = {David E. Shaw and Martin M. Deneroff and Ron O. Dror and Jeffrey S. Kuskin and Richard H. Larson and John K. Salmon and Cliff Young and Brannon Batson and Kevin J. Bowers and Jack C. Chao and Michael P. Eastwood and Joseph Gagliardo and J. P. Grossman and C. Richard Ho and Douglas J. Ierardi and Istv{\'{a}}n Kolossv{\'{a}}ry and John L. Klepeis and Timothy Layman and Christine McLeavey and Mark A. Moraes and Rolf Mueller and Edward C. Priest and Yibing Shan and Jochen Spengler and Michael Theobald and Brian Towles and Stanley C. Wang},
  journal          = {Communications of the {ACM}},
  title            = {Anton, a special-purpose machine for molecular dynamics simulation},
  year             = {2008},
  month            = {jul},
  number           = {7},
  pages            = {91--97},
  volume           = {51},
  creationdate     = {2023-01-29T20:09:03},
  doi              = {10.1145/1364782.1364802},
  file             = {:by-author/S/Shaw/2008_Shaw_91.pdf:PDF},
  keywords         = {ASIC; Computer Architecture; Computer Science (CS); Hardware Acceleration; Hardware Implementation; Molecular Dynamics (MD); Physics},
  modificationdate = {2023-01-29T20:10:01},
  owner            = {saulius},
  publisher        = {Association for Computing Machinery ({ACM})},
}

@Article{Macchi2020,
  author           = {Piero Macchi},
  journal          = {Crystallography Reviews},
  title            = {The connubium between crystallography and quantum mechanics},
  year             = {2020},
  month            = {oct},
  number           = {4},
  pages            = {209--268},
  volume           = {26},
  creationdate     = {2023-01-31T09:26:20},
  doi              = {10.1080/0889311x.2020.1853712},
  file             = {:by-author/M/Macchi/2020_Macchi_209.pdf:PDF;:by-author/M/Macchi/2020_Macchi_209.epub:ePUB},
  keywords         = {Crystallography; Quantum Crystallography; Review},
  modificationdate = {2023-01-31T09:27:58},
  owner            = {saulius},
  publisher        = {Informa {UK} Limited},
}

@Article{Helliwell2021,
  author           = {John R. Helliwell},
  journal          = {Crystallography Reviews},
  title            = {How should we teach crystallography? A review of teaching books' contents pages},
  year             = {2021},
  month            = {oct},
  number           = {3-4},
  pages            = {135--145},
  volume           = {27},
  creationdate     = {2023-01-31T09:30:16},
  doi              = {10.1080/0889311X.2021.1978080},
  file             = {:by-author/H/Helliwell/2021_Helliwell_135.pdf:PDF;:by-author/H/Helliwell/2021_Helliwell_135.epub:ePUB},
  keywords         = {Crystallography; Definition of Crystal; Teaching},
  modificationdate = {2023-01-31T09:32:33},
  owner            = {saulius},
  publisher        = {Informa {UK} Limited},
}

@Article{Macchi2015,
  author           = {Piero Macchi and Jean-Michel Gillet and Francis Taulelle and Javier Campo and Nicolas Claiser and Claude Lecomte},
  journal          = {{IUCrJ}},
  title            = {Modelling the experimental electron density: only the synergy of various approaches can tackle the new challenges},
  year             = {2015},
  month            = {may},
  number           = {4},
  pages            = {441--451},
  volume           = {2},
  creationdate     = {2023-01-31T09:34:12},
  doi              = {10.1107/s2052252515007538},
  file             = {:by-author/M/Macchi/2015_Macchi_441.pdf:PDF},
  keywords         = {Crystallography; Quantum Crystallography; Review},
  modificationdate = {2023-01-31T09:34:41},
  owner            = {saulius},
  publisher        = {International Union of Crystallography ({IUCr})},
}

@Article{Gillet2007,
  author           = {Gillet, Jean Michel},
  journal          = {Acta crystallographica. Section A, Foundations of crystallography},
  title            = {Determination of a one-electron reduced density matrix using a coupled pseudo-atom model and a set of complementary scattering data.},
  year             = {2007},
  issn             = {0108-7673},
  month            = may,
  pages            = {234--238},
  volume           = {63},
  abstract         = {A possible model of one-electron reduced density matrices is presented, adapted from the Hansen-Coppens pseudo-atomic description of electron density [Hansen & Coppens (1978). Acta Cryst. A34, 909-913]. Potential benefits from a joint refinement of the model from X-ray diffraction and deep inelastic scattering data are illustrated.},
  completed        = {2007-06-21},
  country          = {United States},
  creationdate     = {2023-01-31T09:39:22},
  doi              = {10.1107/S0108767307001663},
  file             = {:by-author/G/Gillet/2007_Gillet_234.pdf:PDF},
  issn-linking     = {0108-7673},
  issue            = {Pt 3},
  keywords         = {Charge Density; Crystallography; Quantum Crystallography; Wavefunctions},
  modificationdate = {2023-04-24T12:35:10},
  nlm-id           = {8305825},
  owner            = {saulius},
  pii              = {S0108767307001663},
  pmid             = {17435287},
  pubmodel         = {Print-Electronic},
  pubstate         = {ppublish},
  revised          = {2007-04-16},
}

@Article{Jayatilaka2001,
  author           = {Jayatilaka, D. and Grimwood, D. J.},
  journal          = {Acta crystallographica. Section A, Foundations of crystallography},
  title            = {Wavefunctions derived from experiment. I. Motivation and theory.},
  year             = {2001},
  issn             = {0108-7673},
  month            = jan,
  pages            = {76--86},
  volume           = {57},
  abstract         = {An experimental wavefunction is one that has an assumed form and that is also fitted to experimental measurements according to some well defined procedure. In this paper, the concept of extracting wavefunctions from experimental data is critically examined and past efforts are reviewed. In particular, the importance of scattering experiments for wavefunction fitting schemes is highlighted in relation to the more familiar model, the Hamiltonian paradigm. A general and systematically improvable method for fitting a wavefunction to experimental data is proposed. In this method, the parameters in a model wavefunction are determined according to the variational theorem but subject to an imposed constraint that an agreement statistic between the calculated and observed experimental data has a certain acceptable value. Advantages of the method include the fact that any amount of experimental data can be used in the fitting procedure irrespective of the number of parameters in the model wavefunction, the fact that a unique answer is obtained for a given choice of the model wavefunction, and the fact that the method can be used to model different experiments simultaneously. The wavefunction fitting method is illustrated by developing the theory for extracting a single-determinant wavefunction for a fragment of a molecular crystal, using data obtained from elastic X-ray scattering data. Effects due to thermal motion of the nuclei, secondary extinction of the X-ray scattering and different choices for the crystal fragment are treated.},
  completed        = {2001-03-01},
  country          = {United States},
  creationdate     = {2023-01-31T09:42:29},
  doi              = {10.1107/s0108767300013155},
  file             = {:by-author/J/Jayatilaka/2001_Jayatilaka_76.pdf:PDF},
  issn-linking     = {0108-7673},
  issue            = {Pt 1},
  keywords         = {Charge Density; Crystallography; Quantum Crystallography; Wavefunctions},
  modificationdate = {2023-04-24T12:35:12},
  nlm-id           = {8305825},
  owner            = {saulius},
  pii              = {S0108767300013155},
  pmid             = {11124506},
  pubmodel         = {Print},
  pubstate         = {ppublish},
  revised          = {2019-06-05},
}

@InCollection{Weyrich1996,
  author           = {Wolf Weyrich},
  booktitle        = {Lecture Notes in Chemistry},
  publisher        = {Springer Berlin Heidelberg},
  title            = {One-Electron Density Matrices and Related Observables},
  year             = {1996},
  pages            = {245--272},
  creationdate     = {2023-01-31T09:47:07},
  doi              = {10.1007/978-3-642-61478-1_14},
  file             = {:by-author/W/Weyrich/1996_Weyrich_245.pdf:PDF},
  keywords         = {CRYSTAL Computer Program; Charge Density; Computer Program; Crystallography; Density Matrix; Quantum Crystallography; Wavefunctions},
  modificationdate = {2023-01-31T09:58:51},
  owner            = {saulius},
}

@Presentation{Farrugia2007,
  author           = {Louis J. Farrugia},
  title            = {The multipole model and refinement},
  year             = {2007},
  creationdate     = {2023-01-31T09:51:47},
  file             = {:by-author/F/Farrugia/2007_Farrugia_1.pdf:PDF},
  keywords         = {Crystallography; Electron Density; Multiploe Model; Multipole Expansin; Spherical Harmonics; Structure Refinement; XD Computer Program},
  modificationdate = {2023-01-31T09:58:06},
  owner            = {saulius},
  pages            = {1--36},
  url              = {https://www.chem.gla.ac.uk/~louis/xdworkshop/workshop/documentation/jyvaskla_2.pdf},
}

@Article{Hansen1978,
  author           = {N. K. Hansen and P. Coppens},
  journal          = {Acta Crystallographica Section A},
  title            = {Testing aspherical atom refinements on small-molecule data sets},
  year             = {1978},
  month            = {nov},
  number           = {6},
  pages            = {909--921},
  volume           = {34},
  comment          = {Cited in Farrugia2007.},
  creationdate     = {2023-01-31T09:56:09},
  doi              = {10.1107/s0567739478001886},
  file             = {:by-author/H/Hansen/1978_Hansen_909.pdf:PDF},
  keywords         = {Crystallography; Electron Density; Multiploe Model; Multipole Expansin; Spherical Harmonics; Structure Refinement},
  modificationdate = {2023-01-31T09:56:45},
  owner            = {saulius},
  publisher        = {International Union of Crystallography ({IUCr})},
}

@Article{Huang1999,
  author           = {L. Huang and L. Massa and J. Karle},
  journal          = {International Journal of Quantum Chemistry},
  title            = {Quantum crystallography applied to crystalline maleic anhydride},
  year             = {1999},
  number           = {5},
  pages            = {439--450},
  volume           = {73},
  comment          = {Structure of maleic acid anhydride: COD 2200807 (https://www.crystallography.net/cod/2200807.html).},
  creationdate     = {2023-01-31T10:02:48},
  doi              = {10.1002/(sici)1097-461x(1999)73:5<439::aid-qua7>3.0.co;2-5},
  file             = {:by-author/H/Huang/1999_Huang_439.pdf:PDF},
  keywords         = {Charge Density; Crystallography; Quantum Crystallography; Wavefunctions},
  modificationdate = {2023-01-31T10:12:47},
  owner            = {saulius},
  publisher        = {Wiley},
}

@Lecture{Sandvik2022,
  author           = {Anders W. Sandvik},
  title            = {Numerical solutions of classical equations of motion},
  year             = {2022},
  lecture          = {3},
  school           = {Department of Physics, Boston University},
  creationdate     = {2023-01-31T19:53:20},
  file             = {:by-author/S/Sandvik/2022_Sandvik_1.pdf:PDF},
  keywords         = {Classical Mechanics; Equations of Motion; Euler Method; Integration; Leapfrog Integrator; Numerical Solutions; ODE; Physics; Verlet Integrator},
  modificationdate = {2023-01-31T19:58:57},
  owner            = {saulius},
  pages            = {1--14},
  url              = {http://physics.bu.edu/py502/lectures3/cmotion.pdf},
}

@Manuscript{Kotovych2001,
  author           = {Oksana Kotovych and John C. Bowman},
  title            = {An exactly conservative integrator for the $n$-body problem},
  year             = {2001},
  keywords         = {Conserved Quantities; Equations of Motion; Integration; Mathematics; Numerical Solutions; ODE; Physics},
  url              = {https://www.math.ualberta.ca/~bowman/publications/nbody.pdf},
  creationdate     = {2023-01-31T20:18:18},
  file             = {:by-author/K/Kotovych/2001_Kotovych_1.pdf:PDF},
  modificationdate = {2023-01-31T20:22:10},
  owner            = {saulius},
  pages            = {1--17},
}

@Article{Morse2011,
  author           = {Richard E. Morse and Prakash Nadkarni and David A. Schoenfeld and Dianne M. Finkelstein},
  journal          = {{BMC} Medical Informatics and Decision Making},
  title            = {Web-browser encryption of personal health information},
  year             = {2011},
  month            = {nov},
  number           = {1},
  pages            = {70},
  volume           = {11},
  creationdate     = {2023-02-01T11:30:23},
  doi              = {10.1186/1472-6947-11-70},
  file             = {:by-author/M/Morse/2011_Morse_70.pdf:PDF},
  keywords         = {Data Management; Encription; Medical Data Management; Privacy; Regulations},
  modificationdate = {2023-02-01T11:32:29},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media {LLC}},
}

@Article{Gabelica2022,
  author           = {Gabelica, Mirko and Bojčić, Ružica and Puljak, Livia},
  journal          = {Journal of clinical epidemiology},
  title            = {Many researchers were not compliant with their published data sharing statement: a mixed-methods study.},
  year             = {2022},
  issn             = {1878-5921},
  month            = oct,
  pages            = {33--41},
  volume           = {150},
  abstract         = {The objective of the study was to analyze researchers' compliance with their data availability statement (DAS) from manuscripts published in open-access journals with the mandatory DAS. We analyzed all articles from 333 open-access journals published during January 2019 by BioMed Central. We categorized types of the DAS. We surveyed corresponding authors who wrote in the DAS that they would share the data. Consent to participate in the study was sought for all included manuscripts. After accessing raw data sets, we checked whether data were available in a way that enabled reanalysis. Of 3556 analyzed articles, 3416 contained the DAS. The most frequent DAS category (42%) indicated that the data sets are available on reasonable request. Among 1792 manuscripts in which the DAS indicated that authors are willing to share their data, 1669 (93%) authors either did not respond or declined to share their data with us. Among 254 (14%) of 1792 authors who responded to our query for data sharing, only 123 (6.8%) provided the requested data. Even when authors indicate in their manuscript that they will share data upon request, the compliance rate is the same as for authors who do not provide the DAS, suggesting that the DAS may not be sufficient to ensure data sharing.},
  chemicals        = {amsonic acid},
  citation-subset  = {IM},
  comment          = {Found via https://en.wikipedia.org/wiki/Data_sharing (permanent link: https://en.wikipedia.org/w/index.php?title=Data_sharing&oldid=1102802641).},
  completed        = {2022-12-16},
  country          = {United States},
  creationdate     = {2023-02-02T10:28:56},
  doi              = {10.1016/j.jclinepi.2022.05.019},
  file             = {:by-author/G/Gabelica/2022_Gabelica_33.pdf:PDF},
  issn-linking     = {0895-4356},
  keywords         = {Data Availability Statement; Data Sharing; Humans; Information Dissemination, Methods; Metaresearch; Noncompliance; Open Data; Publications; Reproducibility; Research Personnel},
  modificationdate = {2023-02-02T10:37:31},
  nlm-id           = {8801383},
  owner            = {saulius},
  pii              = {S0895-4356(22)00141-X},
  pmid             = {35654271},
  pubmodel         = {Print-Electronic},
  pubstate         = {ppublish},
  revised          = {2022-12-21},
}

@Article{Glazer2014,
  author           = {A. Michael Glazer and Mois I. Aroyo and Andr{\'{e}} Authier},
  journal          = {Acta Crystallographica Section A Foundations and Advances},
  title            = {Seitz symbols for crystallographic symmetry operations},
  year             = {2014},
  month            = {mar},
  number           = {3},
  pages            = {300--302},
  volume           = {70},
  creationdate     = {2023-02-02T18:49:08},
  doi              = {10.1107/s2053273314004495},
  file             = {:by-author/G/Glazer/2014_Glazer_300.pdf:PDF},
  keywords         = {Crystallography; Notation; Seitz Matrices; Seitz Symbols; Symmetry Operations; Symmetry Operators},
  modificationdate = {2023-02-02T18:50:03},
  owner            = {saulius},
  publisher        = {International Union of Crystallography ({IUCr})},
}

@InCollection{Hestenes2002,
  author           = {David Hestenes},
  booktitle        = {Applications of Geometric Algebra in Computer Science and Engineering},
  publisher        = {Birkhäuser Boston},
  title            = {Point groups and space groups in geometric algebra},
  year             = {2002},
  pages            = {3--34},
  creationdate     = {2023-02-03T09:07:41},
  doi              = {10.1007/978-1-4612-0089-5_1},
  file             = {:by-author/H/Hestenes/2002_Hestenes_3.pdf:PDF},
  keywords         = {Crystallography; Enumeration; Geometric Algebra; Space Groups},
  modificationdate = {2023-02-03T09:10:02},
  owner            = {saulius},
  url              = {https://geocalc.clas.asu.edu/pdf-preAdobe8/crystalsymmetry.pdf},
}

@Manuscript{Dewar2022,
  author           = {Robert Dewar and Olivier Hainque and Dirk Craeynest and Philippe Waroquiers},
  title            = {Exposing uninitialized variables: strengthening and extending run-time checks in {A}da},
  year             = {2022},
  keywords         = {Ada; Computer Science (CS); Programming; Runtime Checks; Software Correctness; Variable Initialisation},
  url              = {https://www.adacore.com/uploads/techPapers/rtchecks.pdf},
  comment          = {Found via https://stackoverflow.com/questions/56793192/check-initialization-of-variable .
"1.5 million Ada source lines for the CFMU application".},
  creationdate     = {2023-02-05T10:14:33},
  file             = {:by-author/D/Dewar/2022_Dewar_1.pdf:PDF},
  modificationdate = {2023-02-05T11:03:09},
  owner            = {saulius},
  pages            = {1--12},
}

@Manuscript{Moeller2005,
  author           = {Niels Möller},
  title            = {On {S}chönhage’s algorithmand subquadratic integer gcd computation},
  year             = {2005},
  keywords         = {Algorithms; Computer Science (CS); Efficiency; GCD; GCD Algorithm; Greatest Common Divisor; Subquadratic Algorithm},
  url              = {http://www.lysator.liu.se/~nisse/archive/sgcd.pdf},
  creationdate     = {2023-02-06T08:11:17},
  file             = {:by-author/M/Möller/2005_Möller_1.pdf:PDF},
  modificationdate = {2023-02-06T08:14:03},
  owner            = {saulius},
  pages            = {1--13},
}

@Article{Moeller2008,
  author           = {Niels Möller},
  journal          = {Mathematics of Computation},
  title            = {On {S}chönhage's algorithm and subquadratic integer gcd computation},
  year             = {2008},
  month            = {jan},
  number           = {261},
  pages            = {589--607},
  volume           = {77},
  creationdate     = {2023-02-06T08:14:14},
  doi              = {10.1090/s0025-5718-07-02017-0},
  file             = {:by-author/M/Möller/2008_Möller_589.pdf:PDF},
  keywords         = {Algorithms; Computer Science (CS); Efficiency; GCD; GCD Algorithm; Greatest Common Divisor; Subquadratic Algorithm},
  modificationdate = {2023-02-06T08:14:58},
  owner            = {saulius},
  publisher        = {American Mathematical Society ({AMS})},
}

@Article{Courtieu2013,
  author           = {Pierre Courtieu and Maria Virginia Aponte and Tristan Crolard and Zhi Zhang and Fnu Robby and Jason Belt and John Hatcliff and Jerome Guitton and Trevor Jennings},
  journal          = {{ACM} {SIGAda} Ada Letters},
  title            = {Towards the formalization of {SPARK} 2014 semantics with explicit run-time checks using coq},
  year             = {2013},
  month            = {nov},
  number           = {3},
  pages            = {21--22},
  volume           = {33},
  creationdate     = {2023-02-06T14:52:20},
  doi              = {10.1145/2658982.2527278},
  file             = {:by-author/C/Courtieu/2013_Courtieu_21.pdf:PDF},
  keywords         = {Ada; Computer Science (CS); Coq; Correctness Proofs; Formal Verification; Program Verification; Proof Assistants; SPARK; SPARK 2014},
  modificationdate = {2023-02-06T14:59:20},
  owner            = {saulius},
  publisher        = {Association for Computing Machinery ({ACM})},
  url              = {https://github.com/AdaCore/sparkformal/blob/master/papers/hilt2013/HILT2013.pdf},
}

@Article{Albert2019,
  author           = {Sahradha Albert and Wojciech Wietrzynski and Chia-Wei Lee and Miroslava Schaffer and Florian Beck and Jan M. Schuller and Patrice A. Salom{\'{e}} and Jürgen M. Plitzko and Wolfgang Baumeister and Benjamin D. Engel},
  journal          = {Proceedings of the National Academy of Sciences},
  title            = {Direct visualization of degradation microcompartments at the {ER} membrane},
  year             = {2019},
  month            = {dec},
  number           = {2},
  pages            = {1069--1080},
  volume           = {117},
  creationdate     = {2023-02-07T07:52:42},
  doi              = {10.1073/pnas.1905641117},
  file             = {:by-author/A/Albert/2019_Albert_1069.pdf:PDF},
  keywords         = {Bioinformatics; Electron MIcroscopy; Electron Tomography; Structural Biology},
  modificationdate = {2023-02-07T07:53:47},
  owner            = {saulius},
  publisher        = {Proceedings of the National Academy of Sciences},
}

@Article{Baumeister2022,
  author           = {Wolfgang Baumeister},
  journal          = {Cell},
  title            = {Cryo-electron tomography: A long journey to the inner space of cells},
  year             = {2022},
  month            = {jul},
  number           = {15},
  pages            = {2649--2652},
  volume           = {185},
  creationdate     = {2023-02-07T07:57:05},
  doi              = {10.1016/j.cell.2022.06.034},
  file             = {:by-author/B/Baumeister/2022_Baumeister_2649.pdf:PDF},
  keywords         = {Bioinformatics; Electron MIcroscopy; Electron Tomography; Structural Biology},
  modificationdate = {2023-02-07T07:58:11},
  owner            = {saulius},
  publisher        = {Elsevier {BV}},
}

@Article{Gotoh1982,
  author           = {Osamu Gotoh},
  journal          = {Journal of Molecular Biology},
  title            = {An improved algorithm for matching biological sequences},
  year             = {1982},
  month            = {dec},
  number           = {3},
  pages            = {705--708},
  volume           = {162},
  comment          = {Cited and criticised by Altschul1986.},
  creationdate     = {2023-02-08T20:08:05},
  doi              = {10.1016/0022-2836(82)90398-9},
  file             = {:by-author/G/Gotoh/1982_Gotoh_705.pdf:PDF},
  keywords         = {Affine Gap Cost; Algorithm Failure; Algorithms; Alignment With Gaps; Bioinformatics; Bugs; Gap Cost; Needleman-Wunsch Algorithm; Sequence Alignment},
  modificationdate = {2023-02-08T20:28:52},
  owner            = {saulius},
  publisher        = {Elsevier {BV}},
}

@InCollection{Needleman1989,
  author           = {Saul B. Needleman and Christian D. Wunsch},
  booktitle        = {Molecular Biology},
  publisher        = {Elsevier},
  title            = {A general method applicable to the search for similarities in the amino acid sequence of two proteins},
  year             = {1989},
  pages            = {453--463},
  creationdate     = {2023-02-08T20:32:05},
  doi              = {10.1016/b978-0-12-131200-8.50031-9},
  file             = {:by-author/N/Needleman/1989_Needleman_453.pdf:PDF},
  keywords         = {Algorithms; Bioinformatics; Needleman-Wunsch Algorithm; Sequence Alignment},
  modificationdate = {2023-02-08T20:33:58},
  owner            = {saulius},
}

@Article{Needleman1970,
  author           = {Needleman, S. B. and Wunsch, C. D.},
  journal          = {Journal of molecular biology},
  title            = {A general method applicable to the search for similarities in the amino acid sequence of two proteins.},
  year             = {1970},
  issn             = {0022-2836},
  month            = mar,
  pages            = {443--453},
  volume           = {48},
  chemicals        = {Hemoglobins, Myoglobin, Ribonucleases, Muramidase},
  citation-subset  = {IM},
  completed        = {1970-07-29},
  country          = {Netherlands},
  creationdate     = {2023-02-08T20:36:47},
  doi              = {10.1016/0022-2836(70)90057-4},
  file             = {:by-author/N/Needleman/1970_Needleman_443.pdf:PDF},
  issn-linking     = {0022-2836},
  issue            = {3},
  keywords         = {Algorithms; Amino Acid Sequence; Bioinformatics; Computers; Hemoglobins; Methods; Muramidase; Myoglobin; Needleman-Wunsch Algorithm; Probability; Ribonucleases; Sequence Alignment},
  modificationdate = {2023-02-08T20:38:14},
  nlm-id           = {2985088R},
  owner            = {saulius},
  pii              = {0022-2836(70)90057-4},
  pmid             = {5420325},
  pubmodel         = {Print},
  pubstate         = {ppublish},
  revised          = {2022-04-09},
}

@Article{Fitch1983,
  author           = {Walter M. Fitch and Temple F. Smith},
  journal          = {Proceedings of the National Academy of Sciences},
  title            = {Optimal sequence alignments},
  year             = {1983},
  month            = {mar},
  number           = {5},
  pages            = {1382--1386},
  volume           = {80},
  comment          = {Cited by Altschul1986.},
  creationdate     = {2023-02-08T20:40:39},
  doi              = {10.1073/pnas.80.5.1382},
  file             = {:by-author/F/Fitch/1983_Fitch_1382.pdf:PDF},
  keywords         = {Algorithms; Bioinformatics; Needleman-Wunsch Algorithm; Sequence Alignment},
  modificationdate = {2023-02-08T20:41:31},
  owner            = {saulius},
  publisher        = {Proceedings of the National Academy of Sciences},
}

@Article{Altschul1986a,
  author           = {S. Altschul and B. Erickson},
  journal          = {Bulletin of Mathematical Biology},
  title            = {A nonlinear measure of subalignment similarity and its significance levels},
  year             = {1986},
  number           = {5-6},
  pages            = {617--632},
  volume           = {48},
  comment          = {Cited by Altschul1986.},
  creationdate     = {2023-02-08T20:42:51},
  doi              = {10.1016/s0092-8240(86)90011-x},
  file             = {:by-author/A/Altschul/1986_Altschul_617.pdf:PDF},
  keywords         = {Algorithms; Bioinformatics; Needleman-Wunsch Algorithm; Sequence Alignment},
  modificationdate = {2023-02-08T20:54:24},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media {LLC}},
}

@Article{Sellers1974,
  author           = {Peter H. Sellers},
  journal          = {{SIAM} Journal on Applied Mathematics},
  title            = {On the theory and computation of evolutionary distances},
  year             = {1974},
  month            = {jun},
  number           = {4},
  pages            = {787--793},
  volume           = {26},
  comment          = {Cited by Altschul1986.},
  creationdate     = {2023-02-08T20:50:49},
  doi              = {10.1137/0126070},
  file             = {:by-author/S/Sellers/1974_Sellers_787.pdf:PDF},
  keywords         = {Algorithms; Alignment Matrices; Bioinformatics; Evolution; Needleman-Wunsch Algorithm; Sequence Alignment},
  modificationdate = {2023-02-08T20:54:27},
  owner            = {saulius},
  publisher        = {Society for Industrial {\&} Applied Mathematics ({SIAM})},
}

@Article{Smith1981a,
  author           = {T. F. Smith and M. S. Waterman and W. M. Fitch},
  journal          = {Journal of Molecular Evolution},
  title            = {Comparative biosequence metrics},
  year             = {1981},
  month            = {jan},
  number           = {1},
  pages            = {38--46},
  volume           = {18},
  comment          = {Cited by Altschul1986.},
  creationdate     = {2023-02-08T20:55:37},
  doi              = {10.1007/bf01733210},
  file             = {:by-author/S/Smith/1981_Smith_38.pdf:PDF},
  keywords         = {Algorithms; Alignment Matrices; Bioinformatics; Evolution; Needleman-Wunsch Algorithm; Sequence Alignment; Smith-Waterman Algorithm},
  modificationdate = {2023-02-08T20:57:10},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media {LLC}},
}

@Article{Taylor1984,
  author           = {Philip Taylor},
  journal          = {Nucleic Acids Research},
  title            = {A fast homology program for aligning biological sequences},
  year             = {1984},
  number           = {1Part2},
  pages            = {447--455},
  volume           = {12},
  comment          = {Cited by Altschul1986.},
  creationdate     = {2023-02-08T20:57:51},
  doi              = {10.1093/nar/12.1part2.447},
  file             = {:by-author/T/Taylor/1984_Taylor_447.pdf:PDF},
  keywords         = {Algorithms; Alignment Matrices; Bioinformatics; Evolution; Needleman-Wunsch Algorithm; Sequence Alignment},
  modificationdate = {2023-02-08T20:59:18},
  owner            = {saulius},
  publisher        = {Oxford University Press ({OUP})},
}

@Article{Waterman1984,
  author           = {Michael S. Waterman},
  journal          = {Journal of Theoretical Biology},
  title            = {Efficient sequence alignment algorithms},
  year             = {1984},
  month            = {jun},
  number           = {3},
  pages            = {333--337},
  volume           = {108},
  comment          = {Cited by Altschul1986.},
  creationdate     = {2023-02-08T21:00:10},
  doi              = {10.1016/s0022-5193(84)80037-5},
  file             = {:by-author/W/Waterman/1984_Waterman_333.pdf:PDF},
  keywords         = {Algorithms; Alignment Matrices; Bioinformatics; Evolution; Needleman-Wunsch Algorithm; Sequence Alignment},
  modificationdate = {2023-02-08T21:00:52},
  owner            = {saulius},
  publisher        = {Elsevier {BV}},
}

@InCollection{Stephen1994,
  author           = {Graham A. Stephen},
  booktitle        = {String Searching Algorithms},
  publisher        = {World Scientific},
  title            = {Approximate string matching},
  year             = {1994},
  month            = {oct},
  pages            = {111--189},
  creationdate     = {2023-02-08T21:01:58},
  doi              = {10.1142/9789814317368_0005},
  file             = {:by-author/S/Stephen/1994_Stephen_111.pdf:PDF},
  keywords         = {Algorithms; Alignment Matrices; Bioinformatics; Evolution; Needleman-Wunsch Algorithm; Sequence Alignment},
  modificationdate = {2023-02-08T21:11:29},
  owner            = {saulius},
}

@InProceedings{Zhang2004c,
  author           = {Qiong Zhang and Roger D. Chamberlain and Ronald S. Indeck and Benjamin West and Jason White},
  booktitle        = {Proc. of Workshop onMassively Parallel Processing},
  title            = {Massively parallel data mining using reconfigurable hardware: approximate string matching},
  year             = {2004},
  pages            = {1--9},
  creationdate     = {2023-02-08T21:11:49},
  file             = {:by-author/Z/Zhang/2004_Zhang_1.pdf:PDF},
  keywords         = {Algorithms; Alignment Matrices; Bioinformatics; Evolution; Needleman-Wunsch Algorithm; Sequence Alignment},
  modificationdate = {2023-02-08T21:15:12},
  owner            = {saulius},
  url              = {https://www.ccrc.wustl.edu/~roger/papers/zciww04.pdf},
}

@InCollection{Ukkonen1983,
  author           = {Esko Ukkonen},
  booktitle        = {Foundations of Computation Theory},
  publisher        = {Springer Berlin Heidelberg},
  title            = {On approximate string matching},
  year             = {1983},
  pages            = {487--495},
  comment          = {Cited by Altschul1986.},
  creationdate     = {2023-02-08T21:16:22},
  doi              = {10.1007/3-540-12689-9_129},
  file             = {:by-author/U/Ukkonen/1983_Ukkonen_487.pdf:PDF},
  keywords         = {Algorithms; Alignment Matrices; Bioinformatics; Evolution; Needleman-Wunsch Algorithm; Sequence Alignment},
  modificationdate = {2023-02-08T21:17:58},
  owner            = {saulius},
}

@Article{Immler2019,
  author           = {Immler, Fabian and Rädle, Jonas and Wenzel, Makarius},
  title            = {Virtualization of HOL4 in Isabelle},
  year             = {2019},
  pages            = {1--18},
  copyright        = {Creative Commons Attribution 3.0 Unported license (CC-BY 3.0)},
  creationdate     = {2023-02-09T12:44:15},
  doi              = {10.4230/LIPICS.ITP.2019.21},
  file             = {:by-author/I/Immler/2019_Immler_1.pdf:PDF},
  keywords         = {Computer Science (CS); Formal Verifcation; HOL; HOL4; Isabelle; Knowledge; Proof Assistants},
  language         = {en},
  modificationdate = {2023-02-09T12:45:40},
  owner            = {saulius},
  publisher        = {Schloss Dagstuhl - Leibniz-Zentrum fuer Informatik GmbH, Wadern/Saarbruecken, Germany},
  url              = {https://drops.dagstuhl.de/opus/volltexte/2019/11076/pdf/LIPIcs-ITP-2019-21.pdf},
}

@Article{Lammich2019,
  author           = {Lammich, Peter},
  title            = {Generating verified {LLVM} from {I}sabelle/{HOL}},
  year             = {2019},
  pages            = {1--19},
  copyright        = {Creative Commons Attribution 3.0 Unported license (CC-BY 3.0)},
  creationdate     = {2023-02-09T12:47:19},
  doi              = {10.4230/LIPICS.ITP.2019.22},
  file             = {:by-author/L/Lammich/2019_Lammich_1.pdf:PDF},
  keywords         = {Computer Science (CS); Formal Verifcation; HOL; HOL4; Isabelle; Knowledge; Proof Assistants},
  language         = {en},
  modificationdate = {2023-02-09T12:48:23},
  owner            = {saulius},
  publisher        = {Schloss Dagstuhl - Leibniz-Zentrum fuer Informatik GmbH, Wadern/Saarbruecken, Germany},
  url              = {https://drops.dagstuhl.de/opus/volltexte/2019/11077/pdf/LIPIcs-ITP-2019-22.pdf},
}

@Webpage{SPARKTeam2011,
  author           = {{SPARK Team}},
  retrieved        = {2023-02-09T12:59+02:00},
  title            = {{SPARK} {S}implifier. {U}ser manual},
  url              = {https://docs.adacore.com/sparkdocs-docs/Simplifier_UM.htm},
  year             = {2011},
  creationdate     = {2023-02-09T12:59:25},
  file             = {:by-author/S/SPARKTeam/2011_SPARKTeam_Simplifier_UM.html:URL},
  keywords         = {Ada; Computer Science (CS); Formal Verifcation; Program Correctness Proofs; SPARK},
  modificationdate = {2023-02-09T13:04:58},
  owner            = {saulius},
}

@Webpage{SPARKTeam2006,
  author           = {{SPARK Team}},
  retrieved        = {2023-02-09T12:59+02:00},
  title            = {{SPARK} {E}xaminer. {U}ser manual – release 7.3 [{NT}]},
  url              = {http://didawikinf.di.unipi.it/lib/exe/fetch.php/magistralesicurezza/sss/examiner_um_win.pdf},
  year             = {2006},
  creationdate     = {2023-02-09T13:03:20},
  file             = {:by-author/S/SPARKTeam/2006_SPARKTeam_Examiner_UM.pdf:PDF},
  keywords         = {Ada; Computer Science (CS); Formal Verifcation; Program Correctness Proofs; SPARK},
  modificationdate = {2023-02-09T13:05:49},
  owner            = {saulius},
}

@Manuscript{Jackson2010,
  author           = {Paul Jackson},
  title            = {{V}ictor: a {SPARK} {VC} translator and prover driver. {U}ser manual for release 0.9.0},
  year             = {2010},
  keywords         = {Ada; Computer Science (CS); Formal Verifcation; Program Correctness Proofs; SPARK},
  url              = {https://homepages.inf.ed.ac.uk/pbj/spark/vct-man.pdf},
  creationdate     = {2023-02-09T13:07:08},
  file             = {:by-author/J/Jackson/2010_Jackson_1.pdf:PDF},
  modificationdate = {2023-02-09T13:09:01},
  owner            = {saulius},
  pages            = {1--28},
}

@MastersThesis{Jedryszek2012,
  author           = {Jakub Jedryszek},
  school           = {Kansas State University},
  title            = {A model-driven development and verification approach for medical devices},
  year             = {2012},
  creationdate     = {2023-02-09T13:10:13},
  file             = {:by-author/J/Jedryszek/2012_Jedryszek_1.pdf:PDF},
  keywords         = {Ada; Computer Science (CS); Formal Verifcation; Medical Devices; Model Driven Verification; Program Correctness Proofs; SPARK},
  modificationdate = {2023-02-09T13:16:55},
  owner            = {saulius},
  pages            = {1--231},
  url              = {https://krex.k-state.edu/bitstream/handle/2097/18222/JakubJedryszek2014.pdf},
}

@Proceedings{Brauer2011,
  title            = {Proceedings of the 6th international {W}orkshop on {S}ystems {S}oftware {V}erification ({SSV} 2011)},
  year             = {2011},
  editor           = {Jörg Brauer and Marco Roveri and Hendrik Tews},
  creationdate     = {2023-02-09T13:14:33},
  file             = {:by-author/B/Brauer/2011_Brauer_1.pdf:PDF},
  keywords         = {Ada; Computer Science (CS); Formal Verifcation; Medical Devices; Model Driven Verification; Program Correctness Proofs; SPARK; Software Verification},
  modificationdate = {2023-02-09T13:17:23},
  owner            = {saulius},
  pages            = {1--101},
  url              = {https://askra.de/papers/ssv2011-proceedings.pdf},
}

@Article{Segura2011,
  author           = {J. Segura and B. Oliva and N. Fernandez-Fuentes},
  journal          = {Nucleic Acids Research},
  title            = {{CAPS}-{DB}: a structural classification of helix-capping motifs},
  year             = {2011},
  month            = {oct},
  number           = {D1},
  pages            = {D479--D485},
  volume           = {40},
  creationdate     = {2023-02-13T11:55:13},
  doi              = {10.1093/nar/gkr879},
  file             = {:by-author/S/Segura/2011_Segura_479.pdf:PDF},
  keywords         = {Bioinformatics; Databases; Helix Cappings; Helix-Capping Motifs; Protein Modelling; Protein Structure Classification; Protein Structure Prediction; Protein Structures; Protein Turn Classification; Rotamer Libraries; Structural Biology},
  modificationdate = {2023-04-22T10:59:12},
  owner            = {saulius},
  publisher        = {Oxford University Press ({OUP})},
}

@Article{McPartlon2022,
  author           = {Matt McPartlon and Jinbo Xu},
  title            = {An end-to-end deep learning method for rotamer-free protein side-chain packing},
  year             = {2022},
  month            = {mar},
  pages            = {1--29},
  creationdate     = {2023-02-13T11:57:31},
  doi              = {10.1101/2022.03.11.483812},
  file             = {:by-author/M/McPartlon/2022_McPartlon_1.pdf:PDF},
  keywords         = {Bioinformatics; Databases; Protein Modelling; Protein Structure Prediction; Protein Structures; Rotamer Libraries; Structural Biology},
  modificationdate = {2023-02-13T12:00:39},
  owner            = {saulius},
  publisher        = {Cold Spring Harbor Laboratory},
}

@Article{Misiura2022,
  author           = {Mikita Misiura and Raghav Shroff and Ross Thyer and Anatoly B. Kolomeisky},
  journal          = {Proteins: Structure, Function, and Bioinformatics},
  title            = {{DLPacker}: Deep learning for prediction of amino acid side chain conformations in proteins},
  year             = {2022},
  month            = {feb},
  number           = {6},
  pages            = {1278--1290},
  volume           = {90},
  creationdate     = {2023-02-13T11:59:34},
  doi              = {10.1002/prot.26311},
  file             = {:by-author/M/Misiura/2022_Misiura_1278.pdf:PDF},
  keywords         = {Bioinformatics; Databases; Protein Modelling; Protein Structure Prediction; Protein Structures; Protein Turn Classification; Rotamer Libraries; Structural Biology},
  modificationdate = {2023-02-13T12:01:01},
  owner            = {saulius},
  publisher        = {Wiley},
}

@Article{Holladay1957,
  author           = {John C. Holladay},
  journal          = {Proceedings of the American Mathematical Society},
  title            = {A note on the {S}tone-{W}eierstrass theorem for quaternions},
  year             = {1957},
  number           = {4},
  pages            = {656--657},
  volume           = {8},
  creationdate     = {2023-02-13T16:25:50},
  doi              = {10.1090/s0002-9939-1957-0087047-7},
  file             = {:by-author/H/Holladay/1957_Holladay_656.pdf:PDF},
  keywords         = {Mathematics; Quatention Calculus; Quaternion Analysis; Quaternions},
  modificationdate = {2023-02-13T21:28:06},
  owner            = {saulius},
  publisher        = {American Mathematical Society ({AMS})},
}

@Article{Harkin2004,
  author           = {Anthony A. Harkin and Joseph B. Harkin},
  journal          = {Mathematics Magazine},
  title            = {Geometry of generalized complex numbers},
  year             = {2004},
  month            = {apr},
  number           = {2},
  pages            = {118--129},
  volume           = {77},
  creationdate     = {2023-02-13T21:27:29},
  doi              = {10.1080/0025570x.2004.11953236},
  file             = {:by-author/H/Harkin/2004_Harkin_118.pdf:PDF},
  keywords         = {Complex Numbers; Dual Numbers; Hypercomplex Numbers; Mathematics; Split-complex Numbers},
  modificationdate = {2023-02-13T21:29:07},
  owner            = {saulius},
  publisher        = {Informa {UK} Limited},
  url              = {https://people.rit.edu/harkin/research/articles/generalized_complex_numbers.pdf},
}

@Article{Shoemake1985,
  author           = {Ken Shoemake},
  journal          = {{ACM} {SIGGRAPH} Computer Graphics},
  title            = {Animating rotation with quaternion curves},
  year             = {1985},
  month            = {jul},
  number           = {3},
  pages            = {245--254},
  volume           = {19},
  creationdate     = {2023-02-13T21:37:14},
  doi              = {10.1145/325165.325242},
  file             = {:by-author/S/Shoemake/1985_Shoemake_245.pdf:PDF},
  keywords         = {Mathematics; Quaternions; Rotations},
  modificationdate = {2023-02-13T21:38:15},
  owner            = {saulius},
  publisher        = {Association for Computing Machinery ({ACM})},
  url              = {https://www.cs.cmu.edu/~kiranb/animation/p245-shoemake.pdf},
}

@Article{Mathov2020,
  author           = {Yael Mathov and Eden Levy and Ziv Katzir and Asaf Shabtai and Yuval Elovici},
  title            = {Not all datasets are born equal: on heterogeneous data and adversarial examples},
  year             = {2020},
  month            = oct,
  pages            = {1--12},
  abstract         = {Recent work on adversarial learning has focused mainly on neural networks and domains where those networks excel, such as computer vision, or audio processing. The data in these domains is typically homogeneous, whereas heterogeneous tabular datasets domains remain underexplored despite their prevalence. When searching for adversarial patterns within heterogeneous input spaces, an attacker must simultaneously preserve the complex domain-specific validity rules of the data, as well as the adversarial nature of the identified samples. As such, applying adversarial manipulations to heterogeneous datasets has proved to be a challenging task, and no generic attack method was suggested thus far. We, however, argue that machine learning models trained on heterogeneous tabular data are as susceptible to adversarial manipulations as those trained on continuous or homogeneous data such as images. To support our claim, we introduce a generic optimization framework for identifying adversarial perturbations in heterogeneous input spaces. We define distribution-aware constraints for preserving the consistency of the adversarial examples and incorporate them by embedding the heterogeneous input into a continuous latent space. Due to the nature of the underlying datasets We focus on $\ell_0$ perturbations, and demonstrate their applicability in real life. We demonstrate the effectiveness of our approach using three datasets from different content domains. Our results demonstrate that despite the constraints imposed on input validity in heterogeneous datasets, machine learning models trained using such data are still equally susceptible to adversarial examples.},
  archiveprefix    = {arXiv},
  creationdate     = {2023-02-15T19:59:48},
  eprint           = {2010.03180},
  file             = {:by-author/M/Mathov/2020_Mathov_1.pdf:PDF},
  keywords         = {Adversarial Networks; Artificial Neural Networks (ANN); CD; Data Quality; Machine Learning (ML); cs.CR; cs.LG},
  modificationdate = {2023-02-15T20:02:07},
  owner            = {saulius},
  primaryclass     = {cs.LG},
}

@Article{Landi2020,
  author           = {Annalisa Landi and Mark Thompson and Viviana Giannuzzi and Fedele Bonifazi and Ignasi Labastida and Luiz Olavo Bonino da Silva Santos and Marco Roos},
  journal          = {Data Intelligence},
  title            = {"{A}" of {FAIR} {\textendash} as open as possible, as closed as necessary},
  year             = {2020},
  month            = {jan},
  number           = {1-2},
  pages            = {47--55},
  volume           = {2},
  comment          = {'data should be "as open as possible and as closed as necessary"'.},
  creationdate     = {2023-02-16T16:15:41},
  doi              = {10.1162/dint_a_00027},
  file             = {:by-author/L/Landi/2020_Landi_47.pdf:PDF},
  keywords         = {EU Requirements; FAIR Data; H2020 Requirements; Open Data; Open Science; Science},
  modificationdate = {2023-02-16T16:18:21},
  owner            = {saulius},
  publisher        = {{MIT} Press - Journals},
}

@Article{Hippalgaonkar2023,
  author           = {Kedar Hippalgaonkar and Qianxiao Li and Xiaonan Wang and John W. Fisher and James Kirkpatrick and Tonio Buonassisi},
  journal          = {Nature Reviews Materials},
  title            = {Knowledge-integrated machine learning for materials: lessons from gameplaying and robotics},
  year             = {2023},
  month            = {jan},
  pages            = {1--20},
  creationdate     = {2023-02-17T18:23:38},
  doi              = {10.1038/s41578-022-00513-1},
  file             = {:by-author/H/Hippalgaonkar/2023_Hippalgaonkar_1.pdf:PDF;:by-author/H/Hippalgaonkar/2023_Hippalgaonkar_supplement.pdf:PDF},
  keywords         = {Computational Materials Science; Materials Science; OPTIMADE; Review},
  modificationdate = {2023-02-17T18:48:04},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media {LLC}},
}

@Article{Kirchenbauer2023,
  author           = {John Kirchenbauer and Jonas Geiping and Yuxin Wen and Jonathan Katz and Ian Miers and Tom Goldstein},
  title            = {A Watermark for Large Language Models},
  year             = {2023},
  month            = jan,
  pages            = {1--24},
  abstract         = {Potential harms of large language models can be mitigated by watermarking model output, i.e., embedding signals into generated text that are invisible to humans but algorithmically detectable from a short span of tokens. We propose a watermarking framework for proprietary language models. The watermark can be embedded with negligible impact on text quality, and can be detected using an efficient open-source algorithm without access to the language model API or parameters. The watermark works by selecting a randomized set of "green" tokens before a word is generated, and then softly promoting use of green tokens during sampling. We propose a statistical test for detecting the watermark with interpretable p-values, and derive an information-theoretic framework for analyzing the sensitivity of the watermark. We test the watermark using a multi-billion parameter model from the Open Pretrained Transformer (OPT) family, and discuss robustness and security.},
  archiveprefix    = {arXiv},
  creationdate     = {2023-02-18T14:35:01},
  eprint           = {2301.10226},
  file             = {:by-author/K/Kirchenbauer/2023_Kirchenbauer_1.pdf:PDF},
  keywords         = {Artificial Intelligence (AI); Artificial Neural Networks (ANN); Chat GPT; Language Models; Machine Learning (ML); cs.CL; cs.CR; cs.LG},
  modificationdate = {2023-02-18T14:37:27},
  owner            = {saulius},
  primaryclass     = {cs.LG},
  url              = {https://arxiv-export3.library.cornell.edu/abs/2301.10226},
}

@Article{Vaswani2017,
  author           = {Ashish Vaswani and Noam Shazeer and Niki Parmar and Jakob Uszkoreit and Llion Jones and Aidan N. Gomez and Lukasz Kaiser and Illia Polosukhin},
  title            = {Attention Is All You Need},
  year             = {2017},
  month            = jun,
  pages            = {1--15},
  abstract         = {The dominant sequence transduction models are based on complex recurrent or convolutional neural networks in an encoder-decoder configuration. The best performing models also connect the encoder and decoder through an attention mechanism. We propose a new simple network architecture, the Transformer, based solely on attention mechanisms, dispensing with recurrence and convolutions entirely. Experiments on two machine translation tasks show these models to be superior in quality while being more parallelizable and requiring significantly less time to train. Our model achieves 28.4 BLEU on the WMT 2014 English-to-German translation task, improving over the existing best results, including ensembles by over 2 BLEU. On the WMT 2014 English-to-French translation task, our model establishes a new single-model state-of-the-art BLEU score of 41.8 after training for 3.5 days on eight GPUs, a small fraction of the training costs of the best models from the literature. We show that the Transformer generalizes well to other tasks by applying it successfully to English constituency parsing both with large and limited training data.},
  archiveprefix    = {arXiv},
  comment          = {Cited in a YouTube video about ChatGTP (https://www.youtube.com/watch?v=kCc8FmEb1nY).},
  creationdate     = {2023-02-18T15:14:32},
  eprint           = {1706.03762},
  file             = {:by-author/V/Vaswani/2017_Vaswani_1.pdf:PDF},
  keywords         = {Artificail Intelligence; Artificial Neural Networks (ANN); ChatGPT; Graph Neural Networks (GNN); Machine Learning (ML); cs.CL; cs.LG},
  modificationdate = {2023-02-18T16:55:33},
  owner            = {saulius},
  primaryclass     = {cs.CL},
}

@Article{Ouyang2022,
  author           = {Long Ouyang and Jeff Wu and Xu Jiang and Diogo Almeida and Carroll L. Wainwright and Pamela Mishkin and Chong Zhang and Sandhini Agarwal and Katarina Slama and Alex Ray and John Schulman and Jacob Hilton and Fraser Kelton and Luke Miller and Maddie Simens and Amanda Askell and Peter Welinder and Paul Christiano and Jan Leike and Ryan Lowe},
  title            = {Training language models to follow instructions with human feedback},
  year             = {2022},
  month            = mar,
  pages            = {1--68},
  abstract         = {Making language models bigger does not inherently make them better at following a user's intent. For example, large language models can generate outputs that are untruthful, toxic, or simply not helpful to the user. In other words, these models are not aligned with their users. In this paper, we show an avenue for aligning language models with user intent on a wide range of tasks by fine-tuning with human feedback. Starting with a set of labeler-written prompts and prompts submitted through the OpenAI API, we collect a dataset of labeler demonstrations of the desired model behavior, which we use to fine-tune GPT-3 using supervised learning. We then collect a dataset of rankings of model outputs, which we use to further fine-tune this supervised model using reinforcement learning from human feedback. We call the resulting models InstructGPT. In human evaluations on our prompt distribution, outputs from the 1.3B parameter InstructGPT model are preferred to outputs from the 175B GPT-3, despite having 100x fewer parameters. Moreover, InstructGPT models show improvements in truthfulness and reductions in toxic output generation while having minimal performance regressions on public NLP datasets. Even though InstructGPT still makes simple mistakes, our results show that fine-tuning with human feedback is a promising direction for aligning language models with human intent.},
  archiveprefix    = {arXiv},
  comment          = {Cited in the Wikipedia article about the ChatGPT (https://en.wikipedia.org/wiki/ChatGPT). This paper (Ouyang2022) described the ChatGPT predecessor, InstructGPR.},
  creationdate     = {2023-02-18T16:56:45},
  eprint           = {2203.02155},
  file             = {:by-author/O/Ouyang/2022_Ouyang_1.pdf:PDF},
  keywords         = {Artificail Intelligence; Artificial Neural Networks (ANN); ChatGPT; Graph Neural Networks (GNN); Machine Learning (ML); cs.AI; cs.CL; cs.LG},
  modificationdate = {2023-02-18T17:00:31},
  owner            = {saulius},
  primaryclass     = {cs.CL},
}

@Article{Bergen2016,
  author           = {Laura A. H. van Bergen and Mercedes Alonso and Anna Palló and Lennart Nilsson and Frank De Proft and Joris Messens},
  journal          = {Scientific Reports},
  title            = {Revisiting sulfur {H}-bonds in proteins: The example of peroxiredoxin {AhpE}},
  year             = {2016},
  month            = {jul},
  number           = {1},
  pages            = {30369},
  volume           = {6},
  creationdate     = {2023-02-21T07:49:28},
  doi              = {10.1038/srep30369},
  file             = {:by-author/B/Bergen/2016_Bergen_30369.pdf:PDF},
  keywords         = {Bioinformatics; Hydrogen Bonds; Sulphur; Sulphur Hydrogen Bonds},
  modificationdate = {2023-02-21T07:51:15},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media {LLC}},
}

@Article{Choudhry2004,
  author           = {Ajai Choudhry},
  journal          = {Linear Algebra and its Applications},
  title            = {Extraction of nth roots of 2{\texttimes}2 matrices},
  year             = {2004},
  month            = {aug},
  pages            = {183--192},
  volume           = {387},
  creationdate     = {2023-02-27T09:50:32},
  doi              = {10.1016/j.laa.2004.02.010},
  file             = {:by-author/C/Choudhry/2004_Choudhry_183.pdf:PDF},
  keywords         = {Algorithms; Linear Algebra; Mathematics; Matrix Algebra; Matrix Equation; Nth Roots of 2×2 Matrices; Quaternions; Split-Quaternions; Square Roots},
  modificationdate = {2023-02-27T09:52:31},
  owner            = {saulius},
  publisher        = {Elsevier {BV}},
}

@Article{Sullivan1993,
  author           = {Donald Sullivan},
  journal          = {Mathematics Magazine},
  title            = {The Square Roots of 2 {\texttimes} 2 Matrices},
  year             = {1993},
  month            = {dec},
  number           = {5},
  pages            = {314--316},
  volume           = {66},
  comment          = {Cited by Choudhry2004.},
  creationdate     = {2023-02-27T09:57:13},
  doi              = {10.1080/0025570x.1993.11996153},
  file             = {:by-author/S/Sullivan/1993_Sullivan_314.pdf:PDF},
  keywords         = {Algorithms; Linear Algebra; Mathematics; Matrix Algebra; Matrix Equation; Quaternions; Split-Quaternions; Square Roots},
  modificationdate = {2023-02-27T09:58:48},
  owner            = {saulius},
  publisher        = {Informa {UK} Limited},
}

@Article{Hintze2016,
  author           = {Bradley J. Hintze and Steven M. Lewis and Jane S. Richardson and David C. Richardson},
  journal          = {Proteins: Structure, Function, and Bioinformatics},
  title            = {Molprobity{\textquotesingle}s ultimate rotamer-library distributions for model validation},
  year             = {2016},
  month            = {jun},
  number           = {9},
  pages            = {1177--1189},
  volume           = {84},
  creationdate     = {2023-02-27T12:45:18},
  doi              = {10.1002/prot.25039},
  file             = {:by-author/H/Hintze/2016_Hintze_1177.pdf:PDF},
  keywords         = {Bioinformatics; Data Quality; Model Quality; Model Validation; Molprobity; Rotamer Libraries; X-ray Crystallography},
  modificationdate = {2023-02-27T12:46:22},
  owner            = {saulius},
  publisher        = {Wiley},
}

@Presentation{Higham2009,
  author           = {Nick Higham},
  title            = {{C}ayley, {S}ylvester, and early matrix theory},
  year             = {2009},
  creationdate     = {2023-02-27T12:49:26},
  file             = {:by-author/H/Higham/2009_Higham_1.pdf:PDF},
  keywords         = {Early Matrix Notation; References; Review},
  modificationdate = {2023-02-27T12:50:57},
  owner            = {saulius},
  pages            = {1--28},
  url              = {https://www.maths.manchester.ac.uk/~higham/talks/talk09_cayley.pdf},
}

@Article{Cayley1858,
  author           = {Arthur Cayley},
  journal          = {Philosophical Transactions of the Royal Society of London},
  title            = {{II}. A memoir on the theory of matrices},
  year             = {1858},
  month            = {dec},
  pages            = {17--37},
  volume           = {148},
  comment          = {Cited in Choudhry2004.},
  creationdate     = {2023-02-27T12:55:18},
  doi              = {10.1098/rstl.1858.0002},
  file             = {:by-author/C/Cayley/1858_Cayley_17.pdf:PDF;:by-author/C/Cayley/1858_Cayley_17alt.pdf:PDF},
  keywords         = {Algorithms; Early Matrix Theory; Hisory of Mathematics; Historic Notation; Linear Algebra; Mathematics; Matrix Algebra; Notation; Square Roots},
  modificationdate = {2023-02-27T13:07:20},
  owner            = {saulius},
  publisher        = {The Royal Society},
}

@Article{Cayley1859,
  author           = {Arthur Cayley},
  journal          = {Proceedings of the Royal Society of London},
  title            = {{III}. A memoir on the theory of matrices},
  year             = {1859},
  month            = {dec},
  pages            = {100--101},
  volume           = {9},
  creationdate     = {2023-02-27T13:00:20},
  doi              = {10.1098/rspl.1857.0017},
  file             = {:by-author/1859_Cayley_100.pdf:PDF},
  keywords         = {Algorithms; Early Matrix Theory; Hisory of Mathematics; Historic Notation; Linear Algebra; Mathematics; Matrix Algebra; Notation; Square Roots},
  modificationdate = {2023-02-27T13:01:34},
  owner            = {saulius},
  publisher        = {The Royal Society},
}

@Article{RadmanLivaja2010,
  author           = {Marta Radman-Livaja and Oliver J. Rando},
  journal          = {Developmental Biology},
  title            = {Nucleosome positioning: How is it established, and why does it matter?},
  year             = {2010},
  month            = {mar},
  number           = {2},
  pages            = {258--266},
  volume           = {339},
  creationdate     = {2023-03-06T20:48:46},
  doi              = {10.1016/j.ydbio.2009.06.012},
  file             = {:by-author/R/Radman-Livaja/2010_Radman-Livaja_258.pdf:PDF},
  keywords         = {Bioinformatics; Chromatin; Molecular Biology; Nucleosomes},
  modificationdate = {2023-03-06T20:50:01},
  owner            = {saulius},
  publisher        = {Elsevier {BV}},
}

@Article{Yuan2008,
  author           = {Guo-Cheng Yuan and Jun S Liu},
  journal          = {{PLoS} Computational Biology},
  title            = {Genomic Sequence Is Highly Predictive of Local Nucleosome Depletion},
  year             = {2008},
  month            = {jan},
  number           = {1},
  pages            = {e13},
  volume           = {4},
  creationdate     = {2023-03-06T20:51:59},
  doi              = {10.1371/journal.pcbi.0040013},
  editor           = {Brad Bernstein},
  file             = {:by-author/Y/Yuan/2008_Yuan_13.pdf:PDF;:by-author/Y/Yuan/2008_Yuan_13 (1).pdf:PDF},
  keywords         = {Bioinformatics; Chromatin; Molecular Biology; Nucleosomes},
  modificationdate = {2023-03-06T20:52:58},
  owner            = {saulius},
  publisher        = {Public Library of Science ({PLoS})},
}

@TechReport{Beaver2010,
  author           = {Doug Beaver and Sanjeev Kumar and Harry C. Li and Jason Sobel and Peter Vajgel},
  institution      = {Facebook},
  title            = {Finding a needle in haystack: {F}acebook’s photo storage},
  year             = {2010},
  creationdate     = {2023-03-01T14:43:50},
  file             = {:by-author/B/Beaver/2010_Beaver_1.pdf:PDF},
  keywords         = {Distributed Storage; Object Storage},
  modificationdate = {2023-03-01T14:53:58},
  owner            = {saulius},
  pages            = {1--14},
  url              = {https://www.usenix.org/legacy/event/osdi10/tech/full_papers/Beaver.pdf},
}

@Article{Dronskowski1993,
  author           = {Richard Dronskowski and Peter E. Bloechl},
  journal          = {The Journal of Physical Chemistry},
  title            = {Crystal orbital {H}amilton populations ({COHP}): energy-resolved visualization of chemical bonding in solids based on density-functional calculations},
  year             = {1993},
  month            = {aug},
  number           = {33},
  pages            = {8617--8624},
  volume           = {97},
  comment          = {Suggested by Andrius. Found via http://www.cohp.de/.},
  creationdate     = {2023-03-10T11:15:40},
  doi              = {10.1021/j100135a014},
  file             = {:by-author/D/Dronskowski/1993_Dronskowski_8617.pdf:PDF},
  keywords         = {Quantum Mechanics (QM); Valence Bond Theory},
  modificationdate = {2023-03-10T13:25:06},
  owner            = {saulius},
  publisher        = {American Chemical Society ({ACS})},
}

@Article{Deringer2011,
  author           = {Volker L. Deringer and Andrei L. Tchougr{\'{e}}eff and Richard Dronskowski},
  journal          = {The Journal of Physical Chemistry A},
  title            = {{C}rystal {O}rbital {H}amilton {P}opulation ({COHP}) analysis as projected from plane-wave basis sets},
  year             = {2011},
  month            = {may},
  number           = {21},
  pages            = {5461--5466},
  volume           = {115},
  comment          = {Suggested by Andrius. Found via http://www.cohp.de/.},
  creationdate     = {2023-03-10T11:22:42},
  doi              = {10.1021/jp202489s},
  file             = {:by-author/D/Deringer/2011_Deringer_5461.pdf:PDF},
  keywords         = {Quantum Mechanics (QM); Valence Bond Theory},
  modificationdate = {2023-03-10T13:24:57},
  owner            = {saulius},
  publisher        = {American Chemical Society ({ACS})},
}

@Article{Maintz2013,
  author           = {Stefan Maintz and Volker L. Deringer and Andrei L. Tchougr{\'{e}}eff and Richard Dronskowski},
  journal          = {Journal of Computational Chemistry},
  title            = {Analytic projection from plane-wave and {PAW} wavefunctions and application to chemical-bonding analysis in solids},
  year             = {2013},
  month            = {sep},
  number           = {29},
  pages            = {2557--2567},
  volume           = {34},
  comment          = {Suggested by Andrius. Found via http://www.cohp.de/.},
  creationdate     = {2023-03-10T13:24:17},
  doi              = {10.1002/jcc.23424},
  file             = {:by-author/M/Maintz/2013_Maintz_2557.pdf:PDF},
  keywords         = {Quantum Mechanics (QM); Valence Bond Theory},
  modificationdate = {2023-03-10T13:41:01},
  owner            = {saulius},
  publisher        = {Wiley},
}

@Article{Maintz2016,
  author           = {Stefan Maintz and Volker L. Deringer and Andrei L. Tchougr{\'{e}}eff and Richard Dronskowski},
  journal          = {Journal of Computational Chemistry},
  title            = {{LOBSTER}: A tool to extract chemical bonding from plane-wave based {DFT}},
  year             = {2016},
  month            = {feb},
  number           = {11},
  pages            = {1030--1035},
  volume           = {37},
  comment          = {Suggested by Andrius. Found via http://www.cohp.de/.},
  creationdate     = {2023-03-10T13:43:02},
  doi              = {10.1002/jcc.24300},
  file             = {:by-author/M/Maintz/2016_Maintz_1030.pdf:PDF},
  keywords         = {Quantum Mechanics (QM); Valence Bond Theory},
  modificationdate = {2023-03-10T13:43:49},
  owner            = {saulius},
  publisher        = {Wiley},
  url              = {http://schmeling.ac.rwth-aachen.de/cohp/download/Maintz_et_al-2016-Journal_of_Computational_Chemistry.pdf},
}

@Article{Maintz2016a,
  author           = {S. Maintz and M. Esser and R. Dronskowski},
  journal          = {Acta Physica Polonica B},
  title            = {Efficient Rotation of Local Basis Functions Using Real Spherical Harmonics},
  year             = {2016},
  number           = {4},
  pages            = {1165},
  volume           = {47},
  comment          = {Suggested by Andrius. Found via http://www.cohp.de/.},
  creationdate     = {2023-03-10T13:44:44},
  doi              = {10.5506/aphyspolb.47.1165},
  file             = {:by-author/M/Maintz/2016_Maintz_1165.pdf:PDF},
  keywords         = {Quantum Mechanics (QM); Valence Bond Theory},
  modificationdate = {2023-03-10T13:45:11},
  owner            = {saulius},
  publisher        = {Jagiellonian University},
}

@Article{Nelson2020,
  author           = {Ryky Nelson and Christina Ertural and Janine George and Volker L. Deringer and Geoffroy Hautier and Richard Dronskowski},
  journal          = {Journal of Computational Chemistry},
  title            = {{LOBSTER}: Local orbital projections, atomic charges, and chemical-bonding analysis from projector-augmented-wave-based density-functional theory},
  year             = {2020},
  month            = {jun},
  number           = {21},
  pages            = {1931--1940},
  volume           = {41},
  comment          = {Suggested by Andrius. Found via http://www.cohp.de/.},
  creationdate     = {2023-03-10T13:46:07},
  doi              = {10.1002/jcc.26353},
  file             = {:by-author/N/Nelson/2020_Nelson_1931.pdf:PDF},
  keywords         = {Quantum Mechanics (QM); Valence Bond Theory},
  modificationdate = {2023-03-10T13:47:43},
  owner            = {saulius},
  publisher        = {Wiley},
}

@Article{Abud2019,
  author           = {Adam Abed Abud},
  title            = {Performance evaluation of distributed file systems forthe phase-{II} upgrade of the {ATLAS} experiment at {CERN}},
  year             = {2019},
  creationdate     = {2023-03-15T12:05:56+0200},
  file             = {:by-author/A/Abud/2019_Abud.pdf:PDF;:https\://iopscience.iop.org/article/10.1088/1742-6596/1525/1/012028/pdf:},
  keywords         = {Distributed Filesystems},
  modificationdate = {2023-04-23T10:08:31},
  owner            = {adam},
}

@InCollection{Olive2017,
  author           = {Antoni Olivé},
  booktitle        = {Conceptual Modeling},
  publisher        = {Springer International Publishing},
  title            = {The {U}niversal {O}ntology: a vision for conceptual modeling and the semantic web ({I}nvited paper)},
  year             = {2017},
  pages            = {1--17},
  creationdate     = {2023-03-16T10:18:23},
  doi              = {10.1007/978-3-319-69904-2_1},
  file             = {:by-author/O/Olivé/2017_Olivé_1.pdf:PDF},
  keywords         = {Computer Science (CS); Conceptual Modelling; Logics; Ontologies},
  modificationdate = {2023-03-16T10:36:58},
  owner            = {saulius},
}

@PhdThesis{Horridge2011,
  author           = {Matthew Horridge},
  school           = {The University of Manchester},
  title            = {Justification based explanation in ontologies},
  year             = {2011},
  comment          = {Prizes: Best Paper Award.
Cites: Description Logics.},
  creationdate     = {2023-03-16T10:31:27},
  eprint           = {https://research.manchester.ac.uk/en/studentTheses/justification-based-explanation-in-ontologies},
  file             = {:by-author/H/Horridge/2011_Horridge_1.pdf:PDF},
  keywords         = {Computer Science (CS); Logics; Ontologies},
  modificationdate = {2023-03-16T10:36:54},
  owner            = {saulius},
  pages            = {1--304},
  url              = {https://pure.manchester.ac.uk/ws/portalfiles/portal/54511395/FULL_TEXT.PDF},
}

@Article{Bergstroem2003,
  author           = {Christel A. S. Bergström and Ulf Norinder and Kristina Luthman and Per Artursson},
  journal          = {Journal of Chemical Information and Computer Sciences},
  title            = {Molecular Descriptors Influencing Melting Point and Their Role in Classification of Solid Drugs},
  year             = {2003},
  month            = {jun},
  number           = {4},
  pages            = {1177--1185},
  volume           = {43},
  creationdate     = {2023-03-17T14:55:02},
  doi              = {10.1021/ci020280x},
  file             = {:by-author/B/Bergström/2003_Bergström_1177.pdf:PDF},
  keywords         = {Melting Point Prediction; Molecular Descriptors; Principal Component Analysis},
  modificationdate = {2023-03-17T15:20:58},
  owner            = {saulius},
  publisher        = {American Chemical Society ({ACS})},
}

@Article{Mi2021,
  author           = {Weiming Mi and Huijun Chen and Donghua (Alan) Zhu and Tao Zhang and Feng Qian},
  journal          = {Chemical Communications},
  title            = {Melting point prediction of organic molecules by deciphering the chemical structure into a natural language},
  year             = {2021},
  number           = {21},
  pages            = {2633--2636},
  volume           = {57},
  creationdate     = {2023-03-17T15:20:41},
  doi              = {10.1039/d0cc07384a},
  file             = {:by-author/M/Mi/2021_Mi_2633.pdf:PDF;:by-author/M/Mi/2021_Mi_2633suppl.pdf:PDF},
  keywords         = {Artificial Neural Networks (ANN); Machine Learning (ML); Melting Point Prediction; Molecular Descriptors; Natural Language Processing},
  modificationdate = {2023-03-17T15:28:36},
  owner            = {saulius},
  publisher        = {Royal Society of Chemistry ({RSC})},
}

@InProceedings{Kalash2018,
  author           = {Mahmoud Kalash and Mrigank Rochan and Noman Mohammed and Neil D. B. Bruce and Yang Wang and Farkhund Iqbal},
  booktitle        = {2018 9th {IFIP} International Conference on New Technologies, Mobility and Security ({NTMS})},
  title            = {Malware Classification with Deep Convolutional Neural Networks},
  year             = {2018},
  month            = {feb},
  pages            = {1--5},
  publisher        = {{IEEE}},
  creationdate     = {2023-03-17T15:31:21},
  doi              = {10.1109/ntms.2018.8328749},
  file             = {:by-author/K/Kalash/2018_Kalash_1.pdf:PDF},
  keywords         = {Artificial Neural Networks (ANN); Code Analysis; Convolutional Neural Networks (CNN); Machine Learning (ML); Malware Detection},
  modificationdate = {2023-03-17T15:34:06},
  owner            = {saulius},
}

@Article{Hofmann2023,
  author           = {Detlef Walter Maria Hofmann and Liudmila Nikolaevna Kuleshova},
  journal          = {Acta Crystallographica Section A Foundations and Advances},
  title            = {A general force field by machine learning on experimental crystal structures. Calculations of intermolecular Gibbs energy with $\less$i$\greater${FlexCryst}$\less$/i$\greater$},
  year             = {2023},
  month            = {feb},
  number           = {2},
  pages            = {132--144},
  volume           = {79},
  creationdate     = {2023-03-17T18:18:55},
  doi              = {10.1107/s2053273323000268},
  file             = {:by-author/H/Hofmann/2023_Hofmann_132.pdf:PDF},
  keywords         = {Force Fields; Material Science; Quantum Mechanics (QM)},
  modificationdate = {2023-03-17T18:24:03},
  owner            = {saulius},
  publisher        = {International Union of Crystallography ({IUCr})},
}

@Article{Massey1983,
  author           = {W. S. Massey},
  journal          = {The American Mathematical Monthly},
  title            = {Cross products of vectors in higher dimensional {E}uclidean spaces},
  year             = {1983},
  month            = {dec},
  number           = {10},
  pages            = {697--701},
  volume           = {90},
  creationdate     = {2023-03-21T13:32:15},
  doi              = {10.2307/2323537},
  file             = {:by-author/M/Massey/1983_Massey_697.pdf:PDF},
  keywords         = {Cross Product; Higher Dimensional Spaces; Vector Algebra},
  modificationdate = {2023-03-23T10:51:16},
  owner            = {saulius},
  publisher        = {{JSTOR}},
}

@Article{Lee1997,
  author           = {DongGill Lee and JoonKyung Lee and Wan Choi and Byung Sun Lee and Chimoon Han},
  journal          = {ETRI Journal},
  title            = {A new integrated software development environment based on {SDL}, {MSC}, and {CHILL} for large-scale switching systems},
  year             = {1997},
  pages            = {265--286},
  creationdate     = {2023-03-25T18:48:06},
  doi              = {10.4218/etrij.97.0197.0044},
  file             = {:by-author/L/Lee/1997_Lee_265.pdf:PDF},
  keywords         = {CHILL; Computer Languages; Computer Science (CS); Programming Languages},
  modificationdate = {2023-03-25T18:52:16},
  owner            = {saulius},
  url              = {https://psc.informatik.uni-jena.de/languages/chill/1997-Lee_et_al-1997-ETRI_Journal.pdf},
}

@Article{Li2022,
  author           = {Li, Qiang and Ma, Shiyong and Zhang, Xuelu and Zhai, Zhaoyu and Zhou, Lu and Tao, Haodong and Wang, Yachen and Pan, Jianbo},
  journal          = {Database : the journal of biological databases and curation},
  title            = {{DDPD} 1.0: a manually curated and standardized database of digital properties of approved drugs for drug-likeness evaluation and drug development},
  year             = {2022},
  issn             = {1758-0463},
  month            = feb,
  pages            = {baab083},
  volume           = {2022},
  abstract         = {Drug-likeness is a vital consideration when selecting compounds in the early stage of drug discovery. A series of drug-like properties are needed to predict the drug-likeness of a given compound and provide useful guidelines to increase the likelihood of converting lead compounds into drugs. Experimental physicochemical properties, pharmacokinetic/toxicokinetic properties and maximum dosages of approved small-molecule drugs from multiple text-based unstructured data resources have been manually assembled, curated, further digitized and processed into structured data, which are deposited in the Database of Digital Properties of approved Drugs (DDPD). DDPD 1.0 contains 30 212 drug property entries, including 2250 approved drugs and 32 properties, in a standardized value/unit format. Moreover, two analysis tools are provided to examine the drug-likeness features of given molecules based on the collected property data of approved drugs. Additionally, three case studies are presented to demonstrate how users can utilize the database. We believe that this database will be a valuable resource for the drug discovery and development field. Database URL:  http://www.inbirg.com/ddpd.},
  chemicals        = {Phenylenediamines, N,N'-diphenyl-4-phenylenediamine},
  citation-subset  = {IM},
  completed        = {2022-04-29},
  country          = {England},
  creationdate     = {2023-03-23T10:52:04},
  doi              = {10.1093/database/baab083},
  file             = {:by-author/L/Li/2022_Li_83.pdf:PDF},
  issn-linking     = {1758-0463},
  keywords         = {Data Management; Databases, Factual; Drug Design; Drug Development; Drug Discovery; Phenylenediamines; Scientific Databases},
  modificationdate = {2023-03-23T10:53:45},
  nlm-id           = {101517697},
  owner            = {saulius},
  pii              = {baab083},
  pmc              = {PMC9245338},
  pmid             = {35139189},
  pubmodel         = {Print},
  pubstate         = {ppublish},
  revised          = {2022-07-16},
}

@Article{Smith2023,
  author           = {David Smith and Joseph Samuel Myers and Craig S. Kaplan and Chaim Goodman-Strauss},
  journal          = {arXiv},
  title            = {An aperiodic monotile},
  year             = {2023},
  month            = mar,
  pages            = {1--89},
  abstract         = {A longstanding open problem asks for an aperiodic monotile, also known as an "einstein": a shape that admits tilings of the plane, but never periodic tilings. We answer this problem for topological disk tiles by exhibiting a continuum of combinatorially equivalent aperiodic polygons. We first show that a representative example, the "hat" polykite, can form clusters called "metatiles", for which substitution rules can be defined. Because the metatiles admit tilings of the plane, so too does the hat. We then prove that generic members of our continuum of polygons are aperiodic, through a new kind of geometric incommensurability argument. Separately, we give a combinatorial, computer-assisted proof that the hat must form hierarchical -- and hence aperiodic -- tilings.},
  archiveprefix    = {arXiv},
  creationdate     = {2023-03-30T17:55:52},
  doi              = {10.48550/arXiv.2303.10798},
  eprint           = {2303.10798},
  file             = {:by-author/S/Smith/2023_Smith_1.pdf:PDF},
  keywords         = {05B45, 52C20 (Primary) 05B50 (Secondary); Aperiodic Tilings; F.2.2; G.2.1; Quasicrystals; cs.DM; math.CO; math.MG},
  modificationdate = {2023-03-30T17:59:05},
  owner            = {saulius},
  primaryclass     = {math.CO},
}

@Article{Beltagy2019,
  author           = {Iz Beltagy and Kyle Lo and Arman Cohan},
  journal          = {EMNLP 2019},
  title            = {{SciBERT}: A pretrained language model for scientific text},
  year             = {2019},
  month            = mar,
  pages            = {1--6},
  abstract         = {Obtaining large-scale annotated data for NLP tasks in the scientific domain is challenging and expensive. We release SciBERT, a pretrained language model based on BERT (Devlin et al., 2018) to address the lack of high-quality, large-scale labeled scientific data. SciBERT leverages unsupervised pretraining on a large multi-domain corpus of scientific publications to improve performance on downstream scientific NLP tasks. We evaluate on a suite of tasks including sequence tagging, sentence classification and dependency parsing, with datasets from a variety of scientific domains. We demonstrate statistically significant improvements over BERT and achieve new state-of-the-art results on several of these tasks. The code and pretrained models are available at https://github.com/allenai/scibert/.},
  archiveprefix    = {arXiv},
  creationdate     = {2023-03-31T16:06:00},
  doi              = {10.48550/arXiv.1903.10676},
  eprint           = {1903.10676},
  file             = {:by-author/B/Beltagy/2019_Beltagy_1.pdf:PDF},
  keywords         = {Artificial Intelligence (AI); Bert; Computer Science (CS); Language Model; Machine Learning (ML); SciBert; cs.CL},
  modificationdate = {2023-03-31T16:14:53},
  owner            = {saulius},
  primaryclass     = {cs.CL},
}

@Article{Catlow2023,
  author           = {Catlow, C. Richard A.},
  journal          = {IUCrJ},
  title            = {Crystal structure prediction: achievements and opportunities.},
  year             = {2023},
  issn             = {2052-2525},
  month            = mar,
  pages            = {143--144},
  volume           = {10},
  abstract         = {This editorial gives gives an update on the current status of crystal structure prediction and its opportunities and challenges.},
  citation-subset  = {IM},
  completed        = {2023-03-03},
  country          = {England},
  creationdate     = {2023-03-31T16:54:58},
  doi              = {10.1107/S2052252523001835},
  file             = {:by-author/C/Catlow/2023_Catlow_143.pdf:PDF},
  issn-linking     = {2052-2525},
  issue            = {Pt 2},
  keywords         = {Computational Modelling of Crystal Structures; Crystal Structure Prediction (CSP); Editorial; Machine Learning (ML); Nano-particle Structures; Structural Science},
  modificationdate = {2023-04-24T12:35:15},
  nlm-id           = {101623101},
  owner            = {saulius},
  pii              = {S2052252523001835},
  pmc              = {PMC9980386},
  pmid             = {36862486},
  pubmodel         = {Electronic},
  pubstate         = {epublish},
  revised          = {2023-03-04},
}

@Presentation{Eon2017,
  author           = {Jean-Guillaume Eon},
  title            = {Topology of crystal structures: applications of graph theory (the vector method)},
  year             = {2017},
  creationdate     = {2023-03-31T17:04:10},
  file             = {:by-author/E/Eon/2017_Eon_1.pdf:PDF},
  modificationdate = {2023-03-31T17:12:49},
  owner            = {saulius},
  pages            = {1--184},
  url              = {http://cloud.crm2.univ-lorraine.fr/pdf/Manila2017/Eon_Topology-of-crystal-structures.pdf},
}

@Article{Helliwell2022,
  author           = {Helliwell, John R.},
  journal          = {Acta crystallographica. Section F, Structural biology communications},
  title            = {Relating protein crystal structure to ligand-binding thermodynamics},
  year             = {2022},
  issn             = {2053-230X},
  month            = dec,
  pages            = {403--407},
  volume           = {78},
  abstract         = {An important interface between biophysical chemistry and biological crystal structures involves whether it is possible to relate experimental calorimetry measurements of protein ligand binding to 3D structures. This has proved to be challenging. The probes of the structure of matter, namely X-rays, neutrons and electrons, have challenges of one type or another in their use. This article focuses on saccharide binding to lectins as a theme, yet after 25 years or so it is still a work in progress to connect 3D structure to binding energies. Whilst this study involved one type of protein (lectins) and one class of ligand (monosaccharides), i.e. it was specific, it was of general importance, as measured for instance by its wide impact. The impetus for writing this update now, as a Scientific Comment, is that a breakthrough in neutron crystal structure determinations of saccharide-bound lectins has been achieved. It is suggested here that this new research from neutron protein crystallography could improve, i.e. reduce, the errors in the estimated binding energies.},
  chemicals        = {Ligands, Lectins},
  citation-subset  = {IM},
  completed        = {2022-12-05},
  country          = {United States},
  creationdate     = {2023-03-31T20:47:55},
  doi              = {10.1107/S2053230X22011244},
  file             = {:by-author/H/Helliwell/2022_Helliwell_403.pdf:PDF},
  issn-linking     = {2053-230X},
  issue            = {Pt 12},
  keywords         = {Calorimetry; Crystallography, X-Ray; Lectins; Ligands; Protein Ligand Binding; Saccharides; Thermodynamics; Thermodynamics and Structure},
  modificationdate = {2024-08-28T11:43:45},
  nlm-id           = {101620319},
  owner            = {saulius},
  pii              = {S2053230X22011244},
  pmc              = {PMC9716570},
  pmid             = {36458619},
  pubmodel         = {Print-Electronic},
  pubstate         = {ppublish},
  revised          = {2022-12-13},
}

@Article{Woodley2020,
  author           = {Scott M. Woodley and Graeme M. Day and R. Catlow},
  journal          = {Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences},
  title            = {Structure prediction of crystals, surfaces and nanoparticles},
  year             = {2020},
  month            = {oct},
  number           = {2186},
  pages            = {20190600},
  volume           = {378},
  creationdate     = {2023-03-31T21:18:06},
  doi              = {10.1098/rsta.2019.0600},
  file             = {:by-author/W/Woodley/2020_Woodley_20190600.pdf:PDF},
  keywords         = {Crystal Structure Prediction (CSP)},
  modificationdate = {2023-03-31T21:19:00},
  owner            = {saulius},
  publisher        = {The Royal Society},
}

@InCollection{Amrollahi2022,
  author           = {Daneshvar Amrollahi and Ezio Bartocci and George Kenison and Laura Kovács and Marcel Moosbrugger and Miroslav Stankovič},
  booktitle        = {Static Analysis},
  publisher        = {Springer Nature Switzerland},
  title            = {Solving invariant generation for unsolvable loops},
  year             = {2022},
  pages            = {19--43},
  comment          = {Cited in Kovacs2023.
Discussed in the "Formalis" seminar on 2023-04-06.},
  creationdate     = {2023-04-06T16:30:52},
  doi              = {10.1007/978-3-031-22308-2_3},
  file             = {:by-author/A/Amrollahi/2022_Amrollahi_19.pdf:PDF},
  keywords         = {Computer Science (CS); Correctness Proofs; Formal Methods; Symbolic Computations},
  modificationdate = {2023-04-10T15:59:14},
  owner            = {saulius},
}

@Article{Leonaviciene2022,
  author           = {Greta Leonaviciene and Linas Mazutis},
  journal          = {Nucleic Acids Research},
  title            = {{RNA} cytometry of single-cells using semi-permeable microcapsules},
  year             = {2022},
  month            = {oct},
  number           = {1},
  pages            = {e2--e2},
  volume           = {51},
  creationdate     = {2023-04-03T17:33:59},
  doi              = {10.1093/nar/gkac918},
  file             = {:by-author/L/Leonaviciene/2022_Leonaviciene_2.pdf:PDF},
  keywords         = {Microfluidics; Single Cell Analysis},
  modificationdate = {2023-04-03T17:35:46},
  owner            = {saulius},
  publisher        = {Oxford University Press ({OUP})},
}

@Manuscript{Wellens2015,
  author           = {Jake Wellens},
  title            = {A friendly introduction to group theory},
  year             = {2015},
  keywords         = {Group Theory; Introduction},
  url              = {https://math.mit.edu/~jwellens/Group Theory Forum.pdf},
  creationdate     = {2023-04-03T17:38:13},
  file             = {:by-author/W/Wellens/2015_Wellens_1.pdf:PDF},
  modificationdate = {2023-04-03T17:41:47},
  owner            = {saulius},
  pages            = {1--16},
}

@Manuscript{Goluguri2019,
  author           = {Ishita Goluguri and Christina Li},
  title            = {Applications of group actions},
  year             = {2019},
  keywords         = {Group Theory; Introduction},
  url              = {https://math.mit.edu/research/highschool/primes/circle/documents/2019/Goluguri_Li_2019.pdf},
  creationdate     = {2023-04-03T17:45:34},
  file             = {:by-author/G/Goluguri/2019_Goluguri_1.pdf:PDF},
  modificationdate = {2023-04-03T17:47:32},
  owner            = {saulius},
  pages            = {1--10},
}

@Article{Tetko2016,
  author           = {Igor V. Tetko and Daniel M. Lowe and Antony J. Williams},
  journal          = {Journal of Cheminformatics},
  title            = {The development of models to predict melting and pyrolysis point data associated with several hundred thousand compounds mined from {PATENTS}},
  year             = {2016},
  month            = {jan},
  number           = {1},
  pages            = {2},
  volume           = {8},
  creationdate     = {2023-04-07T15:03:22},
  doi              = {10.1186/s13321-016-0113-y},
  file             = {:by-author/T/Tetko/2016_Tetko_2.pdf:PDF},
  keywords         = {Chemoinformatics; Machine Learning (ML); Melting Points; Prediction},
  modificationdate = {2023-04-08T15:45:26},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media {LLC}},
}

@InCollection{Smeraldi2010,
  author           = {Fabrizio Smeraldi and Michael Defoin-Platel and Mansoor Saqi},
  booktitle        = {Lecture Notes in Computer Science},
  publisher        = {Springer Berlin Heidelberg},
  title            = {Handling Missing Features with Boosting Algorithms for Protein{\textendash}Protein Interaction Prediction},
  year             = {2010},
  pages            = {132--147},
  comment          = {Cited by Izonin2019.},
  creationdate     = {2023-04-08T15:46:02},
  doi              = {10.1007/978-3-642-15120-0_11},
  file             = {:by-author/S/Smeraldi/2010_Smeraldi_132.pdf:PDF},
  keywords         = {AdaBoost; Bioinformatics; Machine Learning (ML); Missing Data Problem; Protein-protein Interactions},
  modificationdate = {2023-04-08T15:54:09},
  owner            = {saulius},
  url              = {http://www.eecs.qmul.ac.uk/~fabri/Publications/Handling_Missing_Features_with_Boosting_Algorithms_for_Protein-Protein_interaction_prediction/dils2010.pdf},
}

@Article{Izonin2019,
  author           = {Ivan Izonin and Natalia Kryvinska and Roman Tkachenko and Khrystyna Zub},
  journal          = {Procedia Computer Science},
  title            = {An Approach towards Missing Data Recovery within {IoT} Smart System},
  year             = {2019},
  pages            = {11--18},
  volume           = {155},
  abstract         = {Today, the fast development of the hardware for the Internet of things systems creates conditions for the development of loT based Services of various purposes. The imperfect systems of collecting, aggregation and the transmission of large volumes of various types of data, fixed by sensors of IoT devices, as well as possible failures of the latter, cause the occurrence of missing data problems. The paper proposes a regression approach to solving the task of missed data recovery. The authors have developed a composition of the method of the missing data recovery for loT systems based on the use of the Ito decomposition and the AdaBoost algorithm. We transform each data vectors by using Ito decomposition, and searching the coefficients of this decomposition scheme using AdaBoost algorithm. Increasing the dimensionality of the input space due to the use of the second-degree Ito decomposition scheme, as well as its high approximation properties, allowed to increase the accuracy of filling the missed values by the AdaBoost regressor at more than 6% (MAPE). It has been established that the developed method provides the highest accuracy of filling missed data based on all other indicators (MAE, RMSE, SMAPE) among the considered regression methods.},
  comment          = {Cited by the manuscript "machines-2343603-peer-review-v1.pdf" (MD5: ea221dff8ac4e22501f589886bd55927) which I receved for a review.},
  creationdate     = {2023-04-08T15:50:27},
  doi              = {10.1016/j.procs.2019.08.006},
  file             = {:by-author/I/Izonin/2019_Izonin_11.pdf:PDF},
  keywords         = {Internet of Things; IoT; Machine Learning (ML); Missing Data Problem; Regression},
  modificationdate = {2023-04-08T15:59:51},
  owner            = {saulius},
  publisher        = {Elsevier {BV}},
}

@Article{Perera2016,
  author           = {Lokukaluge P. Perera and Brage Mo},
  journal          = {Ocean Engineering},
  title            = {Data analysis on marine engine operating regions in relation to ship navigation},
  year             = {2016},
  month            = {dec},
  pages            = {163--172},
  volume           = {128},
  abstract         = {Data analysis techniques to understand marine engine operating regions as a part of the ship energy efficiency management plan (SEEMP) are proposed in this study. The SEEMP enforces to improve ship energy efficiency under various emission control measures by collecting and analyzing vessel performance and navigation data. The required data analysis techniques to analyze such data sets are presented under the engine-propeller combinator diagram (i.e. one propeller shaft with a direct drive main engine). These techniques consist of implementing Gaussian Mixture Models (GMMs) with an Expectation Maximization (EM) algorithm to classify and Principal Component Analysis (PCA) to analyze frequent operating regions of a marine engine in a selected vessel. Three marine engine operating regions are noted under the combinator diagram and GMMs capture the shape, orientation and boundaries of those operating regions. Then, PCA is used to understand the structure of each GMM with respect to ship performance and navigation parameters. Hence, this approach can be used in the SEEMP to monitor ship navigation with respect to marine engine operating regions.},
  comment          = {Cited by the manuscript "machines-2343603-peer-review-v1.pdf" (MD5: ea221dff8ac4e22501f589886bd55927) which I receved for a review. Contains short elementary explanation of the Expectation Maximisation algorithm.},
  creationdate     = {2023-04-08T16:10:59},
  doi              = {10.1016/j.oceaneng.2016.10.029},
  file             = {:by-author/P/Perera/2016_Perera_163.pdf:PDF},
  keywords         = {Expectation Maximisation; Gaussian Mixture Models; Marine Engines; PCA; Pricipal Component Analysis},
  modificationdate = {2023-04-08T16:26:09},
  owner            = {saulius},
  publisher        = {Elsevier {BV}},
}

@Article{Moon1996,
  author           = {T.K. Moon},
  journal          = {{IEEE} Signal Processing Magazine},
  title            = {The expectation-maximization algorithm},
  year             = {1996},
  number           = {6},
  pages            = {47--60},
  volume           = {13},
  abstract         = {A common task in signal processing is the estimation of the parameters of a probability distribution function. Perhaps the most frequently encountered estimation problem is the estimation of the mean of a signal in noise. In many parameter estimation problems the situation is more complicated because direct access to the data necessary to estimate the parameters is impossible, or some of the data are missing. Such difficulties arise when an outcome is a result of an accumulation of simpler outcomes, or when outcomes are clumped together, for example, in a binning or histogram operation. There may also be data dropouts or clustering in such a way that the number of underlying data points is unknown (censoring and/or truncation). The EM (expectation-maximization) algorithm is ideally suited to problems of this sort, in that it produces maximum-likelihood (ML) estimates of parameters when there is a many-to-one mapping from an underlying distribution to the distribution governing the observation. The EM algorithm is presented at a level suitable for signal processing practitioners who have had some exposure to estimation theory.},
  comment          = {The discussion of the EM algorithm for signal processing practitioners. Cited in Perera2016. Cites Dempster1977.},
  creationdate     = {2023-04-08T16:25:28},
  doi              = {10.1109/79.543975},
  file             = {:by-author/M/Moon/1996_Moon_47.pdf:PDF},
  keywords         = {Expectation Maximisation; Signal Processing},
  modificationdate = {2023-04-08T16:30:25},
  owner            = {saulius},
  publisher        = {Institute of Electrical and Electronics Engineers ({IEEE})},
}

@InCollection{Kovacs2023,
  author           = {Laura Kov{\'{a}}cs},
  booktitle        = {Formal Methods},
  publisher        = {Springer International Publishing},
  title            = {Symbolic Computation in~Automated Program Reasoning},
  year             = {2023},
  pages            = {3--9},
  comment          = {Discussed in the "Formalis" seminar on 2023-04-06.},
  creationdate     = {2023-04-10T15:58:10},
  doi              = {10.1007/978-3-031-27481-7_1},
  file             = {:by-author/K/Kovács/2023_Kovács_3.pdf:PDF},
  keywords         = {Computer Science (CS); Correctness Proofs; Formal Methods; Symbolic Computations},
  modificationdate = {2023-04-10T16:02:51},
  owner            = {saulius},
}

@InCollection{Brucker2023,
  author           = {Achim D. Brucker and Amy Stell},
  booktitle        = {Formal Methods},
  publisher        = {Springer International Publishing},
  title            = {Verifying feedforward neural networks for classification in {I}sabelle/{HOL}},
  year             = {2023},
  pages            = {427--444},
  comment          = {For the discussion in the 2023-04-20 Formalis seminar.},
  creationdate     = {2023-04-10T16:35:08},
  doi              = {10.1007/978-3-031-27481-7_24},
  file             = {:by-author/B/Brucker/2023_Brucker_427.pdf:PDF},
  keywords         = {Artificial Intelligence (AI); Artificial Neural Networks (ANN); Computer Science (CS); Correctness Proofs; Formal Methods; Formal Verification; Machine Learning (ML)},
  modificationdate = {2023-04-13T07:59:45},
  owner            = {saulius},
}

@Manuscript{Imler2012,
  author           = {Fabian Imler},
  title            = {{RIPEMD}-160 - verification of a {SPARK}/{ADA} implementation},
  year             = {2012},
  keywords         = {Ada; Formal Methods; HOL; Isabelle; Program Correctness Proofs; Program Verification; SPARK},
  url              = {https://www.isa-afp.org/browser_info/Isabelle2012/HOL/HOL-Word/RIPEMD-160-SPARK/document.pdf},
  creationdate     = {2023-04-11T21:48:21},
  file             = {:by-author/I/Imler/2012_Imler_1.pdf:PDF},
  modificationdate = {2023-04-11T21:50:35},
  owner            = {saulius},
  pages            = {1--46},
}

@Manuscript{Haftmann2022,
  author           = {Florian Haftmann and Lukas Bulwahn},
  title            = {Code generation from {I}sabelle/{HOL} theories},
  year             = {2022},
  keywords         = {Code Generation; Computer Science (CS); Correctness Proofs; HOL; Isabelle/HOL; Program Verification; Proof Assistants},
  url              = {https://isabelle.in.tum.de/doc/codegen.pdf},
  creationdate     = {2023-04-12T19:55:20},
  file             = {:by-author/H/Haftmann/2022_Haftmann_1.pdf:PDF},
  modificationdate = {2023-04-12T19:58:07},
  owner            = {saulius},
  pages            = {1--51},
}

@Article{Weng2018,
  author           = {Tsui-Wei Weng and Huan Zhang and Hongge Chen and Zhao Song and Cho-Jui Hsieh and Duane Boning and Inderjit S. Dhillon and Luca Daniel},
  journal          = {arXiv},
  title            = {Towards fast computation of certified robustness for {ReLU} networks},
  year             = {2018},
  month            = apr,
  pages            = {1-26},
  abstract         = {Verifying the robustness property of a general Rectified Linear Unit (ReLU) network is an NP-complete problem [Katz, Barrett, Dill, Julian and Kochenderfer CAV17]. Although finding the exact minimum adversarial distortion is hard, giving a certified lower bound of the minimum distortion is possible. Current available methods of computing such a bound are either time-consuming or delivering low quality bounds that are too loose to be useful. In this paper, we exploit the special structure of ReLU networks and provide two computationally efficient algorithms Fast-Lin and Fast-Lip that are able to certify non-trivial lower bounds of minimum distortions, by bounding the ReLU units with appropriate linear functions Fast-Lin, or by bounding the local Lipschitz constant Fast-Lip. Experiments show that (1) our proposed methods deliver bounds close to (the gap is 2-3X) exact minimum distortion found by Reluplex in small MNIST networks while our algorithms are more than 10,000 times faster; (2) our methods deliver similar quality of bounds (the gap is within 35% and usually around 10%; sometimes our bounds are even better) for larger networks compared to the methods based on solving linear programming problems but our algorithms are 33-14,000 times faster; (3) our method is capable of solving large MNIST and CIFAR networks up to 7 layers with more than 10,000 neurons within tens of seconds on a single CPU core. In addition, we show that, in fact, there is no polynomial time algorithm that can approximately find the minimum $\ell_1$ adversarial distortion of a ReLU network with a $0.99\ln n$ approximation ratio unless $\mathsf{NP}$=$\mathsf{P}$, where $n$ is the number of neurons in the network.},
  archiveprefix    = {arXiv},
  comment          = {Cited in Brucker2023.},
  creationdate     = {2023-04-12T20:10:11},
  eprint           = {1804.09699},
  file             = {:by-author/W/Weng/2018_Weng_1.pdf:PDF},
  keywords         = {Artificial Neural Networks (ANN); Computer Science (CS); Machine Learning (ML); cs.CR; cs.CV; cs.LG; stat.ML},
  modificationdate = {2023-08-07T10:24:09},
  owner            = {saulius},
  primaryclass     = {stat.ML},
}

@InProceedings{Taigman2014,
  author           = {Yaniv Taigman and Ming Yang and Marc{\textquotesingle}Aurelio Ranzato and Lior Wolf},
  booktitle        = {2014 {IEEE} Conference on Computer Vision and Pattern Recognition},
  title            = {{DeepFace}: Closing the Gap to Human-Level Performance in Face Verification},
  year             = {2014},
  month            = {jun},
  pages            = {1701-1708},
  publisher        = {{IEEE}},
  comment          = {Cited in Brucker2023.},
  creationdate     = {2023-04-12T20:16:15},
  doi              = {10.1109/cvpr.2014.220},
  file             = {:by-author/T/Taigman/2014_Taigman_1701.pdf:PDF},
  keywords         = {Artificial Neural Networks (ANN); Computer Science (CS); Face Recognition; Machine Learning (ML)},
  modificationdate = {2023-04-12T20:16:47},
  owner            = {saulius},
}

@Article{Szegedy2013,
  author           = {Christian Szegedy and Wojciech Zaremba and Ilya Sutskever and Joan Bruna and Dumitru Erhan and Ian Goodfellow and Rob Fergus},
  title            = {Intriguing properties of neural networks},
  year             = {2013},
  month            = dec,
  pages            = {1--10},
  abstract         = {Deep neural networks are highly expressive models that have recently achieved state of the art performance on speech and visual recognition tasks. While their expressiveness is the reason they succeed, it also causes them to learn uninterpretable solutions that could have counter-intuitive properties. In this paper we report two such properties. First, we find that there is no distinction between individual high level units and random linear combinations of high level units, according to various methods of unit analysis. It suggests that it is the space, rather than the individual units, that contains of the semantic information in the high layers of neural networks. Second, we find that deep neural networks learn input-output mappings that are fairly discontinuous to a significant extend. We can cause the network to misclassify an image by applying a certain imperceptible perturbation, which is found by maximizing the network's prediction error. In addition, the specific nature of these perturbations is not a random artifact of learning: the same perturbation can cause a different network, that was trained on a different subset of the dataset, to misclassify the same input.},
  archiveprefix    = {arXiv},
  comment          = {Cited in Brucker2023.},
  creationdate     = {2023-04-12T20:23:03},
  eprint           = {1312.6199},
  file             = {:by-author/S/Szegedy/2013_Szegedy_1.pdf:PDF},
  keywords         = {Artificial Neural Networks (ANN); Computer Science (CS); Machine Learning (ML); cs.CV; cs.LG; cs.NE},
  modificationdate = {2023-04-12T20:23:03},
  owner            = {saulius},
  primaryclass     = {cs.CV},
}

@Manuscript{Singh2019,
  author           = {Gagandeep Singh and Timon Gehr and Markus Püschel and Martin Vechev},
  title            = {Boosting robustness certification of neural networks},
  year             = {2019},
  keywords         = {Artificial Neural Networks (ANN); Computer Science (CS); Machine Learning (ML)},
  url              = {https://files.sri.inf.ethz.ch/website/papers/RefineZono.pdf},
  comment          = {Cited in Brucker2023.},
  creationdate     = {2023-04-12T21:10:51},
  file             = {:by-author/S/Singh/2019_Singh_1.pdf:PDF},
  modificationdate = {2023-04-12T21:10:51},
  owner            = {saulius},
  pages            = {1--12},
}

@InCollection{Seshia2018,
  author           = {Sanjit A. Seshia and Ankush Desai and Tommaso Dreossi and Daniel J. Fremont and Shromona Ghosh and Edward Kim and Sumukh Shivakumar and Marcell Vazquez-Chanlatte and Xiangyu Yue},
  booktitle        = {Automated Technology for Verification and Analysis},
  publisher        = {Springer International Publishing},
  title            = {Formal Specification for Deep Neural Networks},
  year             = {2018},
  pages            = {20--34},
  comment          = {Cited in Brucker2023.},
  creationdate     = {2023-04-12T21:16:44},
  doi              = {10.1007/978-3-030-01090-4_2},
  file             = {:by-author/S/Seshia/2018_Seshia_20.pdf:PDF},
  keywords         = {Artificial Neural Networks (ANN); Computer Science (CS); Machine Learning (ML)},
  modificationdate = {2023-04-12T21:16:44},
  owner            = {saulius},
  url              = {https://escholarship.org/content/qt3h97c8wb/qt3h97c8wb.pdf?t=qpsszt},
}

@Article{Rumelhart1986,
  author           = {David E. Rumelhart and Geoffrey E. Hinton and Ronald J. Williams},
  journal          = {Nature},
  title            = {Learning representations by back-propagating errors},
  year             = {1986},
  month            = {oct},
  number           = {6088},
  pages            = {533--536},
  volume           = {323},
  comment          = {Cited in Brucker2023.},
  creationdate     = {2023-04-12T21:23:17},
  doi              = {10.1038/323533a0},
  file             = {:by-author/R/Rumelhart/1986_Rumelhart_533.pdf:PDF},
  keywords         = {Artificial Neural Networks (ANN); Computer Science (CS); Machine Learning (ML)},
  modificationdate = {2023-04-12T21:23:17},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media {LLC}},
  url              = {http://www.cs.utoronto.ca/~hinton/absps/naturebp.pdf},
}

@Manuscript{Rintanen2014,
  author           = {Jussi Rintanen},
  title            = {Madagascar: scalable planning with {SAT}},
  year             = {2014},
  keywords         = {Artificial Neural Networks (ANN); Computer Science (CS); Machine Learning (ML)},
  url              = {https://users.aalto.fi/~rintanj1/jussi/papers/Rintanen14IPC.pdf},
  comment          = {Cited in Brucker2023.},
  creationdate     = {2023-04-12T21:31:44},
  file             = {:by-author/R/Rintanen/2014_Rintanen_1.pdf:PDF},
  modificationdate = {2023-04-12T21:31:44},
  owner            = {saulius},
  pages            = {1--5},
}

@InCollection{Pulina2010,
  author           = {Luca Pulina and Armando Tacchella},
  booktitle        = {Computer Aided Verification},
  publisher        = {Springer Berlin Heidelberg},
  title            = {An Abstraction-Refinement Approach to Verification of Artificial Neural Networks},
  year             = {2010},
  pages            = {243--257},
  comment          = {Cited in Brucker2023.},
  creationdate     = {2023-04-12T21:37:08},
  doi              = {10.1007/978-3-642-14295-6_24},
  file             = {:by-author/P/Pulina/2010_Pulina_243.pdf:PDF},
  keywords         = {Artificial Neural Networks (ANN); Computer Science (CS); Machine Learning (ML)},
  modificationdate = {2023-04-12T21:37:08},
  owner            = {saulius},
}

@Article{Larsen2017,
  author           = {Ask Hjorth Larsen and Jens Jørgen Mortensen and Jakob Blomqvist and Ivano E. Castelli and Rune Christensen and Marcin Dułak and Jesper Friis and Michael N. Groves and Bjørk Hammer and Cory Hargus and Eric D. Hermes and Paul C. Jennings and Peter Bjerre Jensen and James Kermode and John R. Kitchin and Esben Leonhard Kolsbjerg and Joseph Kubal and Kristen Kaasbjerg and Steen Lysgaard and Jón Bergmann Maronsson and Tristan Maxson and Thomas Olsen and Lars Pastewka and Andrew Peterson and Carsten Rostgaard and Jakob Schiøtz and Ole Schütt and Mikkel Strange and Kristian S. Thygesen and Tejs Vegge and Lasse Vilhelmsen and Michael Walter and Zhenhua Zeng and Karsten W. Jacobsen},
  journal          = {Journal of Physics: Condensed Matter},
  title            = {The atomic simulation environment -- a {P}ython library for working with atoms},
  year             = {2017},
  month            = {jun},
  number           = {27},
  pages            = {273002},
  volume           = {29},
  creationdate     = {2023-04-13T08:05:34},
  doi              = {10.1088/1361-648x/aa680e},
  file             = {:by-author/L/Larsen/2017_Larsen_273002.pdf:PDF},
  keywords         = {ASE; Atomic Simulation Environment; Atomistic Simulations; Library; Materials Science; Python; Quantum Mechanics (QM)},
  modificationdate = {2023-04-13T08:05:52},
  owner            = {saulius},
  publisher        = {{IOP} Publishing},
}

@Book{Nipkow2002,
  editor           = {Tobias Nipkow and Markus Wenzel and Lawrence C. Paulson},
  publisher        = {Springer Berlin Heidelberg},
  title            = {Isabelle/{HOL}},
  year             = {2002},
  comment          = {Cited in Brucker2023.
Žr. t.p. knygų repo.},
  creationdate     = {2023-04-16T11:43:03},
  doi              = {10.1007/3-540-45949-9},
  file             = {:by-author/N/Nipkow/2002_Nipkow_TOC.pdf:PDF},
  keywords         = {Computer Science (CS); Formal Verificarion; HOL; Isabelle/HOL; Proof Assistants},
  modificationdate = {2023-04-16T11:44:03},
  owner            = {saulius},
}

@InProceedings{Mirman2018,
  author           = {Mirman, Matthew and Gehr, Timon and Vechev, Martin},
  booktitle        = {International Conference on Machine Learning},
  title            = {Differentiable Abstract Interpretation for Provably Robust Neural Networks},
  year             = {2018},
  pages            = {3575--3583},
  comment          = {Cited in Brucker2023.},
  creationdate     = {2023-04-16T11:49:37},
  eprint           = {https://proceedings.mlr.press/v80/mirman18b.html},
  file             = {:by-author/M/Mirman/2018_Mirman_3575.pdf:PDF},
  keywords         = {Artificial Neural Networks (ANN); Computer Science (CS); Machine Learning (ML)},
  modificationdate = {2023-04-16T11:52:55},
  owner            = {saulius},
  url              = {https://files.sri.inf.ethz.ch/website/papers/icml18-diffai.pdf},
}

@Article{Matichuk2016,
  author           = {Daniel Matichuk and Toby Murray and Makarius Wenzel},
  journal          = {Journal of Automated Reasoning},
  title            = {Eisbach: a proof method language for {I}sabelle},
  year             = {2016},
  month            = {jan},
  number           = {3},
  pages            = {261--282},
  volume           = {56},
  comment          = {Cited in Brucker2023.},
  creationdate     = {2023-04-16T12:02:05},
  doi              = {10.1007/s10817-015-9360-2},
  file             = {:by-author/M/Matichuk/2016_Matichuk_261.pdf:PDF},
  keywords         = {Computer Science (CS); Formal Verificarion; HOL; Isabelle/HOL; Proof Assistants},
  modificationdate = {2023-04-16T12:02:17},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media {LLC}},
}

@Article{Kurd2006,
  author           = {Zeshan Kurd and Tim Kelly and Jim Austin},
  journal          = {Neural Computing and Applications},
  title            = {Developing artificial neural networks for safety critical systems},
  year             = {2006},
  month            = {mar},
  number           = {1},
  pages            = {11--19},
  volume           = {16},
  comment          = {Cited in Brucker2023.},
  creationdate     = {2023-04-16T12:10:20},
  doi              = {10.1007/s00521-006-0039-9},
  file             = {:by-author/K/Kurd/2006_Kurd_11.pdf:PDF},
  keywords         = {Computer Science (CS); Formal Methods; Machine Learning (ML); Program Verification},
  modificationdate = {2023-04-16T12:10:20},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media {LLC}},
}

@Article{Krizhevsky2017,
  author           = {Alex Krizhevsky and Ilya Sutskever and Geoffrey E. Hinton},
  journal          = {Communications of the {ACM}},
  title            = {{ImageNet} classification with deep convolutional neural networks},
  year             = {2017},
  month            = {may},
  number           = {6},
  pages            = {84--90},
  volume           = {60},
  comment          = {Cited in Brucker2023.},
  creationdate     = {2023-04-16T14:18:09},
  doi              = {10.1145/3065386},
  file             = {:by-author/K/Krizhevsky/2017_Krizhevsky_84.pdf:PDF},
  keywords         = {Artificial Neural Networks (ANN); Computer Science (CS); ImageNet; Machine Learning (ML)},
  modificationdate = {2023-04-16T14:18:29},
  owner            = {saulius},
  publisher        = {Association for Computing Machinery ({ACM})},
}

@Article{Klein2009,
  author           = {Gerwin Klein},
  journal          = {Sadhana},
  title            = {Operating system verification -- an overview},
  year             = {2009},
  month            = {feb},
  number           = {1},
  pages            = {27--69},
  volume           = {34},
  comment          = {Cited in Brucker2023.},
  creationdate     = {2023-04-16T16:10:00},
  doi              = {10.1007/s12046-009-0002-4},
  file             = {:by-author/K/Klein/2009_Klein_27.pdf:PDF},
  keywords         = {Computer Science (CS); Formal Methods; Operating Systems; Program Correctness Proofs; Review; Software Verification},
  modificationdate = {2023-04-16T16:10:01},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media {LLC}},
  url              = {https://www.ias.ac.in/article/fulltext/sadh/034/01/0027-0069},
}

@InCollection{Katz2019,
  author           = {Guy Katz and Derek A. Huang and Duligur Ibeling and Kyle Julian and Christopher Lazarus and Rachel Lim and Parth Shah and Shantanu Thakoor and Haoze Wu and Aleksandar Zelji{\'{c}} and David L. Dill and Mykel J. Kochenderfer and Clark Barrett},
  booktitle        = {Computer Aided Verification},
  publisher        = {Springer International Publishing},
  title            = {The {M}arabou framework for verification and analysis of deep neural networks},
  year             = {2019},
  pages            = {443--452},
  comment          = {Cited in Brucker2023.},
  creationdate     = {2023-04-16T16:11:09},
  doi              = {10.1007/978-3-030-25540-4_26},
  file             = {:by-author/K/Katz/2019_Katz_443.pdf:PDF},
  keywords         = {Artificial Intelligence (AI); Artificial Neural Networks (ANN); Computer Science (CS); Correctness Proofs; Formal Methods; Formal Verification; Machine Learning (ML)},
  modificationdate = {2023-04-16T16:13:07},
  owner            = {saulius},
}

@InCollection{Katz2017,
  author           = {Guy Katz and Clark Barrett and David L. Dill and Kyle Julian and Mykel J. Kochenderfer},
  booktitle        = {Computer Aided Verification},
  publisher        = {Springer International Publishing},
  title            = {{R}eluplex: an efficient {SMT} solver for verifying deep neural networks},
  year             = {2017},
  pages            = {97--117},
  comment          = {Cited in Brucker2023.},
  creationdate     = {2023-04-16T16:15:39},
  doi              = {10.1007/978-3-319-63387-9_5},
  file             = {:by-author/K/Katz/2017_Katz_97.pdf:PDF},
  keywords         = {Artificial Intelligence (AI); Artificial Neural Networks (ANN); Computer Science (CS); Correctness Proofs; Formal Methods; Formal Verification; Machine Learning (ML); SMT Solvers},
  modificationdate = {2023-04-16T16:15:39},
  owner            = {saulius},
}

@InCollection{Huang2017,
  author           = {Xiaowei Huang and Marta Kwiatkowska and Sen Wang and Min Wu},
  booktitle        = {Computer Aided Verification},
  publisher        = {Springer International Publishing},
  title            = {Safety verification of deep neural networks},
  year             = {2017},
  pages            = {3--29},
  comment          = {Cited in Brucker2023.},
  creationdate     = {2023-04-16T16:17:14},
  doi              = {10.1007/978-3-319-63387-9_1},
  file             = {:by-author/H/Huang/2017_Huang_3.pdf:PDF},
  keywords         = {Artificial Intelligence (AI); Artificial Neural Networks (ANN); Computer Science (CS); Correctness Proofs; Formal Methods; Formal Verification; Machine Learning (ML)},
  modificationdate = {2023-04-16T16:18:08},
  owner            = {saulius},
}

@Article{Harris2020,
  author           = {Charles R. Harris and K. Jarrod Millman and St{\'{e}}fan J. van der Walt and Ralf Gommers and Pauli Virtanen and David Cournapeau and Eric Wieser and Julian Taylor and Sebastian Berg and Nathaniel J. Smith and Robert Kern and Matti Picus and Stephan Hoyer and Marten H. van Kerkwijk and Matthew Brett and Allan Haldane and Jaime Fern{\'{a}}ndez del R{\'{\i}}o and Mark Wiebe and Pearu Peterson and Pierre G{\'{e}}rard-Marchant and Kevin Sheppard and Tyler Reddy and Warren Weckesser and Hameer Abbasi and Christoph Gohlke and Travis E. Oliphant},
  journal          = {Nature},
  title            = {Array programming with {NumPy}},
  year             = {2020},
  month            = {sep},
  number           = {7825},
  pages            = {357--362},
  volume           = {585},
  comment          = {Cited in Brucker2023.},
  creationdate     = {2023-04-16T16:58:59},
  doi              = {10.1038/s41586-020-2649-2},
  file             = {:by-author/H/Harris/2020_Harris_357.pdf:PDF},
  keywords         = {Computer Science (CS); NumPy; Python},
  modificationdate = {2023-04-16T16:58:59},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media {LLC}},
}

@InCollection{Ehlers2017,
  author           = {Rüdiger Ehlers},
  booktitle        = {Automated Technology for Verification and Analysis},
  publisher        = {Springer International Publishing},
  title            = {Formal verification of piece-wise linear feed-forward neural networks},
  year             = {2017},
  pages            = {269--286},
  comment          = {Cited in Brucker2023.},
  creationdate     = {2023-04-16T16:59:52},
  doi              = {10.1007/978-3-319-68167-2_19},
  file             = {:by-author/E/Ehlers/2017_Ehlers_269.pdf:PDF},
  keywords         = {Artificial Intelligence (AI); Artificial Neural Networks (ANN); Computer Science (CS); Correctness Proofs; Formal Methods; Formal Verification; Machine Learning (ML)},
  modificationdate = {2023-04-16T17:00:44},
  owner            = {saulius},
}

@InProceedings{Gowal2019,
  author           = {Sven Gowal and Krishnamurthy Dvijotham and Robert Stanforth and Rudy Bunel and Chongli Qin and Jonathan Uesato and Relja Arandjelovic and Timothy Arthur Mann and Pushmeet Kohli},
  booktitle        = {2019 {IEEE}/{CVF} International Conference on Computer Vision ({ICCV})},
  title            = {Scalable Verified Training for Provably Robust Image Classification},
  year             = {2019},
  month            = {oct},
  pages            = {4842--4851},
  publisher        = {{IEEE}},
  comment          = {Found by DuckDuckGo when searching for bibliographies (Dvijotham2018) of the paper cited in Brucker2023.},
  creationdate     = {2023-04-16T17:10:09},
  doi              = {10.1109/iccv.2019.00494},
  file             = {:by-author/G/Gowal/2019_Gowal_4842.pdf:PDF},
  keywords         = {Artificial Neural Networks (ANN); Computer Science (CS); IMage Processing; Image Classification; Machine Learning (ML)},
  modificationdate = {2023-04-16T17:14:20},
  owner            = {saulius},
  url              = {https://openaccess.thecvf.com/content_ICCV_2019/papers/Gowal_Scalable_Verified_Training_for_Provably_Robust_Image_Classification_ICCV_2019_paper.pdf},
}

@Article{Dvijotham2018,
  author           = {Krishnamurthy Dvijotham and Robert Stanforth and Sven Gowal and Timothy Mann and Pushmeet Kohli},
  title            = {A dual approach to scalable verification of deep networks},
  year             = {2018},
  month            = mar,
  pages            = {1--14},
  abstract         = {This paper addresses the problem of formally verifying desirable properties of neural networks, i.e., obtaining provable guarantees that neural networks satisfy specifications relating their inputs and outputs (robustness to bounded norm adversarial perturbations, for example). Most previous work on this topic was limited in its applicability by the size of the network, network architecture and the complexity of properties to be verified. In contrast, our framework applies to a general class of activation functions and specifications on neural network inputs and outputs. We formulate verification as an optimization problem (seeking to find the largest violation of the specification) and solve a Lagrangian relaxation of the optimization problem to obtain an upper bound on the worst case violation of the specification being verified. Our approach is anytime i.e. it can be stopped at any time and a valid bound on the maximum violation can be obtained. We develop specialized verification algorithms with provable tightness guarantees under special assumptions and demonstrate the practical significance of our general verification approach on a variety of verification tasks.},
  archiveprefix    = {arXiv},
  comment          = {Cited in Brucker2023.},
  creationdate     = {2023-04-16T17:15:44},
  eprint           = {1803.06567},
  file             = {:by-author/D/Dvijotham/2018_Dvijotham_1.pdf:PDF},
  keywords         = {Artificial Neural Networks (ANN); Computer Science (CS); Machine Learning (ML); Software Verification; cs.LG; stat.ML},
  modificationdate = {2023-04-16T17:15:44},
  owner            = {saulius},
  primaryclass     = {cs.LG},
}

@Standard{ICCC2022,
  organization     = {ICCC},
  title            = {Common criteria for information technology security evaluation. Part 1: Introduction and general model},
  author           = {{ICCC}},
  month            = nov,
  number           = {CCMB-2022-11-001},
  revision         = {1},
  url              = {https://www.commoncriteriaportal.org/cc/},
  year             = {2022},
  comment          = {Newer version of the "Common Criteria for Information Technology Security Evaluation" (2017) document (ICCC2022), cited in Brucker2023.},
  creationdate     = {2023-04-16T17:35:45},
  file             = {https://www.commoncriteriaportal.org/files/ccfiles/CC2022PART1R1.pdf},
  keywords         = {Computer Science (CS); Computer Security; Information Security; Standards},
  modificationdate = {2023-04-16T17:35:45},
  owner            = {saulius},
}

@Standard{ICCC2017,
  organization     = {ICCC},
  title            = {Common criteria for information technology security evaluation},
  author           = {{ICCC}},
  url              = {https://www.commoncriteriaportal.org/cc/},
  year             = {2017},
  comment          = {Cited in Brucker2023.},
  creationdate     = {2023-04-16T17:36:27},
  keywords         = {Computer Science (CS); Computer Security; Information Security; Standards},
  modificationdate = {2023-04-16T17:36:27},
  owner            = {saulius},
  release          = {5},
  school           = {ICCC},
  version          = {3.1},
}

@InProceedings{Cohen2016,
  author           = {Nadav Cohen and Or Sharir and Amnon Shashua},
  booktitle        = {JMLR: Workshop and Conference Proceedings},
  title            = {On the expressive power of deep learning: a tensor analysis},
  year             = {2016},
  pages            = {1--31},
  volume           = {49},
  comment          = {Cited in Brucker2023.},
  creationdate     = {2023-04-16T17:50:34},
  file             = {:by-author/C/Cohen/2016_Cohen_1.pdf:PDF},
  keywords         = {Artificial Neural Networks (ANN); Computer Science (CS); Deep Learning (DL); Machine Learning (ML)},
  modificationdate = {2023-04-16T17:50:34},
  owner            = {saulius},
  url              = {https://www.cs.huji.ac.il/w~shashua/papers/colt16.pdf},
}

@Article{Church1940,
  author           = {Alonzo Church},
  journal          = {Journal of Symbolic Logic},
  title            = {A formulation of the simple theory of types},
  year             = {1940},
  month            = {jun},
  number           = {2},
  pages            = {56--68},
  volume           = {5},
  comment          = {Cited in Brucker2023.},
  creationdate     = {2023-04-16T17:53:36},
  doi              = {10.2307/2266170},
  file             = {:by-author/C/Church/1940_Church_56.pdf:PDF},
  keywords         = {Computer Science (CS); Formal Methods; Foundations of Mathematics; Software Verification; Type Theories},
  modificationdate = {2023-04-16T17:54:06},
  owner            = {saulius},
  publisher        = {Cambridge University Press ({CUP})},
}

@Misc{Brucker2022,
  author           = {Brucker, Achim D. and Stell, Amy},
  title            = {Dataset: Feedforward Neural Network Verification in Isabelle/HOL},
  year             = {2022},
  comment          = {Cited in Brucker2023. Contains supplementary materials (Isabelle/HOL theories, trained ANN models) for this paper.},
  copyright        = {BSD 3-Clause "New" or "Revised" License},
  creationdate     = {2023-04-16T18:15:35},
  doi              = {10.5281/ZENODO.7418170},
  file             = {:by-author/B/Brucker/2022_Brucker_7418170.pdf:PDF;:by-author/B/Brucker/2022_Brucker_7418170.tgz:PDF},
  keywords         = {Classification Network; Deep Learning (DL); Feedforward Network; Isabelle/HOL; Neural Networks (NN); Verification},
  language         = {en},
  modificationdate = {2023-04-16T18:15:36},
  owner            = {saulius},
  pages            = {7418170},
  publisher        = {Zenodo},
}

@Electronic{Brucker2022a,
  author           = {Achim D. Brucker},
  month            = jul,
  note             = {\url{http://www.isa-afp.org/entries/Nano_JSON.html}, Formal proof development},
  title            = {Nano {JSON}: Working with {JSON} formatted data in Isabelle/{HOL} and Isabelle/{ML}},
  url              = {https://www.brucker.ch/bibliography/abstract/brucker-nano-json-2022},
  year             = {2022},
  abstract         = {JSON (JavaScript Object Notation) is a common format for exchanging data, based on a collection of
		  key/value-pairs (the JSON objects) and lists. Its syntax is inspired by JavaScript with the aim of
		  being easy to read and write for humans and easy to parse and generate for machines. Despite its
		  origin in the JavaScript world, JSON is language-independent and many programming languages support
		  working with JSON-encoded data. This makes JSON an interesting format for exchanging data with
		  Isabelle/HOL. This AFP entry provides a JSON-like import-expert format for both Isabelle/ML and
		  Isabelle/HOL. On the one hand, this AFP entry provides means for Isabelle/HOL users to work with JSON
		  encoded data without the need using Isabelle/ML. On the other and, the provided Isabelle/ML interfaces
		  allow additional extensions or integration into Isabelle extensions written in Isabelle/ML. While
		  format is not fully JSON compliant (e.g., due to limitations in the range of supported Unicode
		  characters), it works in most situations: the provided implementation in Isabelle/ML and its
		  representation in Isabelle/HOL have been used successfully in several projects for exchanging data
		  sets of several hundredths of megabyte between Isabelle and external tools.},
  areas            = {formal methods, software engineering},
  classification   = {formal},
  comment          = {Cited in Brucker2023.},
  creationdate     = {2023-04-16T18:22:05},
  date             = {2022-07-29},
  eprint           = {https://www.isa-afp.org/entries/Nano_JSON.html},
  file             = {:by-author/B/Brucker/2022_Brucker_1.pdf:PDF},
  issn             = {2150-914x},
  journal          = {Archive of Formal Proofs},
  keywords         = {Computer Science (CS); Formal Proofs; Isabelle/HOL; JSON},
  modificationdate = {2023-04-16T18:29:47},
  owner            = {saulius},
  pages            = {1--29},
  pdf              = {https://www.brucker.ch/bibliography/download/2022/brucker-nano-json-2022.pdf},
  public           = {yes},
}

@InProceedings{Bonaert2021,
  author           = {Gregory Bonaert and Dimitar I. Dimitrov and Maximilian Baader and Martin Vechev},
  booktitle        = {Proceedings of the 42nd {ACM} {SIGPLAN} International Conference on Programming Language Design and Implementation},
  title            = {Fast and precise certification of transformers},
  year             = {2021},
  month            = {jun},
  pages            = {466--481},
  publisher        = {{ACM}},
  comment          = {Cited in Brucker2023.},
  creationdate     = {2023-04-16T18:25:36},
  doi              = {10.1145/3453483.3454056},
  file             = {:by-author/B/Bonaert/2021_Bonaert_466.pdf:PDF},
  keywords         = {Computer Science (CS); Formal Methods; Formal Verification; Program Correctness Proofs; Programming Languages},
  modificationdate = {2023-04-16T18:27:55},
  owner            = {saulius},
}

@Electronic{Bentkamp2016,
  author           = {Alexander Bentkamp},
  month            = {November},
  note             = {\url{https://isa-afp.org/entries/Deep_Learning.html}, Formal proof development},
  title            = {Expressiveness of Deep Learning},
  url              = {https://www.isa-afp.org/browser_info/current/AFP/Deep_Learning/outline.pdf},
  year             = {2016},
  comment          = {Cited in Brucker2023.},
  creationdate     = {2023-04-16T18:35:58},
  eprint           = {https://isa-afp.org/entries/Deep_Learning.html},
  file             = {:by-author/B/Bentkamp/2016_Bentkamp_1.pdf:PDF},
  issn             = {2150-914x},
  journal          = {Archive of Formal Proofs},
  keywords         = {Computer Science (CS); Formal Proof; Formal Proof Archive; Isabelle/HOL},
  modificationdate = {2023-04-16T18:35:58},
  owner            = {saulius},
  pages            = {1--40},
}

@Book{Barocas2022,
  author           = {Solon Barocas and Moritz Hardt and Arvind Narayanan},
  title            = {Fairness and machine learning: limitations and opportunities},
  year             = {2022},
  comment          = {Cited in Brucker2023.},
  creationdate     = {2023-04-16T19:28:30},
  file             = {:by-author/B/Barocas/2022_Barocas_1.pdf:PDF},
  keywords         = {CD; Machine Learning (ML); Social Aspects of ML},
  modificationdate = {2023-04-16T19:29:07},
  owner            = {saulius},
  pages            = {1--294},
  url              = {https://fairmlbook.org/pdf/fairmlbook.pdf},
}

@Article{Banerjee2020,
  author           = {Kunal Banerjee and Vishak Prasad C and Rishi Raj Gupta and Karthik Vyas and Anushree H and Biswajit Mishra},
  title            = {Exploring Alternatives to Softmax Function},
  year             = {2020},
  month            = nov,
  pages            = {1--8},
  abstract         = {Softmax function is widely used in artificial neural networks for multiclass classification, multilabel classification, attention mechanisms, etc. However, its efficacy is often questioned in literature. The log-softmax loss has been shown to belong to a more generic class of loss functions, called spherical family, and its member log-Taylor softmax loss is arguably the best alternative in this class. In another approach which tries to enhance the discriminative nature of the softmax function, soft-margin softmax (SM-softmax) has been proposed to be the most suitable alternative. In this work, we investigate Taylor softmax, SM-softmax and our proposed SM-Taylor softmax, an amalgamation of the earlier two functions, as alternatives to softmax function. Furthermore, we explore the effect of expanding Taylor softmax up to ten terms (original work proposed expanding only to two terms) along with the ramifications of considering Taylor softmax to be a finite or infinite series during backpropagation. Our experiments for the image classification task on different datasets reveal that there is always a configuration of the SM-Taylor softmax function that outperforms the normal softmax function and its other alternatives.},
  archiveprefix    = {arXiv},
  comment          = {Cited in Brucker2023.},
  creationdate     = {2023-04-16T19:31:41},
  doi              = {10.48550/arXiv.2011.11538},
  eprint           = {2011.11538},
  file             = {:by-author/B/Banerjee/2020_Banerjee_1.pdf:PDF},
  keywords         = {Activation Functions; Artificial Neural Networks (ANN); Machine Learning (ML); SofMax; cs.LG},
  modificationdate = {2023-04-16T19:33:16},
  owner            = {saulius},
  primaryclass     = {cs.LG},
}

@Electronic{Abdulaziz2020,
  author           = {Mohammad Abdulaziz and Friedrich Kurz},
  month            = {October},
  note             = {\url{https://isa-afp.org/entries/Verified_SAT_Based_AI_Planning.html}, Formal proof development},
  title            = {Verified SAT-Based AI Planning},
  url              = {https://www.isa-afp.org/browser_info/current/AFP/Verified_SAT_Based_AI_Planning/outline.pdf},
  year             = {2020},
  comment          = {Cited in Brucker2023.},
  creationdate     = {2023-04-16T19:40:52},
  eprint           = {https://www.isa-afp.org/entries/Verified_SAT_Based_AI_Planning.html},
  file             = {:by-author/A/Abdulaziz/2020_Abdulaziz_1.pdf:PDF},
  issn             = {2150-914x},
  journal          = {Archive of Formal Proofs},
  keywords         = {Computer Science (CS); Formal Proof Archive; Formal Proofs; Isabelle/HOL; SAT; SAT Solvers},
  modificationdate = {2023-04-16T19:41:43},
  owner            = {saulius},
  pages            = {1--109},
}

@Electronic{Abadi2015,
  author           = {Abadi, M. and et al.},
  language         = {en},
  title            = {TensorFlow: Large-Scale Machine Learning on HeterogeneousSystems},
  url              = {https://www.tensorflow.org/},
  year             = {2015},
  creationdate     = {2023-04-16T19:42:14},
  modificationdate = {2023-04-16T19:43:55},
  owner            = {saulius},
}

@Manuscript{Manakova2022,
  author           = {Elena Manakova and Edvardas Golovinas and Reda Pocevičiūtė and Giedrius Sasnauskas and Algirdas Grybauskas and Saulius Gražulis and Mindaugas Zaremba},
  title            = {Structural basis for sequence-specific recognition of guide and target strands by the {A}rchaeoglobus fulgidus {A}rgonaute protein},
  year             = {2022},
  doi              = {10.21203/rs.3.rs-2305454/v1},
  month            = {nov},
  creationdate     = {2023-04-17T13:45:53},
  file             = {:by-author/M/Manakova/2022_Manakova_1.pdf:PDF},
  journal          = {Research Square},
  modificationdate = {2023-04-17T13:48:06},
  owner            = {saulius},
  pages            = {1--17},
  publisher        = {Research Square Platform {LLC}},
}

@Article{Manakova2023,
  author           = {Elena Manakova and Edvardas Golovinas and Reda Pocevičiūtė and Giedrius Sasnauskas and Algirdas Grybauskas and Saulius Gražulis and Mindaugas Zaremba},
  journal          = {Scientific Reports},
  title            = {Structural basis for sequence-specific recognition of guide and target strands by the {A}rchaeoglobus fulgidus {A}rgonaute protein},
  year             = {2023},
  month            = {apr},
  number           = {1},
  pages            = {6123},
  volume           = {13},
  creationdate     = {2023-04-17T13:54:20},
  doi              = {10.1038/s41598-023-32600-w},
  file             = {:by-author/M/Manakova/2023_Manakova_6123.pdf:PDF},
  modificationdate = {2023-05-02T10:12:10},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media {LLC}},
}

@Article{Dunitz2001,
  author           = {Jack D. Dunitz},
  journal          = {Angewandte Chemie International Edition},
  title            = {{P}auling's left-handed α-helix},
  year             = {2001},
  month            = {nov},
  number           = {22},
  pages            = {4167--4173},
  volume           = {40},
  creationdate     = {2023-04-18T09:42:12},
  doi              = {10.1002/1521-3773(20011119)40:22<4167::aid-anie4167>3.0.co;2-q},
  file             = {:by-author/D/Dunitz/2001_Dunitz_4167.pdf:PDF},
  keywords         = {Alpha-helix; Asymmetry of Life; Biochemistry; Bioinformatics; Chemistry; Chirality; Helices},
  modificationdate = {2023-04-18T09:48:07},
  owner            = {saulius},
  publisher        = {Wiley},
  url              = {https://williams.chemistry.gatech.edu/course_Information/6572/papers/dunitz_2001.pdf},
}

@Article{Chouaieb2006,
  author           = {Nadia Chouaieb and Alain Goriely and John H. Maddocks},
  journal          = {Proceedings of the National Academy of Sciences},
  title            = {Helices},
  year             = {2006},
  month            = {jun},
  number           = {25},
  pages            = {9398--9403},
  volume           = {103},
  creationdate     = {2023-04-18T09:47:30},
  doi              = {10.1073/pnas.0508370103},
  file             = {:by-author/C/Chouaieb/2006_Chouaieb_9398.pdf:PDF},
  keywords         = {Bioinformatics; Geometry; Helices; Vector Algebra},
  modificationdate = {2023-04-18T09:48:35},
  owner            = {saulius},
  publisher        = {Proceedings of the National Academy of Sciences},
  url              = {https://www.pnas.org/doi/epdf/10.1073/pnas.0508370103},
}

@Article{Foxman2021,
  author           = {Bruce M. Foxman},
  journal          = {Acta Crystallographica Section E Crystallographic Communications},
  title            = {Space groups and crystallographic symmetry: writing a multi-featured tutorial in a new style},
  year             = {2021},
  month            = {jul},
  number           = {9},
  pages            = {857--863},
  volume           = {77},
  creationdate     = {2023-04-19T15:45:34},
  doi              = {10.1107/s2056989021007039},
  file             = {:by-author/F/Foxman/2021_Foxman_857.pdf:PDF},
  keywords         = {Crystallography; IUCr; Spacegroups; Symmetry; Teaching},
  modificationdate = {2023-04-19T15:46:11},
  owner            = {saulius},
  publisher        = {International Union of Crystallography ({IUCr})},
}

@Article{Song2019,
  author           = {Ziyuan Song and Hailin Fu and Ryan Baumgartner and Lingyang Zhu and Kuo-Chih Shih and Yingchun Xia and Xuetao Zheng and Lichen Yin and Christophe Chipot and Yao Lin and Jianjun Cheng},
  journal          = {Nature Communications},
  title            = {Enzyme-mimetic self-catalyzed polymerization of polypeptide helices},
  year             = {2019},
  month            = {nov},
  number           = {1},
  pages            = {5470},
  volume           = {10},
  comment          = {Cites Presta1988.},
  creationdate     = {2023-04-22T10:51:05},
  doi              = {10.1038/s41467-019-13502-w},
  file             = {:by-author/S/Song/2019_Song_5470.pdf:PDF},
  keywords         = {Alpha Helices; Biochemistry; Bioinformatics; Protein Structure; Structural Biology},
  modificationdate = {2023-04-22T10:54:24},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media {LLC}},
}

@Article{Presta1988,
  author           = {Leonard G. Presta and George D. Rose},
  journal          = {Science},
  title            = {Helix Signals in Proteins},
  year             = {1988},
  month            = {jun},
  note             = {"The helix hypothesis, introduced here /.../ states that a necessary condition for helix formation is the presence of residues flanking the helix termini whose side chains can form hydrogen bonds with the initial four-helix >N-H groups and final four-helix >C-O groups; these eight groups would otherwise lack intrahelical partners."},
  number           = {4859},
  pages            = {1632--1641},
  volume           = {240},
  comment          = {Cited by Song2019, Segura2011, Aurora1998. Proposes "The helix hypothesis", see also notes.},
  creationdate     = {2023-04-22T10:55:06},
  doi              = {10.1126/science.2837824},
  file             = {:by-author/P/Presta/1988_Presta_1632.pdf:PDF},
  keywords         = {Alpha Helices; Biochemistry; Bioinformatics; Helix Cappings; Protein Structure; Structural Biology},
  modificationdate = {2023-04-22T12:43:59},
  owner            = {saulius},
  publisher        = {American Association for the Advancement of Science ({AAAS})},
}

@Article{Richardson1988,
  author           = {Jane S. Richardson and David C. Richardson},
  journal          = {Science},
  title            = {Amino acid preferences for specific locations at the ends of α helices},
  year             = {1988},
  month            = {jun},
  number           = {4859},
  pages            = {1648--1652},
  volume           = {240},
  comment          = {Cited by Segura2011.},
  creationdate     = {2023-04-22T11:13:48},
  doi              = {10.1126/science.3381086},
  file             = {:by-author/R/Richardson/1988_Richardson_1648.pdf:PDF},
  keywords         = {Alpha Helices; Biochemistry; Bioinformatics; Helix Cappings; Protein Structure; Structural Biology},
  modificationdate = {2023-04-22T11:19:13},
  owner            = {saulius},
  publisher        = {American Association for the Advancement of Science ({AAAS})},
}

@Article{Oyama2022,
  author           = {Oyama, Linda B. and Olleik, Hamza and Teixeira, Ana Carolina Nery and Guidini, Matheus M. and Pickup, James A. and Hui, Brandon Yeo Pei and Vidal, Nicolas and Cookson, Alan R. and Vallin, Hannah and Wilkinson, Toby and Bazzolli, Denise M. S. and Richards, Jennifer and Wootton, Mandy and Mikut, Ralf and Hilpert, Kai and Maresca, Marc and Perrier, Josette and Hess, Matthias and Mantovani, Hilario C. and Fernandez-Fuentes, Narcis and Creevey, Christopher J. and Huws, Sharon A.},
  journal          = {NPJ biofilms and microbiomes},
  title            = {In silico identification of two peptides with antibacterial activity against multidrug-resistant {S}taphylococcus aureus},
  year             = {2022},
  issn             = {2055-5008},
  month            = jul,
  pages            = {58},
  volume           = {8},
  abstract         = {Here we report two antimicrobial peptides (AMPs), HG2 and HG4 identified from a rumen microbiome metagenomic dataset, with activity against multidrug-resistant (MDR) bacteria, especially methicillin-resistant Staphylococcus aureus (MRSA) strains, a major hospital and community-acquired pathogen. We employed the classifier model design to analyse, visualise, and interpret AMP activities. This approach allowed in silico discrimination of promising lead AMP candidates for experimental evaluation. The lead AMPs, HG2 and HG4, are fast-acting and show anti-biofilm and anti-inflammatory activities in vitro and demonstrated little toxicity to human primary cell lines. The peptides were effective in vivo within a Galleria mellonella model of MRSA USA300 infection. In terms of mechanism of action, HG2 and HG4 appear to interact with the cytoplasmic membrane of target cells and may inhibit other cellular processes, whilst preferentially binding to bacterial lipids over human cell lipids. Therefore, these AMPs may offer additional therapeutic templates for MDR bacterial infections.},
  chemicals        = {Anti-Bacterial Agents, Antimicrobial Cationic Peptides, Lipids},
  citation-subset  = {IM},
  comment          = {Found in EuropePMV in a search for "a-helix nt- and ct capping".},
  completed        = {2022-12-27},
  country          = {United States},
  creationdate     = {2023-04-22T11:24:47},
  doi              = {10.1038/s41522-022-00320-0},
  file             = {:by-author/O/Oyama/2022_Oyama_58.pdf:PDF},
  issn-linking     = {2055-5008},
  issue            = {1},
  keywords         = {Animals; Anti-Bacterial Agents, Pharmacology, Therapeutic Use; Antimicrobial Cationic Peptides, Pharmacology; Humans; Lipids, Therapeutic Use; Methicillin-Resistant Staphylococcus Aureus; Microbial Sensitivity Tests; Staphylococcal Infections, Drug Therapy, Microbiology; Staphylococcus Aureus, Metabolism},
  modificationdate = {2023-04-22T11:50:47},
  nlm-id           = {101666944},
  owner            = {saulius},
  pii              = {58},
  pmc              = {PMC9283466},
  pmid             = {35835775},
  pubmodel         = {Electronic},
  pubstate         = {epublish},
  revised          = {2022-12-27},
}

@Article{Balint2019,
  author           = {Bálint, Mónika and Horváth, István and Mészáros, Nikolett and Hetényi, Csaba},
  journal          = {International journal of molecular sciences},
  title            = {Towards Unraveling the Histone Code by Fragment Blind Docking.},
  year             = {2019},
  issn             = {1422-0067},
  month            = jan,
  pages            = {422},
  volume           = {20},
  abstract         = {Histones serve as protein spools for winding the DNA in the nucleosome. High variability of their post-translational modifications result in a unique code system often responsible for the pathomechanisms of epigenetics-based diseases. Decoding is performed by reader proteins via complex formation with the N-terminal peptide tails of histones. Determination of structures of histone-reader complexes would be a key to unravel the histone code and the design of new drugs. However, the large number of possible histone complex variations imposes a true challenge for experimental structure determination techniques. Calculation of such complexes is difficult due to considerable size and flexibility of peptides and the shallow binding surfaces of the readers. Moreover, location of the binding sites is often unknown, which requires a blind docking search over the entire surface of the target protein. To accelerate the work in this field, a new approach is presented for prediction of the structure of histone H3 peptide tails docked to their targets. Using a fragmenting protocol and a systematic blind docking method, a collection of well-positioned fragments of the H3 peptide is produced. After linking the fragments, reconstitution of anchoring regions of the target-bound H3 peptide conformations was possible. As a first attempt of combination of blind and fragment docking approaches, our new method is named fragment blind docking (FBD).},
  chemicals        = {Histones, Ligands, Peptides, DNA},
  citation-subset  = {IM},
  comment          = {Found in EuropePMV in a search for "a-helix nt- and ct capping".},
  completed        = {2019-05-01},
  country          = {Switzerland},
  creationdate     = {2023-04-22T11:31:18},
  doi              = {10.3390/ijms20020422},
  file             = {:by-author/B/Bálint/2019_Bálint_422.pdf:PDF},
  issn-linking     = {1422-0067},
  issue            = {2},
  keywords         = {Algorithms; Amino Acid Sequence; AutoDock; DNA, Chemistry, Metabolism; Histone Code; Histones, Metabolism; Interaction; Ligand; Ligands; Methylation; Models, Molecular; Molecular Structure; Peptide; Peptides; Protein Binding; Protein Conformation; Structure-activity Relationship (SAR); Target; Translation},
  modificationdate = {2023-04-22T11:50:45},
  nlm-id           = {101092791},
  owner            = {saulius},
  pii              = {422},
  pmc              = {PMC6358888},
  pmid             = {30669446},
  pubmodel         = {Electronic},
  pubstate         = {epublish},
  revised          = {2020-02-25},
}

@Article{Wathen2009,
  author           = {Wathen, Brent and Jia, Zongchao},
  journal          = {International journal of molecular sciences},
  title            = {Folding by numbers: primary sequence statistics and their use in studying protein folding.},
  year             = {2009},
  issn             = {1422-0067},
  month            = apr,
  pages            = {1567--1589},
  volume           = {10},
  abstract         = {The exponential growth over the past several decades in the quantity of both primary sequence data available and the number of protein structures determined has provided a wealth of information describing the relationship between protein primary sequence and tertiary structure. This growing repository of data has served as a prime source for statistical analysis, where underlying relationships between patterns of amino acids and protein structure can be uncovered. Here, we survey the main statistical approaches that have been used for identifying patterns within protein sequences, and discuss sequence pattern research as it relates to both secondary and tertiary protein structure. Limitations to statistical analyses are discussed, and a context for their role within the field of protein folding is given. We conclude by describing a novel statistical study of residue patterning in beta-strands, which finds that hydrophobic (i,i+2) pairing in beta-strands occurs more often than expected at locations near strand termini. Interpretations involving beta-sheet nucleation and growth are discussed.},
  chemicals        = {Proteins},
  citation-subset  = {IM},
  comment          = {Found in EuropePMV in a search for "a-helix nt- and ct capping".
Could be interesting for Bioinformatics students. Pre-AlphaFold?},
  completed        = {2014-01-15},
  country          = {Switzerland},
  creationdate     = {2023-04-22T11:42:48},
  doi              = {10.3390/ijms10041567},
  file             = {:by-author/W/Wathen/2009_Wathen_1567.pdf:PDF},
  issn-linking     = {1422-0067},
  issue            = {4},
  keywords         = {Amino Acid Sequence; Hydrophobic and Hydrophilic Interactions; Models, Molecular; Primary Sequence; Protein Folding; Protein Structure Prediction; Protein Structure, Tertiary; Proteins, Chemistry, Metabolism; Sequence-Structure Relationship},
  modificationdate = {2023-04-22T11:50:41},
  nlm-id           = {101092791},
  owner            = {saulius},
  pii              = {i10041567},
  pmc              = {PMC2680634},
  pmid             = {19468326},
  pubmodel         = {Electronic},
  pubstate         = {epublish},
  revised          = {2022-09-22},
}

@Article{Aurora1998,
  author           = {Aurora, R. and Rose, G. D.},
  journal          = {Protein science : a publication of the Protein Society},
  title            = {Helix capping.},
  year             = {1998},
  issn             = {0961-8368},
  month            = jan,
  pages            = {21--38},
  volume           = {7},
  abstract         = {Helix-capping motifs are specific patterns of hydrogen bonding and hydrophobic interactions found at or near the ends of helices in both proteins and peptides. In an alpha-helix, the first four >N-H groups and last four >C=O groups necessarily lack intrahelical hydrogen bonds. Instead, such groups are often capped by alternative hydrogen bond partners. This review enlarges our earlier hypothesis (Presta LG, Rose GD. 1988. Helix signals in proteins. Science 240:1632-1641) to include hydrophobic capping. A hydrophobic interaction that straddles the helix terminus is always associated with hydrogen-bonded capping. From a global survey among proteins of known structure, seven distinct capping motifs are identified-three at the helix N-terminus and four at the C-terminus. The consensus sequence patterns of these seven motifs, together with results from simple molecular modeling, are used to formulate useful rules of thumb for helix termination. Finally, we examine the role of helix capping as a bridge linking the conformation of secondary structure to supersecondary structure.},
  chemicals        = {Peptides, Proteins},
  citation-subset  = {IM},
  comment          = {Found in EuropePMV in a search for "a-helix nt- and ct capping". Cites (Presta & Rose, 1988)},
  completed        = {1998-05-05},
  country          = {United States},
  creationdate     = {2023-04-22T11:50:13},
  doi              = {10.1002/pro.5560070103},
  file             = {:by-author/A/Aurora/1998_Aurora_21.pdf:PDF},
  issn-linking     = {0961-8368},
  issue            = {1},
  keywords         = {Helix Cappings; Hydrogen Bonding; Models, Molecular; Molecular Conformation; Peptides, Chemistry; Protein Structure, Secondary; Proteins, Chemistry},
  modificationdate = {2023-04-22T11:55:56},
  nlm-id           = {9211750},
  owner            = {saulius},
  pmc              = {PMC2143812},
  pmid             = {9514257},
  pubmodel         = {Print},
  pubstate         = {ppublish},
  revised          = {2018-11-13},
  url              = {https://europepmc.org/article/MED/9514257},
}

@Article{Groebke1996,
  author           = {K Groebke and P Renold and K Y Tsang and T J Allen and K F McClure and D S Kemp},
  journal          = {Proceedings of the National Academy of Sciences},
  title            = {Template-nucleated alanine-lysine helices are stabilized by position-dependent interactions between the lysine side chain and the helix barrel.},
  year             = {1996},
  month            = {apr},
  number           = {9},
  pages            = {4025--4029},
  volume           = {93},
  comment          = {Cited by Aurora1998.},
  creationdate     = {2023-04-22T12:13:45},
  doi              = {10.1073/pnas.93.9.4025},
  file             = {:by-author/G/Groebke/1996_Groebke_4025.pdf:PDF},
  keywords         = {Alpha Helices; Biochemistry; Bioinformatics; Helix Cappings; Protein Structure; Structural Biology},
  modificationdate = {2023-04-22T12:14:36},
  owner            = {saulius},
  publisher        = {Proceedings of the National Academy of Sciences},
}

@Article{Bahar2010,
  author           = {Bahar, Ivet and Lezon, Timothy R. and Bakan, Ahmet and Shrivastava, Indira H.},
  journal          = {Chemical reviews},
  title            = {Normal mode analysis of biomolecular structures: functional mechanisms of membrane proteins.},
  year             = {2010},
  issn             = {1520-6890},
  month            = mar,
  pages            = {1463--1497},
  volume           = {110},
  chemicals        = {Membrane Proteins},
  citation-subset  = {IM},
  comment          = {Found in EuropePMV in a search for "a-helix nt- and ct capping".},
  completed        = {2010-04-19},
  country          = {United States},
  creationdate     = {2023-04-22T12:18:46},
  doi              = {10.1021/cr900095e},
  file             = {:by-author/B/Bahar/2010_Bahar_1463.pdf:PDF},
  issn-linking     = {0009-2665},
  issue            = {3},
  keywords         = {Allosteric Regulation; Animals; Humans; Membrane Proteins, Chemistry, Metabolism; Models, Molecular; Normal Mode Analysis; Protein Conformation; Protein Multimerization},
  mid              = {NIHMS155008},
  modificationdate = {2023-04-24T12:33:41},
  nlm-id           = {2985134R},
  owner            = {saulius},
  pmc              = {PMC2836427},
  pmid             = {19785456},
  pubmodel         = {Print},
  pubstate         = {ppublish},
  revised          = {2021-10-20},
}

@Article{Ballano2008,
  author           = {Ballano, Gema and Zanuy, David and Jiménez, Ana I. and Cativiela, Carlos and Nussinov, Ruth and Alemán, Carlos},
  journal          = {The journal of physical chemistry. B},
  title            = {Structural analysis of a beta-helical protein motif stabilized by targeted replacements with conformationally constrained amino acids.},
  year             = {2008},
  issn             = {1520-6106},
  month            = oct,
  pages            = {13101--13115},
  volume           = {112},
  abstract         = {Here we study conformational stabilization induced in a beta-helical nanostructure by position-specific mutations. The nanostructure is constructed through the self-assembly of the beta-helical building block excised from E. coli galactoside acetyltransferase (PDB code 1krr , chain A; residues 131-165). The mutations involve substitutions by cyclic, conformationally constrained amino acids. Specifically, a complete structural analysis of the Pro-Xaa-Val sequence [with Xaa being Gly, Ac 3c (1-aminocyclopropane-1-carboxylic acid) and Ac 5c (1-aminocyclopentane-1-carboxylic acid)], corresponding to the 148-150 loop region in the wild-type (Gly) and mutated (Ac 3c and Ac 5c) 1krr , has been performed using Molecular Dynamics simulations and X-ray crystallography. Simulations have been performed for the wild-type and mutants of three different systems, namely the building block, the nanoconstruct and the isolated Pro-Xaa-Val tripeptide. Furthermore, the crystalline structures of five peptides of Pro-Xaa-Val or Xaa-Val sequences have been solved by X-ray diffraction analysis and compared with theoretical predictions. Both the theoretical and crystallographic studies indicate that the Pro-Ac n c-Val sequences exhibit a high propensity to adopt turn-like conformations, and this propensity is little affected by the chemical environment. Overall, the results indicate that replacement of Gly149 by Ac 3c or Ac 5c significantly reduce the conformational flexibility of the target site enhancing the structural specificity of the building block and the nanoconstruct derived from the 1krr beta-helical motif.},
  chemicals        = {Amino Acids, Acetyltransferases, galactoside acetyltransferase},
  citation-subset  = {IM},
  comment          = {Found in EuropePMV in a search for "a-helix nt- and ct capping".},
  completed        = {2009-01-06},
  country          = {United States},
  creationdate     = {2023-04-22T12:22:51},
  doi              = {10.1021/jp8032116},
  file             = {:by-author/B/Ballano/2008_Ballano_13101.pdf:PDF;:by-author/B/Ballano/2008_Ballano_13101manuscript.pdf:PDF},
  issn-linking     = {1520-5207},
  issue            = {41},
  keywords         = {Acetyltransferases, Chemistry; Amino Acid Motifs; Amino Acid Sequence; Amino Acid Substitution; Amino Acids, Chemistry; Crystallography, X-Ray; Models, Molecular; Molecular Sequence Data; Molecular Structure; Nanostructures, Chemistry; Protein Structure, Secondary; Protein Structure, Tertiary},
  mid              = {NIHMS112022},
  modificationdate = {2023-04-24T12:33:38},
  nlm-id           = {101157530},
  owner            = {saulius},
  pmc              = {PMC2713822},
  pmid             = {18811190},
  pubmodel         = {Print-Electronic},
  pubstate         = {ppublish},
  revised          = {2018-11-13},
}

@Poster{Baldauf1993,
  author           = {E. A. Baldauf and J. T. J. Lecomte},
  title            = {Study of helix capping in cytochrome {b5} by {NMR} spectroscopy and site-directed mutagenesis},
  year             = {1993},
  conference       = {Thirty-seventh Annual Meeting February 14-18, 1993},
  session          = {Part III},
  comment          = {Found in EuropePMV in a search for "a-helix nt- and ct capping". Apparently contradicts "The helix hypothesis" from Presta1988.},
  creationdate     = {2023-04-22T12:34:43},
  day              = {Wednesday Symposia and Posters},
  file             = {:by-author/B/Baldauf/1993_Baldauf_264.pdf:PDF},
  issue            = {2 Pt 2},
  journal          = {Biophysical Journal},
  location         = {Washington Convention Center Washington, D.C},
  modificationdate = {2023-04-22T12:43:30},
  owner            = {saulius},
  pages            = {A264--A302},
  poster           = {W-Po113},
  url              = {https://europepmc.org/article/PMC/PMC1262548},
  volume           = {64},
}

@Article{Berg2004,
  author           = {Bert van den Berg and Clemons, Jr., William M. and Ian Collinson and Yorgo Modis and Enno Hartmann and Stephen C. Harrison and Tom A. Rapoport},
  journal          = {Nature},
  title            = {X-ray structure of a protein-conducting channel},
  year             = {2004},
  issn             = {1476-4687},
  month            = {dec},
  number           = {6969},
  pages            = {36--44},
  volume           = {427},
  abstract         = {A conserved heterotrimeric membrane protein complex, the Sec61 or SecY complex, forms a protein-conducting channel, allowing polypeptides to be transferred across or integrated into membranes. We report the crystal structure of the complex from Methanococcus jannaschii at a resolution of 3.2 A. The structure suggests that one copy of the heterotrimer serves as a functional translocation channel. The alpha-subunit has two linked halves, transmembrane segments 1-5 and 6-10, clamped together by the gamma-subunit. A cytoplasmic funnel leading into the channel is plugged by a short helix. Plug displacement can open the channel into an 'hourglass' with a ring of hydrophobic residues at its constriction. This ring may form a seal around the translocating polypeptide, hindering the permeation of other molecules. The structure also suggests mechanisms for signal-sequence recognition and for the lateral exit of transmembrane segments of nascent membrane proteins into lipid, and indicates binding sites for partners that provide the driving force for translocation.},
  chemicals        = {Archaeal Proteins, Escherichia coli Proteins, Macromolecular Substances, Protein Subunits, SEC Translocation Channels, SecY protein, E coli},
  citation-subset  = {IM},
  completed        = {2004-01-12},
  country          = {England},
  creationdate     = {2008-07-28T00:00:00},
  doi              = {10.1038/nature02218},
  file             = {:by-author/B/Berg/2004_Berg_36.pdf:PDF},
  issn-linking     = {0028-0836},
  issue            = {6969},
  keywords         = {Archaeal Proteins, Chemistry, Genetics, Metabolism; Crystallography, X-Ray; Escherichia Coli Proteins, Ultrastructure; Macromolecular Substances; Methanococcus, Chemistry; Models, Molecular; Protein Binding; Protein Structure, Quaternary; Protein Structure, Secondary; Protein Subunits, Metabolism; Protein Transport; SEC Translocation Channels; Static Electricity; Suppression, Genetic},
  modificationdate = {2023-04-23T10:35:14},
  nlm-id           = {0410462},
  owner            = {saulius},
  pii              = {nature02218},
  pmid             = {14661030},
  publisher        = {Springer Science and Business Media {LLC}},
  pubmodel         = {Print-Electronic},
  pubstate         = {ppublish},
  revised          = {2022-03-01},
  timestamp        = {2008.07.28},
}

@Article{Westbrook2022,
  author           = {John D. Westbrook and Jasmine Y. Young and Chenghua Shao and Zukang Feng and Vladimir Guranovic and Catherine L. Lawson and Brinda Vallat and Paul D. Adams and John M Berrisford and Gerard Bricogne and Kay Diederichs and Robbie P. Joosten and Peter Keller and Nigel W. Moriarty and Oleg V. Sobolev and Sameer Velankar and Clemens Vonrhein and David G. Waterman and Genji Kurisu and Helen M. Berman and Stephen K. Burley and Ezra Peisach},
  journal          = {Journal of Molecular Biology},
  title            = {{PDBx}/{mmCIF} ecosystem: foundational semantic tools for structural biology},
  year             = {2022},
  month            = {jun},
  number           = {11},
  pages            = {167599},
  volume           = {434},
  creationdate     = {2023-04-23T10:49:59},
  doi              = {10.1016/j.jmb.2022.167599},
  file             = {:by-author/W/Westbrook/2022_Westbrook_167599.pdf:PDF},
  keywords         = {CIF; Crystallography; Databases; PDB; Structural Biology; Validation; {mmCIF}},
  modificationdate = {2023-08-07T10:23:04},
  owner            = {saulius},
  publisher        = {Elsevier {BV}},
}

@Article{Desmet1992,
  author           = {Desmet, Johan and De Maeyer, Marc and Hazes, Bart and Lasters, Ignace},
  journal          = {Nature},
  title            = {The dead-end elimination theorem and its use in protein side-chain positioning},
  year             = {1992},
  number           = {6369},
  pages            = {539--542},
  volume           = {356},
  creationdate     = {2023-04-24T09:52:59},
  doi              = {10.1038/356539a0},
  file             = {:by-author/D/Desmet/1992_Desmet_539.pdf:PDF},
  keywords         = {Algorithms; Bioinformatics; Dead End Elimination},
  modificationdate = {2023-04-28T18:53:19},
  owner            = {saulius},
  publisher        = {Nature Publishing Group},
}

@Article{Naito2020,
  author           = {Hisashi Naito},
  journal          = {Anam Lecture Notes in Mathematics, An introduction to discrete differential geometry, Volume 2, 83-147 (2020)},
  title            = {A short lecture on topological crystallography and a discrete surface theory},
  year             = {2020},
  month            = feb,
  pages            = {1--44},
  abstract         = {This is an unrefereed lecture note based on lectures in 'Introductory Workshop on Discrete Differential Geometry' at Korea University on January 21--24, 2019. In this note, we discuss topological crystallography, which is a mathematical theory of crystal structures. The most symmetric structure among all placements of the graph is obtained by a variational principle in topological crystallography. We also discuss a theory of trivalent discrete surfaces in $3$-dimensional Euclidean space, which are mathematical models of crystal/molecular structures.},
  archiveprefix    = {arXiv},
  creationdate     = {2023-04-28T18:55:34},
  eprint           = {2002.09562},
  file             = {:by-author/N/Naito/2020_Naito_1.pdf:PDF},
  keywords         = {Crystallography; Math-ph; Topology; math.DG; math.MP},
  modificationdate = {2023-04-28T18:57:28},
  owner            = {saulius},
  primaryclass     = {math.DG},
}

@Article{Eon2018,
  author           = {Jean-Guillaume Eon},
  journal          = {Symmetry},
  title            = {Symmetry and topology: the 11 uninodal planar nets revisited},
  year             = {2018},
  month            = {jan},
  number           = {2},
  pages            = {35},
  volume           = {10},
  creationdate     = {2023-04-28T19:33:07},
  doi              = {10.3390/sym10020035},
  file             = {:by-author/E/Eon/2018_Eon_35.pdf:PDF},
  keywords         = {Crystallography; Topology},
  modificationdate = {2023-04-28T19:33:41},
  owner            = {saulius},
  publisher        = {{MDPI} {AG}},
}

@Article{Matthews1968,
  author           = {Matthews, B. W.},
  journal          = {Journal of molecular biology},
  title            = {Solvent content of protein crystals},
  year             = {1968},
  issn             = {0022-2836},
  month            = apr,
  pages            = {491--497},
  volume           = {33},
  chemicals        = {Proteins, Solvents},
  citation-subset  = {IM},
  completed        = {1969-02-14},
  country          = {Netherlands},
  creationdate     = {2023-05-02T10:22:30},
  doi              = {10.1016/0022-2836(68)90205-2},
  file             = {:by-author/M/Matthews/1968_Matthews_491.pdf:PDF},
  issn-linking     = {0022-2836},
  issue            = {2},
  keywords         = {Crystallography; Matthews Coefficient; Molecular Weight (MW); Proteins; Solvents},
  modificationdate = {2023-05-02T10:47:51},
  nlm-id           = {2985088R},
  owner            = {saulius},
  pii              = {0022-2836(68)90205-2},
  pmid             = {5700707},
  pubmodel         = {Print},
  pubstate         = {ppublish},
  revised          = {2022-10-06},
}

@Article{Matthews1976,
  author           = {B. W. Matthews},
  journal          = {Annual Review of Physical Chemistry},
  title            = {{X}-ray crystallographic studies of proteins},
  year             = {1976},
  month            = {oct},
  number           = {1},
  pages            = {493--493},
  volume           = {27},
  creationdate     = {2023-05-02T10:25:55},
  doi              = {10.1146/annurev.pc.27.100176.002425},
  file             = {:by-author/M/Matthews/1976_Matthews_493.pdf:PDF},
  keywords         = {Crystallography; Matthews Coefficient; Molecular Weight (MW); Proteins; Solvents},
  modificationdate = {2023-05-02T10:27:20},
  owner            = {saulius},
  publisher        = {Annual Reviews},
}

@Article{Kantardjieff2003,
  author           = {Kantardjieff, Katherine A. and Rupp, Bernhard},
  journal          = {Protein Science},
  title            = {Matthews coefficient probabilities: Improved estimates for unit cell contents of proteins, {DNA}, and protein–nucleic acid complex crystals},
  year             = {2003},
  issn             = {1469-896X},
  month            = {Sep},
  number           = {9},
  pages            = {1865--1871},
  volume           = {12},
  abstract         = {Estimating the number of molecules in the crystallographic asymmetric unit is one of the first steps in a macromolecular structure determination. Based on a survey of 15,641 crystallographic Protein Data Bank (PDB) entries the distribution of VM, the crystal volume per unit of protein molecular weight, known as Matthews coefficient, has been reanalyzed. The range of values and frequencies has changed in the 30 years since Matthews first analysis of protein crystal solvent content. In the statistical analysis, complexes of proteins and nucleic acids have been treated as a separate group. In addition, the VM distribution for nucleic acid crystals has been examined for the first time. Observing that resolution is a significant discriminator of VM, an improved estimator for the probabilities of the number of molecules in the crystallographic asym- metric unit has been implemented, using resolution as additional information.},
  chemicals        = {DNA-Binding Proteins, Nucleic Acids, Proteins, DNA},
  citation-subset  = {IM},
  completed        = {2004-06-24},
  country          = {United States},
  creationdate     = {2014-05-27T00:00:00},
  doi              = {10.1110/ps.0350503},
  file             = {:by-author/K/Kantardjieff/2003_Kantardjieff_1865.pdf:PDF},
  issn-linking     = {0961-8368},
  issue            = {9},
  keywords         = {Matthews Coefficient; Matthews Probabilities; Protein Crystallography; Protein Crystals; Solvent Content},
  modificationdate = {2023-05-02T11:03:33},
  nlm-id           = {9211750},
  owner            = {em},
  pmc              = {PMC2323984},
  pmid             = {12930986},
  publisher        = {Wiley-Blackwell},
  pubmodel         = {Print},
  pubstate         = {ppublish},
  revised          = {2019-05-13},
  timestamp        = {2014.05.27},
}

@Article{Gilligan2023,
  author           = {Luke P. J. Gilligan and Matteo Cobelli and Valentin Taufour and Stefano Sanvito},
  journal          = {arXiv},
  title            = {A rule-free workflow for the automated generation of databases from scientific literature},
  year             = {2023},
  month            = jan,
  pages            = {1--12},
  abstract         = {In recent times, transformer networks have achieved state-of-the-art performance in a wide range of natural language processing tasks. Here we present a workflow based on the fine-tuning of BERT models for different downstream tasks, which results in the automated extraction of structured information from unstructured natural language in scientific literature. Contrary to other methods for the automated extraction of structured compound-property relations from similar sources, our workflow does not rely on the definition of intricate grammar rules. Hence, it can be adapted to a new task without requiring extensive implementation efforts and knowledge. We test the data extraction performance by automatically generating a database of compounds and their associated Curie temperatures. This is compared with a manually curated database and one obtained with the state-of-the-art rule-based method. Finally, in order to demonstrate that the automatically extracted database can be used in a material-design workflow, we employ it to construct a machine-learning model predicting the Curie temperature based on a compound's chemical composition. This is quantitatively tested and compared with the best model constructed on manually-extracted data.},
  archiveprefix    = {arXiv},
  creationdate     = {2023-05-04T08:42:41},
  doi              = {10.48550/arXiv.2301.11689},
  eprint           = {2301.11689},
  file             = {:by-author/G/Gilligan/2023_Gilligan_1.pdf:PDF},
  keywords         = {Artificial Intelligence (AI); Data Extraction; Databases; Machine Learning (ML); Scientific Publications; cond-mat.mtrl-sci; physics.comp-ph; physics.data-an},
  modificationdate = {2023-05-04T08:44:09},
  owner            = {saulius},
  primaryclass     = {cond-mat.mtrl-sci},
}

@Article{Dickinson2001,
  author           = {Dickinson, S. R. and McGrath, K. M.},
  journal          = {The Analyst},
  title            = {Quantitative determination of binary and tertiary calcium carbonate mixtures using powder {X}-ray diffraction},
  year             = {2001},
  issn             = {0003-2654},
  month            = jul,
  pages            = {1118--1121},
  volume           = {126},
  abstract         = {The ability to determine the calcium carbonate polymorphic ratio of calcite, aragonite and vaterite in a mixture is important for a variety of applications, particularly the fields of biomineralisation and crystal engineering. Raman spectroscopy and powder X-ray diffraction were used to quantitatively determine the polymorphic composition of both binary and tertiary mixtures of calcium carbonate. It was found that the quantitative detection limits of powder X-ray diffraction were superior to both Raman and infrared spectroscopy.},
  chemicals        = {Calcium Carbonate},
  citation-subset  = {IM},
  completed        = {2001-10-04},
  country          = {England},
  creationdate     = {2023-05-04T12:55:05},
  doi              = {10.1039/b103004n},
  file             = {:by-author/D/Dickinson/2001_Dickinson_1118.pdf:PDF},
  issn-linking     = {0003-2654},
  issue            = {7},
  keywords         = {Aragonote; Biomineralisation; Calcite; Calcium Carbonate, Chemistry; Powder Diffraction; Spectrophotometry, Infrared; X-Ray Diffraction, Methods},
  modificationdate = {2023-05-04T13:00:30},
  nlm-id           = {0372652},
  owner            = {saulius},
  pmid             = {11478646},
  pubmodel         = {Print},
  pubstate         = {ppublish},
  revised          = {2019-08-22},
}

@Article{Nesterov2006,
  author           = {Yurii Nesterov and B. T. Polyak},
  journal          = {Mathematical Programming},
  title            = {Cubic regularization of {N}ewton method and its global performance},
  year             = {2006},
  month            = {apr},
  number           = {1},
  pages            = {177--205},
  volume           = {108},
  creationdate     = {2023-05-07T14:21:18},
  doi              = {10.1007/s10107-006-0706-8},
  file             = {:by-author/N/Nesterov/2006_Nesterov_177.pdf:PDF},
  keywords         = {Newton Method; Optimisation},
  modificationdate = {2023-05-07T14:48:57},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media {LLC}},
}

@Manuscript{Lecouat2021,
  author           = {Bruno Lecouat and Jean Ponce and Julien Mairal},
  title            = {{L}ucas-{K}anade reloaded: end-to-end super-resolution from raw image bursts},
  year             = {2021},
  doi              = {10.48550/arXiv.2104.06191},
  keywords         = {Artificial Intelligence (AI); Artificial Neural Networks (ANN); Deep Learning (DL); Image Processing; Image Recognition; Machine Learning (ML); cs.CV; eess.IV},
  month            = apr,
  abstract         = {This presentation addresses the problem of reconstructing a high-resolution image from multiple lower-resolution snapshots captured from slightly different viewpoints in space and time. Key challenges for solving this problem include (i) aligning the input pictures with sub-pixel accuracy, (ii) handling raw (noisy) images for maximal faithfulness to native camera data, and (iii) designing/learning an image prior (regularizer) well suited to the task. We address these three challenges with a hybrid algorithm building on the insight from Wronski et al. that aliasing is an ally in this setting, with parameters that can be learned end to end, while retaining the interpretability of classical approaches to inverse problems. The effectiveness of our approach is demonstrated on synthetic and real image bursts, setting a new state of the art on several benchmarks and delivering excellent qualitative results on real raw bursts captured by smartphones and prosumer cameras.},
  archiveprefix    = {arXiv},
  creationdate     = {2023-05-07T14:51:49},
  eprint           = {2104.06191},
  file             = {:by-author/L/Lecouat/2021_Lecouat_1.pdf:PDF},
  journal          = {arXiv (ICCV 2021)},
  modificationdate = {2023-05-07T14:58:19},
  owner            = {saulius},
  pages            = {1--16},
  primaryclass     = {cs.CV},
}

@InProceedings{Lecouat2021a,
  author           = {Bruno Lecouat and Jean Ponce and Julien Mairal},
  booktitle        = {2021 {IEEE}/{CVF} International Conference on Computer Vision ({ICCV})},
  title            = {{L}ucas-{K}anade reloaded: end-to-end super-resolution from raw image bursts},
  year             = {2021},
  month            = {oct},
  pages            = {2350--2359},
  publisher        = {{IEEE}},
  creationdate     = {2023-05-07T14:56:55},
  doi              = {10.1109/iccv48922.2021.00237},
  file             = {:by-author/L/Lecouat/2021_Lecouat_2350.pdf:PDF},
  keywords         = {Artificial Intelligence (AI); Artificial Neural Networks (ANN); Deep Learning (DL); Image Processing; Image Recognition; Machine Learning (ML)},
  modificationdate = {2023-05-07T15:00:45},
  owner            = {saulius},
}

@Manuscript{Navon2020,
  author           = {Aviv Navon and Idan Achituve and Haggai Maron and Gal Chechik and Ethan Fetaya},
  title            = {Auxiliary learning by implicit differentiation},
  year             = {2020},
  doi              = {10.48550/arXiv.2007.02693},
  keywords         = {Artificial Intelligence (AI); Artificial Neural Networks (ANN); Auxiliary Learning; Deep Learning (DL); Machine Learning (ML); cs.CV; cs.LG; stat.ML},
  month            = jun,
  abstract         = {Training neural networks with auxiliary tasks is a common practice for improving the performance on a main task of interest. Two main challenges arise in this multi-task learning setting: (i) designing useful auxiliary tasks; and (ii) combining auxiliary tasks into a single coherent loss. Here, we propose a novel framework, AuxiLearn, that targets both challenges based on implicit differentiation. First, when useful auxiliaries are known, we propose learning a network that combines all losses into a single coherent objective function. This network can learn non-linear interactions between tasks. Second, when no useful auxiliary task is known, we describe how to learn a network that generates a meaningful, novel auxiliary task. We evaluate AuxiLearn in a series of tasks and domains, including image segmentation and learning with attributes in the low data regime, and find that it consistently outperforms competing methods.},
  archiveprefix    = {arXiv},
  creationdate     = {2023-05-07T17:45:23},
  eprint           = {2007.02693},
  file             = {:by-author/N/Navon/2020_Navon_1.pdf:PDF},
  modificationdate = {2023-05-07T17:47:52},
  owner            = {saulius},
  pages            = {1--20},
  primaryclass     = {cs.CV},
}

@InBook{Gallier2011,
  author           = {Jean H. Gallier},
  chapter          = {12},
  pages            = {447--484},
  title            = {Quadratic optimization problems},
  year             = {2011},
  creationdate     = {2023-05-07T18:09:01},
  file             = {:by-author/G/Gallier/2011_Gallier_447.pdf:PDF},
  keywords         = {Deep Learning (DL); Mathematics; Quadratic Optimisation},
  modificationdate = {2023-05-07T18:11:30},
  owner            = {saulius},
  url              = {https://www.cis.upenn.edu/~cis5150/cis515-11-sl12.pdf},
}

@Article{Levenberg1944,
  author           = {Kenneth Levenberg},
  journal          = {Quarterly of Applied Mathematics},
  title            = {A method for the solution of certain non-linear problems in least squares},
  year             = {1944},
  number           = {2},
  pages            = {164--168},
  volume           = {2},
  comment          = {Cited in Gallier2011.},
  creationdate     = {2023-05-07T18:18:36},
  doi              = {10.1090/qam/10666},
  file             = {:by-author/L/Levenberg/1944_Levenberg_164.pdf:PDF},
  keywords         = {Mathematics; Quadratic Optimisation},
  modificationdate = {2023-05-07T18:19:54},
  owner            = {saulius},
  publisher        = {American Mathematical Society ({AMS})},
  url              = {https://www.ams.org/journals/qam/1944-02-02/S0033-569X-1944-10666-0/},
}

@Article{Marquardt1963,
  author           = {Donald W. Marquardt},
  journal          = {Journal of the Society for Industrial and Applied Mathematics},
  title            = {An algorithm for least-squares estimation of nonlinear parameters},
  year             = {1963},
  month            = {jun},
  number           = {2},
  pages            = {431--441},
  volume           = {11},
  comment          = {Cited in Gallier2011.},
  creationdate     = {2023-05-07T18:22:29},
  doi              = {10.1137/0111030},
  file             = {:by-author/M/Marquardt/1963_Marquardt_431.pdf:PDF},
  keywords         = {Mathematics; Quadratic Optimisation},
  modificationdate = {2023-05-07T18:24:44},
  owner            = {saulius},
  publisher        = {Society for Industrial {\&} Applied Mathematics ({SIAM})},
}

@InCollection{Cassez2023,
  author           = {Franck Cassez and Joanne Fuller and Milad K. Ghale and David J. Pearce and Horacio M. A. Quiles},
  booktitle        = {Formal Methods},
  publisher        = {Springer International Publishing},
  title            = {Formal and~Executable Semantics of~the~Ethereum Virtual Machine in~Dafny},
  year             = {2023},
  pages            = {571--583},
  creationdate     = {2023-05-08T20:51:10},
  doi              = {10.1007/978-3-031-27481-7_32},
  file             = {:by-author/C/Cassez/2023_Cassez_571.pdf:PDF},
  keywords         = {Computer Science (CS); Ethereum; Formal Methods; Formal Verification; Program Correctness; Software Verification},
  modificationdate = {2023-05-08T20:54:27},
  owner            = {saulius},
}

@InCollection{Paganoni2023,
  author           = {Marco Paganoni and Carlo A. Furia},
  booktitle        = {Formal Methods},
  publisher        = {Springer International Publishing},
  title            = {Verifying functional correctness properties at the level of {J}ava bytecode},
  year             = {2023},
  pages            = {343--363},
  creationdate     = {2023-05-08T20:57:44},
  doi              = {10.1007/978-3-031-27481-7_20},
  file             = {:by-author/P/Paganoni/2023_Paganoni_343.pdf:PDF},
  keywords         = {Computer Science (CS); Formal Methods; Formal Verification; JVM; Java; Program Correctness; Software Verification},
  modificationdate = {2023-05-14T09:50:25},
  owner            = {saulius},
}

@InCollection{Ichimiya2004,
  author           = {Ayahiko Ichimiya and Philip I. Cohen},
  booktitle        = {Reflection High-Energy Electron Diffraction},
  publisher        = {Cambridge University Press},
  title            = {Kinematic electron diffraction},
  year             = {2004},
  month            = {dec},
  pages            = {130--153},
  creationdate     = {2023-05-14T09:51:17},
  doi              = {10.1017/cbo9780511735097.011},
  file             = {:by-author/I/Ichimiya/2004_Ichimiya_130.pdf:PDF},
  keywords         = {Crystallography; Diffraction; Electron Diffraction; Kinematic Theory},
  modificationdate = {2023-05-14T09:52:46},
  owner            = {saulius},
  url              = {https://www.cambridge.org/core/books/reflection-highenergy-electron-diffraction/kinematic-electron-diffraction/B196043CC83D033173D02DAE5EDCCB84#},
}

@Article{Diederichs2013a,
  author           = {K. Diederichs and P. A. Karplus},
  journal          = {Acta Crystallographica Section D Biological Crystallography},
  title            = {Better models by discarding data?},
  year             = {2013},
  month            = {jun},
  number           = {7},
  pages            = {1215--1222},
  volume           = {69},
  comment          = {Cited by Takanori Nakane <tnakane.protein@osaka-u.ac.jp> in his 2023-05-14 07:57 e-mail. Contains discussion of CC(1/2) and CC(*).},
  creationdate     = {2023-05-14T10:43:01},
  doi              = {10.1107/s0907444913001121},
  file             = {:by-author/D/Diederichs/2013_Diederichs_1215.pdf:PDF},
  keywords         = {Crystallography; Data Processing; Diffraction; X-ray Crystallography},
  modificationdate = {2023-05-14T10:45:31},
  owner            = {saulius},
  publisher        = {International Union of Crystallography ({IUCr})},
}

@Article{Diederichs1997,
  author           = {Diederichs, K. and Karplus, P. A.},
  journal          = {Nature structural biology},
  title            = {Improved {R}-factors for diffraction data analysis in macromolecular crystallography.},
  year             = {1997},
  issn             = {1072-8368},
  month            = apr,
  pages            = {269--275},
  volume           = {4},
  abstract         = {The quantity Rsym (also called Rmerge) is almost universally used for describing X-ray diffraction data quality. Here, we prove that Rsym is seriously flawed, because it has an implicit dependence on the redundance of the data. A corrected R-factor, Rmeas, is introduced as the equivalent robust indicator of data consistency. In addition, we introduce Rmrgd an R-factor that reflects the gain in accuracy upon averaging of equivalent reflections, as a useful indicator of the quality of reduced data. These new data quality indicators better reveal the benefits of highly redundant data and should stimulate improvements in data quality through increased merging of data from multiple crystals.},
  chemicals        = {Urease},
  citation-subset  = {IM},
  comment          = {Cited by Takanori Nakane <tnakane.protein@osaka-u.ac.jp> in his 2023-05-14 07:57 e-mail.},
  completed        = {1997-04-30},
  country          = {United States},
  creationdate     = {2023-05-14T10:48:36},
  doi              = {10.1038/nsb0497-269},
  file             = {:by-author/D/Diederichs/1997_Diederichs_269.pdf:PDF},
  issn-linking     = {1072-8368},
  issue            = {4},
  keywords         = {Crystallography; Crystallography, X-Ray, Methods; Data Processing; Diffraction; Fourier Analysis; Models, Statistical; Reproducibility of Results; Software; Statistics as Topic; Urease, Chemistry; X-ray Crystallography},
  modificationdate = {2023-05-14T10:51:00},
  nlm-id           = {9421566},
  owner            = {saulius},
  pmid             = {9095194},
  pubmodel         = {Print},
  pubstate         = {ppublish},
  revised          = {2019-10-24},
  url              = {https://kops.uni-konstanz.de/bitstream/123456789/7948/1/Improved_R_factors_for_diffraction_data_analysis_in_macromolecular_crystallography.pdf},
}

@Article{Choudhary2023,
  author           = {Kamal Choudhary and Brian DeCost and Lily Major and Keith Butler and Jeyan Thiyagalingam and Francesca Tavazza},
  journal          = {Digital Discovery},
  title            = {Unified graph neural network force-field for the periodic table: solid state applications},
  year             = {2023},
  number           = {2},
  pages            = {346--355},
  volume           = {2},
  creationdate     = {2023-05-18T07:52:17},
  doi              = {10.1039/d2dd00096b},
  file             = {:by-author/C/Choudhary/2023_Choudhary_346.pdf:PDF},
  keywords         = {Density Functional Theory (DFT); Machine Learning (ML); Phonon Spectra; Rama Spectra},
  modificationdate = {2023-05-18T07:53:27},
  owner            = {saulius},
  publisher        = {Royal Society of Chemistry ({RSC})},
}

@Article{Wilson2021,
  author           = {Samantha L. Wilson and Gregory P. Way and Wout Bittremieux and Jean-Paul Armache and Melissa A. Haendel and Michael M. Hoffman},
  journal          = {{FEBS} Letters},
  title            = {Sharing biological data: why, when, and how},
  year             = {2021},
  month            = {apr},
  number           = {7},
  pages            = {847--863},
  volume           = {595},
  creationdate     = {2023-05-20T09:36:14},
  doi              = {10.1002/1873-3468.14067},
  file             = {:by-author/W/Wilson/2021_Wilson_847.pdf:PDF},
  keywords         = {Data Sharing; FAIR Principles; Metadata},
  modificationdate = {2023-05-20T09:36:57},
  owner            = {saulius},
  publisher        = {Wiley},
}

@Article{Kaiser2023,
  author           = {Jocelyn Kaiser and Jeffrey Brainard},
  journal          = {Science},
  title            = {Ready, set, share!},
  year             = {2023},
  month            = {jan},
  number           = {6630},
  pages            = {322--325},
  volume           = {379},
  creationdate     = {2023-05-20T09:40:19},
  doi              = {10.1126/science.adg8142},
  file             = {:by-author/K/Kaiser/2023_Kaiser_322.pdf:PDF},
  keywords         = {Data Sharing},
  modificationdate = {2023-05-20T09:40:45},
  owner            = {saulius},
  publisher        = {American Association for the Advancement of Science ({AAAS})},
}

@Article{2016,
  author           = {{Editorial}},
  journal          = {Nature Methods},
  title            = {Data sharing comes to structural biology},
  year             = {2016},
  month            = {apr},
  number           = {5},
  pages            = {381--381},
  volume           = {13},
  creationdate     = {2023-05-20T09:42:38},
  doi              = {10.1038/nmeth.3862},
  file             = {:by-author/2016_Editorial_381.pdf:PDF},
  keywords         = {Data Sharing},
  modificationdate = {2023-05-20T09:43:58},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media {LLC}},
}

@Article{Gewin2016,
  author           = {Virginia Gewin},
  journal          = {Nature},
  title            = {Data sharing: An open mind on open data},
  year             = {2016},
  month            = {jan},
  number           = {7584},
  pages            = {117--119},
  volume           = {529},
  creationdate     = {2023-05-20T09:48:56},
  doi              = {10.1038/nj7584-117a},
  file             = {:by-author/G/Gewin/2016_Gewin_117.pdf:PDF},
  keywords         = {Data Sharing},
  modificationdate = {2023-05-20T09:49:33},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media {LLC}},
}

@Article{First2023,
  author           = {First, Emily and Rabe, Markus N. and Ringer, Talia and Brun, Yuriy},
  title            = {Baldur: whole-proof generation and repair with large language models},
  year             = {2023},
  pages            = {1--15},
  comment          = {Recommended by Karolis Petrauskas.},
  copyright        = {arXiv.org perpetual, non-exclusive license},
  creationdate     = {2023-05-22T14:14:40},
  doi              = {10.48550/ARXIV.2303.04910},
  file             = {:by-author/F/First/2023_First_1.pdf:PDF},
  keywords         = {FOS: Computer and Information Sciences; Logic in Computer Science (cs.LO); Machine Learning (cs.LG); Software Engineering (cs.SE)},
  modificationdate = {2023-05-22T14:20:22},
  owner            = {saulius},
  publisher        = {arXiv},
}

@Article{Rombach2021,
  author           = {Robin Rombach and Andreas Blattmann and Dominik Lorenz and Patrick Esser and Björn Ommer},
  title            = {High-resolution image synthesis with latent diffusion models},
  year             = {2021},
  month            = dec,
  pages            = {1--45},
  abstract         = {By decomposing the image formation process into a sequential application of denoising autoencoders, diffusion models (DMs) achieve state-of-the-art synthesis results on image data and beyond. Additionally, their formulation allows for a guiding mechanism to control the image generation process without retraining. However, since these models typically operate directly in pixel space, optimization of powerful DMs often consumes hundreds of GPU days and inference is expensive due to sequential evaluations. To enable DM training on limited computational resources while retaining their quality and flexibility, we apply them in the latent space of powerful pretrained autoencoders. In contrast to previous work, training diffusion models on such a representation allows for the first time to reach a near-optimal point between complexity reduction and detail preservation, greatly boosting visual fidelity. By introducing cross-attention layers into the model architecture, we turn diffusion models into powerful and flexible generators for general conditioning inputs such as text or bounding boxes and high-resolution synthesis becomes possible in a convolutional manner. Our latent diffusion models (LDMs) achieve a new state of the art for image inpainting and highly competitive performance on various tasks, including unconditional image generation, semantic scene synthesis, and super-resolution, while significantly reducing computational requirements compared to pixel-based DMs. Code is available at https://github.com/CompVis/latent-diffusion .},
  archiveprefix    = {arXiv},
  comment          = {Cited in https://www.youtube.com/watch?v=nc9kq9ZkNV8 .},
  creationdate     = {2023-06-03T17:54:45},
  eprint           = {2112.10752},
  file             = {:by-author/R/Rombach/2021_Rombach_1.pdf:PDF},
  keywords         = {Artificial Intelligence (AI); Computer Science (CS); Image Generation; Language Models; cs.CV},
  modificationdate = {2023-06-03T17:57:39},
  owner            = {saulius},
  primaryclass     = {cs.CV},
}

@Article{Racioppi2023,
  author           = {Stefano Racioppi and Maosheng Miao and Eva Zurek},
  journal          = {Chemistry of Materials},
  title            = {Intercalating helium into {A}-site vacant perovskites},
  year             = {2023},
  month            = {may},
  comment          = {Mentioned by Kamil Dziubek <dziubek@lens.unifi.it> in his 2023-06-04 22:39 e-mail to grazulis@ibt.lt.},
  creationdate     = {2023-06-05T10:02:59},
  doi              = {10.1021/acs.chemmater.3c00353},
  file             = {:by-author/R/Racioppi/2023_Racioppi_.pdf:PDF},
  keywords         = {Perovskites; TCOD; Theoretical Structrues},
  modificationdate = {2023-06-05T10:07:27},
  owner            = {saulius},
  publisher        = {American Chemical Society ({ACS})},
}

@Article{Nature2023,
  author           = {{Nature}},
  journal          = {Nature},
  title            = {For chemists, the {AI} revolution has yet to happen},
  year             = {2023},
  month            = {may},
  number           = {7961},
  pages            = {438--438},
  volume           = {617},
  comment          = {From: Andrius Merkys <andrius.merkys@gmail.com>
Date: 2023-05-31 09:57
Sveiki,
Klimentas parodė IMO visai aktualų mums Nature vedamąjį „For chemists, the AI revolution has yet to happen“:
https://www.nature.com/articles/d41586-023-01612-x
Iki,
Andrius},
  creationdate     = {2023-06-05T11:01:46},
  doi              = {10.1038/d41586-023-01612-x},
  file             = {:by-author/N/Nature/2023_Nature_438.pdf:PDF},
  keywords         = {Artificial Intelligence (AI); Chemistry; Chemoinformatics; Machine Learning (ML)},
  modificationdate = {2023-06-05T11:03:59},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media {LLC}},
}

@InBook{Hauser2004,
  author           = {Hauser, Andreas},
  pages            = {155--198},
  publisher        = {Springer Berlin Heidelberg},
  title            = {Light-induced spin crossover and the high-spin{\textrightarrow}low-spin relaxation},
  year             = {2004},
  address          = {Berlin, Heidelberg},
  isbn             = {978-3-540-36774-1},
  abstract         = {The discovery of a light-induced spin transition at cryogenic temperatures in a series of iron(II) spin-crossover compounds in 1984 has had an enormous impact on spin-crossover research. Apart from being an interesting photophysical phenomenon in its own right, it provided the means of studying the dynamics of the intersystem crossing process between the high-spin and the low-spin state in a series of compounds and over a large temperature range. It could thus be firmly established that intersystem crossing in spin-crossover compounds is a tunnelling process, with a limiting low-temperature lifetime below 50 K and a thermally activated region above 100 K. This review begins with an elucidation of the mechanism of the light-induced spin transition, followed by an in depth discussion of the chemical and physical factors, including cooperative effects, governing the lifetimes of the light-induced metastable states.},
  booktitle        = {Spin Crossover in Transition Metal Compounds II},
  comment          = {Cited in https://en.wikipedia.org/wiki/Spin_crossover (https://en.wikipedia.org/w/index.php?title=Spin_crossover&oldid=1122018280).},
  creationdate     = {2023-06-06T10:21:11},
  doi              = {10.1007/b95416},
  file             = {:by-author/H/Hauser/2004_Hauser_155.pdf:PDF},
  keywords         = {Light-sensitive Materials; Spin Crossover},
  modificationdate = {2023-06-06T10:27:07},
  owner            = {saulius},
  url              = {https://doi.org/10.1007/b95416},
}

@Article{Banerjee2021,
  author           = {Amartya S. Banerjee},
  journal          = {Journal of the Mechanics and Physics of Solids},
  title            = {Ab initio framework for systems with helical symmetry: Theory, numerical implementation and applications to torsional deformations in nanostructures},
  year             = {2021},
  month            = {sep},
  pages            = {104515},
  volume           = {154},
  creationdate     = {2023-06-06T11:06:50},
  doi              = {10.1016/j.jmps.2021.104515},
  file             = {:by-author/B/Banerjee/2021_Banerjee_104515.pdf:PDF;:by-author/B/Banerjee/2021_Banerjee_104515_arXiv.pdf:PDF},
  keywords         = {Helical Groups; Symmetry},
  modificationdate = {2023-06-06T11:09:13},
  owner            = {saulius},
  publisher        = {Elsevier {BV}},
}

@InProceedings{Leino2013,
  author           = {Leino, Rustan},
  booktitle        = {ITP 2013},
  title            = {Automating theorem proving with {SMT}},
  year             = {2013},
  month            = {May},
  pages            = {1--15},
  abstract         = {The power and automation offered by modern satisfiability-modulotheories (SMT) solvers is changing the landscape for mechanized formal theorem proving. For instance, the SMT-based program verifier Dafny supports a number of proof features traditionally found only in interactive proof assistants, like inductive, co-inductive, and declarative proofs. To show that proof tools rooted in SMT are growing up, this paper presents, using Dafny, a series of examples that illustrate how theorems are expressed and proved. Since the SMT solver takes care of many formal trivialities automatically, users can focus more of their time on the creative ingredients of proofs.},
  creationdate     = {2023-06-14T18:54:24},
  doi              = {10.1007/978-3-642-39634-2_2},
  edition          = {ITP 2013},
  file             = {:by-author/L/Leino/2013_Leino_1.pdf:PDF},
  keywords         = {Computer Science (CS); Formal Verification; STM Provers; Sofrware Correctness Proofs},
  modificationdate = {2023-06-14T18:56:08},
  owner            = {saulius},
  url              = {https://www.microsoft.com/en-us/research/publication/automating-theorem-proving-smt/},
}

@InProceedings{Zarembo2016,
  author           = {Imants Zarembo and Artis Teilans and Knut Barghorn and Yuri Merkuryev and Gundega Berina},
  booktitle        = {2016 International Conference on Systems Informatics, Modelling and Simulation ({SIMS})},
  title            = {Methodology for similarity assessment of relational data models and semantic ontologies},
  year             = {2016},
  month            = {jun},
  pages            = {119--123},
  publisher        = {{IEEE}},
  comment          = {Barghorn, Knut <knut.barghorn@jade-hs.de> will be visiting our University on June 21st, 2023; this is one of his 3 papers found on ResearcGate and on the Web.},
  creationdate     = {2023-06-16T09:43:58},
  doi              = {10.1109/sims.2016.21},
  file             = {:by-author/Z/Zarembo/2016_Zarembo_119.pdf:PDF},
  keywords         = {Computer Science (CS); Data Management; Ontologies; Relational Databases; Semantic Web},
  modificationdate = {2023-06-16T09:48:36},
  owner            = {saulius},
}

@Article{Zarembo2015,
  author           = {Imants Zarembo},
  journal          = {Environment. Technology. Resources. Proceedings of the International Scientific and Practical Conference},
  title            = {Automatic transformation of relational database schema into {OWL} ontologies},
  year             = {2015},
  month            = {jun},
  pages            = {217},
  volume           = {3},
  comment          = {Cited in Zarembo2016.},
  creationdate     = {2023-06-16T09:49:40},
  doi              = {10.17770/etr2015vol3.170},
  file             = {:by-author/Z/Zarembo/2015_Zarembo_217.pdf:PDF},
  keywords         = {Computer Science (CS); Data Management; Ontologies; Relational Databases; Semantic Web},
  modificationdate = {2023-06-16T09:51:57},
  owner            = {saulius},
  publisher        = {Rezekne Academy of Technologies},
}

@Article{Zarembo2015a,
  author           = {Imants Zarembo and Artis Teilans and Aldis Rausis and Jazeps Buls},
  journal          = {Procedia Computer Science},
  title            = {Assessment of Name Based Algorithms for Land Administration Ontology Matching},
  year             = {2015},
  pages            = {53--61},
  volume           = {43},
  comment          = {Cited in Zarembo2016.},
  creationdate     = {2023-06-16T09:52:20},
  doi              = {10.1016/j.procs.2014.12.008},
  file             = {:by-author/Z/Zarembo/2015_Zarembo_53.pdf:PDF},
  keywords         = {Computer Science (CS); Data Management; Ontologies; Relational Databases; Semantic Web},
  modificationdate = {2023-06-16T09:54:05},
  owner            = {saulius},
  publisher        = {Elsevier {BV}},
}

@Book{Euzenat2013,
  author           = {Jérôme Euzenat and Pavel Shvaiko},
  publisher        = {Springer Berlin Heidelberg},
  title            = {Ontology matching},
  year             = {2013},
  comment          = {Cited in Zarembo2016.
Only table of contents in the PDF... :(.},
  creationdate     = {2023-06-16T09:57:02},
  doi              = {10.1007/978-3-642-38721-0},
  file             = {:by-author/E/Euzenat/2013_Euzenat_1.pdf:PDF},
  keywords         = {Computer Science (CS); Data Management; Ontologies; Semantic Web},
  modificationdate = {2023-06-16T09:59:23},
  owner            = {saulius},
  pages            = {1--14},
}

@InProceedings{Yang2010a,
  author           = {Shihan Yang and Ying Zheng and Xuehui Yang},
  booktitle        = {2010 3rd International Conference on Computer Science and Information Technology},
  title            = {Semi-automatically building ontologies from relational databases},
  year             = {2010},
  month            = {jul},
  pages            = {150--154},
  publisher        = {{IEEE}},
  comment          = {Cited in Zarembo2016.},
  creationdate     = {2023-06-16T10:00:04},
  doi              = {10.1109/iccsit.2010.5563924},
  file             = {:by-author/Y/Yang/2010_Yang_150.pdf:PDF},
  keywords         = {Computer Science (CS); Data Management; Ontologies; Relational Databases; Semantic Web},
  modificationdate = {2023-06-16T10:01:25},
  owner            = {saulius},
}

@InProceedings{Trinkunas2007,
  author           = {Justas Trinkunas and Olegas Vasilecas},
  booktitle        = {Proceedings of the 2007 international conference on Computer systems and technologies - {CompSysTech} {\textquotesingle}07},
  title            = {Building ontologies from relational databases using reverse engineering methods},
  year             = {2007},
  pages            = {1--6},
  publisher        = {{ACM} Press},
  comment          = {Cited in Zarembo2016.},
  creationdate     = {2023-06-16T10:04:12},
  doi              = {10.1145/1330598.1330614},
  file             = {:by-author/T/Trinkunas/2007_Trinkunas_1.pdf:PDF},
  keywords         = {Computer Science (CS); Data Management; Ontologies; Relational Databases; Semantic Web},
  modificationdate = {2023-06-16T10:05:24},
  owner            = {saulius},
}

@InCollection{Shvaiko2005,
  author           = {Pavel Shvaiko and J{\'{e}}r{\^{o}}me Euzenat},
  booktitle        = {Lecture Notes in Computer Science},
  publisher        = {Springer Berlin Heidelberg},
  title            = {A Survey of Schema-Based Matching Approaches},
  year             = {2005},
  pages            = {146--171},
  comment          = {Cited in Zarembo2016.},
  creationdate     = {2023-06-16T10:06:03},
  doi              = {10.1007/11603412_5},
  file             = {:by-author/S/Shvaiko/2005_Shvaiko_146.pdf:PDF},
  keywords         = {Computer Science (CS); Data Management; Ontologies; Relational Databases; Semantic Web},
  modificationdate = {2023-06-16T10:06:32},
  owner            = {saulius},
}

@InCollection{Maedche2002,
  author           = {Alexander Maedche and Steffen Staab},
  booktitle        = {Knowledge Engineering and Knowledge Management: Ontologies and the Semantic Web},
  publisher        = {Springer Berlin Heidelberg},
  title            = {Measuring Similarity between Ontologies},
  year             = {2002},
  pages            = {251--263},
  comment          = {Cited in Zarembo2016.},
  creationdate     = {2023-06-16T10:10:03},
  doi              = {10.1007/3-540-45810-7_24},
  file             = {:by-author/M/Maedche/2002_Maedche_251.pdf:PDF},
  keywords         = {Computer Science (CS); Data Management; Ontologies; Ontology Similarities; Semantic Web; Similarity Measures},
  modificationdate = {2023-06-16T10:10:52},
  owner            = {saulius},
}

@Article{Rahm2001,
  author           = {Erhard Rahm and Philip A. Bernstein},
  journal          = {The {VLDB} Journal},
  title            = {A survey of approaches to automatic schema matching},
  year             = {2001},
  month            = {dec},
  number           = {4},
  pages            = {334--350},
  volume           = {10},
  comment          = {Cited in Zarembo2016.},
  creationdate     = {2023-06-16T10:12:22},
  doi              = {10.1007/s007780100057},
  file             = {:by-author/R/Rahm/2001_Rahm_334.pdf:PDF},
  keywords         = {Computer Science (CS); Data Management; Ontologies; Relational Databases; Semantic Web},
  modificationdate = {2023-06-16T10:13:10},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media {LLC}},
}

@Book{Bundy1994,
  author           = {Bundy, A.},
  publisher        = {Springer Berlin Heidelberg},
  title            = {Automated deduction — {CADE}-12: 12th international conference on automated deduction {N}ancy, {F}rance, {J}une 26--july 1, 1994 proceedings},
  year             = {1994},
  isbn             = {9780387581569},
  series           = {Lecture Notes in Computer Science},
  comment          = {Table of COntents only.
Reportedly contains the QED manifesto (https://en.wikipedia.org/wiki/QED_manifesto).
Bibliography initially taken from the https://books.google.lt/books?id=EeNIAQAAIAAJ url.},
  creationdate     = {2023-06-17T17:01:35},
  file             = {:by-author/B/Bundy/1994_Bundy_1.pdf:PDF},
  keywords         = {Automated Provers; Mathematics; Proof Assistants; Theorem Prooving},
  lccn             = {94017912},
  modificationdate = {2023-06-17T17:05:57},
  owner            = {saulius},
  pages            = {1-15},
  url              = {https://link.springer.com/content/pdf/bfm:978-3-540-48467-7/1},
}

@Manuscript{Boyer1994,
  author           = {Robert S. Boyer and N. G. de Bruijn and Gérard Huet and Andrzej Trybulec},
  title            = {The {QED} manifesto},
  year             = {1994},
  keywords         = {Automated Provers; Mathematics; Proof Assistants; Theorem Prooving},
  url              = {https://www.cs.ru.nl/~freek/qed/qed.pdf},
  comment          = {The document is described in Wikipedia (https://en.wikipedia.org/wiki/QED_manifesto).
The authorship was taken from Bundy1994 TOC, although the title is not present there, just a panel discussion is mentioned. Apparently, the text is published in the Bundy1994 collection, at least the attached PDF claims so.
Another URL is https://www.cse.chalmers.se/research/group/logic/TypesSS05/Extra/wiedijk_2.pdf that yields identical PDF as of now [2023-06-17T17:11+03:00].},
  creationdate     = {2023-06-17T17:06:42},
  file             = {:by-author/B/Boyer/1994_Boyer_238.pdf:PDF},
  modificationdate = {2023-06-17T17:14:33},
  owner            = {saulius},
  pages            = {238--251},
}

@Article{Wiedijk2007,
  author           = {Freek Wiedijk},
  journal          = {Studies in logic, grammar and rhetoric},
  title            = {The {QED} manifesto revisited},
  year             = {2007},
  number           = {23},
  pages            = {121--133},
  volume           = {10},
  creationdate     = {2023-06-17T17:16:59},
  file             = {:by-author/W/Wiedijk/2007_Wiedijk_121.pdf:PDF},
  keywords         = {Automated Provers; Mathematics; Proof Assistants; Theorem Prooving},
  modificationdate = {2023-06-17T17:20:22},
  owner            = {saulius},
  url              = {http://mizar.org/trybulec65/8.pdf},
}

@TechReport{Matuszewski1995,
  institution      = {Warsaw University, Department of Logic},
  title            = {The {QED} workshop {II}},
  year             = {1995},
  address          = {Liniarskiego street 4, 15-420 Białystok, Poland},
  month            = oct,
  number           = {L/1/95},
  type             = {techreport},
  creationdate     = {2023-06-17T17:24:50},
  editor           = {Roman Matuszewski},
  file             = {:by-author/M/Matuszewski/1995_Matuszewski_1.pdf:PDF},
  keywords         = {Automated Provers; Mathematics; Proof Assistants; Theorem Prooving},
  modificationdate = {2023-06-17T17:31:23},
  owner            = {saulius},
  pages            = {1--53},
  url              = {http://mizar.org/people/romat/qed95rep.pdf},
}

@Article{Kamareddine2007,
  author           = {Fairouz Kamareddine and Manuel Maarek and Krzysztof Retel and J. B. Wells},
  journal          = {Studies in logic, grammar and rhetoric},
  title            = {Gradual computerisation/formalisation of mathematical texts into {M}izar},
  year             = {2007},
  number           = {23},
  pages            = {95--120},
  volume           = {10},
  creationdate     = {2023-06-17T17:33:23},
  file             = {:by-author/K/Kamareddine/2007_Kamareddine_95.pdf:PDF},
  keywords         = {Automated Provers; Mathematics; Proof Assistants; The Mizar System; Theorem Prooving},
  modificationdate = {2023-06-17T17:35:53},
  owner            = {saulius},
  url              = {http://mizar.org/trybulec65/7.pdf},
}

@TechReport{Petrulionyte2023,
  author           = {Ieva Petrulionytė},
  institution      = {THOTH team, INRIA},
  title            = {Functional implicit differentiation},
  year             = {2023},
  month            = jun,
  type             = {mathesis},
  comment          = {Sent from ieva.petrulionyte@etu.univ-grenoble-alpes.fr <ieva.petrulionyte@etu.univ-grenoble-alpes.fr> to Saulius Gražulis <grazulis@ibt.lt> on 2023-06-17 12:49.},
  creationdate     = {2023-06-18T09:29:31},
  file             = {:by-author/P/Petrulionytė/2023_Petrulionytė_1.pdf:PDF},
  keywords         = {Artificail Neural Networks; Hessian; Machine Learning (ML); Mathematics; Optimisation},
  modificationdate = {2023-06-18T09:41:04},
  owner            = {saulius},
  pages            = {1--33},
}

@Article{Franceschi2017,
  author           = {Luca Franceschi and Michele Donini and Paolo Frasconi and Massimiliano Pontil},
  journal          = {Franceschi, L., Donini, M., Frasconi, P. & Pontil, M.. (2017). Forward and Reverse Gradient-Based Hyperparameter Optimization. Proceedings of the 34th International Conference on Machine Learning, in PMLR 70:1165-1173},
  title            = {Forward and Reverse Gradient-Based Hyperparameter Optimization},
  year             = {2017},
  month            = mar,
  pages            = {1--11},
  abstract         = {We study two procedures (reverse-mode and forward-mode) for computing the gradient of the validation error with respect to the hyperparameters of any iterative learning algorithm such as stochastic gradient descent. These procedures mirror two methods of computing gradients for recurrent neural networks and have different trade-offs in terms of running time and space requirements. Our formulation of the reverse-mode procedure is linked to previous work by Maclaurin et al. [2015] but does not require reversible dynamics. The forward-mode procedure is suitable for real-time hyperparameter updates, which may significantly speed up hyperparameter optimization on large datasets. We present experiments on data cleaning and on learning task interactions. We also present one large-scale experiment where the use of previous gradient-based methods would be prohibitive.},
  archiveprefix    = {arXiv},
  comment          = {Cited in Petrulionyte2023 (ref [8]).},
  creationdate     = {2023-06-18T09:46:18},
  doi              = {10.48550/arXiv.1703.01785},
  eprint           = {1703.01785},
  file             = {:by-author/F/Franceschi/2017_Franceschi_1.pdf:PDF},
  keywords         = {Bilevel Optimisation; Hyperparameters; Machine Learning (ML); Optimisation; stat.ML},
  modificationdate = {2023-06-18T09:55:16},
  owner            = {saulius},
  primaryclass     = {stat.ML},
}

@Article{Lorraine2019,
  author           = {Jonathan Lorraine and Paul Vicol and David Duvenaud},
  title            = {Optimizing Millions of Hyperparameters by Implicit Differentiation},
  year             = {2019},
  month            = nov,
  pages            = {1--18},
  abstract         = {We propose an algorithm for inexpensive gradient-based hyperparameter optimization that combines the implicit function theorem (IFT) with efficient inverse Hessian approximations. We present results about the relationship between the IFT and differentiating through optimization, motivating our algorithm. We use the proposed approach to train modern network architectures with millions of weights and millions of hyper-parameters. For example, we learn a data-augmentation network - where every weight is a hyperparameter tuned for validation performance - outputting augmented training examples. Jointly tuning weights and hyperparameters with our approach is only a few times more costly in memory and compute than standard training.},
  archiveprefix    = {arXiv},
  comment          = {Cited in Petrulionyte2023 (ref [13]).},
  creationdate     = {2023-06-18T09:48:35},
  doi              = {10.48550/arXiv.1911.02590},
  eprint           = {1911.02590},
  file             = {:by-author/L/Lorraine/2019_Lorraine_1.pdf:PDF},
  keywords         = {Bilevel Optimisation; Hyperparameters; Machine Learning (ML); Optimisation; cs.LG; stat.ML},
  modificationdate = {2023-06-18T09:55:01},
  owner            = {saulius},
  primaryclass     = {cs.LG},
}

@Article{Kingma2014,
  author           = {Diederik P. Kingma and Jimmy Ba},
  title            = {Adam: a method for stochastic optimization},
  year             = {2014},
  month            = dec,
  pages            = {1--15},
  abstract         = {We introduce Adam, an algorithm for first-order gradient-based optimization of stochastic objective functions, based on adaptive estimates of lower-order moments. The method is straightforward to implement, is computationally efficient, has little memory requirements, is invariant to diagonal rescaling of the gradients, and is well suited for problems that are large in terms of data and/or parameters. The method is also appropriate for non-stationary objectives and problems with very noisy and/or sparse gradients. The hyper-parameters have intuitive interpretations and typically require little tuning. Some connections to related algorithms, on which Adam was inspired, are discussed. We also analyze the theoretical convergence properties of the algorithm and provide a regret bound on the convergence rate that is comparable to the best known results under the online convex optimization framework. Empirical results demonstrate that Adam works well in practice and compares favorably to other stochastic optimization methods. Finally, we discuss AdaMax, a variant of Adam based on the infinity norm.},
  archiveprefix    = {arXiv},
  comment          = {Cited in Petrulionyte2023 (ref [6]).},
  creationdate     = {2023-06-18T10:05:33},
  doi              = {10.48550/arXiv.1412.6980},
  eprint           = {1412.6980},
  file             = {:by-author/K/Kingma/2014_Kingma_1.pdf:PDF},
  keywords         = {Algorithms; Machine Learning (ML); Optimisation; cs.LG},
  modificationdate = {2023-06-18T10:07:14},
  owner            = {saulius},
  primaryclass     = {cs.LG},
}

@Article{Baydin2018,
  author           = {Atilim Gunes Baydin and Barak A. Pearlmutter and Alexey Andreyevich Radul and Jeffrey Mark Siskind},
  journal          = {Journal of Machine Learning Research},
  title            = {Automatic Differentiation in Machine Learning: a Survey},
  year             = {2018},
  number           = {153},
  pages            = {1--43},
  volume           = {18},
  abstract         = {Derivatives, mostly in the form of gradients and Hessians, are ubiquitous in machine learning. Automatic differentiation (AD), also called algorithmic differentiation or simply "autodiff", is a family of techniques similar to but more general than backpropagation for efficiently and accurately evaluating derivatives of numeric functions expressed as computer programs. AD is a small but established field with applications in areas including computational fluid dynamics, atmospheric sciences, and engineering design optimization. Until very recently, the fields of machine learning and AD have largely been unaware of each other and, in some cases, have independently discovered each other's results. Despite its relevance, general-purpose AD has been missing from the machine learning toolbox, a situation slowly changing with its ongoing adoption under the names "dynamic computational graphs" and "differentiable programming". We survey the intersection of AD and machine learning, cover applications where AD has direct relevance, and address the main implementation techniques. By precisely defining the main differentiation techniques and their interrelationships, we aim to bring clarity to the usage of the terms "autodiff", "automatic differentiation", and "symbolic differentiation" as these are encountered more and more in machine learning settings.},
  comment          = {Cited in Petrulionyte2023 (ref [7]).},
  creationdate     = {2023-06-18T10:11:30},
  file             = {:by-author/B/Baydin/2018_Baydin_1.pdf:PDF;:by-author/B/Baydin/2018_Baydin_1_arXiv.pdf:PDF},
  keywords         = {Automatic Differentiation; Hyperparameters; Machine Learning (ML); Optimisation},
  modificationdate = {2023-06-18T10:15:53},
  owner            = {saulius},
  url              = {http://jmlr.org/papers/v18/17-468.html},
}

@Article{Duneau1985,
  author           = {Michel Duneau and André Katz},
  journal          = {Physical Review Letters},
  title            = {Quasiperiodic patterns},
  year             = {1985},
  month            = {jun},
  number           = {25},
  pages            = {2688--2691},
  volume           = {54},
  comment          = {Cited in the book "Quasicrystals: A Primer" by C. Janot.},
  creationdate     = {2023-06-18T11:02:56},
  doi              = {10.1103/physrevlett.54.2688},
  file             = {:by-author/D/Duneau/1985_Duneau_2688.pdf:PDF},
  keywords         = {Crystallography; Quasicrystals},
  modificationdate = {2023-06-18T11:10:31},
  owner            = {saulius},
  publisher        = {American Physical Society ({APS})},
}

@Article{Katz1986,
  author           = {A. Katz and M. Duneau},
  journal          = {Journal de Physique},
  title            = {Quasiperiodic patterns and icosahedral symmetry},
  year             = {1986},
  number           = {2},
  pages            = {181--196},
  volume           = {47},
  comment          = {Cited in the book "Quasicrystals: A Primer" by C. Janot.},
  creationdate     = {2023-06-18T11:08:32},
  doi              = {10.1051/jphys:01986004702018100},
  file             = {:by-author/K/Katz/1986_Katz_181.pdf:PDF},
  keywords         = {Crystallography; Quasicrystals},
  modificationdate = {2023-06-18T11:10:25},
  owner            = {saulius},
  publisher        = {{EDP} Sciences},
}

@Article{Jack1978,
  author           = {A. Jack and M. Levitt},
  journal          = {Acta Crystallographica Section A},
  title            = {Refinement of large structures by simultaneous minimization of energy and \textit{R} factor},
  year             = {1978},
  month            = {nov},
  number           = {6},
  pages            = {931--935},
  volume           = {34},
  creationdate     = {2023-06-18T11:18:03},
  doi              = {10.1107/s0567739478001904},
  file             = {:by-author/J/Jack/1978_Jack_931.pdf:PDF},
  keywords         = {Crystallography; Minimisation; Structure Refinement},
  modificationdate = {2023-06-18T11:25:24},
  owner            = {saulius},
  publisher        = {International Union of Crystallography ({IUCr})},
}

@Article{Chen2020a,
  author           = {Chen, Wenyuan and Xiao, Hao and Wang, Xurong and Song, Shuanglin and Han, Zhen and Li, Xiaowu and Yang, Fan and Wang, Li and Song, Jingdong and Liu, Hongrong and Cheng, Lingpeng},
  journal          = {Protein & cell},
  title            = {Structural changes of a bacteriophage upon {DNA} packaging and maturation},
  year             = {2020},
  issn             = {1674-8018},
  month            = may,
  pages            = {374--379},
  volume           = {11},
  chemicals        = {DNA, Viral},
  citation-subset  = {IM},
  completed        = {2020-12-31},
  country          = {Germany},
  creationdate     = {2023-06-18T14:13:55},
  doi              = {10.1007/s13238-020-00715-9},
  file             = {:by-author/C/Chen/2020_Chen_374.pdf:PDF},
  issn-linking     = {1674-800X},
  issue            = {5},
  keywords         = {Bacteriophages, Chemistry, Genetics; DNA Packaging, Genetics; DNA Pressure; DNA, Viral, Genetics; Models, Molecular},
  modificationdate = {2023-06-18T14:15:11},
  nlm-id           = {101532368},
  owner            = {saulius},
  pii              = {10.1007/s13238-020-00715-9},
  pmc              = {PMC7196576},
  pmid             = {32266588},
  pubmodel         = {Print},
  pubstate         = {ppublish},
  revised          = {2020-12-31},
}

@Article{Lander2006,
  author           = {Lander, Gabriel C. and Tang, Liang and Casjens, Sherwood R. and Gilcrease, Eddie B. and Prevelige, Peter and Poliakov, Anton and Potter, Clinton S. and Carragher, Bridget and Johnson, John E.},
  journal          = {Science (New York, N.Y.)},
  title            = {The structure of an infectious {P22} virion shows the signal for headful {DNA} packaging},
  year             = {2006},
  issn             = {1095-9203},
  month            = jun,
  pages            = {1791--1795},
  volume           = {312},
  abstract         = {Bacteriophages, herpesviruses, and other large double-stranded DNA (dsDNA) viruses contain molecular machines that pump DNA into preassembled procapsids, generating internal capsid pressures exceeding, by 10-fold, that of bottled champagne. A 17 angstrom resolution asymmetric reconstruction of the infectious P22 virion reveals that tightly spooled DNA about the portal dodecamer forces a conformation that is significantly different from that observed in isolated portals assembled from ectopically expressed protein. We propose that the tight dsDNA spooling activates the switch that signals the headful chromosome packing density to the particle exterior.},
  chemicals        = {Capsid Proteins, DNA, Viral},
  citation-subset  = {IM},
  comment          = {Cited in Chen2020a.},
  completed        = {2006-07-17},
  country          = {United States},
  creationdate     = {2023-06-18T20:28:00},
  doi              = {10.1126/science.1127981},
  file             = {:by-author/L/Lander/2006_Lander_1791.pdf:PDF},
  issn-linking     = {0036-8075},
  issue            = {5781},
  keywords         = {Bacteriophage P22, Genetics, Physiology, Ultrastructure; Capsid Proteins, Chemistry; Capsid, Chemistry, Ultrastructure; Cryoelectron Microscopy; Crystallography, X-Ray; DNA Packaging; DNA Pressure; DNA, Viral, Analysis, Chemistry; Image Processing, Computer-Assisted; Nucleic Acid Conformation; Pressure; Protein Conformation; Virion, Ultrastructure},
  modificationdate = {2023-06-20T09:17:31},
  nlm-id           = {0404511},
  owner            = {saulius},
  pii              = {1127981},
  pmid             = {16709746},
  pubmodel         = {Print-Electronic},
  pubstate         = {ppublish},
  revised          = {2007-11-14},
}

@Article{Oh2021,
  author           = {Edward Saehong Oh and Art Petronis},
  journal          = {Nature Reviews Genetics},
  title            = {Origins of human disease: the chrono-epigenetic perspective},
  year             = {2021},
  month            = {apr},
  number           = {8},
  pages            = {533--546},
  volume           = {22},
  creationdate     = {2023-06-20T09:18:05},
  doi              = {10.1038/s41576-021-00348-6},
  file             = {:by-author/O/Oh/2021_Oh_533.pdf:PDF},
  keywords         = {DNA Methylation; Epigenetics; Time-dependent Reactions},
  modificationdate = {2023-06-20T09:18:41},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media {LLC}},
}

@Article{Wolff1992,
  author           = {P. M. de Wolff and Y. Billiet and J. D. H. Donnay and W. Fischer and R. B. Galiulin and A. M. Glazer and T. Hahn and M. Senechal and D. P. Shoemaker and H. Wondratschek and A. J. C. Wilson and S. C. Abrahams},
  journal          = {Acta Crystallographica Section A Foundations of Crystallography},
  title            = {Symbols for symmetry elements and symmetry operations. Final report of the {IUCr} {Ad-Hoc} {C}ommittee on the {N}omenclature of {S}ymmetry},
  year             = {1992},
  month            = {sep},
  number           = {5},
  pages            = {727--732},
  volume           = {48},
  creationdate     = {2023-06-22T06:59:04},
  doi              = {10.1107/s0108767392003428},
  file             = {:by-author/W/Wolff/1992_Wolff_727.pdf:PDF},
  keywords         = {Crystallography; Definitions; Hermann-Mauguin Symbols; Notation; Space Groups},
  modificationdate = {2023-06-22T07:00:41},
  owner            = {saulius},
  publisher        = {International Union of Crystallography ({IUCr})},
}

@Article{Velickovic2022,
  author           = {Petar Veličković},
  journal          = {arXiv},
  title            = {Message passing all the way up},
  year             = {2022},
  month            = feb,
  pages            = {1--10},
  abstract         = {The message passing framework is the foundation of the immense success enjoyed by graph neural networks (GNNs) in recent years. In spite of its elegance, there exist many problems it provably cannot solve over given input graphs. This has led to a surge of research on going "beyond message passing", building GNNs which do not suffer from those limitations -- a term which has become ubiquitous in regular discourse. However, have those methods truly moved beyond message passing? In this position paper, I argue about the dangers of using this term -- especially when teaching graph representation learning to newcomers. I show that any function of interest we want to compute over graphs can, in all likelihood, be expressed using pairwise message passing -- just over a potentially modified graph, and argue how most practical implementations subtly do this kind of trick anyway. Hoping to initiate a productive discussion, I propose replacing "beyond message passing" with a more tame term, "augmented message passing".},
  archiveprefix    = {arXiv},
  creationdate     = {2023-06-25T10:57:35},
  doi              = {10.48550/arXiv.2202.11097},
  eprint           = {2202.11097},
  file             = {:by-author/V/Veličković/2022_Veličković_1.pdf:PDF},
  keywords         = {Artificial Neural Networks (ANN); Graph Neural Networks (GNN); Machine Learning (ML); cs.LG; cs.SI; stat.ML},
  modificationdate = {2023-06-25T10:59:09},
  owner            = {saulius},
  primaryclass     = {cs.LG},
}

@Article{Alber2019,
  author           = {Mark Alber and Adrian Buganza Tepole and William R. Cannon and Suvranu De and Salvador Dura-Bernal and Krishna Garikipati and George Karniadakis and William W. Lytton and Paris Perdikaris and Linda Petzold and Ellen Kuhl},
  journal          = {npj Digital Medicine},
  title            = {Integrating machine learning and multiscale modeling -- perspectives, challenges, and opportunities in the biological, biomedical, and behavioral sciences},
  year             = {2019},
  month            = {nov},
  number           = {1},
  pages            = {1--11},
  volume           = {2},
  creationdate     = {2023-06-28T14:52:05},
  doi              = {10.1038/s41746-019-0193-y},
  file             = {:by-author/A/Alber/2019_Alber_1.pdf:PDF},
  keywords         = {Biological Sciences; Macine Learning; Multiscale Modelling},
  modificationdate = {2023-06-28T14:53:35},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media {LLC}},
}

@Article{Chopard2014,
  author           = {B. Chopard and Joris Borgdorff and A. G. Hoekstra},
  journal          = {Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences},
  title            = {A framework for multi-scale modelling},
  year             = {2014},
  month            = {aug},
  number           = {2021},
  pages            = {20130378},
  volume           = {372},
  creationdate     = {2023-06-28T15:22:26},
  doi              = {10.1098/rsta.2013.0378},
  file             = {:by-author/C/Chopard/2014_Chopard_20130378.pdf:PDF},
  keywords         = {Machine Learning (ML); Multiscale Modelling},
  modificationdate = {2023-06-28T15:23:26},
  owner            = {saulius},
  publisher        = {The Royal Society},
}

@Article{Gao2023,
  author           = {Catherine A. Gao and Frederick M. Howard and Nikolay S. Markov and Emma C. Dyer and Siddhi Ramesh and Yuan Luo and Alexander T. Pearson},
  journal          = {npj Digital Medicine},
  title            = {Comparing scientific abstracts generated by {ChatGPT} to real abstracts with detectors and blinded human reviewers},
  year             = {2023},
  month            = {apr},
  number           = {1},
  pages            = {75},
  volume           = {6},
  creationdate     = {2023-06-29T16:23:14},
  doi              = {10.1038/s41746-023-00819-6},
  file             = {:by-author/G/Gao/2023_Gao_75.pdf:PDF},
  keywords         = {Artificial Intelligence (AI); ChatGPT; Expert Reliability; Machine Learning (ML)},
  modificationdate = {2023-06-29T16:26:16},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media {LLC}},
}

@Article{Berselli2022,
  author           = {Alessandro Berselli and Fabio Benfenati and Luca Maragliano and Giulio Alberini},
  journal          = {Computational and Structural Biotechnology Journal},
  title            = {Multiscale modelling of claudin-based assemblies: A magnifying glass for novel structures of biological interfaces},
  year             = {2022},
  pages            = {5984--6010},
  volume           = {20},
  creationdate     = {2023-06-29T17:12:03},
  doi              = {10.1016/j.csbj.2022.10.038},
  file             = {:by-author/B/Berselli/2022_Berselli_5984.pdf:PDF},
  keywords         = {Multiscale Modelling},
  modificationdate = {2023-06-29T17:13:14},
  owner            = {saulius},
  publisher        = {Elsevier {BV}},
}

@Article{Chew2022,
  author           = {Chew, Alvin Wei Ze and Zhang, Limao},
  journal          = {Sustainable cities and society},
  title            = {Data-driven multiscale modelling and analysis of COVID-19 spatiotemporal evolution using explainable AI.},
  year             = {2022},
  issn             = {2210-6715},
  month            = may,
  pages            = {103772},
  volume           = {80},
  abstract         = {To quantificationally identify the optimal control measures for regulators to best minimize COVID-19's growth (G-rate) and death (D-rate) rates in today's context, this paper develops a top-down multiscale engineering approach which encompasses a series of systematic analyses, namely: (global scale) predictive modelling of G-rate and D-rate due to COVID-19 globally, followed by determining the most effective control factors which can best minimize both parameters over time via explainable Artificial Intelligence (AI) with SHAP (SHapley Additive exPlanations) method; (continental scale) same predictive forecasting of G-rate and D-rate in all continents, followed by performing explainable SHAP analysis to determine the most effective control factors for the respective continents; and (country scale) clustering the different countries (> 150 in total) into 3 main clusters to identify the universal set of effective control measures. By using the historical period between 2 May 2020 and 1 Oct 2021, the average MAPE scores for forecasting G-rate and D-rate are within 10%, or less on average, at the global and continental scales. Systematically, we have quantificationally demonstrated that the top 3 most effective control measures for regulators to best minimize G-rate universally are COVID-CONTACT-TRACING, PUBLIC-GATHERING-RULES, and COVID-STRINGENCY-INDEX, while the control factors relating to D-rate depend on the modelling scenario.},
  country          = {Netherlands},
  creationdate     = {2023-06-29T17:15:19},
  doi              = {10.1016/j.scs.2022.103772},
  file             = {:by-author/C/Chew/2022_Chew_103772.pdf:PDF},
  issn-linking     = {2210-6707},
  keywords         = {COVID-19; Data-driven Prediction; Deep Learning (DL); Explainable AI; Multiscale Modelling},
  modificationdate = {2023-06-29T17:16:13},
  nlm-id           = {101735304},
  owner            = {saulius},
  pii              = {S2210-6707(22)00102-0},
  pmc              = {PMC8832881},
  pmid             = {35186668},
  pubmodel         = {Print-Electronic},
  pubstate         = {ppublish},
  revised          = {2022-12-21},
}

@Article{Ponnuchamy2020,
  author           = {Ponnuchamy, Veerapandian and Sandak, Anna and Sandak, Jakub},
  journal          = {Physical chemistry chemical physics : PCCP},
  title            = {Multiscale modelling investigation of wood modification with acetic anhydride},
  year             = {2020},
  issn             = {1463-9084},
  month            = dec,
  pages            = {28448--28458},
  volume           = {22},
  abstract         = {Density functional theory (DFT) and molecular dynamics (MD) simulations were employed to investigate the interaction of cellulose and lignin with acetic anhydride for explaining the wood modification process. Cellulose was modelled with a cellobiose unit and dibenzodioxocin was used to represent the lignin model. Results obtained from both methods revealed that acetic anhydride interacted substantially more with the cellobiose model than the lignin model. The interaction energy of cellobiose-acetic anhydride was higher (about 20 kJ mol-1) than that of lignin-acetic anhydride. DFT results on hydrogen bonding indicated that the hydroxyl group from cellobiose and the aromatic hydroxyl group from lignin models have similar energy values, which explain the equal strength of hydrogen bond interaction. The same trend was also obtained for the substitution of acetyl group in the hydroxyl group. MD results have also predicted that acetic anhydride forms a stronger interaction with cellobiose than with the lignin model, and these findings were in agreement with the DFT results.},
  citation-subset  = {IM},
  completed        = {2020-12-29},
  country          = {England},
  creationdate     = {2023-06-29T17:18:48},
  doi              = {10.1039/d0cp05165a},
  file             = {:by-author/P/Ponnuchamy/2020_Ponnuchamy_28448.pdf:PDF},
  issn-linking     = {1463-9076},
  issue            = {48},
  keywords         = {Multiscale Modelling},
  modificationdate = {2023-06-29T17:19:22},
  nlm-id           = {100888160},
  owner            = {saulius},
  pmid             = {33306769},
  pubmodel         = {Print},
  pubstate         = {ppublish},
  revised          = {2020-12-29},
}

@Article{Suveges2021,
  author           = {Suveges, Szabolcs and Chamseddine, Ibrahim and Rejniak, Katarzyna A. and Eftimie, Raluca and Trucu, Dumitru},
  journal          = {Frontiers in applied mathematics and statistics},
  title            = {Collective cell migration in a fibrous environment: a hybrid multiscale modelling approach.},
  year             = {2021},
  issn             = {2297-4687},
  month            = jun,
  pages            = {1--37},
  volume           = {7},
  abstract         = {The specific structure of the extracellular matrix (ECM), and in particular the density and orientation of collagen fibres, plays an important role in the evolution of solid cancers. While many experimental studies discussed the role of ECM in individual and collective cell migration, there are still unanswered questions about the impact of nonlocal cell sensing of other cells on the overall shape of tumour aggregation and its migration type. There are also unanswered questions about the migration and spread of tumour that arises at the boundary between different tissues with different collagen fibre orientations. To address these questions, in this study we develop a hybrid multi-scale model that considers the cells as individual entities and ECM as a continuous field. The numerical simulations obtained through this model match experimental observations, confirming that tumour aggregations are not moving if the ECM fibres are distributed randomly, and they only move when the ECM fibres are highly aligned. Moreover, the stationary tumour aggregations can have circular shapes or irregular shapes (with finger-like protrusions), while the moving tumour aggregations have elongate shapes (resembling to clusters, strands or files). We also show that the cell sensing radius impacts tumour shape only when there is a low ratio of fibre to non-fibre ECM components. Finally, we investigate the impact of different ECM fibre orientations corresponding to different tissues, on the overall tumour invasion of these neighbouring tissues.},
  country          = {Switzerland},
  creationdate     = {2023-06-29T17:38:35},
  doi              = {10.3389/fams.2021.680029},
  file             = {:by-author/S/Suveges/2021_Suveges_1.pdf:PDF},
  issn-linking     = {2297-4687},
  keywords         = {Agent Based Discrete Cell-cell Interactions; Cell Migration; Continuous Cell-ECM Interactions; Multi-scale Hybrid Mathematical Model; Multiscale Modelling; Numerical Simulations; Orientation of ECM Fibres},
  mid              = {NIHMS1722277},
  modificationdate = {2023-06-30T09:05:42},
  nlm-id           = {101729233},
  owner            = {saulius},
  pii              = {680029},
  pmc              = {PMC8315487},
  pmid             = {34322539},
  pubmodel         = {Print-Electronic},
  pubstate         = {ppublish},
  revised          = {2021-07-30},
}

@Article{Ernest2015,
  author           = {Paul Ernest},
  journal          = {Educational Studies in Mathematics},
  title            = {The problem of certainty in mathematics},
  year             = {2015},
  month            = {nov},
  number           = {3},
  pages            = {379--393},
  volume           = {92},
  creationdate     = {2023-07-08T18:22:05},
  doi              = {10.1007/s10649-015-9651-x},
  file             = {:by-author/E/Ernest/2015_Ernest_379.pdf:PDF},
  keywords         = {Foundations of Mathematics; Mathematics; Philosophy of Science},
  modificationdate = {2023-07-08T18:22:44},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media {LLC}},
}

@Article{Brown2017,
  author           = {James Robert Brown},
  journal          = {The Mathematical Intelligencer},
  title            = {Proofs and Guarantees},
  year             = {2017},
  month            = {oct},
  number           = {4},
  pages            = {47--50},
  volume           = {39},
  creationdate     = {2023-07-08T18:35:35},
  doi              = {10.1007/s00283-017-9730-1},
  file             = {:by-author/B/Brown/2017_Brown_47.pdf:PDF},
  keywords         = {Foundations of Mathematics; Mathematics; Philosophy of Science},
  modificationdate = {2023-07-08T18:37:23},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media {LLC}},
}

@Webpage{CreativeCommons2023,
  author           = {{Creative Commons}},
  retrieved        = {2023-07-09T15:04+03:00},
  title            = {{CC0} 1.0 {U}niversal ({CC0} 1.0). {P}ublic domain dedication},
  url              = {https://creativecommons.org/publicdomain/zero/1.0/},
  year             = {2023},
  creationdate     = {2023-07-09T15:39:44},
  file             = {:by-author/C/CreativeCommons/2023_CreativeCommons.pdf:PDF},
  keywords         = {CC0; Creative Commons; License; Public Domain},
  modificationdate = {2023-07-09T15:39:44},
  note             = {Accessed: 2023-07-09T15:04+03:00},
  owner            = {saulius},
}

@Webpage{LeBail2003,
  author           = {Le Bail, Armel and Michael Berndt and Daniel Chateigner and Lachlan Cranswick and Bob Downs and Rajan Hareesh and Alan Hewat and Fujio Izumi and Luca Lutterotti and Michel Petitjean and Alain Soyer and Brian H. Toby and Brian Toby and Geert Vanhoyland and Alexandre Yokochi},
  retrieved        = {2023-07-09T14:16+03:00},
  title            = {Open crystallographic database - a role for whom?},
  url              = {http://www.crystallography.net/cod/archives/2003/doc/Advisory-Board.txt},
  year             = {2003},
  comment          = {The Michael Berndt letter is also available at http://www.cristal.org/SDPD-list/2003/msg00025.html},
  creationdate     = {2023-07-09T15:39:45},
  file             = {:by-author/L/LeBail/2003_LeBail.txt:TXT},
  keywords         = {COD; Creation of the COD; Crystallographic Databases; History},
  modificationdate = {2023-07-09T15:41:00},
  note             = {Accessed: 2023-07-09T14:16+03:00},
  owner            = {saulius},
}

@Article{Deem2009,
  author           = {Michael W. Deem and Ramdas Pophale and Phillip A. Cheeseman and David J. Earl},
  journal          = {The Journal of Physical Chemistry C},
  title            = {Computational discovery of new zeolite-like materials},
  year             = {2009},
  month            = {oct},
  number           = {51},
  pages            = {21353--21360},
  volume           = {113},
  creationdate     = {2023-07-11T09:16:23},
  doi              = {10.1021/jp906984z},
  file             = {:by-author/D/Deem/2009_Deem_21353.pdf:PDF},
  keywords         = {Crystal Structure Prediction (CSP); Molecular Dynamics (MD); Monte-Carlo Simulations; PCOD; ZEFSA; ZEFSA-II; Zeolites},
  modificationdate = {2024-04-04T10:22:22},
  owner            = {saulius},
  publisher        = {American Chemical Society ({ACS})},
}

@Lecture{Ng2022,
  author           = {Jakin Ng and Sanjana Das and Ethan Yang},
  title            = {Isometries},
  year             = {2022},
  lecture          = {Lecture 13},
  comment          = {Lemma 13.5
If f : Rn → Rn is an isometry such that f (0) = 0, it must be a linear transformation.},
  creationdate     = {2023-07-16T12:09:18},
  file             = {:by-author/N/Ng/2022_Ng_60.pdf:PDF},
  keywords         = {Algebra; Isometires; Linear Algebra; Linear Transforms; Mathematics; Orthogonal Matrices},
  modificationdate = {2023-07-16T12:14:31},
  owner            = {saulius},
  pages            = {60--64},
  url              = {https://ocw.mit.edu/courses/res-18-011-algebra-i-student-notes-fall-2021/mit18_701f21_lect13.pdf},
}

@Lecture{Chandrasekaran2021,
  author           = {Karthik Chandrasekaran},
  title            = {Totally unimodular matrices and applications},
  year             = {2021},
  course           = {IE 511: Integer Programming, Spring 2021},
  lecture          = {Lecture 10},
  comment          = {Proposition 2. If A is TU and $U$ is a nonsingular square submatrix of A, then $U^{−1}$ is integral.},
  creationdate     = {2023-07-16T12:21:08},
  file             = {:by-author/C/Chandrasekaran/2021_Chandrasekaran_10.pdf:PDF},
  keywords         = {Algebra; Isometires; Linear Algebra; Linear Transforms; Mathematics; Orthogonal Matrices; Totally Unimodular Matrices; Unimodular Matrices},
  modificationdate = {2023-07-16T12:25:05},
  owner            = {saulius},
  pages            = {10-1--10-5},
  url              = {http://karthik.ise.illinois.edu/courses/ie511/lectures-sp-21/lecture-10.pdf},
}

@Webpage{Wikipedia2022UnimodularMatrix,
  author           = {{Wikipedia}},
  retrieved        = {2023-07-16T12:29+03:00},
  title            = {Unimodular matrix},
  url              = {https://en.wikipedia.org/wiki/Unimodular_matrix},
  year             = {2022},
  comment          = {Permalink: https://en.wikipedia.org/w/index.php?title=Unimodular_matrix&oldid=1110420484},
  creationdate     = {2023-07-16T12:29:34},
  file             = {:by-author/W/Wikipedia/2022_Wikipedia_Unimodular_matrix.pdf:PDF},
  keywords         = {Algebra; Isometries; Linear Algebra; Linear Transforms; Mathematics; Orthogonal Matrices; Totally Unimodular Matrices; Unimodular Matrices},
  modificationdate = {2023-07-23T20:54:07},
  owner            = {saulius},
}

@Article{Thurston1994,
  author           = {William P. Thurston},
  journal          = {Bull. Amer. Math. Soc. (N.S.) 30 (1994) 161-177},
  title            = {On proof and progress in mathematics},
  year             = {1994},
  month            = apr,
  pages            = {1--17},
  abstract         = {In response to Jaffe and Quinn [math.HO/9307227], the author discusses forms of progress in mathematics that are not captured by formal proofs of theorems, especially in his own work in the theory of foliations and geometrization of 3-manifolds and dynamical systems.},
  archiveprefix    = {arXiv},
  comment          = {Described in: https://www.youtube.com/watch?v=2ptFnIj71SM},
  creationdate     = {2023-07-20T20:21:36},
  eprint           = {math/9404236},
  file             = {:by-author/T/Thurston/1994_Thurston_1.pdf:PDF},
  keywords         = {Derivative; Differential Forms; Differentiation; Interpretations; Mathematics; math.HO},
  modificationdate = {2023-07-20T20:24:51},
  owner            = {saulius},
  primaryclass     = {math.HO},
}

@Article{Kim2022,
  author           = {Sunghwan Kim and Jie Chen and Tiejun Cheng and Asta Gindulyte and Jia He and Siqian He and Qingliang Li and Benjamin A. Shoemaker and Paul A. Thiessen and Bo Yu and Leonid Zaslavsky and Jian Zhang and Evan E. Bolton},
  journal          = {Nucleic Acids Research},
  title            = {{PubChem} 2023 update},
  year             = {2022},
  month            = {oct},
  number           = {D1},
  pages            = {D1373--D1380},
  volume           = {51},
  creationdate     = {2023-07-21T12:09:23},
  doi              = {10.1093/nar/gkac956},
  file             = {:by-author/K/Kim/2022_Kim_1373.pdf:PDF},
  keywords         = {Chemical Databases; Chemistry; Chemoinformatics; Data Management; PubChem; Scientific Databases},
  modificationdate = {2023-07-21T12:12:04},
  owner            = {saulius},
  publisher        = {Oxford University Press ({OUP})},
}

@Article{Liu2023,
  author           = {Yiming Liu and Hongtao Shan and Feng Nie and Gaoyu Zhang and George Xianzhi Yuan},
  journal          = {Information},
  title            = {Document-Level Relation Extraction with Local Relation and Global Inference},
  year             = {2023},
  month            = {jun},
  number           = {7},
  pages            = {365},
  volume           = {14},
  creationdate     = {2023-07-21T14:50:26},
  doi              = {10.3390/info14070365},
  file             = {:by-author/L/Liu/2023_Liu_365.pdf:PDF},
  keywords         = {Artificial Intelligence (AI); Artificial Neural Networks (ANN); Data Management; Document Processing; Knowledge Extraction; Machine Learning (ML)},
  modificationdate = {2023-07-21T14:51:23},
  owner            = {saulius},
  publisher        = {{MDPI} {AG}},
}

@Lecture{Fang2008,
  author           = {S.-C. Fang},
  title            = {Totally unimodular matrices},
  year             = {2008},
  lecture          = {Lecture Notes: ISE/OR/MA 766},
  school           = {North Carolina State University},
  creationdate     = {2023-07-23T20:53:29},
  file             = {:by-author/F/Fang/2008_Fang_1.pdf:PDF},
  keywords         = {Algebra; Isometries; Linear Algebra; Linear Transforms; Mathematics; Orthogonal Matrices; Totally Unimodular Matrices; Unimodular Matrices},
  modificationdate = {2023-07-23T20:59:02},
  owner            = {saulius},
  pages            = {1--24},
  url              = {https://www.ise.ncsu.edu/fuzzy-neural/wp-content/uploads/sites/9/2016/02/or766_TUM.pdf},
}

@TechReport{Tanir1975,
  author           = {Arie Tamir},
  title            = {On totally unimodular matrices},
  year             = {1975},
  number           = {157},
  type             = {Discussion paper},
  creationdate     = {2023-07-23T21:13:18},
  file             = {:by-author/T/Tamir/1975_Tamir_1.pdf:PDF},
  keywords         = {Algebra; Isometries; Linear Algebra; Linear Transforms; Mathematics; Orthogonal Matrices; Totally Unimodular Matrices; Unimodular Matrices},
  modificationdate = {2023-07-23T21:16:02},
  owner            = {saulius},
  pages            = {1--15},
  url              = {https://www.kellogg.northwestern.edu/research/math/papers/157.pdf},
}

@Article{Gerards1989,
  author           = {A. M. H. Gerards},
  journal          = {Linear Algebra and its Applications},
  title            = {A short proof of {T}utte's characterization of totally unimodular matrices},
  year             = {1989},
  month            = {mar},
  pages            = {207--212},
  volume           = {114-115},
  creationdate     = {2023-07-23T21:26:27},
  doi              = {10.1016/0024-3795(89)90461-8},
  file             = {:by-author/G/Gerards/1989_Gerards_207.pdf:PDF;:by-author/G/Gerards/1989_Gerards_207manuscript.pdf:PDF},
  keywords         = {Algebra; Isometries; Linear Algebra; Linear Transforms; Mathematics; Orthogonal Matrices; Totally Unimodular Matrices; Unimodular Matrices},
  modificationdate = {2023-07-23T21:29:36},
  owner            = {saulius},
  publisher        = {Elsevier {BV}},
}

@InCollection{Siek1998,
  author           = {Jeremy G. Siek and Andrew Lumsdaine},
  booktitle        = {Computing in Object-Oriented Parallel Environments},
  publisher        = {Springer Berlin Heidelberg},
  title            = {The Matrix Template Library: A Generic Programming Approach to High Performance Numerical Linear Algebra},
  year             = {1998},
  pages            = {59--70},
  creationdate     = {2023-07-23T21:34:54},
  doi              = {10.1007/3-540-49372-7_6},
  file             = {:by-author/S/Siek/1998_Siek_59.pdf:PDF},
  keywords         = {C++; Matrix Library; Numeric Libraries; Templates},
  modificationdate = {2023-07-23T21:36:00},
  owner            = {saulius},
  url              = {https://www.researchgate.net/publication/2416540_The_Matrix_Template_Library_A_Generic_Programming_Approach_to_High_Performance_Numerical_Linear_Algebra},
}

@Article{Truemper1990,
  author           = {Klaus Truemper},
  journal          = {Journal of Combinatorial Theory, Series B},
  title            = {A decomposition theory for matroids. V. Testing of matrix total unimodularity},
  year             = {1990},
  month            = {aug},
  number           = {2},
  pages            = {241--281},
  volume           = {49},
  creationdate     = {2023-07-23T21:44:04},
  doi              = {10.1016/0095-8956(90)90030-4},
  file             = {:by-author/T/Truemper/1990_Truemper_241.pdf:PDF},
  keywords         = {Algebra; Isometries; Linear Algebra; Linear Transforms; Mathematics; Orthogonal Matrices; Totally Unimodular Matrices; Unimodular Matrices},
  modificationdate = {2023-07-23T21:45:30},
  owner            = {saulius},
  publisher        = {Elsevier {BV}},
}

@Article{Walter2012,
  author           = {Matthias Walter and Klaus Truemper},
  journal          = {Mathematical Programming Computation},
  title            = {Implementation of a unimodularity test},
  year             = {2012},
  month            = {nov},
  number           = {1},
  pages            = {57--73},
  volume           = {5},
  creationdate     = {2023-07-23T21:50:16},
  doi              = {10.1007/s12532-012-0048-x},
  file             = {:by-author/W/Walter/2012_Walter_57.pdf:PDF},
  keywords         = {Algebra; Isometries; Linear Algebra; Linear Transforms; Mathematics; Orthogonal Matrices; Totally Unimodular Matrices; Unimodular Matrices},
  modificationdate = {2023-07-23T21:50:49},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media {LLC}},
}

@TechReport{Higham2021,
  author           = {Higham, Nicholas J. and Lettington, Matthew C.},
  institution      = {Manchester Institute for Mathematical Sciences},
  title            = {Optimizing and factorizing the {W}ilson matrix},
  year             = {2021},
  creationdate     = {2023-07-26T15:13:47},
  doi              = {10.1080/00029890.2022.2038006},
  file             = {:by-author/H/Higham/2021_Higham_1.pdf:PDF},
  issn             = {1749-9097},
  keywords         = {Ill-Conditioned Matrices; Linear Algebra; Matrices; Matrix Algebra; Symmetric Matrices; Unimodular Matrices},
  modificationdate = {2023-07-26T15:20:45},
  owner            = {saulius},
  pages            = {1--13},
  url              = {https://eprints.maths.manchester.ac.uk/2803/3/paper_cropped2.pdf},
}

@Article{Higham2021a,
  author           = {Nicholas J. Higham and Matthew C. Lettington and Karl Michael Schmidt},
  journal          = {Linear Algebra and its Applications},
  title            = {Integer matrix factorisations, superalgebras and the quadratic form obstruction},
  year             = {2021},
  month            = {aug},
  pages            = {250--267},
  volume           = {622},
  creationdate     = {2023-07-26T15:20:26},
  doi              = {10.1016/j.laa.2021.03.028},
  file             = {:by-author/H/Higham/2021_Higham_250.pdf:PDF},
  keywords         = {Linear Algebra; Matrices; Matrix Algebra; Matrix Factorisation; Unimodular Matrices; Wilson Matrix},
  modificationdate = {2023-07-26T15:22:28},
  owner            = {saulius},
  publisher        = {Elsevier {BV}},
}

@Article{Beyene2020,
  author           = {Tewodros A. Beyene and Christian Herrera and Vivek Nigam},
  journal          = {{ACM} {SIGAda} Ada Letters},
  title            = {Verification of {A}da programs with {AdaHorn}},
  year             = {2020},
  month            = {apr},
  number           = {2},
  pages            = {29--34},
  volume           = {39},
  creationdate     = {2023-08-01T19:10:38},
  doi              = {10.1145/3394514.3394517},
  file             = {:by-author/B/Beyene/2020_Beyene_29.pdf:PDF},
  keywords         = {Ada; Formal Specifications; Horn Clauses; SPARK; Software Verification},
  modificationdate = {2023-08-01T19:14:42},
  owner            = {saulius},
  publisher        = {Association for Computing Machinery ({ACM})},
}

@Article{Pearce2022,
  author           = {David J. Pearce and Mark Utting and Lindsay Groves},
  journal          = {Journal of Automated Reasoning},
  title            = {Verifying Whiley Programs with Boogie},
  year             = {2022},
  month            = {mar},
  number           = {4},
  pages            = {747--803},
  volume           = {66},
  creationdate     = {2023-08-01T19:20:14},
  doi              = {10.1007/s10817-022-09619-1},
  file             = {:by-author/P/Pearce/2022_Pearce_747.pdf:PDF},
  keywords         = {Boogie; Correctness Proofs; Formal Methods; Program Verfication; Static Typing; Type Systems; Whiley},
  modificationdate = {2023-08-01T19:21:12},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media {LLC}},
  url              = {https://whileydave.com/publications/PUG22_JAR_preprint.pdf},
}

@Article{Abbasi2023,
  author           = {Rosa Abbasi and Jonas Schiffl and Eva Darulova and Mattias Ulbrich and Wolfgang Ahrendt},
  journal          = {International Journal on Software Tools for Technology Transfer},
  title            = {Combining rule- and {SMT}-based reasoning for verifying floating-point Java programs in {KeY}},
  year             = {2023},
  month            = {mar},
  number           = {2},
  pages            = {185--204},
  volume           = {25},
  creationdate     = {2023-08-01T19:23:07},
  doi              = {10.1007/s10009-022-00691-x},
  file             = {:by-author/A/Abbasi/2023_Abbasi_185.pdf:PDF},
  keywords         = {Floating Point; Formal Methods; Java; Key; Program Verification},
  modificationdate = {2023-08-01T19:23:51},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media {LLC}},
}

@InCollection{Chapman2014,
  author           = {Roderick Chapman and Florian Schanda},
  booktitle        = {Interactive Theorem Proving},
  publisher        = {Springer International Publishing},
  title            = {Are we there yet? 20 years of industrial theorem proving with {SPARK}},
  year             = {2014},
  pages            = {17--26},
  creationdate     = {2023-08-01T19:28:03},
  doi              = {10.1007/978-3-319-08970-6_2},
  file             = {:by-author/C/Chapman/2014_Chapman_17.pdf:PDF},
  keywords         = {Ada; Correctness Proofs; Formal Methods; Program Verfication; SPARK},
  modificationdate = {2023-08-01T19:29:18},
  owner            = {saulius},
  url              = {https://proteancode.com/keynote.pdf},
}

@Article{Blount2012,
  author           = {Zachary D. Blount and Jeffrey E. Barrick and Carla J. Davidson and Richard E. Lenski},
  journal          = {Nature},
  title            = {Genomic analysis of a key innovation in an experimental {E}scherichia coli population},
  year             = {2012},
  month            = {sep},
  number           = {7417},
  pages            = {513--518},
  volume           = {489},
  creationdate     = {2023-08-05T22:25:20},
  doi              = {10.1038/nature11514},
  file             = {:by-author/B/Blount/2012_Blount_513.pdf:PDF},
  keywords         = {Cit; Citrate; Evolution; New Species; Speciation Events},
  modificationdate = {2023-08-05T22:26:06},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media {LLC}},
}

@Article{VanHofwegen2016,
  author           = {Van Hofwegen, Dustin J. and Hovde, Carolyn J. and Minnich, Scott A.},
  journal          = {Journal of bacteriology},
  title            = {Rapid Evolution of Citrate Utilization by Escherichia coli by Direct Selection Requires citT and dctA.},
  year             = {2016},
  issn             = {1098-5530},
  month            = feb,
  pages            = {1022--1034},
  volume           = {198},
  abstract         = {The isolation of aerobic citrate-utilizing Escherichia coli (Cit(+)) in long-term evolution experiments (LTEE) has been termed a rare, innovative, presumptive speciation event. We hypothesized that direct selection would rapidly yield the same class of E. coli Cit(+) mutants and follow the same genetic trajectory: potentiation, actualization, and refinement. This hypothesis was tested with wild-type E. coli strain B and with K-12 and three K-12 derivatives: an E. coli ΔrpoS::kan mutant (impaired for stationary-phase survival), an E. coli ΔcitT::kan mutant (deleted for the anaerobic citrate/succinate antiporter), and an E. coli ΔdctA::kan mutant (deleted for the aerobic succinate transporter). E. coli underwent adaptation to aerobic citrate metabolism that was readily and repeatedly achieved using minimal medium supplemented with citrate (M9C), M9C with 0.005% glycerol, or M9C with 0.0025% glucose. Forty-six independent E. coli Cit(+) mutants were isolated from all E. coli derivatives except the E. coli ΔcitT::kan mutant. Potentiation/actualization mutations occurred within as few as 12 generations, and refinement mutations occurred within 100 generations. Citrate utilization was confirmed using Simmons, Christensen, and LeMaster Richards citrate media and quantified by mass spectrometry. E. coli Cit(+) mutants grew in clumps and in long incompletely divided chains, a phenotype that was reversible in rich media. Genomic DNA sequencing of four E. coli Cit(+) mutants revealed the required sequence of mutational events leading to a refined Cit(+) mutant. These events showed amplified citT and dctA loci followed by DNA rearrangements consistent with promoter capture events for citT. These mutations were equivalent to the amplification and promoter capture CitT-activating mutations identified in the LTEE.IMPORTANCE E. coli cannot use citrate aerobically. Long-term evolution experiments (LTEE) performed by Blount et al. (Z. D. Blount, J. E. Barrick, C. J. Davidson, and R. E. Lenski, Nature 489:513-518, 2012, http://dx.doi.org/10.1038/nature11514 ) found a single aerobic, citrate-utilizing E. coli strain after 33,000 generations (15 years). This was interpreted as a speciation event. Here we show why it probably was not a speciation event. Using similar media, 46 independent citrate-utilizing mutants were isolated in as few as 12 to 100 generations. Genomic DNA sequencing revealed an amplification of the citT and dctA loci and DNA rearrangements to capture a promoter to express CitT, aerobically. These are members of the same class of mutations identified by the LTEE. We conclude that the rarity of the LTEE mutant was an artifact of the experimental conditions and not a unique evolutionary event. No new genetic information (novel gene function) evolved.},
  chemicals        = {CitT protein, E coli, Citrates, Culture Media, DNA, Bacterial, DctA protein, E coli, Dicarboxylic Acid Transporters, Escherichia coli Proteins, Organic Anion Transporters},
  citation-subset  = {IM},
  completed        = {2016-07-28},
  country          = {United States},
  creationdate     = {2023-08-05T22:27:42},
  doi              = {10.1128/JB.00831-15},
  file             = {:by-author/V/Van Hofwegen/2016_Van Hofwegen_1022.pdf:PDF},
  issn-linking     = {0021-9193},
  issue            = {7},
  keywords         = {Biological Evolution; Citrate; Citrates, Metabolism; Culture Media; DNA, Bacterial, Genetics; Dicarboxylic Acid Transporters, Genetics, Metabolism; Escherichia Coli K12, Metabolism; Escherichia Coli Proteins, Metabolism; Gene Expression Regulation, Physiology; Mutation; Organic Anion Transporters, Metabolism; Selection, Genetic; Time Factors},
  modificationdate = {2023-08-05T22:28:38},
  nlm-id           = {2985120R},
  owner            = {saulius},
  pii              = {JB.00831-15},
  pmc              = {PMC4800869},
  pmid             = {26833416},
  pubmodel         = {Electronic},
  pubstate         = {epublish},
  revised          = {2018-11-13},
}

@Article{Britton2016,
  author           = {T.B. Britton and J. Jiang and Y. Guo and A. Vilalta-Clemente and D. Wallis and L.N. Hansen and A. Winkelmann and A.J. Wilkinson},
  journal          = {Materials Characterization},
  title            = {Tutorial: Crystal orientations and {EBSD} {\textemdash} Or which way is up?},
  year             = {2016},
  month            = {jul},
  pages            = {113--126},
  volume           = {117},
  creationdate     = {2023-08-05T22:34:28},
  doi              = {10.1016/j.matchar.2016.04.008},
  file             = {:by-author/B/Britton/2016_Britton_113.pdf:PDF},
  keywords         = {Crystal Orientation; Crystallography},
  modificationdate = {2023-08-05T22:34:52},
  owner            = {saulius},
  publisher        = {Elsevier {BV}},
}

@Article{Blount2020,
  author           = {Zachary D. Blount and Rohan Maddamsetti and Nkrumah A. Grant and Sumaya T. Ahmed and Tanush Jagdish and Jessica A. Baxter and Brooke A. Sommerfeld and Alice Tillman and Jeremy Moore and Joan L. Slonczewski and Jeffrey E. Barrick and Richard E. Lenski},
  journal          = {{eLife}},
  title            = {Genomic and phenotypic evolution of {E}scherichia coli in a novel citrate-only resource environment},
  year             = {2020},
  month            = {may},
  pages            = {e55414},
  volume           = {9},
  creationdate     = {2023-08-05T22:40:21},
  doi              = {10.7554/elife.55414},
  file             = {:by-author/B/Blount/2020_Blount_55414.pdf:PDF},
  keywords         = {Cit; Citrate; Evolution; New Species; Speciation Events},
  modificationdate = {2023-08-07T10:20:09},
  owner            = {saulius},
  publisher        = {{eLife} Sciences Publications, Ltd},
}

@Article{Жегалкин1927,
  author           = {И. И. Жегалкин},
  journal          = {Математический сборник},
  title            = {О технике вычислений предложений в символической логике},
  year             = {1927},
  number           = {1},
  pages            = {9--28},
  volume           = {34},
  comment          = {Other URLs: https://www.mathnet.ru/eng/sm/v34/i1/p9 [accessed 2023-08-07T15:28+03:00], https://www.mathnet.ru/php/archive.phtml?wshow=paper&jrnid=sm&paperid=7433&option_lang=eng [accessed 2023-08-07T15:28+03:00].},
  creationdate     = {2023-08-07T15:25:58},
  eprint           = {https://www.mathnet.ru/eng/sm7433},
  file             = {:by-author/Ж/Жегалкин/1927_Жегалкин_9.pdf:PDF},
  keywords         = {Boolean Algebra; Gégalkine Polynomial; Logical Functions; Logics; Mathematics; Principia Matematica; Zhegalkin Polynomial},
  modificationdate = {2023-08-07T15:33:27},
  owner            = {saulius},
  url              = {https://www.mathnet.ru/links/b51ad95f69b29de3baf6cbec6fe61114/sm7433.pdf},
}

@Article{Cranswick2007,
  author           = {Lachlan Michael David Cranswick},
  journal          = {Acta Crystallographica Section A. Foundations of Crystallography},
  title            = {Busting out of crystallography's {S}isyphean prison: from pencil and paper to structure solving at the press of a button: past, present and future of crystallographic software development, maintenance and distribution},
  year             = {2007},
  month            = {dec},
  number           = {1},
  pages            = {65--87},
  volume           = {64},
  creationdate     = {2023-08-15T06:19:23},
  doi              = {10.1107/s0108767307051355},
  file             = {:by-author/C/Cranswick/2007_Cranswick_65.pdf:PDF},
  keywords         = {Crystallography; History of Crystallography; History of Science; Scientific Software},
  modificationdate = {2023-08-15T06:20:30},
  owner            = {saulius},
  publisher        = {International Union of Crystallography ({IUCr})},
}

@Article{Pujol2007,
  author           = {O Pujol and J Ph Pérez},
  journal          = {European Journal of Physics},
  title            = {On a simple formulation of the golf ball paradox},
  year             = {2007},
  month            = {feb},
  number           = {2},
  pages            = {379--384},
  volume           = {28},
  comment          = {Cited in the YouTube video: https://www.youtube.com/watch?v=5sbM2Isx17A , "The Golf Ball Paradox".},
  creationdate     = {2023-09-06T18:46:33},
  doi              = {10.1088/0143-0807/28/2/024},
  file             = {:by-author/P/Pujol/2007_Pujol_379.pdf:PDF},
  keywords         = {Classical Mechanics; Mechanics; Moment of Inertia; Paradoxes; Physics; The Golf Ball Paradox},
  modificationdate = {2023-09-06T18:50:01},
  owner            = {saulius},
  publisher        = {{IOP} Publishing},
}

@Article{Gualtieri2006,
  author           = {Marco Gualtieri and Tadashi Tokieda and L. Advis-Gaete and B. Carry and E. Reffet and Claude Guthmann},
  journal          = {American Journal of Physics},
  title            = {Golfer's dilemma},
  year             = {2006},
  month            = {jun},
  number           = {6},
  pages            = {497--501},
  volume           = {74},
  comment          = {Cited in the YouTube video: https://www.youtube.com/watch?v=5sbM2Isx17A , "The Golf Ball Paradox".},
  creationdate     = {2023-09-06T18:50:56},
  doi              = {10.1119/1.2180281},
  file             = {:by-author/G/Gualtieri/2006_Gualtieri_497.pdf:PDF},
  keywords         = {Classical Mechanics; Mechanics; Moment of Inertia; Paradoxes; Physics; The Golf Ball Paradox},
  modificationdate = {2023-09-06T18:51:38},
  owner            = {saulius},
  publisher        = {American Association of Physics Teachers ({AAPT})},
}

@Article{Serezhkin2021,
  author           = {Viktor N. Serezhkin and Anton V. Savchenkov},
  journal          = {{CrystEngComm}},
  title            = {Advancing the use of Voronoi{\textendash}Dirichlet polyhedra to describe interactions in organic molecular crystal structures by the example of galunisertib polymorphs},
  year             = {2021},
  number           = {3},
  pages            = {562--568},
  volume           = {23},
  comment          = {Cited in the IUCr26 meeting.},
  creationdate     = {2023-09-06T18:54:09},
  doi              = {10.1039/d0ce01535k},
  file             = {:by-author/S/Serezhkin/2021_Serezhkin_562.pdf:PDF},
  keywords         = {Chemistry; Chemoinformatics; Crystallography; Delaunay Triangulation; Voronoi Tesselation},
  modificationdate = {2023-09-06T18:55:26},
  owner            = {saulius},
  publisher        = {Royal Society of Chemistry ({RSC})},
}

@Article{Weltner1979,
  author           = {Klaus Weltner},
  journal          = {American Journal of Physics},
  title            = {Stable circular orbits of freely moving balls on rotating discs},
  year             = {1979},
  month            = {nov},
  number           = {11},
  pages            = {984--986},
  volume           = {47},
  comment          = {Cited in the YouTube video: https://www.youtube.com/watch?v=3oM7hX3UUEU "The Turntable Paradox".},
  creationdate     = {2023-09-06T20:31:07},
  doi              = {10.1119/1.11602},
  file             = {:by-author/W/Weltner/1979_Weltner_984.pdf:PDF},
  keywords         = {Classical Mechanics; Mechanics; Moment of Inertia; Paradoxes; Physics; Turntable},
  modificationdate = {2023-09-06T20:32:37},
  owner            = {saulius},
  publisher        = {American Association of Physics Teachers ({AAPT})},
  url              = {http://m2.askthephysicist.com/Weltner.pdf},
}

@Article{Bisson2023,
  author           = {Tom Bisson and Michael Franz and O, Isil Dogan and Daniel Romberg and Christoph Jansen and Peter Hufnagl and Norman Zerbe},
  journal          = {Digital Health},
  title            = {Anonymization of whole slide images in histopathology for research and education},
  year             = {2023},
  month            = {jan},
  pages            = {205520762311714},
  volume           = {9},
  creationdate     = {2023-09-08T13:55:15},
  doi              = {10.1177/20552076231171475},
  file             = {:by-author/B/Bisson/2023_Bisson_205520762311714.pdf:PDF;:by-author/B/Bisson/2023_Bisson_205520762311714.epub:ePUB},
  keywords         = {Anonymization; Data Management; Medical Data; Medical Images},
  modificationdate = {2023-09-08T13:59:43},
  owner            = {saulius},
  publisher        = {{SAGE} Publications},
}

@Article{Asif2023,
  author           = {Amina Asif and Kashif Rajpoot and Simon Graham and David Snead and Fayyaz Minhas and Nasir Rajpoot},
  journal          = {The Journal of Pathology},
  title            = {Unleashing the potential of $\less$scp$\greater${AI}$\less$/scp$\greater$ for pathology: challenges and recommendations},
  year             = {2023},
  month            = {aug},
  number           = {5},
  pages            = {564--577},
  volume           = {260},
  creationdate     = {2023-09-08T14:01:15},
  doi              = {10.1002/path.6168},
  file             = {:by-author/A/Asif/2023_Asif_564.pdf:PDF},
  keywords         = {Anonymization; Data Management; Medical Data; Medical Images},
  modificationdate = {2023-09-08T14:02:18},
  owner            = {saulius},
  publisher        = {Wiley},
}

@Article{Desjardins2020,
  author           = {Benoit Desjardins and Yisroel Mirsky and Markel Picado Ortiz and Zeev Glozman and Lawrence Tarbox and Robert Horn and Steven C. Horii},
  journal          = {American Journal of Roentgenology},
  title            = {{DICOM} images have been hacked! Now what?},
  year             = {2020},
  month            = {apr},
  number           = {4},
  pages            = {727--735},
  volume           = {214},
  creationdate     = {2023-09-13T10:17:40},
  doi              = {10.2214/ajr.19.21958},
  file             = {:by-author/D/Desjardins/2020_Desjardins_727.pdf:PDF},
  keywords         = {DICOM; Data Management; Data Security; Digital Signatures; Encryption; Hacking; Health Informatics; Image Standards; Medical Imaging},
  modificationdate = {2023-11-09T15:51:35},
  owner            = {saulius},
  publisher        = {American Roentgen Ray Society},
}

@Article{Mirsky2019,
  author           = {Yisroel Mirsky and Tom Mahler and Ilan Shelef and Yuval Elovici},
  title            = {CT-GAN: Malicious Tampering of 3D Medical Imagery using Deep Learning},
  year             = {2019},
  month            = jan,
  pages            = {03597},
  abstract         = {In 2018, clinics and hospitals were hit with numerous attacks leading to significant data breaches and interruptions in medical services. An attacker with access to medical records can do much more than hold the data for ransom or sell it on the black market. In this paper, we show how an attacker can use deep-learning to add or remove evidence of medical conditions from volumetric (3D) medical scans. An attacker may perform this act in order to stop a political candidate, sabotage research, commit insurance fraud, perform an act of terrorism, or even commit murder. We implement the attack using a 3D conditional GAN and show how the framework (CT-GAN) can be automated. Although the body is complex and 3D medical scans are very large, CT-GAN achieves realistic results which can be executed in milliseconds. To evaluate the attack, we focused on injecting and removing lung cancer from CT scans. We show how three expert radiologists and a state-of-the-art deep learning AI are highly susceptible to the attack. We also explore the attack surface of a modern radiology network and demonstrate one attack vector: we intercepted and manipulated CT scans in an active hospital network with a covert penetration test. Demo video: https://youtu.be/_mkRAArj-x0 Source code: https://github.com/ymirsky/CT-GAN},
  archiveprefix    = {arXiv},
  comment          = {Cited in Desjardins2020.},
  creationdate     = {2023-09-13T10:20:23},
  doi              = {10.48550/arXiv.1901.03597},
  eprint           = {1901.03597},
  file             = {:by-author/M/Mirsky/2019_Mirsky_3597.pdf:PDF},
  keywords         = {Artificial Neural Networks (ANN); DICOM; Data Management; Data Security; Generative Adversarial Networks (GAN); Hacking; Image Standards; Medical Imaging; cs.CR; cs.CV; cs.LG},
  modificationdate = {2023-09-13T10:22:57},
  owner            = {saulius},
  primaryclass     = {cs.CR},
}

@Article{Mantri2022,
  author           = {Mantri, Manisha and Taran, Shruti and Sunder, Gaur},
  journal          = {IEEE reviews in biomedical engineering},
  title            = {DICOM Integration Libraries for Medical Image Interoperability: A Technical Review.},
  year             = {2022},
  issn             = {1941-1189},
  pages            = {247--259},
  volume           = {15},
  abstract         = {Medical images support diagnostic care and research in medicine. The acquisition and availability of medical images in digital form can facilitate quick diagnosis, ease of access, continuity of care, analysis and contribute to modern medical research. Digital Imaging and Communications in Medicine (DICOM) is a universal standard that promises standardized representation and exchange of medical images and related information from various radiological and waveform sources. DICOM software development kits or tools or libraries make it easier to implement DICOM standard in healthcare applications. There are several such API libraries available from different providers that promise DICOM integration. In this paper, we explore available DICOM API libraries and conduct a comparative study between a set of selected libraries on the four major criteria (DICOM features, technical aspects, the robustness of the library, and the level of user support available). The aim is to provide a complete picture of options available that can help in finding a best-fit open-source DICOM standard integration API library for developing standardized and interoperable healthcare applications.},
  citation-subset  = {IM},
  completed        = {2022-03-16},
  country          = {United States},
  creationdate     = {2023-09-13T10:26:28},
  doi              = {10.1109/RBME.2020.3042642},
  file             = {:by-author/M/Mantri/2022_Mantri_247.pdf:PDF},
  issn-linking     = {1937-3333},
  keywords         = {DICOM; Data Management; Data Security; Hacking; Humans; Image Standards; Medical Imaging; Radiology Information Systems; Software},
  modificationdate = {2023-09-13T10:30:40},
  nlm-id           = {101493803},
  owner            = {saulius},
  pmid             = {33275586},
  pubmodel         = {Print-Electronic},
  pubstate         = {ppublish},
  revised          = {2022-05-31},
}

@Standard{MITA2023,
  institution      = {{Medical Imaging \& Technology Alliance}},
  organization     = {{National Electrical Manufacturers Association}},
  title            = {The {DICOM} standard},
  url              = {https://www.dicomstandard.org/current/},
  year             = {2023},
  creationdate     = {2023-09-13T10:54:20},
  eprint           = {https://dicom.nema.org/medical/dicom/current/DocBookDICOM2023d_release_pdf_20230908073327.zip},
  file             = {:by-author/M/MITA/DocBookDICOM2023d_release_pdf_20230908073327.zip:zip;:by-author/M/MITA/2023_MITA_DICOM_d/part01.pdf:PDF;:by-author/M/MITA/2023_MITA_DICOM_d/part02.pdf:PDF;:by-author/M/MITA/2023_MITA_DICOM_d/part03.pdf:PDF;:by-author/M/MITA/2023_MITA_DICOM_d/part04.pdf:PDF;:by-author/M/MITA/2023_MITA_DICOM_d/part05.pdf:PDF;:by-author/M/MITA/2023_MITA_DICOM_d/part06.pdf:PDF;:by-author/M/MITA/2023_MITA_DICOM_d/part07.pdf:PDF;:by-author/M/MITA/2023_MITA_DICOM_d/part08.pdf:PDF;:by-author/M/MITA/2023_MITA_DICOM_d/part10.pdf:PDF;:by-author/M/MITA/2023_MITA_DICOM_d/part11.pdf:PDF;:by-author/M/MITA/2023_MITA_DICOM_d/part12.pdf:PDF;:by-author/M/MITA/2023_MITA_DICOM_d/part14.pdf:PDF;:by-author/M/MITA/2023_MITA_DICOM_d/part15.pdf:PDF;:by-author/M/MITA/2023_MITA_DICOM_d/part16.pdf:PDF;:by-author/M/MITA/2023_MITA_DICOM_d/part17.pdf:PDF;:by-author/M/MITA/2023_MITA_DICOM_d/part18.pdf:PDF;:by-author/M/MITA/2023_MITA_DICOM_d/part19.pdf:PDF;:by-author/M/MITA/2023_MITA_DICOM_d/part20.pdf:PDF;:by-author/M/MITA/2023_MITA_DICOM_d/part21.pdf:PDF;:by-author/M/MITA/2023_MITA_DICOM_d/part22.pdf:PDF},
  modificationdate = {2023-09-13T11:03:30},
  owner            = {saulius},
}

@Article{Blecher2023,
  author           = {Lukas Blecher and Guillem Cucurull and Thomas Scialom and Robert Stojnic},
  journal          = {arXiv},
  title            = {{Nougat}: neural optical understanding for academic documents},
  year             = {2023},
  month            = aug,
  pages            = {1--17},
  abstract         = {Scientific knowledge is predominantly stored in books and scientific journals, often in the form of PDFs. However, the PDF format leads to a loss of semantic information, particularly for mathematical expressions. We propose Nougat (Neural Optical Understanding for Academic Documents), a Visual Transformer model that performs an Optical Character Recognition (OCR) task for processing scientific documents into a markup language, and demonstrate the effectiveness of our model on a new dataset of scientific documents. The proposed approach offers a promising solution to enhance the accessibility of scientific knowledge in the digital age, by bridging the gap between human-readable documents and machine-readable text. We release the models and code to accelerate future work on scientific text recognition.},
  archiveprefix    = {arXiv},
  comment          = {Announced on the 2023-09-18 in the MathML mailing list (see the attached e-mail).},
  creationdate     = {2023-09-19T11:45:29},
  doi              = {10.48550/arXiv.2308.13418},
  eprint           = {2308.13418},
  file             = {:by-author/B/Blecher/2023_Blecher_1.pdf:PDF;:correspondence/2023/2023-09-18_08-49_Adam-Sobieski_adamsobieski-at-hotmail.com.pdf:PDF},
  keywords         = {Data Management; Document Processing; Machine Learning (ML); cs.CV; cs.LG},
  modificationdate = {2023-12-20T09:35:15},
  owner            = {saulius},
  primaryclass     = {cs.LG},
  url              = {https://arxiv.org/abs/2308.13418},
}

@Article{Wang2022a,
  author           = {Teng Wang and Kefei Zhang and Jesse Thé and Hesheng Yu},
  journal          = {Computational Materials Science},
  title            = {Accurate prediction of band gap of materials using stacking machine learning model},
  year             = {2022},
  month            = {jan},
  pages            = {110899},
  volume           = {201},
  creationdate     = {2023-09-28T17:31:15},
  doi              = {10.1016/j.commatsci.2021.110899},
  file             = {:by-author/W/Wang/2022_Wang_110899.pdf:PDF},
  keywords         = {Band Gap; Density Functional Theory (DFT); Material Science},
  modificationdate = {2023-09-28T17:32:39},
  owner            = {saulius},
  publisher        = {Elsevier {BV}},
}

@Article{Zimmerman2003,
  author           = {Daniel M. Zimmerman},
  title            = {A {UNITY}-based formalism for dynamic distributed systems},
  year             = {2003},
  creationdate     = {2023-10-01T16:16:12},
  file             = {:by-author/Z/Zimmerman/2003_Zimmerman_.pdf:PDF},
  modificationdate = {2023-10-01T16:29:48},
  owner            = {saulius},
}

@Article{Clegg2019,
  author           = {William Clegg},
  journal          = {Acta Crystallographica Section C Structural Chemistry},
  title            = {Crystallographic curiosities: polymorphism and structures with {Z}' > 1},
  year             = {2019},
  month            = {jun},
  number           = {7},
  pages            = {833--834},
  volume           = {75},
  creationdate     = {2023-10-07T16:17:26},
  doi              = {10.1107/s2053229619008799},
  file             = {:by-author/C/Clegg/2019_Clegg_833.pdf:PDF},
  keywords         = {Crystallography; Z Prime},
  modificationdate = {2023-10-07T16:18:48},
  owner            = {saulius},
  publisher        = {International Union of Crystallography ({IUCr})},
}

@Article{HaroOlmo2023,
  author           = {Francisco José de Haro-Olmo and Alvaro Valencia-Parra and Ángel Jesús Varela-Vaca and José Antonio Álvarez-Bermejo and Marı́a Teresa Gómez-López},
  journal          = {{PeerJ} Computer Science},
  title            = {{ELI}: an {IoT}-aware big data pipeline with data curation and data quality},
  year             = {2023},
  month            = {oct},
  pages            = {e1605},
  volume           = {9},
  creationdate     = {2023-10-03T09:43:02},
  doi              = {10.7717/peerj-cs.1605},
  file             = {:by-author/H/Haro-Olmo/2023_Haro-Olmo_1605.pdf:PDF},
  keywords         = {Data Curation; Data Management; IoT; Software},
  modificationdate = {2023-10-03T09:44:33},
  owner            = {saulius},
  publisher        = {{PeerJ}},
}

@Presentation{Swaminathan2020,
  author           = {J. Swaminathan},
  title            = {Frama-c demo with simple examples},
  year             = {2020},
  lecture          = {19CSE205 : PROGRAM REASONING},
  school           = {Department of Computer Science and Engineering},
  creationdate     = {2023-10-08T13:27:12},
  file             = {:by-author/S/Swaminathan/2020_Swaminathan_1.pdf:PDF},
  keywords         = {C Programming Language; Computer Science (CS); Correctness Proofs; Formal Methods; Formal Verification; Frama-C; Software Verification},
  modificationdate = {2023-10-08T14:03:27},
  owner            = {saulius},
  pages            = {1--9},
  url              = {https://swaminathanj.github.io/pr/slides/8-frama-c.pdf},
}

@Manual{Correnson2023,
  title            = {Frama-{C} user manual for {F}rama-{C} 27.1 ({C}obalt)},
  author           = {Loïc Correnson and Pascal Cuoq and Florent Kirchner and André Maroneze and Virgile Prevosto and Armand Puccetti and Julien Signoles and Boris Yakobowski},
  year             = {2023},
  creationdate     = {2023-10-08T13:42:23},
  file             = {:by-author/C/Correnson/2023_Correnson_1.pdf:PDF},
  keywords         = {C Programming Language; Computer Science (CS); Correctness Proofs; Formal Methods; Formal Verification; Frama-C; Manual; Software Verification},
  modificationdate = {2023-10-08T14:02:55},
  owner            = {saulius},
  pages            = {1--83},
  url              = {https://frama-c.com/download/frama-c-user-manual.pdf},
}

@Presentation{Frade2023,
  author           = {Maria João Frade},
  title            = {Deductive program verification with {F}rama-{C}},
  year             = {2023},
  creationdate     = {2023-10-08T14:13:05},
  file             = {:by-author/F/Frade/2023_Frade_1.pdf:PDF},
  keywords         = {C Programming Language; Computer Science (CS); Correctness Proofs; Formal Methods; Formal Verification; Frama-C; Software Verification},
  modificationdate = {2023-10-08T14:14:35},
  owner            = {saulius},
  url              = {https://haslab.github.io/MFP/VF/2223/FramaC-WP-part1.pdf},
}

@Manual{Baudin2023,
  title            = {{ANSI/ISO} {C} specification language version 1.19},
  author           = {Patrick Baudin and Pascal Cuoq and Jean-Christophe Filliâtre and Claude Marché and Benjamin Monate and Yannick Moy and Virgile Prevosto},
  year             = {2023},
  creationdate     = {2023-10-08T14:26:44},
  file             = {:by-author/B/Baudin/2023_Baudin_1.pdf:PDF},
  keywords         = {C Programming Language; Computer Science (CS); Correctness Proofs; Formal Methods; Formal Verification; Frama-C; Manual; Software Verification},
  modificationdate = {2023-10-08T14:30:05},
  owner            = {saulius},
  pages            = {1--112},
  url              = {https://frama-c.com/download/acsl-1.19.pdf},
}

@Presentation{Prevosto2014,
  author           = {Virgile Prevosto},
  title            = {Frama-{C} {WP} tutorial},
  year             = {2014},
  creationdate     = {2023-10-08T14:41:14},
  file             = {:by-author/P/Prevosto/2014_Prevosto_1.pdf:PDF},
  keywords         = {C Programming Language; Computer Science (CS); Correctness Proofs; Formal Methods; Formal Verification; Frama-C; Software Verification},
  modificationdate = {2023-10-08T14:42:52},
  owner            = {saulius},
  pages            = {1--70},
  url              = {https://frama-c.com/download/publications/2014-lifo-p/slides.pdf},
}

@Article{Dordowsky2015,
  author           = {Frank Dordowsky},
  journal          = {Electronic Proceedings in Theoretical Computer Science},
  title            = {An experimental study using {ACSL} and {F}rama-{C} to formulate and verify low-level requirements from a {DO}-178{C} compliant avionics project},
  year             = {2015},
  month            = {aug},
  pages            = {28--41},
  volume           = {187},
  creationdate     = {2023-10-08T14:46:02},
  doi              = {10.4204/eptcs.187.3},
  file             = {:by-author/D/Dordowsky/2015_Dordowsky_28.pdf:PDF},
  keywords         = {C Programming Language; Computer Science (CS); Correctness Proofs; Criticism; Formal Methods; Formal Verification; Frama-C; Software Verification},
  modificationdate = {2023-10-12T21:43:10},
  owner            = {saulius},
  publisher        = {Open Publishing Association},
  url              = {https://browse.arxiv.org/pdf/1508.03894.pdf},
}

@Article{Carlstroem2004,
  author           = {Jesper Carlström},
  journal          = {Mathematical Structures in Computer Science},
  title            = {Wheels -- on division by zero},
  year             = {2004},
  month            = {feb},
  number           = {1},
  pages            = {143--184},
  volume           = {14},
  comment          = {Found via https://en.wikipedia.org/wiki/Wheel_theory (https://en.wikipedia.org/w/index.php?title=Wheel_theory&oldid=1179287198).},
  creationdate     = {2023-10-12T21:45:27},
  doi              = {10.1017/s0960129503004110},
  file             = {:by-author/C/Carlström/2004_Carlström_143.pdf:PDF},
  keywords         = {Common Meadows; Division by Zero; Mathematics; Wheels},
  modificationdate = {2023-10-13T12:14:33},
  owner            = {saulius},
  publisher        = {Cambridge University Press ({CUP})},
}

@Article{Bergstra2007,
  author           = {J. A. Bergstra and J. V. Tucker},
  journal          = {Journal of the {ACM}},
  title            = {The rational numbers as an abstract data type},
  year             = {2007},
  month            = {apr},
  number           = {2},
  pages            = {7},
  volume           = {54},
  comment          = {Found via https://en.wikipedia.org/wiki/Wheel_theory (https://en.wikipedia.org/w/index.php?title=Wheel_theory&oldid=1179287198).},
  creationdate     = {2023-10-12T21:50:30},
  doi              = {10.1145/1219092.1219095},
  file             = {:by-author/B/Bergstra/2007_Bergstra_7.pdf:PDF},
  keywords         = {Common Meadows; Computer Science (CS); Division by Zero; Mathematics; Rational Arithmetic; Wheels},
  modificationdate = {2023-10-13T12:14:43},
  owner            = {saulius},
  publisher        = {Association for Computing Machinery ({ACM})},
}

@Article{Moss2001,
  author           = {Lawrence S. Moss},
  journal          = {Discrete Mathematics {\&}amp$\mathsemicolon$ Theoretical Computer Science},
  title            = {Simple equational specifications of rational arithmetic},
  year             = {2001},
  month            = {jan},
  pages            = {291--300},
  volume           = {Vol. 4 no. 2},
  comment          = {Cited by Bergstra2007.},
  creationdate     = {2023-10-12T22:03:32},
  doi              = {10.46298/dmtcs.280},
  file             = {:by-author/M/Moss/2001_Moss_291.pdf:PDF},
  keywords         = {Common Meadows; Computer Science (CS); Division by Zero; Mathematics; Rational Arithmetic; Wheels},
  modificationdate = {2023-10-13T12:13:11},
  owner            = {saulius},
  publisher        = {Centre pour la Communication Scientifique Directe ({CCSD})},
}

@Article{Widdowson2021,
  author           = {Daniel Widdowson and Marco M. Mosca and Angeles Pulido and Andrew I. Cooper and Vitaliy Kurlin},
  journal          = {{MATCH} Communications in Mathematical and in Computer Chemistry},
  title            = {Average minimum distances of periodic point sets {\textendash} foundational invariants for mapping periodic crystals},
  year             = {2021},
  month            = {dec},
  number           = {3},
  pages            = {529--559},
  volume           = {87},
  creationdate     = {2023-10-19T14:26:30},
  doi              = {10.46793/match.87-3.529w},
  file             = {:by-author/W/Widdowson/2021_Widdowson_529.pdf:PDF},
  keywords         = {Computational Geometry; Crystal Structure Comparison; Crystallography; Mathematics},
  modificationdate = {2023-10-19T14:27:13},
  owner            = {saulius},
  publisher        = {University Library in Kragujevac},
}

@Article{Widdowson2020,
  author           = {Widdowson, Daniel and Mosca, Marco and Pulido, Angeles and Kurlin, Vitaliy and Cooper, Andrew I.},
  title            = {The asymptotic behaviour and a near linear time algorithm for isometry invariants of periodic sets},
  year             = {2020},
  copyright        = {arXiv.org perpetual, non-exclusive license},
  creationdate     = {2023-10-19T14:28:05},
  doi              = {10.48550/ARXIV.2009.02488},
  file             = {:by-author/W/Widdowson/2020_Widdowson_1.pdf:PDF},
  keywords         = {Computational Geometry; Crystal Structure Comparison; Crystallography; Materials Science (cond-mat.mtrl-sci); Mathematics},
  modificationdate = {2023-10-19T14:40:48},
  owner            = {saulius},
  publisher        = {arXiv},
}

@InProceedings{Levina2001,
  author           = {E. Levina and P. Bickel},
  booktitle        = {Proceedings Eighth {IEEE} International Conference on Computer Vision. {ICCV} 2001},
  title            = {The {E}arth {M}over's distance is the {M}allows distance: some insights from statistics},
  year             = {2001},
  pages            = {253--256},
  publisher        = {{IEEE} Comput. Soc},
  comment          = {Found via: https://en.wikipedia.org/wiki/Earth_mover%27s_distance [accessed 2023-10-19T14:57+03:00].},
  creationdate     = {2023-10-19T14:53:43},
  doi              = {10.1109/iccv.2001.937632},
  file             = {:by-author/L/Levina/2001_Levina_253.pdf:PDF},
  keywords         = {Computational Geometry; Earth Mover's Distance; Mathematics; Similarity Measures},
  modificationdate = {2023-10-19T14:57:28},
  owner            = {saulius},
}

@Article{Mallows1972,
  author           = {C. L. Mallows},
  journal          = {The Annals of Mathematical Statistics},
  title            = {A note on asymptotic joint normality},
  year             = {1972},
  month            = {apr},
  number           = {2},
  pages            = {508--515},
  volume           = {43},
  comment          = {Found via: https://en.wikipedia.org/wiki/Earth_mover%27s_distance [accessed 2023-10-19T14:57+03:00].},
  creationdate     = {2023-10-19T14:58:41},
  doi              = {10.1214/aoms/1177692631},
  file             = {:by-author/M/Mallows/1972_Mallows_508.pdf:PDF},
  keywords         = {Computational Geometry; Earth Mover's Distance; Mathematics; Similarity Measures},
  modificationdate = {2023-10-19T14:59:25},
  owner            = {saulius},
  publisher        = {Institute of Mathematical Statistics},
}

@Webpage{Fisher2023,
  author           = {Robert Fisher},
  retrieved        = {2023-10-19T15:08+03:00},
  title            = {The {E}arth {M}over's distance},
  url              = {https://homepages.inf.ed.ac.uk/rbf/CVonline/LOCAL_COPIES/RUBNER/emd.htm},
  siteurl          = {https://homepages.inf.ed.ac.uk/rbf/},
  year             = {2023},
  comment          = {Found via: https://en.wikipedia.org/wiki/Earth_mover%27s_distance [accessed 2023-10-19T14:57+03:00].},
  creationdate     = {2023-10-19T15:08:15},
  file             = {:by-author/F/Fisher/2023_Fisher_1.pdf:PDF;:by-author/F/Fisher/2023_Fisher_1.odt:OpenDocument text},
  keywords         = {Computational Geometry; Earth Mover's Distance; Mathematics; Similarity Measures},
  modificationdate = {2023-10-19T15:30:56},
  owner            = {saulius},
}

@Article{Kline2019,
  author           = {Jeffery Kline},
  journal          = {Discrete Applied Mathematics},
  title            = {Properties of the $d$-dimensional earth mover's problem},
  year             = {2019},
  month            = {jul},
  pages            = {128--141},
  volume           = {265},
  comment          = {Found via: https://en.wikipedia.org/wiki/Earth_mover%27s_distance [accessed 2023-10-19T14:57+03:00].},
  creationdate     = {2023-10-19T15:19:10},
  doi              = {10.1016/j.dam.2019.02.042},
  file             = {:by-author/K/Kline/2019_Kline_128.pdf:PDF},
  keywords         = {Computational Geometry; Earth Mover's Distance; Mathematics; Similarity Measures},
  modificationdate = {2023-10-19T15:24:14},
  owner            = {saulius},
  publisher        = {Elsevier {BV}},
}

@InCollection{Pele2008,
  author           = {Ofir Pele and Michael Werman},
  booktitle        = {Lecture Notes in Computer Science},
  publisher        = {Springer Berlin Heidelberg},
  title            = {A linear time histogram metric for improved {SIFT} matching},
  year             = {2008},
  pages            = {495--508},
  comment          = {Found via: https://en.wikipedia.org/wiki/Earth_mover%27s_distance [accessed 2023-10-19T14:57+03:00].},
  creationdate     = {2023-10-19T15:25:42},
  doi              = {10.1007/978-3-540-88690-7_37},
  file             = {:by-author/P/Pele/2008_Pele_495.pdf:PDF},
  keywords         = {Computational Geometry; Earth Mover's Distance; Mathematics; Similarity Measures},
  modificationdate = {2023-10-19T15:29:30},
  owner            = {saulius},
}

@Article{Hitchcock1941,
  author           = {Frank L. Hitchcock},
  journal          = {Journal of Mathematics and Physics},
  title            = {The distribution of a product from several sources to numerous localities},
  year             = {1941},
  month            = {apr},
  number           = {1-4},
  pages            = {224--230},
  volume           = {20},
  comment          = {Cited in Fisher2023.},
  creationdate     = {2023-10-19T15:30:43},
  doi              = {10.1002/sapm1941201224},
  file             = {:by-author/H/Hitchcock/1941_Hitchcock_224.pdf:PDF},
  keywords         = {Computational Geometry; Earth Mover's Distance; Mathematics; Similarity Measures},
  modificationdate = {2023-10-19T15:34:27},
  owner            = {saulius},
  publisher        = {Wiley},
}

@InProceedings{Rubner1998,
  author           = {Y. Rubner and C. Tomasi and L. J. Guibas},
  booktitle        = {Sixth International Conference on Computer Vision ({IEEE} Cat. No.98CH36271)},
  title            = {A metric for distributions with applications to image databases},
  year             = {1998},
  pages            = {59--66},
  publisher        = {Narosa Publishing House},
  comment          = {Cited in Fisher2023 and https://en.wikipedia.org/wiki/Earth_mover%27s_distance [accessed 2023-10-19T14:57+03:00]. Original definition of the EMD (?).},
  creationdate     = {2023-10-19T15:35:37},
  doi              = {10.1109/iccv.1998.710701},
  file             = {:by-author/R/Rubner/1998_Rubner_59.pdf:PDF},
  keywords         = {Computational Geometry; Earth Mover's Distance; Mathematics; Similarity Measures},
  modificationdate = {2023-10-19T16:17:42},
  owner            = {saulius},
}

@Article{Peleg1989,
  author           = {S. Peleg and M. Werman and H. Rom},
  journal          = {{IEEE} Transactions on Pattern Analysis and Machine Intelligence},
  title            = {A unified approach to the change of resolution: space and gray-level},
  year             = {1989},
  month            = {jul},
  number           = {7},
  pages            = {739--742},
  volume           = {11},
  comment          = {Found via: https://en.wikipedia.org/wiki/Earth_mover%27s_distance [accessed 2023-10-20T11:14+03:00].},
  creationdate     = {2023-10-20T11:13:45},
  doi              = {10.1109/34.192468},
  file             = {:by-author/P/Peleg/1989_Peleg_739_from_author_url.pdf:PDF;:by-author/P/Peleg/1989_Peleg_739_from_publisher.pdf:PDF},
  keywords         = {Computational Geometry; Earth Mover's Distance; Mathematics; Similarity Measures},
  modificationdate = {2023-10-20T11:21:07},
  owner            = {saulius},
  publisher        = {Institute of Electrical and Electronics Engineers ({IEEE})},
  url              = {https://www.cs.huji.ac.il/w~werman/Papers/space-gray.pdf},
}

@Article{Orlova2016,
  author           = {Orlova, Darya Y. and Zimmerman, Noah and Meehan, Stephen and Meehan, Connor and Waters, Jeffrey and Ghosn, Eliver E. B. and Filatenkov, Alexander and Kolyagin, Gleb A. and Gernez, Yael and Tsuda, Shanel and Moore, Wayne and Moss, Richard B. and Herzenberg, Leonore A. and Walther, Guenther},
  journal          = {PloS one},
  title            = {{E}arth {M}over's {D}istance ({EMD}): a true metric for comparing biomarker expression levels in cell populations.},
  year             = {2016},
  issn             = {1932-6203},
  pages            = {e0151859},
  volume           = {11},
  abstract         = {Changes in the frequencies of cell subsets that (co)express characteristic biomarkers, or levels of the biomarkers on the subsets, are widely used as indices of drug response, disease prognosis, stem cell reconstitution, etc. However, although the currently available computational "gating" tools accurately reveal subset frequencies and marker expression levels, they fail to enable statistically reliable judgements as to whether these frequencies and expression levels differ significantly between/among subject groups. Here we introduce flow cytometry data analysis pipeline which includes the Earth Mover's Distance (EMD) metric as solution to this problem. Well known as an informative quantitative measure of differences between distributions, we present three exemplary studies showing that EMD 1) reveals clinically-relevant shifts in two markers on blood basophils responding to an offending allergen; 2) shows that ablative tumor radiation induces significant changes in the murine colon cancer tumor microenvironment; and, 3) ranks immunological differences in mouse peritoneal cavity cells harvested from three genetically distinct mouse strains.},
  chemicals        = {Biomarkers},
  citation-subset  = {IM},
  comment          = {Found via: https://en.wikipedia.org/wiki/Earth_mover%27s_distance [accessed 2023-10-20T11:14+03:00].},
  completed        = {2016-08-03},
  country          = {United States},
  creationdate     = {2023-10-20T11:24:44},
  doi              = {10.1371/journal.pone.0151859},
  file             = {:by-author/O/Orlova/2016_Orlova_e151859.pdf:PDF},
  issn-linking     = {1932-6203},
  issue            = {3},
  keywords         = {Algorithms; Biomarkers, Metabolism; Computational Geometry; Earth Mover's Distance; Flow Cytometry; Mathematics; Probability; Similarity Measures},
  modificationdate = {2023-11-08T10:47:16},
  nlm-id           = {101285081},
  owner            = {saulius},
  pii              = {e0151859},
  pmc              = {PMC4805242},
  pmid             = {27008164},
  pubmodel         = {Electronic-eCollection},
  pubstate         = {epublish},
  revised          = {2018-11-13},
}

@Article{Rubner2000,
  author           = {Yossi Rubner},
  journal          = {International Journal of Computer Vision},
  title            = {The {E}arth {M}over's {D}istance as a metric for image retrieval},
  year             = {2000},
  number           = {2},
  pages            = {99--121},
  volume           = {40},
  comment          = {Found via: https://en.wikipedia.org/wiki/Earth_mover%27s_distance [accessed 2023-10-20T11:14+03:00].},
  creationdate     = {2023-10-20T12:02:41},
  doi              = {10.1023/a:1026543900054},
  file             = {:by-author/R/Rubner/2000_Rubner_99.pdf:PDF},
  keywords         = {Computational Geometry; Earth Mover's Distance; Mathematics; Similarity Measures},
  modificationdate = {2023-10-20T12:08:18},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media {LLC}},
}

@Article{Pineda1987,
  author           = {Fernando J. Pineda},
  journal          = {Physical Review Letters},
  title            = {Generalization of back-propagation to recurrent neural networks},
  year             = {1987},
  month            = {nov},
  number           = {19},
  pages            = {2229--2232},
  volume           = {59},
  comment          = {Cited in Gori2005.},
  creationdate     = {2023-10-20T12:23:39},
  doi              = {10.1103/physrevlett.59.2229},
  file             = {:by-author/P/Pineda/1987_Pineda_2229.pdf:PDF},
  keywords         = {Artificial Neural Networks (ANN); Computer Science (CS); Graph Neural Networks (GNN); Graph Neural Neworks; Machine Learning (ML)},
  modificationdate = {2023-10-20T12:26:16},
  owner            = {saulius},
  publisher        = {American Physical Society ({APS})},
}

@Article{Rossi2021,
  author           = {Alberto Rossi and Markus Hagenbuchner and Franco Scarselli and Ah Chung Tsoi},
  journal          = {Neurocomputing},
  title            = {A study on the effects of recursive convolutional layers in convolutional neural networks},
  year             = {2021},
  month            = {oct},
  pages            = {59--70},
  volume           = {460},
  comment          = {Cites},
  creationdate     = {2023-10-20T12:35:38},
  doi              = {10.1016/j.neucom.2021.07.021},
  file             = {:by-author/R/Rossi/2021_Rossi_59.pdf:PDF},
  keywords         = {Artificial Neural Networks (ANN); Computer Science (CS); Graph Neural Networks (GNN); Graph Neural Neworks; Machine Learning (ML)},
  modificationdate = {2023-10-23T20:37:05},
  owner            = {saulius},
  publisher        = {Elsevier {BV}},
}

@Article{Burmester1992,
  author           = {C. P. Burmester and L. T. WilIe and R. Gronsky},
  title            = {{M}onte {C}arlo simulations on {SIMD} computer architectures},
  year             = {1992},
  pages            = {1--9},
  creationdate     = {2023-10-23T20:39:20},
  doi              = {10.1557/proc-278-3},
  file             = {:by-author/B/Burmester/1992_Burmester_1.pdf:PDF},
  keywords         = {Computer Architecture; Computer Science (CS); Computing History; Ising Model; MPP; Monte Carlo Simulation; Parallel Computers; Simulation},
  modificationdate = {2023-10-23T20:48:21},
  owner            = {saulius},
  url              = {https://digital.library.unt.edu/ark:/67531/metadc1400627/m2/1/high_res_d/10184268.pdf},
}

@InProceedings{Kerr1992,
  author           = {J. P. Kerr and E. B. Barlett},
  booktitle        = {[1992] Proceedings Fifth Annual {IEEE} Symposium on Computer-Based Medical Systems},
  title            = {{SPECT} reconstruction using a backpropagation neural network implemented on a massively parallel {SIMD} computer},
  year             = {1992},
  pages            = {465--472},
  publisher        = {{IEEE} Comput. Soc. Press},
  creationdate     = {2023-10-23T20:50:03},
  doi              = {10.1109/cbms.1992.245026},
  file             = {:by-author/K/Kerr/1992_Kerr_465.pdf:PDF},
  keywords         = {Artificial Neural Networks (ANN); Computer Architecture; Computing History; MPP; Neural Networks (NN); Parallel Computers},
  modificationdate = {2023-10-23T20:52:29},
  owner            = {saulius},
  url              = {https://www.osti.gov/servlets/purl/212515},
}

@Book{Webb2007,
  author           = {Peter Webb},
  title            = {Finite group representations for the pure mathematician},
  year             = {2007},
  creationdate     = {2023-10-23T21:34:26},
  file             = {:by-author/W/Webb/2007_Webb_1.pdf:PDF},
  keywords         = {Algebra; Linear Algebra; Mathematics; Represenntation Theory},
  modificationdate = {2023-10-23T21:36:58},
  owner            = {saulius},
  pages            = {1--105},
  url              = {https://math.uchicago.edu/~margalit/repthy/Webb, Finite group reps for the pure mathematician.pdf},
}

@Presentation{Cai2020a,
  author           = {Jiaying Cai and Zheheng Xiao},
  title            = {Induced representations of finite groups},
  year             = {2020},
  creationdate     = {2023-10-23T21:45:06},
  file             = {:by-author/C/Cai/2020_Cai_1.pdf:PDF},
  keywords         = {Algebra; Linear Algebra; Mathematics; Represenntation Theory},
  modificationdate = {2023-10-23T21:47:11},
  owner            = {saulius},
  url              = {https://math.mit.edu/research/highschool/primes/materials/2020/December/4-Cai-Xiao.pdf},
}

@Article{Kim2018a,
  author           = {Sang Hoon Kim},
  title            = {Representations of finite groups},
  year             = {2018},
  creationdate     = {2023-10-23T21:49:03},
  file             = {:by-author/K/Kim/2018_Kim_1a.pdf:PDF},
  keywords         = {Algebra; Linear Algebra; Mathematics; Represenntation Theory},
  modificationdate = {2023-10-23T21:51:50},
  owner            = {saulius},
  url              = {https://math.uchicago.edu/~may/REU2018/REUPapers/Kim.pdf},
}

@Manuscript{DHoker2019,
  author           = {Eric D'Hoker},
  title            = {Mathematical methods in physics - 231{B}. Group theory},
  year             = {2019},
  keywords         = {Algebra; Linear Algebra; Mathematics; Represenntation Theory},
  url              = {https://www.pa.ucla.edu/faculty-websites/dhoker-lecture-notes/graduate-courses/group-theory.pdf},
  creationdate     = {2023-10-23T21:54:16},
  file             = {:by-author/D/D'Hoker/2019_D'Hoker_1.pdf:PDF},
  modificationdate = {2023-10-23T21:56:09},
  owner            = {saulius},
  pages            = {1--105},
}

@Article{Noether1921,
  author           = {Emmy Noether},
  journal          = {Mathematische Annalen},
  title            = {Idealtheorie in Ringbereichen},
  year             = {1921},
  month            = {mar},
  number           = {1-2},
  pages            = {24--66},
  volume           = {83},
  creationdate     = {2023-10-23T22:11:04},
  doi              = {10.1007/bf01464225},
  file             = {:by-author/N/Noether/1921_Noether_24.pdf:PDF},
  keywords         = {Abstract Algebra; Algebra; Group Theory; Mathematics; Ring Theory},
  modificationdate = {2023-10-23T22:11:51},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media {LLC}},
}

@Article{Moreau2011,
  author           = {Luc Moreau and Ben Clifford and Juliana Freire and Joe Futrelle and Yolanda Gil and Paul Groth and Natalia Kwasnikowska and Simon Miles and Paolo Missier and Jim Myers and Beth Plale and Yogesh Simmhan and Eric Stephan and Jan Van den Bussche},
  journal          = {Future Generation Computer Systems},
  title            = {The {O}pen {P}rovenance {M}odel core specification (v1.1)},
  year             = {2011},
  month            = {jun},
  number           = {6},
  pages            = {743--756},
  volume           = {27},
  comment          = {Found in https://openprovenance.org/opm/model/opmo-20101012, via https://openprovenance.org/opm/.},
  creationdate     = {2023-10-30T19:28:05},
  doi              = {10.1016/j.future.2010.07.005},
  eprint           = {https://eprints.soton.ac.uk/268332/1/opm.pdf},
  file             = {:by-author/M/Moreau/2011_Moreau_743.pdf:PDF},
  keywords         = {Bioinformatics; Computer Science (CS); Data Management; Data Provenance; Ontologies; Workflows},
  modificationdate = {2023-10-30T19:32:25},
  owner            = {saulius},
  publisher        = {Elsevier {BV}},
}

@TechReport{PWG2005,
  author           = {{PREMIS Working Group}},
  institution      = {PREMIS},
  title            = {Data dictionary for preservation metadata -- final report ofthe {PREMIS} {W}orking {G}roup},
  year             = {2005},
  comment          = {Cited in Moreau2011.},
  creationdate     = {2023-10-30T19:36:11},
  eprint           = {https://www.oclc.org/content/dam/research/activities/pmwg/premis-final.pdf},
  file             = {:by-author/P/PWG/2005_PWG_1.pdf:PDF},
  keywords         = {Bioinformatics; Computer Science (CS); Data Management; Data Provenance; Metadata; Ontologies; Workflows},
  modificationdate = {2023-10-30T19:41:58},
  owner            = {saulius},
  url              = {http://www.oclc.org/research/projects/pmwg/premis-final.pdf},
}

@Article{Lamport1978,
  author           = {Lamport, Leslie},
  journal          = {Communications of the ACM},
  title            = {Time, clocks and the ordering of events in a distributed system},
  year             = {1978},
  month            = {July},
  note             = {2000 PODC Influential Paper Award (later renamed the Edsger W. Dijkstra Prize in Distributed Computing). Also awarded an ACM SIGOPS Hall of Fame Award in 2007.},
  pages            = {558-565},
  abstract         = {Jim Gray once told me that he had heard two different opinions of this paper: that it's trivial and that it's brilliant. I can't argue with the former, and I am disinclined to argue with the latter.
The origin of this paper was the note The Maintenance of Duplicate Databases by Paul Johnson and Bob Thomas. I believe their note introduced the idea of using message timestamps in a distributed algorithm. I happen to have a solid, visceral understanding of special relativity (see [5]). This enabled me to grasp immediately the essence of what they were trying to do. Special relativity teaches us that there is no invariant total ordering of events in space-time; different observers can disagree about which of two events happened first. There is only a partial order in which an event e1 precedes an event e2 iff e1 can causally affect e2. I realized that the essence of Johnson and Thomas's algorithm was the use of timestamps to provide a total ordering of events that was consistent with the causal order. This realization may have been brilliant. Having realized it, everything else was trivial. Because Thomas and Johnson didn't understand exactly what they were doing, they didn't get the algorithm quite right; their algorithm permitted anomalous behavior that essentially violated causality. I quickly wrote a short note pointing this out and correcting the algorithm.
It didn't take me long to realize that an algorithm for totally ordering events could be used to implement any distributed system. A distributed system can be described as a particular sequential state machine that is implemented with a network of processors. The ability to totally order the input requests leads immediately to an algorithm to implement an arbitrary state machine by a network of processors, and hence to implement any distributed system. So, I wrote this paper, which is about how to implement an arbitrary distributed state machine. As an illustration, I used the simplest example of a distributed system I could think of--a distributed mutual exclusion algorithm.
This is my most often cited paper. Many computer scientists claim to have read it. But I have rarely encountered anyone who was aware that the paper said anything about state machines. People seem to think that it is about either the causality relation on events in a distributed system, or the distributed mutual exclusion problem. People have insisted that there is nothing about state machines in the paper. I've even had to go back and reread it to convince myself that I really did remember what I had written.
The paper describes the synchronization of logical clocks. As something of an afterthought, I decided to see what kind of synchronization it provided for real-time clocks. So, I included a theorem about real-time synchronization. I was rather surprised by how difficult the proof turned out to be. This was an indication of what lay ahead in [62].
This paper won the 2000 PODC Influential Paper Award (later renamed the Edsger W. Dijkstra Prize in Distributed Computing). It won an ACM SIGOPS Hall of Fame Award in 2007.},
  comment          = {Cited in Moreau2011.},
  creationdate     = {2023-10-30T19:55:29},
  doi              = {10.1145/359545.359563},
  edition          = {Communications of the ACM 21, 7 (July 1978), 558-565. Reprinted in several collections, including Distributed Computing: Concepts and Implementations, McEntire et al., ed. IEEE Press, 1984.},
  eprint           = {https://www.microsoft.com/en-us/research/uploads/prod/2016/12/Time-Clocks-and-the-Ordering-of-Events-in-a-Distributed-System.pdf},
  file             = {:by-author/L/Lamport/1978_Lamport_558.pdf:PDF},
  keywords         = {Computer Science (CS); Distributed Systems; Time Management},
  modificationdate = {2023-10-30T19:57:50},
  owner            = {saulius},
  url              = {https://www.microsoft.com/en-us/research/publication/time-clocks-ordering-events-distributed-system/},
}

@InProceedings{Hartig2009a,
  author           = {Olaf Hartig},
  booktitle        = {Proceedingsof the Linked Data on the Web Workshop (LDOW’09)},
  title            = {Provenance information in the web of data},
  year             = {2009},
  comment          = {Cited in Moreau2011.},
  creationdate     = {2023-10-30T20:01:11},
  file             = {:by-author/H/Hartig/2009_Hartig_1.pdf:PDF},
  keywords         = {Computer Science (CS); Data Management; Data Provenance; Linked Data; Workflows},
  modificationdate = {2023-10-30T20:04:35},
  owner            = {saulius},
  url              = {http://events.linkeddata.org/ldow2009/papers/ldow2009_paper18.pdf},
}

@Article{Sahoo2008,
  author           = {Satya S. Sahoo and Amit Sheth and Cory Henson},
  journal          = {{IEEE} Internet Computing},
  title            = {Semantic Provenance for {eScience}: Managing the Deluge of Scientific Data},
  year             = {2008},
  month            = {jul},
  number           = {4},
  pages            = {46--54},
  volume           = {12},
  comment          = {Cited in Moreau2011.},
  creationdate     = {2023-10-30T20:08:50},
  doi              = {10.1109/mic.2008.86},
  file             = {:by-author/S/Sahoo/2008_Sahoo_46.pdf:PDF},
  keywords         = {Computer Science (CS); Data Management; Data Provenance; Linked Data; Workflows},
  modificationdate = {2023-10-30T20:09:47},
  owner            = {saulius},
  publisher        = {Institute of Electrical and Electronics Engineers ({IEEE})},
  url              = {https://corescholar.libraries.wright.edu/cgi/viewcontent.cgi?article=2129&context=knoesis},
}

@Article{Groth2009,
  author           = {Paul Groth and Simon Miles and Luc Moreau},
  journal          = {{ACM} Transactions on Internet Technology},
  title            = {A model of process documentation to determine provenance in mash-ups},
  year             = {2009},
  month            = {feb},
  number           = {1},
  pages            = {1--31},
  volume           = {9},
  comment          = {Cited in Moreau2011.},
  creationdate     = {2023-10-30T20:11:19},
  doi              = {10.1145/1462159.1462162},
  eprint           = {https://eprints.soton.ac.uk/270861/1/toit09.pdf},
  file             = {:by-author/G/Groth/2009_Groth_1.pdf:PDF},
  keywords         = {Computer Science (CS); Data Management; Data Provenance; Linked Data; Workflows},
  modificationdate = {2023-10-30T20:12:09},
  owner            = {saulius},
  publisher        = {Association for Computing Machinery ({ACM})},
  url              = {https://eprints.soton.ac.uk/270861/1/toit09.pdf},
}

@TechReport{Desruisseaux2009,
  title            = {Internet calendaring and scheduling core object specification ({i{C}alendar})},
  year             = {2009},
  month            = {sep},
  creationdate     = {2023-11-08T09:31:25},
  doi              = {10.17487/rfc5545},
  editor           = {B. Desruisseaux},
  file             = {:by-author/D/Desruisseaux/2009_Desruisseaux_1.pdf:PDF},
  keywords         = {Calendar; Computer Science (CS); ICal; RFC},
  modificationdate = {2023-11-08T09:40:43},
  owner            = {saulius},
  pagetotal        = {168},
  publisher        = {{RFC} Editor},
}

@Article{Stokes2013,
  author           = {Harold T. Stokes and Branton J. Campbell and Ryan Cordes},
  journal          = {Acta Crystallographica Section A Foundations of Crystallography},
  title            = {Tabulation of irreducible representations of the crystallographic space groups and their superspace extensions},
  year             = {2013},
  month            = {may},
  number           = {4},
  pages            = {388--395},
  volume           = {69},
  comment          = {Web site with the data: https://stokes.byu.edu/iso/irtables.php [accessed 2023-11-08T09:47+02:00].
Web site for the ISOTROPY software: https://stokes.byu.edu/iso/isotropy.php [accesssed 2023-11-08T10:06+02:00].},
  creationdate     = {2023-11-08T09:43:11},
  doi              = {10.1107/s0108767313007538},
  file             = {:by-author/S/Stokes/2013_Stokes_388.pdf:PDF},
  keywords         = {Algebra; Crystallography; Irreducible Representations; Linear Algebra; Representation Theory; Spacegroups},
  modificationdate = {2023-11-08T10:06:12},
  owner            = {saulius},
  publisher        = {International Union of Crystallography ({IUCr})},
  url              = {https://stokes.byu.edu/iso/2013 Stokes.pdf},
}

@Article{Campbell2006,
  author           = {Branton J. Campbell and Harold T. Stokes and David E. Tanner and Dorian M. Hatch},
  journal          = {Journal of Applied Crystallography},
  title            = {\textit{ISODISPLACE}: a web-based tool for exploring structural distortions},
  year             = {2006},
  month            = {jul},
  number           = {4},
  pages            = {607--614},
  volume           = {39},
  comment          = {Cited in Stokes2013.},
  creationdate     = {2023-11-08T09:51:37},
  doi              = {10.1107/s0021889806014075},
  file             = {:by-author/C/Campbell/2006_Campbell_607.pdf:PDF},
  keywords         = {Algebra; Crystal Distortions; Crystallography; Irreducible Representations; Linear Algebra; Representation Theory; Spacegroups},
  modificationdate = {2023-11-08T09:55:07},
  owner            = {saulius},
  publisher        = {International Union of Crystallography ({IUCr})},
}

@Article{Davies1982,
  author           = {B.L. Davies},
  journal          = {Physica A: Statistical Mechanics and its Applications},
  title            = {Computational group theory in crystal physics: A review},
  year             = {1982},
  month            = {aug},
  number           = {1-3},
  pages            = {507--517},
  volume           = {114},
  comment          = {Found on the Web when searching for "Cracknell, A. P., Davies, B. L., Miller, S. C. & Love, W. F. (1979).
Kronecker Product Tables, Vol. 1. New York: Plenum" using DuckDuckGo.},
  creationdate     = {2023-11-08T09:57:28},
  doi              = {10.1016/0378-4371(82)90340-5},
  file             = {:by-author/D/Davies/1982_Davies_507.pdf:PDF},
  keywords         = {Algebra; Crystallography; Irreducible Representations; Linear Algebra; Representation Theory; Spacegroups},
  modificationdate = {2023-11-08T09:59:54},
  owner            = {saulius},
  publisher        = {Elsevier {BV}},
}

@Manuscript{Li2022a,
  author           = {Rupert Li},
  title            = {{M}ackey-{W}igner’s little group method with an application to {Aff}({q})},
  year             = {2022},
  keywords         = {Linear Algebra; Little Group; Representation Theory},
  url              = {https://math.mit.edu/~mqt/math/teaching/mit/18-704/final-papers/li-r_final.pdf},
  comment          = {Found on the Web using DuckDuckGo when search for "little group of k definition".},
  creationdate     = {2023-11-08T10:15:04},
  file             = {:by-author/L/Li/2022_Li_1.pdf:PDF},
  modificationdate = {2023-11-08T10:19:25},
  owner            = {saulius},
}

@Book{Melnikov2022,
  author           = {Nikolai B. Melnikov and Boris I. Reser},
  publisher        = {Springer International Publishing},
  title            = {Space group representations},
  year             = {2022},
  comment          = {Found on the Web using DuckDuckGo when searching for "irreducible representations and characters of 3D crystallographic space groups".},
  creationdate     = {2023-11-08T10:39:47},
  doi              = {10.1007/978-3-031-13991-8},
  file             = {:by-author/M/Melnikov/2022_Melnikov_Space Group Representations.pdf:PDF;:by-author/M/Melnikov/2022_Melnikov_Space Group Representations.epub:ePUB},
  keywords         = {Algebra; Crystallography; Irreducible Representations; Linear Algebra; Representation Theory; Spacegroups},
  modificationdate = {2023-11-08T11:06:26},
  owner            = {saulius},
  pagetotal        = {343},
}

@InBook{LibreTexts2023,
  author           = {{LibreTexts}},
  chapter          = {12.7},
  publisher        = {LibreTexts},
  title            = {Characters of irreducible representations},
  year             = {2023},
  booktitle        = {Physical Chemistry},
  comment          = {Found on the Web using DuckDuckGo when searching for "irreducible representations and characters of 3D crystallographic space groups".},
  creationdate     = {2023-11-08T10:56:03},
  eprint           = {https://chem.libretexts.org/Bookshelves/Physical_and_Theoretical_Chemistry_Textbook_Maps/Physical_Chemistry_(LibreTexts)/12%3A_Group_Theory_-_The_Exploitation_of_Symmetry/12.07%3A_Characters_of_Irreducible_Representations},
  file             = {:by-author/L/LibreTexts/2023_LibreTexts_Characters of Irreducible Representations.pdf:PDF},
  keywords         = {Chemistry; Irreducible Representations; Representation Theory; Spectroscopy; Symmetry},
  modificationdate = {2023-11-08T11:14:22},
  owner            = {saulius},
}

@Article{Liu2021,
  author           = {Gui-Bin Liu and Miao Chu and Zeying Zhang and Zhi-Ming Yu and Yugui Yao},
  journal          = {Computer Physics Communications},
  title            = {{SpaceGroupIrep}: A package for irreducible representations of space group},
  year             = {2021},
  month            = {aug},
  pages            = {107993},
  volume           = {265},
  comment          = {Found on the Web using DuckDuckGo when searching for "irreducible representations and characters of 3D crystallographic space groups".},
  creationdate     = {2023-11-08T11:05:30},
  doi              = {10.1016/j.cpc.2021.107993},
  file             = {:by-author/L/Liu/2021_Liu_107993.pdf:PDF},
  keywords         = {Algebra; Crystallography; Irreducible Representations; Linear Algebra; Representation Theory; Spacegroups},
  modificationdate = {2023-11-08T11:10:14},
  owner            = {saulius},
  publisher        = {Elsevier {BV}},
}

@Article{Neto1973,
  author           = {N. Neto},
  journal          = {Acta Crystallographica Section A},
  title            = {Irreducible representations of space groups},
  year             = {1973},
  month            = {jul},
  number           = {4},
  pages            = {464--472},
  volume           = {29},
  comment          = {Found on the Web using DuckDuckGo when searching for "irreducible representations and characters of 3D crystallographic space groups".},
  creationdate     = {2023-11-08T11:15:19},
  doi              = {10.1107/s0567739473001129},
  file             = {:by-author/N/Neto/1973_Neto_464.pdf:PDF},
  keywords         = {Algebra; Crystallography; Irreducible Representations; Linear Algebra; Representation Theory; Spacegroups},
  modificationdate = {2023-11-08T11:16:56},
  owner            = {saulius},
  publisher        = {International Union of Crystallography ({IUCr})},
}

@Poster{Paketuryte2021,
  author           = {Vaida Paketurytė and Alexey Smirnov and Elena Manakova and Saulius Gražulis and Daumantas Matulis},
  title            = {Crystallography of human carbonic anhydrases with inhibitors for drug design},
  year             = {2021},
  creationdate     = {2023-11-08T14:13:53},
  file             = {:by-author/P/Paketurytė/2021_Paketurytė_1.pdf:PDF},
  keywords         = {Carbonic Anhydrases; Inhibitors; Structural Biology; X-ray Crystallography},
  modificationdate = {2023-11-08T14:22:02},
  owner            = {saulius},
}

@Article{Makhzani2015,
  author           = {Alireza Makhzani and Jonathon Shlens and Navdeep Jaitly and Ian Goodfellow and Brendan Frey},
  title            = {Adversarial autoencoders},
  year             = {2015},
  month            = nov,
  abstract         = {In this paper, we propose the "adversarial autoencoder" (AAE), which is a probabilistic autoencoder that uses the recently proposed generative adversarial networks (GAN) to perform variational inference by matching the aggregated posterior of the hidden code vector of the autoencoder with an arbitrary prior distribution. Matching the aggregated posterior to the prior ensures that generating from any part of prior space results in meaningful samples. As a result, the decoder of the adversarial autoencoder learns a deep generative model that maps the imposed prior to the data distribution. We show how the adversarial autoencoder can be used in applications such as semi-supervised classification, disentangling style and content of images, unsupervised clustering, dimensionality reduction and data visualization. We performed experiments on MNIST, Street View House Numbers and Toronto Face datasets and show that adversarial autoencoders achieve competitive results in generative modeling and semi-supervised classification tasks.},
  archiveprefix    = {arXiv},
  creationdate     = {2023-11-08T19:14:59},
  doi              = {10.48550/arXiv.1511.05644},
  eprint           = {1511.05644},
  file             = {:by-author/M/Makhzani/2015_Makhzani_1.pdf:PDF},
  keywords         = {cs.LG},
  modificationdate = {2023-11-15T18:24:55},
  owner            = {saulius},
  primaryclass     = {cs.LG},
}

@Book{Steinberg2009,
  author           = {Benjamin Steinberg},
  publisher        = {Benjamin Steinberg},
  title            = {Representation theory of finite groups},
  year             = {2009},
  month            = {Dec},
  note             = {URL: https://www.researchgate.net/publication/228855716\_Representation\_Theory\_of\_Finite\_Groups},
  volume           = {1},
  author_sort      = {Steinberg, Benjamin},
  calibreid        = {1265},
  cover            = {calibre/Benjamin Steinberg/Representation Theory of Finite Groups (1265)/cover.jpg},
  creationdate     = {2023-11-09T11:27:39},
  doi              = {10.1007/978-1-4614-0776-8},
  eprint           = {https://www.researchgate.net/publication/228855716_Representation_Theory_of_Finite_Groups},
  file             = {:by-author/S/Steinberg/2009_Steinberg_Representation Theory of Finite Groups.pdf:PDF},
  formats          = {pdf},
  identifiers      = {url:https://www.researchgate.net/publication/228855716\_Representation\_Theory\_of\_Finite\_Groups},
  keywords         = {Algebra; Mathematics; Representation Theory},
  languages        = {eng},
  library_name     = {calibre},
  modificationdate = {2023-11-09T11:29:18},
  owner            = {saulius},
  size             = {769284 octets},
  tags             = {Mathematics; Algebra; Representation Theory},
  timestamp        = {2023-11-01},
  title_sort       = {Representation Theory of Finite Groups},
  uuid             = {a0fa4d3d-1bf0-427d-9ed2-8c4859c49de8},
}

@Article{Aalst2017,
  author           = {Wil M. P. van der Aalst and Martin Bichler and Armin Heinzl},
  journal          = {Business \& Information Systems Engineering},
  title            = {Responsible data science},
  year             = {2017},
  month            = {jun},
  number           = {5},
  pages            = {311--313},
  volume           = {59},
  comment          = {Cited in Helliwell2019 (in the abstract, in-line).},
  creationdate     = {2023-11-09T15:29:57},
  doi              = {10.1007/s12599-017-0487-z},
  file             = {:by-author/A/Aalst/2017_Aalst_311.pdf:PDF},
  keywords         = {Data Management; Data Quality; FACT; FAIR; Scientific Data},
  modificationdate = {2023-11-09T15:34:57},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media {LLC}},
}

@Book{Braunstein2022,
  author           = {Mark L. Braunstein},
  publisher        = {Springer International Publishing},
  title            = {Health informatics on {FHIR}: how {HL}7's {API} is transforming healthcare},
  year             = {2022},
  creationdate     = {2023-11-09T15:51:00},
  doi              = {10.1007/978-3-030-91563-6},
  file             = {:by-author/B/Braunstein/2022_Braunstein_Health Informatics on FHIR_ How HL7_s API Is Transforming Healthcare.pdf:PDF},
  keywords         = {Health Informatics; Medicine},
  modificationdate = {2023-11-17T10:27:08},
  owner            = {saulius},
  pagetotal        = {482},
}

@Article{Goodfellow2014,
  author           = {Ian J. Goodfellow and Jean Pouget-Abadie and Mehdi Mirza and Bing Xu and David Warde-Farley and Sherjil Ozair and Aaron Courville and Yoshua Bengio},
  journal          = {arXiv},
  title            = {Generative adversarial networks},
  year             = {2014},
  month            = jun,
  abstract         = {We propose a new framework for estimating generative models via an adversarial process, in which we simultaneously train two models: a generative model G that captures the data distribution, and a discriminative model D that estimates the probability that a sample came from the training data rather than G. The training procedure for G is to maximize the probability of D making a mistake. This framework corresponds to a minimax two-player game. In the space of arbitrary functions G and D, a unique solution exists, with G recovering the training data distribution and D equal to 1/2 everywhere. In the case where G and D are defined by multilayer perceptrons, the entire system can be trained with backpropagation. There is no need for any Markov chains or unrolled approximate inference networks during either training or generation of samples. Experiments demonstrate the potential of the framework through qualitative and quantitative evaluation of the generated samples.},
  archiveprefix    = {arXiv},
  creationdate     = {2023-11-15T18:24:24},
  eprint           = {1406.2661},
  file             = {:by-author/G/Goodfellow/2014_Goodfellow_1.pdf:PDF},
  keywords         = {Artificial Neural Networks (ANN); Generative Adversarial Networks (GAN); cs.LG; stat.ML},
  modificationdate = {2023-11-15T18:25:04},
  owner            = {saulius},
  primaryclass     = {stat.ML},
}

 
@Article{Krippendorff2004,
  author           = {Krippendorff, Klaus},
  journal          = {Human Communication Research},
  title            = {Reliability in content analysis: some common misconceptions and recommendations},
  year             = {2004},
  issn             = {1468-2958},
  month            = jul,
  number           = {3},
  pages            = {411--433},
  volume           = {30},
  creationdate     = {2023-11-23T15:45:56},
  doi              = {10.1111/j.1468-2958.2004.tb00738.x},
  file             = {:by-author/K/Krippendorff/2004_Krippendorff_411.pdf:PDF},
  keywords         = {Agreement Between Judges; Krippendorff's Alpha; Reliability; Statistics},
  modificationdate = {2023-11-23T15:54:37},
  owner            = {saulius},
  publisher        = {Oxford University Press (OUP)},
}

@Manuscript{Krippendorff2013,
  author           = {Krippendorff, Klaus},
  title            = {Computing {K}rippendorff’s alpha-reliability},
  year             = {2013},
  keywords         = {Agreement Between Judges; Krippendorff's Alpha; Reliability; Statistics},
  creationdate     = {2023-11-23T15:52:43},
  file             = {:by-author/K/Krippendorff/2013_Krippendorff_1.pdf:PDF},
  modificationdate = {2023-11-23T15:54:44},
  owner            = {saulius},
}

@Article{Altman2005,
  author           = {Altman, Douglas G. and Bland, J. Martin},
  journal          = {BMJ (Clinical research ed.)},
  title            = {Standard deviations and standard errors.},
  year             = {2005},
  issn             = {1756-1833},
  month            = oct,
  pages            = {903},
  volume           = {331},
  citation-subset  = {IM},
  completed        = {2005-10-21},
  country          = {England},
  creationdate     = {2023-11-19T17:40:16},
  doi              = {10.1136/bmj.331.7521.903},
  file             = {:by-author/A/Altman/2005_Altman_903.pdf:PDF},
  issn-linking     = {0959-8138},
  issue            = {7521},
  keywords         = {Normal Distribution; Reproducibility of Results; Standard Deviation; Standard Deviation of the Mean; Standard Error; Statistics; Statistics as Topic, Methods},
  modificationdate = {2023-11-19T17:41:36},
  nlm-id           = {8900488},
  owner            = {saulius},
  pii              = {331/7521/903},
  pmc              = {PMC1255808},
  pmid             = {16223828},
  pubmodel         = {Print},
  pubstate         = {ppublish},
  revised          = {2022-03-17},
  url              = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1255808/},
}

@Article{Nagele2003,
  author           = {Nagele, P.},
  journal          = {British journal of anaesthesia},
  title            = {Misuse of standard error of the mean (SEM) when reporting variability of a sample. A critical evaluation of four anaesthesia journals.},
  year             = {2003},
  issn             = {0007-0912},
  month            = apr,
  pages            = {514--516},
  volume           = {90},
  abstract         = {In biomedical research papers, authors often use descriptive statistics to describe the study sample. The standard deviation (SD) describes the variability between individuals in a sample; the standard error of the mean (SEM) describes the uncertainty of how the sample mean represents the population mean. Authors often, inappropriately, report the SEM when describing the sample. As the SEM is always less than the SD, it misleads the reader into underestimating the variability between individuals within the study sample. The aim of this study was to evaluate the frequency of inappropriate use of the SEM in four leading anaesthesia journals in 2001. The journals were searched manually for descriptive statistics reporting either the mean (SD) or the mean (SEM), and inappropriate use of the SEM was noted. In 2001, all four anaesthesia journals published articles that used the SEM incorrectly: Anesthesia & Analgesia 27.7%, British Journal of Anaesthesia 22.6%, Anesthesiology 18.7% and European Journal of Anaesthesiology 11.5%. Laboratory reports and clinical studies were equally affected, except for Anesthesiology where 90% were basic science reports. One in four articles (n=198/860, 23%) published in four anaesthesia journals in 2001 inappropriately used the SEM in descriptive statistics to describe the variability of the study sample. Anaesthesia journals are encouraged to provide clearer statistical guidelines on how to report data variability in descriptive statistics.},
  citation-subset  = {IM},
  completed        = {2003-05-08},
  country          = {England},
  creationdate     = {2023-11-19T17:55:03},
  doi              = {10.1093/bja/aeg087},
  file             = {:by-author/N/Nagele/2003_Nagele_514.pdf:PDF},
  issn-linking     = {0007-0912},
  issue            = {4},
  keywords         = {Anesthesiology, Standards; Data Interpretation, Statistical; Periodicals as Topic, Standards; Research, Standards; Standard Deviation; Standard Deviation of the Mean; Standard Error; Statistics},
  modificationdate = {2023-11-19T17:57:14},
  nlm-id           = {0372541},
  owner            = {saulius},
  pii              = {S0007-0912(17)38467-2},
  pmid             = {12644429},
  pubmodel         = {Print},
  pubstate         = {ppublish},
  revised          = {2019-12-10},
  url              = {https://pubmed.ncbi.nlm.nih.gov/12644429/},
}

@Article{Lee2015,
  author           = {Lee, Dong Kyu and In, Junyong and Lee, Sangseok},
  journal          = {Korean journal of anesthesiology},
  title            = {Standard deviation and standard error of the mean.},
  year             = {2015},
  issn             = {2005-6419},
  month            = jun,
  pages            = {220--223},
  volume           = {68},
  abstract         = {In most clinical and experimental studies, the standard deviation (SD) and the estimated standard error of the mean (SEM) are used to present the characteristics of sample data and to explain statistical analysis results. However, some authors occasionally muddle the distinctive usage between the SD and SEM in medical literature. Because the process of calculating the SD and SEM includes different statistical inferences, each of them has its own meaning. SD is the dispersion of data in a normal distribution. In other words, SD indicates how accurately the mean represents sample data. However the meaning of SEM includes statistical inference based on the sampling distribution. SEM is the SD of the theoretical distribution of the sample means (the sampling distribution). While either SD or SEM can be applied to describe data and statistical results, one should be aware of reasonable methods with which to use SD and SEM. We aim to elucidate the distinctions between SD and SEM and to provide proper usage guidelines for both, which summarize data and describe statistical results.},
  completed        = {2015-06-05},
  country          = {Korea (South)},
  creationdate     = {2023-11-19T18:00:22},
  doi              = {10.4097/kjae.2015.68.3.220},
  file             = {:by-author/L/Lee/2015_Lee_220.pdf:PDF},
  issn-linking     = {2005-6419},
  issue            = {3},
  keywords         = {Standard Deviation; Standard Deviation of the Mean; Standard Error; Standard Error of the Mean; Statistics},
  modificationdate = {2023-11-19T18:02:07},
  nlm-id           = {101502451},
  owner            = {saulius},
  pmc              = {PMC4452664},
  pmid             = {26045923},
  pubmodel         = {Print-Electronic},
  pubstate         = {ppublish},
  revised          = {2018-11-13},
  url              = {https://pubmed.ncbi.nlm.nih.gov/26045923/},
}

@Article{Andrade2020,
  author           = {Andrade, Chittaranjan},
  journal          = {Indian journal of psychological medicine},
  title            = {Understanding the Difference Between Standard Deviation and Standard Error of the Mean, and Knowing When to Use Which.},
  year             = {2020},
  issn             = {0253-7176},
  month            = jul,
  pages            = {409--410},
  volume           = {42},
  abstract         = {Many authors are unsure of whether to present the mean along with the standard deviation (SD) or along with the standard error of the mean (SEM). The SD is a descriptive statistic that estimates the scatter of values around the sample mean; hence, the SD describes the sample. In contrast, the SEM is an estimate of how close the sample mean is to the population mean; it is an intermediate term in the calculation of the 95% confidence interval around the mean, and (where applicable) statistical significance; the SEM does not describe the sample. Therefore, the mean should always be accompanied by the SD when describing the sample. There are many reasons why the SEM continues to be reported, and it is argued that none of these is justifiable. In fact, presentation of SEMs may mislead readers into believing that the sample data are more precise than they actually are. Given that the standard error is not presented for other parameters, such as difference between means or proportions, and difference between proportions, it is suggested that presentation of SEM values can be done away with, altogether.},
  country          = {United States},
  creationdate     = {2023-11-19T18:07:23},
  doi              = {10.1177/0253717620933419},
  eprint           = {https://journals.sagepub.com/doi/pdf/10.1177/0253717620933419},
  file             = {:by-author/A/Andrade/2020_Andrade_409.pdf:PDF},
  issn-linking     = {0253-7176},
  issue            = {4},
  keywords         = {Confidence Interval; Graphs; Standard Deviation; Standard Deviation of the Mean; Standard Error; Standard Error of the Mean; Statistical Significance; Statistics},
  modificationdate = {2023-11-19T18:09:14},
  nlm-id           = {7910727},
  owner            = {saulius},
  pii              = {10.1177_0253717620933419},
  pmc              = {PMC7746895},
  pmid             = {33402813},
  pubmodel         = {Electronic-eCollection},
  pubstate         = {epublish},
  revised          = {2021-01-11},
  url              = {https://pubmed.ncbi.nlm.nih.gov/33402813/},
}

 
@InBook{Harris2019,
  author           = {Harris, Georgia L.},
  chapter          = {8},
  publisher        = {NIST},
  title            = {Selected laboratory and measurement practices and procedures to support basic mass calibrations: 2019 edition},
  year             = {2019},
  month            = may,
  creationdate     = {2023-11-19T18:41:26},
  doi              = {10.6028/nist.ir.6969-2019},
  file             = {:by-author/H/Harris/2019_Harris_1.pdf:PDF},
  keywords         = {Standard Deviation; Standard Deviation of the Mean; Standard Error; Standard Error of the Mean; Statistics},
  modificationdate = {2023-11-19T18:45:05},
  owner            = {saulius},
  pagetotal        = {12},
  school           = {National Institute of Standards and Technology},
  url              = {https://www.nist.gov/system/files/documents/2019/05/13/section-8-statistics-techniques-20190506.pdf},
}

 
@Article{Krippendorff2004a,
  author           = {Krippendorff, Klaus},
  journal          = {Quality &amp; Quantity},
  title            = {Measuring the reliability of qualitative text analysis data},
  year             = {2004},
  issn             = {1573-7845},
  month            = dec,
  number           = {6},
  pages            = {787--800},
  volume           = {38},
  creationdate     = {2023-11-23T15:59:44},
  doi              = {10.1007/s11135-004-8107-7},
  file             = {:by-author/K/Krippendorff/2004_Krippendorff_787.pdf:PDF},
  keywords         = {Agreement Between Judges; Krippendorff's Alpha; Reliability; Statistics},
  modificationdate = {2023-11-23T16:01:48},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media LLC},
}

 
@Article{Lent2003,
  author           = {Lent, Craig S. and Isaksen, Beth and Lieberman, Marya},
  journal          = {Journal of the American Chemical Society},
  title            = {Molecular quantum-dot cellular automata},
  year             = {2003},
  issn             = {1520-5126},
  month            = jan,
  number           = {4},
  pages            = {1056--1063},
  volume           = {125},
  creationdate     = {2023-11-23T22:05:30},
  doi              = {10.1021/ja026856g},
  file             = {:by-author/L/Lent/2003_Lent_1056.pdf:PDF},
  keywords         = {Cellular Automata; Molecular Computers; Molecular Switches},
  modificationdate = {2023-11-23T22:10:16},
  owner            = {saulius},
  publisher        = {American Chemical Society (ACS)},
}

@Presentation{Lent2009,
  author           = {Craig S. Lent},
  title            = {Molecular quantum-dot cellular automata ({QCA}): beyond transistors},
  year             = {2009},
  creationdate     = {2023-11-23T22:11:48},
  file             = {:by-author/L/Lent/2009_Lent_1.pdf:PDF},
  keywords         = {Cellular Automata; Molecular Computers; Molecular Switches},
  modificationdate = {2023-11-23T22:13:29},
  owner            = {saulius},
  url              = {https://www.cmu.edu/nanotechnology-forum/Forum_6/Presentation/Craig_Lent.pdf},
}

 
@Article{Blair2018,
  author           = {Blair, Enrique and Lent, Craig},
  journal          = {Journal of Low Power Electronics and Applications},
  title            = {Clock Topologies for Molecular Quantum-Dot Cellular Automata},
  year             = {2018},
  issn             = {2079-9268},
  month            = sep,
  number           = {3},
  pages            = {31},
  volume           = {8},
  creationdate     = {2023-11-23T22:16:08},
  doi              = {10.3390/jlpea8030031},
  file             = {:by-author/B/Blair/2018_Blair_31.pdf:PDF},
  keywords         = {Cellular Automata; Molecular Computers; Molecular Switches},
  modificationdate = {2023-11-23T22:16:24},
  owner            = {saulius},
  publisher        = {MDPI AG},
}

 
@Article{Hennessy2001,
  author           = {Hennessy, Kevin and Lent, Craig S.},
  journal          = {Journal of Vacuum Science &amp; Technology B: Microelectronics and Nanometer Structures Processing, Measurement, and Phenomena},
  title            = {Clocking of molecular quantum-dot cellular automata},
  year             = {2001},
  issn             = {1520-8567},
  month            = sep,
  number           = {5},
  pages            = {1752--1755},
  volume           = {19},
  creationdate     = {2023-11-23T22:17:11},
  doi              = {10.1116/1.1394729},
  file             = {:by-author/H/Hennessy/2001_Hennessy_1752.pdf:PDF},
  keywords         = {Cellular Automata; Molecular Computers; Molecular Switches},
  modificationdate = {2023-11-23T22:17:32},
  owner            = {saulius},
  publisher        = {American Vacuum Society},
}

 
@Article{Palii2021,
  author           = {Palii, Andrew and Clemente-Juan, Juan Modesto and Rybakov, Andrey and Aldoshin, Sergey and Tsukerblat, Boris},
  journal          = {Physical Chemistry Chemical Physics},
  title            = {Toward multifunctional molecular cells for quantum cellular automata: exploitation of interconnected charge and spin degrees of freedom},
  year             = {2021},
  issn             = {1463-9084},
  number           = {26},
  pages            = {14511--14528},
  volume           = {23},
  creationdate     = {2023-11-23T22:19:07},
  doi              = {10.1039/d1cp00444a},
  file             = {:by-author/P/Palii/2021_Palii_14511.pdf:PDF},
  keywords         = {Cellular Automata; Molecular Computers; Molecular Switches},
  modificationdate = {2023-11-23T22:20:14},
  owner            = {saulius},
  publisher        = {Royal Society of Chemistry (RSC)},
}

 
@Article{MontenegroPohlhammer2023,
  author           = {Montenegro-Pohlhammer, Nicolás and Palomino, Carlos M. and Calzado, Carmen J.},
  journal          = {Inorganic Chemistry Frontiers},
  title            = {Exploring the potential as molecular quantum-dot cellular automata of a mixed-valence {Ru}2 complex deposited on a {Au}(111) surface},
  year             = {2023},
  issn             = {2052-1553},
  number           = {8},
  pages            = {2484--2492},
  volume           = {10},
  creationdate     = {2023-11-23T22:21:54},
  doi              = {10.1039/d2qi02647c},
  file             = {:by-author/M/Montenegro-Pohlhammer/2023_Montenegro-Pohlhammer_2484.pdf:PDF},
  keywords         = {Cellular Automata; Molecular Computers; Molecular Switches},
  modificationdate = {2023-11-23T22:23:10},
  owner            = {saulius},
  publisher        = {Royal Society of Chemistry (RSC)},
}

 
@Article{Lent1993,
  author           = {Lent, C. S. and Tougaw, P. D. and Porod, W. and Bernstein, G. H.},
  journal          = {Nanotechnology},
  title            = {Quantum cellular automata},
  year             = {1993},
  issn             = {1361-6528},
  month            = jan,
  number           = {1},
  pages            = {49--57},
  volume           = {4},
  comment          = {Cited in MontenegroPohlhammer2023.},
  creationdate     = {2023-11-23T22:24:49},
  doi              = {10.1088/0957-4484/4/1/004},
  file             = {:by-author/L/Lent/1993_Lent_49.pdf:PDF},
  keywords         = {Cellular Automata; Molecular Computers; Molecular Switches},
  modificationdate = {2023-11-23T22:27:05},
  owner            = {saulius},
  publisher        = {IOP Publishing},
}

 
@InBook{Sahu2010,
  author           = {Sahu, Satyajit and Oono, Hiroshi and Ghosh, Subrata and Bandyopadhyay, Anirban and Fujita, Daisuke and Peper, Ferdinand and Isokawa, Teijiro and Pati, Ranjit},
  pages            = {650--659},
  publisher        = {Springer Berlin Heidelberg},
  title            = {Molecular implementations of cellular automata},
  year             = {2010},
  isbn             = {9783642159794},
  booktitle        = {Cellular Automata},
  creationdate     = {2023-11-23T22:30:50},
  doi              = {10.1007/978-3-642-15979-4_73},
  file             = {:by-author/S/Sahu/2010_Sahu_650.pdf:PDF},
  issn             = {1611-3349},
  keywords         = {Cellular Automata; Molecular Computers; Molecular Switches},
  modificationdate = {2023-11-23T22:31:23},
  owner            = {saulius},
}

 
@Article{Lu2007,
  author           = {Lu, Yuhui and Liu, Mo and Lent, Craig},
  journal          = {Journal of Applied Physics},
  title            = {Molecular quantum-dot cellular automata: From molecular structure to circuit dynamics},
  year             = {2007},
  issn             = {1089-7550},
  month            = aug,
  number           = {3},
  volume           = {102},
  creationdate     = {2023-11-23T22:33:04},
  doi              = {10.1063/1.2767382},
  file             = {:by-author/L/Lu/2007_Lu_1.pdf:PDF},
  keywords         = {Cellular Automata; Molecular Computers; Molecular Switches},
  modificationdate = {2023-11-23T22:35:07},
  owner            = {saulius},
  publisher        = {AIP Publishing},
}

 
@Article{Ardesi2018,
  author           = {Ardesi, Yuri and Pulimeno, Azzurra and Graziano, Mariagrazia and Riente, Fabrizio and Piccinini, Gianluca},
  journal          = {Journal of Low Power Electronics and Applications},
  title            = {Effectiveness of Molecules for Quantum Cellular Automata as Computing Devices},
  year             = {2018},
  issn             = {2079-9268},
  month            = jul,
  number           = {3},
  pages            = {24},
  volume           = {8},
  creationdate     = {2023-11-23T22:38:20},
  doi              = {10.3390/jlpea8030024},
  file             = {:by-author/A/Ardesi/2018_Ardesi_24.pdf:PDF},
  keywords         = {Cellular Automata; Molecular Computers; Molecular Switches},
  modificationdate = {2023-11-23T22:38:44},
  owner            = {saulius},
  publisher        = {MDPI AG},
}

 
@Article{Sahu2012,
  author           = {Sahu, Satyajit and Oono, Hiroshi and Ghosh, Subrata and Bandyopadhyay, Anirban and Fujita, Daisuke and Peper, Ferdinand and Isokawa, Teijiro and Pati, Ranjit},
  journal          = {Natural Computing},
  title            = {On Cellular Automata rules of molecular arrays},
  year             = {2012},
  issn             = {1572-9796},
  month            = feb,
  number           = {2},
  pages            = {311--321},
  volume           = {11},
  creationdate     = {2023-11-23T22:40:50},
  doi              = {10.1007/s11047-012-9314-0},
  file             = {:by-author/S/Sahu/2012_Sahu_311.pdf:PDF},
  keywords         = {Cellular Automata; Molecular Computers; Molecular Switches},
  modificationdate = {2023-11-23T22:43:50},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media LLC},
}

 
@InProceedings{Isaksen2003,
  author           = {Isaksen, B. and Lent, C. S.},
  booktitle        = {2003 Third IEEE Conference on Nanotechnology, 2003. IEEE-NANO 2003.},
  title            = {Molecular quantum-dot cellular automata},
  year             = {2003},
  publisher        = {IEEE},
  series           = {NANO-03},
  collection       = {NANO-03},
  creationdate     = {2023-11-23T22:45:12},
  doi              = {10.1109/nano.2003.1231700},
  file             = {:by-author/I/Isaksen/2003_Isaksen_1.pdf:PDF},
  keywords         = {Cellular Automata; Molecular Computers; Molecular Switches},
  modificationdate = {2023-11-23T22:46:52},
  owner            = {saulius},
}

@Manuscript{Miranda2005,
  author           = {Javier Miranda and Edmond Schonberg},
  title            = {{GNAT} and {A}da 2005},
  year             = {2005},
  keywords         = {Ada; Computer Science (CS); GNAT},
  url              = {https://www.adacore.com/uploads/books/pdf/Ada_2005_and_GNAT.pdf},
  creationdate     = {2023-11-25T15:17:25},
  file             = {:by-author/M/Miranda/2005_Miranda_GNAT and Ada 2005.pdf:PDF},
  modificationdate = {2023-11-25T15:19:11},
  owner            = {saulius},
}

@Electronic{AdaCore2023,
  author           = {{AdaCore}},
  language         = {English},
  title            = {{GNAT} and program execution},
  url              = {https://docs.adacore.com/gnat_ugn-docs/html/gnat_ugn/gnat_ugn/gnat_and_program_execution.html#id56},
  year             = {2023},
  creationdate     = {2023-11-25T15:46:02},
  eprint           = {https://docs.adacore.com/gnat_ugn-docs/html/gnat_ugn/gnat_ugn.html},
  file             = {:by-author/A/AdaCore/2023_AdaCore_GNAT and Program Execution.pdf:PDF},
  keywords         = {Ada; Computer Science (CS); GNAT},
  modificationdate = {2023-11-25T15:50:24},
  owner            = {saulius},
}

@Lecture{Bump2020,
  author           = {Daniel Bump},
  title            = {Lecture 9: Permutation representations},
  year             = {2020},
  course           = {Math 122: Modules and Group Representation Theory},
  lecture          = {Lecture 9},
  school           = {Stanford University},
  comment          = {Course URL: http://sporadic.stanford.edu/Math122/ [accessed 2023-11-30T16:57+02:00].},
  creationdate     = {2023-11-30T16:51:49},
  file             = {:by-author/B/Bump/2020_Bump_Lecture 9_ Permutation Representations.pdf:PDF},
  keywords         = {Abstract Algebra; Algebra; Group Theory; Linear Algebra; Math; Permutations; Representation Theory; Symmetry},
  modificationdate = {2023-11-30T21:58:05},
  owner            = {saulius},
  url              = {http://sporadic.stanford.edu/Math122/lecture9.pdf},
}

@Lecture{Bump2020a,
  author           = {Daniel Bump},
  title            = {Lecture 1: Module basics},
  year             = {2020},
  course           = {Math 122: Modules and Group Representation Theory},
  lecture          = {Lecture 1},
  school           = {Stanford University},
  comment          = {Course URL: http://sporadic.stanford.edu/Math122/ [accessed 2023-11-30T16:57+02:00].
The remarks made during the lecture (file with the suffix "(1)") were downloaded from: http://sporadic.stanford.edu/Math122/lecture1-remarks.pdf [accessed 2023-11-30T20:46+02:00].},
  creationdate     = {2023-11-30T18:22:34},
  file             = {:by-author/B/Bump/2020_Bump_Lecture 1_ Module Basics.pdf:PDF;:by-author/B/Bump/2020_Bump_Lecture 1_ Module Basics (1).pdf:PDF},
  keywords         = {Abstract Algebra; Algebra; Group Theory; Linear Algebra; Math; Permutations; Representation Theory; Symmetry},
  modificationdate = {2023-11-30T21:58:02},
  owner            = {saulius},
  url              = {http://sporadic.stanford.edu/Math122/lecture1.pdf},
}

@Lecture{Bump2020b,
  author           = {Daniel Bump},
  title            = {Lecture 6: {M}aschke’s theorem},
  year             = {2020},
  course           = {Math 122: Modules and Group Representation Theory},
  lecture          = {Lecture 1},
  school           = {Stanford University},
  comment          = {Course URL: http://sporadic.stanford.edu/Math122/ [accessed 2023-11-30T16:57+02:00].},
  creationdate     = {2023-11-30T20:38:49},
  file             = {:by-author/B/Bump/2020_Bump_Lecture 6_ Maschke’s Theorem.pdf:PDF},
  keywords         = {Abstract Algebra; Algebra; Group Theory; Linear Algebra; Math; Permutations; Representation Theory; Symmetry},
  modificationdate = {2023-11-30T21:57:59},
  owner            = {saulius},
  url              = {http://sporadic.stanford.edu/Math122/lecture6.pdf},
}

@Lecture{Bump2020c,
  author           = {Daniel Bump},
  title            = {Lecture 5: More on tensors},
  year             = {2020},
  course           = {Math 122: Modules and Group Representation Theory},
  lecture          = {Lecture 1},
  school           = {Stanford University},
  comment          = {Course URL: http://sporadic.stanford.edu/Math122/ [accessed 2023-11-30T16:57+02:00].},
  creationdate     = {2023-11-30T20:48:28},
  file             = {:by-author/B/Bump/2020_Bump_Lecture 5_ More on Tensors.pdf:PDF},
  keywords         = {Abstract Algebra; Algebra; Group Theory; Linear Algebra; Math; Permutations; Representation Theory; Symmetry},
  modificationdate = {2023-11-30T21:57:56},
  owner            = {saulius},
  url              = {http://sporadic.stanford.edu/Math122/lecture5.pdf},
}

@Lecture{Bump2020d,
  author           = {Daniel Bump and Brian Conrad},
  title            = {Maps with tensor products},
  year             = {2020},
  course           = {Math 122: Modules and Group Representation Theory},
  lecture          = {Lecture 1},
  school           = {Stanford University},
  comment          = {Course URL: http://sporadic.stanford.edu/Math122/ [accessed 2023-11-30T16:57+02:00].
Maps with Tensor Products (April 16). Notes by Brian Conrad. Read these instead of Section 10.4 in Dummit and Foote.},
  creationdate     = {2023-11-30T20:52:57},
  file             = {:by-author/B/Bump/2020_Bump_Maps with Tensor Products.pdf:PDF},
  keywords         = {Abstract Algebra; Algebra; Group Theory; Linear Algebra; Math; Permutations; Representation Theory; Symmetry},
  modificationdate = {2023-11-30T21:57:51},
  owner            = {saulius},
  url              = {http://sporadic.stanford.edu/Math122/tensormaps.pdf},
}

@Lecture{Bump2020e,
  author           = {Daniel Bump},
  title            = {Lecture 7: Characters ({I})},
  year             = {2020},
  course           = {Math 122: Modules and Group Representation Theory},
  lecture          = {Lecture 1},
  school           = {Stanford University},
  comment          = {Course URL: http://sporadic.stanford.edu/Math122/ [accessed 2023-11-30T16:57+02:00].},
  creationdate     = {2023-11-30T20:57:04},
  file             = {:by-author/B/Bump/2020_Bump_Lecture 7_ Characters (I).pdf:PDF},
  keywords         = {Abstract Algebra; Algebra; Group Theory; Linear Algebra; Math; Permutations; Representation Theory; Symmetry},
  modificationdate = {2023-11-30T21:57:48},
  owner            = {saulius},
  url              = {http://sporadic.stanford.edu/Math122/lecture7.pdf},
}

@Lecture{Bump2020f,
  author           = {Daniel Bump},
  title            = {Lecture 8. {S}chur orthogonality},
  year             = {2020},
  course           = {Math 122: Modules and Group Representation Theory},
  lecture          = {Lecture 1},
  school           = {Stanford University},
  comment          = {Course URL: http://sporadic.stanford.edu/Math122/ [accessed 2023-11-30T16:57+02:00].
Class notes (file with the suffix "(1)") are taken from: http://sporadic.stanford.edu/Math122/lecture8-notes.pdf [accessed 2023-11-30T21:04+02:00].},
  creationdate     = {2023-11-30T21:02:13},
  file             = {:by-author/B/Bump/2020_Bump_Lecture 8. Schur Orthogonality.pdf:PDF;:by-author/B/Bump/2020_Bump_Lecture 8. Schur Orthogonality (1).pdf:PDF},
  keywords         = {Abstract Algebra; Algebra; Group Theory; Linear Algebra; Math; Permutations; Representation Theory; Symmetry},
  modificationdate = {2023-11-30T21:57:44},
  owner            = {saulius},
  url              = {http://sporadic.stanford.edu/Math122/lecture8.pdf},
}

@Lecture{Bump2020g,
  author           = {Daniel Bump},
  title            = {Lecture 10. {W}edderburn’s theorem ({I})},
  year             = {2020},
  course           = {Math 122: Modules and Group Representation Theory},
  lecture          = {Lecture 1},
  school           = {Stanford University},
  comment          = {Course URL: http://sporadic.stanford.edu/Math122/ [accessed 2023-11-30T16:57+02:00].},
  creationdate     = {2023-11-30T21:08:46},
  file             = {:by-author/B/Bump/2020_Bump_Lecture 10. Wedderburn’s Theorem (I).pdf:PDF},
  keywords         = {Abstract Algebra; Algebra; Group Theory; Linear Algebra; Math; Permutations; Representation Theory; Symmetry},
  modificationdate = {2023-11-30T21:57:41},
  owner            = {saulius},
  url              = {http://sporadic.stanford.edu/Math122/lecture10.pdf},
}

@Lecture{Bump2020h,
  author           = {Daniel Bump},
  title            = {Lecture 11. {W}edderburn’s theorem ({II})},
  year             = {2020},
  course           = {Math 122: Modules and Group Representation Theory},
  lecture          = {Lecture 1},
  school           = {Stanford University},
  comment          = {Course URL: http://sporadic.stanford.edu/Math122/ [accessed 2023-11-30T16:57+02:00].
Lecture notes (file with the suffix "(1)") taken from: http://sporadic.stanford.edu/Math122/lecture11-notes.pdf [accessed 2023-11-30T21:13+02:00].},
  creationdate     = {2023-11-30T21:11:55},
  file             = {:by-author/B/Bump/2020_Bump_Lecture 11. Wedderburn’s Theorem (II).pdf:PDF;:by-author/B/Bump/2020_Bump_Lecture 11. Wedderburn’s Theorem (II) (1).pdf:PDF},
  keywords         = {Abstract Algebra; Algebra; Group Theory; Linear Algebra; Math; Permutations; Representation Theory; Symmetry},
  modificationdate = {2023-11-30T21:57:38},
  owner            = {saulius},
  url              = {http://sporadic.stanford.edu/Math122/lecture11.pdf},
}

@Lecture{Bump2020i,
  author           = {Daniel Bump},
  title            = {Lecture 12. Induced characters},
  year             = {2020},
  course           = {Math 122: Modules and Group Representation Theory},
  lecture          = {Lecture 1},
  school           = {Stanford University},
  comment          = {Course URL: http://sporadic.stanford.edu/Math122/ [accessed 2023-11-30T16:57+02:00].
Lecture notes (the file with the suffix "(1)" is taken from the: http://sporadic.stanford.edu/Math122/lecture12-notes.pdf [accessed 2023-11-30T21:19+02:00].},
  creationdate     = {2023-11-30T21:16:44},
  file             = {:by-author/B/Bump/2020_Bump_Lecture 12. Induced Characters.pdf:PDF;:by-author/B/Bump/2020_Bump_Lecture 12. Induced Characters (1).pdf:PDF},
  keywords         = {Abstract Algebra; Algebra; Group Theory; Linear Algebra; Math; Permutations; Representation Theory; Symmetry},
  modificationdate = {2023-11-30T21:57:32},
  owner            = {saulius},
  url              = {http://sporadic.stanford.edu/Math122/lecture12.pdf},
}

@Lecture{Bump2020j,
  author           = {Daniel Bump},
  title            = {Lecture 13. Permutation characters ({II})},
  year             = {2020},
  course           = {Math 122: Modules and Group Representation Theory},
  lecture          = {Lecture 1},
  school           = {Stanford University},
  comment          = {Course URL: http://sporadic.stanford.edu/Math122/ [accessed 2023-11-30T16:57+02:00].},
  creationdate     = {2023-11-30T21:26:03},
  file             = {:by-author/B/Bump/2020_Bump_Lecture 13. Permutation Characters (II).pdf:PDF},
  keywords         = {Abstract Algebra; Algebra; Group Theory; Linear Algebra; Math; Permutations; Representation Theory; Symmetry},
  modificationdate = {2023-11-30T21:57:29},
  owner            = {saulius},
  url              = {http://sporadic.stanford.edu/Math122/lecture13.pdf},
}

@Lecture{Bump2020k,
  author           = {Daniel Bump},
  title            = {Lecture 14. {F}robenius groups ({I})},
  year             = {2020},
  course           = {Math 122: Modules and Group Representation Theory},
  lecture          = {Lecture 1},
  school           = {Stanford University},
  comment          = {Course URL: http://sporadic.stanford.edu/Math122/ [accessed 2023-11-30T16:57+02:00].
The lecture notes (file with suffix "(1)" is taken from: http://sporadic.stanford.edu/Math122/lecture14-notes.pdf [accessed 2023-11-30T21:32+02:00].},
  creationdate     = {2023-11-30T21:28:51},
  file             = {:by-author/B/Bump/2020_Bump_Lecture 14. Frobenius Groups (I).pdf:PDF;:by-author/B/Bump/2020_Bump_Lecture 14. Frobenius Groups (I) (1).pdf:PDF},
  keywords         = {Abstract Algebra; Algebra; Group Theory; Linear Algebra; Math; Permutations; Representation Theory; Symmetry},
  modificationdate = {2023-11-30T21:57:25},
  owner            = {saulius},
  url              = {http://sporadic.stanford.edu/Math122/lecture14.pdf},
}

@Lecture{Bump2020l,
  author           = {Daniel Bump},
  title            = {Lecture 15. {F}robenius groups ({II})},
  year             = {2020},
  course           = {Math 122: Modules and Group Representation Theory},
  lecture          = {Lecture 1},
  school           = {Stanford University},
  comment          = {Course URL: http://sporadic.stanford.edu/Math122/ [accessed 2023-11-30T16:57+02:00].},
  creationdate     = {2023-11-30T21:37:39},
  file             = {:by-author/B/Bump/2020_Bump_Lecture 15. Frobenius Groups (II).pdf:PDF},
  keywords         = {Abstract Algebra; Algebra; Group Theory; Linear Algebra; Math; Permutations; Representation Theory; Symmetry},
  modificationdate = {2023-11-30T21:57:22},
  owner            = {saulius},
  url              = {http://sporadic.stanford.edu/Math122/lecture15.pdf},
}

@Lecture{Bump2020m,
  author           = {Daniel Bump},
  title            = {Lecture 16. {F}robenius groups ({III})},
  year             = {2020},
  course           = {Math 122: Modules and Group Representation Theory},
  lecture          = {Lecture 1},
  school           = {Stanford University},
  comment          = {Course URL: http://sporadic.stanford.edu/Math122/ [accessed 2023-11-30T16:57+02:00].},
  creationdate     = {2023-11-30T21:40:15},
  file             = {:by-author/B/Bump/2020_Bump_Lecture 16. Frobenius Groups (III).pdf:PDF},
  keywords         = {Abstract Algebra; Algebra; Group Theory; Linear Algebra; Math; Permutations; Representation Theory; Symmetry},
  modificationdate = {2023-11-30T21:57:19},
  owner            = {saulius},
  url              = {http://sporadic.stanford.edu/Math122/lecture16.pdf},
}

@Lecture{Bump2020n,
  author           = {Daniel Bump},
  title            = {Lecture 17: Modules over a {PID}},
  year             = {2020},
  course           = {Math 122: Modules and Group Representation Theory},
  lecture          = {Lecture 1},
  school           = {Stanford University},
  comment          = {Course URL: http://sporadic.stanford.edu/Math122/ [accessed 2023-11-30T16:57+02:00].},
  creationdate     = {2023-11-30T21:45:21},
  file             = {:by-author/B/Bump/2020_Bump_Lecture 17_ Modules Over a PID.pdf:PDF},
  keywords         = {Abstract Algebra; Algebra; Group Theory; Linear Algebra; Math; Permutations; Representation Theory; Symmetry},
  modificationdate = {2023-11-30T21:57:15},
  owner            = {saulius},
  url              = {http://sporadic.stanford.edu/Math122/lecture17.pdf},
}

@Lecture{Bump2020o,
  author           = {Daniel Bump},
  title            = {Lecture 18: character degrees and canonical forms},
  year             = {2020},
  course           = {Math 122: Modules and Group Representation Theory},
  lecture          = {Lecture 1},
  school           = {Stanford University},
  comment          = {Course URL: http://sporadic.stanford.edu/Math122/ [accessed 2023-11-30T16:57+02:00].},
  creationdate     = {2023-11-30T21:49:01},
  file             = {:by-author/B/Bump/2020_Bump_Lecture 18_ Character Degrees and Canonical Forms.pdf:PDF},
  keywords         = {Abstract Algebra; Algebra; Group Theory; Linear Algebra; Math; Permutations; Representation Theory; Symmetry},
  modificationdate = {2023-11-30T21:57:12},
  owner            = {saulius},
  url              = {http://sporadic.stanford.edu/Math122/lecture18.pdf},
}

@Lecture{Bump2020p,
  author           = {Daniel Bump},
  title            = {Lecture 19: {B}urnside’s theorem},
  year             = {2020},
  course           = {Math 122: Modules and Group Representation Theory},
  lecture          = {Lecture 1},
  school           = {Stanford University},
  comment          = {Course URL: http://sporadic.stanford.edu/Math122/ [accessed 2023-11-30T16:57+02:00].},
  creationdate     = {2023-11-30T21:53:40},
  file             = {:by-author/B/Bump/2020_Bump_Lecture 19_ Burnside’s Theorem.pdf:PDF},
  keywords         = {Abstract Algebra; Algebra; Group Theory; Linear Algebra; Math; Permutations; Representation Theory; Symmetry},
  modificationdate = {2023-11-30T21:57:08},
  owner            = {saulius},
  url              = {http://sporadic.stanford.edu/Math122/lecture19.pdf},
}

@Manual{UniOxfordSouthernAfrica2015,
  title            = {{H}arvard style reference guide},
  author           = {{Oxford University Press Southern Africa}},
  year             = {2015},
  creationdate     = {2023-12-03T12:37:09},
  file             = {:by-author/U/UniOxfordSouthernAfrica/2015_UniOxfordSouthernAfrica_Harvard Style Reference Guide.pdf:PDF},
  keywords         = {Citation Styles; Harvard Citation Style; Scholarly Writing},
  modificationdate = {2023-12-03T12:39:26},
  owner            = {saulius},
  url              = {https://www.oxford.co.za/download_files/higher-education/Harvard_Reference_Guide.pdf},
}

@Manual{UniWolverhampton2022,
  title            = {{H}arvard referencing ({C}ite them right): the basics},
  author           = {{University of Wolverhampton}},
  organization     = {University of Wolverhampton},
  year             = {2022},
  creationdate     = {2023-12-03T12:48:56},
  file             = {:by-author/U/UniWolverhampton/2022_UniWolverhampton_Harvard Referencing (Cite Them Right)_ the Basics.pdf:PDF},
  keywords         = {Citation Styles; Harvard Citation Style; Scholarly Writing},
  modificationdate = {2023-12-03T12:51:47},
  owner            = {saulius},
  url              = {https://www.wlv.ac.uk/lib/media/departments/lis/skills/study-guides/LS134-Harvard-Quick-Guide-2022.pdf},
}

@Manual{UniWolverhampton2022a,
  title            = {{H}arvard referencing ({C}ite them right): the basics},
  author           = {{University of Wolverhampton}},
  edition          = {2nd},
  organization     = {University of Wolverhampton},
  year             = {2022},
  creationdate     = {2023-12-03T12:52:56},
  file             = {:by-author/U/UniWolverhampton/2022_UniWolverhampton_Harvard Referencing (Cite Them Right)_ the Basics (1).pdf:PDF},
  keywords         = {Citation Styles; Harvard Citation Style; Scholarly Writing},
  modificationdate = {2023-12-03T12:55:51},
  owner            = {saulius},
  url              = {https://www.wlv.ac.uk/lib/media/departments/lis/skills/study-guides/LS134-Harvard-Quick-Guide.pdf},
}

@Article{Li2023,
  author           = {Zian Li and Xiyuan Wang and Yinan Huang and Muhan Zhang},
  title            = {Is distance matrix enough for geometric deep learning?},
  year             = {2023},
  month            = feb,
  abstract         = {Graph Neural Networks (GNNs) are often used for tasks involving the 3D geometry of a given graph, such as molecular dynamics simulation. While incorporating Euclidean distance into Message Passing Neural Networks (referred to as Vanilla DisGNN) is a straightforward way to learn the geometry, it has been demonstrated that Vanilla DisGNN is geometrically incomplete. In this work, we first construct families of novel and symmetric geometric graphs that Vanilla DisGNN cannot distinguish even when considering all-pair distances, which greatly expands the existing counterexample families. Our counterexamples show the inherent limitation of Vanilla DisGNN to capture symmetric geometric structures. We then propose $k$-DisGNNs, which can effectively exploit the rich geometry contained in the distance matrix. We demonstrate the high expressive power of $k$-DisGNNs from three perspectives: 1. They can learn high-order geometric information that cannot be captured by Vanilla DisGNN. 2. They can unify some existing well-designed geometric models. 3. They are universal function approximators from geometric graphs to scalars (when $k\geq 2$) and vectors (when $k\geq 3$). Most importantly, we establish a connection between geometric deep learning (GDL) and traditional graph representation learning (GRL), showing that those highly expressive GNN models originally designed for GRL can also be applied to GDL with impressive performance, and that existing complicated, equivariant models are not the only solution. Experiments verify our theory. Our $k$-DisGNNs achieve many new state-of-the-art results on MD17.},
  archiveprefix    = {arXiv},
  creationdate     = {2023-12-06T10:59:49},
  eprint           = {2302.05743},
  file             = {:by-author/L/Li/2023_Li_1.pdf:PDF},
  keywords         = {Artificial Neural Networks (ANN); Distance Matrix; Graph Neural Networks (GNN); Machine Learning (ML); cs.AI; cs.LG},
  modificationdate = {2023-12-06T11:04:19},
  owner            = {saulius},
  primaryclass     = {cs.LG},
}

 
@Article{Sola2023,
  author           = {Sola, Fernando and Ayala, Daniel and Hernández, Inma and Ruiz, David},
  journal          = {Applied Intelligence},
  title            = {Deep embeddings and {G}raph {N}eural {N}etworks: using context to improve domain-independent predictions},
  year             = {2023},
  issn             = {1573-7497},
  month            = jun,
  number           = {19},
  pages            = {22415--22428},
  volume           = {53},
  creationdate     = {2023-12-06T19:47:33},
  doi              = {10.1007/s10489-023-04685-3},
  file             = {:by-author/S/Sola/2023_Sola_22415.pdf:PDF},
  keywords         = {Artificial Neural Networks (ANN); Computer Science (CS); Graph Neural Networks (GNN); Machine Learning (ML)},
  modificationdate = {2023-12-06T19:48:19},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media LLC},
}

 
@Article{Merchant2023,
  author           = {Merchant, Amil and Batzner, Simon and Schoenholz, Samuel S. and Aykol, Muratahan and Cheon, Gowoon and Cubuk, Ekin Dogus},
  journal          = {Nature},
  title            = {Scaling deep learning for materials discovery},
  year             = {2023},
  issn             = {1476-4687},
  month            = nov,
  number           = {7990},
  pages            = {80--85},
  volume           = {624},
  creationdate     = {2023-12-06T19:49:09},
  doi              = {10.1038/s41586-023-06735-9},
  file             = {:by-author/M/Merchant/2023_Merchant_80.pdf:PDF},
  keywords         = {Artificial Neural Networks (ANN); Computer Science (CS); Databases; Graph Neural Networks (GNN); Machine Learning (ML); Materials Discovery},
  modificationdate = {2024-02-19T22:32:58},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media LLC},
}

 
@Article{Reiser2022,
  author           = {Reiser, Patrick and Neubert, Marlen and Eberhard, André and Torresi, Luca and Zhou, Chen and Shao, Chen and Metni, Houssam and van Hoesel, Clint and Schopmans, Henrik and Sommer, Timo and Friederich, Pascal},
  journal          = {Communications Materials},
  title            = {Graph neural networks for materials science and chemistry},
  year             = {2022},
  issn             = {2662-4443},
  month            = nov,
  number           = {1},
  volume           = {3},
  creationdate     = {2023-12-06T19:50:09},
  doi              = {10.1038/s43246-022-00315-6},
  file             = {:by-author/R/Reiser/2022_Reiser_1.pdf:PDF},
  keywords         = {Artificial Neural Networks (ANN); Computer Science (CS); Graph Neural Networks (GNN); Machine Learning (ML)},
  modificationdate = {2023-12-06T19:50:26},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media LLC},
}

 
@Article{Xu2021,
  author           = {Xu, Mengjia},
  journal          = {SIAM Review},
  title            = {Understanding Graph Embedding Methods and Their Applications},
  year             = {2021},
  issn             = {1095-7200},
  month            = jan,
  number           = {4},
  pages            = {825--853},
  volume           = {63},
  creationdate     = {2023-12-06T19:51:49},
  doi              = {10.1137/20m1386062},
  file             = {:by-author/X/Xu/2021_Xu_825.pdf:PDF},
  keywords         = {Artificial Neural Networks (ANN); Computer Science (CS); Graph Neural Networks (GNN); Machine Learning (ML)},
  modificationdate = {2023-12-06T19:52:38},
  owner            = {saulius},
  publisher        = {Society for Industrial & Applied Mathematics (SIAM)},
}

@Article{Marinoni2023,
  author           = {Andrea Marinoni and Pietro Lio' and Alessandro Barp and Christian Jutten and Mark Girolami},
  journal          = {arXiv},
  title            = {Improving embedding of graphs with missing data by soft manifolds},
  year             = {2023},
  month            = nov,
  abstract         = {Embedding graphs in continous spaces is a key factor in designing and developing algorithms for automatic information extraction to be applied in diverse tasks (e.g., learning, inferring, predicting). The reliability of graph embeddings directly depends on how much the geometry of the continuous space matches the graph structure. Manifolds are mathematical structure that can enable to incorporate in their topological spaces the graph characteristics, and in particular nodes distances. State-of-the-art of manifold-based graph embedding algorithms take advantage of the assumption that the projection on a tangential space of each point in the manifold (corresponding to a node in the graph) would locally resemble a Euclidean space. Although this condition helps in achieving efficient analytical solutions to the embedding problem, it does not represent an adequate set-up to work with modern real life graphs, that are characterized by weighted connections across nodes often computed over sparse datasets with missing records. In this work, we introduce a new class of manifold, named soft manifold, that can solve this situation. In particular, soft manifolds are mathematical structures with spherical symmetry where the tangent spaces to each point are hypocycloids whose shape is defined according to the velocity of information propagation across the data points. Using soft manifolds for graph embedding, we can provide continuous spaces to pursue any task in data analysis over complex datasets. Experimental results on reconstruction tasks on synthetic and real datasets show how the proposed approach enable more accurate and reliable characterization of graphs in continuous spaces with respect to the state-of-the-art.},
  archiveprefix    = {arXiv},
  creationdate     = {2023-12-06T19:53:41},
  doi              = {10.48550/arXiv.2311.17598},
  eprint           = {2311.17598},
  file             = {:by-author/M/Marinoni/2023_Marinoni_1.pdf:PDF},
  keywords         = {Artificial Neural Networks (ANN); Computer Science (CS); Graph Neural Networks (GNN); Machine Learning (ML); cs.AI; cs.CG; cs.LG},
  modificationdate = {2023-12-06T19:54:27},
  owner            = {saulius},
  primaryclass     = {cs.LG},
}

 
@Article{Butler2018,
  author           = {Butler, Keith T. and Davies, Daniel W. and Cartwright, Hugh and Isayev, Olexandr and Walsh, Aron},
  journal          = {Nature},
  title            = {Machine learning for molecular and materials science},
  year             = {2018},
  issn             = {1476-4687},
  month            = jul,
  number           = {7715},
  pages            = {547--555},
  volume           = {559},
  creationdate     = {2023-12-06T19:56:18},
  doi              = {10.1038/s41586-018-0337-2},
  file             = {:by-author/B/Butler/2018_Butler_547.pdf:PDF},
  keywords         = {Artificial Neural Networks (ANN); Computer Science (CS); Graph Neural Networks (GNN); Machine Learning (ML)},
  modificationdate = {2023-12-06T19:57:11},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media LLC},
  url              = {http://purl.org/net/epubs/manifestation/44000149/STFC-AAM-2019-065.pdf},
}

 
@Article{Wei2019,
  author           = {Wei, Jing and Chu, Xuan and Sun, Xiang‐Yu and Xu, Kun and Deng, Hui‐Xiong and Chen, Jigen and Wei, Zhongming and Lei, Ming},
  journal          = {InfoMat},
  title            = {Machine learning in materials science},
  year             = {2019},
  issn             = {2567-3165},
  month            = sep,
  number           = {3},
  pages            = {338--358},
  volume           = {1},
  creationdate     = {2023-12-06T19:58:13},
  doi              = {10.1002/inf2.12028},
  file             = {:by-author/W/Wei/2019_Wei_338.pdf:PDF},
  keywords         = {Artificial Neural Networks (ANN); Computer Science (CS); Graph Neural Networks (GNN); Machine Learning (ML); Materials Science},
  modificationdate = {2023-12-06T19:59:12},
  owner            = {saulius},
  publisher        = {Wiley},
}

 
@Article{Wang2020a,
  author           = {Wang, Anthony Yu-Tung and Murdock, Ryan J. and Kauwe, Steven K. and Oliynyk, Anton O. and Gurlo, Aleksander and Brgoch, Jakoah and Persson, Kristin A. and Sparks, Taylor D.},
  journal          = {Chemistry of Materials},
  title            = {Machine Learning for Materials Scientists: An Introductory Guide toward Best Practices},
  year             = {2020},
  issn             = {1520-5002},
  month            = may,
  number           = {12},
  pages            = {4954--4965},
  volume           = {32},
  creationdate     = {2023-12-06T20:01:38},
  doi              = {10.1021/acs.chemmater.0c01907},
  file             = {:by-author/W/Wang/2020_Wang_4954.pdf:PDF},
  keywords         = {Artificial Neural Networks (ANN); Computer Science (CS); Graph Neural Networks (GNN); Machine Learning (ML); Materials Science},
  modificationdate = {2023-12-06T20:02:00},
  owner            = {saulius},
  publisher        = {American Chemical Society (ACS)},
}

 
@Article{Zhong2022,
  author           = {Zhong, Xiaoting and Gallagher, Brian and Liu, Shusen and Kailkhura, Bhavya and Hiszpanski, Anna and Han, T. Yong-Jin},
  journal          = {npj Computational Materials},
  title            = {Explainable machine learning in materials science},
  year             = {2022},
  issn             = {2057-3960},
  month            = sep,
  number           = {1},
  volume           = {8},
  creationdate     = {2023-12-06T20:03:12},
  doi              = {10.1038/s41524-022-00884-7},
  file             = {:by-author/Z/Zhong/2022_Zhong_1.pdf:PDF},
  keywords         = {Artificial Neural Networks (ANN); Computer Science (CS); Graph Neural Networks (GNN); Machine Learning (ML); Materials Science},
  modificationdate = {2023-12-06T20:03:29},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media LLC},
}

 
@Article{Ramprasad2017,
  author           = {Ramprasad, Rampi and Batra, Rohit and Pilania, Ghanshyam and Mannodi-Kanakkithodi, Arun and Kim, Chiho},
  journal          = {npj Computational Materials},
  title            = {Machine learning in materials informatics: recent applications and prospects},
  year             = {2017},
  issn             = {2057-3960},
  month            = dec,
  number           = {1},
  volume           = {3},
  creationdate     = {2023-12-06T20:05:56},
  doi              = {10.1038/s41524-017-0056-5},
  file             = {:by-author/R/Ramprasad/2017_Ramprasad_1.pdf:PDF},
  keywords         = {Artificial Neural Networks (ANN); Computer Science (CS); Graph Neural Networks (GNN); Machine Learning (ML); Materials Science},
  modificationdate = {2023-12-06T20:06:11},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media LLC},
}

 
@Article{Isayev2019,
  author           = {Isayev, Olexandr},
  journal          = {Nature},
  title            = {Text mining facilitates materials discovery},
  year             = {2019},
  issn             = {1476-4687},
  month            = jul,
  number           = {7763},
  pages            = {42--43},
  volume           = {571},
  creationdate     = {2023-12-06T20:09:16},
  doi              = {10.1038/d41586-019-01978-x},
  file             = {:by-author/I/Isayev/2019_Isayev_42.pdf:PDF},
  keywords         = {Artificial Neural Networks (ANN); Computer Science (CS); Graph Neural Networks (GNN); Machine Learning (ML); Materials Science},
  modificationdate = {2023-12-06T20:09:43},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media LLC},
}

@Article{Moro2023,
  author           = {Viggo Moro and Charlotte Loh and Rumen Dangovski and Ali Ghorashi and Andrew Ma and Zhuo Chen and Peter Y. Lu and Thomas Christensen and Marin Soljačić},
  title            = {Multimodal Learning for Crystalline Materials},
  year             = {2023},
  month            = nov,
  abstract         = {Artificial intelligence (AI) has revolutionized the field of materials science by improving the prediction of properties and accelerating the discovery of novel materials. In recent years, publicly available material data repositories containing data for various material properties have grown rapidly. In this work, we introduce Multimodal Learning for Crystalline Materials (MLCM), a new method for training a foundation model for crystalline materials via multimodal alignment, where high-dimensional material properties (i.e. modalities) are connected in a shared latent space to produce highly useful material representations. We show the utility of MLCM on multiple axes: (i) MLCM achieves state-of-the-art performance for material property prediction on the challenging Materials Project database; (ii) MLCM enables a novel, highly accurate method for inverse design, allowing one to screen for stable material with desired properties; and (iii) MLCM allows the extraction of interpretable emergent features that may provide insight to material scientists. Further, we explore several novel methods for aligning an arbitrary number of modalities, improving upon prior art in multimodal learning that focuses on bimodal alignment. Our work brings innovations from the ongoing AI revolution into the domain of materials science and identifies materials as a testbed for the next generation of AI.},
  archiveprefix    = {arXiv},
  creationdate     = {2023-12-06T20:10:20},
  eprint           = {2312.00111},
  file             = {:by-author/M/Moro/2023_Moro_1.pdf:PDF},
  keywords         = {Artificial Neural Networks (ANN); Computer Science (CS); Graph Neural Networks (GNN); Machine Learning (ML); Materials Science; cond-mat.mtrl-sci; cs.LG},
  modificationdate = {2023-12-06T20:10:51},
  owner            = {saulius},
  primaryclass     = {cs.LG},
}

 
@Article{Krishnapriyan2021,
  author           = {Krishnapriyan, Aditi S. and Montoya, Joseph and Haranczyk, Maciej and Hummelshøj, Jens and Morozov, Dmitriy},
  journal          = {Scientific Reports},
  title            = {Machine learning with persistent homology and chemical word embeddings improves prediction accuracy and interpretability in metal-organic frameworks},
  year             = {2021},
  issn             = {2045-2322},
  month            = apr,
  number           = {1},
  volume           = {11},
  creationdate     = {2023-12-06T20:11:45},
  doi              = {10.1038/s41598-021-88027-8},
  file             = {:by-author/K/Krishnapriyan/2021_Krishnapriyan_1.pdf:PDF},
  keywords         = {Artificial Neural Networks (ANN); Computer Science (CS); Graph Neural Networks (GNN); Machine Learning (ML); Materials Science; Persistent Homology},
  modificationdate = {2023-12-06T20:12:12},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media LLC},
}

 
@Article{Antunes2022,
  author           = {Antunes, Luis M. and Grau-Crespo, Ricardo and Butler, Keith T.},
  journal          = {npj Computational Materials},
  title            = {Distributed representations of atoms and materials for machine learning},
  year             = {2022},
  issn             = {2057-3960},
  month            = mar,
  number           = {1},
  volume           = {8},
  creationdate     = {2023-12-06T20:12:47},
  doi              = {10.1038/s41524-022-00729-3},
  file             = {:by-author/A/Antunes/2022_Antunes_1.pdf:PDF},
  keywords         = {Artificial Neural Networks (ANN); Computer Science (CS); Graph Neural Networks (GNN); Machine Learning (ML); Materials Science},
  modificationdate = {2023-12-06T20:13:07},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media LLC},
}

 
@Article{Gupta2022,
  author           = {Gupta, Tanishq and Zaki, Mohd and Krishnan, N. M. Anoop and Mausam},
  journal          = {npj Computational Materials},
  title            = {{MatSciBERT}: A materials domain language model for text mining and information extraction},
  year             = {2022},
  issn             = {2057-3960},
  month            = may,
  number           = {1},
  volume           = {8},
  creationdate     = {2023-12-06T20:14:41},
  doi              = {10.1038/s41524-022-00784-w},
  file             = {:by-author/G/Gupta/2022_Gupta_1.pdf:PDF},
  keywords         = {Artificial Neural Networks (ANN); Computer Science (CS); Graph Neural Networks (GNN); Language Models; Machine Learning (ML); Materials Science},
  modificationdate = {2023-12-27T11:21:23},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media LLC},
}

@Article{Venugopal2022,
  author           = {Vineeth Venugopal and Sumit Pai and Elsa Olivetti},
  title            = {MatKG: The Largest Knowledge Graph in Materials Science -- Entities, Relations, and Link Prediction through Graph Representation Learning},
  year             = {2022},
  month            = oct,
  abstract         = {This paper introduces MatKG, a novel graph database of key concepts in material science spanning the traditional material-structure-property-processing paradigm. MatKG is autonomously generated through transformer-based, large language models and generates pseudo ontological schema through statistical co-occurrence mapping. At present, MatKG contains over 2 million unique relationship triples derived from 80,000 entities. This allows the curated analysis, querying, and visualization of materials knowledge at unique resolution and scale. Further, Knowledge Graph Embedding models are used to learn embedding representations of nodes in the graph which are used for downstream tasks such as link prediction and entity disambiguation. MatKG allows the rapid dissemination and assimilation of data when used as a knowledge base, while enabling the discovery of new relations when trained as an embedding model.},
  archiveprefix    = {arXiv},
  creationdate     = {2023-12-06T20:17:28},
  doi              = {10.48550/arXiv.2210.17340},
  eprint           = {2210.17340},
  file             = {:by-author/V/Venugopal/2022_Venugopal_1.pdf:PDF},
  keywords         = {Artificial Neural Networks (ANN); Computer Science (CS); Graph Neural Networks (GNN); Machine Learning (ML); Materials Science; cond-mat.mtrl-sci},
  modificationdate = {2023-12-20T09:38:41},
  owner            = {saulius},
  primaryclass     = {cond-mat.mtrl-sci},
  url              = {https://arxiv.org/abs/2210.17340},
}

@Article{Magar2022,
  author           = {Rishikesh Magar and Yuyang Wang and Amir Barati Farimani},
  title            = {Crystal Twins: Self-supervised Learning for Crystalline Material Property Prediction},
  year             = {2022},
  month            = may,
  abstract         = {Machine learning (ML) models have been widely successful in the prediction of material properties. However, large labeled datasets required for training accurate ML models are elusive and computationally expensive to generate. Recent advances in Self-Supervised Learning (SSL) frameworks capable of training ML models on unlabeled data have mitigated this problem and demonstrated superior performance in computer vision and natural language processing tasks. Drawing inspiration from the developments in SSL, we introduce Crystal Twins (CT): an SSL method for crystalline materials property prediction. Using a large unlabeled dataset, we pre-train a Graph Neural Network (GNN) by applying the redundancy reduction principle to the graph latent embeddings of augmented instances obtained from the same crystalline system. By sharing the pre-trained weights when fine-tuning the GNN for regression tasks, we significantly improve the performance for 7 challenging material property prediction benchmarks},
  archiveprefix    = {arXiv},
  creationdate     = {2023-12-06T20:18:57},
  eprint           = {2205.01893},
  file             = {:by-author/M/Magar/2022_Magar_1.pdf:PDF},
  keywords         = {Artificial Neural Networks (ANN); Computer Science (CS); Graph Neural Networks (GNN); Machine Learning (ML); Materials Science; cond-mat.mtrl-sci; cs.LG},
  modificationdate = {2023-12-06T20:19:27},
  owner            = {saulius},
  primaryclass     = {cs.LG},
}

 
@Article{Krapp2023,
  author           = {Krapp, Lucien F. and Abriata, Luciano A. and Cortés Rodriguez, Fabio and Dal Peraro, Matteo},
  journal          = {Nature Communications},
  title            = {{PeSTo}: parameter-free geometric deep learning for accurate prediction of protein binding interfaces},
  year             = {2023},
  issn             = {2041-1723},
  month            = apr,
  number           = {1},
  volume           = {14},
  creationdate     = {2023-12-20T18:37:08},
  doi              = {10.1038/s41467-023-37701-8},
  file             = {:by-author/K/Krapp/2023_Krapp_1.pdf:PDF},
  keywords         = {Artificial Neural Networks (ANN); Bioinformatics; Graph Neural Networks (GNN); Protein Interection Prediction},
  modificationdate = {2023-12-20T18:37:51},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media LLC},
}

@Article{Duval2023,
  author           = {Alexandre Duval and Simon V. Mathis and Chaitanya K. Joshi and Victor Schmidt and Santiago Miret and Fragkiskos D. Malliaros and Taco Cohen and Pietro Lio and Yoshua Bengio and Michael Bronstein},
  title            = {A hitchhiker's guide to geometric {GNNs} for 3{D} atomic systems},
  year             = {2023},
  month            = dec,
  abstract         = {Recent advances in computational modelling of atomic systems, spanning molecules, proteins, and materials, represent them as geometric graphs with atoms embedded as nodes in 3D Euclidean space. In these graphs, the geometric attributes transform according to the inherent physical symmetries of 3D atomic systems, including rotations and translations in Euclidean space, as well as node permutations. In recent years, Geometric Graph Neural Networks have emerged as the preferred machine learning architecture powering applications ranging from protein structure prediction to molecular simulations and material generation. Their specificity lies in the inductive biases they leverage -- such as physical symmetries and chemical properties -- to learn informative representations of these geometric graphs. In this opinionated paper, we provide a comprehensive and self-contained overview of the field of Geometric GNNs for 3D atomic systems. We cover fundamental background material and introduce a pedagogical taxonomy of Geometric GNN architectures:(1) invariant networks, (2) equivariant networks in Cartesian basis, (3) equivariant networks in spherical basis, and (4) unconstrained networks. Additionally, we outline key datasets and application areas and suggest future research directions. The objective of this work is to present a structured perspective on the field, making it accessible to newcomers and aiding practitioners in gaining an intuition for its mathematical abstractions.},
  archiveprefix    = {arXiv},
  creationdate     = {2023-12-20T18:39:59},
  doi              = {10.48550/arXiv.2312.07511},
  eprint           = {2312.07511},
  file             = {:by-author/D/Duval/2023_Duval_A Hitchhiker's Guide to Geometric GNNs for 3D Atomic Systems.pdf:PDF},
  keywords         = {Artificial Neural Networks (ANN); Graph Neural Networks (GNN); cs.AI; cs.LG; q-bio.QM; stat.ML},
  modificationdate = {2024-01-08T11:23:12},
  owner            = {saulius},
  primaryclass     = {cs.LG},
}

 
@Article{Li2023a,
  author           = {Li, Jie and Zhao, Jing and Sun, Shuchen and Shen, Sen and Zhong, Bincheng and Dong, Xiaohua},
  journal          = {PeerJ},
  title            = {Peptidomics insights: neutrophil extracellular traps ({NETs}) related to the chronic subdural hemorrhage},
  year             = {2023},
  issn             = {2167-8359},
  month            = dec,
  pages            = {e16676},
  volume           = {11},
  creationdate     = {2023-12-22T10:08:53},
  doi              = {10.7717/peerj.16676},
  file             = {:by-author/L/Li/2023_Li_e16676.pdf:PDF},
  keywords         = {Bioinformatics; KEGG; Neurophysiology; Peptidomics; Sequences},
  modificationdate = {2023-12-22T10:11:49},
  owner            = {saulius},
  publisher        = {PeerJ},
  url              = {https://peerj.com/articles/16676.pdf},
}

 
@Article{Jain2023,
  author           = {Jain, Akhil and Gosling, Jonathan and Liu, Shaochuang and Wang, Haowei and Stone, Eloise M. and Chakraborty, Sajib and Jayaraman, Padma-Sheela and Smith, Stuart and Amabilino, David B. and Fromhold, Mark and Long, Yi-Tao and Pérez-García, Lluïsa and Turyanska, Lyudmila and Rahman, Ruman and Rawson, Frankie J.},
  journal          = {Nature Nanotechnology},
  title            = {Wireless electrical–molecular quantum signalling for cancer cell apoptosis},
  year             = {2023},
  issn             = {1748-3395},
  month            = sep,
  creationdate     = {2023-12-24T10:41:50},
  doi              = {10.1038/s41565-023-01496-y},
  file             = {:by-author/J/Jain/2023_Jain_1.pdf:PDF},
  keywords         = {Nanoantenna; Quantum Tunneling; Quantum-basedmedical Diagnostics; Quantum-basedmedical Treatment},
  modificationdate = {2023-12-24T10:44:32},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media LLC},
}

 
@Article{Jain2020,
  author           = {Jain, Akhil and Trindade, Gustavo and Hicks, Jacqueline M. and Pott, Jordan C. and Rahman, Ruman and Hague, Richard and Amabilino, David B. and Pérez-García, Lluïsa and Rawson, Frankie},
  journal          = {ChemRxiv},
  title            = {Modulating the biological function of protein by tailoring the adsorption orientation on nanoparticles},
  year             = {2020},
  month            = jul,
  creationdate     = {2023-12-24T11:06:59},
  doi              = {10.26434/chemrxiv.12721490.v1},
  file             = {:by-author/J/Jain/2020_Jain_1.pdf:PDF},
  keywords         = {Bioelectronics; Functionalisation; Gold Nanopraticles; Nanoparticles; Protein Function; Surface Modification},
  modificationdate = {2023-12-24T11:23:25},
  owner            = {saulius},
  publisher        = {American Chemical Society (ACS)},
}

 
@Article{SanjuanAlberte2018,
  author           = {Sanjuán-Alberte, Paola and Abayzeed, Sidahmed A. and Fuentes-Domínguez, Rafael and Alea-Reyesd, María E. and Clark, Matthew and Hague, Richard and Alexander, Morgan and Pérez-García, Lluïsa and Rawson, Frankie},
  title            = {Wireless bioelectronic nanosystems for intracellular communication},
  year             = {2018},
  month            = sep,
  creationdate     = {2023-12-24T11:22:32},
  doi              = {10.26434/chemrxiv.7106171.v2},
  file             = {:by-author/S/Sanjuán-Alberte/2018_Sanjuán-Alberte_1.pdf:PDF},
  keywords         = {Bioelectronics; Functionalisation; Gold Nanopraticles; Nanoparticles; Surface Modification},
  modificationdate = {2023-12-24T11:24:08},
  owner            = {saulius},
  publisher        = {American Chemical Society (ACS)},
}

 
@Article{CruzCabeza2007,
  author           = {Cruz Cabeza, Aurora J. and Pidcock, Elna and Day, Graeme M. and Motherwell, W. D. Sam and Jones, William},
  journal          = {CrystEngComm},
  title            = {Space group selection for crystal structure prediction of solvates},
  year             = {2007},
  issn             = {1466-8033},
  number           = {7},
  pages            = {556},
  volume           = {9},
  creationdate     = {2023-12-24T11:30:39},
  doi              = {10.1039/b702073b},
  file             = {:by-author/C/Cruz Cabeza/2007_Cruz Cabeza_556.pdf:PDF},
  keywords         = {Crystal Structure Prediction (CSP); Crystal Symmetry; Crystallography; Spacegroup Prediction; Spacegroups},
  modificationdate = {2023-12-24T11:31:34},
  owner            = {saulius},
  publisher        = {Royal Society of Chemistry (RSC)},
}

 
@Article{Nespolo2018,
  author           = {Nespolo, Massimo and Aroyo, Mois Ilia and Souvignier, Bernd},
  journal          = {Journal of Applied Crystallography},
  title            = {Crystallographic shelves: space-group hierarchy explained},
  year             = {2018},
  issn             = {1600-5767},
  month            = sep,
  number           = {5},
  pages            = {1481--1491},
  volume           = {51},
  creationdate     = {2023-12-24T18:55:14},
  doi              = {10.1107/s1600576718012724},
  file             = {:by-author/N/Nespolo/2018_Nespolo_1481.pdf:PDF},
  keywords         = {3D Spacegroups; Chiral Sapcegroups; Classification; Classification of Spacegroups; Crystal Symmetry; Grop Theory; Spacegroups; Symmetry},
  modificationdate = {2023-12-24T19:03:30},
  owner            = {saulius},
  publisher        = {International Union of Crystallography (IUCr)},
}

 
@Article{Hamilton2022,
  author           = {Hamilton, Daniel G. and Page, Matthew J. and Finch, Sue and Everitt, Sarah and Fidler, Fiona},
  journal          = {BMC Medicine},
  title            = {How often do cancer researchers make their data and code available and what factors are associated with sharing?},
  year             = {2022},
  issn             = {1741-7015},
  month            = nov,
  number           = {1},
  pages            = {438},
  volume           = {20},
  creationdate     = {2023-12-27T11:46:40},
  doi              = {10.1186/s12916-022-02644-2},
  file             = {:by-author/H/Hamilton/2022_Hamilton_438.pdf:PDF},
  keywords         = {Data Management; Data Sharing; Open Data; Scientific Data; Scientific Data Management},
  modificationdate = {2023-12-27T11:48:42},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media LLC},
}

@InBook{Fischer2016,
  author           = {W. Fischer and E. Koch},
  chapter          = {3.4},
  pages            = {792--825},
  title            = {Lattice complexes},
  year             = {2016},
  volume           = {A},
  booktitle        = {International Tables for Crystallography},
  creationdate     = {2024-01-05T20:50:22},
  doi              = {10.1107/97809553602060000932},
  file             = {:by-author/F/Fischer/2016_Fischer_792.pdf:PDF},
  keywords         = {Crystallography; Lattice; Lattice Complexes},
  modificationdate = {2024-01-05T20:54:45},
  owner            = {saulius},
  url              = {https://onlinelibrary.wiley.com/iucr/itc/Ac/ch3o4v0001/ch3o4.pdf},
}

 
@Article{Fischer1983,
  author           = {Fischer, W. and Koch, E.},
  journal          = {Acta Crystallographica Section A Foundations of Crystallography},
  title            = {On the equivalence of point configurations due to Euclidean normalizers (Cheshire groups) of space groups},
  year             = {1983},
  issn             = {0108-7673},
  month            = nov,
  number           = {6},
  pages            = {907--915},
  volume           = {39},
  creationdate     = {2024-01-05T20:59:16},
  doi              = {10.1107/s0108767383001828},
  file             = {:by-author/F/Fischer/1983_Fischer_907.pdf:PDF},
  keywords         = {Crystallography; Eucliean Normalisers; Space Groups; Symmetry},
  modificationdate = {2024-01-05T21:00:25},
  owner            = {saulius},
  publisher        = {International Union of Crystallography (IUCr)},
}

@Misc{Bradley2014,
  author           = {Bradley, Jean-Claude and Lang, Andrew and Williams, Antony},
  title            = {{J}ean-{C}laude {B}radley open melting point dataset},
  year             = {2014},
  copyright        = {Creative Commons Zero v1.0 Universal},
  creationdate     = {2024-01-08T16:59:13},
  doi              = {10.6084/m9.figshare.1031637.v2},
  file             = {:by-author/B/Bradley/2014_Bradley_Jean Claude Bradley Open Melting Point Dataset.xlsx:Excel 2007+},
  keywords         = {Chemistry; Dataset; Melting Point; Organic Chemistry; Organic Chemistry, FOS: Chemical Sciences, FOS: Chemical Sciences, Cheminformatics; Reference Data},
  modificationdate = {2024-03-11T17:57:29},
  owner            = {saulius},
  publisher        = {figshare},
  url              = {https://figshare.com/ndownloader/files/1503990},
}

 
@Article{Vaitkus2023,
  author           = {Vaitkus, Antanas and Merkys, Andrius and Sander, Thomas and Quirós, Miguel and Thiessen, Paul A. and Bolton, Evan E. and Gražulis, Saulius},
  journal          = {Journal of Cheminformatics},
  title            = {A workflow for deriving chemical entities from crystallographic data and its application to the {C}rystallography {O}pen {D}atabase},
  year             = {2023},
  issn             = {1758-2946},
  month            = dec,
  number           = {1},
  volume           = {15},
  creationdate     = {2024-01-11T11:54:38},
  doi              = {10.1186/s13321-023-00780-2},
  file             = {:by-author/V/Vaitkus/2023_Vaitkus_123.pdf:PDF},
  keywords         = {COD; COD Derived Data; Chemoinformatics; Crystallography; PubChem; Software},
  modificationdate = {2024-01-12T09:11:10},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media LLC},
}

 
@Article{Balandis2022,
  author           = {Balandis, Benas and Šimkūnas, Tomas and Paketurytė-Latvė, Vaida and Michailovienė, Vilma and Mickevičiūtė, Aurelija and Manakova, Elena and Gražulis, Saulius and Belyakov, Sergey and Kairys, Visvaldas and Mickevičius, Vytautas and Zubrienė, Asta and Matulis, Daumantas},
  journal          = {Pharmaceuticals},
  title            = {Beta and gamma amino acid-substituted benzenesulfonamides as inhibitors of human carbonic anhydrases},
  year             = {2022},
  issn             = {1424-8247},
  month            = apr,
  number           = {4},
  pages            = {477},
  volume           = {15},
  creationdate     = {2024-01-12T09:16:23},
  doi              = {10.3390/ph15040477},
  file             = {:by-author/B/Balandis/2022_Balandis_477.pdf:PDF},
  keywords         = {Carbonic Anhydrases (CA); Drug Design; Inhibitors},
  modificationdate = {2024-01-12T09:17:39},
  owner            = {saulius},
  publisher        = {MDPI AG},
}

@InBook{Aiken2016,
  author           = {Aiken, Alex and Banerjee, Utpal and Kejariwal, Arun and Nicolau, Alexandru},
  pages            = {9--42},
  publisher        = {Springer US},
  title            = {Overview of {ILP} architectures},
  year             = {2016},
  isbn             = {9781489977977},
  booktitle        = {Instruction Level Parallelism},
  creationdate     = {2024-01-22T11:15:50},
  doi              = {10.1007/978-1-4899-7797-7_2},
  file             = {:by-author/A/Aiken/2016_Aiken_9.pdf:PDF},
  keywords         = {Computer Architecture; Computer Science (CS); Instruction Level Parallelism (ILP); Parallel Computations},
  modificationdate = {2024-01-22T11:23:16},
  owner            = {saulius},
  url              = {https://link.springer.com/content/pdf/10.1007/978-1-4899-7797-7_2.pdf},
}

@Electronic{Holzmann2007,
  author           = {Gerard J. Holzmann},
  language         = {English},
  title            = {The power of ten -- rules for developing safety critical code},
  url              = {http://pixelscommander.com/wp-content/uploads/2014/12/P10.pdf},
  year             = {2007},
  creationdate     = {2024-01-22T11:25:39},
  file             = {:by-author/H/Holzmann/2007_Holzmann_1.pdf:PDF},
  keywords         = {Computer Science (CS); Software Design; Software Engineering; Software Requirements},
  modificationdate = {2024-01-24T16:55:43},
  owner            = {saulius},
}

@Article{Mighell1981,
  author           = {Alan D. Mighell and Judith K. Stalick},
  journal          = {Acta Crystallographica Section A Foundations of Crystallography},
  title            = {The {NBS} crystal data file},
  year             = {1981},
  issn             = {0108-7673},
  month            = aug,
  number           = {a1},
  pages            = {C343--C343},
  volume           = {37},
  creationdate     = {2024-01-25T09:24:56},
  doi              = {10.1107/s010876738108940x},
  file             = {:by-author/M/Mighell/1981_Mighell_1.pdf:PDF},
  keywords         = {Crystallographic Databases; Crystallography; Data Management; Material Identification; Scientific Databases},
  modificationdate = {2024-01-25T09:32:30},
  organization     = {Center for Materials Science,National Bureau of Standards, Washington, DC 20234},
  owner            = {saulius},
  publisher        = {International Union of Crystallography (IUCr)},
  url              = {https://journals.iucr.org/a/issues/1981/a1/00/a43612/a43612.pdf},
}

@Article{Carr1989,
  author           = {M. J. Carr and W. F. Chambers and D. Melgaard and V. L. Himes and J. K. Stalick and A. D. Mighell},
  journal          = {Journal of Research of the National Institute of Standards and Technology},
  title            = {{NIST}/{S}andia/{ICDD} {E}lectron {D}iffraction {D}atabase: a database for phase identificationby electron diffraction},
  year             = {1989},
  number           = {1},
  volume           = {94},
  creationdate     = {2024-01-25T09:33:51},
  doi              = {10.6028/jres.094.003},
  file             = {:by-author/C/Carr/1989_Carr_1.pdf:PDF},
  keywords         = {Crystallographic Databases; Crystallography; Data Management; Electron Diffraction; Material Identification; Scientific Databases},
  modificationdate = {2024-01-25T09:40:48},
  owner            = {saulius},
  url              = {https://nvlpubs.nist.gov/nistpubs/jres/094/jresv94n1p15_A1b.pdf},
}

@Article{Heller2013,
  author           = {Heller, Stephen and McNaught, Alan and Stein, Stephen and Tchekhovskoi, Dmitrii and Pletnev, Igor},
  journal          = {Journal of Cheminformatics},
  title            = {{InChI} - the worldwide chemical structure identifier standard},
  year             = {2013},
  issn             = {1758-2946},
  month            = jan,
  number           = {1},
  volume           = {5},
  creationdate     = {2024-01-26T09:46:51},
  doi              = {10.1186/1758-2946-5-7},
  file             = {:by-author/H/Heller/2013_Heller_1.pdf:PDF},
  keywords         = {Chemoinformatics; InChI; Review},
  modificationdate = {2024-01-26T09:47:30},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media LLC},
}

@Article{Besl1992,
  author           = {Besl, P. J. and McKay, Neil D.},
  journal          = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  title            = {A method for registration of 3-{D} shapes},
  year             = {1992},
  issn             = {2160-9292},
  month            = feb,
  number           = {2},
  pages            = {239--256},
  volume           = {14},
  comment          = {Cited in Edelsbrunner2012.},
  creationdate     = {2024-01-26T11:51:38},
  doi              = {10.1109/34.121791},
  file             = {:by-author/B/Besl/1992_Besl_239.pdf:PDF},
  keywords         = {Algorithm; Rotational Superposition; Structure Superposition; Superposition},
  modificationdate = {2024-05-12T11:35:51},
  owner            = {saulius},
  publisher        = {Institute of Electrical and Electronics Engineers (IEEE)},
  url              = {https://www.cs.bu.edu/groups/ivc/exam/papers/besl.pdf},
}

@Article{Bazmi2024,
  author           = {Bazmi, Saman and Wallin, Stefan},
  journal          = {PeerJ Physical Chemistry},
  title            = {Comparing effects of attractive interactions in crowded systems: nonspecific, hydrophobic, and hydrogen bond interactions},
  year             = {2024},
  issn             = {2689-7733},
  month            = jan,
  pages            = {e31},
  volume           = {6},
  creationdate     = {2024-02-01T18:01:29},
  doi              = {10.7717/peerj-pchem.31},
  file             = {:by-author/B/Bazmi/2024_Bazmi_e31.pdf:PDF},
  keywords         = {Crowding, Protein Folding, Molecular Interactions, Hydrophobic Effect, Molecular Simulation, Monte Carlo},
  modificationdate = {2024-02-01T18:02:07},
  owner            = {saulius},
  publisher        = {PeerJ},
}

 
@Article{Bailo2024,
  author           = {Bailo, Daniele and Paciello, Rossana and Michalek, Jan and Mercurio, Daniela and Sangianantoni, Agata and Contell, Kauzar Saleh and Lange, Otto and Maracchia, Giovanna and Atakan, Kuvvet and Jeffery, Keith G. and Freda, Carmela},
  journal          = {Data Science Journal},
  title            = {Data management in distributed, federated research infrastructures: the case of {EPOS}},
  year             = {2024},
  issn             = {1683-1470},
  pages            = {5},
  volume           = {23},
  creationdate     = {2024-02-01T20:36:45},
  doi              = {10.5334/dsj-2024-005},
  file             = {:by-author/B/Bailo/2024_Bailo_5.pdf:PDF},
  keywords         = {Data Management; Data Management Plans; Federated Infrastructures; Infrastructures; Scientific Data},
  modificationdate = {2024-02-01T20:40:04},
  owner            = {saulius},
  publisher        = {Ubiquity Press, Ltd.},
}

 
@Article{Goerzig2024,
  author           = {Görzig, Heike and Gonzalez Beltran, Alejandra N. and Engel, Felix and Matthews, Brian},
  journal          = {Data Science Journal},
  title            = {A framework for active {DMPs} in photon and neutron science large-scale facilities},
  year             = {2024},
  issn             = {1683-1470},
  pages            = {4},
  volume           = {23},
  creationdate     = {2024-02-01T20:39:04},
  doi              = {10.5334/dsj-2024-004},
  file             = {:by-author/G/Görzig/2024_Görzig_4.pdf:PDF},
  keywords         = {Data Management; Data Management Plans; Infrastructures; Scientific Data},
  modificationdate = {2024-02-13T08:33:38},
  owner            = {saulius},
  publisher        = {Ubiquity Press, Ltd.},
}

 
@Article{Kouper2024,
  author           = {Kouper, Inna and Stone, Stacy},
  journal          = {Data Science Journal},
  title            = {Data Sharing and Use in Cybersecurity Research},
  year             = {2024},
  issn             = {1683-1470},
  month            = jan,
  pages            = {3},
  volume           = {23},
  creationdate     = {2024-02-01T20:41:12},
  doi              = {10.5334/dsj-2024-003},
  file             = {:by-author/K/Kouper/2024_Kouper_3.pdf:PDF},
  keywords         = {Data Management; Data Sharing; Scientific Data},
  modificationdate = {2024-02-01T20:42:01},
  owner            = {saulius},
  publisher        = {Ubiquity Press, Ltd.},
}

 
@Article{Gerasimov2024,
  author           = {Gerasimov, Irina and Savtchenko, Andrey and Alfred, Jerome and Acker, James and Wei, Jennifer and Kc, Binita},
  journal          = {Data Science Journal},
  title            = {Bridging the Gap: Enhancing Prominence and Provenance of NASA Datasets in Research Publications},
  year             = {2024},
  issn             = {1683-1470},
  pages            = {1},
  volume           = {23},
  creationdate     = {2024-02-01T20:42:35},
  doi              = {10.5334/dsj-2024-001},
  file             = {:by-author/G/Gerasimov/2024_Gerasimov_1.pdf:PDF},
  keywords         = {Data Management; NASA; Scientific Data; Space Flight},
  modificationdate = {2024-02-01T20:43:13},
  owner            = {saulius},
  publisher        = {Ubiquity Press, Ltd.},
}

 
@Article{Sjoelin2023,
  author           = {Sjølin, Benjamin H. and Jørgensen, Peter B. and Fedrigucci, Andrea and Vegge, Tejs and Bhowmik, Arghya and Castelli, Ivano E.},
  journal          = {Batteries &amp; Supercaps},
  title            = {Accelerated workflow for antiperovskite‐based solid state electrolytes},
  year             = {2023},
  issn             = {2566-6223},
  month            = apr,
  number           = {6},
  pages            = {e202300041},
  volume           = {6},
  creationdate     = {2024-02-02T09:54:43},
  doi              = {10.1002/batt.202300041},
  file             = {:by-author/S/Sjølin/2023_Sjølin_e202300041.pdf:PDF},
  keywords         = {Computational Materials Science; Materials Discovery; Materials Science; MyQueue; Wokflow Managers; Workflow Description Languages; Workflows},
  modificationdate = {2024-02-02T09:58:33},
  owner            = {saulius},
  publisher        = {Wiley},
}

 
@Article{Deng2022,
  author           = {Deng, Zeyu and Kumar, Vipin and Bölle, Felix T. and Caro, Fernando and Franco, Alejandro A. and Castelli, Ivano E. and Canepa, Pieremanuele and Seh, Zhi Wei},
  journal          = {Energy &amp; Environmental Science},
  title            = {Towards autonomous high-throughput multiscale modelling of battery interfaces},
  year             = {2022},
  issn             = {1754-5706},
  number           = {2},
  pages            = {579--594},
  volume           = {15},
  creationdate     = {2024-02-02T14:41:10},
  doi              = {10.1039/d1ee02324a},
  file             = {:by-author/D/Deng/2022_Deng_579.pdf:PDF},
  modificationdate = {2024-02-02T14:46:04},
  owner            = {saulius},
  publisher        = {Royal Society of Chemistry (RSC)},
}

@Article{ChueHong2019,
  author           = {Chue Hong, Neil P. and Allen, Alice and Gonzalez-Beltran and de Waard, Anita and Smith, Arfon M. and Robinson, Carly and Jones, Catherine and Bouquin, Daina and Katz, Daniel S. and Kennedy, David and Ryder, Gerry and Hausman, Jessica and Hwang, Lorraine and Jones, Matthew B. and Harrison, Melissa and Crosas, Mercè and Wu, Mingfang and Löwe, Peter and Haines, Robert and Edmunds, Scott and Stall, Shelley and Swaminathan, Sowmya and Druskat, Stephan and Crick, Tom and Morrell, Tom and Pollard, Tom},
  title            = {Software citation checklist for developers},
  year             = {2019},
  comment          = {Cited in Katz2021.},
  copyright        = {Creative Commons Attribution Share Alike 4.0 International},
  creationdate     = {2024-02-06T10:35:55},
  doi              = {10.5281/ZENODO.3482768},
  file             = {:by-author/C/Chue Hong/2019_Chue Hong_Software Citation Checklist for Developers.md:TXT},
  keywords         = {Checklist; Software Citation},
  language         = {en},
  modificationdate = {2024-02-06T10:46:10},
  owner            = {saulius},
  publisher        = {Zenodo},
  url              = {https://zenodo.org/records/3482769/files/software_citation_checklist_for_developers.md?download=1},
}

@Article{ChueHong2019a,
  author           = {Chue Hong, Neil P. and Allen, Alice and Gonzalez-Beltran, Alejandra and de Waard, Anita and Smith, Arfon M. and Robinson, Carly and Jones, Catherine and Bouquin, Daina and Katz, Daniel S. and Kennedy, David and Ryder, Gerry and Hausman, Jessica and Hwang, Lorraine and Jones, Matthew B. and Harrison, Melissa and Crosas, Mercè and Wu, Mingfang and Löwe, Peter and Haines, Robert and Edmunds, Scott and Stall, Shelley and Swaminathan, Sowmya and Druskat, Stephan and Crick, Tom and Morrell, Tom and Pollard, Tom},
  title            = {Software citation checklist for authors},
  year             = {2019},
  comment          = {Cited in Katz2021.},
  copyright        = {Creative Commons Attribution Share Alike 4.0 International},
  creationdate     = {2024-02-06T10:39:09},
  doi              = {10.5281/ZENODO.3479198},
  eprint           = {https://zenodo.org/records/3479199},
  file             = {:by-author/C/Chue Hong/2019_Chue Hong_Software Citation Checklist for Authors.md:TXT},
  keywords         = {Checklist; Research Software; Software Citation},
  language         = {en},
  modificationdate = {2024-02-06T10:46:16},
  owner            = {saulius},
  publisher        = {Zenodo},
  url              = {https://zenodo.org/records/3479199/files/software_citation_checklist_for_authors.md?download=1},
}

@Article{Dogan2024,
  author           = {Doğan, Mustafa and Öztoprak, Kasım and Tolun, Mehmet Reşit},
  journal          = {PeerJ Computer Science},
  title            = {Teaching computer architecture by designing and simulating processors from their bits and bytes},
  year             = {2024},
  issn             = {2376-5992},
  month            = feb,
  pages            = {e1818},
  volume           = {10},
  creationdate     = {2024-02-20T09:10:45},
  doi              = {10.7717/peerj-cs.1818},
  file             = {:by-author/D/Doğan/2024_Doğan_e1818.pdf:PDF},
  keywords         = {CPU Design; Computer Architecture; Harware Simulation; Teaching},
  modificationdate = {2024-02-20T09:11:51},
  owner            = {saulius},
  publisher        = {PeerJ},
}

@Article{Schmidt2022,
  author           = {Schmidt, Jonathan and Wang, Hai-Chen and Cerqueira, Tiago F. T. and Botti, Silvana and Marques, Miguel A. L.},
  journal          = {Scientific Data},
  title            = {A dataset of 175k stable and metastable materials calculated with the {PBEsol} and {SCAN} functionals},
  year             = {2022},
  issn             = {2052-4463},
  month            = mar,
  number           = {1},
  pages            = {64},
  volume           = {9},
  comment          = {Showcased in 2024 MaRDA Meeting (https://www.marda-alliance.org/materials-data-platforms-and-repositories/).},
  creationdate     = {2024-02-22T18:50:02},
  doi              = {10.1038/s41597-022-01177-w},
  file             = {:by-author/S/Schmidt/2022_Schmidt_64.pdf:PDF},
  keywords         = {Computational Materials Science; Dataset; Materials Discovery; Scientific Databases},
  modificationdate = {2024-02-22T18:52:06},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media LLC},
}

@Article{Ogoshi2023,
  author           = {Ogoshi, Tomoki},
  journal          = {Chemical Reviews},
  title            = {Hierarchical materials from high information content macromolecular building blocks: construction, dynamic interventions, and prediction},
  year             = {2023},
  issn             = {1520-6890},
  month            = jul,
  number           = {13},
  pages            = {8041--8043},
  volume           = {123},
  creationdate     = {2024-03-02T10:55:46},
  doi              = {10.1021/acs.chemrev.3c00355},
  file             = {:by-author/O/Ogoshi/2023_Ogoshi_8041.pdf:PDF},
  keywords         = {Biological Systems; Computational Materials Science; High Information Content Molecules; Materials Design; Materials Science; Review},
  modificationdate = {2024-03-02T11:00:17},
  owner            = {saulius},
  publisher        = {American Chemical Society (ACS)},
}

@Article{Shao2022,
  author           = {Shao, Li and Ma, Jinrong and Prelesnik, Jesse L. and Zhou, Yicheng and Nguyen, Mary and Zhao, Mingfei and Jenekhe, Samson A. and Kalinin, Sergei V. and Ferguson, Andrew L. and Pfaendtner, Jim and Mundy, Christopher J. and De Yoreo, James J. and Baneyx, François and Chen, Chun-Long},
  journal          = {Chemical Reviews},
  title            = {Hierarchical materials from high information content macromolecular building blocks: construction, dynamic interventions, and prediction},
  year             = {2022},
  issn             = {1520-6890},
  month            = oct,
  number           = {24},
  pages            = {17397--17478},
  volume           = {122},
  comment          = {Cited in Ogoshi2023.},
  creationdate     = {2024-03-02T10:58:56},
  doi              = {10.1021/acs.chemrev.2c00220},
  file             = {:by-author/S/Shao/2022_Shao_17397.pdf:PDF},
  keywords         = {Biological Systems; Computational Materials Science; High Information Content Molecules; Materials Design; Materials Science; Review},
  modificationdate = {2024-03-02T11:03:27},
  owner            = {saulius},
  publisher        = {American Chemical Society (ACS)},
}

@Misc{Bradley2014a,
  author           = {Bradley, Jean-Claude and Lang, Andrew and Williams, Antony},
  title            = {Jean-{C}laude {B}radley double plus good (highly curated and validated) melting point dataset},
  year             = {2014},
  copyright        = {Creative Commons Zero v1.0 Universal},
  creationdate     = {2024-03-11T17:27:21},
  doi              = {10.6084/M9.FIGSHARE.1031638.V1},
  file             = {:by-author/B/Bradley/2014_Bradley_Jean Claude Bradley Double Plus Good (highly Curated and Validated) Melting Point Dataset.xlsx:Excel 2007+},
  keywords         = {Chemistry; Dataset; Melting Point; Organic Chemistry; Organic Chemistry, FOS: Chemical Sciences, FOS: Chemical Sciences, Cheminformatics},
  modificationdate = {2024-03-11T17:58:52},
  owner            = {saulius},
  publisher        = {figshare},
  url              = {https://figshare.com/ndownloader/files/1503991},
}

@Article{Grybauskas2023,
  author           = {Grybauskas, Algirdas and Gražulis, Saulius},
  journal          = {Bioinformatics},
  title            = {Building protein structure-specific rotamer libraries},
  year             = {2023},
  issn             = {1367-4811},
  month            = jul,
  number           = {7},
  pages            = {btad429},
  volume           = {39},
  creationdate     = {2024-03-13T14:57:47},
  doi              = {10.1093/bioinformatics/btad429},
  editor           = {Cowen, Lenore},
  file             = {:by-author/G/Grybauskas/2023_Grybauskas_btad429.pdf:PDF},
  keywords         = {Algorithm; Bioinformatics; Protein Side Chains; Rotamers},
  modificationdate = {2024-03-13T15:00:24},
  owner            = {saulius},
  publisher        = {Oxford University Press (OUP)},
}

@Article{Bahar1997,
  author           = {Bahar, Ivet and Atilgan, Ali Rana and Erman, Burak},
  journal          = {Folding and Design},
  title            = {Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential},
  year             = {1997},
  issn             = {1359-0278},
  month            = jun,
  number           = {3},
  pages            = {173--181},
  volume           = {2},
  comment          = {Cited in https://en.wikipedia.org/wiki/Debye%E2%80%93Waller_factor [accessed 2024-03-14T11:05+02:00, permalink https://en.wikipedia.org/w/index.php?title=Debye%E2%80%93Waller_factor&oldid=1198178419]. Gives definition of B as B = 8*π**2*<u**2> / 3 (i.e. it contains the 1/3 factor...).},
  creationdate     = {2024-03-14T11:01:30},
  doi              = {10.1016/s1359-0278(97)00024-2},
  file             = {:by-author/B/Bahar/1997_Bahar_173.pdf:PDF},
  keywords         = {B-factor; Crystallography; Definition; Protein Crystallography; Structural Biology; Thermal Displacement Parameters},
  modificationdate = {2024-03-14T11:06:32},
  owner            = {saulius},
  publisher        = {Elsevier BV},
}

@Article{Sun2019,
  author           = {Sun, Zhoutong and Liu, Qian and Qu, Ge and Feng, Yan and Reetz, Manfred T.},
  journal          = {Chemical Reviews},
  title            = {Utility of {B}-factors in protein science: interpreting rigidity, flexibility, and internal motion and engineering thermostability},
  year             = {2019},
  issn             = {1520-6890},
  month            = jan,
  number           = {3},
  pages            = {1626--1665},
  volume           = {119},
  creationdate     = {2024-03-14T11:10:16},
  doi              = {10.1021/acs.chemrev.8b00290},
  file             = {:by-author/S/Sun/2019_Sun_1626.pdf:PDF},
  keywords         = {B-factor; Crystallography; Definition; Protein Crystallography; Structural Biology; Thermal Displacement Parameters},
  modificationdate = {2024-03-14T11:11:56},
  owner            = {saulius},
  publisher        = {American Chemical Society (ACS)},
}

@Manuscript{Azizollahi2022,
  author           = {Farzaneh Alipoor Azizollahi and Mohammadhosein Razbin and Kavoos Mirabbaszadeh},
  title            = {Migration and size change of a cell inside a microchannel due to adhesive topographical features},
  year             = {2022},
  keywords         = {Cell Migration; Cellular Potts Model (CPM); Hamiltonian; Markov Chain Monte Carlo (MCMC); Microchannel; Topotaxis},
  comment          = {Received via Telegram personally; not to be redistributed!},
  creationdate     = {2024-03-18T10:55:05},
  file             = {:by-author/A/Azizollahi/2022_Azizollahi_Migration and Size Change of a Cell inside a Microchannel Due to Adhesive Topographical Features.pdf:PDF},
  modificationdate = {2024-03-18T11:06:07},
  owner            = {saulius},
}

@Article{Rens2019,
  author           = {Rens, Elisabeth G. and Edelstein-Keshet, Leah},
  journal          = {PLOS Computational Biology},
  title            = {From energy to cellular forces in the {C}ellular {P}otts {M}odel: An algorithmic approach},
  year             = {2019},
  issn             = {1553-7358},
  month            = dec,
  number           = {12},
  pages            = {e1007459},
  volume           = {15},
  comment          = {Cited in Azizollahi2022.},
  creationdate     = {2024-03-18T11:02:49},
  doi              = {10.1371/journal.pcbi.1007459},
  editor           = {Gallo, James},
  file             = {:by-author/R/Rens/2019_Rens_e1007459.pdf:PDF;:by-author/R/Rens/2019_Rens_e1007459_suppl/pcbi.1007459.s001.pdf:PDF;:by-author/R/Rens/2019_Rens_e1007459_suppl/pcbi.1007459.s002.ps:PostScript;:by-author/R/Rens/2019_Rens_e1007459_suppl/pcbi.1007459.s003.ps:PostScript;:by-author/R/Rens/2019_Rens_e1007459_suppl/pcbi.1007459.s004.ps:PostScript;:by-author/R/Rens/2019_Rens_e1007459_suppl/pcbi.1007459.s005.ps:PostScript;:by-author/R/Rens/2019_Rens_e1007459_suppl/pcbi.1007459.s006.ps:PostScript;:by-author/R/Rens/2019_Rens_e1007459_suppl/pcbi.1007459.s007.ps:PostScript;:by-author/R/Rens/2019_Rens_e1007459_suppl/pcbi.1007459.s008.ps:PostScript;:by-author/R/Rens/2019_Rens_e1007459_suppl/pcbi.1007459.s009.ps:PostScript;:by-author/R/Rens/2019_Rens_e1007459_suppl/pcbi.1007459.s010.ps:PostScript;:by-author/R/Rens/2019_Rens_e1007459_suppl/pcbi.1007459.s011.ps:PostScript;:by-author/R/Rens/2019_Rens_e1007459_suppl/pcbi.1007459.s012.ps:PostScript;:by-author/R/Rens/2019_Rens_e1007459_suppl/pcbi.1007459.s013.ps:PostScript;:by-author/R/Rens/2019_Rens_e1007459_suppl/pcbi.1007459.s014.ps:PostScript;:by-author/R/Rens/2019_Rens_e1007459_suppl/pcbi.1007459.s015.ps:PostScript;:by-author/R/Rens/2019_Rens_e1007459_suppl/pcbi.1007459.s016.ps:PostScript;:by-author/R/Rens/2019_Rens_e1007459_suppl/pcbi.1007459.s017.ps:PostScript;:by-author/R/Rens/2019_Rens_e1007459_suppl/pcbi.1007459.s018.ps:PostScript;:by-author/R/Rens/2019_Rens_e1007459_suppl/pcbi.1007459.s019.png:PNG image;:by-author/R/Rens/2019_Rens_e1007459_suppl/pcbi.1007459.s020.png:PNG image;:by-author/R/Rens/2019_Rens_e1007459_suppl/pcbi.1007459.s021.png:PNG image;:by-author/R/Rens/2019_Rens_e1007459_suppl/pcbi.1007459.s022.png:PNG image;:by-author/R/Rens/2019_Rens_e1007459_suppl/pcbi.1007459.s023.png:PNG image;:by-author/R/Rens/2019_Rens_e1007459_suppl/pcbi.1007459.s024.png:PNG image;:by-author/R/Rens/2019_Rens_e1007459_suppl/pcbi.1007459.s025.pdf:PDF;:by-author/R/Rens/2019_Rens_e1007459_suppl/pcbi.1007459.s026.pdf:PDF;:by-author/R/Rens/2019_Rens_e1007459_suppl/pcbi.1007459.s027.avi:avi;:by-author/R/Rens/2019_Rens_e1007459_suppl/pcbi.1007459.s028.avi:avi},
  keywords         = {Cell Migration; Cellular Potts Model (CPM); Hamiltonian; Microchannel; Topotaxis},
  modificationdate = {2024-03-18T21:02:32},
  owner            = {saulius},
  publisher        = {Public Library of Science (PLoS)},
}

@Article{Brink2024,
  author           = {Brink, Alice and Bruno, Ian and Helliwell, John R. and McMahon, Brian},
  journal          = {IUCrJ},
  title            = {The interoperability of crystallographic data and databases},
  year             = {2024},
  issn             = {2052-2525},
  month            = jan,
  number           = {1},
  pages            = {9--15},
  volume           = {11},
  creationdate     = {2024-03-18T21:02:41},
  doi              = {10.1107/s2052252523010424},
  file             = {:by-author/B/Brink/2024_Brink_9.pdf:PDF},
  keywords         = {Crystallography; Databases; Interoperability},
  modificationdate = {2024-03-18T21:03:32},
  owner            = {saulius},
  publisher        = {International Union of Crystallography (IUCr)},
}

@Standard{ISO1975,
  organization     = {ISO/IEC JTC 1/SC 2},
  title            = {The set of control characters of the {ISO} 646},
  author           = {{ISO}},
  language         = {English, French},
  url              = {https://itscj.ipsj.or.jp/ir/001.pdf},
  year             = {1975},
  comment          = {Found via Wikipedia, https://en.wikipedia.org/wiki/C0_and_C1_control_codes [accessed 2024-03-20T11:31+02:00, permalink https://en.wikipedia.org/w/index.php?title=C0_and_C1_control_codes&oldid=1205083220].},
  creationdate     = {2024-03-20T11:25:28},
  file             = {:by-author/I/ISO/1975_ISO_The Set of Control Characters of the ISO 646.pdf:PDF},
  keywords         = {ASCII; C0 Control Codes; Character Encodings; Character Set; Control Characters; File Separator; Group Separator; Record Separator; Unit Separator},
  modificationdate = {2024-03-20T11:32:19},
  owner            = {saulius},
}

@Webpage{Duncan2009,
  author           = {Ronald Duncan},
  retrieved        = {2024-03-20T16:03+02:00},
  title            = {Text file formats – {ASCII} delimited text – not {CSV} or {TAB} delimited text},
  url              = {https://ronaldduncan.wordpress.com/2009/10/31/text-file-formats-ascii-delimited-text-not-csv-or-tab-delimited-text/#comments},
  month            = oct,
  year             = {2009},
  comment          = {Found via https://en.wikipedia.org/wiki/Delimiter#cite_note-19 [accessed 2024-03-20T11:31+02:00, permalink https://en.wikipedia.org/w/index.php?title=C0_and_C1_control_codes&oldid=1205083220].},
  creationdate     = {2024-03-20T16:13:26},
  file             = {:by-author/D/Duncan/2009_Duncan_Text File Formats – ASCII Delimited Text – Not CSV or TAB Delimited Text.pdf:PDF;:delimiters.odt:OpenDocument text},
  keywords         = {ASCII; C0 Control Codes; Character Encodings; Character Set; Control Characters; Development; File Formats; File Separator; Group Separator; Record Separator; Software; Unit Separator},
  modificationdate = {2024-03-20T16:17:12},
  owner            = {saulius},
}

@MastersThesis{Dey2023,
  author           = {Aditya Dey},
  school           = {Norvegian University of Life Sciences},
  title            = {Prediction of melting temperature of organic molecules using machine learning},
  year             = {2023},
  creationdate     = {2024-03-21T17:12:56},
  file             = {:by-author/D/Dey/2023_Dey_Prediction of Melting Temperature of Organic Molecules Using Machine Learning.pdf:PDF},
  keywords         = {Artificial Neural Networks (ANN); Machine Learning (ML); Melting Point Prediction; Random Forest},
  modificationdate = {2024-03-21T17:25:36},
  owner            = {saulius},
  url              = {https://nmbu.brage.unit.no/nmbu-xmlui/handle/11250/3079871},
}

@Article{Lyons2014,
  author           = {Lyons, James and Dehzangi, Abdollah and Heffernan, Rhys and Sharma, Alok and Paliwal, Kuldip and Sattar, Abdul and Zhou, Yaoqi and Yang, Yuedong},
  journal          = {Journal of Computational Chemistry},
  title            = {Predicting backbone {Cα} angles and dihedrals from protein sequences by stacked sparse auto‐encoder deep neural network},
  year             = {2014},
  issn             = {1096-987X},
  month            = sep,
  number           = {28},
  pages            = {2040--2046},
  volume           = {35},
  creationdate     = {2024-03-26T09:37:17},
  doi              = {10.1002/jcc.23718},
  file             = {:by-author/L/Lyons/2014_Lyons_2040.pdf:PDF},
  keywords         = {Artificial Neural Networks (ANN); Autoencoders; Bioinformatics; Deep Learning (DL); Dihedral Angles; Machine Learning (ML); Protein Structure},
  modificationdate = {2024-03-26T09:38:58},
  owner            = {saulius},
  publisher        = {Wiley},
}

@Article{Wu2024,
  author           = {Wu, Kevin E. and Yang, Kevin K. and van den Berg, Rianne and Alamdari, Sarah and Zou, James Y. and Lu, Alex X. and Amini, Ava P.},
  journal          = {Nature Communications},
  title            = {Protein structure generation via folding diffusion},
  year             = {2024},
  issn             = {2041-1723},
  month            = feb,
  number           = {1},
  pages            = {1059},
  volume           = {15},
  creationdate     = {2024-03-26T09:46:36},
  doi              = {10.1038/s41467-024-45051-2},
  file             = {:by-author/W/Wu/2024_Wu_1059.pdf:PDF},
  keywords         = {Algorithm; Bioinformatics; Protein Folding; Protein Structure Prediction},
  modificationdate = {2024-03-26T09:48:14},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media LLC},
}

@Article{Kony2007,
  author           = {Kony, David B. and Damm, Wolfgang and Stoll, Serge and van Gunsteren, Wilfred F. and Hünenberger, Philippe H.},
  journal          = {Biophysical Journal},
  title            = {Explicit-Solvent Molecular Dynamics Simulations of the Polysaccharide Schizophyllan in Water},
  year             = {2007},
  issn             = {0006-3495},
  month            = jul,
  number           = {2},
  pages            = {442--455},
  volume           = {93},
  creationdate     = {2024-03-26T10:41:35},
  doi              = {10.1529/biophysj.106.086116},
  file             = {:by-author/K/Kony/2007_Kony_442.pdf:PDF},
  keywords         = {Bioinformatics; Dihedral Angles; Polysaccharides},
  modificationdate = {2024-03-26T10:42:14},
  owner            = {saulius},
  publisher        = {Elsevier BV},
}

@Article{Turupcu2019,
  author           = {Turupcu, Aysegül and Diem, Matthias and Smith, Lorna J. and Oostenbrink, Chris},
  journal          = {ChemPhysChem},
  title            = {Structural Aspects of the O‐glycosylation Linkage in Glycopeptides via MD Simulations and Comparison with NMR Experiments},
  year             = {2019},
  issn             = {1439-7641},
  month            = may,
  number           = {11},
  pages            = {1527--1537},
  volume           = {20},
  comment-saulius  = {Possible assignment for bioinformatics students?},
  creationdate     = {2024-03-26T10:45:49},
  doi              = {10.1002/cphc.201900079},
  file             = {:by-author/T/Turupcu/2019_Turupcu_1527.pdf:PDF},
  keywords         = {Bioinformatics; Dihedral Angles; Glycosidic Dihedral Angles; Polysaccharides},
  modificationdate = {2024-04-08T14:11:36},
  owner            = {saulius},
  publisher        = {Wiley},
}

@Article{Apweiler1999,
  author           = {Apweiler, R.},
  journal          = {Biochimica et Biophysica Acta (BBA) - General Subjects},
  title            = {On the frequency of protein glycosylation, as deduced from analysis of the {SWISS-PROT} database},
  year             = {1999},
  issn             = {0304-4165},
  month            = dec,
  number           = {1},
  pages            = {4--8},
  volume           = {1473},
  abstract         = {The SWISS-PROT protein sequence data bank contains at present nearly 75,000 entries, almost two thirds of which include the potential N-glycosylation consensus sequence, or sequon, NXS/T (where X can be any amino acid but proline) and thus may be glycoproteins. The number of proteins filed as glycoproteins is however considerably smaller, 7942, of which 749 have been characterized with respect to the total number of their carbohydrate units and sites of attachment of the latter to the protein, as well as the nature of the carbohydrate-peptide linking group. Of these well characterized glycoproteins, about 90% carry either N-linked carbohydrate units alone or both N- and O-linked ones, attached at 1297 N-glycosylation sites (1.9 per glycoprotein molecule) and the rest are O-glycosylated only. Since the total number of sequons in the well characterized glycoproteins is 1968, their rate of occupancy is 2/3. Assuming that the same number of N-linked units and rate of sequon occupancy occur in all sequon containing proteins and that the proportion of solely O-glycosylated proteins (ca. 10%) will also be the same as among the well characterized ones, we conclude that the majority of sequon containing proteins will be found to be glycosylated and that more than half of all proteins are glycoproteins.},
  chemicals        = {DNA, Complementary, alpha-Fetoproteins, Fucosyltransferases, Glycoprotein 6-alpha-L-fucosyltransferase},
  citation-subset  = {IM},
  comment          = {Cited in Turupcu2019.},
  completed        = {2000-01-11},
  country          = {Netherlands},
  creationdate     = {2024-03-26T10:59:04},
  doi              = {10.1016/s0304-4165(99)00165-8},
  file             = {:by-author/A/Apweiler/1999_Apweiler_4.pdf:PDF},
  issn-linking     = {0006-3002},
  issue            = {1},
  keywords         = {Bioinformatics; Glycosilation; Protein Glycosilation; Proteins},
  modificationdate = {2024-03-26T11:00:02},
  nlm-id           = {0217513},
  owner            = {saulius},
  pii              = {S0304-4165(99)00165-8},
  pmid             = {10580125},
  publisher        = {Elsevier BV},
  pubmodel         = {Print},
  pubstate         = {ppublish},
  references       = {94},
  revised          = {2024-01-17},
}

@Article{Forget2013,
  author           = {Forget, Aurelien and Christensen, Jon and Lüdeke, Steffen and Kohler, Esther and Tobias, Simon and Matloubi, Maziar and Thomann, Ralf and Shastri, V. Prasad},
  journal          = {Proceedings of the National Academy of Sciences},
  title            = {Polysaccharide hydrogels with tunable stiffness and provasculogenic properties via α-helix to β-sheet switch in secondary structure},
  year             = {2013},
  issn             = {1091-6490},
  month            = jul,
  number           = {32},
  pages            = {12887--12892},
  volume           = {110},
  comment-saulius  = {Possible assignment for bioinformatics students?},
  creationdate     = {2024-03-26T11:11:41},
  doi              = {10.1073/pnas.1222880110},
  file             = {:by-author/F/Forget/2013_Forget_12887.pdf:PDF;:by-author/F/Forget/2013_Forget_12887_suppl/pnas.201222880si.pdf:PDF},
  keywords         = {Bioinformatics; Dihedral Angles; Glycosidic Dihedral Angles; Polysaccharides},
  modificationdate = {2024-04-08T14:10:42},
  owner            = {saulius},
  publisher        = {Proceedings of the National Academy of Sciences},
}

@Article{Frank2007,
  author           = {Frank, M. and Lütteke, T. and von der Lieth, C.-W.},
  journal          = {Nucleic acids research},
  title            = {{GlycoMapsDB}: a database of the accessible conformational space of glycosidic linkages.},
  year             = {2007},
  issn             = {1362-4962},
  month            = jan,
  pages            = {287--290},
  volume           = {35},
  abstract         = {Conformational energy maps of the glycosidic linkages are a valuable resource to gain information about preferred conformations and flexibility of carbohydrates. Here we present GlycoMapsDB, a new database containing more than 2500 calculated conformational maps for a variety of di- to pentasaccharide fragments contained in N- and O-glycans. Oligosaccharides representing branchpoints of N-glycans are included in the set of fragments, thus the influence of neighbouring residues is reflected in the conformational maps. During refinement of new crystal structures, maps contained in GlycoMapsDB can serve as a valuable resource to check whether the torsion values of a glycosidic linkage are located in an 'allowed' region similar to the Ramachandran plot analysis for proteins. This might help to improve the structural quality of the glycan data contained in the Protein Data Bank (PDB). A link between GlycoMapsDB and the PDB has been established so that the glycosidic torsions of all glycans contained in the PDB can be retrieved and compared to calculated data. The service is available at www.glycosciences.de/modeling/glycomapsdb/.},
  chemicals        = {Oligosaccharides, Polysaccharides},
  citation-subset  = {IM},
  completed        = {2007-03-16},
  country          = {England},
  creationdate     = {2024-03-26T11:16:32},
  doi              = {10.1093/nar/gkl907},
  file             = {:by-author/F/Frank/2007_Frank_287.pdf:PDF},
  issn-linking     = {0305-1048},
  issue            = {Database issue},
  keywords         = {Bioinformatics; Carbohydrate Conformation; Databases, Factual; Glycosilation; Internet; Oligosaccharides, Chemistry; Polysaccharides, Chemistry; Protein Glycosilation; Proteins; User-Computer Interface},
  modificationdate = {2024-03-26T11:19:10},
  nlm-id           = {0411011},
  owner            = {saulius},
  pii              = {35/suppl_1/287},
  pmc              = {PMC1899098},
  pmid             = {17202175},
  pubmodel         = {Print},
  pubstate         = {ppublish},
  revised          = {2023-11-03},
}

@Article{Luetteke2008,
  author           = {Lütteke, Thomas},
  journal          = {ChemBioChem},
  title            = {Web resources for the glycoscientist},
  year             = {2008},
  issn             = {1439-7633},
  month            = aug,
  number           = {13},
  pages            = {2155--2160},
  volume           = {9},
  creationdate     = {2024-03-26T11:18:11},
  doi              = {10.1002/cbic.200800338},
  file             = {:by-author/L/Lütteke/2008_Lütteke_2155.pdf:PDF},
  keywords         = {Bioinformatics; Databases; Polysaccarides},
  modificationdate = {2024-03-26T11:19:51},
  owner            = {saulius},
  publisher        = {Wiley},
}

@Article{Luetteke2004,
  author           = {Lütteke, Thomas and von der Lieth, Claus-W.},
  journal          = {BMC Bioinformatics},
  title            = {{pdb-care} ({PDB} {CA}rbohydrate {RE}sidue check): a program to support annotation of complex carbohydrate structures in {PDB} files},
  year             = {2004},
  issn             = {1471-2105},
  month            = jun,
  number           = {1},
  pages            = {69},
  volume           = {5},
  comment          = {Cited in Turupcu2019.},
  creationdate     = {2024-03-26T11:21:08},
  doi              = {10.1186/1471-2105-5-69},
  file             = {:by-author/L/Lütteke/2004_Lütteke_69.pdf:PDF},
  keywords         = {Bioinformatics; Dihedral Angles; Glycosidic Dihedral Angles; Polysaccharides},
  modificationdate = {2024-03-26T13:45:08},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media LLC},
}

@Article{Rosenberg2023,
  author           = {Rosenberg, Aviv A. and Yehishalom, Nitsan and Marx, Ailie and Bronstein, Alex M.},
  journal          = {Proceedings of the National Academy of Sciences},
  title            = {An amino-domino model described by a cross-peptide-bond {R}amachandran plot defines amino acid pairs as local structural units},
  year             = {2023},
  issn             = {1091-6490},
  month            = oct,
  number           = {44},
  pages            = {e2301064120},
  volume           = {120},
  comment-saulius  = {Good assignment for bioinformatics students :)},
  creationdate     = {2024-03-26T13:45:35},
  doi              = {10.1073/pnas.2301064120},
  file             = {:by-author/R/Rosenberg/2023_Rosenberg_e2301064120.pdf:PDF;:by-author/R/Rosenberg/2023_Rosenberg_e2301064120_suppl/pnas.2301064120.sapp.pdf:PDF;:by-author/R/Rosenberg/2023_Rosenberg_e2301064120_suppl/pnas.2301064120.sd01.txt:Text},
  keywords         = {Bioinformatics; Dihedral Angles; Protein Structure; Ramachandran Plot},
  modificationdate = {2024-04-08T14:04:08},
  owner            = {saulius},
  publisher        = {Proceedings of the National Academy of Sciences},
}

@Article{Lipska2023,
  author           = {Lipska, Agnieszka G. and Sieradzan, Adam K. and Atmaca, Sümeyye and Czaplewski, Cezary and Liwo, Adam},
  journal          = {The Journal of Physical Chemistry Letters},
  title            = {Toward consistent physics-based modeling of local backbone structures and chirality change of proteins in coarse-grained approaches},
  year             = {2023},
  issn             = {1948-7185},
  month            = oct,
  number           = {44},
  pages            = {9824--9833},
  volume           = {14},
  creationdate     = {2024-03-26T15:24:39},
  doi              = {10.1021/acs.jpclett.3c01988},
  file             = {:by-author/L/Lipska/2023_Lipska_9824.pdf:PDF;:by-author/L/Lipska/2023_Lipska_9824_suppl/jz3c01988_si_001.pdf:PDF},
  keywords         = {Bioinformatics; Chirality; Dihedral Angles; Proteins},
  modificationdate = {2024-03-26T20:56:01},
  owner            = {saulius},
  publisher        = {American Chemical Society (ACS)},
}

@Article{Lawson2024,
  author           = {Lawson, Catherine L. and Berman, Helen M. and Chen, Li and Vallat, Brinda and Zirbel, Craig L.},
  journal          = {Nucleic acids research},
  title            = {The {N}ucleic {A}cid {K}nowledgebase: a new portal for 3{D} structural information about nucleic acids.},
  year             = {2024},
  issn             = {1362-4962},
  month            = jan,
  pages            = {D245--D254},
  volume           = {52},
  abstract         = {The Nucleic Acid Knowledgebase (nakb.org) is a new data resource, updated weekly, for experimentally determined 3D structures containing DNA and/or RNA nucleic acid polymers and their biological assemblies. NAKB indexes nucleic acid-containing structures derived from all major structure determination methods (X-ray, NMR and EM), including all held by the Protein Data Bank (PDB). As the planned successor to the Nucleic Acid Database (NDB), NAKB's design preserves all functionality of the NDB and provides novel nucleic acid-centric content, including structural and functional annotations, as well as annotations from and links to external resources. A variety of custom interactive tools have been developed to enable rapid exploration and drill-down of NAKB's content.},
  chemicals        = {DNA, Nucleic Acids, RNA},
  citation-subset  = {IM},
  completed        = {2024-01-11},
  country          = {England},
  creationdate     = {2024-03-26T20:54:53},
  doi              = {10.1093/nar/gkad957},
  file             = {:by-author/L/Lawson/2024_Lawson_D245.pdf:PDF},
  issn-linking     = {0305-1048},
  issue            = {D1},
  keywords         = {DNA, Chemistry; Knowledge Bases; Nucleic Acid Conformation; Nucleic Acids, Genetics; RNA, Chemistry},
  modificationdate = {2024-03-26T20:57:38},
  nlm-id           = {0411011},
  owner            = {saulius},
  pii              = {7416380},
  pmc              = {PMC10767938},
  pmid             = {37953312},
  pubmodel         = {Print},
  pubstate         = {ppublish},
  revised          = {2024-01-11},
}

@Article{Makki2023,
  author           = {Makki, Hesam and Burke, Colm A. and Troisi, Alessandro},
  journal          = {The journal of physical chemistry letters},
  title            = {Microstructural model of indacenodithiophene- co -benzothiadiazole polymer: π-crossing interactions and their potential impact on charge transport},
  year             = {2023},
  issn             = {1948-7185},
  month            = oct,
  pages            = {8867--8873},
  volume           = {14},
  abstract         = {Morphological and electronic properties of indacenodithiophene- co -benzothiadiazole (IDTBT) copolymer with varying molecular weights are calculated through combined molecular dynamics (MD) and quantum chemical (QC) methods. Our study focuses on the polymer chain arrangements, interchain connectivity pathways, and interplay between morphological and electronic structure properties of IDTBT. Our models, which are verified against GIWAXS measurements, show a considerable number of BT-BT π-π interactions with a (preferential) perpendicular local orientation of polymer chains due to the steric hindrance of bulky side chains around IDT. Although our models predict a noncrystalline structure for IDTBT, the BT-BT (interchain) crossing points show a considerable degree of short-range order in spatial arrangement which most likely result in a mesh-like structure for the polymer and provide efficient pathways for interchain charge transport.},
  citation-subset  = {IM},
  country          = {United States},
  creationdate     = {2024-03-26T21:07:50},
  doi              = {10.1021/acs.jpclett.3c02305},
  file             = {:by-author/M/Makki/2023_Makki_8867.pdf:PDF;:by-author/M/Makki/2023_Makki_8867_suppl.pdf:PDF},
  issn-linking     = {1948-7185},
  issue            = {39},
  keywords         = {Dihedral Angles; Semiconducting Polymers; Simulation; Torsion Angles},
  modificationdate = {2024-04-04T09:29:44},
  nlm-id           = {101526034},
  owner            = {saulius},
  pmc              = {PMC10561260},
  pmid             = {37756473},
  pubmodel         = {Print-Electronic},
  pubstate         = {ppublish},
  revised          = {2023-10-11},
}

@Article{Liebschner2023,
  author           = {Liebschner, Dorothee and Moriarty, Nigel W. and Poon, Billy K. and Adams, Paul D.},
  journal          = {Acta crystallographica. Section D, Structural biology},
  title            = {In situ ligand restraints from quantum-mechanical methods.},
  year             = {2023},
  issn             = {2059-7983},
  month            = feb,
  pages            = {100--110},
  volume           = {79},
  abstract         = {In macromolecular crystallographic structure refinement, ligands present challenges for the generation of geometric restraints due to their large chemical variability, their possible novel nature and their specific interaction with the binding pocket of the protein. Quantum-mechanical approaches are useful for providing accurate ligand geometries, but can be plagued by the number of minima in flexible molecules. In an effort to avoid these issues, the Quantum Mechanical Restraints (QMR) procedure optimizes the ligand geometry in situ, thus accounting for the influence of the macromolecule on the local energy minima of the ligand. The optimized ligand geometry is used to generate target values for geometric restraints during the crystallographic refinement. As demonstrated using a sample of >2330 ligand instances in >1700 protein-ligand models, QMR restraints generally result in lower deviations from the target stereochemistry compared with conventionally generated restraints. In particular, the QMR approach provides accurate torsion restraints for ligands and other entities.},
  chemicals        = {Ligands, Proteins},
  citation-subset  = {IM},
  completed        = {2023-02-13},
  country          = {United States},
  creationdate     = {2024-03-26T21:15:50},
  doi              = {10.1107/S2059798323000025},
  file             = {:by-author/L/Liebschner/2023_Liebschner_100.pdf:PDF},
  issn-linking     = {2059-7983},
  issue            = {Pt 2},
  keywords         = {Crystallography, X-Ray; Ligand Restraints; Ligands; Macromolecular Crystallography; Models, Molecular; Protein Conformation; Proteins, Chemistry; Quantum Mechanical Restraints; Quantum Mechanics (QM); Refinement; Software},
  modificationdate = {2024-03-26T21:17:31},
  nlm-id           = {101676043},
  owner            = {saulius},
  pii              = {S2059798323000025},
  pmc              = {PMC9912925},
  pmid             = {36762856},
  pubmodel         = {Print-Electronic},
  pubstate         = {ppublish},
  revised          = {2023-02-15},
}

@Article{Li2022b,
  author           = {Li, Jicun and Song, Xinrui and Li, Pinyuan and Herzfeld, Judith},
  journal          = {The journal of physical chemistry. A},
  title            = {A carbon is a carbon is a carbon: orbital-free simulations of hydrocarbon chemistry without resort to atom types},
  year             = {2022},
  issn             = {1520-5215},
  month            = nov,
  pages            = {8468--8475},
  volume           = {126},
  abstract         = {Semiclassical electrons (aka Lewis dots) have been a mainstay of chemists' thinking about molecular structure, polarizability, and reactivity for over a century. This utility has motivated the development of a corresponding quantitative description. Here we devise pairwise potentials that describe the behavior of valence electron pairs in hydrocarbons, including those in single, double, bridge, and bent bonds of linear, branched, and cyclic compounds, including anionic and cationic states. Beyond predicting structures and energies, the new subatomistic force field, dubbed LEWIS-B, efficiently simulates carbocation addition to a double bond and cation migration to a neighboring carbon. A crucial feature of the semiclassical electrons is variable spread, a fourth degree of freedom in addition to three Cartesian coordinates. In spontaneously adapting to different environments, the spread provides a signature of electron stability, with more contracted clouds where the electron interactions are favorable and expanded clouds where electrons are less tightly held. In addition, the pair potentials provide insight into the subtle trade-offs that govern isomerizations and reactions.},
  citation-subset  = {IM},
  country          = {United States},
  creationdate     = {2024-03-26T21:32:54},
  doi              = {10.1021/acs.jpca.2c05338},
  file             = {:by-author/L/Li/2022_Li_8468.pdf:PDF;:by-author/L/Li/2022_Li_8468_suppl/jp2c05338_si_001.pdf:PDF;:by-author/L/Li/2022_Li_8468_suppl/jp2c05338_si_002.txt:Text},
  issn-linking     = {1089-5639},
  issue            = {45},
  keywords         = {Lewis Theory; Quantitatibe Semi-classical Description; Valence Bond Theory},
  modificationdate = {2024-03-26T21:38:11},
  nlm-id           = {9890903},
  owner            = {saulius},
  pmc              = {PMC9677428},
  pmid             = {36332635},
  pubmodel         = {Print-Electronic},
  pubstate         = {ppublish},
  revised          = {2022-11-23},
}

@Article{Reymond2015,
  author           = {Reymond, Jean-Louis},
  journal          = {Accounts of Chemical Research},
  title            = {The {C}hemical {S}pace {P}roject},
  year             = {2015},
  issn             = {1520-4898},
  month            = feb,
  number           = {3},
  pages            = {722--730},
  volume           = {48},
  creationdate     = {2024-03-31T16:24:42},
  doi              = {10.1021/ar500432k},
  file             = {:by-author/R/Reymond/2015_Reymond_722.pdf:PDF},
  keywords         = {Biological Databases; Database; Molecules; Organic Compounds; Pharmacophores; Receptors; Scientific Databases},
  modificationdate = {2024-03-31T16:38:13},
  owner            = {saulius},
  publisher        = {American Chemical Society (ACS)},
}

@Article{Visini2017,
  author           = {Visini, Ricardo and Awale, Mahendra and Reymond, Jean-Louis},
  journal          = {Journal of chemical information and modeling},
  title            = {Fragment database {FDB}-17.},
  year             = {2017},
  issn             = {1549-960X},
  month            = apr,
  pages            = {700--709},
  volume           = {57},
  abstract         = {To better understand chemical space we recently enumerated the database GDB-17 containing 166.4 billion possible molecules up to 17 atoms of C, N, O, S and halogen following the simple rules of chemical stability and synthetic feasibility. However, due to the combinatorial explosion caused by systematic enumeration GDB-17 is strongly biased toward the largest, functionally and stereochemically most complex molecules and far too large for most virtual screening tools. Herein we selected a much smaller subset of GDB-17, called the fragment database FDB-17, which contains 10 million fragmentlike molecules evenly covering a broad value range for molecular size, polarity, and stereochemical complexity. The database is available at www.gdb.unibe.ch for download and free use, together with an interactive visualization application and a Web-based nearest neighbor search tool to facilitate the selection of new fragment-sized molecules for chemical synthesis.},
  citation-subset  = {IM},
  completed        = {2017-09-21},
  country          = {United States},
  creationdate     = {2024-03-31T16:37:13},
  doi              = {10.1021/acs.jcim.7b00020},
  file             = {:by-author/V/Visini/2017_Visini_700.pdf:PDF},
  issn-linking     = {1549-9596},
  issue            = {4},
  keywords         = {Algorithms; Biological Databases; Database; Databases, Pharmaceutical; Drug Evaluation, Preclinical; Drug Stability; Informatics, Methods; Molecules; Organic Compounds; Pharmacophores; Receptors; Scientific Databases},
  modificationdate = {2024-03-31T16:40:40},
  nlm-id           = {101230060},
  owner            = {saulius},
  pmid             = {28375006},
  pubmodel         = {Print-Electronic},
  pubstate         = {ppublish},
  revised          = {2018-02-27},
}

@Presentation{Wolverton2016,
  author           = {C. Wolverton},
  title            = {The {O}pen {Q}uantum {M}aterials {D}atabase ({OQMD}): features and applications},
  year             = {2016},
  organization     = {Department of Materials Science and Engineering},
  school           = {Northwestern University},
  creationdate     = {2024-04-02T07:12:40},
  file             = {:by-author/W/Wolverton/2016_Wolverton_The Open Quantum Materials Database (OQMD)_ Features and Applications.pdf:PDF},
  keywords         = {Computational Materials Science; Databases; Density Functional Theory (DFT); Materials Science; OQMD; Open Data; Scientific Databases},
  modificationdate = {2024-04-02T07:16:02},
  owner            = {saulius},
  url              = {https://chimad.northwestern.edu/docs/DDD_WS_II/11_Wolverton_The_OQMD_Vinay_Logan.pdf},
}

@Article{Hasanbasri2024,
  author           = {Hasanbasri, Zikri and Tessmer, Maxx H. and Stoll, Stefan and Saxena, Sunil},
  journal          = {Physical chemistry chemical physics : PCCP},
  title            = {Modeling of {C}u({II})-based protein spin labels using rotamer libraries.},
  year             = {2024},
  issn             = {1463-9084},
  month            = feb,
  pages            = {6806--6816},
  volume           = {26},
  abstract         = {The bifunctional spin label double-histidine copper-(II) capped with nitrilotriacetate [dHis-Cu(II)-NTA], used in conjunction with electron paramagnetic resonance (EPR) methods can provide high-resolution distance data for investigating protein structure and backbone conformational diversity. Quantitative utilization of this data is limited due to a lack of rapid and accurate dHis-Cu(II)-NTA modeling methods that can be used to translate experimental data into modeling restraints. Here, we develop two dHis-Cu(II)-NTA rotamer libraries using a set of recently published molecular dynamics simulations and a semi-empirical meta-dynamics-based conformational ensemble sampling tool for use with the recently developed chiLife bifunctional spin label modeling method. The accuracy of both the libraries and the modeling method are tested by comparing model predictions to experimentally determined distance distributions. We show that this method is accurate with absolute deviation between the predicted and experimental modes between 0.0-1.2 Å with an average of 0.6 Å over the test data used. In doing so, we also validate the generality of the chiLife bifunctional label modeling method. Taken together, the increased structural resolution and modeling accuracy of dHis-Cu(II)-NTA over other spin labels promise improvements in the accuracy and resolution of protein models by EPR.},
  chemicals        = {Spin Labels, Copper, Proteins},
  citation-subset  = {IM},
  comment          = {Found in the EuropePMC search: https://europepmc.org/betaSearch?query=protein%20ligand%20dihedral%20angles [accessed 2024-04-03T20:14+03:00, 7256 results]},
  completed        = {2024-02-23},
  country          = {England},
  creationdate     = {2024-04-03T20:13:03},
  doi              = {10.1039/d3cp05951k},
  file             = {:by-author/H/Hasanbasri/2024_Hasanbasri_6806.pdf:PDF},
  issn-linking     = {1463-9076},
  issue            = {8},
  keywords         = {Copper, Chemistry; Dihedral Angles; Electron Paramagnetic Resonance (EPR); Electron Spin Resonance Spectroscopy, Methods; Molecular Dynamics Simulation; Plasticity of Proteins; Proteins, Chemistry; Spin Labels},
  modificationdate = {2024-04-03T20:17:56},
  nlm-id           = {100888160},
  owner            = {saulius},
  pmc              = {PMC10883468},
  pmid             = {38324256},
  pubmodel         = {Electronic},
  pubstate         = {epublish},
  revised          = {2024-02-24},
}

@Article{Cata2024,
  author           = {Căta, Adina and Ienaşcu, Ioana Maria Carmen and Frum, Adina and Ursu, Daniel and Svera, Paula and Orha, Corina and Rusu, Gerlinde and Chiș, Adriana Aurelia and Dobrea, Carmen Maximiliana and Morgovan, Claudiu and Pop, Oana-Raluca},
  journal          = {Pharmaceutics},
  title            = {Preparation and characterization of a novel salicin-cyclodextrin complex},
  year             = {2024},
  issn             = {1999-4923},
  month            = mar,
  pages            = {369},
  volume           = {16},
  abstract         = {Bioactive compounds extracted from plants can provide wide health benefits. However, some molecules have limited applications as pharmaceuticals due to their limited solubility, poor bioavailability, and low stability when exposed to environmental factors. Their integration in formulations that can deliver them to physiological targets while preserving their biological activity can enhance their usage in improving human health. This research provides a delivery system design to enhance the solubility, stability and to mask the bitter taste of salicin. Thus, a novel salicin-β-cyclodextrin complex was prepared and analyzed by X-ray diffraction, scanning electron microscopy, thermogravimetric analysis, FTIR, Raman and UV-Vis spectroscopy. The analytical and computational methods provided clear and distinct evidence for inclusion of salicin within the β-cyclodextrin cavity and brought important findings for the characterization of the inclusion complex. The present study showed that salicin and β-cyclodextrin can form inclusion complexes, both in solution and in solid state, and that the inclusion of salicin in the cavity of β-cyclodextrin leads to the improvement of its solubility and stability. Thus, the study communicates both qualitative and quantitative knowledge about the preparation of a new salicin-β-cyclodextrin inclusion complex suggesting its potential applications in pharmaceutical industry and medical sciences, as formulations with better compliance for the patient, with increased bioavailability, and easier control of dosage.},
  comment          = {Found in the EuropePMC search: https://europepmc.org/betaSearch?query=protein%20ligand%20dihedral%20angles [accessed 2024-04-03T20:14+03:00, 7256 results]},
  country          = {Switzerland},
  creationdate     = {2024-04-03T20:19:04},
  doi              = {10.3390/pharmaceutics16030369},
  file             = {:by-author/C/Căta/2024_Căta_369.pdf:PDF},
  issn-linking     = {1999-4923},
  issue            = {3},
  keywords         = {ADF 2014; ADF Modeling Suite; Anti-inflammatory; BLYP/TZP Level of Theory; Bioactive Compounds; Bioavailability; Chem 3D; ChemBioDraw Ultra 14; Dihedral Angles; HOMO; LUMO; Molecular Modelling; Phytochemicals; Salicin; β-cyclodextrin},
  modificationdate = {2024-04-03T20:26:08},
  nlm-id           = {101534003},
  owner            = {saulius},
  pii              = {369},
  pmc              = {PMC10976097},
  pmid             = {38543263},
  pubmodel         = {Electronic},
  pubstate         = {epublish},
  revised          = {2024-03-30},
}

@Article{Liu2023a,
  author           = {Liu, Kaifeng and Guo, Fangfang and Ma, Yingying and Yu, Xiangyu and Fu, Xueqi and Li, Wannan and Han, Weiwei},
  journal          = {International journal of molecular sciences},
  title            = {Functionalized fullerene potentially inhibits {SARS}-{CoV}-2 infection by modulating spike protein conformational changes},
  year             = {2023},
  issn             = {1422-0067},
  month            = sep,
  pages            = {14471},
  volume           = {24},
  abstract         = {The disease of SARS-CoV-2 has caused considerable morbidity and mortality globally. Spike proteins on the surface of SARS-CoV-2 allow it to bind with human cells, leading to infection. Fullerenes and their derivatives are promising SARS-CoV-2 inhibitors and drug-delivery vehicles. In this study, Gaussian accelerated molecular dynamics simulations and the Markov state model were employed to delve into the inhibitory mechanism of Fullerene-linear-polyglycerol-b-amine sulfate (F-LGPS) on spike proteins. During the study, it was discovered that fullerene derivatives can operate at the interface of the receptor-binding domain (RBD) and the N-terminal domain (NTD), keeping structural domains in a downward conformation. It was also observed that F-LGPS demonstrated superior inhibitory effects on the XBB variant in comparison to the wild-type variant. This study yielded invaluable insights for the potential development of efficient therapeutics targeting the spike protein of SARS-CoV-2.},
  chemicals        = {Fullerenes, spike protein, SARS-CoV-2, Spike Glycoprotein, Coronavirus},
  citation-subset  = {IM},
  comment          = {Found in the EuropePMC search: https://europepmc.org/betaSearch?query=protein%20ligand%20dihedral%20angles [accessed 2024-04-03T20:14+03:00, 7256 results]},
  completed        = {2023-11-01},
  country          = {Switzerland},
  creationdate     = {2024-04-03T20:27:04},
  doi              = {10.3390/ijms241914471},
  file             = {:by-author/L/Liu/2023_Liu_14471.pdf:PDF},
  issn-linking     = {1422-0067},
  issue            = {19},
  keywords         = {COVID-19; Dihedral Angles; Fullerenes, Pharmacology; Functionalized Fullerene; Humans; Markov State Model; Molecular Dynamics Simulation; Protein Binding; SARS-CoV-2; Spike Glycoprotein, Coronavirus; Sulfated Polysaccharide},
  modificationdate = {2024-04-03T20:30:09},
  nlm-id           = {101092791},
  owner            = {saulius},
  pii              = {14471},
  pmc              = {PMC10572755},
  pmid             = {37833919},
  pubmodel         = {Electronic},
  pubstate         = {epublish},
  revised          = {2023-11-01},
}

@Article{Procacci2023,
  author           = {Procacci, Piero},
  journal          = {Journal of chemical theory and computation},
  title            = {Dealing with induced fit, conformational selection, and secondary poses in molecular dynamics simulations for reliable free energy predictions},
  year             = {2023},
  issn             = {1549-9626},
  month            = dec,
  pages            = {8942--8954},
  volume           = {19},
  abstract         = {In this study, we have tested the performance of standard molecular dynamics (MD) simulations, replicates of shorter standard MD simulations, and Hamiltonian Replica Exchange (HREM) simulations for the sampling of two macrocyclic hosts for guest delivery, characterized by induced fit (phenyl-based host) and conformation selection (naphthyl-based host) and of the ODR-BRD4(I) drug-receptor system where the ligand can assume two main poses. For the optimization of the HREM simulation, we have proposed and tested an on-the-fly iterative scheme for equalizing the acceptance ratio along the replica progression at a constant replica number resulting in a moderate impact of the sampling efficiency. Concerning standard MD, we have found that, while splitting the total allocated simulation time in short MD replicates can reproduce the sampling efficiency of HREM in the phenyl-based host and in the ODR-BRD4(I) complex, in the naphthyl-based macrocycle, characterized by long-lived metastable states, enhanced sampling techniques are the only viable alternative for a reliable canonical sampling of the rugged conformational landscape.},
  citation-subset  = {IM},
  comment          = {Found in the EuropePMC search: https://europepmc.org/betaSearch?query=protein%20ligand%20dihedral%20angles [accessed 2024-04-03T20:14+03:00, 7256 results]},
  country          = {United States},
  creationdate     = {2024-04-03T20:29:30},
  doi              = {10.1021/acs.jctc.3c00867},
  file             = {:by-author/P/Procacci/2023_Procacci_8942.pdf:PDF},
  issn-linking     = {1549-9618},
  issue            = {23},
  keywords         = {Alchemical States; Bennett Acceptance Ratio; Binding Free Energy; Dihedral Angles; Drug-receptor System; Free Energy Perturbation (FEP); Hamiltonian Replica Exchange (HREM); Ligand Binding Pose; Ligand Poses; Molecular Dynamics (MD); Solvation Free Energy},
  modificationdate = {2024-04-03T20:39:18},
  nlm-id           = {101232704},
  owner            = {saulius},
  pmc              = {PMC10720345},
  pmid             = {38037326},
  pubmodel         = {Print-Electronic},
  pubstate         = {ppublish},
  revised          = {2023-12-16},
}

@Article{Zinovjev2024,
  author           = {Zinovjev, Kirill and Guénon, Paul and Ramos-Guzmán, Carlos A. and Ruiz-Pernía, J. Javier and Laage, Damien and Tuñón, Iñaki},
  journal          = {Nature communications},
  title            = {Activation and friction in enzymatic loop opening and closing dynamics},
  year             = {2024},
  issn             = {2041-1723},
  month            = mar,
  pages            = {2490},
  volume           = {15},
  abstract         = {Protein loop dynamics have recently been recognized as central to enzymatic activity, specificity and stability. However, the factors controlling loop opening and closing kinetics have remained elusive. Here, we combine molecular dynamics simulations with string-method determination of complex reaction coordinates to elucidate the molecular mechanism and rate-limiting step for WPD-loop dynamics in the PTP1B enzyme. While protein conformational dynamics is often represented as diffusive motion hindered by solvent viscosity and internal friction, we demonstrate that loop opening and closing is activated. It is governed by torsional rearrangement around a single loop peptide group and by significant friction caused by backbone adjustments, which can dynamically trap the loop. Considering both torsional barrier and time-dependent friction, our calculated rate constants exhibit very good agreement with experimental measurements, reproducing the change in loop opening kinetics between proteins. Furthermore, we demonstrate the applicability of our results to other enzymatic loops, including the M20 DHFR loop, thereby offering prospects for loop engineering potentially leading to enhanced designs.},
  chemicals        = {Solvents},
  citation-subset  = {IM},
  comment          = {Found in the EuropePMC search: https://europepmc.org/betaSearch?query=protein%20ligand%20dihedral%20angles [accessed 2024-04-03T20:14+03:00, 7256 results]},
  completed        = {2024-03-22},
  country          = {England},
  creationdate     = {2024-04-03T20:36:11},
  doi              = {10.1038/s41467-024-46723-9},
  file             = {:by-author/Z/Zinovjev/2024_Zinovjev_2490.pdf:PDF},
  issn-linking     = {2041-1723},
  issue            = {1},
  keywords         = {Enzymatic Loops; Friction; Kinetics; Molecular Dynamics Simulation; Protein Conformation; Protein Loops; Solvents},
  modificationdate = {2024-04-03T20:38:20},
  nlm-id           = {101528555},
  owner            = {saulius},
  pii              = {2490},
  pmc              = {PMC10955111},
  pmid             = {38509080},
  pubmodel         = {Electronic},
  pubstate         = {epublish},
  revised          = {2024-03-23},
}

@Article{Galvelis2023,
  author           = {Galvelis, Raimondas and Varela-Rial, Alejandro and Doerr, Stefan and Fino, Roberto and Eastman, Peter and Markland, Thomas E. and Chodera, John D. and De Fabritiis, Gianni},
  journal          = {Journal of chemical information and modeling},
  title            = {{NNP/MM}: accelerating molecular dynamics simulations with machine learning potentials and molecular mechanics},
  year             = {2023},
  issn             = {1549-960X},
  month            = sep,
  pages            = {5701--5708},
  volume           = {63},
  abstract         = {Machine learning potentials have emerged as a means to enhance the accuracy of biomolecular simulations. However, their application is constrained by the significant computational cost arising from the vast number of parameters compared with traditional molecular mechanics. To tackle this issue, we introduce an optimized implementation of the hybrid method (NNP/MM), which combines a neural network potential (NNP) and molecular mechanics (MM). This approach models a portion of the system, such as a small molecule, using NNP while employing MM for the remaining system to boost efficiency. By conducting molecular dynamics (MD) simulations on various protein-ligand complexes and metadynamics (MTD) simulations on a ligand, we showcase the capabilities of our implementation of NNP/MM. It has enabled us to increase the simulation speed by ∼5 times and achieve a combined sampling of 1 μs for each complex, marking the longest simulations ever reported for this class of simulations.},
  chemicals        = {Ligands},
  citation-subset  = {IM},
  comment          = {Found in the EuropePMC search: https://europepmc.org/betaSearch?query=protein%20ligand%20dihedral%20angles [accessed 2024-04-03T20:14+03:00, 7256 results]},
  completed        = {2023-10-23},
  country          = {United States},
  creationdate     = {2024-04-03T20:39:56},
  doi              = {10.1021/acs.jcim.3c00773},
  file             = {:by-author/G/Galvelis/2023_Galvelis_5701.pdf:PDF},
  issn-linking     = {1549-9596},
  issue            = {18},
  keywords         = {Artificial Neural Networks (ANN); Ligands; Machine Learning (ML); Molecular Dynamics (MD); Molecular Dynamics Simulation; Neural Networks, Computer},
  mid              = {NIHMS1934564},
  modificationdate = {2024-04-03T20:43:12},
  nlm-id           = {101230060},
  owner            = {saulius},
  pmc              = {PMC10577237},
  pmid             = {37694852},
  pubmodel         = {Print-Electronic},
  pubstate         = {ppublish},
  revised          = {2024-01-05},
}

@Article{Markham2024,
  author           = {Markham, Lauren E. and Koelblen, Thomas and Chobanian, Harry R. and Follis, Ariele Viacava and Burris, Thomas P. and Micalizio, Glenn C.},
  journal          = {ACS central science},
  title            = {From functional fatty acids to potent and selective natural-product-inspired mimetics via conformational profiling},
  year             = {2024},
  issn             = {2374-7943},
  month            = feb,
  pages            = {477--486},
  volume           = {10},
  abstract         = {Fatty acids play important signaling roles in biology, albeit typically lacking potency or selectivity, due to their substantial conformational flexibility. While being recognized as having properties of potentially great value as therapeutics, it is often the case that the functionally relevant conformation of the natural fatty acid is not known, thereby complicating efforts to develop natural-product-inspired ligands that have similar functional properties along with enhanced potency and selectivity profiles. In other words, without structural information associated with a particular functional relationship and the hopelessly unbiased conformational preferences of the endogenous ligand, one is molecularly ill-informed regarding the precise ligand-receptor interactions that play a role in driving the biological activity of interest. To address this problem, a molecular strategy to query the relevance of distinct subpopulations of fatty acid conformers has been established through "conformational profiling", a process whereby a unique collection of chiral and conformationally constrained fatty acids is employed to deconvolute beneficial structural features that impart natural-product-inspired function. Using oleic acid as an example because it is known to engage a variety of receptors, including GPR40, GPR120, and TLX, a 24-membered collection of mimetics was designed and synthesized. It was then demonstrated that this collection contained members that have enhanced potency and selectivity profiles, with some being clearly biased for engagement of the GPCRs GPR40 and GPR120 while others were identified as potent and selective modulators of the nuclear receptor TLX. A chemical synthesis strategy that exploited the power of modern technology for stereoselective synthesis was critical to achieving success, establishing a common sequence of bond-forming reactions to access a disparate collection of chiral mimetics, whose conformational preferences are impacted by the nature of stereodefined moieties differentially positioned about the C (18)skeleton of the parent fatty acid. Overall, this study establishes a foundation to fuel future programs aimed at developing natural-product-inspired fatty acid mimetics as valuable tools in chemical biology and potential therapeutic leads.},
  comment          = {Found in the EuropePMC search: https://europepmc.org/betaSearch?query=protein%20ligand%20dihedral%20angles [accessed 2024-04-03T20:14+03:00, 7256 results]},
  country          = {United States},
  creationdate     = {2024-04-03T20:52:52},
  doi              = {10.1021/acscentsci.3c01155},
  file             = {:by-author/M/Markham/2024_Markham_477.pdf:PDF},
  issn-linking     = {2374-7943},
  issue            = {2},
  keywords         = {Dihedral Angles; Fatty Acids; Molecular Modelling},
  modificationdate = {2024-04-03T21:01:25},
  nlm-id           = {101660035},
  owner            = {saulius},
  pmc              = {PMC10906247},
  pmid             = {38435518},
  pubmodel         = {Electronic-eCollection},
  pubstate         = {epublish},
  revised          = {2024-03-05},
}

@Article{MejiaRodriguez2023,
  author           = {Mejia-Rodriguez, Daniel and Kim, Hoshin and Sadler, Natalie and Li, Xiaolu and Bohutskyi, Pavlo and Valiev, Marat and Qian, Wei-Jun and Cheung, Margaret S.},
  journal          = {Protein science : a publication of the Protein Society},
  title            = {{PTM-Psi}: A python package to facilitate the computational investigation of post-translational modification on protein structures and their impacts on dynamics and functions},
  year             = {2023},
  issn             = {1469-896X},
  month            = dec,
  pages            = {e4822},
  volume           = {32},
  abstract         = {Post-translational modification (PTM) of a protein occurs after it has been synthesized from its genetic template, and involves chemical modifications of the protein's specific amino acid residues. Despite of the central role played by PTM in regulating molecular interactions, particularly those driven by reversible redox reactions, it remains challenging to interpret PTMs in terms of protein dynamics and function because there are numerous combinatorially enormous means for modifying amino acids in response to changes in the protein environment. In this study, we provide a workflow that allows users to interpret how perturbations caused by PTMs affect a protein's properties, dynamics, and interactions with its binding partners based on inferred or experimentally determined protein structure. This Python-based workflow, called PTM-Psi, integrates several established open-source software packages, thereby enabling the user to infer protein structure from sequence, develop force fields for non-standard amino acids using quantum mechanics, calculate free energy perturbations through molecular dynamics simulations, and score the bound complexes via docking algorithms. Using the S-nitrosylation of several cysteines on the GAP2 protein as an example, we demonstrated the utility of PTM-Psi for interpreting sequence-structure-function relationships derived from thiol redox proteomics data. We demonstrate that the S-nitrosylated cysteine that is exposed to the solvent indirectly affects the catalytic reaction of another buried cysteine over a distance in GAP2 protein through the movement of the two ligands. Our workflow tracks the PTMs on residues that are responsive to changes in the redox environment and lays the foundation for the automation of molecular and systems biology modeling.},
  chemicals        = {Cysteine, Proteins, Amino Acids},
  citation-subset  = {IM},
  comment          = {Found in the EuropePMC search: https://europepmc.org/betaSearch?query=protein%20ligand%20dihedral%20angles [accessed 2024-04-03T20:14+03:00, 7256 results]},
  completed        = {2023-11-29},
  country          = {United States},
  creationdate     = {2024-04-03T20:59:56},
  doi              = {10.1002/pro.4822},
  file             = {:by-author/M/Mejia-Rodriguez/2023_Mejia-Rodriguez_e4822.pdf:PDF},
  issn-linking     = {0961-8368},
  issue            = {12},
  keywords         = {Amino Acids, Metabolism; Cysteine, Metabolism; Dihedral Angles; Molecular Docking; Molecular Dynamics (MD); Protein Processing, Post-Translational; Proteins, Chemistry; Quantum Mechanics (QM); Redox Proteome; Software},
  modificationdate = {2024-04-03T21:10:16},
  nlm-id           = {9211750},
  owner            = {saulius},
  pii              = {e4822},
  pmc              = {PMC10659954},
  pmid             = {37902126},
  pubmodel         = {Print},
  pubstate         = {ppublish},
  revised          = {2023-12-02},
}

@Article{Huang2024,
  author           = {Huang, Lei and Xu, Tingyang and Yu, Yang and Zhao, Peilin and Chen, Xingjian and Han, Jing and Xie, Zhi and Li, Hailong and Zhong, Wenge and Wong, Ka-Chun and Zhang, Hengtong},
  journal          = {Nature communications},
  title            = {A dual diffusion model enables {3D} molecule generation and lead optimization based on target pockets},
  year             = {2024},
  issn             = {2041-1723},
  month            = mar,
  pages            = {2657},
  volume           = {15},
  abstract         = {Structure-based generative chemistry is essential in computer-aided drug discovery by exploring a vast chemical space to design ligands with high binding affinity for targets. However, traditional in silico methods are limited by computational inefficiency, while machine learning approaches face bottlenecks due to auto-regressive sampling. To address these concerns, we have developed a conditional deep generative model, PMDM, for 3D molecule generation fitting specified targets. PMDM consists of a conditional equivariant diffusion model with both local and global molecular dynamics, enabling PMDM to consider the conditioned protein information to generate molecules efficiently. The comprehensive experiments indicate that PMDM outperforms baseline models across multiple evaluation metrics. To evaluate the applications of PMDM under real drug design scenarios, we conduct lead compound optimization for SARS-CoV-2 main protease (M (pro)) and Cyclin-dependent Kinase 2 (CDK2), respectively. The selected lead optimization molecules are synthesized and evaluated for their in-vitro activities against CDK2, displaying improved CDK2 activity.},
  chemicals        = {pyromellitic acid dianhydride-2-hydroxyethyl methacrylate adduct, Anti-HIV Agents, Benzoates, Methacrylates},
  citation-subset  = {IM},
  comment          = {Found in the EuropePMC search: https://europepmc.org/betaSearch?query=protein%20ligand%20dihedral%20angles [accessed 2024-04-03T20:14+03:00, 7256 results]},
  completed        = {2024-03-28},
  country          = {England},
  creationdate     = {2024-04-03T21:11:24},
  doi              = {10.1038/s41467-024-46569-1},
  file             = {:by-author/H/Huang/2024_Huang_2657.pdf:PDF},
  issn-linking     = {2041-1723},
  issue            = {1},
  keywords         = {Anti-HIV Agents; Artificial Neural Networks (ANN); Benchmarking; Benzoates; Chemistry, Physical; Dihedral Angles; Drug Design; Machine Learning (ML); Methacrylates},
  modificationdate = {2024-04-03T21:13:14},
  nlm-id           = {101528555},
  owner            = {saulius},
  pii              = {2657},
  pmc              = {PMC10965937},
  pmid             = {38531837},
  pubmodel         = {Electronic},
  pubstate         = {epublish},
  revised          = {2024-03-29},
}

@Article{O’Shea2023,
  author           = {O’Shea, Jack M. and Richardson, Annis and Doerner, Peter and Wood, Christopher W.},
  journal          = {bioRxiv},
  title            = {Computational design of periplasmic binding protein biosensors guided by molecular dynamics},
  year             = {2023},
  month            = nov,
  comment          = {Found in the EuropePMC search: https://europepmc.org/betaSearch?query=protein%20ligand%20dihedral%20angles [accessed 2024-04-04T09:36+03:00, 7256 results]},
  creationdate     = {2024-04-04T09:41:38},
  doi              = {10.1101/2023.11.10.566541},
  file             = {:by-author/O/O’Shea/2023_O’Shea_Computational Design of Periplasmic Binding Protein Biosensors Guided by Molecular Dynamics.pdf:PDF},
  keywords         = {Dihedral Angles; Molecular Dynamics (MD)},
  modificationdate = {2024-04-04T09:44:22},
  owner            = {saulius},
  publisher        = {Cold Spring Harbor Laboratory},
}

@Article{Lu2024,
  author           = {Lu, Wei and Zhang, Jixian and Huang, Weifeng and Zhang, Ziqiao and Jia, Xiangyu and Wang, Zhenyu and Shi, Leilei and Li, Chengtao and Wolynes, Peter G. and Zheng, Shuangjia},
  journal          = {Nature communications},
  title            = {{DynamicBind}: predicting ligand-specific protein-ligand complex structure with a deep equivariant generative model},
  year             = {2024},
  issn             = {2041-1723},
  month            = feb,
  pages            = {1071},
  volume           = {15},
  abstract         = {While significant advances have been made in predicting static protein structures, the inherent dynamics of proteins, modulated by ligands, are crucial for understanding protein function and facilitating drug discovery. Traditional docking methods, frequently used in studying protein-ligand interactions, typically treat proteins as rigid. While molecular dynamics simulations can propose appropriate protein conformations, they're computationally demanding due to rare transitions between biologically relevant equilibrium states. In this study, we present DynamicBind, a deep learning method that employs equivariant geometric diffusion networks to construct a smooth energy landscape, promoting efficient transitions between different equilibrium states. DynamicBind accurately recovers ligand-specific conformations from unbound protein structures without the need for holo-structures or extensive sampling. Remarkably, it demonstrates state-of-the-art performance in docking and virtual screening benchmarks. Our experiments reveal that DynamicBind can accommodate a wide range of large protein conformational changes and identify cryptic pockets in unseen protein targets. As a result, DynamicBind shows potential in accelerating the development of small molecules for previously undruggable targets and expanding the horizons of computational drug discovery.},
  chemicals        = {Ligands, Proteins},
  citation-subset  = {IM},
  comment          = {Found in the EuropePMC search: https://europepmc.org/betaSearch?query=protein%20ligand%20dihedral%20angles [accessed 2024-04-04T09:36+03:00, 7256 results]},
  completed        = {2024-02-07},
  country          = {England},
  creationdate     = {2024-04-04T09:46:29},
  doi              = {10.1038/s41467-024-45461-2},
  file             = {:by-author/L/Lu/2024_Lu_1071.pdf:PDF},
  issn-linking     = {2041-1723},
  issue            = {1},
  keywords         = {Digedral Angles; Drug Discovery; Ligands; Machine Learning (ML); Molecular Docking Simulation; Molecular Dynamics Simulation; Protein Binding; Protein Conformation; Proteins, Metabolism},
  modificationdate = {2024-04-04T09:50:07},
  nlm-id           = {101528555},
  owner            = {saulius},
  pii              = {1071},
  pmc              = {PMC10844226},
  pmid             = {38316797},
  pubmodel         = {Electronic},
  pubstate         = {epublish},
  revised          = {2024-02-10},
}

@Article{Gadanecz2023,
  author           = {Gadanecz, Márton and Fazekas, Zsolt and Pálfy, Gyula and Karancsiné Menyhárd, Dóra and Perczel, András},
  journal          = {International journal of molecular sciences},
  title            = {{NMR}-chemical-shift-driven protocol reveals the cofactor-bound, complete structure of dynamic intermediates of the catalytic cycle of oncogenic {KRAS} {G12C} protein and the significance of the {Mg} (2+) ion},
  year             = {2023},
  issn             = {1422-0067},
  month            = jul,
  pages            = {12101},
  volume           = {24},
  abstract         = {In this work, catalytically significant states of the oncogenic G12C variant of KRAS, those of Mg (2+)-free and Mg (2+)-bound GDP-loaded forms, have been determined using CS-Rosetta software and NMR-data-driven molecular dynamics simulations. There are several Mg (2+)-bound G12C KRAS/GDP structures deposited in the Protein Data Bank (PDB), so this system was used as a reference, while the structure of the Mg (2+)-free but GDP-bound state of the RAS cycle has not been determined previously. Due to the high flexibility of the Switch-I and Switch-II regions, which also happen to be the catalytically most significant segments, only chemical shift information could be collected for the most important regions of both systems. CS-Rosetta was used to derive an "NMR ensemble" based on the measured chemical shifts, which, however, did not contain the nonprotein components of the complex. We developed a torsional restraint set for backbone torsions based on the CS-Rosetta ensembles for MD simulations, overriding the force-field-based parametrization in the presence of the reinserted cofactors. This protocol (csdMD) resulted in complete models for both systems that also retained the structural features and heterogeneity defined by the measured chemical shifts and allowed a detailed comparison of the Mg (2+)-bound and Mg (2+)-free states of G12C KRAS/GDP.},
  chemicals        = {Proto-Oncogene Proteins p21(ras)},
  citation-subset  = {IM},
  comment          = {Found in the EuropePMC search: https://europepmc.org/betaSearch?query=protein%20ligand%20dihedral%20angles [accessed 2024-04-04T09:36+03:00, 7256 results]},
  completed        = {2023-08-14},
  country          = {Switzerland},
  creationdate     = {2024-04-04T09:57:21},
  doi              = {10.3390/ijms241512101},
  file             = {:by-author/G/Gadanecz/2023_Gadanecz_12101.pdf:PDF},
  issn-linking     = {1422-0067},
  issue            = {15},
  keywords         = {Dihedral Angles; KRAS; Ligand Binding; Magnetic Resonance Imaging; Magnetic Resonance Spectroscopy; Metal Ions; Molecular Dynamics Simulation; Mutation; NMR Spectroscopy; Protein Dynamics; Protein Structure Determination; Proto-Oncogene Proteins {p}21(ras), Genetics},
  modificationdate = {2024-04-21T15:30:45},
  nlm-id           = {101092791},
  owner            = {saulius},
  pii              = {12101},
  pmc              = {PMC10418480},
  pmid             = {37569478},
  pubmodel         = {Electronic},
  pubstate         = {epublish},
  revised          = {2023-08-14},
}

@Article{Hayward2023,
  author           = {Hayward, Steven},
  journal          = {The protein journal},
  title            = {A retrospective on the development of methods for the analysis of protein conformational ensembles},
  year             = {2023},
  issn             = {1875-8355},
  month            = jun,
  pages            = {181--191},
  volume           = {42},
  abstract         = {Analysing protein conformational ensembles whether from molecular dynamics (MD) simulation or other sources for functionally relevant conformational changes can be very challenging. In the nineteen nineties dimensional reduction methods were developed primarily for analysing MD trajectories to determine dominant motions with the aim of understanding their relationship to function. Coarse-graining methods were also developed so the conformational change between two structures could be described in terms of the relative motion of a small number of quasi-rigid regions rather than in terms of a large number of atoms. When these methods are combined, they can characterize the large-scale motions inherent in a conformational ensemble providing insight into possible functional mechanism. The dimensional reduction methods first applied to protein conformational ensembles were referred to as Quasi-Harmonic Analysis, Principal Component Analysis and Essential Dynamics Analysis. A retrospective on the origin of these methods is presented, the relationships between them explained, and more recent developments reviewed.},
  chemicals        = {Proteins},
  citation-subset  = {IM},
  comment          = {Found in the EuropePMC search: https://europepmc.org/betaSearch?query=protein%20ligand%20dihedral%20angles [accessed 2024-04-04T09:36+03:00, 7256 results]},
  comment-saulius  = {Does not cite Grudinin for some reason... (?)},
  completed        = {2023-06-15},
  country          = {Netherlands},
  creationdate     = {2024-04-04T10:04:51},
  doi              = {10.1007/s10930-023-10113-9},
  file             = {:by-author/H/Hayward/2023_Hayward_181.pdf:PDF},
  issn-linking     = {1572-3887},
  issue            = {3},
  keywords         = {Collective Motions; Dihedral Angles; Domain Motions; Essential Dynamics; Molecular Dynamics (MD); Molecular Dynamics Simulation; Principal Component Analysis; Protein Conformation; Proteins, Chemistry; Quasi-Harmonic Analysis; Retrospective Studies; Review},
  modificationdate = {2024-04-04T10:08:05},
  nlm-id           = {101212092},
  owner            = {saulius},
  pii              = {10.1007/s10930-023-10113-9},
  pmc              = {PMC10264293},
  pmid             = {37072659},
  pubmodel         = {Print-Electronic},
  pubstate         = {ppublish},
  revised          = {2023-06-16},
}

@Article{Zhang2023,
  author           = {Zhang, Shuo and Liu, Yang and Xie, Lei},
  journal          = {Scientific reports},
  title            = {A universal framework for accurate and efficient geometric deep learning of molecular systems},
  year             = {2023},
  issn             = {2045-2322},
  month            = nov,
  pages            = {19171},
  volume           = {13},
  abstract         = {Molecular sciences address a wide range of problems involving molecules of different types and sizes and their complexes. Recently, geometric deep learning, especially Graph Neural Networks, has shown promising performance in molecular science applications. However, most existing works often impose targeted inductive biases to a specific molecular system, and are inefficient when applied to macromolecules or large-scale tasks, thereby limiting their applications to many real-world problems. To address these challenges, we present PAMNet, a universal framework for accurately and efficiently learning the representations of three-dimensional (3D) molecules of varying sizes and types in any molecular system. Inspired by molecular mechanics, PAMNet induces a physics-informed bias to explicitly model local and non-local interactions and their combined effects. As a result, PAMNet can reduce expensive operations, making it time and memory efficient. In extensive benchmark studies, PAMNet outperforms state-of-the-art baselines regarding both accuracy and efficiency in three diverse learning tasks: small molecule properties, RNA 3D structures, and protein-ligand binding affinities. Our results highlight the potential for PAMNet in a broad range of molecular science applications.},
  citation-subset  = {IM},
  comment          = {Found in the EuropePMC search: https://europepmc.org/betaSearch?query=protein%20ligand%20dihedral%20angles [accessed 2024-04-04T09:36+03:00, 7256 results]},
  country          = {England},
  creationdate     = {2024-04-04T10:16:22},
  doi              = {10.1038/s41598-023-46382-8},
  file             = {:by-author/Z/Zhang/2023_Zhang_19171.pdf:PDF},
  issn-linking     = {2045-2322},
  issue            = {1},
  keywords         = {Artificial Neural Networks (ANN); Deep Learning (DL); Geometric Deep Learning; Graph Neural Networks (GNN); Machine Learning (ML); Molecular Modelling},
  modificationdate = {2024-04-04T10:18:04},
  nlm-id           = {101563288},
  owner            = {saulius},
  pii              = {19171},
  pmc              = {PMC10628308},
  pmid             = {37932352},
  pubmodel         = {Electronic},
  pubstate         = {epublish},
  revised          = {2023-11-09},
}

@Article{Khuttan2024,
  author           = {Khuttan, Sheenam and Gallicchio, Emilio},
  journal          = {Journal of chemical theory and computation},
  title            = {What to make of zero: resolving the statistical noise from conformational reorganization in alchemical binding free energy estimates with metadynamics sampling},
  year             = {2024},
  issn             = {1549-9626},
  month            = feb,
  pages            = {1489--1501},
  volume           = {20},
  abstract         = {We introduce the self-relative binding free energy (self-RBFE) approach to evaluate the intrinsic statistical variance of dual-topology alchemical binding free energy estimators. The self-RBFE is the relative binding free energy between a ligand and a copy of the same ligand, and its true value is zero. Nevertheless, because the two copies of the ligand move independently, the self-RBFE value produced by a finite-length simulation fluctuates and can be used to measure the variance of the model. The results of this validation provide evidence that a significant fraction of the errors observed in benchmark studies reflect the statistical fluctuations of unconverged estimates rather than the models' accuracy. Furthermore, we find that ligand reorganization is a significant contributing factor to the statistical variance of binding free energy estimates and that metadynamics-accelerated conformational sampling of the torsional degrees of freedom of the ligand can drastically reduce the time to convergence.},
  citation-subset  = {IM},
  comment          = {Found in the EuropePMC search: https://europepmc.org/betaSearch?query=protein%20ligand%20dihedral%20angles [accessed 2024-04-04T09:36+03:00, 7256 results]},
  country          = {United States},
  creationdate     = {2024-04-04T10:28:43},
  doi              = {10.1021/acs.jctc.3c01250},
  file             = {:by-author/K/Khuttan/2024_Khuttan_1489.pdf:PDF},
  issn-linking     = {1549-9618},
  issue            = {3},
  keywords         = {Alchemical Binding Free Energy; Dihedral Angles; Metadynamics; Molecular Dynamics (MD)},
  modificationdate = {2024-04-04T10:32:10},
  nlm-id           = {101232704},
  owner            = {saulius},
  pmc              = {PMC10867849},
  pmid             = {38252868},
  pubmodel         = {Print-Electronic},
  pubstate         = {ppublish},
  revised          = {2024-02-17},
}

@Article{Hirata2023,
  author           = {Hirata, Fumio},
  journal          = {Molecules (Basel, Switzerland)},
  title            = {Structural fluctuation, relaxation, and folding of protein: an approach based on the combined {G}eneralized {L}angevin and {RISM/3D-RISM} theories},
  year             = {2023},
  issn             = {1420-3049},
  month            = oct,
  pages            = {7351},
  volume           = {28},
  abstract         = {In 2012, Kim and Hirata derived two generalized Langevin equations (GLEs) for a biomolecule in water, one for the structural fluctuation of the biomolecule and the other for the density fluctuation of water, by projecting all the mechanical variables in phase space onto the two dynamic variables: the structural fluctuation defined by the displacement of atoms from their equilibrium positions, and the solvent density fluctuation. The equation has an expression similar to the classical Langevin equation (CLE) for a harmonic oscillator, possessing terms corresponding to the restoring force proportional to the structural fluctuation, as well as the frictional and random forces. However, there is a distinct difference between the two expressions that touches on the essential physics of the structural fluctuation, that is, the force constant, or Hessian, in the restoring force. In the CLE, this is given by the second derivative of the potential energy among atoms in a protein. So, the quadratic nature or the harmonicity is only valid at the minimum of the potential surface. On the contrary, the linearity of the restoring force in the GLE originates from the projection of the water's degrees of freedom onto the protein's degrees of freedom . Taking this into consideration, Kim and Hirata proposed an ansatz for the Hessian matrix . The ansatz is used to equate the Hessian matrix with the second derivative of the free-energy surface or the potential of the mean force of a protein in water, defined by the sum of the potential energy among atoms in a protein and the solvation free energy. Since the free energy can be calculated from the molecular mechanics and the RISM/3D-RISM theory, one can perform an analysis similar to the normal mode analysis (NMA) just by diagonalizing the Hessian matrix of the free energy. This method is referred to as the Generalized Langevin Mode Analysis (GLMA). This theory may be realized to explore a variety of biophysical processes, including protein folding, spectroscopy, and chemical reactions. The present article is devoted to reviewing the development of this theory, and to providing perspective in exploring life phenomena.},
  chemicals        = {Proteins, Solvents, Water},
  citation-subset  = {IM},
  comment          = {Found in the EuropePMC search: https://europepmc.org/betaSearch?query=protein%20ligand%20dihedral%20angles [accessed 2024-04-04T09:36+03:00, 7256 results]},
  completed        = {2023-11-15},
  country          = {Switzerland},
  creationdate     = {2024-04-04T10:38:47},
  doi              = {10.3390/molecules28217351},
  file             = {:by-author/H/Hirata/2023_Hirata_7351.pdf:PDF},
  issn-linking     = {1420-3049},
  issue            = {21},
  keywords         = {Central Limiting Theorem; Gaussian Fluctuation; Generalized Langevin Theory; Harmonic Analysis; Hessian; Isomerization; Langevin Molecular Dynamics; Molecular Dynamics (MD); Molecular Dynamics Simulation; Protein Folding; Proteins, Chemistry; RISM/3D-RISM; Review; Solvation Free Energy; Solvents, Chemistry; Structural Fluctuation; Thermodynamics; Water, Chemistry},
  modificationdate = {2024-04-04T10:46:37},
  nlm-id           = {100964009},
  owner            = {saulius},
  pii              = {7351},
  pmc              = {PMC10647392},
  pmid             = {37959769},
  pubmodel         = {Electronic},
  pubstate         = {epublish},
  revised          = {2023-11-17},
}

@Article{GraciaCarmona2023,
  author           = {Gracia Carmona, Oriol and Oostenbrink, Chris},
  journal          = {Journal of chemical theory and computation},
  title            = {Flexible gaussian accelerated molecular dynamics to enhance biological sampling},
  year             = {2023},
  issn             = {1549-9626},
  month            = sep,
  pages            = {6521--6531},
  volume           = {19},
  abstract         = {Molecular dynamics simulations often struggle to obtain sufficient sampling to study complex molecular events due to high energy barriers separating the minima of interest. Multiple enhanced sampling techniques have been developed and improved over the years to tackle this issue. Gaussian accelerated molecular dynamics (GaMD) is a recently developed enhanced sampling technique that works by adding a biasing potential, lifting the energy landscape up, and decreasing the height of its barriers. GaMD allows one to increase the sampling of events of interest without the need of a priori knowledge of the system or the relevant coordinates. All required acceleration parameters can be obtained from a previous search run. Upon its development, several improvements for the methodology have been proposed, among them selective GaMD in which the boosting potential is selectively applied to the region of interest. There are currently four selective GaMD methods that have shown promising results. However, all of these methods are constrained on the number, location, and scenarios in which this selective boosting potential can be applied to ligands, peptides, or protein-protein interactions. In this work, we showcase a GROMOS implementation of the GaMD methodology with a fully flexible selective GaMD approach that allows the user to define, in a straightforward way, multiple boosting potentials for as many regions as desired. We show and analyze the advantages of this flexible selective approach on two previously used test systems, the alanine dipeptide and the chignolin peptide, and extend these examples to study its applicability and potential to study conformational changes of glycans and glycosylated proteins.},
  chemicals        = {Peptides, Dipeptides},
  citation-subset  = {IM},
  comment          = {Found in the EuropePMC search: https://europepmc.org/betaSearch?query=protein%20ligand%20dihedral%20angles [accessed 2024-04-04T09:36+03:00, 7256 results]},
  completed        = {2023-10-04},
  country          = {United States},
  creationdate     = {2024-04-04T10:43:31},
  doi              = {10.1021/acs.jctc.3c00619},
  file             = {:by-author/G/Gracia Carmona/2023_Gracia Carmona_6521.pdf:PDF},
  issn-linking     = {1549-9618},
  issue            = {18},
  keywords         = {Dipeptides, Chemistry; Molecular Dynamics (MD); Molecular Dynamics Simulation; Peptides; Thermodynamics},
  modificationdate = {2024-04-04T10:46:40},
  nlm-id           = {101232704},
  owner            = {saulius},
  pmc              = {PMC10536968},
  pmid             = {37649349},
  pubmodel         = {Print-Electronic},
  pubstate         = {ppublish},
  revised          = {2023-10-04},
}

@Article{Eastman2024,
  author           = {Eastman, Peter and Galvelis, Raimondas and Peláez, Raúl P. and Abreu, Charlles R. A. and Farr, Stephen E. and Gallicchio, Emilio and Gorenko, Anton and Henry, Michael M. and Hu, Frank and Huang, Jing and Krämer, Andreas and Michel, Julien and Mitchell, Joshua A. and Pande, Vijay S. and Rodrigues, João Pglm and Rodriguez-Guerra, Jaime and Simmonett, Andrew C. and Singh, Sukrit and Swails, Jason and Turner, Philip and Wang, Yuanqing and Zhang, Ivy and Chodera, John D. and De Fabritiis, Gianni and Markland, Thomas E.},
  journal          = {The journal of physical chemistry. B},
  title            = {{OpenMM} 8: molecular dynamics simulation with machine learning potentials},
  year             = {2024},
  issn             = {1520-5207},
  month            = jan,
  pages            = {109--116},
  volume           = {128},
  abstract         = {Machine learning plays an important and growing role in molecular simulation. The newest version of the OpenMM molecular dynamics toolkit introduces new features to support the use of machine learning potentials. Arbitrary PyTorch models can be added to a simulation and used to compute forces and energy. A higher-level interface allows users to easily model their molecules of interest with general purpose, pretrained potential functions. A collection of optimized CUDA kernels and custom PyTorch operations greatly improves the speed of simulations. We demonstrate these features in simulations of cyclin-dependent kinase 8 (CDK8) and the green fluorescent protein chromophore in water. Taken together, these features make it practical to use machine learning to improve the accuracy of simulations with only a modest increase in cost.},
  chemicals        = {Water},
  citation-subset  = {IM},
  comment          = {Found in the EuropePMC search: https://europepmc.org/betaSearch?query=protein%20ligand%20dihedral%20angles [accessed 2024-04-04T09:36+03:00, 7256 results]},
  completed        = {2024-01-12},
  country          = {United States},
  creationdate     = {2024-04-04T10:46:04},
  doi              = {10.1021/acs.jpcb.3c06662},
  file             = {:by-author/E/Eastman/2024_Eastman_109.pdf:PDF},
  issn-linking     = {1520-5207},
  issue            = {1},
  keywords         = {CUDA; CUDA Applications; FF; Machine Learning (ML); Molecular Dynamics (MD); Molecular Dynamics Simulation; PyTorch; Water},
  mid              = {NIHMS1963139},
  modificationdate = {2024-04-04T14:57:37},
  nlm-id           = {101157530},
  owner            = {saulius},
  pmc              = {PMC10846090},
  pmid             = {38154096},
  pubmodel         = {Print-Electronic},
  pubstate         = {ppublish},
  revised          = {2024-02-10},
}

@Article{Walsh2015,
  author           = {Walsh, Aron},
  journal          = {Nature Chemistry},
  title            = {The quest for new functionality},
  year             = {2015},
  issn             = {1755-4349},
  month            = mar,
  number           = {4},
  pages            = {274--275},
  volume           = {7},
  comment          = {Mentioned in the COST DAEMON Rome Feb 5 meeting. Can not download the PDF from the VU (no subscription :( ).
65 mln. combinations for a five component materials; 10^100 possible materials.},
  creationdate     = {2024-04-04T15:13:33},
  doi              = {10.1038/nchem.2213},
  keywords         = {Computational Materials Science; Material Generation},
  modificationdate = {2024-04-04T15:15:51},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media LLC},
}

@Article{Antoniuk2023,
  author           = {Antoniuk, Evan R. and Cheon, Gowoon and Wang, George and Bernstein, Daniel and Cai, William and Reed, Evan J.},
  journal          = {npj Computational Materials},
  title            = {Predicting the synthesizability of crystalline inorganic materials from the data of known material compositions},
  year             = {2023},
  issn             = {2057-3960},
  month            = aug,
  number           = {1},
  pages            = {12},
  volume           = {9},
  comment          = {Cites Walsh2015.},
  creationdate     = {2024-04-04T15:16:18},
  doi              = {10.1038/s41524-023-01114-4},
  file             = {:by-author/A/Antoniuk/2023_Antoniuk_12.pdf:PDF},
  keywords         = {Convex Hull; Crystal Structure Prediction (CSP); Density Functional Theory (DFT); Stable Compounds; Thermodynamical Stability},
  modificationdate = {2024-09-10T18:57:12},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media LLC},
}

@Article{Jiang2021a,
  author           = {Jiang, Yi and Chen, Dong and Chen, Xin and Li, Tangyi and Wei, Guo-Wei and Pan, Feng},
  journal          = {npj Computational Materials},
  title            = {Topological representations of crystalline compounds for the machine-learning prediction of materials properties},
  year             = {2021},
  issn             = {2057-3960},
  month            = feb,
  number           = {1},
  pages            = {28},
  volume           = {7},
  comment          = {Cites Walsh2015.},
  creationdate     = {2024-04-04T18:20:44},
  doi              = {10.1038/s41524-021-00493-w},
  file             = {:by-author/J/Jiang/2021_Jiang_28.pdf:PDF},
  keywords         = {Machine Learning (ML); Material Representation of Machine Learning},
  modificationdate = {2024-04-04T18:28:56},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media LLC},
}

@Article{Deringer2021,
  author           = {Deringer, Volker L. and Bernstein, Noam and Csányi, Gábor and Ben Mahmoud, Chiheb and Ceriotti, Michele and Wilson, Mark and Drabold, David A. and Elliott, Stephen R.},
  journal          = {Nature},
  title            = {Origins of structural and electronic transitions in disordered silicon},
  year             = {2021},
  issn             = {1476-4687},
  month            = jan,
  number           = {7840},
  pages            = {59--64},
  volume           = {589},
  comment          = {Mentioned in the COST DAEMON Rome Feb 5 meeting.},
  creationdate     = {2024-04-04T18:42:14},
  doi              = {10.1038/s41586-020-03072-z},
  file             = {:by-author/D/Deringer/2021_Deringer_59.pdf:PDF},
  keywords         = {Amorphous Materials; Computational Materials Science; Disorder; Disordered Materials; Materials Science},
  modificationdate = {2024-04-04T18:43:44},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media LLC},
}

@Article{Wang2021a,
  author           = {Wang, Hai-Chen and Botti, Silvana and Marques, Miguel A. L.},
  journal          = {npj Computational Materials},
  title            = {Predicting stable crystalline compounds using chemical similarity},
  year             = {2021},
  issn             = {2057-3960},
  month            = jan,
  number           = {1},
  pages            = {12},
  volume           = {7},
  comment          = {Cites Walsh2015.},
  creationdate     = {2024-04-04T18:47:13},
  doi              = {10.1038/s41524-020-00481-6},
  file             = {:by-author/W/Wang/2021_Wang_12.pdf:PDF},
  keywords         = {Convex Hull; Crystal Structure Prediction (CSP); Density Functional Theory (DFT); Stable Compounds; Thermodynamical Stability},
  modificationdate = {2024-04-04T18:48:18},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media LLC},
}

@Article{Bag2024,
  author           = {Bag, Sukdev and Liu, Jie and Patil, Sohan and Bonowski, Jana and Koska, Sandra and Schölermann, Beate and Zhang, Ruirui and Wang, Lin and Pahl, Axel and Sievers, Sonja and Brieger, Lukas and Strohmann, Carsten and Ziegler, Slava and Grigalunas, Michael and Waldmann, Herbert},
  journal          = {Nature Chemistry},
  title            = {A divergent intermediate strategy yields biologically diverse pseudo-natural products},
  year             = {2024},
  issn             = {1755-4349},
  month            = feb,
  creationdate     = {2024-04-04T18:51:27},
  doi              = {10.1038/s41557-024-01458-4},
  file             = {:by-author/B/Bag/2024_Bag_1.pdf:PDF},
  keywords         = {Biologically Active Compounds; Chemical Universe; Enumerating Compounds},
  modificationdate = {2024-04-04T18:54:05},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media LLC},
}

@Article{Cui2013,
  author           = {Cui, Xuefeng and Li, Shuai Cheng and Bu, Dongbo and Alipanahi, Babak and Li, Ming},
  journal          = {Algorithms for molecular biology : AMB},
  title            = {Protein structure idealization: how accurately is it possible to model protein structures with dihedral angles?},
  year             = {2013},
  issn             = {1748-7188},
  month            = feb,
  pages            = {5},
  volume           = {8},
  abstract         = {: Previous studies show that the same type of bond lengths and angles fit Gaussian distributions well with small standard deviations on high resolution protein structure data. The mean values of these Gaussian distributions have been widely used as ideal bond lengths and angles in bioinformatics. However, we are not aware of any research done to evaluate how accurately we can model protein structures with dihedral angles and ideal bond lengths and angles.Here, we introduce the protein structure idealization problem. We focus on the protein backbone structure idealization. We describe a fast O(nm/ε) dynamic programming algorithm to find an idealized protein backbone structure that is approximately optimal according to our scoring function. The scoring function evaluates not only the free energy, but also the similarity with the target structure. Thus, the idealized protein structures found by our algorithm are guaranteed to be protein-like and close to the target protein structure.We have implemented our protein structure idealization algorithm and idealized the high resolution protein structures with low sequence identities of the CULLPDB_PC30_RES1.6_R0.25 data set. We demonstrate that idealized backbone structures always exist with small changes and significantly better free energy. We also applied our algorithm to refine protein pseudo-structures determined in NMR experiments.},
  completed        = {2013-05-17},
  country          = {England},
  creationdate     = {2024-04-07T22:09:23},
  doi              = {10.1186/1748-7188-8-5},
  file             = {:by-author/C/Cui/2013_Cui_5.pdf:PDF},
  issn-linking     = {1748-7188},
  issue            = {1},
  keywords         = {Algorithms; Bioinformatics; Dihedral Angles; Proteins},
  modificationdate = {2024-04-07T22:11:08},
  nlm-id           = {101265088},
  owner            = {saulius},
  pii              = {1748-7188-8-5},
  pmc              = {PMC3655034},
  pmid             = {23442792},
  pubmodel         = {Electronic},
  pubstate         = {epublish},
  revised          = {2021-10-21},
}

@Article{Xu2021a,
  author           = {Xu, Yong-Chang and ShangGuan, Tian-Jun and Ding, Xue-Ming and Cheung, Ngaam J.},
  journal          = {Scientific Reports},
  title            = {Accurate prediction of protein torsion angles using evolutionary signatures and recurrent neural network},
  year             = {2021},
  issn             = {2045-2322},
  month            = oct,
  number           = {1},
  pages            = {21033},
  volume           = {11},
  creationdate     = {2024-04-07T22:15:07},
  doi              = {10.1038/s41598-021-00477-2},
  file             = {:by-author/X/Xu/2021_Xu_21033.pdf:PDF},
  keywords         = {Artificial Neural Networks (ANN); Dihedral Angles; Modelling; Proteins},
  modificationdate = {2024-04-07T22:17:29},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media LLC},
}

@Article{Winkler2023,
  author           = {Winkler, Lauren and Galindo-Murillo, Rodrigo and Cheatham, Thomas E.},
  journal          = {Journal of chemical theory and computation},
  title            = {Assessment of {A}- to {B}- {DNA} transitions utilizing the {D}rude polarizable force field},
  year             = {2023},
  issn             = {1549-9626},
  month            = dec,
  pages            = {8955--8966},
  volume           = {19},
  abstract         = {In addition to the well-characterized B-form of DNA, duplex DNA can adopt various conformations, such as A or Z-DNA. Though less common, these structures can be induced biologically through protein or ligand interactions or experimentally with niche environmental conditions, such as high salt concentrations or in mixed water-ethanol. Reproducing these alternate structures through molecular dynamics simulations in recent years has been quite challenging with the currently available force fields, simulation techniques, and time scales. In this study, the Drude polarizable force field is tested for its ability to facilitate transitions between A-DNA and B-DNA or maintain A-DNA. Though transitions away from B-DNA were observed in high concentrations of ethanol, the resulting structures had hybrid properties taken from both B-DNA and A-DNA structures. This was also true for A-DNA in ethanol, which lost some of the A-DNA properties that it was expected to maintain. When B-DNA was tested in high salt environments, the resulting B-DNA structures showed no distinguishable differences with the increasing salt concentrations tested. These results with the Drude FF and recent results with additive force fields suggest that at present the current additive and polarizable force fields do not facilitate a complete transition between B- to A-DNA conformations under the conditions simulated. At present, the Drude FF favors A-B DNA hybrid structures when simulated in nonphysiological conditions.},
  chemicals        = {DNA, B-Form, DNA, A-Form, DNA, Ethanol},
  citation-subset  = {IM},
  comment          = {Discusses DNA backbone dihedral angles. Found on the EuropePMC using the search https://europepmc.org/betaSearch?query=DNA%20backbone%20dihedral%20angles [5114 results, viewed 2024-04-08T14:20+03:00].},
  completed        = {2023-12-16},
  country          = {United States},
  creationdate     = {2024-04-08T14:16:10},
  doi              = {10.1021/acs.jctc.3c01002},
  file             = {:by-author/W/Winkler/2023_Winkler_8955.pdf:PDF},
  issn-linking     = {1549-9618},
  issue            = {23},
  keywords         = {DNA, A-Form; DNA, B-Form; DNA, Chemistry; Dihedral Angles; Ethanol; Molecular Dynamics Simulation},
  modificationdate = {2024-04-08T14:20:31},
  nlm-id           = {101232704},
  owner            = {saulius},
  pmc              = {PMC10720382},
  pmid             = {38014857},
  pubmodel         = {Print-Electronic},
  pubstate         = {ppublish},
  revised          = {2023-12-16},
}

@Article{Skrbic2024,
  author           = {Škrbić, Tatjana and Giacometti, Achille and Hoang, Trinh X. and Maritan, Amos and Banavar, Jayanth R.},
  journal          = {Polymers},
  title            = {A tale of two chains: geometries of a chain model and protein native state structures},
  year             = {2024},
  issn             = {2073-4360},
  month            = feb,
  pages            = {502},
  volume           = {16},
  abstract         = {Linear chain molecules play a central role in polymer physics with innumerable industrial applications. They are also ubiquitous constituents of living cells. Here, we highlight the similarities and differences between two distinct ways of viewing a linear chain. We do this, on the one hand, through the lens of simulations for a standard polymer chain of tethered spheres at low and high temperatures and, on the other hand, through published experimental data on an important class of biopolymers, proteins. We present detailed analyses of their local and non-local structures as well as the maps of their closest contacts. We seek to reconcile the startlingly different behaviors of the two types of chains based on symmetry considerations.},
  comment          = {Found on the EuropePMC using the search https://europepmc.org/betaSearch?query=DNA%20backbone%20dihedral%20angles [5114 results, viewed 2024-04-08T14:20+03:00].},
  country          = {Switzerland},
  creationdate     = {2024-04-08T14:23:00},
  doi              = {10.3390/polym16040502},
  file             = {:by-author/S/Škrbić/2024_Škrbić_502.pdf:PDF},
  issn-linking     = {2073-4360},
  issue            = {4},
  keywords         = {Bioinformatics; Contact Maps; Dihedral Angles; Geometry; Local and Non-local Structure; Symmetry},
  modificationdate = {2024-04-21T15:28:20},
  nlm-id           = {101545357},
  owner            = {saulius},
  pii              = {502},
  pmc              = {PMC10892082},
  pmid             = {38399880},
  pubmodel         = {Electronic},
  pubstate         = {epublish},
  revised          = {2024-02-27},
}

@Article{Skrbic2021,
  author           = {Škrbić, Tatjana and Maritan, Amos and Giacometti, Achille and Banavar, Jayanth R.},
  journal          = {Protein Science},
  title            = {Local sequence‐structure relationships in proteins},
  year             = {2021},
  issn             = {1469-896X},
  month            = feb,
  number           = {4},
  pages            = {818--829},
  volume           = {30},
  comment          = {Cited in Skrbic2024. Contains definitions of the two angles, θ, and μ.},
  creationdate     = {2024-04-08T14:30:02},
  doi              = {10.1002/pro.4032},
  file             = {:by-author/S/Škrbić/2021_Škrbić_818.pdf:PDF;:by-author/S/Škrbić/2021_Škrbić_818_suppl/pro4032-sup-0001-tables1.docx:Word 2007+},
  keywords         = {Amino Acid Groupings, Amino Acid Propensity, Local Structure, Sequence-structure Relationship; Bioinformatics; Dihedral Angles},
  modificationdate = {2024-04-21T16:39:50},
  owner            = {saulius},
  publisher        = {Wiley},
}

@Article{Tamez2023,
  author           = {Tamez, Angel and Nilsson, Lennart and Mihailescu, Mihaela-Rita and Evanseck, Jeffrey D.},
  journal          = {Journal of chemical theory and computation},
  title            = {Parameterization of the {miniPEG}-modified {γPNA} backbone: toward induced {γPNA} duplex dissociation},
  year             = {2023},
  issn             = {1549-9626},
  month            = jun,
  pages            = {3346--3358},
  volume           = {19},
  abstract         = {γ-Modified peptide nucleic acids (γPNAs) serve as potential therapeutic agents against genetic diseases. Miniature poly(ethylene glycol) (miniPEG) has been reported to increase solubility and binding affinity toward genetic targets, yet details of γPNA structure and dynamics are not understood. Within our work, we parameterized missing torsional and electrostatic terms for the miniPEG substituent on the γ-carbon atom of the γPNA backbone in the CHARMM force field. Microsecond timescale molecular dynamics simulations were carried out on six miniPEG-modified γPNA duplexes from NMR structures (PDB ID: 2KVJ). Three NMR models for the γPNA duplex (PDB ID: 2KVJ) were simulated as a reference for structural and dynamic changes captured for the miniPEG-modified γPNA duplex. Principal component analysis performed on the γPNA backbone atoms identified a single isotropic conformational substate (CS) for the NMR simulations, whereas four anisotropic CSs were identified for the ensemble of miniPEG-modified γPNA simulations. The NMR structures were found to have a 23° helical bend toward the major groove, consistent with our simulated CS structure of 19.0°. However, a significant difference between simulated methyl- and miniPEG-modified γPNAs involved the opportunistic invasion of miniPEG through the minor and major groves. Specifically, hydrogen bond fractional analysis showed that the invasion was particularly prone to affect the second G-C base pair, reducing the Watson-Crick base pair hydrogen bond by 60% over the six simulations, whereas the A-T base pairs decreased by only 20%. Ultimately, the invasion led to base stack reshuffling, where the well-ordered base stacking was reduced to segmented nucleobase stacking interactions. Our 6 μs timescale simulations indicate that duplex dissociation suggests the onset toward γPNA single strands, consistent with the experimental observation of decreased aggregation. To complement the insight of miniPEG-modified γPNA structure and dynamics, the new miniPEG force field parameters allow for further exploration of such modified γPNA single strands as potential therapeutic agents against genetic diseases.},
  chemicals        = {Peptide Nucleic Acids},
  citation-subset  = {IM},
  comment          = {Contains discussion of the PNA dihedral angles. Found in the EuropePMC search https://europepmc.org/betaSearch?query=%2BDNA%20%2Bbackbone%20%2Bdihedral%20%2Bangle%20%2Bdefinitions [304 results, accessed 2024-04-08T14:51+03:00] and https://europepmc.org/betaSearch?query=pna%20backbone%20dihedral%20angle%20definition [26 results, accessed 2024-04-08T14:53+03:00].},
  completed        = {2023-06-14},
  country          = {United States},
  creationdate     = {2024-04-08T14:50:10},
  doi              = {10.1021/acs.jctc.2c01163},
  file             = {:by-author/T/Tamez/2023_Tamez_3346.pdf:PDF},
  issn-linking     = {1549-9618},
  issue            = {11},
  keywords         = {Base Pairing; Dihedral Angles; Magnetic Resonance Spectroscopy; Molecular Conformation; Molecular Dynamics Simulation; Nucleic Acid Conformation; Peptide Nucleic Acids (PNA), Chemistry},
  modificationdate = {2024-04-08T15:28:16},
  nlm-id           = {101232704},
  owner            = {saulius},
  pmc              = {PMC10269335},
  pmid             = {37195939},
  pubmodel         = {Print-Electronic},
  pubstate         = {ppublish},
  revised          = {2023-06-17},
}

@Article{Jasinski2018,
  author           = {Jasiński, Maciej and Feig, Michael and Trylska, Joanna},
  journal          = {Journal of Chemical Theory and Computation},
  title            = {Improved force fields for peptide nucleic acids with optimized backbone torsion parameters},
  year             = {2018},
  issn             = {1549-9626},
  month            = may,
  number           = {7},
  pages            = {3603--3620},
  volume           = {14},
  comment          = {Cited in Tamez2023. Contains definitions of the PNA dihedral angles.},
  comment-saulius  = {Possible assignment for bioinformatics students?},
  creationdate     = {2024-04-08T15:12:23},
  doi              = {10.1021/acs.jctc.8b00291},
  file             = {:by-author/J/Jasiński/2018_Jasiński_3603.pdf:PDF},
  keywords         = {Dihedral Angles; Peptide Nucleic Acids (PNA)},
  modificationdate = {2024-04-08T15:35:01},
  owner            = {saulius},
  publisher        = {American Chemical Society (ACS)},
}

@Article{Sen1998,
  author           = {Sen, Srikanta and Nilsson, Lennart},
  journal          = {Journal of the American Chemical Society},
  title            = {Molecular dynamics of duplex systems involving {PNA}: structural and dynamical consequences of the nucleic acid backbone},
  year             = {1998},
  issn             = {1520-5126},
  month            = jan,
  number           = {4},
  pages            = {619--631},
  volume           = {120},
  comment          = {Cited in Tamez2023. Contains definitions of the PNA dihedral angles.},
  creationdate     = {2024-04-08T15:25:18},
  doi              = {10.1021/ja972234x},
  file             = {:by-author/S/Sen/1998_Sen_619.pdf:PDF},
  keywords         = {Dihedral Angles; Peptide Nucleic Acids (PNA)},
  modificationdate = {2024-04-08T15:28:47},
  owner            = {saulius},
  publisher        = {American Chemical Society (ACS)},
}

@Article{IIJCBN1984,
  author           = {{IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN)}},
  journal          = {European Journal of Biochemistry},
  title            = {Nomenclature and symbolism for amino acids and peptides. Recommendations 1983},
  year             = {1984},
  issn             = {1432-1033},
  month            = jan,
  number           = {1},
  pages            = {9--37},
  volume           = {138},
  creationdate     = {2024-04-08T15:54:14},
  doi              = {10.1111/j.1432-1033.1984.tb07877.x},
  file             = {:by-author/I/IIJCBN/1984_IIJCBN_9.pdf:PDF},
  keywords         = {IUPAC; IUPAC Recommendations; Nomenclature; Peptides; Proteins},
  modificationdate = {2024-04-08T16:41:04},
  owner            = {saulius},
  publisher        = {Wiley},
}

@Article{IIJCB1998,
  author           = {{IUPAC-IUBMB Joint Commission on Biochemical Nomenclature (JCBN)}},
  journal          = {Journal of Molecular Biology},
  title            = {Nomenclature. Newsletter 1996},
  year             = {1998},
  issn             = {0022-2836},
  month            = jan,
  number           = {3},
  pages            = {527--537},
  volume           = {275},
  creationdate     = {2024-04-08T16:02:26},
  doi              = {10.1006/jmbi.1997.1433},
  file             = {:by-author/I/IIJCB/1998_IIJCB_527.pdf:PDF},
  keywords         = {IUPAC; IUPAC Recommendations; Nomenclature},
  modificationdate = {2024-04-08T21:45:43},
  owner            = {saulius},
  publisher        = {Elsevier BV},
}

@Article{IIJCBN1983,
  author           = {{IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN)}},
  journal          = {European Journal of Biochemistry},
  title            = {Abbreviations and symbols for the description of conformationsof polynucleotide chains},
  year             = {1983},
  issn             = {1432-1033},
  month            = mar,
  number           = {1},
  pages            = {9--15},
  volume           = {131},
  comment          = {Contains definitions of the DNA dihedral angles. Cited in Bloomfield, V. A.; Crothers, D. M. & Tinoco Jr., I. (2000) Nucleic Acids: Structures, Properties, and Functions. University Science Books, Sausalito, California.},
  creationdate     = {2024-04-08T16:13:09},
  doi              = {10.1111/j.1432-1033.1983.tb07225.x},
  file             = {:by-author/I/IIJCBN/1983_IIJCBN_9.pdf:PDF},
  keywords         = {DNA; Dihedral Angles; IUPAC; IUPAC Recommendations; Nomenclature},
  modificationdate = {2024-04-08T16:27:07},
  owner            = {saulius},
  publisher        = {Wiley},
  url              = {https://febs.onlinelibrary.wiley.com/doi/pdfdirect/10.1111/j.1432-1033.1983.tb07225.x},
}

@Article{IIJCBN1983a,
  author           = {{IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN)}},
  journal          = {Pure & Appl. Chem.},
  title            = {Abbreviations and symbols for the description of conformationsof polynucleotide chains ({PROVISIONAL})},
  year             = {1983},
  number           = {8},
  pages            = {1273--1280},
  volume           = {55},
  comment          = {Contains definitions of the DNA dihedral angles.},
  creationdate     = {2024-04-08T16:30:38},
  file             = {:by-author/I/IIJCBN/1983_IIJCBN_1273.pdf:PDF},
  keywords         = {DNA; Dihedral Angles; IUPAC; IUPAC Recommendations; Nomenclature},
  modificationdate = {2024-04-08T16:35:17},
  owner            = {saulius},
  url              = {https://old.iupac.org/publications/pac/1983/pdf/5508x1273.pdf},
}

@Article{IUPACIUB1974,
  author           = {{International Union of Pure and Applied Chemistry and International Union of Biochemistry}},
  journal          = {Pure and Applied Chemistry},
  title            = {Abbreviations and symbols for description of conformation of polypeptide chains},
  year             = {1974},
  issn             = {0033-4545},
  month            = jan,
  number           = {3},
  pages            = {291--308},
  volume           = {40},
  comment          = {Contains definitions of the peptide dihedral angles.},
  creationdate     = {2024-04-08T16:38:47},
  doi              = {10.1351/pac197440030291},
  file             = {:by-author/I/IUPACIUB/1974_IUPACIUB_291.pdf:PDF},
  keywords         = {Dihedral Angles; IUPAC; IUPAC Recommendations; Nomenclature; Peptides; Proteins},
  modificationdate = {2024-04-08T16:45:24},
  owner            = {saulius},
  publisher        = {Walter de Gruyter GmbH},
}

@Article{Rajan2021,
  author    = {Rajan, Kohulan and Zielesny, Achim and Steinbeck, Christoph},
  title     = {{STOUT}: {SMILES} to {IUPAC} names using neural machine translation},
  journal   = {Journal of Cheminformatics},
  year      = {2021},
  volume    = {13},
  number    = {1},
  month     = apr,
  issn      = {1758-2946},
  doi       = {10.1186/s13321-021-00512-4},
  file      = {:by-author/R/Rajan/2021_Rajan_34.pdf:PDF},
  publisher = {Springer Science and Business Media LLC},
  url       = {https://doi.org/10.1186/s13321-021-00512-4},
}

@Article{Carugo2018,
  author           = {Carugo, Oliviero},
  journal          = {BMC bioinformatics},
  title            = {How large {B}-factors can be in protein crystal structures},
  year             = {2018},
  issn             = {1471-2105},
  month            = feb,
  pages            = {61},
  volume           = {19},
  abstract         = {Protein crystal structures are potentially over-interpreted since they are routinely refined without any restraint on the upper limit of atomic B-factors. Consequently, some of their atoms, undetected in the electron density maps, are allowed to reach extremely large B-factors, even above 100 square Angstroms, and their final positions are purely speculative and not based on any experimental evidence. A strategy to define B-factors upper limits is described here, based on the analysis of protein crystal structures deposited in the Protein Data Bank prior 2008, when the tendency to allow B-factor to arbitrary inflate was limited. This B-factor upper limit (B_max) is determined by extrapolating the relationship between crystal structure average B-factor and percentage of crystal volume occupied by solvent (pcVol) to pcVol =100%, when, ab absurdo, the crystal contains only liquid solvent, the structure of which is, by definition, undetectable in electron density maps. It is thus possible to highlight structures with average B-factors larger than B_max, which should be considered with caution by the users of the information deposited in the Protein Data Bank, in order to avoid scientifically deleterious over-interpretations.},
  chemicals        = {Amino Acids, Proteins, Solvents},
  citation-subset  = {IM},
  completed        = {2018-11-05},
  country          = {England},
  creationdate     = {2024-04-16T11:01:47},
  doi              = {10.1186/s12859-018-2083-8},
  file             = {:by-author/C/Carugo/2018_Carugo_61.pdf:PDF},
  issn-linking     = {1471-2105},
  issue            = {1},
  keywords         = {Amino Acid Sequence; Amino Acids, Chemistry; Atomic Displacement Parameter; B-factor; Crystal Structure; Crystallography, X-Ray; Databases, Protein; Matthews Coefficient; Models, Molecular; Protein Conformation; Protein Structure Validation; Proteins, Chemistry; Solvents},
  modificationdate = {2024-04-16T11:04:02},
  nlm-id           = {100965194},
  owner            = {saulius},
  pii              = {61},
  pmc              = {PMC5824579},
  pmid             = {29471780},
  pubmodel         = {Electronic},
  pubstate         = {epublish},
  revised          = {2024-03-13},
}

@Article{Carugo2022,
  author           = {Carugo, Oliviero},
  journal          = {Acta crystallographica. Section D, Structural biology},
  title            = {B-factor accuracy in protein crystal structures.},
  year             = {2022},
  issn             = {2059-7983},
  month            = jan,
  pages            = {69--74},
  volume           = {78},
  abstract         = {The accuracy of B factors in protein crystal structures has been determined by comparing the same atoms in numerous, independent crystal structures of Gallus gallus lysozyme. Both B-factor absolute differences and normal probability plots indicate that the estimated B-factor errors are quite large, close to 9 Å (2)in ambient-temperature structures and to 6 Å (2)in low-temperature structures, and surprisingly are comparable to values estimated two decades ago. It is well known that B factors are not due to local movements only but reflect several, additional factors from crystal defects, large-scale disorder, diffraction data quality etc. It therefore remains essential to normalize B factors when comparing different crystal structures, although it has clearly been shown that they provide useful information about protein dynamics. Improved, quantitative analyses of raw B factors require novel experimental and computational tools that are able to disaggregate local movements from other features and properties that affect B factors.},
  chemicals        = {hen egg lysozyme, Muramidase},
  citation-subset  = {IM},
  completed        = {2022-03-24},
  country          = {United States},
  creationdate     = {2024-04-16T11:04:43},
  doi              = {10.1107/S2059798321011736},
  file             = {:by-author/C/Carugo/2022_Carugo_69.pdf:PDF},
  issn-linking     = {2059-7983},
  issue            = {Pt 1},
  keywords         = {Accuracy; Algorithms; Animals; B-factor; Chickens; Computational Biology; Crystallization; Crystallography, X-Ray; Molecular Structure; Muramidase, Chemistry, Genetics; Normal Probability Plot; Protein Conformation; Protein Crystal Structures; Reproducibility of Results; Temperature; Validation; X-Ray Diffraction},
  modificationdate = {2024-04-16T11:05:44},
  nlm-id           = {101676043},
  owner            = {saulius},
  pii              = {S2059798321011736},
  pmc              = {PMC8725162},
  pmid             = {34981763},
  pubmodel         = {Print-Electronic},
  pubstate         = {ppublish},
  revised          = {2023-11-05},
}

@Article{Yuan2005,
  author           = {Yuan, Zheng and Bailey, Timothy L. and Teasdale, Rohan D.},
  journal          = {Proteins: Structure, Function, and Bioinformatics},
  title            = {Prediction of protein {B}‐factor profiles},
  year             = {2005},
  issn             = {1097-0134},
  month            = jan,
  number           = {4},
  pages            = {905--912},
  volume           = {58},
  creationdate     = {2024-04-16T11:11:32},
  doi              = {10.1002/prot.20375},
  file             = {:by-author/Y/Yuan/2005_Yuan_905.pdf:PDF},
  keywords         = {B-factor; Bioinformatics; Evolutionary Information; Flexibility; Protein Sequence; Protein Structure; ROC Analysis; Support Vector Regression},
  modificationdate = {2024-04-16T12:22:58},
  owner            = {saulius},
  publisher        = {Wiley},
}

@Article{Touw2014,
  author           = {Touw, W. G. and Vriend, G.},
  journal          = {Protein Engineering Design and Selection},
  title            = {{BDB}: Databank of {PDB} files with consistent {B}-factors},
  year             = {2014},
  issn             = {1741-0134},
  month            = oct,
  number           = {11},
  pages            = {457--462},
  volume           = {27},
  creationdate     = {2024-04-16T11:17:40},
  doi              = {10.1093/protein/gzu044},
  file             = {:by-author/T/Touw/2014_Touw_457.pdf:PDF},
  keywords         = {B-factor; Bioinformatics; PDB; Protein Structure},
  modificationdate = {2024-04-21T15:27:08},
  owner            = {saulius},
  publisher        = {Oxford University Press (OUP)},
}

@Article{Rubin1972,
  author           = {Rubin, B. and Richardson, J. S.},
  journal          = {Biopolymers},
  title            = {The simple construction of protein alpha-carbon models},
  year             = {1972},
  issn             = {0006-3525},
  pages            = {2381--2385},
  volume           = {11},
  chemicals        = {Proteins},
  citation-subset  = {IM},
  comment          = {Cited in Skrbic2021.},
  completed        = {1973-01-30},
  country          = {United States},
  creationdate     = {2024-04-21T16:44:10},
  doi              = {10.1002/bip.1972.360111116},
  file             = {:by-author/R/Rubin/1972_Rubin_2381.pdf:PDF},
  issn-linking     = {0006-3525},
  issue            = {11},
  keywords         = {Dihedral Angles; Methods; Models, Structural; Proteins},
  modificationdate = {2024-04-21T16:46:57},
  nlm-id           = {0372525},
  owner            = {saulius},
  pmid             = {4634874},
  pubmodel         = {Print},
  pubstate         = {ppublish},
  revised          = {2000-12-18},
}

@Article{Skrbic2020,
  author           = {Skrbic, Tatjana and Maritan, Amos and Giacometti, Achille and Rose, George D. and Banavar, Jayanth R.},
  journal          = {bioRxiv},
  title            = {Building blocks of protein structures -- physics meets biology},
  year             = {2020},
  month            = nov,
  creationdate     = {2024-04-21T16:58:48},
  doi              = {10.1101/2020.11.10.375105},
  file             = {:by-author/S/Skrbic/2020_Skrbic_1.pdf:PDF},
  keywords         = {Dihedral Angles; Models, Structural; Proteins},
  modificationdate = {2024-04-21T17:04:28},
  owner            = {saulius},
  publisher        = {Cold Spring Harbor Laboratory},
}

@Article{Bahar1997a,
  author           = {Bahar, I. and Kaplan, M. and Jernigan, R. L.},
  journal          = {Proteins},
  title            = {Short-range conformational energies, secondary structure propensities, and recognition of correct sequence-structure matches},
  year             = {1997},
  issn             = {0887-3585},
  month            = nov,
  pages            = {292--308},
  volume           = {29},
  abstract         = {A statistical analysis of known structures is made for an assessment of the utility of short-range energy considerations. For each type of amino acid, the potentials governing (1) the torsions and bond angle changes of virtual C alpha-C alpha bonds and (2) the coupling between torsion and bond angle changes are derived. These contribute approximately -2 RT per residue to the stability of native proteins, approximately half of which is due to coupling effects. The torsional potentials for the alpha-helical states of different residues are verified to be strongly correlated with the free-energy change measurements made upon single-site mutations at solvent-exposed regions. Likewise, a satisfactory correlation is shown between the beta-sheet potentials of different amino acids and the scales from free-energy measurements, despite the role of tertiary context in stabilizing beta-sheets. Furthermore, there is excellent agreement between our residue-specific potentials for alpha-helical state and other thermodynamic based scales. Threading experiments performed by using an inverse folding protocol show that 50 of 62 test structures correctly recognize their native sequence on the basis of short-range potentials. The performance is improved to 55, upon simultaneous consideration of short-range potentials and the nonbonded interaction potentials between sequentially distant residues. Interactions between near residues along the primary structure, i.e., the local or short-range interactions, are known to be insufficient, alone, for understanding the tertiary structural preferences of proteins alone. Yet, knowledge of short-range conformational potentials permits rationalizing the secondary structure propensities and aids in the discrimination between correct and incorrect tertiary folds.},
  chemicals        = {Amino Acids, Proteins},
  citation-subset  = {IM},
  comment          = {Cited in Skrbic2021.},
  completed        = {1998-02-19},
  country          = {United States},
  creationdate     = {2024-04-21T17:15:39},
  doi              = {10.1002/(sici)1097-0134(199711)29:3<292::aid-prot4>3.0.co;2-d},
  file             = {:by-author/B/Bahar/1997_Bahar_292.pdf:PDF},
  issn-linking     = {0887-3585},
  issue            = {3},
  keywords         = {Amino Acids, Chemistry; Dihedral Angles; Energy Transfer; Mathematical Computing; Probability; Protein Structure, Secondary; Proteins, Chemistry},
  modificationdate = {2024-04-21T17:16:48},
  nlm-id           = {8700181},
  owner            = {saulius},
  pii              = {10.1002/(SICI)1097-0134(199711)29:3<292::AID-PROT4>3.0.CO;2-D},
  pmid             = {9365985},
  pubmodel         = {Print},
  pubstate         = {ppublish},
  revised          = {2019-11-02},
}

@Lecture{Boley2021,
  author           = {Daniel Boley},
  title            = {Floating point arithmethic - error analysis},
  year             = {2021},
  course           = {Computational aspects of matrix theory},
  creationdate     = {2024-04-22T10:22:28},
  file             = {:by-author/B/Boley/2021_Boley_Floating Point Arithmethic Error Analysis.pdf:PDF},
  keywords         = {Floating Point; Rounding Errors},
  modificationdate = {2024-04-22T10:26:18},
  owner            = {saulius},
  url              = {https://www-users.cselabs.umn.edu/classes/Fall-2021/csci5304/LectureNotes/LecN4_R.pdf},
}

@PhdThesis{Cid2000,
  author           = {Samuel A. Figueroa del Cid},
  school           = {Department of Computer Science, New York University},
  title            = {A rigorous frameworkfor fully supporting the {IEEE} standard for floating-point arithmetic in high-level programming languages},
  year             = {2000},
  creationdate     = {2024-04-22T15:48:43},
  file             = {:by-author/C/Cid/2000_Cid_A Rigorous Frameworkfor Fully Supporting the IEEE Standard for Floating Point Arithmetic in High Level Programming Languages.pdf:PDF},
  keywords         = {Ada; Floating Point; IEEE 754; Java; Standard},
  modificationdate = {2024-04-22T15:51:47},
  owner            = {saulius},
  url              = {https://cs.nyu.edu/media/publications/figueroa_sam.pdf},
}

@TechReport{Dross2021,
  author           = {Claire Dross and Johannes Kanig},
  institution      = {AdaCore},
  title            = {Making proofs of floating-point programs accessible to regular developers},
  year             = {2021},
  creationdate     = {2024-04-24T17:15:10},
  file             = {:by-author/D/Dross/2021_Dross_1.pdf:PDF},
  keywords         = {Ada; Correctness Proofs; Floating Point; Formal Methods; IEEE 754; SPARK; Software Verification},
  modificationdate = {2024-04-24T17:18:00},
  owner            = {saulius},
  url              = {https://www.adacore.com/uploads/techPapers/floats_spark.pdf},
}

@Article{Burley2018,
  author           = {Burley, Stephen K. and Berman, Helen M. and Bhikadiya, Charmi and Bi, Chunxiao and Chen, Li and Costanzo, Luigi Di and Christie, Cole and Duarte, Jose M. and Dutta, Shuchismita and Feng, Zukang and Ghosh, Sutapa and Goodsell, David S. and Green, Rachel Kramer and Guranovic, Vladimir and Guzenko, Dmytro and Hudson, Brian P. and Liang, Yuhe and Lowe, Robert and Peisach, Ezra and Periskova, Irina and Randle, Chris and Rose, Alexander and Sekharan, Monica and Shao, Chenghua and Tao, Yi-Ping and Valasatava, Yana and Voigt, Maria and Westbrook, John and Young, Jasmine and Zardecki, Christine and Zhuravleva, Marina and Kurisu, Genji and Nakamura, Haruki and Kengaku, Yumiko and Cho, Hasumi and Sato, Junko and Kim, Ju Yaen and Ikegawa, Yasuyo and Nakagawa, Atsushi and Yamashita, Reiko and Kudou, Takahiro and Bekker, Gert-Jan and Suzuki, Hirofumi and Iwata, Takeshi and Yokochi, Masashi and Kobayashi, Naohiro and Fujiwara, Toshimichi and Velankar, Sameer and Kleywegt, Gerard J. and Anyango, Stephen and Armstrong, David R. and Berrisford, John M. and Conroy, Matthew J. and Dana, Jose M. and Deshpande, Mandar and Gane, Paul and Gáborová, Romana and Gupta, Deepti and Gutmanas, Aleksandras and Koča, Jaroslav and Mak, Lora and Mir, Saqib and Mukhopadhyay, Abhik and Nadzirin, Nurul and Nair, Sreenath and Patwardhan, Ardan and Paysan-Lafosse, Typhaine and Pravda, Lukas and Salih, Osman and Sehnal, David and Varadi, Mihaly and Vařeková, Radka and Markley, John L. and Hoch, Jeffrey C. and Romero, Pedro R. and Baskaran, Kumaran and Maziuk, Dimitri and Ulrich, Eldon L. and Wedell, Jonathan R. and Yao, Hongyang and Livny, Miron and Ioannidis, Yannis E.},
  journal          = {Nucleic Acids Research},
  title            = {{Protein Data Bank}: the single global archive for {3D} macromolecular structure data},
  year             = {2018},
  issn             = {1362-4962},
  month            = oct,
  number           = {D1},
  pages            = {D520--D528},
  volume           = {47},
  creationdate     = {2024-04-27T11:19:53},
  doi              = {10.1093/nar/gky949},
  file             = {:by-author/B/Burley/2018_Burley_D520.pdf:PDF},
  keywords         = {PDB; Scientific Databases},
  modificationdate = {2024-04-27T11:23:51},
  owner            = {saulius},
  publisher        = {Oxford University Press (OUP)},
}

@Article{Liang2023,
  author           = {Liang, Chao and Rouzhahong, Yilimiranmu and Ye, Caiyuan and Li, Chong and Wang, Biao and Li, Huashan},
  journal          = {Nature Communications},
  title            = {Material symmetry recognition and property prediction accomplished by crystal capsule representation},
  year             = {2023},
  issn             = {2041-1723},
  month            = aug,
  number           = {1},
  pages            = {5198},
  volume           = {14},
  abstract         = {Learning the global crystal symmetry and interpreting the equivariant information is crucial for accurately predicting material properties, yet remains to be fully accomplished by existing algorithms based on convolution networks. To overcome this challenge, here we develop a machine learning (ML) model, named symmetry-enhanced equivariance network (SEN), to build material representation with joint structure-chemical patterns, to encode important clusters embedded in the crystal structure, and to learn pattern equivariance in different scales via capsule transformers. Quantitative analyses of the intermediate matrices demonstrate that the intrinsic crystal symmetries and interactions between clusters have been exactly perceived by the SEN model and critically affect the prediction performances by reducing effective feature space. The mean absolute errors (MAEs) of 0.181 eV and 0.0161 eV/atom are obtained for predicting bandgap and formation energy in the MatBench dataset. The general and interpretable SEN model reveals the potential to design ML models by implicitly encoding feature relationship based on physical mechanisms.},
  citation-subset  = {IM},
  comment          = {Found in EuropePMC using the search https://europepmc.org/betaSearch?query=crystal%20structure%20property%20relation%20database [accessed 2024-04-27T12:08+03:00,  3782 results].},
  country          = {England},
  creationdate     = {2024-04-27T12:06:40},
  doi              = {10.1038/s41467-023-40756-2},
  file             = {:by-author/L/Liang/2023_Liang_5198.pdf:PDF},
  issn-linking     = {2041-1723},
  issue            = {1},
  keywords         = {Artificial Intelligence (AI); Computational Materials Science; Crystal Property Prediction; Crystal Symmetry Prediction; Crystallography; Machine Learning (ML); Materials Science; Symmetry},
  modificationdate = {2024-04-27T12:12:19},
  nlm-id           = {101528555},
  owner            = {saulius},
  pii              = {5198},
  pmc              = {PMC10457372},
  pmid             = {37626032},
  publisher        = {Springer Science and Business Media LLC},
  pubmodel         = {Electronic},
  pubstate         = {epublish},
  revised          = {2023-11-19},
}

@Article{Venugopal2024,
  author           = {Venugopal, Vineeth and Olivetti, Elsa},
  journal          = {Scientific Data},
  title            = {MatKG: An autonomously generated knowledge graph in Material Science},
  year             = {2024},
  issn             = {2052-4463},
  month            = feb,
  number           = {1},
  pages            = {217},
  volume           = {11},
  abstract         = {In this paper, we present MatKG, a knowledge graph in materials science that offers a repository of entities and relationships extracted from scientific literature. Using advanced natural language processing techniques, MatKG includes an array of entities, including materials, properties, applications, characterization and synthesis methods, descriptors, and symmetry phase labels. The graph is formulated based on statistical metrics, encompassing over 70,000 entities and 5.4 million unique triples. To enhance accessibility and utility, we have serialized MatKG in both CSV and RDF formats and made these, along with the code base, available to the research community. As the largest knowledge graph in materials science to date, MatKG provides structured organization of domain-specific data. Its deployment holds promise for various applications, including material discovery, recommendation systems, and advanced analytics.},
  citation-subset  = {IM},
  completed        = {2024-02-19},
  country          = {England},
  creationdate     = {2024-04-27T12:16:19},
  doi              = {10.1038/s41597-024-03039-z},
  file             = {:by-author/V/Venugopal/2024_Venugopal_217.pdf:PDF},
  issn-linking     = {2052-4463},
  issue            = {1},
  keywords         = {Data Management; Knowledge Extraction; Knowledge Graph; Text Mining},
  modificationdate = {2024-04-27T12:17:52},
  nlm-id           = {101640192},
  owner            = {saulius},
  pii              = {217},
  pmc              = {PMC10874416},
  pmid             = {38368452},
  publisher        = {Springer Science and Business Media LLC},
  pubmodel         = {Electronic},
  pubstate         = {epublish},
  revised          = {2024-03-19},
}

@Article{Tang2024,
  author           = {Tang, Yidan and Moretti, Rocco and Meiler, Jens},
  journal          = {Journal of chemical information and modeling},
  title            = {Recent advances in automated structure-based de novo drug design},
  year             = {2024},
  issn             = {1549-960X},
  month            = mar,
  pages            = {1794--1805},
  volume           = {64},
  abstract         = {As the number of determined and predicted protein structures and the size of druglike 'make-on-demand' libraries soar, the time-consuming nature of structure-based computer-aided drug design calls for innovative computational algorithms. De novo drug design introduces in silico heuristics to accelerate searching in the vast chemical space. This review focuses on recent advances in structure-based de novo drug design, ranging from conventional fragment-based methods, evolutionary algorithms, and Metropolis Monte Carlo methods to deep generative models. Due to the historical limitation of de novo drug design generating readily available drug-like molecules, we highlight the synthetic accessibility efforts in each category and the benchmarking strategies taken to validate the proposed framework.},
  citation-subset  = {IM},
  completed        = {2024-03-26},
  country          = {United States},
  creationdate     = {2024-04-27T12:19:17},
  doi              = {10.1021/acs.jcim.4c00247},
  file             = {:by-author/T/Tang/2024_Tang_1794.pdf:PDF},
  issn-linking     = {1549-9596},
  issue            = {6},
  keywords         = {Algorithms; Artificial Intelligence (AI); Computer-aided Drug Design; De Novo Drug Design; Drug Design; Evolutionary Algorithm; Fragment Growing; Fragment-based Ligand Design; Genetic Algorithm; Machine Learning (ML); Review; Structure-based Drug Design; Synthetic Accessibility},
  modificationdate = {2024-04-27T12:21:18},
  nlm-id           = {101230060},
  owner            = {saulius},
  pmc              = {PMC10966644},
  pmid             = {38485516},
  pubmodel         = {Print-Electronic},
  pubstate         = {ppublish},
  revised          = {2024-03-30},
}

@Article{Naik2023,
  author           = {Naik, Aakash Ashok and Ertural, Christina and Dhamrait, Nidal and Benner, Philipp and George, Janine},
  journal          = {Scientific Data},
  title            = {A quantum-chemical bonding database for solid-state materials},
  year             = {2023},
  issn             = {2052-4463},
  month            = sep,
  number           = {1},
  pages            = {610},
  volume           = {10},
  abstract         = {An in-depth insight into the chemistry and nature of the individual chemical bonds is essential for understanding materials. Bonding analysis is thus expected to provide important features for large-scale data analysis and machine learning of material properties. Such chemical bonding information can be computed using the LOBSTER software package, which post-processes modern density functional theory data by projecting the plane wave-based wave functions onto an atomic orbital basis. With the help of a fully automatic workflow, the VASP and LOBSTER software packages are used to generate the data. We then perform bonding analyses on 1520 compounds (insulators and semiconductors) and provide the results as a database. The projected densities of states and bonding indicators are benchmarked on standard density-functional theory computations and available heuristics, respectively. Lastly, we illustrate the predictive power of bonding descriptors by constructing a machine learning model for phononic properties, which shows an increase in prediction accuracies by 27% (mean absolute errors) compared to a benchmark model differing only by not relying on any quantum-chemical bonding features.},
  citation-subset  = {IM},
  completed        = {2023-09-13},
  country          = {England},
  creationdate     = {2024-04-27T12:37:36},
  doi              = {10.1038/s41597-023-02477-5},
  file             = {:by-author/N/Naik/2023_Naik_610.pdf:PDF},
  issn-linking     = {2052-4463},
  issue            = {1},
  keywords         = {Chemical Bond Description; Data Management; Scientific Databases},
  modificationdate = {2024-04-27T12:40:10},
  nlm-id           = {101640192},
  owner            = {saulius},
  pii              = {610},
  pmc              = {PMC10495449},
  pmid             = {37696882},
  publisher        = {Springer Science and Business Media LLC},
  pubmodel         = {Electronic},
  pubstate         = {epublish},
  revised          = {2023-11-23},
}

@Article{ReceveurBrechot2023,
  author           = {Receveur-Bréchot, Véronique},
  journal          = {Journal of Applied Crystallography},
  title            = {{AlphaFold}, small-angle {X}-ray scattering and ensemble modelling: a winning combination for intrinsically disordered proteins},
  year             = {2023},
  issn             = {1600-5767},
  month            = sep,
  number           = {5},
  pages            = {1313--1314},
  volume           = {56},
  abstract         = {A recent article by Brookes, Rocco, Vachette & Trewhella [ J. Appl. Cryst. (2023), 56 , 910-926] on improving the accuracy of AlphaFold structural predictions for disordered proteins is discussed.},
  country          = {United States},
  creationdate     = {2024-05-06T18:13:16},
  doi              = {10.1107/s1600576723008403},
  file             = {:by-author/R/Receveur-Bréchot/2023_Receveur-Bréchot_1313.pdf:PDF},
  issn-linking     = {0021-8898},
  issue            = {Pt 5},
  keywords         = {AlphaFold; Ensemble Modelling; Intrinsically Disordered Proteins; Protein Modelling; Proteins; Small-angle Scattering; Small-angle X-ray Scattering (SAXS); Structural Flexibility},
  modificationdate = {2024-05-06T18:15:22},
  nlm-id           = {9876190},
  owner            = {saulius},
  pii              = {S1600576723008403},
  pmc              = {PMC10543683},
  pmid             = {37791368},
  publisher        = {International Union of Crystallography (IUCr)},
  pubmodel         = {Electronic-eCollection},
  pubstate         = {epublish},
  revised          = {2023-10-30},
}

@Article{Agirre2017,
  author           = {Agirre, Jon and Dodson, Eleanor},
  journal          = {Protein Science},
  title            = {Forty years of collaborative computational crystallography},
  year             = {2017},
  issn             = {1469-896X},
  month            = oct,
  number           = {1},
  pages            = {202--206},
  volume           = {27},
  abstract         = {A brief overview is provided of the history of collaborative computational crystallography, with an emphasis on the Collaborative Computational Project No. 4. The key steps in its development are outlined, with consideration also given to the underlying reasons which contributed, and ultimately led to, the unprecedented success of this venture.},
  citation-subset  = {IM},
  comment          = {Found by https://europepmc.org/search?query=teaching%20crystallographic%20computing&page=2 [accessed 2024-05-06T19:05+03:00, 159 results].},
  completed        = {2017-12-26},
  country          = {United States},
  creationdate     = {2024-05-06T18:18:53},
  doi              = {10.1002/pro.3298},
  file             = {:by-author/A/Agirre/2017_Agirre_202.pdf:PDF},
  issn-linking     = {0961-8368},
  issue            = {1},
  keywords         = {C++; Computational Biology, History, Trends; Computational Crystallography; Crystallographic Computing; Crystallography; Crystallography, X-Ray, History; Fortran; History, 20th Century; History, 21st Century; Python; Review},
  modificationdate = {2024-05-06T19:05:46},
  nlm-id           = {9211750},
  owner            = {saulius},
  pmc              = {PMC5734308},
  pmid             = {28901632},
  publisher        = {Wiley},
  pubmodel         = {Print-Electronic},
  pubstate         = {ppublish},
  revised          = {2023-11-12},
}

@Article{Spalvieri2022,
  author           = {Spalvieri, Davide and Mauviel, Anne-Marine and Lambert, Matthieu and Férey, Nicolas and Sacquin-Mora, Sophie and Chavent, Matthieu and Baaden, Marc},
  journal          = {Journal of Integrative Bioinformatics},
  title            = {Design – a new way to look at old molecules},
  year             = {2022},
  issn             = {1613-4516},
  month            = jun,
  number           = {2},
  pages            = {20220020},
  volume           = {19},
  abstract         = {We discuss how design enriches molecular science, particularly structural biology and bioinformatics. We present two use cases, one in academic practice and the other to design for outreach. The first case targets the representation of ion channels and their dynamic properties. In the second, we document a transition process from a research environment to general-purpose designs. Several testimonials from practitioners are given. By describing the design process of abstracted shapes, exploded views of molecular structures, motion-averaged slices, 360-degree panoramic projections, and experiments with lit sphere shading, we document how designers help make scientific data accessible without betraying its meaning, and how a creative mind adds value over purely data-driven visualizations. A similar conclusion was drawn for public outreach, as we found that comic-book-style drawings are better suited for communicating science to a broad audience.},
  citation-subset  = {IM},
  completed        = {2022-08-17},
  country          = {Germany},
  creationdate     = {2024-05-06T19:07:53},
  doi              = {10.1515/jib-2022-0020},
  file             = {:by-author/S/Spalvieri/2022_Spalvieri_20220020.pdf:PDF},
  issn-linking     = {1613-4516},
  issue            = {2},
  keywords         = {Bioinformatics; Exploded Views; Illustration; Ion Channels; Molecular Biology; Molecular Design; Outreach; Teaching; Teaching Crystallography},
  modificationdate = {2024-05-06T19:10:02},
  nlm-id           = {101503361},
  owner            = {saulius},
  pii              = {20220020},
  pmc              = {PMC9377703},
  pmid             = {35776840},
  publisher        = {Walter de Gruyter GmbH},
  pubmodel         = {Electronic},
  pubstate         = {epublish},
  revised          = {2022-08-31},
}

@Article{Phillips2020,
  author           = {Phillips, James C. and Hardy, David J. and Maia, Julio D. C. and Stone, John E. and Ribeiro, João V. and Bernardi, Rafael C. and Buch, Ronak and Fiorin, Giacomo and Hénin, Jérôme and Jiang, Wei and McGreevy, Ryan and Melo, Marcelo C. R. and Radak, Brian K. and Skeel, Robert D. and Singharoy, Abhishek and Wang, Yi and Roux, Benoît and Aksimentiev, Aleksei and Luthey-Schulten, Zaida and Kalé, Laxmikant V. and Schulten, Klaus and Chipot, Christophe and Tajkhorshid, Emad},
  journal          = {The Journal of Chemical Physics},
  title            = {Scalable molecular dynamics on {CPU} and {GPU} architectures with {NAMD}},
  year             = {2020},
  issn             = {1089-7690},
  month            = jul,
  number           = {4},
  pages            = {044130},
  volume           = {153},
  abstract         = {NAMDis a molecular dynamics program designed for high-performance simulations of very large biological objects on CPU- and GPU-based architectures. NAMD offers scalable performance on petascale parallel supercomputers consisting of hundreds of thousands of cores, as well as on inexpensive commodity clusters commonly found in academic environments. It is written in C++ and leans on Charm++ parallel objects for optimal performance on low-latency architectures. NAMD is a versatile, multipurpose code that gathers state-of-the-art algorithms to carry out simulations in apt thermodynamic ensembles, using the widely popular CHARMM, AMBER, OPLS, and GROMOS biomolecular force fields. Here, we review the main features of NAMD that allow both equilibrium and enhanced-sampling molecular dynamics simulations with numerical efficiency. We describe the underlying concepts utilized by NAMD and their implementation, most notably for handling long-range electrostatics; controlling the temperature, pressure, and pH; applying external potentials on tailored grids; leveraging massively parallel resources in multiple-copy simulations; and hybrid quantum-mechanical/molecular-mechanical descriptions. We detail the variety of options offered by NAMD for enhanced-sampling simulations aimed at determining free-energy differences of either alchemical or geometrical transformations and outline their applicability to specific problems. Last, we discuss the roadmap for the development of NAMD and our current efforts toward achieving optimal performance on GPU-based architectures, for pushing back the limitations that have prevented biologically realistic billion-atom objects to be fruitfully simulated, and for making large-scale simulations less expensive and easier to set up, run, and analyze. NAMD is distributed free of charge with its source code at www.ks.uiuc.edu.},
  citation-subset  = {IM},
  completed        = {2020-08-06},
  country          = {United States},
  creationdate     = {2024-05-06T19:12:25},
  doi              = {10.1063/5.0014475},
  file             = {:by-author/P/Phillips/2020_Phillips_44130.pdf:PDF},
  issn-linking     = {0021-9606},
  issue            = {4},
  keywords         = {Bioinformatics; Computer Architecture; Molecular Dynamics (MD); Molecular Modelling; NAMD},
  modificationdate = {2024-05-06T19:14:50},
  nlm-id           = {0375360},
  owner            = {saulius},
  pii              = {044130},
  pmc              = {PMC7395834},
  pmid             = {32752662},
  publisher        = {AIP Publishing},
  pubmodel         = {Print},
  pubstate         = {ppublish},
  revised          = {2024-03-29},
}

@Article{Shao2022a,
  author           = {Shao, Chenghua and Westbrook, John D. and Lu, Changpeng and Bhikadiya, Charmi and Peisach, Ezra and Young, Jasmine Y. and Duarte, Jose M. and Lowe, Robert and Wang, Sijian and Rose, Yana and Feng, Zukang and Burley, Stephen K.},
  journal          = {Structure},
  title            = {Simplified quality assessment for small-molecule ligands in the {P}rotein {D}ata {B}ank},
  year             = {2022},
  issn             = {0969-2126},
  month            = feb,
  number           = {2},
  pages            = {252--262.e4},
  volume           = {30},
  abstract         = {More than 70% of the experimentally determined macromolecular structures in the Protein Data Bank (PDB) contain small-molecule ligands. Quality indicators of ∼643,000 ligands present in ∼106,000 PDB X-ray crystal structures have been analyzed. Ligand quality varies greatly with regard to goodness of fit between ligand structure and experimental data, deviations in bond lengths and angles from known chemical structures, and inappropriate interatomic clashes between the ligand and its surroundings. Based on principal component analysis, correlated quality indicators of ligand structure have been aggregated into two largely orthogonal composite indicators measuring goodness of fit to experimental data and deviation from ideal chemical structure. Ranking of the composite quality indicators across the PDB archive enabled construction of uniformly distributed composite ranking score. This score is implemented at RCSB.org to compare chemically identical ligands in distinct PDB structures with easy-to-interpret two-dimensional ligand quality plots, allowing PDB users to quickly assess ligand structure quality and select the best exemplars.},
  chemicals        = {Ligands, Proteins, Small Molecule Libraries},
  citation-subset  = {IM},
  completed        = {2022-03-21},
  country          = {United States},
  creationdate     = {2024-05-06T21:58:52},
  doi              = {10.1016/j.str.2021.10.003},
  file             = {:by-author/S/Shao/2022_Shao_4.pdf:PDF},
  issn-linking     = {0969-2126},
  issue            = {2},
  keywords         = {Composite Ranking Score; Databases, Protein; Ligand Quality Indicator; Ligand Structure; Ligand Structure Quality; Ligands; Models, Molecular; Multivariate Analysis; PDB; Principal Component Analysis; Protein Conformation; Protein Data Bank; Proteins, Chemistry, Metabolism; RCSB PDB; Small Molecule Libraries, Pharmacology; Small-molecule Ligand},
  mid              = {NIHMS1749090},
  modificationdate = {2024-05-06T22:01:24},
  nlm-id           = {101087697},
  owner            = {saulius},
  pii              = {S0969-2126(21)00371-3},
  pmc              = {PMC8849442},
  pmid             = {35026162},
  publisher        = {Elsevier BV},
  pubmodel         = {Print-Electronic},
  pubstate         = {ppublish},
  revised          = {2023-02-04},
}

@Article{Gallicchio2015,
  author           = {Gallicchio, Emilio and Xia, Junchao and Flynn, William F. and Zhang, Baofeng and Samlalsingh, Sade and Mentes, Ahmet and Levy, Ronald M.},
  journal          = {Computer Physics Communications},
  title            = {Asynchronous replica exchange software for grid and heterogeneous computing},
  year             = {2015},
  issn             = {0010-4655},
  month            = nov,
  pages            = {236--246},
  volume           = {196},
  abstract         = {Parallel replica exchange sampling is an extended ensemble technique often used to accelerate the exploration of the conformational ensemble of atomistic molecular simulations of chemical systems. Inter-process communication and coordination requirements have historically discouraged the deployment of replica exchange on distributed and heterogeneous resources. Here we describe the architecture of a software (named ASyncRE) for performing asynchronous replica exchange molecular simulations on volunteered computing grids and heterogeneous high performance clusters. The asynchronous replica exchange algorithm on which the software is based avoids centralized synchronization steps and the need for direct communication between remote processes. It allows molecular dynamics threads to progress at different rates and enables parameter exchanges among arbitrary sets of replicas independently from other replicas. ASyncRE is written in Python following a modular design conducive to extensions to various replica exchange schemes and molecular dynamics engines. Applications of the software for the modeling of association equilibria of supramolecular and macromolecular complexes on BOINC campus computational grids and on the CPU/MIC heterogeneous hardware of the XSEDE Stampede supercomputer are illustrated. They show the ability of ASyncRE to utilize large grids of desktop computers running the Windows, MacOS, and/or Linux operating systems as well as collections of high performance heterogeneous hardware devices.},
  country          = {Netherlands},
  creationdate     = {2024-05-06T22:04:03},
  doi              = {10.1016/j.cpc.2015.06.010},
  file             = {:by-author/G/Gallicchio/2015_Gallicchio_236_medline.pdf:PDF},
  issn-linking     = {0010-4655},
  keywords         = {BOINC; Distributed Computing; Grid Computing; Peptide Dimerization; Protein-ligand Binding; Replica Exchange Molecular Dynamics},
  mid              = {NIHMS707502},
  modificationdate = {2024-05-06T22:05:24},
  nlm-id           = {100971327},
  owner            = {saulius},
  pmc              = {PMC4834714},
  pmid             = {27103749},
  publisher        = {Elsevier BV},
  pubmodel         = {Print},
  pubstate         = {ppublish},
  revised          = {2024-03-25},
}

@Article{McKinney2016,
  author           = {McKinney, Bill and Meyer, Peter A. and Crosas, Mercè and Sliz, Piotr},
  journal          = {Annals of the New York Academy of Sciences},
  title            = {Extension of research data repository system to support direct compute access to biomedical datasets: enhancing {D}ataverse to support large datasets},
  year             = {2016},
  issn             = {1749-6632},
  month            = nov,
  number           = {1},
  pages            = {95--104},
  volume           = {1387},
  abstract         = {Access to experimental X-ray diffraction image data is important for validation and reproduction of macromolecular models and indispensable for the development of structural biology processing methods. In response to the evolving needs of the structural biology community, we recently established a diffraction data publication system, the Structural Biology Data Grid (SBDG, data.sbgrid.org), to preserve primary experimental datasets supporting scientific publications. All datasets published through the SBDG are freely available to the research community under a public domain dedication license, with metadata compliant with the DataCite Schema (schema.datacite.org). A proof-of-concept study demonstrated community interest and utility. Publication of large datasets is a challenge shared by several fields, and the SBDG has begun collaborating with the Institute for Quantitative Social Science at Harvard University to extend the Dataverse (dataverse.org) open-source data repository system to structural biology datasets. Several extensions are necessary to support the size and metadata requirements for structural biology datasets. In this paper, we describe one such extension-functionality supporting preservation of file system structure within Dataverse-which is essential for both in-place computation and supporting non-HTTP data transfers.},
  citation-subset  = {IM},
  completed        = {2017-07-31},
  country          = {United States},
  creationdate     = {2024-05-06T22:08:30},
  doi              = {10.1111/nyas.13272},
  file             = {:by-author/M/McKinney/2016_McKinney_95_medline.pdf:PDF},
  issn-linking     = {0077-8923},
  issue            = {1},
  keywords         = {Access to Information; Animals; Biomedical Research, Trends; Computational Biology, Instrumentation, Methods, Trends; Computer Communication Networks, Instrumentation, Trends; Crystallography, X-Ray; Data Access Alliance; Data Mining, Trends; Database Management Systems, Trends; Databases, Protein, Trends; Dataverse; Humans; Image Interpretation, Computer-Assisted; Internet; Periodicals as Topic; Protein Conformation; RDMS; Research Data Management System; SBGrid; Software; X-ray Diffraction},
  mid              = {NIHMS817636},
  modificationdate = {2024-05-06T22:09:31},
  nlm-id           = {7506858},
  owner            = {saulius},
  pmc              = {PMC5546227},
  pmid             = {27862010},
  publisher        = {Wiley},
  pubmodel         = {Print-Electronic},
  pubstate         = {ppublish},
  revised          = {2018-11-13},
}

@Article{Woinska2016,
  author           = {Woińska, Magdalena and Grabowsky, Simon and Dominiak, Paulina M. and Woźniak, Krzysztof and Jayatilaka, Dylan},
  journal          = {Science Advances},
  title            = {Hydrogen atoms can be located accurately and precisely by x-ray crystallography},
  year             = {2016},
  issn             = {2375-2548},
  month            = may,
  number           = {5},
  pages            = {e1600192},
  volume           = {2},
  abstract         = {Precise and accurate structural information on hydrogen atoms is crucial to the study of energies of interactions important for crystal engineering, materials science, medicine, and pharmacy, and to the estimation of physical and chemical properties in solids. However, hydrogen atoms only scatter x-radiation weakly, so x-rays have not been used routinely to locate them accurately. Textbooks and teaching classes still emphasize that hydrogen atoms cannot be located with x-rays close to heavy elements; instead, neutron diffraction is needed. We show that, contrary to widespread expectation, hydrogen atoms can be located very accurately using x-ray diffraction, yielding bond lengths involving hydrogen atoms (A-H) that are in agreement with results from neutron diffraction mostly within a single standard deviation. The precision of the determination is also comparable between x-ray and neutron diffraction results. This has been achieved at resolutions as low as 0.8 Å using Hirshfeld atom refinement (HAR). We have applied HAR to 81 crystal structures of organic molecules and compared the A-H bond lengths with those from neutron measurements for A-H bonds sorted into bonds of the same class. We further show in a selection of inorganic compounds that hydrogen atoms can be located in bridging positions and close to heavy transition metals accurately and precisely. We anticipate that, in the future, conventional x-radiation sources at in-house diffractometers can be used routinely for locating hydrogen atoms in small molecules accurately instead of large-scale facilities such as spallation sources or nuclear reactors.},
  chemicals        = {Hydrogen},
  citation-subset  = {IM},
  completed        = {2017-05-04},
  country          = {United States},
  creationdate     = {2024-05-06T22:11:25},
  doi              = {10.1126/sciadv.1600192},
  file             = {:by-author/W/Woińska/2016_Woińska_e1600192.pdf:PDF},
  issn-linking     = {2375-2548},
  issue            = {5},
  keywords         = {Crystallography; Crystallography, X-Ray; Hirshfeld Atom Refinement; Hydrogen Atoms; Hydrogen Bonding; Hydrogen, Chemistry; Models, Molecular; Neutron Diffraction; Neutrons; Quantum Crystallography; X-Ray Diffraction; X-ray Diffraction},
  modificationdate = {2024-05-06T22:13:13},
  nlm-id           = {101653440},
  owner            = {saulius},
  pii              = {e1600192},
  pmc              = {PMC4928899},
  pmid             = {27386545},
  publisher        = {American Association for the Advancement of Science (AAAS)},
  pubmodel         = {Electronic-eCollection},
  pubstate         = {epublish},
  revised          = {2024-03-13},
}

@Article{Axelrod2024,
  author           = {Axelrod, Jeremy J. and Zhang, Jessie T. and Petrov, Petar N. and Glaeser, Robert M. and Müller, Holger},
  journal          = {Current Opinion in Structural Biology},
  title            = {Modern approaches to improving phase contrast electron microscopy},
  year             = {2024},
  issn             = {0959-440X},
  month            = jun,
  pages            = {102805},
  volume           = {86},
  abstract         = {Although defocus can be used to generate partial phase contrast in transmission electron microscope images, cryo-electron microscopy (cryo-EM) can be further improved by the development of phase plates which increase contrast by applying a phase shift to the unscattered part of the electron beam. Many approaches have been investigated, including the ponderomotive interaction between light and electrons. We review the recent successes achieved with this method in high-resolution, single-particle cryo-EM. We also review the status of using pulsed or near-field enhanced laser light as alternatives, along with approaches that use scanning transmission electron microscopy (STEM) with a segmented detector rather than a phase plate.},
  citation-subset  = {IM},
  country          = {England},
  creationdate     = {2024-05-07T06:22:33},
  doi              = {10.1016/j.sbi.2024.102805},
  file             = {:by-author/A/Axelrod/2024_Axelrod_102805_arxiv.pdf:PDF},
  issn-linking     = {0959-440X},
  keywords         = {CryoEM; Electrom Microscopy; Phase Contrast; Review},
  modificationdate = {2024-05-07T06:24:07},
  nlm-id           = {9107784},
  owner            = {saulius},
  pii              = {S0959-440X(24)00032-0},
  pmid             = {38531188},
  publisher        = {Elsevier BV},
  pubmodel         = {Print-Electronic},
  pubstate         = {aheadofprint},
  revised          = {2024-04-08},
  url              = {https://arxiv.org/pdf/2401.11678},
}

@Article{Chen2023,
  author           = {Chen, Lin and Fukata, Yuko and Murata, Kazuyoshi},
  journal          = {The Journal of Biochemistry},
  title            = {In situ cryo-electron tomography: a new method to elucidate cytoplasmic zoning at the molecular level},
  year             = {2023},
  issn             = {1756-2651},
  month            = dec,
  number           = {2},
  pages            = {187--193},
  volume           = {175},
  abstract         = {Cryo-electron microscopy was developed as a powerful tool for imaging biological specimens in near-native conditions. Nowadays, advances in technology, equipment and computations make it possible to obtain structures of biomolecules with near-atomic resolution. Furthermore, cryo-electron tomography combined with continuous specimen tilting allows structural analysis of heterogeneous biological specimens. In particular, when combined with a cryo-focused ion beam scanning electron microscope, it becomes possible to directly analyse the structure of the biomolecules within cells, a process known as in situ cryo-electron tomography. This technique has the potential to visualize cytoplasmic zoning, involving liquid-liquid phase separation, caused by biomolecular networks in aqueous solutions, which has been the subject of recent debate. Here, we review advances in structural studies of biomolecules to study cytoplasmic zoning by in situ cryo-electron tomography.},
  citation-subset  = {IM},
  completed        = {2024-02-19},
  country          = {England},
  creationdate     = {2024-05-07T06:27:04},
  doi              = {10.1093/jb/mvad102},
  file             = {:by-author/C/Chen/2023_Chen_187.pdf:PDF},
  issn-linking     = {0021-924X},
  issue            = {2},
  keywords         = {Cryo-electron Microscopy; Cryo-electron Tomography; Cryo-focused Ion Beam Scanning Electron Microscope; CryoEM; Cryoelectron Microscopy, Methods; Cytoplasmic Zoning; Electron Microscope Tomography, Methods; Liquid–liquid Phase Separation; Review; Tomography},
  modificationdate = {2024-05-07T06:28:31},
  nlm-id           = {0376600},
  owner            = {saulius},
  pii              = {7475814},
  pmid             = {38102736},
  publisher        = {Oxford University Press (OUP)},
  pubmodel         = {Print},
  pubstate         = {ppublish},
  revised          = {2024-02-19},
}

@Article{Murata2018,
  author           = {Murata, Kazuyoshi and Wolf, Matthias},
  journal          = {Biochimica et Biophysica Acta (BBA) - General Subjects},
  title            = {Cryo-electron microscopy for structural analysis of dynamic biological macromolecules},
  year             = {2018},
  issn             = {0304-4165},
  month            = feb,
  number           = {2},
  pages            = {324--334},
  volume           = {1862},
  comment          = {Cited in Chen2023.},
  creationdate     = {2024-05-07T06:30:57},
  doi              = {10.1016/j.bbagen.2017.07.020},
  file             = {:by-author/M/Murata/2018_Murata_324.pdf:PDF},
  keywords         = {CryoEM; Electron Microscopy; Review},
  license          = {CC BY (http://creativecommons.org/licenses/BY/4.0/)},
  modificationdate = {2024-05-07T07:02:03},
  owner            = {saulius},
  publisher        = {Elsevier BV},
}

@Article{Lesk2000,
  author           = {Lesk, Arthur M.},
  journal          = {The Mathematical Intelligencer},
  title            = {The unreasonable effectiveness of mathematics in molecular biology},
  year             = {2000},
  issn             = {0343-6993},
  month            = mar,
  number           = {2},
  pages            = {28--37},
  volume           = {22},
  comment          = {Cited by Konagurthu2014.},
  creationdate     = {2024-05-12T11:12:45},
  doi              = {10.1007/bf03025372},
  file             = {:by-author/L/Lesk/2000_Lesk_28.pdf:PDF},
  keywords         = {Rotational Superposition; Structure Superposition; Superposition},
  modificationdate = {2024-05-12T11:33:54},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media LLC},
}

@Article{Flower1999,
  author           = {Flower, D. R.},
  journal          = {J Mol Graph Model},
  title            = {Rotational superposition: a review of methods},
  year             = {1999},
  issn             = {1093-3263},
  pages            = {238--244},
  volume           = {17},
  abstract         = {Rotational superposition is one of the most commonly used algorithms in molecular modelling. Many different methods of solving superposition have been suggested. Of these, methods based on the quaternion parameterization of rotation are fast, accurate, and robust. Quaternion parameterization-based methods cannot result in rotation inversion and do not have special cases such as co-linearity or co-planarity of points. Thus, quaternion parameterization-based methods are the best choice for rotational superposition applications.},
  citation-subset  = {IM},
  completed        = {2000-05-08},
  country          = {United States},
  creationdate     = {2024-05-12T14:06:11},
  file             = {:by-author/F/Flower/1999_Flower_238.pdf:PDF},
  groups           = {sg/Molecule superposion, sg/Superposition, sg/Bioinf. Algorithms},
  issn-linking     = {1093-3263},
  issue            = {3-4},
  keywords         = {Review; Structure Superposition},
  modificationdate = {2024-05-12T14:06:48},
  nlm-id           = {9716237},
  owner            = {saulius},
  pmid             = {10736782},
  pubmodel         = {Print},
  pubstate         = {ppublish},
  references       = {58},
  revised          = {2004-11-17},
  season           = {Jun-Aug},
  timestamp        = {2012.05.16},
  url              = {https://pubmed.ncbi.nlm.nih.gov/10736782/},
}

@Article{Ernest2017,
  author           = {Ernest, Ampomah and Mensah, Ezekiel and Gilbert, Abilimi},
  journal          = {Communications on Applied Electronics},
  title            = {Qualitative assessment of compiled, interpreted and hybrid programming languages},
  year             = {2017},
  issn             = {2394-4714},
  month            = oct,
  number           = {7},
  pages            = {8--13},
  volume           = {7},
  creationdate     = {2024-05-12T14:11:47},
  doi              = {10.5120/cae2017652685},
  file             = {:by-author/E/Ernest/2017_Ernest_8.pdf:PDF},
  keywords         = {Programming Languages; Review; Scientific Computing},
  modificationdate = {2024-05-12T14:13:04},
  owner            = {saulius},
  publisher        = {Foundation of Computer Science},
}

@Book{Carvalho2009,
  editor           = {J. P. Carvalho},
  title            = {Proceedings of the {J}oint 2009 {I}nternational {F}uzzy {S}ystems {A}ssociation {W}orld {C}ongress and 2009 {E}uropean {S}ociety of {F}uzzy {L}ogic and {T}echnology {C}onference, {L}isbon, {P}ortugal, {J}uly 20 - 24, 2009},
  year             = {2009},
  address          = {Lisbon},
  isbn             = {9789899507968},
  creationdate     = {2024-05-12T14:27:28},
  modificationdate = {2024-05-12T14:29:29},
  owner            = {saulius},
  ppn_gvk          = {779453034},
  subtitle         = {Conference of the European Society for Fuzzy Logic and Technology},
}

@InProceedings{Fober2009a,
  author           = {Thomas Fober and Eyke Hüllermeie},
  booktitle        = {Proceedings of the {J}oint 2009 {I}nternational {F}uzzy {S}ystems {A}ssociation {W}orld {C}ongress and 2009 {E}uropean {S}ociety of {F}uzzy {L}ogic and {T}echnology {C}onference, {L}isbon, {P}ortugal, {J}uly 20 - 24, 2009},
  title            = {Fuzzy modeling of labeled point cloud superpositionfor the comparison of protein binding sites},
  year             = {2009},
  address          = {Lisbon},
  editor           = {J. P. Carvalho},
  pages            = {1299--1304},
  creationdate     = {2024-05-12T14:30:03},
  file             = {:by-author/F/Fober/2009_Fober_1299.pdf:PDF},
  isbn             = {9789899507968},
  keywords         = {Protein Structure; Protein Structure Comparison; Structure Superposition; Superposition},
  modificationdate = {2024-05-12T14:34:41},
  owner            = {saulius},
  ppn_gvk          = {779453034},
  subtitle         = {Conference of the European Society for Fuzzy Logic and Technology},
  url              = {https://web.archive.org/web/20170808161929/http://www.eusflat.org/proceedings/IFSA-EUSFLAT_2009/pdf/tema_1299.pdf},
}

@Article{Wolber2006a,
  author           = {Wolber, Gerhard and Dornhofer, Alois A. and Langer, Thierry},
  journal          = {Journal of computer-aided molecular design},
  title            = {Efficient overlay of small organic molecules using 3{D} pharmacophores},
  year             = {2006},
  issn             = {0920-654X},
  month            = dec,
  pages            = {773--788},
  volume           = {20},
  abstract         = {Aligning and overlaying two or more bio-active molecules is one of the key tasks in computational drug discovery and bio-activity prediction. Especially chemical-functional molecule characteristics from the view point of a macromolecular target represented as a 3D pharmacophore are the most interesting similarity measure when describing and analyzing macromolecule-ligand interaction. In this study, a novel approach for aligning rigid three-dimensional molecules according to their chemical-functional pharmacophoric features is presented and compared to the overlay of experimentally determined poses in a comparable macromolecule coordinate frame. The presented approach identifies optimal chemical feature pairs using distance and density characteristics obtained by correlating pharmacophoric geometries and thus proves to be faster than existing combinatorial alignment methods and creates more reasonable alignments than pure atom-based methods. Examples will be provided to demonstrate the feasibility, speed and intuitiveness of this method.},
  chemicals        = {Enzyme Inhibitors, Enzymes, Ligands, Macromolecular Substances},
  citation-subset  = {IM},
  completed        = {2007-05-03},
  country          = {Netherlands},
  creationdate     = {2024-05-12T16:59:13},
  doi              = {10.1007/s10822-006-9078-7},
  file             = {:by-author/W/Wolber/2006_Wolber_773.pdf:PDF},
  issn-linking     = {0920-654X},
  issue            = {12},
  keywords         = {Algorithms; Computer-Aided Design; Drug Design; Enzyme Inhibitors, Chemistry, Pharmacology; Enzymes, Chemistry; Ligands; Macromolecular Substances; Models, Molecular; Structure Superposition; Superposition},
  modificationdate = {2024-05-12T17:02:36},
  nlm-id           = {8710425},
  owner            = {saulius},
  pmid             = {17051340},
  pubmodel         = {Print-Electronic},
  pubstate         = {ppublish},
  revised          = {2018-11-13},
}

@Article{Lesk1986,
  author           = {Lesk, A. M.},
  journal          = {Acta Crystallographica Section A Foundations of Crystallography},
  title            = {A toolkit for computational molecular biology. {II}. On the optimal superposition of two sets of coordinates},
  year             = {1986},
  issn             = {0108-7673},
  month            = mar,
  number           = {2},
  pages            = {110--113},
  volume           = {42},
  creationdate     = {2024-05-12T21:40:17},
  doi              = {10.1107/s0108767386099786},
  file             = {:by-author/L/Lesk/1986_Lesk_110.pdf:PDF},
  keywords         = {Structure Superposition},
  modificationdate = {2024-05-12T21:45:23},
  owner            = {saulius},
  publisher        = {International Union of Crystallography (IUCr)},
}

@Article{Chen2004c,
  author           = {Chen, Chuanbo and Li, Qishen},
  journal          = {Acta Crystallographica Section A Foundations of Crystallography},
  title            = {A strict solution for the optimal superimposition of protein structures. Retraction},
  year             = {2004},
  issn             = {0108-7673},
  month            = oct,
  number           = {6},
  pages            = {640--640},
  volume           = {60},
  comment          = {Retraction of Chen2004.},
  creationdate     = {2024-05-12T21:51:02},
  doi              = {10.1107/s0108767304024730},
  file             = {:by-author/C/Chen/2004_Chen_640.pdf:PDF},
  keywords         = {Retraction; Structure Superposition},
  modificationdate = {2024-05-12T21:52:18},
  owner            = {saulius},
  publisher        = {International Union of Crystallography (IUCr)},
}

@TechReport{UTSLibary2020,
  author           = {{UTS Libary}},
  institution      = {University of Technology Sydney (UTS)},
  title            = {Differences between {APA} 7th and {H}arvard ({UTS})},
  year             = {2020},
  creationdate     = {2024-05-16T14:57:13},
  file             = {:by-author/U/UTSLibary/2020_UTSLibary_1.pdf:PDF},
  keywords         = {APA 7th; APA Citation Style; Bibliography; Citation Style; Citations; Differences; Harvard Citation Style},
  modificationdate = {2024-05-17T15:27:42},
  owner            = {saulius},
  url              = {https://www.lib.uts.edu.au/sites/default/files/2020-10/Differences between APA 7th and Harvard UTS.pdf},
}

@Article{Peters2015,
  author           = {Peters, A. J. and Sindrilaru, E. A. and Adde, G.},
  journal          = {Journal of Physics: Conference Series},
  title            = {{EOS} as the present and future solution for data storage at {CERN}},
  year             = {2015},
  issn             = {1742-6596},
  month            = dec,
  number           = {4},
  pages            = {042042},
  volume           = {664},
  creationdate     = {2024-05-17T15:24:11},
  doi              = {10.1088/1742-6596/664/4/042042},
  file             = {:by-author/P/Peters/2015_Peters_42042.pdf:PDF},
  keywords         = {Data Management; Data Reuse; Data Storage; Federated Data Storage; Raw Data; Shared File Systems},
  modificationdate = {2024-05-17T15:26:03},
  owner            = {saulius},
  publisher        = {IOP Publishing},
}

@InProceedings{Curcin2008,
  author           = {Curcin, V. and Ghanem, M.},
  booktitle        = {2008 Cairo International Biomedical Engineering Conference},
  title            = {Scientific workflow systems - can one size fit all?},
  year             = {2008},
  month            = dec,
  publisher        = {IEEE},
  creationdate     = {2024-05-17T16:18:55},
  doi              = {10.1109/cibec.2008.4786077},
  file             = {:by-author/C/Curcin/2008_Curcin_1.pdf:PDF},
  keywords         = {Data Management; Data-driven Research; Scientific Data; Workflow Management Systems},
  modificationdate = {2024-05-17T16:22:15},
  owner            = {saulius},
}

@TechReport{Klyne2002,
  author           = {Klyne, G. and Newman, C.},
  institution      = {IETF},
  title            = {Date and time on the internet: timestamps},
  year             = {2002},
  month            = jul,
  creationdate     = {2024-05-22T14:14:49},
  doi              = {10.17487/rfc3339},
  file             = {:by-author/K/Klyne/2002_Klyne_Date and Time on the Internet_ Timestamps.pdf:PDF},
  keywords         = {Date; Date and Time Format; Internet; RFC; Time; Timestamp},
  modificationdate = {2024-05-22T14:19:07},
  owner            = {saulius},
  school           = {RFC Editor},
  url              = {https://www.rfc-editor.org/info/rfc3339},
}

@TechReport{RoyalSociety2024,
  author           = {{The Royal Society}},
  institution      = {The Royal Society},
  title            = {Science in the age of {AI}: How artificial intelligence is changing the nature and method of scientific research},
  year             = {2024},
  type             = {Report},
  comment          = {Recommended by John Helliwell <john.helliwell@manchester.ac.uk> in his 2024-05-31 15:01 via CommDat <commdat@iucr.org>.},
  creationdate     = {2024-06-01T17:34:50},
  file             = {:by-author/R/RoyalSociety/2024_RoyalSociety_Science in the Age of AI_ How Artificial Intelligence Is Changing the Nature and Method of Scientific Research.pdf:PDF},
  isbn             = {978-1-78252-712-1},
  keywords         = {Artificial Intelligence (AI); Disruptive Technologies; Machine Learning (ML); Methodology of Science; Science; Scientific Method},
  license          = {https://creativecommons.org/licenses/by/4.0/},
  modificationdate = {2024-06-01T17:52:02},
  owner            = {saulius},
  url              = {https://royalsociety.org/-/media/policy/projects/science-in-the-age-of-ai/science-in-the-age-of-ai-report.pdf},
}

@TechReport{Berman2023,
  author           = {Glen Berman and Jennifer Chubb and Kate William},
  institution      = {The Royal Society},
  title            = {The use of artificial intelligence in science, technology, engineering, and medicine},
  year             = {2023},
  month            = may,
  type             = {Report},
  comment          = {Downloaded from the same page as (RoyalSociety2024).},
  creationdate     = {2024-06-01T17:48:20},
  file             = {:by-author/B/Berman/2023_Berman_The Use of Artificial Intelligence in Science, Technology, Engineering, and Medicine.pdf:PDF},
  keywords         = {Artificial Intelligence (AI); Disruptive Technologies; Machine Learning (ML); Methodology of Science; Science; Scientific Method},
  modificationdate = {2024-06-01T17:52:48},
  owner            = {saulius},
  url              = {https://royalsociety.org/-/media/policy/projects/science-in-the-age-of-ai/science-ai-taxonomy-report.pdf},
}

@TechReport{Berman2023a,
  author           = {Glen Berman and Jennifer Chubb and Kate Williams},
  institution      = {The Royal Society},
  title            = {Report summary: The use of {AI} in science, technology, engineering, and maths},
  year             = {2023},
  type             = {Executive Summary},
  comment          = {Downloaded from the same page as (RoyalSociety2024).},
  creationdate     = {2024-06-01T17:53:28},
  file             = {:by-author/B/Berman/2023_Berman_Report Summary_ the Use of AI in Science, Technology, Engineering, and Maths.pdf:PDF},
  keywords         = {Artificial Intelligence (AI); Disruptive Technologies; Machine Learning (ML); Methodology of Science; Science; Scientific Method},
  modificationdate = {2024-06-01T18:03:06},
  owner            = {saulius},
  url              = {https://royalsociety.org/-/media/policy/projects/science-in-the-age-of-ai/science-ai-taxonomy-summary.pdf},
}

@TechReport{RoyalSociety2023,
  author           = {{The Royal Society}},
  institution      = {The Royal Society},
  title            = {Science in the age of {AI}: a historical review},
  year             = {2023},
  type             = {Report},
  comment          = {Downloaded from the same page as (RoyalSociety2024).},
  creationdate     = {2024-06-01T17:56:35},
  file             = {:by-author/R/RoyalSociety/2023_RoyalSociety_Science in the Age of AI_ a Historical Review.pdf:PDF},
  keywords         = {Artificial Intelligence (AI); Disruptive Technologies; Machine Learning (ML); Methodology of Science; Science; Scientific Method},
  modificationdate = {2024-06-01T17:58:16},
  owner            = {saulius},
  url              = {https://royalsociety.org/-/media/policy/projects/science-in-the-age-of-ai/science-ai-historical-review.pdf},
}

@TechReport{Silvestre2023,
  author           = {Filip Silvestre and Amy Lam},
  institution      = {The Royal Society},
  title            = {Artificial intelligence related inventions},
  year             = {2023},
  month            = may,
  type             = {Report},
  comment          = {Downloaded from the same page as (RoyalSociety2024).},
  creationdate     = {2024-06-01T17:59:42},
  file             = {:by-author/S/Silvestre/2023_Silvestre_Artificial Intelligence Related Inventions.pdf:PDF},
  keywords         = {Artificial Intelligence (AI); Disruptive Technologies; Machine Learning (ML); Methodology of Science; Patents; Science; Scientific Method},
  modificationdate = {2024-06-01T18:05:56},
  owner            = {saulius},
  url              = {https://royalsociety.org/-/media/policy/projects/science-in-the-age-of-ai/science-ai-related-inventions-report.pdf},
}

@TechReport{Albornoz2023,
  author           = {Denisse Albornoz},
  institution      = {IP Pragmatics Limited},
  title            = {{IP} {P}ragmatics executive summary: Artificial intelligence related inventions},
  year             = {2023},
  type             = {Executive Summary},
  creationdate     = {2024-06-01T18:02:49},
  file             = {:by-author/A/Albornoz/2023_Albornoz_IP Pragmatics Executive Summary_ Artificial Intelligence Related Inventions.pdf:PDF},
  keywords         = {Artificial Intelligence (AI); Disruptive Technologies; Machine Learning (ML); Methodology of Science; Patents; Science; Scientific Method},
  modificationdate = {2024-06-01T18:06:02},
  owner            = {saulius},
  url              = {https://royalsociety.org/-/media/policy/projects/science-in-the-age-of-ai/science-ai-related-inventions-summary.pdf},
}

@Article{Brog2013,
  author           = {Brog, Jean-Pierre and Chanez, Claire-Lise and Crochet, Aurelien and Fromm, Katharina M.},
  journal          = {RSC Advances},
  title            = {Polymorphism, what it is and how to identify it: a systematic review},
  year             = {2013},
  issn             = {2046-2069},
  number           = {38},
  pages            = {16905},
  volume           = {3},
  comment          = {Cited in the reviewed manuscript from the JChemInf.},
  creationdate     = {2024-06-02T16:16:25},
  doi              = {10.1039/c3ra41559g},
  file             = {:by-author/B/Brog/2013_Brog_16905.pdf:PDF},
  keywords         = {Chemical Crystallography; Crystallography; Polymorphism},
  modificationdate = {2024-06-02T16:18:35},
  owner            = {saulius},
  publisher        = {Royal Society of Chemistry (RSC)},
  url              = {http://doc.rero.ch/record/209291/files/fro_pwh.pdf},
}

@Article{Peterson2021,
  author           = {Peterson, Gordon G. C. and Brgoch, Jakoah},
  journal          = {Journal of Physics: Energy},
  title            = {Materials discovery through machine learning formation energy},
  year             = {2021},
  issn             = {2515-7655},
  month            = mar,
  number           = {2},
  pages            = {022002},
  volume           = {3},
  comment          = {Cited in the reviewed manuscript from the JChemInf.},
  creationdate     = {2024-06-02T16:23:54},
  doi              = {10.1088/2515-7655/abe425},
  file             = {:by-author/P/Peterson/2021_Peterson_22002.pdf:PDF},
  keywords         = {Computational Materials Science; Crystal Structure Prediction (CSP); Formation Energies; Machine Learning (ML); Materials Science},
  modificationdate = {2024-06-02T17:44:23},
  owner            = {saulius},
  publisher        = {IOP Publishing},
}

@Article{Togo2018a,
  author           = {Togo, Atsushi and Shinohara, Kohei and Tanaka, Isao},
  journal          = {arXiv},
  title            = {$\texttt{Spglib}$: a software library for crystal symmetry search; v2},
  year             = {2018},
  month            = aug,
  abstract         = {A computer algorithm to search symmetries of crystal structures as implemented in the \texttt{spglib} code is described. An iterative algorithm is employed to robustly identify space group types tolerating a certain amount of distortion in the crystal structures. The source code is distributed under the 3-Clause BSD License, a permissive open-source software license. This paper focuses on the algorithm for identifying the space group symmetry of the crystal structures.},
  archiveprefix    = {arXiv},
  copyright        = {arXiv.org perpetual, non-exclusive license},
  creationdate     = {2024-06-02T17:45:40},
  doi              = {10.48550/ARXIV.1808.01590},
  eprint           = {1808.01590},
  file             = {:by-author/T/Togo/2018_Togo_1v2.pdf:PDF},
  keywords         = {Algorithms; C Library; Crystallography; Materials Science (cond-mat.mtrl-sci), FOS: Physical sciences, FOS: Physical sciences; Spacegroup Determination; Spacegroups; Spglib; Symmetry Determination},
  modificationdate = {2024-06-02T17:52:53},
  owner            = {saulius},
  primaryclass     = {cond-mat.mtrl-sci},
  publisher        = {arXiv},
}

@Article{Zhou2019,
  author           = {Zhou, Jun and Shen, Lei and Costa, Miguel Dias and Persson, Kristin A. and Ong, Shyue Ping and Huck, Patrick and Lu, Yunhao and Ma, Xiaoyang and Chen, Yiming and Tang, Hanmei and Feng, Yuan Ping},
  journal          = {Scientific Data},
  title            = {{2DMatPedia}, an open computational database of two-dimensional materials from top-down and bottom-up approaches},
  year             = {2019},
  issn             = {2052-4463},
  month            = jun,
  number           = {1},
  pages            = {86},
  volume           = {6},
  abstract         = {Two-dimensional (2D) materials have been a hot research topic in the last decade, due to novel fundamental physics in the reduced dimension and appealing applications. Systematic discovery of functional 2D materials has been the focus of many studies. Here, we present a large dataset of 2D materials, with more than 6,000 monolayer structures, obtained from both top-down and bottom-up discovery procedures. First, we screened all bulk materials in the database of Materials Project for layered structures by a topology-based algorithm and theoretically exfoliated them into monolayers. Then, we generated new 2D materials by chemical substitution of elements in known 2D materials by others from the same group in the periodic table. The structural, electronic and energetic properties of these 2D materials are consistently calculated, to provide a starting point for further material screening, data mining, data analysis and artificial intelligence applications. We present the details of computational methodology, data record and technical validation of our publicly available data ( http://www.2dmatpedia.org/ ).},
  comment          = {Cited in the reviewed manuscript from the JChemInf; used as a source of data there.},
  country          = {England},
  creationdate     = {2024-06-02T19:30:03},
  doi              = {10.1038/s41597-019-0097-3},
  file             = {:by-author/Z/Zhou/2019_Zhou_86.pdf:PDF},
  issn-linking     = {2052-4463},
  issue            = {1},
  keywords         = {2D Materials; Computational Materials Science; Materials Science},
  modificationdate = {2024-06-02T19:31:18},
  nlm-id           = {101640192},
  owner            = {saulius},
  pii              = {86},
  pmc              = {PMC6561947},
  pmid             = {31189922},
  publisher        = {Springer Science and Business Media LLC},
  pubmodel         = {Electronic},
  pubstate         = {epublish},
  revised          = {2023-10-12},
}

@Article{Marsh2002,
  author           = {Marsh, Richard E.},
  journal          = {Acta Crystallographica Section B Structural Science},
  title            = {The space groups of point group C 3: some corrections, some comments},
  year             = {2002},
  issn             = {0108-7681},
  month            = sep,
  number           = {5},
  pages            = {893--899},
  volume           = {58},
  creationdate     = {2024-06-02T20:32:39},
  doi              = {10.1107/s0108768102011758},
  file             = {:by-author/M/Marsh/2002_Marsh_893.pdf:PDF},
  keywords         = {Crystallography; Errors in Crystal Structures; Errors in Space Group Assignment; Space Group Determination; Space Groups},
  modificationdate = {2024-06-07T17:12:08},
  owner            = {saulius},
  publisher        = {International Union of Crystallography (IUCr)},
}

@Electronic{NKAB2024,
  author           = {{NKAB}},
  howpublished     = {Web Page},
  organization     = {Nucleic Acid Knowledgebase},
  title            = {Nucleotide geometry standards},
  url              = {https://www.nakb.org/basics/nucleotides.html},
  year             = {2024},
  creationdate     = {2024-06-07T17:05:05},
  file             = {:by-author/N/NKAB/2024_NKAB_Nucleotide Geometry Standards.pdf:PDF;:by-author/N/NKAB/2024_NKAB_Nucleotide Geometry Standards.odt:OpenDocument text;:by-author/N/NKAB/2024_NKAB_Nucleotide Geometry Standards.html:URL},
  keywords         = {Angle Definitions; Nucleic Acid Geometry; Nucleotide Geometry; Standards; Torsion Angles},
  modificationdate = {2024-06-07T17:15:30},
  owner            = {saulius},
}

@InBook{Tramontano2009,
  author           = {Tramontano, A.},
  publisher        = {Wiley},
  title            = {Bioinformatics},
  year             = {2009},
  isbn             = {9780470015902},
  month            = sep,
  booktitle        = {Encyclopedia of Life Sciences (ELS)},
  creationdate     = {2024-06-10T11:38:51},
  doi              = {10.1002/9780470015902.a0001900.pub2},
  file             = {:by-author/T/Tramontano/2009_Tramontano_1.pdf:PDF},
  journal          = {Encyclopedia of Life Sciences},
  keywords         = {Bioinformatics; Review; Software},
  modificationdate = {2024-06-10T11:41:26},
  owner            = {saulius},
}

@Webpage{Rhodes,
  author           = {Gale Rhodes},
  retrieved        = {2024-06-10T11:45+03:00},
  title            = {Get to know histidine. A versatile, important, and confusing amino acid},
  url              = {https://spdbv.unil.ch/TheMolecularLevel/Goodies/Get2NoHistidine.html},
  year             = {2005},
  creationdate     = {2024-06-10T11:42:37},
  file             = {:by-author/R/Rhodes/2005_Rhodes_Get to Know Histidine. a Versatile, Important, and Confusing Amino Acid.pdf:PDF;:by-author/R/Rhodes/2005_Rhodes_Get to Know Histidine. a Versatile, Important, and Confusing Amino Acid.odt:OpenDocument text},
  keywords         = {Biochemistry; Bioinformatics; Histidine; Histidine Properties; Histidine {pKa}; Negatively Charged His Side Chain},
  modificationdate = {2024-06-10T11:52:00},
  owner            = {saulius},
}

@Article{Batatia2024,
  author           = {Batatia, Ilyes and Benner, Philipp and Chiang, Yuan and Elena, Alin M. and Kovács, Dávid P. and Riebesell, Janosh and Advincula, Xavier R. and Asta, Mark and Avaylon, Matthew and Baldwin, William J. and Berger, Fabian and Bernstein, Noam and Bhowmik, Arghya and Blau, Samuel M. and Cărare, Vlad and Darby, James P. and De, Sandip and Della Pia, Flaviano and Deringer, Volker L. and Elijošius, Rokas and El-Machachi, Zakariya and Falcioni, Fabio and Fako, Edvin and Ferrari, Andrea C. and Genreith-Schriever, Annalena and George, Janine and Goodall, Rhys E. A. and Grey, Clare P. and Grigorev, Petr and Han, Shuang and Handley, Will and Heenen, Hendrik H. and Hermansson, Kersti and Holm, Christian and Jaafar, Jad and Hofmann, Stephan and Jakob, Konstantin S. and Jung, Hyunwook and Kapil, Venkat and Kaplan, Aaron D. and Karimitari, Nima and Kermode, James R. and Kroupa, Namu and Kullgren, Jolla and Kuner, Matthew C. and Kuryla, Domantas and Liepuoniute, Guoda and Margraf, Johannes T. and Magdău, Ioan-Bogdan and Michaelides, Angelos and Moore, J. Harry and Naik, Aakash A. and Niblett, Samuel P. and Norwood, Sam Walton and O'Neill, Niamh and Ortner, Christoph and Persson, Kristin A. and Reuter, Karsten and Rosen, Andrew S. and Schaaf, Lars L. and Schran, Christoph and Shi, Benjamin X. and Sivonxay, Eric and Stenczel, Tamás K. and Svahn, Viktor and Sutton, Christopher and Swinburne, Thomas D. and Tilly, Jules and van der Oord, Cas and Varga-Umbrich, Eszter and Vegge, Tejs and Vondrák, Martin and Wang, Yangshuai and Witt, William C. and Zills, Fabian and Csányi, Gábor},
  title            = {A foundation model for atomistic materials chemistry},
  year             = {2024},
  month            = dec,
  abstract         = {Machine-learned force fields have transformed the atomistic modelling of materials by enabling simulations of ab initio quality on unprecedented time and length scales. However, they are currently limited by: (i) the significant computational and human effort that must go into development and validation of potentials for each particular system of interest; and (ii) a general lack of transferability from one chemical system to the next. Here, using the state-of-the-art MACE architecture we introduce a single general-purpose ML model, trained on a public database of 150k inorganic crystals, that is capable of running stable molecular dynamics on molecules and materials. We demonstrate the power of the MACE-MP-0 model - and its qualitative and at times quantitative accuracy - on a diverse set problems in the physical sciences, including the properties of solids, liquids, gases, chemical reactions, interfaces and even the dynamics of a small protein. The model can be applied out of the box and as a starting or "foundation model" for any atomistic system of interest and is thus a step towards democratising the revolution of ML force fields by lowering the barriers to entry.},
  archiveprefix    = {arXiv},
  comment          = {Presented by Gábor Csányi in his OPTIMADE talk 2024-06-12.},
  copyright        = {Creative Commons Attribution Non Commercial No Derivatives 4.0 International},
  creationdate     = {2024-06-12T10:15:59},
  doi              = {10.48550/ARXIV.2401.00096},
  eprint           = {2401.00096},
  file             = {:by-author/B/Batatia/2024_Batatia_A Foundation Model for Atomistic Materials Chemistry.pdf:PDF},
  keywords         = {Chemical Physics (physics.chem-ph), Materials Science (cond-mat.mtrl-sci), FOS: Physical sciences, FOS: Physical sciences},
  modificationdate = {2024-06-12T10:20:14},
  owner            = {saulius},
  primaryclass     = {physics.chem-ph},
  publisher        = {arXiv},
}

@Manuscript{Chapin2008,
  author           = {Peter C. Chapin},
  title            = {{pthread} Tutorial},
  year             = {2008},
  keywords         = {C Programming Language; Computer Science (CS); Concurrent Programming; Multithread Programs; Mutexes; Mutual Exclusion; Pthreads; Semaphors},
  url              = {https://csce.uark.edu/~mqhuang/courses/3513/s2011/materials/Pthreads_Tutorial.pdf},
  creationdate     = {2024-06-19T09:01:03},
  file             = {:by-author/C/Chapin/2008_Chapin_Pthread Tutorial.pdf:PDF},
  modificationdate = {2024-06-19T09:04:44},
  owner            = {saulius},
}

@Article{Huang2024a,
  author           = {Huang, Jiao and Xing, Qianli and Ji, Jinglong and Yang, Bo},
  title            = {{ADA-GNN}: {A}tom-{D}istance-{A}ngle {G}raph {N}eural {N}etwork for crystal material property prediction},
  year             = {2024},
  month            = jan,
  abstract         = {Property prediction is a fundamental task in crystal material research. To model atoms and structures, structures represented as graphs are widely used and graph learning-based methods have achieved significant progress. Bond angles and bond distances are two key structural information that greatly influence crystal properties. However, most of the existing works only consider bond distances and overlook bond angles. The main challenge lies in the time cost of handling bond angles, which leads to a significant increase in inference time. To solve this issue, we first propose a crystal structure modeling based on dual scale neighbor partitioning mechanism, which uses a larger scale cutoff for edge neighbors and a smaller scale cutoff for angle neighbors. Then, we propose a novel Atom-Distance-Angle Graph Neural Network (ADA-GNN) for property prediction tasks, which can process node information and structural information separately. The accuracy of predictions and inference time are improved with the dual scale modeling and the specially designed architecture of ADA-GNN. The experimental results validate that our approach achieves state-of-the-art results in two large-scale material benchmark datasets on property prediction tasks.},
  archiveprefix    = {arXiv},
  copyright        = {arXiv.org perpetual, non-exclusive license},
  creationdate     = {2024-06-25T20:23:45},
  doi              = {10.48550/ARXIV.2401.11768},
  eprint           = {2401.11768},
  file             = {:by-author/H/Huang/2024_Huang_1.pdf:PDF},
  keywords         = {Artificial Neural Networks (ANN); Computational Materials Science; Crystal Property Prediction; FOS: Computer and Information Sciences; FOS: Physical Sciences; Graph Neural Networks (GNN); Machine Learning (ML); Machine Learning (cs.LG); Material Property Prediction; Materials Science; Materials Science (cond-mat.mtrl-sci)},
  modificationdate = {2024-06-25T20:28:16},
  owner            = {saulius},
  primaryclass     = {cs.LG},
  publisher        = {arXiv},
}

@Article{Blank2011,
  author           = {Blank, Martin and Goodman, Reba},
  journal          = {International Journal of Radiation Biology},
  title            = {{DNA} is a fractal antenna in electromagnetic fields},
  year             = {2011},
  issn             = {1362-3095},
  month            = feb,
  number           = {4},
  pages            = {409--415},
  volume           = {87},
  abstract         = {To review the responses of deoxyribonucleic acid (DNA) to electromagnetic fields (EMF) in different frequency ranges, and characterise the properties of DNA as an antenna. We examined published reports of increased stress protein levels and DNA strand breaks due to EMF interactions, both of which are indicative of DNA damage. We also considered antenna properties such as electronic conduction within DNA and its compact structure in the nucleus. EMF interactions with DNA are similar over a range of non-ionising frequencies, i.e., extremely low frequency (ELF) and radio frequency (RF) ranges. There are similar effects in the ionising range, but the reactions are more complex. The wide frequency range of interaction with EMF is the functional characteristic of a fractal antenna, and DNA appears to possess the two structural characteristics of fractal antennas, electronic conduction and self symmetry. These properties contribute to greater reactivity of DNA with EMF in the environment, and the DNA damage could account for increases in cancer epidemiology, as well as variations in the rate of chemical evolution in early geologic history.},
  chemicals        = {DNA},
  citation-subset  = {IM},
  comment          = {Discussed in the YouTube video "Is your DNA an EMF antenna?" at ScottiesTech.Info, URL: https://www.youtube.com/watch?v=B3jf_d_TVc8 [accessed 2024-07-07T15:10+03:00]},
  completed        = {2011-06-01},
  country          = {England},
  creationdate     = {2024-07-07T15:04:45},
  doi              = {10.3109/09553002.2011.538130},
  file             = {:by-author/B/Blank/2011_Blank_409.pdf:PDF},
  issn-linking     = {0955-3002},
  issue            = {4},
  keywords         = {Antenna; DNA Damage; DNA, Chemistry, Genetics, Radiation Effects; Elecrodynamics; Electromagnetic Fields; Fractals; Microwawes; Models, Chemical; Models, Genetic; Radiation Dosage; Radio Frequence; Radio Waves},
  modificationdate = {2024-07-07T15:11:04},
  nlm-id           = {8809243},
  owner            = {saulius},
  pmid             = {21457072},
  publisher        = {Informa UK Limited},
  pubmodel         = {Print-Electronic},
  pubstate         = {ppublish},
  revised          = {2022-04-09},
}

@Article{Yoenyuel2024,
  author           = {Yönyül, Burak and Alatlı, Oylum and Erdur, Rıza Cenk},
  journal          = {PeerJ Computer Science},
  title            = {{MonARCh}: an actor based architecture for dynamic linked data monitoring},
  year             = {2024},
  issn             = {2376-5992},
  month            = jul,
  pages            = {e2133},
  volume           = {10},
  creationdate     = {2024-07-13T10:05:26},
  doi              = {10.7717/peerj-cs.2133},
  file             = {:by-author/Y/Yönyül/2024_Yönyül_e2133.pdf:PDF},
  keywords         = {Computer Science (CS); Data Curation; Data Management; Linked Data; Scientific Data; Web of Data},
  modificationdate = {2024-07-13T10:07:56},
  owner            = {saulius},
  publisher        = {PeerJ},
}

@Article{Cao2024,
  author           = {Cao, Zhendong and Luo, Xiaoshan and Lv, Jian and Wang, Lei},
  title            = {Space group informed transformer for crystalline materials generation},
  year             = {2024},
  month            = mar,
  abstract         = {We introduce CrystalFormer, a transformer-based autoregressive model specifically designed for space group-controlled generation of crystalline materials. The space group symmetry significantly simplifies the crystal space, which is crucial for data and compute efficient generative modeling of crystalline materials. Leveraging the prominent discrete and sequential nature of the Wyckoff positions, CrystalFormer learns to generate crystals by directly predicting the species and locations of symmetry-inequivalent atoms in the unit cell. Our results demonstrate that CrystalFormer matches state-of-the-art performance on standard benchmarks for both validity, novelty, and stability of the generated crystalline materials. Our analysis also shows that CrystalFormer ingests sensible solid-state chemistry information from data for generative modeling. The CrystalFormer unifies symmetry-based structure search and generative pre-training in the realm of crystalline materials. The simplicity, generality, and flexibility of CrystalFormer position it as a promising architecture to be the foundational model of the entire crystalline materials space, heralding a new era in materials modeling and discovery.},
  archiveprefix    = {arXiv},
  copyright        = {arXiv.org perpetual, non-exclusive license},
  creationdate     = {2024-07-19T15:07:54},
  doi              = {10.48550/ARXIV.2403.15734},
  eprint           = {2403.15734},
  file             = {:by-author/C/Cao/2024_Cao_1.pdf:PDF},
  keywords         = {Materials Science (cond-mat.mtrl-sci), Machine Learning (cs.LG), Computational Physics (physics.comp-ph), FOS: Physical sciences, FOS: Physical sciences, FOS: Computer and information sciences, FOS: Computer and information sciences},
  modificationdate = {2024-07-19T15:09:05},
  owner            = {saulius},
  primaryclass     = {cond-mat.mtrl-sci},
  publisher        = {arXiv},
}

@InProceedings{Liu2024,
  author           = {Shengchao Liu and Zichao Rong and Divin Yan and Hongyu Guo and Omar M. Yaghi and Christian Borgs and Anima Anandkumar and Jennifer T. Chayes},
  booktitle        = {ICML 2024 Workshop on Geometry-grounded Representation Learning and Generative Modeling},
  title            = {Equivariant flow matching framework for learning molecular cluster crystallization},
  year             = {2024},
  creationdate     = {2024-07-19T16:46:15},
  eprint           = {https://openreview.net/forum?id=lCVqpQvr4l},
  file             = {:by-author/L/Liu/2024_Liu_1.pdf:PDF},
  keywords         = {Citing COD; Crystal Structure Prediction (CSP); Crystallography; Diffusions Networks; Flow; Machine Learning (ML)},
  modificationdate = {2024-07-19T16:49:47},
  owner            = {saulius},
  url              = {https://openreview.net/pdf?id=lCVqpQvr4l},
}

@Article{Petrauskiene2014,
  author           = {Žibutė Petrauskienė and Saulius Maskeliūnas},
  journal          = {ScieCom Info},
  title            = {Implementing national {O}pen {A}ccess research data archive},
  year             = {2014},
  number           = {1},
  volume           = {10},
  creationdate     = {2024-07-22T12:41:06},
  file             = {:by-author/P/Petrauskienė/2014_Petrauskienė_1.pdf:PDF},
  keywords         = {Data Management; Databases; FAIR Data; MIDAS; Mokslo Duomenys; Mokslo Duomenų Archyvas; Scientific Archives; Scientific Data; Scientific Databases},
  modificationdate = {2024-07-22T12:48:52},
  owner            = {saulius},
  url              = {https://journals.lub.lu.se/sciecominfo/article/view/10233/8623},
}

@Article{Vakser2022,
  author           = {Vakser, Ilya A. and Grudinin, Sergei and Jenkins, Nathan W. and Kundrotas, Petras J. and Deeds, Eric J.},
  journal          = {Proceedings of the National Academy of Sciences},
  title            = {Docking-based long timescale simulation of cell-size protein systems at atomic resolution},
  year             = {2022},
  issn             = {1091-6490},
  month            = oct,
  number           = {41},
  pages            = {e2210249119},
  volume           = {119},
  abstract         = {Computational methodologies are increasingly addressing modeling of the whole cell at the molecular level. Proteins and their interactions are the key component of cellular processes. Techniques for modeling protein interactions, thus far, have included protein docking and molecular simulation. The latter approaches account for the dynamics of the interactions but are relatively slow, if carried out at all-atom resolution, or are significantly coarse grained. Protein docking algorithms are far more efficient in sampling spatial coordinates. However, they do not account for the kinetics of the association (i.e., they do not involve the time coordinate). Our proof-of-concept study bridges the two modeling approaches, developing an approach that can reach unprecedented simulation timescales at all-atom resolution. The global intermolecular energy landscape of a large system of proteins was mapped by the pairwise fast Fourier transform docking and sampled in space and time by Monte Carlo simulations. The simulation protocol was parametrized on existing data and validated on a number of observations from experiments and molecular dynamics simulations. The simulation protocol performed consistently across very different systems of proteins at different protein concentrations. It recapitulated data on the previously observed protein diffusion rates and aggregation. The speed of calculation allows reaching second-long trajectories of protein systems that approach the size of the cells, at atomic resolution.},
  chemicals        = {Proteins},
  citation-subset  = {IM},
  comment          = {Cited by Kliment Olechnovič in his 2024-07-24 09:40 e-mail (PhD position invitation).},
  completed        = {2022-10-05},
  country          = {United States},
  creationdate     = {2024-07-25T10:11:34},
  doi              = {10.1073/pnas.2210249119},
  file             = {:by-author/V/Vakser/2022_Vakser_e2210249119.pdf:PDF},
  issn-linking     = {0027-8424},
  issue            = {41},
  keywords         = {Algorithms; Biophysical Phenomena; Energy Landscape; Kinetics; Macromolecule Fitting to Density; Molecular Dynamics Simulation; Monte Carlo Method; Protein Crowding; Protein Docking; Protein Interaction; Protein Recognition; Proteins; Whole-cell Modelling},
  modificationdate = {2024-07-25T10:13:42},
  nlm-id           = {7505876},
  owner            = {saulius},
  pii              = {e2210249119},
  pmc              = {PMC9565162},
  pmid             = {36191203},
  publisher        = {Proceedings of the National Academy of Sciences},
  pubmodel         = {Print-Electronic},
  pubstate         = {ppublish},
  revised          = {2023-07-02},
}

@Article{Baur1983,
  author           = {Baur, W. H. and Tillmanns, E. and Hofmeister, W.},
  journal          = {Acta Crystallographica Section B Structural Science},
  title            = {Topological analysis of crystal structures},
  year             = {1983},
  issn             = {0108-7681},
  month            = dec,
  number           = {6},
  pages            = {669--674},
  volume           = {39},
  creationdate     = {2024-07-31T16:04:20},
  doi              = {10.1107/s0108768183003201},
  file             = {:by-author/B/Baur/1983_Baur_669.pdf:PDF},
  keywords         = {Crystal Symmetry; Crystallography; Symmetry; Topology; Unnecesarily Low Symmetry; X-ray Crystallography},
  modificationdate = {2024-07-31T16:09:11},
  owner            = {saulius},
  publisher        = {International Union of Crystallography (IUCr)},
}

@Article{Baur1986,
  author           = {Baur, W. H. and Tillmanns, E.},
  journal          = {Acta Crystallographica Section B Structural Science},
  title            = {How to avoid unnecessarily low symmetry in crystal structure determinations},
  year             = {1986},
  issn             = {0108-7681},
  month            = feb,
  number           = {1},
  pages            = {95--111},
  volume           = {42},
  comment          = {Cited in a manuscript to Acta B sent for the review.
"Schomaker & Marsh (1979) recognized two categories: (1) the structure has been described with the wrong Laue symmetry; (2) the Laue symmetry is correct but an inversion center has been omitted. In the second case refinement by full-matrix least-squares methods results either in singular matrices or in high correlation coefficients between related parameters. Convergence is poor and atomic positions can be severely misdetermined."},
  creationdate     = {2024-07-31T16:08:47},
  doi              = {10.1107/s0108768186098518},
  file             = {:by-author/B/Baur/1986_Baur_95.pdf:PDF},
  keywords         = {Crystal Symmetry; Crystallography; Symmetry; Topology; Unnecesarily Low Symmetry; X-ray Crystallography},
  modificationdate = {2024-07-31T16:16:26},
  owner            = {saulius},
  publisher        = {International Union of Crystallography (IUCr)},
}

@Article{Baur2003,
  author           = {Baur, W. H. and Fischer, R. X.},
  journal          = {Mineralogical Magazine},
  title            = {On the significance of small deviations from higher symmetry},
  year             = {2003},
  issn             = {1471-8022},
  month            = aug,
  number           = {4},
  pages            = {793--797},
  volume           = {67},
  comment          = {Cites Baur1992},
  creationdate     = {2024-07-31T16:18:24},
  doi              = {10.1180/0026461036740135},
  file             = {:by-author/B/Baur/2003_Baur_793.pdf:PDF},
  keywords         = {Contains Coordinates; Crystal Symmetry; Crystallography; For COD Deposition; Symmetry; Topology; Unnecesarily Low Symmetry; X-ray Crystallography},
  modificationdate = {2024-07-31T16:36:52},
  owner            = {saulius},
  publisher        = {Mineralogical Society},
}

@InBook{Baur1981,
  author           = {Baur, Werner H.},
  pages            = {31--52},
  publisher        = {Elsevier},
  title            = {Interatomic distance predictions for computer simulation of crystal structures},
  year             = {1981},
  booktitle        = {Industrial Chemistry Library},
  creationdate     = {2024-07-31T16:33:39},
  doi              = {10.1016/b978-0-12-525102-0.50008-6},
  file             = {:by-author/B/Baur/1981_Baur_31.pdf:PDF},
  issn             = {0926-9614},
  keywords         = {Crystallography; Distance Geometry; Interatomic Distances},
  modificationdate = {2024-07-31T16:34:55},
  owner            = {saulius},
}

@Article{Baur1974,
  author           = {Baur, W. H.},
  journal          = {Acta Crystallographica Section B Structural Crystallography and Crystal Chemistry},
  title            = {The geometry of polyhedral distortions. Predictive relationships for the phosphate group},
  year             = {1974},
  issn             = {0567-7408},
  month            = may,
  number           = {5},
  pages            = {1195--1215},
  volume           = {30},
  creationdate     = {2024-07-31T16:38:58},
  doi              = {10.1107/s0567740874004560},
  file             = {:by-author/B/Baur/1974_Baur_1195.pdf:PDF},
  keywords         = {Crystal Symmetry; Crystallography; Symmetry; Topology; Unnecesarily Low Symmetry; X-ray Crystallography},
  modificationdate = {2024-07-31T16:40:10},
  owner            = {saulius},
  publisher        = {International Union of Crystallography (IUCr)},
}

@Article{Hicks2018,
  author           = {David Hicks and Corey Oses and Eric Gossett and Geena Gomez and Richard H. Taylor and Cormac Toher and Michael J. Mehl and Ohad Levy and Stefano Curtarolo},
  journal          = {Acta Crystallographica Section A Foundations and Advances},
  title            = {\textit{{AFLOW}\/}-\textit{{SYM}\/}: platform for the complete, automatic and self-consistent symmetry analysis of crystals},
  year             = {2018},
  issn             = {2053-2733},
  month            = {may},
  number           = {3},
  pages            = {184--203},
  volume           = {74},
  abstract         = {Determination of the symmetry profile of structures is a persistent challenge in materials science. Results often vary amongst standard packages, hindering autonomous materials development by requiring continuous user attention and educated guesses. This article presents a robust procedure for evaluating the complete suite of symmetry properties, featuring various representations for the point, factor and space groups, site symmetries and Wyckoff positions. The protocol determines a system-specific mapping tolerance that yields symmetry operations entirely commensurate with fundamental crystallographic principles. The self-consistent tolerance characterizes the effective spatial resolution of the reported atomic positions. The approach is compared with the most used programs and is successfully validated against the space-group information provided for over 54 000 entries in the Inorganic Crystal Structure Database (ICSD). Subsequently, a complete symmetry analysis is applied to all 1.7+ million entries of the AFLOW data repository. The AFLOW-SYM package has been implemented in, and made available for, public use through the automated ab initio framework AFLOW.},
  completed        = {2018-05-16},
  country          = {United States},
  creationdate     = {2024-07-31T16:47:35},
  doi              = {10.1107/s2053273318003066},
  file             = {:by-author/H/Hicks/2018_Hicks_184.pdf:PDF;:by-author/H/Hicks/2018_Hicks_184_arXiv.pdf:PDF;:by-author/H/Hicks/2018_Hicks_184_suppl/ae5042sup1.pdf:PDF},
  issn-linking     = {2053-2733},
  issue            = {Pt 3},
  keywords         = {Computer Libraries; Crystallography; Software; Symmetry},
  modificationdate = {2024-07-31T16:50:22},
  nlm-id           = {101620182},
  owner            = {saulius},
  pii              = {S2053273318003066},
  pmid             = {29724965},
  publisher        = {International Union of Crystallography ({IUCr})},
  pubmodel         = {Print-Electronic},
  pubstate         = {ppublish},
  revised          = {2018-05-16},
  timestamp        = {2022.06.15},
}

@Article{Griffin2024,
  author           = {Griffin, Benjamin W. and Martin-Silverstone, Elizabeth and Pêgas, Rodrigo V. and Meilak, Erik Anthony and Costa, Fabiana R. and Palmer, Colin and Rayfield, Emily J.},
  journal          = {PeerJ},
  title            = {Modelling take-off moment arms in an ornithocheiraean pterosaur},
  year             = {2024},
  issn             = {2167-8359},
  month            = aug,
  pages            = {e17678},
  volume           = {12},
  comment          = {Full model data downloaded from https://data.bris.ac.uk/data/dataset/314kcutovxtty25yua4ptpjwk1.
The R scripts for randomly varying moment arm outputs are available in the Supplementary Files and Github: https://github.com/BWGriffin/PhD-Codes.
Supplemental information for this article can be found online at http://dx.doi.org/10.7717/
peerj.17678#supplemental-information (all files downloaded and commited here, not all files linked into the bibliography).},
  creationdate     = {2024-08-06T09:45:42},
  doi              = {10.7717/peerj.17678},
  file             = {:by-author/G/Griffin/2024_Griffin_e17678.pdf:PDF;:by-author/G/Griffin/2024_Griffin_e17678_data/314kcutovxtty25yua4ptpjwk1.zip:zip;:by-author/G/Griffin/2024_Griffin_e17678_suppl/10.7717/peerj.17678/supp-1/Graph_Values_Supplement.csv:csv},
  keywords         = {Archeology; Computer Modelling; Mechanics},
  modificationdate = {2024-08-15T16:02:29},
  owner            = {saulius},
  publisher        = {PeerJ},
}

@Article{Kubin2024,
  author           = {Kubin, Markus and Sedeqi, Mojeeb Rahman and Schmidt, Alexander and Gilein, Astrid and Glodowski, Tempest and Serve, Vivien and Günther, Gerrit and Weisweiler, Nina Leonie and Preuß, Gabriel and Mannix, Oonagh},
  journal          = {Data Science Journal},
  title            = {A data-driven approach to monitor and improve open and {FAIR} research data in a federated research ecosystem},
  year             = {2024},
  issn             = {1683-1470},
  pages            = {41},
  volume           = {23},
  creationdate     = {2024-08-15T16:00:39},
  doi              = {10.5334/dsj-2024-041},
  file             = {:by-author/K/Kubin/2024_Kubin_41.pdf:PDF},
  keywords         = {Data Curation; Data Science; Metadata; Scientific Data Repositories},
  modificationdate = {2024-08-15T16:06:38},
  owner            = {saulius},
  publisher        = {Ubiquity Press, Ltd.},
}

@Article{Arkhipova2017,
  author           = {Valentina Arkhipova and Albert Guskov and Dirk-Jan Slotboom},
  journal          = {Journal of General Physiology},
  title            = {Analysis of the quality of crystallographic data and the limitations of structural models},
  year             = {2017},
  month            = {oct},
  number           = {12},
  pages            = {1091--1103},
  volume           = {149},
  creationdate     = {2024-08-15T16:26:27},
  doi              = {10.1085/jgp.201711852},
  file             = {:by-author/A/Arkhipova/2017_Arkhipova_1091.pdf:PDF},
  keywords         = {Crystallography; Data Curation; Data Science; Metadata; Scientific Data Repositories},
  modificationdate = {2024-08-15T16:28:06},
  owner            = {saulius},
  publisher        = {Rockefeller University Press},
}

@Article{Wang2015a,
  author           = {Jimin Wang},
  journal          = {Protein Science},
  title            = {Estimation of the quality of refined protein crystal structures},
  year             = {2015},
  month            = {mar},
  number           = {5},
  pages            = {661--669},
  volume           = {24},
  creationdate     = {2024-08-15T16:30:37},
  doi              = {10.1002/pro.2639},
  file             = {:by-author/W/Wang/2015_Wang_661.pdf:PDF},
  keywords         = {Criticism; Crystallography; Data Curation; Data Science; Macromolecular Crystallography; Metadata; Protein Crystallography; R-factors; X-ray Crystallography},
  modificationdate = {2024-08-15T16:32:17},
  owner            = {saulius},
  publisher        = {Wiley},
}

@Article{Hall1995,
  author           = {Hall, Stephen S.},
  journal          = {Science},
  title            = {Protein images update natural history: a combination of improved biological techniques, hardware, and software has unleashed a flood of brightly colored images of protein structure. They’re changing the way biology is done},
  year             = {1995},
  issn             = {1095-9203},
  month            = feb,
  number           = {5198},
  pages            = {620--624},
  volume           = {267},
  comment          = {Cited in Kleywegt1995.},
  creationdate     = {2024-08-15T17:00:47},
  doi              = {10.1126/science.7839137},
  file             = {:by-author/H/Hall/1995_Hall_620.pdf:PDF},
  keywords         = {Crystallography; Data Reliability; Protein Crystallography; Scientific Method},
  modificationdate = {2024-08-15T17:05:57},
  owner            = {saulius},
  publisher        = {American Association for the Advancement of Science (AAAS)},
}

@Article{Boehm1999a,
  author           = {Boehm, B. and Abts, C.},
  journal          = {Computer},
  title            = {{COTS} integration: plug and pray?},
  year             = {1999},
  issn             = {0018-9162},
  number           = {1},
  pages            = {135--138},
  volume           = {32},
  comment          = {Cites: Council, N. R. (1997) Ada and Beyond: Software Policies for the Department of Defense. National Academies Press.},
  creationdate     = {2024-08-16T11:42:31},
  doi              = {10.1109/2.738311},
  file             = {:by-author/B/Boehm/1999_Boehm_135.pdf:PDF},
  keywords         = {Ada; Commercial Off-The-Shelf Software (COTS); Computer Science (CS)},
  modificationdate = {2024-08-16T11:51:30},
  owner            = {saulius},
  publisher        = {Institute of Electrical and Electronics Engineers (IEEE)},
}

@InProceedings{Carlisle2006,
  author           = {Carlisle, Martin C. and Hamilton, J. A.},
  booktitle        = {Proceedings of the 2006 annual ACM SIGAda international conference on Ada},
  title            = {Integrating {A}da 2005 into visual studio 2005},
  year             = {2006},
  month            = nov,
  pages            = {15--20},
  publisher        = {ACM},
  series           = {SIGAda ’06},
  collection       = {SIGAda ’06},
  comment          = {Cites: Council, N. R. (1997) Ada and Beyond: Software Policies for the Department of Defense. National Academies Press.},
  creationdate     = {2024-08-16T11:50:01},
  doi              = {10.1145/1185642.1185646},
  file             = {:by-author/C/Carlisle/2006_Carlisle_15.pdf:PDF},
  keywords         = {Ada; Commercial Off-The-Shelf Software (COTS); Computer Science (CS)},
  modificationdate = {2024-08-23T09:58:08},
  owner            = {saulius},
}

@InProceedings{Murtagh1998,
  author           = {Murtagh, Jeanne L. and Hamilton, John A.},
  booktitle        = {Proceedings of the 1998 annual ACM SIGAda international conference on Ada},
  title            = {A comparison of {Ada} and {Pascal} in an introductory computer science course},
  year             = {1998},
  month            = nov,
  pages            = {75--80},
  publisher        = {ACM},
  series           = {SIGAda98},
  collection       = {SIGAda98},
  comment          = {Cites: Council, N. R. (1997) Ada and Beyond: Software Policies for the Department of Defense. National Academies Press.},
  creationdate     = {2024-08-16T11:54:55},
  doi              = {10.1145/289524.289535},
  file             = {:by-author/M/Murtagh/1998_Murtagh_75.pdf:PDF},
  keywords         = {Ada; Computer Science (CS); Teaching},
  modificationdate = {2024-08-16T11:56:47},
  owner            = {saulius},
}

@InProceedings{Gargaro1997,
  author           = {Gargaro, Anthony},
  booktitle        = {Proceedings of the conference on TRI-Ada ’97 - TRI-Ada ’97},
  title            = {{A}da-{J}ava communication in {ADEPT}},
  year             = {1997},
  pages            = {231--245},
  publisher        = {ACM Press},
  series           = {TRI-Ada ’97},
  collection       = {TRI-Ada ’97},
  comment          = {Cites: Council, N. R. (1997) Ada and Beyond: Software Policies for the Department of Defense. National Academies Press.},
  creationdate     = {2024-08-16T12:03:31},
  doi              = {10.1145/269629.269653},
  file             = {:by-author/G/Gargaro/1997_Gargaro_231.pdf:PDF},
  keywords         = {Ada; Computer Science (CS); Interoperability; Java; Multi-language Programming},
  modificationdate = {2024-08-16T12:07:02},
  owner            = {saulius},
}

@Article{Garlan1995,
  author           = {Garlan, D. and Allen, R. and Ockerbloom, J.},
  journal          = {IEEE Software},
  title            = {Architectural mismatch: why reuse is so hard},
  year             = {1995},
  issn             = {0740-7459},
  number           = {6},
  pages            = {17--26},
  volume           = {12},
  comment          = {Cited in Boehm1999a.},
  creationdate     = {2024-08-17T09:32:42},
  doi              = {10.1109/52.469757},
  file             = {:by-author/G/Garlan/1995_Garlan_17.pdf:PDF},
  keywords         = {Computer Science (CS); Interface Design; Software Design; Software Engineering; Software Reuse},
  modificationdate = {2024-08-17T09:35:10},
  owner            = {saulius},
  publisher        = {Institute of Electrical and Electronics Engineers (IEEE)},
}

@InProceedings{Gargaro1997a,
  author           = {Gargaro, Anthony and Smith, Gary and Theriault, Ronald J. and Volz, Richard A. and Waldrop, Raymond},
  booktitle        = {Proceedings of the eighth international workshop on Real-Time Ada - IRTAW ’97},
  title            = {Future directions in {A}da---distributed execution and heterogeneous language interoperability toolsets},
  year             = {1997},
  pages            = {51--56},
  publisher        = {ACM Press},
  series           = {IRTAW ’97},
  collection       = {IRTAW ’97},
  creationdate     = {2024-08-17T10:47:58},
  doi              = {10.1145/271658.271690},
  file             = {:by-author/G/Gargaro/1997_Gargaro_51.pdf:PDF},
  issn             = {1094-3641},
  keywords         = {Ada; Ada 95; Ada Programming Language; Computer Science (CS); Interface Design; Software Design; Software Engineering; Software Reuse},
  modificationdate = {2024-08-23T09:57:52},
  owner            = {saulius},
}

@Article{Boulay1981,
  author           = {Boulay, Benedict du and O’Shea, Tim and Monk, John},
  journal          = {International Journal of Man-Machine Studies},
  title            = {The black box inside the glass box: presenting computing concepts to novices},
  year             = {1981},
  issn             = {0020-7373},
  month            = apr,
  number           = {3},
  pages            = {237--249},
  volume           = {14},
  comment          = {Found via: https://en.wikipedia.org/wiki/White_box_(software_engineering) [accessed 2024-08-23T11:41+03:00].},
  creationdate     = {2024-08-23T11:39:47},
  doi              = {10.1016/s0020-7373(81)80056-9},
  file             = {:by-author/B/Boulay/1981_Boulay_237.pdf:PDF},
  keywords         = {Black Box; Computer Science (CS); Glass Box; Programming Languages; Teaching},
  modificationdate = {2024-08-23T11:42:02},
  owner            = {saulius},
  publisher        = {Elsevier BV},
}

@Article{Assmann2016,
  author           = {Assmann, Greta and Brehm, Wolfgang and Diederichs, Kay},
  journal          = {Journal of Applied Crystallography},
  title            = {Identification of rogue datasets in serial crystallography},
  year             = {2016},
  issn             = {1600-5767},
  month            = apr,
  number           = {3},
  pages            = {1021--1028},
  volume           = {49},
  comment          = {Contains definition of CC1/2. Found via https://wiki.uni-konstanz.de/xds/index.php/CC1/2 [accessed 2024-08-25T12:04+03:00].},
  creationdate     = {2024-08-25T12:03:01},
  doi              = {10.1107/s1600576716005471},
  file             = {:by-author/A/Assmann/2016_Assmann_1021.pdf:PDF},
  keywords         = {Crystallography; Data Quality; Data Quality Indicators; X-ray Crystallography},
  modificationdate = {2024-08-25T12:06:19},
  owner            = {saulius},
  publisher        = {International Union of Crystallography (IUCr)},
}

@Article{Fanwick2016,
  author           = {Fanwick, Phillip E.},
  journal          = {Crystallography Reviews},
  title            = {Small molecule crystallography past, present, and future: a career long review of chemical crystallography},
  year             = {2016},
  issn             = {1476-3508},
  month            = jul,
  number           = {4},
  pages            = {250--279},
  volume           = {22},
  creationdate     = {2024-08-26T11:43:23},
  doi              = {10.1080/0889311x.2016.1199550},
  file             = {:by-author/F/Fanwick/2016_Fanwick_250.pdf:PDF},
  keywords         = {Crystallography; Hydrogen Positions; Review; Structure Quality; X-ray Crystallography},
  modificationdate = {2024-08-26T11:45:38},
  owner            = {saulius},
  publisher        = {Informa UK Limited},
}

@Article{Alvarez2018,
  author           = {Alvarez, Santiago},
  journal          = {Inorganica Chimica Acta},
  title            = {Zero- and mono-coordinate transition metals in crystal structures: A box full of surprises},
  year             = {2018},
  issn             = {0020-1693},
  month            = jan,
  pages            = {74--81},
  volume           = {470},
  comment          = {Cites Fanwick2016 and Harlow1996 (under the same ref. number [9]).},
  creationdate     = {2024-08-26T11:47:03},
  doi              = {10.1016/j.ica.2017.03.036},
  file             = {:by-author/A/Alvarez/2018_Alvarez_74.pdf:PDF},
  keywords         = {Crystallography; Metal Coordination; Structure Quality; X-ray Crystallography},
  modificationdate = {2024-08-26T11:49:51},
  owner            = {saulius},
  publisher        = {Elsevier BV},
}

@Article{Hempler2017,
  author           = {Hempler, Daniela and Schmidt, Martin U. and van de Streek, Jacco},
  journal          = {Acta Crystallographica Section B Structural Science, Crystal Engineering and Materials},
  title            = {Validation of missed space-group symmetry in X-ray powder diffraction structures with dispersion-corrected density functional theory},
  year             = {2017},
  issn             = {2052-5206},
  month            = jul,
  number           = {4},
  pages            = {756--766},
  volume           = {73},
  comment          = {Cites Harlow1996.},
  creationdate     = {2024-08-26T12:38:28},
  doi              = {10.1107/s2052520617005935},
  file             = {:by-author/H/Hempler/2017_Hempler_756.pdf:PDF},
  keywords         = {Crystallography; Density Functional Theory (DFT); Structure Quality; X-ray Crystallography},
  modificationdate = {2024-08-26T13:15:10},
  owner            = {saulius},
  publisher        = {International Union of Crystallography (IUCr)},
}

@Article{Mighell1996,
  author           = {Mighell, A. D. and Karen, V. L.},
  journal          = {Journal of Research of the National Institute of Standards and Technology},
  title            = {{NIST} crystallographic databases for research and analysis},
  year             = {1996},
  issn             = {1044-677X},
  month            = may,
  number           = {3},
  pages            = {273},
  volume           = {101},
  comment          = {Cites Harlow1996 (ref. [12]).},
  creationdate     = {2024-08-26T13:26:58},
  doi              = {10.6028/jres.101.028},
  file             = {:by-author/M/Mighell/1996_Mighell_273.pdf:PDF},
  keywords         = {Crystallography; Databases; Scientific Databases; Structure Quality; X-ray Crystallography},
  modificationdate = {2024-08-26T13:29:19},
  owner            = {saulius},
  publisher        = {National Institute of Standards and Technology (NIST)},
}

@Article{Becker2017a,
  author           = {Becker, Sabine and Müller, Peter},
  journal          = {Chemistry – A European Journal},
  title            = {A reinterpretation of the crystal structure analysis of [{K}(crypt‐222)]+{CF3}−: no proof for the trifluoromethanide ion},
  year             = {2017},
  issn             = {1521-3765},
  month            = apr,
  number           = {29},
  pages            = {7081--7086},
  volume           = {23},
  comment          = {Cites Harlow1996.},
  creationdate     = {2024-08-26T13:34:13},
  doi              = {10.1002/chem.201700554},
  file             = {:by-author/B/Becker/2017_Becker_7081.pdf:PDF},
  keywords         = {Crystallography; Structure Correction; Structure Quality; X-ray Crystallography},
  modificationdate = {2024-08-26T14:01:48},
  owner            = {saulius},
  publisher        = {Wiley},
}

@Article{Thompson2023,
  author           = {Thompson, Amber L. and White, Nicholas G.},
  journal          = {Chemical Society Reviews},
  title            = {Hydrogen atoms in supramolecular chemistry: a structural perspective. Where are they, and why does it matter?},
  year             = {2023},
  issn             = {1460-4744},
  number           = {18},
  pages            = {6254--6269},
  volume           = {52},
  comment          = {Cites Harlow1996. Contains extensive bibliography about structure quality.},
  creationdate     = {2024-08-26T13:53:15},
  doi              = {10.1039/d3cs00516j},
  file             = {:by-author/T/Thompson/2023_Thompson_6254.pdf:PDF},
  keywords         = {Crystallography; Hydrogen Atoms; Review; Structure Quality; Tutorial; X-ray Crystallography},
  modificationdate = {2024-08-26T13:59:39},
  owner            = {saulius},
  publisher        = {Royal Society of Chemistry (RSC)},
}

@Article{Shlian2023,
  author           = {Shlian, Daniel G. and Narvaez, Daymieri and Parkin, Gerard},
  journal          = {Polyhedron},
  title            = {Structural characterization of zinc and cadmium complexes derived from {N}-(4-carboxybenzyl)pyridinium: Revisiting the structure of ({Cbp})2{ZnBr2} and influence of the metal on carboxylate coordination mode},
  year             = {2023},
  issn             = {0277-5387},
  month            = jan,
  pages            = {116126},
  volume           = {230},
  comment          = {Cites Harlow1996. Contains extensive bibliography discussing structure quality and X-ray data interpretation.},
  creationdate     = {2024-08-26T14:01:05},
  doi              = {10.1016/j.poly.2022.116126},
  file             = {:by-author/S/Shlian/2023_Shlian_116126.pdf:PDF},
  keywords         = {Crystallography; Structure Correction; Structure Quality; X-ray Crystallography},
  modificationdate = {2024-08-26T14:05:45},
  owner            = {saulius},
  publisher        = {Elsevier BV},
}

@Article{Beebe1994,
  author           = {Nelson H. F. Beebe},
  title            = {Accurate square root computation},
  year             = {1994},
  creationdate     = {2024-08-29T12:41:48},
  file             = {:by-author/B/Beebe/1994_Beebe_Accurate Square Root Computation.pdf:PDF},
  keywords         = {Computer Science (CS); IEEE 745; Math},
  modificationdate = {2024-08-29T12:46:31},
  owner            = {saulius},
  url              = {https://www.math.utah.edu/~beebe/software/ieee/sqrt.pdf},
}

@Poster{Stewart2024,
  author           = {Patrick Shaw Stewart and Stefan Kolek and Peter Baldock and Jack Stubbs and Ivo Tews},
  title            = {Sample preparation for routine and advanced structural biology, including serial datacollection and micro{ED}},
  year             = {2024},
  creationdate     = {2024-08-29T16:39:18},
  file             = {:by-author/S/Stewart/2024_Stewart_Sample Preparation for Routine and Advanced Structural Biology, Including Serial Datacollection and MicroED.pdf:PDF},
  keywords         = {Crystallisation; Crystallography; Oryx; Protein Crystallisation; Sample Preparation; X-ray Crystallography},
  modificationdate = {2024-08-29T16:43:13},
  owner            = {saulius},
}

@InBook{Herman2001,
  author           = {Herman, Ivan and Marshall, M. Scott},
  pages            = {52--62},
  publisher        = {Springer Berlin Heidelberg},
  title            = {{GraphXML} — an {XML}-based graph description format},
  year             = {2001},
  isbn             = {9783540445418},
  booktitle        = {Graph Drawing},
  creationdate     = {2024-09-02T11:00:46},
  doi              = {10.1007/3-540-44541-2_6},
  file             = {:by-author/H/Herman/2001_Herman_52.pdf:PDF},
  issn             = {0302-9743},
  keywords         = {Computer Science (CS); Data Formats; Formats; Graph Representation; Graph Theory; Graphs; XML},
  modificationdate = {2024-09-02T11:05:14},
  owner            = {saulius},
}

@Article{Jumper2021,
  author           = {Jumper, John and Evans, Richard and Pritzel, Alexander and Green, Tim and Figurnov, Michael and Ronneberger, Olaf and Tunyasuvunakool, Kathryn and Bates, Russ and Žídek, Augustin and Potapenko, Anna and Bridgland, Alex and Meyer, Clemens and Kohl, Simon A. A. and Ballard, Andrew J. and Cowie, Andrew and Romera-Paredes, Bernardino and Nikolov, Stanislav and Jain, Rishub and Adler, Jonas and Back, Trevor and Petersen, Stig and Reiman, David and Clancy, Ellen and Zielinski, Michal and Steinegger, Martin and Pacholska, Michalina and Berghammer, Tamas and Bodenstein, Sebastian and Silver, David and Vinyals, Oriol and Senior, Andrew W. and Kavukcuoglu, Koray and Kohli, Pushmeet and Hassabis, Demis},
  journal          = {Nature},
  title            = {Highly accurate protein structure prediction with {AlphaFold}},
  year             = {2021},
  issn             = {1476-4687},
  month            = jul,
  number           = {7873},
  pages            = {583--589},
  volume           = {596},
  comment          = {Recommended by Dmitrii Zhemchuzhnikov <zhemdim@gmail.com>.},
  creationdate     = {2024-09-06T08:30:55},
  doi              = {10.1038/s41586-021-03819-2},
  file             = {:by-author/J/Jumper/2021_Jumper_583.pdf:PDF},
  keywords         = {3D Protein Structures; 3D Structures; AlphaFold; Artificial Intelligence (AI); Artificial Neural Networks (ANN); Bioinformatics; Machine Learning (ML); Protein Structure Prediction},
  modificationdate = {2024-09-06T08:34:16},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media LLC},
}

@Article{Price2014,
  author           = {Price, Sarah L.},
  journal          = {Chem. Soc. Rev.},
  title            = {Predicting crystal structures of organic compounds},
  year             = {2014},
  issn             = {1460-4744},
  number           = {7},
  pages            = {2098--2111},
  volume           = {43},
  creationdate     = {2024-09-10T17:25:29},
  doi              = {10.1039/c3cs60279f},
  file             = {:by-author/P/Price/2014_Price_2098.pdf:PDF},
  keywords         = {Crystal Structure Prediction (CSP); MOLPAK; Review; Tutorial},
  modificationdate = {2024-09-10T17:35:19},
  owner            = {saulius},
  publisher        = {Royal Society of Chemistry (RSC)},
}

@Article{Hao2021,
  author           = {Hao, Xuan and Liu, Jinfeng and Ali, Imran and Luo, Hongyuan and Han, Yanqiang and Hu, Wenxin and Liu, Jinyun and He, Xiao and Li, Jinjin},
  journal          = {Scientific Reports},
  title            = {Ab initio determination of crystal stability of di-p-tolyl disulfide},
  year             = {2021},
  issn             = {2045-2322},
  month            = mar,
  number           = {1},
  pages            = {7076},
  volume           = {11},
  creationdate     = {2024-09-10T17:32:38},
  doi              = {10.1038/s41598-021-86519-1},
  file             = {:by-author/H/Hao/2021_Hao_7076.pdf:PDF},
  keywords         = {Ab Initio; Crystal Structure Prediction (CSP); MOLPAK},
  modificationdate = {2024-09-10T17:34:20},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media LLC},
}

@Article{Nikhar2022,
  author           = {Nikhar, Rahul and Szalewicz, Krzysztof},
  journal          = {Nature Communications},
  title            = {Reliable crystal structure predictions from first principles},
  year             = {2022},
  issn             = {2041-1723},
  month            = jun,
  number           = {1},
  pages            = {3095},
  volume           = {13},
  creationdate     = {2024-09-10T17:40:31},
  doi              = {10.1038/s41467-022-30692-y},
  file             = {:by-author/N/Nikhar/2022_Nikhar_3095.pdf:PDF;:by-author/N/Nikhar/2022_Nikhar_3095_supp/41467_2022_30692_MOESM1_ESM.pdf:PDF;:by-author/N/Nikhar/2022_Nikhar_3095_supp/41467_2022_30692_MOESM3_ESM.zip:zip},
  keywords         = {Crystal Structure Prediction (CSP); Review},
  modificationdate = {2024-09-10T17:48:04},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media LLC},
}

@TechReport{Rice2004,
  author           = {Betsy M. Rice and Dan C. Sorescu},
  institution      = {U. S. Army Research Laboratory; U. S. Department of Energy, National Energy Technology Laboratory},
  title            = {{\em Ab initio} predictions of structures and densities of energetic solids},
  year             = {2004},
  creationdate     = {2024-09-10T17:52:27},
  file             = {:by-author/R/Rice/2004_Rice_1.pdf:PDF},
  keywords         = {Crystal Structure Prediction (CSP)},
  modificationdate = {2024-09-10T17:57:18},
  owner            = {saulius},
  url              = {https://apps.dtic.mil/sti/pdfs/ADA433279.pdf},
}

@Article{Zoubritzky2022,
  author           = {Zoubritzky, Lionel and Coudert, François-Xavier},
  title            = {{CrystalNets.jl}: identification of crystal topologies},
  year             = {2022},
  month            = may,
  pages            = {5},
  creationdate     = {2024-09-11T17:12:55},
  doi              = {10.26434/chemrxiv-2022-bl6mf-v2},
  eprint           = {https://scipost.org/submissions/10.26434/chemrxiv-2022-bl6mf-v2/},
  file             = {:by-author/Z/Zoubritzky/2022_Zoubritzky_5.pdf:PDF},
  keywords         = {Crystal Nets; Crystallography; Topology},
  modificationdate = {2024-09-11T17:16:26},
  owner            = {saulius},
  publisher        = {American Chemical Society (ACS)},
}

@Article{Alexandrov2017,
  author           = {Alexandrov, Eugeny V. and Blatov, Vladislav A. and Proserpio, Davide M.},
  journal          = {CrystEngComm},
  title            = {How 2-periodic coordination networks are interweaved: entanglement isomerism and polymorphism},
  year             = {2017},
  issn             = {1466-8033},
  number           = {15},
  pages            = {1993--2006},
  volume           = {19},
  cites            = {Baburin2016,Alexandrov2015,Carlucci2014,Mitina2013,Zhao2012a,Yang2012,Hu2012,Liu2012d,Alexandrov2011,Zhuang2009,Zhang2009,Baburin2008,Baburin2008a,OKeeffe2008,Wang2008,Qi2007a,Baburin2007,Lin2007,Blatov2004,Carlucci2004,Carlucci2003,,Carlucci2003a,Abourahma2002,Fu2002,Moulton2001,Kondo2000,Batten1998,Bonneau2015,Batten2001,Zaworotko2001,Withersby1999,Alexandrov2012,Wang2009},
  creationdate     = {2024-09-12T11:25:58},
  doi              = {10.1039/c7ce00313g},
  file             = {:by-author/A/Alexandrov/2017_Alexandrov_1993.pdf:PDF;:by-author/A/Alexandrov/2017_Alexandrov_1993_suppl/c7ce00313g1.pdf:PDF;:by-author/A/Alexandrov/2017_Alexandrov_1993_suppl/c7ce00313g2.xls:Excel},
  keywords         = {Crystallography; Entangled Nets; Infinite Nets; Interpenetrated Nets; Nets; Polymers},
  modificationdate = {2024-09-15T09:13:28},
  owner            = {saulius},
  priority         = {prio1},
  publisher        = {Royal Society of Chemistry (RSC)},
}

@Article{Pitteri1996,
  author           = {Pitteri, M. and Zanzotto, G.},
  journal          = {Acta Crystallographica Section A Foundations of Crystallography},
  title            = {On the definition and classification of {B}ravais lattices},
  year             = {1996},
  issn             = {0108-7673},
  month            = nov,
  number           = {6},
  pages            = {830--838},
  volume           = {52},
  comment          = {Recommended by Davide Proserpio at the ECM34.},
  creationdate     = {2024-09-12T11:35:37},
  doi              = {10.1107/s0108767396005971},
  file             = {:by-author/P/Pitteri/1996_Pitteri_830.pdf:PDF},
  keywords         = {Bravais Lattices; Crystallography; Space Groups; Symmetry},
  modificationdate = {2024-09-12T11:39:22},
  owner            = {saulius},
  publisher        = {International Union of Crystallography (IUCr)},
}

@Article{Fadda2001,
  author           = {Fadda, Giuseppe and Zanzotto, Giovanni},
  journal          = {Acta Crystallographica Section A Foundations of Crystallography},
  title            = {On the arithmetic classification of crystal structures},
  year             = {2001},
  issn             = {0108-7673},
  month            = aug,
  number           = {5},
  pages            = {492--506},
  volume           = {57},
  creationdate     = {2024-09-12T11:40:36},
  doi              = {10.1107/s0108767301005165},
  file             = {:by-author/F/Fadda/2001_Fadda_492.pdf:PDF},
  keywords         = {Bravais Lattices; Classification; Crystallography; Space Groups; Symmetry},
  modificationdate = {2024-09-12T11:41:28},
  owner            = {saulius},
  publisher        = {International Union of Crystallography (IUCr)},
}

@Article{Horner2016,
  author           = {Horner, Kate E. and Miller, Mark A. and Steed, Jonathan W. and Sutcliffe, Paul M.},
  journal          = {Chemical Society Reviews},
  title            = {Knot theory in modern chemistry},
  year             = {2016},
  issn             = {1460-4744},
  month            = nov,
  number           = {23},
  pages            = {6432--6448},
  volume           = {45},
  abstract         = {Knot theory is a branch of pure mathematics, but it is increasingly being applied in a variety of sciences. Knots appear in chemistry, not only in synthetic molecular design, but also in an array of materials and media, including some not traditionally associated with knots. Mathematics and chemistry can now be used synergistically to identify, characterise and create knots, as well as to understand and predict their physical properties. This tutorial review provides a brief introduction to the mathematics of knots and related topological concepts in the context of the chemical sciences. We then survey the broad range of applications of the theory to contemporary research in the field.},
  comment          = {Cited in Alexandrov2017 (ref. [1]).},
  completed        = {2018-01-18},
  country          = {England},
  creationdate     = {2024-09-12T14:44:14},
  doi              = {10.1039/c6cs00448b},
  file             = {:by-author/H/Horner/2016_Horner_6432.pdf:PDF},
  issn-linking     = {0306-0012},
  issue            = {23},
  keywords         = {Crystallography; Entangled Nets; Infinite Nets; Interpenetrated Nets; Nets; Polymers; Review; Tutorial},
  modificationdate = {2024-09-13T16:32:06},
  nlm-id           = {0335405},
  owner            = {saulius},
  pmid             = {27868114},
  publisher        = {Royal Society of Chemistry (RSC)},
  pubmodel         = {Print},
  pubstate         = {ppublish},
  revised          = {2018-01-18},
}

@Article{Batten1998,
  author           = {Batten, Stuart R. and Robson, Richard},
  journal          = {Angewandte Chemie International Edition},
  title            = {Interpenetrating nets: ordered, periodic entanglement},
  year             = {1998},
  issn             = {1521-3773},
  month            = jun,
  number           = {11},
  pages            = {1460--1494},
  volume           = {37},
  comment          = {Cited in Alexandrov2017 (ref. [3]).},
  creationdate     = {2024-09-13T16:42:07},
  doi              = {10.1002/(sici)1521-3773(19980619)37:11<1460::aid-anie1460>3.0.co;2-z},
  file             = {:by-author/B/Batten/1998_Batten_1460.pdf:PDF},
  keywords         = {Crystallography; Entangled Nets; Infinite Nets; Interpenetrated Nets; Nets; Polymers; Review},
  modificationdate = {2024-09-13T16:43:45},
  owner            = {saulius},
  publisher        = {Wiley},
}

@Article{Carlucci2014,
  author           = {Carlucci, Lucia and Ciani, Gianfranco and Proserpio, Davide M. and Mitina, Tatiana G. and Blatov, Vladislav A.},
  journal          = {Chemical Reviews},
  title            = {Entangled two-dimensional coordination networks: a general survey},
  year             = {2014},
  issn             = {1520-6890},
  month            = jun,
  number           = {15},
  pages            = {7557--7580},
  volume           = {114},
  comment          = {Cited in Alexandrov2017 (ref. [4]).},
  completed        = {2015-05-12},
  country          = {United States},
  creationdate     = {2024-09-13T16:47:56},
  doi              = {10.1021/cr500150m},
  file             = {:by-author/C/Carlucci/2014_Carlucci_7557.pdf:PDF;:by-author/C/Carlucci/2014_Carlucci_7557_suppl/cr500150m_si_001.pdf:PDF;:by-author/C/Carlucci/2014_Carlucci_7557_suppl/cr500150m_si_002.xls:Excel},
  issn-linking     = {0009-2665},
  issue            = {15},
  keywords         = {Crystallography; Entangled Nets; Infinite Nets; Interpenetrated Nets; Nets; Polymers; Review},
  modificationdate = {2024-09-13T17:21:55},
  nlm-id           = {2985134R},
  owner            = {saulius},
  pmid             = {24918284},
  publisher        = {American Chemical Society (ACS)},
  pubmodel         = {Print-Electronic},
  pubstate         = {ppublish},
  revised          = {2014-08-13},
}

@Article{Carlucci2003,
  author           = {Carlucci, Lucia and Ciani, Gianfranco and Proserpio, Davide M.},
  journal          = {Coordination Chemistry Reviews},
  title            = {Polycatenation, polythreading and polyknotting in coordination network chemistry},
  year             = {2003},
  issn             = {0010-8545},
  month            = nov,
  number           = {1–2},
  pages            = {247--289},
  volume           = {246},
  comment          = {Cited in Alexandrov2017.},
  creationdate     = {2024-09-13T16:50:53},
  doi              = {10.1016/s0010-8545(03)00126-7},
  file             = {:by-author/C/Carlucci/2003_Carlucci_247.pdf:PDF},
  keywords         = {Crystallography; Entangled Nets; Infinite Nets; Interpenetrated Nets; Nets; Polymers; Review},
  modificationdate = {2024-09-15T08:54:19},
  owner            = {saulius},
  publisher        = {Elsevier BV},
}

@Article{Campbell1983,
  author           = {Campbell, J. and Synnott, S. and Bierman, G.},
  journal          = {IEEE Transactions on Automatic Control},
  title            = {Voyager orbit determination at {J}upiter},
  year             = {1983},
  issn             = {0018-9286},
  month            = mar,
  number           = {3},
  pages            = {256--268},
  volume           = {28},
  creationdate     = {2024-09-13T17:17:10},
  doi              = {10.1109/tac.1983.1103223},
  file             = {:by-author/C/Campbell/1983_Campbell_256.pdf:PDF},
  keywords         = {Computer Science (CS); Computers in Space; Jupiter; Space Flight; Voyager},
  modificationdate = {2024-09-13T17:20:32},
  owner            = {saulius},
  publisher        = {Institute of Electrical and Electronics Engineers (IEEE)},
  url              = {http://users.cecs.anu.edu.au/~Jonghyuk.Kim/teaching/KF Voyager.pdf},
}

@Article{Kuang2010,
  author           = {Kuang, Xiaofei and Wu, Xiaoyuan and Yu, Rongmin and Donahue, James P. and Huang, Jinshun and Lu, Can-Zhong},
  journal          = {Nature Chemistry},
  title            = {Assembly of a metal–organic framework by sextuple intercatenation of discrete adamantane-like cages},
  year             = {2010},
  issn             = {1755-4349},
  month            = apr,
  number           = {6},
  pages            = {461--465},
  volume           = {2},
  abstract         = {Metal-organic frameworks form a unique class of multifunctional hybrid materials and have myriad applications, including gas storage and catalysis. Their structure is usually achieved through the infinite coordination of metal ions and multidentate organic ligands by means of strong covalent bonds. Threaded molecules such as catenanes and rotaxanes have largely been restricted to comprising components of two-dimensional interlocking rings or polygons. There are very few examples of the catenation of polyhedral cages. Although it has been postulated that the infinite extended architecture can be obtained from the polycatenation of a discrete cage based on such threading, this has not been documented to date. Here we describe an infinite three-dimensional metal-organic framework composed of catenated polyhedral cages, in which the framework is achieved by mechanical interlocking of all of the vertices of the cages. The three-dimensional polycatenated framework shows twofold self-interpenetration in its crystal packing. The penetration of polycatenanes creates nanosized voids into which the Keggin polyoxometalate anions are perfectly accommodated as counteranions.},
  chemicals        = {Anthracenes, Metals, Organometallic Compounds, Rotaxanes, catenane, Adamantane},
  citation-subset  = {IM},
  comment          = {Cited in Alexandrov2017 (ref. [5]).},
  completed        = {2010-07-08},
  country          = {England},
  creationdate     = {2024-09-13T17:28:53},
  doi              = {10.1038/nchem.618},
  file             = {:by-author/K/Kuang/2010_Kuang_461.pdf:PDF},
  issn-linking     = {1755-4330},
  issue            = {6},
  keywords         = {Adamantane, Chemistry; Anthracenes, Chemistry; Coordination Polymers; Crystallography; Crystallography, X-Ray; Entangled Nets; Infinite Nets; Interpenetrated Nets; Metals, Chemistry; Models, Chemical; Nets; Organometallic Compounds, Chemistry; Polymers; Rotaxanes, Chemistry},
  modificationdate = {2024-09-13T17:30:29},
  nlm-id           = {101499734},
  owner            = {saulius},
  pii              = {nchem.618},
  pmid             = {20489714},
  publisher        = {Springer Science and Business Media LLC},
  pubmodel         = {Print-Electronic},
  pubstate         = {ppublish},
  revised          = {2021-10-20},
}

@Article{Gonzalez2009,
  author           = {González, Álvaro},
  journal          = {Mathematical Geosciences},
  title            = {Measurement of areas on a sphere using {F}ibonacci and latitude-longitude lattices},
  year             = {2009},
  issn             = {1874-8953},
  month            = nov,
  number           = {1},
  pages            = {49--64},
  volume           = {42},
  abstract         = {The area of a spherical region can be easily measured by considering which sampling points of a lattice are located inside or outside the region. This point-counting technique is frequently used for measuring the Earth coverage of satellite constellations, employing a latitude-longitude lattice. This paper analyzes the numerical errors of such measurements, and shows that they could be greatly reduced if the Fibonacci lattice were used instead. The latter is a mathematical idealization of natural patterns with optimal packing, where the area represented by each point is almost identical. Using the Fibonacci lattice would reduce the root mean squared error by at least 40%. If, as is commonly the case, around a million lattice points are used, the maximum error would be an order of magnitude smaller.},
  archiveprefix    = {arXiv},
  comment          = {Contains the formula and the pseudocode for generation of the Fibonacci grid.},
  copyright        = {arXiv.org perpetual, non-exclusive license},
  creationdate     = {2024-09-13T22:30:02},
  date             = {2009-12-23},
  doi              = {10.1007/s11004-009-9257-x},
  eprint           = {0912.4540},
  file             = {:by-author/G/González/2009_González_49.pdf:PDF},
  keywords         = {Algorithm; FOS: Mathematics; Fibonacci Grids; History and Overview (math.HO); Metric Geometry (math.MG); Sphere Tesselation; Tesselation},
  modificationdate = {2024-09-15T12:32:25},
  owner            = {saulius},
  primaryclass     = {math.MG},
  publisher        = {Springer Science and Business Media LLC},
}

@Article{Proserpio2010,
  author           = {Proserpio, Davide M.},
  journal          = {Nature Chemistry},
  title            = {Polycatenation weaves a 3{D} web},
  year             = {2010},
  issn             = {1755-4349},
  month            = jun,
  number           = {6},
  pages            = {435--436},
  volume           = {2},
  comment          = {Cited in Alexandrov2017 (ref. [6]).},
  creationdate     = {2024-09-14T11:59:23},
  doi              = {10.1038/nchem.674},
  file             = {:by-author/P/Proserpio/2010_Proserpio_435.pdf:PDF},
  keywords         = {Crystallography; Entangled Nets; Infinite Nets; Interpenetrated Nets; Nets; Polymers},
  modificationdate = {2024-09-14T12:00:31},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media LLC},
}

@Article{Alexandrov2015,
  author           = {E. Alexandrov and A. P. Shevchenko and Abdullah A. Asiri and V. Blatov},
  journal          = {CrystEngComm},
  title            = {New knowledge and tools for crystal design: local coordination versus overall network topology and much more},
  year             = {2015},
  issn             = {1466-8033},
  number           = {15},
  pages            = {2913--2924},
  volume           = {17},
  comment          = {Cited in Alexandrov2017.},
  creationdate     = {2024-09-14T12:22:25},
  doi              = {10.1039/c4ce02418d},
  file             = {:by-author/A/Alexandrov/2015_Alexandrov_2913.pdf:PDF},
  keywords         = {Crystallography; Entangled Nets; Infinite Nets; Interpenetrated Nets; Nets; Polymers},
  modificationdate = {2024-09-15T09:56:17},
  owner            = {saulius},
  publisher        = {Royal Society of Chemistry (RSC)},
}

@Article{Mitina2013,
  author           = {T. G. Mitina and V. Blatov},
  journal          = {Crystal Growth \& Design},
  title            = {Topology of 2-periodic coordination networks: toward expert systems in crystal design},
  year             = {2013},
  issn             = {1528-7505},
  month            = mar,
  number           = {4},
  pages            = {1655--1664},
  volume           = {13},
  comment          = {Cited in Alexandrov2017.},
  creationdate     = {2024-09-14T12:22:25},
  doi              = {10.1021/cg301873m},
  file             = {:by-author/M/Mitina/2013_Mitina_1655.pdf:PDF},
  keywords         = {Crystallography; Entangled Nets; Infinite Nets; Interpenetrated Nets; Nets; Polymers},
  modificationdate = {2024-09-15T10:10:38},
  owner            = {saulius},
  publisher        = {American Chemical Society (ACS)},
}

@Article{Zhao2012a,
  author           = {Fang-Hua Zhao and Yun-xia Che and Ji-min Zheng},
  journal          = {CrystEngComm},
  title            = {A {2D}→{3D} net with coexistence of polycatenation and polythreading constructed by long rigid and flexible ligands},
  year             = {2012},
  issn             = {1466-8033},
  number           = {20},
  pages            = {6397},
  volume           = {14},
  comment          = {Cited in Alexandrov2017.},
  creationdate     = {2024-09-14T12:22:25},
  doi              = {10.1039/c2ce25911g},
  file             = {:by-author/Z/Zhao/2012_Zhao_6397.pdf:PDF},
  keywords         = {Crystallography; Entangled Nets; Infinite Nets; Interpenetrated Nets; Nets; Polymers},
  modificationdate = {2024-09-15T10:18:48},
  owner            = {saulius},
  publisher        = {Royal Society of Chemistry (RSC)},
}

@Article{Yang2012,
  author           = {Jin Yang and Jian‐Fang Ma and S. Batten},
  journal          = {Chemical Communications},
  title            = {Polyrotaxane metal-organic frameworks ({PMOFs})},
  year             = {2012},
  issn             = {1364-548X},
  number           = {64},
  pages            = {7899},
  volume           = {48},
  comment          = {Cited in Alexandrov2017.},
  creationdate     = {2024-09-14T12:22:25},
  doi              = {10.1039/c2cc33060a},
  file             = {:by-author/Y/Yang/2012_Yang_7899.pdf:PDF},
  keywords         = {Crystallography; Entangled Nets; Infinite Nets; Interpenetrated Nets; Nets; Polymers},
  modificationdate = {2024-09-15T10:15:40},
  owner            = {saulius},
  publisher        = {Royal Society of Chemistry (RSC)},
}

@Article{Hu2012,
  author           = {Jin Hu and L. Qin and Mingdao Zhang and X. Yao and Yi-zhi Li and Ziyuan Guo and Hegen Zheng and Z. Xue},
  journal          = {Chem. Commun.},
  title            = {Three self-penetrated, interlocked, and polycatenated supramolecular isomers via one-pot synthesis and crystallization},
  year             = {2012},
  issn             = {1364-548X},
  number           = {5},
  pages            = {681--683},
  volume           = {48},
  comment          = {Cited in Alexandrov2017.},
  creationdate     = {2024-09-14T12:22:25},
  doi              = {10.1039/c1cc16147d},
  file             = {:by-author/H/Hu/2012_Hu_681.pdf:PDF},
  keywords         = {Crystallography; Entangled Nets; Infinite Nets; Interpenetrated Nets; Nets; Polymers},
  modificationdate = {2024-09-15T10:03:15},
  owner            = {saulius},
  publisher        = {Royal Society of Chemistry (RSC)},
}

@Article{Liu2012d,
  author           = {Guang-Zhen Liu and Jian-ge Wang and Liya Wang},
  journal          = {CrystEngComm},
  title            = {Divalent metal coordination polymers assembled from dual linkers – semirigid carboxyphenylpropionate and dipyridyl type molecule},
  year             = {2012},
  issn             = {1466-8033},
  number           = {3},
  pages            = {951--960},
  volume           = {14},
  comment          = {Cited in Alexandrov2017.},
  creationdate     = {2024-09-14T12:22:25},
  doi              = {10.1039/c1ce05760j},
  file             = {:by-author/L/Liu/2012_Liu_951.pdf:PDF},
  keywords         = {Crystallography; Entangled Nets; Infinite Nets; Interpenetrated Nets; Nets; Polymers},
  modificationdate = {2024-09-15T10:09:27},
  owner            = {saulius},
  publisher        = {Royal Society of Chemistry (RSC)},
}

@Article{Zhuang2009,
  author           = {C. Zhuang and Jianyong Zhang and Qing Wang and Zhaojie Chu and D. Fenske and C. Su},
  journal          = {Chemistry – A European Journal},
  title            = {Temperature-dependent guest-driven single-crystal-to-single-crystal ligand exchange in a two-fold interpenetrated {Cd(II)} grid network},
  year             = {2009},
  issn             = {1521-3765},
  month            = jul,
  number           = {31},
  pages            = {7578--7585},
  volume           = {15},
  comment          = {Cited in Alexandrov2017.},
  creationdate     = {2024-09-14T12:22:25},
  doi              = {10.1002/chem.200900552},
  file             = {:by-author/Z/Zhuang/2009_Zhuang_7578.pdf:PDF},
  keywords         = {Crystallography; Entangled Nets; Infinite Nets; Interpenetrated Nets; Nets; Polymers},
  modificationdate = {2024-09-15T10:20:04},
  owner            = {saulius},
  publisher        = {Wiley},
}

@Article{Zhang2009,
  author           = {Jie‐Peng Zhang and Xiao-Chun Huang and Xiao‐Ming Chen},
  journal          = {Chemical Society Reviews},
  title            = {Supramolecular isomerism in coordination polymers},
  year             = {2009},
  issn             = {1460-4744},
  number           = {8},
  pages            = {2385},
  volume           = {38},
  comment          = {Cited in Alexandrov2017.},
  creationdate     = {2024-09-14T12:22:25},
  doi              = {10.1039/b900317g},
  file             = {:by-author/Z/Zhang/2009_Zhang_2385.pdf:PDF},
  keywords         = {Crystallography; Entangled Nets; Infinite Nets; Interpenetrated Nets; Nets; Polymers},
  modificationdate = {2024-09-15T10:17:50},
  owner            = {saulius},
  publisher        = {Royal Society of Chemistry (RSC)},
}

@Article{Baburin2008a,
  author           = {I. Baburin and V. Blatov and L. Carlucci and G. Ciani and D. Proserpio},
  journal          = {CrystEngComm},
  title            = {Interpenetrated three-dimensional hydrogen-bonded networks from metal–organic molecular and one- or two-dimensional polymeric motifs},
  year             = {2008},
  issn             = {1466-8033},
  number           = {12},
  pages            = {1822},
  volume           = {10},
  comment          = {Cited in Alexandrov2017.},
  creationdate     = {2024-09-14T12:22:25},
  doi              = {10.1039/b811855h},
  file             = {:by-author/B/Baburin/2008_Baburin_1822.pdf:PDF},
  keywords         = {Crystallography; Entangled Nets; Infinite Nets; Interpenetrated Nets; Nets; Polymers},
  modificationdate = {2024-09-15T09:59:25},
  owner            = {saulius},
  publisher        = {Royal Society of Chemistry (RSC)},
}

@Article{Wang2008,
  author           = {X. Wang and Hong-yan Lin and Yanfeng Bi and Baokuan Chen and Guocheng Liu},
  journal          = {Journal of Solid State Chemistry},
  title            = {An unprecedented extended architecture constructed from a 2-{D} interpenetrating cationic coordination framework templated by {Si} {W}12 {O}40$^{4-}$ anion},
  year             = {2008},
  issn             = {0022-4596},
  month            = mar,
  number           = {3},
  pages            = {556--561},
  volume           = {181},
  comment          = {Cited in Alexandrov2017.},
  creationdate     = {2024-09-14T12:22:25},
  doi              = {10.1016/j.jssc.2007.12.029},
  file             = {:by-author/W/Wang/2008_Wang_556.pdf:PDF},
  keywords         = {Crystallography; Entangled Nets; Infinite Nets; Interpenetrated Nets; Nets; Polymers},
  modificationdate = {2024-09-15T10:14:26},
  owner            = {saulius},
  publisher        = {Elsevier BV},
}

@Article{Baburin2008,
  author           = {I. Baburin and V. Blatov and L. Carlucci and G. Ciani and D. Proserpio},
  journal          = {Crystal Growth &amp; Design},
  title            = {Interpenetrated three-dimensional networks of hydrogen-bonded organic species: a systematic analysis of the cambridge structural database},
  year             = {2008},
  issn             = {1528-7505},
  month            = jan,
  number           = {2},
  pages            = {519--539},
  volume           = {8},
  comment          = {Cited in Alexandrov2017.},
  creationdate     = {2024-09-14T12:22:25},
  doi              = {10.1021/cg0705660},
  file             = {:by-author/B/Baburin/2008_Baburin_519.pdf:PDF},
  keywords         = {Crystallography; Entangled Nets; Infinite Nets; Interpenetrated Nets; Nets; Polymers},
  modificationdate = {2024-09-15T09:58:09},
  owner            = {saulius},
  publisher        = {American Chemical Society (ACS)},
}

@Article{Qi2007a,
  author           = {Y. Qi and A. Xiao and A. E. Wang and B. Z. Zhang and Xinlong Wang},
  journal          = {Australian Journal of Chemistry},
  title            = {Two new three-dimensional networks constructed on polyoxovanadates},
  year             = {2007},
  issn             = {0004-9425},
  number           = {11},
  pages            = {871},
  volume           = {60},
  comment          = {Cited in Alexandrov2017.},
  creationdate     = {2024-09-14T12:22:25},
  doi              = {10.1071/ch07182},
  file             = {:by-author/Q/Qi/2007_Qi_871.pdf:PDF},
  keywords         = {Crystallography; Entangled Nets; Infinite Nets; Interpenetrated Nets; Nets; Polymers},
  modificationdate = {2024-09-15T10:26:19},
  owner            = {saulius},
  publisher        = {CSIRO Publishing},
}

@Article{Baburin2007,
  author           = {I. Baburin and V. Blatov},
  journal          = {Acta Crystallographica Section B Structural Science},
  title            = {Three-dimensional hydrogen-bonded frameworks in organic crystals: a topological study},
  year             = {2007},
  issn             = {0108-7681},
  month            = sep,
  number           = {5},
  pages            = {791--802},
  volume           = {63},
  comment          = {Cited in Alexandrov2017.},
  creationdate     = {2024-09-14T12:22:25},
  doi              = {10.1107/s0108768107033137},
  file             = {:by-author/B/Baburin/2007_Baburin_791.pdf:PDF},
  keywords         = {Crystallography; Entangled Nets; Infinite Nets; Interpenetrated Nets; Nets; Polymers},
  modificationdate = {2024-09-15T10:28:06},
  owner            = {saulius},
  publisher        = {International Union of Crystallography (IUCr)},
}

@Article{Lin2007,
  author           = {Jian-Di Lin and Zhihua Li and Jian-Rong Li and S. Du},
  journal          = {Polyhedron},
  title            = {Synthesis and crystal structures of three novel coordination polymers generated from {AgCN} and {AgSCN} with flexible {N}-donor ligands},
  year             = {2007},
  issn             = {0277-5387},
  month            = jan,
  number           = {1},
  pages            = {107--114},
  volume           = {26},
  comment          = {Cited in Alexandrov2017.},
  creationdate     = {2024-09-14T12:22:25},
  doi              = {10.1016/j.poly.2006.07.034},
  file             = {:by-author/L/Lin/2007_Lin_107.pdf:PDF},
  keywords         = {Crystallography; Entangled Nets; Infinite Nets; Interpenetrated Nets; Nets; Polymers},
  modificationdate = {2024-09-15T10:06:18},
  owner            = {saulius},
  publisher        = {Elsevier BV},
}

@Article{Carlucci2004,
  author           = {L. Carlucci and G. Ciani and D. Proserpio and L. Spadacini},
  journal          = {CrystEngComm},
  title            = {Supramolecular isomers in the same crystal: a new case involving two different types of layers polycatenated in the {3D} architecture of [{Cu}(bix)2({SO4})]·7.5{H2O} [bix = 1,4-bis(imidazol-1-ylmethyl)benzene]},
  year             = {2004},
  issn             = {1466-8033},
  number           = {20},
  pages            = {96--101},
  volume           = {6},
  comment          = {Cited in Alexandrov2017.},
  creationdate     = {2024-09-14T12:22:25},
  doi              = {10.1039/B402935F},
  file             = {:by-author/C/Carlucci/2004_Carlucci_96.pdf:PDF},
  keywords         = {Crystallography; Entangled Nets; Infinite Nets; Interpenetrated Nets; Nets; Polymers},
  modificationdate = {2024-09-15T10:29:17},
  owner            = {saulius},
  publisher        = {Royal Society of Chemistry (RSC)},
}

@Article{Carlucci2003a,
  author           = {L. Carlucci and G. Ciani and D. Proserpio},
  journal          = {CrystEngComm},
  title            = {Borromean links and other non-conventional links in ‘polycatenated’ coordination polymers: re-examination of some puzzling networks},
  year             = {2003},
  issn             = {1466-8033},
  number           = {47},
  pages            = {269--279},
  volume           = {5},
  comment          = {Cited in Alexandrov2017.},
  creationdate     = {2024-09-14T12:22:25},
  doi              = {10.1039/b305246j},
  file             = {:by-author/C/Carlucci/2003_Carlucci_269.pdf:PDF},
  keywords         = {Crystallography; Entangled Nets; Infinite Nets; Interpenetrated Nets; Nets; Polymers},
  modificationdate = {2024-09-15T10:30:26},
  owner            = {saulius},
  publisher        = {Royal Society of Chemistry (RSC)},
}

@Article{Abourahma2002,
  author           = {H. Abourahma and B. Moulton and V. Kravtsov and M. Zaworotko},
  journal          = {Journal of the American Chemical Society},
  title            = {Supramolecular isomerism in coordination compounds: nanoscale molecular hexagons and chains},
  year             = {2002},
  issn             = {1520-5126},
  month            = aug,
  number           = {34},
  pages            = {9990--9991},
  volume           = {124},
  comment          = {Cited in Alexandrov2017.},
  creationdate     = {2024-09-14T12:22:25},
  doi              = {10.1021/ja027371v},
  file             = {:by-author/A/Abourahma/2002_Abourahma_9990.pdf:PDF},
  keywords         = {Crystallography; Entangled Nets; Infinite Nets; Interpenetrated Nets; Nets; Polymers},
  modificationdate = {2024-09-15T09:55:14},
  owner            = {saulius},
  publisher        = {American Chemical Society (ACS)},
}

@Article{Fu2002,
  author           = {Z. Fu and Xintao Wu and J. Dai and Shengmin Hu and W. Du},
  journal          = {New Journal of Chemistry},
  title            = {A novel mixed-ligand molecular bilayer generated by self-assembly of “{T}-shaped” moieties, displaying an unusual entanglement},
  year             = {2002},
  issn             = {1369-9261},
  month            = jul,
  number           = {8},
  pages            = {978--980},
  volume           = {26},
  comment          = {Cited in Alexandrov2017.},
  creationdate     = {2024-09-14T12:22:25},
  doi              = {10.1039/b202762c},
  file             = {:by-author/F/Fu/2002_Fu_978.pdf:PDF},
  keywords         = {Crystallography; Entangled Nets; Infinite Nets; Interpenetrated Nets; Nets; Polymers},
  modificationdate = {2024-09-15T10:31:42},
  owner            = {saulius},
  publisher        = {Royal Society of Chemistry (RSC)},
}

@Article{Moulton2001,
  author           = {B. Moulton and M. Zaworotko},
  journal          = {Chemical Reviews},
  title            = {From molecules to crystal engineering: supramolecular isomerism and polymorphism in network solids},
  year             = {2001},
  issn             = {1520-6890},
  month            = may,
  number           = {6},
  pages            = {1629--1658},
  volume           = {101},
  comment          = {Cited in Alexandrov2017.},
  creationdate     = {2024-09-14T12:22:25},
  doi              = {10.1021/cr9900432},
  file             = {:by-author/M/Moulton/2001_Moulton_1629.pdf:PDF},
  keywords         = {Crystallography; Entangled Nets; Infinite Nets; Interpenetrated Nets; Nets; Polymers},
  modificationdate = {2024-09-15T10:12:51},
  owner            = {saulius},
  publisher        = {American Chemical Society (ACS)},
}

@Article{Kondo2000,
  author           = {M. Kondo and Mari Shimamura and S. Noro and S. Minakoshi and A. Asami and K. Seki and S. Kitagawa},
  journal          = {Chemistry of Materials},
  title            = {Microporous materials constructed from the interpenetrated coordination networks. Structures and methane adsorption properties},
  year             = {2000},
  issn             = {1520-5002},
  month            = apr,
  number           = {5},
  pages            = {1288--1299},
  volume           = {12},
  comment          = {Cited in Alexandrov2017.},
  creationdate     = {2024-09-14T12:22:25},
  doi              = {10.1021/cm990612m},
  file             = {:by-author/K/Kondo/2000_Kondo_1288.pdf:PDF},
  keywords         = {Crystallography; Entangled Nets; Infinite Nets; Interpenetrated Nets; Nets; Polymers},
  modificationdate = {2024-09-15T10:05:01},
  owner            = {saulius},
  publisher        = {American Chemical Society (ACS)},
}

@Article{Bonneau2015,
  author           = {Charlotte Bonneau and M. O'Keeffe},
  journal          = {Acta Crystallographica Section A Foundations and Advances},
  title            = {High-symmetry embeddings of interpenetrating periodic nets. Essential rings and patterns of catenation},
  year             = {2015},
  issn             = {2053-2733},
  month            = jan,
  number           = {1},
  pages            = {82--91},
  volume           = {71},
  comment          = {Cited in Alexandrov2017.},
  creationdate     = {2024-09-14T12:22:25},
  doi              = {10.1107/s2053273314019950},
  file             = {:by-author/B/Bonneau/2015_Bonneau_82.pdf:PDF},
  keywords         = {Crystallography; Entangled Nets; Infinite Nets; Interpenetrated Nets; Nets; Polymers},
  modificationdate = {2024-09-15T10:01:13},
  owner            = {saulius},
  publisher        = {International Union of Crystallography (IUCr)},
}

@Article{Batten2001,
  author           = {S. Batten},
  journal          = {CrystEngComm},
  title            = {Topology of interpenetration},
  year             = {2001},
  issn             = {1466-8033},
  number           = {18},
  pages            = {67},
  volume           = {3},
  comment          = {Cited in Alexandrov2017.},
  creationdate     = {2024-09-14T12:22:25},
  doi              = {10.1039/b102400k},
  file             = {:by-author/B/Batten/2001_Batten_67.pdf:PDF},
  keywords         = {Crystallography; Entangled Nets; Infinite Nets; Interpenetrated Nets; Nets; Polymers},
  modificationdate = {2024-09-15T10:33:06},
  owner            = {saulius},
  publisher        = {Royal Society of Chemistry (RSC)},
}

@Article{Zaworotko2001,
  author           = {M. Zaworotko},
  journal          = {Chemical Communications},
  title            = {Superstructural diversity in two dimensions: crystal engineering of laminated solids},
  year             = {2001},
  issn             = {1364-548X},
  number           = {1},
  pages            = {1--9},
  comment          = {Cited in Alexandrov2017.},
  creationdate     = {2024-09-14T12:22:25},
  doi              = {10.1039/b007127g},
  file             = {:by-author/Z/Zaworotko/2001_Zaworotko_1.pdf:PDF},
  keywords         = {Crystallography; Entangled Nets; Infinite Nets; Interpenetrated Nets; Nets; Polymers},
  modificationdate = {2024-09-15T10:16:51},
  owner            = {saulius},
  publisher        = {Royal Society of Chemistry (RSC)},
}

@Article{Withersby1999,
  author           = {Matthew A. Withersby and A. Blake and N. Champness and Paul A. Cooke and P. Hubberstey and M. Schröder},
  journal          = {New Journal of Chemistry},
  title            = {Parallel interpenetration in novel herringbone sheets formed by {Co(II)} and {Cd(II)} complexes with trans-4,4′-azobis(pyridine)},
  year             = {1999},
  issn             = {1369-9261},
  number           = {6},
  pages            = {573--575},
  volume           = {23},
  comment          = {Cited in Alexandrov2017.},
  creationdate     = {2024-09-14T12:22:25},
  doi              = {10.1039/a900947g},
  file             = {:by-author/W/Withersby/1999_Withersby_573.pdf:PDF},
  keywords         = {Crystallography; Entangled Nets; Infinite Nets; Interpenetrated Nets; Nets; Polymers},
  modificationdate = {2024-09-15T10:34:09},
  owner            = {saulius},
  publisher        = {Royal Society of Chemistry (RSC)},
}

@Article{Wang2009,
  author           = {Qing Wang and Jianyong Zhang and C. Zhuang and Yu Tang and C. Su},
  journal          = {Inorganic Chemistry},
  title            = {Guest inclusion and interpenetration tuning of {Cd(II)}/{Mn(II)} coordination grid networks assembled from a rigid linear diimidazole {S}chiff base ligand},
  year             = {2009},
  issn             = {1520-510X},
  month            = nov,
  number           = {1},
  pages            = {287--295},
  volume           = {48},
  abstract         = {Cd(II)/Mn(II) coordination grid networks containing large meshes have been assembled from a long rigid ligand, 2,5-bis(4'-(imidazol-1-yl)benzyl)-3,4-diaza-2,4-hexadiene (ImBNN), and M(CF(3)SO(3))(2) (M = Cd and Mn) salts, and their interpenetration change upon guest inclusion has been investigated with a series of aromatic molecules. Without guest molecules, the grid networks are triply interpenetrated to form closely packed layer structures [M(ImBNN)(2)(CF(3)SO(3))(2)](n) (M = Cd (1) and Mn (2)), but when guest molecules are introduced, the triply interpenetrated frameworks are changed to doubly interpenetrated ones with the inclusion of various aromatic molecules, namely, {[M(ImBNN)(2)(CF(3)SO(3))(2)] superset guest}(n) (M = Cd, guest = o-xylene (3), naphthalene (4), phenanthrene (5), and pyrene (6); M = Mn, guest = benzene (7), p-xylene (8), naphthalene (9), phenanthrene (10), and pyrene (11)). These complexes have been characterized by means of single-crystal X-ray diffraction, X-ray powder diffraction, and IR spectra. The guest-inclusion/desorption behaviors of representative complexes have been studied by thermogravimetric analyses and (1)H NMR measurements. The grid networks display strong preference for aromatic guest inclusion, but less selectivity toward shape and size difference. Tuning of network interpenetration from 3-fold to 2-fold has been successfully achieved through the introduction of guest molecules, when the network displays flexibility to change cavity size to match the guest molecules.},
  chemicals        = {Imidazoles, Ligands, Schiff Bases, Cadmium, Manganese, imidazole},
  citation-subset  = {IM},
  comment          = {Cited in Alexandrov2017.},
  completed        = {2009-02-13},
  country          = {United States},
  creationdate     = {2024-09-14T13:04:12},
  doi              = {10.1021/ic801770n},
  file             = {:by-author/W/Wang/2009_Wang_287.pdf:PDF},
  issn-linking     = {0020-1669},
  issue            = {1},
  keywords         = {Adsorption; Cadmium, Chemistry; Crystallography; Crystallography, X-Ray; Entangled Nets; Imidazoles, Chemistry; Infinite Nets; Interpenetrated Nets; Ligands; Manganese, Chemistry; Models, Molecular; Molecular Conformation; Nets; Polymers; Schiff Bases, Chemistry; Thermogravimetry},
  modificationdate = {2024-09-15T09:52:55},
  nlm-id           = {0366543},
  owner            = {saulius},
  pii              = {10.1021/ic801770n},
  pmid             = {19035763},
  publisher        = {American Chemical Society (ACS)},
  pubmodel         = {Print},
  pubstate         = {ppublish},
  revised          = {2013-11-21},
}

@Article{Dawson2021,
  author           = {Dawson, James A. and Famprikis, Theodosios and Johnston, Karen E.},
  journal          = {Journal of Materials Chemistry A},
  title            = {Anti-perovskites for solid-state batteries: recent developments, current challenges and future prospects},
  year             = {2021},
  issn             = {2050-7496},
  number           = {35},
  pages            = {18746--18772},
  volume           = {9},
  creationdate     = {2024-09-15T10:42:10},
  doi              = {10.1039/d1ta03680g},
  file             = {:by-author/D/Dawson/2021_Dawson_18746.pdf:PDF},
  keywords         = {Antiperovskites; Li Batteries; Solid State Batteries},
  modificationdate = {2024-09-15T10:46:09},
  owner            = {saulius},
  publisher        = {Royal Society of Chemistry (RSC)},
}

@Article{Swinbank2006,
  author           = {Swinbank, Richard and James Purser, R.},
  journal          = {Quarterly Journal of the Royal Meteorological Society},
  title            = {Fibonacci grids: A novel approach to global modelling},
  year             = {2006},
  issn             = {1477-870X},
  month            = jul,
  number           = {619},
  pages            = {1769--1793},
  volume           = {132},
  comment          = {Cited in Gonzalez2009 (ref. [68]).},
  creationdate     = {2024-09-15T12:17:03},
  doi              = {10.1256/qj.05.227},
  file             = {:by-author/S/Swinbank/2006_Swinbank_1769.pdf:PDF},
  keywords         = {Algorithms; Fibonacci Grids; Mathematics; Modelling},
  modificationdate = {2024-09-15T12:32:19},
  owner            = {saulius},
  publisher        = {Wiley},
}

@Article{Coates2018,
  author           = {Coates, Sam and Smerdon, Joseph A. and McGrath, Ronan and Sharma, Hem Raj},
  journal          = {Nature Communications},
  title            = {A molecular overlayer with the {F}ibonacci square grid structure},
  year             = {2018},
  issn             = {2041-1723},
  month            = aug,
  number           = {1},
  volume           = {9},
  comment          = {Found by searching for "three dimensional Fibonacci grid" on DuckDuckGo.},
  creationdate     = {2024-09-15T12:57:33},
  doi              = {10.1038/s41467-018-05950-7},
  file             = {:by-author/C/Coates/2018_Coates_1.pdf:PDF},
  keywords         = {3D Fibonacci Grids; Algorithms; Fibonacci Grids; Mathematics; Modelling; Molecular Overlay; Quasicrystals; Structure Superposition},
  modificationdate = {2024-09-15T13:02:39},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media LLC},
}

@Article{Nagy2024,
  author           = {Nagy, Mariana and Cowell, Simon R. and Beiu, Valeriu},
  journal          = {Mathematics},
  title            = {On the construction of {3D} {F}ibonacci spirals},
  year             = {2024},
  issn             = {2227-7390},
  month            = jan,
  number           = {2},
  pages            = {201},
  volume           = {12},
  comment          = {Found by searching for "three dimensional Fibonacci grid" on DuckDuckGo.},
  creationdate     = {2024-09-15T13:02:08},
  doi              = {10.3390/math12020201},
  file             = {:by-author/N/Nagy/2024_Nagy_201.pdf:PDF},
  keywords         = {3D Fibonacci Grids; Algorithms; Fibonacci Grids; Mathematics},
  modificationdate = {2024-09-18T15:13:47},
  owner            = {saulius},
  publisher        = {MDPI AG},
}

@Article{Satorras2021,
  author           = {Satorras, Victor Garcia and Hoogeboom, Emiel and Welling, Max},
  title            = {{E(n)} equivariant graph neural networks},
  year             = {2021},
  month            = feb,
  abstract         = {This paper introduces a new model to learn graph neural networks equivariant to rotations, translations, reflections and permutations called E(n)-Equivariant Graph Neural Networks (EGNNs). In contrast with existing methods, our work does not require computationally expensive higher-order representations in intermediate layers while it still achieves competitive or better performance. In addition, whereas existing methods are limited to equivariance on 3 dimensional spaces, our model is easily scaled to higher-dimensional spaces. We demonstrate the effectiveness of our method on dynamical systems modelling, representation learning in graph autoencoders and predicting molecular properties.},
  archiveprefix    = {arXiv},
  copyright        = {arXiv.org perpetual, non-exclusive license},
  creationdate     = {2024-09-18T10:09:44},
  doi              = {10.48550/ARXIV.2102.09844},
  eprint           = {2102.09844},
  file             = {:by-author/S/Satorras/2021_Satorras_1.pdf:PDF},
  keywords         = {Artificial Neural Networks (ANN); Equivariance; FOS: Computer and Information Sciences; Graph Neural Networks (GNN); Machine Learning (ML); Machine Learning (cs.LG); Machine Learning (stat.ML)},
  modificationdate = {2024-09-18T10:21:41},
  owner            = {saulius},
  primaryclass     = {cs.LG},
  publisher        = {arXiv},
}

@Presentation{Helliwell2024,
  author           = {Helliwell, John},
  title            = {The scientific truth, the whole truth and nothing but the truth (based on his new book)},
  year             = {2024},
  copyright        = {Creative Commons Attribution 4.0 International},
  creationdate     = {2024-09-20T14:45:46},
  doi              = {10.5281/ZENODO.13777914},
  file             = {:by-author/H/Helliwell/2024_Helliwell_1.pptx:PowerPoint 2007+},
  keywords         = {Crystallographic Data; Crystallography; Data Management; Open Science; Philosopy of Science; Scientific Data; Trust in Science; Truth in Science},
  modificationdate = {2024-09-20T14:48:24},
  owner            = {saulius},
  publisher        = {Zenodo},
}

@Article{GabirondoLopez2024,
  author           = {Gabirondo-López, J. and Gabirondo-López, I. and Tasci, E. S. and Madariaga, G.},
  journal          = {Journal of Applied Crystallography},
  title            = {Towards dynamically configured databases for {CIFs}: the new modulated structures open database at the {B}ilbao {C}rystallographic {S}erver},
  year             = {2024},
  issn             = {1600-5767},
  month            = sep,
  number           = {5},
  volume           = {57},
  comment          = {Recommended by Daniel Chateigner.},
  creationdate     = {2024-09-23T12:58:01},
  doi              = {10.1107/s1600576724007908},
  file             = {:by-author/G/Gabirondo-López/2024_Gabirondo-López_1.pdf:PDF},
  keywords         = {CIF; Crystallographic Databases; Crystallography; Incommensurately Modulated Structures; Sceintific Databases; X-ray Crystallography},
  modificationdate = {2024-09-23T13:01:05},
  owner            = {saulius},
  publisher        = {International Union of Crystallography (IUCr)},
}

@Article{Schoonjans2011,
  author           = {Schoonjans, Tom and Brunetti, Antonio and Golosio, Bruno and Sanchez del Rio, Manuel and Solé, Vicente Armando and Ferrero, Claudio and Vincze, Laszlo},
  journal          = {Spectrochimica Acta Part B: Atomic Spectroscopy},
  title            = {The xraylib library for {X}-ray–matter interactions. Recent developments},
  year             = {2011},
  issn             = {0584-8547},
  month            = nov,
  number           = {11–12},
  pages            = {776--784},
  volume           = {66},
  creationdate     = {2024-09-23T17:45:07},
  doi              = {10.1016/j.sab.2011.09.011},
  file             = {:by-author/S/Schoonjans/2011_Schoonjans_776.pdf:PDF},
  keywords         = {Scientific Databases; X-ray},
  modificationdate = {2024-09-23T18:16:00},
  owner            = {saulius},
  publisher        = {Elsevier BV},
}

@Article{Munteanu2024,
  author           = {Munteanu, Valentin and Starostin, Vladimir and Greco, Alessandro and Pithan, Linus and Gerlach, Alexander and Hinderhofer, Alexander and Kowarik, Stefan and Schreiber, Frank},
  journal          = {Journal of Applied Crystallography},
  title            = {Neural network analysis of neutron and {X}-ray reflectivity data incorporating prior knowledge},
  year             = {2024},
  issn             = {1600-5767},
  month            = mar,
  number           = {2},
  pages            = {456--469},
  volume           = {57},
  comment          = {Cited in the NOBUGS conference talks.},
  creationdate     = {2024-09-24T16:25:47},
  doi              = {10.1107/s1600576724002115},
  file             = {:by-author/M/Munteanu/2024_Munteanu_456.pdf:PDF},
  keywords         = {Artificial Intelligence (AI); Artificial Neural Networks (ANN); Data Management; Machine Learning (ML); Scientific Data; X-ray},
  modificationdate = {2024-09-24T16:29:10},
  owner            = {saulius},
  publisher        = {International Union of Crystallography (IUCr)},
}

@Article{Schmitt1938,
  author           = {Schmitt, Otto H.},
  journal          = {Journal of Scientific Instruments},
  title            = {A thermionic trigger},
  year             = {1938},
  issn             = {0950-7671},
  month            = jan,
  number           = {1},
  pages            = {24--26},
  volume           = {15},
  creationdate     = {2024-10-02T18:29:09},
  doi              = {10.1088/0950-7671/15/1/305},
  file             = {:by-author/S/Schmitt/1938_Schmitt_24.pdf:PDF},
  keywords         = {Electronic CIrcuits; Electronics; Scientific Instruments; Triggers; Vacuum Tubes},
  modificationdate = {2024-10-02T18:30:37},
  owner            = {saulius},
  publisher        = {IOP Publishing},
}

@Article{NatureEditorial2024,
  author           = {{Nature Editorial}},
  journal          = {Nature},
  title            = {Use citizen science to turbocharge big-data projects},
  year             = {2024},
  issn             = {1476-4687},
  month            = oct,
  number           = {8032},
  pages            = {7--7},
  volume           = {634},
  creationdate     = {2024-10-04T14:19:18},
  doi              = {10.1038/d41586-024-03182-y},
  file             = {:by-author/N/NatureEditorial/2024_NatureEditorial_7.pdf:PDF},
  keywords         = {Citizen Science; Data; Data Science; Scientific Data},
  modificationdate = {2024-10-11T09:50:44},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media LLC},
}

@Article{Alser2017,
  author           = {Alser, Mohammed and Hassan, Hasan and Xin, Hongyi and Ergin, Oğuz and Mutlu, Onur and Alkan, Can},
  journal          = {Bioinformatics},
  title            = {{GateKeeper}: a new hardware architecture for accelerating pre-alignment in {DNA} short read mapping},
  year             = {2017},
  issn             = {1367-4811},
  month            = may,
  number           = {21},
  pages            = {3355--3363},
  volume           = {33},
  comment          = {Advertised in the introductory ETH course on Computer Architecture by Onur Mutlu et al. (https://www.youtube.com/watch?v=0U2OMvvsyl8&list=PL5Q2soXY2Zi-NVn779PBtYziKiW-zdW5i, accessed 2024-10-08T15:07+03:00).},
  creationdate     = {2024-10-08T15:03:41},
  doi              = {10.1093/bioinformatics/btx342},
  editor           = {Berger, Bonnie},
  file             = {:by-author/A/Alser/2017_Alser_3355.pdf:PDF},
  keywords         = {Bioinformatics; FPGA},
  modificationdate = {2024-10-08T15:08:58},
  owner            = {saulius},
  publisher        = {Oxford University Press (OUP)},
}

@Article{Alser2020,
  author           = {Alser, Mohammed and Shahroodi, Taha and Gómez-Luna, Juan and Alkan, Can and Mutlu, Onur},
  journal          = {Bioinformatics},
  title            = {{SneakySnake}: a fast and accurate universal genome pre-alignment filter for {CPUs}, {GPUs} and {FPGAs}},
  year             = {2020},
  issn             = {1367-4811},
  month            = dec,
  number           = {22–23},
  pages            = {5282--5290},
  volume           = {36},
  comment          = {Advertised in the introductory ETH course on Computer Architecture by Onur Mutlu et al. (https://www.youtube.com/watch?v=0U2OMvvsyl8&list=PL5Q2soXY2Zi-NVn779PBtYziKiW-zdW5i, accessed 2024-10-08T15:07+03:00).},
  creationdate     = {2024-10-08T15:04:13},
  doi              = {10.1093/bioinformatics/btaa1015},
  editor           = {Robinson, Peter},
  file             = {:by-author/A/Alser/2020_Alser_5282.pdf:PDF},
  keywords         = {Bioinformatics; FPGA},
  modificationdate = {2024-10-08T15:08:46},
  owner            = {saulius},
  publisher        = {Oxford University Press (OUP)},
}

@Article{Henkelman2000,
  author           = {Henkelman, Graeme and Jónsson, Hannes},
  journal          = {The Journal of Chemical Physics},
  title            = {Improved tangent estimate in the nudged elastic band method for finding minimum energy paths and saddle points},
  year             = {2000},
  issn             = {1089-7690},
  month            = dec,
  number           = {22},
  pages            = {9978--9985},
  volume           = {113},
  comment          = {Recommended by Ivano Eligi Casteli; obtained via https://wiki.fysik.dtu.dk/ase/ase/neb.html.},
  creationdate     = {2024-10-11T09:47:58},
  doi              = {10.1063/1.1323224},
  file             = {:by-author/H/Henkelman/2000_Henkelman_9978.pdf:PDF},
  keywords         = {Atomic Simulation Anvironment (ASE); Comuptational Materials Science; IN-CHARGE; Materials Science; Nudged Elastic Band; Review},
  modificationdate = {2024-10-11T09:54:08},
  owner            = {saulius},
  publisher        = {AIP Publishing},
}

@Article{Henkelman2000a,
  author           = {Henkelman, Graeme and Uberuaga, Blas P. and Jónsson, Hannes},
  journal          = {The Journal of Chemical Physics},
  title            = {A climbing image nudged elastic band method for finding saddle points and minimum energy paths},
  year             = {2000},
  issn             = {1089-7690},
  month            = dec,
  number           = {22},
  pages            = {9901--9904},
  volume           = {113},
  comment          = {Recommended by Ivano Eligi Casteli; obtained via https://wiki.fysik.dtu.dk/ase/ase/neb.html.},
  creationdate     = {2024-10-11T09:51:08},
  doi              = {10.1063/1.1329672},
  file             = {:by-author/H/Henkelman/2000_Henkelman_9901.pdf:PDF},
  keywords         = {Atomic Simulation Anvironment (ASE); Comuptational Materials Science; IN-CHARGE; Materials Science; Nudged Elastic Band; Review},
  modificationdate = {2024-10-11T09:54:38},
  owner            = {saulius},
  publisher        = {AIP Publishing},
}

@Article{Kolsbjerg2016,
  author           = {Kolsbjerg, Esben L. and Groves, Michael N. and Hammer, Bjørk},
  journal          = {The Journal of Chemical Physics},
  title            = {An automated nudged elastic band method},
  year             = {2016},
  issn             = {1089-7690},
  month            = sep,
  number           = {9},
  pages            = {094107},
  volume           = {145},
  comment          = {Recommended by Ivano Eligi Casteli; obtained via https://wiki.fysik.dtu.dk/ase/ase/neb.html.},
  creationdate     = {2024-10-11T09:52:11},
  doi              = {10.1063/1.4961868},
  file             = {:by-author/K/Kolsbjerg/2016_Kolsbjerg_94107.pdf:PDF},
  keywords         = {Atomic Simulation Anvironment (ASE); Comuptational Materials Science; IN-CHARGE; Materials Science; Nudged Elastic Band; Review},
  modificationdate = {2024-10-11T09:57:53},
  owner            = {saulius},
  publisher        = {AIP Publishing},
}

@Article{Makri2019,
  author           = {Makri, Stela and Ortner, Christoph and Kermode, James R.},
  journal          = {The Journal of Chemical Physics},
  title            = {A preconditioning scheme for minimum energy path finding methods},
  year             = {2019},
  issn             = {1089-7690},
  month            = mar,
  number           = {9},
  pages            = {094109},
  volume           = {150},
  comment          = {Recommended by Ivano Eligi Casteli; obtained via https://wiki.fysik.dtu.dk/ase/ase/neb.html.},
  creationdate     = {2024-10-11T09:52:23},
  doi              = {10.1063/1.5064465},
  file             = {:by-author/M/Makri/2019_Makri_94109.pdf:PDF},
  keywords         = {Atomic Simulation Anvironment (ASE); Comuptational Materials Science; IN-CHARGE; Materials Science; Nudged Elastic Band; Review},
  modificationdate = {2024-10-11T09:57:25},
  owner            = {saulius},
  publisher        = {AIP Publishing},
}

@InProceedings{Goldwasser1985,
  author           = {Goldwasser, S. and Micali, S. and Rackoff, C.},
  booktitle        = {Proceedings of the seventeenth annual ACM symposium on Theory of computing - STOC ’85},
  title            = {The knowledge complexity of interactive proof-systems},
  year             = {1985},
  pages            = {291--304},
  publisher        = {ACM Press},
  series           = {STOC ’85},
  collection       = {STOC ’85},
  comment          = {Cited and criticised by Goldreich1991.},
  creationdate     = {2024-10-13T08:59:30},
  doi              = {10.1145/22145.22178},
  file             = {:by-author/G/Goldwasser/1985_Goldwasser_291.pdf:PDF},
  keywords         = {Cryptography; Information Theory; NP-completness; Zero-knowledge Proofs; Zero-knowledge Protocols},
  modificationdate = {2024-10-13T09:50:29},
  owner            = {saulius},
}

@Article{Goldwasser1989,
  author           = {Goldwasser, Shafi and Micali, Silvio and Rackoff, Charles},
  journal          = {SIAM Journal on Computing},
  title            = {The knowledge complexity of interactive proof systems},
  year             = {1989},
  issn             = {1095-7111},
  month            = feb,
  number           = {1},
  pages            = {186--208},
  volume           = {18},
  comment          = {A sequel of Goldwasser1985. Goldreich1991 cites it as ref. [GMR2]. It says: "An attempt to formalize the "amount of knowledge" (in case it is not zero) has appeared in [GMR] but was omitted from the later version of this work [GMR2] since the authors themselves found it inadequate (Micali, private communication)"},
  creationdate     = {2024-10-13T09:33:32},
  doi              = {10.1137/0218012},
  file             = {:by-author/G/Goldwasser/1989_Goldwasser_186.pdf:PDF},
  keywords         = {Cryptography; Information Theory; NP-completness; Zero-knowledge Proofs; Zero-knowledge Protocols},
  modificationdate = {2024-10-13T09:51:04},
  owner            = {saulius},
  publisher        = {Society for Industrial & Applied Mathematics (SIAM)},
}

@Article{Feynman1985,
  author           = {Richard P. Feynman},
  journal          = {Optics and Photonics News},
  title            = {Quantum mechanical computers},
  year             = {1985},
  number           = {2},
  pages            = {11--20},
  volume           = {11},
  comment          = {Cited in Aharonov2012, "philosophy" paper SVN repository (svn://saulius.grazulis.lt/philosophy, ref. [11]).},
  creationdate     = {2024-10-13T10:39:31},
  doi              = {10.1364/on.11.000011},
  file             = {:by-author/F/Feynman/1985_Feynman_11.pdf:PDF},
  keywords         = {Computer Architecture; Computer Science (CS); Physics; Quantum Computers; Quantum Computing; Quantum Mechanics (QM)},
  modificationdate = {2024-10-13T10:45:45},
  owner            = {saulius},
}

@Article{Bennett1973,
  author           = {Bennett, C. H.},
  journal          = {IBM Journal of Research and Development},
  title            = {Logical reversibility of computation},
  year             = {1973},
  issn             = {0018-8646},
  month            = nov,
  number           = {6},
  pages            = {525--532},
  volume           = {17},
  comment          = {Cited in Feynman1985 (ref. [1]).},
  creationdate     = {2024-10-13T10:49:55},
  doi              = {10.1147/rd.176.0525},
  file             = {:by-author/B/Bennett/1973_Bennett_525.pdf:PDF},
  keywords         = {Computer Architecture; Computer Science (CS); Energy Cost of Computation; Physics; Quantum Computers; Quantum Computing; Quantum Mechanics (QM); Reversibility of Computation; Thermodynamics},
  modificationdate = {2024-10-13T10:59:45},
  owner            = {saulius},
  publisher        = {IBM},
}

@Article{Bennett1982,
  author           = {Bennett, Charles H.},
  journal          = {International Journal of Theoretical Physics},
  title            = {The thermodynamics of computation—a review},
  year             = {1982},
  issn             = {1572-9575},
  month            = dec,
  number           = {12},
  pages            = {905--940},
  volume           = {21},
  comment          = {Cited in Feynman1985 (ref. [3]).},
  creationdate     = {2024-10-13T10:57:10},
  doi              = {10.1007/bf02084158},
  file             = {:by-author/B/Bennett/1982_Bennett_905.pdf:PDF},
  keywords         = {Computer Architecture; Computer Science (CS); Energy Cost of Computation; Physics; Quantum Computers; Quantum Computing; Quantum Mechanics (QM); Reversibility of Computation; Thermodynamics},
  modificationdate = {2024-10-13T11:00:28},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media LLC},
}

@Article{Fredkin1982,
  author           = {Fredkin, Edward and Toffoli, Tommaso},
  journal          = {International Journal of Theoretical Physics},
  title            = {Conservative logic},
  year             = {1982},
  issn             = {1572-9575},
  month            = apr,
  number           = {3–4},
  pages            = {219--253},
  volume           = {21},
  comment          = {Cited in Feynman1985 (ref. [2]).},
  creationdate     = {2024-10-13T11:03:39},
  doi              = {10.1007/bf01857727},
  file             = {:by-author/F/Fredkin/1982_Fredkin_219.pdf:PDF},
  keywords         = {Computer Architecture; Computer Science (CS); Energy Cost of Computation; Physics; Quantum Computers; Quantum Computing; Quantum Mechanics (QM); Reversibility of Computation; Thermodynamics},
  modificationdate = {2024-10-13T11:05:28},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media LLC},
  url              = {https://cqi.inf.usi.ch/qic/82_Fredkin.pdf},
}

@Article{Toffoli1981,
  author           = {Toffoli, Tommaso},
  journal          = {Mathematical Systems Theory},
  title            = {Bicontinuous extensions of invertible combinatorial functions},
  year             = {1981},
  issn             = {1433-0490},
  month            = dec,
  number           = {1},
  pages            = {13--23},
  volume           = {14},
  comment          = {Cited in Feynman1985 (ref. [4]).},
  creationdate     = {2024-10-13T11:06:29},
  doi              = {10.1007/bf01752388},
  file             = {:by-author/T/Toffoli/1981_Toffoli_13.pdf:PDF},
  keywords         = {Computer Architecture; Computer Science (CS); Energy Cost of Computation; Physics; Quantum Computers; Quantum Computing; Quantum Mechanics (QM); Reversibility of Computation; Thermodynamics},
  modificationdate = {2024-10-13T11:08:22},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media LLC},
}

@Article{Priese1976,
  author           = {Priese, Lutz},
  journal          = {Journal of Cybernetics},
  title            = {On a simple combinatorial structure sufficient for syblying nontrivial self-reproduction},
  year             = {1976},
  issn             = {0022-0280},
  month            = jan,
  number           = {1–2},
  pages            = {101--137},
  volume           = {6},
  comment          = {Cited in Feynman1985 (ref. [5]).},
  creationdate     = {2024-10-13T11:14:27},
  doi              = {10.1080/01969727608927527},
  file             = {:by-author/P/Priese/1976_Priese_101.pdf:PDF},
  keywords         = {Computer Architecture; Computer Science (CS); Energy Cost of Computation; Physics; Quantum Computers; Quantum Computing; Quantum Mechanics (QM); Reversibility of Computation; Self-reproducing Systems; Thermodynamics},
  modificationdate = {2024-10-13T11:17:36},
  owner            = {saulius},
  publisher        = {Informa UK Limited},
}

@Article{Fagundes2021,
  author           = {Fagundes, Daniel Almeida},
  journal          = {European Journal of Physics},
  title            = {Electrostatic potential of a rectangular uniformly charged plate: exact solution and limiting cases},
  year             = {2021},
  issn             = {1361-6404},
  month            = nov,
  number           = {1},
  pages            = {015203},
  volume           = {43},
  creationdate     = {2024-10-17T20:54:36},
  doi              = {10.1088/1361-6404/ac362f},
  file             = {:by-author/F/Fagundes/2021_Fagundes_15203.pdf:PDF},
  keywords         = {Electorstatics; Electricity; Electrodynamics; Physics; Thin PLate},
  modificationdate = {2024-10-17T20:55:43},
  owner            = {saulius},
  publisher        = {IOP Publishing},
}

@Article{Aroyo2006,
  author           = {Aroyo, Mois Ilia and Perez-Mato, Juan Manuel and Capillas, Cesar and Kroumova, Eli and Ivantchev, Svetoslav and Madariaga, Gotzon and Kirov, Asen and Wondratschek, Hans},
  journal          = {Zeitschrift für Kristallographie - Crystalline Materials},
  title            = {{B}ilbao {C}rystallographic {S}erver: {I}. Databases and crystallographic computing programs},
  year             = {2006},
  issn             = {2194-4946},
  month            = jan,
  number           = {1},
  pages            = {15--27},
  volume           = {221},
  creationdate     = {2024-10-21T09:03:44},
  doi              = {10.1524/zkri.2006.221.1.15},
  file             = {:by-author/A/Aroyo/2006_Aroyo_15.pdf:PDF},
  keywords         = {Bilbao Database Server; Crystallographic Databases; Crystallography},
  modificationdate = {2024-10-22T15:05:42},
  owner            = {saulius},
  publisher        = {Walter de Gruyter GmbH},
}

@Article{Aroyo2006a,
  author           = {Aroyo, Mois I. and Kirov, Asen and Capillas, Cesar and Perez-Mato, J. M. and Wondratschek, Hans},
  journal          = {Acta Crystallographica Section A Foundations of Crystallography},
  title            = {{B}ilbao {C}rystallographic {S}erver. {II}. Representations of crystallographic point groups and space groups},
  year             = {2006},
  issn             = {0108-7673},
  month            = mar,
  number           = {2},
  pages            = {115--128},
  volume           = {62},
  creationdate     = {2024-10-21T09:06:46},
  doi              = {10.1107/s0108767305040286},
  file             = {:by-author/A/Aroyo/2006_Aroyo_115.pdf:PDF},
  keywords         = {Bilbao Database Server; Crystallographic Databases; Crystallography},
  modificationdate = {2024-10-22T15:05:28},
  owner            = {saulius},
  publisher        = {International Union of Crystallography (IUCr)},
}

@Article{Abbes2022,
  author           = {Abbes, Ali Ben and Machicao, Jeaneth and Meneguzzi, Leonardo and Corrêa, Pedro Pizzigatti and Specht, Alison and David, Romain and Subsol, Gérard and Vellenich, Danton Ferreira and Devillers, Rodolphe and Stall, Shelley and Mouquet, Nicolas and Chaumont, Marc and Berti-Equille, Laure and Mouillot, David},
  title            = {Checklist strategies to improve the reproducibility of deep learning experiments with an illustration},
  year             = {2022},
  comment          = {Pacituotas Ernesto Filatovo (pranešėjas*), Lino Stripinio, Remigijaus Paulavičiaus pranešime VU Atviro moklso savaitės renginyje.},
  copyright        = {Creative Commons Attribution 4.0 International},
  creationdate     = {2024-10-22T15:14:50},
  doi              = {10.5281/ZENODO.6587702},
  file             = {:by-author/A/Abbes/2022_Abbes_1.pdf:PDF},
  keywords         = {Artificial Intelligence (AI); Deep-learning, Data-sharing; FAIR; Machine Learning (ML); Machine-learning; Reproducibility; Reproducible Research},
  language         = {en},
  modificationdate = {2024-10-23T16:10:05},
  owner            = {saulius},
  publisher        = {Zenodo},
  url              = {https://hal.science/hal-03738323/document},
}

@Article{Zheng2024,
  author           = {Zheng, Kaipeng and Huang, Weiran and Ouyang, Wanli and Zhong, Han-Sen and Li, Yuqiang},
  journal          = {arXiv},
  title            = {{CrystalX}: ultra-precision crystal structure resolution and error correction using deep learning},
  year             = {2024},
  month            = oct,
  abstract         = {Atomic structure analysis of crystalline materials is a paramount endeavor in both chemical and material sciences. This sophisticated technique necessitates not only a solid foundation in crystallography but also a profound comprehension of the intricacies of the accompanying software, posing a significant challenge in meeting the rigorous daily demands. For the first time, we confront this challenge head-on by harnessing the power of deep learning for ultra-precise structural analysis at the full-atom level. To validate the performance of the model, named CrystalX, we employed a vast dataset comprising over 50,000 X-ray diffraction measurements derived from authentic experiments, demonstrating performance that is commensurate with human experts and adept at deciphering intricate geometric patterns. Remarkably, CrystalX revealed that even peer-reviewed publications can harbor errors that are stealthy to human scrutiny, yet CrystalX adeptly rectifies them. This deep learning model revolutionizes the time frame for crystal structure analysis, slashing it down to seconds. It has already been successfully applied in the structure analysis of newly discovered compounds in the latest research without human intervention. Overall, CrystalX marks the beginning of a new era in automating routine structural analysis within self-driving laboratories.},
  archiveprefix    = {arXiv},
  comment          = {Discussed duting the 2024-10-23 KICIS meeting (A.V.); A.V: discussed by Armel Le Bail on the COD Facebook group. Data available at https://doi.org/10.5281/zenodo.13820303 (4.8 GB ZIP file).},
  copyright        = {arXiv.org perpetual, non-exclusive license},
  creationdate     = {2024-10-23T16:11:31},
  doi              = {10.48550/ARXIV.2410.13713},
  eprint           = {2410.13713},
  file             = {:by-author/Z/Zheng/2024_Zheng_1.pdf:PDF},
  keywords         = {Artificial Neural Networks (ANN); COD; Data Quality; Data Reviews; FOS: Computer and Information Sciences; Machine Learning (ML)},
  modificationdate = {2024-10-23T16:28:01},
  owner            = {saulius},
  primaryclass     = {cs.LG},
  publisher        = {arXiv},
}

@Article{Thoelke2022,
  author           = {Thölke, Philipp and De Fabritiis, Gianni},
  title            = {TorchMD-NET: Equivariant Transformers for Neural Network based Molecular Potentials},
  year             = {2022},
  month            = feb,
  abstract         = {The prediction of quantum mechanical properties is historically plagued by a trade-off between accuracy and speed. Machine learning potentials have previously shown great success in this domain, reaching increasingly better accuracy while maintaining computational efficiency comparable with classical force fields. In this work we propose TorchMD-NET, a novel equivariant transformer (ET) architecture, outperforming state-of-the-art on MD17, ANI-1, and many QM9 targets in both accuracy and computational efficiency. Through an extensive attention weight analysis, we gain valuable insights into the black box predictor and show differences in the learned representation of conformers versus conformations sampled from molecular dynamics or normal modes. Furthermore, we highlight the importance of datasets including off-equilibrium conformations for the evaluation of molecular potentials.},
  archiveprefix    = {arXiv},
  comment          = {Cited in Zheng2024 (ref. [39]). Code published in: https://github.com/torchmd/torchmd-net.git.},
  copyright        = {arXiv.org perpetual, non-exclusive license},
  creationdate     = {2024-10-23T16:30:45},
  doi              = {10.48550/ARXIV.2202.02541},
  eprint           = {2202.02541},
  file             = {:by-author/T/Thölke/2022_Thölke_1.pdf:PDF},
  keywords         = {Artificial Intelligence (AI); Chemical Physics; FOS: Computer and Information Sciences; FOS: Physical Sciences; Machine Learning (ML)},
  modificationdate = {2024-10-23T16:37:05},
  owner            = {saulius},
  primaryclass     = {cs.LG},
  publisher        = {arXiv},
}

@Article{Grabowski2017,
  author           = {Grabowski, Marek and Minor, Wladek},
  journal          = {IUCrJ},
  title            = {Sharing {B}ig {D}ata},
  year             = {2017},
  issn             = {2052-2525},
  month            = jan,
  number           = {1},
  pages            = {3--4},
  volume           = {4},
  comment          = {Found on the IUCrJ web page when searching for "sharing data" (1467 articles match your search "sharing data", sorted by relevance).},
  creationdate     = {2024-10-25T10:06:39},
  doi              = {10.1107/s2052252516020364},
  file             = {:by-author/G/Grabowski/2017_Grabowski_3.pdf:PDF},
  keywords         = {Big Data; Data Sharing; Metadata; Open Science; Reproducibility},
  modificationdate = {2024-10-25T10:11:53},
  owner            = {saulius},
  publisher        = {International Union of Crystallography (IUCr)},
}

@Article{Aranda2018,
  author           = {Aranda, Miguel A. G.},
  journal          = {Journal of Applied Crystallography},
  title            = {Sharing powder diffraction raw data: challenges and benefits},
  year             = {2018},
  issn             = {1600-5767},
  month            = nov,
  number           = {6},
  pages            = {1739--1744},
  volume           = {51},
  comment          = {Found on the IUCrJ web page when searching for "sharing data" (1467 articles match your search "sharing data", sorted by relevance).},
  creationdate     = {2024-10-25T10:12:13},
  doi              = {10.1107/s160057671801556x},
  file             = {:by-author/A/Aranda/2018_Aranda_1739.pdf:PDF},
  keywords         = {Data Processing; Powder Diffraction; Raw Data},
  modificationdate = {2024-10-25T10:22:42},
  owner            = {saulius},
  publisher        = {International Union of Crystallography (IUCr)},
}

@Article{Marabini2013,
  author           = {Marabini, Roberto and Macias, Jose Ramon and Vargas, Javier and Quintana, Adrian and Sorzano, Carlos Oscar S. and Carazo, Jose María},
  journal          = {Acta Crystallographica Section D Biological Crystallography},
  title            = {On the development of three new tools for organizing and sharing information in three-dimensional electron microscopy},
  year             = {2013},
  issn             = {0907-4449},
  month            = apr,
  number           = {5},
  pages            = {695--700},
  volume           = {69},
  comment          = {Found on the IUCrJ web page when searching for "sharing data" (1467 articles match your search "sharing data", sorted by relevance).},
  creationdate     = {2024-10-25T10:23:08},
  doi              = {10.1107/s0907444913007038},
  file             = {:by-author/M/Marabini/2013_Marabini_695.pdf:PDF},
  keywords         = {Data Management; Data Processing; Data Sharing; Electron Microscopy; Scientific Data},
  modificationdate = {2024-10-25T10:27:39},
  owner            = {saulius},
  publisher        = {International Union of Crystallography (IUCr)},
}

@Article{Martinez2021,
  author           = {Martinez, Xavier and Baaden, Marc},
  journal          = {Acta Crystallographica Section D Structural Biology},
  title            = {{UnityMol} prototype for {FAIR} sharing of molecular-visualization experiences: from pictures in the cloud to collaborative virtual reality exploration in immersive {3D} environments},
  year             = {2021},
  issn             = {2059-7983},
  month            = may,
  number           = {6},
  pages            = {746--754},
  volume           = {77},
  comment          = {Found on the IUCrJ web page when searching for "sharing data" (1467 articles match your search "sharing data", sorted by relevance).},
  creationdate     = {2024-10-25T10:26:26},
  doi              = {10.1107/s2059798321002941},
  file             = {:by-author/M/Martinez/2021_Martinez_746.pdf:PDF},
  keywords         = {COVID-19; Collaborative Environments; FAIR; FAIR Sharing; Molecular Visualization; Virtual Reality},
  modificationdate = {2024-10-25T10:29:02},
  owner            = {saulius},
  publisher        = {International Union of Crystallography (IUCr)},
}

@Article{Helliwell2017,
  author           = {Helliwell, John R. and McMahon, Brian and Guss, J. Mitchell and Kroon-Batenburg, Loes M. J.},
  journal          = {IUCrJ},
  title            = {The science is in the data},
  year             = {2017},
  issn             = {2052-2525},
  month            = oct,
  number           = {6},
  pages            = {714--722},
  volume           = {4},
  comment          = {Found on the IUCrJ web page when searching for "sharing data" (1467 articles match your search "sharing data", sorted by relevance).},
  creationdate     = {2024-10-25T10:29:42},
  doi              = {10.1107/s2052252517013690},
  file             = {:by-author/H/Helliwell/2017_Helliwell_714.pdf:PDF},
  keywords         = {Crystallographic Science Case Studies; Education; Open Science; Raw Diffraction Data; Sharing Raw Data and Its Reuse},
  modificationdate = {2024-10-25T10:30:58},
  owner            = {saulius},
  publisher        = {International Union of Crystallography (IUCr)},
}

@Article{Gruene2024,
  author           = {Gruene, Tim},
  journal          = {Acta Crystallographica Section C Structural Chemistry},
  title            = {Data collection is your last experiment},
  year             = {2024},
  issn             = {2053-2296},
  month            = jun,
  number           = {7},
  pages            = {262--263},
  volume           = {80},
  comment          = {Found on the IUCrJ web page when searching for "sharing data" (1467 articles match your search "sharing data", sorted by relevance).},
  creationdate     = {2024-10-25T10:31:54},
  doi              = {10.1107/s2053229624005254},
  file             = {:by-author/G/Gruene/2024_Gruene_262.pdf:PDF},
  keywords         = {3D ED; Chemical Crystallography; Electron Diffraction; MicroED},
  modificationdate = {2024-10-25T10:32:49},
  owner            = {saulius},
  publisher        = {International Union of Crystallography (IUCr)},
}

@Article{Hu2021a,
  author           = {Hu, Hao and Qi, Fazhi and Zhang, Hongmei and Tian, Haolai and Luo, Qi},
  journal          = {Journal of Synchrotron Radiation},
  title            = {The design of a data management system at {HEPS}},
  year             = {2021},
  issn             = {1600-5775},
  month            = jan,
  number           = {1},
  pages            = {169--175},
  volume           = {28},
  comment          = {Found on the IUCrJ web page when searching for "sharing data" (1467 articles match your search "sharing data", sorted by relevance).},
  creationdate     = {2024-10-25T10:33:36},
  doi              = {10.1107/s1600577520015167},
  file             = {:by-author/H/Hu/2021_Hu_169.pdf:PDF},
  keywords         = {Data Management; High-energy Photon Sources; Metadata Ingestion},
  modificationdate = {2024-10-25T10:35:21},
  owner            = {saulius},
  publisher        = {International Union of Crystallography (IUCr)},
}

@Article{DeCarlo2014,
  author           = {De Carlo, Francesco and Gürsoy, Dogˇa and Marone, Federica and Rivers, Mark and Parkinson, Dilworth Y. and Khan, Faisal and Schwarz, Nicholas and Vine, David J. and Vogt, Stefan and Gleber, Sophie-Charlotte and Narayanan, Suresh and Newville, Matt and Lanzirotti, Tony and Sun, Yue and Hong, Young Pyo and Jacobsen, Chris},
  journal          = {Journal of Synchrotron Radiation},
  title            = {Scientific data exchange: a schema for {HDF5}-based storage of raw and analyzed data},
  year             = {2014},
  issn             = {1600-5775},
  month            = oct,
  number           = {6},
  pages            = {1224--1230},
  volume           = {21},
  comment          = {Found on the IUCrJ web page when searching for "sharing data" (1467 articles match your search "sharing data", sorted by relevance).},
  creationdate     = {2024-10-25T10:36:02},
  doi              = {10.1107/s160057751401604x},
  file             = {:by-author/D/De Carlo/2014_De Carlo_1224.pdf:PDF},
  keywords         = {Data Formats; Data Management; Data Processing; Data Sharing; HDF5; Raw Diffraction Data; Sharing Raw Data and Its Reuse},
  modificationdate = {2024-10-25T10:39:41},
  owner            = {saulius},
  publisher        = {International Union of Crystallography (IUCr)},
}

@Article{Helliwell2024a,
  author           = {Helliwell, John R. and Hester, James R. and Kroon-Batenburg, Loes M. J. and McMahon, Brian and Storm, Selina L. S.},
  journal          = {IUCrJ},
  title            = {The evolution of raw data archiving and the growth of its importance in crystallography},
  year             = {2024},
  issn             = {2052-2525},
  month            = jun,
  number           = {4},
  pages            = {464--475},
  volume           = {11},
  creationdate     = {2024-10-25T10:42:23},
  doi              = {10.1107/s205225252400455x},
  file             = {:by-author/H/Helliwell/2024_Helliwell_464.pdf:PDF},
  keywords         = {Ground Truth; Raw Data Archive Hardware; Raw Data Measuring Hardware; Raw Data Policies at Photon and Neutron Facilities; Raw Data Processing Software},
  modificationdate = {2024-10-25T10:44:18},
  owner            = {saulius},
  publisher        = {International Union of Crystallography (IUCr)},
}

@Article{Anosova2024,
  author           = {Anosova, Olga and Kurlin, Vitaliy and Senechal, Marjorie},
  journal          = {IUCrJ},
  title            = {The importance of definitions in crystallography},
  year             = {2024},
  issn             = {2052-2525},
  month            = may,
  number           = {4},
  pages            = {453--463},
  volume           = {11},
  creationdate     = {2024-10-25T10:45:35},
  doi              = {10.1107/s2052252524004056},
  file             = {:by-author/A/Anosova/2024_Anosova_453.pdf:PDF},
  keywords         = {Crystal Definition; Materials Modeling; Phase Problem; Structure Prediction},
  modificationdate = {2024-10-25T10:46:32},
  owner            = {saulius},
  publisher        = {International Union of Crystallography (IUCr)},
}

@Article{Gutmanas2013,
  author           = {Gutmanas, Aleksandras and Oldfield, Thomas J. and Patwardhan, Ardan and Sen, Sanchayita and Velankar, Sameer and Kleywegt, Gerard J.},
  journal          = {Acta Crystallographica Section D Biological Crystallography},
  title            = {The role of structural bioinformatics resources in the era of integrative structural biology},
  year             = {2013},
  issn             = {0907-4449},
  month            = apr,
  number           = {5},
  pages            = {710--721},
  volume           = {69},
  comment          = {Found by searching for "ontologies" in the IUCr journals (17 articles match your search "ontologies").},
  creationdate     = {2024-10-25T11:34:49},
  doi              = {10.1107/s0907444913001157},
  file             = {:by-author/G/Gutmanas/2013_Gutmanas_710.pdf:PDF},
  keywords         = {Bioinformatics; Data Sharing; Ontologies; Structural Bioinformatics; Structural Biology},
  modificationdate = {2024-10-25T11:41:35},
  owner            = {saulius},
  publisher        = {International Union of Crystallography (IUCr)},
}

@InBook{Kramer2016,
  author           = {Kramer, Frank and Beißbarth, Tim},
  pages            = {123--135},
  publisher        = {Springer New York},
  title            = {Working with ontologies},
  year             = {2016},
  isbn             = {9781493966226},
  month            = nov,
  volume           = {1525},
  abstract         = {Ontologies are powerful and popular tools to encode data in a structured format and manage knowledge. A large variety of existing ontologies offer users access to biomedical knowledge. This chapter contains a short theoretical background of ontologies and introduces two notable examples: The Gene Ontology and the ontology for Biological Pathways Exchange. For both ontologies a short overview and working bioinformatic applications, i.e., Gene Ontology enrichment analyses and pathway data visualization, are provided.},
  booktitle        = {Bioinformatics},
  citation-subset  = {IM},
  completed        = {2018-01-22},
  country          = {United States},
  creationdate     = {2024-10-25T11:58:57},
  doi              = {10.1007/978-1-4939-6622-6_6},
  file             = {:by-author/K/Kramer/2016_Kramer_123.pdf:PDF},
  issn             = {1940-6029},
  issn-linking     = {1064-3745},
  journal          = {Methods in molecular biology (Clifton, N.J.)},
  keywords         = {BioPAX; Computational Biology, Methods; Data Management; GOstat; Gene Ontology; Information Storage and Retrieval; Knowledge Management; Natural Language Processing; Ontologies; RBiopaxParser; TopGO},
  modificationdate = {2024-10-25T15:22:12},
  nlm-id           = {9214969},
  owner            = {saulius},
  pmid             = {27896720},
  pubmodel         = {Print},
  pubstate         = {ppublish},
  revised          = {2018-04-20},
}

@InBook{Souvignier2016,
  author           = {B. Souvignier and G. Chapuis and H. Wondratschek},
  chapter          = {1.5.4},
  editor           = {Mois I. Aroyo},
  pages            = {91--106},
  publisher        = {Wiley},
  title            = {Synoptic tables of plane and space groups},
  year             = {2016},
  volume           = {A},
  booktitle        = {International Tables for Crystallography},
  creationdate     = {2024-10-30T15:37:24},
  file             = {:by-author/S/Souvignier/2016_Souvignier_91.pdf:PDF},
  keywords         = {Crystallography; International Tables for Crystallography; Space Groups; Spacegroup Settings; Spacegroups},
  modificationdate = {2024-10-30T16:55:03},
  owner            = {saulius},
  section          = {1.5.4},
  url              = {https://onlinelibrary.wiley.com/iucr/itc/Ac/ch1o5v0001/sec1o5o4.pdf},
}

@Webpage{Hall1996,
  author           = {Hall, S. R. and Grosse-Kunstleve, R. W.},
  retrieved        = {2024-10-30T16:55+02:00},
  title            = {Concise space-group symbols},
  url              = {https://cci.lbl.gov/sginfo/hall_symbols.html},
  year             = {1996},
  creationdate     = {2024-10-30T16:52:50},
  file             = {:by-author/H/Hall/1996_Hall_1.html:URL},
  keywords         = {Crystallography; Hall Symbols; International Tables for Crystallography; Space Groups; Spacegroup Settings; Spacegroups},
  modificationdate = {2024-10-30T16:55:44},
  owner            = {saulius},
}

@Article{Kleywegt2024,
  author           = {Kleywegt, Gerard J. and Adams, Paul D. and Butcher, Sarah J. and Lawson, Catherine L. and Rohou, Alexis and Rosenthal, Peter B. and Subramaniam, Sriram and Topf, Maya and Abbott, Sanja and Baldwin, Philip R. and Berrisford, John M. and Bricogne, Gérard and Choudhary, Preeti and Croll, Tristan I. and Danev, Radostin and Ganesan, Sai J. and Grant, Timothy and Gutmanas, Aleksandras and Henderson, Richard and Heymann, J. Bernard and Huiskonen, Juha T. and Istrate, Andrei and Kato, Takayuki and Lander, Gabriel C. and Lok, Shee-Mei and Ludtke, Steven J. and Murshudov, Garib N. and Pye, Ryan and Pintilie, Grigore D. and Richardson, Jane S. and Sachse, Carsten and Salih, Osman and Scheres, Sjors H. W. and Schroeder, Gunnar F. and Sorzano, Carlos Oscar S. and Stagg, Scott M. and Wang, Zhe and Warshamanage, Rangana and Westbrook, John D. and Winn, Martyn D. and Young, Jasmine Y. and Burley, Stephen K. and Hoch, Jeffrey C. and Kurisu, Genji and Morris, Kyle and Patwardhan, Ardan and Velankar, Sameer},
  journal          = {IUCrJ},
  title            = {Community recommendations on {cryoEM} data archiving and validation},
  year             = {2024},
  issn             = {2052-2525},
  month            = feb,
  number           = {2},
  pages            = {140--151},
  volume           = {11},
  creationdate     = {2024-11-08T14:42:44},
  doi              = {10.1107/s2052252524001246},
  file             = {:by-author/K/Kleywegt/2024_Kleywegt_140.pdf:PDF},
  keywords         = {CIF; CryoEM; Crystallographic Databases; Data Deposition; Data Quality; Data Validation},
  modificationdate = {2024-11-08T14:44:03},
  owner            = {saulius},
  publisher        = {International Union of Crystallography (IUCr)},
}

@Presentation{McMahon2019,
  author           = {Brian McMahon},
  title            = {The vital role of {C}rystallographic {I}nformation {F}iles in chemical and biological crystallography to underpin the databases’ validation reports},
  year             = {2019},
  creationdate     = {2024-11-08T17:30:17},
  file             = {:by-author/M/McMahon/2019_McMahon_The Vital Role of Crystallographic Information Files in Chemical and Biological Crystallography to Underpin the Databases’ Validation Reports.pdf:PDF},
  keywords         = {CIF; Crystallographic Data; Crystallographic Databases; Data Management},
  modificationdate = {2024-11-08T17:41:53},
  owner            = {saulius},
  url              = {https://www.iucr.org/__data/assets/pdf_file/0016/144007/03_McMahon_CIF.pdf},
}

@Presentation{McMahon2019a,
  author           = {Brian McMahon},
  title            = {The core {CIF} dictionary and the {mmCIF} dictionary},
  year             = {2019},
  creationdate     = {2024-11-08T17:39:36},
  file             = {:by-author/M/McMahon/2019_McMahon_The Core CIF Dictionary and the MmCIF Dictionary.pdf:PDF:https\://www.iucr.org/__data/assets/pdf_file/0020/145424/McMahon_core_mmcif.pdf},
  keywords         = {CIF; Crystallographic Data; Crystallographic Databases; Data Management},
  modificationdate = {2024-11-08T17:47:12},
  owner            = {saulius},
  url              = {https://www.iucr.org/__data/assets/pdf_file/0020/145424/McMahon_core_mmcif.pdf},
}

@Presentation{McMahon2015,
  author           = {Brian McMahon},
  title            = {The {C}rystallographic {I}nformation {F}ramework as a metadata library},
  year             = {2015},
  creationdate     = {2024-11-08T17:44:48},
  file             = {:by-author/M/McMahon/2015_McMahon_The Crystallographic Information Framework As a Metadata Library.pdf:PDF:https\://www.iucr.org/__data/assets/pdf_file/0011/114131/20_McMahon.pdf},
  keywords         = {CIF; Crystallographic Data; Crystallographic Databases; Data Management},
  modificationdate = {2024-11-08T17:47:39},
  owner            = {saulius},
  url              = {https://www.iucr.org/__data/assets/pdf_file/0011/114131/20_McMahon.pdf},
}

@Presentation{McMahon2015a,
  author           = {Brian McMahon},
  title            = {{CODATA} and (meta)data characterisation in the wider world},
  year             = {2015},
  comment          = {Cited in Brink2024 (ref. McMahon, B. (2017)).},
  creationdate     = {2024-11-08T18:28:55},
  file             = {:by-author/M/McMahon/2015_McMahon_CODATA and (meta)data Characterisation in the Wider World.pdf:PDF:https\://www.iucr.org/__data/assets/pdf_file/0012/114123/15_McMahon.pdf},
  keywords         = {CIF; Crystallographic Data; Crystallographic Databases; Data Management},
  modificationdate = {2024-11-08T18:35:19},
  owner            = {saulius},
  url              = {https://www.iucr.org/__data/assets/pdf_file/0012/114123/15_McMahon.pdf},
}

@InBook{Chapuis2016,
  author           = {G. Chapuis and H. Wondratschek and M. I. Aroyo},
  chapter          = {1.5.3},
  pages            = {87--90},
  title            = {Transformations of coordinate systems. Transformations between different space-group descriptions},
  year             = {2016},
  volume           = {A},
  booktitle        = {International Tables for Crystallography},
  creationdate     = {2024-11-08T18:47:50},
  file             = {:by-author/C/Chapuis/2016_Chapuis_87.pdf:PDF},
  keywords         = {Crystallography; International Tables for Crystallography; Space Groups; Spacegroup Settings; Spacegroups},
  modificationdate = {2024-11-08T18:54:38},
  owner            = {saulius},
  url              = {https://onlinelibrary.wiley.com/iucr/itc/Ac/ch1o5v0001/sec1o5o3.pdf},
}

@Article{Ertl2002a,
  author           = {Ertl, M. Anton and Gregg, David and Krall, Andreas and Paysan, Bernd},
  journal          = {Software: Practice and Experience},
  title            = {Vmgen—a generator of efficient virtual machine interpreters},
  year             = {2002},
  issn             = {1097-024X},
  month            = jan,
  number           = {3},
  pages            = {265--294},
  volume           = {32},
  creationdate     = {2024-11-08T22:10:08},
  doi              = {10.1002/spe.434},
  file             = {:by-author/E/Ertl/2002_Ertl_265.pdf:PDF},
  keywords         = {Compiler Construction; Computer Science (CS); Interpreters; Stack Machines},
  modificationdate = {2024-11-08T22:14:28},
  owner            = {saulius},
  publisher        = {Wiley},
}

@Article{Romer1996,
  author           = {Romer, Theodore H. and Lee, Dennis and Voelker, Geoffrey M. and Wolman, Alec and Wong, Wayne A. and Baer, Jean-Loup and Bershad, Brian N. and Levy, Henry M.},
  journal          = {ACM SIGPLAN Notices},
  title            = {The structure and performance of interpreters},
  year             = {1996},
  issn             = {1558-1160},
  month            = sep,
  number           = {9},
  pages            = {150--159},
  volume           = {31},
  comment          = {Cited in Ertl2002a (ref. [5]).},
  creationdate     = {2024-11-08T22:14:01},
  doi              = {10.1145/248209.237175},
  file             = {:by-author/R/Romer/1996_Romer_150.pdf:PDF},
  keywords         = {Compiler Construction; Computer Science (CS); Interpreters; Stack Machines},
  modificationdate = {2024-11-08T22:16:51},
  owner            = {saulius},
  publisher        = {Association for Computing Machinery (ACM)},
}

@Article{Wlodawer2024,
  author           = {Wlodawer, Alexander and Dauter, Zbigniew and Rubach, Pawel and Minor, Wladek and Loch, Joanna I. and Brzezinski, Dariusz and Gilski, Miroslaw and Jaskolski, Mariusz},
  journal          = {IUCrJ},
  title            = {Waterless structures in the {P}rotein {D}ata {B}ank},
  year             = {2024},
  issn             = {2052-2525},
  month            = oct,
  number           = {6},
  pages            = {966--976},
  volume           = {11},
  creationdate     = {2024-11-10T14:48:10},
  doi              = {10.1107/s2052252524009928},
  file             = {:by-author/W/Wlodawer/2024_Wlodawer_966.pdf:PDF},
  keywords         = {Macromolecular Structures; Missing Water Molecules; PDB; Protein Structures; Structure Quality; Structure Validation; Water; Water Structure},
  modificationdate = {2024-11-10T14:50:19},
  owner            = {saulius},
  publisher        = {International Union of Crystallography (IUCr)},
}

@Article{Breunig2000,
  author           = {Breunig, Markus M. and Kriegel, Hans-Peter and Ng, Raymond T. and Sander, Jörg},
  journal          = {ACM SIGMOD Record},
  title            = {{LOF}: identifying density-based local outliers},
  year             = {2000},
  issn             = {0163-5808},
  month            = may,
  number           = {2},
  pages            = {93--104},
  volume           = {29},
  comment          = {Cited in Wlodawer2024.},
  creationdate     = {2024-11-10T14:53:26},
  doi              = {10.1145/335191.335388},
  file             = {:by-author/B/Breunig/2000_Breunig_93.pdf:PDF},
  keywords         = {Data Processing; Data Quality; Database Mining; Outlier Detection; Statistics},
  modificationdate = {2024-11-12T11:02:15},
  owner            = {saulius},
  publisher        = {Association for Computing Machinery (ACM)},
}

@Article{Liu2024a,
  author           = {Liu, Junyu and Liu, Minzhao and Liu, Jin-Peng and Ye, Ziyu and Wang, Yunfei and Alexeev, Yuri and Eisert, Jens and Jiang, Liang},
  journal          = {Nature Communications},
  title            = {Towards provably efficient quantum algorithms for large-scale machine-learning models},
  year             = {2024},
  issn             = {2041-1723},
  month            = jan,
  number           = {1},
  pages            = {434},
  volume           = {15},
  creationdate     = {2024-11-12T11:02:24},
  doi              = {10.1038/s41467-023-43957-x},
  file             = {:by-author/L/Liu/2024_Liu_434.pdf:PDF:https\://www.nature.com/articles/s41467-023-43957-x.pdf},
  keywords         = {Computer Science (CS); Quantum Algorithms; Quantum Computing},
  modificationdate = {2024-11-12T11:05:48},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media LLC},
}

@Article{Elgendy2024,
  author           = {Elgendy, Rehab and Younes, Ahmed and Abu-Donia, H. M. and Farouk, R. M.},
  journal          = {Scientific Reports},
  title            = {Efficient quantum algorithms for set operations},
  year             = {2024},
  issn             = {2045-2322},
  month            = mar,
  number           = {1},
  pages            = {7015},
  volume           = {14},
  creationdate     = {2024-11-12T11:04:57},
  doi              = {10.1038/s41598-024-56860-2},
  file             = {:by-author/E/Elgendy/2024_Elgendy_7015.pdf:PDF:https\://www.nature.com/articles/s41598-024-56860-2.pdf},
  keywords         = {Computer Science (CS); Quantum Algorithms; Quantum Computing},
  modificationdate = {2024-11-12T11:07:12},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media LLC},
}

@Article{Montanaro2016,
  author           = {Montanaro, Ashley},
  journal          = {npj Quantum Information},
  title            = {Quantum algorithms: an overview},
  year             = {2016},
  issn             = {2056-6387},
  month            = jan,
  number           = {1},
  pages            = {15023},
  volume           = {2},
  creationdate     = {2024-11-12T11:07:57},
  doi              = {10.1038/npjqi.2015.23},
  file             = {:by-author/M/Montanaro/2016_Montanaro_15023.pdf:PDF:https\://www.nature.com/articles/npjqi201523.pdf},
  keywords         = {Computer Science (CS); Quantum Algorithms; Quantum Computing},
  modificationdate = {2024-11-12T11:08:49},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media LLC},
}

@Article{Ma2024,
  author           = {Ma, QuanGong and Hao, ChaoLong and Yang, XuKui and Qian, LongLong and Zhang, Hao and Si, NianWen and Xu, MinChen and Qu, Dan},
  journal          = {EPJ Quantum Technology},
  title            = {Continuous evolution for efficient quantum architecture search},
  year             = {2024},
  issn             = {2196-0763},
  month            = sep,
  number           = {1},
  pages            = {54},
  volume           = {11},
  creationdate     = {2024-11-12T11:10:15},
  doi              = {10.1140/epjqt/s40507-024-00265-7},
  file             = {:by-author/M/Ma/2024_Ma_54.pdf:PDF:https\://epjquantumtechnology.springeropen.com/counter/pdf/10.1140/epjqt/s40507-024-00265-7},
  keywords         = {Computer Science (CS); Quantum Algorithms; Quantum Computing},
  modificationdate = {2024-11-12T11:11:12},
  owner            = {saulius},
  publisher        = {Springer Science and Business Media LLC},
}

@InProceedings{Shor,
  author           = {Shor, P. W.},
  booktitle        = {Proceedings 35th Annual Symposium on Foundations of Computer Science},
  title            = {Algorithms for quantum computation: discrete logarithms and factoring},
  year             = {1994},
  pages            = {124--134},
  publisher        = {IEEE Comput. Soc. Press},
  series           = {SFCS-94},
  collection       = {SFCS-94},
  creationdate     = {2024-11-12T11:14:40},
  doi              = {10.1109/sfcs.1994.365700},
  file             = {:by-author/S/Shor/1994_Shor_124.pdf:PDF},
  keywords         = {Computer Science (CS); Prime Number Factoring; Quantum Algorithms; Quantum Computing},
  modificationdate = {2024-11-12T11:17:01},
  owner            = {saulius},
}

@Article{Shor1997,
  author           = {Shor, Peter W.},
  journal          = {SIAM Journal on Computing},
  title            = {Polynomial-time algorithms for prime factorization and discrete logarithms on a quantum computer},
  year             = {1997},
  issn             = {1095-7111},
  month            = oct,
  number           = {5},
  pages            = {1484--1509},
  volume           = {26},
  creationdate     = {2024-11-12T11:17:44},
  doi              = {10.1137/s0097539795293172},
  file             = {:by-author/S/Shor/1997_Shor_1484.pdf:PDF},
  keywords         = {Computer Science (CS); Prime Number Factoring; Quantum Algorithms; Quantum Computing},
  modificationdate = {2024-11-12T11:24:31},
  owner            = {saulius},
  publisher        = {Society for Industrial & Applied Mathematics (SIAM)},
}

@Article{Shor1995a,
  author           = {Shor, Peter W.},
  journal          = {SIAM J.Sci.Statist.Comput. 26 (1997) 1484},
  title            = {Polynomial-time algorithms for prime factorization and discrete logarithms on a quantum computer},
  year             = {1995},
  issn             = {1095-7111},
  month            = oct,
  number           = {5},
  pages            = {1484--1509},
  volume           = {26},
  abstract         = {A digital computer is generally believed to be an efficient universal computing device; that is, it is believed able to simulate any physical computing device with an increase in computation time of at most a polynomial factor. This may not be true when quantum mechanics is taken into consideration. This paper considers factoring integers and finding discrete logarithms, two problems which are generally thought to be hard on a classical computer and have been used as the basis of several proposed cryptosystems. Efficient randomized algorithms are given for these two problems on a hypothetical quantum computer. These algorithms take a number of steps polynomial in the input size, e.g., the number of digits of the integer to be factored.},
  archiveprefix    = {arXiv},
  copyright        = {Assumed arXiv.org perpetual, non-exclusive license to distribute this article for submissions made before January 2004},
  creationdate     = {2024-11-12T11:19:24},
  date             = {1995-08-30},
  doi              = {10.1137/s0097539795293172},
  eprint           = {quant-ph/9508027},
  file             = {:by-author/S/Shor/1995_Shor_1484.pdf:PDF:http\://arxiv.org/pdf/quant-ph/9508027v2},
  keywords         = {Computer Science (CS); FOS: Physical Sciences; Prime Number Factoring; Quantum Algorithms; Quantum Computing; Quantum Physics (quant-ph)},
  modificationdate = {2024-11-12T11:25:00},
  owner            = {saulius},
  primaryclass     = {quant-ph},
  publisher        = {Society for Industrial & Applied Mathematics (SIAM)},
}

@Manuscript{Chapin2015,
  author           = {Peter Chapin},
  title            = {{A}da–a crash course},
  year             = {2015},
  keywords         = {Ada;Computer Science (CS);Programming Languages;Teaching;Teaching Computer Science},
  url              = {https://www.inf.ed.ac.uk/teaching/courses/fv/spark/Ada-A_Crash_Course.pdf},
  creationdate     = {2024-11-22T14:26:19},
  file             = {:by-author/C/Chapin/2015_Chapin_1.pdf:PDF:https\://www.inf.ed.ac.uk/teaching/courses/fv/spark/Ada-A_Crash_Course.pdf},
  modificationdate = {2024-11-22T14:28:53},
  owner            = {saulius},
}

@Article{Hunnisett2024,
  author           = {Hunnisett, Lily M. and Nyman, Jonas and Francia, Nicholas and Abraham, Nathan S. and Adjiman, Claire S. and Aitipamula, Srinivasulu and Alkhidir, Tamador and Almehairbi, Mubarak and Anelli, Andrea and Anstine, Dylan M. and Anthony, John E. and Arnold, Joseph E. and Bahrami, Faezeh and Bellucci, Michael A. and Bhardwaj, Rajni M. and Bier, Imanuel and Bis, Joanna A. and Boese, A. Daniel and Bowskill, David H. and Bramley, James and Brandenburg, Jan Gerit and Braun, Doris E. and Butler, Patrick W. V. and Cadden, Joseph and Carino, Stephen and Chan, Eric J. and Chang, Chao and Cheng, Bingqing and Clarke, Sarah M. and Coles, Simon J. and Cooper, Richard I. and Couch, Ricky and Cuadrado, Ramon and Darden, Tom and Day, Graeme M. and Dietrich, Hanno and Ding, Yiming and DiPasquale, Antonio and Dhokale, Bhausaheb and van Eijck, Bouke P. and Elsegood, Mark R. J. and Firaha, Dzmitry and Fu, Wenbo and Fukuzawa, Kaori and Glover, Joseph and Goto, Hitoshi and Greenwell, Chandler and Guo, Rui and Harter, Jürgen and Helfferich, Julian and Hofmann, Detlef W. M. and Hoja, Johannes and Hone, John and Hong, Richard and Hutchison, Geoffrey and Ikabata, Yasuhiro and Isayev, Olexandr and Ishaque, Ommair and Jain, Varsha and Jin, Yingdi and Jing, Aling and Johnson, Erin R. and Jones, Ian and Jose, K. V. Jovan and Kabova, Elena A. and Keates, Adam and Kelly, Paul F. and Khakimov, Dmitry and Konstantinopoulos, Stefanos and Kuleshova, Liudmila N. and Li, He and Lin, Xiaolu and List, Alexander and Liu, Congcong and Liu, Yifei Michelle and Liu, Zenghui and Liu, Zhi-Pan and Lubach, Joseph W. and Marom, Noa and Maryewski, Alexander A. and Matsui, Hiroyuki and Mattei, Alessandra and Mayo, R. Alex and Melkumov, John W. and Mohamed, Sharmarke and Momenzadeh Abardeh, Zahrasadat and Muddana, Hari S. and Nakayama, Naofumi and Nayal, Kamal Singh and Neumann, Marcus A. and Nikhar, Rahul and Obata, Shigeaki and O’Connor, Dana and Oganov, Artem R. and Okuwaki, Koji and Otero-de-la-Roza, Alberto and Pantelides, Constantinos C. and Parkin, Sean and Pickard, Chris J. and Pilia, Luca and Pivina, Tatyana and Podeszwa, Rafał and Price, Alastair J. A. and Price, Louise S. and Price, Sarah L. and Probert, Michael R. and Pulido, Angeles and Ramteke, Gunjan Rajendra and Rehman, Atta Ur and Reutzel-Edens, Susan M. and Rogal, Jutta and Ross, Marta J. and Rumson, Adrian F. and Sadiq, Ghazala and Saeed, Zeinab M. and Salimi, Alireza and Salvalaglio, Matteo and Sanders de Almada, Leticia and Sasikumar, Kiran and Sekharan, Sivakumar and Shang, Cheng and Shankland, Kenneth and Shinohara, Kotaro and Shi, Baimei and Shi, Xuekun and Skillman, A. Geoffrey and Song, Hongxing and Strasser, Nina and van de Streek, Jacco and Sugden, Isaac J. and Sun, Guangxu and Szalewicz, Krzysztof and Tan, Benjamin I. and Tan, Lu and Tarczynski, Frank and Taylor, Christopher R. and Tkatchenko, Alexandre and Tom, Rithwik and Tuckerman, Mark E. and Utsumi, Yohei and Vogt-Maranto, Leslie and Weatherston, Jake and Wilkinson, Luke J. and Willacy, Robert D. and Wojtas, Lukasz and Woollam, Grahame R. and Yang, Zhuocen and Yonemochi, Etsuo and Yue, Xin and Zeng, Qun and Zhang, Yizu and Zhou, Tian and Zhou, Yunfei and Zubatyuk, Roman and Cole, Jason C.},
  journal          = {Acta Crystallographica Section B Structural Science, Crystal Engineering and Materials},
  title            = {The seventh blind test of crystal structure prediction: structure generation methods},
  year             = {2024},
  issn             = {2052-5206},
  month            = dec,
  number           = {6},
  pages            = {517--547},
  volume           = {80},
  creationdate     = {2024-12-10T16:21:35},
  doi              = {10.1107/s2052520624007492},
  file             = {:by-author/H/Hunnisett/2024_Hunnisett_517.pdf:PDF:https\://journals.iucr.org/b/issues/2024/06/00/aw5093/aw5093.pdf},
  modificationdate = {2024-12-10T16:22:29},
  owner            = {saulius},
  publisher        = {International Union of Crystallography (IUCr)},
}

@Presentation{Bryant2020,
  author           = {Randal E. Bryant and David R. O'Hallaron},
  title            = {The memory hierarchy},
  year             = {2020},
  creationdate     = {2024-12-16T10:34:15},
  file             = {:by-author/B/Bryant/2020_Bryant_The Memory Hierarchy.pdf:PDF:https\://www.cs.rochester.edu/users/faculty/sandhya/csc252/lectures/lecture-exceptions-processes.pdf},
  keywords         = {Cache Memory;Code Optimisation;Computer Science (CS);Matrix Multiplication;Memory Hierarchy},
  modificationdate = {2024-12-16T10:39:58},
  owner            = {saulius},
  url              = {https://www.cs.rochester.edu/users/faculty/sandhya/csc252/lectures/lecture-exceptions-processes.pdf},
}

@Presentation{Yang2017,
  author           = {T. Yang},
  title            = {Optimizing cache performance in matrix multiplication},
  year             = {2017},
  creationdate     = {2024-12-16T10:38:02},
  file             = {:by-author/Y/Yang/2017_Yang_Optimizing Cache Performance in Matrix Multiplication.pdf:PDF:https\://sites.cs.ucsb.edu/~tyang/class/240a17/slides/Cache3.pdf},
  keywords         = {Cache Memory;Code Optimisation;Computer Science (CS);Matrix Multiplication;Memory Hierarchy},
  modificationdate = {2024-12-16T10:39:51},
  owner            = {saulius},
  url              = {https://sites.cs.ucsb.edu/~tyang/class/240a17/slides/Cache3.pdf},
}

@Presentation{Frigo2020,
  author           = {Matteo Frigo and Charles E. Leiserson and Harald Prokop and Sridhar Ramachandran},
  title            = {Cache-oblivious algorithms},
  year             = {2020},
  creationdate     = {2024-12-16T10:43:40},
  file             = {:by-author/F/Frigo/2020_Frigo_Cache Oblivious Algorithms.pdf:PDF:https\://jshun.csail.mit.edu/6886-s20/lectures/lecture9-1.pdf},
  keywords         = {Cache Memory;Cache-oblivious Algorithms;Code Optimisation;Computer Science (CS);Matrix Multiplication;Memory Hierarchy},
  modificationdate = {2024-12-16T10:45:25},
  owner            = {saulius},
  url              = {https://jshun.csail.mit.edu/6886-s20/lectures/lecture9-1.pdf},
}

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